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Achom M, Sadagopan A, Bao C, McBride F, Li J, Konda P, Tourdot RW, Xu Q, Nakhoul M, Gallant DS, Ahmed UA, O'Toole J, Freeman D, Lee GSM, Hecht JL, Kauffman EC, Einstein DJ, Choueiri TK, Zhang CZ, Viswanathan SR. A genetic basis for sex differences in Xp11 translocation renal cell carcinoma. Cell 2024; 187:5735-5752.e25. [PMID: 39168126 PMCID: PMC11455617 DOI: 10.1016/j.cell.2024.07.038] [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] [Revised: 06/21/2024] [Accepted: 07/23/2024] [Indexed: 08/23/2024]
Abstract
Xp11 translocation renal cell carcinoma (tRCC) is a rare, female-predominant cancer driven by a fusion between the transcription factor binding to IGHM enhancer 3 (TFE3) gene on chromosome Xp11.2 and a partner gene on either chromosome X (chrX) or an autosome. It remains unknown what types of rearrangements underlie TFE3 fusions, whether fusions can arise from both the active (chrXa) and inactive X (chrXi) chromosomes, and whether TFE3 fusions from chrXi translocations account for the female predominance of tRCC. To address these questions, we performed haplotype-specific analyses of chrX rearrangements in tRCC whole genomes. We show that TFE3 fusions universally arise as reciprocal translocations and that oncogenic TFE3 fusions can arise from chrXi:autosomal translocations. Female-specific chrXi:autosomal translocations result in a 2:1 female-to-male ratio of TFE3 fusions involving autosomal partner genes and account for the female predominance of tRCC. Our results highlight how X chromosome genetics constrains somatic chrX alterations and underlies cancer sex differences.
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Affiliation(s)
- Mingkee Achom
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Ananthan Sadagopan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Chunyang Bao
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02215, USA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Fiona McBride
- Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Jiao Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Prathyusha Konda
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Richard W Tourdot
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Qingru Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Maria Nakhoul
- Department of Informatics & Analytics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Daniel S Gallant
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Usman Ali Ahmed
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jillian O'Toole
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Dory Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Gwo-Shu Mary Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jonathan L Hecht
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Eric C Kauffman
- Department of Urology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA
| | - David J Einstein
- Division of Medical Oncology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Cheng-Zhong Zhang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02215, USA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Srinivas R Viswanathan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA.
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2
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Sdeor E, Okada H, Saad R, Ben-Yishay T, Ben-David U. Aneuploidy as a driver of human cancer. Nat Genet 2024:10.1038/s41588-024-01916-2. [PMID: 39358600 DOI: 10.1038/s41588-024-01916-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 08/20/2024] [Indexed: 10/04/2024]
Abstract
Aneuploidy, an abnormal chromosome composition, is a major contributor to cancer development and progression and an important determinant of cancer therapeutic responses and clinical outcomes. Despite being recognized as a hallmark of human cancer, the exact role of aneuploidy as a 'driver' of cancer is still largely unknown. Identifying the specific genetic elements that underlie the recurrence of common aneuploidies remains a major challenge of cancer genetics. In this Review, we discuss recurrent aneuploidies and their function as drivers of tumor development. We then delve into the context-dependent identification and functional characterization of the driver genes underlying driver aneuploidies and examine emerging strategies to uncover these driver genes using cancer genomics data and cancer models. Lastly, we explore opportunities for targeting driver aneuploidies in cancer by leveraging the functional consequences of these common genetic alterations.
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Affiliation(s)
- Eran Sdeor
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Hajime Okada
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ron Saad
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
- The Blavatnik School of Computer Science, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tal Ben-Yishay
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
- The Blavatnik School of Computer Science, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Uri Ben-David
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel.
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3
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André F, Solovieff N, Su F, Bardia A, Neven P, Yap YS, Tripathy D, Lu YS, Slamon D, Chia S, Joshi M, Chakravartty A, Lteif A, Taran T, Arteaga CL. Acquired gene alterations in patients treated with ribociclib plus endocrine therapy or endocrine therapy alone using baseline and end-of-treatment circulating tumor DNA samples in the MONALEESA-2, -3, and -7 trials. Ann Oncol 2024:S0923-7534(24)04018-3. [PMID: 39313156 DOI: 10.1016/j.annonc.2024.09.010] [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: 03/22/2024] [Revised: 09/12/2024] [Accepted: 09/14/2024] [Indexed: 09/25/2024] Open
Abstract
BACKGROUND A prior pooled analysis of the MONALEESA-2, -3, and -7 trials identified baseline markers predictive of sensitivity or resistance to ribociclib plus endocrine therapy (ET). We report the results of an analysis of paired baseline and end-of-treatment (EOT) circulating tumor DNA (ctDNA) samples across the MONALEESA trials. PATIENTS AND METHODS Paired baseline and EOT ctDNA samples from MONALEESA-2, -3, and -7 were sequenced using a targeted next-generation sequencing panel. Genes with an EOT alteration prevalence of >5% were included. A McNemar test was performed on paired samples and adjusted for multiple testing to control the false discovery rate. A Bayesian mixed-effects model was used to adjust for ctDNA fraction at both time points and for study differences. RESULTS The analysis included 523 paired samples. At EOT, 21 genes had a >5% alteration prevalence. A trend for higher ctDNA fraction at EOT vs baseline (P=0.08) was observed. Prevalence of alterations was higher at EOT vs baseline in RB1, SPEN, TPR, PCDH15, and FGFR2 in the ribociclib arm; PBRM1 in the placebo arm; and ESR1 in both arms. The mixed-effects model demonstrated that the same trends for increased prevalence of these alterations at EOT were observed after adjusting for ctDNA fraction and that the increased rate of RB1 and SPEN alterations at EOT were specific to ribociclib plus ET. Analysis of ESR1 indicated a similar increase at EOT in both arms. The most common acquired ESR1 mutations at EOT included Y537C/N/S/D, D538G, E380Q, and L536H/R/P/LC. The prevalence of PIK3CA hotspot mutations at baseline and EOT was similar. CONCLUSIONS This analysis identified acquired gene alterations in patients with HR+/HER2- advanced breast cancer treated with ribociclib plus ET or placebo plus ET. These data may support further studies on acquired resistance mechanisms and inform future systemic interventions in the post-CDK4/6 inhibitor setting.
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Affiliation(s)
- F André
- Department of Medical Oncology, Institut Gustave Roussy, Villejuif, France.
| | - N Solovieff
- Novartis Pharmaceuticals Corporation, Cambridge, MA, USA
| | - F Su
- Novartis Pharmaceuticals Corporation, East Hanover, NJ, USA
| | - A Bardia
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - P Neven
- Multidisciplinary Breast Centre, Universitair Ziekenhuis Leuven, Leuven, Belgium
| | - Y S Yap
- National Cancer Centre Singapore, Singapore
| | - D Tripathy
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Y-S Lu
- National Taiwan University Hospital, Taipei, Taiwan
| | - D Slamon
- David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - S Chia
- British Columbia Cancer Agency, Vancouver, BC, Canada
| | - M Joshi
- Novartis Pharmaceuticals Corporation, Cambridge, MA, USA
| | - A Chakravartty
- Novartis Pharmaceuticals Corporation, East Hanover, NJ, USA
| | - A Lteif
- Novartis Pharmaceuticals Corporation, East Hanover, NJ, USA
| | - T Taran
- Novartis Pharma AG, Basel, Switzerland
| | - C L Arteaga
- UT Southwestern Simmons Comprehensive Cancer Center, Dallas, TX, USA.
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Rodrigues LM, Maistro S, Katayama MLH, Rocha VM, Lopez RVM, Lopes EFDT, Gonçalves FT, Fridman C, Serio PADMP, Barros LRC, Leite LAS, Segatelli V, Estevez-Diz MDP, Guindalini RSC, Ribeiro Junior U, Folgueira MAAK. Prevalence of germline variants in Brazilian pancreatic carcinoma patients. Sci Rep 2024; 14:21083. [PMID: 39256447 PMCID: PMC11387492 DOI: 10.1038/s41598-024-71884-4] [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: 05/06/2024] [Accepted: 09/02/2024] [Indexed: 09/12/2024] Open
Abstract
We evaluated the prevalence of pathogenic/likely pathogenic germline variants (PGV) in Brazilian pancreatic adenocarcinoma (PC) patients, that represent a multiethnic population, in a cross-sectional study. We included 192 PC patients unselected for family history of cancer. We evaluated a panel of 113 cancer genes, through genomic DNA sequencing and 46 ancestry-informative markers, through multiplex PCR. The median age was 61 years; 63.5% of the patients presented disease clinical stages III or IV; 8.3% reported personal history of cancer; 4.7% and 16.1% reported first-degree relatives with PC or breast and/or prostate cancer, respectively. Although the main ancestry was European, there was considerable genetic composition admixture. Twelve patients (6.25%) were PGV carriers in PC predisposition genes (ATM, BRCA1, BRCA2, CDKN2A, MSH2, PALB2) and another 25 (13.0%) were PGV carriers in genes with a limited association or not previously associated with PC (ACD, BLM, BRIP1, CHEK2, ERCC4, FANCA, FANCE, FANCM, GALNT12, MITF, MRE11, MUTYH, POLE, RAD51B, RAD51C, RECQL4, SDHA, TERF2IP). The most frequently affected genes were CHEK2, ATM and FANC. In tumor samples from PGV carriers in ACD, BRIP1, MRE11, POLE, SDHA, TERF2IP, which were examined through exome sequencing, the main single base substitutions (SBS) mutational signature was SBS1+5+18, probably associated with age, tobacco smoking and reactive oxygen species. SBS3 associated with homologous repair deficiency was also represented, but on a lower scale. There was no difference in the frequency of PGV carriers between: (a) patients with or without first-degree relatives with cancer; and (b) patients with admixed ancestry versus those with predominantly European ancestry. Furthermore, there was no difference in overall survival between PGV carriers and non-carriers. Therefore, genetic testing should be offered to all Brazilian pancreatic cancer patients, regardless of their ancestry. Genes with limited or previously unrecognized associations with pancreatic cancer should be further investigated to clarify their role in cancer risk.
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Affiliation(s)
- Lívia Munhoz Rodrigues
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil
| | - Simone Maistro
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil
| | - Maria Lucia Hirata Katayama
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil
| | - Vinícius Marques Rocha
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil
| | - Rossana Veronica Mendoza Lopez
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil
| | - Edia Filomena di Tullio Lopes
- Registro Hospitalar de Cancer, Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, São Paulo, SP, Brazil
| | - Fernanda Toledo Gonçalves
- Departamento de Medicina Legal, Bioetica, Medicina do Trabalho e Medicina Física e Reabilitação, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Sao Paulo, SP, Brazil
| | - Cintia Fridman
- Departamento de Medicina Legal, Bioetica, Medicina do Trabalho e Medicina Física e Reabilitação, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Sao Paulo, SP, Brazil
| | | | - Luciana Rodrigues Carvalho Barros
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil
| | - Luiz Antonio Senna Leite
- Departamento de Radiologia e Oncologia, Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Sao Paulo, SP, Brazil
| | - Vanderlei Segatelli
- Departamento de Patologia Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Sao Paulo, SP, Brazil
| | - Maria Del Pilar Estevez-Diz
- Departamento de Radiologia e Oncologia, Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Sao Paulo, SP, Brazil
| | | | - Ulysses Ribeiro Junior
- Division of Digestive Surgery, Department of Gastroenterology, Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo FMUSP, Sao Paulo, SP, Brazil
| | - Maria Aparecida Azevedo Koike Folgueira
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil.
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Thavaneswaran S, Lin F, Grady JP, Espinoza D, Huang ML, Chinchen S, Sebastian L, Kansara M, Mersiades T, Lee CK, Desai J, Grimison P, Brown M, Millward M, Harrup R, O'Byrne K, Nagrial A, Craft P, Simes J, Joshua AM, Thomas DM. A signal-seeking phase 2 study of Trastuzumab emtansine in tumours harbouring HER2 amplification or mutation. NPJ Precis Oncol 2024; 8:195. [PMID: 39251683 PMCID: PMC11385980 DOI: 10.1038/s41698-024-00698-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 08/29/2024] [Indexed: 09/11/2024] Open
Abstract
This single-arm phase II non-randomised trial (ACTRN12619001265167) evaluated trastuzumab emtansine in solid cancers with HER2 amplification or mutation detected by comprehensive genomic profiling. The primary objective was objective response (OR), while secondary objectives included the time to progression (TTP) on study to TTP on prior therapy ratio, progression-free survival (PFS) and overall survival (OS). The cohort included 16 tumours with HER2 mutations (group 1) and 16 with HER2 amplification (group 2). After 17 months median follow-up, ORs occurred in 19% of group 1 (1 salivary gland carcinoma (SGC), 2 lung cancers) and 25% of group 2 (3 SGCs, 1 uterine carcinoma). Fourteen of 29 TTP-evaluable patients achieved a TTP ratio ≥1.3, including 10 without an OR. Median PFS and OS were 4.5 (95% CI 2.1-7.0) and 18.2 months (95% CI 8.1-not reached) respectively. Trastuzumab emtansine showed modest ORs and a favourable change in disease trajectory in select HER2-altered solid cancers.
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Affiliation(s)
- Subotheni Thavaneswaran
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia.
- The Kinghorn Cancer Centre, St Vincent's Hospital, Sydney, NSW, Australia.
- School of Clinical Medicine, Faculty of Medicine and Health, University of NSW, Sydney, NSW, Australia.
- Garvan Institute of Medical Research, Sydney, NSW, Australia.
| | - Frank Lin
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of NSW, Sydney, NSW, Australia
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, NSW, Australia
| | - John P Grady
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - David Espinoza
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
| | - Min Li Huang
- School of Clinical Medicine, Faculty of Medicine and Health, University of NSW, Sydney, NSW, Australia
- SydPath Department of Anatomical Pathology, St Vincent's Hospital, Sydney, NSW, Australia
| | - Sarah Chinchen
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
| | - Lucille Sebastian
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
| | - Maya Kansara
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Tony Mersiades
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
| | - Chee Khoon Lee
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
| | - Jayesh Desai
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | | | | | - Michael Millward
- Linear Clinical Research & University of Western Australia, Perth, WA, Australia
| | | | - Ken O'Byrne
- Princess Alexandra Hospital and Queensland University of Technology, Brisbane, QLD, Australia
| | | | - Paul Craft
- The Canberra Hospital, Canberra, ACT, Australia
| | - John Simes
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
| | - Anthony M Joshua
- The Kinghorn Cancer Centre, St Vincent's Hospital, Sydney, NSW, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of NSW, Sydney, NSW, Australia
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - David M Thomas
- The Kinghorn Cancer Centre, St Vincent's Hospital, Sydney, NSW, Australia
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Centre for Molecular Oncology, University of New South Wales, Sydney, NSW, Australia
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6
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Lee HH, Chow KL, Wong HS, Chong TY, Wong AS, Cheng GH, Ko JM, Siu HC, Yeung MC, Huen MS, Tse KY, Bray MR, Mak TW, Leung SY, Ip PP. Inhibition of Aberrantly Overexpressed Polo-like Kinase 4 Is a Potential Effective Treatment for DNA Damage Repair-Deficient Uterine Leiomyosarcoma. Clin Cancer Res 2024; 30:3904-3918. [PMID: 38848043 PMCID: PMC11369621 DOI: 10.1158/1078-0432.ccr-23-3720] [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: 12/04/2023] [Revised: 03/13/2024] [Accepted: 06/05/2024] [Indexed: 09/04/2024]
Abstract
PURPOSE Uterine leiomyosarcoma (LMS) is an aggressive sarcoma and a subset of which exhibits DNA repair defects. Polo-like kinase 4 (PLK4) precisely modulates mitosis, and its inhibition causes chromosome missegregation and increased DNA damage. We hypothesize that PLK4 inhibition is an effective LMS treatment. EXPERIMENTAL DESIGN Genomic profiling of clinical uterine LMS samples was performed, and homologous recombination (HR) deficiency scores were calculated. A PLK4 inhibitor (CFI-400945) with and without an ataxia telangiectasia mutated (ATM) inhibitor (AZD0156) was tested in vitro on gynecologic sarcoma cell lines SK-UT-1, SKN, and SK-LMS-1. Findings were validated in vivo using the SK-UT-1 xenograft model in the Balb/c nude mouse model. The effects of CFI-400945 were also evaluated in a BRCA2-knockout SK-UT-1 cell line. The mechanisms of DNA repair were analyzed using a DNA damage reporter assay. RESULTS Uterine LMS had a high HR deficiency score, overexpressed PLK4 mRNA, and displayed mutations in genes responsible for DNA repair. CFI-400945 demonstrated effective antitumor activity in vitro and in vivo. The addition of AZD0156 resulted in drug synergism, largely due to a preference for nonhomologous end-joining DNA repair. Compared with wild-type cells, BRCA2 knockouts were more sensitive to PLK4 inhibition when both HR and nonhomologous end-joining repairs were impaired. CONCLUSIONS Uterine LMS with DNA repair defects is sensitive to PLK4 inhibition because of the effects of chromosome missegregation and increased DNA damage. Loss-of-function BRCA2 alterations or pharmacologic inhibition of ATM enhanced the efficacy of the PLK4 inhibitor. Genomic profiling of an advanced-stage or recurrent uterine LMS may guide therapy.
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Affiliation(s)
- Horace H.Y. Lee
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | - Kin Long Chow
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | - Ho Shing Wong
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | - Tsz Yan Chong
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | - Alice S.T. Wong
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | - Grace H.W. Cheng
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | - Jasmine M.K. Ko
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | - Hoi Cheong Siu
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | - Maximus C.F. Yeung
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | - Michael S.Y. Huen
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | - Ka Yu Tse
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | | | - Tak Wah Mak
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.
| | - Suet Yi Leung
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- The Jockey Club Centre for Clinical Innovation and Discovery, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Centre for PanorOmic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | - Philip P.C. Ip
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
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7
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Nesic M, Rasmussen MH, Henriksen TV, Demuth C, Frydendahl A, Nordentoft I, Dyrskjøt L, Andersen CL. Beyond basics: Key mutation selection features for successful tumor-informed ctDNA detection. Int J Cancer 2024; 155:925-933. [PMID: 38623608 DOI: 10.1002/ijc.34964] [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: 01/11/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/17/2024]
Abstract
Tumor-informed mutation-based approaches are frequently used for detection of circulating tumor DNA (ctDNA). Not all mutations make equally effective ctDNA markers. The objective was to explore if prioritizing mutations using mutational features-such as cancer cell fraction (CCF), multiplicity, and error rate-would improve the success rate of tumor-informed ctDNA analysis. Additionally, we aimed to develop a practical and easily implementable analysis pipeline for identifying and prioritizing candidate mutations from whole-exome sequencing (WES) data. We analyzed WES and ctDNA data from three tumor-informed ctDNA studies, one on bladder cancer (Cohort A) and two on colorectal cancer (Cohorts I and N). The studies included 390 patients. For each patient, a unique set of mutations (median mutations/patient: 6, interquartile 13, range: 1-46, total n = 4023) were used as markers of ctDNA. The tool PureCN was used to assess the CCF and multiplicity of each mutation. High-CCF mutations were detected more frequently than low-CCF mutations (Cohort A: odds ratio [OR] 20.6, 95% confidence interval [CI] 5.72-173, p = 1.73e-12; Cohort I: OR 2.24, 95% CI 1.44-3.52, p = 1.66e-04; and Cohort N: OR 1.78, 95% CI 1.14-2.79, p = 7.86e-03). The detection-likelihood was additionally improved by selecting mutations with multiplicity of two or above (Cohort A: OR 1.55, 95% CI 1. 14-2.11, p = 3.85e-03; Cohort I: OR 1.78, 95% CI 1.23-2.56, p = 1.34e-03; and Cohort N: OR 1.94, 95% CI 1.63-2.31, p = 2.83e-14). Furthermore, selecting the mutations for which the ctDNA detection method had the lowest error rates, additionally improved the detection-likelihood, particularly evident when plasma cell-free DNA tumor fractions were below 0.1% (p = 2.1e-07). Selecting mutational markers with high CCF, high multiplicity, and low error rate significantly improve ctDNA detection likelihood. We provide free access to the analysis pipeline enabling others to perform qualified prioritization of mutations for tumor-informed ctDNA analysis.
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Affiliation(s)
- Marijana Nesic
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Mads H Rasmussen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Tenna V Henriksen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Christina Demuth
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Amanda Frydendahl
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Claus L Andersen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
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8
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Halik A, Tilgner M, Silva P, Estrada N, Altwasser R, Jahn E, Heuser M, Hou HA, Pratcorona M, Hills RK, Metzeler KH, Fenwarth L, Dolnik A, Terre C, Kopp K, Blau O, Szyska M, Christen F, Krönke J, Vasseur L, Löwenberg B, Esteve J, Valk PJM, Duchmann M, Chou WC, Linch DC, Döhner H, Gale RE, Döhner K, Bullinger L, Yoshida K, Damm F. Genomic characterization of AML with aberrations of chromosome 7: a multinational cohort of 519 patients. J Hematol Oncol 2024; 17:70. [PMID: 39160538 PMCID: PMC11331663 DOI: 10.1186/s13045-024-01590-1] [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: 05/19/2024] [Accepted: 08/05/2024] [Indexed: 08/21/2024] Open
Abstract
BACKGROUND Deletions and partial losses of chromosome 7 (chr7) are frequent in acute myeloid leukemia (AML) and are linked to dismal outcome. However, the genomic landscape and prognostic impact of concomitant genetic aberrations remain incompletely understood. METHODS To discover genetic lesions in adult AML patients with aberrations of chromosome 7 [abn(7)], 60 paired diagnostic/remission samples were investigated by whole-exome sequencing in the exploration cohort. Subsequently, a gene panel including 66 genes and a SNP backbone for copy-number variation detection was designed and applied to the remaining samples of the validation cohort. In total, 519 patients were investigated, of which 415 received intensive induction treatment, typically containing a combination of cytarabine and anthracyclines. RESULTS In the exploration cohort, the most frequently mutated gene was TP53 (33%), followed by epigenetic regulators (DNMT3A, KMT2C, IDH2) and signaling genes (NRAS, PTPN11). Thirty percent of 519 patients harbored ≥ 1 mutation in genes located in commonly deleted regions of chr7-most frequently affecting KMT2C (16%) and EZH2 (10%). KMT2C mutations were often subclonal and enriched in patients with del(7q), de novo or core-binding factor AML (45%). Cancer cell fraction analysis and reconstruction of mutation acquisition identified TP53 mutations as mainly disease-initiating events, while del(7q) or -7 appeared as subclonal events in one-third of cases. Multivariable analysis identified five genetic lesions with significant prognostic impact in intensively treated AML patients with abn(7). Mutations in TP53 and PTPN11 (11%) showed the strongest association with worse overall survival (OS, TP53: hazard ratio [HR], 2.53 [95% CI 1.66-3.86]; P < 0.001; PTPN11: HR, 2.24 [95% CI 1.56-3.22]; P < 0.001) and relapse-free survival (RFS, TP53: HR, 2.3 [95% CI 1.25-4.26]; P = 0.008; PTPN11: HR, 2.32 [95% CI 1.33-4.04]; P = 0.003). By contrast, IDH2-mutated patients (9%) displayed prolonged OS (HR, 0.51 [95% CI 0.30-0.88]; P = 0.0015) and durable responses (RFS: HR, 0.5 [95% CI 0.26-0.96]; P = 0.036). CONCLUSION This work unraveled formerly underestimated genetic lesions and provides a comprehensive overview of the spectrum of recurrent gene mutations and their clinical relevance in AML with abn(7). KMT2C mutations are among the most frequent gene mutations in this heterogeneous AML subgroup and warrant further functional investigation.
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MESH Headings
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/mortality
- Female
- Male
- Middle Aged
- Adult
- Chromosomes, Human, Pair 7/genetics
- Aged
- Mutation
- Cohort Studies
- Young Adult
- Chromosome Aberrations
- Prognosis
- Aged, 80 and over
- Adolescent
- Exome Sequencing
- DNA Copy Number Variations
- Tumor Suppressor Protein p53/genetics
- Genomics/methods
- Protein Tyrosine Phosphatase, Non-Receptor Type 11/genetics
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Affiliation(s)
- Adriane Halik
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Marlon Tilgner
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Patricia Silva
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Natalia Estrada
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Robert Altwasser
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Ekaterina Jahn
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
- Department of Internal Medicine IV, University Hospital Halle (Saale), Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Hsin-An Hou
- Division of Hematology, Department of Internal Medicine, and Division of General Medicine, Department of Internal Medicine, National Taiwan University Hospital, No. 7, Chung Shan South Road, Taipei City, Taiwan
| | - Marta Pratcorona
- Hospital de la Santa Creu i Sant Pau. Institut de Recerca Sant Pau. Department of Medicine, Universitat Autonoma of Barcelona, Barcelona, Spain
| | - Robert K Hills
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Klaus H Metzeler
- Department of Hematology, Cell Therapy, Hemostaseology and Infectious Diseases, University Hospital Leipzig, Leipzig, Germany
| | - Laurene Fenwarth
- Unité Mixte de Recherche (UMR) 9020-UMR1277, Canther-Cancer Heterogeneity, Plasticity and Resistance to Therapies, University of Lille, Centre National de la Recherche Scientifique (CNRS), INSERM, Centre Hospitalo-Universitaire (CHU) Lille, Institut de Recherche sur le Cancer de Lille (IRCL), Lille, France
| | - Anna Dolnik
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Christine Terre
- Laboratoire de Cytogénétique, Service de Biologie, CH de Versailles, Le Chesnay, France
| | - Klara Kopp
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Olga Blau
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Martin Szyska
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Friederike Christen
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jan Krönke
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium (Deutsches Konsortium Für Translationale Krebsforschung, DKTK), Partner Site, Berlin, Germany
| | - Loïc Vasseur
- Hematology Department, Saint Louis Hospital, AP-HP, Paris, France
| | - Bob Löwenberg
- Department of Hematology, Erasmus MC Cancer Institute, and Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jordi Esteve
- Hematology Department, IDIBAPS, Hospital Clínic de Barcelona, University of Barcelona, Barcelona, Spain
| | - Peter J M Valk
- Department of Hematology, Erasmus MC Cancer Institute, and Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Matthieu Duchmann
- Institut de Recherche Saint-Louis (IRSL), Institut National de la Santé et de la Recherche Médicale (INSERM) U944, Centre National de la Recherche Scientifique (CNRS) UMR 7212 GenCellDis, Université Paris Cité, Paris, France
| | - Wen-Chien Chou
- Division of Hematology, Department of Internal Medicine, and Division of General Medicine, Department of Internal Medicine, National Taiwan University Hospital, No. 7, Chung Shan South Road, Taipei City, Taiwan
| | - David C Linch
- Department of Haematology, University College London Cancer Institute, London, UK
| | - Hartmut Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Rosemary E Gale
- Department of Haematology, University College London Cancer Institute, London, UK
| | - Konstanze Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Lars Bullinger
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium (Deutsches Konsortium Für Translationale Krebsforschung, DKTK), Partner Site, Berlin, Germany
| | - Kenichi Yoshida
- Division of Cancer Evolution, National Cancer Center Research Institute, Tokyo, Japan
| | - Frederik Damm
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
- German Cancer Consortium (Deutsches Konsortium Für Translationale Krebsforschung, DKTK), Partner Site, Berlin, Germany.
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9
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Nakazawa MS, Silverman IM, Rimkunas V, Veloso A, Glodzik D, Johnson A, Ohsumi TK, Patel SR, Conley AP, Roland CL, Soliman PT, Beird HC, Wu CC, Ingram DR, Lazcano R, Song D, Wani KM, Lazar AJ, Yap TA, Wang WL, Livingston JA. Loss of the DNA Repair Gene RNase H2 Identifies a Unique Subset of DDR-Deficient Leiomyosarcomas. Mol Cancer Ther 2024; 23:1057-1065. [PMID: 38561019 PMCID: PMC11321279 DOI: 10.1158/1535-7163.mct-23-0761] [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: 11/18/2023] [Revised: 01/26/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
Targeting the DNA damage response (DDR) pathway is an emerging therapeutic approach for leiomyosarcoma (LMS), and loss of RNase H2, a DDR pathway member, is a potentially actionable alteration for DDR-targeted treatments. Therefore, we designed a protein- and genomic-based RNase H2 screening assay to determine its prevalence and prognostic significance. Using a selective RNase H2 antibody on a pan-tumor microarray (TMA), RNase H2 loss was more common in LMS (11.5%, 9/78) than across all tumors (3.8%, 32/843). In a separate LMS cohort, RNase H2 deficiency was confirmed in uterine LMS (U-LMS, 21%, 23/108) and soft-tissue LMS (ST-LMS; 30%, 39/102). In the TCGA database, RNASEH2B homozygous deletions (HomDels) were found in 6% (5/80) of LMS cases, with a higher proportion in U-LMS (15%; 4/27) compared with ST-LMS (2%; 1/53). Using the SNiPDx targeted-NGS sequencing assay to detect biallelic loss of function in select DDR-related genes, we found RNASEH2B HomDels in 54% (19/35) of U-LMS cases with RNase H2 loss by IHC, and 7% (3/43) HomDels in RNase H2 intact cases. No RNASEH2B HomDels were detected in ST-LMS. In U-LMS patient cohort (n = 109), no significant overall survival difference was seen in patients with RNase H2 loss versus intact, or RNASEH2B HomDel (n = 12) versus Non-HomDel (n = 37). The overall diagnostic accuracy, sensitivity, and specificity of RNase H2 IHC for detecting RNA-SEH2B HomDels in U-LMS was 76%, 93%, and 71%, respectively, and it is being developed for future predictive biomarker driven clinical trials targeting DDR in U-LMS.
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Affiliation(s)
- Michael S Nakazawa
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | | | | | | | | | - Shreyaskumar R Patel
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anthony P Conley
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christina L Roland
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Pamela T Soliman
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hannah C Beird
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chia-Chin Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Davis R Ingram
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rossana Lazcano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dawon Song
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Khalida M Wani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexander J Lazar
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Timothy A Yap
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wei-Lien Wang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - J Andrew Livingston
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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10
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Prendeville S, Kaur H, Ansari S, Al Qa'qa' S, Stockley TL, Lajkosz K, van der Kwast T, Cheung CC, Selvarajah S. Somatic Tumor Testing in Prostate Cancer: Experience of a Tertiary Care Center Including Pathologist-Driven Reflex Testing of Localized Tumors at Diagnosis. Mod Pathol 2024; 37:100489. [PMID: 38588883 DOI: 10.1016/j.modpat.2024.100489] [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: 11/19/2023] [Revised: 02/17/2024] [Accepted: 03/15/2024] [Indexed: 04/10/2024]
Abstract
Somatic tumor testing in prostate cancer (PCa) can guide treatment options by identifying clinically actionable variants in DNA damage repair genes, including acquired variants not detected using germline testing alone. Guidelines currently recommend performing somatic tumor testing in metastatic PCa, whereas there is no consensus on the role of testing in regional disease, and the optimal testing strategy is only evolving. This study evaluates the frequency, distribution, and pathologic correlates of somatic DNA damage repair mutations in metastatic and localized PCa following the implementation of pathologist-driven reflex testing at diagnosis. A cohort of 516 PCa samples were sequenced using a custom next-generation sequencing panel including homologous recombination repair and mismatch repair genes. Variants were classified based on the Association for Molecular Pathology/American Society of Clinical Oncology/College of American Pathologists guidelines. In total, 183 (35.5%) patients had at least one variant, which is as follows: 72 of 516 (13.9%) patients had at least 1 tier I or tier II variant, whereas 111 of 516 (21.5%) patients had a tier III variant. Tier I/II variant(s) were identified in 27% (12/44) of metastatic biopsy samples and 13% (61/472) of primary samples. Overall, 12% (62/516) of patients had at least 1 tier I/II variant in a homologous recombination repair gene, whereas 2.9% (10/516) had at least 1 tier I/II variant in a mismatch repair gene. The presence of a tier I/II variant was not significantly associated with the grade group (GG) or presence of intraductal/cribriform carcinoma in the primary tumor. Among the 309 reflex-tested hormone-naive primary tumors, tier I/II variants were identified in 10% (31/309) of cases, which is as follows: 9.2% (9/98) GG2; 9% (9/100) GG3; 9.1% (4/44) GG4; and 13.4% (9/67) GG5 cases. Our findings confirm the use of somatic tumor testing in detecting variants of clinical significance in PCa and provide insights that can inform the design of testing strategies. Pathologist-initiated reflex testing streamlines the availability of the results for clinical decision-making; however, pathologic parameters such as GG and the presence of intraductal/cribriform carcinoma may not be reliable to guide patient selection.
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Affiliation(s)
- Susan Prendeville
- Division of Anatomic Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
| | - Harpreet Kaur
- Division of Genome Diagnostics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Shervin Ansari
- Division of Genome Diagnostics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Shifaa' Al Qa'qa'
- Division of Anatomic Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Pathology and Forensic Medicine, Faculty of Medicine, Al-Balqa Applied University, Al-Salt, Jordan
| | - Tracy L Stockley
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Division of Genome Diagnostics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Katherine Lajkosz
- Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Theodorus van der Kwast
- Division of Anatomic Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Carol C Cheung
- Division of Anatomic Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Shamini Selvarajah
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Division of Genome Diagnostics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
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11
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Ingels J, De Cock L, Stevens D, Mayer RL, Théry F, Sanchez GS, Vermijlen D, Weening K, De Smet S, Lootens N, Brusseel M, Verstraete T, Buyle J, Van Houtte E, Devreker P, Heyns K, De Munter S, Van Lint S, Goetgeluk G, Bonte S, Billiet L, Pille M, Jansen H, Pascal E, Deseins L, Vantomme L, Verdonckt M, Roelandt R, Eekhout T, Vandamme N, Leclercq G, Taghon T, Kerre T, Vanommeslaeghe F, Dhondt A, Ferdinande L, Van Dorpe J, Desender L, De Ryck F, Vermassen F, Surmont V, Impens F, Menten B, Vermaelen K, Vandekerckhove B. Neoantigen-targeted dendritic cell vaccination in lung cancer patients induces long-lived T cells exhibiting the full differentiation spectrum. Cell Rep Med 2024; 5:101516. [PMID: 38626769 PMCID: PMC11148567 DOI: 10.1016/j.xcrm.2024.101516] [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: 09/19/2023] [Revised: 02/09/2024] [Accepted: 03/25/2024] [Indexed: 05/24/2024]
Abstract
Non-small cell lung cancer (NSCLC) is known for high relapse rates despite resection in early stages. Here, we present the results of a phase I clinical trial in which a dendritic cell (DC) vaccine targeting patient-individual neoantigens is evaluated in patients with resected NSCLC. Vaccine manufacturing is feasible in six of 10 enrolled patients. Toxicity is limited to grade 1-2 adverse events. Systemic T cell responses are observed in five out of six vaccinated patients, with T cell responses remaining detectable up to 19 months post vaccination. Single-cell analysis indicates that the responsive T cell population is polyclonal and exhibits the near-entire spectrum of T cell differentiation states, including a naive-like state, but excluding exhausted cell states. Three of six vaccinated patients experience disease recurrence during the follow-up period of 2 years. Collectively, these data support the feasibility, safety, and immunogenicity of this treatment in resected NSCLC.
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Affiliation(s)
- Joline Ingels
- Department of Diagnostic Sciences, Ghent University, 9000 Ghent, East-Flanders, Belgium; Cancer Research Institute Ghent (CRIG), 9000 Ghent, Easy-Flanders, Belgium
| | - Laurenz De Cock
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Easy-Flanders, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, East-Flanders, Belgium
| | - Dieter Stevens
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Easy-Flanders, Belgium; Respiratory Medicine, Ghent University Hospital, 9000 Ghent, East-Flanders, Belgium
| | - Rupert L Mayer
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Easy-Flanders, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, East-Flanders, Belgium; VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, East-Flanders, Belgium
| | - Fabien Théry
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, East-Flanders, Belgium; VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, East-Flanders, Belgium
| | - Guillem Sanchez Sanchez
- Department of Pharmacotherapy and Pharmaceutics, Université Libre de Bruxelles, 1050 Brussels, Brussels, Belgium; Institute for Medical Immunology, Université Libre de Bruxelles, 1050 Brussels, Brussels, Belgium; Université Libre de Bruxelles Center for Research in Immunology, Université Libre de Bruxelles, 1050 Brussels, Brussels, Belgium; WELBIO Department, WEL Research Institute, 1300 Wavre, Walloon Brabant, Belgium
| | - David Vermijlen
- Department of Pharmacotherapy and Pharmaceutics, Université Libre de Bruxelles, 1050 Brussels, Brussels, Belgium; Institute for Medical Immunology, Université Libre de Bruxelles, 1050 Brussels, Brussels, Belgium; Université Libre de Bruxelles Center for Research in Immunology, Université Libre de Bruxelles, 1050 Brussels, Brussels, Belgium; WELBIO Department, WEL Research Institute, 1300 Wavre, Walloon Brabant, Belgium
| | - Karin Weening
- Department of Diagnostic Sciences, Ghent University, 9000 Ghent, East-Flanders, Belgium
| | - Saskia De Smet
- GMP Unit Cell Therapy, Ghent University Hospital, 9000 Ghent, East-Flanders, Belgium
| | - Nele Lootens
- GMP Unit Cell Therapy, Ghent University Hospital, 9000 Ghent, East-Flanders, Belgium
| | - Marieke Brusseel
- GMP Unit Cell Therapy, Ghent University Hospital, 9000 Ghent, East-Flanders, Belgium
| | - Tasja Verstraete
- Respiratory Medicine, Ghent University Hospital, 9000 Ghent, East-Flanders, Belgium
| | - Jolien Buyle
- Respiratory Medicine, Ghent University Hospital, 9000 Ghent, East-Flanders, Belgium
| | - Eva Van Houtte
- GMP Unit Cell Therapy, Ghent University Hospital, 9000 Ghent, East-Flanders, Belgium
| | - Pam Devreker
- GMP Unit Cell Therapy, Ghent University Hospital, 9000 Ghent, East-Flanders, Belgium
| | - Kelly Heyns
- GMP Unit Cell Therapy, Ghent University Hospital, 9000 Ghent, East-Flanders, Belgium
| | - Stijn De Munter
- Department of Diagnostic Sciences, Ghent University, 9000 Ghent, East-Flanders, Belgium; Cancer Research Institute Ghent (CRIG), 9000 Ghent, Easy-Flanders, Belgium
| | - Sandra Van Lint
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Easy-Flanders, Belgium; Respiratory Medicine, Ghent University Hospital, 9000 Ghent, East-Flanders, Belgium
| | - Glenn Goetgeluk
- Department of Diagnostic Sciences, Ghent University, 9000 Ghent, East-Flanders, Belgium
| | - Sarah Bonte
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Easy-Flanders, Belgium; VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, East-Flanders, Belgium
| | - Lore Billiet
- Department of Diagnostic Sciences, Ghent University, 9000 Ghent, East-Flanders, Belgium; Cancer Research Institute Ghent (CRIG), 9000 Ghent, Easy-Flanders, Belgium
| | - Melissa Pille
- Department of Diagnostic Sciences, Ghent University, 9000 Ghent, East-Flanders, Belgium
| | - Hanne Jansen
- Department of Diagnostic Sciences, Ghent University, 9000 Ghent, East-Flanders, Belgium
| | - Eva Pascal
- Department of Diagnostic Sciences, Ghent University, 9000 Ghent, East-Flanders, Belgium; Cancer Research Institute Ghent (CRIG), 9000 Ghent, Easy-Flanders, Belgium
| | - Lucas Deseins
- Department of Diagnostic Sciences, Ghent University, 9000 Ghent, East-Flanders, Belgium; Cancer Research Institute Ghent (CRIG), 9000 Ghent, Easy-Flanders, Belgium
| | - Lies Vantomme
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, East-Flanders, Belgium
| | - Maarten Verdonckt
- Department of Diagnostic Sciences, Ghent University, 9000 Ghent, East-Flanders, Belgium
| | - Ria Roelandt
- VIB Single Cell Core, VIB, 9000/3000 Ghent/Leuven, East-Flanders/Flemish Brabant, Belgium
| | - Thomas Eekhout
- VIB Single Cell Core, VIB, 9000/3000 Ghent/Leuven, East-Flanders/Flemish Brabant, Belgium
| | - Niels Vandamme
- VIB Single Cell Core, VIB, 9000/3000 Ghent/Leuven, East-Flanders/Flemish Brabant, Belgium
| | - Georges Leclercq
- Department of Diagnostic Sciences, Ghent University, 9000 Ghent, East-Flanders, Belgium
| | - Tom Taghon
- Department of Diagnostic Sciences, Ghent University, 9000 Ghent, East-Flanders, Belgium
| | - Tessa Kerre
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Easy-Flanders, Belgium; VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, East-Flanders, Belgium; Hematology, Ghent University Hospital, 9000 Ghent, East-Flanders, Belgium
| | - Floris Vanommeslaeghe
- Nephrology, Ghent University Hospital, Ghent University, 9000 Ghent, East-Flanders, Belgium
| | - Annemieke Dhondt
- Nephrology, Ghent University Hospital, Ghent University, 9000 Ghent, East-Flanders, Belgium
| | - Liesbeth Ferdinande
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Easy-Flanders, Belgium; Pathology, Ghent University Hospital, 9000 Ghent, East-Flanders, Belgium
| | - Jo Van Dorpe
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Easy-Flanders, Belgium; Pathology, Ghent University Hospital, 9000 Ghent, East-Flanders, Belgium
| | - Liesbeth Desender
- Thoracic and Vascular Surgery, Ghent University Hospital, 9000 Ghent, East-Flanders, Belgium
| | - Frederic De Ryck
- Thoracic and Vascular Surgery, Ghent University Hospital, 9000 Ghent, East-Flanders, Belgium
| | - Frank Vermassen
- Thoracic and Vascular Surgery, Ghent University Hospital, 9000 Ghent, East-Flanders, Belgium
| | - Veerle Surmont
- Respiratory Medicine, Ghent University Hospital, 9000 Ghent, East-Flanders, Belgium
| | - Francis Impens
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, East-Flanders, Belgium; VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, East-Flanders, Belgium
| | - Björn Menten
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Easy-Flanders, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, East-Flanders, Belgium
| | - Karim Vermaelen
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Easy-Flanders, Belgium; Respiratory Medicine, Ghent University Hospital, 9000 Ghent, East-Flanders, Belgium.
| | - Bart Vandekerckhove
- Department of Diagnostic Sciences, Ghent University, 9000 Ghent, East-Flanders, Belgium; Cancer Research Institute Ghent (CRIG), 9000 Ghent, Easy-Flanders, Belgium; GMP Unit Cell Therapy, Ghent University Hospital, 9000 Ghent, East-Flanders, Belgium.
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12
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Wang K, Zerdes I, Johansson HJ, Sarhan D, Sun Y, Kanellis DC, Sifakis EG, Mezheyeuski A, Liu X, Loman N, Hedenfalk I, Bergh J, Bartek J, Hatschek T, Lehtiö J, Matikas A, Foukakis T. Longitudinal molecular profiling elucidates immunometabolism dynamics in breast cancer. Nat Commun 2024; 15:3837. [PMID: 38714665 PMCID: PMC11076527 DOI: 10.1038/s41467-024-47932-y] [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: 05/08/2023] [Accepted: 04/12/2024] [Indexed: 05/10/2024] Open
Abstract
Although metabolic reprogramming within tumor cells and tumor microenvironment (TME) is well described in breast cancer, little is known about how the interplay of immune state and cancer metabolism evolves during treatment. Here, we characterize the immunometabolic profiles of tumor tissue samples longitudinally collected from individuals with breast cancer before, during and after neoadjuvant chemotherapy (NAC) using proteomics, genomics and histopathology. We show that the pre-, on-treatment and dynamic changes of the immune state, tumor metabolic proteins and tumor cell gene expression profiling-based metabolic phenotype are associated with treatment response. Single-cell/nucleus RNA sequencing revealed distinct tumor and immune cell states in metabolism between cold and hot tumors. Potential drivers of NAC based on above analyses were validated in vitro. In summary, the study shows that the interaction of tumor-intrinsic metabolic states and TME is associated with treatment outcome, supporting the concept of targeting tumor metabolism for immunoregulation.
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Affiliation(s)
- Kang Wang
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Ioannis Zerdes
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Theme Cancer, Karolinska University Hospital and Karolinska Comprehensive Cancer Center, Stockholm, Sweden
| | - Henrik J Johansson
- Department of Oncology-Pathology, Karolinska Institutet, and Science for Life Laboratory, Stockholm, Sweden
| | - Dhifaf Sarhan
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Yizhe Sun
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Dimitris C Kanellis
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Artur Mezheyeuski
- Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, Uppsala, Sweden
- Molecular Oncology Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Xingrong Liu
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Niklas Loman
- Department of Hematology, Oncology and Radiation Physics, Lund University Hospital, Lund, Sweden
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Ingrid Hedenfalk
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Jonas Bergh
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Breast Center, Theme Cancer, Karolinska University Hospital and Karolinska Comprehensive Cancer Center, Stockholm, Sweden
| | - Jiri Bartek
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Danish Cancer Institute, DK-2100, Copenhagen, Denmark
| | - Thomas Hatschek
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Breast Center, Theme Cancer, Karolinska University Hospital and Karolinska Comprehensive Cancer Center, Stockholm, Sweden
| | - Janne Lehtiö
- Department of Oncology-Pathology, Karolinska Institutet, and Science for Life Laboratory, Stockholm, Sweden
- Division of Pathology, Karolinska University Hospital and Karolinska Comprehensive Cancer Center, Stockholm, Sweden
| | - Alexios Matikas
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Breast Center, Theme Cancer, Karolinska University Hospital and Karolinska Comprehensive Cancer Center, Stockholm, Sweden
| | - Theodoros Foukakis
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
- Breast Center, Theme Cancer, Karolinska University Hospital and Karolinska Comprehensive Cancer Center, Stockholm, Sweden.
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13
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Pei G, Sun K, Yang Y, Wang S, Li M, Ma X, Wang H, Chen L, Qin J, Cao S, Liu J, Huang Y. Classification of multiple primary lung cancer in patients with multifocal lung cancer: assessment of a machine learning approach using multidimensional genomic data. Front Oncol 2024; 14:1388575. [PMID: 38764572 PMCID: PMC11100425 DOI: 10.3389/fonc.2024.1388575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 04/08/2024] [Indexed: 05/21/2024] Open
Abstract
Background Multiple primary lung cancer (MPLC) is an increasingly well-known clinical phenomenon. However, its molecular characterizations are poorly understood, and still lacks of effective method to distinguish it from intrapulmonary metastasis (IM). Herein, we propose an identification model based on molecular multidimensional analysis in order to accurately optimize treatment. Methods A total of 112 Chinese lung cancers harboring at least two tumors (n = 270) were enrolled. We retrospectively selected 74 patients with 121 tumor pairs and randomly divided the tumor pairs into a training cohort and a test cohort in a 7:3 ratio. A novel model was established in training cohort, optimized for MPLC identification using comprehensive genomic profiling analyzed by a broad panel with 808 cancer-related genes, and evaluated in the test cohort and a prospective validation cohort of 38 patients with 112 tumors. Results We found differences in molecular characterizations between the two diseases and rigorously selected the characterizations to build an identification model. We evaluated the performance of the classifier using the test cohort data and observed an 89.5% percent agreement (PA) for MPLC and a 100.0% percent agreement for IM. The model showed an excellent area under the curve (AUC) of 0.947 and a 91.3% overall accuracy. Similarly, the assay achieved a considerable performance in the independent validation set with an AUC of 0.938 and an MPLC predictive value of 100%. More importantly, the MPLC predictive value of the classification achieved 100% in both the test set and validation cohort. Compared to our previous mutation-based method, the classifier showed better κ consistencies with clinical classification among all 112 patients (0.84 vs. 0.65, p <.01). Conclusion These data provide novel evidence of MPLC-specific genomic characteristics and demonstrate that our one-step molecular classifier can accurately classify multifocal lung tumors as MPLC or IM, which suggested that broad panel NGS may be a useful tool for assisting with differential diagnoses.
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Affiliation(s)
- Guotian Pei
- Department of Thoracic Surgery, Beijing Haidian Hospital (Haidian Section of Peking University Third Hospital), Beijing, China
| | - Kunkun Sun
- Department of Pathology, Peking University People’s Hospital, Beijing, China
| | - Yingshun Yang
- Department of Thoracic Surgery, Beijing Haidian Hospital (Haidian Section of Peking University Third Hospital), Beijing, China
| | - Shuai Wang
- Department of Thoracic Surgery, Beijing Haidian Hospital (Haidian Section of Peking University Third Hospital), Beijing, China
| | - Mingwei Li
- Department of Medical Affairs, Acornmed Biotechnology Co., Ltd, Beijing, China
| | - Xiaoxue Ma
- Department of Medical Affairs, Acornmed Biotechnology Co., Ltd, Beijing, China
| | - Huina Wang
- Department of Medical Affairs, Acornmed Biotechnology Co., Ltd, Beijing, China
| | - Libin Chen
- Department of Medical Affairs, Acornmed Biotechnology Co., Ltd, Beijing, China
| | - Jiayue Qin
- Department of Medical Affairs, Acornmed Biotechnology Co., Ltd, Beijing, China
| | - Shanbo Cao
- Department of Medical Affairs, Acornmed Biotechnology Co., Ltd, Beijing, China
| | - Jun Liu
- Department of Thoracic Surgery, Beijing Haidian Hospital (Haidian Section of Peking University Third Hospital), Beijing, China
| | - Yuqing Huang
- Department of Thoracic Surgery, Beijing Haidian Hospital (Haidian Section of Peking University Third Hospital), Beijing, China
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14
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Liu Y, Bi X, Leng Y, Chen D, Wang J, Ma Y, Zhang MZ, Han BW, Li Y. A deep-learning-based genomic status estimating framework for homologous recombination deficiency detection from low-pass whole genome sequencing. Heliyon 2024; 10:e26121. [PMID: 38404843 PMCID: PMC10884843 DOI: 10.1016/j.heliyon.2024.e26121] [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: 12/11/2023] [Accepted: 02/07/2024] [Indexed: 02/27/2024] Open
Abstract
Genome-wide sequencing allows for prediction of clinical treatment responses and outcomes by estimating genomic status. Here, we developed Genomic Status scan (GSscan), a long short-term memory (LSTM)-based deep-learning framework, which utilizes low-pass whole genome sequencing (WGS) data to capture genomic instability-related features. In this study, GSscan directly surveys homologous recombination deficiency (HRD) status independent of other existing biomarkers. In breast cancer, GSscan achieved an AUC of 0.980 in simulated low-pass WGS data, and obtained a higher HRD risk score in clinical BRCA-deficient breast cancer samples (p = 1.3 × 10-4, compared with BRCA-intact samples). In ovarian cancer, GSscan obtained higher HRD risk scores in BRCA-deficient samples in both simulated data and clinical samples (p = 2.3 × 10-5 and p = 0.039, respectively, compared with BRCA-intact samples). Moreover, HRD-positive patients predicted by GSscan showed longer progression-free intervals in TCGA datasets (p = 0.0011) treated with platinum-based adjuvant chemotherapy, outperforming existing low-pass WGS-based methods. Furthermore, GSscan can accurately predict HRD status using only 1 ng of input DNA and a minimum sequencing coverage of 0.02 × , providing a reliable, accessible, and cost-effective approach. In summary, GSscan effectively and accurately detected HRD status, and provide a broadly applicable framework for disease diagnosis and selecting appropriate disease treatment.
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Affiliation(s)
- Yang Liu
- Department of BC Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xiang Bi
- Department of Breast Surgery, Yantai Yuhuangding Hospital, Yantai, Shandong, China
| | - Yang Leng
- Guangdong Jiyin Biotech Co. Ltd, Shenzhen, Guangdong, China
| | - Dan Chen
- Guangdong Jiyin Biotech Co. Ltd, Shenzhen, Guangdong, China
| | - Juan Wang
- Guangdong Jiyin Biotech Co. Ltd, Shenzhen, Guangdong, China
| | - Youjia Ma
- Guangdong Jiyin Biotech Co. Ltd, Shenzhen, Guangdong, China
| | - Min-Zhe Zhang
- GeneGenieDx Corp, 160 E Tasman Dr, San Jose, CA, USA
| | - Bo-Wei Han
- Guangdong Jiyin Biotech Co. Ltd, Shenzhen, Guangdong, China
| | - Yalun Li
- Department of Breast Surgery, Yantai Yuhuangding Hospital, Yantai, Shandong, China
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15
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Henriksen TV, Demuth C, Frydendahl A, Nors J, Nesic M, Rasmussen MH, Reinert T, Larsen OH, Jaensch C, Løve US, Andersen PV, Kolbro T, Thorlacius-Ussing O, Monti A, Gögenur M, Kildsig J, Bondeven P, Schlesinger NH, Iversen LH, Gotschalck KA, Andersen CL. Unraveling the potential clinical utility of circulating tumor DNA detection in colorectal cancer-evaluation in a nationwide Danish cohort. Ann Oncol 2024; 35:229-239. [PMID: 37992872 DOI: 10.1016/j.annonc.2023.11.009] [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: 06/19/2023] [Revised: 09/29/2023] [Accepted: 11/13/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Increasingly, circulating tumor DNA (ctDNA) is proposed as a tool for minimal residual disease (MRD) assessment. Digital PCR (dPCR) offers low analysis costs and turnaround times of less than a day, making it ripe for clinical implementation. Here, we used tumor-informed dPCR for ctDNA detection in a large colorectal cancer (CRC) cohort to evaluate the potential for post-operative risk assessment and serial monitoring, and how the metastatic site may impact ctDNA detection. Additionally, we assessed how altering the ctDNA-calling algorithm could customize performance for different clinical settings. PATIENTS AND METHODS Stage II-III CRC patients (N = 851) treated with a curative intent were recruited. Based on whole-exome sequencing on matched tumor and germline DNA, a mutational target was selected for dPCR analysis. Plasma samples (8 ml) were collected within 60 days after operation and-for a patient subset (n = 246)-every 3-4 months for up to 36 months. Single-target dPCR was used for ctDNA detection. RESULTS Both post-operative and serial ctDNA detection were prognostic of recurrence [hazard ratio (HR) = 11.3, 95% confidence interval (CI) 7.8-16.4, P < 0.001; HR = 30.7, 95% CI 20.2-46.7, P < 0.001], with a cumulative ctDNA detection rate of 87% at the end of sample collection in recurrence patients. The ctDNA growth rate was prognostic of survival (HR = 2.6, 95% CI 1.5-4.4, P = 0.001). In recurrence patients, post-operative ctDNA detection was challenging for lung metastases (4/21 detected) and peritoneal metastases (2/10 detected). By modifying the cut-off for calling a sample ctDNA positive, we were able to adjust the sensitivity and specificity of our test for different clinical contexts. CONCLUSIONS The presented results from 851 stage II-III CRC patients demonstrate that our personalized dPCR approach effectively detects MRD after operation and shows promise for serial ctDNA detection for recurrence surveillance. The ability to adjust sensitivity and specificity shows exciting potential to customize the ctDNA caller for specific clinical settings.
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Affiliation(s)
- T V Henriksen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus
| | - C Demuth
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus
| | - A Frydendahl
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus
| | - J Nors
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus
| | - M Nesic
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus
| | - M H Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus
| | - T Reinert
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus
| | - O H Larsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus
| | - C Jaensch
- Department of Surgery, Regional Hospital Gødstrup, Herning
| | - U S Løve
- Department of Surgery, Regional Hospital Viborg, Viborg
| | - P V Andersen
- Department of Surgery, Odense University Hospital, Odense
| | - T Kolbro
- Department of Surgery, Odense University Hospital, Svendborg
| | | | - A Monti
- Department of Surgery, North Denmark Regional Hospital Hjørring, Hjørring
| | - M Gögenur
- Center for Surgical Sciences, Zealand University Hospital, Køge
| | - J Kildsig
- Department of Surgery, Copenhagen University Hospital, Herlev
| | - P Bondeven
- Department of Surgery, Regional Hospital Randers, Randers
| | - N H Schlesinger
- Department of Surgery, Copenhagen University Hospital, Bispebjerg
| | - L H Iversen
- Department of Surgery, Aarhus University Hospital, Aarhus
| | - K A Gotschalck
- Department of Surgery, Regional Hospital Horsens, Horsens, Denmark
| | - C L Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus.
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16
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Fukuhara M, Urabe Y, Nakahara H, Ishikawa A, Ishibashi K, Konishi H, Mizuno J, Tanaka H, Tsuboi A, Yamashita K, Hiyama Y, Takigawa H, Kotachi T, Yuge R, Hayes CN, Oka S. Clinicopathological and genomic features of superficial esophageal squamous cell carcinomas in nondrinker, nonsmoker females. Cancer Med 2024; 13:e7078. [PMID: 38457229 PMCID: PMC10923044 DOI: 10.1002/cam4.7078] [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: 07/24/2023] [Revised: 12/02/2023] [Accepted: 01/26/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) is sometimes detected in non-drinker and non-smoker females who are considered to have very low risk of ESCC development in daily practice. This study examined the clinicopathological and genomic characteristics of ESCCs in females with no history of drinking and smoking. METHODS The sample comprised 118 ESCC lesions occurring in 95 female patients who underwent endoscopic submucosal dissection at our department between January 2008 and December 2019. The patients were categorized into two groups: 51 lesions in 49 patients with no history of drinking and smoking (nondrinker/nonsmoker [NDNS] group) and 69 lesions in 45 patients with a history of drinking or smoking (drinker/smoker [DS] group). We analyzed the differences in clinicopathological and cancerous genomic characteristics between the groups. Significant genomic alterations were validated using immunohistochemistry. RESULTS Multiple logistic regression revealed that older age, fewer multiple Lugol-voiding lesions (LVLs), and reflux esophagitis (RE) were independently associated with the occurrence of ESCCs in the NDNS group. ESCC lesions in the NDNS group were predominantly located in the mid-thoracic esophagus, posterior wall side, with 0-IIa, the aspect ratio of the lesion >2 (vertical/horizontal), and endoscopic keratinization. Genetic analysis showed that CDKN2A driver alterations were significantly more frequent and KMT2D alterations were significantly less frequent in the NDNS group than in the DS group. KMT2D alterations were strongly correlated with immunostaining. CONCLUSION Older nondrinker, nonsmoker females with RE and fewer multiple LVLs may develop longitudinal 0-IIa ESCC with keratinization of the posterior wall of the mid-thoracic esophagus. ESCCs in nondrinker, nonsmoker females had fewer KMT2D alterations and more CDKN2A alterations, which may be a biomarker for treatment.
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Affiliation(s)
- Motomitsu Fukuhara
- Department of GastroenterologyGraduate School of Biomedical and Health Sciences, Hiroshima UniversityHiroshimaJapan
| | - Yuji Urabe
- Gastrointestinal Endoscopy and MedicineHiroshima University HospitalHiroshimaJapan
| | - Hikaru Nakahara
- Department of GastroenterologyGraduate School of Biomedical and Health Sciences, Hiroshima UniversityHiroshimaJapan
| | - Akira Ishikawa
- Department of Molecular PathologyGraduate School of Biomedical and Health Sciences, Hiroshima UniversityHiroshimaJapan
| | - Kazuki Ishibashi
- Department of GastroenterologyGraduate School of Biomedical and Health Sciences, Hiroshima UniversityHiroshimaJapan
| | - Hirona Konishi
- Department of GastroenterologyGraduate School of Biomedical and Health Sciences, Hiroshima UniversityHiroshimaJapan
| | - Junichi Mizuno
- Department of GastroenterologyGraduate School of Biomedical and Health Sciences, Hiroshima UniversityHiroshimaJapan
| | - Hidenori Tanaka
- Department of EndoscopyHiroshima University HospitalHiroshimaJapan
| | - Akiyoshi Tsuboi
- Department of EndoscopyHiroshima University HospitalHiroshimaJapan
| | - Ken Yamashita
- Department of EndoscopyHiroshima University HospitalHiroshimaJapan
| | - Yuichi Hiyama
- Department of Clinical Research CenterHiroshima University HospitalHiroshimaJapan
| | | | - Takahiro Kotachi
- Department of EndoscopyHiroshima University HospitalHiroshimaJapan
| | - Ryo Yuge
- Department of EndoscopyHiroshima University HospitalHiroshimaJapan
| | - C. Nelson Hayes
- Department of GastroenterologyGraduate School of Biomedical and Health Sciences, Hiroshima UniversityHiroshimaJapan
| | - Shiro Oka
- Department of GastroenterologyGraduate School of Biomedical and Health Sciences, Hiroshima UniversityHiroshimaJapan
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17
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Nguyen MTN, Rajavuori A, Huhtinen K, Hietanen S, Hynninen J, Oikkonen J, Hautaniemi S. Circulating tumor DNA-based copy-number profiles enable monitoring treatment effects during therapy in high-grade serous carcinoma. Biomed Pharmacother 2023; 168:115630. [PMID: 37806091 DOI: 10.1016/j.biopha.2023.115630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/23/2023] [Accepted: 10/03/2023] [Indexed: 10/10/2023] Open
Abstract
Circulating tumor DNA (ctDNA) analysis has emerged as a promising tool for detecting and profiling longitudinal genomics changes in cancer. While copy-number alterations (CNAs) play a major role in cancers, treatment effect monitoring using copy-number profiles has received limited attention as compared to mutations. A major reason for this is the insensitivity of CNA analysis for the real-life tumor-fraction ctDNA samples. We performed copy-number analysis on 152 plasma samples obtained from 29 patients with high-grade serous ovarian cancer (HGSC) using a sequencing panel targeting over 500 genes. Twenty-one patients had temporally matched tissue and plasma sample pairs, which enabled assessing concordance with tissues sequenced with the same panel or whole-genome sequencing and to evaluate sensitivity. Our approach could detect concordant CNA profiles in most plasma samples with as low as 5% tumor content and highly amplified regions in samples with ∼1% of tumor content. Longitudinal profiles showed changes in the CNA profiles in seven out of 11 patients with high tumor-content plasma samples at relapse. These changes included focal acquired or lost copy-numbers, even though most of the genome remained stable. Two patients displayed major copy-number profile changes during therapy. Our analysis revealed ctDNA-detectable subclonal selection resulting from both surgical operations and chemotherapy. Overall, longitudinal ctDNA data showed acquired and diminished CNAs at relapse when compared to pre-treatment samples. These results highlight the importance of genomic profiling during treatment as well as underline the usability of ctDNA.
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Affiliation(s)
- Mai T N Nguyen
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki 00291, Finland
| | - Anna Rajavuori
- Department of Obstetrics and Gynecology, Turku University Hospital, Kiinamyllynkatu 4, Turku 20521, Finland
| | - Kaisa Huhtinen
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki 00291, Finland; Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, Turku 20014, Finland
| | - Sakari Hietanen
- Department of Obstetrics and Gynecology, Turku University Hospital, Kiinamyllynkatu 4, Turku 20521, Finland
| | - Johanna Hynninen
- Department of Obstetrics and Gynecology, Turku University Hospital, Kiinamyllynkatu 4, Turku 20521, Finland
| | - Jaana Oikkonen
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki 00291, Finland.
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki 00291, Finland.
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18
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He F, Bandyopadhyay AM, Klesse LJ, Rogojina A, Chun SH, Butler E, Hartshorne T, Holland T, Garcia D, Weldon K, Prado LNP, Langevin AM, Grimes AC, Sugalski A, Shah S, Assanasen C, Lai Z, Zou Y, Kurmashev D, Xu L, Xie Y, Chen Y, Wang X, Tomlinson GE, Skapek SX, Houghton PJ, Kurmasheva RT, Zheng S. Genomic profiling of subcutaneous patient-derived xenografts reveals immune constraints on tumor evolution in childhood solid cancer. Nat Commun 2023; 14:7600. [PMID: 37990009 PMCID: PMC10663468 DOI: 10.1038/s41467-023-43373-1] [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: 03/29/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023] Open
Abstract
Subcutaneous patient-derived xenografts (PDXs) are an important tool for childhood cancer research. Here, we describe a resource of 68 early passage PDXs established from 65 pediatric solid tumor patients. Through genomic profiling of paired PDXs and patient tumors (PTs), we observe low mutational similarity in about 30% of the PT/PDX pairs. Clonal analysis in these pairs show an aggressive PT minor subclone seeds the major clone in the PDX. We show evidence that this subclone is more immunogenic and is likely suppressed by immune responses in the PT. These results suggest interplay between intratumoral heterogeneity and antitumor immunity may underlie the genetic disparity between PTs and PDXs. We further show that PDXs generally recapitulate PTs in copy number and transcriptomic profiles. Finally, we report a gene fusion LRPAP1-PDGFRA. In summary, we report a childhood cancer PDX resource and our study highlights the role of immune constraints on tumor evolution.
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Affiliation(s)
- Funan He
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Population Health Sciences, University of Texas Health Science Center, San Antonio, TX, USA
| | - Abhik M Bandyopadhyay
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Laura J Klesse
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Gill Center for Cancer and Blood Disorders, Children's Health Children's Medical Center, Dallas, TX, USA
| | - Anna Rogojina
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Sang H Chun
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Erin Butler
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Gill Center for Cancer and Blood Disorders, Children's Health Children's Medical Center, Dallas, TX, USA
| | - Taylor Hartshorne
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Trevor Holland
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Dawn Garcia
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Korri Weldon
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Luz-Nereida Perez Prado
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Anne-Marie Langevin
- Department of Pediatrics, University of Texas Health Science Center, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
| | - Allison C Grimes
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Pediatrics, University of Texas Health Science Center, San Antonio, TX, USA
| | - Aaron Sugalski
- Department of Pediatrics, University of Texas Health Science Center, San Antonio, TX, USA
| | - Shafqat Shah
- Department of Pediatrics, University of Texas Health Science Center, San Antonio, TX, USA
| | - Chatchawin Assanasen
- Department of Pediatrics, University of Texas Health Science Center, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
| | - Zhao Lai
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Yi Zou
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Dias Kurmashev
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Lin Xu
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yang Xie
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yidong Chen
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Population Health Sciences, University of Texas Health Science Center, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
| | - Xiaojing Wang
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Population Health Sciences, University of Texas Health Science Center, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
| | - Gail E Tomlinson
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Pediatrics, University of Texas Health Science Center, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
| | - Stephen X Skapek
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Gill Center for Cancer and Blood Disorders, Children's Health Children's Medical Center, Dallas, TX, USA
| | - Peter J Houghton
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Raushan T Kurmasheva
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA.
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA.
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA.
| | - Siyuan Zheng
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA.
- Department of Population Health Sciences, University of Texas Health Science Center, San Antonio, TX, USA.
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA.
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19
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Fitzpatrick A, Iravani M, Mills A, Vicente D, Alaguthurai T, Roxanis I, Turner NC, Haider S, Tutt ANJ, Isacke CM. Genomic profiling and pre-clinical modelling of breast cancer leptomeningeal metastasis reveals acquisition of a lobular-like phenotype. Nat Commun 2023; 14:7408. [PMID: 37973922 PMCID: PMC10654396 DOI: 10.1038/s41467-023-43242-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
Breast cancer leptomeningeal metastasis (BCLM), where tumour cells grow along the lining of the brain and spinal cord, is a devastating development for patients. Investigating this metastatic site is hampered by difficulty in accessing tumour material. Here, we utilise cerebrospinal fluid (CSF) cell-free DNA (cfDNA) and CSF disseminated tumour cells (DTCs) to explore the clonal evolution of BCLM and heterogeneity between leptomeningeal and extracranial metastatic sites. Somatic alterations with potential therapeutic actionability were detected in 81% (17/21) of BCLM cases, with 19% detectable in CSF cfDNA only. BCLM was enriched in genomic aberrations in adherens junction and cytoskeletal genes, revealing a lobular-like breast cancer phenotype. CSF DTCs were cultured in 3D to establish BCLM patient-derived organoids, and used for the successful generation of BCLM in vivo models. These data reveal that BCLM possess a unique genomic aberration profile and highlight potential cellular dependencies in this hard-to-treat form of metastatic disease.
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Affiliation(s)
- Amanda Fitzpatrick
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, King's College London, London, UK
| | - Marjan Iravani
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Adam Mills
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - David Vicente
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - Ioannis Roxanis
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Nicholas C Turner
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Royal Marsden NHS Foundation Trust, London, UK
| | - Syed Haider
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Andrew N J Tutt
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Breast Cancer Now Research Unit, Guy's Hospital, King's College London, London, UK
- Oncology and Haematology Directorate, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Clare M Isacke
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
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20
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André F, Su F, Solovieff N, Hortobagyi G, Chia S, Neven P, Bardia A, Tripathy D, Lu YS, Lteif A, Taran T, Babbar N, Slamon D, Arteaga CL. Pooled ctDNA analysis of MONALEESA phase III advanced breast cancer trials. Ann Oncol 2023; 34:1003-1014. [PMID: 37673211 DOI: 10.1016/j.annonc.2023.08.011] [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: 10/05/2022] [Revised: 08/04/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND The phase III MONALEESA trials tested the efficacy and safety of the cyclin-dependent kinase (CDK)4/6 inhibitor ribociclib with different endocrine therapy partners as first- or second-line treatment of hormone receptor-positive/human epidermal growth factor receptor 2-negative advanced breast cancer (ABC). Using the largest pooled biomarker dataset of the CDK4/6 inhibitor ribociclib in ABC to date, we identified potential biomarkers of response to ribociclib. PATIENTS AND METHODS Baseline circulating tumour DNA from patients in the MONALEESA trials was assessed using next-generation sequencing. An analysis of correlation between gene alteration status and progression-free survival (PFS) was carried out to identify potential biomarkers of response to ribociclib. RESULTS Multiple frequently altered genes were identified. Alterations in ERBB2, FAT3, FRS2, MDM2, SFRP1, and ZNF217 were associated with a greater PFS benefit with ribociclib versus placebo. Patients with high tumour mutational burden (TMB) and with ANO1, CDKN2A/2B/2C, and RB1 alterations exhibited decreased sensitivity to ribociclib versus placebo. CONCLUSIONS Although exploratory, these results provide insight into alterations associated with the improved response to ribociclib treatment and may inform treatment sequencing in patients with actionable alterations following progression on CDK4/6 inhibitors. Validation of potential biomarkers identified here and development of prospective trials testing their clinical utility are warranted. CLINICALTRIALS GOV IDENTIFIERS NCT01958021, NCT02422615, NCT02278120.
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Affiliation(s)
- F André
- Department of Medical Oncology and INSERM U981, Institut Gustave Roussy, Université Paris Saclay, Villejuif, France.
| | - F Su
- Novartis Pharmaceuticals, East Hanover
| | - N Solovieff
- Novartis Institutes for BioMedical Research, Cambridge
| | - G Hortobagyi
- The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S Chia
- British Columbia Cancer Agency, Vancouver, Canada
| | - P Neven
- Multidisciplinary Breast Centre, Universitair Ziekenhuis Leuven, Leuven, Belgium
| | - A Bardia
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, USA
| | - D Tripathy
- The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Y-S Lu
- National Taiwan University Hospital, Taipei, Taiwan
| | - A Lteif
- Novartis Pharmaceuticals, East Hanover
| | - T Taran
- Novartis Pharma AG, Basel, Switzerland
| | - N Babbar
- Novartis Pharmaceuticals, East Hanover
| | - D Slamon
- David Geffen School of Medicine at UCLA, Los Angeles
| | - C L Arteaga
- UT Southwestern Simmons Comprehensive Cancer Center, Dallas, USA
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21
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Cotton JL, Estrada Diez J, Sagar V, Chen J, Piquet M, Alford J, Song Y, Li X, Riester M, DiMare MT, Schumacher K, Boulay G, Sprouffske K, Fan L, Burks T, Mansur L, Wagner J, Bhang HEC, Iartchouk O, Reece-Hoyes J, Morris EJ, Hammerman PS, Ruddy DA, Korn JM, Engelman JA, Niederst MJ. Expressed Barcoding Enables High-Resolution Tracking of the Evolution of Drug Tolerance. Cancer Res 2023; 83:3611-3623. [PMID: 37603596 DOI: 10.1158/0008-5472.can-23-0144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/11/2023] [Accepted: 08/15/2023] [Indexed: 08/23/2023]
Abstract
For a majority of patients with non-small cell lung cancer with EGFR mutations, treatment with EGFR inhibitors (EGFRi) induces a clinical response. Despite this initial reduction in tumor size, residual disease persists that leads to disease relapse. Elucidating the preexisting biological differences between sensitive cells and surviving drug-tolerant persister cells and deciphering how drug-tolerant cells evolve in response to treatment could help identify strategies to improve the efficacy of EGFRi. In this study, we tracked the origins and clonal evolution of drug-tolerant cells at a high resolution by using an expressed barcoding system coupled with single-cell RNA sequencing. This platform enabled longitudinal profiling of gene expression and drug sensitivity in response to EGFRi across a large number of clones. Drug-tolerant cells had higher expression of key survival pathways such as YAP and EMT at baseline and could also differentially adapt their gene expression following EGFRi treatment compared with sensitive cells. In addition, drug combinations targeting common downstream components (MAPK) or orthogonal factors (chemotherapy) showed greater efficacy than EGFRi alone, which is attributable to broader targeting of the heterogeneous EGFRi-tolerance mechanisms present in tumors. Overall, this approach facilitates thorough examination of clonal evolution in response to therapy that could inform the development of improved diagnostic approaches and treatment strategies for targeting drug-tolerant cells. SIGNIFICANCE The evolution and heterogeneity of EGFR inhibitor tolerance are identified in a large number of clones at enhanced cellular and temporal resolution using an expressed barcode technology coupled with single-cell RNA sequencing.
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Affiliation(s)
- Jennifer L Cotton
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Javier Estrada Diez
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Vivek Sagar
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Julie Chen
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Michelle Piquet
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - John Alford
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Youngchul Song
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Xiaoyan Li
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Markus Riester
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Matthew T DiMare
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Katja Schumacher
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Gaylor Boulay
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Kathleen Sprouffske
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Lin Fan
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Tyler Burks
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Leandra Mansur
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Joel Wagner
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Hyo-Eun C Bhang
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Oleg Iartchouk
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - John Reece-Hoyes
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Erick J Morris
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Peter S Hammerman
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - David A Ruddy
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Joshua M Korn
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Jeffrey A Engelman
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Matthew J Niederst
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
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22
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Westcott PMK, Muyas F, Hauck H, Smith OC, Sacks NJ, Ely ZA, Jaeger AM, Rideout WM, Zhang D, Bhutkar A, Beytagh MC, Canner DA, Jaramillo GC, Bronson RT, Naranjo S, Jin A, Patten JJ, Cruz AM, Shanahan SL, Cortes-Ciriano I, Jacks T. Mismatch repair deficiency is not sufficient to elicit tumor immunogenicity. Nat Genet 2023; 55:1686-1695. [PMID: 37709863 PMCID: PMC10562252 DOI: 10.1038/s41588-023-01499-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/07/2023] [Indexed: 09/16/2023]
Abstract
DNA mismatch repair deficiency (MMRd) is associated with a high tumor mutational burden (TMB) and sensitivity to immune checkpoint blockade (ICB) therapy. Nevertheless, most MMRd tumors do not durably respond to ICB and critical questions remain about immunosurveillance and TMB in these tumors. In the present study, we developed autochthonous mouse models of MMRd lung and colon cancer. Surprisingly, these models did not display increased T cell infiltration or ICB response, which we showed to be the result of substantial intratumor heterogeneity of mutations. Furthermore, we found that immunosurveillance shapes the clonal architecture but not the overall burden of neoantigens, and T cell responses against subclonal neoantigens are blunted. Finally, we showed that clonal, but not subclonal, neoantigen burden predicts ICB response in clinical trials of MMRd gastric and colorectal cancer. These results provide important context for understanding immune evasion in cancers with a high TMB and have major implications for therapies aimed at increasing TMB.
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Affiliation(s)
- Peter M K Westcott
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
| | - Francesc Muyas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Haley Hauck
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Olivia C Smith
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nathan J Sacks
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zackery A Ely
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alex M Jaeger
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - William M Rideout
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daniel Zhang
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Arjun Bhutkar
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mary C Beytagh
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David A Canner
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Grissel C Jaramillo
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Santiago Naranjo
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Abbey Jin
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - J J Patten
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Amanda M Cruz
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sean-Luc Shanahan
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Isidro Cortes-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK.
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Rodent Histopathology Core, Harvard Medical School, Boston, MA, USA.
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23
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Hu LS, D'Angelo F, Weiskittel TM, Caruso FP, Fortin Ensign SP, Blomquist MR, Flick MJ, Wang L, Sereduk CP, Meng-Lin K, De Leon G, Nespodzany A, Urcuyo JC, Gonzales AC, Curtin L, Lewis EM, Singleton KW, Dondlinger T, Anil A, Semmineh NB, Noviello T, Patel RA, Wang P, Wang J, Eschbacher JM, Hawkins-Daarud A, Jackson PR, Grunfeld IS, Elrod C, Mazza GL, McGee SC, Paulson L, Clark-Swanson K, Lassiter-Morris Y, Smith KA, Nakaji P, Bendok BR, Zimmerman RS, Krishna C, Patra DP, Patel NP, Lyons M, Neal M, Donev K, Mrugala MM, Porter AB, Beeman SC, Jensen TR, Schmainda KM, Zhou Y, Baxter LC, Plaisier CL, Li J, Li H, Lasorella A, Quarles CC, Swanson KR, Ceccarelli M, Iavarone A, Tran NL. Integrated molecular and multiparametric MRI mapping of high-grade glioma identifies regional biologic signatures. Nat Commun 2023; 14:6066. [PMID: 37770427 PMCID: PMC10539500 DOI: 10.1038/s41467-023-41559-1] [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: 02/14/2023] [Accepted: 09/06/2023] [Indexed: 09/30/2023] Open
Abstract
Sampling restrictions have hindered the comprehensive study of invasive non-enhancing (NE) high-grade glioma (HGG) cell populations driving tumor progression. Here, we present an integrated multi-omic analysis of spatially matched molecular and multi-parametric magnetic resonance imaging (MRI) profiling across 313 multi-regional tumor biopsies, including 111 from the NE, across 68 HGG patients. Whole exome and RNA sequencing uncover unique genomic alterations to unresectable invasive NE tumor, including subclonal events, which inform genomic models predictive of geographic evolution. Infiltrative NE tumor is alternatively enriched with tumor cells exhibiting neuronal or glycolytic/plurimetabolic cellular states, two principal transcriptomic pathway-based glioma subtypes, which respectively demonstrate abundant private mutations or enrichment in immune cell signatures. These NE phenotypes are non-invasively identified through normalized K2 imaging signatures, which discern cell size heterogeneity on dynamic susceptibility contrast (DSC)-MRI. NE tumor populations predicted to display increased cellular proliferation by mean diffusivity (MD) MRI metrics are uniquely associated with EGFR amplification and CDKN2A homozygous deletion. The biophysical mapping of infiltrative HGG potentially enables the clinical recognition of tumor subpopulations with aggressive molecular signatures driving tumor progression, thereby informing precision medicine targeting.
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Affiliation(s)
- Leland S Hu
- Department of Radiology, Mayo Clinic Arizona, Phoenix, AZ, USA.
- Department of Cancer Biology, Mayo Clinic Arizona, Scottsdale, AZ, USA.
- Department of Neurological Surgery, Mayo Clinic Arizona, Scottsdale, AZ, USA.
| | - Fulvio D'Angelo
- Department of Neurological Surgery, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA.
| | - Taylor M Weiskittel
- Mayo Clinic Alix School of Medicine Minnesota, Rochester, MN, USA
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Francesca P Caruso
- Department of Electrical Engineering and Information Technologies, University of Naples, "Federico II", I-80128, Naples, Italy
- BIOGEM Institute of Molecular Biology and Genetics, I-83031, Ariano Irpino, Italy
| | - Shannon P Fortin Ensign
- Department of Cancer Biology, Mayo Clinic Arizona, Scottsdale, AZ, USA
- Department of Hematology and Oncology, Mayo Clinic Arizona, Phoenix, AZ, USA
| | - Mylan R Blomquist
- Department of Cancer Biology, Mayo Clinic Arizona, Scottsdale, AZ, USA
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
- Mayo Clinic Alix School of Medicine Arizona, Scottsdale, AZ, USA
| | - Matthew J Flick
- Department of Radiology, Mayo Clinic Arizona, Phoenix, AZ, USA
- Department of Cancer Biology, Mayo Clinic Arizona, Scottsdale, AZ, USA
- Mayo Clinic Alix School of Medicine Arizona, Scottsdale, AZ, USA
| | - Lujia Wang
- H. Milton Stewart School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Christopher P Sereduk
- Department of Cancer Biology, Mayo Clinic Arizona, Scottsdale, AZ, USA
- Department of Neurological Surgery, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Kevin Meng-Lin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Gustavo De Leon
- Department of Neurological Surgery, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Ashley Nespodzany
- Department of Neuroimaging Research, Barrow Neurological Institute, Dignity Health, Phoenix, AZ, USA
| | - Javier C Urcuyo
- Department of Neurological Surgery, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Ashlyn C Gonzales
- Department of Neuroimaging Research, Barrow Neurological Institute, Dignity Health, Phoenix, AZ, USA
| | - Lee Curtin
- Department of Neurological Surgery, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Erika M Lewis
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Kyle W Singleton
- Department of Neurological Surgery, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | | | - Aliya Anil
- Department of Neuroimaging Research, Barrow Neurological Institute, Dignity Health, Phoenix, AZ, USA
| | - Natenael B Semmineh
- Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Teresa Noviello
- Department of Electrical Engineering and Information Technologies, University of Naples, "Federico II", I-80128, Naples, Italy
- BIOGEM Institute of Molecular Biology and Genetics, I-83031, Ariano Irpino, Italy
| | - Reyna A Patel
- Department of Radiology, Mayo Clinic Arizona, Phoenix, AZ, USA
| | - Panwen Wang
- Quantitative Health Sciences, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Junwen Wang
- Division of Applied Oral Sciences & Community Dental Care, The University of Hong Kong, Hong Kong SAR, China
| | - Jennifer M Eschbacher
- Department of Neuropathology, Barrow Neurological Institute, Dignity Health, Phoenix, AZ, USA
| | | | - Pamela R Jackson
- Department of Neurological Surgery, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Itamar S Grunfeld
- Department of Psychology, Hunter College, The City University of New York, New York, NY, USA
- Department of Psychology, The Graduate Center, The City University of New York, New York, NY, USA
| | | | - Gina L Mazza
- Quantitative Health Sciences, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Sam C McGee
- Department of Speech and Hearing Science, Arizona State University, Tempe, AZ, USA
| | - Lisa Paulson
- Department of Neurological Surgery, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | | | | | - Kris A Smith
- Department of Neurosurgery, Barrow Neurological Institute, Dignity Health, Phoenix, AZ, USA
| | - Peter Nakaji
- Department of Neurosurgery, Banner University Medical Center, University of Arizona, Phoenix, AZ, USA
| | - Bernard R Bendok
- Department of Neurological Surgery, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Richard S Zimmerman
- Department of Neurological Surgery, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Chandan Krishna
- Department of Neurological Surgery, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Devi P Patra
- Department of Neurological Surgery, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Naresh P Patel
- Department of Neurological Surgery, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Mark Lyons
- Department of Neurological Surgery, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Matthew Neal
- Department of Neurological Surgery, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Kliment Donev
- Department of Pathology, Mayo Clinic Arizona, Phoenix, AZ, USA
| | | | - Alyx B Porter
- Department of Neurology, Mayo Clinic Arizona, Phoenix, AZ, USA
| | - Scott C Beeman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | | | - Kathleen M Schmainda
- Departments of Biophysics and Radiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Yuxiang Zhou
- Department of Radiology, Mayo Clinic Arizona, Phoenix, AZ, USA
| | - Leslie C Baxter
- Department of Radiology, Mayo Clinic Arizona, Phoenix, AZ, USA
- Departments of Psychiatry and Psychology, Mayo Clinic, AZ, USA
| | - Christopher L Plaisier
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Jing Li
- H. Milton Stewart School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Anna Lasorella
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - C Chad Quarles
- Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kristin R Swanson
- Department of Cancer Biology, Mayo Clinic Arizona, Scottsdale, AZ, USA
- Department of Neurological Surgery, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Michele Ceccarelli
- Department of Public Health Sciences, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA.
| | - Antonio Iavarone
- Department of Neurological Surgery, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA.
| | - Nhan L Tran
- Department of Cancer Biology, Mayo Clinic Arizona, Scottsdale, AZ, USA.
- Department of Neurological Surgery, Mayo Clinic Arizona, Scottsdale, AZ, USA.
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24
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Chiu J, Su F, Joshi M, Masuda N, Ishikawa T, Aruga T, Zarate JP, Babbar N, Balbin OA, Yap YS. Potential value of ctDNA monitoring in metastatic HR + /HER2 - breast cancer: longitudinal ctDNA analysis in the phase Ib MONALEESASIA trial. BMC Med 2023; 21:306. [PMID: 37580773 PMCID: PMC10426213 DOI: 10.1186/s12916-023-03017-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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 08/01/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND There is increasing interest in the use of liquid biopsies, but data on longitudinal analyses of circulating tumor DNA (ctDNA) remain relatively limited. Here, we report a longitudinal ctDNA analysis of MONALEESASIA, a phase Ib trial evaluating the efficacy and safety of ribociclib plus endocrine therapy (ET) in Asian patients with hormone receptor-positive, human epidermal growth factor receptor-2-negative advanced breast cancer. METHODS MONALEESASIA enrolled premenopausal and postmenopausal Japanese and postmenopausal non-Japanese Asian patients. All patients received ribociclib with ET (letrozole, fulvestrant, or tamoxifen with goserelin). ctDNA was analyzed using a targeted next-generation sequencing panel of 572 cancer-related genes and correlated by best overall response (BOR). RESULTS Five hundred seventy-four cell-free DNA samples from 87 patients were tested. The most frequently altered genes at baseline included PIK3CA (29%) and TP53 (22%). Treatment with ribociclib plus ET decreased ctDNA in most patients at the first on-treatment time point, regardless of dose or ET partner. Patients with partial response and stable disease had lower ctDNA at baseline that remained low until data cutoff if no progressive disease occurred. Most patients with progressive disease as the best response had higher ctDNA at baseline that remained high at the end of treatment. For patients with partial response and stable disease with subsequent progression, ctDNA increased towards the end of treatment in most patients, with a median lead time of 83 days (14-309 days). In some patients with BOR of partial response who experienced disease progression later, specific gene alterations and total ctDNA fraction increased; this was sometimes observed concurrently with the development of new lesions without a change in target lesion size. Patients with alterations in PIK3CA and TP53 at baseline had shorter median progression-free survival compared with patients with wild-type PIK3CA and TP53, 12.7 and 7.3 months vs 19.2 and 19.4 months, respectively (P = .016 and P = .0001, respectively). CONCLUSIONS Higher ctDNA levels and PIK3CA and TP53 alterations detected at baseline were associated with inferior outcomes. On-treatment ctDNA levels were associated with different patterns based on BOR. Longitudinal tracking of ctDNA may be useful for monitoring tumor status and detection of alterations with treatment implications. TRIAL REGISTRATION ClinicalTrials.gov NCT02333370 . Registered on January 7, 2015.
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Affiliation(s)
- Joanne Chiu
- Queen Mary Hospital, 102 Pok Fu Lam Rd, Pok Fu Lam, Hong Kong
| | - Fei Su
- Novartis Pharmaceuticals Corporation, 1 Health Plaza, East Hanover, NJ, USA
| | - Mukta Joshi
- Novartis Institutes for BioMedical Research, 250 Massachusetts Ave, Cambridge, MA, USA
| | - Norikazu Masuda
- Nagoya University Graduate School of Medicine, Building B, Furocho, Chikusa Ward, Nagoya, Japan
| | - Takashi Ishikawa
- Tokyo Medical University Hospital, 6 Chome-7-1 Nishishinjuku, Shinjuku City, Tokyo, Japan
| | - Tomoyuki Aruga
- Tokyo Metropolitan Komagome Hospital, 3 Chome-18 Honkomagome, Bunkyo City, Tokyo, Japan
| | - Juan Pablo Zarate
- Novartis Pharmaceuticals Corporation, 1 Health Plaza, East Hanover, NJ, USA
| | - Naveen Babbar
- Novartis Pharmaceuticals Corporation, 1 Health Plaza, East Hanover, NJ, USA
| | - O Alejandro Balbin
- Novartis Institutes for BioMedical Research, 250 Massachusetts Ave, Cambridge, MA, USA
| | - Yoon-Sim Yap
- Division of Medical Oncology, National Cancer Centre Singapore, 30 Hospital Blvd, Singapore, Singapore.
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25
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Chowdhury S, Kennedy JJ, Ivey RG, Murillo OD, Hosseini N, Song X, Petralia F, Calinawan A, Savage SR, Berry AB, Reva B, Ozbek U, Krek A, Ma W, da Veiga Leprevost F, Ji J, Yoo S, Lin C, Voytovich UJ, Huang Y, Lee SH, Bergan L, Lorentzen TD, Mesri M, Rodriguez H, Hoofnagle AN, Herbert ZT, Nesvizhskii AI, Zhang B, Whiteaker JR, Fenyo D, McKerrow W, Wang J, Schürer SC, Stathias V, Chen XS, Barcellos-Hoff MH, Starr TK, Winterhoff BJ, Nelson AC, Mok SC, Kaufmann SH, Drescher C, Cieslik M, Wang P, Birrer MJ, Paulovich AG. Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer. Cell 2023; 186:3476-3498.e35. [PMID: 37541199 PMCID: PMC10414761 DOI: 10.1016/j.cell.2023.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/23/2023] [Accepted: 07/05/2023] [Indexed: 08/06/2023]
Abstract
To improve the understanding of chemo-refractory high-grade serous ovarian cancers (HGSOCs), we characterized the proteogenomic landscape of 242 (refractory and sensitive) HGSOCs, representing one discovery and two validation cohorts across two biospecimen types (formalin-fixed paraffin-embedded and frozen). We identified a 64-protein signature that predicts with high specificity a subset of HGSOCs refractory to initial platinum-based therapy and is validated in two independent patient cohorts. We detected significant association between lack of Ch17 loss of heterozygosity (LOH) and chemo-refractoriness. Based on pathway protein expression, we identified 5 clusters of HGSOC, which validated across two independent patient cohorts and patient-derived xenograft (PDX) models. These clusters may represent different mechanisms of refractoriness and implicate putative therapeutic vulnerabilities.
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Affiliation(s)
- Shrabanti Chowdhury
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jacob J Kennedy
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Richard G Ivey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Oscar D Murillo
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Noshad Hosseini
- Department of Computational Medicine and Bioinformatics, Michigan Center for Translational Pathology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Xiaoyu Song
- Tisch Cancer Institute, Department of Population Health Science and Policy, Institute for Health Care Delivery Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Calinawan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sara R Savage
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Umut Ozbek
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Weiping Ma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Jiayi Ji
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Chenwei Lin
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Uliana J Voytovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Yajue Huang
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Sun-Hee Lee
- Departments of Oncology and Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Lindsay Bergan
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Travis D Lorentzen
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Zachary T Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, Department of Computational Medicine and Bioinformatics, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeffrey R Whiteaker
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - David Fenyo
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Wilson McKerrow
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Joshua Wang
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Stephan C Schürer
- Department of Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, and Institute for Data Science & Computing, University of Miami, Miami, FL 33136, USA
| | - Vasileios Stathias
- Department of Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, and Institute for Data Science & Computing, University of Miami, Miami, FL 33136, USA
| | - X Steven Chen
- Department of Public Health Sciences, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Mary Helen Barcellos-Hoff
- Helen Diller Family Comprehensive Cancer Center, Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Timothy K Starr
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Boris J Winterhoff
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Andrew C Nelson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samuel C Mok
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Scott H Kaufmann
- Departments of Oncology and Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Charles Drescher
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Marcin Cieslik
- Department of Pathology, Department of Computational Medicine and Bioinformatics, Michigan Center for Translational Pathology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA.
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Michael J Birrer
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Amanda G Paulovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
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26
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Willing EM, Vollbrecht C, Vössing C, Weist P, Schallenberg S, Herbst JM, Schatz S, Jóri B, Bataillon G, Harter P, Salutari V, Martin AG, Vergote I, Colombo N, Roeper J, Berg T, Berger R, Kah B, Noettrup TJ, Falk M, Arndt K, Polten A, Ray-Coquard I, Selzam F, Pirngruber J, Schmidt S, Hummel M, Tiemann M, Horst D, Sehouli J, Pujade-Lauraine E, Tiemann K, Braicu EI, Heukamp LC. Development of the NOGGO GIS v1 Assay, a Comprehensive Hybrid-Capture-Based NGS Assay for Therapeutic Stratification of Homologous Repair Deficiency Driven Tumors and Clinical Validation. Cancers (Basel) 2023; 15:3445. [PMID: 37444554 DOI: 10.3390/cancers15133445] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
The worldwide approval of the combination maintenance therapy of olaparib and bevacizumab in advanced high-grade serous ovarian cancer requires complex molecular diagnostic assays that are sufficiently robust for the routine detection of driver mutations in homologous recombination repair (HRR) genes and genomic instability (GI), employing formalin-fixed (FFPE) paraffin-embedded tumor samples without matched normal tissue. We therefore established a DNA-based hybrid capture NGS assay and an associated bioinformatic pipeline that fulfils our institution's specific needs. The assay´s target regions cover the full exonic territory of relevant cancer-related genes and HRR genes and more than 20,000 evenly distributed single nucleotide polymorphism (SNP) loci to allow for the detection of genome-wide allele specific copy number alterations (CNA). To determine GI status, we implemented an %CNA score that is robust across a broad range of tumor cell content (25-85%) often found in routine FFPE samples. The assay was established using high-grade serous ovarian cancer samples for which BRCA1 and BRCA2 mutation status as well as Myriad MyChoice homologous repair deficiency (HRD) status was known. The NOGGO (Northeastern German Society for Gynecologic Oncology) GIS (GI-Score) v1 assay was clinically validated on more than 400 samples of the ENGOT PAOLA-1 clinical trial as part of the European Network for Gynaecological Oncological Trial groups (ENGOT) HRD European Initiative. The "NOGGO GIS v1 assay" performed using highly robust hazard ratios for progression-free survival (PFS) and overall survival (OS), as well a significantly lower dropout rate than the Myriad MyChoice clinical trial assay supporting the clinical utility of the assay. We also provide proof of a modular and scalable routine diagnostic method, that can be flexibly adapted and adjusted to meet future clinical needs, emerging biomarkers, and further tumor entities.
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Affiliation(s)
- Eva-Maria Willing
- Institut für Hämatopathologie Hamburg, 22547 Hamburg, Germany
- Nord-Ostdeutsche Gesellschaft für Gynäkologische Onkologie NOGGO e. V., 13359 Berlin, Germany
| | - Claudia Vollbrecht
- Nord-Ostdeutsche Gesellschaft für Gynäkologische Onkologie NOGGO e. V., 13359 Berlin, Germany
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Christine Vössing
- Institut für Hämatopathologie Hamburg, 22547 Hamburg, Germany
- Lungenkrebsmedizin Oldenburg, GbR, 26121 Oldenburg, Germany
| | - Peggy Weist
- Institut für Hämatopathologie Hamburg, 22547 Hamburg, Germany
- Lungenkrebsmedizin Oldenburg, GbR, 26121 Oldenburg, Germany
| | - Simon Schallenberg
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | | | - Stefanie Schatz
- Institut für Hämatopathologie Hamburg, 22547 Hamburg, Germany
| | - Balázs Jóri
- Institut für Hämatopathologie Hamburg, 22547 Hamburg, Germany
| | - Guillaume Bataillon
- Department of Pathology, Institut Universitaire du Cancer de Toulouse (IUCT) Oncopole, 31100 Toulouse, France
| | | | - Vanda Salutari
- Department of Woman, Child and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - Antonio Gonzáles Martin
- Medical Oncology Department, Clinica Universidad de Navarra, 28027 Madrid, Spain
- GEICO, 28003 Madrid, Spain
| | - Ignace Vergote
- Leuven Cancer Institute, University Hospital Leuven, 3000 Leuven, Belgium
| | - Nicoletta Colombo
- Gynecologic Oncology Program, European Institute of Oncology, 20141 Milan, Italy
- Department of Medicine and Surgery, University of Milan-Biocca (Colombo), 20141 Milan, Italy
| | - Julia Roeper
- Universitätsklinik für Innere Medizin-Onkologie, Cancer Center Oldenburg, Pius-Hospital, Georgstr. 12, 26121 Oldenburg, Germany
| | - Tobias Berg
- Institut für Hämatopathologie Hamburg, 22547 Hamburg, Germany
| | - Regina Berger
- Department of Obstetrics and Gynecology, AGO Austria Study Center, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Bettina Kah
- Institut für Hämatopathologie Hamburg, 22547 Hamburg, Germany
| | | | - Markus Falk
- Institut für Hämatopathologie Hamburg, 22547 Hamburg, Germany
| | - Kathrin Arndt
- Institut für Hämatopathologie Hamburg, 22547 Hamburg, Germany
| | - Andreas Polten
- Agilent Technologies Deutschland GmbH, 71034 Böblingen, Germany
| | - Isabelle Ray-Coquard
- Centre Léon BERARD, and University Claude Bernard Lyon I, 69008 Lyon, France
- ARCAGY GINECO, 75008 Paris, France
| | | | - Judith Pirngruber
- Institut für Hämatopathologie Hamburg, 22547 Hamburg, Germany
- Lungenkrebsmedizin Oldenburg, GbR, 26121 Oldenburg, Germany
| | | | - Michael Hummel
- Nord-Ostdeutsche Gesellschaft für Gynäkologische Onkologie NOGGO e. V., 13359 Berlin, Germany
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Markus Tiemann
- Institut für Hämatopathologie Hamburg, 22547 Hamburg, Germany
| | - David Horst
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- German Cancer Consortium (DKTK) Partner Site Berlin, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jalid Sehouli
- Nord-Ostdeutsche Gesellschaft für Gynäkologische Onkologie NOGGO e. V., 13359 Berlin, Germany
- Charité University Medicine, Joint Medical Faculty of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Gynecology with Center of Oncological Surgery and European Competence Center for Ovarian Cancer, 10117 Berlin, Germany
| | | | - Katharina Tiemann
- Institut für Hämatopathologie Hamburg, 22547 Hamburg, Germany
- Nord-Ostdeutsche Gesellschaft für Gynäkologische Onkologie NOGGO e. V., 13359 Berlin, Germany
| | - Elena Ioana Braicu
- Nord-Ostdeutsche Gesellschaft für Gynäkologische Onkologie NOGGO e. V., 13359 Berlin, Germany
- Lungenkrebsmedizin Oldenburg, GbR, 26121 Oldenburg, Germany
- Charité University Medicine, Joint Medical Faculty of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Gynecology with Center of Oncological Surgery and European Competence Center for Ovarian Cancer, 10117 Berlin, Germany
- Department of Obstetrics and Gynecology, Stanford University, Stanford, CA 94305, USA
| | - Lukas C Heukamp
- Institut für Hämatopathologie Hamburg, 22547 Hamburg, Germany
- Nord-Ostdeutsche Gesellschaft für Gynäkologische Onkologie NOGGO e. V., 13359 Berlin, Germany
- Lungenkrebsmedizin Oldenburg, GbR, 26121 Oldenburg, Germany
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27
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Ishikawa T, Ogawa T, Shiihara M, Usubuchi H, Omori Y, Hirose K, Itoh T, Yoshida T, Nakanome A, Okoshi A, Higashi K, Ishii R, Rokugo M, Wakamori S, Okamura Y, Kinoshita K, Katori Y, Furukawa T. Salivary gland cancer organoids are valid for preclinical genotype-oriented medical precision trials. iScience 2023; 26:106695. [PMID: 37207275 PMCID: PMC10189274 DOI: 10.1016/j.isci.2023.106695] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/02/2023] [Accepted: 04/13/2023] [Indexed: 05/21/2023] Open
Abstract
Salivary gland cancers (SGCs) are heterogeneous tumors, and precision oncology represents a promising therapeutic approach; however, its impact on SGCs remains obscure. This study aimed to establish a translational model for testing molecular-targeted therapies by combining patient-derived organoids and genomic analyses of SGCs. We enrolled 29 patients, including 24 with SGCs and 5 with benign tumors. Resected tumors were subjected to organoid and monolayer cultures, as well as whole-exome sequencing. Organoid and monolayer cultures of SGCs were successfully established in 70.8% and 62.5% of cases, respectively. Organoids retained most histopathological and genetic profiles of their original tumors. In contrast, 40% of the monolayer-cultured cells did not harbor somatic mutations of their original tumors. The efficacy of molecular-targeted drugs tested on organoids depended on their oncogenic features. Organoids recapitulated the primary tumors and were useful for testing genotype-oriented molecular targeted therapy, which is valuable for precision medicine in patients with SGCs.
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Affiliation(s)
- Tomohiko Ishikawa
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Takenori Ogawa
- Department of Otolaryngology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan
| | - Masahiro Shiihara
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Hajime Usubuchi
- Department of Pathology, Sendai Kousei Hospital, Sendai 980-0873, Japan
| | - Yuko Omori
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Katsuya Hirose
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Taito Itoh
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Takuya Yoshida
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Ayako Nakanome
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| | - Akira Okoshi
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| | - Kenjiro Higashi
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| | - Ryo Ishii
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| | - Masahiro Rokugo
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| | - Shun Wakamori
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| | - Yasunobu Okamura
- Tohoku University Advanced Research Center for Innovations in Next-Generation Medicine, Sendai 980-8573, Japan
- Tohoku University Tohoku Medical Megabank Organization, Sendai 980-8573, Japan
| | - Kengo Kinoshita
- Tohoku University Advanced Research Center for Innovations in Next-Generation Medicine, Sendai 980-8573, Japan
- Tohoku University Tohoku Medical Megabank Organization, Sendai 980-8573, Japan
- Tohoku University Graduate School of Information Sciences, Sendai 980-8579, Japan
| | - Yukio Katori
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| | - Toru Furukawa
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
- Corresponding author
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Jo SY, Hong N, Lee S, Jeong JJ, Won J, Park J, Kim GJ, Kim SK, Kim S, Rhee Y. Genomic and transcriptomic profiling reveal molecular characteristics of parathyroid carcinoma. Exp Mol Med 2023:10.1038/s12276-023-00968-4. [PMID: 37121965 DOI: 10.1038/s12276-023-00968-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/22/2022] [Accepted: 01/03/2023] [Indexed: 05/02/2023] Open
Abstract
Genomic and transcriptomic profiling has enhanced the diagnostic and treatment options for many cancers. However, the molecular characteristics of parathyroid cancer remain largely unexplored, thereby limiting the development of new therapeutic interventions. Herein, we conducted genomic and transcriptomic sequencing of 50 parathyroid tissues (12 carcinomas, 28 adenomas, and 10 normal tissues) to investigate the intrinsic and comparative molecular features of parathyroid carcinoma. We confirmed multiple two-hit mutation patterns in cell division cycle 73 (CDC73) that converged to biallelic inactivation, calling into question the presence of a second hit in other genes. In addition, allele-specific repression of CDC73 in copies with germline-truncating variants suggested selective pressure prior to tumorigenesis. Transcriptomic analysis identified upregulation of the expression of E2F targets, KRAS and TNF-alpha signaling, and epithelial-mesenchymal transition pathways in carcinomas compared to adenomas and normal tissues. A molecular classification model based on carcinoma-specific genes clearly separated carcinomas from adenomas and normal tissues, the clinical utility of which was demonstrated in two patients with uncertain malignant potential. A deeper analysis of gene expression and functional prediction suggested that Wilms tumor 1 (WT1) is a potential biomarker for CDC73-mutant parathyroid carcinoma, which was further validated through immunohistochemistry. Overall, our study revealed the genomic and transcriptomic profiles of parathyroid carcinoma and may help direct future precision diagnostic and therapeutic improvements.
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Affiliation(s)
- Se-Young Jo
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Namki Hong
- Department of Internal Medicine, Severance Hospital, Endocrine Research Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - Seunghyun Lee
- Department of Internal Medicine, Severance Hospital, Endocrine Research Institute, Yonsei University College of Medicine, Seoul, South Korea
- Department of Internal Medicine, Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Jong Ju Jeong
- Department of Surgery, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Jeongsoo Won
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Jiho Park
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Korea
| | - Gi Jeong Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | - Sang Kyum Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Korea.
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea.
- Postech Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang, Korea.
| | - Yumie Rhee
- Department of Internal Medicine, Severance Hospital, Endocrine Research Institute, Yonsei University College of Medicine, Seoul, South Korea.
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Piperno-Neumann S, Carlino MS, Boni V, Loirat D, Speetjens FM, Park JJ, Calvo E, Carvajal RD, Nyakas M, Gonzalez-Maffe J, Zhu X, Shirley MD, Ramkumar T, Fessehatsion A, Burks HE, Yerramilli-Rao P, Kapiteijn E. A phase I trial of LXS196, a protein kinase C (PKC) inhibitor, for metastatic uveal melanoma. Br J Cancer 2023; 128:1040-1051. [PMID: 36624219 PMCID: PMC10006169 DOI: 10.1038/s41416-022-02133-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 12/14/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Up to 50% of patients with uveal melanoma develop metastases (MUM) with a poor prognosis and median overall survival of approximately 1 year. METHODS This phase I study evaluated the safety, tolerability, pharmacokinetics, pharmacodynamics and efficacy of the oral protein kinase C inhibitor LXS196 in 68 patients with MUM (NCT02601378). Patients received LXS196 doses ranging from 100-1000 mg once daily (QD; n = 38) and 200-400 mg twice daily (BID; n = 30). RESULTS First cycle dose-limiting toxicities (DLTs) were observed in 7/38 (18.4%) QD and 2/17 (11.8%) BID patients. Hypotension was the most common DLT, occurring at doses ≥500 mg/day, and manageable with LXS196 interruption and dose reduction. Median duration of exposure to LXS196 was 3.71 months (range: 1.81-15.28) for QD and 4.6 months (range: 0.33-58.32) for BID dosing. Clinical activity was observed in 6/66 (9.1%) evaluable patients achieving response (CR/PR), with a median duration of response of 10.15 months (range: 2.99-41.95); 45/66 had stable disease (SD) per RECIST v1.1. At 300 mg BID, the recommended dose for expansion, 2/18 (11.1%) evaluable patients achieved PR and 12/18 (66.7%) had SD. CONCLUSION These results suggest manageable toxicity and encouraging clinical activity of single-agent LXS196 in patients with MUM.
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Affiliation(s)
| | - M S Carlino
- Blacktown and Westmead Hospitals, Sydney, NSW, Australia.,Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - V Boni
- START Madrid-CIOCC, Centro Integral Oncológico Clara Campal, Madrid, Spain
| | | | - F M Speetjens
- Leiden University Medical Center, Leiden, The Netherlands
| | - J J Park
- Blacktown and Westmead Hospitals, Sydney, NSW, Australia
| | - E Calvo
- START Madrid-CIOCC, Centro Integral Oncológico Clara Campal, Madrid, Spain
| | - R D Carvajal
- Columbia University Irving Medical Center, New York, NY, USA
| | - M Nyakas
- Oslo University Hospital, Oslo, Norway
| | | | - X Zhu
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - M D Shirley
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - T Ramkumar
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - A Fessehatsion
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - H E Burks
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - E Kapiteijn
- Leiden University Medical Center, Leiden, The Netherlands
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Impact of Whole Genome Doubling on Detection of Circulating Tumor DNA in Colorectal Cancer. Cancers (Basel) 2023; 15:cancers15041136. [PMID: 36831479 PMCID: PMC9954709 DOI: 10.3390/cancers15041136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
OBJECTIVE Circulating tumor DNA (ctDNA) is a candidate biomarker of cancer with practice-changing potential in the detection of both early and residual disease. Disease stage and tumor size affect the probability of ctDNA detection, whereas little is known about the influence of other tumor characteristics on ctDNA detection. This study investigates the impact of tumor cell whole-genome doubling (WGD) on the detection of ctDNA in plasma collected preoperatively from newly diagnosed colorectal cancer (CRC) patients. METHODS WGD was estimated from copy numbers derived from whole-exome sequencing (WES) data of matched tumor and normal DNA from 833 Danish CRC patients. To explore if tumor WGD status impacts ctDNA detection, we applied tumor-informed ctDNA analysis to preoperative plasma samples from all patients. RESULTS Patients with WGD+ tumors had 53% increased odds of being ctDNA positive (OR = 1.53, 95%CI: 1.12-2.09). After stratification for UICC stage, the association persisted for Stage I (OR = 2.44, 95%CI: 1.22-5.03) and Stage II (OR = 1.76, 95%CI: 1.11-2.81) but not for Stage III (OR = 0.83, 95%CI: 0.44-1.53) patients. CONCLUSION The presence of WGD significantly increases the probability of detecting ctDNA, particularly for early-stage disease. In patients with more advanced disease, the benefit of WGD on ctDNA detection is less pronounced, consistent with increased DNA shedding from these tumors, making ctDNA detection less dependent on the amount of ctDNA released per tumor cell.
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Niknafs N, Balan A, Cherry C, Hummelink K, Monkhorst K, Shao XM, Belcaid Z, Marrone KA, Murray J, Smith KN, Levy B, Feliciano J, Hann CL, Lam V, Pardoll DM, Karchin R, Seiwert TY, Brahmer JR, Forde PM, Velculescu VE, Anagnostou V. Persistent mutation burden drives sustained anti-tumor immune responses. Nat Med 2023; 29:440-449. [PMID: 36702947 PMCID: PMC9941047 DOI: 10.1038/s41591-022-02163-w] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 11/30/2022] [Indexed: 01/27/2023]
Abstract
Tumor mutation burden is an imperfect proxy of tumor foreignness and has therefore failed to consistently demonstrate clinical utility in predicting responses in the context of immunotherapy. We evaluated mutations in regions of the genome that are unlikely to undergo loss in a pan-cancer analysis across 31 tumor types (n = 9,242) and eight immunotherapy-treated cohorts of patients with non-small-cell lung cancer, melanoma, mesothelioma, and head and neck cancer (n = 524). We discovered that mutations in single-copy regions and those present in multiple copies per cell constitute a persistent tumor mutation burden (pTMB) which is linked with therapeutic response to immune checkpoint blockade. Persistent mutations were retained in the context of tumor evolution under selective pressure of immunotherapy and tumors with a high pTMB content were characterized by a more inflamed tumor microenvironment. pTMB imposes an evolutionary bottleneck that cancer cells cannot overcome and may thus drive sustained immunologic tumor control in the context of immunotherapy.
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Affiliation(s)
- Noushin Niknafs
- 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
| | - Christopher Cherry
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Kim Monkhorst
- Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Xiaoshan M Shao
- 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
| | - Kristen A Marrone
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joseph Murray
- The Sidney Kimmel Comprehensive Cancer Center, 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 for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Benjamin Levy
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Josephine Feliciano
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christine L Hann
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Vincent Lam
- The Sidney Kimmel Comprehensive Cancer Center, 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 for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rachel Karchin
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Tanguy Y Seiwert
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Julie R Brahmer
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Patrick M Forde
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Victor E Velculescu
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, 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 for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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McLaughlin RT, Asthana M, Di Meo M, Ceccarelli M, Jacob HJ, Masica DL. Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning. NPJ Precis Oncol 2023; 7:4. [PMID: 36611079 PMCID: PMC9825621 DOI: 10.1038/s41698-022-00340-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 12/12/2022] [Indexed: 01/08/2023] Open
Abstract
Accurately identifying somatic mutations is essential for precision oncology and crucial for calculating tumor-mutational burden (TMB), an important predictor of response to immunotherapy. For tumor-only variant calling (i.e., when the cancer biopsy but not the patient's normal tissue sample is sequenced), accurately distinguishing somatic mutations from germline variants is a challenging problem that, when unaddressed, results in unreliable, biased, and inflated TMB estimates. Here, we apply machine learning to the task of somatic vs germline classification in tumor-only solid tumor samples using TabNet, XGBoost, and LightGBM, three machine-learning models for tabular data. We constructed a training set for supervised classification using features derived exclusively from tumor-only variant calling and drawing somatic and germline truth labels from an independent pipeline using the patient-matched normal samples. All three trained models achieved state-of-the-art performance on two holdout test datasets: a TCGA dataset including sarcoma, breast adenocarcinoma, and endometrial carcinoma samples (AUC > 94%), and a metastatic melanoma dataset (AUC > 85%). Concordance between matched-normal and tumor-only TMB improves from R2 = 0.006 to 0.71-0.76 with the addition of a machine-learning classifier, with LightGBM performing best. Notably, these machine-learning models generalize across cancer subtypes and capture kits with a call rate of 100%. We reproduce the recent finding that tumor-only TMB estimates for Black patients are extremely inflated relative to that of white patients due to the racial biases of germline databases. We show that our approach with XGBoost and LightGBM eliminates this significant racial bias in tumor-only variant calling.
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Affiliation(s)
| | - Maansi Asthana
- Agricultural and Biological Engineering at Purdue University, West Lafayette, IN, USA
| | - Marc Di Meo
- Johns Hopkins University, Baltimore, MD, USA
| | - Michele Ceccarelli
- Department of Electrical Engineering and Information Technology, University of Naples "Federico II", Naples, Italy
- Biogem, Instituto di Biologia e Genetica Molecolare, Ariano Irpino, Italy
| | | | - David L Masica
- Genomics Research Center, AbbVie, Redwood City, CA, USA.
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Kodgule R, Goldman JW, Monovich AC, Saari T, Aguilar AR, Hall CN, Rajesh N, Gupta J, Chu SCA, Ye L, Gurumurthy A, Iyer A, Brown NA, Chiang MY, Cieslik MP, Ryan RJ. ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia. Blood Cancer Discov 2023; 4:34-53. [PMID: 36350827 PMCID: PMC9820540 DOI: 10.1158/2643-3230.bcd-21-0224] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 08/30/2022] [Accepted: 11/02/2022] [Indexed: 11/11/2022] Open
Abstract
Distal enhancers play critical roles in sustaining oncogenic gene-expression programs. We identify aberrant enhancer-like activation of GGAA tandem repeats as a characteristic feature of B-cell acute lymphoblastic leukemia (B-ALL) with genetic defects of the ETV6 transcriptional repressor, including ETV6-RUNX1+ and ETV6-null B-ALL. We show that GGAA repeat enhancers are direct activators of previously identified ETV6-RUNX1+/- like B-ALL "signature" genes, including the likely leukemogenic driver EPOR. When restored to ETV6-deficient B-ALL cells, ETV6 directly binds to GGAA repeat enhancers, represses their acetylation, downregulates adjacent genes, and inhibits B-ALL growth. In ETV6-deficient B-ALL cells, we find that the ETS transcription factor ERG directly binds to GGAA microsatellite enhancers and is required for sustained activation of repeat enhancer-activated genes. Together, our findings reveal an epigenetic gatekeeper function of the ETV6 tumor suppressor gene and establish microsatellite enhancers as a key mechanism underlying the unique gene-expression program of ETV6-RUNX1+/- like B-ALL. SIGNIFICANCE We find a unifying mechanism underlying a leukemia subtype-defining gene-expression signature that relies on repetitive elements with poor conservation between humans and rodents. The ability of ETV6 to antagonize promiscuous, nonphysiologic ERG activity may shed light on other roles of these key regulators in hematolymphoid development and human disease. See related commentary by Mercher, p. 2. This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Rohan Kodgule
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Joshua W. Goldman
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan
| | | | - Travis Saari
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Athalee R. Aguilar
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Cody N. Hall
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Niharika Rajesh
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Juhi Gupta
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Shih-Chun A. Chu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Li Ye
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Aishwarya Gurumurthy
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Ashwin Iyer
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Noah A. Brown
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Mark Y. Chiang
- Department of Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Marcin P. Cieslik
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Russell J.H. Ryan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
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Belleau P, Deschênes A, Chambwe N, Tuveson DA, Krasnitz A. Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 2023; 83:49-58. [PMID: 36351074 PMCID: PMC9811156 DOI: 10.1158/0008-5472.can-22-0682] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 09/23/2022] [Accepted: 11/02/2022] [Indexed: 11/10/2022]
Abstract
Genetic ancestry-oriented cancer research requires the ability to perform accurate and robust genetic ancestry inference from existing cancer-derived data, including whole-exome sequencing, transcriptome sequencing, and targeted gene panels, very often in the absence of matching cancer-free genomic data. Here we examined the feasibility and accuracy of computational inference of genetic ancestry relying exclusively on cancer-derived data. A data synthesis framework was developed to optimize and assess the performance of the ancestry inference for any given input cancer-derived molecular profile. In its core procedure, the ancestral background of the profiled patient is replaced with one of any number of individuals with known ancestry. The data synthesis framework is applicable to multiple profiling platforms, making it possible to assess the performance of inference specifically for a given molecular profile and separately for each continental-level ancestry; this ability extends to all ancestries, including those without statistically sufficient representation in the existing cancer data. The inference procedure was demonstrated to be accurate and robust in a wide range of sequencing depths. Testing of the approach in four representative cancer types and across three molecular profiling modalities showed that continental-level ancestry of patients can be inferred with high accuracy, as quantified by its agreement with the gold standard of deriving ancestry from matching cancer-free molecular data. This study demonstrates that vast amounts of existing cancer-derived molecular data are potentially amenable to ancestry-oriented studies of the disease without requiring matching cancer-free genomes or patient self-reported ancestry. SIGNIFICANCE The development of a computational approach that enables accurate and robust ancestry inference from cancer-derived molecular profiles without matching cancer-free data provides a valuable methodology for genetic ancestry-oriented cancer research.
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Affiliation(s)
- Pascal Belleau
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
- Cancer Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Astrid Deschênes
- Cancer Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
- Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York
| | - Nyasha Chambwe
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, New York
| | - David A. Tuveson
- Cancer Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
- Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York
| | - Alexander Krasnitz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
- Cancer Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
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Horak J, Kubecek O, Siskova A, Honkova K, Chvojkova I, Krupova M, Manethova M, Vodenkova S, García-Mulero S, John S, Cecka F, Vodickova L, Petera J, Filip S, Vymetalkova V. Differences in genome, transcriptome, miRNAome, and methylome in synchronous and metachronous liver metastasis of colorectal cancer. Front Oncol 2023; 13:1133598. [PMID: 37182133 PMCID: PMC10172672 DOI: 10.3389/fonc.2023.1133598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/20/2023] [Indexed: 05/16/2023] Open
Abstract
Despite distant metastases being the critical factor affecting patients' survival, they remain poorly understood. Our study thus aimed to molecularly characterize colorectal cancer liver metastases (CRCLMs) and explore whether molecular profiles differ between Synchronous (SmCRC) and Metachronous (MmCRC) colorectal cancer. This characterization was performed by whole exome sequencing, whole transcriptome, whole methylome, and miRNAome. The most frequent somatic mutations were in APC, SYNE1, TP53, and TTN genes. Among the differently methylated and expressed genes were those involved in cell adhesion, extracellular matrix organization and degradation, neuroactive ligand-receptor interaction. The top up-regulated microRNAs were hsa-miR-135b-3p and -5p, and the hsa-miR-200-family while the hsa-miR-548-family belonged to the top down-regulated. MmCRC patients evinced higher tumor mutational burden, a wider median of duplications and deletions, and a heterogeneous mutational signature than SmCRC. Regarding chronicity, a significant down-regulation of SMOC2 and PPP1R9A genes in SmCRC compared to MmCRC was observed. Two miRNAs were deregulated between SmCRC and MmCRC, hsa-miR-625-3p and has-miR-1269-3p. The combined data identified the IPO5 gene. Regardless of miRNA expression levels, the combined analysis resulted in 107 deregulated genes related to relaxin, estrogen, PI3K-Akt, WNT signaling pathways, and intracellular second messenger signaling. The intersection between our and validation sets confirmed the validity of our results. We have identified genes and pathways that may be considered as actionable targets in CRCLMs. Our data also provide a valuable resource for understanding molecular distinctions between SmCRC and MmCRC. They have the potential to enhance the diagnosis, prognostication, and management of CRCLMs by a molecularly targeted approach.
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Affiliation(s)
- Josef Horak
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Prague, Czechia
| | - Ondrej Kubecek
- Department of Oncology and Radiotherapy, Faculty of Medicine and University Hospital in Hradec Kralove, Charles University, Hradec Kralove, Czechia
| | - Anna Siskova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czechia
| | - Katerina Honkova
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
| | - Irena Chvojkova
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
| | - Marketa Krupova
- The Fingerland Department of Pathology, University Hospital in Hradec Kralove, Hradec Kralove, Czechia
| | - Monika Manethova
- The Fingerland Department of Pathology, University Hospital in Hradec Kralove, Hradec Kralove, Czechia
| | - Sona Vodenkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
| | - Sandra García-Mulero
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO)-Oncobell Programme, Bellvitge Biomedical Research Institute Oncobell Programme, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Oncobell Programme, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Stanislav John
- Department of Oncology and Radiotherapy, Faculty of Medicine and University Hospital in Hradec Kralove, Charles University, Hradec Kralove, Czechia
| | - Filip Cecka
- Department of Surgery, Faculty of Medicine and University Hospital in Hradec Kralove, Charles University, Hradec Kralove, Czechia
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czechia
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
| | - Jiri Petera
- Department of Oncology and Radiotherapy, Faculty of Medicine and University Hospital in Hradec Kralove, Charles University, Hradec Kralove, Czechia
| | - Stanislav Filip
- Department of Oncology and Radiotherapy, Faculty of Medicine and University Hospital in Hradec Kralove, Charles University, Hradec Kralove, Czechia
- *Correspondence: Veronika Vymetalkova, ; Stanislav Filip,
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czechia
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
- *Correspondence: Veronika Vymetalkova, ; Stanislav Filip,
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Toal TW, Estrada-Florez AP, Polanco-Echeverry GM, Sahasrabudhe RM, Lott PC, Suarez-Olaya JJ, Guevara-Tique AA, Rocha S, Morales-Arana A, Castro-Valencia F, Urayama S, Kirane A, Wei D, Rios-Sarabia N, Medrano R, Mantilla A, Echeverry de Polanco M, Torres J, Bohorquez-Lozano ME, Carvajal-Carmona LG. Multiregional Sequencing Analysis Reveals Extensive Genetic Heterogeneity in Gastric Tumors from Latinos. CANCER RESEARCH COMMUNICATIONS 2022; 2:1487-1496. [PMID: 36970058 PMCID: PMC10035402 DOI: 10.1158/2767-9764.crc-22-0149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/15/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022]
Abstract
UNLABELLED Gastric cancer is a leading cause of cancer mortality and health disparities in Latinos. We evaluated gastric intratumoral heterogeneity using multiregional sequencing of >700 cancer genes in 115 tumor biopsies from 32 patients, 29 who were Latinos. Analyses focused on comparisons with The Cancer Genome Atlas (TCGA) and on mutation clonality, druggability, and signatures. We found that only approximately 30% of all mutations were clonal and that only 61% of the known TCGA gastric cancer drivers harbored clonal mutations. Multiple clonal mutations were found in new candidate gastric cancer drivers such as EYS, FAT4, PCDHA1, RAD50, EXO1, RECQL4, and FSIP2. The genomically stable (GS) molecular subtype, which has the worse prognosis, was identified in 48% of our Latino patients, a fraction that was >2.3-fold higher than in TCGA Asian and White patients. Only a third of all tumors harbored clonal pathogenic mutations in druggable genes, with most (93%) GS tumors lacking actionable clonal mutations. Mutation signature analyses revealed that, in microsatellite-stable (MSS) tumors, DNA repair mutations were common for both tumor initiation and progression, while tobacco, POLE, and inflammation signatures likely initiate carcinogenesis. MSS tumor progression was likely driven by aging- and aflatoxin-associated mutations, as these latter changes were usually nonclonal. In microsatellite-unstable tumors, nonclonal tobacco-associated mutations were common. Our study, therefore, contributed to advancing gastric cancer molecular diagnostics and suggests clonal status is important to understanding gastric tumorigenesis. Our findings of a higher frequency of a poor prognosis associated molecular subtype in Latinos and a possible new aflatoxin gastric cancer etiology also advance cancer disparities research. SIGNIFICANCE Our study contributes to advancing our knowledge of gastric carcinogenesis, diagnostics, and cancer health disparities.
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Affiliation(s)
- Ted W. Toal
- Genome Center, University of California, Davis, California
| | - Ana P. Estrada-Florez
- Genome Center, University of California, Davis, California
- Grupo de Citogenética, Filogenia y Evolución de las Poblaciones, Universidad del Tolima, Ibagué, Colombia
| | | | | | - Paul C. Lott
- Genome Center, University of California, Davis, California
| | - John J. Suarez-Olaya
- Grupo de Citogenética, Filogenia y Evolución de las Poblaciones, Universidad del Tolima, Ibagué, Colombia
| | - Alix A. Guevara-Tique
- Grupo de Citogenética, Filogenia y Evolución de las Poblaciones, Universidad del Tolima, Ibagué, Colombia
| | - Sienna Rocha
- Genome Center, University of California, Davis, California
| | | | - Fabian Castro-Valencia
- Grupo de Citogenética, Filogenia y Evolución de las Poblaciones, Universidad del Tolima, Ibagué, Colombia
| | - Shiro Urayama
- UC Davis Comprehensive Cancer Center, Sacramento, California
- Division of Gastroenterology & Hepatology, University of California, Davis, California
| | - Amanda Kirane
- UC Davis Comprehensive Cancer Center, Sacramento, California
| | - Dongguang Wei
- Department of Pathology and Laboratory Medicine, University of California, Davis, California
| | - Nora Rios-Sarabia
- Unidad de Investigación en Enfermedades Infecciosas y Parasitarias, Unidad Médica de Alta Especialidad en Pediatría, Instituto Mexicano del Seguro Social, México City, México
| | - Rafael Medrano
- Departamento de Sarcomas y Tubo Digestivo Alto, Unidad Medica de Alta Especialidad en Oncología Instituto Mexicano del Seguro Social (IMSS), México City, México
| | - Alejandra Mantilla
- Departamento de Patología, Unidad Medica de Alta Especialidad en Oncología, Instituto Mexicano del Seguro Social (IMSS), México City, México
| | | | - Javier Torres
- Unidad de Investigación en Enfermedades Infecciosas y Parasitarias, Unidad Médica de Alta Especialidad en Pediatría, Instituto Mexicano del Seguro Social, México City, México
| | - Mabel E. Bohorquez-Lozano
- Grupo de Citogenética, Filogenia y Evolución de las Poblaciones, Universidad del Tolima, Ibagué, Colombia
| | - Luis G. Carvajal-Carmona
- Genome Center, University of California, Davis, California
- UC Davis Comprehensive Cancer Center, Sacramento, California
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, California
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Siegmund SE, Manning DK, Davineni PK, Dong F. Deriving tumor purity from cancer next generation sequencing data: applications for quantitative ERBB2 (HER2) copy number analysis and germline inference of BRCA1 and BRCA2 mutations. Mod Pathol 2022; 35:1458-1467. [PMID: 35902772 DOI: 10.1038/s41379-022-01083-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 03/30/2022] [Accepted: 04/03/2022] [Indexed: 11/09/2022]
Abstract
Tumor purity, or the relative contribution of tumor cells out of all cells in a pathological specimen, influences mutation identification and clinical interpretation of cancer panel next generation sequencing results. Here, we describe a method of calculating tumor purity using pathologist-guided copy number analysis from sequencing data. Molecular calculation of tumor purity showed strong linear correlation with purity derived from driver KRAS or BRAF variant allele fractions in colorectal cancers (R2 = 0.79) compared to histological estimation in the same set of colorectal cancers (R2 = 0.01) and in a broader dataset of cancers with various diagnoses (R2 = 0.35). We used calculated tumor purity to quantitate ERBB2 copy number in breast carcinomas with equivocal immunohistochemical staining and demonstrated strong correlation with fluorescence in situ hybridization (R2 = 0.88). Finally, we used calculated tumor purity to infer the germline status of variants in breast and ovarian carcinomas with concurrent germline testing. Tumor-only next generation sequencing correctly predicted the somatic versus germline nature of 26 of 26 (100%) pathogenic TP53, BRCA1 and BRCA2 variants. In this article, we describe a framework for calculating tumor purity from cancer next generation sequencing data. Accurate tumor purity assessment can be assimilated into interpretation pipelines to derive clinically useful information from cancer genomic panels.
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Affiliation(s)
| | | | - Phani K Davineni
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Fei Dong
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
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Del Corvo M, Mazzara S, Pileri SA. TOSCA: an automated Tumor Only Somatic CAlling workflow for somatic mutation detection without matched normal samples. BIOINFORMATICS ADVANCES 2022; 2:vbac070. [PMID: 36699358 PMCID: PMC9710689 DOI: 10.1093/bioadv/vbac070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 09/16/2022] [Accepted: 09/22/2022] [Indexed: 01/28/2023]
Abstract
Motivation Accurate classification of somatic variants in a tumor sample is often accomplished by utilizing a paired normal tissue sample from the same patient to enable the separation of private germline mutations from somatic variants. However, a paired normal sample is not always available, making a reliable somatic variant calling more challenging. In silico screening of variants against public or private databases and other filtering approaches are often used in absence of a paired normal sample. Nevertheless, difficulties in performing a tumor-only calling with sufficient accuracy and lack of open-source software have limited their applications in clinical research. Results To address these limitations, we developed TOSCA, the first automated tumor-only somatic calling workflow in whole-exome sequencing and targeted panel sequencing data which performs an end-to-end analysis from raw read files, via quality checks, alignment and variant calling to functional annotation, databases filtering, tumor purity and ploidy estimation and variant classification. Application of our workflow to tumor-only data provides estimates of somatic and germline variants that are consistent with results from paired analyses. Availability and implementation TOSCA is a Snakemake-based workflow and freely available at https://github.com/mdelcorvo/TOSCA. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
| | - Saveria Mazzara
- Division of Haematopathology, IEO, European Institute of Oncology IRCCS, Milan 20141, Italy
| | - Stefano A Pileri
- Division of Haematopathology, IEO, European Institute of Oncology IRCCS, Milan 20141, Italy
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Renaud G, Nørgaard M, Lindberg J, Grönberg H, De Laere B, Jensen JB, Borre M, Andersen CL, Sørensen KD, Maretty L, Besenbacher S. Unsupervised detection of fragment length signatures of circulating tumor DNA using non-negative matrix factorization. eLife 2022; 11:71569. [PMID: 35894300 PMCID: PMC9363120 DOI: 10.7554/elife.71569] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Sequencing of cell-free DNA (cfDNA) is currently being used to detect cancer by searching both for mutational and non-mutational alterations. Recent work has shown that the length distribution of cfDNA fragments from a cancer patient can inform tumor load and type. Here, we propose non-negative matrix factorization (NMF) of fragment length distributions as a novel and completely unsupervised method for studying fragment length patterns in cfDNA. Using shallow whole-genome sequencing (sWGS) of cfDNA from a cohort of patients with metastatic castration-resistant prostate cancer (mCRPC), we demonstrate how NMF accurately infers the true tumor fragment length distribution as an NMF component - and that the sample weights of this component correlate with ctDNA levels (r=0.75). We further demonstrate how using several NMF components enables accurate cancer detection on data from various early stage cancers (AUC=0.96). Finally, we show that NMF, when applied across genomic regions, can be used to discover fragment length signatures associated with open chromatin.
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Affiliation(s)
- Gabriel Renaud
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Maibritt Nørgaard
- Department of Molecular Medicine, Aarhus University, Aarhus N, Denmark
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Bram De Laere
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | | | - Michael Borre
- Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Lasse Maretty
- Department of Molecular Medicine, Aarhus University, Aarhus N, Denmark
| | - Søren Besenbacher
- Department of Molecular Medicine, Aarhus University, Aarhus N, Denmark
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Responses to the Tepotinib in Gastric Cancers with MET Amplification or MET Exon 14 Skipping Mutations and High Expression of Both PD-L1 and CD44. Cancers (Basel) 2022; 14:cancers14143444. [PMID: 35884507 PMCID: PMC9318186 DOI: 10.3390/cancers14143444] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/30/2022] [Accepted: 07/13/2022] [Indexed: 02/01/2023] Open
Abstract
Both MET exon 14 skipping mutation (METex14SM) and high copy-number variation (CNV) lead to enhanced carcinogenesis; additionally, programmed-death ligand 1 (PD-L1) is often upregulated in cancers. In this study, we characterized the expression of MET (including METex14SM), PD-L1, and CD44 in human gastric cancer (GC) cells as well as the differential susceptibility of these cells to tepotinib. Tepotinib treatments inhibited the growth of five GC cells in a dose-dependent manner with a concomitant induction of cell death. Tepotinib treatments also significantly reduced the expression of phospho-MET, total MET, c-Myc, VEGFR2, and Snail protein in SNU620, MKN45, and Hs746T cells. Notably, tepotinib significantly reduced the expression of CD44 and PD-L1 in METex14SM Hs746T cells. By contrast, tepotinib was only slightly active against SNU638 and KATO III cells. Migration was reduced to a greater extent in the tepotinib-treated group than in the control group. Tepotinib may have therapeutic effects on c-MET-amplified GC, a high expression of both PD-L1 and CD44, and METex14SM. Clinical studies are needed to confirm these therapeutic effects.
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Shui IM, Liu XQ, Zhao Q, Kim ST, Sun Y, Yearley JH, Choudhury T, Webber AL, Krepler C, Cristescu R, Lee J. Baseline and post-treatment biomarkers of resistance to anti-PD-1 therapy in acral and mucosal melanoma: an observational study. J Immunother Cancer 2022; 10:jitc-2022-004879. [PMID: 35793874 PMCID: PMC9260847 DOI: 10.1136/jitc-2022-004879] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2022] [Indexed: 12/14/2022] Open
Abstract
Background Immunotherapies targeting programmed cell death-1 (PD-1) and its ligands have improved clinical outcomes for advanced melanoma. However, many tumors exhibit primary resistance or acquire secondary resistance after an initial positive response. The mechanisms of resistance are not well understood, and no validated predictive biomarkers are available. This exploratory study aimed to characterize baseline differences and molecular changes arising during treatment in acral and mucosal melanomas that exhibited primary or secondary resistance to anti-PD-1 monotherapy. Methods This was an observational retrospective study of 124 patients who had been treated for metastatic acral or mucosal melanoma with anti-PD-1 monotherapy. Tumor samples were collected at baseline (all patients) and post-treatment (resistant tumors only) and were assayed by immunohistochemistry, whole-exome sequencing, and RNA sequencing. Results At baseline, more non-progressor than resistant tumors exhibited expression of PD-L1, immune cell infiltration, and high tumor mutational burden (TMB); baseline PD-L1 expression was also more common in secondary-resistant than in primary-resistant tumors as well as in late versus early secondary-resistant tumors. Non-progressor tumors also had higher median baseline expression of an 18-gene T cell-inflamed gene expression profile (TcellinfGEP). Among resistant tumors, the proportion of PD-L1-positive melanomas and the expression of the TcellinfGEP mRNA signature increased during treatment, while the expression of mRNA signatures related to WNT and INFA1 signaling decreased. There was evidence for greater changes from baseline in secondary-resistant versus primary-resistant tumors for some markers, including expression of RAS-related and WNT-related mRNA signatures and density of CD11c+ and FOXP3+ T cells. Greater changes in CD11c+ cell density were observed in early compared with late secondary-resistant tumors. Conclusions Our findings suggest that TcellinfGEP and PD-L1 expression, TMB, immune cell infiltration, and RAS and WNT signaling warrant further investigation as potential mechanisms and/or biomarkers of anti-PD-1 therapy resistance in acral and mucosal melanomas. Confirmation of these findings in larger populations is needed.
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Affiliation(s)
| | | | - Qing Zhao
- Merck & Co., Inc, Rahway, New Jersey, USA
| | - Seung Tae Kim
- Hematology and Oncology, Samsung Medical Center, Gangnam-gu, South Korea
| | - Yuan Sun
- Merck & Co., Inc, Rahway, New Jersey, USA
| | | | | | | | | | | | - Jeeyun Lee
- Hematology and Oncology, Samsung Medical Center, Gangnam-gu, South Korea
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Molecular characterization of low-grade serous ovarian carcinoma identifies genomic aberrations according to hormone receptor expression. NPJ Precis Oncol 2022; 6:47. [PMID: 35768582 PMCID: PMC9242985 DOI: 10.1038/s41698-022-00288-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/17/2022] [Indexed: 12/03/2022] Open
Abstract
Hormone receptor expression is a characteristic of low-grade serous ovarian carcinoma (LGSOC). Studies investigating estrogen receptor (ER) and progesterone receptor (PR) expression levels suggest its prognostic and predictive significance, although their associations with key molecular aberrations are not well understood. As such, we sought to describe the specific genomic profiles associated with different ER/PR expression patterns and survival outcomes in a cohort of patients with advanced disease. The study comprised fifty-five advanced-staged (III/IV) LGSOCs from the Canadian Ovarian Experimental Unified Resource (COEUR) for which targeted mutation sequencing, copy-number aberration, clinical and follow-up data were available. ER, PR, and p16 expression were assessed by immunohistochemistry. Tumors were divided into low and high ER/PR expression groups based on Allred scoring. Copy number analysis revealed that PR-low tumors (Allred score <2) had a higher fraction of the genome altered by copy number changes compared to PR-high tumors (p = 0.001), with cancer genes affected within specific loci linked to altered peptidyl-tyrosine kinase, MAP-kinase, and PI3-kinase signaling. Cox regression analysis showed that ER-high (p = 0.02), PR-high (p = 0.03), stage III disease (p = 0.02), low residual disease burden (p = 0.01) and normal p16 expression (p<0.001) were all significantly associated with improved overall survival. This study provides evidence that genomic aberrations are linked to ER/PR expression in primary LGSOC.
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Orlando F, Romanel A, Trujillo B, Sigouros M, Wetterskog D, Quaini O, Leone G, Xiang JZ, Wingate A, Tagawa S, Jayaram A, Linch M, Jamal-Hanjani M, Swanton C, Rubin MA, Wyatt AW, Beltran H, Attard G, Demichelis F. Allele-informed copy number evaluation of plasma DNA samples from metastatic prostate cancer patients: the PCF_SELECT consortium assay. NAR Cancer 2022; 4:zcac016. [PMID: 35664542 PMCID: PMC9154344 DOI: 10.1093/narcan/zcac016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/25/2022] [Accepted: 05/05/2022] [Indexed: 02/03/2023] Open
Abstract
Sequencing of cell-free DNA (cfDNA) in cancer patients' plasma offers a minimally-invasive solution to detect tumor cell genomic alterations to aid real-time clinical decision-making. The reliability of copy number detection decreases at lower cfDNA tumor fractions, limiting utility at earlier stages of the disease. To test a novel strategy for detection of allelic imbalance, we developed a prostate cancer bespoke assay, PCF_SELECT, that includes an innovative sequencing panel covering ∼25 000 high minor allele frequency SNPs and tailored analytical solutions to enable allele-informed evaluation. First, we assessed it on plasma samples from 50 advanced prostate cancer patients. We then confirmed improved detection of genomic alterations in samples with <10% tumor fractions when compared against an independent assay. Finally, we applied PCF_SELECT to serial plasma samples intensively collected from three patients previously characterized as harboring alterations involving DNA repair genes and consequently offered PARP inhibition. We identified more extensive pan-genome allelic imbalance than previously recognized in prostate cancer. We confirmed high sensitivity detection of BRCA2 allelic imbalance with decreasing tumor fractions resultant from treatment and identified complex ATM genomic states that may be incongruent with protein losses. Overall, we present a framework for sensitive detection of allele-specific copy number changes in cfDNA.
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Affiliation(s)
- Francesco Orlando
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Alessandro Romanel
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Blanca Trujillo
- UCL Cancer Institute, University College London, London, UK
- Department of Medical Oncology, University College London Hospitals, London NW1 2BU, UK
| | - Michael Sigouros
- Englander Institute for Precision Medicine, Presbyterian Hospital, Weill Cornell Medicine, NY, USA
| | | | - Orsetta Quaini
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Gianmarco Leone
- UCL Cancer Institute, University College London, London, UK
- Department of Medical Oncology, University College London Hospitals, London NW1 2BU, UK
| | - Jenny Z Xiang
- The Genomics Resources Core Facility, Department of Microbiology and Immunology, Weill Cornell Medicine. NY, NY, USA
| | - Anna Wingate
- UCL Cancer Institute, University College London, London, UK
| | - Scott Tagawa
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine. NY, NY, USA
| | - Anuradha Jayaram
- UCL Cancer Institute, University College London, London, UK
- Department of Medical Oncology, University College London Hospitals, London NW1 2BU, UK
| | - Mark Linch
- UCL Cancer Institute, University College London, London, UK
- Department of Medical Oncology, University College London Hospitals, London NW1 2BU, UK
| | - Mariam Jamal-Hanjani
- Department of Medical Oncology, University College London Hospitals, London NW1 2BU, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - Charles Swanton
- UCL Cancer Institute, University College London, London, UK
- Department of Medical Oncology, University College London Hospitals, London NW1 2BU, UK
- The Francis Crick Institute, London NW1 1AT, UK
| | - Mark A Rubin
- Department for BioMedical Research and Bern Center of Precision Medicine, University of Bern and Inselspital, Bern, Switzerland
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Himisha Beltran
- Englander Institute for Precision Medicine, Presbyterian Hospital, Weill Cornell Medicine, NY, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Gerhardt Attard
- UCL Cancer Institute, University College London, London, UK
- Department of Medical Oncology, University College London Hospitals, London NW1 2BU, UK
| | - Francesca Demichelis
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
- Englander Institute for Precision Medicine, Presbyterian Hospital, Weill Cornell Medicine, NY, USA
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Lindh C, Samaratunga H, Delahunt B, Bergström R, Chellappa V, Yaxley J, Lindberg J, Egevad L. Ductal and acinar components of mixed prostatic adenocarcinoma frequently have a common clonal origin. Prostate 2022; 82:576-583. [PMID: 35049068 PMCID: PMC9306900 DOI: 10.1002/pros.24304] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/08/2021] [Accepted: 12/30/2021] [Indexed: 11/09/2022]
Abstract
BACKGROUND Ductal adenocarcinoma (DA) is an aggressive subtype of prostate cancer. It is most commonly seen in mixed tumors together with conventional acinar adenocarcinoma (AA). The genetic profile of DA and its clonal origin is not fully characterized. OBJECTIVE To investigate whether DA represents a distinct genetic subtype and to investigate the somatic relationship between the ductal and acinar components of mixed cancers. DESIGN, SETTING, AND PARTICIPANTS In 17 radical prostatectomy specimens ductal and acinar tumor components from the same tumor foci were dissected. DNA was extracted and genomic sequencing performed. After exclusion of two cases with low cell yield, 15 paired samples remained for analysis. RESULTS In 12 of 15 cases a common somatic denominator was identified, while three cases had clonally separate components. In DA, TMPRSS2-ERG gene fusions were detected in 47% (7/15), clonal FOXA1 alterations in 33% (5/15) and SPOP alterations in 27% (4/15) of cases. In one case KIAA1549-BRAF fusion was identified. Genome doubling events, resulting in an increased ploidy, were identified in the DA in 53% (8/15) of cases, but not seen in any AA. PTEN and CTNNB1 alterations were enriched in DA (6/15) but not seen in any AA. No cancers showed microsatellite instability or high tumor mutation burden. CONCLUSIONS Ductal and acinar prostate adenocarcinoma components of mixed tumors most often share the same origin and are clonally related. DA components in mixed tumor often exhibit genome doubling events resulting in aneuploidy, consistent with the aggressive nature of high grade prostate cancer.
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Affiliation(s)
- Claes Lindh
- Department of Oncology‐PathologyKarolinska InstitutetStockholmSweden
| | | | - Brett Delahunt
- Department of Pathology and Molecular Medicine, Wellington School of Medicine and Health SciencesUniversity of OtagoWellingtonNew Zealand
| | - Rebecka Bergström
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Venkatesh Chellappa
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - John Yaxley
- Wesley Urology ClinicBrisbaneQueenslandAustralia
| | - Johan Lindberg
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Lars Egevad
- Department of Oncology‐PathologyKarolinska InstitutetStockholmSweden
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VHL mosaicism: the added value of multi-tissue analysis. NPJ Genom Med 2022; 7:21. [PMID: 35304467 PMCID: PMC8933488 DOI: 10.1038/s41525-022-00291-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 02/15/2022] [Indexed: 11/09/2022] Open
Abstract
Von Hippel-Lindau disease (VHL) is an autosomal dominant, inherited syndrome with variants in the VHL gene causing predisposition to multi-organ benign and malignant neoplasms. A germline VHL variant is identified in 95-100% of individuals with a clinical diagnosis of VHL. Here, we present the case of an individual with a clinical diagnosis of VHL disease where peripheral blood DNA analysis did not detect a VHL variant. Sequencing of four tumor tissues (ccRCC, pheochromocytoma, lung via sputum, liver) revealed a VHL c.593 T > C (p.Leu198Pro) variant at varying allele fractions (range: 10-55%) in all tissues. Re-examination of the peripheral blood sequencing data identified this variant at 6% allele fraction. Tumor analysis revealed characteristic cytomorphological, immunohistochemical reactivity for alpha-inhibin, and CAIX, and reduced pVHL reactivity supported VHL-related pseudohypoxia. This report of a rare case of VHL mosaicism highlights the value of tissue testing in VHL variant negative cases.
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Ramesh RG, Bigdeli A, Rushton C, Rosenbaum JN. CNViz: An R/Shiny Application for Interactive Copy Number Variant Visualization in Cancer. J Pathol Inform 2022; 13:100089. [PMID: 35251754 PMCID: PMC8888957 DOI: 10.1016/j.jpi.2022.100089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 01/27/2022] [Indexed: 01/10/2023] Open
Abstract
Copy number variants (CNVs) comprise a class of mutation which includes deletion, duplication, or amplification events that range in size from smaller than a single-gene or exon, to the size of a full chromosome. These changes can affect gene expression levels and are thus implicated in disease, including cancer. Although a variety of tools and methodologies exist to detect CNVs using data from massively parallel sequencing (also referred to as next-generation sequencing), it can be difficult to appreciate the copy number profile in a list format or as a static image. CNViz is a freely accessible R/Bioconductor package that launches an interactive R/Shiny visualization tool to facilitate review of copy number data. As inputs, it requires genomic locations and corresponding copy number ratios for probe, gene, and/or segment-level data. If supplied, loss of heterozygosity (LOH), focal variant data [single nucleotide variants (SNVs) and small insertions and deletions (indels)], and metadata (e.g., specimen purity and ploidy) can also be incorporated into the visualization. The CNViz R/Bioconductor package is an easy-to-use tool built with the intent of encouraging visualization and exploration of copy number variation. CNViz can be used in a clinical setting as well as for research to study patterns in human cancers more broadly. The intuitive interface allows users to visualize the copy number profile of a specimen, dynamically change resolution to explore gene and probe-level copy number changes, and simultaneously integrate LOH, SNV, and indel findings. CNViz is available for download as an R package via Bioconductor. An example of the application is available at rebeccagreenblatt.shinyapps.io/cnviz_example.
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Affiliation(s)
- Rebecca G Ramesh
- Center for Personalized Diagnostics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ashkan Bigdeli
- Center for Personalized Diagnostics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Chase Rushton
- Center for Personalized Diagnostics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jason N Rosenbaum
- Center for Personalized Diagnostics, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Pathology, Kaiser Permanente, Oakland, California, USA
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Sitthideatphaiboon P, Teerapakpinyo C, Korphaisarn K, Leelayuwatanakul N, Pornpatrananrak N, Poungvarin N, Chantranuwat P, Shuangshoti S, Aporntewan C, Chintanapakdee W, Sriuranpong V, Vinayanuwattikun C. Co-occurrence CDK4/6 amplification serves as biomarkers of de novo EGFR TKI resistance in sensitizing EGFR mutation non-small cell lung cancer. Sci Rep 2022; 12:2167. [PMID: 35140316 PMCID: PMC8828869 DOI: 10.1038/s41598-022-06239-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 01/17/2022] [Indexed: 12/19/2022] Open
Abstract
Despite the development of predictive biomarkers to shape treatment paradigms and outcomes, de novo EGFR TKI resistance advanced non-small cell lung cancer (NSCLC) remains an issue of concern. We explored clinical factors in 332 advanced NSCLC who received EGFR TKI and molecular characteristics through 65 whole exome sequencing of various EGFR TKI responses including; de novo (progression within 3 months), intermediate response (IRs) and long-term response (LTRs) (durability > 2 years). Uncommon EGFR mutation subtypes were significantly variable enriched in de novo resistance. The remaining sensitizing EGFR mutation subtypes (exon 19 del and L858R) accounted for 75% of de novo resistance. Genomic landscape analysis was conducted, focusing in 10 frequent oncogenic signaling pathways with functional contributions; cell cycle, Hippo, Myc, Notch, Nrf2, PI-3-Kinase/Akt, RTK-RAS, TGF-β, p53 and β-catenin/Wnt signaling. Cell cycle pathway was the only significant alteration pathway among groups with the FDR p-value of 6 × 10-4. We found only significant q-values of < 0.05 in 7 gene alterations; CDK6, CCNE1, CDK4, CCND3, MET, FGFR4 and HRAS which enrich in de novo resistance [range 36-73%] compared to IRs/LTRs [range 4-22%]. Amplification of CDK4/6 was significant in de novo resistance, contrary to IRs and LTRs (91%, 27.9% and 0%, respectively). The presence of co-occurrence CDK4/6 amplification correlated with poor disease outcome with HR of progression-free survival of 3.63 [95% CI 1.80-7.31, p-value < 0.001]. The presence of CDK4/6 amplification in pretreatment specimen serves as a predictive biomarker for de novo resistance in sensitizing EGFR mutation.
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Affiliation(s)
- Piyada Sitthideatphaiboon
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and The King Chulalongkorn Memorial Hospital, Bangkok, 10330, Thailand
| | - Chinachote Teerapakpinyo
- Chula GenePRO Center, Research Affairs, Chulalongkorn University and The King Chulalongkorn Memorial Hospital, Bangkok, 10330, Thailand
| | - Krittiya Korphaisarn
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Siriraj, Bangkok Noi, Bangkok, 10700, Thailand
| | - Nophol Leelayuwatanakul
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Faculty of Medicine, Chulalongkorn University and The King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Nopporn Pornpatrananrak
- Department of Surgery, Faculty of Medicine, Chulalongkorn University and The King Chulalongkorn Memorial Hospital, Bangkok, 10330, Thailand
| | - Naravat Poungvarin
- Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Siriraj, Bangkok Noi, Bangkok, 10700, Thailand
| | - Poonchavist Chantranuwat
- Department of Pathology, Faculty of Medicine, Chulalongkorn University and The King Chulalongkorn Memorial Hospital, Bangkok, 10330, Thailand
| | - Shanop Shuangshoti
- Chula GenePRO Center, Research Affairs, Chulalongkorn University and The King Chulalongkorn Memorial Hospital, Bangkok, 10330, Thailand.,Department of Pathology, Faculty of Medicine, Chulalongkorn University and The King Chulalongkorn Memorial Hospital, Bangkok, 10330, Thailand
| | - Chatchawit Aporntewan
- Department of Mathematics and Computer Science & Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Wariya Chintanapakdee
- Department of Radiology, Faculty of Medicine, Chulalongkorn University and The King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Virote Sriuranpong
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and The King Chulalongkorn Memorial Hospital, Bangkok, 10330, Thailand
| | - Chanida Vinayanuwattikun
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and The King Chulalongkorn Memorial Hospital, Bangkok, 10330, Thailand.
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48
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Identification of Copy Number Alterations from Next-Generation Sequencing Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1361:55-74. [DOI: 10.1007/978-3-030-91836-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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GSA: an independent development algorithm for calling copy number and detecting homologous recombination deficiency (HRD) from target capture sequencing. BMC Bioinformatics 2021; 22:562. [PMID: 34814825 PMCID: PMC8609767 DOI: 10.1186/s12859-021-04487-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/17/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The gain or loss of large chromosomal regions or even whole chromosomes is termed as genomic scarring and can be observed as copy number variations resulting from the failure of DNA damage repair. RESULTS In this study, a new algorithm called genomic scar analysis (GSA) has developed and validated to calculate homologous recombination deficiency (HRD) score. The two critical submodules were tree recursion (TR) segmentation and filtering, and the estimation and correction of the tumor purity and ploidy. Then, this study evaluated the rationality of segmentation and genotype identification by the GSA algorithm and compared with other two algorithms, PureCN and ASCAT, found that the segmentation result of GSA algorithm was more logical. In addition, the results indicated that the GSA algorithm had an excellent predictive effect on tumor purity and ploidy, if the tumor purity was more than 20%. Furtherly, this study evaluated the HRD scores and BRCA1/2 deficiency status of 195 clinical samples, and the results indicated that the accuracy was 0.98 (comparing with Affymetrix OncoScan™ assay) and the sensitivity was 95.2% (comparing with BRCA1/2 deficiency status), both were well-behaved. Finally, HRD scores and 16 genes mutations (TP53 and 15 HRR pathway genes) were analyzed in 17 cell lines, the results showed that there was higher frequency in HRR pathway genes in high HRD score samples. CONCLUSIONS This new algorithm, named as GSA, could effectively and accurately calculate the purity and ploidy of tumor samples through NGS data, and then reflect the degree of genomic instability and large-scale copy number variations of tumor samples.
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50
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Bardia A, Su F, Solovieff N, Im SA, Sohn J, Lee KS, Campos-Gomez S, Jung KH, Colleoni M, Vázquez RV, Franke F, Hurvitz S, Harbeck N, Chow L, Taran T, Rodriguez Lorenc K, Babbar N, Tripathy D, Lu YS. Genomic Profiling of Premenopausal HR+ and HER2- Metastatic Breast Cancer by Circulating Tumor DNA and Association of Genetic Alterations With Therapeutic Response to Endocrine Therapy and Ribociclib. JCO Precis Oncol 2021; 5:PO.20.00445. [PMID: 34504990 PMCID: PMC8423397 DOI: 10.1200/po.20.00445] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 04/14/2021] [Accepted: 07/28/2021] [Indexed: 12/31/2022] Open
Abstract
PURPOSE This analysis evaluated the genomic landscape of premenopausal patients with hormone receptor–positive and human epidermal growth factor receptor 2–negative advanced breast cancer and the association of genetic alterations with response to ribociclib in the phase III MONALEESA-7 trial. METHODS Premenopausal patients were randomly assigned 1:1 to receive endocrine therapy plus ribociclib or placebo. Plasma collected at baseline was sequenced using targeted next-generation sequencing for approximately 600 relevant cancer genes. The association of circulating tumor DNA alterations with progression-free survival (PFS) was evaluated to identify biomarkers of response and resistance to ribociclib. RESULTS Baseline circulating tumor DNA was sequenced in 565 patients; 489 had evidence of ≥ 1 alteration. The most frequent alterations included PIK3CA (28%), TP53 (19%), CCND1 (10%), MYC (8%), GATA3 (8%), receptor tyrosine kinases (17%), and the Chr8p11.23 locus (12%). A treatment benefit of ribociclib was seen with wild-type (hazard ratio [HR] 0.45 [95% CI, 0.33 to 0.62]) and altered (HR 0.57 [95% CI, 0.36 to 0.9]) PIK3CA. Overall, patients with altered CCND1 had shorter PFS regardless of treatment, suggesting CCND1 as a potential prognostic biomarker. Benefit with ribociclib was seen in patients with altered (HR 0.21 [95% CI, 0.08 to 0.54]) or wild-type (HR 0.52 [95% CI, 0.39 to 0.68]) CCND1, but greater benefit was observed with altered, suggesting predictive potential of CCND1. Alterations in TP53, MYC, Chr8p11.23 locus, and receptor tyrosine kinases were associated with worse PFS, but ribociclib benefit was independent of alteration status. CONCLUSION In this study—to our knowledge, the first large study of premenopausal patients with hormone receptor–positive and human epidermal growth factor receptor 2–negative advanced breast cancer—multiple genomic alterations were associated with poor outcome. A PFS benefit of ribociclib was observed regardless of gene alteration status, although in this exploratory analysis, a magnitude of benefits varied by alteration.
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Affiliation(s)
- Aditya Bardia
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA
| | - Fei Su
- Novartis Pharmaceuticals Corporation, East Hanover, NJ
| | | | - Seock-Ah Im
- Seoul National University Hospital, Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Joohyuk Sohn
- Yonsei Cancer Center, Yonsei University Health System, Seoul, South Korea
| | - Keun Seok Lee
- Center for Breast Cancer, National Cancer Center, Goyang, South Korea
| | - Saul Campos-Gomez
- Centro Oncológico Estatal, Instituto de Seguridad Social del Estado de México y Municipios, Toluca, Mexico
| | - Kyung Hae Jung
- Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Marco Colleoni
- Division of Medical Senology, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | | | - Fabio Franke
- Hospital de Caridade de Ijuí, CACON, Ijuí, Brazil
| | - Sara Hurvitz
- University of California, Los Angeles Jonsson Comprehensive Cancer Center, Los Angeles, CA
| | - Nadia Harbeck
- Department of Obstetrics and Gynecology, Breast Center, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Louis Chow
- Organisation for Oncology and Translational Research, Hong Kong, China
| | - Tetiana Taran
- Novartis Pharmaceuticals Corporation, East Hanover, NJ
| | | | | | - Debu Tripathy
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Yen-Shen Lu
- National Taiwan University Hospital, Taipei, Taiwan
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