bims-lifras 2020-11-15 papers

bims-lifras

Biomed News

on Li-Fraumeni syndrome

Issue of 2020–11–15
eleven papers selected by
Joanna Zawacka-Pankau, University of Warsaw

Three Primary Tumors Including EGFR-mutated Non-Small Cell Lung Cancer as First Presentation in Patient With Li-Fraumeni Syndrome.
Hereditary Leiomyomatosis and Renal Cell Cancer Syndrome in Spain: Clinical and Genetic Characterization.
FANCA, TP53, and del(5q)/RPS14 alterations in a patient with T-cell non-Hodgkin lymphoma and concomitant Fanconi anemia and Li-Fraumeni syndrome.
Characteristics of adrenocortical carcinoma associated with Lynch Syndrome.
Gynecological Cancers Caused by Deficient Mismatch Repair and Microsatellite Instability.
Age at diagnosis of cancer in 185delAG BRCA1 mutation carriers of diverse ethnicities: tentative evidence for modifier factors.
Gastric Cancer in BRCA1 Germline Mutation Carriers: Results of Endoscopic Screening and Molecular Analysis of Tumor Tissues.
Clinical, Genetic, and Prognostic Features of Adrenocortical Tumors in Children: A 10-Year Single-Center Experience.
Novel DNMT3A Germline Variant in a Patient with Multiple Paragangliomas and Papillary Thyroid Carcinoma.
Nearly Half of TP53 Germline Variants Predicted To Be Pathogenic in Patients With Osteosarcoma Are De Novo: A Report From the Children's Oncology Group.
The p.Ser64Leu and p,Pro104Leu missense variants of PALB2 identified in familial pancreatic cancer patients compromise the DNA damage response.

Clin Lung Cancer. 2020 Sep 18. pii: S1525-7304(20)30267-9. [Epub ahead of print]

Three Primary Tumors Including EGFR-mutated Non-Small Cell Lung Cancer as First Presentation in Patient With Li-Fraumeni Syndrome.

Arjan Gower, Jong Kim, Kellie Spector, Daniella Menashe, Eric Vail, Ronald Natale.



Keywords:  EGFR; Li-Fraumeni syndrome; NSCLC; Osimertinib; TP53 R337H

DOI:  https://doi.org/10.1016/j.cllc.2020.09.006
Cancers (Basel). 2020 Nov 05. pii: E3277. [Epub ahead of print]12(11):

Hereditary Leiomyomatosis and Renal Cell Cancer Syndrome in Spain: Clinical and Genetic Characterization.

A Beatriz Sánchez-Heras, Adela Castillejo, Juan D García-Díaz, Mercedes Robledo, Alexandre Teulé, Rosario Sánchez, Ángel Zúñiga, Enrique Lastra, Mercedes Durán, Gemma Llort, Carmen Yagüe, Teresa Ramon Y Cajal, Consol López San Martin, Adrià López-Fernández, Judith Balmaña, Luis Robles, José M Mesa-Latorre, Isabel Chirivella, María Fonfria, Raquel Perea Ibañez, M Isabel Castillejo, Inés Escandell, Luis Gomez, Pere Berbel, Jose Luis Soto.

  Hereditary leiomyomatosis and renal cell cancer syndrome (HLRCC) is a very rare hereditary disorder characterized by cutaneous leiomyomas (CLMs), uterine leiomyomas (ULMs), renal cysts (RCys) and renal cell cancers (RCCs). We aimed to describe the genetics, clinical features and potential genotype-phenotype associations in the largest cohort of fumarate hydratase enzyme mutation carriers known from Spain using a multicentre, retrospective study of individuals with a genetic or clinical diagnosis of HLRCC. We collected clinical information from medical records, analysed genetic variants and looked for genotype-phenotype associations. Analyses were performed using R 3.6.0. software. We included 197 individuals: 74 index cases and 123 relatives. CLMs were diagnosed in 65% of patients, ULMs in 90% of women, RCys in 37% and RCC in 10.9%. Twenty-seven different pathogenic variants were detected, 12 (44%) of them not reported previously. Patients with missense pathogenic variants showed higher frequencies of CLMs, ULMs and RCys, than those with loss-of-function variants (p = 0.0380, p = 0.0015 and p = 0.024, respectively). This is the first report of patients with HLRCC from Spain. The frequency of RCCs was lower than those reported in the previously published series. Individuals with missense pathogenic variants had higher frequencies of CLMs, ULMs and RCys.

Keywords:  FH gene; hereditary leiomyomatosis; leiomyomas; missense pathogenic variants, renal cell cancer

DOI:  https://doi.org/10.3390/cancers12113277
Cancer Genet. 2020 Oct 31. pii: S2210-7762(20)30278-7. [Epub ahead of print]

FANCA, TP53, and del(5q)/RPS14 alterations in a patient with T-cell non-Hodgkin lymphoma and concomitant Fanconi anemia and Li-Fraumeni syndrome.

Edoardo Errichiello, Tommaso Mina, Patrizia Morbini, Marco Zecca, Orsetta Zuffardi.

  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.

Keywords:  FANCA; Fanconi anemia (FA); Li-Fraumeni syndrome (LFS); T-cell non-Hodgkin lymphoma (NHL); TP53

DOI:  https://doi.org/10.1016/j.cancergen.2020.10.003
J Clin Endocrinol Metab. 2020 Nov 13. pii: dgaa833. [Epub ahead of print]

Characteristics of adrenocortical carcinoma associated with Lynch Syndrome.

Marta Domènech, Elia Grau, Ares Solanes, Angel Izquierdo, Jesús Del Valle, Cristina Carrato, Marta Pineda, Nuria Dueñas, Magda Pujol, Conxi Lázaro, Gabriel Capellà, Joan Brunet, Matilde Navarro.

   CONTEXT: Lynch syndrome (LS) is the most common inherited colorectal and endometrial cancer syndrome, caused by germline mutations in DNA mismatch repair (MMR) genes. It is also characterized by an increased risk of other tumours with lower prevalence, such as adrenal cortical carcinoma (ACC), an endocrine tumour with an incidence of < two cases/million individuals/year. Most ACC developed during childhood are associated with hereditary syndromes. In adults this association is not as well established as in children. Previous studies showed a 3.2% prevalence of LS among patients with ACC.
EVIDENCE ADQUISITION: The objective of this study is to determine the prevalence of ACC in a Spanish LS cohort and their molecular and histological characteristics. This retrospective study includes 634 patients from 220 LS families registered between 1999 and 2018.
EVIDENCE SYNTHESIS: During the follow-up three patients were diagnosed with ACC (0.47%), all were carriers of a MSH2 germline mutation. The three ACC patients presented loss of expression of MSH2 and MSH6 proteins. One tumour analysis showed loss of heterozygosity of the MSH2 wildtype allele. Our findings support previous data which considered ACC as a LS spectrum tumour.
CONCLUSION: MMR protein immunohistochemistry screening could be an efficient strategy to detect LS in patients with ACC.

Keywords:  Lynch syndrome; adrenocortical carcinoma; molecular characteristics

DOI:  https://doi.org/10.1210/clinem/dgaa833
Cancers (Basel). 2020 Nov 10. pii: E3319. [Epub ahead of print]12(11):

Gynecological Cancers Caused by Deficient Mismatch Repair and Microsatellite Instability.

Madhura Deshpande, Phillip A Romanski, Zev Rosenwaks, Jeannine Gerhardt.

  Mutations in mismatch repair genes leading to mismatch repair (MMR) deficiency (dMMR) and microsatellite instability (MSI) have been implicated in multiple types of gynecologic malignancies. Endometrial carcinoma represents the largest group, with approximately 30% of these cancers caused by dMMR/MSI. Thus, testing for dMMR is now routine for endometrial cancer. Somatic mutations leading to dMMR account for approximately 90% of these cancers. However, in 5-10% of cases, MMR protein deficiency is due to a germline mutation in the mismatch repair genes MLH1, MSH2, MSH6, PMS2, or EPCAM. These germline mutations, known as Lynch syndrome, are associated with an increased risk of both endometrial and ovarian cancer, in addition to colorectal, gastric, urinary tract, and brain malignancies. So far, gynecological cancers with dMMR/MSI are not well characterized and markers for detection of MSI in gynecological cancers are not well defined. In addition, currently advanced endometrial cancers have a poor prognosis and are treated without regard to MSI status. Elucidation of the mechanism causing dMMR/MSI gynecological cancers would aid in diagnosis and therapeutic intervention. Recently, a new immunotherapy was approved for the treatment of solid tumors with MSI that have recurred or progressed after failing traditional treatment strategies. In this review, we summarize the MMR defects and MSI observed in gynecological cancers, their prognostic value, and advances in therapeutic strategies to treat these cancers.

Keywords:  deficient mismatch repair; gynecological cancers; microsatellite instability

DOI:  https://doi.org/10.3390/cancers12113319
Fam Cancer. 2020 Nov 09.

Age at diagnosis of cancer in 185delAG BRCA1 mutation carriers of diverse ethnicities: tentative evidence for modifier factors.

Yael Laitman, Rachel Michaelson-Cohen, Rakefet Chen-Shtoyerman, Yael Goldberg, Orit Reish, Rinat Bernstein-Molho, Ephrat Levy-Lahad, Noa Ephrat Ben Baruch, Inbal Kedar, D Gareth Evans, Sara Haim, Shani Paluch-Shimon, Eitan Friedman.

  Germline pathogenic sequence variants (PSVs) in BRCA1 substantially increase risk for developing breast (BC) and ovarian cancer (OvC). Yet, incomplete penetrance suggests that modifier factors affect phenotypic expression of mutant BRCA1 alleles. Analysis of identical BRCA1 PSV carriers of diverse ethnicities may provide further evidence for modifier factors. Female carriers of the 185delAG BRCA1 PSV identified through high-risk clinics in Israel, and Manchester England from 1998-2018 were eligible. Data were retrieved from patients records and confirmed (in Israel) by cross referencing with the Israeli National Cancer Registry. Overall, 2503 female carriers were included: 1715 (71.4%) Ashkenazi Jews (AJ), 201 (8.3%) Iraqi Jews and 383 (15.9%) of mixed ethnicity. In 102 (4.2%) cases ethnicity could not be ascertained. Of Israeli AJ carriers 649 (37.8%), 256 (14.9%) and 62 (3.6%) were diagnosed with BC, OvC or both cancers, respectively. For the Iraqi Jews these frequencies were 76 (37.8%), 43 (21.4%), and 8 (3.98%), respectively. Age at diagnosis of BC in AJ and Iraqi Jews was 46.7 ± 12.3 years and 52.8 ± 12.2 years, respectively (p = 0.001). For OvC age at diagnosis for AJ was 53.5 ± 10.7 years and for Iraqi Jews 50.1 ± 8.8 years (p = 0.0027). No differences in these parameters were noted between English Jews (n = 110) and non-Jews (n = 32). Age at diagnosis of BC and OvC differs between AJ and Iraqi Jews who carry an identical BRCA1 PSV. This finding supports the existence of modifier factors that may be ethnic specific.

Keywords:  Age at cancer diagnosis; BRCA1 germline pathogenic sequence variants; Incomplete penetrance; Modifier factors

DOI:  https://doi.org/10.1007/s10689-020-00216-y
Pathobiology. 2020 Nov 06. 1-8

Gastric Cancer in BRCA1 Germline Mutation Carriers: Results of Endoscopic Screening and Molecular Analysis of Tumor Tissues.

Albina A Avanesyan, Anna P Sokolenko, Alexandr O Ivantsov, Maxim A Kleshchev, Mikhail A Maydin, Ilya V Bizin, Grigory A Raskin, Ksenia V Shelekhova, Tatiana V Gorodnova, Alexandr A Bessonov, Elena I Anisimova, Olga A Volynshchikova, Alexandr A Romanko, Valeria I Ni, Robert V Broyde, Oleg B Tkachenko, Aldon J Whitehead, Alexandr M Scherbakov, Evgeny N Imyanitov.

   INTRODUCTION: There is some evidence suggesting a link between BRCA1/2 germline mutations and increased risk of gastric cancer.
METHODS: Endoscopic screening for stomach malignancies was performed in 120 BRCA1 mutation carriers in order to evaluate the probability of detecting the tumor disease.
RESULTS: No instances of gastric cancer were revealed at the first visit. The analysis of atrophic changes performed by OLGA (Operative Link for Gastritis Assessment) criteria revealed that OLGA stages I-IV alterations were observed in 26 of 41 (63%) subjects aged >50 years as compared to 29 of 79 (37%) in younger subjects (p = 0.007, χ2 test). One BRCA1 mutation carrier developed gastric cancer 4 years after the first visit for endoscopic examination. We performed next-generation sequencing analysis for this tumor and additional 4 archival gastric cancers obtained from BRCA1/2 mutation carriers. Somatic loss of the remaining BRCA1/2 allele was observed in 3 out of 5 tumors analyzed; all of these carcinomas, but none of the malignancies with the retained BRCA1/2 copy, showed chromosomal instability.
CONCLUSION: Taken together, these data justify further studies on the relationships between the BRCA1/2 and gastric cancer.

Keywords:  Atrophic gastritis; Endoscopy; Gastric cancer; Mutation; Screening

DOI:  https://doi.org/10.1159/000511323
Front Oncol. 2020 ;10 554388

Clinical, Genetic, and Prognostic Features of Adrenocortical Tumors in Children: A 10-Year Single-Center Experience.

Evelina Miele, Angela Di Giannatale, Alessandro Crocoli, Raffaele Cozza, Annalisa Serra, Aurora Castellano, Antonella Cacchione, Maria Giuseppina Cefalo, Rita Alaggio, Maria Debora De Pasquale.

  Background and Aims: Pediatric adrenocortical tumors (ACTs) are very rare endocrine neoplasms in childhood. In this study, we performed a retrospective analysis of children with ACT treated at our institution by examining clinical and genetic disease features, treatment strategies, and outcomes. Methods: We retrospectively analyzed a cohort of 13 children treated at the Bambino Gesù Children's Hospital from November 2010 to March 2020. Results: The median age at diagnosis was 17 months (range = 0-82 months). The female: male ratio was 3.3/1. Mixed symptomatology (>1 hormone abnormality) was the most common presentation (46.1%). In three cases, the tumor was detected during prenatal or perinatal echographic screening. All patients presented with localized disease at diagnosis and underwent total adrenalectomy. Six patients were identified as having malignancies according to the Wieneke scoring system, five benign, and two undetermined. Seven patients underwent mitotane adjuvant therapy for 12 months. There was metastatic disease in three patients, with no correlation with age or Wieneke score. The most common sites of metastases were the liver and lungs. Metastatic patients were treated with surgery (n = 2), mitotane (n = 1), chemotherapy (n = 2) associated with anti-EGFR (n = 1), or immunotherapy with anti-PD1 (pembrolizumab) (n = 1); two patients achieved complete disease remission. Overall 2- and 5-year survival rates were 100%, with a median follow-up of 5 years (range = 2-9.5 years). Two- and 5-year disease free survival was 76.9 and 84.6%, respectively (95% confidence interval = -66.78-114.76 months). All patients are alive, 12 without disease, and one with stable disease. Genetic analyses showed TP53 germline mutations in six of eight patients analyzed (five inherited, one de novo). One patient had Beckwith-Wiedemann syndrome, with mosaic paternal uniparental disomy of chromosome 11, in both neoplastic and healthy adrenal tissue. Conclusion: We report the cases of 13 patients treated for ACT, including 12 aged <4 years at diagnosis, with a relative short time from symptoms onset. Our cohort experienced an excellent prognosis. TP53 mutation was found in 75% of tested patients (6/8) confirming the need to perform genetic tests and familial counseling in this disease.

Keywords:  Beckwith–Wiedeman syndrome; Li-Fraumeni Syndrome; adrenocortical tumors; children; immunotherapy; mitotane; prognosis; targeted therapies

DOI:  https://doi.org/10.3389/fonc.2020.554388
Cancers (Basel). 2020 Nov 09. pii: E3304. [Epub ahead of print]12(11):

Novel DNMT3A Germline Variant in a Patient with Multiple Paragangliomas and Papillary Thyroid Carcinoma.

Sara Mellid, Javier Coloma, Bruna Calsina, María Monteagudo, Juan M Roldán-Romero, María Santos, Luis J Leandro-García, Javier Lanillos, Ángel M Martínez-Montes, Cristina Rodríguez-Antona, Cristina Montero-Conde, Joaquín Martínez-López, Rosa Ayala, Xavier Matias-Guiu, Mercedes Robledo, Alberto Cascón.

  Over the past few years, next generation technologies have been applied to unravel the genetics of rare inherited diseases, facilitating the discovery of new susceptibility genes. We recently found germline DNMT3A gain-of-function variants in two patients with head and neck paragangliomas causing a characteristic hypermethylated DNA profile. Here, whole-exome sequencing identifies a novel germline DNMT3A variant (p.Gly332Arg) in a patient with bilateral carotid paragangliomas, papillary thyroid carcinoma and idiopathic intellectual disability. The variant, located in the Pro-Trp-Trp-Pro (PWWP) domain of the protein involved in chromatin targeting, affects a residue mutated in papillary thyroid tumors and located between the two residues found mutated in microcephalic dwarfism patients. Structural modelling of the variant in the DNMT3A PWWP domain predicts that the interaction with H3K36me3 will be altered. An increased methylation of DNMT3A target genes, compatible with a gain-of-function effect of the alteration, was observed in saliva DNA from the proband and in one independent acute myeloid leukemia sample carrying the same p.Gly332Arg variant. Although further studies are needed to support a causal role of DNMT3A variants in paraganglioma, the description of a new DNMT3A alteration in a patient with multiple clinical features suggests a heterogeneous phenotypic spectrum related to DNMT3A germline variants.

Keywords:  DNMT3A; germline variant; papillary thyroid carcinoma; paraganglioma

DOI:  https://doi.org/10.3390/cancers12113304
JCO Precis Oncol. 2020 ;pii: PO.20.00087. [Epub ahead of print]4

Nearly Half of TP53 Germline Variants Predicted To Be Pathogenic in Patients With Osteosarcoma Are De Novo: A Report From the Children's Oncology Group.

Brandon J Diessner, Nathan Pankratz, Anthony J Hooten, Lisa Mirabello, Aaron L Sarver, Lauren J Mills, David Malkin, Ava C Kelley, Logan G Spector.

PURPOSE: To ascertain the prevalence of recurrent de novo variants among 240 pediatric patients with osteosarcoma (OS; age < 20 years) unselected for family history of cancer.
METHODS: The identification of de novo variants was implemented in 2 phases. In the first, we identified genes with a rare (minor allele frequency < 0.01) de novo variant in > 1 of the 95 case-parent trios examined by whole-exome sequencing (WES) who passed quality control measures. In phase 2, 145 additional patients with OS were evaluated by targeted sequencing to identify rare de novo variants in genes nominated from phase 1. Recurrent rare variants identified from phase 1 and 2 were verified as either de novo or inherited by Sanger sequencing of affected patients and their parents. Categorical and continuous data were analyzed using Fisher exact test and t tests, respectively.
RESULTS: Among 95 case-parent trios who underwent WES, we observed 61 de novo variants in 60 genes among 47 patients, with TP53 identified as the only gene with a pathogenic or likely pathogenic (P/LP) de novo variant in more than one case-parent trio. Among all 240 patients with OS, 13 (5.4%) harbored a P/LP TP53 germline variant, of which 6 (46.2%) were confirmed to be de novo.
CONCLUSION: Apart from TP53, we did not observe any other recurrent de novo P/LP variants in the case-parent trios, suggesting that new mutations in other genes are not a frequent cause of pediatric OS. That nearly half of P/LP TP53 variants in our sample were de novo suggests universal screening for germline TP53 P/LP variants among pediatric patients with OS should be considered.

DOI: https://doi.org/10.1200/PO.20.00087
Hum Mutat. 2020 Nov 10.

The p.Ser64Leu and p,Pro104Leu missense variants of PALB2 identified in familial pancreatic cancer patients compromise the DNA damage response.

Yue Zhang, Jung-Young Park, Fan Zhang, Sara H Olson, Irene Orlow, Yirong Li, Robert C Kurtz, Marc Ladanyi, Jie Chen, Amanda E Toland, Liying Zhang, Paul R Andreassen.

  PALB2 has been identified as a breast and pancreatic cancer susceptibility gene. Utilizing a targeted sequencing approach, we discovered two novel germline missense PALB2 variants c.191C>T and c.311C>T, encoding p.Ser64Leu and p.Pro104Leu, respectively, in individuals in a pancreatic cancer registry. No missense PALB2 variants from familial pancreatic cancer patients, and few PALB2 variants overall, have been functionally characterized. Given the known role of PALB2, we tested the impact of p.Ser64Leu and p.Pro104Leu variants on DNA damage responses. Neither p.Ser64Leu nor p.Pro104Leu had clear effects on interactions with BRCA1 and KEAP1, which are mediated by adjacent motifs in PALB2. However, both variants are associated with defective recruitment of PALB2, and the RAD51 recombinase downstream, to DNA damage foci. Further, p.Ser64Leu and p.Pro104Leu both largely compromise DNA double-strand break-initiated homologous recombination, and confer increased cellular sensitivity to ionizing radiation (IR) and the poly (ADP-ribose) polymerase (PARP) inhibitor Olaparib. Taken together, our results represent the first demonstration of functionally deleterious PALB2 missense variants associated with familial pancreatic cancer and of deleterious variants in the N-terminus outside of the coiled-coil domain. Further, our results suggest the possibility of personalized treatments, using IR or PARP inhibitor, of pancreatic and other cancers that carry a deleterious PALB2 variant. This article is protected by copyright. All rights reserved.

Keywords:  Functional studies; Homologous recombination; Missense variants; PALB2; Pancreatic cancer; Variant of uncertain significance

DOI:  https://doi.org/10.1002/humu.24133