201
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Wood DJ, Endicott JA. Structural insights into the functional diversity of the CDK-cyclin family. Open Biol 2019; 8:rsob.180112. [PMID: 30185601 PMCID: PMC6170502 DOI: 10.1098/rsob.180112] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 08/10/2018] [Indexed: 12/17/2022] Open
Abstract
Since their characterization as conserved modules that regulate progression through the eukaryotic cell cycle, cyclin-dependent protein kinases (CDKs) in higher eukaryotic cells are now also emerging as significant regulators of transcription, metabolism and cell differentiation. The cyclins, though originally characterized as CDK partners, also have CDK-independent roles that include the regulation of DNA damage repair and transcriptional programmes that direct cell differentiation, apoptosis and metabolic flux. This review compares the structures of the members of the CDK and cyclin families determined by X-ray crystallography, and considers what mechanistic insights they provide to guide functional studies and distinguish CDK- and cyclin-specific activities. Aberrant CDK activity is a hallmark of a number of diseases, and structural studies can provide important insights to identify novel routes to therapy.
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Affiliation(s)
- Daniel J Wood
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Jane A Endicott
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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202
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Castillo J, Knol JC, Korver CM, Piersma SR, Pham TV, de Goeij-de Haas RR, van Pelt AMM, Jimenez CR, Jansen BJH. Human Testis Phosphoproteome Reveals Kinases as Potential Targets in Spermatogenesis and Testicular Cancer. Mol Cell Proteomics 2019; 18:S132-S144. [PMID: 30683686 PMCID: PMC6427237 DOI: 10.1074/mcp.ra118.001278] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Indexed: 12/25/2022] Open
Abstract
Spermatogenesis is a complex cell differentiation process that includes marked genetic, cellular, functional and structural changes. It requires tight regulation, because disturbances in any of the spermatogenic processes would lead to fertility deficiencies as well as disorders in offspring. To increase our knowledge of signal transduction during sperm development, we carried out a large-scale identification of the phosphorylation events that occur in the human male gonad. Metal oxide affinity chromatography using TiO2 combined with LC-MS/MS was conducted to profile the phosphoproteome of adult human testes with full spermatogenesis. A total of 8187 phosphopeptides derived from 2661 proteins were identified, resulting in the most complete report of human testicular phosphoproteins to date. Phosphorylation events were enriched in proteins functionally related to spermatogenesis, as well as to highly active processes in the male gonad, such as transcriptional and translational regulation, cytoskeleton organization, DNA packaging, cell cycle and apoptosis. Moreover, 174 phosphorylated kinases were identified. The most active human protein kinases in the testis were predicted both by the number of phosphopeptide spectra identified and the phosphorylation status of the kinase activation loop. The potential function of cyclin-dependent kinase 12 (CDK12) and p21-activated kinase 4 (PAK4) has been explored by in silico, protein-protein interaction analysis, immunodetection in testicular tissue, and a functional assay in a human embryonal carcinoma cell line. The colocalization of CDK12 with Golgi markers suggests a potential crucial role of this protein kinase during sperm formation. PAK4 has been found expressed in human spermatogonia, and a role in embryonal carcinoma cell response to apoptosis has been observed. Together, our protein discovery analysis confirms that phosphoregulation by protein kinases is highly active in sperm differentiation and opens a window to detailed characterization and validation of potential targets for the development of drugs modulating male fertility and tumor behavior.
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Affiliation(s)
- Judit Castillo
- Lead Pharma BV, Pivot Park, Kloosterstraat 9, 5349 AB Oss, The Netherlands;.
| | - Jaco C Knol
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Cindy M Korver
- Center for Reproductive Medicine, Research Institute Amsterdam Reproduction and Development, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Sander R Piersma
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Thang V Pham
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Richard R de Goeij-de Haas
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Ans M M van Pelt
- Center for Reproductive Medicine, Research Institute Amsterdam Reproduction and Development, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Connie R Jimenez
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Bastiaan J H Jansen
- Lead Pharma BV, Pivot Park, Kloosterstraat 9, 5349 AB Oss, The Netherlands;.
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203
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Wu YM, Cieślik M, Lonigro RJ, Vats P, Reimers MA, Cao X, Ning Y, Wang L, Kunju LP, de Sarkar N, Heath EI, Chou J, Feng FY, Nelson PS, de Bono JS, Zou W, Montgomery B, Alva A, Robinson DR, Chinnaiyan AM. Inactivation of CDK12 Delineates a Distinct Immunogenic Class of Advanced Prostate Cancer. Cell 2019; 173:1770-1782.e14. [PMID: 29906450 DOI: 10.1016/j.cell.2018.04.034] [Citation(s) in RCA: 386] [Impact Index Per Article: 77.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 02/23/2018] [Accepted: 04/24/2018] [Indexed: 12/15/2022]
Abstract
Using integrative genomic analysis of 360 metastatic castration-resistant prostate cancer (mCRPC) samples, we identified a novel subtype of prostate cancer typified by biallelic loss of CDK12 that is mutually exclusive with tumors driven by DNA repair deficiency, ETS fusions, and SPOP mutations. CDK12 loss is enriched in mCRPC relative to clinically localized disease and characterized by focal tandem duplications (FTDs) that lead to increased gene fusions and marked differential gene expression. FTDs associated with CDK12 loss result in highly recurrent gains at loci of genes involved in the cell cycle and DNA replication. CDK12 mutant cases are baseline diploid and do not exhibit DNA mutational signatures linked to defects in homologous recombination. CDK12 mutant cases are associated with elevated neoantigen burden ensuing from fusion-induced chimeric open reading frames and increased tumor T cell infiltration/clonal expansion. CDK12 inactivation thereby defines a distinct class of mCRPC that may benefit from immune checkpoint immunotherapy.
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Affiliation(s)
- Yi-Mi Wu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marcin Cieślik
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robert J Lonigro
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pankaj Vats
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Melissa A Reimers
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yu Ning
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lisha Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lakshmi P Kunju
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Navonil de Sarkar
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Elisabeth I Heath
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA; Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, MI 48201, USA
| | - Jonathan Chou
- Department of Medicine, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Felix Y Feng
- Department of Medicine, University of California at San Francisco, San Francisco, CA 94143, USA; Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA 94143, USA; Department of Urology, University of California at San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Peter S Nelson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA; Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Johann S de Bono
- Cancer Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK; Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London SM2 5NG, UK
| | - Weiping Zou
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bruce Montgomery
- Department of Medicine, University of Washington, Seattle, WA 98109, USA; Veterans Affairs Puget Sound Health Care System, University of Washington, Seattle, WA 98109, USA
| | - Ajjai Alva
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Dan R Robinson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA.
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204
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Choi SH, Martinez TF, Kim S, Donaldson C, Shokhirev MN, Saghatelian A, Jones KA. CDK12 phosphorylates 4E-BP1 to enable mTORC1-dependent translation and mitotic genome stability. Genes Dev 2019; 33:418-435. [PMID: 30819820 PMCID: PMC6446539 DOI: 10.1101/gad.322339.118] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/22/2019] [Indexed: 01/23/2023]
Abstract
Here, Choi et al. show that CDK12, the RNA polymerase II C-terminal domain kinase, which regulates genome stability, expression of DNA repair genes, and cancer cell drug resistance, also phosphorylates the mRNA 5′ cap-binding repressor 4E-BP1 to promote translation of mTORC1-dependent mRNAs. Using RIP-seq and Ribo-seq, the authors found that CDK12 regulates binding of eIF4G to many mTORC1 target mRNAs, and identified specific CDK12 “translation-only” target mRNAs. The RNA polymerase II (RNAPII) C-terminal domain kinase, CDK12, regulates genome stability, expression of DNA repair genes, and cancer cell resistance to chemotherapy and immunotherapy. In addition to its role in mRNA biosynthesis of DNA repair genes, we show here that CDK12 phosphorylates the mRNA 5′ cap-binding repressor, 4E-BP1, to promote translation of mTORC1-dependent mRNAs. In particular, we found that phosphorylation of 4E-BP1 by mTORC1 (T37 and T46) facilitates subsequent CDK12 phosphorylation at two Ser–Pro sites (S65 and T70) that control the exchange of 4E-BP1 with eIF4G at the 5′ cap of CHK1 and other target mRNAs. RNA immunoprecipitation coupled with deep sequencing (RIP-seq) revealed that CDK12 regulates release of 4E-BP1, and binding of eIF4G, to many mTORC1 target mRNAs, including those needed for MYC transformation. Genome-wide ribosome profiling (Ribo-seq) further identified specific CDK12 “translation-only” target mRNAs, including many mTORC1 target mRNAs as well as many subunits of mitotic and centromere/centrosome complexes. Accordingly, confocal imaging analyses revealed severe chromosome misalignment, bridging, and segregation defects in cells deprived of CDK12 or CCNK. We conclude that the nuclear RNAPII-CTD kinase CDK12 cooperates with mTORC1, and controls a specialized translation network that is essential for mitotic chromosome stability.
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Affiliation(s)
- Seung H Choi
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Thomas F Martinez
- Clayton Foundation Laboratory for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Seongjae Kim
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Cynthia Donaldson
- Clayton Foundation Laboratory for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Maxim N Shokhirev
- Razavi Newman Integrative Genomics and Bioinformatics Core, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratory for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Katherine A Jones
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
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205
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Omar HA, Tolba MF. Tackling molecular targets beyond PD-1/PD-L1: Novel approaches to boost patients' response to cancer immunotherapy. Crit Rev Oncol Hematol 2019; 135:21-29. [PMID: 30819443 DOI: 10.1016/j.critrevonc.2019.01.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/14/2019] [Accepted: 01/18/2019] [Indexed: 12/31/2022] Open
Abstract
In the new era of immunotherapy, which has changed the clinical oncology practice guidelines, there is a pressing need for finding novel approaches to tune up the clinical outcomes of immunotherapy and extend its benefits to a wider cohort of cancer patients. Several non-classical molecular immune targets beyond PD-1/PD-L1 signaling were shown to be engaged as feedback resistance circuits to shut down the antitumor immune response mediated by the classical immune checkpoint inhibitors. Those include T-cell inducible co-stimulator (ICOS), CD40, CD47, V-domain Ig suppressor of T-cell activation (VISTA), cyclin-dependent kinase (CDK)12, enhancer of Zeste homolog 2 (EZH2), toll-like receptors (TLRs) and OX-40 (CD134). Herein we critically discussed the latest studies concerned with understanding the mechanisms involved in the negative clinical response to classical immunotherapies and strategies to optimize the efficacy of cancer immunotherapy through novel combinatorial approaches.
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Affiliation(s)
- Hany A Omar
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates; College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates; Department of Pharmacology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt.
| | - Mai F Tolba
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt; Biology Department, School of Sciences and Engineering, The American University in Cairo, New Cairo, Egypt.
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206
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Hoshii T, Cifani P, Feng Z, Huang CH, Koche R, Chen CW, Delaney CD, Lowe SW, Kentsis A, Armstrong SA. A Non-catalytic Function of SETD1A Regulates Cyclin K and the DNA Damage Response. Cell 2019; 172:1007-1021.e17. [PMID: 29474905 DOI: 10.1016/j.cell.2018.01.032] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 10/30/2017] [Accepted: 01/24/2018] [Indexed: 12/22/2022]
Abstract
MLL/SET methyltransferases catalyze methylation of histone 3 lysine 4 and play critical roles in development and cancer. We assessed MLL/SET proteins and found that SETD1A is required for survival of acute myeloid leukemia (AML) cells. Mutagenesis studies and CRISPR-Cas9 domain screening show the enzymatic SET domain is not necessary for AML cell survival but that a newly identified region termed the "FLOS" (functional location on SETD1A) domain is indispensable. FLOS disruption suppresses DNA damage response genes and induces p53-dependent apoptosis. The FLOS domain acts as a cyclin-K-binding site that is required for chromosomal recruitment of cyclin K and for DNA-repair-associated gene expression in S phase. These data identify a connection between the chromatin regulator SETD1A and the DNA damage response that is independent of histone methylation and suggests that targeting SETD1A and cyclin K complexes may represent a therapeutic opportunity for AML and, potentially, for other cancers.
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Affiliation(s)
- Takayuki Hoshii
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02210, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Paolo Cifani
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Zhaohui Feng
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02210, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chun-Hao Huang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Cell and Developmental Biology Program, Weill Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Richard Koche
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02210, USA
| | - Chun-Wei Chen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02210, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christopher D Delaney
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02210, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Cell and Developmental Biology Program, Weill Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA; Howard Hughes Medical Institute, New York, NY 10065, USA
| | - Alex Kentsis
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02210, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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207
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Germline and Somatic Defects in DNA Repair Pathways in Prostate Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1210:279-300. [PMID: 31900913 DOI: 10.1007/978-3-030-32656-2_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Recent studies have provided a better understanding of the molecular underpinnings of prostate cancer. Alterations in genes encoding for proteins involved in the different pathways in charge of preserving genomic integrity and repairing DNA damage are common in prostate cancer, particularly in late-stage disease. Generally, these alterations would confer a survival advantage for tumors, resulting in a more aggressive phenotype. However, DNA repair defects can also represent a vulnerability for tumors that can be exploited therapeutically, offering the possibility of precision medicine strategies. Moreover, many of these mutations are linked to hereditary risk for cancers; hence, identification of DNA repair mutations could also be relevant for cancer prevention and screening in healthy individuals, including relatives of prostate cancer patients. In this chapter, we summarize current knowledge about the prevalence of different DNA repair gene alterations across different stages of prostate cancer and review the clinical relevance of such events in terms of prognosis and treatment stratification.
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208
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Ji J, Zhou C, Wu J, Cai Q, Shi M, Zhang H, Yu Y, Zhu Z, Zhang J. Expression pattern of CDK12 protein in gastric cancer and its positive correlation with CD8 + cell density and CCL12 expression. Int J Med Sci 2019; 16:1142-1148. [PMID: 31523177 PMCID: PMC6743279 DOI: 10.7150/ijms.34541] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 07/09/2019] [Indexed: 12/31/2022] Open
Abstract
Background: The aims of this study were to investigate the expression pattern of CDK12 protein in gastric cancer, and to analyze the correlations of CDK12 expression between CD8+ cell density and CCL12 expression. Methods: Eighty-six paired tumor and non-tumor samples were collected from patients who underwent radical surgery and had pathological confirmed gastric adenocarcinoma. Immunohistochemistry was used to assess CDK12 expression and CD8+ cell density. Expression of CDK12 and CCL21 mRNA was detected by quantitative reverse transcription-polymerase chain reaction. Results: CDK12 expression in gastric tumor tissues was significantly higher than it in paired non-tumor tissues (P<0.001). High expression of CDK12 was identified in 43 cases (50%), and it was significantly correlated with Lauren's classification (diffuse type) and number of metastatic lymph nodes (≥15). High CDK12 protein level indicated a relative poorer overall survival than patients with CKD12 low expression, while it was not identified as an independent prognostic factor. Median number of CD8+ cells in tumor tissues was 51 (range: 0-292). Number of CD8+ cells was positively correlated with CDK12 expression score in tumor tissues (r=0.243, P=0.024). Positive correlation was also found between CDK12 and CCL21 mRNA expression (r=0.419, P=0.017). Conclusion: High CDK12 expression was detected in gastric cancer which was correlated with malignant phenotypes and worse outcome. Positive correlations of CD8+ cell number and CCL21 mRNA expression with CDK12 level were identified.
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Affiliation(s)
- Jun Ji
- Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China
| | - Chenfei Zhou
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China
| | - Junwei Wu
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China
| | - Qu Cai
- Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China
| | - Min Shi
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China
| | - Huan Zhang
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China
| | - Yingyan Yu
- Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China
| | - Zhenggang Zhu
- Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China.,Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China
| | - Jun Zhang
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China
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209
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Jarman PJ, Noakes F, Fairbanks S, Smitten K, Griffiths IK, Saeed HK, Thomas JA, Smythe C. Exploring the Cytotoxicity, Uptake, Cellular Response, and Proteomics of Mono- and Dinuclear DNA Light-Switch Complexes. J Am Chem Soc 2018; 141:2925-2937. [DOI: 10.1021/jacs.8b09999] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Paul J. Jarman
- Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, U.K
| | - Felicity Noakes
- Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, U.K
- Department of Chemistry, University of Sheffield, Sheffield S10 2TN, U.K
| | - Simon Fairbanks
- Department of Chemistry, University of Sheffield, Sheffield S10 2TN, U.K
| | - Kirsty Smitten
- Department of Chemistry, University of Sheffield, Sheffield S10 2TN, U.K
| | | | - Hiwa K. Saeed
- Department of Chemistry, University of Sheffield, Sheffield S10 2TN, U.K
| | - Jim A. Thomas
- Department of Chemistry, University of Sheffield, Sheffield S10 2TN, U.K
| | - Carl Smythe
- Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, U.K
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210
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Abstract
Mutations in CDK13 have recently been identified as a novel cause of syndromic intellectual disability. In this chapter, we review the 44 cases of CDK13-related disorder reported to date, highlighting key clinical pointers to this diagnosis including characteristic craniofacial features, feeding difficulties in infancy, and the presence of structural heart or brain malformations. The spectrum of reported mutations is also described, demonstrating an excess of missense mutations arising in the protein kinase domain. Exploration of genotype-phenotype correlations suggests a trend toward milder phenotypes in patients with mutations predicted to cause haploinsufficiency of CDK13, while missense mutations affecting amino acid residue 842 appear most likely to be associated with structural malformations. The greater phenotypic impact of missense variants is hypothesized to occur due to a dominant-negative mechanism, by which the mutant protein acts to sequester cyclin K in inactive complexes. Functional studies to validate this hypothesis have not yet been carried out, however. Differential diagnosis and recommendations for clinical care of patients with CDK13-related disorder are also described, emphasizing baseline echocardiography, vigilance for feeding and swallowing difficulties, and regular developmental evaluation as key components of care. Finally, future directions for CDK13 research are discussed, including the need to resolve uncertainty regarding pathogenicity of CDK13 haploinsufficiency, and to gather further longitudinal data from large cohorts in order to inform the clinical care of patients with this diagnosis.
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Affiliation(s)
- Mark James Hamilton
- Nottingham Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom.
| | - Mohnish Suri
- Nottingham Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom.
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211
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Dubbury SJ, Boutz PL, Sharp PA. CDK12 regulates DNA repair genes by suppressing intronic polyadenylation. Nature 2018; 564:141-145. [PMID: 30487607 PMCID: PMC6328294 DOI: 10.1038/s41586-018-0758-y] [Citation(s) in RCA: 174] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 10/11/2018] [Indexed: 12/28/2022]
Abstract
Mutations that attenuate homologous recombination (HR)-mediated repair promote tumorigenesis and sensitize cells to chemotherapeutics that cause replication fork collapse, a phenotype known as 'BRCAness'1. BRCAness tumours arise from loss-of-function mutations in 22 genes1. Of these genes, all but one (CDK12) function directly in the HR repair pathway1. CDK12 phosphorylates serine 2 of the RNA polymerase II C-terminal domain heptapeptide repeat2-7, a modification that regulates transcription elongation, splicing, and cleavage and polyadenylation8,9. Genome-wide expression studies suggest that depletion of CDK12 abrogates the expression of several HR genes relatively specifically, thereby blunting HR repair3-7,10,11. This observation suggests that the mutational status of CDK12 may predict sensitivity to targeted treatments against BRCAness, such as PARP1 inhibitors, and that CDK12 inhibitors may induce sensitization of HR-competent tumours to these treatments6,7,10,11. Despite growing clinical interest, the mechanism by which CDK12 regulates HR genes remains unknown. Here we show that CDK12 globally suppresses intronic polyadenylation events in mouse embryonic stem cells, enabling the production of full-length gene products. Many HR genes harbour more intronic polyadenylation sites than other expressed genes, and these sites are particularly sensitive to loss of CDK12. The cumulative effect of these sites accounts for the enhanced sensitivity of HR gene expression to CDK12 loss, and we find that this mechanism is conserved in human tumours that contain loss-of-function CDK12 mutations. This work clarifies the function of CDK12 and underscores its potential both as a chemotherapeutic target and as a tumour biomarker.
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Affiliation(s)
- Sara J Dubbury
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Paul L Boutz
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Phillip A Sharp
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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212
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Tam AS, Sihota TS, Milbury KL, Zhang A, Mathew V, Stirling PC. Selective defects in gene expression control genome instability in yeast splicing mutants. Mol Biol Cell 2018; 30:191-200. [PMID: 30462576 PMCID: PMC6589566 DOI: 10.1091/mbc.e18-07-0439] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RNA processing mutants have been broadly implicated in genome stability, but mechanistic links are often unclear. Two predominant models have emerged: one involving changes in gene expression that perturb other genome maintenance factors and another in which genotoxic DNA:RNA hybrids, called R-loops, impair DNA replication. Here we characterize genome instability phenotypes in yeast splicing factor mutants and find that mitotic defects, and in some cases R-loop accumulation, are causes of genome instability. In both cases, alterations in gene expression, rather than direct cis effects, are likely to contribute to instability. Genome instability in splicing mutants is exacerbated by loss of the spindle-assembly checkpoint protein Mad1. Moreover, removal of the intron from the α-tubulin gene TUB1 restores genome integrity. Thus, differing penetrance and selective effects on the transcriptome can lead to a range of phenotypes in conditional mutants of the spliceosome, including multiple routes to genome instability.
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Affiliation(s)
- Annie S Tam
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Tianna S Sihota
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Karissa L Milbury
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Anni Zhang
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Veena Mathew
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Peter C Stirling
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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213
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Abstract
The fact that many cancer types display transcriptional addiction driven by dysregulation of oncogenic enhancers and transcription factors has led to increased interest in a group of protein kinases, known as transcriptional cyclin dependent kinases (tCDKs), as potential therapeutic targets. Despite early reservations about targeting a process that is essential to healthy cell types, there is now evidence that targeting tCDKs could provide enough therapeutic window to be effective in the clinic. Here, we discuss recent developments in this field, with an emphasis on highly-selective inhibitors and the challenges to be addressed before these inhibitors could be used for therapeutic purposes. Abbreviations: CAK: CDK-activating kinase;CDK: cyclin-dependent kinase;CMGC group: CDK-, MAPK-, GSK3-, and CLK-like;CTD: C-terminal repeat domain of the RPB1 subunit of RNA polymerase II;DRB: 5,6-dichloro-1-β-D-ribofuranosylbenzimidazole;mCRPC: metastatic castration-resistant prostate cancer;NSCLC: non-small cell lung cancer;P-TEFb: positive elongation factor b;RNAPII: RNA polymerase II;S2: serine-2 of CTD repeats;S5: serine-5 of CTD repeats;S7: serine-7 of CTD repeats;SEC: super elongation complex;tCDK: transcriptional cyclin-dependent kinase;TNBC: triple-negative breast cancer
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Affiliation(s)
- Matthew D Galbraith
- a Linda Crnic Institute for Down Syndrome, School of Medicine , University of Colorado Anschutz Medical Campus , Aurora , CO , USA.,b Department of Pharmacology, School of Medicine , University of Colorado Anschutz Medical Campus , Aurora , CO , USA
| | - Heather Bender
- a Linda Crnic Institute for Down Syndrome, School of Medicine , University of Colorado Anschutz Medical Campus , Aurora , CO , USA.,b Department of Pharmacology, School of Medicine , University of Colorado Anschutz Medical Campus , Aurora , CO , USA
| | - Joaquín M Espinosa
- a Linda Crnic Institute for Down Syndrome, School of Medicine , University of Colorado Anschutz Medical Campus , Aurora , CO , USA.,b Department of Pharmacology, School of Medicine , University of Colorado Anschutz Medical Campus , Aurora , CO , USA.,c Department of Molecular, Cellular and Developmental Biology , University of Colorado Boulder , Boulder , CO , USA
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214
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Guiro J, Murphy S. Regulation of expression of human RNA polymerase II-transcribed snRNA genes. Open Biol 2018; 7:rsob.170073. [PMID: 28615474 PMCID: PMC5493778 DOI: 10.1098/rsob.170073] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/11/2017] [Indexed: 12/31/2022] Open
Abstract
In addition to protein-coding genes, RNA polymerase II (pol II) transcribes numerous genes for non-coding RNAs, including the small-nuclear (sn)RNA genes. snRNAs are an important class of non-coding RNAs, several of which are involved in pre-mRNA splicing. The molecular mechanisms underlying expression of human pol II-transcribed snRNA genes are less well characterized than for protein-coding genes and there are important differences in expression of these two gene types. Here, we review the DNA features and proteins required for efficient transcription of snRNA genes and co-transcriptional 3′ end formation of the transcripts.
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Affiliation(s)
- Joana Guiro
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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215
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Warner EW, Yip SM, Chi KN, Wyatt AW. DNA repair defects in prostate cancer: impact for screening, prognostication and treatment. BJU Int 2018; 123:769-776. [PMID: 30281887 DOI: 10.1111/bju.14576] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Failure of effective DNA damage repair is a hallmark of cancer, but was previously underappreciated as a driver of aggressive prostate cancer. However, recent international sequencing efforts have revealed that both germline and somatic alterations within the homologous recombination and mismatch repair pathways are relatively common in lethal metastatic disease. BRCA2 gene alterations are particularly prevalent and are linked to poor prognosis as well as poor responses to systemic therapy for castration-resistant prostate cancer, although there is conflicting support for the latter. Defective DNA repair contributes to tumour heterogeneity, evolution and progression, but there are high hopes that management of this aggressive subset will be transformed by biomarker-driven use of poly-ADP ribose polymerase (PARP) inhibitors and platinum-based chemotherapy. In this review, we detail the relationship between DNA repair defects and prostate cancer, highlighting the prevalence of mutations in key genes and their controversial association with clinical outcomes.
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Affiliation(s)
- Evan W Warner
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Steven M Yip
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Kim N Chi
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
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216
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Candidate biomarkers of PARP inhibitor sensitivity in ovarian cancer beyond the BRCA genes. Br J Cancer 2018; 119:1401-1409. [PMID: 30353044 PMCID: PMC6265286 DOI: 10.1038/s41416-018-0274-8] [Citation(s) in RCA: 171] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/20/2018] [Accepted: 09/04/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Olaparib (Lynparza™) is a PARP inhibitor approved for advanced BRCA-mutated (BRCAm) ovarian cancer. PARP inhibitors may benefit patients whose tumours are dysfunctional in DNA repair mechanisms unrelated to BRCA1/2. We report exploratory analyses, including the long-term outcome of candidate biomarkers of sensitivity to olaparib in BRCA wild-type (BRCAwt) tumours. METHODS Tumour samples from an olaparib maintenance monotherapy trial (Study 19, D0810C00019; NCT00753545) were analysed. Analyses included classification of mutations in genes involved in homologous recombination repair (HRR), BRCA1 promoter methylation status, measurement of BRCA1 protein and Myriad HRD score. RESULTS Patients with BRCAm tumours gained most benefit from olaparib; a similar treatment benefit was also observed in 21/95 patients whose tumours were BRCAwt but had loss-of-function HRR mutations compared to patients with no detectable HRR mutations (58/95). A higher median Myriad MyChoice® HRD score was observed in BRCAm and BRCAwt tumours with BRCA1 methylation. Patients without BRCAm tumours derived benefit from olaparib treatment vs placebo although to a lesser extent than BRCAm patients. CONCLUSIONS Ovarian cancer patients with tumours harbouring loss-of-function mutations in HRR genes other than BRCA1/2 may constitute a small, molecularly identifiable and clinically relevant population who derive treatment benefit from olaparib similar to patients with BRCAm.
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217
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Jorda R, Hendrychová D, Voller J, Řezníčková E, Gucký T, Kryštof V. How Selective Are Pharmacological Inhibitors of Cell-Cycle-Regulating Cyclin-Dependent Kinases? J Med Chem 2018; 61:9105-9120. [PMID: 30234987 DOI: 10.1021/acs.jmedchem.8b00049] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cyclin-dependent kinases (CDKs) are an important and emerging class of drug targets for which many small-molecule inhibitors have been developed. However, there is often insufficient data available on the selectivity of CDK inhibitors (CDKi) to attribute the effects on the presumed target CDK to these inhibitors. Here, we highlight discrepancies between the kinase selectivity of CDKi and the phenotype exhibited; we evaluated 31 CDKi (claimed to target CDK1-4) for activity toward CDKs 1, 2, 4, 5, 7, 9 and for effects on the cell cycle. Our results suggest that most CDKi should be reclassified as pan-selective and should not be used as a tool. In addition, some compounds did not even inhibit CDKs as their primary cellular targets; for example, NU6140 showed potent inhibition of Aurora kinases. We also established an online database of commercially available CDKi for critical evaluation of their utility as molecular probes. Our results should help researchers select the most relevant chemical tools for their specific applications.
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Affiliation(s)
- Radek Jorda
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
| | - Denisa Hendrychová
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
| | - Jiří Voller
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
| | - Eva Řezníčková
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
| | - Tomáš Gucký
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
| | - Vladimír Kryštof
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
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218
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Brovkina OI, Shigapova L, Chudakova DA, Gordiev MG, Enikeev RF, Druzhkov MO, Khodyrev DS, Shagimardanova EI, Nikitin AG, Gusev OA. The Ethnic-Specific Spectrum of Germline Nucleotide Variants in DNA Damage Response and Repair Genes in Hereditary Breast and Ovarian Cancer Patients of Tatar Descent. Front Oncol 2018; 8:421. [PMID: 30333958 PMCID: PMC6176317 DOI: 10.3389/fonc.2018.00421] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/11/2018] [Indexed: 12/11/2022] Open
Abstract
The Russian population consists of more than 100 ethnic groups, presenting a unique opportunity for the identification of hereditary pathogenic mutations. To gain insight into the landscape of heredity pathogenic variants, we employed targeted next-generation sequencing to analyze the germline mutation load in the DNA damage response and repair genes of hereditary breast and ovary cancer syndrome (HBOCS) patients of Tatar ethnicity, which represents ~4% of the total Russian population. Several pathogenic mutations were identified in DNA double-strand break repair genes, and the spectrum of these markers in Tatar patients varied from that previously reported for patients of Slavic ancestry. The CDK12 gene encodes cyclin-dependent kinase 12, the key transcriptional regulator of the genes involved in DNA damage response and repair. CDK12 analysis in a cohort of HBOCS patients of Tatar decent identified a c.1047-2A>G nucleotide variant in the CDK12 gene in 8 of the 106 cases (7.6%). The c.1047-2A>G nucleotide variant was identified in 1 of the 93 (1.1%) HBOCS patients with mixed or unknown ethnicity and in 1 of the 238 (0.42%) healthy control patients of mixed ethnicity (Tatars and non-Tatars) (p = 0.0066, OR = 11.18, CI 95% = 1.53-492.95, Tatar and non-Tatar patients vs. healthy controls). In a group of mixed ethnicity patients from Tatarstan, with sporadic breast and/or ovarian cancer, this nucleotide variant was detected in 2 out of 93 (2.2%) cases. In a cohort of participants of Slavic descent from Moscow, comprising of 95 HBOCS patients, 80 patients with sporadic breast and/or ovarian cancer, and 372 healthy controls, this nucleotide variant was absent. Our study demonstrates a strong predisposition for the CDK12 c.1047-2A>G nucleotide variant in HBOCS in patients of Tatar ethnicity and identifies CDK12 as a novel gene involved in HBOCS susceptibility.
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Affiliation(s)
- Olga I Brovkina
- Federal Research and Clinical Center, Federal Medical-Biological Agency of Russia, Moscow, Russia
| | | | - Daria A Chudakova
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Marat G Gordiev
- Republican Clinical Oncology Dispensary of the Ministry of Health of the Republic of Tatarstan, Kazan, Russia
| | - Rafael F Enikeev
- Republican Clinical Oncology Dispensary of the Ministry of Health of the Republic of Tatarstan, Kazan, Russia
| | - Maxim O Druzhkov
- Republican Clinical Oncology Dispensary of the Ministry of Health of the Republic of Tatarstan, Kazan, Russia
| | - Dmitriy S Khodyrev
- Federal Research and Clinical Center, Federal Medical-Biological Agency of Russia, Moscow, Russia
| | | | - Alexey G Nikitin
- Federal Research and Clinical Center, Federal Medical-Biological Agency of Russia, Moscow, Russia.,Pulmonology Research Institute, Federal Medical-Biological Agency of Russia, Moscow, Russia
| | - Oleg A Gusev
- Kazan (Volga Region) Federal University, Kazan, Russia.,RIKEN, Yokohama, Japan
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219
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Zhou C, Feng X, Yuan F, Ji J, Shi M, Yu Y, Zhu Z, Zhang J. Difference of molecular alterations in HER2-positive and HER2-negative gastric cancers by whole-genome sequencing analysis. Cancer Manag Res 2018; 10:3945-3954. [PMID: 30310315 PMCID: PMC6165778 DOI: 10.2147/cmar.s172710] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Objective The aim of this study was to compare the molecular profiling, including somatic mutation and somatic copy number variation (SCNV), between human epidermal growth factor receptor 2 (HER2)-positive (HER2+) and HER2-negative (HER2−) gastric cancer patients. Patients and methods Tumor samples were collected from 15 gastric cancer patients, including 10 HER2+ samples and five HER2− samples, which were diagnosed by immunohistochemistry. Whole-genome sequencing was performed by Illumina HiSeq PE150 instrument, along with somatic single nucleotide variant (SNV), somatic structural variation (SV) and SCNV analyses. Results The average number of somatic SNVs and mutation spectrum were similar between HER2+ and HER2− samples. Transition of C>T was the main type of mutation. For somatic SV, number of intrachromosomal translocation (2,850.3±1,260.4 vs 1,157±586.6, P=0.015) and insertion of large fragment (1,125.6±457.4 vs 500±138.9, P=0.002) in HER2+ samples were higher than those in HER2− samples. For all samples, lysine methyltransferase 2C (KMT2C), ZNF91, TAF1 and MAP4 genes were identified as new significant mutated driver genes. KMT2C gene mutations were mainly detected in HER2+ samples (7/10), which were correlated with the lysine degradation pathway. SERF2 gene mutations were more common in HER2− samples (3/5) than in HER2+ samples (1/10). Copy number gain was the major type of SCNV in both groups, and the average number of SCNVs was similar. In the HER2+ samples, by using the GISTIC algorithm, amplification of known driver genes cyclin-dependent kinase 12 (CDK12, 6/10) and RARA (5/10) was mainly observed, and other amplifications including JUP, GJD3, KRT39, CDC6, RAPGEFL1, WIPF2, FAM65C, KLF5, DACH1 and PIBF1 genes were also observed. Amplifications of solute carrier family 12 member 7 (SLC12A7, 5/5), TTC40 (4/5) and GALNT9 (4/5) genes were mainly detected in HER2− samples. Conclusion Differences in genomic landscape between HER2+ and HER2− gastric cancer samples were revealed in this study. KMT2C mutation and CDK12 amplification were mainly detected in HER2+ gastric cancer, whereas SERF2 mutation and SLC12A7 amplification were detected in HER2− gastric cancer.
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Affiliation(s)
- Chenfei Zhou
- Department of Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China,
| | - Xiaojing Feng
- Department of Clinical Laboratory, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Fei Yuan
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Jun Ji
- Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Min Shi
- Department of Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China,
| | - Yingyan Yu
- Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Zhenggang Zhu
- Department of Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China, .,Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Jun Zhang
- Department of Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China,
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220
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Fan Y, Yin W, Hu B, Kline AD, Zhang VW, Liang D, Sun Y, Wang L, Tang S, Powis Z, Li L, Yan H, Shi Z, Yang X, Chen Y, Wang J, Jiang Y, Tan H, Gu X, Wu L, Yu Y. De Novo Mutations of CCNK Cause a Syndromic Neurodevelopmental Disorder with Distinctive Facial Dysmorphism. Am J Hum Genet 2018; 103:448-455. [PMID: 30122539 DOI: 10.1016/j.ajhg.2018.07.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 07/24/2018] [Indexed: 11/17/2022] Open
Abstract
Neurodevelopment is a transcriptionally orchestrated process. Cyclin K, a regulator of transcription encoded by CCNK, is thought to play a critical role in the RNA polymerase II-mediated activities. However, dysfunction of CCNK has not been linked to genetic disorders. In this study, we identified three unrelated individuals harboring de novo heterozygous copy number loss of CCNK in an overlapping 14q32.3 region and one individual harboring a de novo nonsynonymous variant c.331A>G (p.Lys111Glu) in CCNK. These four individuals, though from different ethnic backgrounds, shared a common phenotype of developmental delay and intellectual disability (DD/ID), language defects, and distinctive facial dysmorphism including high hairline, hypertelorism, thin eyebrows, dysmorphic ears, broad nasal bridge and tip, and narrow jaw. Functional assay in zebrafish larvae showed that Ccnk knockdown resulted in defective brain development, small eyes, and curly spinal cord. These defects were partially rescued by wild-type mRNA coding CCNK but not the mRNA with the identified likely pathogenic variant c.331A>G, supporting a causal role of CCNK variants in neurodevelopmental disorders. Taken together, we reported a syndromic neurodevelopmental disorder with DD/ID and facial characteristics caused by CCNK variations, possibly through a mechanism of haploinsufficiency.
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Affiliation(s)
- Yanjie Fan
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Wu Yin
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China; CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Bing Hu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China; CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Antonie D Kline
- Harvey Institute for Human Genetics, Greater Baltimore Medical Center, Baltimore, MD 21204, USA
| | - Victor Wei Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; AmCare Genomics Lab, GuangZhou 510300, China
| | - Desheng Liang
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410008, China
| | - Yu Sun
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Lili Wang
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Sha Tang
- Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Zöe Powis
- Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Lei Li
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China; CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Huifang Yan
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
| | - Zhen Shi
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
| | - Xiaoping Yang
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China; Department of Neurology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi Province 030001, China
| | - Yinyin Chen
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China; Department of Neurology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi Province 030001, China
| | - Jingmin Wang
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
| | - Yuwu Jiang
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
| | - Hu Tan
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410008, China
| | - Xuefan Gu
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Lingqian Wu
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410008, China.
| | - Yongguo Yu
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China.
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221
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Ito M, Tanaka T, Toita A, Uchiyama N, Kokubo H, Morishita N, Klein MG, Zou H, Murakami M, Kondo M, Sameshima T, Araki S, Endo S, Kawamoto T, Morin GB, Aparicio SA, Nakanishi A, Maezaki H, Imaeda Y. Discovery of 3-Benzyl-1-( trans-4-((5-cyanopyridin-2-yl)amino)cyclohexyl)-1-arylurea Derivatives as Novel and Selective Cyclin-Dependent Kinase 12 (CDK12) Inhibitors. J Med Chem 2018; 61:7710-7728. [PMID: 30067358 DOI: 10.1021/acs.jmedchem.8b00683] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cyclin-dependent kinase 12 (CDK12) plays a key role in the coordination of transcription with elongation and mRNA processing. CDK12 mutations found in tumors and CDK12 inhibition sensitize cancer cells to DNA-damaging reagents and DNA-repair inhibitors. This suggests that CDK12 inhibitors are potential therapeutics for cancer that may cause synthetic lethality. Here, we report the discovery of 3-benzyl-1-( trans-4-((5-cyanopyridin-2-yl)amino)cyclohexyl)-1-arylurea derivatives as novel and selective CDK12 inhibitors. Structure-activity relationship studies of a HTS hit, structure-based drug design, and conformation-oriented design using the Cambridge Structural Database afforded the optimized compound 2, which exhibited not only potent CDK12 (and CDK13) inhibitory activity and excellent selectivity but also good physicochemical properties. Furthermore, 2 inhibited the phosphorylation of Ser2 in the C-terminal domain of RNA polymerase II and induced growth inhibition in SK-BR-3 cells. Therefore, 2 represents an excellent chemical probe for functional studies of CDK12 and could be a promising lead compound for drug discovery.
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Affiliation(s)
- Masahiro Ito
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Toshio Tanaka
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Akinori Toita
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Noriko Uchiyama
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Hironori Kokubo
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Nao Morishita
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Michael G Klein
- Department of Structural Biology , Takeda California Inc. , 10410 Science Center Drive , San Diego , California 92121 , United States
| | - Hua Zou
- Department of Structural Biology , Takeda California Inc. , 10410 Science Center Drive , San Diego , California 92121 , United States
| | - Morio Murakami
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Mitsuyo Kondo
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Tomoya Sameshima
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Shinsuke Araki
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Satoshi Endo
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Tomohiro Kawamoto
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Gregg B Morin
- Genome Sciences Centre , British Columbia Cancer Agency , 675 West 10th Avenue , Vancouver , British Columbia V5Z 1L3 , Canada.,Department of Medical Genetics , University of British Columbia , Vancouver , British Columbia V6H 3N1 , Canada
| | - Samuel A Aparicio
- Department of Molecular Oncology , British Columbia Cancer Agency , 675 West 10th Avenue , Vancouver , British Columbia V5Z 1L3 , Canada
| | - Atsushi Nakanishi
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Hironobu Maezaki
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Yasuhiro Imaeda
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
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222
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Lui GYL, Grandori C, Kemp CJ. CDK12: an emerging therapeutic target for cancer. J Clin Pathol 2018; 71:957-962. [PMID: 30104286 DOI: 10.1136/jclinpath-2018-205356] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 12/20/2022]
Abstract
Cyclin-dependent kinase 12 (CDK12) belongs to the cyclin-dependent kinase (CDK) family of serine/threonine protein kinases that regulate transcriptional and post-transcriptional processes, thereby modulating multiple cellular functions. Early studies characterised CDK12 as a transcriptional CDK that complexes with cyclin K to mediate gene transcription by phosphorylating RNA polymerase II. CDK12 has been demonstrated to specifically upregulate the expression of genes involved in response to DNA damage, stress and heat shock. More recent studies have implicated CDK12 in regulating mRNA splicing, 3' end processing, pre-replication complex assembly and genomic stability during embryonic development. Genomic alterations in CDK12 have been detected in oesophageal, stomach, breast, endometrial, uterine, ovarian, bladder, colorectal and pancreatic cancers, ranging from 5% to 15% of sequenced cases. An increasing number of studies point to CDK12 inhibition as an effective strategy to inhibit tumour growth, and synthetic lethal interactions have been described with MYC, EWS/FLI and PARP/CHK1 inhibition. Herein, we discuss the present literature on CDK12 in cell function and human cancer, highlighting important roles for CDK12 as a clinical biomarker for treatment response and potential as an effective therapeutic target.
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Affiliation(s)
- Goldie Y L Lui
- Fred Hutchinson Cancer Research Center, Human Biology Division, Seattle, Washington, USA
| | | | - Christopher J Kemp
- Fred Hutchinson Cancer Research Center, Human Biology Division, Seattle, Washington, USA
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223
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Menghi F, Barthel FP, Yadav V, Tang M, Ji B, Tang Z, Carter GW, Ruan Y, Scully R, Verhaak RGW, Jonkers J, Liu ET. The Tandem Duplicator Phenotype Is a Prevalent Genome-Wide Cancer Configuration Driven by Distinct Gene Mutations. Cancer Cell 2018; 34:197-210.e5. [PMID: 30017478 PMCID: PMC6481635 DOI: 10.1016/j.ccell.2018.06.008] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 05/04/2018] [Accepted: 06/14/2018] [Indexed: 12/14/2022]
Abstract
The tandem duplicator phenotype (TDP) is a genome-wide instability configuration primarily observed in breast, ovarian, and endometrial carcinomas. Here, we stratify TDP tumors by classifying their tandem duplications (TDs) into three span intervals, with modal values of 11 kb, 231 kb, and 1.7 Mb, respectively. TDPs with ∼11 kb TDs feature loss of TP53 and BRCA1. TDPs with ∼231 kb and ∼1.7 Mb TDs associate with CCNE1 pathway activation and CDK12 disruptions, respectively. We demonstrate that p53 and BRCA1 conjoint abrogation drives TDP induction by generating short-span TDP mammary tumors in genetically modified mice lacking them. Lastly, we show how TDs in TDP tumors disrupt heterogeneous combinations of tumor suppressors and chromatin topologically associating domains while duplicating oncogenes and super-enhancers.
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Affiliation(s)
- Francesca Menghi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Floris P Barthel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Vinod Yadav
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Ming Tang
- MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bo Ji
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Zhonghui Tang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | | | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Ralph Scully
- Division of Hematology Oncology, Department of Medicine, and Cancer Research Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Jos Jonkers
- Oncode Institute and Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam 1066CX, the Netherlands
| | - Edison T Liu
- The Jackson Laboratory, Bar Harbor, ME 04609, USA.
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224
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Meyer SE, Muench DE, Rogers AM, Newkold TJ, Orr E, O'Brien E, Perentesis JP, Doench JG, Lal A, Morris PJ, Thomas CJ, Lieberman J, McGlinn E, Aronow BJ, Salomonis N, Grimes HL. miR-196b target screen reveals mechanisms maintaining leukemia stemness with therapeutic potential. J Exp Med 2018; 215:2115-2136. [PMID: 29997117 PMCID: PMC6080909 DOI: 10.1084/jem.20171312] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 04/30/2018] [Accepted: 06/26/2018] [Indexed: 01/02/2023] Open
Abstract
We have shown that antagomiR inhibition of miRNA miR-21 and miR-196b activity is sufficient to ablate MLL-AF9 leukemia stem cells (LSC) in vivo. Here, we used an shRNA screening approach to mimic miRNA activity on experimentally verified miR-196b targets to identify functionally important and therapeutically relevant pathways downstream of oncogenic miRNA in MLL-r AML. We found Cdkn1b (p27Kip1) is a direct miR-196b target whose repression enhanced an embryonic stem cell-like signature associated with decreased leukemia latency and increased numbers of leukemia stem cells in vivo. Conversely, elevation of p27Kip1 significantly reduced MLL-r leukemia self-renewal, promoted monocytic differentiation of leukemic blasts, and induced cell death. Antagonism of miR-196b activity or pharmacologic inhibition of the Cks1-Skp2-containing SCF E3-ubiquitin ligase complex increased p27Kip1 and inhibited human AML growth. This work illustrates that understanding oncogenic miRNA target pathways can identify actionable targets in leukemia.
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MESH Headings
- Animals
- Carcinogenesis/genetics
- Carcinogenesis/pathology
- Cell Differentiation/genetics
- Cell Line, Tumor
- Cell Proliferation/genetics
- Cell Survival/genetics
- Chromosomes, Human, Pair 11/genetics
- Cyclin-Dependent Kinase Inhibitor p27/metabolism
- Cyclin-Dependent Kinases/metabolism
- Cyclins/metabolism
- Embryonic Stem Cells/metabolism
- Gene Expression Regulation, Leukemic
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/therapy
- Mice, Inbred C57BL
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- Oncogenes
- RNA, Small Interfering/metabolism
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Affiliation(s)
- Sara E Meyer
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - David E Muench
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Andrew M Rogers
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Tess J Newkold
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Emily Orr
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Eric O'Brien
- Division of Oncology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - John P Perentesis
- Division of Oncology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | | | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Patrick J Morris
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Edwina McGlinn
- EMBL Australia, Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Bruce J Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - H Leighton Grimes
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
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225
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Henry KL, Kellner D, Bajrami B, Anderson JE, Beyna M, Bhisetti G, Cameron T, Capacci AG, Bertolotti-Ciarlet A, Feng J, Gao B, Hopkins B, Jenkins T, Li K, May-Dracka T, Murugan P, Wei R, Zeng W, Allaire N, Buckler A, Loh C, Juhasz P, Lucas B, Ennis KA, Vollman E, Cahir-McFarland E, Hett EC, Ols ML. CDK12-mediated transcriptional regulation of noncanonical NF-κB components is essential for signaling. Sci Signal 2018; 11:eaam8216. [PMID: 30065029 DOI: 10.1126/scisignal.aam8216] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Members of the family of nuclear factor κB (NF-κB) transcription factors are critical for multiple cellular processes, including regulating innate and adaptive immune responses, cell proliferation, and cell survival. Canonical NF-κB complexes are retained in the cytoplasm by the inhibitory protein IκBα, whereas noncanonical NF-κB complexes are retained by p100. Although activation of canonical NF-κB signaling through the IκBα kinase complex is well studied, few regulators of the NF-κB-inducing kinase (NIK)-dependent processing of noncanonical p100 to p52 and the subsequent nuclear translocation of p52 have been identified. We discovered a role for cyclin-dependent kinase 12 (CDK12) in transcriptionally regulating the noncanonical NF-κB pathway. High-content phenotypic screening identified the compound 919278 as a specific inhibitor of the lymphotoxin β receptor (LTβR), and tumor necrosis factor (TNF) receptor superfamily member 12A (FN14)-dependent nuclear translocation of p52, but not of the TNF-α receptor-mediated nuclear translocation of p65. Chemoproteomics identified CDK12 as the target of 919278. CDK12 inhibition by 919278, the CDK inhibitor THZ1, or siRNA-mediated knockdown resulted in similar global transcriptional changes and prevented the LTβR- and FN14-dependent expression of MAP3K14 (which encodes NIK) as well as NIK accumulation by reducing phosphorylation of the carboxyl-terminal domain of RNA polymerase II. By coupling a phenotypic screen with chemoproteomics, we identified a pathway for the activation of the noncanonical NF-κB pathway that could serve as a therapeutic target in autoimmunity and cancer.
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Affiliation(s)
- Kate L Henry
- Biogen, 225 Binney Street, Cambridge, MA 02142, USA
- Department of Pharmacology, Boston University School of Medicine, Boston, MA 02118, USA
| | | | | | - John E Anderson
- Biogen, 225 Binney Street, Cambridge, MA 02142, USA
- Department of Pharmacology, Boston University School of Medicine, Boston, MA 02118, USA
| | | | | | - Tom Cameron
- Biogen, 225 Binney Street, Cambridge, MA 02142, USA
| | | | | | - Jun Feng
- Biogen, 225 Binney Street, Cambridge, MA 02142, USA
| | - Benbo Gao
- Biogen, 225 Binney Street, Cambridge, MA 02142, USA
| | | | | | - Kejie Li
- Biogen, 225 Binney Street, Cambridge, MA 02142, USA
| | | | | | - Ru Wei
- Biogen, 225 Binney Street, Cambridge, MA 02142, USA
| | - Weike Zeng
- Biogen, 225 Binney Street, Cambridge, MA 02142, USA
| | - Norm Allaire
- Biogen, 225 Binney Street, Cambridge, MA 02142, USA
| | - Alan Buckler
- Biogen, 225 Binney Street, Cambridge, MA 02142, USA
| | | | - Peter Juhasz
- Biogen, 225 Binney Street, Cambridge, MA 02142, USA
| | - Brian Lucas
- Biogen, 225 Binney Street, Cambridge, MA 02142, USA
| | | | | | | | - Erik C Hett
- Biogen, 225 Binney Street, Cambridge, MA 02142, USA.
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226
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Guffanti F, Fratelli M, Ganzinelli M, Bolis M, Ricci F, Bizzaro F, Chilà R, Sina FP, Fruscio R, Lupia M, Cavallaro U, Cappelletti MR, Generali D, Giavazzi R, Damia G. Platinum sensitivity and DNA repair in a recently established panel of patient-derived ovarian carcinoma xenografts. Oncotarget 2018; 9:24707-24717. [PMID: 29872499 PMCID: PMC5973859 DOI: 10.18632/oncotarget.25185] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/05/2018] [Indexed: 01/22/2023] Open
Abstract
A xenobank of patient-derived (PDX) ovarian tumor samples has been established consisting of tumors with different sensitivity to cisplatin (DDP), from very responsive to resistant. As the DNA repair pathway is an important driver in tumor response to DDP, we analyzed the mRNA expression of 20 genes involved in the nucleotide excision repair, fanconi anemia, homologous recombination, base excision repair, mismatch repair and translesion repair pathways and the methylation patterns of some of these genes. We also investigated the correlation with the response to platinum-based therapy. The mRNA levels of the selected genes were evaluated by Real Time-PCR (RT-PCR) with ad hoc validated primers and gene promoter methylation by pyrosequencing. All the DNA repair genes were variably expressed in all 42 PDX samples analyzed, with no particular histotype-specific pattern of expression. In high-grade serous/endometrioid PDXs, the CDK12 mRNA expression levels positively correlated with the expression of TP53BP1, PALB2, XPF and POLB. High-grade serous/endometrioid PDXs with TP53 mutations had significantly higher levels of POLQ, FANCD2, RAD51 and POLB than high-grade TP53 wild type PDXs. The mRNA levels of CDK12, PALB2 and XPF inversely associated with the in vivo DDP antitumor activity; higher CDK12 mRNA levels were associated with a higher recurrence rate in ovarian patients with low residual tumor. These data support the important role of CDK12 in the response to a platinum based therapy in ovarian patients.
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Affiliation(s)
- Federica Guffanti
- Department of Oncology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Maddalena Fratelli
- Department of Biochemistry, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Monica Ganzinelli
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Marco Bolis
- Department of Biochemistry, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Francesca Ricci
- Department of Oncology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Francesca Bizzaro
- Department of Oncology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Rosaria Chilà
- Department of Oncology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Federica Paola Sina
- Clinic of Obstetrics and Gynecology, San Gerardo Hospital, University of Milan-Bicocca, Department of Medicine and Surgery, Milan, Italy
| | - Robert Fruscio
- Clinic of Obstetrics and Gynecology, San Gerardo Hospital, University of Milan-Bicocca, Department of Medicine and Surgery, Milan, Italy
| | - Michela Lupia
- Unit of Gynecological Oncology Research, European Institute of Oncology, Milan, Italy
| | - Ugo Cavallaro
- Unit of Gynecological Oncology Research, European Institute of Oncology, Milan, Italy
| | | | - Daniele Generali
- Breast Cancer Unit and Translational Research Unit, ASST Cremona, Cremona, Italy.,Department of Medical, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Raffaella Giavazzi
- Department of Oncology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Giovanna Damia
- Department of Oncology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
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227
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Cyclin K regulates prereplicative complex assembly to promote mammalian cell proliferation. Nat Commun 2018; 9:1876. [PMID: 29760377 PMCID: PMC5951916 DOI: 10.1038/s41467-018-04258-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 04/16/2018] [Indexed: 12/14/2022] Open
Abstract
The assembly of prereplicative complex (pre-RC) during G1 phase must be tightly controlled to sustain cell proliferation and maintain genomic stability. Mechanisms to prevent pre-RC formation in G2/M and S phases are well appreciated, whereas how cells ensure efficient pre-RC assembly during G1 is less clear. Here we report that cyclin K regulates pre-RC formation. We find that cyclin K expression positively correlates with cell proliferation, and knockdown of cyclin K or its cognate kinase CDK12 prevents the assembly of pre-RC in G1 phase. Mechanistically we uncover that cyclin K promotes pre-RC assembly by restricting cyclin E1 activity in G1. We identify a cyclin K-dependent, novel phosphorylation site in cyclin E1 that disrupts its interaction with CDK2. Importantly, this antagonistic relationship is largely recapitulated in cyclin E1-overexpressing tumors. We discuss the implications of our findings in light of recent reports linking cyclin K and CDK12 to human tumorigenesis. Prereplicative complex (pre-RC) formation during G1 is fundamental for cell replication. Here the authors report a role for cyclin K in regulating pre-RC formation in mammalian cells by affecting cyclin E1 activity.
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228
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Laarse SAM, Leney AC, Heck AJR. Crosstalk between phosphorylation and O‐Glc
NA
cylation: friend or foe. FEBS J 2018; 285:3152-3167. [DOI: 10.1111/febs.14491] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/27/2018] [Accepted: 04/26/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Saar A. M. Laarse
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University The Netherlands
- Netherlands Proteomics Centre Utrecht The Netherlands
| | - Aneika C. Leney
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University The Netherlands
- Netherlands Proteomics Centre Utrecht The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University The Netherlands
- Netherlands Proteomics Centre Utrecht The Netherlands
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229
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Krasinska L, Fisher D. Non-Cell Cycle Functions of the CDK Network in Ciliogenesis: Recycling the Cell Cycle Oscillator. Bioessays 2018; 40:e1800016. [DOI: 10.1002/bies.201800016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/22/2018] [Indexed: 01/05/2023]
Affiliation(s)
- Liliana Krasinska
- Institut de Génétique Moléculaire de Montpellier (IGMM); University of Montpellier, CNRS 1919 Route de Mende; Montpellier 34293 France
- Equipe Labellisée LIGUE 2018; Ligue Nationale contre le Cancer; 75013 Paris France
| | - Daniel Fisher
- Institut de Génétique Moléculaire de Montpellier (IGMM); University of Montpellier, CNRS 1919 Route de Mende; Montpellier 34293 France
- Equipe Labellisée LIGUE 2018; Ligue Nationale contre le Cancer; 75013 Paris France
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230
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Iniguez AB, Stolte B, Wang EJ, Conway AS, Alexe G, Dharia NV, Kwiatkowski N, Zhang T, Abraham BJ, Mora J, Kalev P, Leggett A, Chowdhury D, Benes CH, Young RA, Gray NS, Stegmaier K. EWS/FLI Confers Tumor Cell Synthetic Lethality to CDK12 Inhibition in Ewing Sarcoma. Cancer Cell 2018; 33:202-216.e6. [PMID: 29358035 PMCID: PMC5846483 DOI: 10.1016/j.ccell.2017.12.009] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 09/15/2017] [Accepted: 12/19/2017] [Indexed: 01/01/2023]
Abstract
Many cancer types are driven by oncogenic transcription factors that have been difficult to drug. Transcriptional inhibitors, however, may offer inroads into targeting these cancers. Through chemical genomics screening, we identified that Ewing sarcoma is a disease with preferential sensitivity to THZ1, a covalent small-molecule CDK7/12/13 inhibitor. The selective CDK12/13 inhibitor, THZ531, impairs DNA damage repair in an EWS/FLI-dependent manner, supporting a synthetic lethal relationship between response to THZ1/THZ531 and EWS/FLI expression. The combination of these molecules with PARP inhibitors showed striking synergy in cell viability and DNA damage assays in vitro and in multiple models of Ewing sarcoma, including a PDX, in vivo without hematopoietic toxicity.
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Affiliation(s)
- Amanda Balboni Iniguez
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Björn Stolte
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA; Ludwig Maximilians University of Munich, Munich 80539, Germany
| | - Emily Jue Wang
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amy Saur Conway
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Gabriela Alexe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA
| | - Neekesh V Dharia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nicholas Kwiatkowski
- The Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Tinghu Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Brian J Abraham
- The Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Jaume Mora
- Development Tumor Biology Laboratory and Department of Pediatric Oncology and Hematology, Hospital Sant Joan de Déu Barcelona, Barcelona 08950, Spain
| | - Peter Kalev
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Alan Leggett
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Dipanjan Chowdhury
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Cyril H Benes
- Massachusetts General Hospital, Center for Cancer Research, Boston, MA 02114, USA
| | - Richard A Young
- The Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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231
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Johannes JW, Denz CR, Su N, Wu A, Impastato AC, Mlynarski S, Varnes JG, Prince DB, Cidado J, Gao N, Haddrick M, Jones NH, Li S, Li X, Liu Y, Nguyen TB, O'Connell N, Rivers E, Robbins DW, Tomlinson R, Yao T, Zhu X, Ferguson AD, Lamb ML, Manchester JI, Guichard S. Structure-Based Design of Selective Noncovalent CDK12 Inhibitors. ChemMedChem 2018; 13:231-235. [PMID: 29266803 DOI: 10.1002/cmdc.201700695] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/13/2017] [Indexed: 12/21/2022]
Abstract
Cyclin-dependent kinase (CDK) 12 knockdown via siRNA decreases the transcription of DNA-damage-response genes and sensitizes BRCA wild-type cells to poly(ADP-ribose) polymerase (PARP) inhibition. To recapitulate this effect with a small molecule, we sought a potent, selective CDK12 inhibitor. Crystal structures and modeling informed hybridization between dinaciclib and SR-3029, resulting in lead compound 5 [(S)-2-(1-(6-(((6,7-difluoro-1H-benzo[d]imidazol-2-yl)methyl)amino)-9-ethyl-9H-purin-2-yl)piperidin-2-yl)ethan-1-ol]. Further structure-guided optimization delivered a series of selective CDK12 inhibitors, including compound 7 [(S)-2-(1-(6-(((6,7-difluoro-1H-benzo[d]imidazol-2-yl)methyl)amino)-9-isopropyl-9H-purin-2-yl)piperidin-2-yl)ethan-1-ol]. Profiling of this compound across CDK9, 7, 2, and 1 at high ATP concentration, single-point kinase panel screening against 352 targets at 0.1 μm, and proteomics via kinase affinity matrix technology demonstrated the selectivity. This series of compounds inhibits phosphorylation of Ser2 on the C-terminal repeat domain of RNA polymerase II, consistent with CDK12 inhibition. These selective compounds were also acutely toxic to OV90 as well as THP1 cells.
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Affiliation(s)
| | | | - Nancy Su
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, MA, USA
| | - Allan Wu
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, MA, USA
| | - Anna C Impastato
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, MA, USA
| | | | | | - D Bryan Prince
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, MA, USA
| | - Justin Cidado
- Oncology, IMED Biotech Unit, AstraZeneca, Boston, MA, USA
| | - Ning Gao
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, MA, USA
| | - Malcolm Haddrick
- Discovery Sciences, IMED Biotech Unit, AstraZeneca Pharmaceuticals LP, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Natalie H Jones
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, MA, USA
| | - Shaobin Li
- Pharmaron Beijing Co. Ltd., 6 Taihe Road BDA, Beijing, 100176, P.R. China
| | - Xiuwei Li
- Pharmaron Beijing Co. Ltd., 6 Taihe Road BDA, Beijing, 100176, P.R. China
| | - Yang Liu
- Pharmaron Beijing Co. Ltd., 6 Taihe Road BDA, Beijing, 100176, P.R. China
| | - Toan B Nguyen
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, MA, USA
| | | | - Emma Rivers
- Discovery Sciences, IMED Biotech Unit, AstraZeneca Pharmaceuticals LP, Unit 310 Darwin Building, Cambridge, CB4 0WG, UK
| | | | - Ronald Tomlinson
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, MA, USA
| | - Tieguang Yao
- Pharmaron Beijing Co. Ltd., 6 Taihe Road BDA, Beijing, 100176, P.R. China
| | - Xiahui Zhu
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, MA, USA
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232
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Carey KT, Wickramasinghe VO. Regulatory Potential of the RNA Processing Machinery: Implications for Human Disease. Trends Genet 2018; 34:279-290. [PMID: 29329719 DOI: 10.1016/j.tig.2017.12.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/14/2017] [Accepted: 12/14/2017] [Indexed: 12/14/2022]
Abstract
Splicing and nuclear export of mRNA are critical steps in the gene expression pathway. While RNA processing factors can perform general, essential functions for intron removal and bulk export of mRNA, emerging evidence highlights that the core RNA splicing and export machineries also display regulatory potential. Here, we discuss recent insights into how this regulatory potential can selectively alter gene expression and regulate important biological processes. We also highlight the participation of RNA processing pathways in the cellular response to DNA damage at multiple levels. These findings have important implications for the contribution of selective mRNA processing and export to the development of human cancers and neurodegenerative disorders.
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Affiliation(s)
- Kirstyn T Carey
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Vihandha O Wickramasinghe
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.
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233
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Naidoo K, Wai PT, Maguire SL, Daley F, Haider S, Kriplani D, Campbell J, Mirza H, Grigoriadis A, Tutt A, Moseley PM, Abdel-Fatah TMA, Chan SYT, Madhusudan S, Rhaka EA, Ellis IO, Lord CJ, Yuan Y, Green AR, Natrajan R. Evaluation of CDK12 Protein Expression as a Potential Novel Biomarker for DNA Damage Response-Targeted Therapies in Breast Cancer. Mol Cancer Ther 2018; 17:306-315. [PMID: 29133620 PMCID: PMC6284786 DOI: 10.1158/1535-7163.mct-17-0760] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 09/19/2017] [Accepted: 10/19/2017] [Indexed: 12/20/2022]
Abstract
Disruption of Cyclin-Dependent Kinase 12 (CDK12) is known to lead to defects in DNA repair and sensitivity to platinum salts and PARP1/2 inhibitors. However, CDK12 has also been proposed as an oncogene in breast cancer. We therefore aimed to assess the frequency and distribution of CDK12 protein expression by IHC in independent cohorts of breast cancer and correlate this with outcome and genomic status. We found that 21% of primary unselected breast cancers were CDK12 high, and 10.5% were absent, by IHC. CDK12 positivity correlated with HER2 positivity but was not an independent predictor of breast cancer-specific survival taking HER2 status into account; however, absent CDK12 protein expression significantly correlated with a triple-negative phenotype. Interestingly, CDK12 protein absence was associated with reduced expression of a number of DDR proteins including ATR, Ku70/Ku80, PARP1, DNA-PK, and γH2AX, suggesting a novel mechanism of CDK12-associated DDR dysregulation in breast cancer. Our data suggest that diagnostic IHC quantification of CDK12 in breast cancer is feasible, with CDK12 absence possibly signifying defective DDR function. This may have important therapeutic implications, particularly for triple-negative breast cancers. Mol Cancer Ther; 17(1); 306-15. ©2017 AACR.
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Affiliation(s)
- Kalnisha Naidoo
- The Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Patty T Wai
- The Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
- Division of Molecular Pathology, Centre for Evolution and Cancer and Centre for Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Sarah L Maguire
- The Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Frances Daley
- The Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Syed Haider
- The Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Divya Kriplani
- The Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - James Campbell
- The Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Hasan Mirza
- Cancer Bioinformatics, Cancer Division, King's College London, London, United Kingdom
| | - Anita Grigoriadis
- Cancer Bioinformatics, Cancer Division, King's College London, London, United Kingdom
| | - Andrew Tutt
- The Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
- Breast Cancer Now Research Unit, King's College London, London, United Kingdom
| | - Paul M Moseley
- Clinical Oncology, The University of Nottingham and Nottingham University Hospitals NHS Trust, Nottingham City Hospital, Nottingham, United Kingdom
| | - Tarek M A Abdel-Fatah
- Clinical Oncology, The University of Nottingham and Nottingham University Hospitals NHS Trust, Nottingham City Hospital, Nottingham, United Kingdom
| | - Stephen Y T Chan
- Clinical Oncology, The University of Nottingham and Nottingham University Hospitals NHS Trust, Nottingham City Hospital, Nottingham, United Kingdom
| | - Srinivasan Madhusudan
- Department of Histopathology and Division of Cancer & Stem Cells, School of Medicine, The University of Nottingham and Nottingham University Hospitals NHS Trust, Nottingham City Hospital, Nottingham, United Kingdom
| | - Emad A Rhaka
- Department of Histopathology and Division of Cancer & Stem Cells, School of Medicine, The University of Nottingham and Nottingham University Hospitals NHS Trust, Nottingham City Hospital, Nottingham, United Kingdom
| | - Ian O Ellis
- Department of Histopathology and Division of Cancer & Stem Cells, School of Medicine, The University of Nottingham and Nottingham University Hospitals NHS Trust, Nottingham City Hospital, Nottingham, United Kingdom
| | - Christopher J Lord
- The Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Yinyin Yuan
- Division of Molecular Pathology, Centre for Evolution and Cancer and Centre for Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Andrew R Green
- Department of Histopathology and Division of Cancer & Stem Cells, School of Medicine, The University of Nottingham and Nottingham University Hospitals NHS Trust, Nottingham City Hospital, Nottingham, United Kingdom
| | - Rachael Natrajan
- The Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom.
- Division of Molecular Pathology, Centre for Evolution and Cancer and Centre for Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
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234
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Meeting Report From the 2016 11th Biennial Ovarian Cancer Research Symposium: Mechanisms of Initiation and Progression of Ovarian Cancers. Int J Gynecol Cancer 2017; 27:S10-S13. [PMID: 29278599 DOI: 10.1097/igc.0000000000001117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVE The aim of this study was to review the latest research advances on the mechanisms of initiation and progression of ovarian cancer. METHODS At the 11th Biennial Ovarian Cancer Research Symposium, which was held in Seattle, Washington in September 2016, leaders in ovarian cancer research convened to present and discuss current advances and future directions in ovarian cancer research. RESULTS One session was dedicated to Mechanisms of Initiation and Progression of Ovarian Cancer, and included a keynote presentation from Dr Ronny Drapkin, MD (University of Pennsylvania), and an invited oral presentation from Laising Yen, PhD (Baylor College of Medicine). Nine additional oral presentations were selected from abstract submissions. Thirty-three abstracts were presented in poster format and were grouped into the categories of mechanisms of the genesis of genomic instability, tumor initiation, metastases of ovarian cancers, innate and acquired chemotherapy resistance, tumor progression, tumor-initiating cell and chemotherapy resistance, and immunomodulation. CONCLUSIONS Eradication of ovarian cancers requires clear understanding of molecular mechanisms of ovarian cancer initiation and progression. These mechanisms will not only drive the precision of early detection, but also discovery of new therapies to target precursor lesions and more advanced stage disease.
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235
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Uehara T, Takenouchi T, Kosaki R, Kurosawa K, Mizuno S, Kosaki K. Redefining the phenotypic spectrum of de novo heterozygous CDK13 variants: Three patients without cardiac defects. Eur J Med Genet 2017; 61:243-247. [PMID: 29222009 DOI: 10.1016/j.ejmg.2017.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 11/08/2017] [Accepted: 12/04/2017] [Indexed: 11/16/2022]
Abstract
Recently, 7 patients with de novo constitutional non-synonymous mutations in the CDK13 gene were ascertained through a trio exome analysis of a large cohort of 610 patients with congenital cardiac diseases. Despite another report describing 9 additional patients, the clinical spectrum of this condition has yet to be defined. Herein, we report 3 patients with heterozygous constitutional CDK13 mutations, who were ascertained through exome analysis of children with intellectual disability and minor anomalies, who lacked cardiac anomalies. Two patients had a c.2149G > A, p.Gly717Arg mutation, and one had a c.2525A > G, p. Asn842Ser mutation. A review of the previously described patients and those described herein has enabled the following points to be clarified. First, congenital heart diseases are not an essential feature (13/19). Second, nasal features may help syndromic recognition (14/16). Third, widely spaced and peg-shaped teeth may represent a previously unappreciated diagnostic clue for this newly identified syndrome. Here, we show that p.Gly717Arg represents a hotspot in addition to p.Asn842Ser. We suggest that this CDK13-related disorder may represent a clinically recognizable syndrome.
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Affiliation(s)
- Tomoko Uehara
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Toshiki Takenouchi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Rika Kosaki
- Division of Medical Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Kenji Kurosawa
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Seiji Mizuno
- Department of Pediatrics, Central Hospital, Aichi Human Service Center, Aichi, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan.
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236
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Johnson SF, Cruz C, Greifenberg AK, Dust S, Stover DG, Chi D, Primack B, Cao S, Bernhardy AJ, Coulson R, Lazaro JB, Kochupurakkal B, Sun H, Unitt C, Moreau LA, Sarosiek KA, Scaltriti M, Juric D, Baselga J, Richardson AL, Rodig SJ, D'Andrea AD, Balmaña J, Johnson N, Geyer M, Serra V, Lim E, Shapiro GI. CDK12 Inhibition Reverses De Novo and Acquired PARP Inhibitor Resistance in BRCA Wild-Type and Mutated Models of Triple-Negative Breast Cancer. Cell Rep 2017; 17:2367-2381. [PMID: 27880910 DOI: 10.1016/j.celrep.2016.10.077] [Citation(s) in RCA: 195] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 09/08/2016] [Accepted: 10/23/2016] [Indexed: 02/04/2023] Open
Abstract
Although poly(ADP-ribose) polymerase (PARP) inhibitors are active in homologous recombination (HR)-deficient cancers, their utility is limited by acquired resistance after restoration of HR. Here, we report that dinaciclib, an inhibitor of cyclin-dependent kinases (CDKs) 1, 2, 5, and 9, additionally has potent activity against CDK12, a transcriptional regulator of HR. In BRCA-mutated triple-negative breast cancer (TNBC) cells and patient-derived xenografts (PDXs), dinaciclib ablates restored HR and reverses PARP inhibitor resistance. Additionally, we show that de novo resistance to PARP inhibition in BRCA1-mutated cell lines and a PDX derived from a PARP-inhibitor-naive BRCA1 carrier is mediated by residual HR and is reversed by CDK12 inhibition. Finally, dinaciclib augments the degree of response in a PARP-inhibitor-sensitive model, converting tumor growth inhibition to durable regression. These results highlight the significance of HR disruption as a therapeutic strategy and support the broad use of combined CDK12 and PARP inhibition in TNBC.
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Affiliation(s)
- Shawn F Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Cristina Cruz
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain; Medical Oncology Department, Hospital Vall d'Hebron, Vall d'Hebron Institute of Oncology, Universitat Autonoma de Barcelona, 08035 Barcelona, Spain
| | - Ann Katrin Greifenberg
- Department of Structural Immunology, Institute of Innate Immunity, University of Bonn, 53127 Bonn, Germany; Group Physical Biochemistry, Center of Advanced European Studies and Research, 53175 Bonn, Germany
| | - Sofia Dust
- Department of Structural Immunology, Institute of Innate Immunity, University of Bonn, 53127 Bonn, Germany; Group Physical Biochemistry, Center of Advanced European Studies and Research, 53175 Bonn, Germany
| | - Daniel G Stover
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - David Chi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Benjamin Primack
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Children's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Shiliang Cao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Andrea J Bernhardy
- Developmental Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Rhiannon Coulson
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, St. Vincent's Health Network, Darlinghurst, NSW 2010, Australia
| | - Jean-Bernard Lazaro
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Bose Kochupurakkal
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Heather Sun
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Christine Unitt
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Lisa A Moreau
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Children's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | | | - Maurizio Scaltriti
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dejan Juric
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - José Baselga
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrea L Richardson
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Alan D D'Andrea
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Children's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Judith Balmaña
- Medical Oncology Department, Hospital Vall d'Hebron, Vall d'Hebron Institute of Oncology, Universitat Autonoma de Barcelona, 08035 Barcelona, Spain
| | - Neil Johnson
- Developmental Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Matthias Geyer
- Department of Structural Immunology, Institute of Innate Immunity, University of Bonn, 53127 Bonn, Germany; Group Physical Biochemistry, Center of Advanced European Studies and Research, 53175 Bonn, Germany
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Elgene Lim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Kinghorn Cancer Centre, Garvan Institute of Medical Research, St. Vincent's Health Network, Darlinghurst, NSW 2010, Australia.
| | - Geoffrey I Shapiro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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237
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Biswas R, Gao S, Cultraro CM, Maity TK, Venugopalan A, Abdullaev Z, Shaytan AK, Carter CA, Thomas A, Rajan A, Song Y, Pitts S, Chen K, Bass S, Boland J, Hanada KI, Chen J, Meltzer PS, Panchenko AR, Yang JC, Pack S, Giaccone G, Schrump DS, Khan J, Guha U. Genomic profiling of multiple sequentially acquired tumor metastatic sites from an "exceptional responder" lung adenocarcinoma patient reveals extensive genomic heterogeneity and novel somatic variants driving treatment response. Cold Spring Harb Mol Case Stud 2017; 2:a001263. [PMID: 27900369 PMCID: PMC5111000 DOI: 10.1101/mcs.a001263] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We used next-generation sequencing to identify somatic alterations in multiple metastatic sites from an “exceptional responder” lung adenocarcinoma patient during his 7-yr course of ERBB2-directed therapies. The degree of heterogeneity was unprecedented, with ∼1% similarity between somatic alterations of the lung and lymph nodes. One novel translocation, PLAG1-ACTA2, present in both sites, up-regulated ACTA2 expression. ERBB2, the predominant driver oncogene, was amplified in both sites, more pronounced in the lung, and harbored an L869R mutation in the lymph node. Functional studies showed increased proliferation, migration, metastasis, and resistance to ERBB2-directed therapy because of L869R mutation and increased migration because of ACTA2 overexpression. Within the lung, a nonfunctional CDK12, due to a novel G879V mutation, correlated with down-regulation of DNA damage response genes, causing genomic instability, and sensitivity to chemotherapy. We propose a model whereby a subclone metastasized early from the primary site and evolved independently in lymph nodes.
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Affiliation(s)
- Romi Biswas
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Shaojian Gao
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Constance M Cultraro
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Tapan K Maity
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Abhilash Venugopalan
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Alexey K Shaytan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Corey A Carter
- Walter Reed National Military Medical Center, Bethesda, Maryland 20889, USA
| | - Anish Thomas
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Arun Rajan
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Young Song
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Stephanie Pitts
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Kevin Chen
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Sara Bass
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, Maryland 20848, USA
| | - Joseph Boland
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, Maryland 20848, USA
| | - Ken-Ichi Hanada
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Jinqiu Chen
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Paul S Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Anna R Panchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - James C Yang
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Svetlana Pack
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Giuseppe Giaccone
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, D.C. 20057, USA
| | - David S Schrump
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Udayan Guha
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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238
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Tien JF, Mazloomian A, Cheng SWG, Hughes CS, Chow CCT, Canapi LT, Oloumi A, Trigo-Gonzalez G, Bashashati A, Xu J, Chang VCD, Shah SP, Aparicio S, Morin GB. CDK12 regulates alternative last exon mRNA splicing and promotes breast cancer cell invasion. Nucleic Acids Res 2017; 45:6698-6716. [PMID: 28334900 PMCID: PMC5499812 DOI: 10.1093/nar/gkx187] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 03/09/2017] [Indexed: 12/31/2022] Open
Abstract
CDK12 (cyclin-dependent kinase 12) is a regulatory kinase with evolutionarily conserved roles in modulating transcription elongation. Recent tumor genome studies of breast and ovarian cancers highlighted recurrent CDK12 mutations, which have been shown to disrupt DNA repair in cell-based assays. In breast cancers, CDK12 is also frequently co-amplified with the HER2 (ERBB2) oncogene. The mechanisms underlying functions of CDK12 in general and in cancer remain poorly defined. Based on global analysis of mRNA transcripts in normal and breast cancer cell lines with and without CDK12 amplification, we demonstrate that CDK12 primarily regulates alternative last exon (ALE) splicing, a specialized subtype of alternative mRNA splicing, that is both gene- and cell type-specific. These are unusual properties for spliceosome regulatory factors, which typically regulate multiple forms of alternative splicing in a global manner. In breast cancer cells, regulation by CDK12 modulates ALE splicing of the DNA damage response activator ATM and a DNAJB6 isoform that influences cell invasion and tumorigenesis in xenografts. We found that there is a direct correlation between CDK12 levels, DNAJB6 isoform levels and the migration capacity and invasiveness of breast tumor cells. This suggests that CDK12 gene amplification can contribute to the pathogenesis of the cancer.
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Affiliation(s)
- Jerry F Tien
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada
| | - Alborz Mazloomian
- Graduate Bioinformatics Training Program, University of British Columbia, Vancouver V5Z 4S6, Canada.,Department of Molecular Oncology, BC Cancer Agency, Vancouver V5Z 1L3, Canada
| | - S-W Grace Cheng
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada
| | - Christopher S Hughes
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada
| | - Christalle C T Chow
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada
| | - Leanna T Canapi
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada
| | - Arusha Oloumi
- Department of Molecular Oncology, BC Cancer Agency, Vancouver V5Z 1L3, Canada
| | - Genny Trigo-Gonzalez
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada
| | - Ali Bashashati
- Department of Molecular Oncology, BC Cancer Agency, Vancouver V5Z 1L3, Canada
| | - James Xu
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver V6T 2B5, Canada
| | - Vicky C-D Chang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada
| | - Sohrab P Shah
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada.,Department of Molecular Oncology, BC Cancer Agency, Vancouver V5Z 1L3, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver V6T 2B5, Canada
| | - Samuel Aparicio
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada.,Department of Molecular Oncology, BC Cancer Agency, Vancouver V5Z 1L3, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver V6T 2B5, Canada
| | - Gregg B Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver V6H 3N1, Canada
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239
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Paculová H, Kohoutek J. The emerging roles of CDK12 in tumorigenesis. Cell Div 2017; 12:7. [PMID: 29090014 PMCID: PMC5658942 DOI: 10.1186/s13008-017-0033-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/16/2017] [Indexed: 12/25/2022] Open
Abstract
Cyclin-dependent kinases (CDKs) are key regulators of both cell cycle progression and transcription. Since dysregulation of CDKs is a frequently occurring event driving tumorigenesis, CDKs have been tested extensively as targets for cancer therapy. Cyclin-dependent kinase 12 (CDK12) is a transcription-associated kinase which participates in various cellular processes, including DNA damage response, development and cellular differentiation, as well as splicing and pre-mRNA processing. CDK12 mutations and amplification have been recently reported in different types of malignancies, including loss-of-function mutations in high-grade serous ovarian carcinomas, and that has led to assumption that CDK12 is a tumor suppressor. On the contrary, CDK12 overexpression in other tumors suggests the possibility that CDK12 has oncogenic properties, similarly to other transcription-associated kinases. In this review, we discuss current knowledge concerning the role of CDK12 in ovarian and breast tumorigenesis and the potential for chemical inhibitors of CDK12 in future cancer treatment.
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Affiliation(s)
- Hana Paculová
- Department of Chemistry and Toxicology, Veterinary Research Institute, Hudcova 296/70, Brno, 621 00 Czech Republic
| | - Jiří Kohoutek
- Department of Chemistry and Toxicology, Veterinary Research Institute, Hudcova 296/70, Brno, 621 00 Czech Republic
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Paculová H, Kramara J, Šimečková Š, Fedr R, Souček K, Hylse O, Paruch K, Svoboda M, Mistrík M, Kohoutek J. BRCA1 or CDK12 loss sensitizes cells to CHK1 inhibitors. Tumour Biol 2017; 39:1010428317727479. [PMID: 29025359 DOI: 10.1177/1010428317727479] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A broad spectrum of tumors develop resistance to classic chemotherapy, necessitating the discovery of new therapies. One successful strategy exploits the synthetic lethality between poly(ADP-ribose) polymerase 1/2 proteins and DNA damage response genes, including BRCA1, a factor involved in homologous recombination-mediated DNA repair, and CDK12, a transcriptional kinase known to regulate the expression of DDR genes. CHK1 inhibitors have been shown to enhance the anti-cancer effect of DNA-damaging compounds. Since loss of BRCA1 increases replication stress and leads to DNA damage, we tested a hypothesis that CDK12- or BRCA1-depleted cells rely extensively on S-phase-related CHK1 functions for survival. The silencing of BRCA1 or CDK12 sensitized tumor cells to CHK1 inhibitors in vitro and in vivo. BRCA1 downregulation combined with CHK1 inhibition induced excessive amounts of DNA damage, resulting in an inability to complete the S-phase. Therefore, we suggest CHK1 inhibition as a strategy for targeting BRCA1- or CDK12-deficient tumors.
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Affiliation(s)
- Hana Paculová
- 1 Department of Chemistry and Toxicology, Veterinary Research Institute, Brno, Czech Republic
| | - Juraj Kramara
- 2 Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Šárka Šimečková
- 3 Institute of Biophysics of the Czech Academy of Sciences, Brno,Czech Republic.,4 Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Radek Fedr
- 3 Institute of Biophysics of the Czech Academy of Sciences, Brno,Czech Republic.,5 International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Karel Souček
- 3 Institute of Biophysics of the Czech Academy of Sciences, Brno,Czech Republic.,4 Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.,5 International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Ondřej Hylse
- 5 International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic.,6 Department of Chemistry, CZ Openscreen, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kamil Paruch
- 5 International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic.,6 Department of Chemistry, CZ Openscreen, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Marek Svoboda
- 7 Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Martin Mistrík
- 2 Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Jiří Kohoutek
- 1 Department of Chemistry and Toxicology, Veterinary Research Institute, Brno, Czech Republic
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241
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Bitler BG, Watson ZL, Wheeler LJ, Behbakht K. PARP inhibitors: Clinical utility and possibilities of overcoming resistance. Gynecol Oncol 2017; 147:695-704. [PMID: 29037806 DOI: 10.1016/j.ygyno.2017.10.003] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/01/2017] [Accepted: 10/03/2017] [Indexed: 12/21/2022]
Abstract
PARP inhibitors represent a major breakthrough in ovarian cancer care. Almost half of all ovarian cancers have deficiencies in the homologous recombination (HR) DNA repair pathway, namely BRCA1/2 mutations. Given the limited therapeutic options for recurrent ovarian cancer patients there has been a significant effort to develop novel therapies to exploit DNA repair deficiencies. In 2005 and 2006, inhibiting PARP enzymes was first observed to be highly effective against cancers with HR deficiencies. PARP inhibitors are being utilized in the clinic to manage recurrent ovarian cancers that display defects in the HR repair pathway. However, PARP inhibitors also show significant clinical benefit in patients without HR deficiencies. There are currently three FDA-approved PARP inhibitors for recurrent ovarian cancer and an additional two PARP inhibitors being evaluated in late stage clinical trials. Given the expanding clinical use of PARP inhibitors and the high likelihood of acquired resistance, there is a significant need for clinical strategies to manage PARP inhibitor resistant disease. This review will examine PARP inhibitors in the context of: indications and toxicities, novel biomarkers to predict response, targeted-therapy resistance, and potential approaches to manage resistant disease.
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Affiliation(s)
- Benjamin G Bitler
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, The University of Colorado, Aurora, CO, United States.
| | - Zachary L Watson
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, The University of Colorado, Aurora, CO, United States
| | - Lindsay J Wheeler
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, The University of Colorado, Aurora, CO, United States; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, The University of Colorado, Aurora, CO, United States
| | - Kian Behbakht
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, The University of Colorado, Aurora, CO, United States; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, The University of Colorado, Aurora, CO, United States.
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242
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Kalra S, Joshi G, Munshi A, Kumar R. Structural insights of cyclin dependent kinases: Implications in design of selective inhibitors. Eur J Med Chem 2017; 142:424-458. [PMID: 28911822 DOI: 10.1016/j.ejmech.2017.08.071] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 08/31/2017] [Accepted: 08/31/2017] [Indexed: 12/17/2022]
Abstract
There are around 20 Cyclin-dependent kinases (CDKs) known till date, and various research groups have reported their role in different types of cancer. The X-ray structures of some CDKs especially CDK2 was exploited in the past few years, and several inhibitors have been found, e.g., flavopiridol, indirubicin, roscovitine, etc., but due to the specificity issues of these inhibitors (binding to all CDKs), these were called as pan inhibitors. The revolutionary outcome of palbociclib in 2015 as CDK4/6 inhibitor added a new charm to the specific inhibitor design for CDKs. Computer-aided drug design (CADD) tools added a benefit to the design and development of new CDK inhibitors by studying the binding pattern of the inhibitors to the ATP binding domain of CDKs. Herein, we have attempted a comparative analysis of structural differences between several CDKs ATP binding sites and their inhibitor specificity by depicting the important ligand-receptor interactions for a particular CDK to be targeted. This perspective provides futuristic implications in the design of inhibitors considering the spatial features and structural insights of the specific CDK.
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Affiliation(s)
- Sourav Kalra
- Centre for Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Gaurav Joshi
- Centre for Pharmaceutical Sciences and Natural Products, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, India
| | - Anjana Munshi
- Centre for Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India.
| | - Raj Kumar
- Centre for Pharmaceutical Sciences and Natural Products, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, India.
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243
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Bostwick BL, McLean S, Posey JE, Streff HE, Gripp KW, Blesson A, Powell-Hamilton N, Tusi J, Stevenson DA, Farrelly E, Hudgins L, Yang Y, Xia F, Wang X, Liu P, Walkiewicz M, McGuire M, Grange DK, Andrews MV, Hummel M, Madan-Khetarpal S, Infante E, Coban-Akdemir Z, Miszalski-Jamka K, Jefferies JL, Rosenfeld JA, Emrick L, Nugent KM, Lupski JR, Belmont JW, Lee B, Lalani SR. Phenotypic and molecular characterisation of CDK13-related congenital heart defects, dysmorphic facial features and intellectual developmental disorders. Genome Med 2017; 9:73. [PMID: 28807008 PMCID: PMC5557075 DOI: 10.1186/s13073-017-0463-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/24/2017] [Indexed: 12/21/2022] Open
Abstract
Background De novo missense variants in CDK13 have been described as the cause of syndromic congenital heart defects in seven individuals ascertained from a large congenital cardiovascular malformations cohort. We aimed to further define the phenotypic and molecular spectrum of this newly described disorder. Methods To minimise ascertainment bias, we recruited nine additional individuals with CDK13 pathogenic variants from clinical and research exome laboratory sequencing cohorts. Each individual underwent dysmorphology exam and comprehensive medical history review. Results We demonstrate greater than expected phenotypic heterogeneity, including 33% (3/9) of individuals without structural heart disease on echocardiogram. There was a high penetrance for a unique constellation of facial dysmorphism and global developmental delay, as well as less frequently seen renal and sacral anomalies. Two individuals had novel CDK13 variants (p.Asn842Asp, p.Lys734Glu), while the remaining seven unrelated individuals had a recurrent, previously published p.Asn842Ser variant. Summary of all variants published to date demonstrates apparent restriction of pathogenic variants to the protein kinase domain with clustering in the ATP and magnesium binding sites. Conclusions Here we provide detailed phenotypic and molecular characterisation of individuals with pathogenic variants in CDK13 and propose management guidelines based upon the estimated prevalence of anomalies identified. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0463-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bret L Bostwick
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.
| | - Scott McLean
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
| | - Haley E Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
| | - Karen W Gripp
- Division of Medical Genetics, A.I. duPont Hospital for Children/Nemours, Wilmington, DE, USA
| | - Alyssa Blesson
- Division of Medical Genetics, A.I. duPont Hospital for Children/Nemours, Wilmington, DE, USA
| | - Nina Powell-Hamilton
- Division of Medical Genetics, A.I. duPont Hospital for Children/Nemours, Wilmington, DE, USA
| | - Jessica Tusi
- Division of Medical Genetics, A.I. duPont Hospital for Children/Nemours, Wilmington, DE, USA
| | - David A Stevenson
- Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ellyn Farrelly
- Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Louanne Hudgins
- Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.,Baylor Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.,Baylor Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.,Baylor Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.,Baylor Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.,Baylor Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Marianne McGuire
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
| | - Dorothy K Grange
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Marisa V Andrews
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Marybeth Hummel
- Department of Pediatrics, Section of Medical Genetics, West Virginia University Health Sciences Center, Morgantown, WV, USA
| | | | - Elena Infante
- Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
| | - Karol Miszalski-Jamka
- Division of Magnetic Resonance Imaging, Silesian Center for Heart Disease, Zabrze, Poland
| | - John L Jefferies
- The Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
| | - Lisa Emrick
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
| | - Kimberly M Nugent
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - John W Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
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244
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Paparidis NFDS, Durvale MC, Canduri F. The emerging picture of CDK9/P-TEFb: more than 20 years of advances since PITALRE. MOLECULAR BIOSYSTEMS 2017; 13:246-276. [PMID: 27833949 DOI: 10.1039/c6mb00387g] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
CDK9 is a prominent member of the transcriptional CDKs subfamily, a group of kinases whose function is to control the primary steps of mRNA synthesis and processing by eukaryotic RNA polymerase II. As a cyclin-dependent kinase, CDK9 activation in vivo depends upon its association with T-type cyclins to assemble the positive transcription elongation factor (P-TEFb). Although CDK9/P-TEFb phosphorylates the C-terminal domain of RNAP II in the same positions targeted by CDK7 (TFIIH) and CDK8 (Mediator), the former does not participate in the transcription initiation, but rather plays a unique role by driving the polymerase to productive elongation. In addition to RNAP II CTD, the negative transcription elongation factors DSIF and NELF also represent major CDK9 substrates, whose phosphorylation is required to overcome the proximal pause of the polymerase. CDK9 is recruited to specific genes through proteins that interact with both P-TEFb and distinct elements in DNA, RNA or chromatin, where it modulates the activity of individual RNAP II transcription complexes. The regulation of CDK9 function is an intricate network that includes post-translational modifications (phosphorylation/dephosphorylation and acetylation/deacetylation of key residues) as well as the association of P-TEFb with various proteins that can stimulate or inhibit its kinase activity. Several cases of CDK9 deregulation have been linked to important human diseases, including various types of cancer and also AIDS (due to its essential role in HIV replication). Not only HIV, but also many other human viruses have been shown to depend strongly on CDK9 activity to be transcribed within host cells. This review summarizes the main advances made on CDK9/P-TEFb field in more than 20 years, introducing the structural, functional and genetic aspects that have been elucidated ever since.
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Affiliation(s)
- Nikolas Ferreira Dos Santos Paparidis
- Department of Chemistry and Molecular Physics, Institute of Chemistry of Sao Carlos, Sao Paulo University, Av. Trabalhador Sãocarlense, 400, Zip Code 780, 13560-970, São Carlos-SP, Brazil.
| | - Maxwell Castro Durvale
- Department of Biochemistry, Institute of Chemistry, Sao Paulo University, Av. Prof. Lineu Prestes, 748, 05508-000, Butantã - São Paulo - SP, Brazil
| | - Fernanda Canduri
- Department of Chemistry and Molecular Physics, Institute of Chemistry of Sao Carlos, Sao Paulo University, Av. Trabalhador Sãocarlense, 400, Zip Code 780, 13560-970, São Carlos-SP, Brazil.
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245
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Schecher S, Walter B, Falkenstein M, Macher-Goeppinger S, Stenzel P, Krümpelmann K, Hadaschik B, Perner S, Kristiansen G, Duensing S, Roth W, Tagscherer KE. Cyclin K dependent regulation of Aurora B affects apoptosis and proliferation by induction of mitotic catastrophe in prostate cancer. Int J Cancer 2017; 141:1643-1653. [PMID: 28670704 DOI: 10.1002/ijc.30864] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/30/2017] [Accepted: 06/12/2017] [Indexed: 12/11/2022]
Abstract
Cyclin K plays a critical role in transcriptional regulation as well as cell development. However, the role of Cyclin K in prostate cancer is unknown. Here, we describe the impact of Cyclin K on prostate cancer cells and examine the clinical relevance of Cyclin K as a biomarker for patients with prostate cancer. We show that Cyclin K depletion in prostate cancer cells induces apoptosis and inhibits proliferation accompanied by an accumulation of cells in the G2/M phase. Moreover, knockdown of Cyclin K causes mitotic catastrophe displayed by multinucleation and spindle multipolarity. Furthermore, we demonstrate a Cyclin K dependent regulation of the mitotic kinase Aurora B and provide evidence for an Aurora B dependent induction of mitotic catastrophe. In addition, we show that Cyclin K expression is associated with poor biochemical recurrence-free survival in patients with prostate cancer treated with an adjuvant therapy. In conclusion, targeting Cyclin K represents a novel, promising anti-cancer strategy to induce cell cycle arrest and apoptotic cell death through induction of mitotic catastrophe in prostate cancer cells. Moreover, our results indicate that Cyclin K is a putative predictive biomarker for clinical outcome and therapy response for patients with prostate cancer.
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Affiliation(s)
- Sabrina Schecher
- Molecular Tumor-Pathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, University of Heidelberg, Heidelberg, Germany.,Institute of Pathology, University Medical Center Mainz, Mainz, Germany
| | - Britta Walter
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Michael Falkenstein
- Molecular Urooncology, Department of Urology, University of Heidelberg, Heidelberg, Germany
| | - Stephan Macher-Goeppinger
- Molecular Tumor-Pathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, University of Heidelberg, Heidelberg, Germany.,Institute of Pathology, University Medical Center Mainz, Mainz, Germany
| | - Philipp Stenzel
- Institute of Pathology, University Medical Center Mainz, Mainz, Germany
| | | | - Boris Hadaschik
- Department of Urology, Essen University Hospital, Essen, Germany.,Department of Urology, University of Heidelberg, Heidelberg, Germany
| | - Sven Perner
- Pathology of the University Medical Center Schleswig-Holstein, Campus Luebeck and the Research Center Borstel, Leibniz Center for Medicine and Biosciences, 23538 Luebeck and 23845 Borstel, Germany
| | | | - Stefan Duensing
- Molecular Urooncology, Department of Urology, University of Heidelberg, Heidelberg, Germany
| | - Wilfried Roth
- Molecular Tumor-Pathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, University of Heidelberg, Heidelberg, Germany.,Institute of Pathology, University Medical Center Mainz, Mainz, Germany
| | - Katrin E Tagscherer
- Molecular Tumor-Pathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, University of Heidelberg, Heidelberg, Germany.,Institute of Pathology, University Medical Center Mainz, Mainz, Germany
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246
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Abstract
Congenital heart disease is the most common congenital abnormality, and advances in medical care mean that this population of individuals is surviving for longer than ever before. It represents a significant healthcare challenge, as many patients require life-long care and individuals may ask about the likelihood of their children being affected. Whilst a number of genes have been identified previously from investigation of families with Mendelian inheritance patterns, sequencing the DNA from large cohorts of individuals with congenital heart disease is now providing fresh insights into the genetics of these conditions. This research has enabled novel gene discovery and uncovered the different genetic mechanisms underlying both isolated congenital heart disease and that which occurs in association with other medical problems. This article discusses the most recent advances in this field and the implications for patient care. In addition, we consider the challenges facing researchers in this field and emphasise the need for close working relationships between clinicians and researchers.
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Affiliation(s)
- Anna Wilsdon
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Alejandro Sifrim
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | | | - Matthew Hurles
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - J David Brook
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
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247
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Abstract
Aflatoxin B1 (AFB1) is widely distributed in nature, especially in a variety of food commodities. It is confirmed to be the most toxic of all the aflatoxins. The toxicity of AFB1 has been well investigated, and it may result in severe health problems including carcinogenesis, mutagenesis, growth retardation, and immune suppression. Epigenetic modifications including DNA methylation, histone modifications and regulation of non-coding RNA play an important role in AFB1-induced disease and carcinogenesis. To better understand the evidence for AFB1-induced epigenetic alterations and the potential mechanisms of the toxicity of AFB1, we conducted a review of published studies of AFB1-induced epigenetic alterations.
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Affiliation(s)
- Yaqi Dai
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China; Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China
| | - Kunlun Huang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China; Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China; The Supervision, Inspection and Testing Center of Genetically Modified Organisms, Ministry of Agriculture, 100083, Beijing, China
| | - Boyang Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China; Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China
| | - Liye Zhu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China; Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China; Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China; The Supervision, Inspection and Testing Center of Genetically Modified Organisms, Ministry of Agriculture, 100083, Beijing, China.
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248
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Abstract
Over the past two decades there has been a great deal of interest in the development of inhibitors of the cyclin-dependent kinases (CDKs). This attention initially stemmed from observations that different CDK isoforms have key roles in cancer cell proliferation through loss of regulation of the cell cycle, a hallmark feature of cancer. CDKs have now been shown to regulate other processes, particularly various aspects of transcription. The early non-selective CDK inhibitors exhibited considerable toxicity and proved to be insufficiently active in most cancers. The lack of patient selection biomarkers and an absence of understanding of the inhibitory profile required for efficacy hampered the development of these inhibitors. However, the advent of potent isoform-selective inhibitors with accompanying biomarkers has re-ignited interest. Palbociclib, a selective CDK4/6 inhibitor, is now approved for the treatment of ER+/HER2- advanced breast cancer. Current developments in the field include the identification of potent and selective inhibitors of the transcriptional CDKs; these include tool compounds that have allowed exploration of individual CDKs as cancer targets and the determination of their potential therapeutic windows. Biomarkers that allow the selection of patients likely to respond are now being discovered. Drug resistance has emerged as a major hurdle in the clinic for most protein kinase inhibitors and resistance mechanism are beginning to be identified for CDK inhibitors. This suggests that the selective inhibitors may be best used combined with standard of care or other molecularly targeted agents now in development rather than in isolation as monotherapies.
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Affiliation(s)
- Steven R Whittaker
- Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Aurélie Mallinger
- Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, United Kingdom; Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Paul Workman
- Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, United Kingdom; Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Paul A Clarke
- Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, United Kingdom; Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, United Kingdom.
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249
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Chen HR, Juan HC, Wong YH, Tsai JW, Fann MJ. Cdk12 Regulates Neurogenesis and Late-Arising Neuronal Migration in the Developing Cerebral Cortex. Cereb Cortex 2017; 27:2289-2302. [PMID: 27073218 DOI: 10.1093/cercor/bhw081] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA damage response (DDR) pathways are critical for ensuring that replication stress and various types of DNA lesion do not perturb production of neural cells during development. Cdk12 maintains genomic stability by regulating expression of DDR genes. Mutant mice in which Cdk12 is conditionally deleted in neural progenitor cells (NPCs) die after birth and exhibit microcephaly with a thinner cortical plate and an aberrant corpus callosum. We show that NPCs of mutant mice accumulate at G2 and M phase, and have lower expression of DDR genes, more DNA double-strand breaks and increased apoptosis. In addition to there being fewer neurons, there is misalignment of layers IV-II neurons and the presence of abnormal axonal tracts of these neurons, suggesting that Cdk12 is also required for the migration of late-arising cortical neurons. Using in utero electroporation, we demonstrate that the migrating mutant cells remain within the intermediate zone and fail to adopt a bipolar morphology. Overexpression of Cdk5 brings about a partially restoration of the neurons reaching layers IV-II in the mutant mice. Thus, Cdk12 is crucial to the repair of DNA damage during the proliferation of NPCs and is also central to the proper migration of late-arising neurons.
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Affiliation(s)
- Hong-Ru Chen
- Department of Life Sciences and Institute of Genome Sciences.,Brain Research Center
| | - Hsien-Chia Juan
- Department of Life Sciences and Institute of Genome Sciences
| | | | - Jin-Wu Tsai
- Brain Research Center.,Institute of Brain Science, National Yang-Ming University, Taipei, Taiwan 11221, Republic of China
| | - Ming-Ji Fann
- Department of Life Sciences and Institute of Genome Sciences.,Brain Research Center
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250
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Gadducci A, Guerrieri ME. PARP inhibitors alone and in combination with other biological agents in homologous recombination deficient epithelial ovarian cancer: From the basic research to the clinic. Crit Rev Oncol Hematol 2017; 114:153-165. [PMID: 28477743 DOI: 10.1016/j.critrevonc.2017.04.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/15/2017] [Accepted: 04/11/2017] [Indexed: 12/21/2022] Open
Abstract
Hereditary epithelial ovarian cancer [EOC] in germline BRCA mutation (gBRCAm) carriers has a distinct clinical behavior characterized by younger age, high- grade serous histology, advanced stage, visceral distribution of disease, high response to platinum and other non-platinum agents and better clinical outcome. Sporadic EOC with homologous recombination deficiency [HDR] but no gBRCAm has the same biological and clinical behavior as EOC in gBRCAm carriers ("BRCAness"phenotype). Biomarkers are in development to enable an accurate definition of molecular features of BRCAness phenotype, and trials are warranted to determine whether such HDR signature will predict sensitivity to PARP inhibitors in sporadic EOC. Moreover, the link between PARP inhibition and angiogenesis suppression, the immunologic properties of EOC in gBRCAm carriers, the HRD induced by PI3K inhibition in EOC cells in vitro strongly support novel clinical trials testing the combination of PARP inhibitors with other biological agents.
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Affiliation(s)
- Angiolo Gadducci
- Department of Clinical and Experimental Medicine, Division of Gynecology and Obstetrics, University of Pisa, Italy.
| | - Maria Elena Guerrieri
- Department of Clinical and Experimental Medicine, Division of Gynecology and Obstetrics, University of Pisa, Italy
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