1
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Pinto EM, Ribeiro EMSF, Wang J, Phillips AH, Kriwacki RW, Zambetti GP. Clinical and functional analysis of the germline TP53 p.K164E acetylation site variant. Cold Spring Harb Mol Case Stud 2023; 9:a006290. [PMID: 38050059 PMCID: PMC10815290 DOI: 10.1101/mcs.a006290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/27/2023] [Indexed: 12/06/2023] Open
Abstract
TP53 plays a critical role as a tumor suppressor by controlling cell cycle progression, DNA repair, and apoptosis. Post-translational modifications such as acetylation of specific lysine residues in the DNA binding and carboxy-terminus regulatory domains modulate its tumor suppressor activities. In this study, we addressed the functional consequences of the germline TP53 p.K164E (NM_000546.5: c.490A>G) variant identified in a patient with early-onset breast cancer and a significant family history of cancer. K164 is a conserved residue located in the L2 loop of the p53 DNA binding domain that is post-translationally modified by acetylation. In silico, in vitro, and in vivo analyses demonstrated that the glutamate substitution at K164 marginally destabilizes the p53 protein structure but significantly impairs sequence-specific DNA binding, transactivation, and tumor cell growth inhibition. Although p.K164E is currently considered a variant of unknown significance by different clinical genetic testing laboratories, the clinical and laboratory-based findings presented here provide strong evidence to reclassify TP53 p.K164E as a likely pathogenic variant.
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Affiliation(s)
- Emilia Modolo Pinto
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA;
| | - Enilze M S F Ribeiro
- Programa de Pós-graduação em Genética, Universidade Federal do Paraná, Curitiba, Paraná, 81531-980, Brazil;
| | - Jinling Wang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Aaron H Phillips
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Gerard P Zambetti
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA;
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2
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Welter L, Xu L, McKinley D, Dago AE, Prabakar RK, Restrepo-Vassalli S, Xu K, Rodriguez-Lee M, Kolatkar A, Nevarez R, Ruiz C, Nieva J, Kuhn P, Hicks J. Treatment response and tumor evolution: lessons from an extended series of multianalyte liquid biopsies in a metastatic breast cancer patient. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005819. [PMID: 33203646 PMCID: PMC7784493 DOI: 10.1101/mcs.a005819] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/15/2020] [Indexed: 12/17/2022] Open
Abstract
Currently, clinical characterization of metastatic breast cancer is based on tissue samples taken at time of diagnosis. However, tissue biopsies are invasive and tumors are continuously evolving, which indicates the need for minimally invasive longitudinal assessment of the tumor. Blood-based liquid biopsies provide minimal invasive means for serial sampling over the course of treatment and the opportunity to adjust therapies based on molecular markers. Here, we aim to identify cellular changes that occur in breast cancer over the lifespan of an affected patient through single-cell proteomic and genomic analysis of longitudinally sampled solid and liquid biopsies. Three solid and 17 liquid biopsies from peripheral blood of an ER+/HER2− metastatic breast cancer patient collected over 4 years and eight treatment regimens were analyzed for morphology, protein expression, copy-number alterations, and single-nucleotide variations. Analysis of 563 single morphometrically similar circulating tumor cells (CTCs) and 13 cell-free DNA (cfDNA) samples along with biopsies of the primary and metastatic tumor revealed progressive genomic evolution away from the primary tumor profiles, along with changes in ER expression and the appearance of resistance mutations. Both the abundance and the genomic alterations of CTCs and cfDNA were highly correlated and consistent with genomic alterations in the tissue samples. We demonstrate that genomic evolution and acquisition of drug resistance can be detected in real time and at single-cell resolution through liquid biopsy analytes and highlight the utility of liquid biopsies to guide treatment decisions.
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Affiliation(s)
- Lisa Welter
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Liya Xu
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Dillon McKinley
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Angel E Dago
- The Scripps Research Institute, La Jolla, California 92037, USA
| | - Rishvanth K Prabakar
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Sara Restrepo-Vassalli
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Kevin Xu
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Mariam Rodriguez-Lee
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Anand Kolatkar
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Rafael Nevarez
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Carmen Ruiz
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Jorge Nieva
- Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
| | - Peter Kuhn
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA.,Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA.,Viterbi School of Engineering, University of Southern California, Los Angeles, California 90089, USA
| | - James Hicks
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
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Quinn EA, Maciaszek JL, Pinto EM, Phillips AH, Berdy D, Khandwala M, Upadhyaya SA, Zambetti GP, Kriwacki RW, Ellison DW, Nichols KE, Kesserwan C. From uncertainty to pathogenicity: clinical and functional interrogation of a rare TP53 in-frame deletion. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a003921. [PMID: 30886117 PMCID: PMC6672031 DOI: 10.1101/mcs.a003921] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/25/2019] [Indexed: 01/07/2023] Open
Abstract
Li–Fraumeni syndrome (LFS) is a highly penetrant cancer predisposition syndrome caused by heterozygous germline mutations in the TP53 gene. Although more than 200 missense and null TP53 mutations are well established as disease-causing, little is known about the pathogenicity and cancer risks associated with small in-frame deletions. This leads to challenges in variant classification and subsequent difficulty making a molecular diagnosis. We report the genetic testing process for a pediatric patient diagnosed with an undifferentiated high-grade brain tumor following his mother's diagnosis of early-onset bilateral breast cancer. Sequential testing revealed that both harbored a heterozygous three-nucleotide deletion in exon 7 of TP53 (c.764_766delTCA; I255del), which was classified as a variant of uncertain significance. Because the maternal family history was void of any other LFS spectrum tumors, additional information was needed to effectively classify the variant. Targeted TP53 testing of the patient's maternal grandparents confirmed that neither carried the variant; this new de novo data upgraded the variant classification to likely pathogenic. To assess the impact of this mutation on the encoded p53 protein, additional in vitro analyses were performed. Structural modeling predicted that the deletion of isoleucine at codon 255 would disrupt the architecture of the DNA-binding domain, suggesting that it might negatively impact p53 function. Consistent with this notion, the I255del mutant protein exhibited significantly impaired transcriptional activity and greatly reduced growth suppressive properties, similar to more well-characterized LFS-associated p53 mutants. This report illustrates the importance of seeking additional evidence to assign proper pathogenicity classification, which enables optimal genetic counseling and medical management of individuals with LFS and their at-risk relatives.
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Affiliation(s)
- Emily A Quinn
- St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Jamie L Maciaszek
- St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Emilia M Pinto
- St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Aaron H Phillips
- St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - David Berdy
- Norwegian American Hospital, Chicago, Illinois 60622, USA
| | | | | | - Gerard P Zambetti
- St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | | | - David W Ellison
- St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Kim E Nichols
- St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Chimene Kesserwan
- St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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Toh MR, Chong ST, Chan SH, Low CE, Ishak NDB, Lim JQ, Courtney E, Ngeow J. Functional analysis of clinical BARD1 germline variants. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a004093. [PMID: 31371347 PMCID: PMC6672023 DOI: 10.1101/mcs.a004093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/10/2019] [Indexed: 12/31/2022] Open
Abstract
Germline pathogenic variants in BRCA1/2 account for one-third of familial breast cancers. The majority of BRCA1 function requires heterodimerization with BARD1. In contrast to BRCA1, BARD1 is a low-penetrance gene with an unclear clinical relevance, partly because of limited functional evidence. Using patient-derived lymphoblastoid cells, we functionally characterized two pathogenic variants (c.1833dupT, c.2099delG) and three variants of uncertain significance (VUSs) (c.73G>C, c.1217G>A, c.1918C>A). Three of these patients had breast cancers, whereas the remaining had colorectal cancers (n = 3). Both patients with pathogenic variants (c.1833dupT, c.2099delG) developed breast cancers with aggressive disease phenotypes such as triple-negative breast cancer and high cancer grades. As BARD1 encompasses multiple functional domains, including those of apoptosis and homologous recombination repair, we hypothesized that the function being impaired would correspond with the domain where the variant was located. Variants c.1918C>A, c.1833dupT, c.1217G>A, and c.2099delG, located within and proximal to apoptotic domains of ankyrin and BRCT, were associated with impaired apoptosis. Conversely, apoptosis function was preserved in c.73G>C, which was distant from the ankyrin domain. All variants displayed normal BRCA1 heterodimerization and RAD51 colocalization, consistent with their location being distal to BRCA1—and RAD51-binding domains. In view of deficient apoptosis, VUSs (c.1217G>A and c.1918C>A) may be pathogenic or likely pathogenic variants. In summary, functional analysis of BARD1 VUSs requires a combination of assays and, more importantly, the use of appropriate functional assays with consideration to the variant's location.
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Affiliation(s)
- Ming Ren Toh
- Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Siao Ting Chong
- Division of Medical Oncology, National Cancer Center, Singapore, 169610, Singapore
| | - Sock Hoai Chan
- Division of Medical Oncology, National Cancer Center, Singapore, 169610, Singapore
| | - Chen Ee Low
- Division of Medical Oncology, National Cancer Center, Singapore, 169610, Singapore
| | | | - Jing Quan Lim
- Division of Medical Oncology, National Cancer Center, Singapore, 169610, Singapore
| | - Eliza Courtney
- Division of Medical Oncology, National Cancer Center, Singapore, 169610, Singapore
| | - Joanne Ngeow
- Duke-NUS Medical School, Singapore, 169857, Singapore.,Division of Medical Oncology, National Cancer Center, Singapore, 169610, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 639798, Singapore.,Institute of Molecular and Cellular Biology, Agency for Science, Technology and Research, Singapore, 138673, Singapore
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5
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Butler TM, Boniface CT, Johnson-Camacho K, Tabatabaei S, Melendez D, Kelley T, Gray J, Corless CL, Spellman PT. Circulating tumor DNA dynamics using patient-customized assays are associated with outcome in neoadjuvantly treated breast cancer. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a003772. [PMID: 30833418 PMCID: PMC6549569 DOI: 10.1101/mcs.a003772] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 02/15/2019] [Indexed: 12/29/2022] Open
Abstract
Pathological complete response (pCR) is an accurate predictor of good outcome following neoadjuvant chemotherapy (NAC) for locally advanced breast cancer. The presence of circulating-tumor DNA (ctDNA) has recently been reported to be strongly predictive of poor outcome in similar patient groups. We monitored ctDNA levels from 10 women undergoing NAC for locally advanced breast cancer using a patient-specific, hybrid-capture sequencing technique sensitive to the level of one altered allele in 10,000. Plasma was collected prior to the start of NAC, prior to each infusion of NAC, and during follow-up for between 350 and 1150 d after the start of NAC. Prior to the start of NAC, ctDNA was detectable in 3/3 triple negative, 3/3 HER2+, and 2/4 HER2−, ER+ breast cancer patients. Total cell-free DNA levels were considerably higher when patients were on NAC than at other times. ctDNA dynamics during NAC showed that patients with pCR experienced rapid declines in ctDNA levels, whereas patients without pCR typically showed evidence of residual ctDNA after initiation of treatment. Intriguingly, two of three patients that showed marked increases in ctDNA while on NAC experienced rapid recurrences (<2 yr following start of NAC). The third patient that had increases in ctDNA levels while on NAC had low-grade ER+ disease and showed residual ctDNA after surgery, which became undetectable after local radiation. Taken together, these results demonstrate the ability of our approach to sensitively serially monitor ctDNA during NAC, and identifies a need to further investigate the possibility of stratifying patients who need additional treatment or identify therapies that are ineffective.
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Affiliation(s)
- Timothy M Butler
- Department of Molecular and Medical Genetics, Oregon Health and Science University (OHSU) Portland, Oregon 97201, USA.,Wellcome Trust Sanger Institute, Cancer Ageing and Somatic Mutation, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Christopher T Boniface
- Department of Molecular and Medical Genetics, Oregon Health and Science University (OHSU) Portland, Oregon 97201, USA
| | - Katie Johnson-Camacho
- Department of Molecular and Medical Genetics, Oregon Health and Science University (OHSU) Portland, Oregon 97201, USA
| | - Shaadi Tabatabaei
- Department of Molecular and Medical Genetics, Oregon Health and Science University (OHSU) Portland, Oregon 97201, USA
| | - Daira Melendez
- Department of Molecular and Medical Genetics, Oregon Health and Science University (OHSU) Portland, Oregon 97201, USA
| | - Taylor Kelley
- Department of Molecular and Medical Genetics, Oregon Health and Science University (OHSU) Portland, Oregon 97201, USA
| | - Joe Gray
- Department of Biomedical Engineering, OHSU Portland, Oregon 97201, USA.,Knight Cancer Institute, OHSU Portland, Oregon 97201, USA.,Center for Spatial Systems Biomedicine, OHSU Portland, Oregon 97201, USA
| | - Christopher L Corless
- Knight Cancer Institute, OHSU Portland, Oregon 97201, USA.,Division of Hematology and Medical Oncology, Portland Veterans Affairs Health Care System, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97201, USA
| | - Paul T Spellman
- Department of Molecular and Medical Genetics, Oregon Health and Science University (OHSU) Portland, Oregon 97201, USA.,Knight Cancer Institute, OHSU Portland, Oregon 97201, USA.,Center for Spatial Systems Biomedicine, OHSU Portland, Oregon 97201, USA
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6
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Thibodeau ML, Zhao EY, Reisle C, Ch'ng C, Wong HL, Shen Y, Jones MR, Lim HJ, Young S, Cremin C, Pleasance E, Zhang W, Holt R, Eirew P, Karasinska J, Kalloger SE, Taylor G, Majounie E, Bonakdar M, Zong Z, Bleile D, Chiu R, Birol I, Gelmon K, Lohrisch C, Mungall KL, Mungall AJ, Moore R, Ma YP, Fok A, Yip S, Karsan A, Huntsman D, Schaeffer DF, Laskin J, Marra MA, Renouf DJ, Jones SJM, Schrader KA. Base excision repair deficiency signatures implicate germline and somatic MUTYH aberrations in pancreatic ductal adenocarcinoma and breast cancer oncogenesis. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a003681. [PMID: 30833417 PMCID: PMC6549570 DOI: 10.1101/mcs.a003681] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/17/2019] [Indexed: 12/21/2022] Open
Abstract
We report a case of early-onset pancreatic ductal adenocarcinoma in a patient harboring biallelic MUTYH germline mutations, whose tumor featured somatic mutational signatures consistent with defective MUTYH-mediated base excision repair and the associated driver KRAS transversion mutation p.Gly12Cys. Analysis of an additional 730 advanced cancer cases (N = 731) was undertaken to determine whether the mutational signatures were also present in tumors from germline MUTYH heterozygote carriers or if instead the signatures were only seen in those with biallelic loss of function. We identified two patients with breast cancer each carrying a pathogenic germline MUTYH variant with a somatic MUTYH copy loss leading to the germline variant being homozygous in the tumor and demonstrating the same somatic signatures. Our results suggest that monoallelic inactivation of MUTYH is not sufficient for C:G>A:T transversion signatures previously linked to MUTYH deficiency to arise (N = 9), but that biallelic complete loss of MUTYH function can cause such signatures to arise even in tumors not classically seen in MUTYH-associated polyposis (N = 3). Although defective MUTYH is not the only determinant of these signatures, MUTYH germline variants may be present in a subset of patients with tumors demonstrating elevated somatic signatures possibly suggestive of MUTYH deficiency (e.g., COSMIC Signature 18, SigProfiler SBS18/SBS36, SignatureAnalyzer SBS18/SBS36).
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Affiliation(s)
- My Linh Thibodeau
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada.,Hereditary Cancer Program, BC Cancer, Vancouver, British Columbia V5Z 1H5, Canada
| | - Eric Y Zhao
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Caralyn Reisle
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Carolyn Ch'ng
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Hui-Li Wong
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Martin R Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Howard J Lim
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - Sean Young
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada.,Cancer Genetics and Genomics Laboratory, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - Carol Cremin
- Hereditary Cancer Program, BC Cancer, Vancouver, British Columbia V5Z 1H5, Canada.,Pancreas Centre BC, Vancouver, British Columbia V5Z 1L8, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Wei Zhang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Robert Holt
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Peter Eirew
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada
| | | | - Steve E Kalloger
- Pancreas Centre BC, Vancouver, British Columbia V5Z 1L8, Canada.,School of Population and Public Health, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,The Canadian Centre for Applied Research in Cancer Control, Vancouver, British Columbia V5Z 1L3, Canada.,Department of Pathology and Laboratory Medicine, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - Greg Taylor
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Elisa Majounie
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Melika Bonakdar
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Zusheng Zong
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Dustin Bleile
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Readman Chiu
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Inanc Birol
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Karen Gelmon
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - Caroline Lohrisch
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Yussanne P Ma
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Alexandra Fok
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada.,Hereditary Cancer Program, BC Cancer, Vancouver, British Columbia V5Z 1H5, Canada
| | - Stephen Yip
- Cancer Genetics and Genomics Laboratory, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada.,Department of Pathology & Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia V5Z 1M9, Canada
| | - Aly Karsan
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada.,Department of Pathology and Laboratory Medicine, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - David Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada.,Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Department of Pathology & Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia V5Z 1M9, Canada
| | - David F Schaeffer
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada.,Pancreas Centre BC, Vancouver, British Columbia V5Z 1L8, Canada.,Department of Pathology & Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia V5Z 1M9, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - Marco A Marra
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Daniel J Renouf
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada.,Pancreas Centre BC, Vancouver, British Columbia V5Z 1L8, Canada
| | - Steven J M Jones
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Kasmintan A Schrader
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Hereditary Cancer Program, BC Cancer, Vancouver, British Columbia V5Z 1H5, Canada.,Pancreas Centre BC, Vancouver, British Columbia V5Z 1L8, Canada.,Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada
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7
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Krempely K, Karam R. A novel de novo CDH1 germline variant aids in the classification of carboxy-terminal E-cadherin alterations predicted to escape nonsense-mediated mRNA decay. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a003012. [PMID: 29798843 PMCID: PMC6071572 DOI: 10.1101/mcs.a003012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/16/2018] [Indexed: 12/30/2022] Open
Abstract
Most truncating cadherin 1 (CDH1) pathogenic alterations confer an elevated lifetime risk of diffuse gastric cancer (DGC) and lobular breast cancer (LBC). However, transcripts containing carboxy-terminal premature stop codons have been demonstrated to escape the nonsense-mediated mRNA decay pathway, and gastric and breast cancer risks associated with these truncations should be carefully evaluated. A female patient underwent multigene panel testing because of a personal history of invasive LBC diagnosed at age 54, which identified the germline CDH1 nonsense alteration, c.2506G>T (p.Glu836*), in the last exon of the gene. Subsequent parental testing for the alteration was negative and additional short tandem repeat analysis confirmed the familial relationships and the de novo occurrence in the proband. Based on the de novo occurrence, clinical history, and rarity in general population databases, this alteration was classified as a likely pathogenic variant. This is the most carboxy-terminal pathogenic alteration reported to date. Additionally, this alteration contributed to the classification of six other upstream CDH1 carboxy-terminal truncating variants as pathogenic or likely pathogenic. Identifying the most distal pathogenic alteration provides evidence to classify other carboxy-terminal truncating variants as either pathogenic or benign, a fundamental step to offering presymptomatic screening and prophylactic procedures to the appropriate patients.
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Affiliation(s)
| | - Rachid Karam
- Ambry Genetics, Aliso Viejo, California 92656, USA
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8
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Dubard Gault M, Mandelker D, DeLair D, Stewart CR, Kemel Y, Sheehan MR, Siegel B, Kennedy J, Marcell V, Arnold A, Al-Ahmadie H, Modak S, Robson M, Shukla N, Roberts S, Vijai J, Topka S, Kentsis A, Cadoo K, Carlo M, Latham Schwark A, Reznik E, Dinatale R, Hechtman J, Borras Flores E, Jairam S, Yang C, Li Y, Bayraktar EC, Ceyhan-Birsoy O, Zhang L, Kohlman W, Schiffman J, Stadler Z, Birsoy K, Kung A, Offit K, Walsh MF. Germline SDHA mutations in children and adults with cancer. Cold Spring Harb Mol Case Stud 2018; 4:a002584. [PMID: 30068732 PMCID: PMC6071569 DOI: 10.1101/mcs.a002584] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 05/10/2018] [Indexed: 11/24/2022] Open
Abstract
Mutations in succinate dehydrogenase complex genes predispose to familial paraganglioma-pheochromocytoma syndrome (FPG) and gastrointestinal stromal tumors (GIST). Here we describe cancer patients undergoing agnostic germline testing at Memorial Sloan Kettering Cancer Center and found to harbor germline SDHA mutations. Using targeted sequencing covering the cancer census genes, we identified 10 patients with SDHA germline mutations. Cancer diagnoses for these patients carrying SDHA germline mutations included neuroblastoma (n = 1), breast (n = 1), colon (n = 1), renal (n = 1), melanoma and uterine (n = 1), prostate (n = 1), endometrial (n = 1), bladder (n = 1), and gastrointestinal stromal tumor (GIST) (n = 2). Immunohistochemical staining and assessment of patient tumors for second hits and loss of heterozygosity in SDHA confirmed GIST as an SDHA-associated tumor and suggests SDHA germline mutations may be a driver in neuroblastoma tumorigenesis.
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Affiliation(s)
- Marianne Dubard Gault
- Graduate Education Memorial, Memorial Sloan Kettering Cancer Center and Weill Cornell Genetics, New York, New York 10065, USA
| | - Diana Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Deborah DeLair
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Carolyn R Stewart
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Yelena Kemel
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
- Niehaus Center for Inherited Cancer Genomics, Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Margaret R Sheehan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Beth Siegel
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Jennifer Kennedy
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Vanessa Marcell
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Angela Arnold
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Hikmat Al-Ahmadie
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Shakeel Modak
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Mark Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
- Niehaus Center for Inherited Cancer Genomics, Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Stephen Roberts
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
- Niehaus Center for Inherited Cancer Genomics, Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Sabine Topka
- Niehaus Center for Inherited Cancer Genomics, Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Alex Kentsis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Karen Cadoo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
- Niehaus Center for Inherited Cancer Genomics, Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Maria Carlo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
- Niehaus Center for Inherited Cancer Genomics, Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Alicia Latham Schwark
- Graduate Education Memorial, Memorial Sloan Kettering Cancer Center and Weill Cornell Genetics, New York, New York 10065, USA
| | - Ed Reznik
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Renzo Dinatale
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Jaclyn Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Ester Borras Flores
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Sowmaya Jairam
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Ciyu Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Yirong Li
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | | | - Ozge Ceyhan-Birsoy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Wendy Kohlman
- Family Cancer Assessment Clinic, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Joshua Schiffman
- Family Cancer Assessment Clinic, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Zsofia Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
- Niehaus Center for Inherited Cancer Genomics, Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Kivanc Birsoy
- Family Cancer Assessment Clinic, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Andrew Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
- Niehaus Center for Inherited Cancer Genomics, Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Michael F Walsh
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
- Niehaus Center for Inherited Cancer Genomics, Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
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9
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Suarez-Kelly LP, Akagi K, Reeser JW, Samorodnitsky E, Reeder M, Smith A, Roychowdhury S, Symer DE, Carson WE. Metaplastic breast cancer in a patient with neurofibromatosis type 1 and somatic loss of heterozygosity. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a002352. [PMID: 29449315 PMCID: PMC5880258 DOI: 10.1101/mcs.a002352] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/30/2018] [Indexed: 01/06/2023] Open
Abstract
Metaplastic breast carcinoma (MBC) is rare and has a poor prognosis. Here we describe genetic analysis of a 41-yr-old female patient with MBC and neurofibromatosis type I (NF1). She initially presented with pT3N1a, grade 3 MBC, but lung metastases were discovered subsequently. To identify the molecular cause of her NF1, we screened for germline mutations disrupting NF1 or SPRED1, revealing a heterozygous germline single-nucleotide variant (SNV) in exon 21 of NF1 at c.2709G>A, Chr 17: 29556342. By report, this variant disrupts pre-mRNA splicing of NF1 transcripts. No pathogenic mutations were identified in SPRED1. A potential association between MBC and NF1 was reported in eight previous cases, but none underwent detailed genomics analysis. To identify additional candidate germline variants potentially predisposing to MBC, we conducted targeted exome sequencing of 279 established cancer-causing genes in a control blood sample, disclosing four rare SNVs. Analysis of her breast tumor showed markedly altered variant allelic fractions (VAFs) for two (50%) of them, revealing somatic loss of heterozygosity (LOH) at germline SNVs. Of these, only the VAF of the pathogenic SNV in NF1 was increased in the tumor. Tumor sequencing demonstrated five somatic mutations altering TP53, BRCA1, and other genes potentially contributing to cancer formation. Because somatic LOH at certain germline SNVs can enhance their impacts, we conclude that increased allelic imbalance of the pathogenic SNV in NF1 likely contributed to tumorigenesis. Our results highlight a need to assess predisposing genetic factors and LOH that can cause rare, aggressive diseases such as MBC in NF1.
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Affiliation(s)
- Lorena P Suarez-Kelly
- The Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Keiko Akagi
- The Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, The Ohio State University, Columbus, Ohio 43210, USA.,Department of Cancer Biology and Genetics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Julie W Reeser
- The Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Eric Samorodnitsky
- The Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Matthew Reeder
- The Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Amy Smith
- The Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Sameek Roychowdhury
- The Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - David E Symer
- The Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, The Ohio State University, Columbus, Ohio 43210, USA.,Department of Cancer Biology and Genetics, The Ohio State University, Columbus, Ohio 43210, USA
| | - William E Carson
- The Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, The Ohio State University, Columbus, Ohio 43210, USA.,Division of Surgical Oncology, Department of Surgery, The Ohio State University, Columbus, Ohio 43210, USA
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10
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Schuh A, Dreau H, Knight SJL, Ridout K, Mizani T, Vavoulis D, Colling R, Antoniou P, Kvikstad EM, Pentony MM, Hamblin A, Protheroe A, Parton M, Shah KA, Orosz Z, Athanasou N, Hassan B, Flanagan AM, Ahmed A, Winter S, Harris A, Tomlinson I, Popitsch N, Church D, Taylor JC. Clinically actionable mutation profiles in patients with cancer identified by whole-genome sequencing. Cold Spring Harb Mol Case Stud 2018; 4:a002279. [PMID: 29610388 PMCID: PMC5880257 DOI: 10.1101/mcs.a002279] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 02/09/2018] [Indexed: 02/07/2023] Open
Abstract
Next-generation sequencing (NGS) efforts have established catalogs of mutations relevant to cancer development. However, the clinical utility of this information remains largely unexplored. Here, we present the results of the first eight patients recruited into a clinical whole-genome sequencing (WGS) program in the United Kingdom. We performed PCR-free WGS of fresh frozen tumors and germline DNA at 75× and 30×, respectively, using the HiSeq2500 HTv4. Subtracted tumor VCFs and paired germlines were subjected to comprehensive analysis of coding and noncoding regions, integration of germline with somatically acquired variants, and global mutation signatures and pathway analyses. Results were classified into tiers and presented to a multidisciplinary tumor board. WGS results helped to clarify an uncertain histopathological diagnosis in one case, led to informed or supported prognosis in two cases, leading to de-escalation of therapy in one, and indicated potential treatments in all eight. Overall 26 different tier 1 potentially clinically actionable findings were identified using WGS compared with six SNVs/indels using routine targeted NGS. These initial results demonstrate the potential of WGS to inform future diagnosis, prognosis, and treatment choice in cancer and justify the systematic evaluation of the clinical utility of WGS in larger cohorts of patients with cancer.
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Affiliation(s)
- Anna Schuh
- Oxford Molecular Diagnostics Centre, Department of Oncology, University of Oxford, Oxford OX3 9DU, United Kingdom
- Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, United Kingdom
| | - Helene Dreau
- Oxford Molecular Diagnostics Centre, Department of Oncology, University of Oxford, Oxford OX3 9DU, United Kingdom
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Samantha J L Knight
- Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Kate Ridout
- Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, United Kingdom
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Tuba Mizani
- Oxford Molecular Diagnostics Centre, Department of Oncology, University of Oxford, Oxford OX3 9DU, United Kingdom
- Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, United Kingdom
| | - Dimitris Vavoulis
- Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, United Kingdom
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Richard Colling
- Oxford Molecular Diagnostics Centre, Department of Oncology, University of Oxford, Oxford OX3 9DU, United Kingdom
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Pavlos Antoniou
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, United Kingdom
| | - Erika M Kvikstad
- Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Melissa M Pentony
- Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Angela Hamblin
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, United Kingdom
| | - Andrew Protheroe
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, United Kingdom
| | - Marina Parton
- Breast Unit, Royal Marsden NHS Foundation Trust and Kingston NHS Foundation Trust, London SW3 6JJ, United Kingdom
| | - Ketan A Shah
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, United Kingdom
| | - Zsolt Orosz
- Breast Unit, Royal Marsden NHS Foundation Trust and Kingston NHS Foundation Trust, London SW3 6JJ, United Kingdom
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, United Kingdom
| | - Nick Athanasou
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, United Kingdom
| | - Bass Hassan
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Adrienne M Flanagan
- University College London, Cancer Institute and Royal National Orthopaedic NHS Hospital, London WC1E 6BT, United Kingdom
| | - Ahmed Ahmed
- Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Stuart Winter
- Department of Ear Nose and Throat-Head and Neck Surgery, Oxford University Hospitals, Oxford OX3 9DU, United Kingdom
| | - Adrian Harris
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Ian Tomlinson
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Niko Popitsch
- The Children's Cancer Research Institute (CCRI), 1090 Vienna, Austria
| | - David Church
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Jenny C Taylor
- Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
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11
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Skurikhin SS, Milkevich IN, Bolotin IA, Odintsov VA, Buynyakova AI, Zhogoleva EB, Suvorova YV. [Vacuum-assisted excision of focal dysplasia of mammary glands. Single-center experience]. Khirurgiia (Mosk) 2018:63-65. [PMID: 29460881 DOI: 10.17116/hirurgia2018263-65] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
AIM To assess the diagnostic significance and safety of vacuum-assisted resection in patients with focal breast cancer BIRADS category 3 and 4. MATERIAL AND METHODS The procedure was performed in 50 women aged 22 to 51 years (35.1±2.6 years). RESULTS There were no any complications immediately after vacuum resection. Tissue of the neoplasm was removed in full in all patients. Benign and malignant tumors were observed in 94 and 6% cases respectively. All cases were identified in BIRADS category 3. CONCLUSION Vacuum-aspiration resection is of great importance in the diagnosis and treatment of focal dysplasia of the mammary glands. It has a high diagnostic accuracy, allows you to remove focal disease in full without serious complications.
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Affiliation(s)
- S S Skurikhin
- St. Petersburg Clinical Hospital of the Russian Academy of Sciences, St. Petersburg, Russia
| | - I N Milkevich
- St. Petersburg Clinical Hospital of the Russian Academy of Sciences, St. Petersburg, Russia
| | - I A Bolotin
- St. Petersburg Clinical Hospital of the Russian Academy of Sciences, St. Petersburg, Russia
| | - V A Odintsov
- St. Petersburg Clinical Hospital of the Russian Academy of Sciences, St. Petersburg, Russia
| | - A I Buynyakova
- St. Petersburg Clinical Hospital of the Russian Academy of Sciences, St. Petersburg, Russia
| | - E B Zhogoleva
- St. Petersburg Clinical Hospital of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Yu V Suvorova
- St. Petersburg Clinical Hospital of the Russian Academy of Sciences, St. Petersburg, Russia
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12
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Grewal JK, Eirew P, Jones M, Chiu K, Tessier-Cloutier B, Karnezis AN, Karsan A, Mungall A, Zhou C, Yip S, Tinker AV, Laskin J, Marra M, Jones SJM. Detection and genomic characterization of a mammary-like adenocarcinoma. Cold Spring Harb Mol Case Stud 2017; 3:a002170. [PMID: 28877932 DOI: 10.1101/mcs.a002170] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 08/02/2017] [Indexed: 12/31/2022] Open
Abstract
Whole-genome and transcriptome sequencing were performed to identify potential therapeutic strategies in the absence of viable treatment options for a patient initially diagnosed with vulvar adenocarcinoma. Genomic events were prioritized by comparison against variant distributions in the TCGA pan-cancer data set and complemented with detailed transcriptome sequencing and copy-number analysis. These findings were considered against published scientific literature in order to evaluate the functional effects of potentially relevant genomic events. Analysis of the transcriptome against a background of 27 TCGA cancer types led to reclassification of the tumor as a primary HER2+ mammary-like adenocarcinoma of the vulva. This revised diagnosis was subsequently confirmed by follow-up immunohistochemistry for a mammary-like adenocarcinoma. The patient was treated with chemotherapy and targeted therapies for HER2+ breast cancer. The detailed pathology and genomic findings of this case are presented herein.
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13
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Thibodeau ML, Reisle C, Zhao E, Martin LA, Alwelaie Y, Mungall KL, Ch'ng C, Thomas R, Ng T, Yip S, J Lim H, Sun S, Young SS, Karsan A, Zhao Y, Mungall AJ, Moore RA, J Renouf D, Gelmon K, Ma YP, Hayes M, Laskin J, Marra MA, Schrader KA, Jones SJM. Genomic profiling of pelvic genital type leiomyosarcoma in a woman with a germline CHEK2:c.1100delC mutation and a concomitant diagnosis of metastatic invasive ductal breast carcinoma. Cold Spring Harb Mol Case Stud 2017; 3:mcs.a001628. [PMID: 28514723 PMCID: PMC5593158 DOI: 10.1101/mcs.a001628] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/14/2017] [Indexed: 12/19/2022] Open
Abstract
We describe a woman with the known pathogenic germline variant CHEK2:c.1100delC and synchronous diagnoses of both pelvic genital type leiomyosarcoma (LMS) and metastatic invasive ductal breast carcinoma. CHEK2 (checkpoint kinase 2) is a tumor-suppressor gene encoding a serine/threonine-protein kinase (CHEK2) involved in double-strand DNA break repair and cell cycle arrest. The CHEK2:c.1100delC variant is a moderate penetrance allele resulting in an approximately twofold increase in breast cancer risk. Whole-genome and whole-transcriptome sequencing were performed on the leiomyosarcoma and matched blood-derived DNA. Despite the presence of several genomic hits within the double-strand DNA damage pathway (CHEK2 germline variant and multiple RAD51B somatic structural variants), tumor profiling did not show an obvious DNA repair deficiency signature. However, even though the LMS displayed clear malignant features, its genomic profiling revealed several characteristics classically associated with leiomyomas including a translocation, t(12;14), with one breakpoint disrupting RAD51B and the other breakpoint upstream of HMGA2 with very high expression of HMGA2 and PLAG1. This is the first report of LMS genomic profiling in a patient with the germline CHEK2:c.1100delC variant and an additional diagnosis of metastatic invasive ductal breast carcinoma. We also describe a possible mechanistic relationship between leiomyoma and LMS based on genomic and transcriptome data. Our findings suggest that RAD51B translocation and HMGA2 overexpression may play an important role in LMS oncogenesis.
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Affiliation(s)
- My Linh Thibodeau
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
| | - Caralyn Reisle
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, British Columbia V5Z 4S6, Canada
| | - Eric Zhao
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, British Columbia V5Z 4S6, Canada
| | - Lee Ann Martin
- Fraser Valley Cancer Centre, British Columbia Cancer Agency, Surrey, British Columbia V3V 1Z2, Canada
| | - Yazeed Alwelaie
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V5Z 1M9, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, British Columbia V5Z 4S6, Canada
| | - Carolyn Ch'ng
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, British Columbia V5Z 4S6, Canada
| | - Ruth Thomas
- Hereditary Cancer Program, British Columbia Cancer Agency-Abbotsford, Abbotsford, British Columbia V2S 0C2, Canada
| | - Tony Ng
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V5Z 1M9, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V5Z 1M9, Canada
| | - Howard J Lim
- British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
| | - Sophie Sun
- British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
| | - Sean S Young
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V5Z 1M9, Canada.,Cancer Genetics Laboratory, Department of Pathology and Laboratory Medicine, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
| | - Aly Karsan
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, British Columbia V5Z 4S6, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V5Z 1M9, Canada.,Cancer Genetics Laboratory, Department of Pathology and Laboratory Medicine, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, British Columbia V5Z 4S6, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, British Columbia V5Z 4S6, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, British Columbia V5Z 4S6, Canada
| | - Daniel J Renouf
- British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
| | - Karen Gelmon
- British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
| | - Yussanne P Ma
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, British Columbia V5Z 4S6, Canada
| | - Malcolm Hayes
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V5Z 1M9, Canada.,Cancer Genetics Laboratory, Department of Pathology and Laboratory Medicine, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
| | - Janessa Laskin
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, British Columbia V5Z 4S6, Canada
| | - Marco A Marra
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, British Columbia V5Z 4S6, Canada
| | - Kasmintan A Schrader
- Hereditary Cancer Program, Department of Medical Genetics, British Columbia Cancer Agency, 614-750 West Broadway, Vancouver British Columbia V5Z 1H5, Canada
| | - Steven J M Jones
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, British Columbia V5Z 4S6, Canada
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14
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Parachoniak CA, Rankin A, Gaffney B, Hartmaier R, Spritz D, Erlich RL, Miller VA, Morosini D, Stephens P, Ross JS, Keech J, Chmielecki J. Exceptional durable response to everolimus in a patient with biphenotypic breast cancer harboring an STK11 variant. Cold Spring Harb Mol Case Stud 2017; 3:mcs.a000778. [PMID: 28550065 PMCID: PMC5593157 DOI: 10.1101/mcs.a000778] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 05/23/2017] [Indexed: 12/31/2022] Open
Abstract
Metastatic triple-negative breast cancer comprises 12%–17% of breast cancers and carries a poor prognosis relative to other breast cancer subtypes. Treatment options in this disease are largely limited to systemic chemotherapy. A majority of clinical studies assessing efficacy of targeted therapeutics (e.g., the mammalian target of rapamycin [mTOR] inhibitor everolimus) in advanced breast cancer patients have not utilized predictive genomic biomarker-based selection and have reported only modest improvement in the clinical outcome relative to standard of care. However, recent reports have highlighted significant clinical responses of breast malignancies harboring alterations in genes involved in the phosphoinositide 3-kinase (PI3K)/AKT/mTOR signaling pathway to mTOR-inhibitor-involving regimens, underscoring the potential clinical benefit of treating subsets of breast cancer patients with molecularly matched targeted therapies. As the paradigm of cancer treatment shifts from chemotherapeutic regimens to more personalized approaches, the identification of additional reliable biomarkers is essential for identifying patients likely to derive maximum benefit from targeted therapies. Herein, we report a near-complete and ongoing 14-mo response to everolimus therapy of a heavily pretreated patient with biphenotypic, metastatic breast cancer. Genomic profiling of the metastatic triple-negative liver specimen identified a single reportable point mutation, STK11 F354L, that appears to have undergone loss of heterozygosity. No other alterations within the PI3K/mTOR pathway were observed. Published functional biochemical data on this variant are conflicting, and germline data, albeit with unclear zygosity status, are suggestive of a benign polymorphism role. Together with the preclinical data, this case suggests further investigation of this variant is warranted to better understand its role as a potential biomarker for mTOR inhibitor sensitivity in the appropriate clinical context.
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Affiliation(s)
| | - Andrew Rankin
- Foundation Medicine, Cambridge, Massachusetts 02141, USA
| | | | - Ryan Hartmaier
- Foundation Medicine, Cambridge, Massachusetts 02141, USA
| | - Dan Spritz
- Foundation Medicine, Cambridge, Massachusetts 02141, USA
| | | | | | | | - Phil Stephens
- Foundation Medicine, Cambridge, Massachusetts 02141, USA
| | - Jeffrey S Ross
- Foundation Medicine, Cambridge, Massachusetts 02141, USA.,Albany Medical College, Albany, New York 12208, USA
| | - John Keech
- MultiCare Regional Cancer Center, Gig Harbor, Washington 98335, USA
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Brannon AR, Frizziero M, Chen D, Hummel J, Gallo J, Riester M, Patel P, Cheung W, Morrissey M, Carbone C, Cottini S, Tortora G, Melisi D. Molecular analysis of a male breast cancer patient with prolonged stable disease under mTOR/PI3K inhibitors BEZ235/everolimus. Cold Spring Harb Mol Case Stud 2016; 2:a000620. [PMID: 27148582 DOI: 10.1101/mcs.a000620] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The mTORC1 inhibitor everolimus (Afinitor/RAD001) has been approved for multiple cancer indications, including ER+/HER2− metastatic breast cancer. However, the combination of everolimus with the dual PI3K/mTOR inhibitor BEZ235 was shown to be more efficacious than either everolimus or BEZ235 alone in preclinical models. Herein, we describe a male breast cancer (MBC) patient who was diagnosed with hormone receptor-positive (HR+)/HER2− stage IIIA invasive ductal carcinoma and sequentially treated with chemoradiotherapy and hormonal therapy. Upon the development of metastases, the patient began a 200 mg twice-daily BEZ235 and 2.5 mg weekly everolimus combination regimen. The patient sustained a prolonged stable disease of 18 mo while undergoing the therapy, before his tumor progressed again. Therefore, we sought to both better understand MBC and investigate the underlying molecular mechanisms of the patient's sensitivity and subsequent resistance to the BEZ235/everolimus combination therapy. Genomic and immunohistochemical analyses were performed on samples collected from the initial invasive ductal carcinoma pretreatment and a metastasis postprogression on the BEZ235/everolimus combination treatment. Both tumors were relatively quiet genomically with no overlap to recurrent MBC alterations in the literature. Markers of PI3K/mTOR pathway hyperactivation were not identified in the pretreatment sample, which complements previous reports of HR+ female breast cancers being responsive to mTOR inhibition without this activation. The postprogression sample, however, demonstrated greater than fivefold increased estrogen receptor and pathogenesis-related protein expression, which could have constrained the PI3K/mTOR pathway inhibition by BEZ235/everolimus. Overall, these analyses have augmented the limited episteme on MBC genetics and treatment.
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