201
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Peng J, Yi B, Wang M, Tan J, Huang Z. CRISPR/Cas9-Mediated Whole Genomic Wide Knockout Screening Identifies Specific Genes Associated With PM 2.5-Induced Mineral Absorption in Liver Toxicity. Front Bioeng Biotechnol 2021; 9:669434. [PMID: 34307318 PMCID: PMC8293916 DOI: 10.3389/fbioe.2021.669434] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/03/2021] [Indexed: 12/15/2022] Open
Abstract
PM2.5, also known as fine particles, refers to particulate matter with a dynamic diameter of ≦2.5 μm in air pollutants, that carries metals (Zn, Co, Cd) which can pass through the alveolar epithelium and enter the circulatory system and tissues. PM2.5 can cause serious health problems, such as non-alcoholic fatty liver and hepatocellular carcinoma, although the underlying mechanisms of its toxic effect are poorly understood. Here, we exposed L02 cells to PM2.5 and performed a pooled genome−wide clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) to assess loss of function and identify new potential PM2.5targets. Enrichr and KEGG pathway analyses were performed to identify candidate genes associated with PM2.5 toxicity. Results revealed that four key genes, namely ATPase Na+/K+ transporting subunit alpha 2 (ATP1A2), metallothionein 1M (MT1M), solute carrier family 6 members 19 (SLC6A19) and transient receptor potential cation channel subfamily V member 6 (TRPV6) were associated with PM2.5 toxicity, mainly in regulating the mineral absorption pathway. Downregulating these genes increased cell viability and attenuated apoptosis in cells exposed to PM2.5. Conversely, overexpressing TRPV6 exacerbated cell apoptosis caused by PM2.5, while a reactive oxygen species (ROS) inhibitor N-acetyl-l-cysteine (NAC) alleviated PM2.5-induced apoptosis. In conclusion, ATP1A2, MT1M, SLC6A19 and TRPV6 may be contributing to absorption of metals in PM2.5 thereby inducing apoptosis mediated by ROS. Therefore, they hold potential as therapeutic targets for PM2.5-related diseases.
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Affiliation(s)
- Jinfu Peng
- Center for Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Bin Yi
- Center for Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Mengyao Wang
- Center for Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Jieqiong Tan
- Center for Medical Genetics, Life Science School, Central South University, Changsha, China
| | - Zhijun Huang
- Center for Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, China
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202
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Setton J, Zinda M, Riaz N, Durocher D, Zimmermann M, Koehler M, Reis-Filho JS, Powell SN. Synthetic Lethality in Cancer Therapeutics: The Next Generation. Cancer Discov 2021; 11:1626-1635. [PMID: 33795234 PMCID: PMC8295179 DOI: 10.1158/2159-8290.cd-20-1503] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/01/2021] [Accepted: 02/23/2021] [Indexed: 12/25/2022]
Abstract
Synthetic lethality (SL) provides a conceptual framework for tackling targets that are not classically "druggable," including loss-of-function mutations in tumor suppressor genes required for carcinogenesis. Recent technological advances have led to an inflection point in our understanding of genetic interaction networks and ability to identify a wide array of novel SL drug targets. Here, we review concepts and lessons emerging from first-generation trials aimed at testing SL drugs, discuss how the nature of the targeted lesion can influence therapeutic outcomes, and highlight the need to develop clinical biomarkers distinct from those based on the paradigms developed to target activated oncogenes. SIGNIFICANCE: SL offers an approach for the targeting of loss of function of tumor suppressor and DNA repair genes, as well as of amplification and/or overexpression of genes that cannot be targeted directly. A next generation of tumor-specific alterations targetable through SL has emerged from high-throughput CRISPR technology, heralding not only new opportunities for drug development, but also important challenges in the development of optimal predictive biomarkers.
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Affiliation(s)
- Jeremy Setton
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Nadeem Riaz
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | | | | | - Simon N Powell
- Memorial Sloan Kettering Cancer Center, New York, New York.
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203
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Ding YY, Kim H, Madden K, Loftus JP, Chen GM, Allen DH, Zhang R, Xu J, Chen CH, Hu Y, Tasian SK, Tan K. Network Analysis Reveals Synergistic Genetic Dependencies for Rational Combination Therapy in Philadelphia Chromosome-Like Acute Lymphoblastic Leukemia. Clin Cancer Res 2021; 27:5109-5122. [PMID: 34210682 DOI: 10.1158/1078-0432.ccr-21-0553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/10/2021] [Accepted: 06/25/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Systems biology approaches can identify critical targets in complex cancer signaling networks to inform new therapy combinations that may overcome conventional treatment resistance. EXPERIMENTAL DESIGN We performed integrated analysis of 1,046 childhood B-ALL cases and developed a data-driven network controllability-based approach to identify synergistic key regulator targets in Philadelphia chromosome-like B-acute lymphoblastic leukemia (Ph-like B-ALL), a common high-risk leukemia subtype associated with hyperactive signal transduction and chemoresistance. RESULTS We identified 14 dysregulated network nodes in Ph-like ALL involved in aberrant JAK/STAT, Ras/MAPK, and apoptosis pathways and other critical processes. Genetic cotargeting of the synergistic key regulator pair STAT5B and BCL2-associated athanogene 1 (BAG1) significantly reduced leukemia cell viability in vitro. Pharmacologic inhibition with dual small molecule inhibitor therapy targeting this pair of key nodes further demonstrated enhanced antileukemia efficacy of combining the BCL-2 inhibitor venetoclax with the tyrosine kinase inhibitors ruxolitinib or dasatinib in vitro in human Ph-like ALL cell lines and in vivo in multiple childhood Ph-like ALL patient-derived xenograft models. Consistent with network controllability theory, co-inhibitor treatment also shifted the transcriptomic state of Ph-like ALL cells to become less like kinase-activated BCR-ABL1-rearranged (Ph+) B-ALL and more similar to prognostically favorable childhood B-ALL subtypes. CONCLUSIONS Our study represents a powerful conceptual framework for combinatorial drug discovery based on systematic interrogation of synergistic vulnerability pathways with pharmacologic inhibitor validation in preclinical human leukemia models.
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Affiliation(s)
- Yang-Yang Ding
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Hannah Kim
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania
| | - Kellyn Madden
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Joseph P Loftus
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Gregory M Chen
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - David Hottman Allen
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Ruitao Zhang
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jason Xu
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Chia-Hui Chen
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Yuxuan Hu
- School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, China
| | - Sarah K Tasian
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania. .,Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kai Tan
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania. .,Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
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204
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Yu LY, Tseng TJ, Lin HC, Hsu CL, Lu TX, Tsai CJ, Lin YC, Chu I, Peng CT, Chen HJ, Tsai FC. Synthetic dysmobility screen unveils an integrated STK40-YAP-MAPK system driving cell migration. SCIENCE ADVANCES 2021; 7:eabg2106. [PMID: 34321207 PMCID: PMC8318371 DOI: 10.1126/sciadv.abg2106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 06/10/2021] [Indexed: 05/05/2023]
Abstract
Integrating signals is essential for cell survival, leading to the concept of synthetic lethality. However, how signaling is integrated to control cell migration remains unclear. By conducting a "two-hit" screen, we revealed the synergistic reduction of cell migration when serine-threonine kinase 40 (STK40) and mitogen-activated protein kinase (MAPK) were simultaneously suppressed. Single-cell analyses showed that STK40 knockdown reduced cell motility and coordination by strengthening focal adhesion (FA) complexes. Furthermore, STK40 knockdown reduced the stability of yes-associated protein (YAP) and subsequently decreased YAP transported into the nucleus, while MAPK inhibition further weakened YAP activities in the nucleus to disturb FA remodeling. Together, we unveiled an integrated STK40-YAP-MAPK system regulating cell migration and introduced "synthetic dysmobility" as a novel strategy to collaboratively control cell migration.
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Affiliation(s)
- Ling-Yea Yu
- Department of Pharmacology, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Ting-Jen Tseng
- Department of Pharmacology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Hsuan-Chao Lin
- Department of Immunology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chi-Lin Hsu
- Department of Pharmacology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ting-Xuan Lu
- Department of Pharmacology, National Taiwan University College of Medicine, Taipei, Taiwan
- Ph.D. Program in Biological Sciences, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Chia-Jung Tsai
- Department of Pharmacology, National Taiwan University College of Medicine, Taipei, Taiwan
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Japan
| | - Yu-Chiao Lin
- Department of Pharmacology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - I Chu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Tzu Peng
- Department of Pharmacology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Hou-Jen Chen
- Department of Pharmacology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Feng-Chiao Tsai
- Department of Pharmacology, National Taiwan University College of Medicine, Taipei, Taiwan.
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
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205
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Chambers CR, Ritchie S, Pereira BA, Timpson P. Overcoming the senescence-associated secretory phenotype (SASP): a complex mechanism of resistance in the treatment of cancer. Mol Oncol 2021; 15:3242-3255. [PMID: 34137158 PMCID: PMC8637570 DOI: 10.1002/1878-0261.13042] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/06/2021] [Accepted: 06/16/2021] [Indexed: 01/10/2023] Open
Abstract
Senescence is a cellular state in which cells undergo persistent cell cycle arrest in response to nonlethal stress. In the treatment of cancer, senescence induction is a potent method of suppressing tumour cell proliferation. In spite of this, senescent cancer cells and adjacent nontransformed cells of the tumour microenvironment can remain metabolically active, resulting in paradoxical secretion of pro-inflammatory factors, collectively termed the senescence-associated secretory phenotype (SASP). The SASP plays a critical role in tumorigenesis, affecting numerous processes including invasion, metastasis, epithelial-to-mesenchymal transition (EMT) induction, therapy resistance and immunosuppression. With increasing evidence, it is becoming clear that cell type, tissue of origin and the primary cellular stressor are key determinants in how the SASP will influence tumour development and progression, including whether it will be pro- or antitumorigenic. In this review, we will focus on recent evidence regarding therapy-induced senescence (TIS) from anticancer agents, including chemotherapy, radiation, immunotherapy, and targeted therapies, and how each therapy can trigger the SASP, which in turn influences treatment efficacy. We will also discuss novel pharmacological manipulation of senescent cancer cells and the SASP, which offers an exciting and contemporary approach to cancer therapeutics. With future research, these adjuvant options may help to mitigate many of the negative side effects and protumorigenic roles that are currently associated with TIS in cancer.
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Affiliation(s)
- Cecilia R Chambers
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Sydney, NSW, Australia.,Faculty of Medicine, St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Shona Ritchie
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Sydney, NSW, Australia.,Faculty of Medicine, St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Brooke A Pereira
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Sydney, NSW, Australia.,Faculty of Medicine, St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Paul Timpson
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Sydney, NSW, Australia.,Faculty of Medicine, St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
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206
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Navarro-Carrasco E, Lazo PA. VRK1 Depletion Facilitates the Synthetic Lethality of Temozolomide and Olaparib in Glioblastoma Cells. Front Cell Dev Biol 2021; 9:683038. [PMID: 34195200 PMCID: PMC8237761 DOI: 10.3389/fcell.2021.683038] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/13/2021] [Indexed: 12/12/2022] Open
Abstract
Background Glioblastomas treated with temozolomide frequently develop resistance to pharmacological treatments. Therefore, there is a need to find alternative drug targets to reduce treatment resistance based on tumor dependencies. A possibility is to target simultaneously two proteins from different DNA-damage repair pathways to facilitate tumor cell death. Therefore, we tested whether targeting the human chromatin kinase VRK1 by RNA interference can identify this protein as a novel molecular target to reduce the dependence on temozolomide in combination with olaparib, based on synthetic lethality. Materials and Methods Depletion of VRK1, an enzyme that regulates chromatin dynamic reorganization and facilitates resistance to DNA damage, was performed in glioblastoma cells treated with temozolomide, an alkylating agent used for GBM treatment; and olaparib, an inhibitor of PARP-1, used as sensitizer. Two genetically different human glioblastoma cell lines, LN-18 and LN-229, were used for these experiments. The effect on the DNA-damage response was followed by determination of sequential steps in this process: H4K16ac, γH2AX, H4K20me2, and 53BP1. Results The combination of temozolomide and olaparib increased DNA damage detected by labeling free DNA ends, and chromatin relaxation detected by H4K16ac. The combination of both drugs, at lower doses, resulted in an increase in the DNA damage response detected by the formation of γH2AX and 53BP1 foci. VRK1 depletion did not prevent the generation of DNA damage in TUNEL assays, but significantly impaired the DNA damage response induced by temozolomide and olaparib, and mediated by γH2AX, H4K20me2, and 53BP1. The combination of these drugs in VRK1 depleted cells resulted in an increase of glioblastoma cell death detected by annexin V and the processing of PARP-1 and caspase-3. Conclusion Depletion of the chromatin kinase VRK1 promotes tumor cell death at lower doses of a combination of temozolomide and olaparib treatments, and can be a novel alternative target for therapies based on synthetic lethality.
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Affiliation(s)
- Elena Navarro-Carrasco
- Molecular Mechanisms of Cancer Program, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Salamanca, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca-IBSAL, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Pedro A Lazo
- Molecular Mechanisms of Cancer Program, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Salamanca, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca-IBSAL, Hospital Universitario de Salamanca, Salamanca, Spain
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207
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Waters AM, Khatib TO, Papke B, Goodwin CM, Hobbs GA, Diehl JN, Yang R, Edwards AC, Walsh KH, Sulahian R, McFarland JM, Kapner KS, Gilbert TSK, Stalnecker CA, Javaid S, Barkovskaya A, Grover KR, Hibshman PS, Blake DR, Schaefer A, Nowak KM, Klomp JE, Hayes TK, Kassner M, Tang N, Tanaseichuk O, Chen K, Zhou Y, Kalkat M, Herring LE, Graves LM, Penn LZ, Yin HH, Aguirre AJ, Hahn WC, Cox AD, Der CJ. Targeting p130Cas- and microtubule-dependent MYC regulation sensitizes pancreatic cancer to ERK MAPK inhibition. Cell Rep 2021; 35:109291. [PMID: 34192548 PMCID: PMC8340308 DOI: 10.1016/j.celrep.2021.109291] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 01/31/2021] [Accepted: 06/03/2021] [Indexed: 12/28/2022] Open
Abstract
To identify therapeutic targets for KRAS mutant pancreatic cancer, we conduct a druggable genome small interfering RNA (siRNA) screen and determine that suppression of BCAR1 sensitizes pancreatic cancer cells to ERK inhibition. Integrative analysis of genome-scale CRISPR-Cas9 screens also identify BCAR1 as a top synthetic lethal interactor with mutant KRAS. BCAR1 encodes the SRC substrate p130Cas. We determine that SRC-inhibitor-mediated suppression of p130Cas phosphorylation impairs MYC transcription through a DOCK1-RAC1-β-catenin-dependent mechanism. Additionally, genetic suppression of TUBB3, encoding the βIII-tubulin subunit of microtubules, or pharmacological inhibition of microtubule function decreases levels of MYC protein in a calpain-dependent manner and potently sensitizes pancreatic cancer cells to ERK inhibition. Accordingly, the combination of a dual SRC/tubulin inhibitor with an ERK inhibitor cooperates to reduce MYC protein and synergistically suppress the growth of KRAS mutant pancreatic cancer. Thus, we demonstrate that mechanistically diverse combinations with ERK inhibition suppress MYC to impair pancreatic cancer proliferation.
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Affiliation(s)
- Andrew M Waters
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tala O Khatib
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bjoern Papke
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Craig M Goodwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - G Aaron Hobbs
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - J Nathaniel Diehl
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Runying Yang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - A Cole Edwards
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Rita Sulahian
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Kevin S Kapner
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Thomas S K Gilbert
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; UNC Michael Hooker Proteomics Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Clint A Stalnecker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sehrish Javaid
- Oral and Craniofacial Biomedicine PhD Program, School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Anna Barkovskaya
- Institute for Cancer Research, Oslo University Hospital, Oslo 0379, Norway
| | - Kajal R Grover
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Priya S Hibshman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Devon R Blake
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Antje Schaefer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Katherine M Nowak
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jennifer E Klomp
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tikvah K Hayes
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michelle Kassner
- Cancer and Cell Biology Division, Translational Genomic Research Institute, Phoenix, AZ 85004, USA
| | - Nanyun Tang
- Cancer and Cell Biology Division, Translational Genomic Research Institute, Phoenix, AZ 85004, USA
| | - Olga Tanaseichuk
- Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Kaisheng Chen
- Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Yingyao Zhou
- Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Manpreet Kalkat
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5S, Canada
| | - Laura E Herring
- UNC Michael Hooker Proteomics Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lee M Graves
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Linda Z Penn
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5S, Canada
| | - Hongwei H Yin
- Cancer and Cell Biology Division, Translational Genomic Research Institute, Phoenix, AZ 85004, USA
| | - Andrew J Aguirre
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02215, USA; Brigham and Women's Hospital, Boston, MA 02215, USA
| | - William C Hahn
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02215, USA; Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Adrienne D Cox
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Oral and Craniofacial Biomedicine PhD Program, School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Channing J Der
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Oral and Craniofacial Biomedicine PhD Program, School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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208
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Zhong L, Li Y, Xiong L, Wang W, Wu M, Yuan T, Yang W, Tian C, Miao Z, Wang T, Yang S. Small molecules in targeted cancer therapy: advances, challenges, and future perspectives. Signal Transduct Target Ther 2021; 6:201. [PMID: 34054126 PMCID: PMC8165101 DOI: 10.1038/s41392-021-00572-w] [Citation(s) in RCA: 595] [Impact Index Per Article: 198.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/23/2021] [Accepted: 03/15/2021] [Indexed: 02/07/2023] Open
Abstract
Due to the advantages in efficacy and safety compared with traditional chemotherapy drugs, targeted therapeutic drugs have become mainstream cancer treatments. Since the first tyrosine kinase inhibitor imatinib was approved to enter the market by the US Food and Drug Administration (FDA) in 2001, an increasing number of small-molecule targeted drugs have been developed for the treatment of malignancies. By December 2020, 89 small-molecule targeted antitumor drugs have been approved by the US FDA and the National Medical Products Administration (NMPA) of China. Despite great progress, small-molecule targeted anti-cancer drugs still face many challenges, such as a low response rate and drug resistance. To better promote the development of targeted anti-cancer drugs, we conducted a comprehensive review of small-molecule targeted anti-cancer drugs according to the target classification. We present all the approved drugs as well as important drug candidates in clinical trials for each target, discuss the current challenges, and provide insights and perspectives for the research and development of anti-cancer drugs.
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Affiliation(s)
- Lei Zhong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, People's Republic of China
| | - Yueshan Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Liang Xiong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Wenjing Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Ming Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Ting Yuan
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, People's Republic of China
| | - Wei Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Chenyu Tian
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Zhuang Miao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Tianqi Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Shengyong Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.
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209
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Alessandrini I, Recagni M, Zaffaroni N, Folini M. On the Road to Fight Cancer: The Potential of G-quadruplex Ligands as Novel Therapeutic Agents. Int J Mol Sci 2021; 22:5947. [PMID: 34073075 PMCID: PMC8198608 DOI: 10.3390/ijms22115947] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/27/2021] [Accepted: 05/27/2021] [Indexed: 12/14/2022] Open
Abstract
Nucleic acid sequences able to adopt a G-quadruplex conformation are overrepresented within the human genome. This evidence strongly suggests that these genomic regions have been evolutionary selected to play a pivotal role in several aspects of cell biology. In the present review article, we provide an overview on the biological impact of targeting G-quadruplexes in cancer. A variety of small molecules showing good G-quadruplex stabilizing properties has been reported to exert an antitumor activity in several preclinical models of human cancers. Moreover, promiscuous binders and multiple targeting G-quadruplex ligands, cancer cell defense responses and synthetic lethal interactions of G-quadruplex targeting have been also highlighted. Overall, evidence gathered thus far indicates that targeting G-quadruplex may represent an innovative and fascinating therapeutic approach for cancer. The continued methodological improvements, the development of specific tools and a careful consideration of the experimental settings in living systems will be useful to deepen our knowledge of G-quadruplex biology in cancer, to better define their role as therapeutic targets and to help design and develop novel and reliable G-quadruplex-based anticancer strategies.
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Affiliation(s)
| | | | | | - Marco Folini
- Molecular Pharmacology Unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via G.A. Amadeo 42, 20133 Milan, Italy; (I.A.); (M.R.); (N.Z.)
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210
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Guccione E, Schwarz M, Di Tullio F, Mzoughi S. Cancer synthetic vulnerabilities to protein arginine methyltransferase inhibitors. Curr Opin Pharmacol 2021; 59:33-42. [PMID: 34052526 DOI: 10.1016/j.coph.2021.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/16/2021] [Indexed: 12/17/2022]
Abstract
Protein arginine methylation is an abundant post-translational modification involved in the modulation of essential cellular processes ranging from transcription, post-transcriptional RNA metabolism, and propagation of signaling cascades to the regulation of the DNA damage response. Excitingly for the field, in the past few years there have been remarkable advances in the development of molecular tools and clinical compounds able to selectively and potently inhibit protein arginine methyltransferase (PRMT) functions. In this review, we first discuss how the somatic mutations that confer advantages to cancer cells are often associated with vulnerabilities that can be exploited by PRMTs' inhibition. In a second part, we discuss strategies to uncover synthetic lethal combinations between existing therapies and PRMT inhibitors.
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Affiliation(s)
- Ernesto Guccione
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Megan Schwarz
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Federico Di Tullio
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Slim Mzoughi
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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211
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Pinoli P, Srihari S, Wong L, Ceri S. Identifying collateral and synthetic lethal vulnerabilities within the DNA-damage response. BMC Bioinformatics 2021; 22:250. [PMID: 33992077 PMCID: PMC8126165 DOI: 10.1186/s12859-021-04168-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 04/27/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND A pair of genes is defined as synthetically lethal if defects on both cause the death of the cell but a defect in only one of the two is compatible with cell viability. Ideally, if A and B are two synthetic lethal genes, inhibiting B should kill cancer cells with a defect on A, and should have no effects on normal cells. Thus, synthetic lethality can be exploited for highly selective cancer therapies, which need to exploit differences between normal and cancer cells. RESULTS In this paper, we present a new method for predicting synthetic lethal (SL) gene pairs. As neighbouring genes in the genome have highly correlated profiles of copy number variations (CNAs), our method clusters proximal genes with a similar CNA profile, then predicts mutually exclusive group pairs, and finally identifies the SL gene pairs within each group pairs. For mutual-exclusion testing we use a graph-based method which takes into account the mutation frequencies of different subjects and genes. We use two different methods for selecting the pair of SL genes; the first is based on the gene essentiality measured in various conditions by means of the "Gene Activity Ranking Profile" GARP score; the second leverages the annotations of gene to biological pathways. CONCLUSIONS This method is unique among current SL prediction approaches, it reduces false-positive SL predictions compared to previous methods, and it allows establishing explicit collateral lethality relationship of gene pairs within mutually exclusive group pairs.
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Affiliation(s)
- Pietro Pinoli
- Department of Electronic, Information and Bioengineering, Politecnico di Milano, Piazza Leonardo da Vinci 32, Milan, Italy
| | - Sriganesh Srihari
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Limsoon Wong
- School of Computing, National University of Singapore, Computing Drive 13, Singapore, Singapore
| | - Stefano Ceri
- Department of Electronic, Information and Bioengineering, Politecnico di Milano, Piazza Leonardo da Vinci 32, Milan, Italy
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212
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Sharp MF, Bythell-Douglas R, Deans AJ, Crismani W. The Fanconi anemia ubiquitin E3 ligase complex as an anti-cancer target. Mol Cell 2021; 81:2278-2289. [PMID: 33984284 DOI: 10.1016/j.molcel.2021.04.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/27/2021] [Accepted: 04/21/2021] [Indexed: 10/21/2022]
Abstract
Agents that induce DNA damage can cure some cancers. However, the side effects of chemotherapy are severe because of the indiscriminate action of DNA-damaging agents on both healthy and cancerous cells. DNA repair pathway inhibition provides a less toxic and targeted alternative to chemotherapy. A compelling DNA repair target is the Fanconi anemia (FA) E3 ligase core complex due to its critical-and likely singular-role in the efficient removal of specific DNA lesions. FA pathway inactivation has been demonstrated to specifically kill some types of cancer cells without the addition of exogenous DNA damage, including cells that lack BRCA1, BRCA2, ATM, or functionally related genes. In this perspective, we discuss the genetic and biochemical evidence in support of the FA core complex as a compelling drug target for cancer therapy. In particular, we discuss the genetic, biochemical, and structural data that could rapidly advance our capacity to identify and implement the use of FA core complex inhibitors in the clinic.
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Affiliation(s)
- Michael F Sharp
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC, Australia
| | - Rohan Bythell-Douglas
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC, Australia
| | - Andrew J Deans
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC, Australia; Department of Medicine (St. Vincent's), University of Melbourne, Fitzroy, VIC, Australia
| | - Wayne Crismani
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC, Australia; Department of Medicine (St. Vincent's), University of Melbourne, Fitzroy, VIC, Australia.
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213
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Ekeke CN, Russell KL, Joubert K, Bartlett DL, Luketich JD, Soloff AC, Guo ZS, Lotze MT, Dhupar R. Fighting Fire With Fire: Oncolytic Virotherapy for Thoracic Malignancies. Ann Surg Oncol 2021; 28:2715-2727. [PMID: 33575873 PMCID: PMC8043873 DOI: 10.1245/s10434-020-09477-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/02/2020] [Indexed: 12/24/2022]
Abstract
Thoracic malignancies are associated with high mortality rates. Conventional therapy for many of the patients with thoracic malignancies is obviated by a high incidence of locoregional recurrence and distant metastasis. Fortunately, developments in immunotherapy provide effective strategies for both local and systemic treatments that have rapidly advanced during the last decade. One promising approach to cancer immunotherapy is to use oncolytic viruses, which have the advantages of relatively high tumor specificity, selective replication-mediated oncolysis, enhanced antigen presentation, and potential for delivery of immunogenic payloads such as cytokines, with subsequent elicitation of effective antitumor immunity. Several oncolytic viruses including adenovirus, coxsackievirus B3, herpes virus, measles virus, reovirus, and vaccinia virus have been developed and applied to thoracic cancers in preclinical murine studies and clinical trials. This review discusses the current state of oncolytic virotherapy in lung cancer, esophageal cancer, and metastatic malignant pleural effusions and considers its potential as an emergent therapeutic for these patients.
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Affiliation(s)
- Chigozirim N Ekeke
- Department of Cardiothoracic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kira L Russell
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kyla Joubert
- Department of Cardiothoracic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - David L Bartlett
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - James D Luketich
- Department of Cardiothoracic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Adam C Soloff
- Department of Cardiothoracic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Zong Sheng Guo
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Michael T Lotze
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Departments of Immunology and Bioengineering, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Rajeev Dhupar
- Department of Cardiothoracic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Veterans Affairs Pittsburgh Healthcare System, Surgical Services Division, Pittsburgh, PA, USA.
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214
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Gallage S, García-Beccaria M, Szydlowska M, Rahbari M, Mohr R, Tacke F, Heikenwalder M. The therapeutic landscape of hepatocellular carcinoma. MED 2021; 2:505-552. [DOI: 10.1016/j.medj.2021.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/23/2021] [Accepted: 03/11/2021] [Indexed: 02/07/2023]
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215
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Saavedra-García P, Roman-Trufero M, Al-Sadah HA, Blighe K, López-Jiménez E, Christoforou M, Penfold L, Capece D, Xiong X, Miao Y, Parzych K, Caputo VS, Siskos AP, Encheva V, Liu Z, Thiel D, Kaiser MF, Piazza P, Chaidos A, Karadimitris A, Franzoso G, Snijders AP, Keun HC, Oyarzún DA, Barahona M, Auner HW. Systems level profiling of chemotherapy-induced stress resolution in cancer cells reveals druggable trade-offs. Proc Natl Acad Sci U S A 2021; 118:e2018229118. [PMID: 33883278 PMCID: PMC8092411 DOI: 10.1073/pnas.2018229118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cancer cells can survive chemotherapy-induced stress, but how they recover from it is not known. Using a temporal multiomics approach, we delineate the global mechanisms of proteotoxic stress resolution in multiple myeloma cells recovering from proteasome inhibition. Our observations define layered and protracted programs for stress resolution that encompass extensive changes across the transcriptome, proteome, and metabolome. Cellular recovery from proteasome inhibition involved protracted and dynamic changes of glucose and lipid metabolism and suppression of mitochondrial function. We demonstrate that recovering cells are more vulnerable to specific insults than acutely stressed cells and identify the general control nonderepressable 2 (GCN2)-driven cellular response to amino acid scarcity as a key recovery-associated vulnerability. Using a transcriptome analysis pipeline, we further show that GCN2 is also a stress-independent bona fide target in transcriptional signature-defined subsets of solid cancers that share molecular characteristics. Thus, identifying cellular trade-offs tied to the resolution of chemotherapy-induced stress in tumor cells may reveal new therapeutic targets and routes for cancer therapy optimization.
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Affiliation(s)
- Paula Saavedra-García
- Cancer Cell Protein Metabolism, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, United Kingdom
- The Hugh and Josseline Langmuir Centre for Myeloma Research, Imperial College London, London W12 0NN, United Kingdom
| | - Monica Roman-Trufero
- Cancer Cell Protein Metabolism, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, United Kingdom
- The Hugh and Josseline Langmuir Centre for Myeloma Research, Imperial College London, London W12 0NN, United Kingdom
| | - Hibah A Al-Sadah
- Cancer Cell Protein Metabolism, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, United Kingdom
- The Hugh and Josseline Langmuir Centre for Myeloma Research, Imperial College London, London W12 0NN, United Kingdom
| | - Kevin Blighe
- Clinical Bioinformatics Research, London W1B 3HH, United Kingdom
| | - Elena López-Jiménez
- Cancer Cell Protein Metabolism, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, United Kingdom
- The Hugh and Josseline Langmuir Centre for Myeloma Research, Imperial College London, London W12 0NN, United Kingdom
| | - Marilena Christoforou
- Cancer Cell Protein Metabolism, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, United Kingdom
- The Hugh and Josseline Langmuir Centre for Myeloma Research, Imperial College London, London W12 0NN, United Kingdom
| | - Lucy Penfold
- Cancer Cell Protein Metabolism, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, United Kingdom
- Cellular Stress, MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom
| | - Daria Capece
- Centre for Molecular Immunology and Inflammation, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, United Kingdom
| | - Xiaobei Xiong
- Cancer Cell Protein Metabolism, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, United Kingdom
- The Hugh and Josseline Langmuir Centre for Myeloma Research, Imperial College London, London W12 0NN, United Kingdom
| | - Yirun Miao
- Cancer Cell Protein Metabolism, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, United Kingdom
- The Hugh and Josseline Langmuir Centre for Myeloma Research, Imperial College London, London W12 0NN, United Kingdom
| | - Katarzyna Parzych
- Cancer Cell Protein Metabolism, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, United Kingdom
| | - Valentina S Caputo
- The Hugh and Josseline Langmuir Centre for Myeloma Research, Imperial College London, London W12 0NN, United Kingdom
| | - Alexandros P Siskos
- Department of Surgery and Cancer, Imperial College London, London W12 0NN, United Kingdom
| | - Vesela Encheva
- Proteomics Platform, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Zijing Liu
- Department of Mathematics, Imperial College London, London SW7 2AZ, United Kingdom
- Department of Brain Sciences, Imperial College London, London W12 0NN, United Kingdom
- UK Dementia Research Institute at Imperial College, London W12 0NN, United Kingdom
| | - Denise Thiel
- Department of Mathematics, Imperial College London, London SW7 2AZ, United Kingdom
| | - Martin F Kaiser
- Myeloma Molecular Therapy, The Institute of Cancer Research, Sutton SW7 3RP, United Kingdom
| | - Paolo Piazza
- Imperial BRC Genomics Facility, Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, United Kingdom
| | - Aristeidis Chaidos
- The Hugh and Josseline Langmuir Centre for Myeloma Research, Imperial College London, London W12 0NN, United Kingdom
| | - Anastasios Karadimitris
- The Hugh and Josseline Langmuir Centre for Myeloma Research, Imperial College London, London W12 0NN, United Kingdom
| | - Guido Franzoso
- Centre for Molecular Immunology and Inflammation, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, United Kingdom
| | - Ambrosius P Snijders
- Proteomics Platform, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Hector C Keun
- Department of Surgery and Cancer, Imperial College London, London W12 0NN, United Kingdom
| | - Diego A Oyarzún
- School of Informatics, The University of Edinburgh, Edinburgh EH8 9AB, United Kingdom
- School of Biological Sciences, The University of Edinburgh, Edinburgh EH8 9AB, United Kingdom
| | - Mauricio Barahona
- Department of Mathematics, Imperial College London, London SW7 2AZ, United Kingdom
| | - Holger W Auner
- Cancer Cell Protein Metabolism, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, United Kingdom;
- The Hugh and Josseline Langmuir Centre for Myeloma Research, Imperial College London, London W12 0NN, United Kingdom
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216
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Overexpression of lncRNA SNGH3 Predicts Unfavorable Prognosis and Clinical Outcomes in Human Cancers: Evidence from a Meta-Analysis. BIOMED RESEARCH INTERNATIONAL 2021; 2020:7974034. [PMID: 32802874 PMCID: PMC7335396 DOI: 10.1155/2020/7974034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/23/2020] [Accepted: 05/28/2020] [Indexed: 12/22/2022]
Abstract
Long noncoding RNAs (lncRNAs) have been confirmed to play a crucial role in human disease, especially in tumor development and progression. Small nucleolar RNA host gene (SNHG3), a newly identified lncRNA, has been found dysregulated in various cancers. Nevertheless, the results remain controversial. Thus, we aim to analyze the comprehensive data to elaborate the association between SNHG3 expression and clinical outcomes in multiple cancers. We searched PubMed, Web of Science, Cochrane Library, Embase, and MEDLINE database to identify eligible articles. STATA software was applied to calculate the hazard ratio (HR) and odds ratio (OR) with 95% confidence interval (95% CI) for survival outcomes and clinical parameters, respectively. Besides, the data from The Cancer Genome Atlas (TCGA) dataset was extracted to verify the results in our meta-analysis. There were thirteen studies totaling 919 cancer patients involved in this meta-analysis. The results demonstrated that high SNHG3 expression was significantly associated with poor overall survival (OS) (HR = 2.53, 95% CI: 1.94-3.31) in cancers, disease-free survival (DFS) (HR = 3.89, 95% CI: 1.34-11.3), and recurrence-free survival (RFS) (HR = 2.42, 95% CI: 1.14-5.15) in hepatocellular carcinoma. Analysis stratified by analysis method, sample size, follow-up time, and cancer type further verified the prognostic value of SNHG3. Additionally, patients with high SNHG3 expression tended to have more advanced clinical stage, higher histological grade, earlier distant metastasis, and earlier lymph node metastasis. Excavation of TCGA dataset valuated that SNHG3 was upregulated in various cancers and predicted worse OS and DFS. Overexpressed SNHG3 was strongly associated with poor survival and clinical outcomes in human cancers and therefore can serve as a promising biomarker for predicting patients' prognosis.
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217
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Chang L, Ruiz P, Ito T, Sellers WR. Targeting pan-essential genes in cancer: Challenges and opportunities. Cancer Cell 2021; 39:466-479. [PMID: 33450197 PMCID: PMC8157671 DOI: 10.1016/j.ccell.2020.12.008] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/02/2020] [Accepted: 12/09/2020] [Indexed: 12/22/2022]
Abstract
Despite remarkable successes in the clinic, cancer targeted therapy development remains challenging and the failure rate is disappointingly high. This problem is partly due to the misapplication of the targeted therapy paradigm to therapeutics targeting pan-essential genes, which can result in therapeutics whereby efficacy is attenuated by dose-limiting toxicity. Here we summarize the key features of successful chemotherapy and targeted therapy agents, and use case studies to outline recurrent challenges to drug development efforts targeting pan-essential genes. Finally, we suggest strategies to avoid previous pitfalls for ongoing and future development of pan-essential therapeutics.
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Affiliation(s)
- Liang Chang
- Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paloma Ruiz
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Takahiro Ito
- Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - William R Sellers
- Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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218
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Gonzalez-Leal C, Ladurner AG. A triskelion of nucleic acids drives protein aggregation in A-T. Mol Cell 2021; 81:1367-1369. [PMID: 33798413 DOI: 10.1016/j.molcel.2021.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Mutations in ataxia telangiectasia mutated (ATM) kinase lead to cerebellar neurodegeneration. In this issue of Molecular Cell, Lee et al. (2021) revealed how transcription-induced reactive oxygen species and DNA-RNA hybrids activate PARP enzymes, generating the nucleic acid poly-ADP-ribose, which promotes the accumulation of protein aggregates in A-T-like disorders.
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Affiliation(s)
- Claudia Gonzalez-Leal
- Department of Physiological Chemistry, Biomedical Center, Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany; International Max Planck Research School for Molecular Life Sciences, 82152 Planegg-Martinsried, Germany
| | - Andreas G Ladurner
- Department of Physiological Chemistry, Biomedical Center, Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany; International Max Planck Research School for Molecular Life Sciences, 82152 Planegg-Martinsried, Germany; Eisbach Bio GmbH, Am Klopferspitz 19, 82152 Planegg-Martinsried, Germany.
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219
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Breslauer KJ. The shaping of a molecular linguist: How a career studying DNA energetics revealed the language of molecular communication. J Biol Chem 2021; 296:100522. [PMID: 34237886 PMCID: PMC8058554 DOI: 10.1016/j.jbc.2021.100522] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 01/31/2023] Open
Abstract
My personal and professional journeys have been far from predictable based on my early childhood. Owing to a range of serendipitous influences, I miraculously transitioned from a rebellious, apathetic teenage street urchin who did poorly in school to a highly motivated, disciplined, and ambitious academic honors student. I was the proverbial “late bloomer.” Ultimately, I earned my PhD in biophysical chemistry at Yale, followed by a postdoc fellowship at Berkeley. These two meccas of thermodynamics, coupled with my deep fascination with biology, instilled in me a passion to pursue an academic career focused on mapping the energy landscapes of biological systems. I viewed differential energetics as the language of molecular communication that would dictate and control biological structures, as well as modulate the modes of action associated with biological functions. I wanted to be a “molecular linguist.” For the next 50 years, my group and I used a combination of spectroscopic and calorimetric techniques to characterize the energy profiles of the polymorphic conformational space of DNA molecules, their differential ligand-binding properties, and the energy landscapes associated with mutagenic DNA damage recognition, repair, and replication. As elaborated below, the resultant energy databases have enabled the development of quantitative molecular biology through the rational design of primers, probes, and arrays for diagnostic, therapeutic, and molecular-profiling protocols, which collectively have contributed to a myriad of biomedical assays. Such profiling is further justified by yielding unique energy-based insights that complement and expand elegant, structure-based understandings of biological processes.
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Affiliation(s)
- Kenneth J Breslauer
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA; The Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA.
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220
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Research Techniques Made Simple: Preclinical Development of Combination Antitumor Targeted Therapies in Dermatology. J Invest Dermatol 2021; 140:2319-2325.e1. [PMID: 33222758 DOI: 10.1016/j.jid.2020.09.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/24/2020] [Accepted: 09/01/2020] [Indexed: 10/22/2022]
Abstract
The identification and application of targeted therapies that inhibit critical pathways in malignant cells have shown tremendous promise for improving clinical outcomes for patients with advanced cutaneous malignancies. However, tumor cell heterogeneity, development of drug resistance, and risks of off-target effects remain barriers to prolonged remission and definitive cure. Herein, we describe the potential that combinations of antitumor targeted agents may offer in overcoming these challenges and detail techniques whereby promising combination regimens can be identified and further evaluated preclinically. Cancer cell lines and primary patient-derived malignant cells can be utilized to perform dose-response screenings in vitro for individual targeted agents before moving toward the evaluation of potential synergistic combinations. Mathematical analyses, including the Chou-Talalay method, determine combination indices and Hill slopes that permit relative comparisons among various drug combinations by quantification of synergistic activities. Further preclinical in vivo evaluation of promising single versus combination regimens may be studied in relevant mouse models of cutaneous malignancy. Ultimately, the formulation of combination targeted therapy regimens may be more broadly effective and less toxic, helping to better inform clinical trial design and prioritization.
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221
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Castells-Roca L, Tejero E, Rodríguez-Santiago B, Surrallés J. CRISPR Screens in Synthetic Lethality and Combinatorial Therapies for Cancer. Cancers (Basel) 2021; 13:1591. [PMID: 33808217 PMCID: PMC8037779 DOI: 10.3390/cancers13071591] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 12/26/2022] Open
Abstract
Cancer is a complex disease resulting from the accumulation of genetic dysfunctions. Tumor heterogeneity causes the molecular variety that divergently controls responses to chemotherapy, leading to the recurrent problem of cancer reappearance. For many decades, efforts have focused on identifying essential tumoral genes and cancer driver mutations. More recently, prompted by the clinical success of the synthetic lethality (SL)-based therapy of the PARP inhibitors in homologous recombinant deficient tumors, scientists have centered their novel research on SL interactions (SLI). The state of the art to find new genetic interactions are currently large-scale forward genetic CRISPR screens. CRISPR technology has rapidly evolved to be a common tool in the vast majority of laboratories, as tools to implement CRISPR screen protocols are available to all researchers. Taking advantage of SLI, combinatorial therapies have become the ultimate model to treat cancer with lower toxicity, and therefore better efficiency. This review explores the CRISPR screen methodology, integrates the up-to-date published findings on CRISPR screens in the cancer field and proposes future directions to uncover cancer regulation and individual responses to chemotherapy.
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Affiliation(s)
- Laia Castells-Roca
- Genome Instability and DNA Repair Syndromes Group, Sant Pau Biomedical Research Institute (IIB Sant Pau) and Join Unit UAB-IR Sant Pau on Genomic Medicine, 08041 Barcelona, Spain
- Genetics Department, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain;
- Genetics and Microbiology Department, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Eudald Tejero
- Sant Pau Biomedical Research Institute (IIB Sant Pau), 08041 Barcelona, Spain;
| | - Benjamín Rodríguez-Santiago
- Genetics Department, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain;
- Center for Biomedical Network Research on Rare Diseases (CIBERER) and Sant Pau Biomedical Research Institute (IIB Sant Pau), 08041 Barcelona, Spain
| | - Jordi Surrallés
- Genome Instability and DNA Repair Syndromes Group, Sant Pau Biomedical Research Institute (IIB Sant Pau) and Join Unit UAB-IR Sant Pau on Genomic Medicine, 08041 Barcelona, Spain
- Genetics Department, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain;
- Genetics and Microbiology Department, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER) and Sant Pau Biomedical Research Institute (IIB Sant Pau), 08041 Barcelona, Spain
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222
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Angers S. Wnt signaling inhibition confers induced synthetic lethality to PARP inhibitors. EMBO Mol Med 2021; 13:e14002. [PMID: 33787008 PMCID: PMC8033510 DOI: 10.15252/emmm.202114002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 01/16/2023] Open
Abstract
Despite considerable efforts, therapeutic strategies targeting the Wnt pathway are still not clinically available. The pervasive role of Wnt‐βcatenin signaling for the control of stem cells during normal tissue homeostasis makes the on‐target toxicity of available therapeutic grade molecules an important limitation preventing their clinical introduction. The article in this issue of EMBO Molecular Medicine by Kaur et al (2021) reveals that treatment of Wnt‐addicted cancer cells with inhibitors of Wnt signaling induces a state of BRCAness leading to hypersensitivity to PARP inhibitors. This is a new example of induced synthetic lethality that could pave the way for new indications for PARP inhibitors or may contribute to the long‐awaited clinical introduction of therapeutic agents targeting the Wnt pathway.
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Affiliation(s)
- Stephane Angers
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
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223
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Gilad Y, Eliaz Y, Yu Y, Dean AM, Han SJ, Qin L, O’Malley BW, Lonard DM. A genome-scale CRISPR Cas9 dropout screen identifies synthetically lethal targets in SRC-3 inhibited cancer cells. Commun Biol 2021; 4:399. [PMID: 33767353 PMCID: PMC7994904 DOI: 10.1038/s42003-021-01929-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 02/24/2021] [Indexed: 02/01/2023] Open
Abstract
Steroid receptor coactivator 3 (SRC-3/NCoA3/AIB1), is a key regulator of gene transcription and it plays a central role in breast cancer (BC) tumorigenesis, making it a potential therapeutic target. Beyond its function as an important regulator of estrogen receptor transcriptional activity, SRC-3 also functions as a coactivator for a wide range of other transcription factors, suggesting SRC-3 inhibition can be beneficial in hormone-independent cancers as well. The recent discovery of a potent SRC-3 small molecule inhibitor, SI-2, enabled the further development of additional related compounds. SI-12 is an improved version of SI-2 that like SI-2 has anti-proliferative activity in various cancer types, including BC. Here, we sought to identify gene targets, that when inhibited in the presence of SI-12, would lead to enhanced BC cell cytotoxicity. We performed a genome-scale CRISPR-Cas9 screen in MCF-7 BC cells under conditions of pharmacological pressure with SI-12. A parallel screen was performed with an ER inhibitor, fulvestrant, to shed light on both common and distinct activities between SRC-3 and ERα inhibition. Bearing in mind the key role of SRC-3 in tumorigenesis of other types of cancer, we extended our study by validating potential hits identified from the MCF-7 screen in other cancer cell lines.
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Affiliation(s)
- Yosi Gilad
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - Yossi Eliaz
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Yang Yu
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - Adam M. Dean
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - San Jung Han
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - Li Qin
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - Bert W. O’Malley
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - David M. Lonard
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
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224
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Metcalf KJ, Alazzeh A, Werb Z, Weaver VM. Leveraging microenvironmental synthetic lethalities to treat cancer. J Clin Invest 2021; 131:143765. [PMID: 33720045 PMCID: PMC7954586 DOI: 10.1172/jci143765] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Treatment resistance leads to cancer patient mortality. Therapeutic approaches that employ synthetic lethality to target mutational vulnerabilities in key tumor cell signaling pathways have proven effective in overcoming therapeutic resistance in some cancers. Yet, tumors are organs composed of malignant cells residing within a cellular and noncellular stroma. Tumor evolution and resistance to anticancer treatment are mediated through a dynamic and reciprocal dialogue with the tumor microenvironment (TME). Accordingly, expanding tumor cell synthetic lethality to encompass contextual synthetic lethality has the potential to eradicate tumors by targeting critical TME circuits that promote tumor progression and therapeutic resistance. In this Review, we summarize current knowledge about the TME and discuss its role in treatment. We outline the concept of tumor cell-specific synthetic lethality and describe therapeutic approaches to expand this paradigm to leverage TME synthetic lethality to improve cancer therapy.
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Affiliation(s)
| | | | - Zena Werb
- Department of Anatomy
- Helen Diller Family Comprehensive Cancer Center
| | - Valerie M. Weaver
- Department of Surgery
- Helen Diller Family Comprehensive Cancer Center
- Center for Bioengineering and Tissue Regeneration, and
- Radiation Oncology, Department of Bioengineering and Therapeutic Sciences, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, California, USA
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225
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Petroni G, Buqué A, Zitvogel L, Kroemer G, Galluzzi L. Immunomodulation by targeted anticancer agents. Cancer Cell 2021; 39:310-345. [PMID: 33338426 DOI: 10.1016/j.ccell.2020.11.009] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/17/2020] [Accepted: 11/17/2020] [Indexed: 02/08/2023]
Abstract
At odds with conventional chemotherapeutics, targeted anticancer agents are designed to inhibit precise molecular alterations that support oncogenesis or tumor progression. Despite such an elevated degree of molecular specificity, many clinically employed and experimental targeted anticancer agents also mediate immunostimulatory or immunosuppressive effects that (at least in some settings) influence therapeutic efficacy. Here, we discuss the main immunomodulatory effects of targeted anticancer agents and explore potential avenues to harness them in support of superior clinical efficacy.
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Affiliation(s)
- Giulia Petroni
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
| | - Aitziber Buqué
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
| | - Laurence Zitvogel
- Gustave Roussy Cancer Center, Villejuif, France; INSERM U1015, Villejuif, France; Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428, Villejuif, France; Faculty of Medicine, Paris-Saclay University, Le Kremlin-Bicêtre, France
| | - Guido Kroemer
- Equipe Labellisée Par La Ligue Contre le Cancer, Centre de Recherche des Cordeliers, INSERM U1138, Université de Paris, Sorbonne Université, Paris, France; Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France; Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France; Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China; Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden.
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA; Sandra and Edward Meyer Cancer Center, New York, NY, USA; Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA; Department of Dermatology, Yale School of Medicine, New Haven, CT, USA; Université de Paris, Paris, France.
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226
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Gerard L, Duvivier L, Gillet JP. Targeting tumor resistance mechanisms. Fac Rev 2021; 10:6. [PMID: 33659924 PMCID: PMC7894262 DOI: 10.12703/r/10-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cancer develops resistance to treatments through many mechanisms. Single-cell analyses reveal the intratumor heterogeneity and dynamic relationships between cancer cell subpopulations. These analyses also highlight that various mechanisms of resistance may coexist in a given tumor. Studies have unraveled how the microenvironment affects tumor response to treatments and how cancer cells may adapt to these treatments. Though challenging, individualized treatment based on the molecular characterization of the tumor should become the new standard of care. In the meantime, the success rate of clinical trials in oncology remains dramatically low. There is a need to do better and improve the predictability of preclinical models. This requires innovative changes in ex vivo models and the culture system currently being used. An innovative ligand design is also urgently needed. The limited arsenal of medicinal chemistry reactions and the biases of scaffold selection favor structurally similar compounds with linear shapes at the expense of disc and spherical shapes, which leave a large chemical shape space untouched. In this regard, venoms have received increasing interest as a wellspring for drug candidates. Overall, the characterization of tumor heterogeneity has contributed to advancing our understanding of the mechanisms that underlie cancer resistance to treatments. Targeting these mechanisms will require setting key milestones to significantly improve the translatability of preclinical studies to the clinic with the hope of increasing the success rate of clinical trials.
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Affiliation(s)
- Louise Gerard
- Laboratory of Molecular Cancer Biology, Molecular Physiology Research Unit (URPhyM), Namur Research Institute for Life Sciences (NARILIS), Faculty of Medicine, University of Namur, Namur, Belgium
| | - Laurent Duvivier
- Laboratory of Molecular Cancer Biology, Molecular Physiology Research Unit (URPhyM), Namur Research Institute for Life Sciences (NARILIS), Faculty of Medicine, University of Namur, Namur, Belgium
| | - Jean-Pierre Gillet
- Laboratory of Molecular Cancer Biology, Molecular Physiology Research Unit (URPhyM), Namur Research Institute for Life Sciences (NARILIS), Faculty of Medicine, University of Namur, Namur, Belgium
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227
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Ramnaraign B, Altshuler E. Complete clinical response of a patient with BRCA1-mutant cervical esophageal squamous cell carcinoma treated with oxaliplatin-based chemotherapy highlights the importance of performing genomic profiling in cancer treatment. CURRENT PROBLEMS IN CANCER: CASE REPORTS 2021. [DOI: 10.1016/j.cpccr.2021.100069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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228
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Jaiswal A, Gautam P, Pietilä EA, Timonen S, Nordström N, Akimov Y, Sipari N, Tanoli Z, Fleischer T, Lehti K, Wennerberg K, Aittokallio T. Multi-modal meta-analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor. Mol Syst Biol 2021; 17:e9526. [PMID: 33750001 PMCID: PMC7983037 DOI: 10.15252/msb.20209526] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 12/12/2022] Open
Abstract
Molecular and functional profiling of cancer cell lines is subject to laboratory-specific experimental practices and data analysis protocols. The current challenge therefore is how to make an integrated use of the omics profiles of cancer cell lines for reliable biological discoveries. Here, we carried out a systematic analysis of nine types of data modalities using meta-analysis of 53 omics studies across 12 research laboratories for 2,018 cell lines. To account for a relatively low consistency observed for certain data modalities, we developed a robust data integration approach that identifies reproducible signals shared among multiple data modalities and studies. We demonstrated the power of the integrative analyses by identifying a novel driver gene, ECHDC1, with tumor suppressive role validated both in breast cancer cells and patient tumors. The multi-modal meta-analysis approach also identified synthetic lethal partners of cancer drivers, including a co-dependency of PTEN deficient endometrial cancer cells on RNA helicases.
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Affiliation(s)
- Alok Jaiswal
- Institute for Molecular Medicine Finland (FIMM)Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
- Present address:
The Broad Institute of MIT and HarvardCambridgeMAUSA
| | - Prson Gautam
- Institute for Molecular Medicine Finland (FIMM)Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
| | - Elina A Pietilä
- Individualized Drug Therapy, Research Programs UnitUniversity of HelsinkiHelsinkiFinland
| | - Sanna Timonen
- Institute for Molecular Medicine Finland (FIMM)Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
- Hematology Research Unit HelsinkiUniversity of Helsinki and Helsinki University Hospital Comprehensive Cancer CenterHelsinkiFinland
- Translational Immunology Research Program and Department of Clinical Chemistry and HematologyUniversity of HelsinkiHelsinkiFinland
| | - Nora Nordström
- Institute for Molecular Medicine Finland (FIMM)Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
| | - Yevhen Akimov
- Institute for Molecular Medicine Finland (FIMM)Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
| | - Nina Sipari
- Viikki Metabolomics UnitHelsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
| | - Ziaurrehman Tanoli
- Institute for Molecular Medicine Finland (FIMM)Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
| | - Thomas Fleischer
- Department of Cancer GeneticsInstitute for Cancer ResearchOslo University HospitalOsloNorway
| | - Kaisa Lehti
- Individualized Drug Therapy, Research Programs UnitUniversity of HelsinkiHelsinkiFinland
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
- Department of Biomedical Laboratory ScienceNorwegian University of Science and TechnologyTrondheimNorway
| | - Krister Wennerberg
- Institute for Molecular Medicine Finland (FIMM)Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
- Biotech Research & Innovation Centre (BRIC) and Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM)Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
- Department of Cancer GeneticsInstitute for Cancer ResearchOslo University HospitalOsloNorway
- Department of Mathematics and StatisticsUniversity of TurkuTurkuFinland
- Oslo Centre for Biostatistics and Epidemiology (OCBE)University of OsloOsloNorway
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229
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Akimov Y, Aittokallio T. Re-defining synthetic lethality by phenotypic profiling for precision oncology. Cell Chem Biol 2021; 28:246-256. [PMID: 33631125 DOI: 10.1016/j.chembiol.2021.01.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 12/28/2020] [Accepted: 01/28/2021] [Indexed: 12/31/2022]
Abstract
High-throughput functional and genomic screening techniques provide systematic means for phenotypic discovery. Using synthetic lethality (SL) as a paradigm for anticancer drug and target discovery, we describe how these screening technologies may offer new possibilities to identify therapeutically relevant and selective SL interactions by addressing some of the challenges that have made robust discovery of SL candidates difficult. We further introduce an extended concept of SL interaction, in which a simultaneous perturbation of two or more cellular components reduces cell viability more than expected by their individual effects, which we feel is highly befitting for anticancer applications. We also highlight the potential benefits and challenges related to computational quantification of synergistic interactions and cancer selectivity. Finally, we explore how tumoral heterogeneity can be exploited to find phenotype-specific SL interactions for precision oncology using high-throughput functional screening and the exciting opportunities these methods provide for the identification of subclonal SL interactions.
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Affiliation(s)
- Yevhen Akimov
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland; Institute for Cancer Research, Department of Cancer Genetics, Oslo University Hospital, Oslo, Norway; Centre for Biostatistics and Epidemiology (OCBE), Faculty of Medicine, University of Oslo, Oslo, Norway.
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230
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Dodge MJ, MacNeil KM, Tessier TM, Weinberg JB, Mymryk JS. Emerging antiviral therapeutics for human adenovirus infection: Recent developments and novel strategies. Antiviral Res 2021; 188:105034. [PMID: 33577808 DOI: 10.1016/j.antiviral.2021.105034] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 12/11/2022]
Abstract
Human adenoviruses (HAdV) are ubiquitous human pathogens that cause a significant burden of respiratory, ocular, and gastrointestinal illnesses. Although HAdV infections are generally self-limiting, pediatric and immunocompromised individuals are at particular risk for developing severe disease. Currently, no approved antiviral therapies specific to HAdV exist. Recent outbreaks underscore the need for effective antiviral agents to treat life-threatening infections. In this review we will focus on recent developments in search of potential therapeutic agents for controlling HAdV infections, with a focus on those targeting post-entry stages of the virus replicative cycle.
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Affiliation(s)
- Mackenzie J Dodge
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Katelyn M MacNeil
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Tanner M Tessier
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Jason B Weinberg
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Joe S Mymryk
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada; Department of Otolaryngology, Head & Neck Surgery, The University of Western Ontario, London, ON, Canada; Department of Oncology, The University of Western Ontario, London, ON, Canada; London Regional Cancer Program, Lawson Health Research Institute, London, ON, Canada.
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231
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Gilad Y, Gellerman G, Lonard DM, O’Malley BW. Drug Combination in Cancer Treatment-From Cocktails to Conjugated Combinations. Cancers (Basel) 2021; 13:669. [PMID: 33562300 PMCID: PMC7915944 DOI: 10.3390/cancers13040669] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 02/02/2021] [Indexed: 12/14/2022] Open
Abstract
It is well recognized today that anticancer drugs often are most effective when used in combination. However, the establishment of chemotherapy as key modality in clinical oncology began with sporadic discoveries of chemicals that showed antiproliferative properties and which as a first attempt were used as single agents. In this review we describe the development of chemotherapy from its origins as a single drug treatment with cytotoxic agents to polydrug therapy that includes targeted drugs. We discuss the limitations of the first chemotherapeutic drugs as a motivation for the establishment of combined drug treatment as standard practice in spite of concerns about frequent severe, dose limiting toxicities. Next, we introduce the development of targeted treatment as a concept for advancement within the broader field of small-molecule drug combination therapy in cancer and its accelerating progress that was boosted by recent scientific and technological progresses. Finally, we describe an alternative strategy of drug combinations using drug-conjugates for selective delivery of cytotoxic drugs to tumor cells that potentiates future improvement of drug combinations in cancer treatment. Overall, in this review we outline the development of chemotherapy from a pharmacological perspective, from its early stages to modern concepts of using targeted therapies for combinational treatment.
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Affiliation(s)
- Yosi Gilad
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Gary Gellerman
- Department of Chemical Sciences, Ariel University, Ariel 40700, Israel;
| | - David M. Lonard
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Bert W. O’Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA;
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232
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Schneeweis C, Hassan Z, Schick M, Keller U, Schneider G. The SUMO pathway in pancreatic cancer: insights and inhibition. Br J Cancer 2021; 124:531-538. [PMID: 33071285 PMCID: PMC7851129 DOI: 10.1038/s41416-020-01119-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 08/31/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022] Open
Abstract
An urgent medical need to develop novel treatment strategies for patients with pancreatic ductal adenocarcinoma (PDAC) exists. However, despite various efforts in the histopathological and molecular subtyping of PDAC, novel targeted or specific therapies have not been established. Posttranslational modifications (PTMs) with ubiquitin-like proteins, including small ubiquitin-like modifiers (SUMOs), mediate numerous processes that can contribute to the fitness and survival of cancer cells. The contribution of SUMOylation to transcriptional control, DNA repair pathways, mitotic progression, and oncogenic signalling has been described. Here we review functions of the SUMO pathway in PDAC, with a special focus on its connection to an aggressive subtype of the disease characterised by high MYC activity, and discuss SUMOylation inhibitors under development for precise PDAC therapies.
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Affiliation(s)
- Christian Schneeweis
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, 81675, München, Germany
| | - Zonera Hassan
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, 81675, München, Germany
| | - Markus Schick
- Department of Hematology, Oncology and Tumor Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Hindenburgdamm 30, 12203, Berlin, Germany
| | - Ulrich Keller
- Department of Hematology, Oncology and Tumor Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Hindenburgdamm 30, 12203, Berlin, Germany.
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120, Heidelberg, Germany.
- Max-Delbrück-Center for Molecular Medicine, 13092, Berlin, Germany.
| | - Günter Schneider
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, 81675, München, Germany.
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120, Heidelberg, Germany.
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233
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Gallage S, Barragan Avila JE, Heikenwalder M. Lethal lipotoxicity for liver cancer therapy. NATURE CANCER 2021; 2:138-140. [PMID: 35122080 DOI: 10.1038/s43018-021-00175-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Suchira Gallage
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jose Efren Barragan Avila
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mathias Heikenwalder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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234
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Chen A, Wen S, Liu F, Zhang Z, Liu M, Wu Y, He B, Yan M, Kang T, Lam EWF, Wang Z, Liu Q. CRISPR/Cas9 screening identifies a kinetochore-microtubule dependent mechanism for Aurora-A inhibitor resistance in breast cancer. Cancer Commun (Lond) 2021; 41:121-139. [PMID: 33471959 PMCID: PMC7896750 DOI: 10.1002/cac2.12125] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/04/2020] [Accepted: 12/16/2020] [Indexed: 12/31/2022] Open
Abstract
Background Overexpression of Aurora‐A (AURKA) is a feature of breast cancer and associates with adverse prognosis. The selective Aurora‐A inhibitor alisertib (MLN8237) has recently demonstrated promising antitumor responses as a single agent in various cancer types but its phase III clinical trial was reported as a failure since MLN8237 did not show an apparent effect in prolonging the survival of patients. Thus, identification of potential targets that could enhance the activity of MLN8237 would provide a rationale for drug combination to achieve better therapeutic outcome. Methods Here, we conducted a systematic synthetic lethality CRISPR/Cas9 screening of 507 kinases using MLN8237 in breast cancer cells and identified a number of targetable kinases that displayed synthetic lethality interactions with MLN8237. Then, we performed competitive growth assays, colony formation assays, cell viability assays, apoptosis assays, and xenograft murine model to evaluate the synergistic therapeutic effects of Haspin (GSG2) depletion or inhibition with MLN8237. For mechanistic studies, immunofluorescence was used to detect the state of microtubules and the localization of Aurora‐B and mitotic centromere‐associated kinesin (MCAK). Results Among the hits, we observed that Haspin depletion or inhibition marginally inhibited breast cancer cell growth but could substantially enhance the killing effects of MLN8237. Mechanistic studies showed that co‐treatment with Aurora‐A and Haspin inhibitors abolished the recruitment of Aurora‐B and mitotic centromere‐associated kinesin (MCAK) to centromeres which were associated with excessive microtubule depolymerization, kinetochore‐microtubule (KT‐MT) attachment failure, and severe mitotic catastrophe. We further showed that the combination of MLN8237 and the Haspin inhibitor CHR‐6494 synergistically reduced breast cancer cell viability and significantly inhibited both in vitro and in vivo tumor growth. Conclusions These findings establish Haspin as a synthetic lethal target and demonstrate CHR‐6494 as a potential combinational drug for promoting the therapeutic effects of MLN8237 on breast cancer.
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Affiliation(s)
- Ailin Chen
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P. R. China
| | - Shijun Wen
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P. R. China
| | - Fang Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P. R. China
| | - Zijian Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P. R. China
| | - Meiling Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P. R. China
| | - Yuanzhong Wu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P. R. China
| | - Bin He
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P. R. China
| | - Min Yan
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P. R. China
| | - Tiebang Kang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P. R. China
| | - Eric W-F Lam
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P. R. China.,Department of Surgery and Cancer, Imperial College London, W12 0NN, London, UK
| | - Zifeng Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P. R. China
| | - Quentin Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P. R. China.,Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, 116044, P. R. China
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235
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Lin PH, Huang CY, Yu KJ, Kan HC, Liu CY, Chuang CK, Lu YC, Chang YH, Shao IH, Pang ST. Genomic characterization of clear cell renal cell carcinoma using targeted gene sequencing. Oncol Lett 2021; 21:169. [PMID: 33456545 PMCID: PMC7802514 DOI: 10.3892/ol.2021.12430] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 11/10/2020] [Indexed: 01/04/2023] Open
Abstract
Kidney cancer is one of the most lethal cancer types worldwide. The most common subtype of kidney cancer is clear cell renal cell carcinoma (ccRCC), and the somatic mutations of ccRCC have been identified through the development of large databases. The present study aimed to validate the status of the associated gene mutations in a Taiwanese cohort. Targeted sequencing was used to validate the mutation status of genes related to ccRCC in Taiwanese patients who had nephrectomy for kidney cancer. The top eight mutated genes in the Catalogue Of Somatic Mutations In Cancer (COSMIC) were selected. These genes were VHL, protein polybromo-1 (PBRM1), histone-lysine N-methyltransferase SETD2, BRCA1-associated protein-1 (BAP1), lysine-specific demethylase 5C (KDM5C), TP53, MTOR and PTEN. The association between the gene mutation status of VHL, PBRM1, SETD2 and BAP1 was validated with clinicopathological parameters as well as overall survival time. Tumor cells from 96 patients with ccRCC were target sequenced. The order of mutation rate of the eight aforementioned genes was similar to that reported within COSMIC. The present Taiwanese cohort exhibited lower PBRM1 and BAP1 mutation rates compared with average, with increased mutation rates for SETD2 and KDM5C. BAP1 mutation was associated with the tumor and cancerous stage. None of these four genes were positively associated with the overall survival of patients. The PBRM1 and SETD2 mutations were mutually exclusive to BAP1 mutation. Overall, the present study provided data confirming gene alteration in Taiwanese patients with ccRCC and showed some differences when compared with Western countries. Further comprehensive genomic and epigenomic studies, as well as downstream validation, are necessary to evaluate the impact of these differences.
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Affiliation(s)
- Po-Hung Lin
- Division of Urology, Department of Surgery, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan, R.O.C.,Graduate Institute of Clinical Medical Science, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan, R.O.C
| | - Chao-Yuan Huang
- Department of Urology, National Taiwan University Hospital, Taipei 10022, Taiwan, R.O.C
| | - Kai-Jie Yu
- Division of Urology, Department of Surgery, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan, R.O.C
| | - Hung-Cheng Kan
- Division of Urology, Department of Surgery, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan, R.O.C
| | - Chung-Yi Liu
- Division of Urology, Department of Surgery, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan, R.O.C
| | - Cheng-Keng Chuang
- Division of Urology, Department of Surgery, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan, R.O.C
| | - Yu-Chuan Lu
- Department of Urology, National Taiwan University Hospital, Taipei 10022, Taiwan, R.O.C.,Institute of Biomedical Engineering, National Taiwan University, Taipei 10022, Taiwan, R.O.C
| | - Ying-Hsu Chang
- Division of Urology, Department of Surgery, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan, R.O.C
| | - I-Hung Shao
- Division of Urology, Department of Surgery, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan, R.O.C
| | - See-Tong Pang
- Division of Urology, Department of Surgery, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan, R.O.C
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236
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Weyemi U, Galluzzi L. Chromatin and genomic instability in cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 364:ix-xvii. [PMID: 34507786 DOI: 10.1016/s1937-6448(21)00116-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Urbain Weyemi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States.
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, United States; Sandra and Edward Meyer Cancer Center, New York, NY, United States; Caryl and Israel Englander Institute for Precision Medicine, New York, NY, United States; Department of Dermatology, Yale School of Medicine, New Haven, CT, United States; Université de Paris, Paris, France.
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237
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Blessing C, Mandemaker IK, Gonzalez-Leal C, Preisser J, Schomburg A, Ladurner AG. The Oncogenic Helicase ALC1 Regulates PARP Inhibitor Potency by Trapping PARP2 at DNA Breaks. Mol Cell 2020; 80:862-875.e6. [PMID: 33275888 DOI: 10.1016/j.molcel.2020.10.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/27/2020] [Accepted: 10/04/2020] [Indexed: 12/16/2022]
Abstract
The anti-tumor potency of poly(ADP-ribose) polymerase (PARP) inhibitors (PARPis) has been linked to trapping of PARP1 on damaged chromatin. However, little is known about their impact on PARP2, an isoform with overlapping functions at DNA lesions. Whether the release of PARP1/2 from DNA lesions is actively catalyzed by molecular machines is also not known. We found that PARPis robustly trap PARP2 and that the helicase ALC1 (CHD1L) is strictly required for PARP2 release. Catalytic inactivation of ALC1 quantitatively traps PARP2 but not PARP1. ALC1 manipulation impacts the response to single-strand DNA breaks through PARP2 trapping, potentiates PARPi-induced cancer cell killing, and mediates synthetic lethality upon BRCA deficiency. The chromatin remodeler ALC1 actively drives PARP2 turnover from DNA lesions, and PARP2 contributes to the cellular responses of PARPi. This suggests that disrupting the ATP-fueled remodeling forces of ALC1 might enable therapies that selectively target the DNA repair functions of PARPs in cancer.
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Affiliation(s)
- Charlotte Blessing
- Department of Physiological Chemistry, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany; International Max Planck Research School (IMPRS) for Molecular Life Sciences, 82152 Planegg-Martinsried, Germany
| | - Imke Karlijn Mandemaker
- Department of Physiological Chemistry, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Claudia Gonzalez-Leal
- Department of Physiological Chemistry, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany; International Max Planck Research School (IMPRS) for Molecular Life Sciences, 82152 Planegg-Martinsried, Germany
| | - Julia Preisser
- Department of Physiological Chemistry, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Adrian Schomburg
- Department of Physiological Chemistry, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany; Eisbach Bio GmbH, Am Klopferspitz 19, 82152 Planegg-Martinsried, Germany
| | - Andreas Gerhard Ladurner
- Department of Physiological Chemistry, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany; International Max Planck Research School (IMPRS) for Molecular Life Sciences, 82152 Planegg-Martinsried, Germany; Eisbach Bio GmbH, Am Klopferspitz 19, 82152 Planegg-Martinsried, Germany.
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238
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Myers S, Ortega JA, Cavalli A. Synthetic Lethality through the Lens of Medicinal Chemistry. J Med Chem 2020; 63:14151-14183. [PMID: 33135887 PMCID: PMC8015234 DOI: 10.1021/acs.jmedchem.0c00766] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Indexed: 02/07/2023]
Abstract
Personalized medicine and therapies represent the goal of modern medicine, as drug discovery strives to move away from one-cure-for-all and makes use of the various targets and biomarkers within differing disease areas. This approach, especially in oncology, is often undermined when the cells make use of alternative survival pathways. As such, acquired resistance is unfortunately common. In order to combat this phenomenon, synthetic lethality is being investigated, making use of existing genetic fragilities within the cancer cell. This Perspective highlights exciting targets within synthetic lethality, (PARP, ATR, ATM, DNA-PKcs, WEE1, CDK12, RAD51, RAD52, and PD-1) and discusses the medicinal chemistry programs being used to interrogate them, the challenges these programs face, and what the future holds for this promising field.
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Affiliation(s)
- Samuel
H. Myers
- Computational
& Chemical Biology, Istituto Italiano
di Tecnologia, 16163 Genova, Italy
| | - Jose Antonio Ortega
- Computational
& Chemical Biology, Istituto Italiano
di Tecnologia, 16163 Genova, Italy
| | - Andrea Cavalli
- Computational
& Chemical Biology, Istituto Italiano
di Tecnologia, 16163 Genova, Italy
- Department
of Pharmacy and Biotechnology, University
of Bologna, 40126 Bologna, Italy
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239
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Hans F, Senarisoy M, Bhaskar Naidu C, Timmins J. Focus on DNA Glycosylases-A Set of Tightly Regulated Enzymes with a High Potential as Anticancer Drug Targets. Int J Mol Sci 2020; 21:ijms21239226. [PMID: 33287345 PMCID: PMC7730500 DOI: 10.3390/ijms21239226] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 12/01/2020] [Indexed: 12/25/2022] Open
Abstract
Cancer is the second leading cause of death with tens of millions of people diagnosed with cancer every year around the world. Most radio- and chemotherapies aim to eliminate cancer cells, notably by causing severe damage to the DNA. However, efficient repair of such damage represents a common mechanism of resistance to initially effective cytotoxic agents. Thus, development of new generation anticancer drugs that target DNA repair pathways, and more particularly the base excision repair (BER) pathway that is responsible for removal of damaged bases, is of growing interest. The BER pathway is initiated by a set of enzymes known as DNA glycosylases. Unlike several downstream BER enzymes, DNA glycosylases have so far received little attention and the development of specific inhibitors of these enzymes has been lagging. Yet, dysregulation of DNA glycosylases is also known to play a central role in numerous cancers and at different stages of the disease, and thus inhibiting DNA glycosylases is now considered a valid strategy to eliminate cancer cells. This review provides a detailed overview of the activities of DNA glycosylases in normal and cancer cells, their modes of regulation, and their potential as anticancer drug targets.
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240
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Neggers JE, Paolella BR, Asfaw A, Rothberg MV, Skipper TA, Yang A, Kalekar RL, Krill-Burger JM, Dharia NV, Kugener G, Kalfon J, Yuan C, Dumont N, Gonzalez A, Abdusamad M, Li YY, Spurr LF, Wu WW, Durbin AD, Wolpin BM, Piccioni F, Root DE, Boehm JS, Cherniack AD, Tsherniak A, Hong AL, Hahn WC, Stegmaier K, Golub TR, Vazquez F, Aguirre AJ. Synthetic Lethal Interaction between the ESCRT Paralog Enzymes VPS4A and VPS4B in Cancers Harboring Loss of Chromosome 18q or 16q. Cell Rep 2020; 33:108493. [PMID: 33326793 PMCID: PMC8374858 DOI: 10.1016/j.celrep.2020.108493] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/04/2020] [Accepted: 11/17/2020] [Indexed: 12/26/2022] Open
Abstract
Few therapies target the loss of tumor suppressor genes in cancer. We examine CRISPR-SpCas9 and RNA-interference loss-of-function screens to identify new therapeutic targets associated with genomic loss of tumor suppressor genes. The endosomal sorting complexes required for transport (ESCRT) ATPases VPS4A and VPS4B score as strong synthetic lethal dependencies. VPS4A is essential in cancers harboring loss of VPS4B adjacent to SMAD4 on chromosome 18q and VPS4B is required in tumors with co-deletion of VPS4A and CDH1 (E-cadherin) on chromosome 16q. We demonstrate that more than 30% of cancers selectively require VPS4A or VPS4B. VPS4A suppression in VPS4B-deficient cells selectively leads to ESCRT-III filament accumulation, cytokinesis defects, nuclear deformation, G2/M arrest, apoptosis, and potent tumor regression. CRISPR-SpCas9 screening and integrative genomic analysis reveal other ESCRT members, regulators of abscission, and interferon signaling as modifiers of VPS4A dependency. We describe a compendium of synthetic lethal vulnerabilities and nominate VPS4A and VPS4B as high-priority therapeutic targets for cancers with 18q or 16q loss. Neggers, Paolella, and colleagues identify the ATPases VPS4A and VPS4B as selective vulnerabilities and potential therapeutic targets in cancers harboring loss of chromosome 18q or 16q. In VPS4B-deficient cancers, VPS4A suppression leads to ESCRT-III dysfunction, nuclear deformation, and abscission defects. Moreover, ESCRT proteins and interferons can modulate dependency on VPS4A.
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Affiliation(s)
- Jasper E Neggers
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Brenton R Paolella
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Adhana Asfaw
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael V Rothberg
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Thomas A Skipper
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Annan Yang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Radha L Kalekar
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - John M Krill-Burger
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Neekesh V Dharia
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Cancer and Blood Disorders Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Guillaume Kugener
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jérémie Kalfon
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Chen Yuan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Nancy Dumont
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alfredo Gonzalez
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mai Abdusamad
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yvonne Y Li
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Liam F Spurr
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Westley W Wu
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Adam D Durbin
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Cancer and Blood Disorders Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Federica Piccioni
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David E Root
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jesse S Boehm
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andrew D Cherniack
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Aviad Tsherniak
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andrew L Hong
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Cancer and Blood Disorders Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - William C Hahn
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Kimberly Stegmaier
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Cancer and Blood Disorders Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Todd R Golub
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Francisca Vazquez
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.
| | - Andrew J Aguirre
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.
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241
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Persi E, Wolf YI, Horn D, Ruppin E, Demichelis F, Gatenby RA, Gillies RJ, Koonin EV. Mutation-selection balance and compensatory mechanisms in tumour evolution. Nat Rev Genet 2020; 22:251-262. [PMID: 33257848 DOI: 10.1038/s41576-020-00299-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2020] [Indexed: 12/11/2022]
Abstract
Intratumour heterogeneity and phenotypic plasticity, sustained by a range of somatic aberrations, as well as epigenetic and metabolic adaptations, are the principal mechanisms that enable cancers to resist treatment and survive under environmental stress. A comprehensive picture of the interplay between different somatic aberrations, from point mutations to whole-genome duplications, in tumour initiation and progression is lacking. We posit that different genomic aberrations generally exhibit a temporal order, shaped by a balance between the levels of mutations and selective pressures. Repeat instability emerges first, followed by larger aberrations, with compensatory effects leading to robust tumour fitness maintained throughout the tumour progression. A better understanding of the interplay between genetic aberrations, the microenvironment, and epigenetic and metabolic cellular states is essential for early detection and prevention of cancer as well as development of efficient therapeutic strategies.
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Affiliation(s)
- Erez Persi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - David Horn
- School of Physics and Astronomy, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Eytan Ruppin
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Francesca Demichelis
- Department for Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy.,Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY, USA
| | - Robert A Gatenby
- Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Robert J Gillies
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
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242
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Haykal MM, Nahmias C, Varon C, Martin OCB. Organotypic Modeling of the Tumor Landscape. Front Cell Dev Biol 2020; 8:606039. [PMID: 33330508 PMCID: PMC7732527 DOI: 10.3389/fcell.2020.606039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/03/2020] [Indexed: 12/21/2022] Open
Abstract
Cancer is a complex disease and it is now clear that not only epithelial tumor cells play a role in carcinogenesis. The tumor microenvironment is composed of non-stromal cells, including endothelial cells, adipocytes, immune and nerve cells, and a stromal compartment composed of extracellular matrix, cancer-associated fibroblasts and mesenchymal cells. Tumorigenesis is a dynamic process with constant interactions occurring between the tumor cells and their surroundings. Even though all connections have not yet been discovered, it is now known that crosstalk between actors of the microenvironment drives cancer progression. Taking into account this complexity, it is important to develop relevant models to study carcinogenesis. Conventional 2D culture models fail to represent the entire tumor microenvironment properly and the use of animal models should be decreased with respect to the 3Rs rule. To this aim, in vitro organotypic models have been significantly developed these past few years. These models have different levels of complexity and allow the study of tumor cells alone or in interaction with the microenvironment actors during the multiple stages of carcinogenesis. This review depicts recent insights into organotypic modeling of the tumor and its microenvironment all throughout cancer progression. It offers an overview of the crosstalk between epithelial cancer cells and their microenvironment during the different phases of carcinogenesis, from the early cell autonomous events to the late metastatic stages. The advantages of 3D over classical 2D or in vivo models are presented as well as the most promising organotypic models. A particular focus is made on organotypic models used for studying cancer progression, from the less complex spheroids to the more sophisticated body-on-a-chip. Last but not least, we address the potential benefits of these models in personalized medicine which is undoubtedly a domain paving the path to new hopes in terms of cancer care and cure.
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Affiliation(s)
- Maria M. Haykal
- Université Paris-Saclay, Institut Gustave Roussy, Inserm U981, Biomarqueurs Prédictifs et Nouvelles Stratégies Thérapeutiques en Oncologie, Villejuif, France
| | - Clara Nahmias
- Université Paris-Saclay, Institut Gustave Roussy, Inserm U981, Biomarqueurs Prédictifs et Nouvelles Stratégies Thérapeutiques en Oncologie, Villejuif, France
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243
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Zimmer Y, Reinhardt HC, Medová M. Editorial: Exploiting DNA Damage Response in the Era of Precision Oncology. Front Oncol 2020; 10:611127. [PMID: 33178619 PMCID: PMC7593708 DOI: 10.3389/fonc.2020.611127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 11/24/2022] Open
Affiliation(s)
- Yitzhak Zimmer
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Hans Christian Reinhardt
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,German Consortium for Translational Cancer Research (DKTK), Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Michaela Medová
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
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244
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Pan YR, Wu CE, Yeh CN. ATM Inhibitor Suppresses Gemcitabine-Resistant BTC Growth in a Polymerase θ Deficiency-Dependent Manner. Biomolecules 2020; 10:E1529. [PMID: 33182492 PMCID: PMC7697425 DOI: 10.3390/biom10111529] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/05/2020] [Accepted: 11/05/2020] [Indexed: 12/19/2022] Open
Abstract
Patients with advanced biliary tract cancer (BTC) inevitably experience progression after first-line, gemcitabine-based chemotherapy, due to chemo-resistance. The genetic alterations of DNA damage repair (DDR) genes are usually determined in BTC tumors. In this study, we found that the POLQ mRNA levels are downregulated and the ataxia-telangiectasia mutated (ATM) inhibitor AZD0156 was more sensitive in gemcitabine-resistant BTC sublines than in the parental cell lines. The knockdown of DNA polymerase θ does not affect cell proliferation, but its combination with the ATM inhibitor facilitated cell death in gemcitabine-resistant and gemcitabine-intensive BTC cells. Moreover, in the DNA damage caused by photon, hydrogen peroxide, or chemotherapy drugs, synthetic lethal interactions were found in combination with ATM inhibition by AZD0156 and DNA polymerase θ depletion, resulting in increased DNA damage accumulation and micronucleus formation, as well as reduced cell survival and colony formation. Collectively, our results reveal that ATM acts as a potential target in gemcitabine-resistant and DNA polymerase θ-deficient BTC.
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Affiliation(s)
- Yi-Ru Pan
- Department of General Surgery and Liver Research Center, Chang Gung Memorial Hospital, Linkou branch, Chang Gung University, Taoyuan 333, Taiwan;
| | - Chiao-En Wu
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou, Chang Gung University College of Medicine, Taoyuan 333, Taiwan;
| | - Chun-Nan Yeh
- Department of General Surgery and Liver Research Center, Chang Gung Memorial Hospital, Linkou branch, Chang Gung University, Taoyuan 333, Taiwan;
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245
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Lankes K, Hassan Z, Doffo MJ, Schneeweis C, Lier S, Öllinger R, Rad R, Krämer OH, Keller U, Saur D, Reichert M, Schneider G, Wirth M. Targeting the ubiquitin-proteasome system in a pancreatic cancer subtype with hyperactive MYC. Mol Oncol 2020; 14:3048-3064. [PMID: 33099868 PMCID: PMC7718946 DOI: 10.1002/1878-0261.12835] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 09/11/2020] [Accepted: 10/04/2020] [Indexed: 12/12/2022] Open
Abstract
The myelocytomatosis oncogene (MYC) is an important driver in a subtype of pancreatic ductal adenocarcinoma (PDAC). However, MYC remains a challenging therapeutic target; therefore, identifying druggable synthetic lethal interactions in MYC‐active PDAC may lead to novel precise therapies. First, to identify networks with hyperactive MYC, we profiled transcriptomes of established human cell lines, murine primary PDAC cell lines, and accessed publicly available repositories to analyze transcriptomes of primary human PDAC. Networks active in MYC‐hyperactive subtypes were analyzed by gene set enrichment analysis. Next, we performed an unbiased pharmacological screen to define MYC‐associated vulnerabilities. Hits were validated by analysis of drug response repositories and genetic gain‐ and loss‐of‐function experiments. In these experiments, we discovered that the proteasome inhibitor bortezomib triggers a MYC‐associated vulnerability. In addition, by integrating publicly available data, we found the unfolded protein response as a signature connected to MYC. Furthermore, increased sensitivity of MYC‐hyperactive PDACs to bortezomib was validated in genetically modified PDAC cells. In sum, we provide evidence that perturbing the ubiquitin–proteasome system (UPS) might be an option to target MYC‐hyperactive PDAC cells. Our data provide the rationale to further develop precise targeting of the UPS as a subtype‐specific therapeutic approach.
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Affiliation(s)
- Katharina Lankes
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Munich, Germany
| | - Zonera Hassan
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Munich, Germany
| | - María Josefina Doffo
- Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Campus Benjamin Franklin, Berlin, Germany
| | - Christian Schneeweis
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Munich, Germany
| | - Svenja Lier
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Munich, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, Technical University Munich, Munich, Germany.,German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, Technical University Munich, Munich, Germany.,German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Oliver H Krämer
- Department of Toxicology, University Medical Center, Mainz, Germany
| | - Ulrich Keller
- Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Campus Benjamin Franklin, Berlin, Germany.,German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Dieter Saur
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany.,Institute for Translational Cancer Research and Experimental Cancer Therapy, Technical University Munich, Munich, Germany
| | - Maximilian Reichert
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Munich, Germany.,German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Günter Schneider
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Munich, Germany.,German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Matthias Wirth
- Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Campus Benjamin Franklin, Berlin, Germany
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246
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PROTACs to address the challenges facing small molecule inhibitors. Eur J Med Chem 2020; 210:112993. [PMID: 33189436 DOI: 10.1016/j.ejmech.2020.112993] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/01/2020] [Accepted: 11/01/2020] [Indexed: 02/07/2023]
Abstract
Small molecule inhibitors of proteins represent important medicines and critical chemical tools to investigate the biology of the target proteins. Advances in various -omics technologies have fueled the pace of discovery of disease-relevant proteins. Translating these discoveries into human benefits requires us to develop specific chemicals to inhibit the proteins. However, traditional small molecule inhibitors binding to orthosteric or allosteric sites face significant challenges. These challenges include drug selectivity, therapy resistance as well as drugging undruggable proteins and multi-domain proteins. To address these challenges, PROteolysis TArgeting Chimera (PROTAC) has been proposed. PROTACs are heterobifunctional molecules containing a binding ligand for a protein of interest and E3 ligase-recruiting ligand that are connected through a chemical linker. Binding of a PROTAC to its target protein will bring a E3 ligase in close proximity to initiate polyubiquitination of the target protein ensuing its proteasome-mediated degradation. Unlike small molecule inhibitors, PROTACs achieve target protein degradation in its entirety in a catalytical fashion. In this review, we analyze recent advances in PROTAC design to discuss how PROTACs can address the challenges facing small molecule inhibitors to potentially deliver next-generation medicines and chemical tools with high selectivity and efficacy. We also offer our perspectives on the future promise and potential limitations facing PROTACs. Investigations to overcome these limitations of PROTACs will further help realize the promise of PROTACs for human benefits.
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247
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Abstract
Cancer cells die when their decimated DNA damage response (DDR) unsuccessfully handles DNA damage. This notion has been successfully exploited when targeting PARP (poly ADP-ribose polymerase) in homologous recombination-deficient cells. With the greater understanding of DDR achieved in the last decade, new cancer therapy targets within the DDR network have been identified. Intriguingly, many of the molecules that have advanced into clinical trials are inhibitors of DDR kinases. This special issue is devoted to discussing the mechanism of cell killing and the level of success that such inhibitors have reached in pre-clinical and clinical settings.
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Affiliation(s)
- Vanesa Gottifredi
- Fundación Instituto Leloir - Instituto de Investigaciones Bioquímicas de Buenos Aires. Consejo de Investigaciones Científicas y Técnicas. Avenida Patricias Argentinas 435, C1405BWE, Buenos Aires, Argentina.
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248
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Sinha A, Saleh A, Endersby R, Yuan SH, Chokshi CR, Brown KR, Kuzio B, Kauppinen T, Singh SK, Baker SJ, McKinnon PJ, Katyal S. RAD51-Mediated DNA Homologous Recombination Is Independent of PTEN Mutational Status. Cancers (Basel) 2020; 12:cancers12113178. [PMID: 33138032 PMCID: PMC7693555 DOI: 10.3390/cancers12113178] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 10/20/2020] [Indexed: 12/22/2022] Open
Abstract
Simple Summary PTEN is an important tumor suppressor that is frequently mutated in malignancy. PTEN mutational loss has been associated with reduced RAD51 expression and homologous recombination deficiency (HRD), however; recent studies have failed to recapitulate these findings. Here, we show that RAD51 expression, foci formation and homologous recombination repair activity are unaltered in normal and tumorigenic PTEN-deficient cells and patient samples. Furthermore, we show that PTEN-deficient tumor cell lines do not synergize with the clinical PARP inhibitor olaparib, underscoring a need to discontinue its use in treating patients with PTEN-deficient tumors that do not otherwise exhibit HRD. Abstract PTEN mutation occurs in a variety of aggressive cancers and is associated with poor patient outcomes. Recent studies have linked mutational loss of PTEN to reduced RAD51 expression and function, a key factor involved in the homologous recombination (HR) pathway. However, these studies remain controversial, as they fail to establish a definitive causal link to RAD51 expression that is PTEN-dependent, while other studies have not been able to recapitulate the relationship between the PTEN expression and the RAD51/HR function. Resolution of this apparent conundrum is essential due to the clinically-significant implication that PTEN-deficient tumors may be sensitive to poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi) commonly used in the clinical management of BRCA-mutated and other HR-deficient (HRD) tumors. Methods: Primary Pten-deficient (and corresponding wild-type) mouse embryonic fibroblasts (MEFs) and astrocytes and PTEN-null human tumor cell lines and primary cells were assessed for RAD51 expression (via the Western blot analysis) and DNA damage repair analyses (via alkali comet and γH2AX foci assays). RAD51 foci analysis was used to measure HR-dependent DNA repair. Xrcc2-deficient MEFs served as an HR-deficient control, while the stable knockdown of RAD51 (shRAD51) served to control for the relative RAD51/HR-mediated repair and the phospho-53BP1 foci analysis served to confirm and measure non-homologous end joining (NHEJ) activity in PTEN-deficient and shRAD51-expressing (HRD) lines. Cell proliferation studies were used to measure any potential added sensitivity of PTEN-null cells to the clinically-relevant PARPi, olaparib. RAD51 levels and DNA damage response signaling were assessed in PTEN-mutant brain tumor initiating cells (BTICs) derived from primary and recurrent glioblastoma multiforme (GBM) patients, while expression of RAD51 and its paralogs were examined as a function of the PTEN status in the RNA expression datasets isolated from primary GBM tumor specimens and BTICs. Results: Pten knockout primary murine cells display unaltered RAD51 expression, endogenous and DNA strand break-induced RAD51 foci and robust DNA repair activity. Defective HR was only observed in the cells lacking Xrcc2. Likewise, human glioblastoma multiforme (GBM) cell lines with known PTEN deficiency (U87, PTEN-mutated; U251 and U373, PTEN-null) show apparent expression of RAD51 and display efficient DNA repair activity. Only GBM cells stably expressing shRNAs against RAD51 (shRAD51) display dysfunctional DNA repair activity and reduced proliferative capacity, which is exacerbated by PARPi treatment. Furthermore, GBM patient-derived BTICs displayed robust RAD51 expression and intact DNA damage response signaling in spite of PTEN-inactivating mutations. RNA expression analysis of primary GBM tissue specimens and BTICs demonstrate stable levels of RAD51 and its paralogs (RAD51B, RAD51C, RAD51D, XRCC2, XRCC3, and DMC1), regardless of the PTEN mutational status. Conclusions: Our findings demonstrate definitively that PTEN loss does not alter the RAD51 expression, its paralogs, or the HR activity. Furthermore, deficiency in PTEN alone is not sufficient to impart enhanced sensitivity to PARPi associated with HRD. This study is the first to unequivocally demonstrate that PTEN deficiency is not linked to the RAD51 expression or the HR activity amongst primary neural and non-neural Pten-null cells, PTEN-deficient tumor cell lines, and primary PTEN-mutant GBM patient-derived tissue specimens and BTICs.
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Affiliation(s)
- Asha Sinha
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB R3E 0T6, Canada; (A.S.); (A.S.); (S.H.Y.); (B.K.); (T.K.)
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Ali Saleh
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB R3E 0T6, Canada; (A.S.); (A.S.); (S.H.Y.); (B.K.); (T.K.)
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Raelene Endersby
- Telethon Kids Institute, Perth Children’s Hospital, 15 Hospital Avenue, Perth, WA 6009, Australia;
- Centre for Child Health Research, University of Western Australia, 15 Hospital Avenue, Perth, WA 6009, Australia
| | - Shek H. Yuan
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB R3E 0T6, Canada; (A.S.); (A.S.); (S.H.Y.); (B.K.); (T.K.)
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Chirayu R. Chokshi
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, ON L8S 4L8, Canada; (C.R.C.); (S.K.S.)
| | - Kevin R. Brown
- Donnelly Centre, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada;
| | - Bozena Kuzio
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB R3E 0T6, Canada; (A.S.); (A.S.); (S.H.Y.); (B.K.); (T.K.)
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Tiina Kauppinen
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB R3E 0T6, Canada; (A.S.); (A.S.); (S.H.Y.); (B.K.); (T.K.)
- Neuroscience Research Program, Kleysen Institute for Advanced Medicine, Health Sciences Centre, 710 William Avenue, Winnipeg, MB R3E 0Z3, Canada
| | - Sheila K. Singh
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, ON L8S 4L8, Canada; (C.R.C.); (S.K.S.)
- Department of Surgery, Faculty of Health Sciences, McMaster University, 1200 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Suzanne J. Baker
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, TN 38105-3678, USA;
| | - Peter J. McKinnon
- Department of Genetics, St Jude Children’s Research Hospital, Memphis, TN 38105-3678, USA;
| | - Sachin Katyal
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB R3E 0T6, Canada; (A.S.); (A.S.); (S.H.Y.); (B.K.); (T.K.)
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
- Correspondence: ; Tel.: +1-204-787-2765; Fax: +1-204-787-2190
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249
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Integrative omics analysis reveals relationships of genes with synthetic lethal interactions through a pan-cancer analysis. Comput Struct Biotechnol J 2020; 18:3243-3254. [PMID: 33240468 PMCID: PMC7658657 DOI: 10.1016/j.csbj.2020.10.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 10/10/2020] [Accepted: 10/12/2020] [Indexed: 02/07/2023] Open
Abstract
Synthetic lethality is thought to play an important role in anticancer therapies. Herein, to understand the potential distributions and relationships between synthetic lethal interactions between genes, especially for pairs deriving from different sources, we performed an integrative analysis of genes at multiple molecular levels. Based on inter-species phylogenetic conservation of synthetic lethal interactions, gene pairs from yeast and humans were analyzed; a total of 37,588 candidate gene pairs containing 7,816 genes were collected. Of these, 49.74% of genes had 2–10 interactions, 22.93% were involved in hallmarks of cancer, and 21.61% were identified as core essential genes. Many genes were shown to have important biological roles via functional enrichment analysis, and 65 were identified as potentially crucial in the pathophysiology of cancer. Gene pairs with dysregulated expression patterns had higher prognostic values. Further screening based on mutation and expression levels showed that remaining gene pairs were mainly derived from human predicted or validated pairs, while most predicted pairs from yeast were filtered from analysis. Genes with synthetic lethality were further analyzed with their interactive microRNAs (miRNAs) at the isomiR level which have been widely studied as negatively regulatory molecules. The miRNA–mRNA interaction network revealed that many synthetic lethal genes contributed to the cell cycle (seven of 12 genes), cancer pathways (five of 12 genes), oocyte meiosis, the p53 signaling pathway, and hallmarks of cancer. Our study contributes to the understanding of synthetic lethal interactions and promotes the application of genetic interactions in further cancer precision medicine.
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Key Words
- ACC, adrenocortical carcinoma
- BLCA, bladder urothelial carcinoma
- BRCA, breast invasive carcinoma
- CESC, cervical squamous cell carcinoma and endocervical adenocarcinoma
- CHOL, cholangiocarcinoma
- COAD, colon adenocarcinoma
- Cancer therapy
- DLBC, lymphoid neoplasm diffuse large B-cell lymphoma
- ESCA, esophageal carcinoma
- GBM, glioblastoma multiforme
- HNSC, head and neck squamous cell carcinoma
- KICH, kidney chromophobe
- KIRC, kidney renal clear cell carcinoma
- KIRP, kidney renal papillary cell carcinoma
- LAML, acute myeloid leukemia
- LGG, brain lower grade glioma
- LIHC, liver hepatocellular carcinoma
- LUAD, lung adenocarcinoma
- LUSC, lung squamous cell carcinoma
- MESO, mesothelioma
- OV, ovarian serous cystadenocarcinoma
- PAAD, pancreatic adenocarcinoma
- PCPG, pheochromocytoma and paraganglioma
- PRAD, prostate adenocarcinoma
- Pan-cancer analysis
- READ, rectum adenocarcinoma
- RNA interaction
- SARC, sarcoma
- SKCM, skin cutaneous melanoma
- STAD, stomach adenocarcinoma
- Synthetic lethality
- TGCT, testicular germ cell tumors
- THCA, thyroid carcinoma
- THYM, thymoma
- TSG, tumor suppressor gene
- UCEC, uterine corpus endometrial carcinoma
- UCS, uterine carcinosarcoma
- UVM, uveal melanoma
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250
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Development of synthetic lethality in cancer: molecular and cellular classification. Signal Transduct Target Ther 2020; 5:241. [PMID: 33077733 PMCID: PMC7573576 DOI: 10.1038/s41392-020-00358-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 12/27/2022] Open
Abstract
Recently, genetically targeted cancer therapies have been a topic of great interest. Synthetic lethality provides a new approach for the treatment of mutated genes that were previously considered unable to be targeted in traditional genotype-targeted treatments. The increasing researches and applications in the clinical setting made synthetic lethality a promising anticancer treatment option. However, the current understandings on different conditions of synthetic lethality have not been systematically assessed and the application of synthetic lethality in clinical practice still faces many challenges. Here, we propose a novel and systematic classification of synthetic lethality divided into gene level, pathway level, organelle level, and conditional synthetic lethality, according to the degree of specificity into its biological mechanism. Multiple preclinical findings of synthetic lethality in recent years will be reviewed and classified under these different categories. Moreover, synthetic lethality targeted drugs in clinical practice will be briefly discussed. Finally, we will explore the essential implications of this classification as well as its prospects in eliminating existing challenges and the future directions of synthetic lethality.
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