ACLY ubiquitination by CUL3-KLHL25 induces the reprogramming of fatty acid metabolism to facilitate iTreg differentiation

Miaomiao Tian; Fengqi Hao; Xin Jin; Xue Sun; Ying Jiang; Yang Wang; Dan Li; Tianyi Chang; Yingying Zou; Pinghui Peng; Chaoyi Xia; Jia Liu; Yuanxi Li; Ping Wang; Yunpeng Feng; Min Wei

doi:10.7554/eLife.62394

. 2021 Sep 7;10:e62394. doi: 10.7554/eLife.62394

ACLY ubiquitination by CUL3-KLHL25 induces the reprogramming of fatty acid metabolism to facilitate iTreg differentiation

Miaomiao Tian ^1,^†, Fengqi Hao ^1,^†, Xin Jin ¹, Xue Sun ¹, Ying Jiang ¹, Yang Wang ¹, Dan Li ^2,³, Tianyi Chang ¹, Yingying Zou ¹, Pinghui Peng ¹, Chaoyi Xia ¹, Jia Liu ¹, Yuanxi Li ¹, Ping Wang ⁴, Yunpeng Feng ^1,^✉, Min Wei ^1,^✉

Editors: Kiyoshi Takeda⁵, Tadatsugu Taniguchi⁶

PMCID: PMC8423445 PMID: 34491895

Abstract

Inducible regulatory T (iTreg) cells play a central role in immune suppression. As iTreg cells are differentiated from activated T (Th0) cells, cell metabolism undergoes dramatic changes, including a shift from fatty acid synthesis (FAS) to fatty acid oxidation (FAO). Although the reprogramming in fatty acid metabolism is critical, the mechanism regulating this process during iTreg differentiation is still unclear. Here we have revealed that the enzymatic activity of ATP-citrate lyase (ACLY) declined significantly during iTreg differentiation upon transforming growth factor β1 (TGFβ1) stimulation. This reduction was due to CUL3-KLHL25-mediated ACLY ubiquitination and degradation. As a consequence, malonyl-CoA, a metabolic intermediate in FAS that is capable of inhibiting the rate-limiting enzyme in FAO, carnitine palmitoyltransferase 1 (CPT1), was decreased. Therefore, ACLY ubiquitination and degradation facilitate FAO and thereby iTreg differentiation. Together, we suggest TGFβ1-CUL3-KLHL25-ACLY axis as an important means regulating iTreg differentiation and bring insights into the maintenance of immune homeostasis for the prevention of immune diseases.

Research organism: E. coli, Human, Mouse, Virus

Introduction

As a critical subset of immunosuppressive cells, regulatory T (Treg) cells play a central role in the suppression of aberrant or excessive immune responses and are critical for the maintenance of immune homeostasis (Dominguez-Villar and Hafler, 2018). Defects in Treg frequency or function are often associated with distinct autoimmune disorders, such as system lupus erythematosus (SLE), rheumatoid arthritis (RA), and inflammatory bowel disease (IBD) (Sakaguchi et al., 2008; Tao et al., 2017). Treg cells are composed of thymus-derived natural Treg (nTreg) and peripheral inducible Treg (iTreg) cells, which are originated and matured at different locations in the body (Lee et al., 2009; Noack and Miossec, 2014). In general, nTreg cells are dominant in the periphery under unperturbed conditions, whereas iTreg cells are often boosted upon special immune challenges to balance inflammatory responses (Murai et al., 2010). Furthermore, enhancing iTreg cells by stimulating iTreg differentiation or employing adoptive transfer appeared to be effective in the therapeutic treatment for several immune diseases (Dall'Era et al., 2019; Esensten et al., 2018; Göschl et al., 2019; Ryba-Stanisławowska et al., 2019).

iTreg cells are derived from activated T (Th0) cells, which can also differentiate into effector CD4⁺ T cells (Teffs), including Th1, Th2, and Th17, depending on cytokine contexts, and the establishment of iTreg cells relies on transforming growth factor β1 (TGFβ1) (Chen et al., 2003; Maciolek et al., 2014). It has been characterized that TGFβ1 stimulates the phosphorylation of transcription factors Smad2 and Smad3 to facilitate the formation of a heterotrimeric complex containing Smad2/3/4 (Derynck and Zhang, 2003; Souchelnytskyi et al., 1997). Subsequently, this Smad2/3/4 complex binds to the conservative non-coding sequence 1 (CNS1) in Foxp3, which encodes the master transcription factor critical for the establishment and maintenance of iTreg cells, thereby promoting iTreg differentiation (Chen et al., 2011; Fontenot et al., 2003; Hori et al., 2003; Schlenner et al., 2012).

Accumulating evidence has revealed that different types of T cells are usually associated with distinct metabolic characteristics (Chen et al., 2015; Kempkes et al., 2019). For instance, Th0, Th1, Th2, and Th17 prefer de novo fatty acid synthesis (FAS) that substantially supports anabolism to meet the need for biological macromolecules during rapid proliferation (Lochner et al., 2015; Ma et al., 2017; Maciolek et al., 2014; Wang et al., 2011). In contrast, iTreg relies on fatty acid oxidation (FAO) (Chen et al., 2015; Gerriets et al., 2015; Ma et al., 2017; Michalek et al., 2011). Because carnitine palmitoyltransferase 1 (CPT1) is the rate-limiting enzyme in FAO, upregulating CPT1 by its substrate palmitate and downregulating CPT1 by the specific inhibitor etomoxir, respectively, could result in enhancement and impairment in FAO and iTreg differentiation (Gualdoni et al., 2016; Michalek et al., 2011). Obviously, FAS and FAO are reciprocal pathways, only one of which can be dominant in a specific type of T cells (Foster, 2012; Wolfgang and Lane, 2006). During iTreg differentiation, cell metabolism undergoes a series of dramatic changes, including a shift from FAS to FAO. Although the downregulation of FAS appears to be important (Berod et al., 2014), the mechanism regulating FAS in the process of iTreg differentiation is still unclear.

FAS is directly controlled by a series of metabolic enzymes in cytoplasm, including three rate-limiting enzymes ATP-citrate lyase (ACLY), acetyl-CoA carboxylase (ACC), and fatty acid synthase (FASN) (Lochner et al., 2015). In brief, ACLY converts mitochondrial-derived citrate into acetyl-CoA and oxaloacetic acid (OAA), and provides the main acetyl-CoA source for de novo FAS. ACC catalyzes acetyl-CoA into malonyl-CoA to provide an active two-carbon-unit donor for carbon chain extension. FASN uses both malonyl-CoA and acetyl-CoA as substrates to continuously synthesize long-chain fatty acids. Although regulation of the three enzymes at the transcriptional level was reported (Kidani et al., 2013), direct modulation of their activities by posttranslational modifications (PTMs), particularly ubiquitination that is tightly coupled with protein degradation, has set a new stage for the exploration of FAS control. For instance, nutrient deficiency induced ACLY ubiquitination at K540/K546/K554 in human lung cancer cells. This change resulted in the degradation of ACLY proteins and suppressed de novo lipid synthesis, eventually causing impairment in cell proliferation (Lin et al., 2013; Zhang et al., 2016). ACC stability as well as de novo lipid synthesis in mouse adipocytes was found to be regulated by ubiquitination (Qi et al., 2006). Additionally, FASN ubiquitination in HEK293T cells was also linked to its degradation, which in turn compromised de novo lipid synthesis (Lin et al., 2016). However, it still remains poorly understood whether and how ubiquitination is involved in the control of FAS during iTreg differentiation.

In this study, we have revealed that ACLY activity declined significantly as iTreg cells were differentiated. Upregulation in ACLY expression hindered the switch from FAS to FAO and thereby impaired iTreg differentiation. ACLY-dependent malonyl-CoA, an intermediate in FAS, could directly finetune CPT1 activity and therefore FAO. In response to TGFβ1 stimulation, CUL3-KLHL25 mediated ACLY ubiquitination to facilitate its degradation. When we removed CUL3 to block ACLY degradation, iTreg differentiation and colitis alleviation by adoptive iTreg cells in mice were compromised. Simultaneous depletion of ACLY partially rescued CUL3 deficiency-induced defects in iTreg differentiation and colitis alleviation. Overall, we demonstrated the regulation of iTreg differentiation via TGFβ1-CUL3-KLHL25-ACLY axis and bring insights into the maintenance of immune homeostasis for the prevention of colitis.

Results

ACLY is critical for the efficient differentiation of iTreg cells

To understand the alteration in FAS during iTreg differentiation, we examined the three rate-limiting enzymes ACLY, ACC, and FASN in FAS pathway. It appeared that the enzymatic activity of ACLY was reduced markedly, while ACC and FASN activities remained largely unchanged (Figure 1A, Figure 1—figure supplement 1A). Meanwhile, acetyl-CoA and OAA, the two products of ACLY-mediated reaction, were also reduced upon TGFβ1 treatment, confirming the decreased ACLY activity during iTreg differentiation (Figure 1B, Figure 1—figure supplement 1B). Importantly, preventing the decline in ACLY activity by supplementing cells with exogenous ACLY drastically impaired iTreg differentiation (Figure 1C, Figure 1—figure supplement 1C). In contrast, knocking down Acly by small interfering RNAs (siRNAs) or blocking ACLY activity by the specific inhibitor SB204990 led to elevated iTreg differentiation (Figure 1D–E, Figure 1—figure supplement 1D-E). Together, these data suggest that ACLY regulates iTreg differentiation.

Figure 1. — (**A, B**) Detection of ATP-citrate lyase (ACLY) activity in inducible regulatory T (iTreg) cells. Naive CD4⁺ T cells isolated from mice were cultured with Dynabeads Mouse T-Activator CD3/CD28 and rmIL-2 for 72 hr to obtain activated T (Th0) cells or simultaneously supplemented with rhTGFβ1 (2 ng/ml) to generate iTreg cells. (A) Assessment of enzymatic activity for ACLY, acetyl-CoA carboxylase (ACC), and fatty acid synthase (FASN) from Th0 or iTreg cells. (B) Assay for cytosol acetyl-CoA and oxaloacetic acid (OAA) from Th0 or iTreg cells. (C) ACLY overexpression affects iTreg differentiation. Naive CD4⁺ T cells were transfected with GFP-ACLY and cultured under Th0- or iTreg-polarization condition as in (A). Cells were analyzed by flow cytometry (FCM) to evaluate GFP⁺CD25⁺Foxp3⁺ iTreg cells. (**D, E**) Inhibition of ACLY influences iTreg differentiation. Naive CD4⁺ T cells transfected with small interfering RNAs (siRNAs) against *Acly* (D) or treated with SB204990 (100 μM) (E) were cultured under Th0- or iTreg (with 0.5 ng/ml rhTGFβ1)-polarization condition for 72 hr. CD4⁺CD25⁺Foxp3⁺ iTreg cells were assayed by FCM (left) and quantified (right). Data represent mean ± SD of three independent experiments, with significance determined by Student's t-test (**A, B**) or one-way analysis of variance (ANOVA) test (**C–E**). *p<0.05, **p<0.01, ***p<0.001, and ****p<0.0001; ns, nonsignificant.

Figure 1—figure supplement 1. — (**A, B**) Detection of ATP-citrate lyase (ACLY) activity in inducible regulatory T (iTreg) cells. Naive CD4⁺ T cells isolated from mice were cultured with Dynabeads Mouse T-Activator CD3/CD28 and rmIL-2 for 72 hr to obtain activated T (Th0) cells or simultaneously supplemented with rhTGFβ1 (2 ng/ml) to generate iTreg cells. (A) Assessment of enzymatic activity for ACLY, acetyl-CoA carboxylase (ACC), and fatty acid synthase (FASN) from Th0 or iTreg cells. (B) Assay for cytosol acetyl-CoA and oxaloacetic acid (OAA) from Th0 or iTreg cells. (C) ACLY overexpression affects iTreg differentiation. Naive CD4⁺ T cells were transfected with GFP-ACLY and cultured under Th0- or iTreg-polarization condition as in (A). Cells were analyzed by flow cytometry (FCM) to evaluate GFP⁺CD25⁺Foxp3⁺ iTreg cells. (**D, E**) Inhibition of ACLY influences iTreg differentiation. Naive CD4⁺ T cells transfected with small interfering RNAs (siRNAs) against *Acly* (D) or treated with SB204990 (100 μM) (E) were cultured under Th0- or iTreg (with 0.5 ng/ml rhTGFβ1)-polarization condition for 72 hr. CD4⁺CD25⁺Foxp3⁺ iTreg cells were assayed by FCM (left) and quantified (right). Data represent mean ± SD of three independent experiments, with significance determined by Student's t-test (**A, B**) or one-way analysis of variance (ANOVA) test (**C–E**). *p<0.05, **p<0.01, ***p<0.001, and ****p<0.0001; ns, nonsignificant.

ACLY is required for the reprogramming of fatty acid metabolism during iTreg differentiation

ACLY converts citrate into acetyl-CoA and OAA, and acetyl-CoA is the main source supporting de novo FAS, mevalonate-cholesterol synthesis, and histone acetylation (Zaidi et al., 2012). To further understand ACLY-dependent regulation of metabolic reprogramming during iTreg differentiation, we performed [U-¹³C] glucose-tracing experiment. Upon ACLY inhibition, ¹³C-labeled fatty acids were reduced as expected (Figure 2A). However, key intermediates in mevalonate-cholesterol synthesis, including 3-hydroxy-3-methyl glutaryl coenzyme A (HMG-CoA), mevalonate, mevalonate 5-pyrophosphate, and cholesterol remained rather stable irrespective of the presence of ACLY inhibitor (Figure 2—figure supplement 1A–D). Exogenous supplement of mevalonate and cholesterol failed to affect ACLY-inhibition-induced enhancement in iTreg differentiation (Figure 2—figure supplement 2A–C), confirming a dispensable role of mevalonate-cholesterol synthesis in ACLY-dependent regulation of iTreg differentiation. Meanwhile, we examined the level of nuclear acetyl-CoA that directly supports histone acetylation and found that it remained relatively stable, regardless of the presence of ACLY inhibitor (Figure 2—figure supplement 3A–B). In line with this observation, acetylation in total histones and H3/H4 was not influenced by ACLY inhibition (Figure 2—figure supplement 3C–D).

Figure 2—figure supplement 1. — (A) ATP-citrate lyase (ACLY) inhibition reduces de novo fatty acid synthesis (FAS). Naive CD4⁺ T cells were treated with SB204990 (100 μM) and cultured under inducible regulatory T (iTreg)-polarization condition as in Figure 1E for 24 hr in the presence of [U-¹³C] glucose (11 mM). Cells were collected and subjected to metabolic flux analysis for FAS by ultra-high performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS) analysis. n = 4, Student's t-test, mean ± SD. *p<0.05, **p<0.01, ****p<0.0001; ns, nonsignificant. (**B, C**) Functional evaluation of metabolic intermediates from FAS on iTreg differentiation. Naive CD4⁺ T cells were treated with SB204990 (100 μM) and cultured as in Figure 1E in the presence of different doses of palmitate (B) or malonyl-CoA (C). CD4⁺CD25⁺Foxp3⁺ iTreg cells were assayed by flow cytometry (FCM) (left) and quantified (right). (**D, E**) ACLY inhibition increases carnitine palmitoyltransferase 1 (CPT1) activity and fatty acid oxidation (FAO). In the presence of malonyl-CoA (50 μM) or cerulenin (4 μM), naive CD4⁺ T cells treated with SB204990 were cultured as in Figure 1E for 24 hr. Cell lysates were used for analyzing CPT1 activity (D). For oxygen consumption rate (OCR) detection, cells were transferred to XF Base Medium containing palmitate and carnitine. Diagram (left) illustrating the OCR at various conditions and associated quantifications (right) are shown (E). (F) Impact of *Cpt1* knockdown on iTreg differentiation. Naive CD4⁺ T cells transfected with small interfering RNA (siRNA) against *Cpt1* were cultured as in Figure 1E. CD4⁺CD25⁺Foxp3⁺ iTreg cells were assayed by FCM (left) and quantified (right). (**B–F**) Data represent mean ± SD of three (**D–F**) or four (**B, C**) independent experiments, with significance determined by one-way analysis of variance (ANOVA) test. **p<0.01, ***p<0.001, and ****p<0.0001; ns, nonsignificant.

Intriguingly, adding back palmitate did not change ACLY-inhibition-induced iTreg differentiation (Figure 2B, Figure 2—figure supplement 4A), despite a significant reduction in FAS upon ACLY inhibition (Figure 2A). Considering that palmitate, the terminal product of FAS, may not be the limiting factor coordinating ACLY-dependent impact and iTreg differentiation, other intermediate products in FAS can be potentially at play (Figure 2—figure supplement 4B). Next, we targeted key enzymes in FAS separately with different inhibitors to gain insights into the pivotal metabolite(s). While FASN inhibition abolished ACLY-inhibition-induced iTreg differentiation, the inhibition of ACC barely had any effect (Figure 2—figure supplement 4C). This strongly indicates that malonyl-CoA, the substrate of FASN, might be important for ACLY-inhibition-induced iTreg differentiation. Upon ACLY inhibition, we did observe a clear reduction in malony-CoA (Figure 2—figure supplement 4D). More importantly, add-back of malonyl-CoA completely abolished ACLY-inhibition-induced iTreg differentiation (Figure 2C). These data suggest that ACLY-dependent regulation of iTreg differentiation is probably through malonyl-CoA.

Because malonyl-CoA is a well-characterized metabolic intermediate capable of inhibiting CPT1, the key enzyme in FAO, we asked whether ACLY inhibition could regulate CPT1 activity and thereby FAO to promote iTreg differentiation (Figure 2—figure supplement 4B). When ACLY was inhibited by SB204990, both CPT1 activity (Figure 2D) and FAO (Figure 2E) were enhanced. Under the same condition, upregulating the cellular level of malonyl-CoA by exogenous supplementation of malonyl-CoA or FASN inhibition abrogated ACLY-inhibition-induced upregulation in CPT1 activity (Figure 2D, Figure 2—figure supplement 5A) and FAO (Figure 2E). Importantly, knockdown or inhibition of CPT1 abolished ACLY-inhibition-induced iTreg differentiation (Figure 2F, Figure 2—figure supplement 5B). Collectively, the reduction in malonyl-CoA resulted from ACLY inhibition mediates the derepression of CPT1 to facilitate FAO and iTreg differentiation.

TGFβ1 induces ACLY ubiquitination and degradation during iTreg differentiation

To further understand the decline in ACLY activity during iTreg differentiation, we first isolated ACLY proteins from Th0 and iTreg cells and normalized them to the same level (Figure 3—figure supplement 1A–B). Interestingly, both ACLY activity and Ser455 phosphorylation, which is a marker directly reflecting the enzymatic activity of ACLY (Das et al., 2015; Sivanand et al., 2017), remained unchanged (Figure 3—figure supplement 1A–B). However, a dramatic decrease in ACLY protein, but not in its mRNA, was observed in the process of iTreg differentiation (Figure 3A, Figure 3—figure supplement 1C), strongly arguing a mechanism regulating ACLY at its protein level.

Figure 3. — (A) Assay of ATP-citrate lyase (ACLY) protein level. Activated T (Th0) and inducible regulatory T (iTreg) cells prepared as in Figure 1A were subjected to western blot (WB) with antibodies against ACLY (left). Quantification of ACLY levels (right). (B) Impact of transforming growth factor β1 (TGFβ1) on ACLY degradation. Naive CD4⁺ T cells were cultured as in Figure 1A for 24 hr and treated with cycloheximide (CHX) (10 μg/ml) as indicated prior to WB analysis (left). Quantification of ACLY levels (right). (C) Pathway analysis for ACLY degradation. Th0 and iTreg cells polarized as in Figure 1A for 24 hr were treated with MG132 (left) or leupeptin (right) and analyzed with WB for ACLY protein. (**D, E**) Impact of TGFβ1 on ACLY ubiquitination. Cells polarized as in Figure 1A for 24 hr were treated with MG132 (10 μM) and cell extracts were immunoprecipitated with antibodies against ACLY (D) or ubiquitin (Ub) (E). IgG serves as a negative control. (**F–H**) Functional comparison between ACLY^WT and ACLY^3KR. Naive CD4⁺ T cells transfected with GFP-ACLY^WT or -ACLY^3KR were polarized as in Figure 1A for 24 hr. (F) Extracts from cells pre-treated with MG132 were assayed with immunoprecipitation (IP) for ACLY ubiquitination. IgG serves as a negative control. (G) WB analysis for ACLY protein. (H) Cell lysates were prepared for the analysis of carnitine palmitoyltransferase 1 (CPT1) activity. (I) ACLY ubiquitination impacts on iTreg differentiation. Cells transfected with GFP-ACLY^WT or -ACLY^3KR were polarized as in Figure 1A and assessed with flow cytometry (FCM) (left). Quantification of GFP⁺CD25⁺Foxp3⁺ iTreg cells (right). (**A–C, G–I**) Quantification shows mean ± SD based on three independent experiments. Student's t-test (A), two-way analysis of variance (ANOVA) test (B), or one-way ANOVA test (**C, G–I**) was used. *p<0.05, **p<0.01, ***p<0.001, and ****p<0.0001; ns, nonsignificant. For WB in (**A–G**), one representative experiment out of three is represented. Associated scores indicate mean intensities based on three biological replicas.

Figure 3—figure supplement 1. — (A) Assay of ATP-citrate lyase (ACLY) protein level. Activated T (Th0) and inducible regulatory T (iTreg) cells prepared as in Figure 1A were subjected to western blot (WB) with antibodies against ACLY (left). Quantification of ACLY levels (right). (B) Impact of transforming growth factor β1 (TGFβ1) on ACLY degradation. Naive CD4⁺ T cells were cultured as in Figure 1A for 24 hr and treated with cycloheximide (CHX) (10 μg/ml) as indicated prior to WB analysis (left). Quantification of ACLY levels (right). (C) Pathway analysis for ACLY degradation. Th0 and iTreg cells polarized as in Figure 1A for 24 hr were treated with MG132 (left) or leupeptin (right) and analyzed with WB for ACLY protein. (**D, E**) Impact of TGFβ1 on ACLY ubiquitination. Cells polarized as in Figure 1A for 24 hr were treated with MG132 (10 μM) and cell extracts were immunoprecipitated with antibodies against ACLY (D) or ubiquitin (Ub) (E). IgG serves as a negative control. (**F–H**) Functional comparison between ACLY^WT and ACLY^3KR. Naive CD4⁺ T cells transfected with GFP-ACLY^WT or -ACLY^3KR were polarized as in Figure 1A for 24 hr. (F) Extracts from cells pre-treated with MG132 were assayed with immunoprecipitation (IP) for ACLY ubiquitination. IgG serves as a negative control. (G) WB analysis for ACLY protein. (H) Cell lysates were prepared for the analysis of carnitine palmitoyltransferase 1 (CPT1) activity. (I) ACLY ubiquitination impacts on iTreg differentiation. Cells transfected with GFP-ACLY^WT or -ACLY^3KR were polarized as in Figure 1A and assessed with flow cytometry (FCM) (left). Quantification of GFP⁺CD25⁺Foxp3⁺ iTreg cells (right). (**A–C, G–I**) Quantification shows mean ± SD based on three independent experiments. Student's t-test (A), two-way analysis of variance (ANOVA) test (B), or one-way ANOVA test (**C, G–I**) was used. *p<0.05, **p<0.01, ***p<0.001, and ****p<0.0001; ns, nonsignificant. For WB in (**A–G**), one representative experiment out of three is represented. Associated scores indicate mean intensities based on three biological replicas.

Given that protein levels are controlled by both synthesis and degradation, we next examined ACLY protein level upon the treatment of cycloheximide (CHX), a well-documented ribosome inhibitor, often used for blocking protein synthesis (Schneider-Poetsch et al., 2010). Our time-course analysis showed that TGFβ1 stimulation caused a reduction in ACLY protein even in the presence of CHX (Figure 3B), indicating that protein degradation played an important role in TGFβ1-mediated ACLY downregulation. Indeed, when we blocked protein degradation with MG132, which inhibits ubiquitination-proteasome degradation (Liu et al., 2016), TGFβ1-induced downregulation in ACLY was abolished (Figure 3C). In contrast, the addition of leupeptin, which blocks autophagy-lysosome degradation (Liu et al., 2016), did not affect ACLY protein level (Figure 3C). These results suggested that, during iTreg differentiation, TGFβ1 induced ACLY downregulation via ubiquitination-proteasome degradation.

Subsequently, we carried on confirming whether ubiquitination determined ACLY stability during iTreg differentiation. In response to TGFβ1 stimulation, ACLY ubiquitination was evidently increased (Figure 3D–E). Mutation of ACLY at K530, K536, and K544 (3KR), which are homologous to the three ubiquitination sites (K540, K546, and K554) reported in human ACLY (Figure 3—figure supplement 2A; Lin et al., 2013; Zhang et al., 2016), abolished TGFβ1-dependent upregulation in ACLY ubiquitination (Figure 3F). Importantly, the reduction of ACLY stimulated by TGFβ1 was blocked when K530, K536, and K544 were mutated (Figure 3G, Figure 3—figure supplement 2B). As a consequence, TGFβ1-induced increase in CPT1 activity and iTreg differentiation were diminished (Figure 3H–I). Together, TGFβ1 promotes ACLY ubiquitination at K530, K536, and K544 to induce ACLY degradation, which in turn facilitates iTreg differentiation.

CUL3-KLHL25 is responsible for TGFβ1-mediated ACLY ubiquitination

In human cells, ACLY ubiquitination was found to be regulated by ubiquitin ligases UBR4 and CUL3-KLHL25 and deubiquitinase USP13 (Han et al., 2016; Lin et al., 2013; Zhang et al., 2016). To substantiate the determinants for ACLY ubiquitination in iTreg cells, we examined which of these candidate regulators interacted with ACLY. CUL3-KLHL25 and USP13, but not UBR4, appeared to interact with ACLY in iTreg cells (Figure 4—figure supplement 1A–B). Importantly, co-immunoprecipitation demonstrated that CUL3-KLHL25 association, rather than USP13 interaction, with ACLY was dramatically changed by TGFβ1 (Figure 4A, Figure 4—figure supplement 1C). This strongly suggested an important role for CUL3-KLHL25 in TGFβ1-dependent ACLY ubiquitination during iTreg differentiation.

Figure 4. — (A) Assay of ATP-citrate lyase (ACLY) interaction with CUL3-KLHL25. Cells polarized as in Figure 1A for 24 hr were treated with MG132 and assayed by immunoprecipitation (IP) with ACLY antibody. IgG serves as a negative control. (**B–E**) Functional assessment of CUL3-KLHL25 depletion in inducible regulatory T (iTreg) differentiation. Naive CD4⁺ T cells transfected with desired small interfering RNAs (siRNAs) were polarized as in Figure 1A for 24 hr (**B–D**) or 72 hr (E). They were pre-treated with MG132 before IP for the detection of ACLY ubiquitination (B), analyzed by western blotting (WB) with indicated antibodies (C), evaluated for carnitine palmitoyltransferase 1 (CPT1) activity (D), and stained for CD4/CD25/Foxp3 to identify iTreg cells prior to flow cytometry (FCM) analysis (E). (**F–H**) Functional assays for ACLY ubiquitination in cells derived from *Cul3* knockout mice. Naive CD4⁺ T cells isolated from wild-type (WT) or *Cd4^CreCul3^fl/fl* mice were polarized as in Figure 1A for 24 hr. Cells were pre-treated with MG132 before IP with antibodies against ACLY (F) or ubiquitin (Ub) (G), or analyzed for ACLY expression with WB (H). (**I, J**) Impact of CUL3 deficiency on fatty acid oxidation (FAO) and iTreg differentiation. Naive CD4⁺ T cells transfected with siRNAs were induced as in Figure 1A for 24 hr (I) or 72 hr (J). Cells were lysed for CPT1 activity detection (I) or stained for CD4/CD25/Foxp3 to identify iTreg cells prior to FCM analysis (J). (**C–E, H–J**) Quantification shows mean ± SD based on three independent experiments, with significance determined by one-way analysis of variance (ANOVA) test. *p<0.05, **p<0.01, ***p<0.001, and ****p<0.0001; ns, nonsignificant. For WB in (**A–D, F–I**), one representative experiment out of three is represented. Associated scores indicate mean intensities based on three biological replicas.

Figure 4—figure supplement 1. — (A) Assay of ATP-citrate lyase (ACLY) interaction with CUL3-KLHL25. Cells polarized as in Figure 1A for 24 hr were treated with MG132 and assayed by immunoprecipitation (IP) with ACLY antibody. IgG serves as a negative control. (**B–E**) Functional assessment of CUL3-KLHL25 depletion in inducible regulatory T (iTreg) differentiation. Naive CD4⁺ T cells transfected with desired small interfering RNAs (siRNAs) were polarized as in Figure 1A for 24 hr (**B–D**) or 72 hr (E). They were pre-treated with MG132 before IP for the detection of ACLY ubiquitination (B), analyzed by western blotting (WB) with indicated antibodies (C), evaluated for carnitine palmitoyltransferase 1 (CPT1) activity (D), and stained for CD4/CD25/Foxp3 to identify iTreg cells prior to flow cytometry (FCM) analysis (E). (**F–H**) Functional assays for ACLY ubiquitination in cells derived from *Cul3* knockout mice. Naive CD4⁺ T cells isolated from wild-type (WT) or *Cd4^CreCul3^fl/fl* mice were polarized as in Figure 1A for 24 hr. Cells were pre-treated with MG132 before IP with antibodies against ACLY (F) or ubiquitin (Ub) (G), or analyzed for ACLY expression with WB (H). (**I, J**) Impact of CUL3 deficiency on fatty acid oxidation (FAO) and iTreg differentiation. Naive CD4⁺ T cells transfected with siRNAs were induced as in Figure 1A for 24 hr (I) or 72 hr (J). Cells were lysed for CPT1 activity detection (I) or stained for CD4/CD25/Foxp3 to identify iTreg cells prior to FCM analysis (J). (**C–E, H–J**) Quantification shows mean ± SD based on three independent experiments, with significance determined by one-way analysis of variance (ANOVA) test. *p<0.05, **p<0.01, ***p<0.001, and ****p<0.0001; ns, nonsignificant. For WB in (**A–D, F–I**), one representative experiment out of three is represented. Associated scores indicate mean intensities based on three biological replicas.

It is known that CUL3-KLHL25 complex belongs to Cullin–RING ubiquitin ligase family, the largest class of ubiquitin ligases (Chen and Chen, 2016; Zheng and Shabek, 2017). In brief, CUL3 is the core scaffolding protein holding the entire complex together, while KLHL25 serves as an adaptor for substrate recognition (Zhang et al., 2016). When we knocked down Cul3 or Klhl25 with targeting siRNAs, ACLY ubiquitination was dramatically reduced (Figure 4B, Figure 4—figure supplement 2A). Also, both ACLY ubiquitination and degradation induced by TGFβ1 were blocked upon the depletion of CUL3 or KLHL25 (Figure 4B–C, Figure 4—figure supplement 2B). Moreover, the removal of CUL3 also resulted in an upregulated malonyl-CoA level (Figure 4—figure supplement 2C), reduced CPT1 activity, and downregulated iTreg differentiation (Figure 4D–E). Importantly, ACLY depletion partially rescued Cul3-knockdown-induced alterations in malonyl-CoA level, CPT1 activity, and iTreg differentiation (Figure 4—figure supplement 2C, Figure 4D–E). These data demonstrated that TGFβ1-mediated ACLY ubiquitination and degradation rely on CUL3-KLHL25.

In addition, we generated CD4⁺ T-cell-specific CUL3-deficient mice (Cd4^CreCul3^fl/fl) by crossing Cd4^Cre mice (Dong et al., 2008) with Cul3^fl/fl mice (McEvoy et al., 2007; Figure 4—figure supplement 3A–B). Due to the lack of CUL3, the frequency of CD4⁺Foxp3⁺Treg cells in colon was reduced as expected (Figure 4—figure supplement 3C). Notably, when naive CD4⁺ T cells from these CUL3-deficient mice were induced into iTreg cells in vitro, both ACLY ubiquitination and degradation induced by TGFβ1 were blocked (Figure 4F–H). These observations fully recapitulated what we previously found in siRNA-mediated CUL3-depleted cells. More importantly, alterations induced by CUL3 deficiency, including increase in malonyl-CoA level and decrease in CPT1 activity and iTreg differentiation, were dampened by ACLY depletion (Figure 4—figure supplement 3D, Figure 4I–J). Together, TGFβ1 induces CUL3-KLHL25-mediated ACLY ubiquitination and degradation for iTreg differentiation.

It is worth mentioning that the suppressive function of iTreg cells did not seem to be affected by ACLY ubiquitination and degradation. When we knocked down Cul3 and/or Acly with targeting siRNAs, levels of distinct surrogate molecules typically associated with the suppressive activity of iTreg cells, including CTLA4, ICOS, TIGIT, and IL-10, remained rather stable (Figure 4—figure supplement 4A). In agreement with this observation, we took the advantage of the available Foxp3^YFP-Cre mice (Priyadharshini et al., 2018) and induced YFP-iTreg cell differentiation under various conditions in vitro. We found that YFP-iTreg cells lacking CUL3 alone or in combination with ACLY could still retain the potent suppressive function (Figure 4—figure supplement 4B). Hence, instead of the suppressive function of iTreg, ACLY ubiquitination and degradation mainly affect iTreg differentiation.

CUL3-KLHL25-ACLY ubiquitination axis regulates human iTreg differentiation

To further corroborate the role of CUL3-KLHL25-mediated ACLY ubiquitination in human iTreg differentiation, we isolated naive CD4⁺ T cells from human peripheral blood and induced them into either Th0 or iTreg cells. As expected, the level of ACLY in iTreg dropped significantly as compared with Th0 (Figure 5A). ACLY overexpression and inhibition resulted in downregulation and upregulation in iTreg differentiation, respectively (Figure 5B–C). Furthermore, TGFβ1 treatment promoted CUL3-KLHL25 association with ACLY, resulting in ACLY ubiquitination and degradation (Figure 5D–F). Upon the mutation of K540/546/554 in ACLY (ACLY^3KR), TGFβ1-induced ACLY ubiquitination and degradation, as well as iTreg differentiation, were remarkably dampened (Figure 5E–G). Taken together, these data corroborate the important role of CUL3-KLHL25-mediated ACLY ubiquitination in human iTreg differentiation.

Figure 5. — (A) Assay of ATP-citrate lyase (ACLY) expression in human inducible regulatory T (iTreg) cells. Naive CD4⁺ T cells isolated from human peripheral blood were cultured with Dynabeads Human T-Activator CD3/CD28 and rhIL-2 to induce activated T (Th0) cells or simultaneously supplemented with rhTGFβ1 (2 ng/ml) to induce iTreg cells for 24 hr. Cell extracts were subsequently analyzed for ACLY expression by western blotting (WB). (B) ACLY overexpression affects iTreg cell differentiation. Human naive CD4⁺ T cells transfected with GFP-ACLY^WT were polarized as in (A) for 72 hr prior to the assessment of iTreg cells by flow cytometry (FCM) (left). Quantification of iTreg populations (right). (C) ACLY inhibition affects iTreg differentiation. Cells treated with SB204990 were cultured under Th0- or iTreg (with 0.5 ng/ml rhTGFβ1)-polarization condition for 72 hr and subjected to the analysis (left) and quantification (right) of iTreg cells. (D) ACLY interaction with CUL3-KLHL25. Cells prepared as in (A) were pre-treated with MG132 before immunoprecipitation (IP) with ACLY antibody. IgG serves as a negative control. (**E–G**) ACLY ubiquitination regulates human iTreg differentiation. Cells transfected with GFP-ACLY^WT or -ACLY^3KR were induced under Th0- or iTreg-polarization condition as described in (A) for 24 hr (**E, F**) or 72 hr (G). Cells were pre-treated with MG132 before IP for the assessment of protein ubiquitination (E), examined by WB (F), or evaluated for GFP/CD25/Foxp3 expression with FCM (left), and quantified (right) (G). (**A–C, F, G**) Quantification shows mean ± SD based on three independent experiments, with significance determined by Student's t-test (**A, C**) or one-way analysis of variance (ANOVA) test (**B, F, G**). *p<0.05, **p<0.01, ***p<0.001; ns, nonsignificant. For WB in (A) and (**D–F**), one representative experiment out of three is represented. Associated scores indicate mean intensities based on three biological replicas.

ACLY inhibition alleviates mouse colitis by promoting iTreg cell generation

As a common digestive system disease, IBD poses a serious threat to public health, and the number of patients with IBD keeps growing (Bernstein et al., 2010). Manipulation of iTreg functions holds promise for the therapeutic treatment of IBD (Clough et al., 2020; Izcue et al., 2006; van Herk and Te Velde, 2016). Next, we performed a functional assay for CUL3-KLHL25-mediated ACLY ubiquitination in a classic mouse IBD model (Wirtz and Neurath, 2007). Same amount of naive CD4⁺ T cells was isolated from wild-type (WT) or Cd4^CreCul3^fl/fl (Cul3^-/-) mice and transfected with siRNAs prior to polarization to obtain Th0 (WT), iTreg (WT), iTreg (Cul3^-/-), or iTreg (Cul3^-/-+siAcly) cells (Figure 6A). Compared to control, the lack of CUL3 impaired iTreg differentiation, while ACLY depletion compromised CUL3-deficiency-induced changes (Figure 6—figure supplement 1, Figure 6B). Upon the adoptive transfer of these cells along with WT-mice-derived naive CD4⁺ T cells used to induce colitis into Rag1^-/- recipient mice (Figure 6A), Th0 (WT) group suffered serious colitis lying in body weight loss, disease activity index (DAI) score increase, colon length shortening, inflammatory cell infiltration, mucosal edema and injury as well as crypt damage increase (Figure 6C–E). As expected, iTreg (WT) mice showed significantly alleviated pathological alterations associated with colitis (Figure 6C–E). When we injected recipient mice with iTreg (Cul3^-/-) cells, less alleviation in colitis was observed as compared to that in iTreg (WT) group (Figure 6C–E). Importantly, knocking down Acly in iTreg (Cul3^-/-+siAcly) cells prior to the adoptive transfer rescued CUL3-deficiency-induced failures in colitis alleviation (Figure 6C–E). Using the same T-cell adoptive transfer strategy, we found that direct inhibition of ACLY by SB204990, which led to elevation in iTreg population from both mesenteric lymphatic node (MLN) and colonic lamina propria (cLP) and alleviation of dextran sodium sulfate (DSS)-induced colitis (Figure 6—figure supplement 2A–F), also effectively relieved T-cell-transfer-induced colitis in mice (Figure 6—figure supplement 3A–E). Together, these in vivo data confirm the important role of CUL3-KLHL25-mediated ACLY ubiquitination in colitis alleviation.

Figure 6. — (A) Experimental design. (B) Impact of inducible regulatory T (iTreg) cells on T-cell proliferation. Activated T (Th0) (wild-type, WT), iTreg (WT), iTreg (*Cul3^-/-*), and iTreg (*Cul3^-/-*+siAcly#1) cells were cocultured with carboxyfluorescein diacetate succinimidyl ester (CFSE)-stained naive CD4⁺ T cells and treated with Dynabeads Mouse T-Activator CD3/CD28 for 72 hr. T-cell proliferation was evaluated using flow cytometry (FCM) (left). Quantification analysis for CD4⁺ T-cell proliferation (right) based on three independent experiments. One-way analysis of variance (ANOVA) test, mean ± SD. **p<0.01, ***p<0.001, ****p<0.0001. (**C–E**) Systematic evaluation of colitis in mice adoptively transferred with different cells. (C) Body weight (left) and disease activity index (DAI) score (right) based on body weight loss, stool consistency, and blood in the stool were recorded weekly. 7 weeks later, entire colons from mice treated in different ways were removed for length assessment (D) and hematoxylin and eosin (H and E) staining, which is used for revealing histopathological changes (E). Scale bar, 200 μm. One representative experiment out of four biological replicas is represented. (**C, D**) Data represent mean ± SD (n = 4), with significance determined by two-way ANOVA test (C) or one-way ANOVA test (D). *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001.

Figure 6—figure supplement 1. — (A) Experimental design. (B) Impact of inducible regulatory T (iTreg) cells on T-cell proliferation. Activated T (Th0) (wild-type, WT), iTreg (WT), iTreg (*Cul3^-/-*), and iTreg (*Cul3^-/-*+siAcly#1) cells were cocultured with carboxyfluorescein diacetate succinimidyl ester (CFSE)-stained naive CD4⁺ T cells and treated with Dynabeads Mouse T-Activator CD3/CD28 for 72 hr. T-cell proliferation was evaluated using flow cytometry (FCM) (left). Quantification analysis for CD4⁺ T-cell proliferation (right) based on three independent experiments. One-way analysis of variance (ANOVA) test, mean ± SD. **p<0.01, ***p<0.001, ****p<0.0001. (**C–E**) Systematic evaluation of colitis in mice adoptively transferred with different cells. (C) Body weight (left) and disease activity index (DAI) score (right) based on body weight loss, stool consistency, and blood in the stool were recorded weekly. 7 weeks later, entire colons from mice treated in different ways were removed for length assessment (D) and hematoxylin and eosin (H and E) staining, which is used for revealing histopathological changes (E). Scale bar, 200 μm. One representative experiment out of four biological replicas is represented. (**C, D**) Data represent mean ± SD (n = 4), with significance determined by two-way ANOVA test (C) or one-way ANOVA test (D). *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001.

In addition, we also investigated the role of CUL3-dependent ACLY regulation in an alternative inflammatory disease associated with deregulated Treg function, namely allergic diarrhea (Kordowski et al., 2019; Wang et al., 2018; Yamamoto et al., 2019). Adoptive transfer of WT iTreg cells, but not CUL3-deficient cells (Cul3^-/-), into recipient mice remarkably alleviated the defects associated with ovalbumin (OVA)-induced allergic diarrhea, including upregulation of OVA-specific IgE antibodies and mastocyte protease (MCPT-1) in serum (Kordowski et al., 2019; Figure 6—figure supplement 4A–E). Knockdown of Acly rescued the effect of CUL3 deficiency on diarrhea (Figure 6—figure supplement 4B–E). Hence, these results suggest an important role for ‘CUL3-ACLY’ axis in the regulation of diarrhea.

Discussion

iTreg cells are essential for the regulation of immune homeostasis, and their establishment relies on TGFβ1 induction (Chen et al., 2003; Dominguez-Villar and Hafler, 2018). Recent findings suggest that a shift from FAS to FAO is required for efficient iTreg differentiation (Berod et al., 2014; Michalek et al., 2011), but the control of this process is still unclear. Here we unveiled a TGFβ1-CUL3-KLHL25-ACLY axis that is important for the metabolic reprogramming in fatty acid metabolism during iTreg differentiation.

As one of the most well-studied signaling pathways, TGFβ1 governs a number of signaling cascades, including canonical Smad signals and non-canonical MAPK (ERK/JNK/P38), PI3K/Akt, and Rho-like GTPase signals, mainly by regulating different kinases to phosphorylate their downstream factors (Vander Ark et al., 2018; Zhang, 2017). In the process of iTreg differentiation, TGFβ1 activates TGFRI/II, which are transmembrane protein serine/threonine kinases and directly phosphorylate Smad2/3, to improve Foxp3 expression (Schlenner et al., 2012). Interestingly, our work here demonstrated that, through ubiquitination of a key metabolic enzyme, TGFβ1 launched a reprogramming in fatty acid metabolism and promoted iTreg differentiation. These findings indicate ubiquitination as a useful means for TGFβ1 to coordinate fatty acid metabolism and induce iTreg differentiation.

Moreover, CUL3-KLHL25 is a part of the biggest ubiquitin ligase Cullin-Ring family and is involved in the regulation of numerous biological processes, such as cell cycle regulation, DNA damage responses, and cell apoptosis (Davidge et al., 2019; Genschik et al., 2013). The lack of CUL3 has been associated with defects in embryogenesis, hypertension, diminished angiogenesis, progressive interstitial inflammation, exacerbated colonic inflammation, and swelled spleens and lymph nodes (Agbor et al., 2019; Li et al., 2017; Maekawa et al., 2017; Mathew et al., 2012; Saritas et al., 2019; Singer et al., 1999). Interestingly, some of these defects, for example, progressive interstitial inflammation, exacerbated colonic inflammation, and swelled spleens and lymph nodes, are clearly relevant to immune system imbalance. In this study, the functional characterization of CUL3-KLHL25 in iTreg differentiation implies that disturbed iTreg cell homeostasis may contribute to CUL3-deficiency-associated defects, in particular, inflammatory-related phenomena. In addition, this may provide a new angle for re-evaluating and understanding severe pathological changes induced by the loss of CUL3.

It is also worth mentioning that the loss of CUL3 did not affect the differentiation of Th1, Th2, or Th17 in vitro, but enhanced follicular helper T (Tfh) cell number and responses in the germinal center (GC). These observations and our findings suggest that CUL3 may play distinct roles in different types of T cells, such as Tfh and Treg cells. In GC, Tfh cells can be suppressed by follicular regulatory T (Tfr) cells, which are also crucial for the maintenance of immune homeostasis (Essig et al., 2017; Huang et al., 2019). This specific type of T cells is actually derived from Treg cells (Essig et al., 2017; Huang et al., 2019). Whether CUL3 could finetune the balance between Tfh and Tfr for the control of GC function remains to be addressed in future.

Growing evidence shows that the regulation of cell metabolism is vital for T-cell proliferation, differentiation, and functions (Galgani et al., 2015; Guo, 2017; Maciolek et al., 2014; Wang and Solt, 2016). Different types of T cells are usually associated with distinct metabolic status and features. Unlike effector T cells, including Th1, Th2, and Th17, which ‘prefer’ FAS, iTreg cells ‘favor’ FAO (Maciolek et al., 2014; Michalek et al., 2011; Wang et al., 2011). During iTreg differentiation, suppressing FAS could probably be advantageous to keep the differentiation process on the right track and prevent differentiating cells from rushing into unwanted pathways. Also, we found that downregulation of FAS reduced malonyl-CoA, the potent physiological inhibitor of CPT1, and this could facilitate the unleashing of CPT1 activity for FAO and thereby iTreg differentiation. Therefore, reprogramming in fatty acid metabolism, in particular, the switch from FAS to FAO, is vital for the efficient differentiation of iTreg cells.

Although the essential role of FAO and CPT1 in iTreg differentiation has been documented (MacIver et al., 2013; Michalek et al., 2011; Patel and Powell, 2017; Zhang et al., 2017), a more recent investigation challenged this conclusion and proposed that CPT1 is dispensable for iTreg differentiation (Raud et al., 2018). Raud et al., 2018 found that naive CD4⁺ T cells isolated from mice with CPT1 deletion in T cells (TCPT1 mice) did not seem to have any defect in iTreg differentiation and proposed that the phenotypes induced by high-dose CPT1 inhibitor, etomoxir (>100 μM), were due to the off-target effect. However, we found that siRNA-mediated Cpt1 knockdown or low-dose etomoxir (5 μM), which inhibits CPT1 without introducing off-target effects, impaired iTreg differentiation in vitro (Hao et al., 2021; O'Connor et al., 2018; Figure 2F, Figure 2—figure supplement 5B). Of note, TCPT1 mice reported in Raud et al., 2018 survived from the lack of CPT1. One thus can envision that various metabolic genes/regulators have to be re-adjusted to compensate for the loss of CPT1, and metabolic homeostasis needs to be re-established. As a consequence, the defect(s) associated with the loss of CPT1 would be gradually compensated or masked during mouse development. In contrast, blocking CPT1 function by a specific inhibitor or siRNA that mimics an acute disruption in FAO might be useful for minimizing long-term metabolic adaption and directly evaluating CPT1 function in iTreg differentiation. In addition, our in vitro functional assays showed that alterations in CPT1 activity induced by ACLY and/or CUL3 depletion failed to change the suppressive function of iTreg cells (Figure 4D,I, Figure 4—figure supplement 4A–B). In a recent study, Saravia et al., 2020 also showed that the deletion of CPT1 in Foxp3⁺ Treg cells did not influence cell proliferation or function (Saravia et al., 2020). Together, these findings argue that CPT1 may be dispensable for the regulation and maintenance of iTreg function.

FAS is controlled by a series of enzymes, three of which are rate-limiting enzymes, namely ACLY, ACC, and FASN. During iTreg differentiation, only ACLY changed significantly. These observations suggest that, rather than ACC and FASN, ACLY is apt to function as a sensor for FAS to respond to TGFβ1 signal. ACLY is responsible for the conversion of citrate into acetyl-CoA and OAA. Its enzymatic activity and expression are tightly coupled with the level of citrate, which could block glycolysis by inhibiting phosphofructokinase (PFK) (Iacobazzi and Infantino, 2014; Zaidi et al., 2012). Notably, inhibition of glycolysis has a positive impact on iTreg differentiation (Shi et al., 2011). Therefore, TGFβ1-induced downregulation of ACLY, which is probably accompanied by citrate accumulation, might also contribute to the repression of glycolysis for iTreg differentiation.

Because of the great potential as a target for pharmaceutical intervention against hyperlipidemia, hypercholesterolemia, obesity, and cancer, ACLY has attracted considerable amount of attention over the recent decade (Feng et al., 2020; Migita et al., 2008). A growing list of ACLY inhibitors, including bempedoic acid (BemA), SB204990, curcumin, cinnamon polyphenol, and hydroxycitric acid, is under extensive investigation. It is worth mentioning that BemA, a small molecule inhibiting liver-specific ACLY, has been tested in a phase-three clinical trial for the control and treatment of hypercholesterolemia (Feng et al., 2020; Pinkosky et al., 2016). Results in this work have shown that ACLY inhibition by SB204990 effectively alleviated colitis in mice, suggesting that this small-molecule inhibitor (SB204990) may have a promising role in the clinical treatment for IBD. Thus, future investigations systematically evaluating ACLY as a drugable target for IBD and other immune diseases are in need.

Functional characterization of CUL3-KLHL25-mediated ACLY ubiquitination pinpoints ACLY as a regulatory node integrating TGFβ1 signaling with iTreg differentiation and therefore brings insights into the modulation and maintenance of immune homeostasis. Moreover, ACLY inhibitors with pharmaceutical potentials are apparently of interest for immunotherapy of autoimmunity and unwanted inflammation and certainly require further investigations.

Materials and methods

Key resources table.

Reagent type (species) or resource	Designation	Source or reference	Identifiers	Additional information
Strain, strain background (Mus musculus)	C57BL/6J	Beijing HFK Bioscience
Strain, strain background (M. musculus)	Cd4 ^Cre	Dong et al., 2008
Strain, strain background (M. musculus)	Cul3^fl/fl	The Jackson Laboratory	Stock #: 028349
Strain, strain background (M. musculus)	Cd4^CreCul3^fl/fl	This paper
Strain, strain background (M. musculus)	Foxp3^YFP-Cre	The Jackson Laboratory	Stock #: 016959
Strain, strain background (M. musculus)	B6/Rag1^-/-	Jiangsu Gempharmatech	Stock #: T011699
Cell line (Homo sapiens)	HEK293T	ATCC	Cat. #: ACS-4500
Biological sample (Homo sapiens)	Healthy adult peripheral blood	Jilin blood center
Antibody	Mouse anti-CD3/CD28 beads	Gibco	Cat. #: 11453D	T-cell activation (beads:cells, 1:1)
Antibody	Human anti-CD3/CD28 beads	Gibco	Cat. #: 11132D	T-cell activation (beads:cells, 1:1)
Antibody	Anti-mouse CD4-FITC	BD Biosciences	Cat. #: 553046 RRID:AB_394582	FCM (1:200)
Antibody	Anti-mouse CD25-PE	BD Biosciences	Cat. #: 561065 RRID:AB_10563211	FCM (1:200)
Antibody	Anti-mouse Foxp3- Alexa Fluor 647	BD Biosciences	Cat. #: 560401 RRID:AB_1645201	FCM (1:200)
Antibody	Anti-human CD4-FITC	Biolegend	Cat. #: 357406 RRID:AB_2562357	FCM (1:200)
Antibody	Anti-human CD25-PE	Biolegend	Cat. #: 302605 RRID:AB_314275	FCM (1:200)
Antibody	Anti-human Foxp3- Alexa Fluor 647	Biolegend	Cat. #: 320114 RRID:AB_439754	FCM (1:200)
Antibody	Anti-mouse CTLA4-PE-Cy7	Biolegend	Cat. #: 106311 RRID:AB_10901170	FCM (1:200)
Antibody	Anti-mouse ICOS-PE-Cy7	Biolegend	Cat. #: 117421 RRID:AB_2860636	FCM (1:200)
Antibody	Anti-mouse TIGIT-PE-Cy7	Biolegend	Cat. #: 142107 RRID:AB_2565648	FCM (1:200)
Antibody	Anti-mouse IL-10-PE-Cy7	Biolegend	Cat. #: 505025 RRID:AB_11149682	FCM (1:200)
Antibody	Anti-ACLY	Abcam	Cat. #: Ab40793 RRID:AB_722533	IP (1:100) WB (1:1000)
Antibody	Anti-eGFP	Proteintech	Cat. #: 66002–1-Ig RRID:AB_11182611	IP (1:100) WB (1:1000)
Antibody	Anti-Actin	Proteintech	Cat. #: 66009–1-Ig RRID:AB_2687938	WB (1:1000)
Antibody	Anti-CUL3	Santa Cruz	Cat. #: sc-166110 RRID:AB_2245478	IP (1:50) WB (1:200)
Antibody	Anti-KLHL25	Santa Cruz	Cat. #: sc-100774 RRID:AB_1124139	IP (1:50) WB (1:200)
Antibody	Anti-UBR4	Abcam	Cat. #: Ab86738 RRID:AB_1952666	IP (1:100) WB (1:1000)
Antibody	Anti-USP13	Santa Cruz	Cat. #: sc-514416	IP (1:50) WB (1:200)
Antibody	Anti-Ubiquitin	Abcam	Cat. #: ab7780 RRID:AB_306069	IP (1:100) WB (1:1000)
Antibody	Anti-Lamin b1	CST	Cat. #: 12586	WB (1:1000)
Antibody	Anti-β-Tubulin	Sigma	Cat. #: T0198 RRID:AB_2210695	WB (1:1000)
Antibody	Anti-ATP5A1	Bimake	Cat. #: A5288	WB (1:1000)
Antibody	Anti-Pan-acetylation	CST	Cat. #: 9441 RRID:AB_331805	WB (1:1000)
Antibody	Goat anti-Rabbit	Signalway Antibody	Cat. #: L3012-2	WB (1:10,000)
Antibody	Goat anti-Mouse	Signalway Antibody	Cat. #: L3032-2	WB (1:10,000)
Commercial assay or kit	Mouse CD4⁺Naïve T Cell isolation kit	Biolegend	Cat. #: 480040
Commercial assay or kit	Human CD4⁺Naïve T Cell isolation kit	Biolegend	Cat. #: 480042
Commercial assay or kit	Mouse T cell nucleofection kit	Lonza	Cat. #: VPA1006
Commercial assay or kit	Mouse mevalonate ELISA kit	Sino Best Biological Technology	Cat. #: YX-132201M
Commercial assay or kit	Mouse MCPT1 ELISA kit	Sino Best Biological Technology	Cat. #: YX-130316M
Commercial assay or kit	Mouse OVA-specific IgE ELISA kit	Sino Best Biological Technology	Cat. #: YX-152201M
Commercial assay or kit	Mouse mevalonate-5-pyrophosphate ELISA kit	Shanghai Ruifan Biological Technology	Cat. #: RF8872
Commercial assay or kit	Mouse HMG-CoA ELISA kit	Shanghai Ruifan Biological Technology	Cat. #: RF8726
Commercial assay or kit	Mitochondrial isolation kit	Beyotime Biotechnology	Cat. #: C3601
Commercial assay or kit	Cell Nuclear/Cytoplasm Protein Isolation Kit	Beyotime Biotechnology	Cat. #: P0028
Commercial assay or kit	ACLY activity assay kit	Suzhou comin Biotechnology	Cat. #: ACL-1-Y
Commercial assay or kit	ACC activity assay kit	Suzhou comin Biotechnology	Cat. #: ACC-1-Y
Commercial assay or kit	FASN activity assay kit	Suzhou comin Biotechnology	Cat. #: FASN-1-Y
Commercial assay or kit	CPT1 activity assay kit	Suzhou comin Biotechnology	Cat. #: CPT1-1-Y
Commercial assay or kit	Acetyl-CoA Fluorometric Assay kit	BioVision	Cat. #: K317-100
Commercial assay or kit	OAA assay kit	Sigma	Cat. #: MAK070
Commercial assay or kit	Transcriptional factor buffer set	BD	Cat. #: 562574
Commercial assay or kit	CFSE	Biolegend	Cat. #: 423801	1 μM
Commercial assay or kit	CellTrace Violet	Thermo Fisher	Cat. #: C34557	1 μM
Commercial assay or kit	Mito Stress Test kits	Agilent	Cat. #: 103010–100
Commercial assay or kit	Seahorse XF Palmitate-BSA FAO substrate	Agilent	Cat. #: 102720–100
Recombinant DNA reagent	pWPXLD-mACLY (plasmid)	This paper
Recombinant DNA reagent	pWPXLD-mACLY^{3KR(K530/536/544)}(plasmid)	This paper
Recombinant DNA reagent	pWPXLD-hACLY (plasmid)	This paper
Recombinant DNA reagent	pWPXLD-hACLY^{3KR(K540/546/554)}(plasmid)	This paper
Peptide, recombinant protein	Recombinant mouse IL-2	Peprotech	Cat. #: 212–12	7.5 ng/ml
Peptide, recombinant protein	Recombinant human IL-2	Gibco	Cat. #: PHC0026	7.5 ng/ml
Peptide, recombinant protein	Recombinant human TGFβ1	Peprotech	Cat. #: 100-21-10	0.5 or 2 ng/ml
Chemical compound, drug	SB204990	Tocris Bioscience	Cat. #: 154566-12-8	100 μM
Chemical compound, drug	MG132	Selleck	Cat. #: S2619	10, 20, or 40 μM
Chemical compound, drug	CHX	Tocris Bioscience	Cat. #: 0970	10 μg/ml
Chemical compound, drug	Leupeptin	Selleck	Cat. #: S7380	0.4 or 0.8 mM
Chemical compound, drug	Dextran sulfate sodium (36,000–50,000)	MP Biomedicals	Cat. #: 0216011080	2%
Chemical compound, drug	PF05175157	TOCRIS	Cat. #: 5709	5 μM
Chemical compound, drug	Cerulenin	Biovision	Cat. #: 1579–5	4 μM
Software, algorithm	FlowJo 10.1	FlowJo LLC	https://www.flowjo.com/
Software, algorithm	GraphPad Prism 6	GraphPad Software	https://www.graphpad.com
Other	RPMI 1640	Sigma-Aldrich	Cat. #: R66504
Other	Fetal bovine serum	Biological Industries	Cat. #: 04-001-01
Other	XF Base Medium	Agilent	Cat. #: 103193–100
Other	OVA	Sigma-Aldrich	Cat. #: A5503
Other	Polybrene	Solarbio	Cat. #: H8761	8 μg/ml

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Animals

C57BL/6J (B6) and B6/Rag1^-/- mice were purchased from Beijing HFK Bioscience Co, Ltd, China, and Jiangsu Gempharmatech Co, Ltd, China, respectively. Cul3^fl/fl mice were generously sponsored by Jeffrey D Singer (Department of Biology, Portland State University, Portland, OR, USA.). Cd4^Cre transgenic mice were generously provided by Zichun Hua (The State Key Laboratory of Pharmaceutical Biotechnology, Department of Biochemistry, College of Life Sciences, Nanjing University, Nanjing). Cd4^Cre and Cul3^fl/fl mice were crossed to generate mice specifically lacking CUL3 in their CD4⁺ T cells. Polymerase chain reaction (PCR) primers used for amplifying Cd4^Cre transgene and Cul3^fl/fl mutant are shown in Supplementary file 1. Foxp3^YFP-Cre mice were purchased from the Jackson laboratory.

Mice were bred and cohoused, four to six mice per cage, in a specific pathogen-free facility with a standard 12-hr alternate light/dark cycle at an ambient temperature of 22 ± 2°C and 30–70% humidity at the Animal Research Center of Northeast Normal University (Changchun, China). Health status of mice was determined via daily observation by technicians supported by veterinary care. All mouse experiments were conducted in accordance with the protocols for animal use, treatment, and euthanasia approved by the local ethics committee (reference number: AP2019085, the institutional animal care and use committee (IACUC) of the Northeast Normal University).

Induction of mouse iTreg in vitro

Naive CD4⁺ T cells were isolated from the spleen of female mice at the age of 6–8 weeks with MojoSort Mouse CD4⁺ Naïve T Cell Isolation Kit (Biolegend) according to the manufacturer’s instructions. For Th0 induction, 2 to 3 × 10⁵ naive CD4⁺ T cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Sigma-Aldrich) supplemented with 10% fetal bovine serum (FBS) (Biological Industries), penicillin-streptomycin (500 U; PAN biotech), and β-mercaptoethanol (50 μM; Sigma-Aldrich) and stimulated with Dynabeads Mouse T-Activator CD3/CD28 (Gibco) at a cell:bead ratio of 1:1 in the presence of rmIL-2 (200 U/ml; Peprotech) (Wang et al., 2019). To obtain iTreg cells, rhTGFβ1 (2 or 0.5 ng/ml; Peprotech) was simultaneously added along with the reagents used for inducing Th0 cells. ACLY inhibitor: SB204990 (Tocris Bioscience), ACC inhibitor: PF05175157 (Tocris Bioscience), FASN inhibitor: cerulenin (Biovision), protein synthesis inhibitor: CHX (Tocris Bioscience), proteasome inhibitor: MG132 (Selleck), lysosome inhibitor: leupeptin (Selleck).

Induction of human iTreg in vitro

Human peripheral blood samples were obtained from Jilin Blood Center (Changchun, China). All work with human blood samples was approved by the local ethics committee (reference number: AP2019085, the ethical committee of the Northeast Normal University), and informed consent was obtained from all subjects. After Ficoll (GENVIEW) gradient, naive CD4⁺ T cells were isolated with MojoSort human CD4⁺ Naïve T Cell Isolation Kit (Biolegend) according to the manufacturer’s instructions (Ghosh et al., 2016). For Th0 induction, 2 to 3 × 10⁵ naive CD4⁺ T cells were cultured in RPMI 1640 medium (Sigma) supplemented with 10% FBS (Biological Industries), penicillin-streptomycin (500 U; PAN biotech), and β-mercaptoethanol (50 μM; Sigma-Aldrich) and stimulated with Dynabeads human T-Activator CD3/CD28 (Gibco) at a cell:bead ratio of 1:1 in the presence of rhIL-2 (200 U/ml; Gibco). To obtain iTreg cells, rhTGFβ1 (2 or 0.5 ng/ml; Peprotech) was simultaneously added along with the reagents used for inducing Th0 cells.

Flow cytometry analysis

Cells were collected in phosphate-buffered saline (PBS) containing 1% FBS (v/v) and fixed/permeabilized using the Transcription Factor Buffer Set (BD Biosciences) according to the manufacturer’s instructions. For mouse iTreg analysis, selected protein markers were stained with fluorescein isothiocyanate (FITC) rat anti-mouse CD4, phycoerythrin (PE) rat anti-mouse CD25, and Alexa Fluor 647 rat anti-mouse Foxp3 monoclonal antibodies (BD Biosciences). For human iTreg analysis, protein markers were stained with FITC rat anti-human CD4, PE mouse anti-human CD25, and Alexa Fluor 647 mouse anti-human Foxp3 monoclonal antibodies (Biolegend).

Quantitative real-time PCR

Total RNA was isolated using the TRIzol reagent (Invitrogen). Complementary DNA (cDNA) was synthesized with the PrimeScript RT reagent Kit plus gDNA Eraser (Takara) according to the manufacturer’s instructions. Real-time PCR was performed on the QuantStudio 3 Real-Time PCR Instrument (Applied Biosystems) with a TB Green Premix Ex Taq (Tli RNaseH Plus) reagent (Takara). The mRNA expression of genes was normalized to the expression of β-actin gene. Data were analyzed using the comparative cycling threshold method. Quantitative PCR primers are shown in Supplementary file 1.

siRNA transfection

All siRNA transfections were performed with Mouse T-cell nucleofection kit (Lonza) according to the instructions using X-001 progress as described previously (Mantei et al., 2008). Cells were transiently transfected with siRNAs (siRNAs against Acly, Cul3, and Klhl25 were commercially synthesized; Shanghai GenePharma) at a final concentration of 20 nM and rested in RPMI-1640 (with 10% FBS) for 4–5 hr before incubation under different conditions (Th0 or iTreg) for a desired period of time. siRNA sequences are shown in Supplementary file 1.

Plasmid construction

DNA sequences coding mouse Acly gene (NCBI Accession No. NM_001199296.1) from mouse CD4⁺ T cells and human Acly gene (NCBI Accession No. NM_001096.3) from human CD4⁺ T cells were amplified by PCR and subsequently cloned into pWPXLd vector (containing green fluorescent protein (GFP) sequence) to construct pWPXLd-mACLY and pWPXLd-hACLY, respectively. K530, K536, and K544 mutations in mACLY and K540, K546, and K554 in hACLY were introduced by whole-plasmid PCR followed by DpnI digestion to obtain pWPXLd-mACLY^{3KR (K530/K536/K544)} and pWPXLd-hACLY^{3KR (K540/K546/K554)}.

Lentivirus transduction of CD4⁺ T cells

HEK293T cells (without mycoplasma contamination) were grown in 10-cm cell-culture dishes to 70% confluence and were transfected with a three-plasmid system (pWPXLd-ACLY, PAX, PMD). The supernatant was harvested at 48, 72, and 96 hr after transfection and was concentrated 100-fold in an ultracentrifuge. Aliquots were stored at −80°C. Naive CD4⁺ T cells were cultured under Th0-inducing condition as described above for 16–24 hr and were spin infected for two rounds with lentivirus supernatants (ACLY^WT, ACLY^3KR, or Empty) in the presence of 8 μg/ml polybrene (Solarbio) at 1000 ×g, 90 min, at 32°C as described previously (Lin et al., 2019; Sun et al., 2015). After 24 hr of infection, supernatants were removed and cells were selectively cultured under either Th0- or iTreg-inducing condition for a desired period of time.

Assessment of metabolic molecules

For acetyl-CoA and OAA detection, cytosolic fractions from Th0 or iTreg cells were separated using Cell Mitochondria Isolation Kit (Beyotime). In brief, cells were washed with cold PBS, followed by homogenation for 20 s, and then centrifuged twice (first round, 600 ×g for 5 min; second round, 11,000 ×g for 5 min). Supernatants that represent cytosolic fractions without nuclei and mitochondria were confirmed by western blotting (WB) and deproteinized with a 10-kD spin filter by centrifuge for effluent preparation. Nuclear fraction was separated using Cell Nuclear/Cytoplasm Protein Isolation Kit (Beyotime) and also confirmed by WB. Cytosolic/nuclear acetyl-CoA and cytosolic OAA were assessed using PicoProbe acetyl-CoA fluorometric assay kit (Biovision) and OAA assay kit (Sigma), respectively, according to the manufacturer’s protocol. For the analysis of malonyl-CoA, cells were cultured under iTreg-polarization condition for 24 hr and lysed with ice-cold 5% sulfosalicylic acid (Sigma-Aldrich) containing 50 μM dithioerythritol (DTE) (Sigma-Aldrich). After 600 ×g centrifugation for 10 min at 4°C, the supernatants were collected for the detection of malonyl-CoA by high-performance liquid chromatography (HPLC). For the detection of HMG-CoA, mevalonate, and mevalonate-5-pyrophosphate, cells were homogenized in PBS and the supernatants were collected for detection of HMG-CoA, mevalonate, and mevalonate-5-pyrophosphate using HMG-CoA enzyme-linked immunosorbent assay (ELISA) kit (Shanghai Ruifan Biological Technology), Mevalonate ELISA kit (Sino Best Biological Technology), and Mevalonate-5-pyrophosphate ELISA kit (Shanghai Ruifan Biological Technology) according to the manufacturers’ instructions. Equal amount of cells was used for different groups in the same assay.

Extracellular flux analysis

For the FAO-associated oxygen consumption rate (OCR) assay by Seahorse XFp Analyzer (Agilent), Palmitate-BSA reagent (Agilent) and Mito Stress Test Kits (Agilent) were used according to the manufacturers’ instructions with minor modifications. In brief, cells were collected and adhered to poly-D-lysine-coated XFp plates (4 to 6 × 10⁵ cells/well) via centrifugation in serum-free XF Base Medium (Agilent). For evaluation of palmitate oxidation, cells were cultured with XF Base Medium (Agilent) in a non-CO₂ incubator for 15–20 min at 37°C. Subsequently, the XF Palmitate-BSA FAO Substrates (Agilent) palmitate-BSA (167 μM palmitate conjugated with 28 μM BSA) and 0.5 mM L-carnitine (Sigma Aldrich) were added to the medium for the assessment of OCR. Immediately, XF Cell Mito Stress Test was performed in a Seahorse XFp Analyzer (Agilent) by sequentially adding several modulators of mitochondrial function, including 1 mM oligomycin (Oligo) (Agilent), 1.5 mM fluorocarbonyl cyanide phenylhydrazone (FCCP) (Agilent), and 100 nM rotenone plus 1 mM antimycin A (Rot/Ant A) (Agilent). Data were analyzed with Wave software version 2.3.0 (Agilent) and proper statistical methods using GraphPad Prism version 6 (GraphPad Software).

¹³C-tracing assessment

Cell samples cultured in a medium containing [U-¹³C] glucose (11 mM) were mixed with 10 μl formate and 800 μl chloroform, and processed by four cycles of 1 min ultra-sonication and 1 min interval in ice-water bath followed by standing for 30 min at room temperature prior to centrifugation at 3000 ×g for 15 min. All chloroform was transferred to a new glass vial and mixed with 500 μl 75% ethanol (containing 0.5 M KOH) prior to incubation at 80°C for 60 min. Then, the mixture was added with 600 μl of hexane and vortexed for 1 min and made to stand for 30 min. After centrifugation at 3000 ×g for 15 min, all hexane layers were evaporated to dryness. The dry residue deposit was mixed with 10 μl 1-hydroxybenzotriazole (HoBt) (in dimethyl sulfoxide [DMSO]), 20 μl cholamine (in DMSO with 200 mM triethylamine [TEA]), and 10 μl O-(7-azabenzotriazol-1yl)-N,N,N',N'-tetramethyluronium hexafluorophosphate (HATU) (in DMSO) followed by incubating for 5 min at room temperature. 60 μl acetonitrile was added, followed by centrifuging at 3000 ×g for 15 min at 4°C prior to UHPLC-HRMS analysis.

The ultra-high performance liquid chromatography-tandem mass-spectrometry (UHPLC-MS/MS) analysis was performed on an Agilent 1290 Infinity II UHPLC system coupled to a 6470A Triple Quadrupole mass spectrometre (Santa Clara, CA, United States). Samples were injected onto a Waters UPLC BEH C18 column (100 mm × 2.1 mm, 1.7 μm) at a flow rate of 0.3 ml/min. The mobile phase consisted of water (phase A) and acetonitrile (phase B), both with 0.1% formate. The chromatographic separation was conducted by a gradient elution program as follows: 0 min, 10% B; 4 min, 40% B; 8 min, 45% B; 11 min, 50% B; 14 min, 70% B; 15 min, 90% B; 15.5 min, 100% B; 18 min, 100% B; 18.1 min, 10% B; 20 min, 10% B. The column temperature was 40°C. The raw data were processed by Agilent MassHunter Workstation Software (version B.08.00) by using the default parameters and assisting manual inspection to ensure the qualitative and quantitative accuracies of each compound. The peak areas of target compounds were integrated and the output was run for IsoCorrection analysis.

Assessment of metabolic enzyme activities

Cells were lysed by ultrasonic treatment in extracting buffer from the kits. Supernatants were collected and used for the analyses of enzymatic activities. ACC Activity Assay Kit (Suzhou Comin), ACLY Activity Assay Kit (Suzhou Comin), FASN Activity Assay Kit (Suzhou Comin), and CPT1 Activity Assay Kit (Suzhou Comin) were used according to the manufacturers’ instructions.

Immunoprecipitation and western blotting

Cells were lysed in cold western blot-immunoprecipitation (WB-IP) lysis buffer (Beyotime) for 30 min and centrifuged (at 4°C, 5 min, at 14,000 ×g) to remove cell debris. The supernatant was collected as a whole-cell lysate. ACLY, ubiquitin (Ub), and CUL3 were immunoprecipitated from the whole-cell lysates using anti-ACLY (Abcam), anti-ubiquitin (Abcam), and anti-CUL3 (Santa Cruz Biotechnology) antibodies coupling to Protein A/G PLUS Agarose Beads (Santa Cruz Biotechnology) overnight at 4°C. Nonspecific rabbit or mouse IgG antibody was used as a negative control. Immunoprecipitated proteins were mixed with 1× loading buffer and boiled at 100°C for 10 min followed by WB. For WB, protein samples were resolved by sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels and then proteins were transferred to polyvinylidene fluoride membranes (Millipore). The membranes were blocked with 5% nonfat milk for 1 hr at room temperature before incubation with primary antibodies overnight at 4°C. Mouse- or rabbit-conjugated horseradish peroxidase (HRP) secondary antibodies were added to the membranes for 50 min at room temperature, followed by washing three times with 1× Tris-buffered saline with Tween 20 (TBST), and visualized using Chemiluminescent HRP Substrate (Millipore) on Chemiluminescence Image System (Tanon Science and Technology Co, Ltd). The antibodies for WB are shown in Key Resources Table.

In vitro iTreg suppression assay

Naive CD4⁺ T cells from WT or Cd4^CreCul3^fl/fl mice were transfected with Acly-specific or scramble siRNA and cultured under Th0- or iTreg-polarization condition for 72 hr to obtain Th0 (WT), iTreg (WT), iTreg (Cul3^-/-), and iTreg (Cul3^-/-+siAcly) cells. Meanwhile, 2 × 10⁵ freshly isolated naive CD4⁺ T cells from WT mice pulse-labeled with carboxyfluorescein diacetate succinimidyl ester (CFSE) (Biolegend) at 0.5 μM for 20 min were co-cultured with different groups of iTreg cells at a ratio of 1:1 in the presence of Dynabeads Mouse T-Activator CD3/CD28 for 72 hr as described previously (De Rosa et al., 2015). The flow cytometry was used for the assessment of CFSE dilution, which indicates the suppressive function of iTreg cells in vitro.

Naive CD4⁺ T cells from Foxp3^YFP-Cre mice were transfected with siRNAs against Acly and (or) Cul3 and cultured under Th0- or iTreg-polarization condition for 72 hr followed by sorting yellow fluorescent protein (YFP)-positive cells to obtain Th0, YFP-iTreg, YFP-iTreg (siCul3), and YFP-iTreg (siCul3+siAcly) cells. Meanwhile, 2 × 10⁵ freshly isolated naive CD4⁺ T cells from WT mice pulse-labeled with CellTrace Violet (CTV) (Thermo Fisher) at 1 μM for 20 min were co-cultured with different groups of iTreg cells at a ratio of 1:1 in the presence of Dynabeads Mouse T-Activator CD3/CD28 for 72 hr as described previously. The flow cytometry was used for the assessment of CTV dilution (Johnson et al., 2018), which indicates the suppressive function of iTreg cells in vitro.

Mouse model of colitis

T-cell transfer colitis based on adoptive transfer of naive CD4⁺ T cells into Rag1^-/- mice is widely used for studying chronic intestinal inflammation (Furusawa et al., 2013). As described previously, 5 × 10⁵ freshly isolated naive CD4⁺ T cells were administrated into Rag1^-/- mice by intraperitoneal injection to induce colitis. Concomitant injection of 5 × 10⁵ Th0 (WT), iTreg (WT), iTreg (Cul3^-/-), or iTreg (Cul3^-/-+siAcly) cells was conducted for the evaluation of CUL3 and ACLY function. Meanwhile, Rag1^-/- mice of blank control group were administrated with PBS. Moreover, the function of ACLY in acute colitis was also assessed in DSS-induced colitis model. DSS (MP Biomedicals) dissolved in drinking water (2%, w/v) was given ad libitum to 6- to 8-week-old female C57BL/6J mice for 7 days followed by water for 3 days (Wirtz et al., 2017; Wirtz et al., 2007). Mice supplied with regular drinking water were included as a negative control. ACLY inhibitor, SB204990 (37.5 mg/kg/d) (Tocris Bioscience), was administrated orally every 2 days before the assessment of colitis.

Evaluation of colitis in mice

To assess the severity of colitis, DAI was weekly (T-cell transfer colitis) or daily (DSS-induced colitis) recorded by scoring the body weight loss, stool consistency, and blood in the stool as described in the literature (Furusawa et al., 2013; Wirtz et al., 2017; Wirtz et al., 2007). 7 weeks later (T-cell transfer colitis) or 10 days later (DSS-induced colitis), mice were euthanized for the examination of histopathological changes in colon tissues. Entire colons were removed and colon length was determined. Following cleaning with saline and fixation with formalin, colon samples were embedded in paraffin. Sections (3 μm) were stained with hematoxylin and eosin (H and E) and slides were blindly analyzed for intestinal inflammation according to the previous description (Wirtz et al., 2017; Wirtz et al., 2007). In addition, for DSS-induced colitis, the mononuclear cells from MLNs and the cLP were prepared as described previously (Atarashi et al., 2011) for the analysis of Treg cells by flow cytometry.

Induction of allergic diarrhea

Mice were sensitized with 50 μg of OVA (Sigma Aldrich) and 1 mg of alum (Thermo) in sterile saline by interperitoneal (ip) injection. From day 14 on, mice were challenged by oral gavage with 50 mg of OVA in saline three times per week for 3 weeks as described. Mice showing profuse liquid stool within 60 min after oral OVA challenge were recorded as diarrhea-positive. Th0 and iTreg cells under various conditions were adoptively transferred into mice, respectively, by tail vein injection (iv) after the first and forth challenge. 2 hr after the last oral administration, mice were sacrificed and blood samples and intestinal tissues were collected for detection of OVA-specific IgE and MCPT1 in serum by ELISA and eosnophil infiltration by H and E staining.

Data analysis and statistics

All experiments were done at least three times independently. Statistical analysis was performed using GraphPad Prism version 6 (GraphPad Software). Data are displayed as mean ± standard (SD). The p-values were calculated from Student’s unpaired t-test when comparing within two groups. One-way or two-way analysis of variance (ANOVA) was performed in the indicated figures when more than two groups were compared. p-values <0.05 were considered significant. p-values were indicated on graphs as *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001; ns, nonsignificant.

Acknowledgements

We thank Jeffrey D Singer (Department of Biology, Portland State University, Portland, OR, USA) and Zichun Hua (The State Key Laboratory of Pharmaceutical Biotechnology, Department of Biochemistry, College of Life Sciences, Nanjing University, Nanjing) for generously sponsoring the Cul3^fl/fl and Cd4^Cre mice, respectively. We also thank Weiwei Yang (Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, China) for critical comments. This work was supported by grants from the National Natural Science Foundation of China (32070896 and 31870896) and the Fundamental Research Funds for the Central Universities (2412019FZ028).

Funding Statement

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Contributor Information

Yunpeng Feng, Email: fengyp0108@nenu.edu.cn.

Min Wei, Email: weim750@nenu.edu.cn.

Kiyoshi Takeda, Osaka University, Japan.

Tadatsugu Taniguchi, Institute of Industrial Science, The University of Tokyo, Japan.

Funding Information

This paper was supported by the following grants:

National Natural Science Foundation of China 32070896 to Min Wei.
National Natural Science Foundation of China 31870896 to Min Wei.
Fundamental Research Funds for the Central Universities 2412019FZ028 to Yunpeng Feng.

Additional information

Competing interests

No competing interests declared.

Author contributions

Conceptualization, Data curation, Software, Formal analysis, Validation, Visualization, Methodology, Writing - original draft, Writing - review and editing.

Software, Formal analysis, Methodology, Writing - original draft, Writing - review and editing.

Data curation, Formal analysis, Visualization, Methodology.

Formal analysis, Methodology.

Resources.

Data curation.

Software, Methodology.

Data curation.

Formal analysis.

Data curation.

Conceptualization, Resources, Formal analysis.

Conceptualization, Supervision, Funding acquisition, Writing - original draft, Writing - review and editing.

Conceptualization, Supervision, Funding acquisition, Validation, Writing - original draft, Project administration, Writing - review and editing.

Ethics

Human subjects: All work with human blood samples was approved by the local ethics committee (Reference number: AP2019085, the ethical committee of the Northeast Normal University), and informed consent was obtained from all subjects.

Animal experimentation: All mouse experiments were conducted in accordance with the protocols for animal use, treatment, and euthanasia approved by the institutional animal care and use committee (IACUC) of Northeast Normal University (Reference number: AP2019085). The number of experimental mice used for research purposes is reduced as far as possible while still allowing the scientific purpose of the research to be achieved.

Additional files

Source data 1. Original data and blots supporting main figures and figure supplements.

elife-62394-data1.zip^{(36.5MB, zip)}

Supplementary file 1. List of oligonucleotides.

Primers for PCR and quantitative PCR, and sequences of siRNAs are included.

elife-62394-supp1.docx^{(37KB, docx)}

Transparent reporting form

elife-62394-transrepform.docx^{(112.1KB, docx)}

Data availability

All data generated or analysed during this study are included in the manuscript and supporting file; Source Data files have been provided for Figures 1-6.

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eLife. doi: 10.7554/eLife.62394.sa1

Decision letter

Editor: Kiyoshi Takeda¹

In the interests of transparency, eLife publishes the most substantive revision requests and the accompanying author responses.

Acceptance summary:

In this study, the authors reveal downregulation of ACLY expression as a metabolic determinant of iTreg cell generation induced by TGFβ1. The authors show that neutral lipid content is decreased during iTreg compared to Th0 differentiation. Using complementary systems of overexpression, gene repression, and drug inhibition, the authors established that ACLY expression or activity is correlated with alterations in neutral lipid content in iTreg cells, and more importantly, changes in iTreg differentiation in both mouse and human cells. Mechanistically, the authors show that ACLY is targeted for ubiquitination and proteasomal degradation by CUL3-KLHL25 and further demonstrate that the CUL3-ACLY axis is important for regulating iTreg cell-dependent suppression of T cell proliferation and development of colitis and allergic diarrhea in vivo. This study will be of interest to those in the immunometabolism field and will have broader interest to those studying the therapeutic efficacy of ACLY inhibition in certain diseases.

Decision letter after peer review:

Thank you for submitting your article "ACLY ubiquitination by CUL3-KLHL25 coordinates fatty acid synthesis to promote iTreg differentiation" for consideration by eLife. Your article has been reviewed by 2 peer reviewers, one of whom is a member of our Board of Reviewing Editors, and the evaluation has been overseen by Tadatsugu Taniguchi as the Senior Editor. The reviewers have opted to remain anonymous.

The reviewers have discussed the reviews with one another and the Reviewing Editor has drafted this decision to help you prepare a revised submission.

Summary:

In this study, the authors show that neutral lipid content is decreased during iTreg compared to Th0 differentiation. Using complementary systems of overexpression, gene repression, and drug inhibition, the authors established that ACLY expression or activity is correlated with alterations in neutral lipid content in iTreg cells, and more importantly, changes in iTreg differentiation in both mouse and human cells. Mechanistically, the authors show that ACLY is targeted for ubiquitination and proteasomal degradation by CUL3-KLHL25 and further demonstrate that the CUL3-ACLY axis is important for regulating iTreg cell-dependent suppression of T cell proliferation and development of colitis in vivo.

This is a well performed study that reveals downregulation of ACLY expression as a metabolic determinant of iTreg cell differentiation induced by TGFβ1.

Overall, the experiments were well performed and the study clearly shows the important roles of CUL3-KLHL25-mediated ACLY ubiquitination in iTreg differentiation. We have the following suggestions to improve the manuscript.

Essential revisions:

1. The authors provide convincing, but correlative, data for decreased neutral lipid staining (using BODIPY) in iTreg cells that is impacted by altered expression or activity of ACLY. BODIPY staining alone cannot distinguish if these changes are due only to alterations of de novo fatty acid synthesis. Indeed, such differences may also reflect changes in lipid uptake or even degradation via the fatty acid oxidation pathway. In addition, ACLY-derived acetyl-CoA can also serve as a precursor for the mevalonate-cholesterol biosynthesis pathway, as well as a substrate for acetyltransferase enzymes. Additional experiments are therefore required to demonstrate that downregulation of ACLY-dependent fatty acid synthesis is essential for iTreg cell differentiation, including:

a. Assess de novo lipid synthesis using radiolabeled acetate or glucose in ACLY-sufficient or -deficient iTreg (or SB204990-treated) cells to establish that the change in BODIPY staining is attributed to reduced lipid synthesis.

b. Add back palmitate, mevalonate, cholesterol, or acetate to iTreg cell cultures to establish a more direct relationship between ACLY downregulation/inhibition and fatty acid synthesis for iTreg cell generation.

c. Assess changes in histone acetylation by immunoblot, imaging, or flow cytometry analysis.

d. Measure nuclear levels of acetyl-CoA, as ACLY has been reported to enter the nucleus and influence histone acetylation (Sivanand et al., 2017 Mol Cell). The authors currently only assess changes in non-nuclear acetyl-CoA levels.

2. The authors suggest that downregulation of ACLY is important for promoting activation of CPT1a-dependent fatty acid oxidation, which has been implicated for iTreg cell generation in vitro. Do ACLY-deficient or SB204990-treated iTreg cells have increased rates of fatty acid oxidation?

3. TGFβ1 is also important for the development of thymic-derived Treg cells (Liu et al. 2008 Nat Immunol; Ouyang et al. 2010 Immunity). Is ACLY expression altered as cells differentiate from double-positive thymocytes to Treg precursors to mature Treg cells in the thymus?

4. For data presented in Figure 5, it remains unclear if the altered suppressive activity of CUL3- +/- ACLY-deficient iTreg cells in vitro or in vivo is due to differences in the proportion of iTreg cells or changes in suppressive function. To address this, the authors should perform the below experiments:

a. Assess the expression of surrogate molecules associated with Treg cell suppressive activity on Foxp3⁺ iTreg cells under the various conditions (e.g. CTLA4, ICOS, TIGIT, IL-10, etc.).

b. Assess the number of Treg cells in the intestine of Cd4-cre:Cul3-deficient mice. Also, the authors should co-stain the intestinal Treg cells with RORγt and Helios to better distinguish peripherally-induced and thymic-derived Treg cells in the intestines (Sefik et al., 2015 Science; Ohnmacht et al., 2015 Science).

c. Use naïve T cells from Foxp3 reporter mice and sort purify Foxp3⁺ iTreg cells for the in vitro suppressive assay.

d. Would be interesting if the authors investigate, for ex, allergic diarrhea, in which intestinal Treg cells are implicated in the prevention.

5. The therapeutic relevance of SB204990 in the DSS colitis model shown in Figure S8 should be discussed in the Results section of the manuscript, not only the Discussion.

eLife. 2021 Sep 7;10:e62394. doi: 10.7554/eLife.62394.sa2

Author response

Essential revisions:

1. The authors provide convincing, but correlative, data for decreased neutral lipid staining (using BODIPY) in iTreg cells that is impacted by altered expression or activity of ACLY. BODIPY staining alone cannot distinguish if these changes are due only to alterations of de novo fatty acid synthesis. Indeed, such differences may also reflect changes in lipid uptake or even degradation via the fatty acid oxidation pathway. In addition, ACLY-derived acetyl-CoA can also serve as a precursor for the mevalonate-cholesterol biosynthesis pathway, as well as a substrate for acetyltransferase enzymes. Additional experiments are therefore required to demonstrate that downregulation of ACLY-dependent fatty acid synthesis is essential for iTreg cell differentiation, including:

We totally agree with reviewers that comprehensive characterization of ACLY-repression-induced alterations in cell metabolism during iTreg cell differentiation is critical and pivotal. Thus we have performed a series of new experiments including radio-labelling and rescue assays as suggested to improve this manuscript.

a. Assess de novo lipid synthesis using radiolabeled acetate or glucose in ACLY-sufficient or -deficient iTreg (or SB204990-treated) cells to establish that the change in BODIPY staining is attributed to reduced lipid synthesis.

As the reviewer pointed out, BODIPY staining alone cannot pinpoint the contribution from ACLY-dependent alteration in FAS to de novo lipid synthesis. We thus have tracked [U-¹³C] glucose in iTreg cells inhibited for ACLY by SB204990 and found moderate to significant reductions in different ¹³C-labelled fatty acids (new Figure 2A). This is consistent with decreased BODIPY staining in response to ACLY inhibition (previous Figure 1H) and again supports an important role for ACLY in de novo lipid synthesis. In addition, we have explained the isotope tracing analysis of FAS in the revised manuscript (please see page 6 line 135-138).

b. Add back palmitate, mevalonate, cholesterol, or acetate to iTreg cell cultures to establish a more direct relationship between ACLY downregulation/inhibition and fatty acid synthesis for iTreg cell generation.

Following the reviewer’s constructive suggestion, we have performed a series of rescue assays to carefully evaluate the functional consequences of ACLY-dependent metabolic alterations in iTreg differentiation. Upon the addition of mevalonate, cholesterol or acetate, upregulated iTreg differentiation induced by ACLY inhibition remained unchanged (new Figure 2—figure supplement 2A-C, Figure R1A-B). In line with this observation, levels of HMG-CoA, mevalonate, mevalonate-5-pyrophosphate, cholesterol as well as nuclear acetyl-CoA were unaffected in response to ACLY inhibition (new Figure 2—figure supplement 1A-D, Figure 2—figure supplement 3A-B). In addition, histone acetylation remained rather stable regardless of whether ACLY was inhibited or not (new Figure 2—figure supplement 3C-D). These results indicate that ACLY are unlikely to regulate iTreg differentiation via mevalonate-cholesterol biosynthesis pathway or histone acetylation.

Despite a reduction in FAS resulted from ACLY inhibition (new Figure 2A), addback of palmitate still could not rescue changes in iTreg differentiation induced by ACLY inhibition (new Figure 2—figure supplement 4A, Figure 2B). One may consider that the supplement of a single end-product is probably not sufficient enough to rescue the whole FAS. To evaluate the role of individual intermediate metabolite from FAS in ACLY-dependent regulation of iTreg differentiation, we separately blocked ACC and FASN in cells inhibited for ACLY by SB204990 (new Figure 2—figure supplement 4B). FASN inhibition by cerulenin, but not ACC inhibition by PF05175157, effectively abrogated ACLY-inhibition-induced iTreg differentiation (new Figure 2—figure supplement 4C), suggesting an important role for malonyl-CoA in ACLY-dependent regulation of iTreg differentiation. As the substrate of FASN, malonyl-CoA declined upon ACLY inhibition (new Figure 2—figure supplement 4D). Importantly, adding malonyl-CoA back totally blocked ACLY-inhibition-induced changes in iTreg differentiation (new Figure 2C). Together, these data argue that ACLY inhibition promotes iTreg differentiation probably by reducing malonyl-CoA. In the revised manuscript, these data have been selectively integrated and the main text has been modified accordingly (please see page 6-7 line 138-165).

c. Assess changes in histone acetylation by immunoblot, imaging, or flow cytometry analysis.

As suggested, we have assayed histone acetylation, which remained largely unchanged irrespective of the presence or absence of ACLY inhibitor (new Figure 2—figure supplement 3C-D). We also compared histone acetylation levels in Th0 and iTreg cells and found they were rather similar (Figure R2A-B). These results indicate that ACLY-dependent regulation of iTreg differentiation may not through histone acetylation. In the revised manuscript, this point has been integrated (please see page 7 line 147-149).

d. Measure nuclear levels of acetyl-CoA, as ACLY has been reported to enter the nucleus and influence histone acetylation (Sivanand et al., 2017 Mol Cell). The authors currently only assess changes in non-nuclear acetyl-CoA levels.

Following the reviewer’s suggestion, we have assessed nuclear acetyl-CoA levels at different conditions. Upon ACLY inhibition, the level of acetyl-CoA in nuclear fraction failed to change significantly (new Figure 2—figure supplement 3A-B). In a parallel assay comparing Th0 to iTreg cells, levels of nuclear acetyl-CoA also seemed rather similar (Figure R2C-D). In line with unchanged histone acetylation upon ACLY inhibition (new Figure 2—figure supplement 3C-D), these results suggest a dispensable role for ACLY in the regulation of nuclear acetyl-CoA level as well as histone acetylation during iTreg differentiation. In addition, we have also discussed the assessment of nuclear acetyl-CoA level in the revised manuscript (please see page 6-7 line 144-147).

2. The authors suggest that downregulation of ACLY is important for promoting activation of CPT1a-dependent fatty acid oxidation, which has been implicated for iTreg cell generation in vitro. Do ACLY-deficient or SB204990-treated iTreg cells have increased rates of fatty acid oxidation?

To address this point, we examined palmitate-dependent oxidation and CPT1 activity, which have been widely used for evaluating the rate of FAO (Hao et al., 2021; Kim et al., 2002). Upon ACLY inhibition, both palmitate-dependent oxidation and CPT1 activity were significantly elevated (new Figure 2D-E, R3A-B). In the revised manuscript, these data have been selectively integrated and the main text has been modified accordingly (please see page 7 line 169-170).

3. TGFβ1 is also important for the development of thymic-derived Treg cells (Liu et al. 2008 Nat Immunol; Ouyang et al. 2010 Immunity). Is ACLY expression altered as cells differentiate from double-positive thymocytes to Treg precursors to mature Treg cells in the thymus?

As suggested, we examined ACLY expression as cells differentiate from double-positive thymocytes to Treg precursors and mature Treg cells. During thymic-derived Treg cell development, ACLY expression increased gradually (Figure R5). Levels of ACLY in Treg precursors (CD4⁺CD8^-CD25⁺Foxp3^-) and mature Treg cells (CD4⁺CD8^-CD25⁺Foxp3⁺) are significantly higher than that in double-positive thymocytes (CD4⁺CD8⁺) (Figure R5).

In contrast to iTreg cells that are dependent on FAO, tTreg cells have been found to rely on glycolysis and lipid synthesis (Priyadharshini et al., 2018; Zeng et al., 2013). Although both iTreg and tTreg differentiation are reliant on TGFβ1, different levels of ACLY may be of help for cells to establish distinct metabolic patterns. For instance, relatively high level of ACLY in tTreg cells (Figure R5) can support efficient lipid synthesis, which is known to be important for the suppressive function of tTreg cells (Zeng et al., 2013).

4. For data presented in Figure 5, it remains unclear if the altered suppressive activity of CUL3- +/- ACLY-deficient iTreg cells in vitro or in vivo is due to differences in the proportion of iTreg cells or changes in suppressive function. To address this, the authors should perform the below experiments:

a. Assess the expression of surrogate molecules associated with Treg cell suppressive activity on Foxp3⁺ iTreg cells under the various conditions (e.g. CTLA4, ICOS, TIGIT, IL-10, etc.).

We truly appreciate the reviewer’s suggestion and have assessed the expression of surrogate molecules associated with the suppressive activity of iTreg cells under various conditions. Neither CUL3 deficiency (Cul3^-/-) nor the lack of CUL3 and ACLY (Cul3^-/- and siAcly) changed the expression of representative surrogate molecules, such as CTLA4, ICOS, TIGIT and IL-10, in Foxp3⁺ iTreg cells (new Figure 4—figure supplement 4A). These data suggest that ACLY-dependent regulation of iTreg is probably not through modulation of its suppressive function. In the revised manuscript, we have integrated these new data and modified the main text accordingly (please see page 10 line 256-259).

b. Assess the number of Treg cells in the intestine of Cd4-cre:Cul3-deficient mice. Also, the authors should co-stain the intestinal Treg cells with RORγt and Helios to better distinguish peripherally-induced and thymic-derived Treg cells in the intestines (Sefik et al., 2015 Science; Ohnmacht et al., 2015 Science).

As the reviewer suggested, we have assessed the number of CD4⁺Foxp3⁺ Treg cells in intestines from Cd4^CreCul3^fl/fl mice and found a dramatic decrease as compared to WT mice (new Figure 4—figure supplement 3C, Figure R6). Furthermore, both peripherally-induced (Foxp3⁺RORγt⁺) and thymic-derived (Foxp3⁺Helios⁺) Treg cells were reduced (Figure R6). Together, these data confirmed the CUL3-deletion-induced impairment in iTreg differentiation in vivo. In the revised manuscript, these data have been selectively integrated and the main text has been modified accordingly (please see page 10 line 244-246).

c. Use naïve T cells from Foxp3 reporter mice and sort purify Foxp3⁺ iTreg cells for the in vitro suppressive assay.

We took the advantage of the established Foxp3^YFP-Cre mice (Rubtsov et al., 2008) and isolated naïve CD4⁺ T cells for functional assays. Following the transfection of siRNAs against Cul3 and (or) Acly, naïve CD4⁺ T cells were induced under iTreg differentiation condition prior to the analysis of Foxp3-YFP⁺ iTreg cells. Clearly, Cul3 knockdown by siRNA caused a reduction in Foxp3-YFP⁺ iTreg cell number, which could be blocked by a simultaneous depletion of ACLY (new Figure 4—figure supplement 4B). These observations completely recapitulated our previous in vitro findings (new Figure 4E) and confirmed the important role of CUL3-ACLY axis during iTreg differentiation. In addition, the lack of CUL3 and (or) ACLY did not seem to affect the suppressive function of Foxp3-YFP⁺ iTreg cells, because T cell proliferation remained unchanged, regardless of whether wild-type, siCul3- or siCul3/siAcly-treated Foxp3-YFP⁺ iTreg cells were presented in the co-culture system (new Figure 4—figure supplement 4B). Meanwhile, the main text of the revised manuscript has been modified accordingly (please see page 10 line 259-264).

d. Would be interesting if the authors investigate, for ex, allergic diarrhea, in which intestinal Treg cells are implicated in the prevention.

Following the reviewer’s suggestion, we established an OVA-induced allergic diarrhea mouse model for the functional evaluation of CUL3-dependent ACLY degradation in iTreg differentiation (new Figure 6—figure supplement 4A). Upon OVA stimulation, mice developed diarrhea and exhibited upregulated OVA-specific IgE antibodies and mastocyte protease (MCPT-1) in the serum as expected (Kordowski et al., 2019) (new Figure 6—figure supplement 4B-E). Importantly, the adoptive transfer of wild-type (WT) iTreg cells, but not CUL3 deficient (Cul3^-/-) cells, into recipient mice remarkably alleviated diarrhea-associated defects (new Figure 6—figure supplement 4B-E). The alleviation effect from CUL3 deficiency on the diarrhea was rescued, when we used targeting siRNA to knock down Acly (new Figure 6—figure supplement 4B-E). Together, these in vivo data argue an important role for CUL3-mediated ACLY ubiquitination in the regulation of diarrhea. In the revised manuscript, we have explained the functional assessment for Treg cells derived from CUL3 and (or) ACLY deficiency in allergic diarrhea (please see page 12 line 311-320).

5. The therapeutic relevance of SB204990 in the DSS colitis model shown in Figure S8 should be discussed in the Results section of the manuscript, not only the Discussion.

Following the reviewer’s suggestion, we have discussed the therapeutic relevance of SB204990 in the DSS colitis model in the Results section of the manuscript (Page 12 line 304-307).

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Source data 1. Original data and blots supporting main figures and figure supplements.

elife-62394-data1.zip^{(36.5MB, zip)}

Supplementary file 1. List of oligonucleotides.

Primers for PCR and quantitative PCR, and sequences of siRNAs are included.

elife-62394-supp1.docx^{(37KB, docx)}

Transparent reporting form

elife-62394-transrepform.docx^{(112.1KB, docx)}

Data Availability Statement

All data generated or analysed during this study are included in the manuscript and supporting file; Source Data files have been provided for Figures 1-6.

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PERMALINK

ACLY ubiquitination by CUL3-KLHL25 induces the reprogramming of fatty acid metabolism to facilitate iTreg differentiation

Miaomiao Tian

Fengqi Hao

Xin Jin

Xue Sun

Ying Jiang

Yang Wang

Dan Li

Tianyi Chang

Yingying Zou

Pinghui Peng

Chaoyi Xia

Jia Liu

Yuanxi Li

Ping Wang

Yunpeng Feng

Min Wei

Roles

Abstract

Introduction

Results

ACLY is critical for the efficient differentiation of iTreg cells

Figure 1. ACLY is critical for iTreg cell differentiation.

Figure 1—figure supplement 1. Analyses of ACLY activity during iTreg differentiation.

ACLY is required for the reprogramming of fatty acid metabolism during iTreg differentiation

Figure 2. ACLY inhibition induces the reprogramming in fatty acid metabolism during iTreg differentiation.

Figure 2—figure supplement 1. Detection of metabolic intermediates in mevalonate-cholesterol synthesis pathway upon ACLY inhibition.

Figure 2—figure supplement 2. Impact of mevalonate and cholesterol on iTreg differentiation.

Figure 2—figure supplement 3. Examination of nuclear acetyl-CoA and histone acetylation upon ACLY inhibition.

Figure 2—figure supplement 4. Functional comparison between ACC and FASN in ACLY-inhibition-induced iTreg differentiation.

Figure 2—figure supplement 5. Functional evaluation of CPT1 in ACLY-inhibition-induced iTreg differentiation.

TGFβ1 induces ACLY ubiquitination and degradation during iTreg differentiation

Figure 3. TGFβ1 induces ACLY ubiquitination and degradation during iTreg differentiation.

Figure 3—figure supplement 1. Assessment of ACLY activity and mRNA in Th0 and iTreg cells.

Figure 3—figure supplement 2. K530/536/544 are important for ACLY degradation.

CUL3-KLHL25 is responsible for TGFβ1-mediated ACLY ubiquitination

Figure 4. CUL3-KLHL25 is responsible for TGFβ1-mediated ACLY ubiquitination.

Figure 4—figure supplement 1. Examination of ACLY association with ubiquitin ligases and deubiquitinase.

Figure 4—figure supplement 2. Knockdown of CUL3-KLHL25 blocks TGFβ1-induced ACLY degradation.

Figure 4—figure supplement 3. Analysis of Treg number in the intestines of Cd4CreCul3fl/fl mice.

Figure 4—figure supplement 4. Functional analysis of ACLY ubiquitination for iTreg cells.

CUL3-KLHL25-ACLY ubiquitination axis regulates human iTreg differentiation

Figure 5. CUL3-KLHL25-ACLY ubiquitination axis regulates human iTreg differentiation.

ACLY inhibition alleviates mouse colitis by promoting iTreg cell generation

Figure 6. ACLY ubiquitination promotes iTreg cell generation and alleviates mouse colitis.

Figure 6—figure supplement 1. ACLY knockdown influences the differentiation of naive CD4+ T cells derived from Cul3 knockout mice.

Figure 6—figure supplement 2. SB204990 administration elevates iTreg population in vivo and alleviates mice colitis.

Figure 6—figure supplement 3. ACLY inhibition promotes iTreg differentiation and relieves mice colitis.

Figure 6—figure supplement 4. ACLY ubiquitination is involved in the regulation of iTreg differentiation and allergic diarrhea in mice.

Discussion

Materials and methods

Key resources table.

Animals

Induction of mouse iTreg in vitro

Induction of human iTreg in vitro

Flow cytometry analysis

Quantitative real-time PCR

siRNA transfection

Plasmid construction

Lentivirus transduction of CD4+ T cells

Assessment of metabolic molecules

Extracellular flux analysis

13C-tracing assessment

Assessment of metabolic enzyme activities

Immunoprecipitation and western blotting

In vitro iTreg suppression assay

Mouse model of colitis

Evaluation of colitis in mice

Induction of allergic diarrhea

Data analysis and statistics

Acknowledgements

Funding Statement

Contributor Information

Funding Information

Additional information

Competing interests

Author contributions

Ethics

Additional files

Figure 4—figure supplement 3. Analysis of Treg number in the intestines of Cd4^CreCul3^fl/fl mice.

Figure 6—figure supplement 1. ACLY knockdown influences the differentiation of naive CD4⁺ T cells derived from Cul3 knockout mice.

Lentivirus transduction of CD4⁺ T cells

¹³C-tracing assessment