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Dobner J, Nguyen T, Pavez-Giani MG, Cyganek L, Distelmaier F, Krutmann J, Prigione A, Rossi A. mtDNA analysis using Mitopore. Mol Ther Methods Clin Dev 2024; 32:101231. [PMID: 38572068 PMCID: PMC10988129 DOI: 10.1016/j.omtm.2024.101231] [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: 09/14/2023] [Accepted: 03/08/2024] [Indexed: 04/05/2024]
Abstract
Mitochondrial DNA (mtDNA) analysis is crucial for the diagnosis of mitochondrial disorders, forensic investigations, and basic research. Existing pipelines are complex, expensive, and require specialized personnel. In many cases, including the diagnosis of detrimental single nucleotide variants (SNVs), mtDNA analysis is still carried out using Sanger sequencing. Here, we developed a simple workflow and a publicly available webserver named Mitopore that allows the detection of mtDNA SNVs, indels, and haplogroups. To simplify mtDNA analysis, we tailored our workflow to process noisy long-read sequencing data for mtDNA analysis, focusing on sequence alignment and parameter optimization. We implemented Mitopore with eliBQ (eliminate bad quality reads), an innovative quality enhancement that permits the increase of per-base quality of over 20% for low-quality data. The whole Mitopore workflow and webserver were validated using patient-derived and induced pluripotent stem cells harboring mtDNA mutations. Mitopore streamlines mtDNA analysis as an easy-to-use fast, reliable, and cost-effective analysis method for both long- and short-read sequencing data. This significantly enhances the accessibility of mtDNA analysis and reduces the cost per sample, contributing to the progress of mtDNA-related research and diagnosis.
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Affiliation(s)
- Jochen Dobner
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Thach Nguyen
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Mario Gustavo Pavez-Giani
- Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany
| | - Lukas Cyganek
- Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Jean Krutmann
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
- Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Alessandro Prigione
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Andrea Rossi
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
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2
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Choudhury AD, Kwak L, Cheung A, Allaire KM, Marquez J, Yang DD, Tripathi A, Kilar JM, Flynn M, Maynard B, Reichel R, Pace AF, Chen BK, Van Allen EM, Kilbridge K, Wei XX, McGregor BA, Pomerantz MM, Bhatt RS, Sweeney CJ, Bubley GJ, Jacene HA, Taplin ME, Huang FW, Harshman LC, Fong L. Randomized Phase II Study Evaluating the Addition of Pembrolizumab to Radium-223 in Metastatic Castration-resistant Prostate Cancer. Cancer Immunol Res 2024; 12:704-718. [PMID: 38552171 PMCID: PMC11148544 DOI: 10.1158/2326-6066.cir-22-0306] [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: 04/26/2022] [Revised: 08/15/2023] [Accepted: 03/08/2024] [Indexed: 06/05/2024]
Abstract
The checkpoint immunotherapeutic pembrolizumab induces responses in a small minority of patients with metastatic castration-resistant prostate cancer (mCRPC). Radium-223 (R223) may increase immunogenicity of bone metastases and increase pembrolizumab (P) activity. In a randomized phase II study, we assessed the effect of R223+P compared with R223 on tumor immune infiltration, safety, and clinical outcomes in patients with mCRPC. The primary endpoint was differences in CD4+ and CD8+ T-cell infiltrate in 8-week versus baseline bone metastasis biopsies; secondary endpoints were safety, radiographic progression-free survival (rPFS), and overall survival (OS). Of the 42 treated patients (29 R223+P, 13 R223), 18 R223+P and 8 R223 patients had evaluable paired tumor biopsies. Median fold-change of CD4+ T cells was -0.7 (range: -9.3 to 4.7) with R223+P and 0.1 (-11.1 to 3.7) with R223 (P = 0.66); for CD8+ T cells, median fold-change was -0.6 (-7.4 to 5.3) with R223+P and -1.3 (-3.1 to 4.8) with R223 (P = 0.66). Median rPFS and OS was 6.1 (95% confidence interval: 2.7-11.0) and 16.9 months [12.7-not reached (NR)], respectively, with R223+P and 5.7 (2.6-NR) and 16.0 (9.0-NR), respectively, with R223. Although R223+P was well tolerated with no unexpected toxicity, the combination did not improve efficacy. High-dimensional flow cytometry demonstrated minimal immune modulation with R223, whereas R223+P induced CTLA-4 expression on circulating CD4+ T cells. Clinical responders possessed lower circulating frequencies of Ki67+ T and myeloid cells at baseline and higher circulating frequencies of TIM-3+ T and myeloid cells by week 9. Although R223+P did not induce T-cell infiltration into the tumor microenvironment, exhaustion of induced peripheral T-cell immune responses may dampen the combination's clinical activity.
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Affiliation(s)
- Atish D Choudhury
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Lucia Kwak
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Alexander Cheung
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Kathryn M Allaire
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Jaqueline Marquez
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - David D Yang
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | | | | | | | | | - Rebecca Reichel
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Brandon K Chen
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Eliezer M Van Allen
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Kerry Kilbridge
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Xiao X Wei
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Bradley A McGregor
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Mark M Pomerantz
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Rupal S Bhatt
- Harvard Medical School, Boston, Massachusetts
- Beth-Israel Deaconess Medical Center, Boston, Massachusetts
| | | | - Glenn J Bubley
- Harvard Medical School, Boston, Massachusetts
- Beth-Israel Deaconess Medical Center, Boston, Massachusetts
| | - Heather A Jacene
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Mary-Ellen Taplin
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Franklin W Huang
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | | | - Lawrence Fong
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, California
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3
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Yao P, Gao M, Hu W, Wang J, Wang Y, Wang Q, Ji J. Proteogenomic analysis identifies neoantigens and bacterial peptides as immunotherapy targets in colorectal cancer. Pharmacol Res 2024; 204:107209. [PMID: 38740147 DOI: 10.1016/j.phrs.2024.107209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 05/08/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024]
Abstract
Considerable progress has recently been made in cancer immunotherapy, including immune checkpoint blockade, cancer vaccine, and adoptive T cell methods. The lack of effective targets is a major cause of the low immunotherapy response rate in colorectal cancer (CRC). Here, we used a proteogenomic strategy comprising immunopeptidomics, whole exome sequencing, and 16 S ribosomal DNA sequencing analyses of 8 patients with CRC to identify neoantigens and bacterial peptides that can serve as antitumor targets. This study directly identified several personalized neoantigens and bacterial immunopeptides. Immunoassays showed that all neoantigens and 5 of 8 bacterial immunopeptides could be recognized by autologous T cells. Additionally, T cell receptor (TCR) αβ sequencing revealed the TCR repertoire of epitope-reactive CD8+ T cells. Functional studies showed that T cell receptor-T (TCR-T) could be activated by epitope pulsed lymphoblastoid cells. Overall, this study comprehensively profiled the CRC immunopeptidome, revealing several neoantigens and bacterial peptides with potential to serve as immunotherapy targets in CRC.
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Affiliation(s)
- Pengju Yao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Mingjie Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Weiyi Hu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Jiahao Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Institute of Molecular Medicine, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Yuhao Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Qingsong Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Jianguo Ji
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
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4
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Johnson TS, Sudha P, Liu E, Becker N, Robertson S, Blaney P, Morgan G, Chopra VS, Dos Santos C, Nixon M, Huang K, Suvannasankha A, Zaid MA, Abonour R, Walker BA. 1q amplification and PHF19 expressing high-risk cells are associated with relapsed/refractory multiple myeloma. Nat Commun 2024; 15:4144. [PMID: 38755140 PMCID: PMC11099140 DOI: 10.1038/s41467-024-48327-9] [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: 08/09/2023] [Accepted: 04/29/2024] [Indexed: 05/18/2024] Open
Abstract
Multiple Myeloma is an incurable plasma cell malignancy with a poor survival rate that is usually treated with immunomodulatory drugs (iMiDs) and proteosome inhibitors (PIs). The malignant plasma cells quickly become resistant to these agents causing relapse and uncontrolled growth of resistant clones. From whole genome sequencing (WGS) and RNA sequencing (RNA-seq) studies, different high-risk translocation, copy number, mutational, and transcriptional markers can be identified. One of these markers, PHF19, epigenetically regulates cell cycle and other processes and is already studied using RNA-seq. In this study, we generate a large (325,025 cells and 49 patients) single cell multi-omic dataset and jointly quantify ATAC- and RNA-seq for each cell and matched genomic profiles for each patient. We identify an association between one plasma cell subtype with myeloma progression that we call relapsed/refractory plasma cells (RRPCs). These cells are associated with chromosome 1q alterations, TP53 mutations, and higher expression of PHF19. We also identify downstream regulation of cell cycle inhibitors in these cells, possible regulation by the transcription factor (TF) PBX1 on chromosome 1q, and determine that PHF19 may be acting primarily through this subset of cells.
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Affiliation(s)
- Travis S Johnson
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN, USA
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
- Melvin and Bren Simon Comprehensive Cancer Center, Experimental and Developmental Therapeutics, School of Medicine, Indiana University, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Parvathi Sudha
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Enze Liu
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Nathan Becker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | | | - Patrick Blaney
- Perlmutter Cancer Center, Langone Health, New York University, New York, NY, USA
| | - Gareth Morgan
- Perlmutter Cancer Center, Langone Health, New York University, New York, NY, USA
| | | | | | | | - Kun Huang
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN, USA
- Melvin and Bren Simon Comprehensive Cancer Center, Experimental and Developmental Therapeutics, School of Medicine, Indiana University, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Attaya Suvannasankha
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
- Roudebush VAMC, Indianapolis, IN, USA
| | - Mohammad Abu Zaid
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Rafat Abonour
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Brian A Walker
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, USA.
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA.
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5
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Deyell RJ, Shen Y, Titmuss E, Dixon K, Williamson LM, Pleasance E, Nelson JMT, Abbasi S, Krzywinski M, Armstrong L, Bonakdar M, Ch'ng C, Chuah E, Dunham C, Fok A, Jones M, Lee AF, Ma Y, Moore RA, Mungall AJ, Mungall KL, Rogers PC, Schrader KA, Virani A, Wee K, Young SS, Zhao Y, Jones SJM, Laskin J, Marra MA, Rassekh SR. Whole genome and transcriptome integrated analyses guide clinical care of pediatric poor prognosis cancers. Nat Commun 2024; 15:4165. [PMID: 38755180 PMCID: PMC11099106 DOI: 10.1038/s41467-024-48363-5] [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: 05/08/2023] [Accepted: 04/29/2024] [Indexed: 05/18/2024] Open
Abstract
The role for routine whole genome and transcriptome analysis (WGTA) for poor prognosis pediatric cancers remains undetermined. Here, we characterize somatic mutations, structural rearrangements, copy number variants, gene expression, immuno-profiles and germline cancer predisposition variants in children and adolescents with relapsed, refractory or poor prognosis malignancies who underwent somatic WGTA and matched germline sequencing. Seventy-nine participants with a median age at enrollment of 8.8 y (range 6 months to 21.2 y) are included. Germline pathogenic/likely pathogenic variants are identified in 12% of participants, of which 60% were not known prior. Therapeutically actionable variants are identified by targeted gene report and whole genome in 32% and 62% of participants, respectively, and increase to 96% after integrating transcriptome analyses. Thirty-two molecularly informed therapies are pursued in 28 participants with 54% achieving a clinical benefit rate; objective response or stable disease ≥6 months. Integrated WGTA identifies therapeutically actionable variants in almost all tumors and are directly translatable to clinical care of children with poor prognosis cancers.
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Affiliation(s)
- Rebecca J Deyell
- Department of Pediatrics, BC Children's Hospital and Research Institute, Vancouver, BC, Canada.
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Emma Titmuss
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Katherine Dixon
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Jessica M T Nelson
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Sanna Abbasi
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Martin Krzywinski
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Linlea Armstrong
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Melika Bonakdar
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Carolyn Ch'ng
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Chris Dunham
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Alexandra Fok
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Martin Jones
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Anna F Lee
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Paul C Rogers
- Department of Pediatrics, BC Children's Hospital and Research Institute, Vancouver, BC, Canada
| | - Kasmintan A Schrader
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Alice Virani
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Kathleen Wee
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Sean S Young
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Cancer Genetics and Genomics Laboratory, Department of Pathology and Laboratory Medicine, BC Cancer, Vancouver, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Shahrad R Rassekh
- Department of Pediatrics, BC Children's Hospital and Research Institute, Vancouver, BC, Canada.
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6
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Giubellino A, He Y, Munro SA, Zhou Y, Song KY, Plaza JA, Torres-Cabala CA, Nelson AC. Gene Expression Profile of Benign, Intermediate, and Malignant Spitz and Spitzoid Melanocytic Lesions. Cancers (Basel) 2024; 16:1798. [PMID: 38791877 PMCID: PMC11119593 DOI: 10.3390/cancers16101798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/19/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Spitz and Spitzoid lesions represent one of the most challenging melanocytic neoplasms in dermatopathology. Nosologic classification has been more recently improved by the discovery of novel molecular drivers, particularly translocations. In the current study, we aimed to use an unbiased approach to explore the gene expression profile of a group of melanocytic Spitz and Spitzoid melanocytic lesions ranging from benign lesions to melanoma, including intermediate lesions such as SPARK nevi and atypical Spitz tumors/melanocytomas. Using unsupervised analysis of gene expression data, we found some distinct hierarchical clusters of lesions, including groups characterized by ALK and NTRK translocations. Few non-ALK translocated tumors demonstrated increased ALK expression, confirmed by immunohistochemistry. Spitz tumors with overlapping features of dysplastic nevi, so-called SPARK nevi, appear to have a common gene expression profile by hierarchical clustering. Finally, weighted gene correlation network analysis identified gene modules variably regulated in subtypes of these cases. Thus, gene expression profiling of Spitz and Spitzoid lesions represents a viable instrument for the characterization of these lesions.
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Affiliation(s)
- Alessio Giubellino
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA; (Y.H.); (Y.Z.); (K.Y.S.); (A.C.N.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yuyu He
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA; (Y.H.); (Y.Z.); (K.Y.S.); (A.C.N.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sarah A. Munro
- Minnesota Supercomputing Institute, Minneapolis, MN 55455, USA;
| | - Yan Zhou
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA; (Y.H.); (Y.Z.); (K.Y.S.); (A.C.N.)
| | - Kyu Young Song
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA; (Y.H.); (Y.Z.); (K.Y.S.); (A.C.N.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jose A. Plaza
- Department of Pathology, The Ohio State University Wexner Medical Center (OOSUWMC), Columbus, OH 43210, USA;
| | | | - Andrew C. Nelson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA; (Y.H.); (Y.Z.); (K.Y.S.); (A.C.N.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
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7
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Gupta A, Gazzo A, Selenica P, Safonov A, Pareja F, da Silva EM, Brown DN, Zhu Y, Patel J, Blanco-Heredia J, Stefanovska B, Carpenter MA, Pei X, Frosina D, Jungbluth AA, Ladanyi M, Curigliano G, Weigelt B, Riaz N, Powell SN, Razavi P, Harris RS, Reis-Filho JS, Marra A, Chandarlapaty S. APOBEC3 mutagenesis drives therapy resistance in breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591453. [PMID: 38746158 PMCID: PMC11092499 DOI: 10.1101/2024.04.29.591453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Acquired genetic alterations commonly drive resistance to endocrine and targeted therapies in metastatic breast cancer 1-7 , however the underlying processes engendering these diverse alterations are largely uncharacterized. To identify the mutational processes operant in breast cancer and their impact on clinical outcomes, we utilized a well-annotated cohort of 3,880 patient samples with paired tumor-normal sequencing data. The mutational signatures associated with apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) enzymes were highly prevalent and enriched in post-treatment compared to treatment-naïve hormone receptor-positive (HR+) cancers. APOBEC3 mutational signatures were independently associated with shorter progression-free survival on antiestrogen plus CDK4/6 inhibitor combination therapy in patients with HR+ metastatic breast cancer. Whole genome sequencing (WGS) of breast cancer models and selected paired primary-metastatic samples demonstrated that active APOBEC3 mutagenesis promoted resistance to both endocrine and targeted therapies through characteristic alterations such as RB1 loss-of-function mutations. Evidence of APOBEC3 activity in pre-treatment samples illustrated a pervasive role for this mutational process in breast cancer evolution. The study reveals APOBEC3 mutagenesis to be a frequent mediator of therapy resistance in breast cancer and highlights its potential as a biomarker and target for overcoming resistance.
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8
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George B, Kudryashova O, Kravets A, Thalji S, Malarkannan S, Kurzrock R, Chernyavskaya E, Gusakova M, Kravchenko D, Tychinin D, Savin E, Alekseeva L, Butusova A, Bagaev A, Shin N, Brown JH, Sethi I, Wang D, Taylor B, McFall T, Kamgar M, Hall WA, Erickson B, Christians KK, Evans DB, Tsai S. Transcriptomic-Based Microenvironment Classification Reveals Precision Medicine Strategies for Pancreatic Ductal Adenocarcinoma. Gastroenterology 2024; 166:859-871.e3. [PMID: 38280684 DOI: 10.1053/j.gastro.2024.01.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 12/11/2023] [Accepted: 01/18/2024] [Indexed: 01/29/2024]
Abstract
BACKGROUND & AIMS The complex tumor microenvironment (TME) of pancreatic ductal adenocarcinoma (PDAC) has hindered the development of reliable predictive biomarkers for targeted therapy and immunomodulatory strategies. A comprehensive characterization of the TME is necessary to advance precision therapeutics in PDAC. METHODS A transcriptomic profiling platform for TME classification based on functional gene signatures was applied to 14 publicly available PDAC datasets (n = 1657) and validated in a clinically annotated independent cohort of patients with PDAC (n = 79). Four distinct subtypes were identified using unsupervised clustering and assessed to evaluate predictive and prognostic utility. RESULTS TME classification using transcriptomic profiling identified 4 biologically distinct subtypes based on their TME immune composition: immune enriched (IE); immune enriched, fibrotic (IE/F); fibrotic (F); and immune depleted (D). The IE and IE/F subtypes demonstrated a more favorable prognosis and potential for response to immunotherapy compared with the F and D subtypes. Most lung metastases and liver metastases were subtypes IE and D, respectively, indicating the role of clonal phenotype and immune milieu in developing personalized therapeutic strategies. In addition, distinct TMEs with potential therapeutic implications were identified in treatment-naive primary tumors compared with tumors that underwent neoadjuvant therapy. CONCLUSIONS This novel approach defines a distinct subgroup of PADC patients that may benefit from immunotherapeutic strategies based on their TME subtype and provides a framework to select patients for prospective clinical trials investigating precision immunotherapy in PDAC. Further, the predictive utility and real-world clinical applicability espoused by this transcriptomic-based TME classification approach will accelerate the advancement of precision medicine in PDAC.
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Affiliation(s)
- Ben George
- LaBahn Pancreatic Cancer Program, Division of Hematology and Oncology, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin.
| | | | | | - Samih Thalji
- LaBahn Pancreatic Cancer Program, Department of Surgery, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Subramaniam Malarkannan
- Versiti Blood Research Institute, Department of Medicine, Microbiology & Molecular Genetics, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Razelle Kurzrock
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Division of Hematology and Oncology, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | | | | | | | | | - Egor Savin
- BostonGene Corporation, Waltham, Massachusetts
| | | | | | | | - Nara Shin
- BostonGene Corporation, Waltham, Massachusetts
| | | | - Isha Sethi
- BostonGene Corporation, Waltham, Massachusetts
| | - Dandan Wang
- Versiti Blood Research Institute, Department of Medicine, Microbiology & Molecular Genetics, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Bradley Taylor
- Clinical and Translational Science Institute, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Thomas McFall
- LaBahn Pancreatic Cancer Program, Department of Biochemistry, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Mandana Kamgar
- LaBahn Pancreatic Cancer Program, Division of Hematology and Oncology, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - William A Hall
- LaBahn Pancreatic Cancer Program, Department of Radiation Oncology, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Beth Erickson
- LaBahn Pancreatic Cancer Program, Department of Radiation Oncology, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Kathleen K Christians
- LaBahn Pancreatic Cancer Program, Department of Surgery, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Douglas B Evans
- LaBahn Pancreatic Cancer Program, Department of Surgery, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Susan Tsai
- LaBahn Pancreatic Cancer Program, Department of Surgery, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
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9
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Kapur P, Zhong H, Le D, Mukhopadhyay R, Miyata J, Carrillo D, Rakheja D, Rajaram S, Durinck S, Modrusan Z, Brugarolas J. Molecular underpinnings of dedifferentiation and aggressiveness in chromophobe renal cell carcinoma. JCI Insight 2024; 9:e176743. [PMID: 38775158 PMCID: PMC11141915 DOI: 10.1172/jci.insight.176743] [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: 10/19/2023] [Accepted: 04/10/2024] [Indexed: 06/02/2024] Open
Abstract
Sarcomatoid dedifferentiation is common to multiple renal cell carcinoma (RCC) subtypes, including chromophobe RCC (ChRCC), and is associated with increased aggressiveness, resistance to targeted therapies, and heightened sensitivity to immunotherapy. To study ChRCC dedifferentiation, we performed multiregion integrated paired pathological and genomic analyses. Interestingly, ChRCC dedifferentiates not only into sarcomatoid but also into anaplastic and glandular subtypes, which are similarly associated with increased aggressiveness and metastases. Dedifferentiated ChRCC shows loss of epithelial markers, convergent gene expression, and whole genome duplication from a hypodiploid state characteristic of classic ChRCC. We identified an intermediate state with atypia and increased mitosis but preserved epithelial markers. Our data suggest that dedifferentiation is initiated by hemizygous mutation of TP53, which can be observed in differentiated areas, as well as mutation of PTEN. Notably, these mutations become homozygous with duplication of preexisting monosomes (i.e., chromosomes 17 and 10), which characterizes the transition to dedifferentiated ChRCC. Serving as potential biomarkers, dedifferentiated areas become accentuated by mTORC1 activation (phospho-S6) and p53 stabilization. Notably, dedifferentiated ChRCC share gene enrichment and pathway activation features with other sarcomatoid RCC, suggesting convergent evolutionary trajectories. This study expands our understanding of aggressive ChRCC, provides insight into molecular mechanisms of tumor progression, and informs pathologic classification and diagnostics.
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Affiliation(s)
- Payal Kapur
- Department of Pathology and
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Kidney Cancer Program at Simmons Comprehensive Cancer Center, Dallas, Texas, USA
| | - Hua Zhong
- Department of Pathology and
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Daniel Le
- Molecular Biology Department, Genentech Inc., South San Francisco, California, USA
| | | | - Jeffrey Miyata
- Kidney Cancer Program at Simmons Comprehensive Cancer Center, Dallas, Texas, USA
- Hematology-Oncology Division of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Deyssy Carrillo
- Kidney Cancer Program at Simmons Comprehensive Cancer Center, Dallas, Texas, USA
- Hematology-Oncology Division of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | | | - Satwik Rajaram
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Steffen Durinck
- Molecular Biology Department, Genentech Inc., South San Francisco, California, USA
| | - Zora Modrusan
- Molecular Biology Department, Genentech Inc., South San Francisco, California, USA
| | - James Brugarolas
- Kidney Cancer Program at Simmons Comprehensive Cancer Center, Dallas, Texas, USA
- Hematology-Oncology Division of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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10
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Kosugi S, Terao C. Comparative evaluation of SNVs, indels, and structural variations detected with short- and long-read sequencing data. Hum Genome Var 2024; 11:18. [PMID: 38632226 PMCID: PMC11024196 DOI: 10.1038/s41439-024-00276-x] [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: 01/18/2024] [Revised: 03/12/2024] [Accepted: 03/20/2024] [Indexed: 04/19/2024] Open
Abstract
Short- and long-read sequencing technologies are routinely used to detect DNA variants, including SNVs, indels, and structural variations (SVs). However, the differences in the quality and quantity of variants detected between short- and long-read data are not fully understood. In this study, we comprehensively evaluated the variant calling performance of short- and long-read-based SNV, indel, and SV detection algorithms (6 for SNVs, 12 for indels, and 13 for SVs) using a novel evaluation framework incorporating manual visual inspection. The results showed that indel-insertion calls greater than 10 bp were poorly detected by short-read-based detection algorithms compared to long-read-based algorithms; however, the recall and precision of SNV and indel-deletion detection were similar between short- and long-read data. The recall of SV detection with short-read-based algorithms was significantly lower in repetitive regions, especially for small- to intermediate-sized SVs, than that detected with long-read-based algorithms. In contrast, the recall and precision of SV detection in nonrepetitive regions were similar between short- and long-read data. These findings suggest the need for refined strategies, such as incorporating multiple variant detection algorithms, to generate a more complete set of variants using short-read data.
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Affiliation(s)
- Shunichi Kosugi
- Center for Genome Informatics, Research Organization of Information and Systems, Joint Support-Center for Data Science Research, Shizuoka, Japan.
- Advanced Genomics Center, National Institute of Genetics, Shizuoka, Japan.
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan.
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
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11
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Tumuluru S, Godfrey JK, Cooper A, Yu J, Chen X, MacNabb BW, Venkataraman G, Zha Y, Pelzer B, Song J, Duns G, Sworder BJ, Bolen C, Penuel E, Postovalova E, Kotlov N, Bagaev A, Fowler N, Smith SM, Alizadeh AA, Steidl C, Kline J. Integrative genomic analysis identifies unique immune environments associated with immunotherapy response in diffuse large B cell lymphoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.17.576100. [PMID: 38328071 PMCID: PMC10849512 DOI: 10.1101/2024.01.17.576100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Most diffuse large B-cell lymphoma (DLBCL) patients treated with bispecific antibodies (BsAb) or chimeric antigen receptor (CAR) T cells fail to achieve durable treatment responses, underscoring the need for a deeper understanding of mechanisms that regulate the immune environment and response to treatment. Here, an integrative, multi-omic approach was employed to characterize DLBCL immune environments, which effectively segregated DLBCLs into four quadrants - termed DLBCL-immune quadrants (IQ) - defined by cell-of-origin and immune-related gene set expression scores. Recurrent genomic alterations were enriched in each IQ, suggesting that lymphoma cell-intrinsic alterations contribute to orchestrating unique DLBCL immune environments. In relapsed/refractory DLBCL patients, DLBCL-IQ assignment correlated significantly with clinical benefit with the CD20 x CD3 BsAb, mosunetuzumab, but not with CD19-directed CAR T cells. DLBCL-IQ provides a new framework to conceptualize the DLBCL immune landscape and uncovers the differential impact of the endogenous immune environment on outcomes to BsAb and CAR T cell treatment.
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12
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Kelly RJ, Landon BV, Zaidi AH, Singh D, Canzoniero JV, Balan A, Hales RK, Voong KR, Battafarano RJ, Jobe BA, Yang SC, Broderick S, Ha J, Marrone KA, Pereira G, Rao N, Borole A, Karaindrou K, Belcaid Z, White JR, Ke S, Amjad AI, Weksler B, Shin EJ, Thompson E, Smith KN, Pardoll DM, Hu C, Feliciano JL, Anagnostou V, Lam VK. Neoadjuvant nivolumab or nivolumab plus LAG-3 inhibitor relatlimab in resectable esophageal/gastroesophageal junction cancer: a phase Ib trial and ctDNA analyses. Nat Med 2024; 30:1023-1034. [PMID: 38504015 PMCID: PMC11031406 DOI: 10.1038/s41591-024-02877-z] [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: 06/05/2023] [Accepted: 02/16/2024] [Indexed: 03/21/2024]
Abstract
Gastroesophageal cancer dynamics and drivers of clinical responses with immune checkpoint inhibitors (ICI) remain poorly understood. Potential synergistic activity of dual programmed cell death protein 1 (PD-1) and lymphocyte-activation gene 3 (LAG-3) inhibition may help improve immunotherapy responses for these tumors. We report a phase Ib trial that evaluated neoadjuvant nivolumab (Arm A, n = 16) or nivolumab-relatlimab (Arm B, n = 16) in combination with chemoradiotherapy in 32 patients with resectable stage II/stage III gastroesophageal cancer together with an in-depth evaluation of pathological, molecular and functional immune responses. Primary endpoint was safety; the secondary endpoint was feasibility; exploratory endpoints included pathological complete (pCR) and major pathological response (MPR), recurrence-free survival (RFS) and overall survival (OS). The study met its primary safety endpoint in Arm A, although Arm B required modification to mitigate toxicity. pCR and MPR rates were 40% and 53.5% for Arm A and 21.4% and 57.1% for Arm B. Most common adverse events were fatigue, nausea, thrombocytopenia and dermatitis. Overall, 2-year RFS and OS rates were 72.5% and 82.6%, respectively. Higher baseline programmed cell death ligand 1 (PD-L1) and LAG-3 expression were associated with deeper pathological responses. Exploratory analyses of circulating tumor DNA (ctDNA) showed that patients with undetectable ctDNA post-ICI induction, preoperatively and postoperatively had a significantly longer RFS and OS; ctDNA clearance was reflective of neoantigen-specific T cell responses. Our findings provide insights into the safety profile of combined PD-1 and LAG-3 blockade in gastroesophageal cancer and highlight the potential of ctDNA analysis to dynamically assess systemic tumor burden during neoadjuvant ICI that may open a therapeutic window for future intervention. ClinicalTrials.gov registration: NCT03044613 .
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Affiliation(s)
- Ronan J Kelly
- The Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA.
| | - Blair V Landon
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ali H Zaidi
- Allegheny Health Network Cancer Institute, Allegheny Health Network, Pittsburgh, PA, USA
| | - Dipika Singh
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Bloomberg-Kimmel Institute of Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jenna V Canzoniero
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Archana Balan
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Russell K Hales
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Radiation Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - K Ranh Voong
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Radiation Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Richard J Battafarano
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Blair A Jobe
- Allegheny Health Network Cancer Institute, Allegheny Health Network, Pittsburgh, PA, USA
| | - Stephen C Yang
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stephen Broderick
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jinny Ha
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kristen A Marrone
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Bloomberg-Kimmel Institute of Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Gavin Pereira
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nisha Rao
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aryan Borole
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Katerina Karaindrou
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zineb Belcaid
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James R White
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Suqi Ke
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Ali I Amjad
- Allegheny Health Network Cancer Institute, Allegheny Health Network, Pittsburgh, PA, USA
| | - Benny Weksler
- Allegheny Health Network Cancer Institute, Allegheny Health Network, Pittsburgh, PA, USA
| | - Eun Ji Shin
- Department of Gastroenterology & Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth Thompson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kellie N Smith
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Bloomberg-Kimmel Institute of Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Drew M Pardoll
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Bloomberg-Kimmel Institute of Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chen Hu
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Josephine L Feliciano
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valsamo Anagnostou
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- The Bloomberg-Kimmel Institute of Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Lung Cancer Precision Medicine Center of Excellence, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Vincent K Lam
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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13
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Nakashima T, Yamamoto R, Ohno M, Sugino H, Takahashi M, Funakoshi Y, Nambu S, Uneda A, Yanagisawa S, Uzuka T, Arakawa Y, Hanaya R, Ishida J, Yoshimoto K, Saito R, Narita Y, Suzuki H. Development of a rapid and comprehensive genomic profiling test supporting diagnosis and research for gliomas. Brain Tumor Pathol 2024; 41:50-60. [PMID: 38332448 DOI: 10.1007/s10014-023-00476-3] [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: 09/15/2023] [Accepted: 12/25/2023] [Indexed: 02/10/2024]
Abstract
A prompt and reliable molecular diagnosis for brain tumors has become crucial in precision medicine. While Comprehensive Genomic Profiling (CGP) has become feasible, there remains room for enhancement in brain tumor diagnosis due to the partial lack of essential genes and limitations in broad copy number analysis. In addition, the long turnaround time of commercially available CGPs poses an additional obstacle to the timely implementation of results in clinics. To address these challenges, we developed a CGP encompassing 113 genes, genome-wide copy number changes, and MGMT promoter methylation. Our CGP incorporates not only diagnostic genes but also supplementary genes valuable for research. Our CGP enables us to simultaneous identification of mutations, gene fusions, focal and broad copy number alterations, and MGMT promoter methylation status, with results delivered within a minimum of 4 days. Validation of our CGP, through comparisons with whole-genome sequencing, RNA sequencing, and pyrosequencing, has certified its accuracy and reliability. We applied our CGP for 23 consecutive cases of intracranial mass lesions, which demonstrated its efficacy in aiding diagnosis and prognostication. Our CGP offers a comprehensive and rapid molecular profiling for gliomas, which could potentially apply to clinical practices and research primarily in the field of brain tumors.
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Affiliation(s)
- Takuma Nakashima
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
- Department of Neurosurgery, Nagoya University School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Ryo Yamamoto
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
- Department of Neurosurgery, Nagoya University School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Makoto Ohno
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Hirokazu Sugino
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Masamichi Takahashi
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Yusuke Funakoshi
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Shohei Nambu
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Atsuhito Uneda
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Shunsuke Yanagisawa
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Takeo Uzuka
- Department of Neurosurgery, Dokkyo Medical University, 880 Kitakobaya-Shi, Mibu, Shimotsuga-Gun, Tochigi, 321-0293, Japan
| | - Yoshiki Arakawa
- Department of Neurosurgery, Kyoto University Graduate School of Medicine, 54 Kawahara-Cho Shogoin Sakyo-Ku, Kyoto, 606-8507, Japan
| | - Ryosuke Hanaya
- Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1, Sakuragaoka, Kagoshima, 890-8544, Japan
| | - Joji Ishida
- Department of Neurosurgery, Okayama University Graduate School of Medicine, 2-5-1 Shikata-Cho, Kita-Ku, Okayama, 700-8558, Japan
| | - Koji Yoshimoto
- Department of Neurosurgery, Graduate School of Medical Science, Kyushu University, 3-1-1, Maidashi, Higashi-Ku, Fukuoka City, 812-8582, Japan
| | - Ryuta Saito
- Department of Neurosurgery, Nagoya University School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Yoshitaka Narita
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Hiromichi Suzuki
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan.
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14
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Rahman CR, Wong L. How much can ChatGPT really help computational biologists in programming? J Bioinform Comput Biol 2024; 22:2471001. [PMID: 38779779 DOI: 10.1142/s021972002471001x] [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] [Indexed: 05/25/2024]
Abstract
ChatGPT, a recently developed product by openAI, is successfully leaving its mark as a multi-purpose natural language based chatbot. In this paper, we are more interested in analyzing its potential in the field of computational biology. A major share of work done by computational biologists these days involve coding up bioinformatics algorithms, analyzing data, creating pipelining scripts and even machine learning modeling and feature extraction. This paper focuses on the potential influence (both positive and negative) of ChatGPT in the mentioned aspects with illustrative examples from different perspectives. Compared to other fields of computer science, computational biology has (1) less coding resources, (2) more sensitivity and bias issues (deals with medical data), and (3) more necessity of coding assistance (people from diverse background come to this field). Keeping such issues in mind, we cover use cases such as code writing, reviewing, debugging, converting, refactoring, and pipelining using ChatGPT from the perspective of computational biologists in this paper.
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Affiliation(s)
| | - Limsoon Wong
- School of Computing, National University of Singapore, 13 Computing Drive, Singapore 117417
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15
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Pelster MS, Silverman IM, Schonhoft JD, Johnson A, Selenica P, Ulanet D, Rimkunas V, Reis-Filho JS. Post-therapy emergence of an NBN reversion mutation in a patient with pancreatic acinar cell carcinoma. NPJ Precis Oncol 2024; 8:82. [PMID: 38561473 PMCID: PMC10985087 DOI: 10.1038/s41698-024-00497-x] [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: 03/06/2023] [Accepted: 12/21/2023] [Indexed: 04/04/2024] Open
Abstract
Pancreatic acinar cell carcinoma (PACC) is a rare form of pancreatic cancer that commonly harbors targetable alterations, including activating fusions in the MAPK pathway and loss-of-function (LOF) alterations in DNA damage response/homologous recombination DNA repair-related genes. Here, we describe a patient with PACC harboring both somatic biallelic LOF of NBN and an activating NTRK1 fusion. Upon disease progression following 13 months of treatment with folinic acid, fluorouracil, irinotecan, and oxaliplatin (FOLFIRINOX), genomic analysis of a metastatic liver biopsy revealed the emergence of a novel reversion mutation restoring the reading frame of NBN. To our knowledge, genomic reversion of NBN has not been previously reported as a resistance mechanism in any tumor type. The patient was treated with, but did not respond to, targeted treatment with a selective NTRK inhibitor. This case highlights the complex but highly actionable genomic landscape of PACC and underlines the value of genomic profiling of rare tumor types such as PACC.
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Affiliation(s)
| | | | | | | | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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16
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Titmuss E, Yu IS, Pleasance ED, Williamson LM, Mungall K, Mungall AJ, Renouf DJ, Moore R, Jones SJM, Marra MA, Laskin JJ, Savage KJ. Exploration of Germline Correlates and Risk of Immune-Related Adverse Events in Advanced Cancer Patients Treated with Immune Checkpoint Inhibitors. Curr Oncol 2024; 31:1865-1875. [PMID: 38668043 PMCID: PMC11048877 DOI: 10.3390/curroncol31040140] [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: 02/16/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Immune checkpoint inhibitors (ICIs) are increasingly used in the treatment of many tumor types, and durable responses can be observed in select populations. However, patients may exhibit significant immune-related adverse events (irAEs) that may lead to morbidity. There is limited information on whether the presence of specific germline mutations may highlight those at elevated risk of irAEs. We evaluated 117 patients with metastatic solid tumors or hematologic malignancies who underwent genomic analysis through the ongoing Personalized OncoGenomics (POG) program at BC Cancer and received an ICI during their treatment history. Charts were reviewed for irAEs. Whole genome sequencing of a fresh biopsy and matched normal specimens (blood) was performed at the time of POG enrollment. Notably, we found that MHC class I alleles in the HLA-B27 family, which have been previously associated with autoimmune conditions, were associated with grade 3 hepatitis and pneumonitis (q = 0.007) in patients treated with combination PD-1/PD-L1 and CTLA-4 inhibitors, and PD-1 inhibitors in combination with IDO-1 inhibitors. These data highlight that some patients may have a genetic predisposition to developing irAEs.
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Affiliation(s)
- Emma Titmuss
- Department of Medical Oncology, BC Cancer, Vancouver, BC V5Z 4E6, Canada; (E.T.); (D.J.R.); (J.J.L.)
| | - Irene S. Yu
- Department of Medical Oncology, BC Cancer, Surrey, BC V3V 1Z2, Canada;
| | - Erin D. Pleasance
- Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada; (E.D.P.); (A.J.M.); (R.M.); (S.J.M.J.); (M.A.M.)
| | - Laura M. Williamson
- Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada; (E.D.P.); (A.J.M.); (R.M.); (S.J.M.J.); (M.A.M.)
| | - Karen Mungall
- Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada; (E.D.P.); (A.J.M.); (R.M.); (S.J.M.J.); (M.A.M.)
| | - Andrew J. Mungall
- Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada; (E.D.P.); (A.J.M.); (R.M.); (S.J.M.J.); (M.A.M.)
| | - Daniel J. Renouf
- Department of Medical Oncology, BC Cancer, Vancouver, BC V5Z 4E6, Canada; (E.T.); (D.J.R.); (J.J.L.)
- Pancreas Centre BC, Vancouver, BC V5Z 1G1, Canada
| | - Richard Moore
- Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada; (E.D.P.); (A.J.M.); (R.M.); (S.J.M.J.); (M.A.M.)
| | - Steven J. M. Jones
- Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada; (E.D.P.); (A.J.M.); (R.M.); (S.J.M.J.); (M.A.M.)
| | - Marco A. Marra
- Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada; (E.D.P.); (A.J.M.); (R.M.); (S.J.M.J.); (M.A.M.)
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 2A1, Canada
| | - Janessa J. Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, BC V5Z 4E6, Canada; (E.T.); (D.J.R.); (J.J.L.)
| | - Kerry J. Savage
- Department of Medical Oncology, BC Cancer, Vancouver, BC V5Z 4E6, Canada; (E.T.); (D.J.R.); (J.J.L.)
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17
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Larkin J, Marais R, Porta N, Gonzalez de Castro D, Parsons L, Messiou C, Stamp G, Thompson L, Edmonds K, Sarker S, Banerji J, Lorigan P, Evans TRJ, Corrie P, Marshall E, Middleton MR, Nathan P, Nicholson S, Ottensmeier C, Plummer R, Bliss J, Valpione S, Turajlic S. Nilotinib in KIT-driven advanced melanoma: Results from the phase II single-arm NICAM trial. Cell Rep Med 2024; 5:101435. [PMID: 38417447 PMCID: PMC10982988 DOI: 10.1016/j.xcrm.2024.101435] [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: 08/16/2023] [Revised: 12/01/2023] [Accepted: 01/26/2024] [Indexed: 03/01/2024]
Abstract
Mucosal (MM) and acral melanomas (AM) are rare melanoma subtypes of unmet clinical need; 15%-20% harbor KIT mutations potentially targeted by small-molecule inhibitors, but none yet approved in melanoma. This multicenter, single-arm Phase II trial (NICAM) investigates nilotinib safety and activity in KIT mutated metastatic MM and AM. KIT mutations are identified in 39/219 screened patients (18%); of 29/39 treated, 26 are evaluable for primary analysis. Six patients were alive and progression free at 6 months (local radiology review, 25%); 5/26 (19%) had objective response at 12 weeks; median OS was 7.7 months; ddPCR assay correctly identifies KIT alterations in circulating tumor DNA (ctDNA) in 16/17 patients. Nilotinib is active in KIT-mutant AM and MM, comparable to other KIT inhibitors, with demonstrable activity in nonhotspot KIT mutations, supporting broadening of KIT evaluation in AM and MM. Our results endorse further investigations of nilotinib for the treatment of KIT-mutated melanoma. This clinical trial was registered with ISRCTN (ISRCTN39058880) and EudraCT (2009-012945-49).
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Affiliation(s)
- James Larkin
- Skin and Renal Units, The Royal Marsden Hospital NHS Foundation Trust, London, UK; Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London, UK
| | - Richard Marais
- Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK
| | - Nuria Porta
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - David Gonzalez de Castro
- Molecular Diagnostics, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
| | - Lisa Parsons
- University of Edinburgh, Edinburgh, UK; PDD - Thermo Fisher Scientific, Bend, Oregon, USA
| | - Christina Messiou
- Department of Radiology, The Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - Gordon Stamp
- Department of Histopathology, The Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - Lisa Thompson
- Centre for Molecular Pathology, The Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - Kim Edmonds
- Skin and Renal Units, The Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - Sarah Sarker
- Skin and Renal Units, The Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - Jane Banerji
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - Paul Lorigan
- Division of Cancer Sciences, Unviersity of Manchester, Manchester, UK; The Christie NHS Foundation Trust, Manchester, UK
| | | | - Pippa Corrie
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Ernest Marshall
- The Clatterbridge Cancer Centre NHS Foundation Trust, Liverpool, UK
| | | | - Paul Nathan
- Mount Vernon Cancer Centre, East & North Herts NHS Trust, Northwood, UK
| | - Steve Nicholson
- University Hospitals of Leicester NHS Foundation Trust, Leicester, UK
| | | | - Ruth Plummer
- Newcastle University and Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK
| | - Judith Bliss
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - Sara Valpione
- Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK; The Christie NHS Foundation Trust, Manchester, UK.
| | - Samra Turajlic
- Skin and Renal Units, The Royal Marsden Hospital NHS Foundation Trust, London, UK; Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London, UK; Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK.
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18
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Matejcic M, Teer JK, Hoehn HJ, Diaz DB, Shankar K, Gong J, Nguyen NT, Lorona N, Coppola D, Fulmer C, Saglam O, Jiang K, Cress D, Muñoz-Antonia T, Flores I, Gordian E, Oliveras Torres JA, Felder SI, Sanchez JA, Fleming J, Siegel EM, Freedman JA, Dutil J, Stern MC, Fridley BL, Figueiredo JC, Schmit SL. Spectrum of somatic mutational features of colorectal tumors in ancestrally diverse populations. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.11.24303880. [PMID: 38558992 PMCID: PMC10980113 DOI: 10.1101/2024.03.11.24303880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Ancestrally diverse and admixed populations, including the Hispanic/Latino/a/x/e community, are underrepresented in cancer genetic and genomic studies. Leveraging the Latino Colorectal Cancer Consortium, we analyzed whole exome sequencing data on tumor/normal pairs from 718 individuals with colorectal cancer (128 Latino, 469 non-Latino) to map somatic mutational features by ethnicity and genetic ancestry. Global proportions of African, East Asian, European, and Native American ancestries were estimated using ADMIXTURE. Associations between global genetic ancestry and somatic mutational features across genes were examined using logistic regression. TP53 , APC , and KRAS were the most recurrently mutated genes. Compared to non-Latino individuals, tumors from Latino individuals had fewer KRAS (OR=0.64, 95%CI=0.41-0.97, p=0.037) and PIK3CA mutations (OR=0.55, 95%CI=0.31-0.98, p=0.043). Genetic ancestry was associated with presence of somatic mutations in 39 genes (FDR-adjusted LRT p<0.05). Among these genes, a 10% increase in African ancestry was associated with significantly higher odds of mutation in KNCN (OR=1.34, 95%CI=1.09-1.66, p=5.74×10 -3 ) and TMEM184B (OR=1.53, 95%CI=1.10-2.12, p=0.011). Among RMGs, we found evidence of association between genetic ancestry and mutation status in CDC27 (LRT p=0.0084) and between SMAD2 mutation status and AFR ancestry (OR=1.14, 95%CI=1.00-1.30, p=0.046). Ancestry was not associated with tumor mutational burden. Individuals with above-average Native American ancestry had a lower frequency of microsatellite instable (MSI-H) vs microsatellite stable tumors (OR=0.45, 95%CI=0.21-0.99, p=0.048). Our findings provide new knowledge about the relationship between ancestral haplotypes and somatic mutational profiles that may be useful in developing precision medicine approaches and provide additional insight into genomic contributions to cancer disparities. Significance Our data in ancestrally diverse populations adds essential information to characterize mutational features in the colorectal cancer genome. These results will help enhance equity in the development of precision medicine strategies.
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19
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Srivatsa A, Schwartz R. Optimizing Design of Genomics Studies for Clonal Evolution Analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.14.585055. [PMID: 38559253 PMCID: PMC10980045 DOI: 10.1101/2024.03.14.585055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Genomic biotechnologies have seen rapid development over the past two decades, allowing for both the inference and modification of genetic and epigenetic information at the single cell level. While these tools present enormous potential for basic research, diagnostics, and treatment, they also raise difficult issues of how to design research studies to deploy these tools most effectively. In designing a study at the population or individual level, a researcher might combine several different sequencing modalities and sampling protocols, each with different utility, costs, and other tradeoffs. The central problem this paper attempts to address is then how one might create an optimal study design for a genomic analysis, with particular focus on studies involving somatic variation, typically for applications in cancer genomics. We pose the study design problem as a stochastic constrained nonlinear optimization problem and introduce a simulation-centered optimization procedure that iteratively optimizes the objective function using surrogate modeling combined with pattern and gradient search. Finally, we demonstrate the use of our procedure on diverse test cases to derive resource and study design allocations optimized for various objectives for the study of somatic cell populations.
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Affiliation(s)
- Arjun Srivatsa
- Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, Pittsburgh PA 15213, USA
| | - Russell Schwartz
- Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, Pittsburgh PA 15213, USA
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh PA 15213, USA
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20
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Radtke AJ, Postovalova E, Varlamova A, Bagaev A, Sorokina M, Kudryashova O, Meerson M, Polyakova M, Galkin I, Svekolkin V, Isaev S, Wiebe D, Sharun A, Sarachakov A, Perelman G, Lozinsky Y, Yaniv Z, Lowekamp BC, Speranza E, Yao L, Pittaluga S, Shaffer AL, Jonigk D, Phelan JD, Davies-Hill T, Huang DW, Ovcharov P, Nomie K, Nuzhdina E, Kotlov N, Ataullakhanov R, Fowler N, Kelly M, Muppidi J, Davis JL, Hernandez JM, Wilson WH, Jaffe ES, Staudt LM, Roschewski M, Germain RN. Multi-omic profiling of follicular lymphoma reveals changes in tissue architecture and enhanced stromal remodeling in high-risk patients. Cancer Cell 2024; 42:444-463.e10. [PMID: 38428410 PMCID: PMC10966827 DOI: 10.1016/j.ccell.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 12/04/2023] [Accepted: 02/05/2024] [Indexed: 03/03/2024]
Abstract
Follicular lymphoma (FL) is a generally incurable malignancy that evolves from developmentally blocked germinal center (GC) B cells. To promote survival and immune escape, tumor B cells undergo significant genetic changes and extensively remodel the lymphoid microenvironment. Dynamic interactions between tumor B cells and the tumor microenvironment (TME) are hypothesized to contribute to the broad spectrum of clinical behaviors observed among FL patients. Despite the urgent need, existing clinical tools do not reliably predict disease behavior. Using a multi-modal strategy, we examined cell-intrinsic and -extrinsic factors governing progression and therapeutic outcomes in FL patients enrolled onto a prospective clinical trial. By leveraging the strengths of each platform, we identify several tumor-specific features and microenvironmental patterns enriched in individuals who experience early relapse, the most high-risk FL patients. These features include stromal desmoplasia and changes to the follicular growth pattern present 20 months before first progression and first relapse.
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Affiliation(s)
- Andrea J Radtke
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ziv Yaniv
- Bioinformatics and Computational Bioscience Branch, NIAID, NIH, Bethesda, MD 20892, USA
| | - Bradley C Lowekamp
- Bioinformatics and Computational Bioscience Branch, NIAID, NIH, Bethesda, MD 20892, USA
| | - Emily Speranza
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA; Florida Research and Innovation Center, Cleveland Clinic Lerner Research Institute, Port Saint Lucie, FL 34987, USA
| | - Li Yao
- Li Yao Visuals, Rockville, MD 20855, USA
| | | | - Arthur L Shaffer
- Lymphoid Malignancies Branch, NCI, NIH, Bethesda, MD 20892, USA; Tumor Targeted Delivery, Heme Malignancy Target Discovery Group, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Danny Jonigk
- Institute of Pathology, Aachen Medical University, RWTH Aachen, 52074 Aachen, Germany; German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), 30625 Hannover, Germany
| | - James D Phelan
- Lymphoid Malignancies Branch, NCI, NIH, Bethesda, MD 20892, USA
| | | | - Da Wei Huang
- Lymphoid Malignancies Branch, NCI, NIH, Bethesda, MD 20892, USA
| | | | | | | | | | | | | | - Michael Kelly
- CCR Single Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Bethesda, MD 20892, USA
| | - Jagan Muppidi
- Lymphoid Malignancies Branch, NCI, NIH, Bethesda, MD 20892, USA
| | - Jeremy L Davis
- Surgical Oncology Program, Metastasis Biology Section, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jonathan M Hernandez
- Surgical Oncology Program, Metastasis Biology Section, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | - Elaine S Jaffe
- Laboratory of Pathology, NCI, NIH, Bethesda, MD 20892, USA
| | - Louis M Staudt
- Lymphoid Malignancies Branch, NCI, NIH, Bethesda, MD 20892, USA
| | - Mark Roschewski
- Lymphoid Malignancies Branch, NCI, NIH, Bethesda, MD 20892, USA
| | - Ronald N Germain
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
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21
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Kim KH, Migliozzi S, Koo H, Hong JH, Park SM, Kim S, Kwon HJ, Ha S, Garofano L, Oh YT, D'Angelo F, Kim CI, Kim S, Lee JY, Kim J, Hong J, Jang EH, Mathon B, Di Stefano AL, Bielle F, Laurenge A, Nesvizhskii AI, Hur EM, Yin J, Shi B, Kim Y, Moon KS, Kwon JT, Lee SH, Lee SH, Gwak HS, Lasorella A, Yoo H, Sanson M, Sa JK, Park CK, Nam DH, Iavarone A, Park JB. Integrated proteogenomic characterization of glioblastoma evolution. Cancer Cell 2024; 42:358-377.e8. [PMID: 38215747 PMCID: PMC10939876 DOI: 10.1016/j.ccell.2023.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 07/11/2023] [Accepted: 12/14/2023] [Indexed: 01/14/2024]
Abstract
The evolutionary trajectory of glioblastoma (GBM) is a multifaceted biological process that extends beyond genetic alterations alone. Here, we perform an integrative proteogenomic analysis of 123 longitudinal glioblastoma pairs and identify a highly proliferative cellular state at diagnosis and replacement by activation of neuronal transition and synaptogenic pathways in recurrent tumors. Proteomic and phosphoproteomic analyses reveal that the molecular transition to neuronal state at recurrence is marked by post-translational activation of the wingless-related integration site (WNT)/ planar cell polarity (PCP) signaling pathway and BRAF protein kinase. Consistently, multi-omic analysis of patient-derived xenograft (PDX) models mirror similar patterns of evolutionary trajectory. Inhibition of B-raf proto-oncogene (BRAF) kinase impairs both neuronal transition and migration capability of recurrent tumor cells, phenotypic hallmarks of post-therapy progression. Combinatorial treatment of temozolomide (TMZ) with BRAF inhibitor, vemurafenib, significantly extends the survival of PDX models. This study provides comprehensive insights into the biological mechanisms of glioblastoma evolution and treatment resistance, highlighting promising therapeutic strategies for clinical intervention.
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Affiliation(s)
- Kyung-Hee Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea; Proteomics Core Facility, Research Core Center, Research Institute, National Cancer Center, Goyang, Korea
| | - Simona Migliozzi
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Harim Koo
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea; Department of Biomedical Informatics, Korea University College of Medicine, Seoul, Korea; Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea
| | - Jun-Hee Hong
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Seung Min Park
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Sooheon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Hyung Joon Kwon
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Seokjun Ha
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Luciano Garofano
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Young Taek Oh
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Fulvio D'Angelo
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Chan Il Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Seongsoo Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Ji Yoon Lee
- Department of Biomedical Informatics, Korea University College of Medicine, Seoul, Korea; Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea
| | - Jiwon Kim
- Department of Biomedical Informatics, Korea University College of Medicine, Seoul, Korea; Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea
| | - Jisoo Hong
- Department of Biomedical Informatics, Korea University College of Medicine, Seoul, Korea; Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea
| | - Eun-Hae Jang
- Laboratory of Neuroscience, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Bertrand Mathon
- Service de Neurochirurgie, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France
| | - Anna-Luisa Di Stefano
- Institut de Neurologie, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Sorbonne Université, Inserm, CNRS, UMR S 1127, Paris Brain Institute (ICM), Equipe labellisée LNCC, Paris, France; Onconeurotek, AP-HP, Hôpital Pitié-Salpêtrière, F-75013 Paris, France; Department of Neurology, Foch Hospital, Suresnes, France
| | - Franck Bielle
- Institut de Neurologie, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Sorbonne Université, Inserm, CNRS, UMR S 1127, Paris Brain Institute (ICM), Equipe labellisée LNCC, Paris, France; Onconeurotek, AP-HP, Hôpital Pitié-Salpêtrière, F-75013 Paris, France
| | - Alice Laurenge
- Institut de Neurologie, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Sorbonne Université, Inserm, CNRS, UMR S 1127, Paris Brain Institute (ICM), Equipe labellisée LNCC, Paris, France; Onconeurotek, AP-HP, Hôpital Pitié-Salpêtrière, F-75013 Paris, France
| | | | - Eun-Mi Hur
- Laboratory of Neuroscience, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea; BK21 Four Future Veterinary Medicine Leading Education & Research Center, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Jinlong Yin
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea; Henan-Macquarie University Joint Centre for Biomedical Innovation, School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Bingyang Shi
- Henan-Macquarie University Joint Centre for Biomedical Innovation, School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Youngwook Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Kyung-Sub Moon
- Department of Neurosurgery, Chonnam National University Hwasun Hospital and Medical School, Hwasun, Korea
| | - Jeong Taik Kwon
- Department of Neurosurgery, Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul, Korea
| | - Shin Heon Lee
- Department of Neurosurgery, Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul, Korea
| | - Seung Hoon Lee
- Department of Neurosurgery, Eulji University School of Medicine, Daejeon, Korea
| | - Ho Shin Gwak
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Anna Lasorella
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Biochemistry, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Heon Yoo
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Marc Sanson
- Institut de Neurologie, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Sorbonne Université, Inserm, CNRS, UMR S 1127, Paris Brain Institute (ICM), Equipe labellisée LNCC, Paris, France; Onconeurotek, AP-HP, Hôpital Pitié-Salpêtrière, F-75013 Paris, France.
| | - Jason K Sa
- Department of Biomedical Informatics, Korea University College of Medicine, Seoul, Korea; Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea.
| | - Chul-Kee Park
- Deparment of Neurosurgery, Seoul National University College of Medicine, Seoul, Korea.
| | - Do-Hyun Nam
- Department of Neurosurgery and Samsung Advanced Institute for Health Sciences and Technology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
| | - Antonio Iavarone
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Neurological Surgery and Department of Biochemistry, University of Miami Miller School of Medicine, Miami, FL, USA.
| | - Jong Bae Park
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea; Department of Clinical Research, Research Institute and Hospital, National Cancer Center, Goyang, Korea.
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22
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Nabet BY, Hamidi H, Lee MC, Banchereau R, Morris S, Adler L, Gayevskiy V, Elhossiny AM, Srivastava MK, Patil NS, Smith KA, Jesudason R, Chan C, Chang PS, Fernandez M, Rost S, McGinnis LM, Koeppen H, Gay CM, Minna JD, Heymach JV, Chan JM, Rudin CM, Byers LA, Liu SV, Reck M, Shames DS. Immune heterogeneity in small-cell lung cancer and vulnerability to immune checkpoint blockade. Cancer Cell 2024; 42:429-443.e4. [PMID: 38366589 DOI: 10.1016/j.ccell.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 12/02/2023] [Accepted: 01/23/2024] [Indexed: 02/18/2024]
Abstract
Atezolizumab (anti-PD-L1), combined with carboplatin and etoposide (CE), is now a standard of care for extensive-stage small-cell lung cancer (ES-SCLC). A clearer understanding of therapeutically relevant SCLC subsets could identify rational combination strategies and improve outcomes. We conduct transcriptomic analyses and non-negative matrix factorization on 271 pre-treatment patient tumor samples from IMpower133 and identify four subsets with general concordance to previously reported SCLC subtypes (SCLC-A, -N, -P, and -I). Deeper investigation into the immune heterogeneity uncovers two subsets with differing neuroendocrine (NE) versus non-neuroendocrine (non-NE) phenotypes, demonstrating immune cell infiltration hallmarks. The NE tumors with low tumor-associated macrophage (TAM) but high T-effector signals demonstrate longer overall survival with PD-L1 blockade and CE versus CE alone than non-NE tumors with high TAM and high T-effector signal. Our study offers a clinically relevant approach to discriminate SCLC patients likely benefitting most from immunotherapies and highlights the complex mechanisms underlying immunotherapy responses.
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Affiliation(s)
| | | | | | | | | | - Leah Adler
- F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Velimir Gayevskiy
- Genentech Inc., South San Francisco CA, USA; Rancho Biosciences, San Diego, CA, USA
| | | | | | | | | | | | - Caleb Chan
- Genentech Inc., South San Francisco CA, USA
| | | | | | | | | | | | - Carl M Gay
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390-8593, USA; Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA; Departments of Internal Medicine and Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - John V Heymach
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph M Chan
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10016, USA
| | - Charles M Rudin
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10016, USA; Weill Cornell Medical College, New York, NY 10065, USA
| | - Lauren A Byers
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephen V Liu
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Martin Reck
- Lung Clinic Grosshansdorf, Airway Research Center North, German Center of Lung Research, Grosshansdorf, Germany
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23
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Wang Z, Xia Y, Mills L, Nikolakopoulos AN, Maeser N, Dehm SM, Sheltzer JM, Sun R. Evolving copy number gains promote tumor expansion and bolster mutational diversification. Nat Commun 2024; 15:2025. [PMID: 38448455 PMCID: PMC10918155 DOI: 10.1038/s41467-024-46414-5] [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: 06/06/2023] [Accepted: 02/20/2024] [Indexed: 03/08/2024] Open
Abstract
The timing and fitness effect of somatic copy number alterations (SCNA) in cancer evolution remains poorly understood. Here we present a framework to determine the timing of a clonal SCNA that encompasses multiple gains. This involves calculating the proportion of time from its last gain to the onset of population expansion (lead time) as well as the proportion of time prior to its first gain (initiation time). Our method capitalizes on the observation that a genomic segment, while in a specific copy number (CN) state, accumulates point mutations proportionally to its CN. Analyzing 184 whole genome sequenced samples from 75 patients across five tumor types, we commonly observe late gains following early initiating events, occurring just before the clonal expansion relevant to the sampling. These include gains acquired after genome doubling in more than 60% of cases. Notably, mathematical modeling suggests that late clonal gains may contain final-expansion drivers. Lastly, SCNAs bolster mutational diversification between subpopulations, exacerbating the circle of proliferation and increasing heterogeneity.
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Affiliation(s)
- Zicheng Wang
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- School of Data Science, The Chinese University of Hong Kong (CUHK-Shenzhen), Shenzhen, China
| | - Yunong Xia
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Lauren Mills
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Athanasios N Nikolakopoulos
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Nicole Maeser
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Scott M Dehm
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Department of Urology, University of Minnesota, Minneapolis, MN, USA
| | | | - Ruping Sun
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA.
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
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Yang Z, Zhou B, Guo W, Peng Y, Tian H, Xu J, Wang S, Chen X, Hu B, Liu C, Wang Z, Li C, Gao S, He J. Genomic characteristics and immune landscape of super multiple primary lung cancer. EBioMedicine 2024; 101:105019. [PMID: 38364701 PMCID: PMC10878856 DOI: 10.1016/j.ebiom.2024.105019] [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: 10/30/2023] [Revised: 02/03/2024] [Accepted: 02/04/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND In recent years, a growing number of patients with multiple primary lung cancer (MPLC) are being diagnosed, and a subset of these patients is found to have a large number of lesions at the time of diagnosis, which are referred to as 'super MPLC'. METHODS Here, we perform whole exome sequencing (WES) and immunohistochemistry (IHC) analysis of PD-L1 and CD8 on 212 tumor samples from 42 patients with super MPLC. FINDINGS We report the genomic alteration landscape of super MPLC. EGFR, RBM10 and TP53 mutation and TERT amplification are important molecular events in the evolution of super MPLC. We propose the conception of early intrapulmonary metastasis, which exhibits different clinical features from conventional metastasis. The IHC analyses of PD-L1 and CD8 reveal a less inflamed microenvironment of super MPLC than that of traditional non-small cell lung cancer (NSCLC). We identify the potentially susceptible germline mutations for super MPLC. INTERPRETATION Our study depicts the genomic characteristics and immune landscape, providing insights into the pathogenesis and possible therapeutic guidance of super MPLC. FUNDING A full list of funding bodies that supported this study can be found in the Acknowledgements section.
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Affiliation(s)
- Zhenlin Yang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Bolun Zhou
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Wei Guo
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Yue Peng
- Department of Thoracic Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - He Tian
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Jiachen Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China; Guangdong Provincial People's Hospital/Guangdong Provincial Academy of Medical Sciences, Guangdong Provincial Key Lab of Translational Medicine in Lung Cancer, Guangdong, 519041, China
| | - Shuaibo Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Xiaowei Chen
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Bin Hu
- Department of Thoracic Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Chengming Liu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Zhijie Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Chunxiang Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China.
| | - Shugeng Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China.
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China.
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25
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Beckabir W, Wobker SE, Damrauer JS, Midkiff B, De la Cruz G, Makarov V, Flick L, Woodcock MG, Grivas P, Bjurlin MA, Harrison MR, Vincent BG, Rose TL, Gupta S, Kim WY, Milowsky MI. Spatial Relationships in the Tumor Microenvironment Demonstrate Association with Pathologic Response to Neoadjuvant Chemoimmunotherapy in Muscle-invasive Bladder Cancer. Eur Urol 2024; 85:242-253. [PMID: 38092611 PMCID: PMC11022933 DOI: 10.1016/j.eururo.2023.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/11/2023] [Accepted: 11/09/2023] [Indexed: 03/09/2024]
Abstract
BACKGROUND Platinum-based neoadjuvant chemotherapy (NAC) is standard for patients with muscle-invasive bladder cancer (MIBC). Pathologic response (complete: ypT0N0 and partial: OBJECTIVE Using the NanoString GeoMx platform, we performed proteomic digital spatial profiling (DSP) on transurethral resections of bladder tumors from 18 responders ( DESIGN, SETTING, AND PARTICIPANTS Pretreatment tumor samples were stained by hematoxylin and eosin and immunofluorescence (panCK and CD45) to select four regions of interest (ROIs): tumor enriched (TE), immune enriched (IE), tumor/immune interface (tumor interface = TX and immune interface = IX). OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS DSP was performed with 52 protein markers from immune cell profiling, immunotherapy drug target, immune activation status, immune cell typing, and pan-tumor panels. RESULTS AND LIMITATIONS Protein marker expression patterns were analyzed to determine their association with pathologic response, incorporating or agnostic of their ROI designation (TE/IE/TX/IX). Overall, DSP-based marker expression showed high intratumoral heterogeneity; however, response was associated with markers including PD-L1 (ROI agnostic), Ki-67 (ROI agnostic, TE, IE, and TX), HLA-DR (TX), and HER2 (TE). An elastic net model of response with ROI-inclusive markers demonstrated better validation set performance (area under the curve [AUC] = 0.827) than an ROI-agnostic model (AUC = 0.432). A model including DSP, tumor mutational burden, and clinical data performed no better (AUC = 0.821) than the DSP-only model. CONCLUSIONS Despite high intratumoral heterogeneity of DSP-based marker expression, we observed associations between pathologic response and specific DSP-based markers in a spatially dependent context. Further exploration of tumor region-specific biomarkers may help predict response to neoadjuvant chemoimmunotherapy in MIBC. PATIENT SUMMARY In this study, we used the GeoMx platform to perform proteomic digital spatial profiling on transurethral resections of bladder tumors from 18 responders and 18 nonresponders from two studies of neoadjuvant chemotherapy (gemcitabine and cisplatin) plus immune checkpoint inhibitor therapy (LCCC1520 [pembrolizumab] and BLASST-1 [nivolumab]). We found that assessing protein marker expression in the context of tumor architecture improved response prediction.
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Affiliation(s)
- Wolfgang Beckabir
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Sara E Wobker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Pathology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeffrey S Damrauer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Division of Oncology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bentley Midkiff
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gabriela De la Cruz
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vladmir Makarov
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Leah Flick
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mark G Woodcock
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Petros Grivas
- Department of Medicine, Division of Medical Oncology, University of Washington, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Marc A Bjurlin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Urology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael R Harrison
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University, Durham, NC, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA; Division of Hematology, Department of Medicine, UNC School of Medicine, Chapel Hill, NC, USA; Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA; Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Tracy L Rose
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Division of Oncology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shilpa Gupta
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - William Y Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Division of Oncology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Matthew I Milowsky
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Division of Oncology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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26
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Simpson JT. Detecting Somatic Mutations Without Matched Normal Samples Using Long Reads. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582089. [PMID: 38464143 PMCID: PMC10925087 DOI: 10.1101/2024.02.26.582089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
DNA sequencing of tumours to identify somatic mutations has become a critical tool to guide the type of treatment given to cancer patients. The gold standard for mutation calling is comparing sequencing data from the tumour to a matched normal sample to avoid mis-classifying inherited SNPs as mutations. This procedure works extremely well, but in certain situations only a tumour sample is available. While approaches have been developed to find mutations without a matched normal, they have limited accuracy or require specific types of input data (e.g. ultra-deep sequencing). Here we explore the application of single molecule long read sequencing to calling somatic mutations without matched normal samples. We develop a simple theoretical framework to show how haplotype phasing is an important source of information for determining whether a variant is a somatic mutation. We then use simulations to assess the range of experimental parameters (tumour purity, sequencing depth) where this approach is effective. These ideas are developed into a prototype somatic mutation caller, smrest, and its use is demonstrated on two highly mutated cancer cell lines. Finally, we argue that this approach has potential to measure clinically important biomarkers that are based on the genome-wide distribution of mutations: tumour mutation burden and mutation signatures.
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Affiliation(s)
- Jared T. Simpson
- Ontario Institute for Cancer Research, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
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27
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Thng DKH, Hooi L, Siew BE, Lee KY, Tan IJW, Lieske B, Lin NS, Kow AWC, Wang S, Rashid MBMA, Ang C, Koh JJM, Toh TB, Tan KK, Chow EKH. A functional personalised oncology approach against metastatic colorectal cancer in matched patient derived organoids. NPJ Precis Oncol 2024; 8:52. [PMID: 38413740 PMCID: PMC10899621 DOI: 10.1038/s41698-024-00543-8] [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: 11/16/2023] [Accepted: 02/08/2024] [Indexed: 02/29/2024] Open
Abstract
Globally, colorectal cancer (CRC) is the third most frequently occurring cancer. Progression on to an advanced metastatic malignancy (metCRC) is often indicative of poor prognosis, as the 5-year survival rates of patients decline rapidly. Despite the availability of many systemic therapies for the management of metCRC, the long-term efficacies of these regimens are often hindered by the emergence of treatment resistance due to intratumoral and intertumoral heterogeneity. Furthermore, not all systemic therapies have associated biomarkers that can accurately predict patient responses. Hence, a functional personalised oncology (FPO) approach can enable the identification of patient-specific combinatorial vulnerabilities and synergistic combinations as effective treatment strategies. To this end, we established a panel of CRC patient-derived organoids (PDOs) as clinically relevant biological systems, of which three pairs of matched metCRC PDOs were derived from the primary sites (ptCRC) and metastatic lesions (mCRC). Histological and genomic characterisation of these PDOs demonstrated the preservation of histopathological and genetic features found in the parental tumours. Subsequent application of the phenotypic-analytical drug combination interrogation platform, Quadratic Phenotypic Optimisation Platform, in these pairs of PDOs identified patient-specific drug sensitivity profiles to epigenetic-based combination therapies. Most notably, matched PDOs from one patient exhibited differential sensitivity patterns to the rationally designed drug combinations despite being genetically similar. These findings collectively highlight the limitations of current genomic-driven precision medicine in guiding treatment strategies for metCRC patients. Instead, it suggests that epigenomic profiling and application of FPO could complement the identification of novel combinatorial vulnerabilities to target synchronous ptCRC and mCRC.
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Affiliation(s)
- Dexter Kai Hao Thng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Lissa Hooi
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Bei En Siew
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Kai-Yin Lee
- Division of Colorectal Surgery, Department of Surgery, National University Hospital, National University Health System, Singapore, Singapore
| | - Ian Jse-Wei Tan
- Division of Colorectal Surgery, Department of Surgery, National University Hospital, National University Health System, Singapore, Singapore
| | - Bettina Lieske
- Division of Colorectal Surgery, Department of Surgery, National University Hospital, National University Health System, Singapore, Singapore
| | - Norman Sihan Lin
- Division of Colorectal Surgery, Department of Surgery, National University Hospital, National University Health System, Singapore, Singapore
| | - Alfred Wei Chieh Kow
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, National University Hospital, National University Health System, Singapore, Singapore
| | - Shi Wang
- Department of Pathology, National University Hospital, National University Health System, Singapore, Singapore
| | | | - Chermaine Ang
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jasmin Jia Min Koh
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tan Boon Toh
- The N.1 Institute for Health, National University of Singapore, Singapore, Singapore
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ker-Kan Tan
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Division of Colorectal Surgery, Department of Surgery, National University Hospital, National University Health System, Singapore, Singapore.
| | - Edward Kai-Hua Chow
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
- NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- The N.1 Institute for Health, National University of Singapore, Singapore, Singapore.
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore.
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28
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Coorens THH, Spencer Chapman M, Williams N, Martincorena I, Stratton MR, Nangalia J, Campbell PJ. Reconstructing phylogenetic trees from genome-wide somatic mutations in clonal samples. Nat Protoc 2024:10.1038/s41596-024-00962-8. [PMID: 38396041 DOI: 10.1038/s41596-024-00962-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/13/2023] [Indexed: 02/25/2024]
Abstract
Phylogenetic trees are a powerful means to display the evolutionary history of species, pathogens and, more recently, individual cells of the human body. Whole-genome sequencing of laser capture microdissections or expanded stem cells has allowed the discovery of somatic mutations in clones, which can be used as natural barcodes to reconstruct the developmental history of individual cells. Here we describe Sequoia, our pipeline to reconstruct lineage trees from clones of normal cells. Candidate somatic mutations are called against the human reference genome and filtered to exclude germline mutations and artifactual variants. These filtered somatic mutations form the basis for phylogeny reconstruction using a maximum parsimony framework. Lastly, we use a maximum likelihood framework to explicitly map mutations to branches in the phylogenetic tree. The resulting phylogenies can then serve as a basis for many subsequent analyses, including investigating embryonic development, tissue dynamics in health and disease, and mutational signatures. Sequoia can be readily applied to any clonal somatic mutation dataset, including single-cell DNA sequencing datasets, using the commands and scripts provided. Moreover, Sequoia is highly flexible and can be easily customized. Typically, the runtime of the core script ranges from minutes to an hour for datasets with a moderate number (50,000-150,000) of variants. Competent bioinformatic skills, including in-depth knowledge of the R programming language, are required. A high-performance computing cluster (one that is capable of running mutation-calling algorithms and other aspects of the analysis at scale) is also required, especially if handling large datasets.
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Affiliation(s)
- Tim H H Coorens
- Wellcome Sanger Institute, Hinxton, UK.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Michael Spencer Chapman
- Wellcome Sanger Institute, Hinxton, UK.
- Department of Haematology, Barts Health NHS Trust, London, UK.
- Department of Haemato-oncology, Barts Cancer Institute, Queen Mary University of London, London, UK.
| | | | | | | | - Jyoti Nangalia
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Peter J Campbell
- Wellcome Sanger Institute, Hinxton, UK.
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK.
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29
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Blanco-Heredia J, Souza CA, Trincado JL, Gonzalez-Cao M, Gonçalves-Ribeiro S, Gil SR, Pravdyvets D, Cedeño S, Callari M, Marra A, Gazzo AM, Weigelt B, Pareja F, Vougiouklakis T, Jungbluth AA, Rosell R, Brander C, Tresserra F, Reis-Filho JS, Tiezzi DG, de la Iglesia N, Heyn H, De Mattos-Arruda L. Converging and evolving immuno-genomic routes toward immune escape in breast cancer. Nat Commun 2024; 15:1302. [PMID: 38383522 PMCID: PMC10882008 DOI: 10.1038/s41467-024-45292-1] [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: 08/21/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024] Open
Abstract
The interactions between tumor and immune cells along the course of breast cancer progression remain largely unknown. Here, we extensively characterize multiple sequential and parallel multiregion tumor and blood specimens of an index patient and a cohort of metastatic triple-negative breast cancers. We demonstrate that a continuous increase in tumor genomic heterogeneity and distinct molecular clocks correlated with resistance to treatment, eventually allowing tumors to escape from immune control. TCR repertoire loses diversity over time, leading to convergent evolution as breast cancer progresses. Although mixed populations of effector memory and cytotoxic single T cells coexist in the peripheral blood, defects in the antigen presentation machinery coupled with subdued T cell recruitment into metastases are observed, indicating a potent immune avoidance microenvironment not compatible with an effective antitumor response in lethal metastatic disease. Our results demonstrate that the immune responses against cancer are not static, but rather follow dynamic processes that match cancer genomic progression, illustrating the complex nature of tumor and immune cell interactions.
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Affiliation(s)
- Juan Blanco-Heredia
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Carla Anjos Souza
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Juan L Trincado
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
- Josep Carreras Leukemia Research Institute, Barcelona, Spain
| | | | | | - Sara Ruiz Gil
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | | | - Samandhy Cedeño
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain
| | - Maurizio Callari
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Antonio Marra
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrea M Gazzo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fresia Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Theodore Vougiouklakis
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Achim A Jungbluth
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rafael Rosell
- Dexeus Institute of Oncology, Quironsalud Group, Barcelona, Spain
| | - Christian Brander
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain
- ICREA, Passeig de Lluís Companys, 23, Barcelona, Spain
- Universitat de Vic-Universitat Central de Catalunya, Catalunya, Spain
| | | | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Guimarães Tiezzi
- Department of Gynecology and Obstetrics - Breast Disease Division and Laboratory for Translational Data Science, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
- Advanced Research Center in Medicine (CEPAM), Union of the Colleges of the Great Lakes (UNILAGO), São José do Rio Preto, Brazil
| | | | - Holger Heyn
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
- Omniscope, Barcelona, Spain
| | - Leticia De Mattos-Arruda
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain.
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.
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30
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Clay S, Evans A, Zambrano R, Otohinoyi D, Hicks C, Tsien F. Bioinformatics characterization of variants of uncertain significance in pediatric sensorineural hearing loss. Front Pediatr 2024; 12:1299341. [PMID: 38450295 PMCID: PMC10915201 DOI: 10.3389/fped.2024.1299341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 01/31/2024] [Indexed: 03/08/2024] Open
Abstract
Introduction Rapid advancements in Next Generation Sequencing (NGS) and bioinformatics tools have allowed physicians to obtain genetic testing results in a more rapid, cost-effective, and comprehensive manner than ever before. Around 50% of pediatric sensorineural hearing loss (SNHL) cases are due to a genetic etiology, thus physicians regularly utilize targeted sequencing panels that identify variants in genes related to SNHL. These panels allow for early detection of pathogenic variants which allows physicians to provide anticipatory guidance to families. Molecular testing does not always reveal a clear etiology due to the presence of multigenic variants with varying classifications, including the presence of Variants of Uncertain Significance (VUS). This study aims to perform a preliminary bioinformatics characterization of patients with variants associated with Type II Usher Syndrome in the presence of other multigenic variants. We also provide an interpretation algorithm for physicians reviewing molecular results with medical geneticists. Methods Review of records for multigenic and/or VUS results identified several potential subjects of interest. For the purposes of this study, two ADGRV1 compound heterozygotes met inclusion criteria. Sequencing, data processing, and variant calling (the process by which variants are identified from sequence data) was performed at Invitae (San Francisco CA). The preliminary analysis followed the recommendations outlined by the American College of Medical Genetics and Association for Molecular Pathology (ACMG-AMP) in 2015 and 2019. The present study utilizes computational analysis, predictive data, and population data as well as clinical information from chart review and publicly available information in the ClinVar database. Results Two subjects were identified as compound heterozygotes for variants in the gene ADGRV1. Subject 1's variants were predicted as deleterious, while Subject 2's variants were predicted as non-deleterious. These results were based on known information of the variants from ClinVar, multiple lines of computational data, population databases, as well as the clinical presentation. Discussion Early molecular diagnosis through NGS is ideal, as families are then able to access a wide range of resources that will ultimately support the child as their condition progresses. We recommend that physicians build strong relationships with medical geneticists and carefully review their interpretation before making recommendations to families, particularly when addressing the VUS. Reclassification efforts of VUS are supported by studies like ours that provide evidence of pathogenic or benign effects of variants.
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Affiliation(s)
- Sloane Clay
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Adele Evans
- Department of Otolaryngology, Children's Hospital of New Orleans, New Orleans, LA, United States
| | - Regina Zambrano
- Department of Pediatrics, Division of Clinical Genetics, Louisiana State University Health Sciences Center and Children’s Hospital of New Orleans, New Orleans, LA, United States
| | - David Otohinoyi
- Department of Genetics, Bioinformatics and Genomics Program, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Chindo Hicks
- Department of Genetics, Bioinformatics and Genomics Program, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Fern Tsien
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States
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31
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Zhou X, Cai X, Jing F, Li X, Zhang J, Zhang H, Li T. Genomic alterations in oral multiple primary cancers. Int J Oral Sci 2024; 16:13. [PMID: 38368361 PMCID: PMC10874441 DOI: 10.1038/s41368-023-00265-w] [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: 08/09/2023] [Revised: 12/02/2023] [Accepted: 12/04/2023] [Indexed: 02/19/2024] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the predominant type of oral cancer, while some patients may develop oral multiple primary cancers (MPCs) with unclear etiology. This study aimed to investigate the clinicopathological characteristics and genomic alterations of oral MPCs. Clinicopathological data from patients with oral single primary carcinoma (SPC, n = 202) and oral MPCs (n = 34) were collected and compared. Copy number alteration (CNA) analysis was conducted to identify chromosomal-instability differences among oral MPCs, recurrent OSCC cases, and OSCC patients with lymph node metastasis. Whole-exome sequencing was employed to identify potential unique gene mutations in oral MPCs patients. Additionally, CNA and phylogenetic tree analyses were used to gain preliminary insights into the molecular characteristics of different primary tumors within individual patients. Our findings revealed that, in contrast to oral SPC, females predominated the oral MPCs (70.59%), while smoking and alcohol use were not frequent in MPCs. Moreover, long-term survival outcomes were poorer in oral MPCs. From a CNA perspective, no significant differences were observed between oral MPCs patients and those with recurrence and lymph node metastasis. In addition to commonly mutated genes such as CASP8, TP53 and MUC16, in oral MPCs we also detected relatively rare mutations, such as HS3ST6 and RFPL4A. Furthermore, this study also demonstrated that most MPCs patients exhibited similarities in certain genomic regions within individuals, and distinct differences of the similarity degree were observed between synchronous and metachronous oral MPCs.
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Affiliation(s)
- Xuan Zhou
- Department of Oral Pathology, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental Materials, Beijing, China
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, China
| | - Xinjia Cai
- Department of Oral Pathology, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental Materials, Beijing, China
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, China
| | - Fengyang Jing
- Department of Oral Pathology, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental Materials, Beijing, China
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, China
| | - Xuefen Li
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China
| | - Jianyun Zhang
- Department of Oral Pathology, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental Materials, Beijing, China
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, China
| | - Heyu Zhang
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, China.
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China.
| | - Tiejun Li
- Department of Oral Pathology, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental Materials, Beijing, China.
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, China.
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Feinberg J, Da Cruz Paula A, da Silva EM, Pareja F, Patel J, Zhu Y, Selenica P, Leitao MM, Abu-Rustum NR, Reis-Filho JS, Joehlin-Price A, Weigelt B. Adenoid cystic carcinoma of the Bartholin's gland is underpinned by MYB- and MYBL1- rearrangements. Gynecol Oncol 2024; 185:58-67. [PMID: 38368814 DOI: 10.1016/j.ygyno.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 02/09/2024] [Indexed: 02/20/2024]
Abstract
OBJECTIVE Adenoid cystic carcinoma (AdCC) of the Bartholin's gland (AdCC-BG) is a very rare gynecologic vulvar malignancy. AdCC-BGs are slow-growing but locally aggressive and are associated with high recurrence rates. Here we sought to characterize the molecular underpinning of AdCC-BGs. METHODS AdCC-BGs (n = 6) were subjected to a combination of RNA-sequencing, targeted DNA-sequencing, reverse-transcription PCR, fluorescence in situ hybridization (FISH) and MYB immunohistochemistry (IHC). Clinicopathologic variables, somatic mutations, copy number alterations and chimeric transcripts were assessed. RESULTS All six AdCC-BGs were biphasic, composed of ductal and myoepithelial cells. Akin to salivary gland and breast AdCCs, three AdCC-BGs had the MYB::NFIB fusion gene with varying breakpoints, all of which were associated with MYB overexpression by IHC. Two AdCC-BGs were underpinned by MYBL1 fusion genes with different gene partners, including MYBL1::RAD51B and MYBL1::EWSR1 gene fusions, and showed MYB protein expression. Although the final AdCC-BG studied had MYB protein overexpression, no gene fusion was identified. AdCC-BGs harbored few additional somatic genetic alterations, and only few mutations in cancer-related genes were identified, including GNAQ, GNAS, KDM6A, AKT1 and BCL2, none of which were recurrent. Two AdCC-BGs, both with a MYB::NFIB fusion gene, developed metastatic disease. CONCLUSIONS AdCC-BGs constitute a convergent phenotype, whereby activation of MYB or MYBL1 can be driven by the MYB::NFIB fusion gene or MYBL1 rearrangements. Our observations further support the notion that AdCCs, irrespective of organ site, constitute a genotypic-phenotypic correlation. Assessment of MYB or MYBL1 rearrangements may be used as an ancillary marker for the diagnosis of AdCC-BGs.
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Affiliation(s)
- Jacqueline Feinberg
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arnaud Da Cruz Paula
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edaise M da Silva
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fresia Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juber Patel
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yingjie Zhu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pier Selenica
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mario M Leitao
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem R Abu-Rustum
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amy Joehlin-Price
- Cleveland Clinic Pathology and Laboratory Medicine Institute, Cleveland, OH, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Schott CR, Koehne AL, Sayles LC, Young EP, Luck C, Yu K, Lee AG, Breese MR, Leung SG, Xu H, Shah AT, Liu HY, Spillinger A, Behroozfard IH, Marini KD, Dinh PT, Pons Ventura MV, Vanderboon EN, Hazard FK, Cho SJ, Avedian RS, Mohler DG, Zimel M, Wustrack R, Curtis C, Sirota M, Sweet-Cordero EA. Osteosarcoma PDX-Derived Cell Line Models for Preclinical Drug Evaluation Demonstrate Metastasis Inhibition by Dinaciclib through a Genome-Targeted Approach. Clin Cancer Res 2024; 30:849-864. [PMID: 37703185 PMCID: PMC10870121 DOI: 10.1158/1078-0432.ccr-23-0873] [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: 03/21/2023] [Revised: 03/26/2023] [Accepted: 08/08/2023] [Indexed: 09/15/2023]
Abstract
PURPOSE Models to study metastatic disease in rare cancers are needed to advance preclinical therapeutics and to gain insight into disease biology. Osteosarcoma is a rare cancer with a complex genomic landscape in which outcomes for patients with metastatic disease are poor. As osteosarcoma genomes are highly heterogeneous, multiple models are needed to fully elucidate key aspects of disease biology and to recapitulate clinically relevant phenotypes. EXPERIMENTAL DESIGN Matched patient samples, patient-derived xenografts (PDX), and PDX-derived cell lines were comprehensively evaluated using whole-genome sequencing and RNA sequencing. The in vivo metastatic phenotype of the PDX-derived cell lines was characterized in both an intravenous and an orthotopic murine model. As a proof-of-concept study, we tested the preclinical effectiveness of a cyclin-dependent kinase inhibitor on the growth of metastatic tumors in an orthotopic amputation model. RESULTS PDXs and PDX-derived cell lines largely maintained the expression profiles of the patient from which they were derived despite the emergence of whole-genome duplication in a subset of cell lines. The cell lines were heterogeneous in their metastatic capacity, and heterogeneous tissue tropism was observed in both intravenous and orthotopic models. Single-agent dinaciclib was effective at dramatically reducing the metastatic burden. CONCLUSIONS The variation in metastasis predilection sites between osteosarcoma PDX-derived cell lines demonstrates their ability to recapitulate the spectrum of the disease observed in patients. We describe here a panel of new osteosarcoma PDX-derived cell lines that we believe will be of wide use to the osteosarcoma research community.
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Affiliation(s)
- Courtney R. Schott
- Department of Pediatrics, University of California San Francisco, San Francisco, California
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Amanda L. Koehne
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Leanne C. Sayles
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Elizabeth P. Young
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Cuyler Luck
- Department of Pediatrics, University of California San Francisco, San Francisco, California
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California
| | - Katherine Yu
- Department of Pediatrics, University of California San Francisco, San Francisco, California
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California
| | - Alex G. Lee
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Marcus R. Breese
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Stanley G. Leung
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Hang Xu
- Departments of Genetics and Medicine, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Avanthi Tayi Shah
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Heng-Yi Liu
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Aviv Spillinger
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Inge H. Behroozfard
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Kieren D. Marini
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Phuong T. Dinh
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - María V. Pons Ventura
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Emma N. Vanderboon
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Florette K. Hazard
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Soo-Jin Cho
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Raffi S. Avedian
- Department of Orthopedic Surgery, Stanford University School of Medicine, Stanford University, Stanford, California
| | - David G. Mohler
- Department of Orthopedic Surgery, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Melissa Zimel
- Department of Orthopedic Surgery, University of California San Francisco, San Francisco, California
| | - Rosanna Wustrack
- Department of Orthopedic Surgery, University of California San Francisco, San Francisco, California
| | - Christina Curtis
- Departments of Genetics and Medicine, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Marina Sirota
- Department of Pediatrics, University of California San Francisco, San Francisco, California
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California
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Adams AC, Macy AM, Borden ES, Herrmann LM, Brambley CA, Ma T, Li X, Hughes A, Roe DJ, Mangold AR, Buetow KH, Wilson MA, Baker BM, Hastings KT. Distinct sets of molecular characteristics define tumor-rejecting neoantigens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.579546. [PMID: 38405868 PMCID: PMC10888839 DOI: 10.1101/2024.02.13.579546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Challenges in identifying tumor-rejecting neoantigens limit the efficacy of neoantigen vaccines to treat cancers, including cutaneous squamous cell carcinoma (cSCC). A minority of human cSCC tumors shared neoantigens, supporting the need for personalized vaccines. Using a UV-induced mouse cSCC model which recapitulated the mutational signature and driver mutations found in human disease, we found that CD8 T cells constrain cSCC. Two MHC class I neoantigens were identified that constrained cSCC growth. Compared to the wild-type peptides, one tumor-rejecting neoantigen exhibited improved MHC binding and the other had increased solvent accessibility of the mutated residue. Across known neoantigens that do not impact MHC binding, structural modeling of the peptide/MHC complexes indicated that increased solvent accessibility, which will facilitate TCR recognition of the neoantigen, distinguished tumor-rejecting from non-immunogenic neoantigens. This work reveals characteristics of tumor-rejecting neoantigens that may be of considerable importance in identifying optimal vaccine candidates in cSCC and other cancers.
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Dopeso H, Gazzo AM, Derakhshan F, Brown DN, Selenica P, Jalali S, Da Cruz Paula A, Marra A, da Silva EM, Basili T, Gusain L, Colon-Cartagena L, Bhaloo SI, Green H, Vanderbilt C, Oesterreich S, Grabenstetter A, Kuba MG, Ross D, Giri D, Wen HY, Zhang H, Brogi E, Weigelt B, Pareja F, Reis-Filho JS. Genomic and epigenomic basis of breast invasive lobular carcinomas lacking CDH1 genetic alterations. NPJ Precis Oncol 2024; 8:33. [PMID: 38347189 PMCID: PMC10861500 DOI: 10.1038/s41698-024-00508-x] [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: 05/10/2023] [Accepted: 12/14/2023] [Indexed: 02/15/2024] Open
Abstract
CDH1 (E-cadherin) bi-allelic inactivation is the hallmark alteration of breast invasive lobular carcinoma (ILC), resulting in its discohesive phenotype. A subset of ILCs, however, lack CDH1 genetic/epigenetic inactivation, and their genetic underpinning is unknown. Through clinical targeted sequencing data reanalysis of 364 primary ILCs, we identified 25 ILCs lacking CDH1 bi-allelic genetic alterations. CDH1 promoter methylation was frequent (63%) in these cases. Targeted sequencing reanalysis revealed 3 ILCs harboring AXIN2 deleterious fusions (n = 2) or loss-of-function mutation (n = 1). Whole-genome sequencing of 3 cases lacking bi-allelic CDH1 genetic/epigenetic inactivation confirmed the AXIN2 mutation and no other cell-cell adhesion genetic alterations but revealed a new CTNND1 (p120) deleterious fusion. AXIN2 knock-out in MCF7 cells resulted in lobular-like features, including increased cellular migration and resistance to anoikis. Taken together, ILCs lacking CDH1 genetic/epigenetic alterations are driven by inactivating alterations in other cell adhesion genes (CTNND1 or AXIN2), endorsing a convergent phenotype in ILC.
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Affiliation(s)
- Higinio Dopeso
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrea M Gazzo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fatemeh Derakhshan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - David N Brown
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pier Selenica
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sahar Jalali
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arnaud Da Cruz Paula
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Antonio Marra
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edaise M da Silva
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Thais Basili
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laxmi Gusain
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lorraine Colon-Cartagena
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shirin Issa Bhaloo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hunter Green
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chad Vanderbilt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Steffi Oesterreich
- Department of Pharmacology & Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Anne Grabenstetter
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Gabriela Kuba
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dara Ross
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dilip Giri
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hannah Y Wen
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hong Zhang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edi Brogi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fresia Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Varkaris A, Fece de la Cruz F, Martin EE, Norden BL, Chevalier N, Kehlmann AM, Leshchiner I, Barnes H, Ehnstrom S, Stavridi AM, Yuan X, Kim JS, Ellis H, Papatheodoridi A, Gunaydin H, Danysh BP, Parida L, Sanidas I, Ji Y, Lau K, Wulf GM, Bardia A, Spring LM, Isakoff SJ, Lennerz JK, Del Vecchio K, Pierce L, Pazolli E, Getz G, Corcoran RB, Juric D. Allosteric PI3Kα Inhibition Overcomes On-target Resistance to Orthosteric Inhibitors Mediated by Secondary PIK3CA Mutations. Cancer Discov 2024; 14:227-239. [PMID: 37916958 PMCID: PMC10850944 DOI: 10.1158/2159-8290.cd-23-0704] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/20/2023] [Accepted: 10/23/2023] [Indexed: 11/03/2023]
Abstract
PIK3CA mutations occur in ∼8% of cancers, including ∼40% of HR-positive breast cancers, where the PI3K-alpha (PI3Kα)-selective inhibitor alpelisib is FDA approved in combination with fulvestrant. Although prior studies have identified resistance mechanisms, such as PTEN loss, clinically acquired resistance to PI3Kα inhibitors remains poorly understood. Through serial liquid biopsies and rapid autopsies in 39 patients with advanced breast cancer developing acquired resistance to PI3Kα inhibitors, we observe that 50% of patients acquire genomic alterations within the PI3K pathway, including PTEN loss and activating AKT1 mutations. Notably, although secondary PIK3CA mutations were previously reported to increase sensitivity to PI3Kα inhibitors, we identified emergent secondary resistance mutations in PIK3CA that alter the inhibitor binding pocket. Some mutations had differential effects on PI3Kα-selective versus pan-PI3K inhibitors, but resistance induced by all mutations could be overcome by the novel allosteric pan-mutant-selective PI3Kα-inhibitor RLY-2608. Together, these findings provide insights to guide strategies to overcome resistance in PIK3CA-mutated cancers. SIGNIFICANCE In one of the largest patient cohorts analyzed to date, this study defines the clinical landscape of acquired resistance to PI3Kα inhibitors. Genomic alterations within the PI3K pathway represent a major mode of resistance and identify a novel class of secondary PIK3CA resistance mutations that can be overcome by an allosteric PI3Kα inhibitor. See related commentary by Gong and Vanhaesebroeck, p. 204 . See related article by Varkaris et al., p. 240 . This article is featured in Selected Articles from This Issue, p. 201.
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Affiliation(s)
- Andreas Varkaris
- Mass General Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Ferran Fece de la Cruz
- Mass General Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | | | - Bryanna L. Norden
- Mass General Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Nicholas Chevalier
- Mass General Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Allison M. Kehlmann
- Mass General Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | | | - Haley Barnes
- Mass General Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Sara Ehnstrom
- Mass General Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | | | - Xin Yuan
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Janice S. Kim
- Mass General Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Haley Ellis
- Mass General Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | | | | | - Brian P. Danysh
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Ioannis Sanidas
- Mass General Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Yongli Ji
- Hematology-Oncology, Exeter Hospital, New Haven
| | - Kayao Lau
- Mass General Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Gerburg M. Wulf
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Aditya Bardia
- Mass General Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Laura M. Spring
- Mass General Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Steven J. Isakoff
- Mass General Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Jochen K. Lennerz
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Levi Pierce
- Relay Therapeutics, Cambridge, Massachusetts
| | | | - Gad Getz
- Mass General Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Ryan B. Corcoran
- Mass General Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Dejan Juric
- Mass General Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
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Wu J, Mao L, Lei W, Sun W, Yang X, Zhang Y, Huang X, Lin D. Genomic discordances and heterogeneous mutational burden, PD-L1 expression and immune infiltrates of non-small cell lung cancer metastasis. J Clin Pathol 2024:jcp-2023-209328. [PMID: 38307721 DOI: 10.1136/jcp-2023-209328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 01/21/2024] [Indexed: 02/04/2024]
Abstract
AIMS To investigate the genomic discordances and heterogeneous mutational burden, PD-L1 expression and immune cell (IC) infiltrates of non-small cell lung cancer (NSCLC) metastasis. METHODS Surgical samples from 41 cases of NSCLC with metastatic tumours (MTs) and paired primary tumours (PTs) were collected. PD-L1 expression and ICs were quantified using image-based immunohistochemistry profiling. Whole exome sequencing was employed to explore discrepancies in genomic characteristics, tumour mutational burden (TMB) and tumour neoantigen burden (TNB) in 28 cases. RESULTS Non-synonymous mutations in MTs were slightly more than in PTs, with only 42.34% of mutations shared between paired PTs and MTs. The heterogeneity of TMB showed no significant difference (p=0.785) between MTs and PTs, while TNB significantly increased in MTs (p=0.013). MTs generally exhibited a higher density of PD-L1+ cells and a higher tumour proportion score with a lower density of IC infiltrates. Subgroup analysis considering clinicopathological factors revealed that the heterogeneity of immune biomarkers was closely associated with the histology of lung adenocarcinoma, metastatic sites of extrapulmonary, time intervals and treatment history. Prognosis analysis indicated that a high density of CD8+ T cells was a low-risk factor, whereas a high density of PD-L1+ cells in MTs was a high-risk factor for cancer-related death in metastatic NSCLC. CONCLUSIONS The mutational burden, PD-L1 expression and IC infiltrates undergo changes during NSCLC metastasis, which may impact the immunotherapeutic benefits in patients with NSCLC with metastatic progression and should be monitored according to clinical scenarios.
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Affiliation(s)
- Jianghua Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Luning Mao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Wanjun Lei
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Wei Sun
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xin Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yanhui Zhang
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital; National Clinical Research Center of Cancer; Key Laboratory of Cancer Prevention and Therapy; Tianjin's Clinical Research Center of Cancer, Tianjin, China
| | - Xiaozheng Huang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Dongmei Lin
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
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Lee CAA, Wu S, Chow YT, Kofman E, Williams V, Riddle M, Eide C, Ebens CL, Frank MH, Tolar J, Hook KP, AlDubayan SH, Frank NY. Accelerated Aging and Microsatellite Instability in Recessive Dystrophic Epidermolysis Bullosa-Associated Cutaneous Squamous Cell Carcinoma. J Invest Dermatol 2024:S0022-202X(24)00022-8. [PMID: 38272206 DOI: 10.1016/j.jid.2023.11.025] [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: 08/25/2023] [Revised: 10/22/2023] [Accepted: 11/06/2023] [Indexed: 01/27/2024]
Abstract
Recessive dystrophic epidermolysis bullosa (RDEB) is a severely debilitating disorder caused by pathogenic variants in COL7A1 and is characterized by extreme skin fragility, chronic inflammation, and fibrosis. A majority of patients with RDEB develop squamous cell carcinoma, a highly aggressive skin cancer with limited treatment options currently available. In this study, we utilized an approach leveraging whole-genome sequencing and RNA sequencing across 3 different tissues in a single patient with RDEB to gain insight into possible mechanisms of RDEB-associated squamous cell carcinoma progression and to identify potential therapeutic options. As a result, we identified PLK-1 as a possible candidate for targeted therapy and discovered microsatellite instability and accelerated aging as factors potentially contributing to the aggressive nature and early onset of RDEB squamous cell carcinoma. By integrating multitissue genomic and transcriptomic analyses in a single patient, we demonstrate the promise of bridging the gap between genomic research and clinical applications for developing tailored therapies for patients with rare genetic disorders such as RDEB.
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Affiliation(s)
- Catherine A A Lee
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA; Transplant Research Program, Division of Nephrology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Siyuan Wu
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA; Transplant Research Program, Division of Nephrology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Yuen Ting Chow
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Boston, Massachusetts, USA
| | - Eric Kofman
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Boston, Massachusetts, USA; Broad Institute, Cambridge, Massachusetts, USA
| | - Valencia Williams
- Division of Pediatric Blood and Marrow Transplantation & Cellular Therapy, Department of Pediatrics, University of Minnesota Twin Cities, Minneapolis, Minnesota, USA
| | - Megan Riddle
- Division of Pediatric Blood and Marrow Transplantation & Cellular Therapy, Department of Pediatrics, University of Minnesota Twin Cities, Minneapolis, Minnesota, USA
| | - Cindy Eide
- Division of Pediatric Blood and Marrow Transplantation & Cellular Therapy, Department of Pediatrics, University of Minnesota Twin Cities, Minneapolis, Minnesota, USA
| | - Christen L Ebens
- Division of Pediatric Blood and Marrow Transplantation & Cellular Therapy, Department of Pediatrics, University of Minnesota Twin Cities, Minneapolis, Minnesota, USA
| | - Markus H Frank
- Harvard Medical School, Boston, Massachusetts, USA; Transplant Research Program, Division of Nephrology, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA; Department of Dermatology, Brigham & Women's Hospital, Boston, Massachusetts, USA
| | - Jakub Tolar
- Division of Pediatric Blood and Marrow Transplantation & Cellular Therapy, Department of Pediatrics, University of Minnesota Twin Cities, Minneapolis, Minnesota, USA; Medical School, University of Minnesota Twin Cities, Minneapolis, Minnesota, USA; Stem Cell Institute, Medical School, University of Minnesota Twin Cities, Minneapolis, Minnesota, USA
| | - Kristen P Hook
- Department of Dermatology, Medical School, University of Minnesota Twin Cities, Minneapolis, Minnesota, USA
| | - Saud H AlDubayan
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Boston, Massachusetts, USA; Broad Institute, Cambridge, Massachusetts, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Natasha Y Frank
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA; Transplant Research Program, Division of Nephrology, Boston Children's Hospital, Boston, Massachusetts, USA; Department of Medicine, VA Boston Healthcare System, West Roxbury, Massachusetts, USA.
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Zhang Y, Fu F, Zhang Q, Li L, Liu H, Deng C, Xue Q, Zhao Y, Sun W, Han H, Gao Z, Guo C, Zheng Q, Hu H, Sun Y, Li Y, Ding C, Chen H. Evolutionary proteogenomic landscape from pre-invasive to invasive lung adenocarcinoma. Cell Rep Med 2024; 5:101358. [PMID: 38183982 PMCID: PMC10829798 DOI: 10.1016/j.xcrm.2023.101358] [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: 01/24/2023] [Revised: 08/29/2023] [Accepted: 12/11/2023] [Indexed: 01/08/2024]
Abstract
Lung adenocarcinoma follows a stepwise progression from pre-invasive to invasive. However, there remains a knowledge gap regarding molecular events from pre-invasive to invasive. Here, we conduct a comprehensive proteogenomic analysis comprising whole-exon sequencing, RNA sequencing, and proteomic and phosphoproteomic profiling on 98 pre-invasive and 99 invasive lung adenocarcinomas. The deletion of chr4q12 contributes to the progression from pre-invasive to invasive adenocarcinoma by downregulating SPATA18, thus suppressing mitophagy and promoting cell invasion. Proteomics reveals diverse enriched pathways in normal lung tissues and pre-invasive and invasive adenocarcinoma. Proteomic analyses identify three proteomic subtypes, which represent different stages of tumor progression. We also illustrate the molecular characterization of four immune clusters, including endothelial cells, B cells, DCs, and immune depression subtype. In conclusion, this comprehensive proteogenomic study characterizes the molecular architecture and hallmarks from pre-invasive to invasive lung adenocarcinoma, guiding the way to a deeper understanding of the tumorigenesis and progression of this disease.
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Affiliation(s)
- Yang Zhang
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Fangqiu Fu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Qiao Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Lingling Li
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Hui Liu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai 200433, China; State Key Laboratory Cell Differentiation and Regulation, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), College of Life Science, Henan Normal University, Xinxiang, Henan 453007, China
| | - Chaoqiang Deng
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Qianqian Xue
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Yue Zhao
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Wenrui Sun
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Han Han
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Zhendong Gao
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Chunmei Guo
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Qiang Zheng
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Hong Hu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yihua Sun
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yuan Li
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China.
| | - Chen Ding
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai 200433, China.
| | - Haiquan Chen
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
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Dhanushkumar T, M E S, Selvam PK, Rambabu M, Dasegowda KR, Vasudevan K, George Priya Doss C. Advancements and hurdles in the development of a vaccine for triple-negative breast cancer: A comprehensive review of multi-omics and immunomics strategies. Life Sci 2024; 337:122360. [PMID: 38135117 DOI: 10.1016/j.lfs.2023.122360] [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: 10/12/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023]
Abstract
Triple-Negative Breast Cancer (TNBC) presents a significant challenge in oncology due to its aggressive behavior and limited therapeutic options. This review explores the potential of immunotherapy, particularly vaccine-based approaches, in addressing TNBC. It delves into the role of immunoinformatics in creating effective vaccines against TNBC. The review first underscores the distinct attributes of TNBC and the importance of tumor antigens in vaccine development. It then elaborates on antigen detection techniques such as exome sequencing, HLA typing, and RNA sequencing, which are instrumental in identifying TNBC-specific antigens and selecting vaccine candidates. The discussion then shifts to the in-silico vaccine development process, encompassing antigen selection, epitope prediction, and rational vaccine design. This process merges computational simulations with immunological insights. The role of Artificial Intelligence (AI) in expediting the prediction of antigens and epitopes is also emphasized. The review concludes by encapsulating how Immunoinformatics can augment the design of TNBC vaccines, integrating tumor antigens, advanced detection methods, in-silico strategies, and AI-driven insights to advance TNBC immunotherapy. This could potentially pave the way for more targeted and efficacious treatments.
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Affiliation(s)
- T Dhanushkumar
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Santhosh M E
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Prasanna Kumar Selvam
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Majji Rambabu
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - K R Dasegowda
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Karthick Vasudevan
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India.
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore, India.
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Sveen A, Johannessen B, Klokkerud SM, Kraggerud SM, Meza-Zepeda LA, Bjørnslett M, Bischof K, Myklebost O, Taskén K, Skotheim RI, Dørum A, Davidson B, Lothe RA. Evolutionary mode and timing of dissemination of high-grade serous carcinomas. JCI Insight 2024; 9:e170423. [PMID: 38175731 PMCID: PMC11143962 DOI: 10.1172/jci.insight.170423] [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: 12/21/2023] [Accepted: 12/26/2023] [Indexed: 01/06/2024] Open
Abstract
Dissemination within the peritoneal cavity is a main determinant of poor patient outcomes from high-grade serous carcinomas (HGSCs). The dissemination process is poorly understood from a cancer evolutionary perspective. We reconstructed the evolutionary trajectories across a median of 5 tumor sites and regions from each of 23 patients based on deep whole-exome sequencing. Polyclonal cancer origin was detected in 1 patient. Ovarian tumors had more complex subclonal architectures than other intraperitoneal tumors in each patient, which indicated that tumors developed earlier in the ovaries. Three common modes of dissemination were identified, including monoclonal or polyclonal dissemination of monophyletic (linear) or polyphyletic (branched) subclones. Mutation profiles of initial or disseminated clones varied greatly among cancers, but recurrent mutations were found in 7 cancer-critical genes, including TP53, BRCA1, BRCA2, and DNMT3A, and in the PI3K/AKT1 pathway. Disseminated clones developed late in the evolutionary trajectory models of most cancers, in particular in cancers with DNA damage repair deficiency. Polyclonal dissemination was predicted to occur predominantly as a single and rapid wave, but chemotherapy exposure was associated with higher genomic diversity of disseminated clones. In conclusion, we described three common evolutionary dissemination modes across HGSCs and proposed factors associated with dissemination diversity.
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Affiliation(s)
- Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Bjarne Johannessen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Solveig M.K. Klokkerud
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Sigrid M. Kraggerud
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Leonardo A. Meza-Zepeda
- Department of Tumor Biology, Institute for Cancer Research
- Genomics Core Facility, Department of Core Facilities, Institute for Cancer Research
| | - Merete Bjørnslett
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Katharina Bischof
- Department of Gynecological Oncology, The Norwegian Radium Hospital, and
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Ola Myklebost
- Department of Tumor Biology, Institute for Cancer Research
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kjetil Taskén
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Rolf I. Skotheim
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Anne Dørum
- Department of Gynecological Oncology, The Norwegian Radium Hospital, and
| | - Ben Davidson
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Ragnhild A. Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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Lin YL, Zhu JQ, Ma RQ, Meng W, Wang ZY, Li XB, Ma R, Wu HL, Xu HB, Gao Y, Li Y. Whole-Exome Sequencing Identifies Mutation Profile and Mutation Signature-Based Clustering Associated with Prognosis in Appendiceal Pseudomyxoma Peritonei. Mol Cancer Res 2024; 22:70-81. [PMID: 37768171 DOI: 10.1158/1541-7786.mcr-22-0801] [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: 10/11/2022] [Revised: 01/18/2023] [Accepted: 09/25/2023] [Indexed: 09/29/2023]
Abstract
Pseudomyxoma peritonei (PMP) is a rare malignant clinical syndrome with little known about the global mutation profile. In this study, whole-exome sequencing (WES) was performed in 49 appendiceal PMP to investigate mutation profiles and mutation signatures. A total of 4,020 somatic mutations were detected, with a median mutation number of 56 (1-402). Tumor mutation burden (TMB) was generally low (median 1.55 mutations/Mb, 0.12-11.26 mutations/Mb). Mutations were mainly enriched in the function of cancer-related axonogenesis, extracellular matrix-related processes, calcium signaling pathway, and cAMP signaling pathway. Mutations in FCGBP, RBFOX1, SPEG, RTK-RAS, PI3K-AKT, and focal adhesion pathways were associated with high-grade mucinous carcinoma peritonei. These findings revealed distinct mutation profile in appendiceal PMP. Ten mutation signatures were identified, dividing patients into mutation signature cluster (MSC) 1 (N = 28, 57.1%) and MSC 2 (N = 21, 42.9%) groups. MSC (P = 0.007) was one of the four independent factors associated with 3-year survival. TMB (P = 0.003) and microsatellite instability (P = 0.002) were independent factors associated with MSC 2 grouping. Taken together, our findings provided a broader view in the understanding of molecular pathologic mechanism in appendiceal PMP and may be critical to developing an individualized approach to appendiceal PMP treatment. IMPLICATIONS This work describes exhaustive mutation profile of PMP based on WES data and derives ten mutation signatures, which divides patients into two clusters and serve as an independent prognostic factor associated with 3-year survival.
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Affiliation(s)
- Yu-Lin Lin
- Department of Peritoneal Cancer Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | | | - Rui-Qing Ma
- Department of Myxoma, Aerospace Center Hospital, Beijing, China
| | - Wei Meng
- Department of Pathology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Zi-Yue Wang
- Department of Pathology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Xin-Bao Li
- Department of Peritoneal Cancer Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Ru Ma
- Department of Peritoneal Cancer Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - He-Liang Wu
- Department of Peritoneal Cancer Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Department of Peritoneal Cancer Surgery, Beijing Shijitan Hospital, Peking University Ninth School of Clinical Medicine, Beijing, China
| | - Hong-Bin Xu
- Department of Myxoma, Aerospace Center Hospital, Beijing, China
| | - Ying Gao
- Department of Pathology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Yan Li
- Department of Peritoneal Cancer Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Department of Surgical Oncology, Beijing Tsinghua Changgung Hospital affiliated to Tsinghua University, Beijing, China
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Zhou Z, Zhang Y, Zhu L, Cui Y, Gao Y, Zhou C. Familial gigantiform cementoma with recurrent ANO5 p.Cys356Tyr mutations: Clinicopathological and genetic study with literature review. Mol Genet Genomic Med 2024; 12:e2277. [PMID: 37649308 PMCID: PMC10767285 DOI: 10.1002/mgg3.2277] [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: 04/10/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND Familial gigantiform cementoma (FGC) is a rare tumor characterized by the early onset of multi-quadrant fibro-osseous lesions in the jaws, causing severe maxillofacial deformities. Its clinicopathological features overlap with those of other benign fibro-osseous lesions. FGC eventually exhibits progressively rapid growth, but no suspected causative gene has been identified. METHODS In this study, three patients with FGC were recruited, and genomic DNA from the tumor tissue and peripheral blood was extracted for whole-exome sequencing. RESULTS Results showed that all three patients harbored the heterozygous mutation c.1067G > A (p.Cys356Tyr) in the ANO5 gene. Furthermore, autosomal dominant mutations in ANO5 at this locus have been identified in patients with gnathodiaphyseal dysplasia (GDD) and are considered a potential causative agent, suggesting a genetic association between FGC and GDD. In addition, multifocal fibrous bone lesions with similar clinical presentations were detected, including five cases of florid cemento-osseous dysplasia, five cases of polyostotic fibrous dysplasia, and eight cases of juvenile ossifying fibromas; however, none of them harbored mutations in the ANO5 gene. CONCLUSION Our findings indicate that FGC may be an atypical variant of GDD, providing evidence for the feasibility of ANO5 gene testing as an auxiliary diagnostic method for complex cases with multiple quadrants.
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Affiliation(s)
- Zheng Zhou
- Department of Oral PathologyPeking University School and Hospital of StomatologyBeijingP.R. China
- National Engineering Laboratory for Digital and Material Technology of StomatologyPeking University School and Hospital of StomatologyBeijingP.R. China
| | - Ye Zhang
- Department of Oral PathologyPeking University School and Hospital of StomatologyBeijingP.R. China
- National Engineering Laboratory for Digital and Material Technology of StomatologyPeking University School and Hospital of StomatologyBeijingP.R. China
| | - Lijing Zhu
- Department of Oral PathologyPeking University School and Hospital of StomatologyBeijingP.R. China
- National Engineering Laboratory for Digital and Material Technology of StomatologyPeking University School and Hospital of StomatologyBeijingP.R. China
| | - Yajuan Cui
- Department of Oral PathologyPeking University School and Hospital of StomatologyBeijingP.R. China
- National Engineering Laboratory for Digital and Material Technology of StomatologyPeking University School and Hospital of StomatologyBeijingP.R. China
| | - Yan Gao
- Department of Oral PathologyPeking University School and Hospital of StomatologyBeijingP.R. China
- National Engineering Laboratory for Digital and Material Technology of StomatologyPeking University School and Hospital of StomatologyBeijingP.R. China
| | - Chuan‐Xiang Zhou
- Department of Oral PathologyPeking University School and Hospital of StomatologyBeijingP.R. China
- National Engineering Laboratory for Digital and Material Technology of StomatologyPeking University School and Hospital of StomatologyBeijingP.R. China
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Zhao L, Wang J, Zhang Y, Wang P, Lv C, Zhao S, Guo T, Li F, Gu C, Zhu Y. Genomic heterogeneity of multiple synchronous lung cancers in Chinese population. Cancer Med 2024; 13:e6928. [PMID: 38348924 PMCID: PMC10839131 DOI: 10.1002/cam4.6928] [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: 07/31/2023] [Revised: 12/24/2023] [Accepted: 12/31/2023] [Indexed: 02/15/2024] Open
Abstract
INTRODUCTION It is clinically challenging to infer the phylogenetic relationship between different tumor lesions of patients with multiple synchronous lung cancers (MSLC), whether these lesions are the result of independently evolved tumor or intrapulmonary metastases. METHODS We used the Illumina X10 platform to sequence 128 stage I lung cancer samples collected from 64 patients with MSLC. All samples were analyzed for mutation spectra and phylogenetic inference. RESULTS We detected genetic aberrations within genes previously reported to be recurrently altered in lung adenocarcinoma including, EGFR, ERBB2, TP53, BRAF, and KRAS. Other putative driver mutations identified were enriched in RTK-RAS signaling, TP53 signaling, and cell cycle. Also, we found some interesting cases, two cases that carried EGFR L858R and T790M co-mutation in one tumor and another tumor with only EGFR 19del, and 1 case with two KRAS hotspots in the same tumor. Due to the short follow-up time and early stage, further investigation is needed to determine whether this unique mutation profile will affect their progression-free survival (PFS) and overall survival (OS). Regarding genetic evolution analysis among 64 tumor samples, 50 of them display distinct mutational profiles, suggesting these are independently evolved tumors, which is consistent with histopathological assessment. On the other hand, six patients were identified to be intrapulmonary metastasis as the mutations harbored in different lesions are clonally related. CONCLUSION In summary, unlike intrapulmonary metastases, patients with MSLC harbor distinct genomic profiles in different tumor lesions, and we could distinguish MSLC from intrapulmonary metastases via clonality estimation.
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Affiliation(s)
- Lei Zhao
- Department of Thoracic Surgerythe First Affiliated Hospital of Dalian Medical UniversityDalianChina
| | - Jin Wang
- Department of Thoracic Surgerythe First Affiliated Hospital of Dalian Medical UniversityDalianChina
| | - Yixiang Zhang
- Department of Thoracic Surgerythe First Affiliated Hospital of Dalian Medical UniversityDalianChina
| | - Peng Wang
- Department of Thoracic Surgerythe First Affiliated Hospital of Dalian Medical UniversityDalianChina
| | - Changsheng Lv
- Department of Thoracic Surgerythe First Affiliated Hospital of Dalian Medical UniversityDalianChina
| | - Shilei Zhao
- Department of Thoracic Surgerythe First Affiliated Hospital of Dalian Medical UniversityDalianChina
| | - Tao Guo
- Department of Thoracic Surgerythe First Affiliated Hospital of Dalian Medical UniversityDalianChina
| | - Fengzhou Li
- Department of Thoracic Surgerythe First Affiliated Hospital of Dalian Medical UniversityDalianChina
| | - Chundong Gu
- Department of Thoracic Surgerythe First Affiliated Hospital of Dalian Medical UniversityDalianChina
| | - Yuntao Zhu
- Department of Thoracic Surgerythe First Affiliated Hospital of Dalian Medical UniversityDalianChina
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Contreras Yametti GP, Robbins G, Chowdhury A, Narang S, Ostrow TH, Kilberg H, Greenberg J, Kramer L, Raetz E, Tsirigos A, Evensen NA, Carroll WL. SETD2 mutations do not contribute to clonal fitness in response to chemotherapy in childhood B cell acute lymphoblastic leukemia. Leuk Lymphoma 2024; 65:78-90. [PMID: 37874744 DOI: 10.1080/10428194.2023.2273752] [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: 06/19/2023] [Accepted: 10/14/2023] [Indexed: 10/26/2023]
Abstract
Mutations in genes encoding epigenetic regulators are commonly observed at relapse in B cell acute lymphoblastic leukemia (B-ALL). Loss-of-function mutations in SETD2, an H3K36 methyltransferase, have been observed in B-ALL and other cancers. Previous studies on mutated SETD2 in solid tumors and acute myelogenous leukemia support a role in promoting resistance to DNA damaging agents. We did not observe chemoresistance, an impaired DNA damage response, nor increased mutation frequency in response to thiopurines using CRISPR-mediated knockout in wild-type B-ALL cell lines. Likewise, restoration of SETD2 in cell lines with hemizygous mutations did not increase sensitivity. SETD2 mutations affected the chromatin landscape and transcriptional output that was unique to each cell line. Collectively our data does not support a role for SETD2 mutations in driving clonal evolution and relapse in B-ALL, which is consistent with the lack of enrichment of SETD2 mutations at relapse in most studies.
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Affiliation(s)
- Gloria P Contreras Yametti
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Gabriel Robbins
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Ashfiyah Chowdhury
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Sonali Narang
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Talia H Ostrow
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Harrison Kilberg
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Joshua Greenberg
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Lindsay Kramer
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Elizabeth Raetz
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Aristotelis Tsirigos
- Departments of Pediatrics and Pathology, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Nikki A Evensen
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - William L Carroll
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Department of Pathology, NYU Langone Health, New York, NY, USA
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Difilippo V, Saba KH, Styring E, Magnusson L, Nilsson J, Nathrath M, Baumhoer D, Nord KH. Osteosarcomas With Few Chromosomal Alterations or Adult Onset Are Genetically Heterogeneous. J Transl Med 2024; 104:100283. [PMID: 37931683 DOI: 10.1016/j.labinv.2023.100283] [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: 06/22/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/08/2023] Open
Abstract
Osteosarcoma is the most common primary bone malignancy, often detected in children and adolescents and commonly associated with TP53 alterations along with a high number of chromosomal rearrangements. However, osteosarcoma can affect patients of any age, and some tumors display less genetic complexity. Besides TP53 variants, data on key driving mutations are lacking for many osteosarcomas, particularly those affecting adults. To detect osteosarcoma-specific alterations, we screened transcriptomic and genomic sequencing and copy number data from 150 bone tumors originally diagnosed as osteosarcomas. To increase the precision in gene fusion detection, we developed a bioinformatic tool denoted as NAFuse, which extracts gene fusions that are verified at both the genomic and transcriptomic levels. Apart from the already reported genetic subgroups of osteosarcoma with TP53 structural variants, or MDM2 and/or CDK4 amplification, we did not identify any recurrent genetic driver that signifies the remaining cases. Among the plethora of mutations identified, we found genetic alterations characteristic of, or similar to, those of other bone and soft tissue tumors in 8 cases. These mutations were found in tumors with relatively few other genetic alterations or in adults. Due to the lack of clinical context and available tissue, we can question the diagnosis only on a genetic basis. However, our findings support the notion that osteosarcomas with few chromosomal alterations or adult onset seem genetically distinct from conventional osteosarcomas of children and adolescents.
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Affiliation(s)
- Valeria Difilippo
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Karim H Saba
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Emelie Styring
- Department of Orthopedics, Lund University, Skåne University Hospital, Lund, Sweden
| | - Linda Magnusson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Jenny Nilsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Michaela Nathrath
- Children's Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany; Department of Pediatric Oncology, Klinikum Kassel, Kassel, Germany
| | - Daniel Baumhoer
- Bone Tumour Reference Centre at the Institute of Pathology, University Hospital and University of Basel, Basel, Switzerland
| | - Karolin H Nord
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden.
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47
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Mouhieddine TH, Nzerem C, Redd R, Dunford A, Leventhal M, Sklavenitis-Pistofidis R, Tahri S, El-Khoury H, Steensma DP, Ebert BL, Soiffer RJ, Keats JJ, Mehr S, Auclair D, Ghobrial IM, Sperling AS, Stewart C, Getz G. Clinical Outcomes and Evolution of Clonal Hematopoiesis in Patients with Newly Diagnosed Multiple Myeloma. CANCER RESEARCH COMMUNICATIONS 2023; 3:2560-2571. [PMID: 38019104 PMCID: PMC10730502 DOI: 10.1158/2767-9764.crc-23-0093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/23/2023] [Accepted: 11/22/2023] [Indexed: 11/30/2023]
Abstract
Clonal hematopoiesis (CH) at time of autologous stem cell transplant (ASCT) has been shown to be associated with decreased overall survival (OS) and progression-free survival (PFS) in patients with multiple myeloma not receiving immunomodulatory drugs (IMiD). However, the significance of CH in newly diagnosed patients, including transplant ineligible patients, and its effect on clonal evolution during multiple myeloma therapy in the era of novel agents, has not been well studied. Using our new algorithm to differentiate tumor and germline mutations from CH, we detected CH in approximately 10% of 986 patients with multiple myeloma from the Clinical Outcomes in MM to Personal Assessment of Genetic Profile (CoMMpass) cohort (40/529 transplanted and 59/457 non-transplanted patients). CH was associated with increased age, risk of recurrent bacterial infections and cardiovascular disease. CH at time of multiple myeloma diagnosis was not associated with inferior OS or PFS regardless of undergoing ASCT, and all patients benefited from IMiD-based therapies, irrespective of the presence of CH. Serial sampling of 52 patients revealed the emergence of CH over a median of 3 years of treatment, increasing its prevalence to 25%, mostly with DNMT3A mutations. SIGNIFICANCE Using our algorithm to differentiate tumor and germline mutations from CH mutations, we detected CH in approximately 10% of patients with newly diagnosed myeloma, including both transplant eligible and ineligible patients. Receiving IMiDs improved outcomes irrespective of CH status, but the prevalence of CH significantly rose throughout myeloma-directed therapy.
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Affiliation(s)
- Tarek H. Mouhieddine
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Chidimma Nzerem
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Robert Redd
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Andrew Dunford
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Romanos Sklavenitis-Pistofidis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sabrin Tahri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Hematology, Erasmus MC Cancer Centre, Rotterdam, the Netherlands
| | - Habib El-Khoury
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - David P. Steensma
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Robert J. Soiffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jonathan J. Keats
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Shaadi Mehr
- Multiple Myeloma Research Foundation, Norwalk, Connecticut
| | - Daniel Auclair
- Multiple Myeloma Research Foundation, Norwalk, Connecticut
| | - Irene M. Ghobrial
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Adam S. Sperling
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Division of Hematology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Chip Stewart
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Gad Getz
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
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48
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Kamran SC, Zhou Y, Otani K, Drumm M, Otani Y, Wu S, Wu CL, Feldman AS, Wszolek M, Lee RJ, Saylor PJ, Lennerz J, Van Allen E, Willers H, Hong TS, Liu Y, Davicioni E, Gibb EA, Shipley WU, Mouw KW, Efstathiou JA, Miyamoto DT. Genomic Tumor Correlates of Clinical Outcomes Following Organ-Sparing Chemoradiation Therapy for Bladder Cancer. Clin Cancer Res 2023; 29:5116-5127. [PMID: 37870965 PMCID: PMC10722135 DOI: 10.1158/1078-0432.ccr-23-0792] [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: 03/15/2023] [Revised: 05/20/2023] [Accepted: 09/27/2023] [Indexed: 10/25/2023]
Abstract
PURPOSE There is an urgent need for biomarkers of radiation response in organ-sparing therapies. Bladder preservation with trimodality therapy (TMT), consisting of transurethral tumor resection followed by chemoradiation, is an alternative to radical cystectomy for muscle-invasive bladder cancer (MIBC), but molecular determinants of response are poorly understood. EXPERIMENTAL DESIGN We characterized genomic and transcriptomic features correlated with long-term response in a single institution cohort of patients with MIBC homogeneously treated with TMT. Pretreatment tumors from 76 patients with MIBC underwent whole-exome sequencing; 67 underwent matched transcriptomic profiling. Molecular features were correlated with clinical outcomes including modified bladder-intact event-free survival (mBI-EFS), a composite endpoint that reflects long-term cancer control with bladder preservation. RESULTS With a median follow-up of 74.6 months in alive patients, 37 patients had favorable long-term response to TMT while 39 had unfavorable long-term response. Tumor mutational burden was not associated with outcomes after TMT. DNA damage response gene alterations were associated with improved locoregional control and mBI-EFS. Of these alterations, somatic ERCC2 mutations stood out as significantly associated with favorable long-term outcomes; patients with ERCC2 mutations had significantly improved mBI-EFS [HR, 0.15; 95% confidence interval (CI), 0.06-0.37; P = 0.030] and improved BI-EFS, an endpoint that includes all-cause mortality (HR, 0.33; 95% CI, 0.15-0.68; P = 0.044). ERCC2 mutant bladder cancer cell lines were significantly more sensitive to concurrent cisplatin and radiation treatment in vitro than isogenic ERCC2 wild-type cells. CONCLUSIONS Our data identify ERCC2 mutation as a candidate biomarker associated with sensitivity and long-term response to chemoradiation in MIBC. These findings warrant validation in independent cohorts.
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Affiliation(s)
- Sophia C. Kamran
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Yuzhen Zhou
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Keisuke Otani
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Michael Drumm
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Yukako Otani
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Shulin Wu
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Chin-Lee Wu
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Adam S. Feldman
- Harvard Medical School, Boston, Massachusetts
- Department of Urology, Massachusetts General Hospital, Boston, Massachusetts
| | - Matthew Wszolek
- Harvard Medical School, Boston, Massachusetts
- Department of Urology, Massachusetts General Hospital, Boston, Massachusetts
| | - Richard J. Lee
- Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Philip J. Saylor
- Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Jochen Lennerz
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Eliezer Van Allen
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Department of Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Henning Willers
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Theodore S. Hong
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Yang Liu
- Veracyte, San Francisco, California
| | | | | | - William U. Shipley
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Kent W. Mouw
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jason A. Efstathiou
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - David T. Miyamoto
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts
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49
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Burdett NL, Willis MO, Pandey A, Fereday S, DeFazio A, Bowtell DDL, Christie EL. Small-scale mutations are infrequent as mechanisms of resistance in post-PARP inhibitor tumour samples in high grade serous ovarian cancer. Sci Rep 2023; 13:21884. [PMID: 38072854 PMCID: PMC10711013 DOI: 10.1038/s41598-023-48153-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
While the introduction of poly-(ADP)-ribose polymerase (PARP) inhibitors in homologous recombination DNA repair (HR) deficient high grade serous ovarian, fallopian tube and primary peritoneal cancers (HGSC) has improved patient survival, resistance to PARP inhibitors frequently occurs. Preclinical and translational studies have identified multiple mechanisms of resistance; here we examined tumour samples collected from 26 women following treatment with PARP inhibitors as part of standard of care or their enrolment in clinical trials. Twenty-one had a germline or somatic BRCA1/2 mutation. We performed targeted sequencing of 63 genes involved in DNA repair processes or implicated in ovarian cancer resistance. We found that just three individuals had a small-scale mutation as a definitive resistance mechanism detected, having reversion mutations, while six had potential mechanisms of resistance detected, with alterations related to BRCA1 function and mutations in SHLD2. This study indicates that mutations in genes related to DNA repair are detected in a minority of HGSC patients as genetic mechanisms of resistance. Future research into resistance in HGSC should focus on copy number, transcriptional and epigenetic aberrations, and the contribution of the tumour microenvironment.
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Affiliation(s)
- Nikki L Burdett
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
- Box Hill Hospital, Eastern Health, Box Hill, Victoria, 3128, Australia
| | | | - Ahwan Pandey
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Sian Fereday
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Anna DeFazio
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, NSW, 2145, Australia
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, NSW, 2006, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, NSW, 2145, Australia
| | - David D L Bowtell
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
| | - Elizabeth L Christie
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia.
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50
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Kim SR, Oldfield L, Tone A, Pollett A, Pedersen S, Wellum J, Cesari M, Lajkosz K, Pugh TJ, Ferguson SE. Comprehensive molecular assessment of mismatch repair deficiency in Lynch associated ovarian cancers using next generation sequencing panel. Int J Gynecol Cancer 2023:ijgc-2023-004815. [PMID: 37940339 DOI: 10.1136/ijgc-2023-004815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023] Open
Abstract
OBJECTIVES Abnormalities in mismatch repair have been described in ovarian cancer, but few studies have examined the causes of mismatch repair deficiency (MMRd). To address this, we completed targeted mutational and methylation sequencing on MMRd ovarian cancer cases. The objective of this study was to explore the molecular mechanism of MMRd using our targeted next generation sequencing panel. METHODS Newly diagnosed non-serous/mucinous ovarian cancers (n=215) were prospectively recruited from three cancer centers in Ontario, Canada, between 2015 and 2018. Tumors were reflexively assessed for mismatch repair protein by immunohistochemistry. Matched tumor-normal MMRd cases were analyzed on a custom next generation sequencing panel to identify germline and somatic mutations, copy number variants, rearrangements, and promoter methylation in mismatch repair and associated genes. RESULTS Of 215 cases, 28 (13%) were MMRd. The MMRd cohort had a median age of 52.3 years (range 33.6-62.2), with mostly stage I (50%) and grade 1 or 2 endometrioid histotype (57%). Of the 28 cases, 22 were available for molecular analysis, and Lynch syndrome was detected in 50% of MMRd cases (11/22; seven ovarian cancer and four synchronous ovarian and endometrial cancer: seven MSH6, two MLH1, one PMS2, and one MSH2). An explanation for the observed mismatch repair phenotype was available for 22/22 deficient cases, including 12 MLH1/PMS2 deficient (nine somatic methylation, one bi-allelic somatic deletion, and two pathogenic germline variant), one PMS2 deficient (one pathogenic germline variant), seven MSH6 deficient (seven pathogenic germline variant), and two MSH2/MSH6 deficient (one pathogenic germline variant and one bi-allelic somatic mutation). Concordance between clinical germline testing and panel sequencing results was 100%. CONCLUSIONS Use of our custom next generation sequencing panel allowed for the streamlined assessment of hereditary and somatic causes of MMRd in ovarian cancers.
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Affiliation(s)
- Soyoun Rachel Kim
- Princess Margaret Cancer Center/University Health Network/Sinai Health Systems, Toronto, Ontario, Canada
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, Ontario, Canada
- Gynecologic Oncology, Princess Margaret Hospital Cancer Center, Toronto, Ontario, Canada
| | - Leslie Oldfield
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Alicia Tone
- Gynecologic Oncology, Princess Margaret Hospital Cancer Center, Toronto, Ontario, Canada
| | - Aaron Pollett
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Stephanie Pedersen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Johanna Wellum
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Matthew Cesari
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Katherine Lajkosz
- Department of Biostatistics, University of Toronto, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, University Health Network, Toronto, Ontario, Canada
| | - Sarah Elizabeth Ferguson
- Princess Margaret Cancer Center/University Health Network/Sinai Health Systems, Toronto, Ontario, Canada
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, Ontario, Canada
- Gynecologic Oncology, Princess Margaret Hospital Cancer Center, Toronto, Ontario, Canada
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