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Tlemsani C, Heske CM, Elloumi F, Pongor L, Khandagale P, Varma S, Luna A, Meltzer PS, Khan J, Reinhold WC, Pommier Y. Sarcoma_CellminerCDB: A tool to interrogate the genomic and functional characteristics of a comprehensive collection of sarcoma cell lines. iScience 2024; 27:109781. [PMID: 38868205 PMCID: PMC11167437 DOI: 10.1016/j.isci.2024.109781] [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] [Received: 10/26/2023] [Revised: 12/28/2023] [Accepted: 04/15/2024] [Indexed: 06/14/2024] Open
Abstract
Sarcomas are a diverse group of rare malignancies composed of multiple different clinical and molecular subtypes. Due to their rarity and heterogeneity, basic, translational, and clinical research in sarcoma has trailed behind that of other cancers. Outcomes for patients remain generally poor due to an incomplete understanding of disease biology and a lack of novel therapies. To address some of the limitations impeding preclinical sarcoma research, we have developed Sarcoma_CellMinerCDB, a publicly available interactive tool that merges publicly available sarcoma cell line data and newly generated omics data to create a comprehensive database of genomic, transcriptomic, methylomic, proteomic, metabolic, and pharmacologic data on 133 annotated sarcoma cell lines. The reproducibility, functionality, biological relevance, and therapeutic applications of Sarcoma_CellMinerCDB described herein are powerful tools to address and generate biological questions and test hypotheses for translational research. Sarcoma_CellMinerCDB (https://discover.nci.nih.gov/SarcomaCellMinerCDB) aims to contribute to advancing the preclinical study of sarcoma.
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Affiliation(s)
- Camille Tlemsani
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
- Department of Medical Oncology, Cochin Hospital, Paris Cancer Institute CARPEM, Université Paris Cité, APHP. Centre, Paris, France
- Institut Cochin, INSERM U1016, CNRS UMR8104, Paris Cancer Institute CARPEM, Université Paris Cité, Paris, France
| | - Christine M. Heske
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fathi Elloumi
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Lorinc Pongor
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
- Hungarian Centre of Excellence for Molecular Medicine, Cancer Genomics and Epigenetics Core Group, Szeged, Hungary
| | - Prashant Khandagale
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sudhir Varma
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Augustin Luna
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
- Computational Biology Branch, National Library of Medicine, NIH, Bethesda, Maryland 20892, USA
| | - Paul S. Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - William C. Reinhold
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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Pal Choudhuri S, Girard L, Lim JYS, Wise JF, Freitas B, Yang D, Wong E, Hamilton S, Chien VD, Kim YJ, Gilbreath C, Zhong J, Phat S, Myers DT, Christensen CL, Mazloom-Farsibaf H, Stanzione M, Wong KK, Hung YP, Farago AF, Meador CB, Dyson NJ, Lawrence MS, Wu S, Drapkin BJ. Acquired Cross-Resistance in Small Cell Lung Cancer due to Extrachromosomal DNA Amplification of MYC Paralogs. Cancer Discov 2024; 14:804-827. [PMID: 38386926 PMCID: PMC11061613 DOI: 10.1158/2159-8290.cd-23-0656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 12/15/2023] [Accepted: 02/20/2024] [Indexed: 02/24/2024]
Abstract
Small cell lung cancer (SCLC) presents as a highly chemosensitive malignancy but acquires cross-resistance after relapse. This transformation is nearly inevitable in patients but has been difficult to capture in laboratory models. Here, we present a preclinical system that recapitulates acquired cross-resistance, developed from 51 patient-derived xenograft (PDX) models. Each model was tested in vivo against three clinical regimens: cisplatin plus etoposide, olaparib plus temozolomide, and topotecan. These drug-response profiles captured hallmark clinical features of SCLC, such as the emergence of treatment-refractory disease after early relapse. For one patient, serial PDX models revealed that cross-resistance was acquired through MYC amplification on extrachromosomal DNA (ecDNA). Genomic and transcriptional profiles of the full PDX panel revealed that MYC paralog amplifications on ecDNAs were recurrent in relapsed cross-resistant SCLC, and this was corroborated in tumor biopsies from relapsed patients. We conclude that ecDNAs with MYC paralogs are recurrent drivers of cross-resistance in SCLC. SIGNIFICANCE SCLC is initially chemosensitive, but acquired cross-resistance renders this disease refractory to further treatment and ultimately fatal. The genomic drivers of this transformation are unknown. We use a population of PDX models to discover that amplifications of MYC paralogs on ecDNA are recurrent drivers of acquired cross-resistance in SCLC. This article is featured in Selected Articles from This Issue, p. 695.
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Affiliation(s)
- Shreoshi Pal Choudhuri
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Internal Medicine and Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Luc Girard
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jun Yi Stanley Lim
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jillian F. Wise
- Massachusetts General Hospital Cancer Center, Krantz Family Center for Cancer Research, Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Braeden Freitas
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Internal Medicine and Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Di Yang
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Internal Medicine and Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Edmond Wong
- Massachusetts General Hospital Cancer Center, Krantz Family Center for Cancer Research, Harvard Medical School, Boston, Massachusetts
| | - Seth Hamilton
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Internal Medicine and Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Victor D. Chien
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Internal Medicine and Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yoon Jung Kim
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Collin Gilbreath
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jun Zhong
- Massachusetts General Hospital Cancer Center, Krantz Family Center for Cancer Research, Harvard Medical School, Boston, Massachusetts
| | - Sarah Phat
- Massachusetts General Hospital Cancer Center, Krantz Family Center for Cancer Research, Harvard Medical School, Boston, Massachusetts
| | - David T. Myers
- Massachusetts General Hospital Cancer Center, Krantz Family Center for Cancer Research, Harvard Medical School, Boston, Massachusetts
| | | | - Hanieh Mazloom-Farsibaf
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Marcello Stanzione
- Massachusetts General Hospital Cancer Center, Krantz Family Center for Cancer Research, Harvard Medical School, Boston, Massachusetts
| | - Kwok-Kin Wong
- Perlmutter Cancer Center, NYU Langone Health, New York, New York
| | - Yin P. Hung
- Massachusetts General Hospital Cancer Center, Krantz Family Center for Cancer Research, Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Anna F. Farago
- Massachusetts General Hospital Cancer Center, Krantz Family Center for Cancer Research, Harvard Medical School, Boston, Massachusetts
| | - Catherine B. Meador
- Massachusetts General Hospital Cancer Center, Krantz Family Center for Cancer Research, Harvard Medical School, Boston, Massachusetts
| | - Nicholas J. Dyson
- Massachusetts General Hospital Cancer Center, Krantz Family Center for Cancer Research, Harvard Medical School, Boston, Massachusetts
| | - Michael S. Lawrence
- Massachusetts General Hospital Cancer Center, Krantz Family Center for Cancer Research, Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Sihan Wu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Benjamin J. Drapkin
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Internal Medicine and Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
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Barata T, Pereira V, Pires das Neves R, Rocha M. Reconstruction of cell-specific models capturing the influence of metabolism on DNA methylation in cancer. Comput Biol Med 2024; 170:108052. [PMID: 38308868 DOI: 10.1016/j.compbiomed.2024.108052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 02/05/2024]
Abstract
The imbalance of epigenetic regulatory mechanisms such as DNA methylation, which can promote aberrant gene expression profiles without affecting the DNA sequence, may cause the deregulation of signaling, regulatory, and metabolic processes, contributing to a cancerous phenotype. Since some metabolites are substrates and cofactors of epigenetic regulators, their availability can be affected by characteristic cancer cell metabolic shifts, feeding cancer onset and progression through epigenetic deregulation. Hence, there is a need to study the influence of cancer metabolic reprogramming in DNA methylation to design new effective treatments. In this study, a generic Genome-Scale Metabolic Model (GSMM) of a human cell, integrating DNA methylation or demethylation reactions, was obtained and used for the reconstruction of Genome-Scale Metabolic Models enhanced with Enzymatic Constraints using Kinetic and Omics data (GECKOs) of 31 cancer cell lines. Furthermore, cell-line-specific DNA methylation levels were included in the models, as coefficients of a DNA composition pseudo-reaction, to depict the influence of metabolism over global DNA methylation in each of the cancer cell lines. Flux simulations demonstrated the ability of these models to provide simulated fluxes of exchange reactions similar to the equivalent experimentally measured uptake/secretion rates and to make good functional predictions. In addition, simulations found metabolic pathways, reactions and enzymes directly or inversely associated with the gene promoter methylation. Two potential candidates for targeted cancer epigenetic therapy were identified.
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Affiliation(s)
- Tânia Barata
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal; CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Vítor Pereira
- Centre of Biological Engineering, University of Minho - Campus de Gualtar, Braga, Portugal; LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Ricardo Pires das Neves
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal; CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-517 Coimbra, Portugal; IIIUC-Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Miguel Rocha
- Centre of Biological Engineering, University of Minho - Campus de Gualtar, Braga, Portugal; LABBELS - Associate Laboratory, Braga/Guimarães, Portugal; Department of Informatics, University of Minho, Portugal.
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Luo N, Mei Z, Zhang Q, Tang H, Wan R, Deng A, Zou X, Lv C. TMX family genes and their association with prognosis, immune infiltration, and chemotherapy in human pan-cancer. Aging (Albany NY) 2023; 15:15064-15083. [PMID: 38147024 PMCID: PMC10781458 DOI: 10.18632/aging.205332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/10/2023] [Indexed: 12/27/2023]
Abstract
BACKGROUND The thioredoxin (TMX) system, an important redox system, plays crucial roles in several immune-related diseases. However, there is limited research on the correlation of TMX family gene expression with human pan-cancer prognosis, tumor microenvironment (TME), and immunotherapy. METHODS Based on the integration of several bioinformatics analysis methods, we explored the expression levels and prognostic value of TMX family members in pan-cancer and analyzed their association between TME, immune infiltration, stemness scores, and drug sensitivity. Using KEGG enrichment analysis, we explored the potential signaling pathways of their regulation. Additionally, we conducted a transwell assay to verify the relationship between TMX family gene expression and epithelial-mesenchymal transition (EMT) in liver cancer. RESULTS Expression of the TMX family genes was shown to have an obvious intratumoral heterogeneity. In some cancers, TMX family members expression was also been found to correlate with poor prognosis of patients. Furthermore, TMX family genes may serve important roles in TME. The expression of TMX family genes was found to have a strong correlation with the stromal scores, immune scores, DNAss and RNAss in pan-cancer. Specifically, the expression levels of TMX family genes have been found to be associated with immune subtypes of renal clear cell carcinoma and liver hepatocellular carcinoma. High TMX2 expression promote EMT in liver cancer. CONCLUSIONS The findings of this study may elucidate the biological roles of TMX family genes as potential targets for pan-cancer and also offer valuable insights for further investigating how these genes function in the development and spreading of cancer.
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Affiliation(s)
- Na Luo
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, China
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Zhiqiang Mei
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Qiqi Zhang
- Degree Office, The Graduate School of Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Hong Tang
- Department of Pathology, Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Runlan Wan
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Anni Deng
- Department of Pediatrics, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Xiaopan Zou
- Breast and Thyroid Surgery, Renmin Hospital, Jilin University, Changchun 130024, Jilin, China
| | - Chaoxiang Lv
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, China
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5
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Tejedor JR, Peñarroya A, Gancedo-Verdejo J, Santamarina-Ojeda P, Pérez RF, López-Tamargo S, Díez-Borge A, Alba-Linares JJ, González-Del-Rey N, Urdinguio RG, Mangas C, Roberti A, López V, Morales-Ruiz T, Ariza RR, Roldán-Arjona T, Meijón M, Valledor L, Cañal MJ, Fernández-Martínez D, Fernández-Hevia M, Jiménez-Fonseca P, García-Flórez LJ, Fernández AF, Fraga MF. CRISPR/dCAS9-mediated DNA demethylation screen identifies functional epigenetic determinants of colorectal cancer. Clin Epigenetics 2023; 15:133. [PMID: 37612734 PMCID: PMC10464368 DOI: 10.1186/s13148-023-01546-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/03/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND Promoter hypermethylation of tumour suppressor genes is frequently observed during the malignant transformation of colorectal cancer (CRC). However, whether this epigenetic mechanism is functional in cancer or is a mere consequence of the carcinogenic process remains to be elucidated. RESULTS In this work, we performed an integrative multi-omic approach to identify gene candidates with strong correlations between DNA methylation and gene expression in human CRC samples and a set of 8 colon cancer cell lines. As a proof of concept, we combined recent CRISPR-Cas9 epigenome editing tools (dCas9-TET1, dCas9-TET-IM) with a customized arrayed gRNA library to modulate the DNA methylation status of 56 promoters previously linked with strong epigenetic repression in CRC, and we monitored the potential functional consequences of this DNA methylation loss by means of a high-content cell proliferation screen. Overall, the epigenetic modulation of most of these DNA methylated regions had a mild impact on the reactivation of gene expression and on the viability of cancer cells. Interestingly, we found that epigenetic reactivation of RSPO2 in the tumour context was associated with a significant impairment in cell proliferation in p53-/- cancer cell lines, and further validation with human samples demonstrated that the epigenetic silencing of RSPO2 is a mid-late event in the adenoma to carcinoma sequence. CONCLUSIONS These results highlight the potential role of DNA methylation as a driver mechanism of CRC and paves the way for the identification of novel therapeutic windows based on the epigenetic reactivation of certain tumour suppressor genes.
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Affiliation(s)
- Juan Ramón Tejedor
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), 33940, El Entrego, Asturias, Spain
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), 28029, Madrid, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Alfonso Peñarroya
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), 33940, El Entrego, Asturias, Spain
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
| | - Javier Gancedo-Verdejo
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), 33940, El Entrego, Asturias, Spain
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), 28029, Madrid, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Pablo Santamarina-Ojeda
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), 28029, Madrid, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Raúl F Pérez
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), 33940, El Entrego, Asturias, Spain
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), 28029, Madrid, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Sara López-Tamargo
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Ana Díez-Borge
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Viralgen Vector Core, 20009, San Sebastián, Gipuzkoa, Spain
| | - Juan J Alba-Linares
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), 33940, El Entrego, Asturias, Spain
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Nerea González-Del-Rey
- Department of Organisms and Systems Biology, Institute of Biotechnology of Asturias, University of Oviedo, 33071, Oviedo, Asturias, Spain
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Rocío G Urdinguio
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), 28029, Madrid, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Cristina Mangas
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Annalisa Roberti
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), 33940, El Entrego, Asturias, Spain
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
| | - Virginia López
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Teresa Morales-Ruiz
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain
- Department of Genetics, University of Córdoba, 14071, Córdoba, Spain
| | - Rafael R Ariza
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain
- Department of Genetics, University of Córdoba, 14071, Córdoba, Spain
| | - Teresa Roldán-Arjona
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain
- Department of Genetics, University of Córdoba, 14071, Córdoba, Spain
| | - Mónica Meijón
- Department of Organisms and Systems Biology, Institute of Biotechnology of Asturias, University of Oviedo, 33071, Oviedo, Asturias, Spain
| | - Luis Valledor
- Department of Organisms and Systems Biology, Institute of Biotechnology of Asturias, University of Oviedo, 33071, Oviedo, Asturias, Spain
| | - María Jesús Cañal
- Department of Organisms and Systems Biology, Institute of Biotechnology of Asturias, University of Oviedo, 33071, Oviedo, Asturias, Spain
| | - Daniel Fernández-Martínez
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
- Division of General Surgery, Department of Colorectal Surgery, Central University Hospital of Asturias (HUCA), 33011, Oviedo, Asturias, Spain
| | - María Fernández-Hevia
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
- Division of General Surgery, Department of Colorectal Surgery, Central University Hospital of Asturias (HUCA), 33011, Oviedo, Asturias, Spain
| | - Paula Jiménez-Fonseca
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Division of Oncology, Department of Medical Oncology, Central University Hospital of Asturias (HUCA), 33011, Oviedo, Asturias, Spain
| | - Luis J García-Flórez
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
- Division of General Surgery, Department of Colorectal Surgery, Central University Hospital of Asturias (HUCA), 33011, Oviedo, Asturias, Spain
- Department of Surgery and Medical Surgical Specialties, University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Agustín F Fernández
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), 33940, El Entrego, Asturias, Spain.
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain.
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), 28029, Madrid, Spain.
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain.
| | - Mario F Fraga
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), 33940, El Entrego, Asturias, Spain.
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain.
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), 28029, Madrid, Spain.
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain.
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Choudhuri SP, Girard L, Lim JYS, Wise JF, Freitas B, Yang D, Wong E, Hamilton S, Chien VD, Gilbreath C, Zhong J, Phat S, Myers DT, Christensen CL, Stanzione M, Wong KK, Farago AF, Meador CB, Dyson NJ, Lawrence MS, Wu S, Drapkin BJ. Acquired Cross-resistance in Small Cell Lung Cancer due to Extrachromosomal DNA Amplification of MYC paralogs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.23.546278. [PMID: 37425738 PMCID: PMC10327110 DOI: 10.1101/2023.06.23.546278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Small cell lung cancer (SCLC) presents as a highly chemosensitive malignancy but acquires cross-resistance after relapse. This transformation is nearly inevitable in patients but has been difficult to capture in laboratory models. Here we present a pre-clinical system that recapitulates acquired cross-resistance in SCLC, developed from 51 patient-derived xenografts (PDXs). Each model was tested for in vivo sensitivity to three clinical regimens: cisplatin plus etoposide, olaparib plus temozolomide, and topotecan. These functional profiles captured hallmark clinical features, such as the emergence of treatment-refractory disease after early relapse. Serially derived PDX models from the same patient revealed that cross-resistance was acquired through a MYC amplification on extrachromosomal DNA (ecDNA). Genomic and transcriptional profiles of the full PDX panel revealed that this was not unique to one patient, as MYC paralog amplifications on ecDNAs were recurrent among cross-resistant models derived from patients after relapse. We conclude that ecDNAs with MYC paralogs are recurrent drivers of cross-resistance in SCLC. SIGNIFICANCE SCLC is initially chemosensitive, but acquired cross-resistance renders this disease refractory to further treatment and ultimately fatal. The genomic drivers of this transformation are unknown. We use a population of PDX models to discover that amplifications of MYC paralogs on ecDNA are recurrent drivers of acquired cross-resistance in SCLC.
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7
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Reinhold WC, Wilson K, Elloumi F, Bradwell KR, Ceribelli M, Varma S, Wang Y, Duveau D, Menon N, Trepel J, Zhang X, Klumpp-Thomas C, Micheal S, Shinn P, Luna A, Thomas C, Pommier Y. CellMinerCDB: NCATS Is a Web-Based Portal Integrating Public Cancer Cell Line Databases for Pharmacogenomic Explorations. Cancer Res 2023; 83:1941-1952. [PMID: 37140427 PMCID: PMC10330642 DOI: 10.1158/0008-5472.can-22-2996] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/27/2023] [Accepted: 04/25/2023] [Indexed: 05/05/2023]
Abstract
Major advances have been made in the field of precision medicine for treating cancer. However, many open questions remain that need to be answered to realize the goal of matching every patient with cancer to the most efficacious therapy. To facilitate these efforts, we have developed CellMinerCDB: National Center for Advancing Translational Sciences (NCATS; https://discover.nci.nih.gov/rsconnect/cellminercdb_ncats/), which makes available activity information for 2,675 drugs and compounds, including multiple nononcology drugs and 1,866 drugs and compounds unique to the NCATS. CellMinerCDB: NCATS comprises 183 cancer cell lines, with 72 unique to NCATS, including some from previously understudied tissues of origin. Multiple forms of data from different institutes are integrated, including single and combination drug activity, DNA copy number, methylation and mutation, transcriptome, protein levels, histone acetylation and methylation, metabolites, CRISPR, and miscellaneous signatures. Curation of cell lines and drug names enables cross-database (CDB) analyses. Comparison of the datasets is made possible by the overlap between cell lines and drugs across databases. Multiple univariate and multivariate analysis tools are built-in, including linear regression and LASSO. Examples have been presented here for the clinical topoisomerase I (TOP1) inhibitors topotecan and irinotecan/SN-38. This web application provides both substantial new data and significant pharmacogenomic integration, allowing exploration of interrelationships. SIGNIFICANCE CellMinerCDB: NCATS provides activity information for 2,675 drugs in 183 cancer cell lines and analysis tools to facilitate pharmacogenomic research and to identify determinants of response.
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Affiliation(s)
- William C. Reinhold
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Kelli Wilson
- National Center for Advancing Translational Sciences, NIH Bethesda, MD 20892, USA
| | - Fathi Elloumi
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | - Michele Ceribelli
- National Center for Advancing Translational Sciences, NIH Bethesda, MD 20892, USA
| | - Sudhir Varma
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
- HiThru Analytics LLC, Princeton, NJ 08540, USA
| | - Yanghsin Wang
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
- ICF International Inc., Fairfax, VA 22031, USA
| | - Damien Duveau
- National Center for Advancing Translational Sciences, NIH Bethesda, MD 20892, USA
| | - Nikhil Menon
- National Center for Advancing Translational Sciences, NIH Bethesda, MD 20892, USA
| | - Jane Trepel
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Xiaohu Zhang
- National Center for Advancing Translational Sciences, NIH Bethesda, MD 20892, USA
| | | | - Samuel Micheal
- National Center for Advancing Translational Sciences, NIH Bethesda, MD 20892, USA
| | - Paul Shinn
- National Center for Advancing Translational Sciences, NIH Bethesda, MD 20892, USA
| | - Augustin Luna
- cBio Center, Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA
| | - Craig Thomas
- National Center for Advancing Translational Sciences, NIH Bethesda, MD 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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8
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Jiang J, Qu H, Zhan X, Liu D, Liang T, Chen L, Huang S, Sun X, Chen J, Chen T, Li H, Yao Y, Liu C. Identification of osteosarcoma m6A-related prognostic biomarkers using artificial intelligence: RBM15. Sci Rep 2023; 13:5255. [PMID: 37002245 PMCID: PMC10066227 DOI: 10.1038/s41598-023-28739-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 01/24/2023] [Indexed: 04/03/2023] Open
Abstract
Osteosarcoma has the worst prognosis among malignant bone tumors, and effective biomarkers are lacking. Our study aims to explore m6A-related and immune-related biomarkers. Gene expression profiles of osteosarcoma and healthy controls were downloaded from multiple public databases, and their m6A-based gene expression was utilized for tumor typing using bioinformatics. Subsequently, a prognostic model for osteosarcoma was constructed using the least absolute shrinkage and selection operator and multivariate Cox regression analysis, and its immune cell composition was calculated using the CIBERSORTx algorithm. We also performed drug sensitivity analysis for these two genes. Finally, analysis was validated using immunohistochemistry. We also examined the RBM15 gene by qRT-PCR in an in vitro experiment. We collected routine blood data from 1738 patients diagnosed with osteosarcoma and 24,344 non-osteosarcoma patients and used two independent sample t tests to verify the accuracy of the CIBERSORTx analysis for immune cell differences. The analysis based on m6A gene expression tumor typing was most reliable using the two typing methods. The prognostic model based on the two genes constituting RNA-binding motif protein 15 (RBM15) and YTDC1 had a much lower survival rate for patients in the high-risk group than those in the low-risk group (P < 0.05). CIBERSORTx immune cell component analysis demonstrated that RBM15 showed a negative and positive correlation with T cells gamma delta and activated natural killer cells, respectively. Drug sensitivity analysis showed that these two genes showed varying degrees of correlation with multiple drugs. The results of immunohistochemistry revealed that the expression of these two genes was significantly higher in osteosarcoma than in paraneoplastic tissues. The results of qRT-PCR experiments showed that the expression of RBM15 was significantly higher in both osteosarcomas than in the control cell lines. Absolute lymphocyte value, lymphocyte percentage, hematocrit and erythrocyte count were lower in osteosarcoma than in the control group (P < 0.001). RBM15 and YTHDC1 can serve as potential prognostic biomarkers associated with m6A in osteosarcoma.
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Affiliation(s)
- Jie Jiang
- The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Haishun Qu
- Department of Traditional Chinese Medicine, The People's Hospital of Guangxi Zhuang Autonmous Region, Nanning, 530016, People's Republic of China
| | - Xinli Zhan
- The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Dachang Liu
- The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Tuo Liang
- The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Liyi Chen
- The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Shengsheng Huang
- The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Xuhua Sun
- The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Jiarui Chen
- The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Tianyou Chen
- The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Hao Li
- The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Yuanlin Yao
- The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Chong Liu
- The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China.
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9
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Reddin IG, Fenton TR, Wass MN, Michaelis M. Large inherent variability in data derived from highly standardised cell culture experiments. Pharmacol Res 2023; 188:106671. [PMID: 36681368 DOI: 10.1016/j.phrs.2023.106671] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 01/12/2023] [Accepted: 01/17/2023] [Indexed: 01/19/2023]
Abstract
Cancer drug development is hindered by high clinical attrition rates, which are blamed on weak predictive power by preclinical models and limited replicability of preclinical findings. However, the technically feasible level of replicability remains unknown. To fill this gap, we conducted an analysis of data from the NCI60 cancer cell line screen (2.8 million compound/cell line experiments), which is to our knowledge the largest depository of experiments that have been repeatedly performed over decades. The findings revealed profound intra-laboratory data variability, although all experiments were executed following highly standardised protocols that avoid all known confounders of data quality. All compound/ cell line combinations with > 100 independent biological replicates displayed maximum GI50 (50% growth inhibition) fold changes (highest/ lowest GI50) > 5% and 70.5% displayed maximum fold changes > 1000. The highest maximum fold change was 3.16 × 1010 (lowest GI50: 7.93 ×10-10 µM, highest GI50: 25.0 µM). FDA-approved drugs and experimental agents displayed similar variation. Variability remained high after outlier removal, when only considering experiments that tested drugs at the same concentration range, and when only considering NCI60-provided quality-controlled data. In conclusion, high variability is an intrinsic feature of anti-cancer drug testing, even among standardised experiments in a world-leading research environment. Awareness of this inherent variability will support realistic data interpretation and inspire research to improve data robustness. Further research will have to show whether the inclusion of a wider variety of model systems, such as animal and/ or patient-derived models, may improve data robustness.
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Affiliation(s)
- Ian G Reddin
- School of Biosciences, University of Kent, Canterbury, UK; Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Tim R Fenton
- School of Biosciences, University of Kent, Canterbury, UK; Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Mark N Wass
- School of Biosciences, University of Kent, Canterbury, UK.
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10
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Martín A, Epifano C, Vilaplana-Marti B, Hernández I, Macías RIR, Martínez-Ramírez Á, Cerezo A, Cabezas-Sainz P, Garranzo-Asensio M, Amarilla-Quintana S, Gómez-Domínguez D, Caleiras E, Camps J, Gómez-López G, Gómez de Cedrón M, Ramírez de Molina A, Barderas R, Sánchez L, Velasco-Miguel S, Pérez de Castro I. Mitochondrial RNA methyltransferase TRMT61B is a new, potential biomarker and therapeutic target for highly aneuploid cancers. Cell Death Differ 2023; 30:37-53. [PMID: 35869285 PMCID: PMC9883398 DOI: 10.1038/s41418-022-01044-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/27/2022] [Accepted: 07/09/2022] [Indexed: 02/01/2023] Open
Abstract
Despite being frequently observed in cancer cells, chromosomal instability (CIN) and its immediate consequence, aneuploidy, trigger adverse effects on cellular homeostasis that need to be overcome by anti-stress mechanisms. As such, these safeguard responses represent a tumor-specific Achilles heel, since CIN and aneuploidy are rarely observed in normal cells. Recent data have revealed that epitranscriptomic marks catalyzed by RNA-modifying enzymes change under various stress insults. However, whether aneuploidy is associated with such RNA modifying pathways remains to be determined. Through an in silico search for aneuploidy biomarkers in cancer cells, we found TRMT61B, a mitochondrial RNA methyltransferase enzyme, to be associated with high levels of aneuploidy. Accordingly, TRMT61B protein levels are increased in tumor cell lines with an imbalanced karyotype as well as in different tumor types when compared to control tissues. Interestingly, while TRMT61B depletion induces senescence in melanoma cell lines with low levels of aneuploidy, it leads to apoptosis in cells with high levels. The therapeutic potential of these results was further validated by targeting TRMT61B in transwell and xenografts assays. We show that TRM61B depletion reduces the expression of several mitochondrial encoded proteins and limits mitochondrial function. Taken together, these results identify a new biomarker of aneuploidy in cancer cells that could potentially be used to selectively target highly aneuploid tumors.
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Affiliation(s)
- Alberto Martín
- Gene Therapy Unit, Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III (ISCIII), Madrid, Spain.
| | - Carolina Epifano
- Gene Therapy Unit, Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Borja Vilaplana-Marti
- Gene Therapy Unit, Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Iván Hernández
- Gene Therapy Unit, Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Rocío I R Macías
- Experimental Hepatology and Drug Targeting (HEVEPHARM) Group, University of Salamanca, Biomedical Research Institute of Salamanca (IBSAL), Salamanca, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, Madrid, Spain
| | - Ángel Martínez-Ramírez
- Department of Molecular Cytogenetics, MD Anderson Cancer Center, Madrid, Spain
- Oncohematology Cytogenetics Laboratory, Eurofins-Megalab, Madrid, Spain
| | - Ana Cerezo
- Lilly Cell Signaling and Immunometabolism Section, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Pablo Cabezas-Sainz
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Campus de Lugo, 27002, Lugo, Spain
| | - Maria Garranzo-Asensio
- Chronic Disease Program (UFIEC), Instituto de Salud Carlos III (ISCIII), E-28220, Madrid, Spain
| | - Sandra Amarilla-Quintana
- Gene Therapy Unit, Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Programa de Doctorado UNED-ISCIII Ciencias Biomédicas y Salud Pública, Universidad Nacional de Educación a Distancia (UNED), Madrid, Spain
| | - Déborah Gómez-Domínguez
- Gene Therapy Unit, Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Eduardo Caleiras
- Histopathology Core Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Jordi Camps
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, Institut d'Investigacio´ Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Gonzalo Gómez-López
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Marta Gómez de Cedrón
- Molecular Oncology Group, Precision Nutrition and Cancer Program, IMDEA FOOD, CEI UAM+CSIC, Madrid, Spain
| | - Ana Ramírez de Molina
- Molecular Oncology Group, Precision Nutrition and Cancer Program, IMDEA FOOD, CEI UAM+CSIC, Madrid, Spain
| | - Rodrigo Barderas
- Chronic Disease Program (UFIEC), Instituto de Salud Carlos III (ISCIII), E-28220, Madrid, Spain
| | - Laura Sánchez
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Campus de Lugo, 27002, Lugo, Spain
| | - Susana Velasco-Miguel
- Lilly Cell Signaling and Immunometabolism Section, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ignacio Pérez de Castro
- Gene Therapy Unit, Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III (ISCIII), Madrid, Spain.
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11
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Pongor LS, Tlemsani C, Elloumi F, Arakawa Y, Jo U, Gross JM, Mosavarpour S, Varma S, Kollipara RK, Roper N, Teicher BA, Aladjem MI, Reinhold W, Thomas A, Minna JD, Johnson JE, Pommier Y. Integrative epigenomic analyses of small cell lung cancer cells demonstrates the clinical translational relevance of gene body methylation. iScience 2022; 25:105338. [DOI: 10.1016/j.isci.2022.105338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/15/2022] [Accepted: 10/10/2022] [Indexed: 10/31/2022] Open
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12
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Heumos S, Dehn S, Bräutigam K, Codrea MC, Schürch CM, Lauer UM, Nahnsen S, Schindler M. Multiomics surface receptor profiling of the NCI-60 tumor cell panel uncovers novel theranostics for cancer immunotherapy. Cancer Cell Int 2022; 22:311. [PMID: 36221114 PMCID: PMC9555072 DOI: 10.1186/s12935-022-02710-y] [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] [Received: 07/25/2022] [Accepted: 08/30/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Immunotherapy with immune checkpoint inhibitors (ICI) has revolutionized cancer therapy. However, therapeutic targeting of inhibitory T cell receptors such as PD-1 not only initiates a broad immune response against tumors, but also causes severe adverse effects. An ideal future stratified immunotherapy would interfere with cancer-specific cell surface receptors only. METHODS To identify such candidates, we profiled the surface receptors of the NCI-60 tumor cell panel via flow cytometry. The resulting surface receptor expression data were integrated into proteomic and transcriptomic NCI-60 datasets applying a sophisticated multiomics multiple co-inertia analysis (MCIA). This allowed us to identify surface profiles for skin, brain, colon, kidney, and bone marrow derived cell lines and cancer entity-specific cell surface receptor biomarkers for colon and renal cancer. RESULTS For colon cancer, identified biomarkers are CD15, CD104, CD324, CD326, CD49f, and for renal cancer, CD24, CD26, CD106 (VCAM1), EGFR, SSEA-3 (B3GALT5), SSEA-4 (TMCC1), TIM1 (HAVCR1), and TRA-1-60R (PODXL). Further data mining revealed that CD106 (VCAM1) in particular is a promising novel immunotherapeutic target for the treatment of renal cancer. CONCLUSION Altogether, our innovative multiomics analysis of the NCI-60 panel represents a highly valuable resource for uncovering surface receptors that could be further exploited for diagnostic and therapeutic purposes in the context of cancer immunotherapy.
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Affiliation(s)
- Simon Heumos
- Quantitative Biology Center (QBiC), University of Tübingen, 72076, Tübingen, Germany.,Biomedical Data Science, Dept. of Computer Science, University of Tübingen, 72076, Tübingen, Germany
| | - Sandra Dehn
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | | | - Marius C Codrea
- Quantitative Biology Center (QBiC), University of Tübingen, 72076, Tübingen, Germany
| | - Christian M Schürch
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Ulrich M Lauer
- Department of Internal Medicine VIII, Medical Oncology and Pneumology, Virotherapy Center Tübingen (VCT), Medical University Hospital Tübingen, 72076, Tübingen, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Partner Site Tübingen, 72076, Tübingen, Germany
| | - Sven Nahnsen
- Quantitative Biology Center (QBiC), University of Tübingen, 72076, Tübingen, Germany.,Biomedical Data Science, Dept. of Computer Science, University of Tübingen, 72076, Tübingen, Germany
| | - Michael Schindler
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany.
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13
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Can Schlafen 11 Help to Stratify Ovarian Cancer Patients Treated with DNA-Damaging Agents? Cancers (Basel) 2022; 14:cancers14102353. [PMID: 35625957 PMCID: PMC9139752 DOI: 10.3390/cancers14102353] [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] [Received: 03/25/2022] [Revised: 04/25/2022] [Accepted: 05/06/2022] [Indexed: 02/04/2023] Open
Abstract
Platinum-based chemotherapy has been the cornerstone of systemic treatment in ovarian cancer. Since no validated molecular predictive markers have been identified yet, the response to platinum-based chemotherapy has been evaluated clinically, based on platinum-free interval. The new promising marker Schlafen 11 seems to correlate with sensitivity or resistance to DNA-damaging agents, including platinum compounds or PARP inhibitors in various types of cancer. We provide background information about the function of Schlafen 11, its evaluation in tumor tissue, and its prevalence in ovarian cancer. We discuss the current evidence of the correlation of Schlafen 11 expression in ovarian cancer with treatment outcomes and the potential use of Schlafen 11 as the key predictive and prognostic marker that could help to better stratify ovarian cancer patients treated with platinum-based chemotherapy or PARP inhibitors. We also provide perspectives on future directions in the research on this promising marker.
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14
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Zhu C, Zhang S, Liu D, Wang Q, Yang N, Zheng Z, Wu Q, Zhou Y. A Novel Gene Prognostic Signature Based on Differential DNA Methylation in Breast Cancer. Front Genet 2021; 12:742578. [PMID: 34956313 PMCID: PMC8693898 DOI: 10.3389/fgene.2021.742578] [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: 07/16/2021] [Accepted: 11/15/2021] [Indexed: 12/11/2022] Open
Abstract
Background: DNA methylation played essential roles in regulating gene expression. The impact of DNA methylation status on the occurrence and development of cancers has been well demonstrated. However, little is known about its prognostic role in breast cancer (BC). Materials: The Illumina Human Methylation450 array (450k array) data of BC was downloaded from the UCSC xena database. Transcriptomic data of BC was downloaded from the Cancer Genome Atlas (TCGA) database. Firstly, we used univariate and multivariate Cox regression analysis to screen out independent prognostic CpGs, and then we identified methylation-associated prognosis subgroups by consensus clustering. Next, a methylation prognostic model was developed using multivariate Cox analysis and was validated with the Illumina Human Methylation27 array (27k array) dataset of BC. We then screened out differentially expressed genes (DEGs) between methylation high-risk and low-risk groups and constructed a methylation-based gene prognostic signature. Further, we validated the gene signature with three subgroups of the TCGA-BRCA dataset and an external dataset GSE146558 from the Gene Expression Omnibus (GEO) database. Results: We established a methylation prognostic signature and a methylation-based gene prognostic signature, and there was a close positive correlation between them. The gene prognostic signature involved six genes: IRF2, KCNJ11, ZDHHC9, LRP11, PCMT1, and TMEM70. We verified their expression in mRNA and protein levels in BC. Both methylation and methylation-based gene prognostic signatures showed good prognostic stratification ability. The AUC values of 3-years, 5-years overall survival (OS) were 0.737, 0.744 in the methylation signature and 0.725, 0.715 in the gene signature, respectively. In the validation groups, high-risk patients were confirmed to have poorer OS. The AUC values of 3 years were 0.757, 0.735, 0.733 in the three subgroups of TCGA dataset and 0.635 in GSE146558 dataset. Conclusion: This study revealed the DNA methylation landscape and established promising methylation and methylation-based gene prognostic signatures that could serve as potential prognostic biomarkers and therapeutic targets.
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Affiliation(s)
- Chunmei Zhu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Shuyuan Zhang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Di Liu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qingqing Wang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ningning Yang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhewen Zheng
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qiuji Wu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yunfeng Zhou
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
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15
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Taniyama D, Sakamoto N, Takashima T, Takeda M, Pham QT, Ukai S, Maruyama R, Harada K, Babasaki T, Sekino Y, Hayashi T, Sentani K, Pommier Y, Murai J, Yasui W. Prognostic impact of Schlafen 11 in bladder cancer patients treated with platinum-based chemotherapy. Cancer Sci 2021; 113:784-795. [PMID: 34808009 PMCID: PMC8819307 DOI: 10.1111/cas.15207] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/28/2021] [Accepted: 11/04/2021] [Indexed: 12/15/2022] Open
Abstract
The utility of Schlafen 11 (SLFN11) expression as a predictive biomarker for platinum‐based chemotherapy has been established for cancers from different histologies. However, the therapeutic relevance of SLFN11 in bladder cancer (BC) is unknown. Here, we examined the clinicopathologic significance of SLFN11 expression across 120 BC cases by immunohistochemistry. We divided the cases into two cohorts, one including 50 patients who received adjuvant or neoadjuvant platinum‐based chemotherapy, and the other including 70 BC patients treated by surgical resection without chemotherapy. In the cohort of 50 BC cases treated with platinum‐based chemotherapy, the SLFN11‐positive group (n = 25) showed significantly better overall survival than the SLFN11‐negative group (n = 25, P = .012). Schlafen 11 expression correlated significantly with the expression of luminal subtype marker GATA3. Multivariate analyses identified SLFN11 expression as an independent prognostic predictor (odds ratio, 0.32; 95% confidence interval, 0.11‐0.91; P = .033). Conversely, in the cohort of 70 BC cases not receiving platinum‐based chemotherapy, the SLFN11‐positive group (n = 29) showed significantly worse overall survival than the SLFN11‐negative group (n = 41, P = .034). In vitro analyses using multiple BC cell lines confirmed that SLFN11 KO rendered cells resistant to cisplatin. The epigenetic modifying drugs 5‐azacytidine and entinostat restored SLFN11 expression and resensitized cells to cisplatin and carboplatin in SLFN11‐negative BC cell lines. We conclude that SLFN11 is a predictive biomarker for BC patients who undergo platinum‐based chemotherapy and that the combination of epigenetic modifiers could rescue refractory BC patients to platinum derivatives by reactivating SLFN11 expression.
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Affiliation(s)
- Daiki Taniyama
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Naoya Sakamoto
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Tsuyoshi Takashima
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Masahiko Takeda
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Quoc Thang Pham
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Shoichi Ukai
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Ryota Maruyama
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kenji Harada
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takashi Babasaki
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Department of Urology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yohei Sekino
- Department of Urology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Tetsutaro Hayashi
- Department of Urology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kazuhiro Sentani
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Junko Murai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Wataru Yasui
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
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16
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Murai Y, Jo U, Murai J, Fukuda S, Takebe N, Pommier Y. Schlafen 11 expression in human acute leukemia cells with gain-of-function mutations in the interferon-JAK signaling pathway. iScience 2021; 24:103173. [PMID: 34693224 PMCID: PMC8517841 DOI: 10.1016/j.isci.2021.103173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/16/2021] [Accepted: 09/22/2021] [Indexed: 12/28/2022] Open
Abstract
Schlafen11 (SLFN11) is referred to as interferon (IFN)-inducible. Based on cancer genomic databases, we identified human acute myeloid and lymphoblastic leukemia cells with gain-of-function mutations in the Janus kinase (JAK) family as exhibiting high SLFN11 expression. In these cells, the clinical JAK inhibitors cerdulatinib, ruxolitinib, and tofacitinib reduced SLFN11 expression, but IFN did not further induce SLFN11 despite phosphorylated STAT1. We provide evidence that suppression of SLFN11 by JAK inhibitors is caused by inactivation of the non-canonical IFN pathway controlled by AKT and ERK. Accordingly, the AKT and ERK inhibitors MK-2206 and SCH77284 suppressed SLFN11 expression. Both also suppressed the E26 transformation-specific (ETS)-family genes ETS-1 and FLI-1 that act as transcription factors for SLFN11. Moreover, SLFN11 expression was inhibited by the ETS inhibitor TK216. Our study reveals that SLFN11 expression is regulated via the JAK, AKT and ERK, and ETS axis. Pharmacological suppression of SLFN11 warrants future studies.
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Affiliation(s)
- Yasuhisa Murai
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
- Department of Gastroenterology and Hematology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Ukhyun Jo
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Junko Murai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Shinsaku Fukuda
- Department of Gastroenterology and Hematology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Naoko Takebe
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
- Developmental Therapeutics Branch and Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
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17
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Jo U, Murai Y, Takebe N, Thomas A, Pommier Y. Precision Oncology with Drugs Targeting the Replication Stress, ATR, and Schlafen 11. Cancers (Basel) 2021; 13:4601. [PMID: 34572827 PMCID: PMC8465591 DOI: 10.3390/cancers13184601] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/14/2022] Open
Abstract
Precision medicine aims to implement strategies based on the molecular features of tumors and optimized drug delivery to improve cancer diagnosis and treatment. DNA replication is a logical approach because it can be targeted by a broad range of anticancer drugs that are both clinically approved and in development. These drugs increase deleterious replication stress (RepStress); however, how to selectively target and identify the tumors with specific molecular characteristics are unmet clinical needs. Here, we provide background information on the molecular processes of DNA replication and its checkpoints, and discuss how to target replication, checkpoint, and repair pathways with ATR inhibitors and exploit Schlafen 11 (SLFN11) as a predictive biomarker.
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Affiliation(s)
- Ukhyun Jo
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-4264, USA; (Y.M.); (A.T.)
| | - Yasuhisa Murai
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-4264, USA; (Y.M.); (A.T.)
- Department of Gastroenterology and Hematology, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan
| | - Naoko Takebe
- Developmental Therapeutics Branch and Division of Cancer Treatment and Diagnosis, NCI, NIH, Bethesda, MD 20892-4264, USA;
| | - Anish Thomas
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-4264, USA; (Y.M.); (A.T.)
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-4264, USA; (Y.M.); (A.T.)
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18
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Chen Q, Wu Q, Peng Y. ADHFE1 is a correlative factor of patient survival in cancer. Open Life Sci 2021; 16:571-582. [PMID: 34179501 PMCID: PMC8216228 DOI: 10.1515/biol-2021-0065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 12/23/2022] Open
Abstract
Alcohol dehydrogenase iron containing 1 (ADHFE1) encodes a hydroxyacid-oxoacid transhydrogenase participating in multiple biological processes. The role of ADHFE1 in cancer has not been fully uncovered. Herein, we performed data analysis to investigate the expression of ADHFE1 and the underlying regulatory mechanisms, its relationship with cancer patients’ survival, and the relevant pathways in cancer. A range of recognized, web-available databases and bioinformatics tools were used in this in silico study. We found that ADHFE1 was frequently downregulated and hypermethylated in various cancer cell lines and tissue samples. High expression of ADHFE1 was positively associated with favorable patient prognosis in breast, colon, and gastric cancers. Pathway analysis revealed its potential role in cancer-related biological processes, including energy metabolism, DNA replication, and cell cycle regulation. AHDFE1 mRNA expression and DNA methylation can potentially be used as diagnostic markers in cancer and might be of great value in predicting the survival of patients with cancer.
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Affiliation(s)
- Qi Chen
- Department of Traditional Chinese Medicine, The First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Qiyan Wu
- Cancer Center Key Lab, The First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Yaojun Peng
- Department of Emergency, The First Medical Centre, Chinese PLA General Hospital, #28 Fuxing Road, Beijing 100853, China
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19
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Chromatin Remodeling and Immediate Early Gene Activation by SLFN11 in Response to Replication Stress. Cell Rep 2021; 30:4137-4151.e6. [PMID: 32209474 DOI: 10.1016/j.celrep.2020.02.117] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 02/06/2020] [Accepted: 02/28/2020] [Indexed: 12/12/2022] Open
Abstract
Schlafen 11 (SLFN11) was recently discovered as a cellular restriction factor against replication stress. Here, we show that SLFN11 increases chromatin accessibility genome wide, prominently at active promoters in response to replication stress induced by the checkpoint kinase 1 (CHK1) inhibitor prexasertib or the topoisomerase I (TOP1) inhibitor camptothecin. Concomitantly, SLFN11 selectively activates cellular stress response pathways by inducing the transcription of the immediate early genes (IEGs), including JUN, FOS, EGR1, NFKB2, and ATF3, together with the cell cycle arrest genes CDKN1A (p21WAF1) and GADD45. Both chromatin remodeling and IEG activation require the putative ATPase and helicase activity of SLFN11, whereas canonical extrinsic IEG activation is SLFN11 independent. SLFN11-dependent IEG activation by camptothecin is also observed across 55 non-isogenic NCI-60 cell lines. We conclude that SLFN11 acts as a global regulator of chromatin structure and an intrinsic IEG activator with the potential to engage the innate immune activation in response to replicative stress.
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20
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Drapkin BJ, Rudin CM. Advances in Small-Cell Lung Cancer (SCLC) Translational Research. Cold Spring Harb Perspect Med 2021; 11:cshperspect.a038240. [PMID: 32513672 DOI: 10.1101/cshperspect.a038240] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Over the past several years, we have witnessed a resurgence of interest in the biology and therapeutic vulnerabilities of small-cell lung cancer (SCLC). This has been driven in part through the development of a more extensive array of representative models of disease, including a diverse variety of genetically engineered mouse models and human tumor xenografts. Herein, we review recent progress in SCLC model development, and consider some of the particularly active avenues of translational research in SCLC, including interrogation of intratumoral heterogeneity, insights into the cell of origin and oncogenic drivers, mechanisms of chemoresistance, and new therapeutic opportunities including biomarker-directed targeted therapies and immunotherapies. Whereas SCLC remains a highly lethal disease, these new avenues of translational research, bringing together mechanism-based preclinical and clinical research, offer new hope for patients with SCLC.
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Affiliation(s)
- Benjamin J Drapkin
- University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Charles M Rudin
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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21
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Chen P, Guo H, Liu Y, Chen B, Zhao S, Wu S, Li W, Wang L, Jia K, Wang H, Jiang M, Tang X, Qi H, Dai C, Ye J, He Y. Aberrant methylation modifications reflect specific drug responses in small cell lung cancer. Genomics 2021; 113:1114-1126. [PMID: 33705885 DOI: 10.1016/j.ygeno.2020.12.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/10/2020] [Accepted: 12/15/2020] [Indexed: 12/14/2022]
Abstract
In the study, Methylated DNA immunoprecipitation sequencing, RNA sequencing, and whole-exome sequencing were employed to clinical small cell lung cancer (SCLC) patients. Then, we verified the therapeutic predictive effects of differentially methylated genes (DMGs) in 62 SCLC cell lines. Of 4552 DMGs between chemo-sensitive and chemo-insensitive group, coding genes constituted the largest percentage (85.08%), followed by lncRNAs (10.52%) and miRNAs (3.56%). Both two groups demonstrated two methylation peaks near transcription start site and transcription end site. Two lncRNA-miRNA-mRNA networks suggested the extensive genome connection between chemotherapy efficacy-related non-coding RNAs (ncRNAs) and mRNAs. Combing miRNAs and lncRNAs could effectively predict chemotherapy response in SCLC. In addition, we also verified the predictive values of mutated genes in SCLC cell lines. This study was the first to evaluate multiple drugs efficacy-related ncRNAs and mRNAs which were modified by methylation in SCLC. DMGs identified in our research might serve as promising therapeutic targets to reverse drugs-insensitivity by complex lncRNA-miRNA-mRNA mechanisms in SCLC.
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Affiliation(s)
- Peixin Chen
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, No 507 Zhengmin Road, Shanghai 200433, China; Medical School, Tongji University, No 1239 Siping Road, Shanghai 200433, China
| | - Haoyue Guo
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, No 507 Zhengmin Road, Shanghai 200433, China; Medical School, Tongji University, No 1239 Siping Road, Shanghai 200433, China
| | - Yu Liu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, No 507 Zhengmin Road, Shanghai 200433, China; Medical School, Tongji University, No 1239 Siping Road, Shanghai 200433, China
| | - Bin Chen
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, No 507 Zhengmin Road, Shanghai 200433, China
| | - Sha Zhao
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, No 507 Zhengmin Road, Shanghai 200433, China
| | - Shengyu Wu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, No 507 Zhengmin Road, Shanghai 200433, China; Medical School, Tongji University, No 1239 Siping Road, Shanghai 200433, China
| | - Wei Li
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, No 507 Zhengmin Road, Shanghai 200433, China
| | - Lei Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, No 507 Zhengmin Road, Shanghai 200433, China
| | - Keyi Jia
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, No 507 Zhengmin Road, Shanghai 200433, China; Medical School, Tongji University, No 1239 Siping Road, Shanghai 200433, China
| | - Hao Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, No 507 Zhengmin Road, Shanghai 200433, China; Medical School, Tongji University, No 1239 Siping Road, Shanghai 200433, China
| | - Minlin Jiang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, No 507 Zhengmin Road, Shanghai 200433, China; Medical School, Tongji University, No 1239 Siping Road, Shanghai 200433, China
| | - Xuzhen Tang
- Oncology and Immunology BU, Research Service Division, WuXi Apptec, Shanghai, China
| | - Hui Qi
- Oncology and Immunology BU, Research Service Division, WuXi Apptec, Shanghai, China
| | - Chunlei Dai
- Oncology and Immunology BU, Research Service Division, WuXi Apptec, Shanghai, China
| | - Junyan Ye
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, No 507 Zhengmin Road, Shanghai 200433, China
| | - Yayi He
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, No 507 Zhengmin Road, Shanghai 200433, China.
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22
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Vural S, Palmisano A, Reinhold WC, Pommier Y, Teicher BA, Krushkal J. Association of expression of epigenetic molecular factors with DNA methylation and sensitivity to chemotherapeutic agents in cancer cell lines. Clin Epigenetics 2021; 13:49. [PMID: 33676569 PMCID: PMC7936435 DOI: 10.1186/s13148-021-01026-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 02/10/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Altered DNA methylation patterns play important roles in cancer development and progression. We examined whether expression levels of genes directly or indirectly involved in DNA methylation and demethylation may be associated with response of cancer cell lines to chemotherapy treatment with a variety of antitumor agents. RESULTS We analyzed 72 genes encoding epigenetic factors directly or indirectly involved in DNA methylation and demethylation processes. We examined association of their pretreatment expression levels with methylation beta-values of individual DNA methylation probes, DNA methylation averaged within gene regions, and average epigenome-wide methylation levels. We analyzed data from 645 cancer cell lines and 23 cancer types from the Cancer Cell Line Encyclopedia and Genomics of Drug Sensitivity in Cancer datasets. We observed numerous correlations between expression of genes encoding epigenetic factors and response to chemotherapeutic agents. Expression of genes encoding a variety of epigenetic factors, including KDM2B, DNMT1, EHMT2, SETDB1, EZH2, APOBEC3G, and other genes, was correlated with response to multiple agents. DNA methylation of numerous target probes and gene regions was associated with expression of multiple genes encoding epigenetic factors, underscoring complex regulation of epigenome methylation by multiple intersecting molecular pathways. The genes whose expression was associated with methylation of multiple epigenome targets encode DNA methyltransferases, TET DNA methylcytosine dioxygenases, the methylated DNA-binding protein ZBTB38, KDM2B, SETDB1, and other molecular factors which are involved in diverse epigenetic processes affecting DNA methylation. While baseline DNA methylation of numerous epigenome targets was correlated with cell line response to antitumor agents, the complex relationships between the overlapping effects of each epigenetic factor on methylation of specific targets and the importance of such influences in tumor response to individual agents require further investigation. CONCLUSIONS Expression of multiple genes encoding epigenetic factors is associated with drug response and with DNA methylation of numerous epigenome targets that may affect response to therapeutic agents. Our findings suggest complex and interconnected pathways regulating DNA methylation in the epigenome, which may both directly and indirectly affect response to chemotherapy.
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Affiliation(s)
- Suleyman Vural
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD, 20850, USA
| | - Alida Palmisano
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD, 20850, USA
- General Dynamics Information Technology (GDIT), 3150 Fairview Park Drive, Falls Church, VA, 22042, USA
| | - William C Reinhold
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Beverly A Teicher
- Molecular Pharmacology Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD, 20850, USA.
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23
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Integrative pan cancer analysis reveals epigenomic variation in cancer type and cell specific chromatin domains. Nat Commun 2021; 12:1419. [PMID: 33658503 PMCID: PMC7930052 DOI: 10.1038/s41467-021-21707-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 02/09/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetic mechanisms contribute to the initiation and development of cancer, and epigenetic variation promotes dynamic gene expression patterns that facilitate tumor evolution and adaptation. While the NCI-60 panel represents a diverse set of human cancer cell lines that has been used to screen chemical compounds, a comprehensive epigenomic atlas of these cells has been lacking. Here, we report an integrative analysis of 60 human cancer epigenomes, representing a catalog of activating and repressive histone modifications. We identify genome-wide maps of canonical sharp and broad H3K4me3 domains at promoter regions of tumor suppressors, H3K27ac-marked conventional enhancers and super enhancers, and widespread inter-cancer and intra-cancer specific variability in H3K9me3 and H4K20me3-marked heterochromatin domains. Furthermore, we identify features of chromatin states, including chromatin state switching along chromosomes, correlation of histone modification density with genetic mutations, DNA methylation, enrichment of DNA binding motifs in regulatory regions, and gene activity and inactivity. These findings underscore the importance of integrating epigenomic maps with gene expression and genetic variation data to understand the molecular basis of human cancer. Our findings provide a resource for mining epigenomic maps of human cancer cells and for identifying epigenetic therapeutic targets.
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24
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Luna A, Elloumi F, Varma S, Wang Y, Rajapakse VN, Aladjem MI, Robert J, Sander C, Pommier Y, Reinhold WC. CellMiner Cross-Database (CellMinerCDB) version 1.2: Exploration of patient-derived cancer cell line pharmacogenomics. Nucleic Acids Res 2021; 49:D1083-D1093. [PMID: 33196823 DOI: 10.1093/nar/gkaa968] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/25/2020] [Accepted: 10/19/2020] [Indexed: 12/13/2022] Open
Abstract
CellMiner Cross-Database (CellMinerCDB, discover.nci.nih.gov/cellminercdb) allows integration and analysis of molecular and pharmacological data within and across cancer cell line datasets from the National Cancer Institute (NCI), Broad Institute, Sanger/MGH and MD Anderson Cancer Center (MDACC). We present CellMinerCDB 1.2 with updates to datasets from NCI-60, Broad Cancer Cell Line Encyclopedia and Sanger/MGH, and the addition of new datasets, including NCI-ALMANAC drug combination, MDACC Cell Line Project proteomic, NCI-SCLC DNA copy number and methylation data, and Broad methylation, genetic dependency and metabolomic datasets. CellMinerCDB (v1.2) includes several improvements over the previously published version: (i) new and updated datasets; (ii) support for pattern comparisons and multivariate analyses across data sources; (iii) updated annotations with drug mechanism of action information and biologically relevant multigene signatures; (iv) analysis speedups via caching; (v) a new dataset download feature; (vi) improved visualization of subsets of multiple tissue types; (vii) breakdown of univariate associations by tissue type; and (viii) enhanced help information. The curation and common annotations (e.g. tissues of origin and identifiers) provided here across pharmacogenomic datasets increase the utility of the individual datasets to address multiple researcher question types, including data reproducibility, biomarker discovery and multivariate analysis of drug activity.
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Affiliation(s)
- Augustin Luna
- cBio Center, Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA
| | - Fathi Elloumi
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.,General Dynamics Information Technology Inc., Fairfax, VA 22042, USA
| | - Sudhir Varma
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.,HiThru Analytics LLC, Princeton, NJ 08540, USA
| | - Yanghsin Wang
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.,General Dynamics Information Technology Inc., Fairfax, VA 22042, USA
| | - Vinodh N Rajapakse
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jacques Robert
- Inserm unité 1218, Université de Bordeaux, Bordeaux 33076, France
| | - Chris Sander
- cBio Center, Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - William C Reinhold
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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25
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Krushkal J, Negi S, Yee LM, Evans JR, Grkovic T, Palmisano A, Fang J, Sankaran H, McShane LM, Zhao Y, O'Keefe BR. Molecular genomic features associated with in vitro response of the NCI-60 cancer cell line panel to natural products. Mol Oncol 2021; 15:381-406. [PMID: 33169510 PMCID: PMC7858122 DOI: 10.1002/1878-0261.12849] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/29/2020] [Accepted: 11/06/2020] [Indexed: 12/17/2022] Open
Abstract
Natural products remain a significant source of anticancer chemotherapeutics. The search for targeted drugs for cancer treatment includes consideration of natural products, which may provide new opportunities for antitumor cytotoxicity as single agents or in combination therapy. We examined the association of molecular genomic features in the well-characterized NCI-60 cancer cell line panel with in vitro response to treatment with 1302 small molecules which included natural products, semisynthetic natural product derivatives, and synthetic compounds based on a natural product pharmacophore from the Developmental Therapeutics Program of the US National Cancer Institute's database. These compounds were obtained from a variety of plant, marine, and microbial species. Molecular information utilized for the analysis included expression measures for 23059 annotated transcripts, lncRNAs, and miRNAs, and data on protein-changing single nucleotide variants in 211 cancer-related genes. We found associations of expression of multiple genes including SLFN11, CYP2J2, EPHX1, GPC1, ELF3, and MGMT involved in DNA damage repair, NOTCH family members, ABC and SLC transporters, and both mutations in tyrosine kinases and BRAF V600E with NCI-60 responses to specific categories of natural products. Hierarchical clustering identified groups of natural products, which correlated with a specific mechanism of action. Specifically, several natural product clusters were associated with SLFN11 gene expression, suggesting that potential action of these compounds may involve DNA damage. The associations between gene expression or genome alterations of functionally relevant genes with the response of cancer cells to natural products provide new information about potential mechanisms of action of these identified clusters of compounds with potentially similar biological effects. This information will assist in future drug discovery and in design of new targeted cancer chemotherapy agents.
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Affiliation(s)
- Julia Krushkal
- Biometric Research ProgramDivision of Cancer Treatment and DiagnosisNational Cancer InstituteNIHRockvilleMDUSA
| | - Simarjeet Negi
- Biometric Research ProgramDivision of Cancer Treatment and DiagnosisNational Cancer InstituteNIHRockvilleMDUSA
| | - Laura M. Yee
- Biometric Research ProgramDivision of Cancer Treatment and DiagnosisNational Cancer InstituteNIHRockvilleMDUSA
| | - Jason R. Evans
- Natural Products BranchDevelopmental Therapeutics ProgramDivision of Cancer Treatment and DiagnosisNational Cancer InstituteFrederickMDUSA
| | - Tanja Grkovic
- Natural Products Support GroupFrederick National Laboratory for Cancer ResearchFrederickMDUSA
| | - Alida Palmisano
- Biometric Research ProgramDivision of Cancer Treatment and DiagnosisNational Cancer InstituteNIHRockvilleMDUSA
- General Dynamics Information Technology (GDIT)Falls ChurchVAUSA
| | - Jianwen Fang
- Biometric Research ProgramDivision of Cancer Treatment and DiagnosisNational Cancer InstituteNIHRockvilleMDUSA
| | - Hari Sankaran
- Biometric Research ProgramDivision of Cancer Treatment and DiagnosisNational Cancer InstituteNIHRockvilleMDUSA
| | - Lisa M. McShane
- Biometric Research ProgramDivision of Cancer Treatment and DiagnosisNational Cancer InstituteNIHRockvilleMDUSA
| | - Yingdong Zhao
- Biometric Research ProgramDivision of Cancer Treatment and DiagnosisNational Cancer InstituteNIHRockvilleMDUSA
| | - Barry R. O'Keefe
- Natural Products BranchDevelopmental Therapeutics ProgramDivision of Cancer Treatment and DiagnosisNational Cancer InstituteFrederickMDUSA
- Molecular Targets ProgramCenter for Cancer ResearchNational Cancer InstituteFrederickMDUSA
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26
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Waters T, Goss KL, Koppenhafer SL, Terry WW, Gordon DJ. Eltrombopag inhibits the proliferation of Ewing sarcoma cells via iron chelation and impaired DNA replication. BMC Cancer 2020; 20:1171. [PMID: 33256675 PMCID: PMC7706234 DOI: 10.1186/s12885-020-07668-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/20/2020] [Indexed: 12/30/2022] Open
Abstract
Background The treatment of Ewing sarcoma, an aggressive bone and soft tissue sarcoma, is associated with suboptimal outcomes and significant side-effects. Consequently, there is an urgent need to identify novel therapies that will improve outcomes for children and adults with Ewing sarcoma tumors while also decreasing treatment-related toxicities. Methods We analyzed data from the PRISM drug repurposing screen, which tested the activity of 4518 drugs across 578 cancer cell lines, to identify drugs that selectively inhibit the growth of Ewing sarcoma cell lines. We then tested the effects of a top hit from the screen on cell proliferation, cell cycle progression, and activation of the DNA damage pathway using Ewing sarcoma cell lines. We also used a CRISPR/Cas9 gene knockout approach to investigate the role of Schlafen 11 (SLFN11), a restriction factor for DNA replication stress that is overexpressed in Ewing sarcoma tumors, in mediating the sensitivity of Ewing sarcoma cells to the drug. Results We found that eltrombopag, an FDA-approved thrombopoietin-receptor agonist (TPO-RA) that is currently being evaluated as a treatment for chemotherapy-induced thrombocytopenia, inhibits the growth of Ewing sarcoma cell lines in vitro in proliferation and colony formation assays. However, from a mechanistic standpoint, the thrombopoietin receptor is not expressed in Ewing sarcoma cells and we show that eltrombopag impairs DNA replication and causes DNA damage in Ewing sarcoma cells by chelating iron, a known “off-target” effect of the drug. We also found that the sensitivity of Ewing sarcoma cells to eltrombopag is mediated, in part, by SLFN11, which regulates the cellular response to DNA replication stress. Conclusions Ewing sarcoma cell lines are sensitive to eltrombopag and this drug could improve outcomes for patients with Ewing sarcoma tumors by both targeting the tumor, via chelation of iron and inhibition of DNA replication, and reducing chemotherapy-induced thrombocytopenia, via stimulation of the thrombopoietin receptor. Supplementary Information Supplementary information accompanies this paper at 10.1186/s12885-020-07668-6.
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Affiliation(s)
- Torin Waters
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Iowa, 25 S Grand Avenue, Iowa City, Iowa, 52242, USA
| | - Kelli L Goss
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Iowa, 25 S Grand Avenue, Iowa City, Iowa, 52242, USA
| | - Stacia L Koppenhafer
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Iowa, 25 S Grand Avenue, Iowa City, Iowa, 52242, USA
| | - William W Terry
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Iowa, 25 S Grand Avenue, Iowa City, Iowa, 52242, USA
| | - David J Gordon
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Iowa, 25 S Grand Avenue, Iowa City, Iowa, 52242, USA.
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27
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Tlemsani C, Pongor L, Elloumi F, Girard L, Huffman KE, Roper N, Varma S, Luna A, Rajapakse VN, Sebastian R, Kohn KW, Krushkal J, Aladjem MI, Teicher BA, Meltzer PS, Reinhold WC, Minna JD, Thomas A, Pommier Y. SCLC-CellMiner: A Resource for Small Cell Lung Cancer Cell Line Genomics and Pharmacology Based on Genomic Signatures. Cell Rep 2020; 33:108296. [PMID: 33086069 PMCID: PMC7643325 DOI: 10.1016/j.celrep.2020.108296] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 08/06/2020] [Accepted: 09/30/2020] [Indexed: 01/23/2023] Open
Abstract
CellMiner-SCLC (https://discover.nci.nih.gov/SclcCellMinerCDB/) integrates drug sensitivity and genomic data, including high-resolution methylome and transcriptome from 118 patient-derived small cell lung cancer (SCLC) cell lines, providing a resource for research into this "recalcitrant cancer." We demonstrate the reproducibility and stability of data from multiple sources and validate the SCLC consensus nomenclature on the basis of expression of master transcription factors NEUROD1, ASCL1, POU2F3, and YAP1. Our analyses reveal transcription networks linking SCLC subtypes with MYC and its paralogs and the NOTCH and HIPPO pathways. SCLC subsets express specific surface markers, providing potential opportunities for antibody-based targeted therapies. YAP1-driven SCLCs are notable for differential expression of the NOTCH pathway, epithelial-mesenchymal transition (EMT), and antigen-presenting machinery (APM) genes and sensitivity to mTOR and AKT inhibitors. These analyses provide insights into SCLC biology and a framework for future investigations into subtype-specific SCLC vulnerabilities.
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Affiliation(s)
- Camille Tlemsani
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Lorinc Pongor
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Fathi Elloumi
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Luc Girard
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kenneth E Huffman
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nitin Roper
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sudhir Varma
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Augustin Luna
- cBio Center, Division of Biostatistics, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Vinodh N Rajapakse
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Robin Sebastian
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Kurt W Kohn
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Beverly A Teicher
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Paul S Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - William C Reinhold
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Anish Thomas
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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Yao X, Watkins NH, Brown-Harding H, Bierbach U. A membrane transporter determines the spectrum of activity of a potent platinum-acridine hybrid anticancer agent. Sci Rep 2020; 10:15201. [PMID: 32939009 PMCID: PMC7494928 DOI: 10.1038/s41598-020-72099-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/24/2020] [Indexed: 01/22/2023] Open
Abstract
Cytotoxic drugs that are mechanistically distinct from current chemotherapies are attractive components of personalized combination regimens for combatting aggressive forms of cancer. To gain insight into the cellular mechanism of a potent platinum-acridine anticancer agent (compound 1), a correlation analysis of NCI-60 compound screening results and gene expression profiles was performed. A plasma membrane transporter, the solute carrier (SLC) human multidrug and toxin extrusion protein 1 (hMATE1, SLC47A1), emerged as the dominant predictor of cancer cell chemosensitivity to the hybrid agent (Pearson correlation analysis, p < 10-5) across a wide range of tissues of origin. The crucial role of hMATE1 was validated in lung adenocarcinoma cells (A549), which expresses high levels of the membrane transporter, using transporter inhibition assays and transient knockdown of the SLC47A1 gene, in conjunction with quantification of intracellular accumulation of compound 1 and cell viability screening. Preliminary data also show that HCT-116 colon cancer cells, in which hMATE1 is epigenetically repressed, can be sensitized to compound 1 by priming the cells with the drugs EPZ-6438 (tazemetostat) and EED226. Collectively, these results suggest that hMATE1 may have applications as a pan-cancer molecular marker to identify and target tumors that are likely to respond to platinum-acridines.
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Affiliation(s)
- Xiyuan Yao
- Department of Chemistry, Wake Forest University, Wake Forest Innovation Quarter, 455 Vine St., Winston-Salem, NC, 27101, USA
| | - Noah H Watkins
- Department of Chemistry, Wake Forest University, Wake Forest Innovation Quarter, 455 Vine St., Winston-Salem, NC, 27101, USA
| | - Heather Brown-Harding
- Department of Biology, Wake Forest University, Wake Forest Innovation Quarter, 455 Vine St., Winston-Salem, NC, 27101, USA
| | - Ulrich Bierbach
- Department of Chemistry, Wake Forest University, Wake Forest Innovation Quarter, 455 Vine St., Winston-Salem, NC, 27101, USA.
- Comprehensive Cancer Center, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, 27157, USA.
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29
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Krushkal J, Silvers T, Reinhold WC, Sonkin D, Vural S, Connelly J, Varma S, Meltzer PS, Kunkel M, Rapisarda A, Evans D, Pommier Y, Teicher BA. Epigenome-wide DNA methylation analysis of small cell lung cancer cell lines suggests potential chemotherapy targets. Clin Epigenetics 2020; 12:93. [PMID: 32586373 PMCID: PMC7318526 DOI: 10.1186/s13148-020-00876-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/26/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Small cell lung cancer (SCLC) is an aggressive neuroendocrine lung cancer. SCLC progression and treatment resistance involve epigenetic processes. However, links between SCLC DNA methylation and drug response remain unclear. We performed an epigenome-wide study of 66 human SCLC cell lines using the Illumina Infinium MethylationEPIC BeadChip array. Correlations of SCLC DNA methylation and gene expression with in vitro response to 526 antitumor agents were examined. RESULTS We found multiple significant correlations between DNA methylation and chemosensitivity. A potentially important association was observed for TREX1, which encodes the 3' exonuclease I that serves as a STING antagonist in the regulation of a cytosolic DNA-sensing pathway. Increased methylation and low expression of TREX1 were associated with the sensitivity to Aurora kinase inhibitors AZD-1152, SCH-1473759, SNS-314, and TAK-901; the CDK inhibitor R-547; the Vertex ATR inhibitor Cpd 45; and the mitotic spindle disruptor vinorelbine. Compared with cell lines of other cancer types, TREX1 had low mRNA expression and increased upstream region methylation in SCLC, suggesting a possible relationship with SCLC sensitivity to Aurora kinase inhibitors. We also identified multiple additional correlations indicative of potential mechanisms of chemosensitivity. Methylation of the 3'UTR of CEP350 and MLPH, involved in centrosome machinery and microtubule tracking, respectively, was associated with response to Aurora kinase inhibitors and other agents. EPAS1 methylation was associated with response to Aurora kinase inhibitors, a PLK-1 inhibitor and a Bcl-2 inhibitor. KDM1A methylation was associated with PLK-1 inhibitors and a KSP inhibitor. Increased promoter methylation of SLFN11 was correlated with resistance to DNA damaging agents, as a result of low or no SLFN11 expression. The 5' UTR of the epigenetic modifier EZH2 was associated with response to Aurora kinase inhibitors and a FGFR inhibitor. Methylation and expression of YAP1 were correlated with response to an mTOR inhibitor. Among non-neuroendocrine markers, EPHA2 was associated with response to Aurora kinase inhibitors and a PLK-1 inhibitor and CD151 with Bcl-2 inhibitors. CONCLUSIONS Multiple associations indicate potential epigenetic mechanisms affecting SCLC response to chemotherapy and suggest targets for combination therapies. While many correlations were not specific to SCLC lineages, several lineage markers were associated with specific agents.
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Affiliation(s)
- Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, 9609 Medical Center Dr., Rockville, MD, 20850, USA.
| | - Thomas Silvers
- Molecular Pharmacology Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - William C Reinhold
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Dmitriy Sonkin
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, 9609 Medical Center Dr., Rockville, MD, 20850, USA
| | - Suleyman Vural
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, 9609 Medical Center Dr., Rockville, MD, 20850, USA
| | - John Connelly
- Molecular Pharmacology Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Sudhir Varma
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Paul S Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Mark Kunkel
- Drug Synthesis and Chemistry Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Annamaria Rapisarda
- Molecular Pharmacology Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - David Evans
- Molecular Pharmacology Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Beverly A Teicher
- Molecular Pharmacology Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, 20892, USA.
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30
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Joshi R, Castro De Moura M, Piñeyro D, Alvarez-Errico D, Arribas C, Esteller M. The DNA methylation landscape of human cancer organoids available at the American type culture collection. Epigenetics 2020; 15:1167-1177. [PMID: 32396494 PMCID: PMC7595613 DOI: 10.1080/15592294.2020.1762398] [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] [Indexed: 12/29/2022] Open
Abstract
One caveat in cancer research is the dependence of certain experimental systems that might not really reflect the properties of the primary tumours. The recent irruption of 3D cultured cells termed organoids could render a better representation of the original tumour sample. However, every laboratory has its own protocol and tissue-provider to establish these cancer models, preventing further dissemination and validation of the obtained data. To address this problem, the Human Cancer Models Initiative (HCMI) has selected the American Type Culture Collection (ATCC) to make available organoid models to the scientific community. In this regard, no epigenetic information is available for these samples and, overall, the DNA methylation profiles of human cancer organoids are largely unknown. Herein, we provide the DNA methylation landscape of 25 human cancer organoids available at the ATCC using a microarray that interrogates more than 850,000 CpG sites. We observed that the studied organoids retain the epigenetic setting of their original primary cancer type; that exhibit a DNA methylation landscape characteristic of transformed tissues excluding an overgrowth of normal-matched cells; and that are closer to the DNA methylation profiles of the corresponding primary tumours than to established 2D cell lines. Most importantly, the obtained DNA methylation results are freely available to everyone for further data mining. Thus, our findings support from the epigenetic standpoint that the ATCC human cancer organoids recapitulate many of the features of the disorder in the patient and are excellent tools to be shared among investigators for further tumour biology research.
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Affiliation(s)
- Ricky Joshi
- Josep Carreras Leukaemia Research Institute (IJC), Badalona , Barcelona, Spain
| | | | - David Piñeyro
- Josep Carreras Leukaemia Research Institute (IJC), Badalona , Barcelona, Spain
| | | | - Carles Arribas
- Josep Carreras Leukaemia Research Institute (IJC), Badalona , Barcelona, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona , Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA) , Barcelona, Spain.,Centro de Investigacion Biomedica en Red Cancer (CIBERONC) , Madrid, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB) , Barcelona, Spain
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31
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Zhou C, Liu C, Liu W, Chen W, Yin Y, Li CW, Hsu JL, Sun J, Zhou Q, Li H, Hu B, Fu P, Atyah M, Ma Q, Xu Y, Dong Q, Hung MC, Ren N. SLFN11 inhibits hepatocellular carcinoma tumorigenesis and metastasis by targeting RPS4X via mTOR pathway. Theranostics 2020; 10:4627-4643. [PMID: 32292519 PMCID: PMC7150495 DOI: 10.7150/thno.42869] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/05/2020] [Indexed: 12/19/2022] Open
Abstract
Hepatocellular carcinoma (HCC) remains one of the most refractory malignancies worldwide. Schlafen family member 11 (SLFN11) has been reported to play an important role in inhibiting the production of human immunodeficiency virus 1 (HIV-1). However, whether SLFN11 also inhibits hepatitis B virus (HBV), and affects HBV-induced HCC remain to be systematically investigated. Methods: qRT-PCR, western blot and immunohistochemical (IHC) staining were conducted to investigate the potential role and prognostic value of SLFN11 in HCC. Then SLFN11 was stably overexpressed or knocked down in HCC cell lines. To further explore the potential biological function of SLFN11 in HCC, cell counting kit-8 (CCK-8) assays, colony formation assays, wound healing assays and transwell cell migration and invasion assays were performed in vitro. Meanwhile, HCC subcutaneous xenograft tumor models were established for in vivo assays. Subsequently, immunoprecipitation (IP) and liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) analyses were applied to understand the molecular mechanisms of SLFN11 in HCC. Co-IP, immunofluorescence and IHC staining were used to analyze the relationship between ribosomal protein S4 X-linked (RPS4X) and SLFN11. Finally, the therapeutic potential of SLFN11 with mTOR pathway inhibitor INK128 on inhibiting HCC growth and metastasis was evaluated in vitro and in vivo orthotopic xenograft mouse models. Results: We demonstrate that SLFN11 expression is decreased in HCC, which is associated with shorter overall survival and higher recurrence rates in patients. In addition, we show that low SLFN11 expression is associated with aggressive clinicopathologic characteristics. Moreover, overexpression of SLFN11 inhibits HCC cell proliferation, migration, and invasion, facilitates apoptosis in vitro, and impedes HCC growth and metastasis in vivo, all of which are attenuated by SLFN11 knockdown. Mechanistically, SLFN11 physically associates with RPS4X and blocks the mTOR signaling pathway. In orthotopic mouse models, overexpression of SLFN11 or inhibition of mTOR pathway inhibitor by INK128 reverses HCC progression and metastasis. Conclusions: SLFN11 may serve as a powerful prognostic biomarker and putative tumor suppressor by suppressing the mTOR signaling pathway via RPS4X in HCC. Our study may therefore offer a novel therapeutic strategy for treating HCC patients with the mTOR pathway inhibitor INK128.
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Affiliation(s)
- Chenhao Zhou
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chunxiao Liu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wenjie Liu
- Biomedical Research Centre, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wanyong Chen
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
- Institute of Fudan Minhang Academic Health System, and Key Laboratory of Whole-period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital & AHS, Fudan University, Shanghai, China
| | - Yirui Yin
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Chia-Wei Li
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer L. Hsu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jialei Sun
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Qiang Zhou
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Hui Li
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bo Hu
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Peiyao Fu
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Manar Atyah
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Qianni Ma
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Yang Xu
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Qiongzhu Dong
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Institute of Fudan Minhang Academic Health System, and Key Laboratory of Whole-period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital & AHS, Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate Institute of Biomedical Sciences and Center for Molecular Medicine, China Medical University, Taichung, Taiwan
| | - Ning Ren
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
- Institute of Fudan Minhang Academic Health System, and Key Laboratory of Whole-period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital & AHS, Fudan University, Shanghai, China
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Marzi L, Szabova L, Gordon M, Weaver Ohler Z, Sharan SK, Beshiri ML, Etemadi M, Murai J, Kelly K, Pommier Y. The Indenoisoquinoline TOP1 Inhibitors Selectively Target Homologous Recombination-Deficient and Schlafen 11-Positive Cancer Cells and Synergize with Olaparib. Clin Cancer Res 2019; 25:6206-6216. [PMID: 31409613 PMCID: PMC6801079 DOI: 10.1158/1078-0432.ccr-19-0419] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/24/2019] [Accepted: 07/19/2019] [Indexed: 02/07/2023]
Abstract
PURPOSE Irinotecan and topotecan are used to treat a variety of different cancers. However, they have limitations, including chemical instability and severe side effects. To overcome these limitations, we developed the clinical indenoisoquinolines: LMP400 (indotecan), LMP776 (indimitecan), and LMP744. The purpose of the study is to build the molecular rationale for phase II clinical trials. EXPERIMENTAL DESIGN CellMinerCDB (http://discover.nci.nih.gov/cellminercdb) was used to mine the cancer cell lines genomic databases. The causality of Schlafen11 (SLFN11) was validated in isogenic cell lines. Because topoisomerase I (TOP1)-mediated replication DNA damage is repaired by homologous recombination (HR), we tested the "synthetic lethality" of HR-deficient (HRD) cells. Survival and cell-cycle alterations were performed after drug treatments in isogenic DT40, DLD1, and OVCAR cell lines with BRCA1, BRCA2, or PALB2 deficiencies and in organoids cultured from prostate cancer patient-derived xenografts with BRCA2 loss. We also used an ovarian orthotopic allograft model with BRCA1 loss to validate the efficacy of LMP400 and olaparib combination. RESULTS CellMinerCDB reveals that SLFN11, which kills cells undergoing replicative stress, is a dominant drug determinant to the clinical indenoisoquinolines. In addition, BRCA1-, BRCA2-, and PALB2-deficient cells were hypersensitive to the indenoisoquinolines. All 3 clinical indenoisoquinolines were also synergistic with olaparib, especially in the HRD cells. The synergy between LMP400 and olaparib was confirmed in the orthotopic allograft model harboring BRCA1 loss. CONCLUSIONS Our results provide a rationale for molecularly designed clinical trials with the indenoisoquinolines as single agents and in combination with PARP inhibitors in HRD cancers expressing SLFN11.
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Affiliation(s)
- Laetitia Marzi
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Ludmila Szabova
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research at the National Cancer Institute-Frederick, Frederick, Maryland
| | - Melanie Gordon
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research at the National Cancer Institute-Frederick, Frederick, Maryland
| | - Zoe Weaver Ohler
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research at the National Cancer Institute-Frederick, Frederick, Maryland
| | - Shyam K Sharan
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research at the National Cancer Institute-Frederick, Frederick, Maryland
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, Maryland
| | - Michael L Beshiri
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Moudjib Etemadi
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Junko Murai
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Kathleen Kelly
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland.
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33
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Murai J, Thomas A, Miettinen M, Pommier Y. Schlafen 11 (SLFN11), a restriction factor for replicative stress induced by DNA-targeting anti-cancer therapies. Pharmacol Ther 2019; 201:94-102. [PMID: 31128155 PMCID: PMC6708787 DOI: 10.1016/j.pharmthera.2019.05.009] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/14/2019] [Indexed: 12/13/2022]
Abstract
Schlafen 11 (SLFN11) sensitizes cells to a broad range of anti-cancer drugs including platinum derivatives (cisplatin and carboplatin), inhibitors of topoisomerases (irinotecan, topotecan, doxorubicin, daunorubicin, mitoxantrone and etoposide), DNA synthesis inhibitors (gemcitabine, cytarabine, hydroxyurea and nucleoside analogues), and poly(ADPribose) polymerase (PARP) inhibitors (olaparib, rucaparib, niraparib and talazoparib). In spite of their different primary mechanisms of action, all these drugs damage DNA during S-phase, activate the intra-S-phase checkpoint and induce replication fork slowing and stalling with single-stranded DNA segments coated with replication protein A. Such situation with abnormal replication forks is known as replication stress. SLFN11 irreversibly blocks replication in cells under replication stress, explaining why SLFN11-positive cells are markedly more efficiently killed by DNA-targeting drugs than SLFN11-negative cells. SLFN11 is inactivated in ~50% of cancer cell lines and in a large fraction of tumors, and is linked with the native immune, interferon and T-cells responses, implying the translational relevance of measuring SLFN11 expression as a predictive biomarker of response and resistance in patients. SLFN11 is also a plausible epigenetic target for reactivation by inhibitors of histone deacetylases (HDAC), DNA methyltransferases (DNMT) and EZH2 histone methyltransferase and for combination of these epigenetic inhibitors with DNA-targeting drugs in cells lacking SLFN11 expression. In addition, resistance due to lack of SLFN11 expression in tumors is a potential indication for cell-cycle checkpoint inhibitors in combination with DNA-targeting therapies.
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Affiliation(s)
- Junko Murai
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| | - Anish Thomas
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Markku Miettinen
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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Luan J, Gao X, Hu F, Zhang Y, Gou X. SLFN11 is a general target for enhancing the sensitivity of cancer to chemotherapy (DNA-damaging agents). J Drug Target 2019; 28:33-40. [PMID: 31092045 DOI: 10.1080/1061186x.2019.1616746] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
In patients with cancer, drug tolerance often occurs during the use of chemotherapy drugs, seriously affecting patient prognosis and survival. Therefore, scientists began to study the factors that affect chemotherapy drug sensitivity, and the high correlation between Schlafen-11 (SLFN11) and sensitivity to chemical drugs (mainly DNA-damaging agents, DDAs) has received increasing attention since it was discovered through bioinformatics analyses. Regarding the mechanism, SLFN11 may sensitise cells to chemotherapy drugs by preventing DNA damage repair. In recent years, SLFN11 has gradually become a hot research topic, and the results are enriching our understanding of this molecule. Indeed, the biological functions of SLFN11 under normal physiological conditions and in cancer, changes in its expression levels and mechanisms promoting apoptosis within the context of chemotherapeutic interventions have gradually been uncovered. Studies to date provide knowledge and the experimental and theoretical bases underlying SLFN11 and its effects on sensitivity to chemotherapy drugs. This review summarises the existing research on SLFN11 with the aim of achieving a more comprehensive understanding and furthering the development of strategies to target SLFN11 in the treatment of cancer.
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Affiliation(s)
- Jing Luan
- Shaanxi Key Laboratory of Brain Disorders & Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, Shaanxi, China
| | - Xingchun Gao
- Shaanxi Key Laboratory of Brain Disorders & Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, Shaanxi, China
| | - Fengrui Hu
- Shaanxi Key Laboratory of Brain Disorders & Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, Shaanxi, China
| | - Yuelin Zhang
- Shaanxi Key Laboratory of Brain Disorders & Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, Shaanxi, China
| | - Xingchun Gou
- Shaanxi Key Laboratory of Brain Disorders & Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, Shaanxi, China
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Reinhold WC, Varma S, Sunshine M, Elloumi F, Ofori-Atta K, Lee S, Trepel JB, Meltzer PS, Doroshow JH, Pommier Y. RNA Sequencing of the NCI-60: Integration into CellMiner and CellMiner CDB. Cancer Res 2019; 79:3514-3524. [PMID: 31113817 DOI: 10.1158/0008-5472.can-18-2047] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 02/15/2019] [Accepted: 05/15/2019] [Indexed: 02/06/2023]
Abstract
CellMiner (http://discover.nci.nih.gov/cellminer) and CellMinerCDB (https://discover.nci.nih.gov/cellminercdb/) are web-based applications for mining publicly available genomic, molecular, and pharmacologic datasets of human cancer cell lines including the NCI-60, Cancer Cell Line Encyclopedia, Genomics of Drug Sensitivity in Cancer, Cancer Therapeutics Response Portal, NCI/DTP small cell lung cancer, and NCI Almanac cell line sets. Here, we introduce our RNA sequencing (RNA-seq) data for the NCI-60 and their access and integration with the other databases. Correlation to transcript microarray expression levels for identical genes and identical cell lines across CellMinerCDB demonstrates the high quality of these new RNA-seq data. We provide composite and isoform transcript expression data and demonstrate diversity in isoform composition for individual cancer- and pharmacologically relevant genes, including HRAS, PTEN, EGFR, RAD51, ALKBH2, BRCA1, ERBB2, TP53, FGFR2, and CTNND1. We reveal cell-specific differences in the overall levels of isoforms and show their linkage to expression of RNA processing and splicing genes as well as resultant alterations in cancer and pharmacologic gene sets. Gene-drug pairings linked by pathways or functions show specific correlations to isoforms compared with composite gene expression, including ALKBH2-benzaldehyde, AKT3-vandetanib, BCR-imatinib, CDK1 and 20-palbociclib, CASP1-imexon, and FGFR3-pazopanib. Loss of MUC1 20 amino acid variable number tandem repeats, which is used to elicit immune response, and the presence of the androgen receptor AR-V4 and -V7 isoforms in all NCI-60 tissue of origin types demonstrate translational relevance. In summary, we introduce RNA-seq data to our CellMiner and CellMinerCDB web applications, allowing their exploration for both research and translational purposes. SIGNIFICANCE: The current study provides RNA sequencing data for the NCI-60 cell lines made accessible through both CellMiner and CellMinerCDB and is an important pharmacogenomics resource for the field.
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Affiliation(s)
- William C Reinhold
- Developmental Therapeutic Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
| | - Sudhir Varma
- Developmental Therapeutic Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.,HiThru Analytics LLC, Princeton, New Jersey
| | - Margot Sunshine
- Developmental Therapeutic Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.,General Dynamics Information Technology, Falls Church, Virginia
| | - Fathi Elloumi
- Developmental Therapeutic Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.,General Dynamics Information Technology, Falls Church, Virginia
| | - Kwabena Ofori-Atta
- Massachusetts Institute of Technology, Computer Science and Molecular Biology, Cambridge, Massachusetts
| | - Sunmin Lee
- Developmental Therapeutic Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Jane B Trepel
- Developmental Therapeutic Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Paul S Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - James H Doroshow
- Developmental Therapeutic Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.,Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Yves Pommier
- Developmental Therapeutic Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
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Rajapakse VN, Luna A, Yamade M, Loman L, Varma S, Sunshine M, Iorio F, Sousa FG, Elloumi F, Aladjem MI, Thomas A, Sander C, Kohn KW, Benes CH, Garnett M, Reinhold WC, Pommier Y. CellMinerCDB for Integrative Cross-Database Genomics and Pharmacogenomics Analyses of Cancer Cell Lines. iScience 2018; 10:247-264. [PMID: 30553813 PMCID: PMC6302245 DOI: 10.1016/j.isci.2018.11.029] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 10/11/2018] [Accepted: 11/15/2018] [Indexed: 12/13/2022] Open
Abstract
CellMinerCDB provides a web-based resource (https://discover.nci.nih.gov/cellminercdb/) for integrating multiple forms of pharmacological and genomic analyses, and unifying the richest cancer cell line datasets (the NCI-60, NCI-SCLC, Sanger/MGH GDSC, and Broad CCLE/CTRP). CellMinerCDB enables data queries for genomics and gene regulatory network analyses, and exploration of pharmacogenomic determinants and drug signatures. It leverages overlaps of cell lines and drugs across databases to examine reproducibility and expand pathway analyses. We illustrate the value of CellMinerCDB for elucidating gene expression determinants, such as DNA methylation and copy number variations, and highlight complexities in assessing mutational burden. We demonstrate the value of CellMinerCDB in selecting drugs with reproducible activity, expand on the dominant role of SLFN11 for drug response, and present novel response determinants and genomic signatures for topoisomerase inhibitors and schweinfurthins. We also introduce LIX1L as a gene associated with mesenchymal signature and regulation of cellular migration and invasiveness.
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Affiliation(s)
- Vinodh N Rajapakse
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| | - Augustin Luna
- cBio Center, Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA.
| | - Mihoko Yamade
- First Department of Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Lisa Loman
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sudhir Varma
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Margot Sunshine
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; General Dynamics Information Technology Inc., 3211 Jermantown Road, Fairfax, VA 22030, USA
| | - Francesco Iorio
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Fabricio G Sousa
- Centro De Estudos Em Células Tronco, Terapia Celular E Genética Toxicológica, Programa De Pós-Graduação Em Farmácia, Universidade Federal De Mato Grosso Do Sul, Campo Grande, MS 79070-900, Brazil
| | - Fathi Elloumi
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; General Dynamics Information Technology Inc., 3211 Jermantown Road, Fairfax, VA 22030, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Anish Thomas
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Chris Sander
- cBio Center, Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA
| | - Kurt W Kohn
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Cyril H Benes
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA
| | - Mathew Garnett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - William C Reinhold
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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A pan-cancer study of the transcriptional regulation of uricogenesis in human tumours: pathological and pharmacological correlates. Biosci Rep 2018; 38:BSR20171716. [PMID: 30104401 PMCID: PMC6146287 DOI: 10.1042/bsr20171716] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 08/07/2018] [Accepted: 08/10/2018] [Indexed: 02/04/2023] Open
Abstract
Uric acid (UA) is the end product of the catabolism of purines, and its serum levels are commonly increased in cancer patients. We aimed to explore the transcriptional regulation of tumour uricogenesis in human tumours, and relate uricogenesis with tumour pathological and pharmacological findings. Using data from The Cancer Genome Atlas (TCGA), we analysed the expression levels of xanthine dehydrogenase (XDH) and adenine phosphoribosyltransferase (APRT), two key enzymes in UA production and the purine salvage pathway, respectively. We found large differences between tumour types and individual tumours in their expression of XDH and APRT. Variations in locus-specific DNA methylation and gene copy number correlated with the expression levels of XDH and APRT in human tumours respectively. We explored the consequences of this differential regulation of uricogenesis. Tumours with high levels of XDH mRNA were characterised by higher expression of several genes encoding pro-inflammatory and immune cytokines, and increased levels of tumour infiltration with immune cells. Finally, we studied cancer drug sensitivity using data from the National Cancer Institute-60 (NCI-60) database. A specific correlation was found between the expression levels of APRT and cell sensitivity to the chemotherapeutic agent 5-fluorouracil (5-FU). Our findings underline the existence of great differences in uricogenesis between different types of human tumours. The study of uricogenesis offers promising perspectives for the identification of clinically relevant molecular biomarkers and for tumour stratification in the therapeutic context.
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Kaina B, Izzotti A, Xu J, Christmann M, Pulliero A, Zhao X, Dobreanu M, Au WW. Inherent and toxicant-provoked reduction in DNA repair capacity: A key mechanism for personalized risk assessment, cancer prevention and intervention, and response to therapy. Int J Hyg Environ Health 2018; 221:993-1006. [PMID: 30041861 DOI: 10.1016/j.ijheh.2018.07.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/03/2018] [Accepted: 07/04/2018] [Indexed: 02/05/2023]
Abstract
Genomic investigations reveal novel evidence which indicates that genetic predisposition and inherent drug response are key factors for development of cancer and for poor response to therapy. However, mechanisms for these outcomes and interactions with environmental factors have not been well-characterized. Therefore, cancer risk, prevention, intervention and prognosis determinations have still mainly been based on population, rather than on individualized, evaluations. The objective of this review was to demonstrate that a key mechanism which contributes to the determination is inherent and/or toxicant-provoked reduction in DNA repair capacity. In addition, functional and quantitative determination of DNA repair capacity on an individual basis would dramatically change the evaluation and management of health problems from a population to a personalized basis. In this review, justifications for the scenario were delineated. Topics to be presented include assays for detection of functional DNA repair deficiency, mechanisms for DNA repair defects, toxicant-perturbed DNA repair capacity, epigenetic mechanisms (methylation and miRNA expression) for alteration of DNA repair function, and bioinformatics approach to analyze large amount of genomic data. Information from these topics has recently been and will be used for better understanding of cancer causation and of response to therapeutic interventions. Consequently, innovative genomic- and mechanism-based evidence can be increasingly used to develop more precise cancer risk assessment, and target-specific and personalized medicine.
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Affiliation(s)
| | - Alberto Izzotti
- University of Genoa, Genoa, Italy; IRCCS Policlinico San Martino Genoa, Italy
| | - Jianzhen Xu
- Shantou University Medical College, Shantou, China
| | | | | | - Xing Zhao
- Shantou University Medical College, Shantou, China
| | | | - William W Au
- Shantou University Medical College, Shantou, China; University of Medicine and Pharmacy, Tirgu Mures, Romania; University of Texas Medical Branch, Galveston, TX, USA.
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Marzi L, Agama K, Murai J, Difilippantonio S, James A, Peer CJ, Figg WD, Beck D, Elsayed MSA, Cushman M, Pommier Y. Novel Fluoroindenoisoquinoline Non-Camptothecin Topoisomerase I Inhibitors. Mol Cancer Ther 2018; 17:1694-1704. [PMID: 29748210 PMCID: PMC6072611 DOI: 10.1158/1535-7163.mct-18-0028] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/29/2018] [Accepted: 05/04/2018] [Indexed: 01/12/2023]
Abstract
Contrary to other anticancer targets, topoisomerase I (TOP1) is targeted by only one chemical class of FDA-approved drugs: topotecan and irinotecan, the derivatives of the plant alkaloid, camptothecin. The indenoisoquinolines LMP400, LMP744, and LMP776 are novel noncamptothecin TOP1 inhibitors in clinical trial, which overcome the limitations of camptothecins. To further improve metabolic stability, their methoxy groups have been replaced by fluorine, as in the fluoroindenoisoquinolines NSC 781517 (LMP517), NSC 779135 (LMP135), and NSC 779134 (LMP134). We tested the induction and stability of TOP1 cleavage complexes (TOP1cc), and the induction and persistence of DNA damage measured by histone H2AX phosphorylation (γH2AX) compared with their parent compounds LMP744 and LMP776 in leukemia CCRF-CEM and colon carcinoma HCT116 cells. The fluoroindenoisoquinolines induced TOP1cc and γH2AX at nanomolar concentrations, and at higher levels than the parent indenoisoquinolines. The fluoroindenoisoquinoline LMP135 showed greater antitumor activity than topotecan in small-cell lung cancer cell H82 xenografts. It was also more potent than topotecan in the NCI-60 cancer cell line panel. Bioinformatics tools (http://discover.nci.nih.gov/cellminercdb) were used to investigate the following: (i) the correlations of fluoroindenoisoquinolines activity with other drugs, and (ii) genomic determinants of response in the NCI-60. The activity of the fluoroindenoisoquinolines was mostly correlated with camptothecin derivatives and the parent indenoisoquinolines, consistent with TOP1 targeting. Genomic analyses and activity assays in CCRF-CEM SLFN11-deleted cells showed that SLFN11 expression is a dominant determinant of response to LMP135. This study shows the potential value of the fluoroindenoisoquinolines for further development as novel anticancer agents targeting TOP1. Mol Cancer Ther; 17(8); 1694-704. ©2018 AACR.
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Affiliation(s)
- Laetitia Marzi
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Keli Agama
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Junko Murai
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Simone Difilippantonio
- Laboratory of Animal Sciences Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Amy James
- Laboratory of Animal Sciences Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Cody J Peer
- Clinical Pharmacology Program, Genitourinary Malignancy Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - William D Figg
- Clinical Pharmacology Program, Genitourinary Malignancy Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Daniel Beck
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and The Purdue Center for Cancer Research, Purdue University, Lafayette, Indiana
| | - Mohamed S A Elsayed
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and The Purdue Center for Cancer Research, Purdue University, Lafayette, Indiana
| | - Mark Cushman
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and The Purdue Center for Cancer Research, Purdue University, Lafayette, Indiana
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland.
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Clark DJ, Hu Y, Bocik W, Chen L, Schnaubelt M, Roberts R, Shah P, Whiteley G, Zhang H. Evaluation of NCI-7 Cell Line Panel as a Reference Material for Clinical Proteomics. J Proteome Res 2018; 17:2205-2215. [PMID: 29718670 PMCID: PMC6670293 DOI: 10.1021/acs.jproteome.8b00165] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Reference materials are vital to benchmarking the reproducibility of clinical tests and essential for monitoring laboratory performance for clinical proteomics. The reference material utilized for mass spectrometric analysis of the human proteome would ideally contain enough proteins to be suitably representative of the human proteome, as well as exhibit a stable protein composition in different batches of sample regeneration. Previously, The Clinical Proteomic Tumor Analysis Consortium (CPTAC) utilized a PDX-derived comparative reference (CompRef) materials for the longitudinal assessment of proteomic performance; however, inherent drawbacks of PDX-derived material, including extended time needed to grow tumors and high level of expertise needed, have resulted in efforts to identify a new source of CompRef material. In this study, we examined the utility of using a panel of seven cancer cell lines, NCI-7 Cell Line Panel, as a reference material for mass spectrometric analysis of human proteome. Our results showed that not only is the NCI-7 material suitable for benchmarking laboratory sample preparation methods, but also NCI-7 sample generation is highly reproducible at both the global and phosphoprotein levels. In addition, the predicted genomic and experimental coverage of the NCI-7 proteome suggests the NCI-7 material may also have applications as a universal standard proteomic reference.
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Affiliation(s)
- David J. Clark
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - William Bocik
- Antibody Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Lijun Chen
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Michael Schnaubelt
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Rhonda Roberts
- Antibody Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Punit Shah
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Gordon Whiteley
- Antibody Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
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Tang SW, Thomas A, Murai J, Trepel JB, Bates SE, Rajapakse VN, Pommier Y. Overcoming Resistance to DNA-Targeted Agents by Epigenetic Activation of Schlafen 11 ( SLFN11) Expression with Class I Histone Deacetylase Inhibitors. Clin Cancer Res 2018; 24:1944-1953. [PMID: 29391350 DOI: 10.1158/1078-0432.ccr-17-0443] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 11/07/2017] [Accepted: 01/26/2018] [Indexed: 12/30/2022]
Abstract
Purpose: Schlafen 11 (SLFN11), a putative DNA/RNA helicase is a dominant genomic determinant of response to DNA-damaging agents and is frequently not expressed in cancer cells. Whether histone deacetylase (HDAC) inhibitors can be used to release SLFN11 and sensitize SLFN11-inactivated cancers to DNA-targeted agents is tested here.Experimental Design:SLFN11 expression was examined in The Cancer Genome Atlas (TCGA), in cancer cell line databases and in patients treated with romidepsin. Isogenic cells overexpressing or genetically inactivated for SLFN11 were used to investigate the effect of HDAC inhibitors on SLFN11 expression and sensitivity to DNA-damaging agents.Results:SLFN11 expression is suppressed in a broad fraction of common cancers and cancer cell lines. In cancer cells not expressing SLFN11, transfection of SLFN11 sensitized the cells to camptothecin, topotecan, hydroxyurea, and cisplatin but not to paclitaxel. SLFN11 mRNA and protein levels were strongly induced by class I (romidepsin, entinostat), but not class II (roclinostat) HDAC inhibitors in a broad panel of cancer cells. SLFN11 expression was also enhanced in peripheral blood mononuclear cells of patients with circulating cutaneous T-cell lymphoma treated with romidepsin. Consistent with the epigenetic regulation of SLFN11, camptothecin and class I HDAC inhibitors were synergistic in many of the cell lines tested.Conclusions: This study reports the prevalent epigenetic regulation of SLFN11 and the dominant stimulatory effect of HDAC inhibitors on SLFN11 expression. Our results provide a rationale for combining class I HDAC inhibitors and DNA-damaging agents to overcome epigenetic inactivation of SLFN11-mediated resistance to DNA-targeted agents. Clin Cancer Res; 24(8); 1944-53. ©2018 AACR.
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Affiliation(s)
- Sai-Wen Tang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Anish Thomas
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Junko Murai
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Jane B Trepel
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Susan E Bates
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland.,Division of Hematology/Oncology, Columbia University, New York, New York
| | - Vinodh N Rajapakse
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland.
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Abstract
Approximately half of high-grade serous epithelial ovarian cancers incur alterations in genes of homologous recombination (BRCA1, BRCA2, RAD51C, Fanconi anemia genes), and the rest incur alterations in other DNA repair pathways at high frequencies. Such cancer-specific gene alterations can confer selective sensitivity to DNA damaging agents such as cisplatin and carboplatin, topotecan, etoposide, doxorubicin, and gemcitabine. Originally presumed to inhibit DNA repair, PARP inhibitors that have recently been approved by the FDA for the treatment of advanced ovarian cancer also act as DNA damaging agents by inducing PARP-DNA complexes. These DNA damaging agents induce different types of DNA lesions that require various DNA repair genes for the repair, but commonly induce replication fork slowing or stalling, also referred to as replication stress. Replication stress activates DNA repair checkpoint proteins (ATR, CHK1), which prevent further DNA damage. Hence, targeting DNA repair genes or DNA repair checkpoint genes augments the anti-tumor activity of DNA damaging agents. This review describes the rational basis for using DNA repair and DNA repair checkpoint inhibitors as single agents. The review also presents the strategies combining these inhibitors with DNA damaging agents for ovarian cancer therapy based on specific gene alterations.
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