scholarly journals 3548 De novo germline variants in Histone 3 Family 3A (H3F3A) and Histone 3 Family 3B (H3F3B) cause a severe neurodegenerative disorder and functional effects unique from their somatic mutations

2019 ◽  
Vol 3 (s1) ◽  
pp. 103-103 ◽  
Author(s):  
Divya R Nair ◽  
Elizabeth Bhoj
Keyword(s):  
Somatic Mutations ◽  
De Novo ◽  
Neurodegenerative Disorder ◽  
Germline Mutations ◽  
Dominant Negative ◽  
Missense Mutations ◽  
Repair Gene ◽  
Histone 3 ◽  
Expression Of Genes ◽  
Dna Repair Gene

OBJECTIVES/SPECIFIC AIMS: Histones are nuclear proteins that associate with DNA to facilitate packaging into condensed chromatin. Histones are dynamically decorated with post-translational modifications (PTMs), which regulate such processes as DNA repair, gene expression, mitosis, and meiosis. Histone 3 Family 3 (H3F3) histones (H3.3), encoded by H3F3A and H3F3B, mark active genes, maintain epigenetic memory, and maintain heterochromatin and telomeric integrity. Specific somatic mutations in H3F3A and H3F3B have been strongly associated with pediatric glia and other tumors, but no germline mutations have been reported. The goal of our study was to further understand the functional effects of germline mutations of H3F3A and H3F3B. METHODS/STUDY POPULATION: We analyzed 32 patients bearing de novo germline missense mutations in H3F3A or H3F3B with core phenotypes of progressive neurologic dysfunction and congenital anomalies, but no malignancies. Patient histones were analyzed by quantitative mass spectrometry (qMS). RESULTS/ANTICIPATED RESULTS: qMS results revealed that the mutant histone proteins are present at a concentration similar to that of wild-type H3.3. qMS analysis showed strikingly aberrant PTM patterns that suggested local dysregulation. These patterns are distinct from the dominant negative somatic mutations, which cause more global PTM dysregulation. Patient cells also demonstrated upregulation of the expression of genes related to mitosis and cell division, and had a greater proliferative capacity. DISCUSSION/SIGNIFICANCE OF IMPACT: Our data suggests that the pathogenic mechanism of germline histone mutations is distinct from that of the published cancer-associated somatic histone mutations, but may converge on control of cell proliferation. Further clarification of the pathophysiology in these patients can elucidate the roles of histones and histone PTMs in human development and non-syndromic neurodegeneration. In addition, it provides a framework for targeted therapy development for this and related progressive neurologic disorders.

scholarly journals Histone H3.3 beyond cancer: Germline mutations in Histone 3 Family 3A and 3B cause a previously unidentified neurodegenerative disorder in 46 patients

2020 ◽  
Vol 6 (49) ◽  
pp. eabc9207
Author(s):  
Laura Bryant ◽  
Dong Li ◽  
Samuel G. Cox ◽  
Dylan Marchione ◽  
Evan F. Joiner ◽  
...  
Keyword(s):  
Posttranslational Modifications ◽  
De Novo ◽  
Neurodegenerative Disorder ◽  
Germline Mutations ◽  
Zebrafish Model ◽  
Cellular Assays ◽  
Histone 3 ◽  
Regulated Gene Expression ◽  
Cancer Germline

Although somatic mutations in Histone 3.3 (H3.3) are well-studied drivers of oncogenesis, the role of germline mutations remains unreported. We analyze 46 patients bearing de novo germline mutations in histone 3 family 3A (H3F3A) or H3F3B with progressive neurologic dysfunction and congenital anomalies without malignancies. Molecular modeling of all 37 variants demonstrated clear disruptions in interactions with DNA, other histones, and histone chaperone proteins. Patient histone posttranslational modifications (PTMs) analysis revealed notably aberrant local PTM patterns distinct from the somatic lysine mutations that cause global PTM dysregulation. RNA sequencing on patient cells demonstrated up-regulated gene expression related to mitosis and cell division, and cellular assays confirmed an increased proliferative capacity. A zebrafish model showed craniofacial anomalies and a defect in Foxd3-derived glia. These data suggest that the mechanism of germline mutations are distinct from cancer-associated somatic histone mutations but may converge on control of cell proliferation.

scholarly journals STK11 (LKB1) missense somatic mutant isoforms promote tumor growth, motility and inflammation

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Paula Granado-Martínez ◽  
Sara Garcia-Ortega ◽  
Elena González-Sánchez ◽  
Kimberley McGrail ◽  
Rafael Selgas ◽  
...  
Keyword(s):  
Tumor Growth ◽  
Somatic Mutations ◽  
Human Cancer ◽  
Tumor Biology ◽  
Missense Mutations ◽  
Expression Of Genes ◽  
Promote Tumor Growth ◽  
Genes Encoding ◽  
Differential Gene ◽  
Somatic Mutant

AbstractElucidating the contribution of somatic mutations to cancer is essential for personalized medicine. STK11 (LKB1) appears to be inactivated in human cancer. However, somatic missense mutations also occur, and the role/s of these alterations to this disease remain unknown. Here, we investigated the contribution of four missense LKB1 somatic mutations in tumor biology. Three out of the four mutants lost their tumor suppressor capabilities and showed deficient kinase activity. The remaining mutant retained the enzymatic activity of wild type LKB1, but induced increased cell motility. Mechanistically, LKB1 mutants resulted in differential gene expression of genes encoding vesicle trafficking regulating molecules, adhesion molecules and cytokines. The differentially regulated genes correlated with protein networks identified through comparative secretome analysis. Notably, three mutant isoforms promoted tumor growth, and one induced inflammation-like features together with dysregulated levels of cytokines. These findings uncover oncogenic roles of LKB1 somatic mutations, and will aid in further understanding their contributions to cancer development and progression.

scholarly journals Genetic, Phenotypic, and Interferon Biomarker Status in ADAR1-Related Neurological Disease

2017 ◽  
Vol 48 (03) ◽  
pp. 166-184 ◽  
Author(s):  
Gillian Rice ◽  
Naoki Kitabayashi ◽  
Magalie Barth ◽  
Tracy Briggs ◽  
Annabel Burton ◽  
...  
Keyword(s):  
Neurological Disease ◽  
De Novo ◽  
Phenotypic Variability ◽  
Spastic Paraparesis ◽  
Dominant Negative ◽  
Compound Heterozygous ◽  
Motor Disorder ◽  
Type I ◽  
Missense Mutations ◽  
Dominant Negative Mutation

AbstractWe investigated the genetic, phenotypic, and interferon status of 46 patients from 37 families with neurological disease due to mutations in ADAR1. The clinicoradiological phenotype encompassed a spectrum of Aicardi–Goutières syndrome, isolated bilateral striatal necrosis, spastic paraparesis with normal neuroimaging, a progressive spastic dystonic motor disorder, and adult-onset psychological difficulties with intracranial calcification. Homozygous missense mutations were recorded in five families. We observed a p.Pro193Ala variant in the heterozygous state in 22 of 23 families with compound heterozygous mutations. We also ascertained 11 cases from nine families with a p.Gly1007Arg dominant-negative mutation, which occurred de novo in four patients, and was inherited in three families in association with marked phenotypic variability. In 50 of 52 samples from 34 patients, we identified a marked upregulation of type I interferon-stimulated gene transcripts in peripheral blood, with a median interferon score of 16.99 (interquartile range [IQR]: 10.64–25.71) compared with controls (median: 0.93, IQR: 0.57–1.30). Thus, mutations in ADAR1 are associated with a variety of clinically distinct neurological phenotypes presenting from early infancy to adulthood, inherited either as an autosomal recessive or dominant trait. Testing for an interferon signature in blood represents a useful biomarker in this context.

Randomized phase II study of second-line modified FOLFIRI with PARP inhibitor ABT-888 (Veliparib) (NSC-737664) versus FOLFIRI in metastatic pancreatic cancer (mPC): SWOG S1513.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. 4014-4014 ◽  
Author(s):  
E. Gabriela Chiorean ◽  
Katherine A Guthrie ◽  
Philip Agop Philip ◽  
Elizabeth M. Swisher ◽  
Florencia Jalikis ◽  
...  
Keyword(s):  
Dna Repair ◽  
Phase Ii ◽  
Somatic Mutations ◽  
Phase Ii Study ◽  
Parp Inhibitor ◽  
Gene Mutations ◽  
Control Treatment ◽  
Repair Gene ◽  
Randomized Phase Ii ◽  
Dna Repair Gene

4014 Background: PC is characterized by DNA Damage Repair (DDR) deficiencies, including in BRCA1/2, ATM, and FANC genes. Given preclinical synergism between veliparib with irinotecan, safety and preliminary efficacy, we designed a randomized phase II study of mFOLFIRI (no 5-FU bolus) + veliparib vs FOLFIRI alone for 2nd line mPC patients (pts). Methods: Eligible pts had mPC, adequate organ function, ECOG PS 0-1, and 1 prior non-irinotecan systemic therapy.143 pts were to be randomized (1:1) to veliparib vs control. Primary endpoint was overall survival (OS). All pts had blood and tumor biopsies at baseline to assess germline and somatic BRCA1/2 mutations (integrated), and homologous recombination (HR) or DDR biomarkers (exploratory). Results: 123 pts were accrued between 09/2016 to 12/2017, and 108 were included in this analysis. 117 pts were biomarker evaluable: 109 blood/106 tumors. 11 cancers (9%) had HR deficiency (HRD), including 4 germline ( BRCA1, BRCA2, ATM) and 7 somatic mutations ( BRCA2, PALB2, ATM, CDK12). Additional 24 cancers (20%) had germline (n = 11, e.g., FANC, BLM, SLX4, CHEK2) or somatic mutations (n = 13, e.g., FANC, BLM, POLD1, RIF1, MSH2, MSH6) in other DNA repair genes, not classified as HRD. A planned interim futility analysis at 35% of expected PFS events determined the veliparib arm was unlikely to be superior to control. Most common grade 3/4 treatment related toxicities were neutropenia (33% vs 20%), fatigue (19% vs 4%), and nausea (11% vs 4%), for veliparib vs control. Treatment exposure was similar for veliparib vs control: median 4 cycles (range 1-31 vs 1-32). Median OS was 5.1 vs 5.9 mos (HR 1.3, 95%CI 0.9-2.0, p = 0.21), and median PFS was 2.1 vs 2.9 mos (HR 1.5, 95%CI 1.0-2.2, p = 0.05) for veliparib vs control arms, respectively. Correlations of gene mutations and signatures with efficacy outcomes will be presented. Conclusions: Nearly 30% of mPC pts had DNA repair gene abnormalities, including 9% with HRD. Veliparib increased toxicity and did not improve OS when added to mFOLFIRI in biomarker unselected pts. BRCA1/2 and DDR biomarkers will be correlated with efficacy to inform patient selection for future PARP inhibitor clinical trials. Clinical trial information: NCT02890355.

Effect of germline ATM mutations on clonal hematopoiesis.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. 1509-1509
Author(s):  
Thomas Paul Slavin ◽  
Kar Wing Kevin Tsang ◽  
Jeffrey Longmate ◽  
Danielle Castillo ◽  
Josef Herzog ◽  
...  
Keyword(s):  
Germline Mutation ◽  
White Blood Cells ◽  
Germline Mutations ◽  
Lymphocytic Leukemia ◽  
Repair Gene ◽  
Clonal Hematopoiesis ◽  
Mutation Carriers ◽  
Dna Repair Gene ◽  
Increased Risk ◽  
Allele Fraction

1509 Background: Clonal hematopoiesis (CH) in myeloid related-genes is associated with development of primary and secondary leukemia and atherosclerotic disease, as well as, decreased overall survival. Identification of factors beyond age and cytotoxic exposures that predispose to CH may be useful to both recognize individuals at increased risk for CH and to better understand how CH develops. We have previously shown that germline mutations in the DNA repair gene ATM may predispose to CH. We hypothesized here that heterozygous ATM germline mutation carriers would have higher rates of CH in myeloid genes compared to controls. Methods: Germline DNA samples from 34 heterozygous ATM germline mutation carriers (cases) and 22 controls without ATM germline mutations were sequenced on an Illumina 2500 using a custom 79-gene-myeloid-CH-coding-exon-amplicon-based Qiaseq panel. Read depth averaged 130x. Pathogenic and likely pathogenic CH variants (PV) above an allele fraction of 2% were used for analyses. Cases and controls were compared using a rank-sum test. Results: Cases had a higher median age (56 years, range 30-82) than controls (48 years, range 5-72). Cases and controls were similar in solid tumor cancer history and known exposure to cancer cytotoxic therapy; 73.5% vs 86.4%, and 18.1 vs 20.6%, respectively. The number of CH PV was similarly associated with age in both cases and controls (cor = 0.31, p = 0.01). Cases displayed more CH PVs than controls (total 62 vs 3 PVs, median 2 PVs vs 0, p = 10-6). Of note, cases frequently had a concomitant second (n = 10; 29% of cases) or third (n = 4; 11.8% of cases) unique ATM CH PV, whereas no ATM CH PVs were seen in controls. Even after excluding ATM CH PVs, CH PVs were more frequent in cases (p = 0.00003). After ATM CH PVs, the most frequent CH PVs in cases were in NF1 (5 PVs), BCORL1 (4 PVs), and DMNT3A (4 PVs). Conclusions: Our study supports ATM as a strong predisposition locus for myeloid gene CH. CH in ATM germline mutation carriers frequently involved unique low allele fraction PVs in ATM, suggesting ATM germline PVs are driving production of likely bi-allelic ATM inactivation in white blood cells, or complete ATM loss. Complete ATM loss may be a nidus particularly for lymphocytic leukemia, as bi-allelic ATM inactivation is a frequent somatic finding.

scholarly journals Mice harboring a SCA28 patient mutation in AFG3L2 develop late-onset ataxia associated with enhanced mitochondrial proteotoxicity.

2018 ◽  
Author(s):  
Cecilia Mancini ◽  
Eriola Hoxha ◽  
Luisa Iommarini ◽  
Alessandro Brussino ◽  
Uwe Richter ◽  
...  
Keyword(s):  
Network Formation ◽  
De Novo ◽  
Neurodegenerative Disorder ◽  
Late Onset ◽  
Mitochondrial Protein ◽  
Atp Synthesis ◽  
Protein Translation ◽  
Mutant Mice ◽  
Mitochondrial Morphology ◽  
Missense Mutations

Spinocerebellar ataxia 28 is an autosomal dominant neurodegenerative disorder caused by missense mutations affecting the proteolytic domain of AFG3L2, a major component of the mitochondrial m-AAA protease. However, little is known of the underlying pathogenetic mechanisms or how to treat patients with SCA28. Currently available Afg3l2 mutant mice harbour deletions that lead to severe, early-onset neurological phenotypes that do not faithfully reproduce the late-onset and slowly progressing SCA28 phenotype. Here we describe production and detailed analysis of a new knock-in murine model harbouring an Afg3l2 allele carrying the p.Met665Arg patient-derived mutation. Heterozygous mutant mice developed normally but signs of ataxia were detectable by beam test at 18 months. Cerebellar pathology was negative; electrophysiological analysis showed increased spontaneous firing in Purkinje cells from heterozygous mutants with respect to wild-type controls, although not statistically significant. As homozygous mutants died perinatally with evidence of cardiac atrophy, for each genotype we generated mouse embryonic fibroblasts (MEFs) to investigate mitochondrial function. MEFs from mutant mice showed altered mitochondrial bioenergetics, with decreased basal oxygen consumption rate, ATP synthesis and mitochondrial membrane potential. Mitochondrial network formation and morphology was also altered, in line with greatly reduced expression of Opa1 fusogenic protein L-isoforms. The mitochondrial alterations observed in MEFs were also detected in cerebella of 18-month-old heterozygous mutants, suggesting they may be a hallmark of disease. Pharmacological inhibition of de novo mitochondrial protein translation with chloramphenicol caused reversal of mitochondrial morphology in homozygous mutant MEFs, supporting the relevance of mitochondrial proteotoxicity for SCA28 pathogenesis and therapy development.

Germline genetic mutational landscape and characteristics of men with prostate cancer (PCa): A single institution experience.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e13679-e13679
Author(s):  
Sunil Adige ◽  
Lisa Bealin ◽  
Nicole Ventriglia ◽  
Daniel M. Geynisman ◽  
Fern Anari ◽  
...  
Keyword(s):  
Dna Repair ◽  
Single Gene ◽  
Specific Antigen ◽  
Gene Mutations ◽  
Germline Mutations ◽  
Disease Stage ◽  
Single Institution ◽  
Repair Gene ◽  
Dna Repair Gene ◽  
New Guidelines

e13679 Background: The role of germline genetic testing (GGT) is rapidly changing for men with PCa. We describe the characteristics of men with PCa diagnosed with pathogenic (P) and likely pathogenic (LP) mutations on GGT. Methods: We conducted a retrospective single-institution study for all men with PCa who received single gene or multi-gene GGT from 1997-2019, unselected for disease stage, Gleason score, or age at diagnosis, and while most had a family history of cancer, some did not. All participants were from the Risk Assessment Program (RAP) database at FCCC and consented for research purposes at the time of GGT. Results: 160 men with PCa had GGT. 72/160 (45%) patients had no mutations. 41/160 (26%) patients had a variant of undetermined significance (VUS) (13 with 2 VUS, 1 with 3 VUS). 47/160 (29%) men were found to have a P or LP germline mutation. 26/47 (55%) with recurrent disease, and 1/47 (2%) unknown. 46 were Caucasian, and 1 was African American ( PALB2). 28/47 (60%) had Gleason Scores (GS) ≤7. 6/47 (13%) had a Prostate Specific Antigen (PSA) at diagnosis < 4.0 ng/mL. 23/47 (49%) were diagnosed < 60 years of age, and 8/47 (17%) at ≤ 50. 19/23 (83%) PCa cases with P/LP diagnosed below age 60 had DNA repair genes: BRCA2 (8), BRCA1 (4), CHEK2 (4), ATM (2), and PALB2 (1). 74/160 (46%) were tested after PCa NCCN genetics guidelines changed (October 2017), of which 19/74 (25%) had P/LP, and of those positive for P/LP, 6/19 (32%) had non-metastatic disease. Two patients had small cell neuroendocrine PCa ( CHEK2 and BRCA2), the remaining had adenocarcinoma PCa. Please see Table for full results. Conclusions: To our knowledge, this is the largest single-institution study reporting PCa characteristics and incidence of P/LP germline mutations. Rates of DNA-repair gene mutations were higher than previously reported, possibly reflecting our specialized cancer center’s population. While BRCA1/2 mutations were the most represented (55%), we describe PCa patients with mutations in ATM, CHEK2, NBN, PALB2, CFTR, and MUTYH, recognizing a few are not known to be linked to PCa. More than half of P/LP mutation carriers had GS ≤7. Additionally, 13% of the men with P/LP germline mutations had low PSA ( < 4.0 ng/mL) at diagnosis. Our findings highlight the importance of the new guidelines and GGT importance in some men with PCa, particularly if they could benefit from a different therapeutic approach, or be influenced into cascade GGT. [Table: see text]

Azacytidine-induced reactivation of a DNA repair gene in Chinese hamster ovary cells

1986 ◽  
Vol 6 (8) ◽  
pp. 2944-2949
Author(s):  
P A Jeggo ◽  
R Holliday
Keyword(s):  
De Novo ◽  
Chinese Hamster Ovary Cells ◽  
Chinese Hamster ◽  
Very High Frequency ◽  
Repair Gene ◽  
Ovary Cells ◽  
Mammalian Cell Lines ◽  
Dna Repair Gene ◽  
Type Gene ◽  
Very High

Six X-ray-sensitive (xrs) strains of the CHO-K1 cell line were shown to revert at a very high frequency after treatment with 5-azacytidine. This suggested that there was a methylated xrs+ gene in these strains which was structurally intact, but not expressed. The xrs strains did not complement one another, and the locus was autosomally located. In view of the frequency of their isolation and their somewhat different phenotypes, we propose that the xrs strains are mutants derived from an active wild-type gene. However, there is in addition a methylated silent gene present in the genome. Azacytidine treatment reactivated this gene. We present a model for the functional hemizygosity of mammalian cell lines, which is based on the inactivation of genes by de novo hypermethylation. In contrast to results with xrs strains, other repair-defective lines were found not to be reverted by azacytidine.

scholarly journals Frequent germline mutations of HAVCR2 in sporadic subcutaneous panniculitis-like T-cell lymphoma

2019 ◽  
Vol 3 (4) ◽  
pp. 588-595 ◽  
Author(s):  
Chantana Polprasert ◽  
Yasuhide Takeuchi ◽  
Nobuyuki Kakiuchi ◽  
Kenichi Yoshida ◽  
Thamathorn Assanasen ◽  
...  
Keyword(s):  
T Cell ◽  
Somatic Mutations ◽  
Cell Lymphoma ◽  
Germline Mutations ◽  
T Cell Lymphoma ◽  
Compound Heterozygous ◽  
Missense Mutations ◽  
Whole Exome ◽  
History Of ◽  
Underlying Diseases

Abstract Subcutaneous panniculitis-like T-cell lymphoma (SPTCL) is a rare subtype of peripheral T-cell lymphoma affecting younger patients and associated with hemophagocytic lymphohistiocytosis. To clarify the molecular pathogenesis of SPTCL, we analyzed paired tumor and germline DNAs from 13 patients by whole-exome sequencing. All cases were Asians and were phenotypically sporadic with no family history of SPTCL. Consistent with a recent report, germline mutations in HAVCR2, encoding T-cell immunoglobulin mucin 3 (TIM3), were identified in 11 of 13 (85%) cases. All mutated cases were primary SPTCL, whereas the 2 cases without mutation were secondary SPTCL associated with underlying diseases, including viral infection and autoimmune disease. Ten patients harbored homozygous p.Y82C mutations, and 1 showed compound heterozygous mutations (p.Y82C and p.T101I). Both missense mutations altered highly conserved residues located in the extracellular immunoglobulin variable–like domain. According to the Genome Aggregation Database of &gt;138 500 general individuals, both mutations were documented with minor allele frequencies &lt; 0.007, indicating remarkable enrichment of these HAVCR2 alleles in SPTCL. SPTCL cells also harbored somatic mutations (6.2 per patient) that are frequently identified in genes associated with epigenetic regulation and signal transduction. In conclusion, individuals harboring biallelic HAVCR2 (TIM3) germline mutations were highly susceptible to sporadic SPTCL, which was also associated with clonal somatic mutations.

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