Long non-coding RNAs in tuberculosis: Immune regulation and clinical biomarker potential

Summary

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains the leading infectious cause of mortality worldwide, with an estimated 1.25 million deaths in 2023. Despite therapeutic advances, the lack of precise early screening tools continues to impede epidemic control. Long non-coding RNAs (lncRNAs) have emerged as essential modulators of host anti-Mtb immunity, and elucidating their functional mechanisms is pivotal for developing effective interventions. This review systematically synthesizes lncRNA-mediated immune regulation during Mtb infection, with emphasis on their roles in modulating immune cell death, extending beyond apoptosis to encompass necrosis and pyroptosis. Importantly, we provide a comprehensive analysis of lncRNAs and related gene polymorphisms as predictive biomarkers for anti-TB drug-induced adverse reactions. Current research gaps and future priorities are also discussed. Together, the dual potential of lncRNAs as molecular diagnostics and candidate targets for host-directed therapy represents a promising frontier in TB management.

Graphical abstract

Immunology; Medical microbiology; Molecular biology

Introduction

Tuberculosis (TB), an enduring infectious disease caused by Mycobacterium tuberculosis (Mtb), remains the leading cause of death from a single infectious agent worldwide. The WHO 2024 Global Tuberculosis Report documented 10.8 million new cases, marking a 6.9% increase compared with 2020 and reversing the previous declining trend.¹ Alarmingly, approximately one-quarter of the world’s population harbors latent TB infection (LTBI), in which bacilli persist asymptomatically within granulomatous niches of the lung for decades.^2,3,4 Although host immunity typically contains LTBI, 5%–15% of infected individuals progress to active disease because of failures in immune containment, allowing bacteria to reactivate and spread.⁵

Accurate TB diagnosis remains a persistent challenge for clinicians and microbiologists, as no laboratory test achieves 100% predictive accuracy for this treatment-intensive disease. Conventional diagnostic methods—including smear microscopy and mycobacterial culture—exhibit suboptimal sensitivity (40%–60%), prolonged turnaround times (2–6 weeks), and limited specificity.⁶ Tests such as the tuberculin skin test (TST) and interferon-gamma release assays (IGRAs) cannot reliably distinguish LTBI from active tuberculosis as both elicit similar antigenic responses.^7,8 Furthermore, Mtb, a highly successful pathogen living alongside humans, has developed a variety of immune escape mechanisms (e.g., phagosome maturation arrest and antigen masking) to achieve long-term survival in host cells.^9,10 These collective limitations highlight the urgent need for new diagnostic and treatment methods to reduce the global TB burden.

Advancements have recently quickened the process of finding biomarkers for TB risk evaluation and therapeutic targeting. Importantly, numerous long non-coding RNAs (lncRNAs) have been found to be dysregulated in TB and are crucial in managing biological processes, including immune responses and host-pathogen interactions.¹¹ LncRNAs are RNA molecules over 200 nucleotides long that do not have a substantial open reading frame (ORF).¹² Although functional characterization remains incomplete, lncRNAs are now recognized as master epigenetic regulators governing genomic architecture and key pathological pathways.^13,14 Groundbreaking findings over the past decade have transformed research frameworks, highlighting the importance of non-coding genomes in the etiology of TB, beyond just protein-coding genes.^{15,16,17,18,19,20}

This review systematically synthesizes lncRNA expression profiles in TB patients (Table 1) and elucidates their emerging immunomodulatory functions during Mtb infection. We further evaluate the translational potential of lncRNAs as diagnostic and prognostic biomarkers and delineate critical knowledge gaps requiring further investigation.

Table 1.

Investigations into the changes of lncRNAs in TB

Study design	Sample source	LncRNAs		p-value	Techniques	AUCs	Biological effect	Reference
		Up	Down
30 ATB vs.25 LTBI vs.30 HC	T cells	BC010527 ENST00000457582 AK055252 chr2:192293450–192304436+	ENST00000429730 ENST00000515242 ENST00000456688 uc011dma.1	<0.05	microarray RT-qPCR	0.75 – – –	deregulated lncRNAs were largely connected to the MAPK pathway, cytokine-cytokine receptor interactions, and the Toll-like receptor pathway, among other pathways.their potential functions are still largely unknown	Yi et al.21
31 ATB vs. 35 HC	B cells	RP11-99H8.1 RP11-478H13.3 ENST00000507373 KIAA0664L3	RP1-90G24.6 TCONS_00024847 LINC00324 AC109826.2	<0.05	microarray RT-qPCR	– – –	TLR signaling pathway and TGF-β signaling pathway were the primary pathways linked to these lncRNAs	Fu et al.18
26 untreated TB vs.24 cured TB vs.29 HC	plasma	ENST00000416708 T150805 T274995	uc.48+ NR_105053 NR_126366	<0.01	microarray RT-qPCR	– 0.94 –	the identification of potential biomarkers to differentiate untreated from cured TB offers an experimental basis for assessing TB treatment efficacy	Li et al.22
56 ATB vs.49 HC	PBMCs	NR_047626 NR_001545 NR_047614 TCONS_00017629	ENST00000434839 (lncRNA-CGB) ENST00000421322 uc004ebm.1 NR_003255	<0.05	microarray RT-qPCR	– – – – –	the interaction between LncRNA-CGB and EZH2 negatively affected H3K27Me3 epigenetic programming, which led to higher IFN-γ expression, suggesting that the gut bacteria-lncRNA-H3K27Me3 pathway contributes to immune defense against TB	Yang et al.23
31 PTB vs.32 HC	PBMCs	MIR3945HG V1 MIR3945HG V2 NR_046398 NR_026913	ENST00000360485 ENST00000551898 (PCED1B-AS1) ENST00000429482	<0.001	RT-qPCR microarray	0.93 0.96 – –	despite the unclear mechanisms, they have been introduced as promising candidates for TB diagnostic biomarkers	Yang et al.24
20 ATB vs.20 HC	macrophages	–	ENST00000551898 (PCED1B-AS1)	<0.05	WB TEM	– –	reduce monocyte apoptosis and increase autophagy	Li et al.25
637 PTB vs.1127 HC	PBMCs	n335265 (0.89) ENST00000518552 TCONS_00013664	ENST00000497872 n333737 n344917	<0.05	microarray RT-qPCR	0.89 0.89 0.88	enable the early detection of PTB cases in patients suspected of having TB but showing negative microbiological results, warranting further examination	Hu et al.26
238 PTB vs.298 HC	PBMCs	–	n344917	<0.001	microarray RT-qPCR	–	prospective molecular marker for PTB diagnosed in clinical settings	Meng et al.27
805 PTB vs.1954 HC	PBMCs	TCONS_00001838 TCONS_00013664 ENST00000416679	n406498	<0.001	microarray RT-qPCR	0.86 0.86 –	the lncRNAs that are expressed differently might play a role in controlling various biological processes; TCONS_00001838 and n406498 could serve as novel molecular indicators for TB	Chen et al.28
ATB vs.HC	T cells	BC050410 (lncRNA-CD244) ENST00000484151 ENST00000457582 NR_002161	CR592555 AK097103	<0.001	microarray RT-qPCR flow cytometry	– – – –	contributing to TB infection pathology through the inhibition of IFN-γ and TNF-α	Wang et al.29
467 TB vs. 473 HC	whole blood	–	AC145676.1–6 TGS1-1	<0.001	RT-qPCR	– –	results in thrombocytopenia occurring during anti-TB therapy due to interference with the TLR pathway and other immune interactions	Bai et al.30
53 ATB vs.106 HC	plasma	ENST00000354432 ENST00000427151 ENST00000442037 NR_044997 uc004cov.4	ENST00000428188 TCONS_00019972 TCONS_00004316 ENST00000568137 ENST00000584688	<0.05	microarray RT-qPCR	– – – – –	exhibit a space-specific expression pattern (ENST00000354432); widespread expression in adipose tissue (RPKM 5.1), endometrium (RPKM 3.8), and 25 additional tissues. (ENST00000427151), as possible molecular biomarkers for the quick diagnosis of TB	He et al.31
106 TB vs.55 HC	PBMCs	NEAT1-1 NEAT1-2	–	<0.01	RT-qPCR	–	involved with TB outcomes and may regulate the transcription of various genes	Huang et al.32
11 Sputum negative TB	Lung tissue (low and high metabolic activity)	ENST00000429730.1 MSTRG.93124.1	ENST00000602711.1	<0.001	RNA-seq RT-qPCR	– –	possible signs of metabolic activity in TB lesions for cases of sputum-negative TB	Wang et al.33
90 PTB vs.85 HC	serum	NORAD	–	<0.001	RT-qPCR	0.92	by targeting miR-618, it serves as a potential biomarker for diagnosing PTB and enhances the survival of Mtb-infected macrophages along with the inflammatory immune response	Sun et al.34
114 ATB vs.105 HC	plasma	ENST00000570366 LINC00870 NR_003142	ENST00000422183	<0.01 <0.05 <0.05	microarray RT-qPCR	0.67 0.74 0.66	management of T cell activation, Th1 immune response, selection of T cells either positively or negatively, and reaction of cells to IFN-γ, causing atypical immune functions	Chen et al.35
32 TB vs.20 LTBI vs.25 HC	plasma/sputum	NR_038221 (LINC00870)	–	<0.05	RT-qPCR	0.68 –	modulates Th1/Th2 type immune response via the JAK/STAT signaling pathway in Mtb-infected PBMCs	Jianfang et al.36
34 ATB vs. 35 HC	T cells	XLOC-014219 LOC152742 LINC00229	LOC200772 LINC00278 AC016683.6	<0.05	RT-qPCR microarray	– 0.85 –	the malfunction of CD8+ T cells is involved in the development of active TB	Fu et al.37
48 ATB/Obsolete TB/BCG patients vs.44 HC	plasma/sputum	LOC152742	–	<0.0001	RT-qPCR	–	while the mechanisms are not yet clear, it has potential as a biomarker for ATB diagnosis and treatment	Wang et al.38
79 ATB vs.79 HC	plasma	NONHSAT257478.1	NONHSAT067134.2 HSAT148822.1 NONHSAT101518.2 HSAT078957.2	<0.0001	RT-qPCR	0.87 0.71 0.95 0.89	in the plasma of ATB patients, four lncRNAs are downregulated and could serve as potential diagnostic biomarkers for ATB	Fang et al.39

Biogenesis and regulation of LncRNAs

LncRNAs comprise diverse subtypes including antisense RNAs, pseudogenes, long intergenic non-coding RNAs (lincRNAs), and circular RNAs (circRNAs). Among these, lincRNAs represent the most extensively characterized class, exhibiting transcriptional activation mechanisms analogous to mRNAs and higher cross-species conservation than antisense RNAs.^40,41 Their expression demonstrates superior tissue specificity and stability relative to other lncRNA subtypes.^42,43 LncRNAs are mainly synthesized by RNA polymerase II (Pol II) and, after transcription, they experience splicing similar to mRNA processing, leading to transcripts with 5′ 7-methylguanosine caps and 3' polyadenylated tails. Beyond these canonical processing steps, certain lncRNAs require specialized maturation pathways.¹⁴ For instance, the nuclear-retained lncRNAs MALAT1 and NEAT1 depend on RNase P-mediated cleavage for generation of functional isoforms.^44,45,46 The complete understanding of lncRNA biogenesis is still lacking, yet innovative technologies hold the promise of revealing more about the underlying mechanisms. Elucidating the intricacies of lncRNA processing, including subtype-specific synthesis, modification, and subcellular trafficking, is essential for comprehending their biological functions.

Recent findings indicate that lncRNAs are crucial in regulating biological processes by interacting intricately with DNA, RNA, and proteins, acting as decoys, scaffolds, guides, sponges, or enhancers (Figure 1). The subcellular localization of lncRNAs is crucial in determining their molecular interactions and functional consequences. For instance, lncRNAs localized in the nucleus interact with chromatin modifiers, transcription factors, and genomic DNA to regulate transcriptional activation or repression via cis- or trans-regulatory mechanisms.⁴⁷ This enables gene expression control across pre-transcriptional, transcriptional, and post-transcriptional stages.^48,49 Notably, emerging studies reveal that lncRNAs can regulate gene expression through sequence-specific pairing with DNA. This pairing forms RNA-DNA triplex structures that facilitate DNA methylation and transcriptional silencing.⁵⁰ A paradigm is the lncRNA PARTICLE, which forms a triplex complex near the CpG island of the methionine adenosyltransferase 2A (MAT2A) promoter. Following irradiation, this complex recruits methylation machinery to epigenetically silence MAT2A. The association of lncRNA PARTICLE with MAT2A indicates that lncRNA plays a role in cell-to-cell communication and acts as a recruitment platform for gene silencing mechanisms via triplex formation in response to radiation exposure.⁵¹

Figure 1.

Cellular localization and general functions of lncRNAs

LncRNAs exert distinct regulatory functions depending on their subcellular localization, acting within the nucleus (A–D) or the cytoplasm (E–I) to control gene expression at the epigenetic, transcriptional, post-transcriptional, and translational levels.

(A) Nuclear lncRNAs modulate downstream gene transcription by interacting with transcriptional activators and repressors.

(B) The expression of genes is regulated by lncRNAs through the recruitment of complexes that modify chromatin.

(C) lncRNAs function as scaffolds for phosphorylation and ubiquitination processes.

(D) lncRNAs modulate gene expression by influencing the splicing process of pre-mRNA and facilitating the production of mature RNA.

(E and F) In the cytoplasm, lncRNAs play a role in regulating mRNA by impacting its stability and translation.

(G) A subset of lncRNAs contains small ORFs that can be translated into biologically active small peptides.

(H) lncRNAs can compete with miRNAs by occupying their binding sites.

(I) lncRNAs function as sponges for miRNAs to regulate their target genes.

lncRNA, long non-coding RNA; mRNA, messenger RNA; pre-mRNA, precursor messenger RNA; miRNA, microRNA; sORF, small open reading frame. Arrows indicate activation/promotion; blunt-ended lines indicate inhibition.

While nuclear localization predominates among lncRNAs, a substantial fraction resides within the cytoplasm. Cytoplasmic lncRNAs engage ribosomes, govern the translation and stability of mRNA, and modulate RNA terminal structures. Critically, they function as competing endogenous RNAs (ceRNAs) by binding to microRNAs (miRNAs), which leads to the release of miRNA-targeted mRNAs from repression.^48,51 For instance, the nuclear lncRNAs MALAT1 and NEAT1 exhibit cytoplasmic miRNA-sponging activity that modulates specific gene expression. Mounting evidence implicates lncRNA ceRNA networks in regulating apoptosis and autophagy during TB pathogenesis. Notably, lncRNA PCED1B-AS1 attenuates macrophage apoptosis and enhances autophagy through miR-155 sponging, which consequently derepresses the FOXO3/Rheb pathway—a mechanism with significant implications for TB control.²⁵ Beyond RNA interference, cytoplasmic lncRNAs influence protein translation through ribosome-associated small open reading frames (smORFs) that encode functional micropeptides regulating diverse biological processes.⁴⁶ Simultaneously, lncRNAs orchestrate epigenetic reprogramming; for example, the lncRNA HOTAIR recruits histone modifiers including enhancer of zeste homolog 2 (EZH2; an H3K27 methyltransferase) and lysine-specific demethylase 1 (LSD1; an H3K4 demethylase) to impact intracellular Mtb survival.⁵² Beyond epigenetic regulation, lncRNAs critically modulate post-translational modifications (PTMs). They facilitate kinase-mediated phosphorylation cascades and orchestrate ubiquitin-dependent protein degradation pathways. A prime example is HOTAIR, which scaffolds E3 ubiquitin ligases to enhance targeted ubiquitination and subsequent proteasomal degradation of substrate proteins.^13,53 This spatiotemporal complexity underscores lncRNAs as multifaceted regulators with context-dependent functions, providing critical insights for mechanistic prediction.

LncRNA-mediated regulation of host immune responses to Mtb

A substantial number of lncRNAs have been identified within mammalian genomes, although only a small, yet progressively increasing, fraction has been functionally characterized in a range of biological mechanisms, including TB immunity. The regulation of innate and adaptive immune cells during TB infection has been associated with specific expression patterns of host lncRNAs. Furthermore, models of viral infection offer a valuable framework for elucidating the biology and regulatory mechanisms of lncRNAs. Consequently, a comprehensive understanding of the mechanisms governing lncRNA expression and function during immune responses is crucial for developing more effective TB prevention and treatment strategies.

LncRNA dysregulation in macrophages

As frontline defenders against Mtb infection, macrophages are essential for phagocytosis and pathogen clearance. Recent research indicates that following Mtb infection, lncRNAs modulate the immune response of host macrophages through diverse expression patterns. These regulatory mechanisms are involved in critical cellular processes, including inflammation, apoptosis, autophagy, necrosis, pyroptosis, and macrophage polarization (Figure 2).

Figure 2.

Diagrammatic depiction of how lncRNAs influence the immune response of macrophages during Mtb infection

During Mtb infection, lncRNAs act as critical regulators of macrophage survival, apoptosis, autophagy, pyroptosis, and inflammatory cytokine production through distinct cytosolic and nuclear pathways.

(A) Pro-inflammatory and survival pathways. TLR engagement activates MYD88-dependent signaling, converging on NF-κB. GAS5 functions as a ceRNA by sponging miR-18a-5p, thereby promoting macrophage survival and pro-inflammatory responses. lncRNA-COX2 and lncRNA-XIST further amplify NF-κB signaling, with XIST also modulating miR-125b-5p. Activated NF-κB translocates into the nucleus and binds promoter regions to drive the induced transcription of downstream effector cytokines, including TNF-α, IFN-γ, pro-IL-1β, and pro-IL-6, which are subsequently processed and secreted to amplify inflammation. NEAT1 modulates inflammation and programmed cell death via interaction with miR-377-3p, feeding into the NLRP3 inflammasome axis. XIST also generates ROS that contribute to NLRP3 inflammasome activation.

(B) Autophagy regulation. LincRNA-EPS activates the JNK2/MAPK pathway to inhibit cell death while promoting protective autophagy. PCED1B-AS1 directly sequesters miR-155 and miR-233, thereby suppressing apoptosis (via the Foxo3–Bim axis) and enhancing autophagy to restrict intracellular Mtb survival.

(C) Apoptosis regulation. FasL engagement induces lncRNA-COX2 expression, triggering ER stress-mediated apoptosis via the PERK–eIF2α–CHOP–Caspase-8–Caspase-3 cascade. In parallel, downregulation of lncRNA-MEG3 releases miR-145-5p, which promotes Bak/Bax-mediated mitochondrial apoptosis through caspase-9 and caspase-3 activation.

(D) Pyroptosis and cytokine suppression. The Mtb effector protein EST12 suppresses lnc-EST12 expression. Downregulation of lnc-EST12 recruits the transcription factor FUBP3, resulting in inhibition of pro-inflammatory IL-1β production, suppression of NLRP3 inflammasome assembly, and downstream GSDMD-mediated pyroptosis. miR-379-5p additionally regulates GSDMD-mediated pyroptosis.

Mtb, Mycobacterium tuberculosis; lncRNA, long non-coding RNA; miRNA, microRNA; ceRNA, competing endogenous RNA; TLRs, Toll-like receptors; IL-1R, interleukin-1 receptor; TNFR, tumor necrosis factor receptor; FasL, Fas ligand; MYD88, myeloid differentiation primary response 88; PRRs, pattern recognition receptors; ROS, reactive oxygen species; ER, endoplasmic reticulum; TNF-α, tumor necrosis factor-alpha; IFN-γ, interferon-gamma; IL-1β/IL-6, interleukin-1 beta/interleukin-6; NF-κB, nuclear factor kappa B; PERK, protein kinase RNA-like ER kinase; CHOP, C/EBP homologous protein; JNK, c-Jun N-terminal kinase; MAPK, mitogen-activated protein kinase; NLRP3, NOD-like receptor family pyrin domain containing 3; GSDMD, gasdermin D; FUBP3, far upstream element-binding protein 3; Foxo3, forkhead box O3.

Regulation of inflammatory responses

Upon invasion by Mtb, macrophages are activated and release inflammatory mediators, such as cytokines and chemokines, to attract more immune cells facilitate pathogen clearance. This inflammatory reaction aids in the granuloma formation, which in turn restricts the spread of the pathogen. Recent findings suggest that lncRNAs have a regulatory function in TB-related inflammation, consequently affecting the progression of the disease.⁵⁴ For example, a study employing high-throughput microarray analysis in RAW264.7 macrophages, both infected and uninfected with Mtb, identified 1,487 lncRNAs and 910 mRNAs with altered expression profiles due to Mtb infection. Bioinformatics analysis revealed that the mRNAs with increased expression were related to immune responses, TNF pathways, and antigen processing and presentation, whereas the mRNAs with decreased expression were connected to the regulation of biological processes and the PPAR pathway. Notably, lncRNA AK151345 was observed to be elevated in macrophages infected by Mtb and presented significant correlation with its adjacent coding gene Irgm1, implying that Irgm1 could be involved in altering the effects of lncRNA AK151345 on Mtb infection.⁵⁵

Mtb-mediated evasion of host immunity drives pulmonary inflammation, presenting a major therapeutic challenge in tuberculosis. Recent findings suggest that lncRNA CCAT1 plays a crucial role in controlling inflammatory responses in macrophages. Notably, CCAT1 exacerbates intestinal barrier dysfunction in inflammatory bowel disease via the miR-185-3p/myosin light-chain kinase (MLCK) pathway,⁵⁶ suggesting potential parallels in TB immunopathology. Supporting this notion, CCAT1 is significantly upregulated in both recurrent and patients with newly diagnosed TB compared to healthy controls. Early detection of CCAT1 upon hospital admission may inform personalized treatment strategies to improve clinical outcomes. Similarly, the inflammation-associated lincRNA-Cox2 has been shown to be induced in Mtb-infected macrophages. Mechanistically, lincRNA-Cox2 acts as a scaffold for ribonucleoprotein complexes and regulates the transcription of immune response genes.^17,57,58 In macrophages infected with Mtb H37Ra, suppression of lincRNA-Cox2 expression attenuated NF-κB and STAT3 activation (Figure 2), suggesting its involvement in the orchestration of inflammatory signaling pathways.⁵⁹ Importantly, analysis of peripheral blood samples from 56 patients with active pulmonary TB (PTB) and 60 healthy controls demonstrated elevated lincRNA-Cox2 expression in TB patients, supporting its potential association with disease-related inflammation. Collectively, these findings suggest that lincRNA-Cox2 may represent a candidate host-response biomarker reflecting inflammatory activation in TB. In addition, a recently identified pathogen-responsive lncRNA, LINC02528, modulates mitochondrial redox homeostasis during Mtb infection. By interacting with the mitochondrial outer membrane protein TOMM22, LINC02528 restrains mitochondrial reactive oxygen species (mtROS) production and IL-1β-mediated antimicrobial responses,⁶⁰ thereby influencing intracellular Mtb survival.

Research indicates that drugs can influence the roles of lncRNAs in the inflammatory process triggered by Mtb infection. Mtb infection has been demonstrated to increase the levels of p50-associated lncRNA-PACER and lincRNA-p21. In monocyte-derived macrophages (MDMs), these lncRNAs are further elevated when exposed to triptolide, either before or after infection.⁶¹ The genes targeted by lncRNA PACER and lincRNA-p21, Ptgs2 and IL-6, are identified as pro-inflammatory and vital to the immune response against Mtb.⁶² Mtb is recognized for using host non-coding RNA to evade immune responses, yet PACER facilitates macrophage activation transitioning to the pro-inflammatory M1 phenotype, aiding in Mtb clearance.^63,64

Recent research has demonstrated that in Mtb-infected THP-1 cells, transformation of anti-inflammatory M2 macrophages into the pro-inflammatory M1 phenotype is aided by the overexpression of lncRNA GAS5. Moreover, lncRNA GAS5 is involved in the Th17/Treg imbalance seen in childhood pneumonia by interacting with the miR-217/STAT5 pathway.^65,66 This suggests that modulation of GAS5 expression could be instrumental in managing TB progression. Additionally, another study explored how negative pressure and lncRNA XIST together influence the regulation of Mtb infection. Findings showed that negative pressure treatment after Mtb infection enhances the polarization of macrophages to the pro-inflammatory M1 phenotype by modulating the XIST/miR-125b-5p/A20/NF-κB pathway.⁶⁷ These results add to the growing understanding of lncRNA mechanisms in TB, providing new perspectives for understanding the disease and developing possible treatments.

Regulation of autophagy and apoptosis

Apoptosis in Mtb-infected macrophages helps prevent intracellular release of Mtb and spreading to other healthy macrophages by packaging the bacteria in apoptotic vesicles. Autophagy, an essential physiological mechanism for preserving intracellular balance, inhibits intracellular Mtb survival by forming autophagic lysosomes. Mtb-induced macrophage apoptosis and autophagy constitute essential host defense mechanisms, with lncRNAs emerging as pivotal regulators. LncRNA MEG3 is significantly upregulated in PTB patients; reducing its expression in Bacillus Calmette-Guérin (BCG)-infected RAW264.7 macrophages boosts autophagy and aids in clearing mycobacteria.¹⁹ Similarly, lncRNA PCED1B-AS1 acts as a ceRNA by capturing miR-155, which in turn activates FOXO3/Rheb signaling (Figure 2). Silencing PCED1B-AS1 reduces apoptosis while augmenting autophagy in infected macrophages.²⁵ LincRNA-EPS (erythroid prosurvival) expression is notably lower in monocytes from TB patients, where its downregulation regulates the balance between apoptosis and autophagy via the JNK/MAPK pathway (Figure 2), indicating its potential for diagnostic and therapeutic applications. LincRNA-Cox2 facilitates apoptosis in BCG-infected macrophages via the PERK-eIF-2α-CHOP pathway, leading to the accumulation of ROS.⁵⁸ While it has been reported to influence macrophage polarization in cancer models by enhancing pro-apoptotic M1 function and suppressing M2 activity, its specific mechanisms in TB remain to be validated.⁶⁴ Similarly, lncRNA MIAT (myocardial infarction associated transcript) influences the balance between autophagy and apoptosis via the miR-665/ULK1 pathway in macrophages infected with BCG.⁶⁸ Taken together, these lncRNAs are promising molecular targets for the advancement of new TB interventions.

Regulation of necrosis and pyroptosis

Eukaryotic cells mainly experience cell death through two primary processes: apoptosis and necrosis. Apoptosis is a selfless mechanism of programmed cell death marked by the condensation of the nucleus; fragmentation of chromosomal DNA into nucleosome-sized, ladder-like fragments; cellular shrinkage; and the subsequent formation of apoptotic bodies.⁶⁹ Conversely, necrosis is a passive process characterized by morphological changes, including the enlargement of granulomas, organelle swelling, and cellular expansion. Necrosis is commonly observed in pathological conditions, such as during pathogen invasion, where it triggers an inflammatory response and facilitates bacterial transmission.⁷⁰

Programmed necrotic cell death, governed by a multitude of factors including lncRNAs, is increasingly acknowledged for its significance in host-pathogen interactions. For instance, lncCRLA inhibits RIPK1-induced necroptosis by obstructing the interaction between RIPK1 and RIPK3.⁷¹ While prior research on lncRNAs in TB has predominantly concentrated on their influence on immune cell apoptosis, emerging studies suggest that the dysregulated expression of lncRNAs also contributes to immune cell necrosis during Mtb infection. Mechanistically, BCG infection induces cell necrosis and upregulates lncRNA NR003508 expression. LncRNA NR003508 acts as a ceRNA, capturing miR-346-3p, which is directed at RIPK1. The increased levels of RIPK1 in the peripheral blood of TB patients, compared to healthy people, support this mechanism. Reducing lncRNA NR003508 levels or increasing miR-346-3p expression lessens cell necrosis and ROS buildup in RAW264.7 cells. Consequently, lncRNA NR003508 modulates RIPK1 by sponging miR-346-3p, thereby exerting a positive regulatory role in Mtb-induced necrosis.⁷²

This research offers initial understanding of how the NR003508-miR-346-3p-RIPK1 pathway influences cell necrosis, which could serve as a potential intervention strategy for TB.

Pyroptosis, a programmed cell death pathway dependent on caspase-1/4/5 and activated by intracellular pathogens, integrates characteristics of both apoptosis and necrosis. This process enhances antimicrobial defense through the substantial release of pro-inflammatory cytokines.⁷³ LncRNA NEAT1 represents a well-characterized regulator of inflammasome-mediated pyroptosis. Mechanistically, NEAT1 has been shown to associate with components of multiple inflammasomes, including NLRP3, NLRC4, and AIM2, thereby facilitating inflammasome assembly and promoting pro-caspase-1 processing (Figure 2).⁷⁴ Upon inflammasome activation, NEAT1 can translocate from paraspeckles to the cytoplasm, where it enhances caspase-1 maturation and stabilizes active caspase-1, ultimately leading to increased interleukin 1β (IL-1β) production and pyroptotic cell death. Clinically, NEAT1 levels are elevated in PBMCs from active TB patients and normalize following successful treatment, serving as a potential indicator of therapeutic response. Importantly, silencing NEAT1 in macrophages impairs IL-6 production and weakens intracellular bacterial clearance, underscoring its essential role in orchestrating effective antimicrobial immunity via pyroptotic cell death.³²

Notably, the Mtb-secreted protein EST12 activates NF-κB/AP-1-NLRP3-gasdermin D (GSDMD)-mediated pyroptosis, thereby strengthening anti-mycobacterial immunity.⁷⁵ Subsequent transcriptomic analyses have identified lnc-EST12 as a differentially expressed regulator during Mtb infection. Mechanistically, the EST12 protein inhibits lnc-EST12 transcription via the p-JAK2/p-STAT5a pathway in murine immune cells. Lnc-EST12 hinders the assembly of the NLRP3 inflammasome and the cleavage of GSDMD by binding to the transcription factor FUBP3, leading to a decrease in the release of IL-6 and IL-1β, as well as CCL5 and CCL8, along with reduced pyroptosis.⁷⁶ Although knowledge regarding Mtb-modulated pyroptotic effectors remains limited, these findings illuminate a pathogen-host regulatory axis: Mtb EST12 promotes pyroptosis while concurrently suppressing its lncRNA counterpart to modulate inflammation. Targeting this dual pathway presents new therapeutic opportunities for TB.

LncRNA dysregulation in T cells

Effective containment of Mtb requires coordinated interactions between innate and adaptive immunity. Among adaptive immune components, T cells are indispensable for controlling bacterial replication and limiting tissue damage. Impairment of T cell immunity, as exemplified by the markedly increased TB susceptibility in HIV-infected individuals, underscores their central role in host defense.^77,78,79

LncRNAs in CD4⁺ T cell differentiation and function

CD4⁺ T helper 1 (Th1) cells are the primary orchestrators of protective immunity against TB. Upon antigen recognition, Th1 cells secrete IFN-γ and TNF-α, which activate infected macrophages to enhance phagolysosomal maturation, reactive nitrogen intermediate production, and intracellular bacterial killing. Disruption of this axis leads to impaired granuloma integrity and progressive disease.⁸⁰

Transcriptomic profiling of CD4⁺ T cells from individuals with active TB (ATB), LTBI, and healthy controls has revealed substantial dysregulation of lncRNA expression in both ATB and LTBI, with more extensive alterations observed in ATB.²¹ Enrichment analyses identified perturbations in pathways central to T cell activation and effector function, including MAPK signaling, cytokine-cytokine receptor interactions, and Toll-like receptor signaling. Several differentially expressed lncRNAs were located in proximity to immune-related protein-coding genes. For instance, coordinated downregulation of lncRNA NR_024586 and its associated mRNA MLL5, as well as ENST00000431999 and CYP1B1, suggests potential regulatory coupling.²¹ Although direct mechanistic links remain to be experimentally validated, such dysregulation may influence T cell differentiation, cytokine production, or responsiveness to antigenic stimulation.^79,81 These findings suggest that altered lncRNA expression profiles in CD4⁺ T cells could contribute to impaired Th1 polarization or suboptimal cytokine secretion, thereby weakening macrophage activation and compromising bacterial containment during active disease.

LncRNAs in CD8⁺ T cell cytotoxicity and functional exhaustion

Although historically considered secondary to CD4⁺ T cells, CD8⁺ T cells are now recognized as critical contributors to anti-TB immunity. CD8⁺ T cells exert antibacterial effects through perforin- and granzyme-mediated cytotoxicity, secretion of granulysin that directly damages intracellular mycobacteria, and production of IFN-γ to support macrophage activation.⁸² Reduced proliferative capacity, impaired degranulation, and diminished cytokine secretion in CD8⁺ T cells have been associated with increased bacterial burden and more severe disease manifestations.⁸³

Transcriptomic analyses of CD8⁺ T cells from ATB patients identified 328 differentially expressed lncRNAs and 356 mRNAs compared with controls.³⁷ Upregulated mRNAs were enriched in calcium signaling, cAMP signaling, and transforming growth factor β (TGF-β) pathways, whereas downregulated genes were associated with antigen processing and cytotoxicity pathways. Among the dysregulated lncRNAs, lincRNA XLOC_014219 was markedly upregulated, while its neighboring gene HMOX1—previously implicated in TB pathophysiology—was suppressed.⁸⁴ This inverse relationship raises the possibility of transcriptional or epigenetic repression, although functional validation is required.

In addition, inhibitory receptor pathways contribute to CD8⁺ T cell dysfunction during TB. CD244-mediated recruitment of the epigenetic modifier EZH2 promotes H3K27 trimethylation at the loci encoding IFN-γ and TNF-α, resulting in reduced cytokine production. Experimental depletion of CD244 in murine models has been associated with improved T cell function and reduced bacterial burden.²⁹ While the precise contribution of lncRNAs to this regulatory axis remains to be fully clarified, these findings collectively suggest that lncRNA-associated epigenetic and transcriptional programs may participate in shaping CD8⁺ T cell exhaustion during active TB. Taken together, dysregulated lncRNAs in T cells may influence disease progression by modulating cytokine production, cytotoxic capacity, and epigenetic programming, ultimately affecting bacterial clearance and immunopathology.

LncRNA dysregulation in B cells

Although T cells and macrophages dominate TB immunology research due to their established roles in granuloma formation and intracellular bacterial killing, B cells are increasingly recognized as active participants in TB immunity. Beyond antibody production, B cells contribute to antigen presentation, cytokine secretion, and modulation of T cell responses within granulomatous lesions.^45,77 Antibodies generated during Mtb infection may facilitate opsonization and enhance Fc receptor-mediated phagocytosis by macrophages. B cells can also produce cytokines such as IL-10 and IL-6, thereby influencing local inflammatory balance and T cell polarization.⁸⁵ Alterations in B cell numbers, phenotype, or function have been associated with TB disease severity and treatment response, highlighting their immunomodulatory relevance.

Emerging transcriptomic data indicate extensive lncRNA dysregulation in B cells from TB patients. One study identified 844 differentially expressed lncRNAs in primary B cells from individuals with TB, many of which were co-dysregulated with adjacent protein-coding genes. Notably, lncRNA XLOC_012582 and the nearby gene SOCS3 were both significantly upregulated. SOCS3 is a key negative regulator of cytokine signaling and modulates responses downstream of STAT pathways, which are critical for inflammatory control during Mtb infection.⁸⁶ The coordinated upregulation of XLOC_012582 and SOCS3 raises the possibility of cis-regulatory interactions that may dampen cytokine signaling in B cells.

Although direct functional evidence is still limited, altered lncRNA expression in B cells could theoretically influence antibody production, class-switch recombination, or cytokine secretion, thereby reshaping adaptive immune responses and granuloma dynamics.^87,88 Further mechanistic studies are required to determine whether specific lncRNAs actively regulate B cell-mediated immunity or primarily reflect systemic inflammatory states. Overall, while the role of B cell-specific lncRNAs in TB remains less defined than in macrophages and T cells, accumulating transcriptomic evidence supports their involvement in adaptive immune regulation and warrants deeper investigation.

Collectively, the evidence discussed previously suggests that lncRNAs regulate TB pathogenesis through convergent immune pathways rather than isolated mechanisms. Across macrophages, T cells, and B cells, several recurring signaling hubs—including NF-κB, STAT3, MAPK, and inflammasome pathways—emerge as central nodes of lncRNA-mediated regulation. Notably, multiple lncRNAs converge on inflammatory cytokine production (e.g., IL-1β, TNF-α, IFN-γ) and epigenetic modifiers such as EZH2, indicating shared regulatory frameworks across immune cell types. However, inconsistencies remain regarding whether specific lncRNAs act predominantly as protective regulators or drivers of immunopathology, underscoring the context-dependent nature of their function. These observations highlight the need to interpret individual lncRNA studies within broader immune network models.

LncRNAs as candidate diagnostic biomarkers in TB

Existing methods for diagnosing TB in a clinical setting exhibit several limitations, including the limited sensitivity and speed of smear microscopy and mycobacterial culture, the low detection rate of smear-negative PTB, and the inability of the IGRA to distinguish between LTBI and active TB. These challenges impede effective TB control.^89,90 Consequently, improving the management of the TB epidemic requires early, fast, and precise diagnosis. Given the crucial roles of lncRNAs in the immune response to TB, they present promising opportunities to address these diagnostic challenges.

Unlike sputum culture, which directly detects viable Mtb and remains the microbiological gold standard, lncRNA-based assays reflect host immune responses to infection. Therefore, lncRNA signatures are not intended to replace microbiological confirmation but may serve as complementary tools, particularly in smear-negative, extrapulmonary, or pediatric TB where bacteriological evidence is limited. The dysregulated expression of lncRNAs in different tissues and cell types linked to infectious diseases suggests their potential as innovative TB biomarkers.

LncRNAs from PBMCs as potential biomarkers

Peripheral blood mononuclear cells (PBMCs) are a clinically viable source for TB biomarker development, attributed to their accessibility via minimally invasive sampling and straightforward isolation protocols that are feasible in routine diagnostic laboratories. Importantly, in vitro cultures of PBMCs effectively replicate systemic immune environments, thereby providing valuable models for clinical diagnostics.^91,92 Increasing evidence suggests that dysregulation of lncRNAs in PBMCs from TB patients presents significant potential as biomarkers. A significant observation is the increased levels of CD244 and its signaling pathways in CD8⁺ T cells among active TB patients, which is associated with diminished IFN-γ and TNF-α production. Notably, knockout of CD244 reverses this suppression,²⁹ highlighting this lncRNA-associated epigenetic pathway as a promising therapeutic target with implications for the development of vaccines and diagnostics. Complementing this, lncRNA NEAT1 isoforms demonstrate consistently increased levels in TB patients that normalize following anti-TB treatment, serving as treatment-response indicators.³²

Transcriptomic analyses identified four differentially expressed lncRNAs in PBMCs from PTB patients, including MIR3945HG V1, MIR3945HG V2, ENST00000360485, and ENST00000417932. Quantitative reverse-transcription PCR (RT-qPCR) validation demonstrated that MIR3945HG V1 and MIR3945HG V2 were significantly upregulated in PTB patients compared with healthy controls, whereas ENST00000360485 was downregulated and ENST00000417932 showed no significant change. Receiver operating characteristic (ROC) curve analysis further evaluated their diagnostic performance. The area under the curve (AUC) values for MIR3945HG V1 and MIR3945HG V2 both exceeded 0.90, indicating strong discriminative capacity between PTB patients and healthy controls. Specifically, MIR3945HG V1 showed a sensitivity of 90.0% (95% confidence interval [CI]: 73.47–97.89) and a specificity of 81.25% (95% CI: 63.56–92.79), while MIR3945HG V2 demonstrated a sensitivity of 89.66% (95% CI: 72.65–97.81) and a specificity of 90.63% (95% CI: 74.98–98.02). In contrast, ENST00000360485 exhibited a lower diagnostic performance, with an AUC of 0.7984 (95% CI: 0.687–0.909) and a specificity of 71.88% (95% CI: 53.25–86.25), suggesting comparatively reduced accuracy (Table 1).²⁴ These findings suggest that selected PBMC-derived lncRNAs may have potential utility as host-response biomarkers for TB. However, validation in larger and clinically diverse cohorts is required to confirm their reproducibility and disease specificity. Similarly, PCED1B-AS1 was found to be downregulated in both THP-1 cells and PBMCs.²⁵

While this observation suggests a possible role in immune regulation during Mtb infection, further mechanistic and clinical validation is necessary before translational implications can be drawn. Overall, PBMC-derived lncRNAs represent a promising area of investigation for adjunctive TB diagnostics and disease monitoring, although their clinical applicability remains to be rigorously established.

The misdiagnosis of PTB continues to pose a significant challenge due to inadequate pathogenic and diagnostic evidence.⁹³ Researchers are increasingly focusing on the development of predictive models that target lncRNAs to enhance PTB diagnosis. For instance, lncRNA n344917 has been identified as significantly downregulated in the PBMCs of PTB patients. By integrating lncRNA n344917 with patients’ electronic health record (EHR) data, researchers have developed a predictive model that exhibits strong clinical utility, consistency, and discriminative power.²⁷ Additional examination with the NONCODE database showed an increase in lncRNA n344917 levels in lymphocytes and leukocytes, suggesting its possible involvement in the immune response to Mtb infection. Furthermore, a separate study utilized the differential expression of lncRNAs (n333737, n335265, and ENST00000497872) in PTB patients to construct a heatmap that accurately predicted infection.²⁶ This model demonstrated superior discriminative ability in distinguishing PTB patients from non-PTB disease control groups compared to models based solely on electronic medical records. Additionally, novel specific lncRNAs, n406498 and TCONS_00001838, identified from PBMC samples, exhibited potential as molecular markers for PTB diagnosis when combined with EHR parameters in a logistic regression model and heatmap.²⁸ Therefore, embedding the “LncRNA + EHR” model within a heatmap framework holds potential for the rapid diagnosis of TB in medical settings.

LncRNAs in plasma or serum as potential biomarkers

Currently, a definitive test for confirming the cure of TB is not available, which could result in the premature discharge of patients and heightened risks of transmission, recurrence, and the development of drug resistance. Plasma, owing to its closer resemblance to the interstitial fluid of the human body, provides a more precise and sensitive representation of physiological status. This characteristic of plasma helps to mitigate potential inaccuracies that arise from the complex cellular components found in whole blood.⁹⁴ Consequently, plasma analysis is frequently employed in clinical blood testing. Recent research has indicated that certain lncRNAs can distinguish between TB patients and those who have been cured in plasma samples. For instance, there are significant differences in the expression levels of lncRNA uc.48+ and lncRNA NR-105053 in plasma from PTB patients who are untreated compared to those who are cured.²² By integrating their expression levels, a model was created to predict TB cure, demonstrating high sensitivity and specificity, which implies that these lncRNAs could be potential biomarkers for distinguishing between PTB patients who are untreated and those who have been cured.

Transcriptome analysis in an independent study revealed four lncRNAs (NR_038221/NR_003142, lncRNA ENST00000570366/ENST00000422183) showing altered expression in TB patients versus healthy controls. Notably, the lncRNAs NR_003142, NR_038221, and ENST00000570366 were significantly upregulated, whereas ENST00000422183 was reduced in the plasma of individuals with TB. A diagnostic model incorporating these four lncRNAs exhibited enhanced performance compared to individual biomarkers. Further investigation revealed that the genes targeted by NR_003142 are involved in immune pathways, including TLR6, NOD2, HLA-DQB, and IL6ST.³⁵ Prior investigations have recognized hsa-miR-378a-3p as a potential indicator for TB, connected with NR_038221,⁹⁵ suggesting that NR_038221 and hsa-miR-378a-3p may serve analogous roles in the biological processes of TB and might together play a role in the development of TB infection.

Additionally, the research examined LOC152742 expression levels in the plasma of healthy people, ATB patients, former PTB patients, and individuals vaccinated with BCG.³⁸ The findings revealed that LOC152742 exhibited greater specificity for active PTB in both sputum and plasma compared to its specificity for past PTB and BCG-vaccinated individuals. Furthermore, the levels of LOC152742 significantly rose in pulmonary epithelial macrophages infected with H37Ra or H37Rv strains compared to the uninfected group. These findings imply that LOC152742 holds potential as an innovative biomarker for the diagnosis and management of active PTB. Moreover, the identification of lncRNAs ENST00000354432 and ENST00000427151 in plasma samples suggests their potential as biomarkers for TB diagnosis and treatment.³³

Serologic diagnosis has the advantage of being rapid, easy to operate, and not requiring specialized precision instruments. Commonly used TB antigens for detecting serum antibodies to Mtb include the 38 kDa antigen, A60 antigen, P32 antigen, glycolipid antigen, and lipoarabinomannan. Multiple purified specific antigens can be assayed together to improve detection rates.⁹⁶ However, little has been reported on the regulatory relationship between abnormal lncRNA expression in serum samples and TB. Researchers examined the expression of lncRNA NORAD in serum samples from 90 patients with PTB and 85 healthy controls. Elevated lncRNA NORAD levels in PTB patients correlated with elevated concentrations of inflammatory cytokines IL-6 and TNF-α, suggesting its involvement in excessive inflammation in PTB. Further ROC curve analysis revealed that NORAD may serve as a clinical diagnostic biomarker for PTB due to its significant ability to differentiate TB patients from healthy individuals.

Exosomal LncRNAs as potential biomarkers

Exosomes are extracellular vesicles ranging from 30 to 100 nm in diameter that mediate intercellular communication by transporting bioactive molecules, including proteins, lipids, microRNAs, and lncRNAs.⁹⁷ Encapsulation within a lipid bilayer protects RNA cargo from extracellular degradation,⁹⁸ ensuring distinct and detectable signatures even in complex clinical samples and making them attractive candidates for minimally invasive biomarker development.

Recent advances in isolation technologies have accelerated the exploration of exosomal lncRNAs in respiratory diseases.⁹⁹ Fang et al. first characterized the lncRNA landscape in serum exosomes from TB patients, identifying a specific signature of four downregulated lncRNAs (NONHSAT101518.2, NONHSAT067134.2, NONHSAT148822.1, and NONHSAT078957.2) compared to healthy controls.³⁹ These markers exhibited high sensitivity and specificity for active TB detection. These preliminary findings suggest that exosomal lncRNAs may reflect systemic immune alterations during active infection.

Overall, these findings suggest that exosomal lncRNAs offer a robust, non-invasive platform for early TB diagnosis, overcoming the stability issues often associated with free-circulating transcripts. However, current evidence is limited to small cohorts and requires validation in larger, multi-center studies with appropriate disease controls.¹⁰⁰ In addition, it remains unclear whether exosomal lncRNA signatures are specific to TB or represent broader inflammatory responses. Therefore, while circulating exosomal lncRNAs may represent promising non-invasive biomarker candidates, their diagnostic performance and clinical utility remain to be rigorously established.

LncRNA gene polymorphisms in TB

Relationship between LncRNA gene polymorphisms and susceptibility to TB

Recent studies have clarified that single nucleotide polymorphisms (SNPs) in lncRNAs act as key regulators in numerous diseases, such as cancer and TB.^14,43 The impact of host genetic characteristics on TB susceptibility has been strongly proven through studies on twins, linkage analyses, and candidate gene investigations.¹⁰¹ For instance, a comprehensive study analyzing 7.6 million genetic variations in a cohort comprising 5,530 TB participants and 5,607 healthy controls (HCs) identified a significant relationship between TB and the variants situated within an intron of the ASAP1 gene on chromosome 8q24. The rs10956514 variant was correlated with decreased expression levels of ASAP1, resulting in impaired dendritic cell migration during Mtb infection, thereby suggesting a potential mechanism underlying TB susceptibility.¹⁰²

Furthermore, polymorphisms in lncRNA genes have garnered attention for their potential to differentiate between ATB and LTBI (Table 2). Yi et al. conducted microarray analyses that revealed differential expression of the lncRNA transcript AC079767.4 among participants with ATB, LTBI, and HC group. The expression of AC079767.4 transcript was observed to decrease in both ATB and LTBI participants compared to the HC, while it was higher in the LTBI participants than in ATB participants. The aforementioned findings were validated using RT-qPCR, demonstrating a high concordance with the microarray results (Table 2).²¹ Based on this evidence, the lncRNA AC079767.4 gene may be implicated in the initiation and development of TB infection.

Table 2.

Clinical relevance of the lncRNAs genetic polymorphisms in TB patients

Study design	Sample source	LncRNAs	Technique	SNPs	Biological effect	Reference
554 TB vs. 561 HC	whole blood	ENST00000429730 (AC079767.4)	iMLDR	rs10178277 rs12477677 rs1055228 rs1055229	in the subgroup analysis of 4 SNPs in AC079767.4, only the C allele of rs12477677 was linked to reduced PTB susceptibility. Additionally, the CC genotype of rs12477677 was associated with fewer fever incidents (p = 0.016), and the T allele was linked to lower ESR levels in the dominant model of rs1055229.	Zhao et al.103
526 TB vs. 561 HC	peripheral blood	HNF1B-3:1	iMLDR	rs1416 rs2542670 rs4262994 rs8075185 rs2688 rs12939622	there were no notable links between TB susceptibility and the 7 SNPs of lnc-HNF1B-3:1. However, the AA genotype of rs12939622 (dominant model) and rs4262994 (recessive model) increased fever susceptibility. The Rs2542670 G allele was linked to a higher risk of thrombocytopenia, leukopenia, and chronic kidney damage after drug use.	Wu et al.104
1359 TB vs.1534 HC	whole blood	RIPK2	iMLDR	rs10956271 rs39509 rs7015630 rs2697668 rs989384	after Bonferroni correction, rs39509 was linked to TB risk in allelic, additive, and recessive models. It may be located in functional regions and serve as an eQTL for RIPK2 and lncRNA RP11-37B2.1, according to the GTEx Project.	Song et al.105
554 PTB vs.561 HC	whole blood	RP11-37B2.1	iMLDR	rs218921 rs160441 rs218916 rs218936	no meaningful connection was identified between TB susceptibility and SNPs in lncRNA RP11-37B2.1. However, the SNPs of rs218916 and rs160441 were associated with thrombocytopenia during anti-TB therapy under the dominant model.	Song et al.106
467 TB vs. 473 HC	whole blood	TGS1-1	iMLDR	rs4737420	among TB patients undergoing therapy, lower TGS1-1 expression was associated with thrombocytopenia, while the CC genotype of rs4737420 was tied to a lesser risk of leukopenia than the T allele.	Bai et al.30
467 TB vs. 473 HC	whole blood	AC145676.1–6	iMLDR	rs111352767	the SNPs of rs111352767 do not show a significant connection with TB susceptibility.	Bai et al.30
900 ATB vs.1534 HC	whole blood	CASC8	iMLDR	rs7825118 rs6981424 rs9297758 rs7836840	the lncRNA CASC8 variant rs7836840 is linked to higher TB risk, with the C allele significantly associated with susceptibility. Individuals with AG and GG genotypes (rs7825118/rs9297758) exhibited reduced hemoglobin and neutrophil counts, respectively, whereas those with AG and AA genotypes in rs6981424 had higher ALT and AST levels, suggesting a potential rise in TB risk.	Liu et al.107

Based on the studies mentioned earlier, an in-depth analysis of SNPs within the AC079767.4 gene was conducted in a case study involving a Han Chinese population from Western China, focusing on their relationship with clinical phenotypes and susceptibility to TB.¹⁰³ The study employed the improved multiplex ligation detection reaction (iMLDR) method to genotype four SNPs (rs12477677, rs10178277, rs1055228, and rs1055229) in a cohort comprising 554 TB participants and 561 HC. The data revealed that only the C allele of rs12477677 was significantly associated with a decreased susceptibility to TB. Furthermore, within the dominant model for rs1055229, people possessing the CC genotype demonstrated a decreased probability of developing fevers, whereas those carrying the T allele were less prone to elevated ESR. Haplotype analysis revealed that the ACAC haplotype, which includes the C allele at rs12477677, is associated with a slight decrease in TB risk, supporting previous SNP analysis.¹⁰³ These findings suggest that AC079767.4 polymorphisms may contribute to genetic susceptibility to TB and could serve as candidate markers for risk stratification, pending further validation.

Mechanistically, SNPs within lncRNA genes may influence TB susceptibility through multiple pathways. Variants located in promoter or enhancer regions can alter transcriptional efficiency, thereby modifying lncRNA expression levels. Intronic or exonic polymorphisms may affect RNA secondary structure, stability, or subcellular localization, potentially reshaping interactions with RNA-binding proteins, transcription factors, or epigenetic modifiers such as EZH2. In this context, the protective C allele of rs12477677 within AC079767.4 may influence the expression or structural configuration of this lncRNA, thereby modulating baseline inflammatory responsiveness or immune activation thresholds during Mtb infection. Although the precise molecular mechanisms remain to be elucidated, these findings suggest that lncRNA polymorphisms may contribute to interindividual differences in host immune regulation and TB susceptibility. However, more research with larger patient groups is needed to confirm these results and understand the mechanisms of LTBI and its reactivation.

Association between LncRNA gene polymorphisms and ATD-ADRs

Clinically, prolonged anti-TB treatment regimens are associated with a variety of adverse drug reactions (ADRs), which may necessitate the modification or discontinuation of therapy, potentially resulting in treatment failure or even mortality.¹⁰⁸ Adherence to treatment is essential for the successful eradication of TB. However, ADRs can adversely affect patient compliance by requiring alterations in the treatment regimen, thereby potentially compromising treatment outcomes. The incidence of anti-TB drug-induced hepatotoxicity, recognized as the most severe and possibly life-threatening ADR, ranges from 2% to 28%.^109,110 In China, particularly in the western regions, TB poses a substantial public health challenge, with an ADR incidence exceeding 10%.¹¹¹ Accurately predicting which patients will develop hepatotoxicity during TB treatment remains a formidable challenge.

A case-control study in western China examined the associations of lnc-AC145676.2.1-6 and its variant rs111352767, as well as lnc-TGS1-1 and its variant rs4737420, with TB susceptibility, clinical features, and anti-tuberculosis drug-induced adverse reactions (ATD-ADRs). The study found that both lncRNAs were significantly downregulated in TB patients, suggesting a protective role against TB. Additionally, lower lnc-TGS1-1 expression was linked to thrombocytopenia during treatment, and patients with the CC genotype of rs4737420 had a reduced risk of leukopenia compared to those with the T allele.³⁰ This highlights the importance of studying SNP loci related to ATD-ADRs.

The relationship between the lnc-HNF1B-3:1 variant and TB susceptibility, clinical manifestations, and ADRs was thoroughly examined in another study. A total of seven SNPs within lnc-HNF1B-3:1 were genotyped in a cohort consisting of 526 TB patients and 561 healthy controls. Single-locus analysis indicated no significant association between TB susceptibility and the presence of these SNPs. Nevertheless, the AA genotype of rs12939622, under the dominant model, and the AA genotype of rs4262994, under the recessive model, were associated with an increased susceptibility to fever. Additionally, the G allele of rs2542670 was correlated with a heightened risk of thrombocytopenia, leukopenia, and chronic kidney injury following drug administration.¹⁰⁴ These findings suggest that specific lncRNA polymorphisms may be associated with hematological and renal adverse reactions during anti-TB treatment. Although these associations require replication in larger and ethnically diverse cohorts, they indicate that lncRNA genetic variants may contribute to interindividual variability in drug tolerance. Further functional studies are needed to clarify whether these polymorphisms influence lncRNA expression, stability, or downstream immune and metabolic pathways involved in drug-induced toxicity.

Challenges and future perspectives

Despite the rapidly expanding body of literature on lncRNAs in TB, significant challenges remain before these molecules can be translated into reliable clinical biomarkers or therapeutic targets. Addressing these limitations will be essential for advancing the field from exploratory transcriptomic observations to clinically actionable applications.

Disease specificity and population heterogeneity

One of the major challenges in developing lncRNA-based diagnostics for TB is disease specificity. Many of the signaling pathways regulated by lncRNAs in TB—such as NF-κB, STAT3, PPAR, and inflammasome-related pathways—are central components of general inflammatory and immune responses.¹¹² Consequently, dysregulated lncRNAs identified in TB patients may also be altered in other pulmonary diseases, including bacterial pneumonia, viral infections (e.g., influenza), chronic obstructive pulmonary disease (COPD), and lung cancer.^46,113 Furthermore, TB is a highly heterogeneous disease influenced by host genetics, age, sex, nutritional status, HIV co-infection, and geographic background.¹¹⁴ Most currently available studies have been conducted in relatively small, single-center cohorts. The lack of large-scale, multi-center validation studies limits the generalizability of reported lncRNA signatures. Future research should prioritize well-characterized cohorts with appropriate disease controls and stratification by latent versus active TB, drug-sensitive versus drug-resistant TB, and co-morbid conditions.

Standardization of detection platforms and analytical pipelines

Technical variability represents another critical barrier. Current studies employ diverse detection platforms, including RNA sequencing, microarrays, and RT-qPCR, often using different normalization strategies and reference genes. Pre-analytical variables—such as sample type (PBMCs, whole blood, plasma, serum, and exosomes), RNA extraction methods, storage conditions, and hemolysis—can significantly influence lncRNA measurements.^93,115 To enhance reproducibility and clinical applicability, standardized protocols for sample processing, RNA quantification, and data normalization are urgently needed. Additionally, the development of robust, cost-effective, and rapid detection platforms suitable for routine clinical laboratories—particularly in high TB-burden, resource-limited settings—remains a key priority.

Functional validation and mechanistic depth

Although numerous studies report differential expression of lncRNAs in TB, many remain descriptive and lack in-depth mechanistic validation. In particular, transcriptomic alterations observed in peripheral blood immune cells are not always examined under direct Mtb infection conditions, making it difficult to establish causal relationships between lncRNA expression and antibacterial immune function. Future studies should integrate multi-omics approaches—combining transcriptomics, epigenomics, proteomics, and single-cell analyses—to clarify cell type-specific functions of lncRNAs during Mtb infection. Functional experiments using gene knockdown, overexpression, CRISPR-based RNA modulation, and in vivo infection models will be essential to distinguish correlation from causation and to identify convergent regulatory networks.

Translational considerations for LncRNA-based therapeutic modulation

Although currently theoretical, targeting lncRNAs represents a long-term goal for host-directed therapies. Conceptually, lncRNAs could be modulated using antisense oligonucleotides (ASOs), small interfering RNAs (siRNAs), or CRISPR-based RNA-targeting systems.¹¹⁶ However, efficient and cell type-specific delivery to infected macrophages or granulomatous lesions in the lung remains technically challenging. Moreover, given that many lncRNAs regulate fundamental immune pathways, systemic modulation may carry risks of unintended immunosuppression or excessive inflammation.¹⁷ Comprehensive safety assessments, pharmacokinetic studies, and tissue-specific delivery strategies—such as nanoparticle-based systems or engineered extracellular vesicles—will be required before lncRNA-targeted therapies can be considered feasible in TB.

Polymorphisms, drug responses, and precision medicine

The association between lncRNA polymorphisms and TB susceptibility or ATD-ADRs offers promising avenues for precision medicine.^117,118 However, most studies to date involve limited sample sizes and specific ethnic populations. Replication in independent cohorts and functional validation of risk-associated SNPs are necessary to confirm biological relevance. In the future, integrating lncRNA expression profiles, genetic variants, and clinical parameters into predictive models may improve individualized risk assessment for disease progression and treatment-related toxicity.

Toward integrative and systems-level models

Emerging evidence suggests that lncRNAs function within complex regulatory networks involving microRNAs, transcription factors, epigenetic modifiers, and signaling cascades.^11,119 Rather than acting in isolation, lncRNAs likely contribute to coordinated immune programs that determine infection control, granuloma stability, and tissue pathology. This systemic view must also encompass cross-talk with the host microbiome. The discovery of the “gut-lung axis”—where gut commensals induce lncRNA-CGB to epigenetically regulate IFN-γ production—exemplifies how distal signals can shape pulmonary immunity via lncRNA intermediates.^23,120 Therefore, future research should move beyond single-lncRNA analyses toward integrative systems-level frameworks. The development of network-based models and machine learning approaches, incorporating multi-omics data from both the host and its microbiome, may help identify convergent nodes and prioritize the most biologically and clinically relevant lncRNAs.

Conclusions

In summary, lncRNAs represent an important layer of host regulation in TB, with potential applications in diagnostics, prognosis, and host-directed therapy. However, substantial methodological, biological, and translational challenges remain. Rigorous validation, mechanistic clarification, and standardized clinical studies will be crucial to determine whether lncRNAs can transition from promising molecular signatures to reliable tools in TB management.

Acknowledgments

This study was supported by the Prevention and Control of Emerging and Major Infectious Diseases-National Science and Technology Major Project (2025ZD01907000), the National Natural Science Foundation of China (82572593), the Natural Science Foundation of Guangdong Province (2025A1515012728), the Science and Technology Program of Guangzhou (2023A03J0539, 2023A03J0991, 2023B03J1303, and 2024A03J0437), and the Guangzhou Municipal Health Science and Technology Project (20261A011036).

Author contributions

N.T. drafted the manuscript. J.L. and N.T. drew the figures. J.Z., D.J., and Y.T. revised the review. All authors contributed to the article and approved the submitted version.

Declaration of interests

All authors declared no potential conflicts of interest.