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Huang X, Chen C, Lin Y, Wang C, Zhou X, Xu Y, Sun Q, Zhou Y. Pedigree analysis exploring the inconsistency between diverse phenotypes and testing criteria for germline TP53 mutations in Chinese women with breast cancer. Breast Cancer Res Treat 2024; 206:653-666. [PMID: 38878125 PMCID: PMC11208215 DOI: 10.1007/s10549-024-07341-7] [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: 11/28/2023] [Accepted: 04/10/2024] [Indexed: 06/27/2024]
Abstract
PURPOSE In the present study, we addressed the inconsistency between the testing criteria and diverse phenotypes for germline TP53 mutation in patients with breast cancer in the Chinese population. METHOD We proposed a new added item (synchronous or metachronous bilateral breast cancer) as one of the testing criteria (aimed at high-penetrance breast cancer susceptibility genes) and applied it for determining TP53 germline mutation status in 420 female patients with breast cancer using multigene panel-based next-generation sequencing, Sanger sequencing, and mass spectrometry. RESULTS We found that 1.4% of patients carried a pathogenic or likely pathogenic germline TP53 mutation. Compared with BRCA mutation carriers (8.0%) and non-carriers (7.1%), TP53 mutation carriers (33.3%) developed breast cancer earlier. The majority of TP53 mutation carriers (66.7%) developed breast cancer after age 30 and had bilateral breast cancer (33.3%). Pedigree investigation of four TP53 carriers and a patient with a TP53 variant of unknown significance revealed that neither of their parents harbored the same mutations as the probands, indicating that the mutations might occur de novo. CONCLUSION Our study revealed distinguishing features of TP53 carriers among Chinese women with breast cancer, which is inconsistent with the currently used testing criteria; therefore, the newly proposed testing criteria may be more appropriate.
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Affiliation(s)
- Xin Huang
- Department of Breast Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Chang Chen
- Department of Breast Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Yan Lin
- Department of Breast Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Changjun Wang
- Department of Breast Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Xingtong Zhou
- Department of Breast Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Ying Xu
- Department of Breast Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Qiang Sun
- Department of Breast Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Yidong Zhou
- Department of Breast Surgery, Peking Union Medical College Hospital, Beijing, China.
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Scatolini M, Grisanti S, Tomaiuolo P, Grosso E, Basile V, Cosentini D, Puglisi S, Laganà M, Perotti P, Saba L, Rossini E, Palermo F, Sigala S, Volante M, Berruti A, Terzolo M. Germline NGS targeted analysis in adult patients with sporadic adrenocortical carcinoma. Eur J Cancer 2024; 205:114088. [PMID: 38714106 DOI: 10.1016/j.ejca.2024.114088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/11/2024] [Accepted: 04/21/2024] [Indexed: 05/09/2024]
Abstract
BACKGROUND Adrenocortical carcinoma (ACC) is a rare cancer that arises sporadically or due to hereditary syndromes. Data on germline variants (GVs) in sporadic ACC are limited. Our aim was to characterize GVs of genes potentially related to adrenal diseases in 150 adult patients with sporadic ACC. METHODS This was a retrospective analysis of stage I-IV ACC patients with sporadic ACC from two reference centers for ACC in Italy. Patients were included in the analysis if they had confirmed diagnosis of ACC, a frozen peripheral blood sample and complete clinical and follow-up data. Next generation sequencing technology was used to analyze the prevalence of GVs in a custom panel of 17 genes belonging to either cancer-predisposition genes or adrenocortical-differentiation genes categories. RESULTS We identified 18 GVs based on their frequency, enrichment and predicted functional characteristics. We found six pathogenic (P) or likely pathogenic (LP) variants in ARMC5, CTNNB1, MSH2, PDE11A and TP53 genes; and twelve variants lacking evidence of pathogenicity. New unique P/LP variants were identified in TP53 (p.G105D) and, for the first time, in ARMC5 (p.P731R). The presence of P/LP GVs was associated with reduced survival outcomes and had a significant and independent impact on both progression-free survival and overall survival. CONCLUSIONS GVs were present in 6.7 % of patients with sporadic ACC, and we identified novel variants of ARMC5 and TP53. These findings may improve understanding of ACC pathogenesis and enable genetic counseling of patients and their families.
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Affiliation(s)
- Maria Scatolini
- Molecular Oncology Laboratory, Fondazione Edo ed Elvo Tempia, 13875 Ponderano, BI, Italy
| | - Salvatore Grisanti
- Medical Oncology Unit, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, ASST Spedali Civili, 25123 Brescia, Italy
| | - Pasquale Tomaiuolo
- Molecular Oncology Laboratory, Fondazione Edo ed Elvo Tempia, 13875 Ponderano, BI, Italy; Internal Medicine, Department of Clinical and Biological Sciences, S. Luigi Gonzaga Hospital, University of Turin, 10043 Orbassano, Italy
| | - Enrico Grosso
- Molecular Oncology Laboratory, Fondazione Edo ed Elvo Tempia, 13875 Ponderano, BI, Italy
| | - Vittoria Basile
- Internal Medicine, Department of Clinical and Biological Sciences, S. Luigi Gonzaga Hospital, University of Turin, 10043 Orbassano, Italy
| | - Deborah Cosentini
- Medical Oncology Unit, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, ASST Spedali Civili, 25123 Brescia, Italy
| | - Soraya Puglisi
- Internal Medicine, Department of Clinical and Biological Sciences, S. Luigi Gonzaga Hospital, University of Turin, 10043 Orbassano, Italy.
| | - Marta Laganà
- Medical Oncology Unit, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, ASST Spedali Civili, 25123 Brescia, Italy
| | - Paola Perotti
- Internal Medicine, Department of Clinical and Biological Sciences, S. Luigi Gonzaga Hospital, University of Turin, 10043 Orbassano, Italy
| | - Laura Saba
- Internal Medicine, Department of Clinical and Biological Sciences, S. Luigi Gonzaga Hospital, University of Turin, 10043 Orbassano, Italy
| | - Elisa Rossini
- Department of Molecular & Translational Medicine, Section of Pharmacology, University of Brescia, 25123 Brescia, Italy
| | - Flavia Palermo
- Molecular Oncology Laboratory, Fondazione Edo ed Elvo Tempia, 13875 Ponderano, BI, Italy
| | - Sandra Sigala
- Department of Molecular & Translational Medicine, Section of Pharmacology, University of Brescia, 25123 Brescia, Italy
| | - Marco Volante
- Pathology Unit, Oncology department, University of Turin, San Luigi Gonzaga University Hospital, Regione Gonzole 10, 10043 Orbassano, Turin, Italy
| | - Alfredo Berruti
- Medical Oncology Unit, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, ASST Spedali Civili, 25123 Brescia, Italy
| | - Massimo Terzolo
- Internal Medicine, Department of Clinical and Biological Sciences, S. Luigi Gonzaga Hospital, University of Turin, 10043 Orbassano, Italy
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3
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Ea V, Berthozat C, Dreyfus H, Legrand C, Rousselet E, Peysselon M, Baudet L, Martinez G, Coutton C, Bidart M. BRCA1 Intragenic Duplication Combined with a Likely Pathogenic TP53 Variant in a Patient with Triple-Negative Breast Cancer: Clinical Risk and Management. Int J Mol Sci 2024; 25:6274. [PMID: 38892462 PMCID: PMC11173113 DOI: 10.3390/ijms25116274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
For patients with hereditary breast and ovarian cancer, the probability of carrying two pathogenic variants (PVs) in dominant cancer-predisposing genes is rare. Using targeted next-generation sequencing (NGS), we investigated a 49-year-old Caucasian woman who developed a highly aggressive breast tumor. Our analyses identified an intragenic germline heterozygous duplication in BRCA1 with an additional likely PV in the TP53 gene. The BRCA1 variant was confirmed by multiplex ligation probe amplification (MLPA), and genomic breakpoints were characterized at the nucleotide level (c.135-2578_442-1104dup). mRNA extracted from lymphocytes was amplified by RT-PCR and then Sanger sequenced, revealing a tandem duplication r.135_441dup; p.(Gln148Ilefs*20). This duplication results in the synthesis of a truncated and, most likely, nonfunctional protein. Following functional studies, the TP53 exon 5 c.472C > T; p.(Arg158Cys) missense variant was classified as likely pathogenic by the Li-Fraumeni Syndrome (LFS) working group. This type of unexpected association will be increasingly identified in the future, with the switch from targeted BRCA sequencing to hereditary breast and ovarian cancer (HBOC) panel sequencing, raising the question of how these patients should be managed. It is therefore important to record and investigate these rare double-heterozygous genotypes.
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Affiliation(s)
- Vuthy Ea
- UM Génétique Moléculaire: Maladies Héréditaires et Oncologie, University Hospital Grenoble Alpes, 38000 Grenoble, France;
- INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Grenoble Alpes University, 38000 Grenoble, France; (G.M.); (C.C.)
| | - Claudine Berthozat
- Department of Medical Oncology, Cancer and Blood Diseases, Grenoble Alpes University Hospital, 38000 Grenoble, France;
| | - Hélène Dreyfus
- Genetic Service, Department of Genetics and Procreation, University Hospital Grenoble Alpes, 38000 Grenoble, France; (H.D.); (C.L.); (E.R.); (M.P.); (L.B.)
| | - Clémentine Legrand
- Genetic Service, Department of Genetics and Procreation, University Hospital Grenoble Alpes, 38000 Grenoble, France; (H.D.); (C.L.); (E.R.); (M.P.); (L.B.)
| | - Estelle Rousselet
- Genetic Service, Department of Genetics and Procreation, University Hospital Grenoble Alpes, 38000 Grenoble, France; (H.D.); (C.L.); (E.R.); (M.P.); (L.B.)
| | - Magalie Peysselon
- Genetic Service, Department of Genetics and Procreation, University Hospital Grenoble Alpes, 38000 Grenoble, France; (H.D.); (C.L.); (E.R.); (M.P.); (L.B.)
| | - Laura Baudet
- Genetic Service, Department of Genetics and Procreation, University Hospital Grenoble Alpes, 38000 Grenoble, France; (H.D.); (C.L.); (E.R.); (M.P.); (L.B.)
| | - Guillaume Martinez
- INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Grenoble Alpes University, 38000 Grenoble, France; (G.M.); (C.C.)
- UM de Génétique Chromosomique, University Hospital Grenoble Alpes, 38000 Grenoble, France
| | - Charles Coutton
- INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Grenoble Alpes University, 38000 Grenoble, France; (G.M.); (C.C.)
- UM de Génétique Chromosomique, University Hospital Grenoble Alpes, 38000 Grenoble, France
| | - Marie Bidart
- UM Génétique Moléculaire: Maladies Héréditaires et Oncologie, University Hospital Grenoble Alpes, 38000 Grenoble, France;
- INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Grenoble Alpes University, 38000 Grenoble, France; (G.M.); (C.C.)
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Ward A, Farengo-Clark D, McKenna DB, Safonov A, Good M, Le A, Kessler L, Shah PD, Bradbury AR, Domchek SM, Nathanson KL, Powers J, Maxwell KN. Clinical management of TP53 mosaic variants found on germline genetic testing. Cancer Genet 2024; 284-285:43-47. [PMID: 38677009 PMCID: PMC11168919 DOI: 10.1016/j.cancergen.2024.04.002] [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: 09/11/2023] [Revised: 03/23/2024] [Accepted: 04/22/2024] [Indexed: 04/29/2024]
Abstract
BACKGROUND Germline heterozygous TP53 pathogenic variants (PVs) cause Li Fraumeni Syndrome (LFS, OMIM#151623). TP53 PVs at lower-than-expected variant allele frequencies (VAF) may reflect postzygotic mosaicism (PZM) or clonal hematopoiesis (CH); however, no guidelines exist for workup and clinical management. PATIENTS AND METHODS Retrospective analysis of probands who presented to an academic cancer genetics program with a TP53 PV result on germline genetic testing. RESULTS Twenty-one of 125 unrelated probands (17 %) were found to harbor a TP53 PV with VAF<30 % or a designation of "mosaic". A diagnosis of PZM was made in nine (43 %) due to a clinical phenotype consistent with LFS with (n = 8) or without (n = 1) positive ancillary tissue testing. Twelve patients (57 %) were diagnosed with presumed CH (pCH) due to a diagnosis of a myeloproliferative neoplasm, negative ancillary tissue testing, clinical phenotype not meeting LFS criteria, no cancer, and/or no first cancer age<50. Of the 19 patients with biological offspring, nine had either partial or complete offspring testing, all negative. CONCLUSIONS Determining the etiology of low VAF TP53 PVs requires ancillary tissue testing and incorporation of clinical phenotype. Discerning PZM versus CH is important to provide optimal care and follow-up.
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Affiliation(s)
- Abigail Ward
- Master of Science in Genetic Counseling Program, Perelman School of Medicine, University of Pennsylvania, USA
| | - Dana Farengo-Clark
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, USA
| | - Danielle B McKenna
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, USA
| | - Anton Safonov
- Division of Translational Medicine and Human Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Madeline Good
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, USA
| | - Anh Le
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, USA
| | - Lisa Kessler
- Master of Science in Genetic Counseling Program, Perelman School of Medicine, University of Pennsylvania, USA
| | - Payal D Shah
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, USA
| | - Angela R Bradbury
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, USA
| | - Susan M Domchek
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, USA; Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Katherine L Nathanson
- Division of Translational Medicine and Human Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jacquelyn Powers
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, USA
| | - Kara N Maxwell
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, USA; Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Corporal Michael Crescenz Veterans Affairs Medical Center, Philadelphia, PA, USA.
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5
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Linga BG, Mohammed SGAA, Farrell T, Rifai HA, Al-Dewik N, Qoronfleh MW. Genomic Newborn Screening for Pediatric Cancer Predisposition Syndromes: A Holistic Approach. Cancers (Basel) 2024; 16:2017. [PMID: 38893137 PMCID: PMC11171256 DOI: 10.3390/cancers16112017] [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: 04/19/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
As next-generation sequencing (NGS) has become more widely used, germline and rare genetic variations responsible for inherited illnesses, including cancer predisposition syndromes (CPSs) that account for up to 10% of childhood malignancies, have been found. The CPSs are a group of germline genetic disorders that have been identified as risk factors for pediatric cancer development. Excluding a few "classic" CPSs, there is no agreement regarding when and how to conduct germline genetic diagnostic studies in children with cancer due to the constant evolution of knowledge in NGS technologies. Various clinical screening tools have been suggested to aid in the identification of individuals who are at greater risk, using diverse strategies and with varied outcomes. We present here an overview of the primary clinical and molecular characteristics of various CPSs and summarize the existing clinical genomics data on the prevalence of CPSs in pediatric cancer patients. Additionally, we discuss several ethical issues, challenges, limitations, cost-effectiveness, and integration of genomic newborn screening for CPSs into a healthcare system. Furthermore, we assess the effectiveness of commonly utilized decision-support tools in identifying patients who may benefit from genetic counseling and/or direct genetic testing. This investigation highlights a tailored and systematic approach utilizing medical newborn screening tools such as the genome sequencing of high-risk newborns for CPSs, which could be a practical and cost-effective strategy in pediatric cancer care.
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Affiliation(s)
- BalaSubramani Gattu Linga
- Department of Research, Women’s Wellness and Research Center, Hamad Medical Corporation (HMC), P.O. Box 3050, Doha 0974, Qatar
- Translational and Precision Medicine Research, Women’s Wellness and Research Center (WWRC), Hamad Medical Corporation (HMC), Doha 0974, Qatar
| | | | - Thomas Farrell
- Department of Research, Women’s Wellness and Research Center, Hamad Medical Corporation (HMC), P.O. Box 3050, Doha 0974, Qatar
| | - Hilal Al Rifai
- Neonatal Intensive Care Unit (NICU), Newborn Screening Unit, Department of Pediatrics and Neonatology, Women’s Wellness and Research Center (WWRC), Hamad Medical Corporation (HMC), Doha 0974, Qatar
| | - Nader Al-Dewik
- Department of Research, Women’s Wellness and Research Center, Hamad Medical Corporation (HMC), P.O. Box 3050, Doha 0974, Qatar
- Translational and Precision Medicine Research, Women’s Wellness and Research Center (WWRC), Hamad Medical Corporation (HMC), Doha 0974, Qatar
- Neonatal Intensive Care Unit (NICU), Newborn Screening Unit, Department of Pediatrics and Neonatology, Women’s Wellness and Research Center (WWRC), Hamad Medical Corporation (HMC), Doha 0974, Qatar
- Genomics and Precision Medicine (GPM), College of Health & Life Science (CHLS), Hamad Bin Khalifa University (HBKU), Doha 0974, Qatar
- Faculty of Health and Social Care Sciences, Kingston University and St George’s University of London, Kingston upon Thames, Surrey, London KT1 2EE, UK
| | - M. Walid Qoronfleh
- Healthcare Research & Policy Division, Q3 Research Institute (QRI), Ann Arbor, MI 48197, USA
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Bundrant B, Gerstein Y, Arun B, DiNardo CD. Hematologic malignancies in Li-Fraumeni syndrome: A case report. Am J Med Genet A 2024:e63573. [PMID: 38410872 DOI: 10.1002/ajmg.a.63573] [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: 11/29/2023] [Revised: 01/29/2024] [Accepted: 02/12/2024] [Indexed: 02/28/2024]
Abstract
Li-Fraumeni syndrome (LFS) is a rare syndrome characterized by an increased lifetime risk of cancer development in multiple organ systems, typically caused by de novo or inherited germline pathogenic variants in the tumor suppressor TP53 gene. LFS is more classically associated with solid tumors; however, it is also associated with hematologic malignancies such as therapy-related acute myeloid leukemia (AML). We present the case of a female patient with a strong family and personal history of cancer who presented to our institution with therapy-related AML with next-generation sequencing showing a pathogenic TP53 mutation. She received several lines of systemic therapy and underwent stem cell transplant using her adult daughter as a haploidentical donor after achieving minimal residual disease (MRD). Her posttransplant bone marrow evaluations demonstrated persistence of the same pathogenic TP53 mutation despite ongoing clinical remission with full donor engraftment and negative MRD. Genetic testing was performed which confirmed the germline origin of the TP53 pathogenic variant in the patient. The patient's adult donor daughter was also identified to have the same pathogenic variant in TP53 consistent with LFS. The presented case highlights the need for increased awareness of LFS in the adult hematologic community, particularly for patients undergoing evaluation for stem cell transplant.
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Affiliation(s)
- Bethany Bundrant
- Internal Medicine Department, Baylor College of Medicine, Houston, Texas, USA
- Division of Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yoheved Gerstein
- Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Banu Arun
- Department of Breast Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Clinical Cancer Prevention, Division of OVP, Cancer Prevention, and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Courtney D DiNardo
- Department of Leukemia, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Barili V, Ambrosini E, Bortesi B, Minari R, De Sensi E, Cannizzaro IR, Taiani A, Michiara M, Sikokis A, Boggiani D, Tommasi C, Serra O, Bonatti F, Adorni A, Luberto A, Caggiati P, Martorana D, Uliana V, Percesepe A, Musolino A, Pellegrino B. Genetic Basis of Breast and Ovarian Cancer: Approaches and Lessons Learnt from Three Decades of Inherited Predisposition Testing. Genes (Basel) 2024; 15:219. [PMID: 38397209 PMCID: PMC10888198 DOI: 10.3390/genes15020219] [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: 12/30/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Germline variants occurring in BRCA1 and BRCA2 give rise to hereditary breast and ovarian cancer (HBOC) syndrome, predisposing to breast, ovarian, fallopian tube, and peritoneal cancers marked by elevated incidences of genomic aberrations that correspond to poor prognoses. These genes are in fact involved in genetic integrity, particularly in the process of homologous recombination (HR) DNA repair, a high-fidelity repair system for mending DNA double-strand breaks. In addition to its implication in HBOC pathogenesis, the impairment of HR has become a prime target for therapeutic intervention utilizing poly (ADP-ribose) polymerase (PARP) inhibitors. In the present review, we introduce the molecular roles of HR orchestrated by BRCA1 and BRCA2 within the framework of sensitivity to PARP inhibitors. We examine the genetic architecture underneath breast and ovarian cancer ranging from high- and mid- to low-penetrant predisposing genes and taking into account both germline and somatic variations. Finally, we consider higher levels of complexity of the genomic landscape such as polygenic risk scores and other approaches aiming to optimize therapeutic and preventive strategies for breast and ovarian cancer.
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Affiliation(s)
- Valeria Barili
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Enrico Ambrosini
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
| | - Beatrice Bortesi
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Roberta Minari
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Erika De Sensi
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | | | - Antonietta Taiani
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Maria Michiara
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Angelica Sikokis
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Daniela Boggiani
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Chiara Tommasi
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Olga Serra
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Francesco Bonatti
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Alessia Adorni
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Anita Luberto
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | | | - Davide Martorana
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
| | - Vera Uliana
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
| | - Antonio Percesepe
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
| | - Antonino Musolino
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Benedetta Pellegrino
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
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8
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Kast K, Rhiem K, Larsen M, Wappenschmidt B, Schmutzler R. Phenotype analysis of families with TP53 germline variants at the Center for Familial Breast and Ovarian Cancer, Cologne. Cancer Med 2024; 13:e6920. [PMID: 38230850 PMCID: PMC10905677 DOI: 10.1002/cam4.6920] [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: 05/31/2023] [Revised: 12/07/2023] [Accepted: 12/31/2023] [Indexed: 01/18/2024] Open
Abstract
PURPOSE Tumor protein p53 (TP53) pathogenic variant (PV) carriers are identified during genetic testing for hereditary causes of cancer. PVs in TP53 are associated with the Li-Fraumeni syndrome (LFS), and thus, surveillance and preventive measures are important for TP53 PV carriers. However, the penetrance of TP53 PVs can be low if the Chompret criteria are not fulfilled. In this study, we compared the phenotypic characteristics of families that did and did not fulfill the LFS criteria according to Chompret. METHODS The German Consortium for Hereditary Breast and Ovarian Cancer (GC-HBOC) database was used to identify index patients with a likely pathogenic/pathogenic TP53 variant and their family members. The study investigated the type of variant, pedigree, age of onset, number of primary tumors, and histological type of BC. RESULTS TP53 PV were present in the index cases of 35 families, 57% (20/35) of which fulfilled the Chompret criteria. The median age of onset at first BC diagnosis was lower in families that fulfilled the Chompret criteria compared to those who did not. Four of all diseased individuals were minors (4%; 4/105) when malignancy was first diagnosed. Sarcomas and brain tumors occurred in 10% (10/105) and in 7% (7/105) of all diseased persons, respectively. BC was the most frequently occurring first tumor (60%; 62/105) and additional malignancy (45%; 20/44) in this cohort. Subsequent malignancies developed in 31% (20/65) of the individuals who fulfilled the Chompret criteria compared with 15% (6/40) of those who did not. CONCLUSION The tumor spectrum and age of onset found in this study showed that tumors other than BC had low disease penetrance in TP53 PV carriers identified using the GC-HBOC criteria for genetic testing.
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Affiliation(s)
- K. Kast
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical FacultyUniversity Hospital CologneCologneGermany
| | - K. Rhiem
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical FacultyUniversity Hospital CologneCologneGermany
| | - M. Larsen
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical FacultyUniversity Hospital CologneCologneGermany
| | - B. Wappenschmidt
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical FacultyUniversity Hospital CologneCologneGermany
| | - R. Schmutzler
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical FacultyUniversity Hospital CologneCologneGermany
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9
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Guerrini-Rousseau L, Masliah-Planchon J, Filser M, Tauziède-Espariat A, Entz-Werle N, Maugard CM, Hopman SMJ, Torrejon J, Gauthier-Villars M, Simaga F, Blauwblomme T, Beccaria K, Rouleau E, Dimaria M, Grill J, Abbou S, Claret B, Brugières L, Doz F, Bouchoucha Y, Faure-Conter C, Bonadona V, Mansuy L, de Carli E, Ingster O, Legrand C, Pagnier A, Berthet P, Bodet D, Julia S, Bertozzi AI, Wilems M, Maurage CA, Delattre O, Ayrault O, Dufour C, Bourdeaut F. Medulloblastomas with ELP1 pathogenic variants: A weakly penetrant syndrome with a restricted spectrum in a limited age window. Neurooncol Adv 2024; 6:vdae075. [PMID: 38962751 PMCID: PMC11221071 DOI: 10.1093/noajnl/vdae075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024] Open
Abstract
Background ELP1 pathogenic variants (PV) have been recently identified as the most frequent variants predisposing to Sonic Hedgehog (SHH) medulloblastomas (MB); however, guidelines are still lacking for genetic counseling in this new syndrome. Methods We retrospectively reviewed clinical and genetic data of a French series of 29 ELP1-mutated MB. Results All patients developed SHH-MB, with a biallelic inactivation of PTCH1 found in 24 tumors. Other recurrent alterations encompassed the TP53 pathway and activation of MYCN/MYCL signaling. The median age at diagnosis was 7.3 years (range: 3-14). ELP1-mutated MB behave as sporadic cases, with similar distribution within clinical and molecular risk groups and similar outcomes (5 y - OS = 86%); no unusual side effect of treatments was noticed. Remarkably, a germline ELP1 PV was identified in all patients with available constitutional DNA (n = 26); moreover, all tested familial trio (n = 11) revealed that the PVs were inherited. Two of the 26 index cases from the French series had a family history of MB; pedigrees from these patients and from 1 additional Dutch family suggested a weak penetrance. Apart from MB, no cancer was associated with ELP1 PVs; second tumors reported in 4 patients occurred within the irradiation fields, in the usual time-lapse for expected radiotherapy-induced neoplasms. Conclusions The low penetrance, the "at risk' age window limited to childhood and the narrow tumor spectrum, question the actual benefit of genetic screening in these patients and their family. Our results suggest restricting ELP1 germline sequencing to patients with SHH-MB, depending on the parents" request.
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Affiliation(s)
- Léa Guerrini-Rousseau
- Molecular Predictors and New Targets in Oncology, Inserm U981 Team “Genomics and Oncogenesis of Pediatric Brain Tumors,” Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Department of Children and Adolescents Oncology, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Julien Masliah-Planchon
- Department of Pathology and Diagnostic, Prognostic and Theranostic Medicine, Somatic Genetic Unit, Institut Curie, Paris Sciences Lettres Research University, Paris, France
| | - Mathilde Filser
- Department of Pathology and Diagnostic, Prognostic and Theranostic Medicine, Somatic Genetic Unit, Institut Curie, Paris Sciences Lettres Research University, Paris, France
| | | | - Natacha Entz-Werle
- Pediatric Hematology and Oncology Department, Strasbourg University Hospital, University of Strasbourg, Strasbourg, France
| | - Christine M Maugard
- Department of Clinical Genetics, Strasbourg University Hospital, Strasbourg, France
| | - Saskia M J Hopman
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jacob Torrejon
- Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
- Institut Curie, Paris Sciences Lettres Research University, CNRS UMR, INSERM, Orsay, France
| | - Marion Gauthier-Villars
- Department of Genetics, Institut Curie, Paris Sciences Lettres Research University, Paris, France
| | - Fatoumata Simaga
- Department of Genetics, Institut Curie, Paris Sciences Lettres Research University, Paris, France
| | - Thomas Blauwblomme
- Necker-Enfants Malades University Hospital, Department of Pediatric Neurosurgery, Paris-Cité University, Paris, France
| | - Kevin Beccaria
- Necker-Enfants Malades University Hospital, Department of Pediatric Neurosurgery, Paris-Cité University, Paris, France
| | - Etienne Rouleau
- Cancer Genetics Unit, Department of Biology and Pathology, Institut Gustave Roussy, Villejuif, France
| | - Marina Dimaria
- Department of Children and Adolescents Oncology, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Jacques Grill
- Molecular Predictors and New Targets in Oncology, Inserm U981 Team “Genomics and Oncogenesis of Pediatric Brain Tumors,” Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Department of Children and Adolescents Oncology, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Samuel Abbou
- Department of Children and Adolescents Oncology, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy, Villejuif, France
| | - Béatrice Claret
- Psycho-Oncology Unit, Interdisciplinary Department of Supportive Care, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Laurence Brugières
- Department of Children and Adolescents Oncology, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - François Doz
- Université Paris Cité, SIREDO Pediatric Cancer Center, Institut Curie, Paris, France
- SIREDO Center (Care, Innovation Research in Pediatric, Adolescent and Young Adult Oncology), Institut Curie, Paris, France
| | - Yassine Bouchoucha
- SIREDO Center (Care, Innovation Research in Pediatric, Adolescent and Young Adult Oncology), Institut Curie, Paris, France
| | - Cécile Faure-Conter
- Pediatric Hematology and Oncology Institut, Centre Léon Berard, Lyon, France
| | - Valerie Bonadona
- Clinical Oncogenetics Unit, Department of Prevention and Public Health, Centre Léon Bérard, Lyon, France
| | - Ludovic Mansuy
- Department of Pediatric Hematology and Oncology, Centre Hospitalo-Universitaire de Nancy, Vandœuvre-lès-Nancy, France
| | - Emilie de Carli
- Pediatric Hematology and Oncology Department, Angers University Hospital, Nancy, France
| | - Olivier Ingster
- Department of Genetics, Angers University Hospital, Angers, France
| | | | - Anne Pagnier
- Department of Pediatric Hematology and Oncology, Centre Hospitalo-Universitaire de Grenoble, Grenoble, France
| | | | - Damien Bodet
- Pediatric Hematology and Oncology Department, Caen University Hospital, Caen, France
| | - Sophie Julia
- Department of Genetics, Toulouse University Hospital, Toulouse, France
| | - Anne-Isabelle Bertozzi
- Pediatric Hematology and Oncology Department, Toulouse University Hospital, Toulouse, France
| | - Marjolaine Wilems
- Department of Medical Genetics, Montpellier University Hospital, Institute for Neurosciences of Montpellier, Univ Montpellier, INSERM, Montpellier, France
| | | | - Olivier Delattre
- INSERM U830, Cancer, Heterogeneity, Instability and Plasticity Laboratory Institut Curie, Paris, France
| | - Olivier Ayrault
- Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
- Institut Curie, Paris Sciences Lettres Research University, CNRS UMR, INSERM, Orsay, France
| | - Christelle Dufour
- Molecular Predictors and New Targets in Oncology, Inserm U981 Team “Genomics and Oncogenesis of Pediatric Brain Tumors,” Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Department of Children and Adolescents Oncology, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Franck Bourdeaut
- Université Paris Cité, SIREDO Pediatric Cancer Center, Institut Curie, Paris, France
- SIREDO Center (Care, Innovation Research in Pediatric, Adolescent and Young Adult Oncology), Institut Curie, Paris, France
- INSERM U830, Cancer, Heterogeneity, Instability and Plasticity Laboratory Institut Curie, Paris, France
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10
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Gebhart P, Tan Y, Muhr D, Stein C, Singer C. A de Novo BRCA1 Pathogenic Variant in a 29-Year-Old Woman with Triple-Negative Breast Cancer. Breast Care (Basel) 2023; 18:412-416. [PMID: 37901051 PMCID: PMC10601672 DOI: 10.1159/000531612] [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: 04/18/2023] [Accepted: 06/14/2023] [Indexed: 10/31/2023] Open
Abstract
Introduction Germline pathogenic variants in the BRCA1 and BRCA2 genes lead to a highly increased lifetime risk for breast and ovarian cancer. These variants are usually inherited and reports of de novo occurrences are a very rare phenomenon. Case Presentation We report on a breast cancer patient with a de novo BRCA1 variant c.121C>T (p.His41Tyr). The pathogenic variant was detected in leukocyte DNA of a patient with negative family history who had developed early onset, triple-negative breast cancer. The variant was not found in any of the maternal and paternal tissues tested, but it was detected in multiple samples representing all three germ layers of the affected carrier, which renders somatic mosaicism unlikely. Conclusion This case highlights the importance of including early onset of disease and triple negativity of the tumor as criteria for genetic testing, even in patients without family history. Considering the availability of effective breast cancer treatments in patients with pathogenic variants in the BRCA genes, this finding underscores the importance of genetic testing in breast cancer patients.
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Affiliation(s)
- Paulina Gebhart
- Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Yen Tan
- Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Daniela Muhr
- Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Christina Stein
- Center for Forensic Medicine, DNA Central Laboratory, Medical University of Vienna, Vienna, Austria
| | - Christian Singer
- Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
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11
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Burr R, Leshchiner I, Costantino CL, Blohmer M, Sundaresan T, Cha J, Seeger K, Guay S, Danysh BP, Gore I, Jacobs RA, Slowik K, Utro F, Rhrissorrakrai K, Levovitz C, Barth JL, Dubash T, Chirn B, Parida L, Sequist LV, Lennerz JK, Mino-Kenudson M, Maheswaran S, Naxerova K, Getz G, Haber DA. Germline mutations and developmental mosaicism underlying EGFR-mutant lung cancer. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.28.23296274. [PMID: 37808694 PMCID: PMC10557804 DOI: 10.1101/2023.09.28.23296274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
While the development of multiple primary tumors in smokers with lung cancer can be attributed to carcinogen-induced field cancerization, the occurrence of multiple primary tumors in individuals with EGFR-mutant lung cancer who lack known environmental exposures remains unexplained. We identified ten patients with early-stage, resectable non-small cell lung cancer who presented with multiple anatomically distinct EGFR-mutant tumors. We analyzed the phylogenetic relationships among multiple tumors from each patient using whole exome sequencing (WES) and hypermutable poly-guanine (poly-G) repeat genotyping, as orthogonal methods for lineage tracing. In two patients, we identified germline EGFR variants, which confer moderately enhanced signaling when modeled in vitro. In four other patients, developmental mosaicism is supported by the poly-G lineage tracing and WES, indicating a common non-germline cell-of-origin. Thus, developmental mosaicism and germline variants define two distinct mechanisms of genetic predisposition to multiple EGFR-mutant primary tumors, with implications for understanding their etiology and clinical management.
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Affiliation(s)
- Risa Burr
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Ignaty Leshchiner
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christina L Costantino
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Martin Blohmer
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Justin Cha
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Karsen Seeger
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Sara Guay
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Brian P Danysh
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ira Gore
- St Vincent’s Hospital, Birmingham, AL, USA
| | - Raquel A Jacobs
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kara Slowik
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | - Jaimie L Barth
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Taronish Dubash
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Brian Chirn
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | | | - Lecia V Sequist
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Shyamala Maheswaran
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kamila Naxerova
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Gad Getz
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel A Haber
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Bethesda, MD, USA
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12
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Sánchez-Heras AB, Ramon y Cajal T, Pineda M, Aguirre E, Graña B, Chirivella I, Balmaña J, Brunet J. SEOM clinical guideline on heritable TP53-related cancer syndrome (2022). Clin Transl Oncol 2023; 25:2627-2633. [PMID: 37133731 PMCID: PMC10425559 DOI: 10.1007/s12094-023-03202-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 04/11/2023] [Indexed: 05/04/2023]
Abstract
Li-Fraumeni syndrome is caused by heterozygous germline pathogenic variants in the TP53 gene. It involves a high risk of a variety of malignant tumors in childhood and adulthood, the main ones being premenopausal breast cancer, soft tissue sarcomas and osteosarcomas, central nervous system tumors, and adrenocortical carcinomas. The variability of the associated clinical manifestations, which do not always fit the classic criteria of Li-Fraumeni syndrome, has led the concept of SLF to extend to a more overarching cancer predisposition syndrome, termed hereditable TP53-related cancer syndrome (hTP53rc). However, prospective studies are needed to assess genotype-phenotype characteristics, as well as to evaluate and validate risk-adjusted recommendations. This guideline aims to establish the basis for interpreting pathogenic variants in the TP53 gene and provide recommendations for effective screening and prevention of associated cancers in carrier individuals.
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Affiliation(s)
| | | | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, L’Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Cancer, CIBERONC, Carlos III Institute of Health, Madrid, Spain
| | - Elena Aguirre
- Medical Oncology Department, Hospital Quironsalud, Zaragoza, Spain
| | - Begoña Graña
- Medical Oncology Department, University Hospital A Coruña, 15006 A Coruña, Spain
| | - Isabel Chirivella
- Medical Oncology Department, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain
| | - Judit Balmaña
- Medical Oncology Department, Hospital Vall d’Hebron, and Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology, Barcelona, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, L’Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Cancer, CIBERONC, Carlos III Institute of Health, Madrid, Spain
- Medical Oncology Department, Catalan Institute of Oncology, University Hospital Josep Trueta, University of Girona, Girona, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, Girona Biomedical Research Instiute (IDIBGI), Girona, Spain
| | - the SEOM Hereditary Cancer Working Group and AEGH Hereditary Cancer Committee
- Medical Oncology Department, Hospital General Universitario de Elche, Elche, Alicante, Spain
- Medical Oncology Service, Hospital Sant Pau, Barcelona, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, L’Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Cancer, CIBERONC, Carlos III Institute of Health, Madrid, Spain
- Medical Oncology Department, Hospital Quironsalud, Zaragoza, Spain
- Medical Oncology Department, University Hospital A Coruña, 15006 A Coruña, Spain
- Medical Oncology Department, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain
- Medical Oncology Department, Hospital Vall d’Hebron, and Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology, Barcelona, Spain
- Medical Oncology Department, Catalan Institute of Oncology, University Hospital Josep Trueta, University of Girona, Girona, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, Girona Biomedical Research Instiute (IDIBGI), Girona, Spain
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13
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Öfverholm A, Törngren T, Rosén A, Arver B, Einbeigi Z, Haraldsson K, Ståhlbom AK, Kuchinskaya E, Lindblom A, Melin B, Paulsson-Karlsson Y, Stenmark-Askmalm M, Tham E, von Wachenfeldt A, Kvist A, Borg Å, Ehrencrona H. Extended genetic analysis and tumor characteristics in over 4600 women with suspected hereditary breast and ovarian cancer. BMC Cancer 2023; 23:738. [PMID: 37563628 PMCID: PMC10413543 DOI: 10.1186/s12885-023-11229-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 07/24/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUND Genetic screening for pathogenic variants (PVs) in cancer predisposition genes can affect treatment strategies, risk prediction and preventive measures for patients and families. For decades, hereditary breast and ovarian cancer (HBOC) has been attributed to PVs in the genes BRCA1 and BRCA2, and more recently other rare alleles have been firmly established as associated with a high or moderate increased risk of developing breast and/or ovarian cancer. Here, we assess the genetic variation and tumor characteristics in a large cohort of women with suspected HBOC in a clinical oncogenetic setting. METHODS Women with suspected HBOC referred from all oncogenetic clinics in Sweden over a six-year inclusion period were screened for PVs in 13 clinically relevant genes. The genetic outcome was compared with tumor characteristics and other clinical data collected from national cancer registries and hospital records. RESULTS In 4622 women with breast and/or ovarian cancer the overall diagnostic yield (the proportion of women carrying at least one PV) was 16.6%. BRCA1/2 PVs were found in 8.9% of women (BRCA1 5.95% and BRCA2 2.94%) and PVs in the other breast and ovarian cancer predisposition genes in 8.2%: ATM (1.58%), BARD1 (0.45%), BRIP1 (0.43%), CDH1 (0.11%), CHEK2 (3.46%), PALB2 (0.84%), PTEN (0.02%), RAD51C (0.54%), RAD51D (0.15%), STK11 (0) and TP53 (0.56%). Thus, inclusion of the 11 genes in addition to BRCA1/2 increased diagnostic yield by 7.7%. The yield was, as expected, significantly higher in certain subgroups such as younger patients, medullary breast cancer, higher Nottingham Histologic Grade, ER-negative breast cancer, triple-negative breast cancer and high grade serous ovarian cancer. Age and tumor subtype distributions differed substantially depending on genetic finding. CONCLUSIONS This study contributes to understanding the clinical and genetic landscape of breast and ovarian cancer susceptibility. Extending clinical genetic screening from BRCA1 and BRCA2 to 13 established cancer predisposition genes almost doubles the diagnostic yield, which has implications for genetic counseling and clinical guidelines. The very low yield in the syndrome genes CDH1, PTEN and STK11 questions the usefulness of including these genes on routine gene panels.
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Affiliation(s)
- Anna Öfverholm
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Therese Törngren
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Anna Rosén
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Brita Arver
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Zakaria Einbeigi
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
- Department of Medicine and Oncology, Southern Älvsborg Hospital, Borås, Sweden
| | - Karin Haraldsson
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | | | - Ekaterina Kuchinskaya
- Department of Clinical Pathology and Clinical Genetics, Department of Clinical Experimental Medicine, Linköping University, Linköping, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Beatrice Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Ylva Paulsson-Karlsson
- Department of Immunology, Genetics and Pathology, Uppsala University Hospital, Uppsala, Sweden
| | - Marie Stenmark-Askmalm
- Department of Clinical Pathology and Clinical Genetics, Department of Clinical Experimental Medicine, Linköping University, Linköping, Sweden
- Department of Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna von Wachenfeldt
- Department of Clinical Science and Education at Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Anders Kvist
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Åke Borg
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Hans Ehrencrona
- Department of Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden.
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.
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14
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Ryckx S, De Schepper J, Giron P, Maes K, Vaeyens F, Wilgenhof K, Lefesvre P, Ernst C, Vanderlinden K, Klink D, Hes F, Vanbesien J, Gies I, Staels W. Peripheral precocious puberty in Li-Fraumeni syndrome: a case report and literature review of pure androgen-secreting adrenocortical tumors. J Med Case Rep 2023; 17:195. [PMID: 37179382 PMCID: PMC10183130 DOI: 10.1186/s13256-023-03889-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 03/14/2023] [Indexed: 05/15/2023] Open
Abstract
INTRODUCTION Pure androgen-secreting adrenocortical tumors are a rare but important cause of peripheral precocious puberty. CASE PRESENTATION Here, we report a pure androgen-secreting adrenocortical tumor in a 2.5-year-old boy presenting with penile enlargement, pubic hair, frequent erections, and rapid linear growth. We confirmed the diagnosis through laboratory tests, medical imaging, and histology. Furthermore, genetic testing detected a pathogenic germline variant in the TP53 gene, molecularly confirming underlying Li-Fraumeni syndrome. DISCUSSION Only 15 well-documented cases of pure androgen-secreting adrenocortical tumors have been reported so far. No clinical or imaging signs were identified to differentiate adenomas from carcinomas, and no other cases of Li-Fraumeni syndrome were diagnosed in the four patients that underwent genetic testing. However, diagnosing Li-Fraumeni syndrome is important as it implies a need for intensive tumor surveillance and avoidance of ionizing radiation. CONCLUSION In this article, we emphasize the need to screen for TP53 gene variants in children with androgen-producing adrenal adenomas and report an association with arterial hypertension.
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Affiliation(s)
- Sofie Ryckx
- Division of Pediatric Endocrinology and Diabetology, Department of Pediatrics, ZNA Queen Paola Child Hospital, Lindendreef 1, 2020, Antwerp, Belgium.
- Division of Pediatric Endocrinology, Department of Pediatrics, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090, Brussels, Belgium.
| | - Jean De Schepper
- Division of Pediatric Endocrinology, Department of Pediatrics, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090, Brussels, Belgium
| | - Philippe Giron
- Centre for Medical Genetics, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Ken Maes
- Centre for Medical Genetics, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Freya Vaeyens
- Centre for Medical Genetics, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Kaat Wilgenhof
- Department of Pathology, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Pierre Lefesvre
- Department of Pathology, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Caroline Ernst
- Department of Radiology, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Kim Vanderlinden
- Division of Pediatric Surgery, Department of Surgery, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Daniel Klink
- Division of Pediatric Endocrinology and Diabetology, Department of Pediatrics, ZNA Queen Paola Child Hospital, Lindendreef 1, 2020, Antwerp, Belgium
| | - Frederik Hes
- Centre for Medical Genetics, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Jesse Vanbesien
- Division of Pediatric Endocrinology, Department of Pediatrics, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090, Brussels, Belgium
| | - Inge Gies
- Division of Pediatric Endocrinology, Department of Pediatrics, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090, Brussels, Belgium
| | - Willem Staels
- Division of Pediatric Endocrinology, Department of Pediatrics, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090, Brussels, Belgium
- Beta Cell Neogenesis (BENE) Research Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
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15
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Truty R, Rojahn S, Ouyang K, Kautzer C, Kennemer M, Pineda-Alvarez D, Johnson B, Stafford A, Basel-Salmon L, Saitta S, Slavotinek A, Chandrasekharappa SC, Suarez CJ, Burnett L, Nussbaum RL, Aradhya S. Patterns of mosaicism for sequence and copy-number variants discovered through clinical deep sequencing of disease-related genes in one million individuals. Am J Hum Genet 2023; 110:551-564. [PMID: 36933558 PMCID: PMC10119133 DOI: 10.1016/j.ajhg.2023.02.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 02/23/2023] [Indexed: 03/19/2023] Open
Abstract
DNA variants that arise after conception can show mosaicism, varying in presence and extent among tissues. Mosaic variants have been reported in Mendelian diseases, but further investigation is necessary to broadly understand their incidence, transmission, and clinical impact. A mosaic pathogenic variant in a disease-related gene may cause an atypical phenotype in terms of severity, clinical features, or timing of disease onset. Using high-depth sequencing, we studied results from one million unrelated individuals referred for genetic testing for almost 1,900 disease-related genes. We observed 5,939 mosaic sequence or intragenic copy number variants distributed across 509 genes in nearly 5,700 individuals, constituting approximately 2% of molecular diagnoses in the cohort. Cancer-related genes had the most mosaic variants and showed age-specific enrichment, in part reflecting clonal hematopoiesis in older individuals. We also observed many mosaic variants in genes related to early-onset conditions. Additional mosaic variants were observed in genes analyzed for reproductive carrier screening or associated with dominant disorders with low penetrance, posing challenges for interpreting their clinical significance. When we controlled for the potential involvement of clonal hematopoiesis, most mosaic variants were enriched in younger individuals and were present at higher levels than in older individuals. Furthermore, individuals with mosaicism showed later disease onset or milder phenotypes than individuals with non-mosaic variants in the same genes. Collectively, the large compendium of variants, disease correlations, and age-specific results identified in this study expand our understanding of the implications of mosaic DNA variation for diagnosis and genetic counseling.
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Affiliation(s)
- Rebecca Truty
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | - Susan Rojahn
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | - Karen Ouyang
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | | | | | | | - Britt Johnson
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | | | - Lina Basel-Salmon
- Rabin Medical Center-Beilinson Hospital and Schneider Children's Medical Center of Israel, Petach Tikva, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Sulagna Saitta
- Division of Clinical Genetics, Departments of Pediatrics and Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Anne Slavotinek
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Settara C Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carlos Jose Suarez
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94301, USA
| | | | - Robert L Nussbaum
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA; School of Medicine, University of California - San Francisco, San Francisco, CA, USA
| | - Swaroop Aradhya
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94301, USA.
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16
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Förster A, Davenport C, Duployez N, Erlacher M, Ferster A, Fitzgibbon J, Göhring G, Hasle H, Jongmans MC, Kolenova A, Kronnie G, Lammens T, Mecucci C, Mlynarski W, Niemeyer CM, Sole F, Szczepanski T, Waanders E, Biondi A, Wlodarski M, Schlegelberger B, Ripperger T. European standard clinical practice - Key issues for the medical care of individuals with familial leukemia. Eur J Med Genet 2023; 66:104727. [PMID: 36775010 DOI: 10.1016/j.ejmg.2023.104727] [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: 03/22/2022] [Revised: 02/02/2023] [Accepted: 02/10/2023] [Indexed: 02/12/2023]
Abstract
Although hematologic malignancies (HM) are no longer considered exclusively sporadic, additional awareness of familial cases has yet to be created. Individuals carrying a (likely) pathogenic germline variant (e.g., in ETV6, GATA2, SAMD9, SAMD9L, or RUNX1) are at an increased risk for developing HM. Given the clinical and psychological impact associated with the diagnosis of a genetic predisposition to HM, it is of utmost importance to provide high-quality, standardized patient care. To address these issues and harmonize care across Europe, the Familial Leukemia Subnetwork within the ERN PaedCan has been assigned to draft an European Standard Clinical Practice (ESCP) document reflecting current best practices for pediatric patients and (healthy) relatives with (suspected) familial leukemia. The group was supported by members of the German network for rare diseases MyPred, of the Host Genome Working Group of SIOPE, and of the COST action LEGEND. The ESCP on familial leukemia is proposed by an interdisciplinary team of experts including hematologists, oncologists, and human geneticists. It is intended to provide general recommendations in areas where disease-specific recommendations do not yet exist. Here, we describe key issues for the medical care of familial leukemia that shall pave the way for a future consensus guideline: (i) identification of individuals with or suggestive of familial leukemia, (ii) genetic analysis and variant interpretation, (iii) genetic counseling and patient education, and (iv) surveillance and (psychological) support. To address the question on how to proceed with individuals suggestive of or at risk of familial leukemia, we developed an algorithm covering four different, partially linked clinical scenarios, and additionally a decision tree to guide clinicians in their considerations regarding familial leukemia in minors with HM. Our recommendations cover, not only patients but also relatives that both should have access to adequate medical care. We illustrate the importance of natural history studies and the need for respective registries for future evidence-based recommendations that shall be updated as new evidence-based standards are established.
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Affiliation(s)
- Alisa Förster
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Claudia Davenport
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Nicolas Duployez
- Department of Hematology, CHU Lille, INSERM, University Lille, Lille, France
| | - Miriam Erlacher
- Division of Pediatric Hematology-Oncology, Department of Pediatric and Adolescent Medicine, University of Freiburg, Freiburg, Germany
| | - Alina Ferster
- Department of Pediatric Rheumatology, Hôpital Universitaire des Enfants Reine Fabiola, Brussels, Belgium
| | - Jude Fitzgibbon
- Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Gudrun Göhring
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Henrik Hasle
- Department of Paediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Marjolijn C Jongmans
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Alexandra Kolenova
- Department of Pediatric Hematology and Oncology, Comenius University Medical School and University Children's Hospital, Bratislava, Slovakia
| | | | - Tim Lammens
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Cristina Mecucci
- Institute of Hematology and Center for Hemato-Oncology Research, University and Hospital of Perugia, Perugia, Italy
| | - Wojciech Mlynarski
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Lodz, Poland
| | - Charlotte M Niemeyer
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Francesc Sole
- Josep Carreras Leukemia Research Institute (IJC), Campus ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Tomasz Szczepanski
- Polish Pediatric Leukemia/Lymphoma Study Group, Zabrze, Poland; Medical University of Silesia, Katowice, Poland
| | - Esmé Waanders
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands; Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Andrea Biondi
- Clinica Pediatrica and Centro Ricerca Tettamanti, Università di Milano-Bicocca, Monza, Italy
| | - Marcin Wlodarski
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Tim Ripperger
- Department of Human Genetics, Hannover Medical School, Hannover, Germany.
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17
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Blondeaux E, Arecco L, Punie K, Graffeo R, Toss A, De Angelis C, Trevisan L, Buzzatti G, Linn SC, Dubsky P, Cruellas M, Partridge AH, Balmaña J, Paluch-Shimon S, Lambertini M. Germline TP53 pathogenic variants and breast cancer: A narrative review. Cancer Treat Rev 2023; 114:102522. [PMID: 36739824 DOI: 10.1016/j.ctrv.2023.102522] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 02/02/2023]
Abstract
Approximately 10% of breast cancers are associated with the inheritance of a pathogenic variant (PV) in one of the breast cancer susceptibility genes. Multiple breast cancer predisposing genes, including TP53, are responsible for the increased breast cancer risk. Tumor protein-53 (TP53) germline PVs are associated with Li-Fraumeni syndrome, a rare autosomal dominant inherited cancer predisposition syndrome associated with early-onset pediatric and multiple primary cancers such as soft tissue and bone sarcomas, breast cancer, brain tumors, adrenocortical carcinomas and leukemias. Women harboring a TP53 PV carry a lifetime risk of developing breast cancer of 80-90%. The aim of the present narrative review is to provide a comprehensive overview of the criteria for offering TP53 testing, prevalence of TP53 carriers among patients with breast cancer, and what is known about its prognostic and therapeutic implications. A summary of the current indications of secondary cancer surveillance and survivorship issues are also provided. Finally, the spectrum of TP53 alteration and testing is discussed. The optimal strategies for the treatment of breast cancer in patients harboring TP53 PVs poses certain challenges. Current guidelines favor the option of performing mastectomy rather than lumpectomy to avoid adjuvant radiotherapy and subsequent risk of radiation-induced second primary malignancies, with careful consideration of radiation when indicated post-mastectomy. Some studies suggest that patients with breast cancer and germline TP53 PV might have worse survival outcomes compared to patients with breast cancer and wild type germline TP53 status. Annual breast magnetic resonance imaging (MRI) and whole-body MRI are recommended as secondary prevention.
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Affiliation(s)
- Eva Blondeaux
- Clinical Epidemiology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.
| | - Luca Arecco
- Department of Internal Medicine and Medical Specialties (DiMI), School of Medicine, University of Genova, Genoa, Italy; Department of Medical Oncology, U.O. Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Kevin Punie
- Department of General Medical Oncology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Rossella Graffeo
- Oncology Institute of Southern Switzerland, EOC, Bellinzona, Switzerland
| | - Angela Toss
- Department of Oncology and Hematology, University Hospital of Modena, Modena, Italy
| | - Carmine De Angelis
- Department of Clinical Medicine and Surgery, University Federico II, Naples, Italy
| | - Lucia Trevisan
- Hereditary Cancer Unit, Oncologia Medica 2, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Giulia Buzzatti
- Hereditary Cancer Unit, Oncologia Medica 2, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Sabine C Linn
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Peter Dubsky
- Breast Centre, Hirslanden Klinik St Anna, Luzern, Switzerland
| | - Mara Cruellas
- Department of Medical Oncology, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Ann H Partridge
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Judith Balmaña
- Department of Medical Oncology, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Shani Paluch-Shimon
- Breast Cancer Unit, Sharett Institute of Oncology, Hadassah Medical Center & Faculty of Medicine, Hebrew University, 91120 Jerusalem, Israel
| | - Matteo Lambertini
- Department of Internal Medicine and Medical Specialties (DiMI), School of Medicine, University of Genova, Genoa, Italy; Department of Medical Oncology, U.O. Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
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18
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Kirsche M, Prabhu G, Sherman R, Ni B, Battle A, Aganezov S, Schatz MC. Jasmine and Iris: population-scale structural variant comparison and analysis. Nat Methods 2023; 20:408-417. [PMID: 36658279 PMCID: PMC10006329 DOI: 10.1038/s41592-022-01753-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 12/15/2022] [Indexed: 01/21/2023]
Abstract
The availability of long reads is revolutionizing studies of structural variants (SVs). However, because SVs vary across individuals and are discovered through imprecise read technologies and methods, they can be difficult to compare. Addressing this, we present Jasmine and Iris ( https://github.com/mkirsche/Jasmine/ ), for fast and accurate SV refinement, comparison and population analysis. Using an SV proximity graph, Jasmine outperforms six widely used comparison methods, including reducing the rate of Mendelian discordance in trio datasets by more than fivefold, and reveals a set of high-confidence de novo SVs confirmed by multiple technologies. We also present a unified callset of 122,813 SVs and 82,379 indels from 31 samples of diverse ancestry sequenced with long reads. We genotype these variants in 1,317 samples from the 1000 Genomes Project and the Genotype-Tissue Expression project with DNA and RNA-sequencing data and assess their widespread impact on gene expression, including within medically relevant genes.
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Affiliation(s)
- Melanie Kirsche
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Gautam Prabhu
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Rachel Sherman
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Bohan Ni
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Sergey Aganezov
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA.
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19
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Splicing-Disrupting Mutations in Inherited Predisposition to Solid Pediatric Cancer. Cancers (Basel) 2022; 14:cancers14235967. [PMID: 36497448 PMCID: PMC9739414 DOI: 10.3390/cancers14235967] [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: 10/17/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/09/2022] Open
Abstract
The prevalence of hereditary cancer in children was estimated to be very low until recent studies suggested that at least 10% of pediatric cancer patients carry a germline mutation in a cancer predisposition gene. A significant proportion of pathogenic variants associated with an increased risk of hereditary cancer are variants affecting splicing. RNA splicing is an essential process involved in different cellular processes such as proliferation, survival, and differentiation, and alterations in this pathway have been implicated in many human cancers. Hereditary cancer genes are highly susceptible to splicing mutations, and among them there are several genes that may contribute to pediatric solid tumors when mutated in the germline. In this review, we have focused on the analysis of germline splicing-disrupting mutations found in pediatric solid tumors, as the discovery of pathogenic splice variants in pediatric cancer is a growing field for the development of personalized therapies. Therapies developed to correct aberrant splicing in cancer are also discussed as well as the options to improve the diagnostic yield based on the increase in the knowledge in splicing.
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20
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Bachega FS, Suartz CV, Almeida MQ, Brondani VB, Charchar HLS, Lacombe AMF, Martins-Filho SN, Soares IC, Zerbini MCN, Dénes FT, Mendonca B, Lopes RI, Latronico AC, Fragoso MCBV. Retrospective Analysis of Prognostic Factors in Pediatric Patients with Adrenocortical Tumor from Unique Tertiary Center with Long-Term Follow-Up. J Clin Med 2022; 11:jcm11226641. [PMID: 36431124 PMCID: PMC9692695 DOI: 10.3390/jcm11226641] [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: 09/28/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
Pediatric adrenocortical tumors (PACTs) represent rare causes of malignancies. However, the south/southeast regions of Brazil are known to have a high incidence of PACTs because of the founder effect associated with a germline pathogenic variant of tumor suppressor gene TP53. We aimed to retrospectively analyze the types of variables among hormone production, radiological imaging, tumor staging, histological and genetic features that were associated with the occurrence of malignancy in 95 patients (71% females) with PACTs from a unique center. The worst prognosis was associated with those aged > 3 years (p < 0.05), high serum levels of 11-desoxicortisol (p < 0.001), tumor weight ≥ 200 g (p < 0.001), tumor size ≥ 5 cm (p < 0.05), Weiss score ≥ 5 (p < 0.05), Wieneke index ≥ 3 (p < 0.001) and Ki67 ≥ 15% (p < 0.05). Furthermore, patients with MacFarlane stage IV had an overall survival rate almost two times shorter than patients with other stages (p < 0.001). Additionally, the subtractions of BUB1B-PINK1 (<6.95) expression (p < 0.05) and IGF-IR overexpression (p = 0.0001) were associated with malignant behavior. These results helped identify patients who are likely to have an aggressive course; further multicenter prospective studies are required to confirm our results. In conclusion, PACTs with these patterns of prognostic factors could be treated using an adjuvant approach that may improve the overall survival in such patients.
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Affiliation(s)
- Fernanda S. Bachega
- Unidade de Suprarrenal, Laboratório de Hormônios e Genética Molecular LIM/42, Disciplina de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05466-040, SP, Brazil
| | - Caio V. Suartz
- Divisão de Urologia, Departamento de Cirurgia da Faculdade de Medicina da Universidade de São Paulo, São Paulo 1964-2007, SP, Brazil
| | - Madson Q. Almeida
- Unidade de Suprarrenal, Laboratório de Hormônios e Genética Molecular LIM/42, Disciplina de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05466-040, SP, Brazil
| | - Vania B. Brondani
- Unidade de Suprarrenal, Laboratório de Hormônios e Genética Molecular LIM/42, Disciplina de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05466-040, SP, Brazil
| | - Helaine L. S. Charchar
- Unidade de Suprarrenal, Laboratório de Hormônios e Genética Molecular LIM/42, Disciplina de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05466-040, SP, Brazil
| | - Amanda M. F. Lacombe
- Unidade de Suprarrenal, Laboratório de Hormônios e Genética Molecular LIM/42, Disciplina de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05466-040, SP, Brazil
| | - Sebastião N. Martins-Filho
- Departamento de Patologia, Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-903, SP, Brazil
| | - Iberê C. Soares
- Departamento de Patologia, Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-903, SP, Brazil
| | - Maria Claudia N. Zerbini
- Departamento de Patologia, Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-903, SP, Brazil
| | - Francisco T. Dénes
- Divisão de Urologia, Departamento de Cirurgia da Faculdade de Medicina da Universidade de São Paulo, São Paulo 1964-2007, SP, Brazil
| | - Berenice Mendonca
- Unidade de Suprarrenal, Laboratório de Hormônios e Genética Molecular LIM/42, Disciplina de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05466-040, SP, Brazil
| | - Roberto I. Lopes
- Divisão de Urologia, Departamento de Cirurgia da Faculdade de Medicina da Universidade de São Paulo, São Paulo 1964-2007, SP, Brazil
| | - Ana Claudia Latronico
- Unidade de Suprarrenal, Laboratório de Hormônios e Genética Molecular LIM/42, Disciplina de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05466-040, SP, Brazil
| | - Maria Candida B. V. Fragoso
- Unidade de Suprarrenal, Laboratório de Hormônios e Genética Molecular LIM/42, Disciplina de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05466-040, SP, Brazil
- Correspondence:
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21
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Wenger D, Kurumety S, Aydi ZB. A case report: invasive ductal carcinoma in mosaic Li-Fraumeni syndrome. J Surg Case Rep 2022; 2022:rjac408. [PMID: 36168441 PMCID: PMC9509207 DOI: 10.1093/jscr/rjac408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 08/23/2022] [Indexed: 11/22/2022] Open
Abstract
Li-Fraumeni syndrome (LFS) is a rare autosomal dominant condition caused by pathogenic variants in the TP53 tumor suppressor gene and characterized by a high lifetime risk of various cancers with a very early age of onset. We are presenting a 41-year-old woman with right invasive ductal cancer and no family history of cancers, diagnosed with mosaic LFS confirmed with blood and skin punch biopsy samples. She was treated with neoadjuvant chemotherapy, mastectomy and sentinel node biopsy with completion axillary dissection. Adjuvant radiation was not recommended due to increased risk of secondary cancers. She also elected to undergo risk reducing contralateral mastectomy. Further research is warranted to determine the appropriate clinical management and surveillance strategies in patients with mosaic LFS as whether individuals with mosaic LFS have differing cancer risks in comparison to classic germline LFS is unknown.
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Affiliation(s)
- Danielle Wenger
- University of Arizona College of Medicine – Phoenix , Phoenix, AZ 85006 , USA
| | - Sasha Kurumety
- Department of Radiology, Houston Methodist Hospital , Houston, TX 77030 , USA
| | - Zeynep B Aydi
- Department of Surgery, University of Arizona College of Medicine – Phoenix , Phoenix, AZ 85006 , USA
- Department of Surgical Oncology, Banner MD Anderson Cancer Center , Phoenix, AZ 85006 , USA
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22
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Chen JL, Miller DT, Schmidt LS, Malkin D, Korf BR, Eng C, Kwiatkowski DJ, Giannikou K. Mosaicism in Tumor Suppressor Gene Syndromes: Prevalence, Diagnostic Strategies, and Transmission Risk. Annu Rev Genomics Hum Genet 2022; 23:331-361. [PMID: 36044908 DOI: 10.1146/annurev-genom-120121-105450] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A mosaic state arises when pathogenic variants are acquired in certain cell lineages during postzygotic development, and mosaic individuals may present with a generalized or localized phenotype. Here, we review the current state of knowledge regarding mosaicism for eight common tumor suppressor genes-NF1, NF2, TSC1, TSC2, PTEN, VHL, RB1, and TP53-and their related genetic syndromes/entities. We compare and discuss approaches for comprehensive diagnostic genetic testing, the spectrum of variant allele frequency, and disease severity. We also review affected individuals who have no mutation identified after conventional genetic analysis, as well as genotype-phenotype correlations and transmission risk for each tumor suppressor gene in full heterozygous and mosaic patients. This review provides new insight into similarities as well as marked differences regarding the appreciation of mosaicism in these tumor suppressor syndromes.
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Affiliation(s)
- Jillian L Chen
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine and Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA; .,Boston University School of Medicine, Boston, Massachusetts, USA
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Laura S Schmidt
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.,Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - David Malkin
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.,Germline High Risk Cancer Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
| | - David J Kwiatkowski
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine and Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA;
| | - Krinio Giannikou
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine and Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA; .,Division of Hematology and Oncology, Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, California, USA;
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23
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SASAKI RITSUKO, HORIMOTO YOSHIYA, SAEKI HARUMI, SATO SHOJI, SANO KATSUHIRO, SHIKAMA NAOTO, UENO MAYUMI, SAITO MITSUE, ARAI MASAMI. Lessons Learned in Practice with Li-Fraumeni Syndrome: LFS-Related Breast Cancer Treatment Strategy and Establishment of a Surveillance System. JUNTENDO IJI ZASSHI = JUNTENDO MEDICAL JOURNAL 2022; 68:405-412. [PMID: 39021431 PMCID: PMC11249967 DOI: 10.14789/jmj.jmj22-0012-cr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/31/2022] [Indexed: 07/20/2024]
Abstract
We herein present the case of a 33-year-old woman with no family history of metachronous bilateral breast cancer and osteosarcoma, diagnosed with Li-Fraumeni syndrome (LFS), which is a rare autosomal dominant hereditary cancer syndrome associated with a germline TP53 variant. She was diagnosed with left distal femoral osteosarcoma at the age of 16, and metachronous bilateral breast cancer at the ages of 29 and 33. When the third cancer was diagnosed, a hereditary tumor syndrome was suspected and the patient was referred to our genetic outpatient clinic. There was no family history of the 'core' cancers for LFS, but since the patient met Chompret's criteria, germline TP53 genetic testing was performed with the patient's will. A pathogenic variant, TP53:c.216dupC (p.Val73ArgfsX76) was found in exon 4 of the gene. This case is didactic because radiotherapy was performed on the first breast cancer before the diagnosis of LFS was made; radiation should be avoided if there are other options in LFS because of the inability to repair DNA damage. As a lesson learned, oncologists reaffirmed the importance of being aware of hereditary tumors from the keywords "multiple," "young," "familial," and "rare," and consulting the genetic department. In addition, surveillance using whole-body magnetic resonance imaging is recommended in LFS. However, this system is not yet provided nationwide, but we have newly settled it in our hospital.
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Affiliation(s)
| | | | | | | | | | | | | | | | - MASAMI ARAI
- Corresponding author: Masami Arai, Department of Clinical Genetics, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan, TEL: +81-3-3813-3111 E-mail:
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Castillo D, Yuan TA, Nehoray B, Cervantes A, Tsang KK, Yang K, Sand SR, Mokhnatkin J, Herzog J, Slavin TP, Hyman S, Schwartz A, Ebert BL, Amos CI, Garber JE, Weitzel JN. Clonal Hematopoiesis and Mosaicism Revealed by a Multi-Tissue Analysis of Constitutional TP53 Status. Cancer Epidemiol Biomarkers Prev 2022; 31:1621-1629. [PMID: 35654360 PMCID: PMC9866580 DOI: 10.1158/1055-9965.epi-21-1296] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 02/02/2022] [Accepted: 05/20/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Though germline TP53 pathogenic/likely pathogenic variants (PV) are associated with Li-Fraumeni syndrome, many detected by multigene panels represent aberrant clonal expansion (ACE), most due to clonal hematopoiesis (CH). Discerning ACE/CH from germline variants and postzygotic mosaicism (PZM) is critically needed for risk assessment and management. METHODS Participants in the Li-Fraumeni & TP53 Understanding & Progress (LiFT UP) study with a TP53 PV were eligible. Demographics, personal/family cancer history, and clinical laboratory test reports were obtained. DNA from multiple tissues was analyzed using a custom QIAseq assay (ACE panel) that included TP53 and other CH-associated genes; the ACE panel and eyebrow follicles were assessed in a workflow to discern TP53 PV clinical categories. RESULTS Among 134 participants there was a significant difference for the age at diagnosis (P < 0.001), component cancers (P = 0.007), and clinical testing criteria (P < 0.001), comparing germline with PZM or ACE. ACE panel analysis of DNA from 55 sets of eyebrow follicles (mean 1.4 ug) and 36 formalin-fixed, paraffin imbedded tissues demonstrated low variance (SE, 3%; P = 0.993) for TP53 variant allele fraction, with no significant difference (P = 0.965) between tissue types, and detected CH gene PVs. Of 55 multi-tissue cases, germline status was confirmed for 20, PZM in seven, ACE for 25, and three were indeterminate. Additional CH variants were detected in six ACE and two germline cases. CONCLUSIONS We demonstrated an effective approach and tools for discerning germline TP53 status. IMPACT Discernment of PZM and TP53-driven CH increases diagnostic accuracy and enables risk-appropriate care.
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Affiliation(s)
| | - Tze-An Yuan
- City of Hope Cancer Center, Duarte, CA 91010, USA
| | - Bita Nehoray
- City of Hope Cancer Center, Duarte, CA 91010, USA
| | | | | | - Kai Yang
- City of Hope Cancer Center, Duarte, CA 91010, USA
| | | | | | - Josef Herzog
- City of Hope Cancer Center, Duarte, CA 91010, USA
| | | | - Sophie Hyman
- Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | | | | | | | - Jeffrey N. Weitzel
- City of Hope Cancer Center, Duarte, CA 91010, USA,Latin American School of Oncology, Los Angeles, CA, USA
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Werner-Lin A, Forbes Shepherd R, Young JL, Wilsnack C, Merrill SL, Greene MH, Khincha PP. Embodied risk for families with Li-Fraumeni syndrome: Like electricity through my body. Soc Sci Med 2022; 301:114905. [PMID: 35367908 PMCID: PMC9237847 DOI: 10.1016/j.socscimed.2022.114905] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 12/17/2021] [Accepted: 03/11/2022] [Indexed: 10/18/2022]
Abstract
INTRODUCTION Experiences of illness change the physical body and embodiments, or the ways in which the world and the self are known through the body. When illness is anticipated, such as with inherited cancer predisposition syndromes, risk becomes embodied and shared in family groups. Embodied risk is experienced whether or not symptoms have manifested. To examine how individuals and families with genetic risk experience the world and understand their disease through their bodies, we employ Li-Fraumeni syndrome (LFS) as an exemplar. LFS is a rare, genetic, cancer predisposition syndrome with nearly 100% lifetime cancer risk starting from birth, limited opportunities for prevention, rigorous screening protocols, and early mortality. METHODS Forty-five families, including 117 individuals aged 13-81 years, enrolled in the National Cancer Insitute's LFS study (NCT01443468) completed 66 open-ended interviews regarding LFS experiences. An interdisciplinary team used modified grounded theory to explore physical aspects of living with LFS in psychosocial contexts. FINDINGS The physicality of living with LFS included constant monitoring of LFS bodies across the family to identify physical change that might indicate carcinogenesis. Cancer screening, risk reduction, and treatment acted as dually protective and invasive, and as an unavoidable features of LFS. Connections between family members with similar embodiments normalized aesthetic changes and supported coping with visible markers of difference. In some circumstances, participants objectified the body to preserve the self and important relationships. In others, intense pain or loss created thresholds beyond which the self could no longer be separated from the body to support coping. DISCUSSION This paper focuses on Li-Fraumeni syndrome, a familial condition with a well-established genetic identity in which the body-self is experienced in relation to important others, to medical imaging, and to historical experiences with cancer. We expand on theories of embodied risk and inter-embodiment to describe experiences across disease trajectories, with attention to division and union between body, self, and other.
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Affiliation(s)
- Allison Werner-Lin
- School of Social Policy and Practice, University of Pennsylvania, Philadelphia, PA, USA; Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
| | - Rowan Forbes Shepherd
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jennifer L Young
- Stanford Center for Biomedical Ethics, Stanford University, Stanford, CA, USA
| | - Catherine Wilsnack
- Steve Hicks School of Social Work, The University of Texas at Austin, Austin, TX, USA
| | - Shana L Merrill
- School of Social Policy and Practice, University of Pennsylvania, Philadelphia, PA, USA; Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Mark H Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Payal P Khincha
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
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26
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van der Graaf W, Tesselaar M, McVeigh T, Oyen W, Fröhling S. Biology-Guided Precision Medicine in Rare Cancers: Lessons from Sarcomas and Neuroendocrine Tumours. Semin Cancer Biol 2022; 84:228-241. [DOI: 10.1016/j.semcancer.2022.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 05/19/2022] [Accepted: 05/19/2022] [Indexed: 11/26/2022]
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Rhiem K, Auber B, Briest S, Dikow N, Ditsch N, Dragicevic N, Grill S, Hahnen E, Horvath J, Jaeger B, Kast K, Kiechle M, Leinert E, Morlot S, Püsken M, Schäfer D, Schott S, Schroeder C, Siebers-Renelt U, Solbach C, Weber-Lassalle N, Witzel I, Zeder-Göß C, Schmutzler RK. Consensus Recommendations of the German Consortium for Hereditary Breast and Ovarian Cancer. Breast Care (Basel) 2022; 17:199-207. [PMID: 35702495 PMCID: PMC9149395 DOI: 10.1159/000516376] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/17/2021] [Indexed: 08/01/2023] Open
Abstract
BACKGROUND The German Consortium for Hereditary Breast and Ovarian Cancer (GC-HBOC) has established a multigene panel (TruRisk®) for the analysis of risk genes for familial breast and ovarian cancer. SUMMARY An interdisciplinary team of experts from the GC-HBOC has evaluated the available data on risk modification in the presence of pathogenic mutations in these genes based on a structured literature search and through a formal consensus process. KEY MESSAGES The goal of this work is to better assess individual disease risk and, on this basis, to derive clinical recommendations for patient counseling and care at the centers of the GC-HBOC from the initial consultation prior to genetic testing to the use of individual risk-adapted preventive/therapeutic measures.
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Affiliation(s)
- Kerstin Rhiem
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology, Cologne, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Bernd Auber
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Susanne Briest
- Department of Obstetrics and Gynaecology, University Hospital of Leipzig, Leipzig, Germany
| | - Nicola Dikow
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Nina Ditsch
- Department of Gynecology and Obstetrics, University Hospital of Augsburg, Augsburg, Germany
| | - Neda Dragicevic
- Institute of Human Genetics, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Sabine Grill
- Department of Gynecology and Obstetrics, University Hospital Klinikum Rechts der Isar, Technical University Munich (TUM), Munich, Germany
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology, Cologne, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Judit Horvath
- Institute for Human Genetics, University Hospital Münster, Münster, Germany
| | - Bernadette Jaeger
- Department of Gynaecology and Obstetrics, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Karin Kast
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology, Cologne, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Marion Kiechle
- Department of Gynecology and Obstetrics, University Hospital Klinikum Rechts der Isar, Technical University Munich (TUM), Munich, Germany
| | - Elena Leinert
- Department of Gynaecology and Obstetrics, University Hospital Ulm, Ulm, Germany
| | - Susanne Morlot
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Michael Püsken
- Department of Radiology, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Dieter Schäfer
- Institute for Human Genetics, University of Frankfurt, Frankfurt, Germany
| | - Sarah Schott
- Department of Obstetrics and Gynaecology, University of Heidelberg, Heidelberg, Germany
| | - Christopher Schroeder
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | | | - Christine Solbach
- Department of Gynecology and Obstetrics, University Hospital Frankfurt, Frankfurt, Germany
| | - Nana Weber-Lassalle
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology, Cologne, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Isabell Witzel
- Department of Obstetrics and Gynaecology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christine Zeder-Göß
- Department of Gynecology and Obstetrics, University Hospital of Augsburg, Augsburg, Germany
| | - Rita K. Schmutzler
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology, Cologne, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
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Ben-Cohen G, Doffe F, Devir M, Leroy B, Soussi T, Rosenberg S. TP53_PROF: a machine learning model to predict impact of missense mutations in TP53. Brief Bioinform 2022; 23:6510957. [PMID: 35043155 PMCID: PMC8921628 DOI: 10.1093/bib/bbab524] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/04/2021] [Accepted: 11/15/2021] [Indexed: 11/27/2022] Open
Abstract
Correctly identifying the true driver mutations in a patient’s tumor is a major challenge in precision oncology. Most efforts address frequent mutations, leaving medium- and low-frequency variants mostly unaddressed. For TP53, this identification is crucial for both somatic and germline mutations, with the latter associated with the Li-Fraumeni syndrome (LFS), a multiorgan cancer predisposition. We present TP53_PROF (prediction of functionality), a gene specific machine learning model to predict the functional consequences of every possible missense mutation in TP53, integrating human cell- and yeast-based functional assays scores along with computational scores. Variants were labeled for the training set using well-defined criteria of prevalence in four cancer genomics databases. The model’s predictions provided accuracy of 96.5%. They were validated experimentally, and were compared to population data, LFS datasets, ClinVar annotations and to TCGA survival data. Very high accuracy was shown through all methods of validation. TP53_PROF allows accurate classification of TP53 missense mutations applicable for clinical practice. Our gene specific approach integrated machine learning, highly reliable features and biological knowledge, to create an unprecedented, thoroughly validated and clinically oriented classification model. This approach currently addresses TP53 mutations and will be applied in the future to other important cancer genes.
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Affiliation(s)
- Gil Ben-Cohen
- Corresponding authors: Gil Ben Cohen, Gaffin Center for Neuro-Oncology, Sharett Institute for Oncology, The Wohl Institute for Translational Medicine. Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel. Tel.: +972549410946. E-mail: ; Shai Rosenberg, Gaffin Center for Neuro-Oncology, Sharett Institute for Oncology, The Wohl Institute for Translational Medicine. Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel. Tel.: 972-2-6776289. E-mail:
| | - Flora Doffe
- INSERM UMR 1186, Integrative Tumor Immunology and Immunotherapy, Gustave Roussy, Faculté de Médecine, Université Paris-Sud, Université Paris-Saclay, 94805 Villejuif, France
| | - Michal Devir
- Gaffin Center for Neuro-Oncology, Sharett Institute for Oncology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
- The Wohl Institute for Translational Medicine, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Bernard Leroy
- Sorbonne Université, UPMC Univ Paris 06, F- 75005 Paris, France
| | | | - Shai Rosenberg
- Corresponding authors: Gil Ben Cohen, Gaffin Center for Neuro-Oncology, Sharett Institute for Oncology, The Wohl Institute for Translational Medicine. Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel. Tel.: +972549410946. E-mail: ; Shai Rosenberg, Gaffin Center for Neuro-Oncology, Sharett Institute for Oncology, The Wohl Institute for Translational Medicine. Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel. Tel.: 972-2-6776289. E-mail:
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Kratz CP, Steinke-Lange V, Spier I, Aretz S, Schröck E, Holinski-Feder E. Overview of the Clinical Features of Li-Fraumeni Syndrome and the Current European ERN GENTURIS Guideline. Geburtshilfe Frauenheilkd 2022; 82:42-49. [PMID: 35027859 PMCID: PMC8747895 DOI: 10.1055/a-1541-7912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/29/2021] [Indexed: 01/18/2023] Open
Abstract
Patients with a tumour-risk syndrome have a significantly increased risk of developing cancer during their lifetime. A positive family history of tumour disease or an unusually early age of onset may be indicative of a tumour risk syndrome. With the diagnosis of a tumour risk syndrome it is possible to recommend a risk-adapted tumour surveillance programme for the patient and (asymptomatic) family members at risk. This facilitates early detection of possible tumours and thus often prevents advanced tumour stages. Li-Fraumeni syndrome is associated with a significantly increased risk of sarcoma and breast cancer in particular, but it is often not diagnosed clinically in those affected. This article reviews the clinical picture, genetic cause and special aspects in the diagnosis and care of patients with Li-Fraumeni syndrome. The initiative resulted from the European reference network GENTURIS, which has set itself the task of improving the identification and care of
patients with tumour risk syndromes. A first step is the recent publication of a European guideline for Li-Fraumeni syndrome, which is summarised here and discussed in the context of existing recommendations.
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Affiliation(s)
- Christian Peter Kratz
- Klinik für Pädiatrische Hämatologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Verena Steinke-Lange
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, München, Germany.,MGZ Medizinisch Genetisches Zentrum, München, Germany
| | - Isabel Spier
- Institut für Humangenetik, Universitätsklinikum Bonn, Bonn, Germany
| | - Stefan Aretz
- Institut für Humangenetik, Universitätsklinikum Bonn, Bonn, Germany
| | - Evelin Schröck
- Institut für Klinische Genetik, Technische Universität Dresden, Dresden, Germany
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, München, Germany.,MGZ Medizinisch Genetisches Zentrum, München, Germany
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Avoidance or adaptation of radiotherapy in patients with cancer with Li-Fraumeni and heritable TP53-related cancer syndromes. Lancet Oncol 2021; 22:e562-e574. [PMID: 34856153 DOI: 10.1016/s1470-2045(21)00425-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/14/2021] [Accepted: 07/21/2021] [Indexed: 12/18/2022]
Abstract
The management of patients with cancer and Li-Fraumeni or heritable TP53-related cancer syndromes is complex because of their increased risk of developing second malignant neoplasms after genotoxic stresses such as systemic treatments or radiotherapy (radiosusceptibility). Clinical decision making also integrates the risks of normal tissue toxicity and sequelae (radiosensitivity) and tumour response to radiotherapy (radioresistance and radiocurability). Radiotherapy should be avoided in patients with cancer and Li-Fraumeni or heritable TP53 cancer-related syndromes, but overall prognosis might be poor without radiotherapy: radioresistance in these patients seems similar to or worse than that of the general population. Radiosensitivity in germline TP53 variant carriers seems similar to that in the general population. The risk of second malignant neoplasms according to germline TP53 variant and the patient's overall oncological prognosis should be assessed during specialised multidisciplinary staff meetings. Radiotherapy should be avoided whenever other similarly curative treatment options are available. In other cases, it should be adapted to minimise the risk of second malignant neoplasms in patients who still require radiotherapy despite its genotoxicity, in view of its potential benefit. Adaptations might be achieved through the reduction of irradiated volumes using proton therapy, non-ionising diagnostic procedures, image guidance, and minimal stray radiation. Non-ionising imaging should become more systematic. Radiotherapy approaches that might result in a lower probability of misrepaired DNA damage (eg, particle therapy biology and tumour targeting) are an area of investigation.
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31
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Fortuno C, McGoldrick K, Pesaran T, Dolinsky J, Hoang L, Weitzel JN, Beshay V, San Leong H, James PA, Spurdle AB. Suspected clonal hematopoiesis as a natural functional assay of TP53 germline variant pathogenicity. Genet Med 2021; 24:673-680. [PMID: 34906512 DOI: 10.1016/j.gim.2021.10.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 10/19/2022] Open
Abstract
PURPOSE Some variants identified by multigene panel testing of DNA from blood present with low variant allele fraction (VAF), often a manifestation of clonal hematopoiesis. Research has shown that the proportion of variants with low VAF is especially high in TP53, the Li-Fraumeni syndrome gene. Based on the hypothesis that variants with low VAF are positively selected as drivers of clonal hematopoiesis, we investigated the use of VAF as a predictor of TP53 germline variant pathogenicity. METHODS We used data from 260,681 TP53 variants identified at 2 laboratories to compare the distribution of pathogenic and benign variants at different VAF intervals. RESULTS Likelihood ratios toward pathogenicity associated with a VAF < 26% equated to the American College of Medical Genetics/Association of Molecular Pathology strong strength level and were applicable for 1 in 5 variants of unknown significance. CONCLUSION In conclusion, detection of variants with low VAF in blood can be considered an in vivo functional assay to aid assessment of TP53 variant pathogenicity.
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Affiliation(s)
- Cristina Fortuno
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | | | | | | | | | - Victoria Beshay
- Molecular Pathology Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Huei San Leong
- Molecular Pathology Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, and Royal Melbourne Hospital, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia.
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
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Schwartz AN, Hyman SR, Stokes SM, Castillo D, Tung NM, Weitzel JN, Rana HQ, Garber JE. Evaluation of TP53 Variants Detected on Peripheral Blood or Saliva Testing: Discerning Germline From Somatic TP53 Variants. JCO Precis Oncol 2021; 5:1677-1686. [PMID: 34994652 DOI: 10.1200/po.21.00278] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/15/2021] [Accepted: 09/24/2021] [Indexed: 01/04/2023] Open
Abstract
PURPOSE Multigene panel testing (MGPT) identifies TP53 pathogenic or likely pathogenic (P/LP) variants in patients with diverse phenotypes, of which only one is classic Li-Fraumeni syndrome. Low variant allelic fraction (VAF) in TP53 found on germline testing may suggest aberrant clonal expansion or constitutional mosaicism. We evaluated TP53-positive probands seen in a cancer genetics program to determine germline versus somatic status. METHODS We reviewed TP53-positive probands from 2012 to 2019 identified by MGPT on blood or saliva (N = 84). Available VAFs were collected. Probands with a familial variant, who met Li-Fraumeni syndrome testing criteria or who carried a founder variant, were considered germline. For those with uncertain germline status, TP53 variants were further examined using ancillary data of family members and somatic tissue. RESULTS Of the 84 probands, 54.7% had germline variants with 33.3% meeting criteria for germline status and 21.4% confirmed through ancillary testing. Aberrant clonal expansion comprised 13.1% with clonal hematopoiesis of indeterminate potential and 2.4% with a hematologic malignancy. Constitutional mosaicism was confirmed in 8.3% probands. Definitive status could not be determined in 3.6% despite ancillary assessment, and 17.9% did not have ancillary testing. CONCLUSION A TP53 P/LP variant found on peripheral blood or saliva MGPT does not always originate in the germline. In a clinical cancer genetics cohort, approximately half of the patients had TP53 P/LP germline variants; these patients plus those with constitutional mosaicism require intensified surveillance. A framework of multiple strategies enables discernment of germline from constitutional mosaic and acquired variants, which is essential for appropriate management.
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Affiliation(s)
- Alison N Schwartz
- Division of Cancer Genetics and Prevention, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Sophie R Hyman
- Division of Cancer Genetics and Prevention, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Samantha M Stokes
- Division of Cancer Genetics and Prevention, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Danielle Castillo
- Division of Clinical Cancer Genomics, Beckman Research Institute, City of Hope, Duarte, CA
| | - Nadine M Tung
- Harvard Medical School, Boston, MA
- Division of Hematology and Oncology, Beth Israel Deaconess Medical Center, Boston, MA
| | | | - Huma Q Rana
- Division of Cancer Genetics and Prevention, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Judy E Garber
- Division of Cancer Genetics and Prevention, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
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Pinto EM, Maxwell KN, Halalsheh H, Phillips A, Powers J, MacFarland S, Walsh MF, Breen K, Formiga MN, Kriwacki R, Nichols KE, Mostafavi R, Wang J, Clay MR, Rodriguez-Galindo C, Ribeiro RC, Zambetti GP. Clinical and Functional Significance of TP53 Exon 4-Intron 4 Splice Junction Variants. Mol Cancer Res 2021; 20:207-216. [PMID: 34675114 DOI: 10.1158/1541-7786.mcr-21-0583] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/15/2021] [Accepted: 10/19/2021] [Indexed: 11/16/2022]
Abstract
Germline TP53 splicing variants are uncommon, and their clinical relevance is unknown. However, splice-altering variants at exon 4-intron 4 junctions are relatively enriched in pediatric adrenocortical tumors (ACT). Nevertheless, family histories of cancer compatible with classic Li-Fraumeni syndrome are rarely seen in these patients. We used conventional and in silico assays to determine protein stability, splicing, and transcriptional activity of 10 TP53 variants at exon 4-intron 4 junctions and analyzed their clinical correlates. We reviewed public databases that report the impact of TP53 variants in human cancer and examined individual reports, focusing on family history of cancer. TP53 exon 4-intron 4 junction germline variants were identified in 9 of 75 pediatric ACTs enrolled in the International Pediatric Adrenocortical Tumor Registry and Children's Oncology Group ARAR0332 study. An additional eight independent TP53 variants involving exon 4 splicing were identified in the Pediatric Cancer Genome Project (n = 5,213). These variants resulted in improper expression due to ineffective splicing, protein instability, altered subcellular localization, and loss of function. Clinical case review of carriers of TP53 exon 4-intron 4 junction variants revealed a high incidence of pediatric ACTs and atypical tumor types not consistent with classic Li-Fraumeni syndrome. Germline variants involving TP53 exon 4-intron 4 junctions are frequent in ACT and rare in other pediatric tumors. The collective impact of these germline TP53 variants on the fidelity of splicing, protein structure, and function must be considered in evaluating cancer susceptibility. IMPLICATIONS: Taken together, the data indicate that splice variants at TP53 codon 125 and surrounding bases differentially impacted p53 gene expression and function.
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Affiliation(s)
- Emilia M Pinto
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | - Kara N Maxwell
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Aaron Phillips
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jacquelyn Powers
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Suzanne MacFarland
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Michael F Walsh
- Department of Pediatrics and Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kelsey Breen
- Department of Pediatrics and Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria N Formiga
- Department of Oncogenetics, A.C. Camargo Center, Sao Paulo, Brazil
| | - Richard Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Kim E Nichols
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Roya Mostafavi
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jinling Wang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael R Clay
- Department of Pathology, University of Colorado, Boulder, Colorado
| | - Carlos Rodriguez-Galindo
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
- Global Pediatric Medicine at St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Raul C Ribeiro
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | - Gerard P Zambetti
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee.
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34
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Steinke-Lange V, de Putter R, Holinski-Feder E, Claes KB. Somatic mosaics in hereditary tumor predisposition syndromes. Eur J Med Genet 2021; 64:104360. [PMID: 34655802 DOI: 10.1016/j.ejmg.2021.104360] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 10/04/2021] [Accepted: 10/08/2021] [Indexed: 01/05/2023]
Abstract
Historically, it is estimated that 5-10% of cancer patients carry a causative genetic variant for a tumor predisposition syndrome. These conditions have high clinical relevance as they are actionable regarding risk-specific surveillance, predictive genetic testing, reproductive options, and - in some cases - risk reducing surgery or targeted therapy. Every individual is born with on average 0.5-1 exonic mosaic variants prevalent in single or multiple tissues. Depending on the tissues affected, mosaic conditions can abrogate the clinical phenotype of a tumor predisposition syndrome and can even go unrecognized, because it can be impossible or difficult to detect them with routine genetic testing in blood/leucocytes. On the other hand, it is estimated that at least 4% of presumed de novo variants are the result of low-level mosaicism (variant allele frequency <10%) in a parent, while around 7% are true mosaic variants with a higher variant allele frequency, which can sometimes be confused for heterozygous variants. Clonal hematopoiesis however can simulate a mosaic tumor predisposition in genetic diagnostics and has to be taken into account, especially for TP53 variants. Depending on the technique, variant allele frequencies of 2-3% can be detected for single nucleotide variants by next generation sequencing, copy number variants with variant allele frequencies of 5-30% can be detected by array-based technologies or MLPA. Mosaic tumor predisposition syndromes are more common than previously thought and may often remain undiagnosed. The clinical suspicion and diagnostic procedure for several cases with mosaic tumor predisposition syndromes are presented.
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Affiliation(s)
- Verena Steinke-Lange
- MGZ - Medical Genetics Center, Germany; Arbeitsgruppe Erbliche Gastrointestinale Tumore, Medizinische Klinik und Poliklinik IV - Campus Innenstadt, Klinikum der Universität München, Germany.
| | - Robin de Putter
- Center for Medical Genetics, Ghent University Hospital, Belgium
| | - Elke Holinski-Feder
- MGZ - Medical Genetics Center, Germany; Arbeitsgruppe Erbliche Gastrointestinale Tumore, Medizinische Klinik und Poliklinik IV - Campus Innenstadt, Klinikum der Universität München, Germany
| | - Kathleen Bm Claes
- Center for Medical Genetics, Ghent University Hospital, Belgium; CRIG (Cancer Research Institute Ghent) and Department of Biomolecular Medicine, Ghent University, Belgium
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35
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A de novo pathogenic variant in the MSH6 gene in a 52 years-old woman. Fam Cancer 2021; 21:319-324. [PMID: 34519923 DOI: 10.1007/s10689-021-00274-w] [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: 05/03/2021] [Accepted: 08/29/2021] [Indexed: 10/20/2022]
Abstract
Lynch syndrome (LS) is a condition which predisposes individuals primarily to early-onset colorectal and endometrial cancer. LS is characterized by a germline pathogenic variant in one of the MMR (MisMatch Repair) gene, inducing a phenotype of microsatellite instability in the tumor, which may be associated with a loss of expression of MMR proteins detected by standard immunohistochemistry on tumor tissue. Most of the time, LS is inherited from a parent in whom the condition may not be known due to incomplete penetrance, but de novo pathogenic variant is a rare occurrence. Here, we describe the case of a 52-year-old woman with no family history of LS, referred to the genetics department for colorectal cancer at the age of 50. Genetic analysis revealed a de novo germline pathogenic variant in the MSH6 gene. To date, this case is only the second report of a de novo pathogenic variant in the MSH6 gene in Lynch syndrome. De novo mutations have been extensively studied over the past years, but little is known about their origin and mechanism of occurrence in MMR genes. However, knowledge of mutation status allows better cancer risk management for the patient and an appropriate genetic testing and counseling for her family.
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36
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Maani N, Panabaker K, McCuaig JM, Buckley K, Semotiuk K, Farncombe KM, Ainsworth P, Panchal S, Sadikovic B, Armel SR, Lin H, Kim RH. Incidental findings from cancer next generation sequencing panels. NPJ Genom Med 2021; 6:63. [PMID: 34282142 PMCID: PMC8289933 DOI: 10.1038/s41525-021-00224-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 06/09/2021] [Indexed: 11/09/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have facilitated multi-gene panel (MGP) testing to detect germline DNA variants in hereditary cancer patients. This sensitive technique can uncover unexpected, non-germline incidental findings indicative of mosaicism, clonal hematopoiesis (CH), or hematologic malignancies. A retrospective chart review was conducted to identify cases of incidental findings from NGS-MGP testing. Inclusion criteria included: 1) multiple pathogenic variants in the same patient; 2) pathogenic variants at a low allele fraction; and/or 3) the presence of pathogenic variants not consistent with family history. Secondary tissue analysis, complete blood count (CBC) and medical record review were conducted to further delineate the etiology of the pathogenic variants. Of 6060 NGS-MGP tests, 24 cases fulfilling our inclusion criteria were identified. Pathogenic variants were detected in TP53, ATM, CHEK2, BRCA1 and APC. 18/24 (75.0%) patients were classified as CH, 3/24 (12.5%) as mosaic, 2/24 (8.3%) related to a hematologic malignancy, and 1/24 (4.2%) as true germline. We describe a case-specific workflow to identify and interpret the nature of incidental findings on NGS-MGP. This workflow will provide oncology and genetic clinics a practical guide for the management and counselling of patients with unexpected NGS-MGP findings.
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Affiliation(s)
- Nika Maani
- Program for Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Karen Panabaker
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Jeanna M McCuaig
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Familial Cancer Clinic, Princess Margaret Hospital Cancer Centre, Toronto, ON, Canada
| | | | - Kara Semotiuk
- Zane Cohen Centre for Digestive Diseases, Familial Gastrointestinal Cancer Registry, Mount Sinai Hospital, Toronto, ON, Canada
| | - Kirsten M Farncombe
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Peter Ainsworth
- Molecular Genetics Laboratory, Division of Molecular Diagnostics, London Health Sciences Centre, London, ON, Canada
| | - Seema Panchal
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Familial Breast Cancer Clinic, Mount Sinai Hospital, Toronto, ON, Canada
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Division of Molecular Diagnostics, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Susan Randall Armel
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Familial Cancer Clinic, Princess Margaret Hospital Cancer Centre, Toronto, ON, Canada
| | - Hanxin Lin
- Molecular Genetics Laboratory, Division of Molecular Diagnostics, London Health Sciences Centre, London, ON, Canada. .,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
| | - Raymond H Kim
- Familial Cancer Clinic, Princess Margaret Hospital Cancer Centre, Toronto, ON, Canada. .,Department of Medicine, University of Toronto, Toronto, ON, Canada.
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Ceyhan-Birsoy O, Selenica P, Chui MH, Jayakumaran G, Ptashkin R, Misyura M, Aypar U, Jairam S, Yang C, Li Y, Mehta N, Kemel Y, Salo-Mullen E, Maio A, Sheehan M, Zehir A, Carlo M, Latham A, Stadler Z, Robson M, Offit K, Ladanyi M, Walsh M, Reis-Filho JS, Mandelker D. Paired Tumor-Normal Sequencing Provides Insights Into the TP53-Related Cancer Spectrum in Patients With Li-Fraumeni Syndrome. J Natl Cancer Inst 2021; 113:1751-1760. [PMID: 34240179 PMCID: PMC9891110 DOI: 10.1093/jnci/djab117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/12/2021] [Accepted: 07/01/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Genetic testing for Li-Fraumeni syndrome (LFS) is performed by using blood specimens from patients selected based on phenotype-dependent guidelines. This approach is problematic for understanding the LFS clinical spectrum because patients with nonclassical presentations are missed, clonal hematopoiesis-related somatic blood alterations cannot be distinguished from germline variants, and unrelated tumors cannot be differentiated from those driven by germline TP53 defects. METHODS To provide insights into the LFS-related cancer spectrum, we analyzed paired tumor-blood DNA sequencing results in 17 922 patients with cancer and distinguished clonal hematopoiesis-related, mosaic, and germline TP53 variants. Loss of heterozygosity and TP53 mutational status were assessed in tumors, followed by immunohistochemistry for p53 expression on a subset to identify those lacking biallelic TP53 inactivation. RESULTS Pathogenic/likely pathogenic TP53 variants were identified in 50 patients, 12 (24.0%) of which were clonal hematopoiesis related and 4 (8.0%) of which were mosaic. Twelve (35.3%) of 34 patients with germline TP53 variants did not meet LFS testing criteria. Loss of heterozygosity of germline TP53 variant was observed in 96.0% (95% confidence interval [CI] = 79.7% to 99.9%) of core LFS spectrum-type tumors vs 45.5% (95% CI = 16.8% to 76.6%) of other tumors and 91.3% (95% CI = 72.0% to 98.9%) of tumors from patients who met LFS testing criteria vs 61.5% (95% CI = 31.6% to 86.1%) of tumors from patients who did not. Tumors retaining the wild-type TP53 allele exhibited wild-type p53 expression. CONCLUSIONS Our results indicate that some TP53 variants identified in blood-only sequencing are not germline and a substantial proportion of patients with LFS are missed based on current testing guidelines. Additionally, a subset of tumors from patients with LFS do not have biallelic TP53 inactivation and may represent cancers unrelated to their germline TP53 defect.
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Affiliation(s)
- Ozge Ceyhan-Birsoy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Herman Chui
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gowtham Jayakumaran
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryan Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maksym Misyura
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Umut Aypar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sowmya Jairam
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ciyu Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yirong Li
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikita Mehta
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yelena Kemel
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Erin Salo-Mullen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna Maio
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Margaret Sheehan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Carlo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alicia Latham
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zsofia Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Walsh
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Diana Mandelker
- Correspondence to: Diana Mandelker, MD, PhD, Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA (e-mail: )
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38
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Byrjalsen A, Diets IJ, Bakhuizen J, Hansen TVO, Schmiegelow K, Gerdes AM, Stoltze U, Kuiper RP, Merks JHM, Wadt K, Jongmans M. Selection criteria for assembling a pediatric cancer predisposition syndrome gene panel. Fam Cancer 2021; 20:279-287. [PMID: 34061292 PMCID: PMC8484084 DOI: 10.1007/s10689-021-00254-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 04/07/2021] [Indexed: 11/16/2022]
Abstract
Increasing use of genomic sequencing enables standardized screening of all childhood cancer predisposition syndromes (CPS) in children with cancer. Gene panels currently used often include adult-onset CPS genes and genes without substantial evidence linking them to cancer predisposition. We have developed criteria to select genes relevant for childhood-onset CPS and assembled a gene panel for use in children with cancer. We applied our criteria to 381 candidate genes, which were selected through two in-house panels (n = 338), a literature search (n = 39), and by assessing two Genomics England’s PanelApp panels (n = 4). We developed evaluation criteria that determined a gene’s eligibility for inclusion on a childhood-onset CPS gene panel. These criteria assessed (1) relevance in childhood cancer by a minimum of five childhood cancer patients reported carrying a pathogenic variant in the gene and (2) evidence supporting a causal relation between variants in this gene and cancer development. 138 genes fulfilled the criteria. In this study we have developed criteria to compile a childhood cancer predisposition gene panel which might ultimately be used in a clinical setting, regardless of the specific type of childhood cancer. This panel will be evaluated in a prospective study. The panel is available on (pediatric-cancer-predisposition-genepanel.nl) and will be regularly updated.
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Affiliation(s)
- Anna Byrjalsen
- Department of Clinical Genetics, Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen East, Denmark
| | - Illja J Diets
- Department of Human Genetics, Radboudumc, Geert Grooteplein Zuid 10, 6525 GA, Nijmegen, The Netherlands
| | - Jette Bakhuizen
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.,Department of Genetics, University Medical Center Utrecht, 3508 AB, Utrecht, The Netherlands
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen East, Denmark.,Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen East, Denmark
| | - Kjeld Schmiegelow
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen East, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen East, Denmark
| | - Ulrik Stoltze
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen East, Denmark
| | - Roland P Kuiper
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.,Department of Genetics, University Medical Center Utrecht, 3508 AB, Utrecht, The Netherlands
| | - Johannes H M Merks
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Karin Wadt
- Department of Clinical Genetics, Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen East, Denmark
| | - Marjolijn Jongmans
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands. .,Department of Genetics, University Medical Center Utrecht, 3508 AB, Utrecht, The Netherlands.
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39
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Rodriguez KD, Schneider KW, Suttman A, Garrington T, Jellins T, Tholen K, Francom CR, Herrmann BW. Pediatric Head and Neck Tumors Associated with Li-Fraumeni Syndrome. Ann Otol Rhinol Laryngol 2021:34894211014786. [PMID: 33971750 DOI: 10.1177/00034894211014786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
INTRODUCTION Cancer predisposition syndromes are germline pathogenic variants in genes that greatly raise the risk of developing neoplastic diseases. One of the most well-known is Li-Fraumeni syndrome (LFS), which is due to pathogenic variants in the TP53 gene. Children with LFS have higher risks for multiple malignancies before adulthood, often with rare and aggressive subtypes. OBJECTIVE To examine head and neck manifestations of LFS in children treated at a tertiary children's hospital over a 20-year period. METHODS A retrospective review of LFS children with neoplastic disease presenting in traditional Otolaryngologic head and neck subsites from 2000 to 2019, with patient charts reviewed for relevant clinical, imaging, and operative data. RESULTS Of the 40 LFS patients initially identified, 27 neoplastic tumors were identified in 20 children within this cohort (20 primary, 7 second primary). Head and neck subsites aside from the brain or orbit were involved in 22% (6/27) of these tumors, representing 20% (4/20) of primary tumors and 29% (2/7) of second primary tumors. Both second primaries within the head and neck were within the radiation fields of the first primary tumor. The mean ages at primary and second primary diagnosis were 4.6 years (SD 3.5) and 12 years (SD 1.4), respectively. The male/female ratio was 1:6 among all patients with head and neck tumors. All 6 head and neck tumors were sarcomas. Rhabdomyosarcoma (N = 3, 50%) was the most common pathology, and the other 3 demonstrated rare tumor pathological subtypes (synovial cell sarcoma, pleomorphic myxoid liposarcoma, mandibular osteosarcoma). The neck was the most common subsite (75%) within this group for primary tumor presentation. CONCLUSION This study identifies a high potential for head and neck involvement in children with LFS, which has not been previously described in the literature. Otolaryngological care should be included in a multidisciplinary care team surveilling these patients.
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Affiliation(s)
- Kenny D Rodriguez
- Department of Otolaryngology-Head and Neck Surgery, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Kami Wolfe Schneider
- Department of Hematology, Oncology, Bone Marrow Transplantation, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Alexandra Suttman
- Department of Hematology, Oncology, Bone Marrow Transplantation, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Timothy Garrington
- Department of Hematology, Oncology, Bone Marrow Transplantation, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | | | - Kaitlyn Tholen
- Department of Otolaryngology-Head and Neck Surgery, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Christian R Francom
- Department of Otolaryngology-Head and Neck Surgery, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Brian W Herrmann
- Department of Otolaryngology-Head and Neck Surgery, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
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40
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Le Duc D, Hentschel J, Neuser S, Stiller M, Meier C, Jäger E, Abou Jamra R, Platzer K, Monecke A, Ziemer M, Markovic A, Bläker H, Lemke JR. In cis TP53 and RAD51C pathogenic variants may predispose to sebaceous gland carcinomas. Eur J Hum Genet 2020; 29:489-494. [PMID: 33319852 PMCID: PMC7940394 DOI: 10.1038/s41431-020-00781-x] [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: 06/22/2020] [Revised: 11/07/2020] [Accepted: 11/17/2020] [Indexed: 11/22/2022] Open
Abstract
Pathogenic variants in TP53 have been classically thought to cause Li-Fraumeni syndrome (LFS), a cancer predisposition with high risks for various childhood- and adult-onset malignancies. However, increased genetic testing has lately revealed, that pathogenic variant carriers exhibit a broader range of phenotypes and that penetrance may be dependent both on variant type and modifiers. Using next generation sequencing and short tandem repeat analysis, we identified germline pathogenic variants in TP53 and RAD51C located in cis on chromosome 17 in a 43-year-old male, who has developed a rare sebaceous gland carcinoma (SGC) but so far no tumors of the LFS spectrum. This course mirrors a Trp53-Rad51c-double-mutant cis mouse-model, which similarly develops SGC, while the characteristic Trp53-associated tumor spectrum occurs with significantly lower frequency. Therefore, we propose that co-occurent pathogenic variants in RAD51C and TP53 may predispose to SGC, reminiscent of Muir-Torre syndrome. Further, this report supports the diversity of clinical presentations associated with germline TP53 alterations, and thus, the proposed expansion of LFS to heritable TP53-related cancer syndrome.
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Affiliation(s)
- Diana Le Duc
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany. .,Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
| | - Julia Hentschel
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Sonja Neuser
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Mathias Stiller
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany.,Institute of Pathology, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Carolin Meier
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Elisabeth Jäger
- Department of Endocrinology, Nephrology, and Rheumatology, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Astrid Monecke
- Institute of Pathology, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Mirjana Ziemer
- Department of Dermatology, Venereology and Allergology, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Aleksander Markovic
- Department of Dermatology, Venereology and Allergology, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Hendrik Bläker
- Institute of Pathology, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany.
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41
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Liu APY, Wu G, Orr BA, Lin T, Ashford JM, Bass JK, Bowers DC, Hassall T, Fisher PG, Indelicato DJ, Klimo P, Boop F, Conklin H, Onar-Thomas A, Merchant TE, Ellison DW, Gajjar A, Robinson GW. Outcome and molecular analysis of young children with choroid plexus carcinoma treated with non-myeloablative therapy: results from the SJYC07 trial. Neurooncol Adv 2020; 3:vdaa168. [PMID: 33506206 PMCID: PMC7813199 DOI: 10.1093/noajnl/vdaa168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Choroid plexus carcinoma (CPC) is a rare and aggressive tumor of infancy without a clear treatment strategy. This study describes the outcomes of children with CPC treated on the multi-institutional phase 2 SJYC07 trial and reports on the significance of clinical and molecular characteristics. Methods Eligible children <3 years-old with CPC were postoperatively stratified to intermediate-risk (IR) stratum if disease was localized or high-risk (HR) stratum, if metastatic. All received high-dose methotrexate-containing induction chemotherapy. IR-stratum patients received focal irradiation as consolidation whereas HR-stratum patients received additional chemotherapy. Consolidation was followed by oral antiangiogenic maintenance regimen. Survival rates and potential prognostic factors were analyzed. Results Thirteen patients (median age: 1.41 years, range: 0.21-2.93) were enrolled; 5 IR, 8 HR. Gross-total resection or near-total resection was achieved in ten patients and subtotal resection in 3. Seven patients had TP53-mutant tumors, including 4 who were germline carriers. Five patients experienced progression and died of disease; 8 (including 5 HR) are alive without progression. The 5-year progression-free survival (PFS) and overall survival rates were 61.5 ± 13.5% and 68.4 ± 13.1%. Patients with TP53-wild-type tumors had a 5-year PFS of 100% as compared to 28.6 ± 17.1% for TP53-mutant tumors (P = .012). Extent of resection, metastatic status, and use of radiation therapy were not significantly associated with survival. Conclusions Non-myeloablative high-dose methotrexate-containing therapy with maximal surgical resection resulted in long-term PFS in more than half of patients with CPC. TP53-mutational status was the only significant prognostic variable and should form the basis of risk-stratification in future trials.
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Affiliation(s)
- Anthony P Y Liu
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Gang Wu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Brent A Orr
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Tong Lin
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jason M Ashford
- Department of Psychology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Johnnie K Bass
- Department of Rehabilitation Services, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Daniel C Bowers
- Division of Pediatric Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Tim Hassall
- Queensland Children's Hospital, Brisbane, Queensland, Australia
| | - Paul G Fisher
- Department of Neurology, Stanford University, Palo Alto, California, USA
| | - Daniel J Indelicato
- Department of Radiation Oncology, University of Florida College of Medicine-Jacksonville, Semmes Murphey Clinic, Memphis, Tennessee, USA
| | - Paul Klimo
- Department of Surgery, St. Jude Children's Research Hospital, Semmes Murphey Clinic, Memphis, Tennessee, USA.,Department of Neurosurgery, University of Tennessee Health Science Center, Semmes Murphey Clinic, Memphis, Tennessee, USA.,Le Bonheur Neuroscience Institute, Le Bonheur Children's Hospital, Semmes Murphey Clinic, Memphis, Tennessee, USA.,Semmes Murphey Clinic, Memphis, Tennessee, USA
| | - Frederick Boop
- Department of Surgery, St. Jude Children's Research Hospital, Semmes Murphey Clinic, Memphis, Tennessee, USA.,Department of Neurosurgery, University of Tennessee Health Science Center, Semmes Murphey Clinic, Memphis, Tennessee, USA.,Le Bonheur Neuroscience Institute, Le Bonheur Children's Hospital, Semmes Murphey Clinic, Memphis, Tennessee, USA.,Semmes Murphey Clinic, Memphis, Tennessee, USA
| | - Heather Conklin
- Department of Psychology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Arzu Onar-Thomas
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Thomas E Merchant
- Department of Radiation Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Amar Gajjar
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Giles W Robinson
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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Evans DG, Woodward ER, Bajalica-Lagercrantz S, Oliveira C, Frebourg T. Germline TP53 Testing in Breast Cancers: Why, When and How? Cancers (Basel) 2020; 12:cancers12123762. [PMID: 33327514 PMCID: PMC7764913 DOI: 10.3390/cancers12123762] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/05/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary TP53 variants detected in blood represent a main genetic cause of breast cancers occurring before 31 years of age. TP53 being included in most of the cancer gene panels, patients with breast cancer are offered germline TP53 testing, independently of the age of tumour onset and familial history. Interpretation of TP53 variants is remarkably complex, and detection of a germline disease-causing TP53 variant in a breast cancer patient has drastic medical consequences: radiotherapy contributing to the development of subsequent tumours should be, if possible, avoided. In her family, variant carriers should be offered annual follow-up, including whole-body MRI. Therefore, we consider that, in breast cancer patients, germline TP53 testing should be performed before treatment and that the decision of TP53 testing should not be systematic but based on the age of tumour onset, type of breast cancer, personal and familial history of cancer. Abstract Germline TP53 variants represent a main genetic cause of breast cancers before 31 years of age. Development of cancer multi-gene panels has resulted in an exponential increase of germline TP53 testing in breast cancer patients. Interpretation of TP53 variants, which are mostly missense, is complex and requires excluding clonal haematopoiesis and circulating tumour DNA. In breast cancer patients harbouring germline disease-causing TP53 variants, radiotherapy contributing to the development of subsequent tumours should be, if possible, avoided and, within families, annual follow-up including whole-body MRI should be offered to carriers. We consider that, in breast cancer patients, germline TP53 testing should be performed before treatment and offered systematically only to patients with: (i) invasive breast carcinoma or ductal carcinoma in situ (DCIS) before 31; or (ii) bilateral or multifocal or HER2+ invasive breast carcinoma/DCIS or phyllode tumour before 36; or (iii) invasive breast carcinoma before 46 and another TP53 core tumour (breast cancer, soft-tissue sarcoma, osteosarcoma, central nervous system tumour, adrenocortical carcinoma); or (iv) invasive breast carcinoma before 46 and one first- or second-degree relative with a TP53 core tumour before 56. In contrast, women presenting with breast cancer after 46, without suggestive personal or familial history, should not be tested for TP53.
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Affiliation(s)
- D. Gareth Evans
- Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, University of Manchester, Manchester M13 9WL, UK;
- Manchester Centre for Genomic Medicine St Mary’s Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WL, UK
- Correspondence: (D.G.E.); (T.F.)
| | - Emma R. Woodward
- Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, University of Manchester, Manchester M13 9WL, UK;
- Manchester Centre for Genomic Medicine St Mary’s Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WL, UK
| | - Svetlana Bajalica-Lagercrantz
- Hereditary Cancer Unit, Department of Clinical Genetics, Karolinska University Hospital, SE-17176 Stockholm, Sweden;
| | - Carla Oliveira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal;
- Ipatimup-Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
- Porto Comprehensive Cancer Center, 4200-072 Porto, Portugal
| | - Thierry Frebourg
- Department of Genetics, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, 76000 Rouen, France
- Inserm U1245, Normandie University, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76183 Rouen, France
- Correspondence: (D.G.E.); (T.F.)
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Mehta S, Kuo DJ. To test or not to test: genetic cancer predisposition testing in paediatric patients with cancer. JOURNAL OF MEDICAL ETHICS 2020; 47:medethics-2020-106656. [PMID: 33303646 DOI: 10.1136/medethics-2020-106656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/07/2020] [Accepted: 11/16/2020] [Indexed: 06/12/2023]
Abstract
Genetic cancer predisposition testing in the paediatric population poses unique ethical dilemmas. Using the hypothetical example of a teenager with cancer with a high probability of having an underlying cancer predisposition syndrome, we discuss the ethical considerations that affect the decision-making process. Because legally these decisions are made by parents, genetic testing in paediatrics can remove a child's autonomy to preserve his or her own 'open future'. However, knowledge of results confirming a predisposition syndrome can potentially be beneficial in modifying treatment and surveillance plans and enabling at-risk family members to obtain cascade testing for themselves. Considering virtue ethics to envision the best characters of the patient, parents and healthcare providers can guide them to the better choice to test or not to test, with the ultimate goal of achieving the best outcome for survival and eudaimonia, human flourishing reliably sought out.
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Affiliation(s)
- Sapna Mehta
- Global Health, Biology, University of California San Diego, La Jolla, California, USA
| | - Dennis John Kuo
- Pediatric Hematology-Oncology, University of California San Diego School of Medicine, La Jolla, California, USA
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Peacock EG, Grenon LM, Batalini F, Tung N. Challenges in Interpreting TP53 Pathogenic Variants With a Low Minor Allele Frequency in Germline Genetic Testing: A Case Report of a Patient With Mosaic Li-Fraumeni Syndrome. JCO Precis Oncol 2020; 4:91-95. [DOI: 10.1200/po.19.00279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
| | | | | | - Nadine Tung
- Beth Israel Deaconess Medical Center, Boston, MA
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45
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FANCA, TP53, and del(5q)/RPS14 alterations in a patient with T-cell non-Hodgkin lymphoma and concomitant Fanconi anemia and Li-Fraumeni syndrome. Cancer Genet 2020; 256-257:179-183. [PMID: 33183999 DOI: 10.1016/j.cancergen.2020.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/01/2020] [Accepted: 10/25/2020] [Indexed: 11/23/2022]
Abstract
We traced the neoplastic history (from 5 to 11 years of age) of a child with concomitant Fanconi anemia and Li-Fraumeni syndrome. Interestingly, the patient developed a highly malignant T-cell non-Hodgkin lymphoma (NHL), which does not represent the typical tumor type in the two aforementioned syndromes, presumably due to the underlying genomic instability. By using a combination of molecular and immunohistochemical approaches, we characterized the accumulation of multiple genetic alterations in a single patient, with both germline (parentally inherited biallelic FANCA variants and a likely de novo nonsense variant in TP53) and somatic (TP53 loss of heterozygosity and 5q interstitial deletion) contributions. Our findings support the interplay of TP53 and FANC genes in DNA damage response pathways and further highlight the genetic heterogeneity of lymphomas as well as the contribution of genomic instability to lymphomagenesis.
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46
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Pre- and Post-Zygotic TP53 De Novo Mutations in SHH-Medulloblastoma. Cancers (Basel) 2020; 12:cancers12092503. [PMID: 32899294 PMCID: PMC7564492 DOI: 10.3390/cancers12092503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/26/2020] [Accepted: 09/01/2020] [Indexed: 11/26/2022] Open
Abstract
Simple Summary Medulloblastoma is the most common malignant brain tumor in children. In a subset of cases, a causal factor is a constitutive mutation of the TP53 gene, which may be inherited or arise for the first time in a patient (de novo). Using an immunohistochemistry assay as a screening tool, we selected patients suspected of harboring a TP53 mutation and offered genetic counseling and germline testing. Our study, which was the first to investigate the parental origin of TP53 mutations in medulloblastoma, allowed the identification of two additional cases with de novo mutations. Moreover, we demonstrated that in one patient the mutation originated at a post-zygotic stage, resulting in somatic mosaicism. These findings have important implications for genetic counseling since they highlight the occurrence of both pre- and post-zygotic TP53 de novo mutations in medulloblastoma, pointing out that in a specific subgroup of patients genetic testing should be offered regardless of family history. Abstract Li-Fraumeni syndrome (LFS) is an autosomal dominant disorder caused by mutations in the TP53 gene, predisposing to a wide spectrum of early-onset cancers, including brain tumors. In medulloblastoma patients, the role of TP53 has been extensively investigated, though the prevalence of de novo mutations has not been addressed. We characterized TP53 mutations in a monocentric cohort of consecutive Sonic Hedgehog (SHH)-activated medulloblastoma patients. Germline testing was offered based on tumor p53 immunostaining positivity. Among 24 patients, three (12.5%) showed tumor p53 overexpression, of whom two consented to undergo germline testing and resulted as carriers of TP53 mutations. In the first case, family history was uneventful and the mutation was not found in either of the parents. The second patient, with a family history suggestive of LFS, unexpectedly resulted as a carrier of the mosaic mutation c.742=/C>T p.(Arg248=/Trp). The allele frequency was 26% in normal tissues and 42–77% in tumor specimens. Loss of heterozygosity (LOH) in the tumor was also confirmed. Notably, the mosaic case has been in complete remission for more than one year, while the first patient, as most TP53-mutated medulloblastoma cases from other cohorts, showed a severe and rapidly progressive disease. Our study reported the first TP53 mosaic mutation in medulloblastoma patients and confirmed the importance of germline testing in p53 overexpressed SHH-medulloblastoma, regardless of family history.
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47
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Pondrom M, Bougeard G, Karanian M, Bonneau-Lagacherie J, Boulanger C, Boutroux H, Briandet C, Chevreau C, Corradini N, Coze C, Defachelles AS, Galmiche-Roland L, Orbach D, Piguet C, Scoazec JY, Vérité C, Willems M, Frebourg T, Minard V, Brugières L. Rhabdomyosarcoma associated with germline TP53 alteration in children and adolescents: The French experience. Pediatr Blood Cancer 2020; 67:e28486. [PMID: 32658383 DOI: 10.1002/pbc.28486] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/06/2020] [Accepted: 05/13/2020] [Indexed: 01/07/2023]
Abstract
OBJECTIVE To describe the clinical characteristics and outcome of patients with Li-Fraumeni-associated rhabdomyosarcoma (RMS). METHOD Retrospective analysis of data from 31 French patients with RMS diagnosed before the age of 20 years associated with a TP53 pathogenic germline variant. Cases were identified through the French Li-Fraumeni database. Central histologic review was performed in 16 cases. RESULTS The median age at diagnosis was 2.3 years, and the median follow-up was 9.1 years (0.3-34.8). The main tumor sites were head and neck (n = 13), extremities (n = 8), and trunk (n = 8). The local pathology report classified the 31 tumors in embryonal (n = 26), alveolar (n = 1), pleomorphic (n = 1), and spindle-cell (n = 1) RMS (missing = 2). After histological review, anaplasia (diffuse or focal) was reported in 12/16 patients. Twenty-five patients had localized disease, three had lymph node involvement, and three distant metastases. First-line therapy combined surgery (n = 27), chemotherapy (n = 30), and radiotherapy (n = 14) and led to RMS control in all, but one patient. Eleven patients relapsed, and 18 patients had second malignancies. The 10-year event-free, progression-free, and overall survival rates were 36% (95% CI: 20-56), 62% (95% CI: 43-77) and 76% (95% CI: 56-88), respectively. The 10-year cumulative risk of second malignancies was 40% (95% CI: 22-60). CONCLUSION The high incidence of multiple primary tumors strongly influences the long-term prognosis of RMS associated with TP53 pathogenic germline variants. Anaplastic RMS in childhood, independently of the familial history, should lead to TP53 analysis at treatment initiation to reduce, whenever possible, the burden of genotoxic drugs and radiotherapy in carriers and to ensure the early detection of second malignancies.
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Affiliation(s)
- Morgane Pondrom
- Gustave Roussy Cancer Center, Department of Children and Adolescents Oncology, Paris-Saclay University, Villejuif, France.,Department of Pediatric Hemato-Oncology, Nice University Hospital, Nice, France
| | - Gaelle Bougeard
- Rouen University Hospital, Normandy University, UNIROUEN, Inserm, Department of Genetics, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Marie Karanian
- Department of Pathology, Lyon University Hospital, Lyon, France
| | | | - Cécile Boulanger
- Department of Pediatric Onco-Hematology, Toulouse University Hospital, Toulouse, France
| | - Hélène Boutroux
- Department of Pediatric Onco-Hematology, Trousseau Hospital, Paris, France
| | - Claire Briandet
- Department of Pediatric Onco-Hematology, Dijon University Hospital, Dijon, France
| | | | | | - Carole Coze
- Hôpital d'Enfants La Timone, Department of Pediatric Onco-Hematology, Aix-Marseille University, APHM, Marseille, France
| | | | | | - Daniel Orbach
- SIREDO Oncology Center (Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer), Institut Curie, PSL University, Paris, France
| | - Christophe Piguet
- Department of Pediatric Onco-Hematology, Limoges University Hospital, Limoges, France
| | - Jean Yves Scoazec
- Gustave Roussy Cancer Center, Department of Pathology, Paris-Saclay University, Villejuif, France
| | - Cécile Vérité
- Department of Pediatric Onco-Hematology, Bordeaux University Hospital, Bordeaux, France
| | - Marjolaine Willems
- Department of Genetics, Montpellier University Hospital, Montpellier, France
| | - Thierry Frebourg
- Rouen University Hospital, Normandy University, UNIROUEN, Inserm, Department of Genetics, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Véronique Minard
- Gustave Roussy Cancer Center, Department of Children and Adolescents Oncology, Paris-Saclay University, Villejuif, France
| | - Laurence Brugières
- Gustave Roussy Cancer Center, Department of Children and Adolescents Oncology, Paris-Saclay University, Villejuif, France
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Gao F, Pan X, Dodd-Eaton EB, Recio CV, Montierth MD, Bojadzieva J, Mai PL, Zelley K, Johnson VE, Braun D, Nichols KE, Garber JE, Savage SA, Strong LC, Wang W. A pedigree-based prediction model identifies carriers of deleterious de novo mutations in families with Li-Fraumeni syndrome. Genome Res 2020; 30:1170-1180. [PMID: 32817165 PMCID: PMC7462073 DOI: 10.1101/gr.249599.119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 06/25/2020] [Indexed: 01/14/2023]
Abstract
De novo mutations (DNMs) are increasingly recognized as rare disease causal factors. Identifying DNM carriers will allow researchers to study the likely distinct molecular mechanisms of DNMs. We developed Famdenovo to predict DNM status (DNM or familial mutation [FM]) of deleterious autosomal dominant germline mutations for any syndrome. We introduce Famdenovo.TP53 for Li-Fraumeni syndrome (LFS) and analyze 324 LFS family pedigrees from four US cohorts: a validation set of 186 pedigrees and a discovery set of 138 pedigrees. The concordance index for Famdenovo.TP53 prediction was 0.95 (95% CI: [0.92, 0.98]). Forty individuals (95% CI: [30, 50]) were predicted as DNM carriers, increasing the total number from 42 to 82. We compared clinical and biological features of FM versus DNM carriers: (1) cancer and mutation spectra along with parental ages were similarly distributed; (2) ascertainment criteria like early-onset breast cancer (age 20-35 yr) provides a condition for an unbiased estimate of the DNM rate: 48% (23 DNMs vs. 25 FMs); and (3) hotspot mutation R248W was not observed in DNMs, although it was as prevalent as hotspot mutation R248Q in FMs. Furthermore, we introduce Famdenovo.BRCA for hereditary breast and ovarian cancer syndrome and apply it to a small set of family data from the Cancer Genetics Network. In summary, we introduce a novel statistical approach to systematically evaluate deleterious DNMs in inherited cancer syndromes. Our approach may serve as a foundation for future studies evaluating how new deleterious mutations can be established in the germline, such as those in TP53.
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Affiliation(s)
- Fan Gao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Department of Statistics, Rice University, Houston, Texas 77005, USA
| | - Xuedong Pan
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Department of Statistics, Texas A&M University, College Station, Texas 77843, USA
| | - Elissa B Dodd-Eaton
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Carlos Vera Recio
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Matthew D Montierth
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jasmina Bojadzieva
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Phuong L Mai
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Kristin Zelley
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Valen E Johnson
- Department of Statistics, Texas A&M University, College Station, Texas 77843, USA
| | - Danielle Braun
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Kim E Nichols
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Judy E Garber
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Louise C Strong
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Wenyi Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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Carbone M, Harbour JW, Brugarolas J, Bononi A, Pagano I, Dey A, Krausz T, Pass HI, Yang H, Gaudino G. Biological Mechanisms and Clinical Significance of BAP1 Mutations in Human Cancer. Cancer Discov 2020; 10:1103-1120. [PMID: 32690542 DOI: 10.1158/2159-8290.cd-19-1220] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/03/2020] [Accepted: 05/07/2020] [Indexed: 11/16/2022]
Abstract
Among more than 200 BAP1-mutant families affected by the "BAP1 cancer syndrome," nearly all individuals inheriting a BAP1 mutant allele developed one or more malignancies during their lifetime, mostly uveal and cutaneous melanoma, mesothelioma, and clear-cell renal cell carcinoma. These cancer types are also those that, when they occur sporadically, are more likely to carry somatic biallelic BAP1 mutations. Mechanistic studies revealed that the tumor suppressor function of BAP1 is linked to its dual activity in the nucleus, where it is implicated in a variety of processes including DNA repair and transcription, and in the cytoplasm, where it regulates cell death and mitochondrial metabolism. BAP1 activity in tumor suppression is cell type- and context-dependent. BAP1 has emerged as a critical tumor suppressor across multiple cancer types, predisposing to tumor development when mutated in the germline as well as somatically. Moreover, BAP1 has emerged as a key regulator of gene-environment interaction.This article is highlighted in the In This Issue feature, p. 1079.
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Affiliation(s)
| | - J William Harbour
- Bascom Palmer Eye Institute, Sylvester Comprehensive Cancer Center, and Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, Florida
| | - James Brugarolas
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Angela Bononi
- University of Hawai'i Cancer Center, Honolulu, Hawai'i
| | - Ian Pagano
- University of Hawai'i Cancer Center, Honolulu, Hawai'i
| | - Anwesha Dey
- Department of Discovery Oncology, Genentech, South San Francisco, California
| | - Thomas Krausz
- Department of Pathology, University of Chicago, Chicago, Illinois
| | - Harvey I Pass
- Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York
| | - Haining Yang
- University of Hawai'i Cancer Center, Honolulu, Hawai'i
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50
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Donovan LN, Kohlmann W, Snow AK, Neklason DW, Schiffman JD, Maese L. Germ Cell Mosaicism: A Rare Cause of Li-Fraumeni Recurrence Among Siblings. JCO Precis Oncol 2020; 4:PO.20.00064. [PMID: 32923893 PMCID: PMC7446446 DOI: 10.1200/po.20.00064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2020] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Wendy Kohlmann
- University of Utah Huntsman Cancer Institute, Salt Lake City, UT
| | - Angela K. Snow
- University of Utah Huntsman Cancer Institute, Salt Lake City, UT
| | - Deborah W. Neklason
- University of Utah Huntsman Cancer Institute, Salt Lake City, UT
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT
| | - Joshua D. Schiffman
- University of Utah Huntsman Cancer Institute, Salt Lake City, UT
- University of Utah Department of Pediatrics, Salt Lake City, UT
| | - Luke Maese
- University of Utah Huntsman Cancer Institute, Salt Lake City, UT
- University of Utah Department of Pediatrics, Salt Lake City, UT
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