bims-lifras Biomed News
on Li-Fraumeni syndrome
Issue of 2022–10–23
fourteen papers selected by
Joanna Zawacka-Pankau, Karolinska Institutet



  1. Cureus. 2022 Sep;14(9): e29240
      Li-Fraumeni syndrome (LFS) is an inherited genetic condition that makes individuals predisposed to specific types of cancer. As a result, cancer risk can be passed down from generation to generation. TP53 is the genetic blueprint for a protein called p53 and most commonly causes this condition by mutations or alterations in that gene. Mutations prevent the gene from functioning properly. LFS is associated with TP53 gene mutations in approximately 70% of families. Most patients with LFS have one normal copy of TP53 and one mutated copy of TP53, usually inherited from a parent with the condition. This is a case report of a 40-year-old female who underwent genetic testing to determine her p53 mutation status. Her mother was diagnosed with breast cancer at a young age, despite the fact that her brothers and sisters' genetic tests came out normal. The genetic testing showed her as a carrier for the TP53 gene mutation. Despite the fact that she had no signs or symptoms of any linked tumors associated with the condition, she was diagnosed with LFS.
    Keywords:  cancer; family medicine; hereditary diseases; internal medicine; le fraumeni syndrome
    DOI:  https://doi.org/10.7759/cureus.29240
  2. Hematol Oncol Clin North Am. 2022 Oct;pii: S0889-8588(22)00076-4. [Epub ahead of print]36(5): 943-960
      Germline genetic variants implicated in increasing lifetime risk of pancreatic cancer (PDAC) have been identified in ∼4% to 10% of cases. Clinical features such as family history have poor sensitivity in identifying carriers of these risk variants. Genetic testing for these germline variants has potential to guide risk assessment and surveillance recommendations in high-risk individuals to promote prevention and early detection measures. Furthermore, identification of novel germline variants can offer important insights into pathogenesis that may inform precision medicine approaches. This article reviews current understanding of germline mutations associated with PDAC risk and implications of genetic testing.
    Keywords:  Genetic testing; Germline mutations; Pancreatic ductal adenocarcinoma
    DOI:  https://doi.org/10.1016/j.hoc.2022.07.008
  3. Fam Cancer. 2022 Oct 20.
      Variants in hereditary cancer risk genes are frequently identified following tumor-based DNA sequencing and represent an opportunity to diagnose hereditary cancer. We implemented an automated hereditary cancer screening program in a large HMO for all patients who underwent tumor-based DNA sequencing to identify patients with hereditary cancer and determine if this approach augmented existing genetic counseling approaches driven by personal/family history criteria. Regular automated searches of a centralized tumor DNA variant database were performed for ATM, BRCA1, BRCA2, MLH1, MSH2, MSH6, PALB2, and/or PMS2 variants, and germline hereditary cancer gene panel testing was offered to patients with tumor variants who had never undergone germline testing. Patients completing germline testing due to their tumor DNA test results were considered part of the tumor DNA safety net. Patients previously completing germline testing via traditional genetic counseling and tumor DNA safety net were compared for demographics, tumor type, presence of germline pathogenic/likely pathogenic (P/LP) variant, and whether NCCN criteria were met for hereditary cancer genetic testing. Germline P/LP variants were common in both groups. Patients who received germline testing through traditional genetic counseling were more likely to have cardinal hereditary tumors than the tumor DNA safety net group. Patients identified with hereditary cancer through traditional genetic counseling were more likely to meet NCCN personal/family history criteria for germline testing than the tumor DNA safety net group (99% versus 34%). A universal tumor DNA safety net screen is an important diagnostic strategy which augments traditional genetic counseling approaches based on personal/family history.
    DOI:  https://doi.org/10.1007/s10689-022-00317-w
  4. J Hepatol. 2022 Oct 12. pii: S0168-8278(22)03137-3. [Epub ahead of print]
       BACKGROUND & AIMS: The heritability and actionability of molecular therapies for biliary tract cancer are uncertain. Although associations between biliary tract cancer and BRCA germline variants have been reported, homologous recombination deficiency has not been investigated in BTCs.
    METHODS: We sequenced germline variants in 27 cancer-predisposing genes in 1,292 biliary tract cancer cases and 37,583 controls without a personal and family history of cancer. We compared pathogenic germline variant frequencies between cases and controls and documented the demographic and clinical characteristics of carrier patients. In addition, whole-genome sequencing of 45 biliary tract cancers was performed to evaluate homologous recombination deficiency status.
    RESULTS: Targeted sequencing identified 5,018 germline variants, which were classified into 317 pathogenic, 3,611 variants of uncertain significance, and 1,090 benign variants. Seventy-one BTC cases (5.5%) had at least one pathogenic variant among 27 cancer-predisposing genes. Pathogenic germline variants enriched in biliary tract cancers were in BRCA1, BRCA2, APC, and MSH6 (P < 0.00185). PALB2 variants were marginally associated with BTC (P = 0.01). APC variants were predominantly found in ampulla of Vater carcinomas. Whole-genome sequencing demonstrated that three biliary tract cancers with pathogenic germline variants in BRCA2 and PALB2 accompanied with loss of heterozygosity displayed HRD. Conversely, pathogenic germline variants without in homologous recombination-related genes showed homologous recombination proficient phenotypes.
    CONCLUSIONS: This study described the heritability and the actionability of homologous recombination deficiency targeted treatments and provides possibilities for expanding therapeutic strategies and screening for BTCs.
    Keywords:  Biliary tract cancer; germline pathogenic variant; hereditary cancer; homologous recombination deficiency
    DOI:  https://doi.org/10.1016/j.jhep.2022.09.025
  5. JCO Precis Oncol. 2022 Oct;6 e2200033
       PURPOSE: In 2020, ASCO recommended that all women with epithelial ovarian cancer have germline testing for BRCA1/2 mutations, and those without a germline pathogenic variant (PV) should have somatic tumor testing to determine eligibility for a poly (ADP-ribose) polymerase inhibitor. Consequently, the majority of patients with ovarian cancer will have both germline testing and somatic testing. An alternate strategy is tumor testing first and then germline testing if there is a PV in the tumor and/or significant family history. The objective was to conduct a cost-effectiveness analysis comparing the two testing strategies.
    METHODS: The Markov model compared the costs (US dollars) and benefits of two testing strategies for newly diagnosed ovarian cancer: (1) ASCO strategy and (2) tumor testing triage for germline testing. Data were applied from SOLO-1, and costs were from wholesale acquisition prices, Medicare, and published sources. Sensitivity analyses accounted for uncertainty around various parameters. Monte Carlo simulation estimated the number tested and identified with germline and somatic BRCA PV for olaparib maintenance treatment annually in the US population.
    RESULTS: The ASCO strategy was more effective but more costly than tumor testing triage in identifying patients for olaparib, with an incremental cost-effectiveness ratio of $281,296 US dollars per progression-free life year gained. Assuming 10,000 eligible patients with ovarian cancer annually, Monte Carlo simulation yielded comparable numbers of patients with BRCA PV in the germline and tumor with the ASCO and tumor testing triage strategies (2,080 v 2,062, respectively), but substantially higher number of patients tested using the ASCO strategy (8,052 v 3,076).
    CONCLUSION: The ASCO strategy may identify more BRCA PVs but is not cost-effective. Tumor testing in epithelial ovarian cancer as triage for germline testing is the favored strategy in this health care system.
    DOI:  https://doi.org/10.1200/PO.22.00033
  6. Front Genet. 2022 ;13 1012025
      Pathogenic and likely pathogenic (P/LP) germline variants in the tumor suppressor gene CDH1 (E-cadherin) result in increased lifetime risk of diffuse-type gastric cancer and lobular breast cancer. CDH1 variants are also associated with hereditary cleft lip and palate (CLP), the mechanism of which is not well understood. We sought to determine the prevalence of CLP in families who carry P/LP CDH1 variants. Patients with P/LP CDH1 variants who were enrolled in a prospective clinical trial were reviewed (NCT03030404). The cohort included 299 individuals from 153 families that had 80 unique P/LP variants in CDH1. The rate of CLP was 19% (29/153) in families reporting CLP in at least one family member, and 2.7% (8/299) among individuals with confirmed germline CDH1 P/LP variants. There were 22 unique variants in CDH1 among the 29 families that reported CLP, or a CLP rate of 27.5% per variant (22/80). 10 of the variants were not previously reported to be associated with CLP. We observed that 24% (7/29) of CLP-associated gene variants involved large-scale (≥1 exon) deletions. Among families with CLP, 69% (20/29) had a member diagnosed with gastric cancer, and 79% (23/29) had a member with breast cancer, which were similar to rates observed in non-CLP families (p >0.3 for both). Our analysis suggests that the prevalence of CLP in families with germline CDH1 P/LP variants was high in this large cohort, and there was no genotype-phenotype pattern. Genetic testing for CDH1 variants should be considered in families with CLP and history of either diffuse-type gastric or lobular breast cancer.
    Keywords:  CDH1; E-cadherin; cleft lip; cleft lip/palate; cleft palate; hereditary diffuse gastric cancer syndrome
    DOI:  https://doi.org/10.3389/fgene.2022.1012025
  7. Leukemia. 2022 Oct 20.
      Broader genetic screening has led to the growing recognition of the role of germline variants associated with adult bone marrow failure (BMF) and myeloid neoplasia (MN) not exclusively in children and young adults. In this study, we applied a germline variant panel to 3008 adult BMF and MN cases to assess the importance of germline genetics and its impact on disease phenotype and prognosis. In our cohort, up to 9.7% of BMF and 5.3% of MN cases carried germline variants. Our cohort also included heterozygous carriers of recessive traits, suggesting they contribute to the risk of BMF and MN. By gene category, variants of Fanconi anemia gene family represented the highest-frequency category for both BMF and MN cases, found in 4.9% and 1.7% cases, respectively. In addition, about 1.4% of BMF and 0.19% of MN cases harbored multiple germline variants affecting often functionally related genes as compound heterozygous. The burden of germline variants in BMF and MN was clearly associated with acquisition of monosomy 7. While BMF cases carrying germline variants showed similar overall survival as compared to the wild-type (WT) cases, MN cases with germline variants experienced a significantly shorter overall survival as compared to WT cases.
    DOI:  https://doi.org/10.1038/s41375-022-01729-4
  8. Curr Oncol Rep. 2022 Oct 18.
       PURPOSE OF REVIEW: In this article, we discuss recent advances in germline genetic testing for patients with breast cancer and highlight current limitations and impacts on clinical care. We also provide an update on the therapeutic implications of having a germline mutation, including targeted systemic therapy options for treating early and metastatic breast cancer.
    RECENT FINDINGS: Approximately 5 to 10% of women diagnosed with breast cancer have a pathogenic variant in a hereditary cancer susceptibility gene, which has significant implications for managing these patients. Previously, testing was done mainly to inform screening and risk-reduction treatment; however, more recently, germline genetic results have significant systemic therapy implications that can meaningfully improve outcomes in breast cancer patients, especially with oral poly-ADP-ribose polymerase (PARP) inhibitors. These systemic therapy advances implore a shift in paradigm for whom to test moving forward and how to modify the existing testing models to meet the increasing demand for germline testing, which is expected to grow exponentially.
    Keywords:  BRCA1; BRCA2; Breast cancer; Germline genetic testing; Olaparib; PARP inhibitors; Systemic therapy; Targeted therapies
    DOI:  https://doi.org/10.1007/s11912-022-01340-x
  9. JNCI Cancer Spectr. 2022 Oct 21. pii: pkac074. [Epub ahead of print]
       BACKGROUND: Few studies have evaluated the relationship between CDKN2A germline pathogenic variants (GPV), transcript (p16, p14ARF) alteration, and cancer risk.
    METHODS: Standardized incidence ratios (SIRs) comparing cancer risk to the general population were calculated for 385 CDKN2A GPV carriers from two large cohorts (259 United States and 126 Swedish individuals) using Poisson regression; statistical significance was defined as P<.002 (Bonferroni correction). Cumulative incidence is reported for melanoma and non-melanoma cancer.
    RESULTS: Incidence was significantly increased for melanoma (SIR = 159.8, 95% confidence interval [CI] = 132.1 to 193.2), pancreatic cancer (SIR = 24.1, 95% CI = 14.7 to 39.4), head and neck squamous cell carcinoma (HNSCC; SIR = 16.2, 95% CI = 9.5 to 27.6), and lung cancer (SIR = 5.6, 95% CI = 3.4 to 9.1) in GPV carriers. Similar associations were observed with p16 alteration. Combined p16 and p14ARF alteration was associated with increased incidence of esophageal cancer (SIR = 16.7, 95% CI = 5.7 to 48.9) and malignant peripheral nerve sheath tumor (SIR = 113.0, 95% CI = 16.4 to 780.9), although cancer events were limited (n < 5 for each malignancy). Cumulative incidence at age 70 for melanoma and non-melanoma cancer was 68.3% (95% CI = 68.0 to 68.6) and 35.2% (95% CI = 34.9 to 35.6), respectively. 89% of smoking-related cancers (lung, HNSCC, pancreatic, esophageal) occurred in ever smokers.
    CONCLUSION: These findings highlight the impact of p16 and p14ARF alteration on cancer risk. Smoking was an important risk factor for smoking-related cancers in our study.
    DOI:  https://doi.org/10.1093/jncics/pkac074
  10. Gastroenterology. 2022 Oct 12. pii: S0016-5085(22)01169-6. [Epub ahead of print]
      
    DOI:  https://doi.org/10.1053/j.gastro.2022.09.045
  11. Gastrointest Endosc. 2022 Oct 17. pii: S0016-5107(22)02079-X. [Epub ahead of print]
       BACKGROUND AND AIMS: The true rate of gastric cancer (GC) in Juvenile Polyposis Syndrome (JPS) is unknown due to its rarity and ascertainment bias in published literature. To better assess this, we conducted a systematic review and meta-analysis.
    METHODS: Medline, Embase and Scopus databases were searched for keywords 'Juvenile polyposis syndrome, juvenile polyps, stomach cancer, gastric cancer, SMAD4, BMPR1A, hamartomatous polyposis syndrome, hamartomas and hereditary cancers' for studies reporting upper GI manifestations in JPS. The primary outcome was the reported occurrence of GC in JPS. Secondarily, we compared GC occurrence based on presence or absence of pathogenic germline variants (PGVs) and in untested patients.
    RESULTS: Eleven studies including 637 patients were included. The pooled occurrence of GC was 3.5% (95%CI:1.8, 5.2; I2:12.3%) at a median age of 42.5 (range: 15-57.6) years. The pooled occurrence of GC in patients with SMAD4 PGV was 10.1% (95%CI:3.2%, 16.8%, I2:54.7%). GC was only reported in only one BMPR1A PGV carrier, and was not reported in patients without an identifiable PGV.In patients with prior germline testing, the risk of GC was higher in SMAD4 PGV carriers (Odds Ratio:11.6, 95% CI:4.6, 29.4, I2=18.3%) compared to patients without SMAD4 PGV.In JPS patients with unknown status of germline testing, pooled occurrence of GC was 7.5% (95%CI: 0, 15.5%). There was an overall moderate risk of bias in the studies.
    CONCLUSION: GC is highest in SMAD4-associated JPS and was not reported in patients without identifiable PGVs. The value of GC surveillance in BMPR1A PGV carriers and JPS patients without an identifiable PGV is questionable. Germline testing should be performed in all JPS patients to inform GC risk discussion and utility of surveillance.
    Keywords:  BMPR1A; Juvenile polyposis syndrome; SMAD4; gastric cancer; gastric polyposis; hamartomatous polyps; hereditary cancers
    DOI:  https://doi.org/10.1016/j.gie.2022.10.026
  12. J Med Genet. 2022 Oct 21. pii: jmedgenet-2022-108684. [Epub ahead of print]
       BACKGROUND: Patients with serrated polyposis syndrome (SPS) have multiple and/or large serrated colonic polyps and higher risk for colorectal cancer. SPS inherited genetic basis is mostly unknown. We aimed to identify new germline predisposition factors for SPS by functionally evaluating a candidate gene and replicating it in additional SPS cohorts.
    METHODS: After a previous whole-exome sequencing in 39 SPS patients from 16 families (discovery cohort), we sequenced specific genes in an independent validation cohort of 211 unrelated SPS cases. Additional external replication was also available in 297 SPS cases. The WNK2 gene was disrupted in HT-29 cells by gene editing, and WNK2 variants were transfected using a lentiviral delivery system. Cells were analysed by immunoblots, real-time PCR and functional assays monitoring the mitogen-activated protein kinase (MAPK) pathway, cell cycle progression, survival and adhesion.
    RESULTS: We identified 2 rare germline variants in the WNK2 gene in the discovery cohort, 3 additional variants in the validation cohort and 10 other variants in the external cohorts. Variants c.2105C>T (p.Pro702Leu), c.4820C>T (p.Ala1607Val) and c.6157G>A (p.Val2053Ile) were functionally characterised, displaying higher levels of phospho-PAK1/2, phospho-ERK1/2, CCND1, clonogenic capacity and MMP2.
    CONCLUSION: After whole-exome sequencing in SPS cases with familial aggregation and replication of results in additional cohorts, we identified rare germline variants in the WNK2 gene. Functional studies suggested germline WNK2 variants affect protein function in the context of the MAPK pathway, a molecular hallmark in this disease.
    Keywords:  Digestive System Disease; Gastroenterology; Gene Editing; Genetic Predisposition to Disease; Loss of Function Mutation
    DOI:  https://doi.org/10.1136/jmg-2022-108684
  13. J Med Genet. 2022 Oct 21. pii: jmedgenet-2022-108467. [Epub ahead of print]
      APC germline pathogenic variants result in predisposition to familial adenomatous polyposis and extraintestinal tumours such as desmoid fibromatosis, medulloblastomas and thyroid cancers. They have also been recently involved in ovarian microcystic stromal tumours. APC inactivation has been described at the tumour level in epithelial ovarian cancers (EOCs). Here, we report the identification of APC germline pathogenic variants in two patients diagnosed with premenopausal EOC in early 30s, with no other pathogenic variant detected in the known ovarian cancer predisposing genes. Subsequent tumour analysis showed neither a second hit of APC inactivation nor β-catenin activation. Both tumours did not have a homologous recombination (HR) deficiency, pointing towards the implication of other genes than those involved in HR. APC may contribute to the carcinogenesis of EOC in a multifactorial context. Further studies are required to clarify the role of APC in predisposition to EOC.
    Keywords:  Genetics
    DOI:  https://doi.org/10.1136/jmg-2022-108467
  14. Hematol Oncol Clin North Am. 2022 Oct;pii: S0889-8588(22)00062-4. [Epub ahead of print]36(5): 929-942
      Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease with high mortality, largely due to late stage at diagnosis. Approximately 10% to 15% are hereditary, and detection of early stage PDAC or precursor lesions through pancreatic surveillance programs may improve outcomes. Current surveillance is annual, typically with endoscopic ultrasound and/or magnetic resonance imaging.
    Keywords:  Cancer screening; Consensus guidelines; Familial pancreatic cancer; High-risk; Pancreatic ductal adenocarcinoma; Pancreatic surveillance
    DOI:  https://doi.org/10.1016/j.hoc.2022.06.004