bims-lifras Biomed News
on Li-Fraumeni syndrome
Issue of 2020–05–10
nine papers selected by
Joanna Zawacka-Pankau
  1. Significant Benefits of Osimertinib against Adenosquamous Carcinoma Harboring Germline T790M Mutation.
  2. Germline RBBP8 variants associated with early-onset breast cancer compromise replication fork stability.
  3. Case report: acute abdominal pain in a 37-year-old patient and the consequences for his family.
  4. A novel germline BMPR1A variant (c.72_73delGA) in a Japanese family with hereditary mixed polyposis syndrome.
  5. MLH1 intronic variants mapping to + 5 position of splice donor sites lead to deleterious effects on RNA splicing.
  6. Hereditary Breast and Ovarian Cancer in Families from Southern Italy (Sicily)-Prevalence and Geographic Distribution of Pathogenic Variants in BRCA1/2 Genes.
  7. Optimal age for genetic cancer predisposition testing in hereditary SMARCA4 Ovarian Cancer Families: How young is too young?
  8. Development and validation of next generation sequencing based 35-gene hereditary cancer panel.
  9. Ancestry and frequency of genetic variants in the general population are confounders in the characterization of germline variants linked to cancer.
  1. Oncologist. 2020 May 04.
    Significant Benefits of Osimertinib against Adenosquamous Carcinoma Harboring Germline T790M Mutation.
    Ran Huo, Jinghua Li, Xiaofang Li, Junping Shi, Kunjie Wang, Jin Jiao, Yanhong Shang.
       BACKGROUND: The identification of epidermal growth factor receptor (EGFR) mutations represents a milestone in the treatment of advanced non-small-cell lung cancer (NSCLC). Patients with lung adenosquamous carcinomas (ASCs) rarely present with germline EGFR T790M mutation. The optimal treatment for cancers with germline EGFR T790M mutation (especially ASC) is not clear.
    MATERIALS AND METHODS: Using next-generation sequencing (NGS), we tested 450 cancer-related genes in a 27-year-old patient's lung adenosquamous carcinoma and matched blood samples. Germline mutations in samples from the patient's available relatives were identified by Sanger sequencing.
    RESULTS: We identified germline EGFR T790M mutation in the patient's lung adenosquamous carcinoma. He was treated with osimertinib, and achieved complete response (CR) for more than 30 months, without significant drug-related adverse events. Genetic testing showed that germline EGFR T790M mutation might be a characteristic of inherited lung cancer.
    CONCLUSION: Osimertinib can be a treatment option for patients with lung ASC harboring germline EGFR T790M mutation.
    Keywords:  Adenosquamous carcinoma; Osimertinib; germline EGFR T790M mutation; inherited lung cancer; progression-free survival
    DOI:  https://doi.org/10.1634/theoncologist.2019-0938
  2. J Clin Invest. 2020 May 07. pii: 127521. [Epub ahead of print]
    Germline RBBP8 variants associated with early-onset breast cancer compromise replication fork stability.
    Reihaneh Zarrizi, Martin R Higgs, Karolin Voßgröne, Maria Rossing, Birgitte Bertelsen, Muthiah Bose, Arne N Kousholt, Heike I Rösner, Bent Ejlertsen, Grant S Stewart, Finn Cilius Nielsen, Claus Sørensen.
      Haploinsufficiency of factors governing genome stability underlies hereditary breast and ovarian cancer. Homologous recombination (HR) repair is a major pathway disabled in these cancers. With the aim of identifying new candidate genes, we examined early onset breast cancer patients negative for BRCA1 and BRCA2 pathogenic variants. Here, we focused on CtIP (RBBP8 gene) that mediates HR repair through the end-resection of DNA double-strand breaks (DSB). Notably, the patients exhibited a number of rare germline RBBP8 variants, and functional analysis revealed that these variants did not affect DNA DSB end-resection efficiency. However, expression of a subset of variants led to deleterious nucleolytic degradation of stalled DNA replication forks in a manner similar to cells lacking BRCA1 or BRCA2. In contrast to BRCA1 and BRCA2, CtIP deficiency promoted the helicase-driven destabilization of RAD51 nucleofilaments at damaged DNA replication forks. Taken together, our work identifies CtIP as a critical regulator of DNA replication fork integrity, which when compromised, may predispose to the development of early onset breast cancer.
    Keywords:  Cell Biology; Genetic instability; Genetics
    DOI:  https://doi.org/10.1172/JCI127521
  3. BMC Gastroenterol. 2020 May 03. 20(1): 129
    Case report: acute abdominal pain in a 37-year-old patient and the consequences for his family.
    Elisabeth Niemeyer, Hamid Mofid, Carsten Zornig, Eike-Christian Burandt, Alexander Stein, Andreas Block, Alexander E Volk.
       BACKGROUND: Hereditary diffuse gastric cancer is a rare condition that accounts for approximately 1-3% of all gastric cancer cases. Due to its rapid and invasive growth pattern, it is associated with a very poor prognosis. As a result, comprehensive genetic testing is imperative in patients who meet the current testing criteria in order to identify relatives at risk. This case report illustrates the substantial benefit of genetic testing in the family of a patient diagnosed with hereditary diffuse gastric cancer.
    CASE PRESENTATION: A 37-year-old patient was admitted to the emergency department with acute abdominal pain. Following explorative laparoscopy, locally advanced diffuse gastric cancer was diagnosed. The indication for genetic testing of CDH1 was given due to the patient's young age. A germline mutation in CDH1 was identified in the index patient. As a result, several family members underwent genetic testing. The patient's father, brother and one aunt were identified as carriers of the familial CDH1 mutation and subsequently received gastrectomy. In both the father and the aunt, histology of the surgical specimen revealed a diffuse growing adenocarcinoma after an unremarkable preoperative gastroscopy.
    CONCLUSION: Awareness and recognition of a potential hereditary diffuse gastric cancer can provide a substantial health benefit not only for the patient but especially for affected family members.
    Keywords:  CDH1 germline mutation; Hereditary diffuse gastric cancer; Prophylactic gastrectomy
    DOI:  https://doi.org/10.1186/s12876-020-01283-2
  4. Jpn J Clin Oncol. 2020 May 07. pii: hyaa059. [Epub ahead of print]
    A novel germline BMPR1A variant (c.72_73delGA) in a Japanese family with hereditary mixed polyposis syndrome.
    Yosuke Miyahara, Hideyuki Ishida, Koichi Kawabe, Hiroyuki Eto, Toyotaka Kasai, Tetsuya Ito, Kou Kaneko, Motohiro Arai, Nao Kamae, Shuji Momose, Hidetaka Eguchi, Yasushi Okazaki.
      Hereditary mixed polyposis syndrome (HMPS) is a rare autosomal dominant disorder characterized by a mixture of typical and/or atypical juvenile polyps, adenomas and hyperplastic polyps, resulting in an increased risk of colorectal cancer. In HMPS, four different germline BMPR1A variants from five unrelated families have been reported. This study is the first to report HMPS within a Japanese family. The proband underwent repeated colonoscopic polypectomies over a 5-year period, since the age of 67. Histological examination of these resected polyps revealed adenomas, juvenile-like polyps and hyperplastic changes. Genetic testing was conducted to identify the causative genes for hereditary gastrointestinal cancer syndromes, including BMPR1A. We detected a germline variant, c.72_73delGA, in BMPR1A. The proband's elder brother, younger sister and nephew have also undergone repeated colonoscopic polypectomies at other clinics. His sister and nephew underwent genetic testing, and the same BMPR1A variant was identified.
    Keywords:   BMPR1A ; hereditary mixed polyposis syndrome; juvenile polyposis syndrome
    DOI:  https://doi.org/10.1093/jjco/hyaa059
  5. Fam Cancer. 2020 May 04.
    MLH1 intronic variants mapping to + 5 position of splice donor sites lead to deleterious effects on RNA splicing.
    Tamara Alejandra Piñero, Omar Soukarieh, Marion Rolain, Karin Alvarez, Francisco López-Köstner, Giovana Tardin Torrezan, Dirce Maria Carraro, Ivana Lucia De Oliveira Nascimento, Thaís Ferreira Bomfim, Taísa Manuela Bonfim Machado-Lopes, Juliana Côrtes Freitas, Maria Betânia Toralles, Kiyoko Abe Sandes, Benedito Mauro Rossi, Samuel Aguiar Junior, Joanna Meira, Mev Dominguez-Valentin, Pål Møller, Carlos Alberto Vaccaro, Alexandra Martins, Walter Hernán Pavicic.
      Germline pathogenic variants in the DNA mismatch repair genes (MMR): MLH1, MSH2, MSH6, and PMS2, are causative of Lynch syndrome (LS). However, many of the variants mapping outside the invariant splice site positions (IVS ± 1, IVS ± 2) are classified as variants of unknown significance (VUS). Three such variants (MLH1 c.588+5G>C, c.588+5G>T and c.677+5G>A) were identified in 8 unrelated LS families from Argentina, Brazil and Chile. Herein, we collected clinical information on these families and performed segregation analysis and RNA splicing studies to assess the implication of these VUS in LS etiology. Pedigrees showed a clear pattern of variant co-segregation with colorectal cancer and/or other LS-associated malignancies. Tumors presented deficient expression of MLH1-PMS2 proteins in 7/7 of the LS families, and MSI-high status in 3/3 cases. Moreover, RNA analyses revealed that c.588+5G>C and c.588+5G>T induce skipping of exon 7 whereas c.677+5G>A causes skipping of exon 8. In sum, we report that the combined clinical findings in the families and the molecular studies provided the evidences needed to demonstrate that the three MLH1 variants are causative of LS and to classify c.588+5G>C and c.677+5G>A as class 5 (pathogenic), and c.588+5G>T as class 4 (likely-pathogenic). Our findings underline the importance of performing clinical and family analyses, as well as RNA splicing assays in order to determine the clinical significance of intronic variants, and contribute to the genetic counseling and clinical management of patients and their relatives.
    Keywords:  Lynch syndrome; MLH1; Mismatch repair genes; Splicing assay; Splicing defect; Variants of unknown significance
    DOI:  https://doi.org/10.1007/s10689-020-00182-5
  6. Cancers (Basel). 2020 May 05. pii: E1158. [Epub ahead of print]12(5):
    Hereditary Breast and Ovarian Cancer in Families from Southern Italy (Sicily)-Prevalence and Geographic Distribution of Pathogenic Variants in BRCA1/2 Genes.
    Lorena Incorvaia, Daniele Fanale, Giuseppe Badalamenti, Marco Bono, Valentina Calò, Daniela Cancelliere, Marta Castiglia, Alessia Fiorino, Alessia Pivetti, Nadia Barraco, Sofia Cutaia, Antonio Russo, Viviana Bazan.
      Recent advances in the detection of germline pathogenic variants (PVs) in BRCA1/2 genes have allowed a deeper understanding of the BRCA-related cancer risk. Several studies showed a significant heterogeneity in the prevalence of PVs across different populations. Because little is known about this in the Sicilian population, our study was aimed at investigating the prevalence and geographic distribution of inherited BRCA1/2 PVs in families from this specific geographical area of Southern Italy. We retrospectively collected and analyzed all clinical information of 1346 hereditary breast and/or ovarian cancer patients genetically tested for germline BRCA1/2 PVs at University Hospital Policlinico "P. Giaccone" of Palermo from January 1999 to October 2019. Thirty PVs were more frequently observed in the Sicilian population but only some of these showed a specific territorial prevalence, unlike other Italian and European regions. This difference could be attributed to the genetic heterogeneity of the Sicilian people and its historical background. Therefore hereditary breast and ovarian cancers could be predominantly due to BRCA1/2 PVs different from those usually detected in other geographical areas of Italy and Europe. Our investigation led us to hypothesize that a higher prevalence of some germline BRCA PVs in Sicily could be a population-specific genetic feature of BRCA-positive carriers.
    Keywords:  BRCA1; BRCA2; Sicilian population; breast cancer; founder variants; genetic testing; germline pathogenic variants; hereditary breast and ovarian cancer; ovarian cancer
    DOI:  https://doi.org/10.3390/cancers12051158
  7. Gynecol Oncol Rep. 2020 May;32 100569
    Optimal age for genetic cancer predisposition testing in hereditary SMARCA4 Ovarian Cancer Families: How young is too young?
    Sarah E Podwika, Taylor M Jenkins, Joyti K Khokhar, Sarah H Erickson, Susan C Modesitt.
      Small cell carcinoma of the ovary, hypercalcemic type is a rare, aggressive, and typically fatal ovarian cancer that primarily affects young women less than 40 years of age. It is caused by a pathogenic variant in the SMARCA4 gene, with nearly half of patients found to have germline pathogenic variants and the remainder demonstrating somatic SMARCA4 pathogenic variants. This case report discusses an illustrative case and explores the existing data and potential recommendations to optimize timing of genetic testing in family members, given the presence of a familial germline pathogenic variant.
    Keywords:  Genetic testing; SMARCA4; Small Cell Ovarian Cancer
    DOI:  https://doi.org/10.1016/j.gore.2020.100569
  8. Hered Cancer Clin Pract. 2020 ;18 9
    Development and validation of next generation sequencing based 35-gene hereditary cancer panel.
    Wing Chan, Mianne Lee, Zhen Xuan Yeo, Dingge Ying, Keith A Grimaldi, Craig Pickering, Michael M S Yang, Senthil K Sundaram, Lawrence C H Tzang.
       Background: Understanding the genetic basis of cancer risk is a major international endeavor. The emergence of next-generation sequencing (NGS) in late 2000's has further accelerated the discovery of many cancer susceptibility genes. The use of targeted NGS-based multigene testing panels to provide comprehensive analysis of cancer susceptible genes has proven to be a viable option, with the accurate and robust detection of a wide range of clinically relevant variants in the targeted genes being crucial.
    Methods: We have developed and validated a targeted NGS-based test for hereditary cancer risk assessment using Illumina's NGS platform by analyzing the protein-coding regions of 35 hereditary cancer genes with a bioinformatics pipeline that utilizes standard practices in the field. This 35-gene hereditary cancer panel is designed to identify germline cancer-causing mutations for 8 different cancers: breast, ovarian, prostate, uterine, colorectal, pancreatic, stomach cancers and melanoma. The panel was validated using well-characterized DNA specimens [NIGMS Human Genetic Cell Repository], where DNA had been extracted using blood of individuals whose genetic variants had been previously characterized by the 1000 Genome Project and the Coriell Catalog.
    Results: The 35-gene hereditary cancer panel shows high sensitivity (99.9%) and specificity (100%) across 4820 variants including single nucleotide variants (SNVs) and small insertions and deletions (indel; up to 25 bp). The reproducibility and repeatability are 99.8 and 100%, respectively.
    Conclusions: The use of targeted NGS-based multigene testing panels to provide comprehensive analysis of cancer susceptible genes has been considered a viable option. In the present study, we developed and validated a 35-gene panel for testing 8 common cancers using next-generation sequencing (NGS). The performance of our hereditary cancer panel is assessed across a board range of variants in the 35 genes to support clinical use.
    Keywords:  Analytical validation; Genetic testing; Hereditary cancer; Multigene panel testing; Next generation sequencing
    DOI:  https://doi.org/10.1186/s13053-020-00141-2
  9. BMC Med Genet. 2020 May 06. 21(1): 92
    Ancestry and frequency of genetic variants in the general population are confounders in the characterization of germline variants linked to cancer.
    Anna Bobyn, Mehdi Zarrei, Yuankun Zhu, Mary Hoffman, Darren Brenner, Adam C Resnick, Stephen W Scherer, Marco Gallo.
       BACKGROUND: Pediatric high-grade gliomas (pHGGs) are incurable malignant brain cancers. Clear somatic genetic drivers are difficult to identify in the majority of cases. We hypothesized that this may be due to the existence of germline variants that influence tumor etiology and/or progression and are filtered out using traditional pipelines for somatic mutation calling.
    METHODS: In this study, we analyzed whole-genome sequencing (WGS) datasets of matched germlines and tumor tissues to identify recurrent germline variants in pHGG patients.
    RESULTS: We identified two structural variants that were highly recurrent in a discovery cohort of 8 pHGG patients. One was a ~ 40 kb deletion immediately upstream of the NEGR1 locus and predicted to remove the promoter region of this gene. This copy number variant (CNV) was present in all patients in our discovery cohort (n = 8) and in 86.3% of patients in our validation cohort (n = 73 cases). We also identified a second recurrent deletion 55.7 kb in size affecting the BTNL3 and BTNL8 loci. This BTNL3-8 deletion was observed in 62.5% patients in our discovery cohort, and in 17.8% of the patients in the validation cohort. Our single-cell RNA sequencing (scRNA-seq) data showed that both deletions result in disruption of transcription of the affected genes. However, analysis of genomic information from multiple non-cancer cohorts showed that both the NEGR1 promoter deletion and the BTNL3-8 deletion were CNVs occurring at high frequencies in the general population. Intriguingly, the upstream NEGR1 CNV deletion was homozygous in ~ 40% of individuals in the non-cancer population. This finding was immediately relevant because the affected genes have important physiological functions, and our analyses showed that NEGR1 expression levels have prognostic value for pHGG patient survival. We also found that these deletions occurred at different frequencies among different ethnic groups.
    CONCLUSIONS: Our study highlights the need to integrate cancer genomic analyses and genomic data from large control populations. Failure to do so may lead to spurious association of genes with cancer etiology. Importantly, our results showcase the need for careful evaluation of differences in the frequency of genetic variants among different ethnic groups.
    Keywords:  Germline variants; Pediatric high-grade glioma; Single-cell RNA-seq; Whole-genome sequencing
    DOI:  https://doi.org/10.1186/s12881-020-01033-x
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