Adaptive chromatin remodeling and transcriptional changes of the functional kinome in tumor cells in response to targeted kinase inhibition
2021; Elsevier BV; Volume: 298; Issue: 2 Linguagem: Inglês
10.1016/j.jbc.2021.101525
ISSN1083-351X
AutoresMichael P. East, Gary L. Johnson,
Tópico(s)Melanoma and MAPK Pathways
ResumoPharmacological inhibition of protein kinases induces adaptive reprogramming of tumor cell regulatory networks by altering expression of genes that regulate signaling, including protein kinases. Adaptive responses are dependent on transcriptional changes resulting from remodeling of enhancer and promoter landscapes. Enhancer and promoter remodeling in response to targeted kinase inhibition is controlled by changes in open chromatin state and by activity of specific transcription factors, such as c-MYC. This review focuses on the dynamic plasticity of protein kinase expression of the tumor cell kinome and the resulting adaptive resistance to targeted kinase inhibition. Plasticity of the functional kinome has been shown in patient window trials where triple-negative and human epidermal growth factor receptor 2–positive breast cancer patient tumors were characterized by RNAseq after biopsies before and after 1 week of therapy. The expressed kinome changed dramatically during drug treatment, and these changes in kinase expression were shown in cell lines and xenografts in mice to be correlated with adaptive tumor cell drug resistance. The dynamic transcriptional nature of the kinome also differs for inhibitors targeting different kinase signaling pathways (e.g., BRAF-MEK-ERK versus PI3K-AKT) that are commonly activated in cancers. Heterogeneity arising from differences in gene regulation and mutations represents a challenge to therapeutic durability and prevention of clinical drug resistance with drug-tolerant tumor cell populations developing and persisting through treatment. We conclude that understanding the heterogeneity of kinase expression at baseline and in response to therapy is imperative for development of combinations and timing intervals of therapies making interventions durable. Pharmacological inhibition of protein kinases induces adaptive reprogramming of tumor cell regulatory networks by altering expression of genes that regulate signaling, including protein kinases. Adaptive responses are dependent on transcriptional changes resulting from remodeling of enhancer and promoter landscapes. Enhancer and promoter remodeling in response to targeted kinase inhibition is controlled by changes in open chromatin state and by activity of specific transcription factors, such as c-MYC. This review focuses on the dynamic plasticity of protein kinase expression of the tumor cell kinome and the resulting adaptive resistance to targeted kinase inhibition. Plasticity of the functional kinome has been shown in patient window trials where triple-negative and human epidermal growth factor receptor 2–positive breast cancer patient tumors were characterized by RNAseq after biopsies before and after 1 week of therapy. The expressed kinome changed dramatically during drug treatment, and these changes in kinase expression were shown in cell lines and xenografts in mice to be correlated with adaptive tumor cell drug resistance. The dynamic transcriptional nature of the kinome also differs for inhibitors targeting different kinase signaling pathways (e.g., BRAF-MEK-ERK versus PI3K-AKT) that are commonly activated in cancers. Heterogeneity arising from differences in gene regulation and mutations represents a challenge to therapeutic durability and prevention of clinical drug resistance with drug-tolerant tumor cell populations developing and persisting through treatment. We conclude that understanding the heterogeneity of kinase expression at baseline and in response to therapy is imperative for development of combinations and timing intervals of therapies making interventions durable. Protein kinases function in signaling networks controlling most cellular functions and their dysfunction contributes to many human diseases, most notably cancer. Most human cell lines express ∼350–400 protein kinases that are integrated into canonical signaling networks. In different cancers, kinases are frequently mutated or amplified making them excellent targets for inhibition to inhibit growth and/or induce apoptosis of the tumor cell (1Fleuren E.D. Zhang L. Wu J. Daly R.J. The kinome 'at large' in cancer.Nat. Rev. Cancer. 2016; 16: 83-98Google Scholar). The first targeted kinase inhibitor, gleevec (imatinib also known as STI571), was approved in 2001 to treat chronic myelogenous leukemia (CML). CML is generally caused by the fusion of the ABL1 gene (Abelson tyrosine kinase 1) and BCR gene (Breakpoint Cluster Region gene) resulting in the constitutive activation of the ABL1 tyrosine kinase (2Lugo T.G. Pendergast A.M. Muller A.J. Witte O.N. 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HER2 inhibition drastically improves patient outcome, but efficacy can be short-lived, and resistance frequently develops. Small-molecule inhibitors of the HER2 and EGFR kinases include lapatinib, tucatinib, and the irreversible inhibitor neratinib (5Schlam I. Swain S.M. HER2-positive breast cancer and tyrosine kinase inhibitors: The time is now.NPJ Breast Cancer. 2021; 7: 56Google Scholar). Monoclonal antibodies such as trastuzumab and pertuzumab are also effective in HER2+ breast cancer and have different mechanisms of action. Trastuzumab targets the HER2 extracellular domain and in combination with chemotherapy in early breast cancer decreases death by nearly 40%. A major mechanism of trastuzumab involves the recruitment of immune cells to the HER2+ tumor (6Hudis C.A. Trastuzumab--Mechanism of action and use in clinical practice.N. Engl. J. Med. 2007; 357: 39-51Google Scholar). 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Drugging the human kinome with targeted inhibitors has been hampered by the development of drug resistance, and many if not most kinase inhibitors as single agents fail to produce durable responses in the clinic as monotherapies. While Darwinian selection of cells harboring acquired kinase mutations may be overcome by development of new inhibitors effective against the mutant kinase (15Duong-Ly K.C. Devarajan K. Liang S. Horiuchi K.Y. Wang Y. Ma H. Peterson J.R. Kinase inhibitor profiling reveals unexpected opportunities to inhibit disease-associated mutant kinases.Cell Rep. 2016; 14: 772-781Google Scholar, 16Sullivan I. Planchard D. Next-generation EGFR tyrosine kinase inhibitors for treating EGFR-mutant lung cancer beyond first line.Front. Med. (Lausanne). 2016; 3: 76Google Scholar, 17Zhou W. Ercan D. Chen L. Yun C.H. Li D. Capelletti M. Cortot A.B. Chirieac L. Iacob R.E. Padera R. Engen J.R. Wong K.K. Eck M.J. Gray N.S. Janne P.A. Novel mutant-selective EGFR kinase inhibitors against EGFR T790M.Nature. 2009; 462: 1070-1074Google Scholar, 18Lu X. Smaill J.B. Ding K. Medicinal chemistry strategies for the development of kinase inhibitors targeting point mutations.J. Med. Chem. 2020; 63: 10726-10741Google Scholar), resistance mediated by adaptive kinome reprogramming remains a significant clinical concern. In this review, we address the mechanisms of adaptive reprogramming of the kinome in response to targeted kinase inhibition and how this must be overcome by combination and timing of treatments to make kinase inhibitor therapies durable. Tumor cells can acquire genetic mutations that render the targeted protein insensitive to a drug to induce acquired drug resistance (19Rosenzweig S.A. Acquired resistance to drugs targeting tyrosine kinases.Adv. Cancer Res. 2018; 138: 71-98Google Scholar, 20Shah N.P. Sawyers C.L. 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An example of the adaptive resistance mechanism was described for a "drug tolerant state" in the non-small-cell lung cancer (NSCLC) PC9 cell line (22Sharma S.V. Lee D.Y. Li B. Quinlan M.P. Takahashi F. Maheswaran S. McDermott U. Azizian N. Zou L. Fischbach M.A. Wong K.K. Brandstetter K. Wittner B. Ramaswamy S. Classon M. et al.A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations.Cell. 2010; 141: 69-80Google Scholar). PC9 cells express an activated mutant form of EGFR having deletion of Glu746–Ala750 in exon 19 that drives cellular proliferation and a dependency for survival of PC9 cells. The cells are extremely sensitive to the EGFR inhibitors gefitinib and erlotinib with growth arrest and loss of viability (22Sharma S.V. Lee D.Y. Li B. Quinlan M.P. Takahashi F. Maheswaran S. McDermott U. Azizian N. Zou L. Fischbach M.A. Wong K.K. Brandstetter K. Wittner B. Ramaswamy S. Classon M. et al.A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations.Cell. 2010; 141: 69-80Google Scholar). However, a small number of EGFR inhibitor-treated PC9 cells "persist" and escape cell death during EGFR inhibitor treatment, and with several days of continuous inhibitor treatment, drug-tolerant persister cells begin to propagate. There was no acquired mutation or amplification of the EGFR or expression of the receptor tyrosine kinase MET in the drug-tolerant PC9 cells that is often seen in drug-resistant patient NSCLC (23Stewart E.L. Tan S.Z. Liu G. Tsao M.S. Known and putative mechanisms of resistance to EGFR targeted therapies in NSCLC patients with EGFR mutations-a review.Transl. Lung Cancer Res. 2015; 4: 67-81Google Scholar). Notably, the drug-tolerant state was reversible, as cells reacquired drug sensitivity after drug withdrawal and could emerge de novo from clonally isolated, drug-sensitive cells. The persister cells were driven by IGF-1 receptor tyrosine kinase signaling and upregulation of the histone demethylase KDM5A, which regulates function of histones in chromatin by regulating their methylation of specific lysine residues (22Sharma S.V. Lee D.Y. Li B. Quinlan M.P. Takahashi F. Maheswaran S. McDermott U. Azizian N. Zou L. Fischbach M.A. Wong K.K. Brandstetter K. Wittner B. Ramaswamy S. Classon M. et al.A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations.Cell. 2010; 141: 69-80Google Scholar). IGF-1 receptor inhibition or knockdown of KDM5A was sufficient to restore drug sensitivity, demonstrating a chromatin-dependent regulation of the drug-tolerant state. Selective inhibitors of KDM5A were unavailable, but inhibitors of histone deacetylases (HDACs) killed cells in the drug-tolerant state but not parental cells. These data are consistent with a mechanism for acute drug tolerance that is mediated by chromatin remodeling, where chromatin accessibility is heavily regulated by the posttranslational modification of histones by enzymes such as KDM5A and different HDACs to control gene transcription and is comprehensively reviewed elsewhere (24Bannister A.J. Kouzarides T. Regulation of chromatin by histone modifications.Cell Res. 2011; 21: 381-395Google Scholar). A second study in EGFR-mutant NSCLC showed similar epigenetic reprogramming in the drug-tolerant persister cells using histone mass spectrometry assays (25Guler G.D. Tindell C.A. Pitti R. Wilson C. Nichols K. KaiWai Cheung T. Kim H.J. Wongchenko M. Yan Y. Haley B. Cuellar T. Webster J. Alag N. Hegde G. Jackson E. et al.Repression of stress-induced LINE-1 expression protects cancer cell subpopulations from lethal drug exposure.Cancer Cell. 2017; 32: 221-237.e13Google Scholar). Drug-tolerant cells showed higher global H3K27me3 and H3K9me3 marks combined with a decrease in multiple H3Kacetylation (H3Kac) marks. H3K27me3 and H3K9me3 are associated with heterochromatin and a decrease in expression of nearby genes, whereas increased H3Kac is associated with a more open chromatin state and an increase in transcription of nearby genes. An siRNA screen of chromatin regulators also revealed dependencies on the histone methyltransferase EZH2, H3K9 methylation-dependent chromatin regulators, and several HDACs. In a study in triple-negative breast cancer (TNBC), targeted inhibition of kinases in the two primary proliferative kinase cascades-MEK1/2-ERK1/2 pathway (MEK-ERK) or PI3K-AKT pathway resulted in a reversible drug-tolerant state with profound effects on chromatin accessibility of specific transcription factor motifs (26Risom T. Langer E.M. Chapman M.P. Rantala J. Fields A.J. Boniface C. Alvarez M.J. Kendsersky N.D. Pelz C.R. Johnson-Camacho K. Dobrolecki L.E. Chin K. Aswani A.J. Wang N.J. Califano A. et al.Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer.Nat. Commun. 2018; 9: 3815Google Scholar). MEK or PI3K inhibition showed upregulation in activity of BRD4, which binds acetylated histones to promote gene expression. A BRD4 bromo- and extra-terminal domain (BET) inhibitor, JQ1, suppressed the drug-tolerant state and synergized with MEK and PI3K inhibitors. JQ1 also inhibited the changes in open chromatin state, bringing open motifs back to near DMSO control states. Similar epigenetic reprogramming was observed in glioblastoma in response to targeted kinase inhibitors with epigenetic reprogramming of H3K27ac and H3K27me3 marks accompanied by a dependency on the histone demethylase KDM6A/B for drug tolerance (27Liau B.B. Sievers C. Donohue L.K. Gillespie S.M. Flavahan W.A. Miller T.E. Venteicher A.S. Hebert C.H. Carey C.D. Rodig S.J. Shareef S.J. Najm F.J. van Galen P. Wakimoto H. Cahill D.P. et al.Adaptive chromatin remodeling drives glioblastoma stem cell plasticity and drug tolerance.Cell Stem Cell. 2017; 20: 233-246.e7Google Scholar). Changes in expression of protein kinases represent adaptive kinome reprogramming, which has been shown to regulate the onset of resistance to targeted kinase inhibitors. Using Multiplexed Inhibitor Beads coupled with Mass spectrometry (MIB/MS) to capture and identify functional protein kinases, Duncan et al. showed that treatment of TNBC cell lines with selumetinib, an allosteric inhibitor of MEK in the MEK1/2-ERK1/2 MAPK pathway, resulted in the expression and activation of multiple protein kinases including several receptor tyrosine kinases (RTKs) (28Duncan J.S. Whittle M.C. Nakamura K. Abell A.N. Midland A.A. Zawistowski J.S. Johnson N.L. Granger D.A. Jordan N.V. Darr D.B. Usary J. Kuan P.F. Smalley D.M. Major B. 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Other studies have defined adaptive kinome reprogramming in different tumor types (e.g., renal cell carcinoma, ovarian cancer, leukemia, glioblastoma lymphoma) and with inhibitors targeting kinases in pathways different from the MEK-ERK pathway such as targeting inhibition of the PI3K-AKT pathway (11Stuhlmiller T.J. Miller S.M. Zawistowski J.S. Nakamura K. Beltran A.S. Duncan J.S. Angus S.P. Collins K.A. Granger D.A. Reuther R.A. Graves L.M. Gomez S.M. Kuan P.F. Parker J.S. Chen X. et al.Inhibition of lapatinib-induced kinome reprogramming in ERBB2-positive breast cancer by targeting BET family bromodomains.Cell Rep. 2015; 11: 390-404Google Scholar, 30McNeill R.S. Canoutas D.A. Stuhlmiller T.J. Dhruv H.D. Irvin D.M. Bash R.E. Angus S.P. Herring L.E. Simon J.M. Skinner K.R. Limas J.C. Chen X. Schmid R.S. Siegel M.B. 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The claudin-low tumor showed unique adaptive kinome reprogramming compared with the basal-like tumors. The findings were similar to what has been characterized for the adaptive kinome reprogramming response to trametinib in basal-like and claudin-low TNBC cell lines and mouse xenografts (28Duncan J.S. Whittle M.C. Nakamura K. Abell A.N. Midland A.A. Zawistowski J.S. Johnson N.L. Granger D.A. Jordan N.V. Darr D.B. Usary J. Kuan P.F. Smalley D.M. Major B. He X. et al.Dynamic reprogramming of the kinome in response to targeted MEK inhibition in triple-negative breast cancer.Cell. 2012; 149: 307-321Google Scholar, 29Zawistowski J.S. Bevill S.M. Goulet D.R. Stuhlmiller T.J. Beltran A.S. Olivares-Quintero J.F. Singh D. Sciaky N. Parker J.S. Rashid N.U. Chen X. Duncan J.S. Whittle M.C. Angus S.P. Velarde S.H. et al.Enhancer remodeling during adaptive bypass to MEK inhibition is attenuated by pharmacologic targeting of the P-TEFb complex.Cancer Discov. 2017; 7: 302-321Google Scholar). Using DEseq2 for differential expression analysis showed six protein kinases were transcriptionally upregulated in both patient basal-like breast cancers and three basal-like cell lines: DDR1, HER2, FRK, CDC42BPG, CDK19, and CDKL5 (Fig. 1). DDR1, HER2, and FRK are tyrosine kinases that would have the ability to activate both the MEK-ERK and PI3K-AKT pathways to overcome trametinib inhibition of the MEK-ERK pathway. CDC42BPG, CDKL5, and CDK19 are serine/threonine kinases. CDC42BPG is an understudied kinase predicted to be downstream of CDC42 involved in cytoskeletal regulation based upon the functions of its two closest paralogs CDC42BPA/B (41Leung T. Chen X.Q. Tan I. Manser E. Lim L. Myotonic dystrophy kinase-related Cdc42-binding kinase acts as a Cdc42 effector in promoting cytoskeletal reorganization.Mol. Cell. Biol. 1998; 18: 130-140Google Scholar). CDK19 is a member of the mediator complex controlling transcriptional activation (42Sato S. Tomomori-Sato C. Parmely T.J. Florens L. 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The upregulation of protein kinases including RTKs was largely the result of increased transcription resulting from a rapid degradation of the super transcription factor c-MYC, which regulates expression of up to 15% of the human genome (28Duncan J.S. Whittle M.C. Nakamura K. Abell A.N. Midland A.A. Zawistowski J.S. Johnson N.L. Granger D.A. Jordan N.V. Darr D.B. Usary J. Kuan P.F. Smalley D.M. Major B. He X. et al.Dynamic reprogramming of the kinome in response to targeted MEK inhibition in triple-negative breast cancer.Cell. 2012; 149: 307-321Google Scholar, 29Zawistowski J.S. Bevill S.M. Goulet D.R. Stuhlmiller T.J. Beltran A.S. Olivares-Quintero J.F. Singh D. Sciaky N. Parker J.S. Rashid N.U. Chen X. Duncan J.S. Whittle M.C. Angus S.P. Velarde S.H. et al.Enhancer remodeling during adaptive bypass to MEK inhibition is attenuated by pharmacologic targeting of the P-TEFb complex.Cancer Discov. 2017; 7: 302-321Google Scholar, 35Kurimchak A.M. Shelton C. Herrera-Montavez C. Duncan K.E. Chernoff J. Duncan J.S. Intrinsic resistance to MEK inhibition through BET protein-mediated kinome reprogramming in NF1-deficient ovarian cancer.Mol. Cancer Res. 2019; 17: 1721-1734Google Scholar, 45Sun C. Hobor S. Bertotti A. Zecchin D. Huang S. Galimi F. Cottino F. Prahallad A. Grernrum W. Tzani A. Schlicker A. Wessels L.F. Smit E.F. Thunnissen E. Halonen P. et al.Intrinsic resistance to MEK inhibition in KRAS mutant lung and colon cancer through transcriptional induction of ERBB3.Cell Rep. 2014; 7: 86-93Google Scholar). c-MYC is stabilized by phosphorylation at Ser62 and inhibition of the MEK-ERK pathway by selumetinib or trametinib resulted in loss of P-Ser62 and rapid degradation of c-MYC (28Duncan J.S. Whittle M.C. Nakamura K. Abell A.N. Midland A.A. Zawistowski J.S. Johnson N.L. Granger D.A. Jordan N.V. Darr D.B. Usary J. Kuan P.F. Smalley D.M. Major B. He X. et al.Dynamic reprogramming of the kinome in response to targeted MEK inhibition in triple-negative breast cancer.Cell. 2012; 149: 307-321Google Scholar, 29Zawistowski J.S. Bevill S.M. Goulet D.R. Stuhlmiller T.J. Beltran A.S. Olivares-Quintero J.F. Singh D. Sciaky N. Parker J.S. Rashid N.U. Chen X. Duncan J.S. Whittle M.C. Angus S.P. Velarde S.H. et al.Enhancer remodeling during adaptive bypass to MEK inhibition is attenuated by pharmacologic targeting of the P-TEFb complex.Cancer Discov. 2017; 7: 302-321Google Scholar). Turnover of c-MYC has been shown to regulate genomic reorganization and recruitment of transcriptional complexes to genomic loci including those regulating tr
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