bims-lifras Biomed News
on Li-Fraumeni syndrome
Issue of 2020‒07‒12
sixteen papers selected by
Joanna Zawacka-Pankau
University of Warsaw


  1. Mod Pathol. 2020 Jul 07.
    Kuba MG, Lester SC, Bowman T, Stokes SM, Taneja KL, Garber JE, Dillon DA.
      Breast cancer is the most common malignancy in female patients with Li-Fraumeni syndrome (LFS), a rare autosomal dominant hereditary syndrome characterized by germline TP53 mutations. Recent studies have shown that the majority of these tumors are estrogen receptor (ER) positive with frequent HER2 co-expression. However, the morphologic features of these tumors have not been as well studied as other germline-associated breast cancers. We evaluated the pathologic features of 27 invasive and in situ carcinomas from patients with known germline TP53 mutations collected through the Li-Fraumeni Consortium. Overall, 60% of cases were HER2 positive and 44% showed ER co-expression. Most DCIS was high nuclear grade with central necrosis and associated periductal fibrosis and lymphocytic response. Invasive carcinomas were mostly of ductal type (NOS), modified Scarff-Bloom-Richardson (mSBR) high grade, with marked nuclear atypia and high mitotic rate. Prominent tumor infiltrating lymphocytes, syncytial growth pattern, or pushing borders were not seen in these tumors. High p53 IHC expression was seen in tumors from individuals with germline TP53 missense mutations whereas little or no protein expression (<1% nuclear expression, null pattern) was seen in tumors from carriers of non-missense mutations. In this study, we report in detail the morphologic features of invasive and in situ carcinomas in LFS. We found that these tumors share features with cancers harboring somatic TP53 mutations but are distinct from BRCA-associated breast cancers.
    DOI:  https://doi.org/10.1038/s41379-020-0610-4
  2. Best Pract Res Clin Endocrinol Metab. 2020 Jul 03. pii: S1521-690X(20)30075-0. [Epub ahead of print] 101448
    Pinto EM, Zambetti GP, Rodriguez-Galindo C.
      Childhood adrenocortical tumors (ACTs) are rare, representing ∼0.2% of all pediatric malignancies and having an incidence of 0.2-0.3 new cases per million per year in the United States, but incidences are remarkably higher in Southern Brazil. At diagnosis, most children show signs and symptoms of virilization, Cushing syndrome, or both. Less than 10% of patients with ACT exhibit no endocrine syndrome at presentation, although some show abnormal concentrations of adrenal cortex hormones. Pediatric ACT is commonly associated with constitutional genetic and/or epigenetic alterations, represented by germline TP53 mutations or chromosome 11p abnormalities. Complete tumor resection is required to achieve cure. The role of chemotherapy is not established, although definitive responses to several anticancer drugs are documented. For patients undergoing complete tumor resection, favorable prognostic factors include young age, small tumor size, virilization, and adenoma histology. Prospective studies are necessary to further elucidate the pathogenesis of ACT and improve patient outcomes.
    Keywords:  11p15; TP53; adrenal; carcinoma; pediatric
    DOI:  https://doi.org/10.1016/j.beem.2020.101448
  3. Genet Med. 2020 Jul 06.
    Thibodeau ML, O'Neill K, Dixon K, Reisle C, Mungall KL, Krzywinski M, Shen Y, Lim HJ, Cheng D, Tse K, Wong T, Chuah E, Fok A, Sun S, Renouf D, Schaeffer DF, Cremin C, Chia S, Young S, Pandoh P, Pleasance S, Pleasance E, Mungall AJ, Moore R, Yip S, Karsan A, Laskin J, Marra MA, Schrader KA, Jones SJM.
      PURPOSE: Structural variants (SVs) may be an underestimated cause of hereditary cancer syndromes given the current limitations of short-read next-generation sequencing. Here we investigated the utility of long-read sequencing in resolving germline SVs in cancer susceptibility genes detected through short-read genome sequencing.METHODS: Known or suspected deleterious germline SVs were identified using Illumina genome sequencing across a cohort of 669 advanced cancer patients with paired tumor genome and transcriptome sequencing. Candidate SVs were subsequently assessed by Oxford Nanopore long-read sequencing.
    RESULTS: Nanopore sequencing confirmed eight simple pathogenic or likely pathogenic SVs, resolving three additional variants whose impact could not be fully elucidated through short-read sequencing. A recurrent sequencing artifact on chromosome 16p13 and one complex rearrangement on chromosome 5q35 were subsequently classified as likely benign, obviating the need for further clinical assessment. Variant configuration was further resolved in one case with a complex pathogenic rearrangement affecting TSC2.
    CONCLUSION: Our findings demonstrate that long-read sequencing can improve the validation, resolution, and classification of germline SVs. This has important implications for return of results, cascade carrier testing, cancer screening, and prophylactic interventions.
    Keywords:  genome sequencing; hereditary cancer; long-read sequencing; structural variants; variant interpretation
    DOI:  https://doi.org/10.1038/s41436-020-0880-8
  4. Hum Mutat. 2020 Jul 05.
    Canson D, Glubb D, Spurdle AB.
      It is possible to estimate the prior probability of pathogenicity for germline disease gene variants based on bioinformatic prediction of variant effect/s. However, routinely used approaches have likely led to the underestimation and underreporting of variants located outside donor and acceptor splice site motifs that affect mRNA processing. This review presents information about hereditary cancer gene germline variants, outside native splice sites, with experimentally validated splicing effects. We list 95 exonic variants that impact splicing regulatory elements in BRCA1, BRCA2, MLH1, MSH2, MSH6 and PMS2. We utilized a pre-existing large-scale BRCA1 functional dataset to map functional splicing regulatory elements, and assess the relative performance of different tools to predict effects of 283 variants on such elements. We also describe rare examples of intronic variants that impact branchpoint sites and create pseudoexons. We discuss the challenges in predicting variant effect on branchpoint site usage and pseudoexonization, and suggest strategies to improve the bioinformatic prioritization of such variants for experimental validation. Importantly, our review and analysis highlights the value of considering impact of variants outside donor and acceptor motifs on mRNA splicing and disease causation. This article is protected by copyright. All rights reserved.
    Keywords:  ESE; ESS; Splicing regulatory elements; branchpoint; hereditary cancer genes; pseudoexon
    DOI:  https://doi.org/10.1002/humu.24074
  5. Front Oncol. 2020 ;10 983
    Li J, Li Y, Ni H, Yang Z, Chen J, Li Y, Ding S, Jiang X, Wang M, Li L, Lv X, Ruan X, Jiang Q, Lei Z, Cheng Y, Huang J, Deng A.
      Lynch syndrome (LS) is an inherited autosomal dominant disorder caused by germline mutations of mismatch repair (MMR) genes, including MSH2, MSH6, PMS2, and MLH1. This study aimed to analyze the molecular defects and clinical manifestations of an affected family and propose appropriate individual prevention strategies for all mutation carriers. A novel splicing mutation (c.1661+2 T>G) was identified in the MSH2 gene, which was found to co-segregate among affected family members by Whole exome sequencing (WES). RT-PCR analysis confirmed that c.1661+2 T>G could produce 3 transcripts, including 1 normal transcript and 2 aberrant transcripts. The 2 aberrant transcripts resulted in premature termination at the 6th nucleotide codon of MSH2 exon 11, so that the predicted products of the mutant MSH2 mRNAs were truncated proteins of 505 amino acids (with all of exon 10 deleted) and 528 amino acids (with a deletion of 82-nucleotides in exon 10), resulting in the loss of the interaction domain, the ATP domain and post-translationally modified residues. Quantitative RT-PCR (qRT-PCR) analysis showed that MSH2 mRNA levels in all patients were reduced to only 1/4 of the control levels. Our study reveals that a novel splicing mutation (c.1661+2 T>G) in the MSH2 gene causes LS and reaffirms the importance of genetic testing for LS.
    Keywords:  Lynch syndrome; MSH2; aberrant splicing; genetic counseling; hereditary non-polyposis colorectal cancer; microsatellite instability
    DOI:  https://doi.org/10.3389/fonc.2020.00983
  6. Int J Mol Sci. 2020 Jun 30. pii: E4650. [Epub ahead of print]21(13):
    Bozsik A, Pócza T, Papp J, Vaszkó T, Butz H, Patócs A, Oláh E.
      Large genomic rearrangements (LGRs) affecting one or more exons of BRCA1 and BRCA2 constitute a significant part of the mutation spectrum of these genes. Since 2004, the National Institute of Oncology, Hungary, has been involved in screening for LGRs of breast or ovarian cancer families enrolled for genetic testing. LGRs were detected by multiplex ligation probe amplification method, or next-generation sequencing. Where it was possible, transcript-level characterization of LGRs was performed. Phenotype data were collected and analyzed too. Altogether 28 different types of LGRs in 51 probands were detected. Sixteen LGRs were novel. Forty-nine cases were deletions or duplications in BRCA1 and two affected BRCA2. Rearrangements accounted for 10% of the BRCA1 mutations. Three exon copy gains, two complex rearrangements, and 23 exon losses were characterized by exact breakpoint determinations. The inferred mechanisms for LGR formation were mainly end-joining repairs utilizing short direct homologies. Comparing phenotype features of the LGR-carriers to that of the non-LGR BRCA1 mutation carriers, revealed no significant differences. Our study is the largest comprehensive report of LGRs of BRCA1/2 in familial breast and ovarian cancer patients in the Middle and Eastern European region. Our data add novel insights to genetic interpretation associated to the LGRs.
    Keywords:  BRCA1; BRCA2; breakpoint characterization; copy number analysis; deletion; duplication; familial breast cancer; large genomic rearrangement
    DOI:  https://doi.org/10.3390/ijms21134650
  7. Sci Adv. 2020 Jun;6(26): eaba3231
    Pinto EM, Figueiredo BC, Chen W, Galvao HCR, Formiga MN, Fragoso MCBV, Ashton-Prolla P, Ribeiro EMSF, Felix G, Costa TEB, Savage SA, Yeager M, Palmero EI, Volc S, Salvador H, Fuster-Soler JL, Lavarino C, Chantada G, Vaur D, Odone-Filho V, Brugières L, Else T, Stoffel EM, Maxwell KN, Achatz MI, Kowalski L, de Andrade KC, Pappo A, Letouze E, Latronico AC, Mendonca BB, Almeida MQ, Brondani VB, Bittar CM, Soares EWS, Mathias C, Ramos CRN, Machado M, Zhou W, Jones K, Vogt A, Klincha PP, Santiago KM, Komechen H, Paraizo MM, Parise IZS, Hamilton KV, Wang J, Rampersaud E, Clay MR, Murphy AJ, Lalli E, Nichols KE, Ribeiro RC, Rodriguez-Galindo C, Korbonits M, Zhang J, Thomas MG, Connelly JP, Pruett-Miller S, Diekmann Y, Neale G, Wu G, Zambetti GP.
      Cancer risk is highly variable in carriers of the common TP53-R337H founder allele, possibly due to the influence of modifier genes. Whole-genome sequencing identified a variant in the tumor suppressor XAF1 (E134*/Glu134Ter/rs146752602) in a subset of R337H carriers. Haplotype-defining variants were verified in 203 patients with cancer, 582 relatives, and 42,438 newborns. The compound mutant haplotype was enriched in patients with cancer, conferring risk for sarcoma (P = 0.003) and subsequent malignancies (P = 0.006). Functional analyses demonstrated that wild-type XAF1 enhances transactivation of wild-type and hypomorphic TP53 variants, whereas XAF1-E134* is markedly attenuated in this activity. We propose that cosegregation of XAF1-E134* and TP53-R337H mutations leads to a more aggressive cancer phenotype than TP53-R337H alone, with implications for genetic counseling and clinical management of hypomorphic TP53 mutant carriers.
    DOI:  https://doi.org/10.1126/sciadv.aba3231
  8. Front Pharmacol. 2020 ;11 897
    De Mattia E, Roncato R, Palazzari E, Toffoli G, Cecchin E.
      Neoadjuvant chemoradiotherapy (nCRT) followed by radical surgery is the standard of care for patients with Locally Advanced Rectal Cancer (LARC). Current selection for nCRT is based on clinical criteria regardless of any molecular marker. Pharmacogenomics may be a useful strategy to personalize and optimize nCRT in LARC. This review aims to summarize the most recent and relevant findings about the role of germline and somatic pharmacogenomics in the prediction of nCRT outcome in patients with LARC, discussing the state of the art of their application in the clinical practice. A systematic literature search of the PubMed database was completed to identify relevant English-language papers published up to January 2020. The chemotherapeutic backbone of nCRT is represented by fluoropyrimidines, mainly metabolized by DPD (Dihydro-Pyrimidine Dehydrogenase, DPYD). The clinical impact of testing DPYD*2A, DPYD*13, c.2846A > T and c.1236G > A-HapB3 before a fluoropyrimidines administration to increase treatment safety is widely acknowledged. Other relevant target genes are TYMS (Thymidylate Synthase) and MTHFR (Methylene-Tetrahydro-Folate Reductase), whose polymorphisms were mainly studied as potential markers of treatment efficacy in LARC. A pivotal role of a TYMS polymorphism in the gene promoter region (rs34743033) was reported and was pioneeringly used to guide nCRT treatment in a phase II study. The pharmacogenomic analysis of other pathways mostly involved in the cellular response to radiation damage, as the DNA repair and the activation of the inflammatory cascade, provided less consistent results. A high rate of somatic mutation in genes belonging to PI3K (Phosphatidyl-Inositol 3-Kinase) and MAPK (Mitogen-Activated Protein Kinase) pathways, as BRAF (V-raf murine sarcoma viral oncogene homolog B1), KRAS (Kirsten Rat Sarcoma viral oncogene homolog), NRAS (Neuroblastoma RAS viral (v-ras) oncogene homolog), PIK3CA (Phosphatidyl-Inositol-4,5-bisphosphate 3-Kinase, Catalytic Subunit Alpha), as well as TP53 (Tumor Protein 53) was reported in LARC. Their pharmacogenomic role, already defined in colorectal cancer, is under investigation in LARC with promising results concerning specific somatic mutations in KRAS and TP53, as predictors of tumor response and prognosis. The availability of circulating tumor DNA in plasma may also represent an opportunity to monitor somatic mutations in course of therapy.
    Keywords:  germline; mutation; neo-adjuvant chemoradiotherapy; pharmacogenomics; polymorphism; rectal cancer; somatic
    DOI:  https://doi.org/10.3389/fphar.2020.00897
  9. Clin Chem. 2020 Jul 01. 66(7): 886
    Lockwood CM.
      
    Keywords:   BRCA1 ; PARP inhibitor; germline mutation; next-generation sequencing; ovarian cancer; precision medicine
    DOI:  https://doi.org/10.1093/clinchem/hvaa055
  10. Cancer Genet. 2020 Jun 26. pii: S2210-7762(20)30248-9. [Epub ahead of print]245 49-52
    Zhu Z, Wang J, Jiang L, Lin L, Meng P, Zhao J, Cai Q.
      This study recruited a Chinese family with hereditary cancer-predisposing syndrome. To investigate the causative mutations, disease-associated exome sequencing was conducted using peripheral blood of three members with malignant disease. As a result, three variants (PLD2 c. C1951T, RAB3GAP1 c.A701G and POLB c.C1002A) came out to be the potential candidate pathogenic mutations, which were not reported before. Sanger sequencing was used to validate the candidate variant in seven healthy members of this family. The candidate variant POLB c.C1002A was proved to co-segregate with malignant diseases, which was selected through a series of filtering criteria. This study thus identified POLB c.C1002A as a potential causative variant for hereditary cancer-predisposing syndrome.
    Keywords:  Hereditary cancer-predisposing syndrome; Next-generation sequencing; POLB
    DOI:  https://doi.org/10.1016/j.cancergen.2020.06.003
  11. Medicine (Baltimore). 2020 Jul 02. 99(27): e20806
    Zhang Y, Ren M, Hong Y, Zhong Y, Cong X, Chen C, Liu Z, Man Y, Yang L.
      RATIONALE: DICER1 syndrome is an autosomal-dominant tumor predisposition syndrome associated with numerous cancerous and noncancerous conditions. The most common sex cord-stromal tumor associated with DICER1 syndrome is Sertoli-Leydig cell tumor of the ovary (SLCT), which is extremely unusual and accounts for < 0.5% of all ovarian neoplasms. SLCT predominantly affects adolescents and young female adults. To date, there are only a few case reports of ovarian SLCT with underlying germline DICER1 mutations. The diagnosis and treatment of this rare malignancy remains challenging in the clinic mainly due to its rarity and varied presentation.PATIENT CONCERNS: A 21-year-old Chinese girl (proband) was admitted in hospital for experiencing a lower abdominal pain and irregular vaginal bleeding for half a year. She was initially diagnosed with abdominal cavity mass prior to surgical operation. The other 20-year-old patient is the younger sister of the proband, who was diagnosed with ovarian cysts and had irregular menstruation and amenorrhea for 4 months. The elder sister underwent an uncomplicated bilateral ovarian tumor resection. Given a high degree of malignancy, comprehensive staged fertility-preserving surgery, including left adnexectomy, omentectomy, pelvic, and para-aortic lymphadenectomy, was performed. Since the other patient requested to maintain her fertility, tumor resection was only conducted in the right ovary.
    DIAGNOSES: The elder sister was diagnosed as poorly differentiated SLCT accompanied with heterologous stage IC rhabdomyosarcoma (RMS) based on its typical pathology features and molecular characteristics from immunohistochemistry (IHC) staining. The younger sister was diagnosed as poorly differentiated SLCT. Targeted next-generation sequencing (NGS) detected DICER1 mutation in the plasma samples and postoperative tumor tissues of both patients.
    INTERVENTIONS: Both patients underwent surgical tumor resection, followed by combination chemotherapy with bleomycin, etoposide, and cisplatin for 4 cycles.
    OUTCOMES: Patients received the above clinical interventions but eventually died from disease recurrence. The elder sister died from disease relapse after one and a half years postsurgery. The younger sister had a relapse of the disease 1 year later, but she refused the comprehensive staged surgery and died from disease relapse quickly.
    LESSONS: Ovarian SLCT patients with DICER1 mutations and a family history have a high degree of malignancy and are associated with a poor prognosis. With ongoing research efforts on DICER1 mutations, genetic screening and counselling on a regular basis is recommended for predicting potential future cancer risk of individuals with DICER1 syndrome family history.
    DOI:  https://doi.org/10.1097/MD.0000000000020806
  12. Breast Cancer. 2020 Jul 06.
    Tozaki M, Nakamura S.
      Overseas, the importance for breast MRI screening for high-risk groups has been shown. However, the evidence among Japanese population was lacking. Therefore, we collaborated with the "Study on clinical and genetic characterization of hereditary breast and ovarian cancer and improvement in prognosis using genetic information in Japan" group, as part of the Comprehensive Research Project on the Promotion of Cancer Control, Health and Labour Sciences Research, and have been conducting the study entitled, "Study of the usefulness of MRI surveillance of BRCA1/2 mutation carriers" since 2014. In addition, we found that in the Japanese population also, the pathological and imaging characteristics differ between BRCA1 and BRCA2 mutation carriers, like in non-Japanese populations by the several reports. In high-risk females, risk categories such as BRCA1 or BRCA2 mutation carriers are very important. Furthermore, in the future, the optimal surveillance modalities and examination intervals would also vary according to the age, thinness of the breast (constitution), breast density (individual differences on mammography), etc.; this would be "personalized surveillance", and quality-assured MRI examination is of the essence. This review will present clinical trial data of prospective MRI surveillance in Japan, and summarize the current status of breast cancer screening in high-risk Japanese women.
    Keywords:  BRCA; Breast cancer screening; Hereditary breast and ovarian cancer syndrome; Magnetic resonance imaging
    DOI:  https://doi.org/10.1007/s12282-020-01103-1
  13. Breast J. 2020 Jul 06.
    Desai NV, Tung NM.
      Germline BRCA1/2 mutations may be infrequent in unselected breast cancer population but are concentrated in those with triple-negative breast cancer or high-risk family history. Insight into the biology of BRCA mutation is now allowing a targeted therapeutic approach to these carriers with breast cancer. Functional BRCA genes play a critical role in DNA damage repair. Agents such as platinum salts and poly (ADP-ribose) polymerase (PARP) inhibitors exploit this vulnerability of impaired DNA damage repair mechanism in BRCA mutant cancers to leverage therapeutic benefit. Research has demonstrated improved response rates to platinum salts in BRCA-mutated compared with non-BRCA-mutated breast cancer, particularly in the metastatic setting. Additionally, clinical trials of single-agent PARP inhibitors have shown encouraging response rates and progression-free survival in patients with BRCA1/2-mutated breast cancer. In this review, we summarize the medical management of BRCA-associated breast cancer.
    Keywords:  BRCA; DNA damage repair; PARP inhibitors; breast cancer; platinum
    DOI:  https://doi.org/10.1111/tbj.13972
  14. Neurooncol Adv. 2019 May-Dec;1(1):1(1): vdz033
    Guerrini-Rousseau L, Varlet P, Colas C, Andreiuolo F, Bourdeaut F, Dahan K, Devalck C, Faure-Conter C, Genuardi M, Goldberg Y, Kuhlen M, Moalla S, Opocher E, Perez-Alonso V, Sehested A, Slavc I, Unger S, Wimmer K, Grill J, Brugières L.
      Background: Malignant brain tumors (BT) are among the cancers most frequently associated with constitutional mismatch repair deficiency (CMMRD), a rare childhood cancer predisposition syndrome resulting from biallelic germline mutations in mismatch repair genes. This study analyzed data from the European "Care for CMMRD" (C4CMMRD) database to describe their clinical characteristics, treatments, and outcome with the aim of improving its diagnosis/treatment.Methods: Retrospective analysis of data on patients with CMMRD and malignant BT from the C4CMMRD database up to July 2017.
    Results: Among the 87 registered patients, 49 developed 56 malignant BTs: 50 high-grade gliomas (HGG) (with giant multinucleated cells in 16/21 histologically reviewed tumors) and 6 embryonal tumors. The median age at first BT was 9.2 years [1.1-40.6], with nine patients older than 18. Twenty-seven patients developed multiple malignancies (including16 before the BT). Most patients received standard treatment, and eight patients immunotherapy for relapsed HGG. The 3- and 5-year overall survival (OS) rates were 30% (95% CI: 19-45) and 22% (95% CI: 12-37) after the first BT, with worse prognosis for HGG (3-year OS = 20.5%). Six patients were alive (median follow-up 2.5 years) and 43 dead (38 deaths, 88%, were BT-related). Other CMMRD-specific features were café-au-lait macules (40/41), multiple BTs (5/15), developmental brain anomalies (11/15), and consanguinity (20/38 families).
    Conclusions: Several characteristics could help suspecting CMMRD in pediatric malignant BTs: giant cells on histology, previous malignancies, parental consanguinity, café-au-lait macules, multiple BTs, and developmental brain anomalies. The prognosis of CMMRD-associated BT treated with standard therapies is poor requiring new therapeutic up-front approaches.
    Keywords:  MMR biallelic germline mutation; brain tumor; café-au-lait spot; childhood cancer; constitutional mismatch repair deficiency; high-grade glioma; predisposition
    DOI:  https://doi.org/10.1093/noajnl/vdz033