PKCδ Regulates Chromatin Remodeling and DNA Repair through SIRT6

Irradiation (IR) is a highly effective cancer therapy; however, IR damage to tumor-adjacent healthy tissues can result in significant comorbidities and potentially limit the course of therapy. We have previously shown that protein kinase C delta (PKCδ) is required for IR-induced apoptosis and that inhibition of PKCδ activity provides radioprotection in vivo. Here we show that PKCδ regulates histone modification, chromatin accessibility, and double-stranded break (DSB) repair through a mechanism that requires Sirtuin 6 (SIRT6). Overexpression of PKCδ promotes genomic instability and increases DNA damage and apoptosis. Conversely, depletion of PKCδ increases DNA repair via nonhomologous end joining (NHEJ) and homologous recombination (HR) as evidenced by increased formation of DNA damage foci, increased expression of DNA repair proteins, and increased repair of NHEJ and HR fluorescent reporter constructs. Nuclease sensitivity indicates that PKCδ depletion is associated with more open chromatin, while overexpression of PKCδ reduces chromatin accessibility. Epiproteome analysis reveals increased chromatin associated H3K36me2 in PKCδ-depleted cells which is accompanied by chromatin disassociation of KDM2A. We identify SIRT6 as a downstream mediator of PKCδ. PKCδ-depleted cells have increased SIRT6 expression, and depletion of SIRT6 reverses changes in chromatin accessibility, histone modification and DSB repair in PKCδ-depleted cells. Furthermore, depletion of SIRT6 reverses radioprotection in PKCδ-depleted cells. Our studies describe a novel pathway whereby PKCδ orchestrates SIRT6-dependent changes in chromatin accessibility to regulate DNA repair, and define a mechanism for regulation of radiation-induced apoptosis by PKCδ.

IMPLICATIONS

PKCδ controls sensitivity to irradiation by regulating DNA repair.

Metabolic reprogramming contributes to radioprotection by protein kinase Cδ

Loss of protein kinase Cδ (PKCδ) activity renders cells resistant to DNA damaging agents, including irradiation; however, the mechanism(s) underlying resistance is poorly understood. Here, we have asked if metabolic reprogramming by PKCδ contributes to radioprotection. Analysis of global metabolomics showed that depletion of PKCδ affects metabolic pathways that control energy production and antioxidant, nucleotide, and amino acid biosynthesis. Increased NADPH and nucleotide production in PKCδ-depleted cells is associated with upregulation of the pentose phosphate pathway (PPP) as evidenced by increased activation of G6PD and an increase in the nucleotide precursor, 5-phosphoribosyl-1-pyrophosphate. Stable isotope tracing with U-[13C6] glucose showed reduced utilization of glucose for glycolysis in PKCδ-depleted cells and no increase in U-[13C6] glucose incorporation into purines or pyrimidines. In contrast, isotope tracing with [13C5, 15N2] glutamine showed increased utilization of glutamine for synthesis of nucleotides, glutathione, and tricarboxylic acid intermediates and increased incorporation of labeled glutamine into pyruvate and lactate. Using a glycolytic rate assay, we confirmed that anaerobic glycolysis is increased in PKCδ-depleted cells; this was accompanied by a reduction in oxidative phosphorylation, as assayed using a mitochondrial stress assay. Importantly, pretreatment of cells with specific inhibitors of the PPP or glutaminase prior to irradiation reversed radioprotection in PKCδ-depleted cells, indicating that these cells have acquired codependency on the PPP and glutamine for survival. Our studies demonstrate that metabolic reprogramming to increase utilization of glutamine and nucleotide synthesis contributes to radioprotection in the context of PKCδ inhibition.

PKCδ regulates chromatin remodeling and DNA repair through SIRT6

Protein kinase C delta (PKCδ) is a ubiquitous kinase whose function is defined in part by localization to specific cellular compartments. Nuclear PKCδ is both necessary and sufficient for IR-induced apoptosis, while inhibition of PKCδ activity provides radioprotection in vivo. How nuclear PKCδ regulates DNA-damage induced cell death is poorly understood. Here we show that PKCδ regulates histone modification, chromatin accessibility, and double stranded break (DSB) repair through a mechanism that requires SIRT6. Overexpression of PKCδ promotes genomic instability and increases DNA damage and apoptosis. Conversely, depletion of PKCδ increases DNA repair via non-homologous end joining (NHEJ) and homologous recombination (HR) as evidenced by more rapid formation of NHEJ (DNA-PK) and HR (Rad51) DNA damage foci, increased expression of repair proteins, and increased repair of NHEJ and HR fluorescent reporter constructs. Nuclease sensitivity indicates that PKCδ depletion is associated with more open chromatin, while overexpression of PKCδ reduces chromatin accessibility. Epiproteome analysis revealed that PKCδ depletion increases chromatin associated H3K36me2, and reduces ribosylation of KDM2A and chromatin bound KDM2A. We identify SIRT6 as a downstream mediator of PKCδ. PKCδ-depleted cells have increased expression of SIRT6, and depletion of SIRT6 reverses the changes in chromatin accessibility, histone modification and NHEJ and HR DNA repair seen with PKCδ-depletion. Furthermore, depletion of SIRT6 reverses radioprotection in PKCδ-depleted cells. Our studies describe a novel pathway whereby PKCδ orchestrates SIRT6-dependent changes in chromatin accessibility to increase DNA repair, and define a mechanism for regulation of radiation-induced apoptosis by PKCδ.

Loss of MAP3K7 Sensitizes Prostate Cancer Cells to CDK1/2 Inhibition and DNA Damage by Disrupting Homologous Recombination

The combined loss of CHD1 and MAP3K7 promotes aggressive prostate cancer by unknown mechanisms. Because both of these genes are lost genetically in prostate cancer, they cannot be directly targeted. We applied an established computational systems pharmacology approach (TRAP) to identify altered signaling pathways and associated druggable targets. We compared gene expression profiles of prostate cancer with coloss of CHD1 and MAP3K7 with prostate cancer diploid for these genes using The Cancer Genome Atlas patient samples. This analysis prioritized druggable target genes that included CDK1 and CDK2. We validated that inhibitors of these druggable target genes, including the CDK1/CDK2 inhibitor dinaciclib, had antiproliferative and cytotoxic effects selectively on mouse prostate cells with knockdown of Chd1 and Map3k7. Dinaciclib had stronger effects on prostate cells with suppression of Map3k7 independent of Chd1 and also compared with cells without loss of Map3k7. Dinaciclib treatment reduced expression of homologous recombination (HR) repair genes such as ATM, ATR, BRCA2, and RAD51, blocked BRCA1 phosphorylation, reduced RAD51 foci formation, and increased γH2AX foci selectively in prostate cells with suppression of Map3k7, thus inhibiting HR repair of chromosomal double-strand breaks. Dinaciclib-induced HR disruption was also observed in human prostate cells with knockdown of MAP3K7. Cotreatment of dinaciclib with DNA-damaging agents or PARP inhibitor resulted in a stronger cytotoxic effect on prostate cells with suppression of MAP3K7 compared with those without loss of MAP3K7, or to each single agent. IMPLICATIONS: These findings demonstrate that loss of MAP3K7 is a main contributing factor to drug response through disruption of HR in prostate cancer.

EGF receptor and PKCδ kinase activate DNA damage-induced pro-survival and pro-apoptotic signaling via biphasic activation of ERK and MSK1 kinases

DNA damage-mediated activation of extracellular signal-regulated kinase (ERK) can regulate both cell survival and cell death. We show here that ERK activation in this context is biphasic and that early and late activation events are mediated by distinct upstream signals that drive cell survival and apoptosis, respectively. We identified the nuclear kinase mitogen-sensitive kinase 1 (MSK1) as a downstream target of both early and late ERK activation. We also observed that activation of ERK→MSK1 up to 4 h after DNA damage depends on epidermal growth factor receptor (EGFR), as EGFR or mitogen-activated protein kinase/extracellular signal-regulated kinase kinase (MEK)/ERK inhibitors or short hairpin RNA-mediated MSK1 depletion enhanced cell death. This prosurvival response was partially mediated through enhanced DNA repair, as EGFR or MEK/ERK inhibitors delayed DNA damage resolution. In contrast, the second phase of ERK→MSK1 activation drove apoptosis and required protein kinase Cδ (PKCδ) but not EGFR. Genetic disruption of PKCδ reduced ERK activation in an in vivo irradiation model, as did short hairpin RNA-mediated depletion of PKCδ in vitro In both models, PKCδ inhibition preferentially suppressed late activation of ERK. We have shown previously that nuclear localization of PKCδ is necessary and sufficient for apoptosis. Here we identified a nuclear PKCδ→ERK→MSK1 signaling module that regulates apoptosis. We also show that expression of nuclear PKCδ activates ERK and MSK1, that ERK activation is required for MSK1 activation, and that both ERK and MSK1 activation are required for apoptosis. Our findings suggest that location-specific activation by distinct upstream regulators may enable distinct functional outputs from common signaling pathways.

PKCδ regulates integrin αVβ3 expression and transformed growth of K-ras dependent lung cancer cells

We have previously shown that Protein Kinase C delta (PKCδ) functions as a tumor promoter in non-small cell lung cancer (NSCLC), specifically in the context of K-ras addiction. Here we define a novel PKCδ -> integrin α_Vβ₃->Extracellular signal-Regulated Kinase (ERK) pathway that regulates the transformed growth of K-ras dependent NSCLC cells. To explore how PKCδ regulates tumorigenesis, we performed mRNA expression analysis in four KRAS mutant NSCLC cell lines that stably express scrambled shRNA or a PKCδ targeted shRNA. Analysis of PKCδ-dependent mRNA expression identified 3183 regulated genes, 210 of which were specifically regulated in K-ras dependent cells. Genes that regulate extracellular matrix and focal adhesion pathways were most highly represented in this later group. In particular, expression of the integrin pair, α_Vβ₃, was specifically reduced in K-ras dependent cells with depletion of PKCδ, and correlated with reduced ERK activation and reduced transformed growth as assayed by clonogenic survival. Re-expression of PKCδ restored ITGAV and ITGB3 mRNA expression, ERK activation and transformed growth, and this could be blocked by pretreatment with a α_Vβ₃ function-blocking antibody, demonstrating a requirement for integrin α_Vβ₃ downstream of PKCδ. Similarly, expression of integrin α_V restored ERK activation and transformed growth in PKCδ depleted cells, and this could also be inhibited by pretreatment with PD98059. Our studies demonstrate an essential role for α_Vβ₃ and ERK signalingdownstream of PKCδ in regulating the survival of K-ras dependent NSCLC cells, and identify PKCδ as a novel therapeutic target for the subset of NSCLC patients with K-ras dependent tumors.

Abstract 3319: PKCδ switches from a pro-apoptotic to a pro-survival signal in K-ras “dependent” lung cancer

Oncogenic mutations in KRAS are found in about 25% of non-small cell lung cancers (NSCLC), however only a subset of these tumors are dependent upon K-ras for survival. We have previously shown that PKCδ is required for transformed growth of NSCLC cells that are dependent on K-ras, and for growth of K-ras driven lung tumors in vivo. PKCδ also plays an essential role in DNA damage-induced apoptosis in many cell types. Analysis of 14 mutant KRAS NSCLC cell lines that are K-ras “independent” for survival (A549, H157, H460, SW1573, H1155, H1792), or K-ras “dependent” (H2009, H727, HCC44, H2122, SW900, H1573, H358, H441) reveals that the pro-tumorigenic and pro-apoptotic functions of PKCδ segregate with the K-ras dependency status, and reflect differential regulation of survival signaling by PKCδ in these two cell populations. K-ras-independent NSCLC cells are sensitive to DNA-damage-induced apoptosis, and shRNA mediated depletion of PKCδ in these cells results in suppression of apoptosis and increased activation of the MEK/ERK pathway. In contrast, K-ras dependent NSCLC cells are resistance to DNA-damage-induced apoptosis and depletion of PKCδ enhances apoptosis and suppresses MEK/ERK activation, anchorage-independent growth, and invasion/migration. To explore why K-ras dependent NSCLC cells are resistant to apoptosis, we analyzed PKCδ Y64 phosphorylation and nuclear translocation, events we have previously shown are critical for the pro-apoptotic function of PKCδ. Surprisingly, K-ras dependent cells have an up to 7-fold increase in the nuclear:cytoplasmic ratio of PKCδ, increased phosphorylation of PKCδ Y64, and increased (1.5-3 fold) PKCδ mRNA and protein, suggesting that these cells may be refractive to PKCδ driven apoptosis. To test this we expressed a mutant of PKCδ targeted to the nucleus by the addition of a SV40 nuclear localization signal. Expression of PKCδNLS induced apoptosis and increased DNA damage-induced apoptosis in K-ras independent but not K-ras dependent NSCLC cells, confirming that the later are unable to activate apoptotic pathways downstream of PKCδ. These studies define two distinct subsets of NSCLC cell lines in the context of mutant KRAS. NSCLC cells that are “independent” of K-ras preferentially utilize PKCδ for apoptosis, while cells “dependent” on oncogenic K-ras preferentially use PKCδ for proliferation and survival. We are currently using two large, publicly available lung cancer cell line gene expression datasets (GEO accession #'s GSE4824 and GSE36133) to identify pathways and signaling networks unique to these two populations of NSCLC cells.

Citation Format: Mary E. Reyland, Angela M. Ohm, Michael G. Edwards, Jennifer Symonds. PKCδ switches from a pro-apoptotic to a pro-survival signal in K-ras “dependent” lung cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3319. doi:10.1158/1538-7445.AM2014-3319

Protein kinase Cδ is required for ErbB2-driven mammary gland tumorigenesis and negatively correlates with prognosis in human breast cancer

Protein kinase C δ (PKCδ) regulates apoptosis in the mammary gland, however, the functional contribution of PKCδ to the development or progression of breast cancer has yet to be determined. Meta-analysis of ErbB2-positive breast cancers shows increased PKCδ expression, and a negative correlation between PKCδ expression and prognosis. Here, we present in-vivo evidence that PKCδ is essential for the development of mammary gland tumors in a ErbB2-overexpressing transgenic mouse model, and in-vitro evidence that PKCδ is required for proliferative signaling downstream of the ErbB2 receptor. Mouse mammary tumor virus (MMTV)-ErbB2 mice lacking PKCδ (δKO) have increased tumor latency compared with MMTV-ErbB2 wild-type (δWT) mice, and the tumors show a dramatic decrease in Ki-67 staining. To explore the relationship between PKCδ and ErbB2-driven proliferation more directly, we used MCF-10A cells engineered to express a synthetic ligand-inducible form of the ErbB2 receptor. Depletion of PKCδ with short hairpin RNA inhibited ligand-induced growth in both two-dimensional (2D) (plastic) and three-dimensional (3D) (Matrigel) culture, and correlated with decreased phosphorylation of the ErbB2 receptor and reduced activation of Src and MAPK/ERK pathways. Similarly, in human breast cancer cell lines in which ErbB2 is overexpressed, depletion of PKCδ suppresses proliferation, Src and ERK activation. PKCδ appears to drive proliferation through the formation of an active ErbB2/PKCδ/Src signaling complex, as depletion of PKCδ disrupts association of Src with the ErbB2 receptor. Taken together, our studies present the first evidence that PKCδ is a critical regulator of ErbB2-mediated tumorigenesis, and suggest further investigation of PKCδ as a target in ErbB2-positive breast cancer.

Abstract B29: Oncogenic K-ras addiction in NSCLC switches PKCδ from a pro-apoptotic to a pro-survival signal

Oncogenic mutations in K-ras occur in about 25% of lung cancers, however only a subset of lung tumors with KRAS mutations are functionally dependent upon oncogenic K-ras for survival. Our previous studies show that the function of Protein Kinase C-δ (PKCδ), a serine/threonine kinase that regulates apoptosis in non-transformed cells, is altered in non-small cell lung cancers (NSCLC) that are dependent on oncogenic K-ras, such that these cells now require PKCδ for survival and transformed growth (Symonds et al, Cancer Research, 2011). The purpose of the current studies was to determine if this switch in PKCδ function alters the response of lung cancer cells to chemotherapeutic drugs. We analyzed apoptosis and PKCδ function in five NSCLC cells lines previously characterized in our laboratory as dependent on oncogenic K-ras for survival, and five NSCLC cell lines characterized as K-ras independent. Our results show that NSCLC cell lines that are functionally dependent on K-ras are highly resistant to apoptosis induced by DNA damaging agents such as etoposide. In contrast, K-ras independent NSCLC cell lines are highly sensitive to apoptosis. Our previous studies have shown that PKCδ translocates to the nucleus in response to apoptotic agents and that nuclear localization of PKCδ is essential for apoptosis. To determine the mechanism underlying the switch in PKCδ function from pro-apoptotic to pro-survival, we analyzed PKCδ expression and cytoplasmic/nuclear localization in apoptosis sensitive (K-ras independent) and apoptosis resistant (K-ras dependent) NCSCL cells. Relative to insensitive NSCLC cells, apoptosis sensitive cells showed increased expression of PKCδ by qrtPCR, a reduced cytoplasmic:nuclear ratio of PKCδ under basal conditions, and increased nuclear import of PKCδ in response to etoposide. This suggests that PKCδ may be a pro-apoptotic signal in K-ras independent cells, similar to what we have shown for non-transformed cells. In contrast, nuclear import of PKCδ in response to etoposide was suppressed in K-ras dependent/apoptosis resistant NSCLC cells as was phosphorylation of PKCδ on tyrosines Y64 and Y155, which we have previously shown is required for importin -α binding and nuclear import. Exclusion of PKCδ from the nucleus may explain the resistance of K-ras dependent cells to apoptotic agents. To probe the contribution of PKCδ to these two phenotypes more directly, we depleted PKCδ from K-ras independent/apoptosis sensitive A549 and K-ras dependent/apoptosis resistant H2009 cells using an lentivirus delivered shRNA to PKCδ or a scrambled shRNA control. Depletion of PKCδ in A549 cells resulted in suppression of etoposide-induced apoptosis, similar to what we have previously reported in non-transformed cells. Suppression of apoptosis was accompanied by increased activation of the Akt and MEK/ERK cell survival pathways in A549 cells. In contrast, depletion of PKCδ in H2009 cells resulted in increased apoptosis in response to etoposide, and suppression of the Akt and MEK/ERK cell survival pathways. Our studies suggest NSCLC cells functionally dependent on oncogenic K-ras may be resistant to chemotherapeutic agents in part due to loss of the pro-apoptotic function of PKCδ.

Regulated binding of importin-α to protein kinase Cδ in response to apoptotic signals facilitates nuclear import

PKCδ translocates into the nucleus in response to apoptotic agents and functions as a potent cell death signal. Cytoplasmic retention of PKCδ and its transport into the nucleus are essential for cell homeostasis, but how these processes are regulated is poorly understood. We show that PKCδ resides in the cytoplasm in a conformation that precludes binding of importin-α. A structural model of PKCδ in the inactive state suggests that the nuclear localization sequence (NLS) is prevented from binding to importin-α through intramolecular contacts between the C2 and catalytic domains. We have previously shown that PKCδ is phosphorylated on specific tyrosine residues in response to apoptotic agents. Here, we show that phosphorylation of PKCδ at Tyr-64 and Tyr-155 results in a conformational change that allows exposure of the NLS and binding of importin-α. In addition, Hsp90 binds to PKCδ with similar kinetics as importin-α and is required for the interaction of importin-α with the NLS. Finally, we elucidate a role for a conserved PPxxP motif, which overlaps the NLS, in nuclear exclusion of PKCδ. Mutagenesis of the conserved prolines to alanines enhanced importin-α binding to PKCδ and induced its nuclear import in resting cells. Thus, the PPxxP motif is important for maintaining a conformation that facilitates cytosplasmic retention of PKCδ. Taken together, this study establishes a novel mechanism that retains PKCδ in the cytoplasm of resting cells and regulates its nuclear import in response to apoptotic stimuli.

Protein kinase C δ is a downstream effector of oncogenic K-ras in lung tumors

Oncogenic activation of K-ras occurs commonly in non-small cell lung cancer (NSCLC), but strategies to therapeutically target this pathway have been challenging to develop. Information about downstream effectors of K-ras remains incomplete, and tractable targets are yet to be defined. In this study, we investigated the role of protein kinase C δ (PKCδ) in K-ras-dependent lung tumorigenesis by using a mouse carcinogen model and human NSCLC cells. The incidence of urethane-induced lung tumors was decreased by 69% in PKCδ-deficient knockout (δKO) mice compared with wild-type (δWT) mice. δKO tumors are smaller and showed reduced proliferation. DNA sequencing indicated that all δWT tumors had activating mutations in KRAS, whereas only 69% of δKO tumors did, suggesting that PKCδ acts as a tumor promoter downstream of oncogenic K-ras while acting as a tumor suppressor in other oncogenic contexts. Similar results were obtained in a panel of NSCLC cell lines with oncogenic K-ras but which differ in their dependence on K-ras for survival. RNA interference-mediated attenuation of PKCδ inhibited anchorage-independent growth, invasion, migration, and tumorigenesis in K-ras-dependent cells. These effects were associated with suppression of mitogen-activated protein kinase pathway activation. In contrast, PKCδ attenuation enhanced anchorage-independent growth, invasion, and migration in NSCLC cells that were either K-ras-independent or that had WT KRAS. Unexpectedly, our studies indicate that the function of PKCδ in tumor cells depends on a specific oncogenic context, as loss of PKCδ in NSCLC cells suppressed transformed growth only in cells dependent on oncogenic K-ras for proliferation and survival.

Induction of apoptosis is driven by nuclear retention of protein kinase C delta

Protein kinase C delta (PKC delta) mediates apoptosis downstream of many apoptotic stimuli. Because of its ubiquitous expression, tight regulation of the proapoptotic function of PKC delta is critical for cell survival. Full-length PKC delta is found in all cells, whereas the catalytic fragment of PKC delta, generated by caspase cleavage, is only present in cells undergoing apoptosis. Here we show that full-length PKC delta transiently accumulates in the nucleus in response to etoposide and that nuclear translocation precedes caspase cleavage of PKC delta. Nuclear PKC delta is either cleaved by caspase 3, resulting in accumulation of the catalytic fragment in the nucleus, or rapidly exported by a Crm1-sensitive pathway, thereby assuring that sustained nuclear accumulation of PKC delta is coupled to caspase activation. Nuclear accumulation of PKC delta is necessary for caspase cleavage, as mutants of PKC delta that do not translocate to the nucleus are not cleaved. However, caspase cleavage of PKC delta per se is not required for apoptosis, as an uncleavable form of PKC delta induces apoptosis when retained in the nucleus by the addition of an SV-40 nuclear localization signal. Finally, we show that kinase negative full-length PKC delta does not translocate to the nucleus in apoptotic cells but instead inhibits apoptosis by blocking nuclear import of endogenous PKC delta. These studies demonstrate that generation of the PKC delta catalytic fragment is a critical step for commitment to apoptosis and that nuclear import and export of PKC delta plays a key role in regulating the survival/death pathway.