Germline Mutations In Genes Research Articles

Prevalence of Pathogenic Germline Mutations in Solid Tumor Predisposition Genes Detected By Tumor-Normal Whole Exome Sequencing Analysis Among Adults with Hematologic Malignancies

Background Approximately 7-10% of cancer patients have pathogenic germline variants (PGVs) in cancer predisposition genes. However, most studies to date have focused on PGVs in patients with solid tumors. Less is known about the prevalence of PGVs in patients with hematologic malignancies (HM). We investigated the prevalence of PGVs in 72 cancer predisposition genes in a cohort of HM cases from our tumor-normal whole exome sequencing (TN-WES) database. Methods We identified 363 unique HM patients with TN-WES performed at our lab (Sema4, Branford, CT) since 2020. Our analysis pipeline calls germline pathogenic/likely pathogenic variants (PGVs) in 72 cancer-predisposing genes (PGV-72) from normal tissue, predominantly buccal samples. These are reported clinically as secondary findings, with the patient's consent. Results The cohort (N=363) was comprised predominantly of patients with lymphoid malignancies (N=299, 82.4%), most commonly myeloma (N=222) and CLL/SLL (N=27). The most common myeloid malignancy was myelodysplastic syndrome (N=25). Of 363 unique HM patients with TN-WES, 33 (9.1%) were found to have PGVs in one of the PGV-72 genes. There was no significant difference between those with lymphoid and myeloid malignancies (8.0% vs. 14.1%, Fisher's exact p=0.15). Among patients with germline findings (N=33), the median age was 67 years (range 23-84). The most commonly mutated genes were APC (N=7), CHEK2 (N=7), MUTYH (N=6), and LZTR1 (N=4). LZTR1 and ATM PGVs were more common in patients with myeloid versus lymphoid malignancies (LZTR1: 4.7% vs 0.3%, p=0.02; ATM: 3.1% vs. 0%, p=0.03). Several founder mutations were identified: all APC variants were p.I1307K; four CHEK2 variants were p.T367Mfs*15 (c.100delC); five MUTYH variants were p.G396D. Two patients had more than one PGV: one patient with myeloma (APC p.I1307K and CHEK2 p.S428F) and one patient with CLL/SLL (CHEK2 p.T367Mfs*15 and HOXB13 p.G84E). One patient with myeloma had a BRCA2 p.S1982Rfs*22 germline variant. All PGVs were heterozygous, and none were associated with a somatic second hit. Conclusions The prevalence of PGVs in 72 cancer predisposition genes was approximately 9% in a set of patients with HM undergoing TN-WES. Most PGVs identified were associated with moderately increased risk for solid tumors. Many of the PGVs identified were founder mutations in APC, CHEK2, and MUTYH, likely reflecting the racial/ethnic composition of our cohort. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Characterizing Immunodeficiency in Patients with Telomere Biology Disorders

Telomere biology disorders (TBD) are caused by germline mutations in telomere related genes that lead to excessive telomere shortening. Affected genes include TERT and TERC, which encode two components of the telomerase complex. TBDs are multisystem disorders that present with a constellation of findings including bone marrow failure and lung and/or liver disease. Immunodeficiency has been described but is not well characterized in a large cohort of TBD patients. In the present study, we report the clinical incidence and severity of infections, as well as laboratory evidence of immunodeficiency in 83 patients with TBD. The electronic medical record was queried for the clinical history of patients with TBD who were evaluated at the National Institutes of Health Clinical Center from 2002 to present. Laboratory data included immunoglobulins (IgG, IgA, IgM) and peripheral blood lymphocyte subsets (CD4, CD19). Fifteen patients did not have immunoglobulin levels and 29 patients did not have lymphocyte subsets available. A significant infection history was defined as occurrence of infections that were opportunistic, recurrent, and/or required hospitalization. Recurrent infections were defined as two or more severe infections in one year, three or more respiratory infections (e.g. sinusitis, otitis, bronchitis) in one year, or the need for antibiotics for two months per year. Diminished immune function was defined by CD4 T cell counts: patients with CD4 < 200 cells x 106/L were classified as immunodeficient, and CD4 >200 cells x 106/L but < 500 cells x 106/L as immune impaired. Reference ranges for female and male patients were used to determine whether levels are below or within normal limits. Development of lung and/or liver fibrosis were also assessed. Chi-square tests were used to test the association between the two categorical variables. Kaplan-Meier curves and log rank tests were used to estimate overall survival (OS) and test the differences of survival time distributions among infection groups and immune status groups. Patient characteristics are in Table 1. TERT and TERC were the most commonly mutated genes, and others included DKC1, PARN, TINF2, CTC1, RTEL1, and NAF1. Of 49 patients with laboratory data available, the majority (65%) had depressed CD4 counts with 11 immunodeficient patients, 21 immune impaired patients, and 17 patients with normal counts. Median age was similar in the 3 groups. Three (27%) immunodeficient patients and 2 (10%) immune impaired patients had an opportunistic infection. Two (18%) immunodeficient patients and 6 (29%) immune impaired patients reported recurrent infections. Nine (43%) immune impaired patients required hospitalization from infection. No patients with normal CD4 count had opportunistic or recurrent infections, but 4 had required hospitalization for infection. Lower CD4 count was associated with having a significant infection history, and specifically recurrent infections, and being hospitalized for infection (p=0.0417, p=0.0471, p=0.0154 respectively). We observed varied associations between other clinical factors and immune dysfunction or infection. Low levels of CD19 B cells were observed in 14 patients, and associated with development of recurrent infections (P = 0.0003) but not opportunistic or infections requiring hospitalization. Two patients had deficient IgG and IgA levels while 8 had deficient IgM. However, immunoglobulins were not associated with any significant infection history. All immunodeficient and immune impaired patients had concurrent bone marrow failure. Lung fibrosis was recorded in 6 (54%) immunodeficient and 6 (27%) immune impaired patients, and liver fibrosis in 4 (36%) immunodeficient and 4 (19%) immune impaired patients. Of 11 patients with both lung and liver fibrosis, 4 (36%) were immunodeficient, 2 (18%) were immune impaired, and 5 (45%) did not have CD4 counts available. There was no association between gene mutation and development of low CD4 count or clinically significant infections. OS was lower in TBD patients with clinically significant infections (p=0.00011) or low CD4 counts (p=0.016) (Figure 1). Immune dysfunction is common in TBD and patients are at increased risk of clinically significant infections. Low CD4 counts are associated with worse OS. TBD patients should be routinely screened for immunodeficiency to allow appropriate clinical monitoring, antimicrobial prophylaxis, and education. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

CTIM-02. TIP: PHASE I/II STUDY OF STEREOTACTIC RADIOSURGERY WITH CONCURRENT OLAPARIB FOLLOWED BY ADJUVANT DURVALUMAB AND PHYSICIAN’S CHOICE SYSTEMIC THERAPY IN SUBJECTS WITH BREAST CANCER BRAIN METASTASES

Abstract BACKGROUND Despite progress in the treatment of brain metastasis (BrM) for HER2+ breast cancer (BC), outcomes for patients with HER2-negative BC BrM remain poor. Current standard of care consists of local therapies, including surgery and radiotherapy, followed by systemic therapy. Preclinical studies show inhibitors of poly(ADP-ribose) polymerase (PARP) are effective with radiation therapy as a DNA damage response inhibitor. Triple negative BC (TNBC) has higher rates of homologous recombination deficiency compared to other BC subtypes, and together with HER2-negative, BRCA-mutated BC would be particularly sensitive to PARP inhibition. PARP inhibition also shows promising efficacy combined with immunotherapy in patients with germline BRCA-mutant and metastatic TNBC in clinical trials (MEDIOLA, TOPACIO). In addition, immunotherapy with stereotactic radiosurgery (SRS) is associated with favorable intracranial control and survival in patients with BrM. We hypothesize that this biologically-rational combination will enhance local control of SRS-treated BrM through synergy with PARP inhibition, while controlling micrometastatic disease in the brain and extracranial sites via potentiation of the immune response. METHOD We are conducting a multi-institution, Phase I/II trial of SRS plus olaparib, followed by durvalumab (with physician’s choice systemic therapy), for patients with TNBC (any BRCA status) or HER2-negative with BRCA-mutated (germline or somatic) BC BrM [NCT04711824]. The primary objectives are to evaluate safety and tolerability (Phase I) and determine intracranial disease control at 6 months (Phase II) of this treatment combination. Secondary objectives include determining clinical activity via intracranial and global progression-free survival, overall survival, and intracranial and extracranial response rate. Exploratory objectives will assess potential biomarkers of treatment response, including changes in circulating tumor cells and DNA in blood and cerebrospinal fluid, germline and tumor mutations in DNA repair pathway genes, and PD-L1 expression, as well as quality of life and patient-reported outcomes. A surgical sub-study will evaluate olaparib concentration/distribution in resected BrM.

Checking for CHEK2 Hereditary Mutations in Ukrainian Women: Lack of CHECK2 Variants Contribution to Breast Cancer Susceptibility

Abstract Introduction/Objective Although the role of homologous recombination repair (HRR) machinery in breast cancer susceptibility has been clearly established, the range and frequency of HRR gene mutations vary profoundly in different populations. Previously high incidence of CHEK2 (Checkpoint kinase 2) mutations was shown in Eastern Europe, however, there is still limited data on the rate of CHEK2 gene mutations and their clinical implications in the Ukrainian population. The aim of this study was to assess the frequency of CHEK2 mutations and investigate whether CHEK2 variants confer susceptibility to breast cancer in Ukrainian women. Methods/Case Report This was a retrospective case-control study performed on 320 female breast cancer patients and 146 unaffected women (control), aged 42,3±0,51 and 40,3±0,84 respectively, who underwent NGS-testing for germline mutations in multiple genes including CHEK2. Only pathogenic (PV) and likely pathogenic (LPV) variants were considered for further analysis. Results (if a Case Study enter NA) The frequency of CHEK2 mutations did not differ significantly between the observed groups: there were 27 (8,4%) carriers among female breast cancer patients and 15 (10,27%) carriers in unaffected women. To note, the breast cancer patients demonstrated a high rate of CHEK2 co-mutations with BRCA1 (PV, n=3) and BRCA2 (n=2, PV). Within the range of CHEK2 genetic alterations, we reported variant c.470T&amp;gt;C (p.Ile157Thr) found in 22 carriers (52,4%) and deletions of exons 9-10 detected in 7 women (16,7%) as most prevalent in Ukrainian population. The rates of CHEK2 c.470T&amp;gt;C (p.Ile157Thr) variant were comparable among the unaffected women (n=5; 3,4%) and breast cancer group (n=17; 5,3%); exon 9-10 deletions were found in 2 (1,36%) and 5 (1,56%) cases respectively. Less frequent CHEK2 mutations were detected in ≤3 cases per group. In this study we report no contribution of CHEK2 genetic alterations to breast cancer susceptibility (OR=1,24; 95%CI 0,64-2,41; p=0,521) in Ukrainian women. Conclusion The frequency of CHEK2 mutation in Ukrainian women is relatively high as compared to available data on other populations. However, we did not find any contribution of CHEK2 pathogenic/likely pathogenic variants to breast cancer susceptibility.

RF21 | PSUN07 Germline Genetic Testing in a Cohort of Adults with Adrenocortical Carcinoma : Insights From a Clinical Care Setting

Abstract Context About 5-10% of adrenocortical cancer (ACC) arise in patients with genetic predisposition syndromes, including Li-Fraumeni, Lynch, MEN1, or Familial Adenomatous Polyposis (APC). Recent European (2018) and American guidelines (2020) recommend that all adults with ACC should be offered clinical genetic counseling. There is a paucity of data regarding systematic germline testing in adults with ACC and the extent of the genetic evaluation is unclear. Objective To describe the germline genetic characteristics in a cohort of adult patients with ACC evaluated in a tertiary clinical care center. Methods Data including demographics, personal and family history of neoplasia, pathology reports, clinical features and genetic testing were retrospectively collected from charts of patients treated at Centre hospitalier de l'Université de Montréal (CHUM). After genetic counseling, genetic testing was proposed to patients with a pathologic diagnosis of ACC. From 2005 to 2015, TP53 gene analysis was performed using direct sequencing and MLPA. Since 2016, multigene testing was performed for a progressively increasing number of oncogenic genes using a custom next-generation panel for germline leucocyte DNA including at least the TP53, MSH2, MSH6, MLH1,PMS2, EPCAM, MEN1, BRCA1 and BRCA2 genes (Invitae, CA). An extended panel, based on past medical and familial history, was performed at the discretion of the geneticist. Patient data was retrospectively investigated. Results We analyzed data from 44 patients with available germline genetic results. Median age of the patients was 46 years (ranging from 22 to 79 years), including 11 males (25.0%) and 33 females (75.0%). Ten patients (22.7%) underwent only TP53 gene analysis and 32 patients (72.7%) were studied using the larger oncogenic genetic panel. Germline pathogenic or likely pathogenic variants were identified in 5 of the 44 patients (11.4%) while genetic variants of unknown significance (VUS) were found in 7 of the 44 patients (15.9%). Among patients with pathogenic variants, one had a family history and known germline mutation in the BRCA2 gene (8765delAG, p.Glu2846GlyfsX23). One patient had a personal and familial medical history suggesting a MEN1 syndrome that was confirmed with the finding of a germline MEN1 mutation (c.1556delC, p.Pro519Leu fs40). Unsuspected germline pathogenic variants were found in three patients: 1) TP53 (c.425delC, p.Pro142fs), 2) MUTYH (c.536A&amp;gt;G, p.Tyr179Cys) and 3) MSH6 (c.3649-3655, p.Arg1217Leu fs9) genes. Variants of unknown significance (VUS) were found in the following genes: POT1, MSH3, PALB2, RAD51d, APC, ATM and BRCA2. Conclusions Germline pathogenic variants were found in 11.4% of our cohort of patients with ACC. VUS were found in 15.9% of patients but their significance remains to be determined. Genetic counseling and germline genetic testing should be offered to all patients with ACC; however the optimal use and extent of oncogenic gene panels need to be better defined. Presentation: Sunday, June 12, 2022 12:30 p.m. - 2:30 p.m., Sunday, June 12, 2022 12:48 p.m. - 12:53 p.m.

P015 - A dedicated screening for early detection of Prostate cancer (Pca) in men with germline mutations in DNA-Repair Genes (DRG)

P015 - A dedicated screening for early detection of Prostate cancer (Pca) in men with germline mutations in DNA-Repair Genes (DRG)

43. Association between Clonal Hematopoiesis and Inherited Cancer Susceptibility Genes

<h3>Background</h3> Understanding how germline mutations affect Clonal Hematopoiesis (CH) will provide insights into germline predisposition to MN. <h3>Methods</h3> We leveraged blood whole-exome sequencing data from 200,643 individuals in the UK Biobank (UKBB). The association between CH and germline mutations in 211 cancer susceptibility genes were tested among participants without hematologic malignancies at baseline using logistic regression adjusted for known confounders. Genes suggestive of association with CH were validated in 17,037 solid tumor patients with blood sequenced using Memorial Sloan Kettering (MSK) IMPACT panel. <h3>Results</h3> Germline pathogenic/likely pathogenic mutations were detected in 8,967 UKBB participants (4.5%). Germline mutations in TP53, ATR, ATM, and MPL were associated with increased risk of CH with odds ratios (ORs) and confidence intervals (CIs) of 4.33(1.31-14.32), 2.53(1.11-5.76), 2.21(1.23-3.97) and 1.44(1.00-2.08), correspondingly. Among 37 subjects with Li Fraumeni in the MSK-IMPACT cohort, TP53 was also associated with CH (OR: 3.75, 95% CI: 1.40-8.94) and this association was independent of cancer therapy (ORuntreated: 13.52, 95% CI: 2.94-57.48). The significant positive associations between germline TP53 mutations and CH were driven by somatic mutations in TP53 (OR:18.5, 95% CI: 2.8-72.8) and DNMT3A (OR: 5.1, 95% CI: 1.8-12.4). The rate of MN in TP53 mutation carriers was significantly increased (incidence rate ratio: 23.3; 95% CI: 6.0-65.4). The transition to MN was demarcated by a second TP53 loss of function mutation or deletion and by complex karyotype. <h3>Conclusions</h3> Germline mutations in cancer susceptibility genes, particularly those in the DNA damage response pathway are independent risk factors for CH and MN development.

Bladder paraganglioma, gastrointestinal stromal tumor, and SDHB germline mutation in a patient with Carney-Stratakis syndrome: A case report and literature review.

Carney-Stratakis syndrome (CSS) is a rare dyad of paraganglioma (PGL)/pheochromocytoma (PHEO) and gastrointestinal stromal tumor (GIST). PGLs are neuroendocrine tumors of neural crest origin which are mostly found in the head, neck, and retroperitoneal space. GISTs are the most common mesenchymal tumors of the digestive tract, usually caused by KIT/PDGFRA mutations. Here, we reported a case of CSS with unusual bladder PGL and succinate dehydrogenase (SDH) deficient GIST due to a germline mutation in SDH-subunit B (SDHB) gene. A 39-year-old female patient initially diagnosed with gastric GIST and isolated pelvic metastasis was eventually found to be CSS with bladder PGL and SDH-deficient GIST after surgery. This patient underwent resection of gastric and bladder tumors, and postoperative pathology confirmed the diagnosis of CSS. According to the next-generation sequencing (NGS), the patient carried a germline mutation in the SDHB gene, which was the cause of the disorder. The patient had no tumor recurrence with regular follow-up in 10 months. CSS is an autosomal genetic disorder with no gender difference in incidence, and PGLs are more frequent than GISTs. SDH germline mutation is the molecular biological mechanism of CSS while the most common type is SDHB mutation. The unique mechanism of tumorigenesis including hypoxia and hypermethylation caused by SDH deficiency renders target therapy with tyrosine kinase inhibitors ineffective, therefore complete surgical resection is the optimal treatment in the absence of tumor metastases.

Deficient mismatch repair is detected in large-to-giant congenital melanocytic naevi: providing new insight into aetiology and diagnosis.

The aetiologies of large-to-giant congenital melanocytic naevi (LGCMN) remain ambiguous. A previous study discovered signatures associated with deficient mismatch repair (dMMR) in patients with LGCMN. However, a screening diagnostic immunohistochemistry (IHC) panel of dMMR in patients with LGCMN has not been performed to date. To identify the MMR status and aetiologies of LGCMN. A total of 110 patients with CMN, including 30 giant CMN, 30 large CMN, 30 medium CMN and 20 small CMN, underwent diagnostic IHC (for MSH6, MSH2, PMS2 and MLH1) screening of dMMR. The control group comprised normal skin samples from 20 healthy people. MMR proteins with little effect (MSH3 and PMS1) on the MMR system were stained in all samples. The surgical procedures conducted on each patient were noted because they might alter the behaviour of CMN and confound the results. Binary logistic regression analyses were performed between the phenotypic data and MMR status to identify associations. Whole-exome sequencing was performed on the main naevi, satellite naevi and normal skin tissues of four patients to detect variants. Mutational signature analyses were conducted to explore the aetiologies of LGCMN. dMMR was detected in 37% (11 of 30) of giant, 23% (7 of 30) of large and 7% (2 of 30) of medium CMNs, but were not identified in small CMNs or normal skin tissues. Moreover, multiple LGCMNs had a much higher dMMR rate than did single LGCMNs. The regression analyses showed that MMR status was significantly associated with CMN size and the presence of satellites, but was not correlated with age, sex, location, satellite diversity or tissue expansion. Notably, the pattern of protein loss in LGCMN mainly consisted of PMS2 loss. Mutational signature analyses detected dMMR-related signatures in patients with LGCMN. Additionally, rare deleterious germline mutations in DNA repair genes were detected in LGCMN, mainly in MSH6, ATM, RAD50, BRCA1 and ERCC8. These germline mutations were single-patient variants with unknown significance. dMMR is one of the aetiologies underlying LGCMN, particularly in patients with giant main lesions and multiple satellite lesions. Further studies are necessary to investigate the role of the DNA repair system, particularly MMR, in LGCMN.

Prospects for the use of statins in the treatment of neurofibromatosis type 1

Neurofibromatosis type 1 is caused by a germline mutation in the NF1 gene encoding the tumor suppressor neurofibromin. Deficiency of this protein causes hyperactivation of Ras proto-oncogenes. This leads to the development of tumors. Ras proteins undergo prenylation, which is inhibited by inhibitors of 3-hydroxy-3-methylglutaryl-coenzyme-A reductase. Therefore, statins can be proposed as anticancer drugs in the complex treatment of neurofibromatosis type 1. Clinical studies have proven the effectiveness of statins in the treatment of sporadic malignant neoplasms, in the pathogenesis of which mutations in the NF1 gene play an important role. Various pathways of the influence of these drugs on the development of tumors are described, including the activation of autophagy, ferroptosis, suppression of proliferation, stimulation of antitumor immunity, and effects on the microenvironment of neoplasms. Data on the effect of statins on the development and progression of neurofibromas in patients with neurofibromatosis type 1 are not presented in the scientific literature. However, it was found that statins enhance the effect of anticancer drugs, the use of which in monotherapy against malignant neoplasms associated with neurofibromatosis is ineffective. In this regard, despite the inefficiency of statins in cognitive disorders in patients with neurofibromatosis type 1, the introduction of these drugs into clinical practice in combination with other drugs could provide a pleiotropic effect, affect various links in the pathogenesis of the disease.

SC142 - A dedicated screening for early detection of prostate cancer in men with germline mutations in DNA-repair genes

SC142 - A dedicated screening for early detection of prostate cancer in men with germline mutations in DNA-repair genes

S2334 Incidentally Diagnosed Triple Cancers Within 2 Years: A Novel Case of Rare Metachronous Cancers, Renal Cell Carcinoma, Cholangiocarcinoma, and Squamous Cell Carcinoma of the Gastroesophageal Junction

Introduction: The gastrointestinal (GI) tract is involved in many familial cancer syndromes usually involving the colon or stomach. We present a patient with 3 rare cancers that were detected within a span of 2 years in a single individual: clear cell renal cell carcinoma (ccRCC), cholangiocarcinoma (CCA), and esophageal squamous cell carcinoma (SCC); a combination not previously described in the literature Case Description/Methods: A 50-year-old male with a history of ccRCC, GERD, and CCA was admitted for evaluation of chronic abdominal pain during chemotherapy for CCA. Regarding his cancer history, ccRCC was incidentally diagnosed 18 months prior on a CT scan for diverticulitis. He underwent a left partial nephrectomy. Surveillance CT imaging 6 months after surgery revealed new incidental liver lesions. Biopsies confirmed metastatic CCA and he started chemotherapy. He noted a 15-year history of episodic abdominal pain and vomiting with no dysphagia or weight loss. Upper endoscopy 16 months prior was normal. He was a former smoker, drank alcohol a few times per month, used marijuana daily, and used cocaine rarely. His family history was significant for multiple cancers at a young age on his maternal side of unknown type. Physical exam showed diffuse abdominal tenderness, worse in the epigastrium without guarding. Labs showed mild anemia, normal BMP/LFTs, and negative H. pylori stool antigen. Upper endoscopy found nodularity adjacent to the esophagogastric junction (EGJ) with abnormal pit pattern under narrow band imaging (Figure). Biopsies confirmed invasive SCC. Staging endoscopic ultrasound showed T3N3 EGJ SCC. He was referred to oncology to discuss treatment options. Genetic testing was positive for BAP1 tumor predisposition syndrome (BAP1-TPDS) Discussion: A review of published literature did not yield a previous description of this combination of cancers in a single individual. BAP1-TPDS is an uncommon autosomal dominant syndrome caused by germline mutation in a tumor suppressor gene. Patients typically present with melanocytic tumors or malignant mesotheliomas but are at risk for RCC, hepatocellular carcinoma, meningioma and CCA. Literature has not revealed esophageal SCC to be associated. In addition to the incidental nature and timing of diagnosis of all 3 of these cancers within a short period of 2 years, the EGJ involvement is unusual. This case suggests atypical EGJ-SCC may be considered as part of the BAP1-TPDS tumor spectrum and warrant additional screening for at-risk individuals.Figure 1.: Left panel showing abnormal nodular mucosa adjacent to the gastro-esophageal junction under high-definition white light imaging. Right panel showing the same area under narrow band imaging.

SC99 - Male awareness of prostate cancer risk remains poor in families with germline mutations in dna-repair genes

SC99 - Male awareness of prostate cancer risk remains poor in families with germline mutations in dna-repair genes

Genomic profiling for clinical decision making in myeloid neoplasms and acute leukemia

AbstractMyeloid neoplasms and acute leukemias derive from the clonal expansion of hematopoietic cells driven by somatic gene mutations. Although assessment of morphology plays a crucial role in the diagnostic evaluation of patients with these malignancies, genomic characterization has become increasingly important for accurate diagnosis, risk assessment, and therapeutic decision making. Conventional cytogenetics, a comprehensive and unbiased method for assessing chromosomal abnormalities, has been the mainstay of genomic testing over the past several decades and remains relevant today. However, more recent advances in sequencing technology have increased our ability to detect somatic mutations through the use of targeted gene panels, whole-exome sequencing, whole-genome sequencing, and whole-transcriptome sequencing or RNA sequencing. In patients with myeloid neoplasms, whole-genome sequencing represents a potential replacement for both conventional cytogenetic and sequencing approaches, providing rapid and accurate comprehensive genomic profiling. DNA sequencing methods are used not only for detecting somatically acquired gene mutations but also for identifying germline gene mutations associated with inherited predisposition to hematologic neoplasms. The 2022 International Consensus Classification of myeloid neoplasms and acute leukemias makes extensive use of genomic data. The aim of this report is to help physicians and laboratorians implement genomic testing for diagnosis, risk stratification, and clinical decision making and illustrates the potential of genomic profiling for enabling personalized medicine in patients with hematologic neoplasms.

A novel germline HAVCR2 (TIM-3) compound heterozygous mutation is related to hemophagocytic lymphohistiocytic syndrome in EBV-positive peripheral T-cell lymphoma (NOS) with down-regulated TIM-3 signaling.

Recently, it have been reported that Hepatitis A Virus-Cellular Receptor 2(HAVCR2,encoding T-cell immunoglobulin and Mucin-Containing Protein 3[TIM3]) mutations are associated with severe hemophagocytic syndrome(HLH) in subcutaneous panniculitis-like T-cell lymphoma(SPTCL),and there are also frequent mutations in sporadic SPTCL, suggesting the individuals harboring HAVCR2(TIM-3) germline mutations are highly susceptible to familial or sporadic SPTCL. Here, we identify a novel germline compound heterozygous mutation of TIM-3 gene,c.245A>G (p.Tyr82Cys) and c.265C>T(p.Arg89Cys) variations in a single familial case with EBV-positive peripheral T-cell lymphoma(NOS),accompanied HLH;we also detected Tyr82Cys germline mutation in TIM-3 gene in one sporadic patient with cutaneous T cell lymphoma. We screened the distributive frequencies for TIM-3 mutations in healthy controls(n=87), B-(n=79) or T-cell lymphoma(n=25) not SPTCL, and the results showed that the mutation was found in two out of 25 patients with T-cell lymphoma but was not detected in 79 patients with B-cell lymphoma nor in a group of 87 controls. The mRNA expression of TIM-3 on primary cells and transfected HEK293 cells reduced significantly, indicating Tyr82Cys and Arg89Cys mutations is a loss-of function mutations on TIM-3,resulting in a weakened TIM-3 signaling. Our results suggest Tyr82Cys TIM-3 germline mutations are not only limited in SPTCL, and also occurred in other types of T-cell lymphoma, especially complicated HLH. TIM-3 mutations may be an predisposing factor for T-cell lymphoma and molecular marker for auxiliary diagnosis in T cell lymphoma,especially complicated with HLH.

Increased Risk of Hereditary Prostate Cancer in Italian Families with Hereditary Breast and Ovarian Cancer Syndrome Harboring Mutations in BRCA and in Other Susceptibility Genes.

Hereditary prostate cancer (HPCa) has the highest heritability of any cancer in men. Interestingly, it occurs in several hereditary syndromes, including breast and ovarian cancer (HBOC) and Lynch syndrome (LS). Several gene mutations related to these syndromes have been identified as biomarkers in HPCa. The goal of this study was to screen for germline mutations in susceptibility genes by using a multigene panel, and to subsequently correlate the results with clinical and laboratory parameters. This was undertaken in 180 HBOC families, which included 217 males with prostate cancer (PCa). Mutational analysis was further extended to 104 family members of mutated patients. Screening of HBOC families revealed that 30.5% harbored germline mutations in susceptibility genes, with 21.6% harboring pathogenic variants (PVs) and 8.9% having variants of uncertain significance (VUS). We found PVs at similar frequency in BRCA1 and BRCA2 genes (8.8% and 9.4%, respectively), while 0.56% of PVs were present in well-established susceptibility genes PALB2, TP53 and RAD51C. Moreover, 0.56% of monoallelic PVs were present in MUTYH, a gene whose function in tumorigenesis in the context of PCa is still unclear. Finally, we reported double heterozygosity (DH) in BRCA1/2 genes in a single family, and found double mutation (DM) present in BRCA2 in a separate family. There was no significant difference between the mean age of onset of PCa in HBOC families with or without germline mutations in susceptibility genes, while the mean survival was highest in mutated patients compared to wild type. Furthermore, PCa is the second most recurrent cancer in our cohort, resulting in 18% of cases in both mutated and non-mutated families. Our investigation shows that PVs were located mostly in the 3′ of BRCA1 and BRCA2 genes, and in BRCA2, most PVs fell in exon 11, suggesting a mutation cluster region relating to risk of HPCa. A total of 65 family members inherited the proband’s mutation; of these, 24 developed cancer, with 41 remaining unaffected.

Germline mutations in high penetrance genes are associated with worse clinical outcomes in patients with non–small cell lung cancer

ObjectiveTo determine the frequency of pathogenic mutations in high-penetrance genes (HPGs) in patients with non–small cell lung cancer (NSCLC) and identify whether such mutations are associated with clinicopathologic outcomes. MethodsPatients with NSCLC who had consented to participate in a linked clinical database and biorepository underwent germline DNA sequencing using a next-generation sequencing panel that included cancer-associated HPGs and cancer risk–associated single nucleotide polymorphisms (SNPs). These data were linked to the clinical database to assess for associations between germline variants and clinical phenotype using Fisher's exact test and multivariable logistic and Cox regression. ResultsWe analyzed 151 patients, among whom 33% carried any pathogenic HPG mutation and 23% had a genetic risk score (GRS) >1.5. Among the patients without any pathogenic mutation, 31% were at cancer stage II or higher, compared with 55% of those with 2 types of HPG mutations (P = .0293); 40% of patients with both types of HPG mutations had cancer recurrence, compared with 21% of patients without both types (P = .0644). In multivariable analysis, the presence of 2 types of HPG mutations was associated with higher cancer stage (odds ratio [OR], 3.32; P = .0228), increased recurrence of primary tumor (OR, 2.93; P = .0527), shorter time to recurrence (hazard ratio [HR], 3.03; P = .0119), and decreased cancer-specific (HR, 3.53; P = .0039) and overall survival (HR, 2.44; P = .0114). ConclusionsThe presence of mutations in HPGs is associated with higher cancer stage, increased risk of recurrence, and worse cancer-specific and overall survival in patients with NSCLC. Further large studies are needed to better delineate the role of HPGs in cancer recurrence and the potential benefit of adjuvant treatment in patients harboring such mutations.

Genomic landscape of multiple Bowen's disease using whole-exome sequencing.

The genomic landscape of Bowen's disease (BD), with multiple manifestations, has not yet been determined. This study aimed to investigate the genomic alterations in multiple BD. We performed whole-exome sequencing of BD lesions (n=9) and matched germlines collected from three patients with multiple (≥3) BD to detect somatic and germline mutations. We found a median of 64 somatic mutations in each sample (range 20-267). UV-signature mutations accounted for 64.9% (median, range 26.0%-82.1%) of point mutations. Putative driver mutations were found in five BDs (RB1 p.R445*, ARID2 p.R274*, TP53 p.Y163D/p.Y205D/p.R342*, KMT2C p.R4549C) but not in the other four lesions. Somatic mutations were not shared between multiple BD lesions collected from the same patient, indicating a different clonal origin. We also found no known pathogenic germline mutations in cancer-related genes. The mutational signature analysis revealed that UV signatures (SBS7a/7b) and age-related signatures (SBS1/5) were the main active signatures. Copy number alterations (CNAs) were found in two BDs: one with extensive CNA regions (21.7% of the genome), including driver genes (PIK3CA/SOX2/TP63 and MYC gain, and CDKN2A loss), and the other with 1q gain. Our study revealed that multiple BD lesions harbor distinct genomic landscapes, suggesting that they have different risks of malignant progression.

Error-prone repair of stalled replication forks drives mutagenesis and loss of heterozygosity in haploinsufficient BRCA1 cells

Germline mutations in the BRCA genes are associated with a higher risk of carcinogenesis, which is linked to an increased mutation rate and loss of the second unaffected BRCA allele (loss of heterozygosity, LOH). However, the mechanisms triggering mutagenesis are not clearly understood. The BRCA genes contain high numbers of repetitive DNA sequences. We detected replication forks stalling, DNA breaks, and deletions at these sites in haploinsufficient BRCA cells, thus identifying the BRCA genes as fragile sites. Next, we found that stalled forks are repaired by error-prone pathways, such as microhomology-mediated break-induced replication (MMBIR) in haploinsufficient BRCA1 breast epithelial cells. We detected MMBIR mutations in BRCA1 tumor cells and noticed deletions-insertions (>50bp) at the BRCA1 genes in BRCA1 patients. Altogether, these results suggest that under stress, error-prone repair of stalled forks is upregulated and induces mutations, including complex genomic rearrangements at the BRCA genes (LOH), in haploinsufficient BRCA1 cells.

Progress on the diagnosis and therapy about atopic diseases and primary immunodeficiency diseases

Primary immunodeficiency diseases (PID) is a congenital disease caused by single gene germline mutation related to the immune system. PID patients have immune dysregulation, and are susceptible to infectious diseases, autoimmune diseases, autoimmune diseases, allergic diseases, and malignant tumors. The first symptom of some PID patients is atopic disease, therefore they go to the department of allergy, department of pediatrics and other relevant departments. How to identify and diagnose PID in allergic patients, to reduce diagnosis delay and prevent disease aggravation are the abilities that allergists, pediatricians, and doctors in other relevant departments need to master. This article summarizes the warning signs of PID in allergic patients and the mechanism of allergy combined with PID, and then summarizes the common types of PID in allergic patients, the evaluation, treatment and prevention in patients with PID and allergy.