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Obermayr E, Mohr T, Schuster E, Braicu EI, Taube E, Sehouli J, Vergote I, Pujade-Lauraine E, Ray-Coquard I, Harter P, Wimberger P, Joly-Lobbedez F, Mahner S, Moll UM, Concin N, Zeillinger R. Gene expression markers in peripheral blood and outcome in patients with platinum-resistant ovarian cancer: A study of the European GANNET53 consortium. Int J Cancer 2024. [PMID: 38676430 DOI: 10.1002/ijc.34978] [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: 09/25/2023] [Revised: 03/01/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024]
Abstract
Disease progression is a major problem in ovarian cancer. There are very few treatment options for patients with platinum-resistant ovarian cancer (PROC), and therefore, these patients have a particularly poor prognosis. The aim of the present study was to identify markers for monitoring the response of 123 PROC patients enrolled in the Phase I/II GANNET53 clinical trial, which evaluated the efficacy of Ganetespib in combination with standard chemotherapy versus standard chemotherapy alone. In total, 474 blood samples were collected, comprising baseline samples taken before the first administration of the study drugs and serial samples taken during treatment until further disease progression (PD). After microfluidic enrichment, 27 gene transcripts were analyzed using quantitative polymerase chain reaction and their utility for disease monitoring was evaluated. At baseline, ERCC1 was associated with an increased risk of PD (hazard ratio [HR] 1.75, 95% confidence interval [CI]: 1.20-2.55; p = 0.005), while baseline CDH1 and ESR1 may have a risk-reducing effect (CDH1 HR 0.66, 95% CI: 0.46-0.96; p = 0.024; ESR1 HR 0.58, 95% CI: 0.39-0.86; p = 0.002). ERCC1 was observed significantly more often (72.7% vs. 53.9%; p = 0.032) and ESR1 significantly less frequently (59.1% vs. 78.3%; p = 0.018) in blood samples taken at radiologically confirmed PD than at controlled disease. At any time during treatment, ERCC1-presence and ESR1-absence were associated with short PFS and with higher odds of PD within 6 months (odds ratio 12.77, 95% CI: 4.08-39.97; p < 0.001). Our study demonstrates the clinical relevance of ESR1 and ERCC1 and may encourage the analysis of liquid biopsy samples for the management of PROC patients.
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Affiliation(s)
- Eva Obermayr
- Molecular Oncology Group, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Thomas Mohr
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Eva Schuster
- Molecular Oncology Group, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Elena Ioana Braicu
- Department of Gynecology, European Competence Center for Ovarian Cancer, Campus 3 Virchow Klinikum, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Eliane Taube
- Institute of Pathology, Campus Charité Mitte, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jalid Sehouli
- Department of Gynecology, European Competence Center for Ovarian Cancer, Campus 3 Virchow Klinikum, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Ignace Vergote
- Division of Gynecological Oncology, Department of Obstetrics and Gynecology, Leuven Cancer Institute, University Hospitals Leuven, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Isabelle Ray-Coquard
- Centre Anticancereux Léon Bérard, University Claude Bernard Lyon, GINECO Group, Lyon, France
| | - Philipp Harter
- Department of Gyneacologic Oncology, Kliniken Essen Mitte, Evang. Huyssens-Stiftung/Knappschaft GmbH, Essen, Germany
| | - Pauline Wimberger
- Department of Gynecology and Obstetrics, Technische Universität Dresden, Dresden, Germany and National Center for Tumor Diseases (NCT/UCC), Dresden, Germany
| | | | - Sven Mahner
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, AGO, Hamburg, Germany
| | - Ute Martha Moll
- Universitätsmedizin Göttingen, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Nicole Concin
- Department of Obstetrics and Gynecology, Innsbruck Medical University, Innsbruck, Austria
| | - Robert Zeillinger
- Molecular Oncology Group, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
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2
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Sherina V, McMurray HR, Powers W, Land H, Love TMT, McCall MN. Correction: Multiple imputation and direct estimation for qPCR data with non-detects. BMC Bioinformatics 2024; 25:63. [PMID: 38326767 PMCID: PMC10848451 DOI: 10.1186/s12859-024-05653-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024] Open
Affiliation(s)
- Valeriia Sherina
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, 265 Crittenden Blvd., Rochester, NY, 14642, USA
| | - Helene R McMurray
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, 601 Elmwood Ave., Rochester, NY, 14642, USA
| | - Winslow Powers
- Department of Biomedical Engineering, University of Rochester, 201 Robert B. Goergen Hall, Rochester, NY, 14627, USA
| | - Harmut Land
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA
| | - Tanzy M T Love
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, 265 Crittenden Blvd., Rochester, NY, 14642, USA
| | - Matthew N McCall
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, 265 Crittenden Blvd., Rochester, NY, 14642, USA.
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA.
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Barnett KR, Mobley RJ, Diedrich JD, Bergeron BP, Bhattarai KR, Monovich AC, Narina S, Yang W, Crews KR, Manring CS, Jabbour E, Paietta E, Litzow MR, Kornblau SM, Stock W, Inaba H, Jeha S, Pui CH, Mullighan CG, Relling MV, Pruett-Miller SM, Ryan RJ, Yang JJ, Evans WE, Savic D. Epigenomic mapping reveals distinct B cell acute lymphoblastic leukemia chromatin architectures and regulators. CELL GENOMICS 2023; 3:100442. [PMID: 38116118 PMCID: PMC10726428 DOI: 10.1016/j.xgen.2023.100442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 08/30/2023] [Accepted: 10/20/2023] [Indexed: 12/21/2023]
Abstract
B cell lineage acute lymphoblastic leukemia (B-ALL) is composed of diverse molecular subtypes, and while transcriptional and DNA methylation profiling has been extensively examined, the chromatin landscape is not well characterized for many subtypes. We therefore mapped chromatin accessibility using ATAC-seq in primary B-ALL cells from 156 patients spanning ten molecular subtypes and present this dataset as a resource. Differential chromatin accessibility and transcription factor (TF) footprint profiling were employed and identified B-ALL cell of origin, TF-target gene interactions enriched in B-ALL, and key TFs associated with accessible chromatin sites preferentially active in B-ALL. We further identified over 20% of accessible chromatin sites exhibiting strong subtype enrichment and candidate TFs that maintain subtype-specific chromatin architectures. Over 9,000 genetic variants were uncovered, contributing to variability in chromatin accessibility among patient samples. Our data suggest that distinct chromatin architectures are driven by diverse TFs and inherited genetic variants that promote unique gene-regulatory networks.
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Affiliation(s)
- Kelly R. Barnett
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Robert J. Mobley
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jonathan D. Diedrich
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Brennan P. Bergeron
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Kashi Raj Bhattarai
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Alexander C. Monovich
- Department of Pathology, University of Michigan–Ann Arbor, Rogel Cancer Center, Ann Arbor, MI 48109, USA
| | - Shilpa Narina
- Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Wenjian Yang
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Kristine R. Crews
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Christopher S. Manring
- Alliance Hematologic Malignancy Biorepository, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH 43210, USA
| | - Elias Jabbour
- Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Elisabeth Paietta
- Department of Oncology, Montefiore Medical Center, Bronx, NY 10467, USA
| | - Mark R. Litzow
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Steven M. Kornblau
- Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Wendy Stock
- University of Chicago Comprehensive Cancer Center, Chicago, IL 60637, USA
| | - Hiroto Inaba
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Sima Jeha
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ching-Hon Pui
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Charles G. Mullighan
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Mary V. Relling
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shondra M. Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Russell J.H. Ryan
- Department of Pathology, University of Michigan–Ann Arbor, Rogel Cancer Center, Ann Arbor, MI 48109, USA
| | - Jun J. Yang
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38105, USA
| | - William E. Evans
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Daniel Savic
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38105, USA
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4
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Dabbish AM, Abdelzaher HM, Abohawya M, Shamma S, Mahmoud YH, Maged A, Manaa M, Hassany M, Kobeissy F, Bazgir O, El-Fawal H, Azzazy HME, Abdelnaser A. Prognostic MicroRNA Panel for HCV-Associated HCC: Integrating Computational Biology and Clinical Validation. Cancers (Basel) 2022; 14:3036. [PMID: 35804809 PMCID: PMC9265118 DOI: 10.3390/cancers14133036] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/29/2022] [Accepted: 02/05/2022] [Indexed: 02/06/2023] Open
Abstract
Early detection of hepatocellular carcinoma (HCC) will reduce morbidity and mortality rates of this widely spread disease. Dysregulation in microRNA (miRNA) expression is associated with HCC progression. The objective is to identify a panel of differentially expressed miRNAs (DE-miRNAs) to enhance HCC early prediction in hepatitis C virus (HCV) infected patients. Candidate miRNAs were selected using a bioinformatic analysis of microarray and RNA-sequencing datasets, resulting in nine DE-miRNAs (miR-142, miR-150, miR-183, miR-199a, miR-215, miR-217, miR-224, miR-424, and miR-3607). Their expressions were validated in the serum of 44 healthy individuals, 62 non-cirrhotic HCV patients, 67 cirrhotic-HCV, and 72 HCV-associated-HCC patients using real-time PCR (qPCR). There was a significant increase in serum concentrations of the nine-candidate miRNAs in HCC and HCV patients relative to healthy individuals. MiR-424, miR-199a, miR-142, and miR-224 expressions were significantly altered in HCC compared to non-cirrhotic patients. A panel of five miRNAs improved sensitivity and specificity of HCC detection to 100% and 95.12% relative to healthy controls. Distinguishing HCC from HCV-treated patients was achieved by 70.8% sensitivity and 61.9% specificity using the combined panel, compared to alpha-fetoprotein (51.4% sensitivity and 60.67% specificity). These preliminary data show that the novel miRNAs panel (miR-150, miR-199a, miR-224, miR-424, and miR-3607) could serve as a potential non-invasive biomarker for HCC early prediction in chronic HCV patients. Further prospective studies on a larger cohort of patients should be conducted to assess the potential prognostic ability of the miRNAs panel.
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Affiliation(s)
- Areeg M. Dabbish
- Biotechnology Graduate Program, Department of Biology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (A.M.D.); (M.A.)
| | - Hana M. Abdelzaher
- Institute of Global Health and Human Ecology (IGHHE), The American University in Cairo, New Cairo 11835, Egypt; (H.M.A.); (S.S.); (H.E.-F.)
| | - Moustafa Abohawya
- Biotechnology Graduate Program, Department of Biology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (A.M.D.); (M.A.)
| | - Samir Shamma
- Institute of Global Health and Human Ecology (IGHHE), The American University in Cairo, New Cairo 11835, Egypt; (H.M.A.); (S.S.); (H.E.-F.)
| | - Yosra H. Mahmoud
- Fellow of Clinical Pathology, National Hepatology and Tropical Medicine Research Institute (NHTMRI), Cairo 11562, Egypt;
| | - Amr Maged
- Tropical Medicine Department, National Hepatology and Tropical Medicine Research Institute (NHTMRI), Cairo 11562, Egypt; (A.M.); (M.M.); (M.H.)
| | - Mohamed Manaa
- Tropical Medicine Department, National Hepatology and Tropical Medicine Research Institute (NHTMRI), Cairo 11562, Egypt; (A.M.); (M.M.); (M.H.)
| | - Mohamed Hassany
- Tropical Medicine Department, National Hepatology and Tropical Medicine Research Institute (NHTMRI), Cairo 11562, Egypt; (A.M.); (M.M.); (M.H.)
| | - Firas Kobeissy
- Program for Neurotrauma, Neuroproteomics & Biomarkers Research, Departments of Emergency Medicine, Psychiatry, Neuroscience and Chemistry, University of Florida, Gainesville, FL 32611, USA;
- Department of Biochemistry and Molecular Biology, American University of Beirut, Beirut 11-0236, Lebanon
| | - Omid Bazgir
- Modeling and Simulation/Clinical Pharmacology, Genentech, CA 94080, USA;
| | - Hassan El-Fawal
- Institute of Global Health and Human Ecology (IGHHE), The American University in Cairo, New Cairo 11835, Egypt; (H.M.A.); (S.S.); (H.E.-F.)
| | - Hassan M. E. Azzazy
- Department of Chemistry, The American University in Cairo, New Cairo 11835, Egypt;
| | - Anwar Abdelnaser
- Institute of Global Health and Human Ecology (IGHHE), The American University in Cairo, New Cairo 11835, Egypt; (H.M.A.); (S.S.); (H.E.-F.)
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