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. 2014 Dec 31;3:e03751. doi: 10.7554/eLife.03751

A kinase-independent function of AKT promotes cancer cell survival

Igor Vivanco 1,*,†,‡, Zhi C Chen 1,†, Barbara Tanos 2, Barbara Oldrini 3, Wan-Ying Hsieh 4, Nicolas Yannuzzi 1, Carl Campos 1, Ingo K Mellinghoff 1,4,5,*
Editor: Roger Davis6
PMCID: PMC4337624  PMID: 25551293

Abstract

The serine–threonine kinase AKT regulates proliferation and survival by phosphorylating a network of protein substrates. In this study, we describe a kinase-independent function of AKT. In cancer cells harboring gain-of-function alterations in MET, HER2, or Phosphatidyl-Inositol-3-Kinase (PI3K), catalytically inactive AKT (K179M) protected from drug induced cell death in a PH-domain dependent manner. An AKT kinase domain mutant found in human melanoma (G161V) lacked enzymatic activity in vitro and in AKT1/AKT2 double knockout cells, but promoted growth factor independent survival of primary human melanocytes. ATP-competitive AKT inhibitors failed to block the kinase-independent function of AKT, a liability that limits their effectiveness compared to allosteric AKT inhibitors. Our results broaden the current view of AKT function and have important implications for the development of AKT inhibitors for cancer.

DOI: http://dx.doi.org/10.7554/eLife.03751.001

Research organism: human, mouse

eLife digest

To maintain a healthy body, the ability of our cells to survive and divide is normally strictly controlled. If any cells manage to escape these restrictions, they may rapidly divide and form tumors, which can lead to cancer.

A protein called AKT can encourage cells to survive and divide, and in healthy cells it is only allowed to be active at specific times. However, in many cancer cells, the genes that make and control AKT activity can be altered by mutations, which can result in AKT being active at the wrong times.

Part of the AKT protein acts as an enzyme called a kinase and adds chemical groups called phosphates to other proteins. The phosphate groups can activate or deactivate these proteins to control cell survival and cell division. However, there are other sections to the AKT protein and it is not clear how they are involved in this protein's activity.

In this study, Vivanco et al. show that AKT has another role in cell survival that does not depend on its kinase. The experiments show that even when the kinase part of the protein is missing, AKT can help cancer cells to survive drug treatments and external conditions that would normally kill them. This role requires another section of the protein called the PH-domain.

There are several chemicals—called inhibitors—that can stop AKT from working properly, and they have the potential to be used to treat some types of cancer. These inhibitors work in different ways: some were able to block the activity of the kinase, but others inhibited AKT by binding to other parts of the protein. Therefore, to develop AKT inhibitors into effective drugs, it will be important to know precisely what role the protein plays in different types of cancers.

DOI: http://dx.doi.org/10.7554/eLife.03751.002

Introduction

The serine–threonine kinase AKT is a non-receptor kinase that plays critical roles in growth and metabolism (Pearce et al., 2010). AKT is aberrantly activated in many human cancers, usually due to mutations in upstream components of the Phosphatidyl-Inositol-3-Kinase (PI3K) pathway. AKT signaling is required for tumor maintenance in certain genetic contexts, as has been shown for some cancer cell lines harboring PI3K mutations or amplification of the HER2 receptor tyrosine kinase (She et al., 2008). Encouraged by these results, several ATP-competitive and allosteric AKT inhibitors have been identified (Engelman, 2009), but optimal strategies for the clinical development of these agents are currently unknown.

Results

To address this question, we compared the activity of the allosteric AKT inhibitor MK2206 (Hirai et al., 2010) with the ATP-competitive AKT inhibitors GSK690693 (Heerding et al., 2008; Rhodes et al., 2008) and GDC0068 (Lin et al., 2013). Each of these AKT inhibitors dose dependently inhibited AKT kinase activity in the non-small-cell lung carcinoma (NSCLC) cell line EBC1 as determined by phosphorylation of three AKT substrates (PRAS40, GSK3β, and BAD) in whole-cell lysates (Figure 1A and Figure 1—figure supplement 1). Consistent with previous reports (Okuzumi et al., 2009), the ATP-competitive AKT inhibitors induced hyper-phosphorylation of AKT at the two regulatory phosphorylation sites threonine 308 and serine 473. When we compared the ability of the AKT inhibitors to induce cell death using a trypan blue exclusion assay, we observed significantly greater cell death induction by the allosteric inhibitor MK2206 compared to the ATP-competitive AKT inhibitors GSK690693 (Figure 1B—source data 1) and GDC0068 (Figure 1C—source data 1) despite less complete inhibition of AKT substrate phosphorylation at these drug concentrations (Figure 1A).

Figure 1. Differential sensitivity of human cancer cells to different classes of AKT inhibitors.

(A) Effect of AKT inhibitors on phosphorylation of AKT and AKT protein substrates. EBC1 cells were treated with the indicated doses of MK2206 and GSK690693 (top), or GDC0068 (bottom) for 24 hr. Treated cells were lysed and analyzed by immunoblot with the indicated antibodies. Phosphorylation of PRAS40, BAD, and GSK3β was quantified by image densitometry (middle). (B) Allosteric AKT inhibitor MK2206 induces more cell death than ATP-competitive inhibitor GSK690693 in EBC1 human lung cancer cells. Cells were treated with drug or vehicle for 96 hr. Cell death was determined by the trypan blue method. Error bars denote standard error of the mean (t-test *p ≤ 0.05, **p ≤ 0.01, treatment vs vehicle). (C) Allosteric AKT inhibitor MK2206 induces more cell death than ATP-competitive inhibitor GDC0068. Experimental conditions were as in Figure 1B. (D) Allosteric AKT inhibitor MK2206 induces more cell death than the ATP-competitive inhibitor GSK690693 in MDA-MB-361 human breast cancer cells. Cell death was assessed on day 1, day 3, day 5, and day 7 following treatment with vehicle or 2 µM of MK2206 or 2 µM of GSK690693(top) (t-test *p ≤ 0.05,**p ≤ 0.01, treatment vs vehicle). An additional plate from each treatment group was lysed 24 hr after drug treatment and analyzed by Western blot with the indicated antibodies (bottom). (E) Suppression of MK2206-induced cell death by a drug-resistant allele of AKT1. MDA-MB-361 cells were stably transduced with HA-tagged wild-type AKT1 or AKT1-W80A and treated with 2 µM MK2206 for 96 hr. Cell death was assessed as above. Expression of the transgenes was confirmed by immunoblot using an HA antibody, and loading was controlled with a vinculin antibody (inset).

DOI: http://dx.doi.org/10.7554/eLife.03751.003

Figure 1—source data 1. Contains source data for Figure 1 and all accompanying Figure 1—figure supplements.
DOI: http://dx.doi.org/10.7554/eLife.03751.004
elife03751s001.xlsx (42.7KB, xlsx)
DOI: 10.7554/eLife.03751.004

Figure 1.

Figure 1—figure supplement 1. MK2206 and GSK690693 cause sustained suppression of AKT-dependent BAD phosphorylation.

Figure 1—figure supplement 1.

EBC1 cells were treated with either 2 µM MK2206 or 2 µM GSK690693 and lysates were collected at the indicated times. Ser136 BAD phosphorylation was analyzed by immunoblot as indicated.
DOI: http://dx.doi.org/10.7554/eLife.03751.005

Figure 1—figure supplement 2. MET-amplified cancer cell lines die in response to an allosteric but not an ATP-competitive AKT inhibitor.

Figure 1—figure supplement 2.

EBC1, H1993, H1648, and GTL6 cells were treated with vehicle, 2 µM GSK690693, or 2 µM MK2206 for 96 hr. Cell death was assessed by the trypan blue method as detailed in the ‘Methods’ section.
DOI: http://dx.doi.org/10.7554/eLife.03751.006

Figure 1—figure supplement 3. Breast cancer cell lines with HER2 amplification and/or activating PIK3CA-mutations die in response to an allosteric but not an ATP competitive AKT inhibitor.

Figure 1—figure supplement 3.

MDA-MB-361, MCF7, and BT-474 breast cancer cells were treated with the indicated doses of GSK690693 or MK2206 for 96 hr. Cell death was assessed by the trypan blue method.
DOI: http://dx.doi.org/10.7554/eLife.03751.007

Figure 1—figure supplement 4. Non-small-cell lung cancer (NSCLC) cell lines with EGFR gene amplification and/or activating EGFR mutations are resistant to cell death induction by AKT inhibitors.

Figure 1—figure supplement 4.

HCC827 (EGFR-Δ74-750/AMP) (top right), HCC4006 (EGFR-Δ747-749/AMP) (bottom left), and H1975 (EGFR-T790M-L858R) (bottom right) lung cancer cells were treated with the indicated doses of GSK690693 or MK2206 for 96 hr. Cell death was assessed by the trypan blue method.
DOI: http://dx.doi.org/10.7554/eLife.03751.008

Figure 1—figure supplement 5. A drug-resistant allele of AKT2 suppresses MK2206-induced cell death.

Figure 1—figure supplement 5.

MDA-MB-361 cells were stably transduced with HA-tagged wild-type AKT2 or AKT2-W80A and treated with the indicated concentrations of MK2206 for 96 hr. Cell death was assessed by the trypan blue method (left). Expression of the transgenes was confirmed by immunoblot using an anti-HA antibody, and anti-vinculin was used to control for loading (right).
DOI: http://dx.doi.org/10.7554/eLife.03751.009

Figure 1—figure supplement 6. W80A mutation renders AKT1 and AKT2 resistant to MK2206.

Figure 1—figure supplement 6.

MDA-MB-361 cells were stably transduced with HA-tagged AKT1-W80A or AKT2-W80A and treated with 2 µM MK2206 for 96 hr. Cell death was assessed by the trypan blue method (left). Parental MDA-MB-361 cells or MDA-MB-361 cells stably expressing AKT1-W80A or AKT2-W80A were treated with the indicated doses of MK2206 for 24 hr and lysed. To assess drug effects, lysates were subjected to immunoblot analysis with the indicated antibodies (right).
DOI: http://dx.doi.org/10.7554/eLife.03751.010

Figure 1—figure supplement 7. Near-complete inhibition of tumor cell proliferation by both allosteric and ATP-competitive inhibitors of AKT.

Figure 1—figure supplement 7.

PIK3CA-mutant MDA-MB-361 cells were treated with vehicle, 2 µM MK2206, or 2 µM GSK690693 (left panel), or vehicle, 2 µM MK2206, or 4 µM GDC0068 (right panel). The number of viable cells was counted on day 1, day 3, day 5, and day 7.
DOI: http://dx.doi.org/10.7554/eLife.03751.011

Figure 1—figure supplement 8. Comparison of AKT kinase inhibition by GSK690693 and MK2206.

Figure 1—figure supplement 8.

BT474 cells (left) and MDA-MB-361 cells (right) were treated with the indicated doses of either MK2206 or GSK690693 for 24 hr and lysed. Lysates were analyzed by immunoblot with the indicated antibodies.
DOI: http://dx.doi.org/10.7554/eLife.03751.012

Figure 1—figure supplement 9. De-inhibition of ErbB3 and p-IGF-IRβ by GSK690693 and MK2206.

Figure 1—figure supplement 9.

EBC1 and BT474 cells were treated with the indicated doses of MK2206 and GSK690693 for 24 hr and lysates were analyzed by Western blot with the indicated antibodies.
DOI: http://dx.doi.org/10.7554/eLife.03751.013
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We had selected EBC1 lung cancer cells for our initial studies because they harbor amplification of MET, a receptor tyrosine kinase that mediates critical oncogenic signals through the PI3K/AKT axis (Gherardi et al., 2012). To test whether other MET-amplified human cancer cells show a similar drug response pattern, we extended our experiments to MET-amplified H1993 and H1648 NSCLC cell lines and GTL-16 gastric cancer cells. MK2206 again induced significantly more cell death than GSK690693 (Figure 1—figure supplement 2, Figure 1—source data 1). In cell lines with other PI3K pathway alterations previously associated with ‘AKT-dependence’ (She et al., 2008), we also found that MK2006 induced significantly more cell death than ATP-competitive AKT inhibitors. These cell lines included breast cancer cells with HER2 amplification and/or PIK3CA-mutation (Figure 1D and Figure 1—figure supplement 3, Figure 1—source data 1). In contrast, MK2206 did not induce cell death in non-transformed bronchial epithelial cells (data not shown). MK2206 also did not induce cell death in lung cancer cell lines with activating EGFR mutations (Figure 1—figure supplement 4, Figure 1—source data 1) which have been linked with aberrant PI3K pathway activation (Engelman et al., 2005), suggesting that the mode of PI3K activation is critical in establishing AKT addiction in cancer.

To exclude the possibility that the greater cell death induction by the allosteric AKT inhibitor was due to additional effects on proteins other than AKT, we stably expressed a synthetic AKT mutant in which a residue critical for allosteric inhibitor binding (tryptophan 80) (Green et al., 2008; Calleja et al., 2009; Wu et al., 2010) had been replaced by an alanine. Expression of AKT1 W80A or AKT2 W80A but not wild-type AKT1 or wild-type AKT2 completely rescued MK2206-induced cell death (Figure 1E and Figure 1—figure supplement 5, Figure 1—source data 1). Western blot analysis confirmed that these AKT alleles are biochemically insensitive to MK2206 and prevented the induction of PARP cleavage, a marker of apoptosis (Figure 1—figure supplement 6, Figure 1—source data 1).

Of note, all three inhibitors were able to induce near-complete proliferation arrest (Figure 1—figure supplement 7, Figure 1—source data 1). These results demonstrate that allosteric and ATP-competitive AKT inhibitors differ in their ability to block AKT-mediated survival, and that this survival signal can be mediated by AKT1 or AKT2.

AKT regulates survival through phosphorylation of several protein substrates. We were therefore surprised that ATP-competitive inhibitors induced less cell death than MK2206 despite greater or equal inhibition of AKT substrate phosphorylation (Figure 1A and Figure 1—figure supplement 8). We could not explain these results by differential effects on induction of ErbB3 expression or IGF-IRβ phosphorylation (Figure 1—figure supplement 9) which can accompany AKT inhibition and mediate resistance to AKT inhibitors (Chandarlapaty et al., 2011).

One potential explanation for our observations is that ATP-competitive AKT inhibitors might induce an AKT conformation which can serve as a platform for a kinase-independent survival signal (Figure 2A). If true, ATP-competitive AKT inhibitors might antagonize cell death induction by a variety of cell death stimuli, for example, inhibition of the MET kinase in MET-amplified EBC1 cells. We found this to be the case. Despite inducing a modest amount of cell death as single agent, GSK690693 antagonized the ability of crizotinib to kill EBC1 cells. The allosteric AKT inhibitor MK2206, in contrast, did not compromise the ability of crizotinib to induce cell death (Figure 2B, Figure 2—source data 1).

Figure 2. Catalytically inactive AKT supports the survival of AKT-dependent human cancer cells.

(A) Cartoon illustrating how ATP-competitive AKT inhibitors may promote a kinase-independent pro-survival function of AKT. In this model, ATP-competitive inhibitors of AKT block kinase activity, induce AKT hyper-phosphorylation, and induce the formation of a pro-survival complex. (B) EBC1 cells were treated with either 25 nM crizotinib, 1 µM GSK690693, 1 µM MK2206, or the indicated combinations for 96 hr. Cell death was assessed following treatment by the trypan blue assay. (C) MCF7 cells or a sub-line generated by stable transduction with kinase-deficient AKT1-K179M were treated with either vehicle or 1 µM MK2206 for 96 hr. Cell death was assessed by the trypan blue method (left). A duplicate set of plates was lysed and analyzed by immunoblot with the indicated antibodies (right) to confirm kinase inhibition and transgene expression. (D) MDA-MB-361 cells or a sub-line stably expressing AKT1-K179M were treated with the indicated doses of MK2206 for 96 hr. Cell death was assessed by the trypan blue assay. (E) Parental EBC1 cells of EBC1 cells stably expressing AKT1-K179M or AKT2-K181M were treated with MK2206 as indicated. After 96 hr, cell death was assessed as elsewhere. (F) EBC1 cells expressing doxycycline-inducible hairpins targeting both hAKT1 and hAKT2 and a sub-line expressing a hairpin-resistant kinase-deficient mAKT1-K179M allele were grown in the presence or absence of 2.5 µg/ml doxycycline for 7 days. Cell death was assessed on day 7 by the trypan blue assay (bottom). Replicate plates were cultured with or without doxycycline for the indicated times and lysed. Lysates were analyzed by immunoblot (top) using the indicated antibodies.

DOI: http://dx.doi.org/10.7554/eLife.03751.014

Figure 2—source data 1. Contains source data for Figure 2 and Figure 2—figure supplement 1.
DOI: http://dx.doi.org/10.7554/eLife.03751.015
elife03751s002.xlsx (41.7KB, xlsx)
DOI: 10.7554/eLife.03751.015

Figure 2.

Figure 2—figure supplement 1. Kinase-dead AKT2-K181M but not wild-type AKT2 protects from MK2206-induced cell death.

Figure 2—figure supplement 1.

EBC1 cells were stably transduced with either HA-tagged wild-type AKT2 or AKT2-K181M. Cells were treated with the indicated doses of MK2206 for 96 hr and cell death was analyzed by the trypan blue method (left). Expression of the transgenes was confirmed by immunoblot with the indicated antibodies (right).
DOI: http://dx.doi.org/10.7554/eLife.03751.016
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To provide genetic evidence for the kinase-independent AKT function, we took advantage of a synthetic AKT mutant which is catalytically inactive due to substitution of lysine by methionine at position 179 at the ATP-binding site (AKT K179M) (Franke et al., 1995). When we expressed this mutant in MCF7 breast cancer cells, MDA-MB-361 breast cancer cells and EBC1 lung cancer cells, catalytically inactive AKT (Figure 2C/D/E, Figure 2—source data 1) but not wild-type AKT (Figure 2—figure supplement 1, Figure 2—source data 1), protected from MK2206-induced cell death. Compared to the complete cell death protection provided by the drug-resistant W80A-AKT allele (Figure 1E, Figure 1—source data 1), the protection by the K179M-AKT allele was only partial, consistent with the coexistence of kinase-independent and kinase-dependent AKT signals.

We also used an AKT knockdown strategy to minimize the effect of AKT overexpression on the stoichiometry of the AKT signaling complex. For this purpose, we first generated EBC1 cells with doxycycline-inducible human-specific shRNAs for both AKT 1 and AKT 2 and then expressed a kinase-deficient (AKT1-K179M) AKT1 cDNA of murine origin that is partially resistant to knockdown due to mismatches in the mouse sequence. Protein levels of the hairpin-resistant AKT allele after doxycycline induction were similar to the levels of endogenous AKT in parental EBC1 cells (Figure 2F, top, lanes 6 and 8 vs lanes 1 and 3). Similar to our results with pharmacological AKT blockade, catalytically inactive AKT protected from cell death following doxycycline treatment and AKT depletion of these cells (Figure 2F, bottom, Figure 2—source data 1).

We next examined the effects of AKT inhibitors on phosphoinositide (PI) binding. In the absence of growth factors, AKT is inactive because intermolecular interactions between the pleckstrin homology (PH) and kinase domain (KD) keep the kinase in a closed conformation (Calleja et al., 2009). Following growth factor stimulation, AKT shifts to an open conformation and becomes accessible to phosphorylation on threonine 308 and serine 473, a process that requires localization of AKT to the plasma membrane through the interaction with the phospholipid products of PI3K, phosphatidyl-inositol-3,4,5-trisphosphate [PtdIns (3,4,5)P3], and PtdIns(3,4)P2. Using a PI pull-down assay, we observed that MK2206 markedly impaired phosphoinositide binding (Figure 3A). This result is consistent with findings from structural studies that allosteric AKT inhibitors lock AKT in a closed conformation with its phospholipid binding site blocked by the kinase domain (Wu et al., 2010). In contrast to our findings with MK2206, incubation with the ATP-competitive inhibitor GSK690693 increased binding of AKT to PtdIns(3,4)P2 and PtdIns (3,4,5)P3 and this was associated with increased localization of AKT to the plasma membrane (Figure 3B).

Figure 3. Kinase-dead AKT protects from drug-induced cell death in a PH-domain-dependent manner.

(A) HCT116 AKT1−/− AKT2 −/− cells stably transduced with human influenza hemagglutinin (HA) epitope-tagged AKT2 were treated with vehicle, MK2206, or GSK690693 for 4 hr and lysed. Lysates were subjected to a PIP-binding assay to assess phosphoinositide binding preference. AKT binding was assessed by immunoblot using an AKT-specific antibody. (B) The localization of AKT2 was assessed in the same cells as in A by HA immunofluorescence following 24 hr treatment with the indicated drugs. Arrows indicate HA staining. (C) Parental MCF10A cells and MCF10A cells stably transduced with HA-tagged wild-type (WT) AKT1 (lane 2) or AKT1-K179M (lane 3) were analyzed by Western blot with the indicated antibodies. (D) The localization of WT and K179M-AKT1 in MCF10A cells was assessed by HA immunostaining. Shown are representative immunofluorescence images. Arrows indicate HA staining. (E) Parental MDA-MB-361 cells or sub-lines stably expressing AKT1-K179M or ΔPH-Myr-AKT1-K179M were treated with the indicated doses of MK2206 for 96 hr. Cell death was assessed by the trypan blue assay. (F) Parental MDA-MB-361 cells, or sub-lines stably expressing kinase-dead AKT1-K179M, or the PIP-binding-deficient variant AKT1-R86A-K179M were treated with the indicated doses of MK2206 for 96 hr. Cell death was measured by the trypan blue assay.

DOI: http://dx.doi.org/10.7554/eLife.03751.017

Figure 3—source data 1. Contains source data for Figure 3 and Figure 3—figure supplement 2.
DOI: http://dx.doi.org/10.7554/eLife.03751.018
elife03751s003.xlsx (15.1KB, xlsx)
DOI: 10.7554/eLife.03751.018

Figure 3.

Figure 3—figure supplement 1. Kinase-deficient AKT mutants display enhanced activation loop phosphorylation at threonine 308.

Figure 3—figure supplement 1.

HCT116 AKT1−/− AKT2 −/− cells were stably transduced with wild-type and kinase-deficient alleles (K179M for AKT1 and K181M for AKT2) of either AKT1 or AKT2. Stably transduced cells were lysed and analyzed by immunoblot with the indicated antibodies. The ratio of phosphorylated AKT (Thr308)/total AKT was determined for each AKT isoform by image quantification densitometry and is indicated below each lane.
DOI: http://dx.doi.org/10.7554/eLife.03751.019

Figure 3—figure supplement 2. Kinase-deficient mutant AKT2 exhibits enhanced membrane localization.

Figure 3—figure supplement 2.

EBC1 cells stably transduced with HA-tagged wild-type AKT2 (top) or kinase-dead AKT2-K181M (bottom) were stained with antibodies against HA. Cells were also stained with DAPI and phalloidin, which binds F-actin and marks membrane ruffles. Note, increased membrane localization of mutant AKT2 even in the absence of membrane ruffles. Shown are representative confocal images of each sample.
DOI: http://dx.doi.org/10.7554/eLife.03751.020

Figure 3—figure supplement 3. Biochemical effects of PH-domain removal in kinase-dead AKT.

Figure 3—figure supplement 3.

Parental MDA-MB-361 cells or MDA-MB-361 cells stably expressing AKT1-K179M or ΔPH-Myr-AKT1-K179M were treated with the indicated doses of MK2206 for 24 hr and lysed. Lysates were subjected to immunoblot analysis with the indicated antibodies.
DOI: http://dx.doi.org/10.7554/eLife.03751.021

Figure 3—figure supplement 4. Phosphoinositide binding deficient kinase-dead AKT can protect from drug-induced cell death.

Figure 3—figure supplement 4.

(A) To assess AKT and AKT substrate phosphorylation of mutant AKT1 alleles, parental HCT116 AKT1−/− AKT2 −/− cells, or HCT116 AKT1−/− AKT2 −/− cells stably expressing WT AKT1, AKT1-K179M, or AKT1-R86A-K179M were lysed and analyzed by Western blot with the indicated antibodies. (B) Parental MDA-MB-361 cells or MDA-MB-361 cells stably expressing AKT1-K179M or AKT1-R86A-K179M were lysed and analyzed by Western blot with the indicated antibodies. Relative levels of AKT1 and vinculin were quantified by image densitometry and are indicated under each lane. (C) Parental MDA-MB-361 cells or sub-lines stably expressing kinase-dead AKT1-K179M or the PIP-binding-deficient variant AKT1-R25C-K179M were treated with the indicated doses of MK2206 for 96 hr. Cell death was measured by the trypan blue assay. Lysates from MDA-MB-361 cells expressing AKT1-R25C-K179M were collected after treatment with vehicle or 2 µM MK2206 for 24 hr.
DOI: http://dx.doi.org/10.7554/eLife.03751.022
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We next explored the structural requirements for the pro-survival signal of catalytically inactive AKT. Similar to GSK690693-bound AKT, the AKT1-K179M (or AKT2-K181M) mutant was hyper-phosphorylated at T308 (Figure 3C and Figure 3—figure supplement 1). This phosphorylation event occurs at the plasma membrane (Stephens et al., 1998) and immunofluorescence in MCF10A and EBC1 cells confirmed that kinase-dead AKT was constitutively localized to the plasma membrane (Figure 3D and Figure 3—figure supplement 2).

To examine whether membrane localization was sufficient for the pro-survival function of AKT1-K179M, we replaced the PH-domain of AKT1-K179M by a membrane-targeting myristoylation signal and expressed this mutant in EBC1 cells. This mutant was unable to inhibit MK2206-induced cell death (Figure 3E, Figure 3—source data 1) despite being constitutively phosphorylated in the presence of MK2206 (Figure 3—figure supplement 3). Lastly, we abolished the ability of the AKT1-K179M mutant to bind phospholipids by introducing a second substitution at an amino acid residue (R86) critical for binding of AKT to PtdIns (3,4,5)P3 and PtdIns(3,4)P2 (Thomas et al., 2002). Consistent with a loss of membrane localization, the R86A/K179M double mutant showed loss of AKT phosphorylation at threonine 308 when expressed in HCT116 cells that express no endogenous AKT (Ericson et al., 2010) (Figure 3—figure supplement 4A) and it did not protect from MK2206-induced dephosphorylation in cells which do express endogenous AKT (Figure 3—figure supplement 4B). Abrogation of phosphoinositide binding by the R86A substitution did not impair the pro-survival function of kinase-defective AKT (Figure 3F, Figure 3—source data 1). We observed a similar result with a second mutation (R25C) known to abolish phosphoinositide binding (Thomas et al., 2002) (Figure 3—figure supplement 4C, Figure 3—source data 1).

Mutations in the coding sequence of AKT are rare in human cancers but provide important insights into AKT regulation (Parikh et al., 2012). We wondered whether there was precedence in human cancer for kinase-dead AKT mutations. Our survey of published cancer sequencing data identified five AKT2 kinase domain mutations that occurred in at least two independent samples (G161V/E, R170W, I289M, H355Y, R368C/H) (Figure 4A). We engineered each of these mutations into an AKT2 expression vector and stably expressed the mutant protein in HCT116 cells with targeted deletions of AKT1 and AKT2 (HCT116-DKO). AKT2-G161V, but none of the other four kinase domain mutants, showed complete loss of in vitro AKT substrate phosphorylation, comparable to the synthetic kinase-dead K181M-AKT2 mutant included as control in our experiments (Figure 4B). Whole-cell lysates from G161V-AKT2 expressing cells showed loss of phosphorylation for the endogenous AKT kinase substrates PRAS40 and BAD (Figure 4C). In the phosphoinositide pull-down assay, AKT2-G161V showed altered phosphoinositide binding with acquired preference for PtdIns(4,5)P2, again similar to the synthetic kinase-dead AKT2 mutant (Figure 4D).

Figure 4. AKT mutants found in human cancer can promote cell survival independently of kinase activity.

Figure 4.

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(A) Distribution of AKT2 mutations that occur in human cancers in 2 or more independent samples. (B) HA-tagged wild-type and the indicated AKT2 mutant proteins were immunoprecipitated with an HA antibody from stably transduced HCT116 AKT1−/− AKT2 −/− cells and subjected to non-radioactive in vitro kinase assay. ‘No kinase’ control consists of an HA-immunoprecipitate from parental HCT116 AKT1−/− AKT2 −/− cells. Substrate phosphorylation, substrate loading, and AKT2 loading were all measured by immunoblot (for further details see ‘Methods’). (C) To evaluate the in vivo kinase activity of various AKT2 alleles, cells described in B were also lysed and analyzed by immunoblot with the indicated antibodies. (D) To determine the PIP-binding preference of WT and mutant AKT2, HCT116 AKT1−/− AKT2 −/− cells expressing WT, K181M, or G161V alleles of AKT2 were subjected to PIP-binding assay. AKT binding was assessed by immunoblot using an HA antibody. (E) Parental or AKT2-G161-expressing immortalized human epidermal melanocytes were plated on melanocyte media and allowed to attach overnight. Cells were then given fresh melanocyte media or switched to RMPI media containing 10% fetal bovine serum. 96 hr following media switch, cell death was assessed as elsewhere. Expression of the transgene was confirmed by immunoblot (inset). Vinculin was used as a loading control. (F) Parental EBC1 cells or EBC1 cells stably expressing exogenous WT AKT1, AKT1-E17K or AKT1-E17K-K179M were treated with the indicated doses of MK2206 for 24 hr and lysed. To asses target inactivation, lysates were analyzed by Western blot with the indicated antibodies. (G) Cells described in F were treated with the indicated doses of MK2206 for 96 hr. Cell death was assessed as before. (H) Model of AKT-dependent protection from apoptosis. AKT becomes fully activated following PI3K activation and subsequent phosphorylation at the T308 and S473 regulatory sites. Fully active AKT negatively regulates pro-apoptotic signals such as BAD and FKHR and positively regulates anti-apoptotic signals such as NFκB through phosphorylation (kinase-dependent functions). Fully AKT also regulates survival signals through kinase-independent activities.

DOI: http://dx.doi.org/10.7554/eLife.03751.023

Figure 4—source data 1. Contains source data for Figure 4.
DOI: http://dx.doi.org/10.7554/eLife.03751.024
elife03751s004.xlsx (34.3KB, xlsx)
DOI: 10.7554/eLife.03751.024

Since AKT2-G161V was found in a human melanoma sample, we explored the pro-survival potential of this mutant in immortalized human melanocytes. These cells required 12-O-tetradecanoylphorbol-13-acetate (TPA) for survival in culture, as has previously been reported (Arita et al., 1992), but acquired the ability to survive in TPA-deficient media (RPMI) after stable expression of AKT2-G161V (Figure 4E, Figure 4—source data 1).

The increased PI(4,5)P2 binding of the kinase-dead G161V-AKT2 mutant (Figure 4D) was reminiscent of the most common somatic AKT mutation in human cancer (E17K-AKT1) which localizes to the plasma membrane due to increased affinity for the constitutive plasma membrane lipid PI(4,5)P2 (Carpten et al., 2007; Landgraf et al., 2008). This raised the question whether kinase activity might be dispensable for the pro-survival functions of the oncogenic E17K-AKT1 mutant. To explore this question, we compared the effects of E17K-AKT1 and a kinase-defective allele of this mutant (E17K/K179M-AKT1) in EBC1 cells. Compared to cells transduced with wild-type AKT, cells transduced with the E17K-AKT1 mutant showed residual AKT phosphorylation at equimolar concentrations of MK2206 (Figure 4F), consistent with the reported reduced sensitivity of E17K-AKT1 to allosteric ATP kinase inhibitors (Calleja et al., 2009; Wu et al., 2010; Parikh et al., 2012). Expression of E17K-AKT1 provided partial protection from MK2206-induced cell death (Figure 4G, Figure 4—source data 1). Interestingly, the E17K/K179M-AKT1 double mutant provided a similar degree of protection as the E17K-AKT1 single mutant, suggesting that this cancer-associated PH-domain mutant can mediate survival signals independent of its catalytic activity in certain cellular contexts.

Lastly, we identified a human endometrial cancer cell line with a kinase domain mutation in AKT1 (G311D) (Barretina et al., 2012) that failed to induce phosphorylation of endogenous AKT substrates in AKT1/2 DKO HCT116 cells (Figure 5A). While knockdown of endogenous AKT1 or AKT2 resulted in growth inhibition, knockdown of AKT1 resulted in substantially greater cell death induction than knockdown of AKT2 (Figure 5B, Figure 5—source data 1), suggesting a state of addiction to signals provided by the mutant AKT1.

Figure 5. Endometrial cancer cells expressing endogenous kinase-deficient AKT1 are sensitive to AKT1 but not AKT2 knockdown.

Figure 5.

Open in a new tab

(A) AKT-deficient HCT116 cells were stably transduced with wild-type or the indicated mutant AKT1 alleles. In cell AKT kinase activity was determined by assessing the phosphorylation of the AKT substrates PRAS40 and BAD by immunoblot as shown. Expression of vinculin was used as a loading control. Note that AKT1-G311D does not promote AKT substrate phosphorylation. (B) MFE-319 endometrial cancer cells which carry and endogenous AKT1-G311D mutation (http://www.broadinstitute.org/ccle/home) were engineered to express tetracycline-inducible hairpins targeting either AKT1 or AKT2. Cells were grown in the presence or absence of 2.5 µg/ml doxycycline for 6 days. Cell death was assessed on day 7 as before (left). To confirm knockdown of AKT and selectivity of the hairpins, a separate set of plates was grown with or without doxycycline for the indicated times and lysed. Vinculin expression was used as a loading control.

DOI: http://dx.doi.org/10.7554/eLife.03751.025

Figure 5—source data 1. Contains source data for Figure 5.
DOI: http://dx.doi.org/10.7554/eLife.03751.026
elife03751s005.xlsx (35.6KB, xlsx)
DOI: 10.7554/eLife.03751.026

Discussion

The work presented here represents the first example of a kinase-independent function of AKT (Figure 4H). Our findings that catalytically inactivating kinase domain mutations (AKT1-K179M, AKT2-K181M, AKT2-G161V) or ATP-competitive inhibitor binding to wild-type AKT can promote phosphoinositide binding document the critical importance of the kinase domain conformation on AKT PH-domain functions. It also suggests that hyper-phosphorylation of AKT in response to ATP-competitive inhibitors (Okuzumi et al., 2009) may not only be due to impaired phosphatase access (Chan et al., 2011) but also due to increased phosphorylation at the plasma membrane. Furthermore, given that the loss of phosphoinositide binding does not completely abolish the pro-survival function of kinase-deficient AKT, we suspect that the PH-domain promotes cell survival through regulation of interacting protein partners, and that perturbations in the kinase domain can influence PH-domain function by altering the ability of AKT to reach the appropriate sub-cellular compartment (likely those richest in PI(4,5)P2) and/or interact with specific effector proteins. Further studies are required to identify the effectors of catalytically inactive AKT and define its contribution to other AKT-regulated cellular processes.

Our findings have implications for the development of drugs to block AKT in cancer. Previous studies have shown that cancer-associated AKT mutations that favor an open conformation show reduced sensitivity to allosteric AKT inhibitors but retain sensitivity to ATP-competitive inhibitors (Calleja et al., 2009; Wu et al., 2010; Parikh et al., 2012). Here, we show that cancer cells with aberrant AKT activation by common PI3K pathway lesions (HER2, PIK3CA, MET) show the opposite drug sensitivity profile with reduced sensitivity to ATP-competitive AKT inhibitors. The inability of ATP-competitive inhibitors to suppress non-catalytic AKT functions in certain genetic contexts may represent a liability compared to allosteric AKT inhibitors. This concept remains to be tested in ongoing clinical trials.

Materials

Chemicals and antibodies

MK2206, GSK690693, and crizotinib were purchased from Selleck Chemicals (Houston, TX). GDC0068 was purchased from Active Biochem. Antibodies for immunoblots against pPRAS40 (T246), PRAS40, AKT, AKT1, AKT2, pAKT1 (S473), pAKT2 (S474), pAKT (T308), pAKT (S473), pAKT substrate (RXRXXS*/T*), BAD, pBAD, cleaved PARP, pMET (Y1349), Met, pErk1/2 (T202/Y204), Erk, pGSK3β (S9), GSK3β, pFoxo3a (S253), and Foxo3a were purchased from Cell Signaling Technologies (Danvers, MA, USA). HA, vinculin, and β-actin antibodies for immunoblots were purchased from Sigma-Aldrich (St. Louis, MO). HA.11 Clone 16B12 monoclonal antibody for immunofluorescence was purchased from Covance (Princeton, NJ). DAPI, Alexa-488 anti-mouse secondary antibody, Phalloidin 546, and Prolong Gold Antifade reagent were purchased from Life Technologies (Carlsbad, CA). HA-Tag antibody Sepharose bead conjugate and non-radioactive AKT kinase assay kit were purchased from Cell Signaling Technologies. PIP Beads Sample pack was purchased from Echelon Biosciences Incorporated (Salt Lake City, UT).

Cells

EBC1 cells were obtained from the Japanese Collection of Research Bioresources (JCRB) Cell Bank. GTL-16 cells were the generous gift of Dr Silvia Giordano (Instituto di Candiolo, Italy). HCT116 AKT1−/− AKT2 −/− (HCT116-DKO) cells were kindly provided by Dr Bert Vogelstein (Johns Hopkins University School of Medicine). BT474, H1648, H1975, HCC827, HCC4006, MCF7, MCF10A, and MDA-MB-361 cells were purchased from the American Type Culture Collection (ATCC). Human epidermal melanocytes were purchased from ScienCell Research Laboratories (Carlsbad, CA, Catalog #2200). HCT116-DKO cells were maintained in McCoy’s 5a Medium supplemented with 10% fetal bovine serum (FBS). MCF10A cells were maintained in Mammary Epithelial Cell Growth Medium (Lonza, Allendale, NJ). Human melanocytes were maintained in melanocyte media (ScienCell, Catalog #2201). All other cell lines were maintained in DMEM media supplemented with 10% FBS.

Plasmids and mutagenesis

TRIPZ tetracycline-inducible lentiviral shRNAs targeting human AKT1 and AKT2 were purchased from Thermo Scientific (Lafayette, CO) (AKT1 clones: V3THS_358718 and V3THS_358718; AKT2 clones: V2THS_237948, V3THS_325553, and V3THS_325558). pLNCX1-HA-mAKT1 (murine) was generated by Dr Morris Birnbaum and obtained from Addgene (Plasmid #15990). pLNCX-HA-mAKT1-K179M was generated by site-directed mutagenesis. All site-directed mutagenesis was carried out using the QuikChange Lightning Site-Directed Mutagenesis Kit from Agilent Technologies (Santa Clara, CA) and verified by Sanger sequencing. pLNCX1-ΔPH-Myr-AKT1-K179M was generated by site-directed mutagenesis using pLNCX1-ΔPH myr-AKT1 (generated by Dr Morris Birnbaum and obtained from Addgene, plasmid #15989) as template. pLNCX1-HA-AKT2 (human #27295) was generated by Dr Morris Birnbaum and obtained from Addgene (Plasmid #15990). From pLNCX1-HA-AKT2 a HindIII/ClaI restriction fragment was used to subclone AKT2 into pLPCX (Clontech) to create pLPCX-HA-AKT2. All AKT2 mutants used in this study were generated by site-directed mutagenesis using pLPCX-HA-AKT2 as template. pLNCX-HA-AKT1 (human) was generated by Dr William Sellers and obtained from Addgene (Plasmid #9004). pLNCX-HA-AKT1-K179M and pLNCX-HA-AKT1-W80A were generated by site-directed mutagenesis using pLNCX-HA-AKT1 as template. pbabe-hTERT+p53DD was generated by Dr Christopher Counter and obtained from Addgene (Plasmid #11128).

Site directed mutagenesis was done using the following primers:

  • AKT1-E17K (human): Sense: 5′-gctgcacaaacgagggaagtacatcaagacctg-3′, Antisense: 5′-caggtcttgatgtacttccctcgtttgtgcagc-3′.

  • mAKT1-K179M (murine): Sense: 5′-ccgctactatgccatgatgatcctcaagaaggagg-3′, Antisense: 5′-cctccttcttgaggatcatcatggcatagtagcgg-3′.

  • AKT1-K179M (human): Sense: 5′-ccgctactacgccatgatgatcctcaagaaggaag-3′, Antisense: 5′-cttccttcttgaggatcatcatggcgtagtagcgg-3′.

  • AKT1-R25C (human): Sense: 5′-aagacctggcggccatgctacttcctcc-3′, Antisense: 5′-ggaggaagtagcatggccgccaggtctt-3′.

  • AKT1-R86A (human): Sense: 5′-cagtggaccactgtcatcgaagccaccttccatgtg-3′, Antisense: 5′-cacatggaaggtggcttcgatgacagtggtccactg-3′.

  • AKT1-W80A (human): Sense: 5′-tccgctgcctgcaggcgaccactgtcatcg-3′, Antisense: 5′-cgatgacagtggtcgcctgcaggcagcgga-3′.

  • AKT2-K181M (human): Sense: 5′- gctactacgccatgatgatcctgcggaagga-3′, Antisense: 5′- tccttccgcaggatcatcatggcgtagtagc-3′.

  • AKT2-G161V (human): Sense: 5′-caaactccttggcaaggtaacctttggcaaagtca-3′, Antisense: 5′-tgactttgccaaaggttaccttgccaaggagtttg-3′.

  • AKT2-R170W (human): Sense: 5′-aaagtcatcctggtgtgggagaaggccactg-3′, Antisense: 5′-cagtggccttctcccacaccaggatgacttt-3′.

  • AKT2-R368C (human): Sense: 5′-tcatggaagagatctgcttcccgcgcacg-3′, Antisense: 5′-cgtgcgcgggaagcagatctcttccatga-3′.

  • AKT2-H355Y (human): Sense: 5′-cttctacaaccaggactatgagcgcctcttcgagc-3′, Antisense: 5′-gctcgaagaggcgctcatagtcctggttgtagaag-3′.

  • AKT2-I289M (human): Sense: 5′-tggacaaagatggccacatgaagatcactgactttg-3′, Antisense: 5′-caaagtcagtgatcttcatgtggccatctttgtcca-3′.

Methods

Western blots

Cells were harvested directly on tissue culture plates with 1% triton cell lysis buffer (Cell Signaling Technologies) supplemented with protease and phosphatase inhibitors. Lysates were sonicated, cleared by centrifugation, and normalized to equal amounts of total protein using the DC protein assay (Biorad).

Retroviral infections

For transduction of wild-type and mutant AKT alleles into EBC1, HCT116 AKT1−/− AKT2 −/−, MCF7, and MDA-MB-361 cells, amphotropic retroviruses were generated by co-transfection of retroviral constructs carrying the appropriate cDNA and the packaging plasmid pCL-Ampho (IMGENEX, San Diego, CA) into 293T cells. Viral particles were collected after 36 and 60 hr following transfection and target cells were infected for 18 hr with the respective virus. Stable expressors were derived through antibiotic selection. To immortalize human epidermal melanocytes (iHEM), primary melanocytes (ScienCell) were retrovirally infected with amphotropic pbabe-hTERT + p53DD virus using the above transduction protocol. For lentiviral transduction of Tet-inducible shRNAs targeting AKT1 and AKT2, viral particles were produced by co-transfection of shRNA constructs (listed above) with two packaging plasmids (pMD2G and pPAX2) into 293T cells. Five different viruses were generated (2 AKT1 hairpins and 3 AKT2 hairpins). Viral particles were collected at 36 and 60 hr after transfection. All five viruses were mixed, and infection of EBC1 cells was carried out for 8 hr after each virus collection. 36 hours after the last infection, cells were selected with 10 µM puromycin to derive stable expressors. Following selection, cells were also transduced with pLNCX-HA-mAKT1-K179M retrovirus and selected with 1 mg/ml G148 to generate cells with a hairpin-resistant AKT1-K179M allele.

Cell death assay

Cells were seeded on 6 cm dishes and allowed to attach overnight. Cells were then treated with the indicated drugs at the indicated doses. Each treatment group was seeded in triplicate. Following treatment, both attached and unattached cells were harvested and counted on a ViCell Cell Viability analyzer. The instrument uses trypan blue to assess cell death. Cell death was expressed as the fraction of trypan blue-positive cells over the total number of cells. Statistical significance was assessed by one-tailed unequal variance t-test (ns = p > 0.05; * = p ≤ 0.05; ** = p ≤ 0.01, *** = p ≤ 0.001).

AKT kinase assay

AKT kinase assays were carried out using the non-radioactive AKT Kinase Assay Kit from Cell Signaling Technologies (Catalog #9840) according to the manufacturer's instructions with the following modification: HA-Tag antibody Sepharose bead conjugate was used to isolate AKT kinase. Briefly, HCT116 AKT1/2 DKO cells expressing exogenous HA-tagged AKT alleles were lysed in 1× lysis buffer and sonicated. Sonicated lysates were normalized to equal amounts of total protein. AKT was then purified from normalized lysates by HA immunoprecipitation for 3 hr at 4°C. HA beads were then washed two times with 500 µl lysis buffer and once with 1× kinase buffer. Beads were then resuspended in 50 µl kinase buffer, and kinase reaction was carried out for 30 min after addition of 1 µg of substrate and ATP to a final concentration of 200 µM. Reaction was terminated by adding 3× Laemmli buffer. 10 µl of kinase reaction were analyzed by immunoblot. Substrate phosphorylation and AKT content in each reaction was measured by immunoblot.

PIP binding assay

HCT116 AKT1−/− AKT2 −/− (with or without exogenous AKT) cells were grown on a monolayer, washed once with cold PBS, and harvested on the dish using lysis buffer (10 mM HEPES pH 7.4, 150 mM NaCl, 1% Triton, and EDTA-free protease and phosphatase inhibitors). Lysates were sonicated and cleared by centrifugation. Cleared lysates were then normalized to equal amounts of total protein. The amount of AKT in each lysate was then quantified by Western blot using an HA antibody and the lysates normalized for AKT content using image analysis of AKT immunoreactive bands. Lysate from parental HCT116 AKT1−/− AKT2 −/− cells was used to normalize a second time for total protein amount. Each lysate was then divided into 10 aliquots to verify the final normalization by Western blot and for PIP binding analysis. PIP beads were obtained from Echelon Biosciences Inc. (Echelon Inc, Salt Lake City, UT). Each lysate was incubated with one PIP variant (30 μl of 50% bead slurry equivalent to approximately 200 pmoles) for 3 hr at 4°C. Beads were washed three times with 10 vol of lysis buffer. Bound proteins were eluted by boiling PIP beads in 3× Laemmli Sample Buffer at 95°C.

Immunofluorescence

Cells were washed with 1× PBS at room temperature, fixed in 4% PFA for 10 min, and permeabilized for 2 min in 1× PBS containing 0.1% Triton X-100. Coverslips were blocked with 3% bovine serum albumin (wt/vol) and 0.1% Triton X-100 in PBS for 30 min. Primary antibody incubation was done for 1 hr in blocking solution, followed by five 1× PBS, 0.1% Triton X-100 washes. Secondary antibody incubation was carried out for 1 hr followed by five washes and incubated with DAPI for 2 min to visualize DNA. Fluorescent images were acquired on an upright microscope (Axio imager; Carl Zeiss) equipped with 100× oil objectives, NA of 1.45, a camera (ORCA ER; Hamamatsu Photonics), and a computer loaded with image-processing software (Axiovision).

For confocal analysis, EBC1 cells were plated on fibronectin coated coverslips, washed with 1× PBS, fixed in 4% PFA for 10 min at room temperature, and permeabilized with 0.1% Triton X-100 for 10 min. Coverslips were then incubated in blocking solution (10% donkey serum, 0.1% BSA in PBS) for 1 hr, followed by incubation with a primary antibody (anti-HA) in blocking solution for 1 hr. Alexa-488 anti-mouse antibodies were used for detection. Coverslips were then incubated with Phalloidin 546 for 30 min. Nuclei were stained with DAPI for 3 min. Coverslips were then mounted using Prolong Gold Antifade reagent and images were acquired with a 40× magnification lens in a Leica TCS-SP5 (WLL) multiphoton confocal microscope.

Acknowledgements

We thank members of the Mellinghoff Laboratory, Dr Charles Sawyers, Dr Neal Rosen, and Dr Michelle Garrett for helpful suggestions. This work was supported by the National Institutes of Health (1R01NS080944–01, U54CA143798, F32 GM096558), the James S McDonnell Foundation, and National Brain Tumor Society Defeat GBM initiative.

Funding Statement

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

Funding Information

This paper was supported by the following grants:

  • National Institutes of Health 1R01NS080944–01, U54CA143798 to Igor Vivanco, Zhi C Chen, Nicolas Yannuzzi, Carl Campos.

  • National Institutes of Health F32 GM096558 to Barbara Tanos.

  • James S. McDonnell Foundation to Igor Vivanco, Zhi C Chen, Nicolas Yannuzzi, Carl Campos.

  • National Brain Tumor Society to Igor Vivanco, Zhi C Chen, Nicolas Yannuzzi, Carl Campos.

Additional information

Competing interests

The authors declare that no competing interests exist.

Author contributions

IV, Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article.

ZCC, Acquisition of data, Analysis and interpretation of data.

BO, Acquisition of data, Analysis and interpretation of data.

W-YH, Acquisition of data, Analysis and interpretation of data.

NY, Acquisition of data, Analysis and interpretation of data.

CC, Acquisition of data, Analysis and interpretation of data.

BT, Conception and design, Acquisition of data, Analysis and interpretation of data.

IKM, Conception and design, Analysis and interpretation of data, Drafting or revising the article.

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eLife. 2014 Dec 31;3:e03751. doi: 10.7554/eLife.03751.027

Decision letter

Editor: Roger Davis1

eLife posts the editorial decision letter and author response on a selection of the published articles (subject to the approval of the authors). An edited version of the letter sent to the authors after peer review is shown, indicating the substantive concerns or comments; minor concerns are not usually shown. Reviewers have the opportunity to discuss the decision before the letter is sent (see review process). Similarly, the author response typically shows only responses to the major concerns raised by the reviewers.

Thank you for sending your work entitled and Senior, Thank you for sending your work entitled “A kinase-independent function of AKT promotes cancer cell survival” for consideration at eLife. Your article has been favorably evaluated by Tony Hunter (Senior Editor) and 3 reviewers, one of whom is a member of our Board of Reviewing Editors.

The Reviewing and the other reviewers discussed their comments before we reached this decision, The Reviewing editor and the other reviewers discussed their comments before we reached this decision, and the Reviewing editor has assembled the following comments to help you prepare a revised submission.

Previous studies have established that AKT provides important survival signals mediated by the phosphorylation of protein substrates, Previous studies have established that AKT provides important survival signals mediated by the phosphorylation of protein substrates. Here the authors demonstrate that AKT also promotes survival by a mechanism that is independent of AKT substrate phosphorylation. The identity of this mechanism is not described. Nevertheless, the conclusions of the paper are novel, interesting, and potentially significant for cancer therapy. However, the conclusions of this study are not fully supported by the data presented.

Major points:

1) One weakness of this study is that it is largely based on over-expression of mutant AKT. Controls using WT AKT are not presented (with the exception of Figure 4G); this important control should be included in each experiment. Moreover, studies of AKT expressed at endogenous levels are essential. Only two studies designed to examine AKT expressed at endogenous levels are presented. The first is a shRNA knock-down/rescue with a shRNA-resistant mutant (Figure 2G). This experiment is difficult to interpret because the mutant AKT is clearly over-expressed and knocked down by the shRNA (despite being stated to be shRNA-resistant). The experiment also lacks controls for off-target actions of the shRNA pools. The second study is an shRNA experiment on endometrial cancer cells (Figure 5B) that lacks controls for off-target effects of the shRNA pools. Additional validation of a kinase-independent function of AKT expressed at endogenous levels is required. For example, can the survival function of kinase-dead AKT be phenocopied by blocking upstream pathways that lead to AKT activation?

2) Figure 2C: The authors argue that the ability of ATP-competitive AKT inhibitors to create complexes with their target(s) that are capable of providing survival signals is revealed by their ability to suppress crizotinib-induced cell death. This would be more clearly validated by a comparison with an “allosteric” inhibitor.

3) The protein localization data are unclear (Figures 3B, D), because the conclusions regarding membrane localization are compromised by the apparent membrane ruffling that causes a higher local density of membrane that can give the false appearance of concentration.

4) Figure 3E: The data obtained with mAKT1-K179M lacking a PH domain are difficult to interpret. Is it targeted to the plasma membrane? Is it substantially resident in other membrane compartments? Could these data indicate that membrane targeting is important, rather than indicating that the survival signals are generated away from membranes, as stated?

5) The analysis is focused on cells with gain-of-function of pathways leading to Akt activation, including MET and PI3K-pathway mutations. Data on survival in response to allosteric vs ATP-competitive AKT inhibitors using cells without this gain-of-function would provide some initial insight into the potential cancer v normal-cell therapeutic window.

6) The HA blot in Figure 3–figure supplement 2B is difficult to interpret.

eLife. 2014 Dec 31;3:e03751. doi: 10.7554/eLife.03751.028

Author response

In response to the reviewers’ excellent suggestions, we have conducted a series of additional experiments that clarified several key points brought up by several reviewers:

To address the role of AKT protein levels in our observations with kinase-dead AKT allels, To address the role of AKT protein levels in our observations with kinase-dead AKT allels, we now expressed wildtype AKT in multiple cell lines (EBC1, MCF7, MDA-MB-361) and show that wild-type AKT is not sufficient to promote cell survival. We also provided more experimental detail regarding our experiment where we knocked down endogenous (human) AKT and replaced it with a murine, kinase dead AKT protein.

Regarding the subcellular localization of kinase-deficient AKT mutants, Regarding the subcellular localization of kinase-deficient AKT mutants, we performed additional confocal microscopy experiments. We again found increased plasma membrane localization of kinase-deficient AKT. Furthermore, by re-introducing wild type or kinase-deficient AKT alleles into AKT1/2 double knockout cells, we show enhanced activation loop phosphorylation (T308) in mutant AKT, a phosphorylation event that occurs at the cytoplasmic membrane.

We now document that the allosteric AKT inhibitor, We now document that the allosteric AKT inhibitor, unlike ATP-competitive AKT inhibitors, does not antagonize the ability of a MET kinase inhibitor to induce cell death in MET-amplified cancer cells. This important control was missing from our original manuscript.

Major points:

1) One weakness of this study is that it is largely based on over-expression of mutant AKT. Controls using WT AKT are not presented (with the exception of Figure 4G); this important control should be included in each experiment.

We thank the reviewers for this suggestion and agree that assessing the effects of ectopically expressed wild type AKT represents an important control, We thank the reviewers for this suggestion and agree that assessing the effects of ectopically expressed wild type AKT represents an important control. To address this question, we now overexpressed wild type AKT1 or wild type AKT2 in several cancer cell lines and repeated key experiments with this additional control. Unlike the W80A-AKT mutants, which cannot bind MK2206, expression of wild type AKT1 (Author response image 1A) or AKT2 (Author response image 1B) does not rescue MDA-MB361 breast cancer cells from MK2206-induced cell death (indicated by red arrows below). We made similar observation in EBC1 lung cancer cells (Author response image 1C). These new data are included in our revised manuscript as Figure 1E, Figure 1–figure supplement 5, Figure 2–figure supplement 1, and Figure 4G (also shown below as Author response image 1A, 1B, 1C, and 1D, respectively).

Author response image 1.

Author response image 1.

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A) and B) MDA‐MB‐361 cells were stably transduced with wild type or MK‐2206‐resistant AKT1 (AKT1‐W80A) or AKT2 (AKT2‐W80A) and assessed for MK2206 response as shown. Note that overexpression of wild type AKT alleles does not change the response to MK2206. C) EBC1 cells were stably transduced with wild type or kinase‐dead AKT2 (AKT2‐K181M) and assessed for MK2206 response as in A. Note that mutant, but not wild type AKT overexpression, confers resistance to MK2206.

Moreover, studies of AKT expressed at endogenous levels are essential. Only two studies designed to examine AKT expressed at endogenous levels are presented. The first is a shRNA knock-down/rescue with a shRNA-resistant mutant (Figure 2G). This experiment is difficult to interpret because the mutant AKT is clearly over-expressed and knocked down by the shRNA (despite being stated to be shRNA-resistant). The experiment also lacks controls for off-target actions of the shRNA pools. The second study is an shRNA experiment on endometrial cancer cells (Figure 5B) that lacks controls for off-target effects of the shRNA pools. Additional validation of a kinase-independent function of AKT expressed at endogenous levels is required. For example, can the survival function of kinase-dead AKT be phenocopied by blocking upstream pathways that lead to AKT activation?

We thank the reviewers for the opportunity to clarify these important points.

The reviewer is correct that the shRNA-“resistant” cDNA is, in fact, only partially resistant to our shRNAs. The targeting sequences used to knock down AKT1 in our experiments (CCCGAGGTGCTGGAGGACA and GGCAAGGTGATCCTGGTGA) are based on human AKT1 and we used murine AKT as a “rescue” allele. As indicated in the Materials and methods section of our revised manuscript, human and murine AKT1 are mismatched only at one or two nucleotides (underlined) relative to each of the targeting sequences (CCTGAGGTGCTGGAGGACA and GGGAAGGTGATTCTGGTGA), likely explaining the incomplete rescue. Nonetheless, despite the effects of the shRNA-hairpins on the murine mRNA, only cells expressing the murine AKT1 cDNA show residual AKT1 following doxycycline treatment. [Please compare, in Author response image 2 below, lanes 6 and 8 (green arrows) to lanes 2 and 4 (red arrows).] Of note, levels of residual K179M-mAKT1 (lanes 6 and 8, green arrows) are roughly equivalent to the endogenous AKT levels seen in the absence of doxycycline (lanes 1 and 3, blue arrows), an effect not seen with AKT2 expression. In our revised manuscript, we have revised the figure and text to explain this point more clearly.

Author response image 2.

Author response image 2.

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EBC1 cells were stably transduced with doxycycline‐inducible human‐specific AKT1 and AKT2 shRNAs (Control) and subsequently transduced with a murine kinase‐deficient AKT1 cDNA (mAKT1‐K179M). Cells were treated with doxycycline for the indicated times. AKT levels were measured at each time point by western blot as shown. Note that the levels of shRNA‐resistant AKT1 expression (green arrows) are equivalent to those seen in untreated control cells (blue arrows).

We also examined the question whether the survival function of kinase-dead AKT can be phenocopied by blocking upstream pathways that lead to AKT activation. We found that the ATP-competitive AKT inhibitor GSK690693 does not promote cell survival if we block all AKT activating signals through pharmacological PI3-kinase inhibition with the PI3K inhibitor BKM-120 (Author response image 3). These data suggests that even the kinase-independent functions of AKT require a PI3K input. We are therefore unable to experimentally phenocopy the pro-survival functions of kinase-deficient AKT by blockade of upstream signals.

Author response image 3.

Author response image 3.

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EBC1 cells were treated with the pan‐class‐I PI3K inhibitor, and/or the AKT inhibitor GSK690693. Cells were allowed to grow for 96 hours and assessed for cell death following this incubation period by the trypan blue method (left). A duplicate set of samples was analysed by western blot to document drug activity. Note that GSK690693 does not protect (red arrow) from PI3K‐inhibitor‐induced cell death (green arrow).

2) Figure 2C: The authors argue that the ability of ATP-competitive AKT inhibitors to create complexes with their target(s) that are capable of providing survival signals is revealed by their ability to suppress crizotinib-induced cell death. This would be more clearly validated by a comparison with an “allosteric” inhibitor.

We apologize for not including these data in our prior submission. In our revised manuscript, we are showing the full experiment which included the allosteric AKT inhibitor MK2206 and the crizotinib/MK2206 combination. The results show that the allosteric AKT inhibitor MK2206, unlike the ATP-competitive inhibitor GSK690693, does not protect from crizotinib-induced cell death (Author response image 4), consistent with our model. These data are included as Figure 2B in the revised manuscript.

Author response image 4.

Author response image 4.

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EBC1 cells were treated with the MET inhibitor crizotinib and/or AKT inhibitors GSK690693 and MK2206, and assessed for cell death. Panel (A) was shown in the original manuscript as Figure 2B and only contained data with crizotinib and GSK690693. Panel (B) has now replaced this figure in the revised manuscript and contains additional data using MK2206 (red arrows).

3) The protein localization data are unclear (Figures 3B, D), because the conclusions regarding membrane localization are compromised by the apparent membrane ruffling that causes a higher local density of membrane that can give the false appearance of concentration.

We thank the reviewers for the opportunity to clarify this important point. In our original manuscript, we showed increased phosphorylation of the kinase-deficient AKT1 mutant (K179M) at Serine 308 (Author response image 5A). Other investigators have shown that phosphorylation of AKT at T308 occurs at the plasma membrane (Stephens et al., Science 1998, PMID: 9445477), and we believe that this is consistent with our previously provided immunofluorescence data (Author response image 5B).

Author response image 5.

Author response image 5.

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MCF10A cells were stably transduced with wild type or kinase‐dead (K179M) AKT1. Western blot analysis (A) (Figure 3C of revised manuscript) shows enhanced pAKT(T308) in mutant‐AKT‐expressing cells, and immunofluorescence analysis indicates this increase corresponds to enhanced membrane localization (B) (Figure 3D of revised manuscript). (C) EBC1 cells were stably transduced with WT or kinase‐dead AKT2 (K181M). Cells were stained as indicated and imaged using confocal microscopy. Note the enhanced membrane localization of mutant AKT2 (bottom left, green arrow), compared to wild type AKT2 (top left, green arrow). Insets are an enlarged images of the region indicated by the red arrows.

In response to the reviewers, we have now also examined the cellular localization of kinase deficient AKT2 (K181M). As shown in confocal images of wild type vs. mutant AKT2 in stably-transduced EBC1 cells (Author response image 5C, left column), kinase-deficient AKT2 more robustly colocalizes with the plasma membrane marker Na+/K+ ATPase than its wild type counterpart. Furthermore, following the reviewer’s suggestion, we co-stained these cells with phalloidin which binds F-actin and marks membrane ruffles. We found increased membrane localization of mutant AKT2 even in the absence of membrane ruffles (red arrows in Author response image 5C, right column). These data are included in Figure 3–figure supplement 2 of our revised manuscript.

We thus conclude that kinase-deficient AKT1 and AKT2 show increased localization to the plasma membraneOur results with engineered and naturally occurring kinase-dead AKT mutants are reminiscent of the findings from Kevan Shokat’s group at UCSFwhich documented relocalization of AKT to the plasma membrane in response to ATP-competitive Akt kinase inhibitors (Okuzumi et al., 2009 We thus conclude that kinase-deficient AKT1 and AKT2 show increased localization to the plasma membrane. Our results with engineered and naturally occurring kinase-dead AKT mutants are reminiscent of the findings from Kevan Shokat’s group at UCSF, which documented relocalization of AKT to the plasma membrane in response to ATP-competitive Akt kinase inhibitors (Okuzumi et al., Nature Chemical Biology, 2009, PMID: 19465931). In contrast, the allosteric AKT inhibitor MK2206 does not promote membrane relocalization of AKT.

4) Figure 3E: The data obtained with my-Akt1-K179M lacking a PH domain are difficult to interpret. Is it targeted to the plasma membrane? Is it substantially resident in other membrane compartments? Could these data indicate that membrane targeting is important, rather than indicating that the survival signals are generated away from membranes, as stated?

We completely agree with the reviewers’ interpretation of the data and have rephrased our conclusions to express this more clearly. The non-catalytic function of AKT requires the presence of the PH domain, as demonstrated by our data with the Δ PH-Myr-Akt1-K179M mutant. Together with the results of our experiments using the R86C and R25C mutants, this data suggest that the kinase-independent function of AKT might require targeting to specific membranes or membrane subdomains, likely those richest in PI(4,5)P2, to which the mutants show enhanced binding.

5) The analysis is focused on cells with gain-of-function of pathways leading to Akt activation, including MET and PI3K-pathway mutations. Data on survival in response to allosteric vs ATP-competitive AKT inhibitors using cells without this gain-of-function would provide some initial insight into the potential cancer v normal-cell therapeutic window.

We thank the reviewers for this insightful suggestion, We thank the reviewers for this insightful suggestion.

To address the issue, To address the issue, we have treated BEAS-2B immortalized (non-transformed) bronchial epithelial cells with MK2206, and found that it could not induce any appreciable amount of cell death (Author response image 6).

Author response image 6.

Immortalized bronchial epithelial cells (BEAS‐2B) and EGFR‐mutant non‐small‐cell lung carcinoma cell lines (HCC827, HCC4006, and H1975) do not die in response to MK2206.

Author response image 6.

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We have also treated three NSCLC cell lines carrying endogenous activating EGFR mutations with AKT inhibitors (also shown in Author response image 6), We have also treated three NSCLC cell lines carrying endogenous activating EGFR mutations with AKT inhibitors (also shown in Author response image 6). While we have found that amplification of MET and activating PIK3CA-mutations are associated with sensitivity to AKT allosteric inhibitors, we find that the EGFR-mutant lung cancer cell lines are completely refractory to cell death induction by either MK2206 or GSK690693. Given that these EGFR mutations are capable of activating AKT (PMID: 15731348), these data suggest that the mechanism of PI3K activation (e.g. EGFR activation vs MET activation) is likely critical in establishing AKT dependence. These data have been added to the revised manuscript as Figure 1–figure supplement 4.

6) The HA blot in Figure 3–figure supplement 2B is difficult to interpret.

We apologize for the poor quality of this blot. We have now performed additional western blot analysis with an AKT1-specific antibody to quantify AKT1 expression in the transduced sublines, relative to the parental controls. The results show increased AKT1 expression in cells transduced with wild type or mutant AKT1 cells (see image quantification below each lane in Author response image 7). Of note, it also again shows that the kinase-dead K179M-AKT1 mutant exhibits increased phosphorylation at threonine 308 (lanes 5) compared to wild type AKt1 (lane 3) and that this hyperphosphorylation is lost when PIP3-binding is disrupted by the second R86A mutation (lane 7). These new data have been included as Figure 3–figure supplement 4B of the revised manuscript.

Author response image 7.

MDA‐MB‐361 cells were stably transduced with the indicated alleles of AKT1. Cells were treated with vehicle or MK2206 and lysed for western blot analysis as indicated. AKT1 levels and the levels of the loading control (vinculin) were quantified by image densitometry, and the relative levels are indicated under each band. Note that all samples from transduced cells express higher AKT1 levels, and that Akt1‐K179M exhibits enhanced pAKT(T308) levels.

Author response image 7.

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Associated Data

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

    Supplementary Materials

    Figure 1—source data 1. Contains source data for Figure 1 and all accompanying Figure 1—figure supplements.

    DOI: http://dx.doi.org/10.7554/eLife.03751.004

    elife03751s001.xlsx (42.7KB, xlsx)
    DOI: 10.7554/eLife.03751.004
    Figure 2—source data 1. Contains source data for Figure 2 and Figure 2—figure supplement 1.

    DOI: http://dx.doi.org/10.7554/eLife.03751.015

    elife03751s002.xlsx (41.7KB, xlsx)
    DOI: 10.7554/eLife.03751.015
    Figure 3—source data 1. Contains source data for Figure 3 and Figure 3—figure supplement 2.

    DOI: http://dx.doi.org/10.7554/eLife.03751.018

    elife03751s003.xlsx (15.1KB, xlsx)
    DOI: 10.7554/eLife.03751.018
    Figure 4—source data 1. Contains source data for Figure 4.

    DOI: http://dx.doi.org/10.7554/eLife.03751.024

    elife03751s004.xlsx (34.3KB, xlsx)
    DOI: 10.7554/eLife.03751.024
    Figure 5—source data 1. Contains source data for Figure 5.

    DOI: http://dx.doi.org/10.7554/eLife.03751.026

    elife03751s005.xlsx (35.6KB, xlsx)
    DOI: 10.7554/eLife.03751.026

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