SF3B1 Mutations Frequently Occur With Both ATM Mutations and TP53 Mutations In CLL Patients

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 2868-2868
Author(s):  
Veronika Navrkalova ◽  
Jitka Malcikova ◽  
Barbara Kantorova ◽  
Ludmila Sebejova ◽  
Karla Plevova ◽  
...  
Keyword(s):  
Conflicts Of Interest ◽  
Hot Spot ◽  
Statistical Significance ◽  
Missense Mutations ◽  
Loss Of Function ◽  
Protein Loss ◽  
Tp53 Mutations ◽  
Active Involvement ◽  
Mutation Profile ◽  
Complete Protein

Abstract Abnormalities of TP53 and ATM genes are well established adverse prognostic markers in CLL. Mutations in splicing factor SF3B1 have recently been described as recurrent and predominantly subclonal aberration. Previous studies inconsistently suggested mutual exclusivity or partial overlap with TP53 mutations. Concerning ATM defects, the association between SF3B1 mutations and del(11q) was reported, but relation to ATM mutations remains unclear. The aims were: (a) to assess association between SF3B1 mutations and the most adverse classic genetic lesions represented by TP53 mutations and del(11q); (b) to investigate association between SF3B1 mutations and ATM mutations in a subset of ATM-characterized patients, and (c) to delineate SF3B1 mutation profile and proportion. We used Sanger sequencing of SF3B1 hot-spot exons 14-16, FASAY analysis of TP53 exons 4-10 and resequencing microarray for ATM mutation detection (all 62 coding exons). We analyzed unfavorable cohort of 338 patients characterized by prevalence of unmutated IGHV (72%). At the time of analysis, 82.5% of the patients were previously untreated. We observed SF3B1 mutation in 17.5% (59/338), TP53 mutation in 20% (68/338), and del(11q) in 27.5% (93/338) of cases. All these genetic defects were significantly more frequent in treated patients (SF3B1: P=0.008, TP53: P<0.0001, del(11q): P=0.0295). Interestingly, we observed quite frequent co-occurrence of SF3B1 and TP53 mutations; 28% (19/68) of p53-affected patients in comparison with 15% (40/270) of p53-wt patients harbored SF3B1 mutation (P=0.019). This co-occurrence was apparent (albeit without statistical significance, P=0.166) also in patients investigated at diagnosis, when 20.6% (7/34) of p53-affected patients but only 11.5% (19/165) of p53-wt patients exhibited SF3B1 mutation. The previously reported increased SF3B1 mutation frequency in patients with del(11q) was also apparent but not significant (P=0.078) in our cohort since mutation frequencies were 24% (22/93) and 15% (37/244) in groups with and without del(11q). To analyze the relation of SF3B1 and ATM mutations we used samples with characterized ATM mutation status (n=112). The p53-defective samples and samples with sole del(11q) were omitted since these more frequently harbored SF3B1 mutation. In the remaining 37 patients we observed that SF3B1 and ATM mutations frequently co-occur: 8/21 ATM-mutated patients (38%) but only 2/16 ATM-TP53-wt patients (12.5%) exhibited SF3B1 mutation (P=0.137). This association should be, however, verified on larger cohort. Concerning the SF3B1 mutation profile, we observed previously reported hot-spot missense mutations with the most abundant mutation K700E (21/59, 36%). In addition, we found 2 short in-frame deletions. Altogether it shows that rather than SF3B1 loss-of-function only partial impairment or gain-of-function is possible. The vast majority of samples had mutation in heterozygous state that correlates with presumably preserved second allele. Interestingly, we found 4 mutations in a proportion around 90% that could be explained by loss of heterozygosity in the locus 2q33.1 by any cause. Our study indicates that SF3B1 mutations frequently overlap with mutations in the DNA damage response pathway genes at least in prognostically unfavorable cohort. It seems that SF3B1 mutations do not lead to complete protein loss indicating rather active involvement of mutated SF3B1 in splicing processes in CLL cells. The work was supported by grants NT13519-4, NT11218-6, MSM0021622430, MUNI/A/0723/2012. Disclosures: No relevant conflicts of interest to declare.

TP53 Abnormalities in Chronic Lymphocytic Leukemia Exhibit a Disease Specific Profile: Meta-Analysis of 270 Mutations.

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 2077-2077
Author(s):  
Thorsten Zenz ◽  
Jana Smadova ◽  
Dominik Vollmer ◽  
Martin Trbusek ◽  
Axel Benner ◽  
...  
Keyword(s):  
Mutation Analysis ◽  
Tp53 Mutation ◽  
Hot Spot ◽  
Statistical Significance ◽  
Residual Activity ◽  
Missense Mutations ◽  
Tp53 Mutations ◽  
Cpg Sites ◽  
Frame Shift ◽  
Mutation Pattern

Abstract TP53 mutations have been shown to occur in 5–40% of CLL patients depending on the clinical background (early stage/refractory disease). They are associated with a poor response to standard chemotherapy with alkylators and purine analogues and dismal clinical course. Because previous studies have examined small cohorts without detailed molecular characterization, the exact TP53 mutation profile and a correlation of TP53 mutation pattern, allele status and associated molecular genetics has not been possible. We performed a large scale mutation analysis of TP53 at four centres and pooled the data to characterize the pattern of TP53 mutations in CLL. The methods of mutational analysis included DHPLC (n=149 mutations), FASAY assay (n=63), direct sequencing (n=28) and a TP53 custom re-sequencing chip (n=30). We performed a comparison to a group of 463 patients without TP53 mutation. We found 270 mutations in 256 patients with CLL (14 with 2 mutations) out of over 1000 screened cases. Transversions, small deletions and insertions were observed less commonly (86/270; 44/270; 9/270 resp.). Missense mutations appeared in 74% of cases, compared to frameshift (20%), nonsense (4%) and splice site (2%) mutations. As expected, the majority (246/270) of mutations were located in the DNA binding domain of p53, predominantly represented by missense mutations (80%). Outside this central core domain, frame-shift (52%) and nonsense mutations (26%) were more frequent. Transitions were found in 131 of 270 mutations, with only 41 occurring at methylated CpG sites (15%). Interestingly, the number of G-A mutations was markedly higher in comparison with C-T mutations at the CpGs (27 vs. 14). Since the former alteration may reflect a C-T transition on non-coding, transcribed DNA strand, we hypothesize that these mutations might be selected for during a prolonged G1-phase, which is characteristic for CLL cells. Genomic aberrations detected by FISH were available for 261/270 cases. Most mutations (201/270) were accompanied by deletion of the other allele (17p-). Nonetheless, TP53 mutations were also found in cases with no aberrations (n=18) and 13q- as the sole abnormality (n=24). There appeared to be a higher frequency of frameshift mutations in the 17p- subgroup (22% vs. 13%) although the comparison did not reach statistical significance. Interestingly, trisomy 12 (without 17p- or 11q-) was only found in a single case with TP53 mutation compared to 54/463 in the cohort without mutation (P&lt;0.0001). We quite frequently observed a deletion 11q- (36/270) accompanying the abnormalities of one (14/60) as well as of both (22/201) TP53 alleles (mutation/deletion). 11q deletion may not be a simple alternative to p53 inactivation, as it has been proposed previously. Chemotherapy before mutation analysis was noted in 106 cases. The mutational profile was not different in the cohorts with and without prior therapy suggesting that the mechanism underlying the development of mutations may be similar independent of treatment. When comparing the predicted functional activity of the mutated TP53 in different cytogenetic subgroups (http://p53.free.fr/Database/p53_recomendations.html) we observed a significantly lower residual activity (WAF1 promotor) of the missense mutations in the 17p- subgroup compared to the patients with 13q- (single) and a TP53 mutation (median 6,815 vs. 10,31 p&lt;0,0001). Seventy percent of missense mutations (140/201) were located in 30 different codons. The amino acids most frequently mutated were at positions 179, 209, 248 and 273. This indicates that the classical hot spots are also commonly mutated in CLL. Codons 175, 248, and 273 made up for 11% of the mutations, but we identified three other commonly mutated codons (179, 209, 220) that also made up for 10% of the mutations in CLL. The mutation pattern of TP53 shows a comparatively small amount of transitions at CpG sites indicating a relatively negligible contribution of endogenous mutability at methylated cytosine. In addition, CLL is characterized by a high incidence of deleterious frame-shift mutations compared to other cancers. The high frequency of mutations at codon 209 in our cohort suggests this as a new hot spot of TP53 abnormalities associated with CLL.

scholarly journals The association of microcephaly protein WDR62 with CPAP/IFT88 is required for cilia formation and neocortical development

2019 ◽  
Vol 29 (2) ◽  
pp. 248-263 ◽  
Author(s):  
Belal Shohayeb ◽  
Uda Ho ◽  
Yvonne Y Yeap ◽  
Robert G Parton ◽  
S Sean Millard ◽  
...  
Keyword(s):  
Radial Glia ◽  
Single Amino Acid ◽  
Missense Mutations ◽  
Loss Of Function ◽  
Protein Loss ◽  
Mutant Proteins ◽  
Cilia Formation ◽  
Morphological Defects ◽  
Cell Processes ◽  
Radial Glial

Abstract WDR62 mutations that result in protein loss, truncation or single amino-acid substitutions are causative for human microcephaly, indicating critical roles in cell expansion required for brain development. WDR62 missense mutations that retain protein expression represent partial loss-of-function mutants that may therefore provide specific insights into radial glial cell processes critical for brain growth. Here we utilized CRISPR/Cas9 approaches to generate three strains of WDR62 mutant mice; WDR62 V66M/V66M and WDR62R439H/R439H mice recapitulate conserved missense mutations found in humans with microcephaly, with the third strain being a null allele (WDR62stop/stop). Each of these mutations resulted in embryonic lethality to varying degrees and gross morphological defects consistent with ciliopathies (dwarfism, anophthalmia and microcephaly). We find that WDR62 mutant proteins (V66M and R439H) localize to the basal body but fail to recruit CPAP. As a consequence, we observe deficient recruitment of IFT88, a protein that is required for cilia formation. This underpins the maintenance of radial glia as WDR62 mutations caused premature differentiation of radial glia resulting in reduced generation of neurons and cortical thinning. These findings highlight the important role of the primary cilium in neocortical expansion and implicate ciliary dysfunction as underlying the pathology of MCPH2 patients.

Loss of PERK Signaling Results in Impaired Granulopoiesis in Transgenic Mice Expressing Mutant Ela2.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 551-551
Author(s):  
Suparna Nanua ◽  
Jun Xia ◽  
Mark Murakami ◽  
Jill Woloszynek ◽  
Daniel C. Link
Keyword(s):  
Er Stress ◽  
Protein Misfolding ◽  
Conflicts Of Interest ◽  
Fetal Liver ◽  
Clinical Samples ◽  
Missense Mutations ◽  
Loss Of Function ◽  
Granulocytic Differentiation ◽  
Disease Pathogenesis ◽  
Chemical Inducers

Abstract Abstract 551 Severe congenital neutropenia (SCN) is an inborn disorder of granulopoiesis characterized by chronic neutropenia, a block in granulocytic differentiation at the promyelocyte/myelocyte stage, and a marked propensity to develop acute myeloid leukemia. Approximately 50% of cases of SCN are associated with germline heterozygous mutations of ELA2, encoding neutrophil elastase (NE). To date, 59 different, mostly missense, mutations of ELA2 have been reported. A unifying mechanism by which all of the different ELA2 mutants disrupt granulopoiesis is lacking. We and others previously proposed a model in which the ELA2 mutations result in NE protein misfolding, induction of endoplasmic reticulum (ER) stress, activation of the unfolded protein response (UPR), and ultimately apoptosis of granulocytic precursors. Testing this (and other) models has been limited by the rarity of SCN and difficulty in obtaining clinical samples for testing. We previously reported preliminary findings of a novel transgenic mouse expressing a truncation mutation of Ela2 (G193X) reproducing a similar mutation found in some patients with SCN (2008 ASH abstract #314). We showed that the G193X Ela2 allele produced the expected truncated protein that was rapidly degraded. Surprisingly, basal and stress granulopoiesis were normal. We hypothesized that reduced expression of Ela2 in murine compared with human granulocytic precursors resulted in less delivery of misfolded mutant NE protein to the ER, attenuating UPR activation and preserving granulopoiesis in G193X Ela2 mice. Consistent with this hypothesis, only modest evidence of UPR activation was observed in G193X Ela2 granulocytic precursors, and these cells displayed increased sensitivity to chemical inducers of ER stress compared with wildtype granulocytic precursors. The UPR model of disease pathogenesis predicts that inhibition of the cellular pathways that handle misfolded proteins may sensitize G193X Ela2 cells to ER stress and result in impaired granulocytic differentiation. To test this prediction, we crossed G193X Ela2 mice with mice lacking protein kinase RNA (PKR)-like ER kinase (PERK); PERK is one of three major ER-resident proteins that sense ER stress and activate the UPR. Of note, homozygous loss-of-function mutations of PERK (EIF2AK3) are responsible for Wolcott-Rallison syndrome, which is characterized by infantile diabetes and neutropenia in approximately 50% of cases. Since PERK deficiency is embryonic lethal, we transplanted fetal liver cells from PERK-/-, PERK-/- × G193X Ela2, and wild type embryos into irradiated recipients. Complete donor engraftment was observed in all cohorts. Basal granulopoiesis was normal in mice reconstituted with PERK-/- cells. However, in the PERK-/- × G193X Ela2 chimeras, though blood neutrophil counts were normal, a significant reduction in bone marrow neutrophils was observed [6.01 × 106/femur ± 0.92 (PERK-/-) versus 3.14 × 106 ± 0.88 (PERK-/- × G193X Ela2); p < 0.001]. These data show that loss of PERK signaling combined with G193X Ela2 expression results in impaired granulopoiesis, providing new evidence in support of the UPR model of disease pathogenesis. Disclosures: No relevant conflicts of interest to declare.

scholarly journals The Association Between SERPINC1 C.883G>a and VT in the Chinese Population

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 3505-3505
Author(s):  
Jingdi Liu ◽  
Liang Tang ◽  
Wei Zeng ◽  
Yu Hu ◽  
Han Liu
Keyword(s):  
Venous Thrombosis ◽  
Chinese Population ◽  
Case Control Study ◽  
Conflicts Of Interest ◽  
Hot Spot ◽  
Case Control ◽  
Missense Mutations ◽  
Increased Risk ◽  
Control Study

Abstract Background: Antithrombin(AT) is a major anticoagulation molecule in vivo and is encoded by the gene SERPINC1. AT plays a key role as an inhibitor of physiological haemostasis by inhibiting the procoagulation factors, especially the factor Xa and thrombin. Objectives: To explore the variations of SERPINC1 gene associated with venous thrombosis in the Chinese population. Methods: SERPINC1 gene sequencing was carried out. A case-control study involving 1335 patients diagnosed with VT and 1315 Age- and sex-matched control individuals without a history of thrombosis were further carried out. Furthermore, plasma AT activity, AT antigen, and thrombin generation tests (TGT) were performed to evaluate the influences of the mutations. Results: Four different missense mutations were identified in an unreported hot spot region of SERPINC1. They were c.880C>T(p.Arg294Cys), c.881G>T(p.Arg294Leu), c.881G>A(p.Arg294His) and c.883G>A(p.Val295Met). All of the affected individuals were heterozygotes. In addition, c.883G>A was found to be a predominant mutation. In the case-control study, the mutation was proved to be a strong risk factor for venous thrombosis with an OR of 10.92(p<0.01, 95%CI 1.41-84.68). Functional assays showed that both the activities and antigens of plasma AT decreased mildly. Conclusion: A hot spot mutation region of SERPINC1 gene was discovered. The predominant mutation of SERPINC1 c.883G>A is the most frequent cause of AT deficiency and is associated with an increased risk of venous thrombosis in the Chinese population. Disclosures No relevant conflicts of interest to declare.

Pan-HER tyrosine-kinase inhibitors (TKI) dacomitinib and afatinib in penile squamous cell carcinoma (PSCC): Results from an ongoing open-label, single-group, phase 2 trial of dacomitinib in chemonaive patients (pts).

2016 ◽  
Vol 34 (2_suppl) ◽  
pp. 483-483
Author(s):  
Daniele Raggi ◽  
Andrea Necchi ◽  
Patrizia Giannatempo ◽  
Nicola Nicolai ◽  
Maurizio Colecchia ◽  
...  
Keyword(s):  
Kinase Inhibitors ◽  
Hot Spot ◽  
Objective Response ◽  
Skin Toxicity ◽  
Pelvic Lymphadenectomy ◽  
Missense Mutations ◽  
Loss Of Function ◽  
Open Label ◽  
Molecular Alterations ◽  
Phase 2 Trial

483 Background: Prognosis of pts with advanced/metastatic PSCC is poor and chemotherapy exerts a low efficacy. Targeting HER pathway is rational and promising in PSCC. Two companion trials are enrolling in the 1st-line/neoadjuvant setting (Dacomitinib, NCT01728233) and salvage setting (Afatinib, NCT02541903). Here we present the ongoing results of the former study. Dacomitinib is a potent, irreversible TKI of human EGFR/HER1, HER2 and HER4. Methods: 37 pts with clinical N2-3 or M1 disease receive oral Dacomitinib 45 mg daily until surgery or disease progression (PD)/unacceptable toxicity. No prior systemic therapy is allowed. Computed tomography and PET scan are repeated q2 months. Simon’s Optimal 2-stage design is applied. The primary endpoint is the objective response-rate (ORR = CR/PR according to RECIST v1.1: H0 ≤ 5%, H1 ≥ 20%, α and β = 10%). Next generation sequencing (NGS) with “Hot-spot cancer panel” (Ion Torrent, Life Technologies) is being performed for all enrolled pts. Results: From 06/13 to 05/15, 14 pts were treated. Median age was 57 yrs (IQR: 54-72). 4 had received inguinal/pelvic lymphadenectomy, 4 had inguinal+pelvic nodes, 10 bilateral disease, and 4 distant mets. Two pts achieved a PR (ORR: 14.3%), 8 a SD, 4 a PD. 8 pts (57.1%) had a metabolic PR. 9 pts underwent post-Dacomitinib lymphadenectomy: > 90% necrosis was seen in one patient. After a median follow-up of 6.97 months, 6 pts (42.8%) were progression-free (median PFS was 4.47 months). Median OS was 11.9 months, 1-year OS was 50% (95%CI: 8.05-82.63). Skin toxicity was observed in 7 pts (6 G1, 1 G3), G2 diarrhea in two, and bleeding of cutaneous mets in one. Tissue from one PR pt harbored missense mutations in FBXW7 (R505S), PTEN (A3T), and TP53 (R273H, loss of function mutation) genes. Conclusions: Dacomitinib is endowed with antitumor activity in PSCC. Results are pending confirmation in the whole sample size. Dacomitinib and Afatinib trials will provide insights into the targeting of HER pathway in PSCC based on prior chemotherapy administration. Preliminary data on molecular alterations linked to clinical benefit are being observed. Clinical trial information: NCT01728233.

p53 Inactivation in CLL: Pattern of 110 TP53 Mutations.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 2064-2064 ◽  
Author(s):  
Thorsten Zenz ◽  
Martin Trbusek ◽  
Jana Smardova ◽  
Sonja Häbe ◽  
Tina Denzel ◽  
...  
Keyword(s):  
Mutation Analysis ◽  
Tp53 Mutation ◽  
Hot Spot ◽  
Statistical Significance ◽  
Residual Activity ◽  
The Other ◽  
Response To Treatment ◽  
Tp53 Mutations ◽  
Mutation Pattern ◽  
P53 Inactivation

Abstract TP53 mutations have been shown to occur in 5–15% of CLL patients and are associated with a poor response to treatment. Because previous studies have examined small cohorts without detailed molecular characterization, the exact correlation of TP53 mutation pattern, allele status and associated molecular genetics has not been possible. We undertook a large scale mutation analysis of TP53 in two centres and pooled the data to characterize the mutation pattern of TP53 in CLL. Two methods of mutational analysis (DHPLC exons 2–11 / FASAY assay) were used. We found 110 mutations in 106 patients with CLL. As expected, most mutations were located in the DNA binding domain of p53. Transitions were found in 54 of 110 mutations (9/110 at CpG sites), while transversions, small deletions and especially insertions were less common (33/110; 22/110; 1/110 resp.). Cytogenetics by FISH were available for 100/106 patients. Most mutations were accompanied by deletion of the other allele (17p-)(n=67). Nonetheless, TP53 mutations were also found in the good prognostic subgroups with normal karyotype (n=6) and 13q- as the sole abnormality (n=15). 17 patients with TP53 mutations had a mutated VH status vs. 79 with an unmutated VH status. We quite frequently observed a deletion 11q- (16/100), accompanying evenly the abnormalities of one as well as of both TP53 alleles (deletion/mutation). It indicates that this deletion may not be a simple alternative to p53 inactivation, as it has been proposed previously. Chemotherapy before mutation analysis was noted in 43/92 patients and was more frequent in those with aberration of one TP53 allele without reaching statistical significance (64% vs. 51% of previously treated patients bearing both inactivated alleles). The transitions, transversions and small deletions were evenly distributed among both untreated and treated patients. When comparing the predicted functional activity of the mutated TP53 in different cytogenetic subgroups (http://p53.free.fr/Database/p53_recomendations.html) we observed significantly lower residual activity of the missense mutations in the 17p- subgroup compared to the patients with 13q- (single) and a TP53 mutation (median 3,1 vs. 10,4 p=0,037). The codons most frequently mutated were at positions 209, 220, 234, suggesting that the classical hot spots (codons 175, 248, 273) may not be commonly mutated in CLL. The very low number of mutations which were identified at CpG dinucleotides implies a relatively negligible contribution of endogenous mutability at methylated cytosine. This is manifested also by a finding of only two mutations at the very prominent, heavily methylated hot-spot at position 248Arg. We assume that some other mechanisms of mutagenesis may play a relevant role in B-CLL. The current study characterizes the mutational profile of TP53 mutations in CLL. While the classical hot spot mutants were not observed at high frequencies we could identify 3 codons that made up for 12,7% of the mutations. The majority of mutations are accompanied by the inactivation of the other allele (deletion 17p). For the first time, the analysis of a large cohort of TP53 mutations will allow to investigate potential differences in the clinical course of monoallelic vs. biallelic aberrations of TP53.

scholarly journals DNMT3A Mutations in Acute Myeloid Leukemia

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. SCI-31-SCI-31
Author(s):  
Timothy J. Ley ◽  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
De Novo ◽  
Conflicts Of Interest ◽  
Myeloproliferative Neoplasms ◽  
Gene Expression Signature ◽  
Adverse Outcomes ◽  
Missense Mutations ◽  
Loss Of Function ◽  
Hematopoietic Stem

Abstract Abstract SCI-31 DNMT3A is one of the two human de novo methyltransferases; both are essential for methylating specific cytosine residues, a process that is critical for regulating gene expression during early development. In 2010, recurring mutations in DNMT3A were discovered in patients with AML (1, 2); mutations were not found in the other de novo methyltransferase (DNMT3B) or in the binding partner for both (DNMT3L). After discovering the first mutation by whole genome sequencing, we sequenced all of the exons of DNMT3A in 281 additional AML patients and found a total of 62 mutations (22% of all cases) in the gene that were predicted to affect translation. Eighteen different missense mutations were found, the most common of which was at amino acid R882 (37 patients). We identified six frameshift, six nonsense, and three splice site mutations, and also a 1.5 MB deletion that included the entire DNMT3A gene. DNMT3A mutations are highly enriched in patients with intermediate risk cytogenetics (56 of 166 patients, 33.7%) and were absent in 79 patients with favorable risk cytogenetics (p < 0.001 for both). In our series, DNMT3A mutations were independently associated with poor outcomes in multivariate analyses. Since the initial reports, DNMT3A mutations have been identified in ∼5%–10% of patients with myelodysplastic syndromes (3, 4), in 10%–20% of patients with myeloproliferative neoplasms and secondary AML (5), and in pediatric AML cases, but at much lower frequencies than adult AML (0%–1%) (6, 7). The adverse clinical outcomes associated with DNMT3A mutations have been confirmed by Yan et al (8) and by Thol et al (9). DNMT3A mutations are therefore among the most common in AML and other myeloid malignancies, and may be important for identifying patients with adverse outcomes. However, the mechanisms by which DNMT3A mutations influence AML pathogenesis are not yet clear. In our original study, we did not identify a clear gene expression signature associated with DNMT3A mutations, nor were we able to identify global or focal alterations in DNA methylation patterns that are clearly caused by the mutations. Yan et al (8) reported that DNMT3A mutations were associated with increased expression and hypomethylation of several HOXB genes, but this could not be validated with our data. Many important questions about DNMT3A mutations remain to be answered, including: 1) What are the relationships between DNMT3A mutations and other mutations that affect outcomes?, 2) Do DNMT3A mutations predict responses to hypomethylating agents or other regimens?, 3) Are the recurring mutations at R882 associated with a gain-of-function activity or do they act as dominant negatives?, and 4) Do the missense mutations alter methylase activity, DNA binding and/or methylation specificity, protein/protein interactions, or other (as yet unknown) functions of DNMT3A? Although the mechanism of action of DNMT3A mutations is currently unknown, Challen et al (10) noted that loss of Dnmt3a in the hematopoietic cells of mice caused a dramatic expansion of stem cells upon serial transplantation. These results strongly suggest that loss-of-function mutations in DNMT3A may affect the self-renewal properties of hematopoietic stem cells, which may be relevant for AML pathogenesis. Disclosures: No relevant conflicts of interest to declare.

Correlation of tumor mutational burden (TMB) with CDKN2A and TP53 mutation in HPV-negative head and neck squamous cell carcinoma (HNSCC).

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. 6552-6552 ◽  
Author(s):  
Barbara Burtness ◽  
Alexander Deneka ◽  
Yasmine Baca ◽  
Ilya Serebriiskii ◽  
Mitchell I. Parker ◽  
...  
Keyword(s):  
Oral Cavity ◽  
Tp53 Mutation ◽  
Predictive Biomarker ◽  
Dominant Negative ◽  
Alternative Methods ◽  
Missense Mutations ◽  
Loss Of Function ◽  
Tp53 Mutations ◽  
Cdkn2a Mutation ◽  
Mutational Status

6552 Background: The tumor suppressors TP53 and CDKN2A are commonly mutated or lost in HNSCC, impairing G1 checkpoints. This reduces ability to repair DNA damage arising from hypoxia, replication stress, and mutagen exposure, thus increasing TMB, a potential predictive biomarker for immunotherapy benefit. TP53 mutations can be classified as loss-of-function (LOF) with or without dominant negative (DNE) activity, gain-of-function (GOF) and benign. We investigated whether specific categories of TP53 mutation were associated with increased TMB, and whether these cooperated with CDKN2A mutation to elevate TMB. Methods: We analyzed 1010 HPV- HNSCC tumor samples (246 female) profiled with a 592-gene panel by Caris Life Sciences from 2015 to 2019. Predominant subsites were oral cavity (285), oropharynx (225) and larynx (153). TMB reflected all somatic nonsynonymous missense mutations detected. We report mean TMB per megabase (MB). Pathogenicity of TP53 and CDKN2A mutations was determined according to American College of Medical Genetics (ACMG) guidelines. We also used four alternative methods of characterizing TP53 mutations based on analysis of protein structure, public databases (IARC, ClinVar, InterVar), and publications (PMID: 25108461 and others) assessing structure-function relations. Results: 60% of cases had TP53 mutations ( TP53mut) designated pathogenic by ACMG guidelines. Estimates of frequency of LOF/DNE mutations ranged from 30-42.8% of cases among the alternative classification methods. Damaging CDKN2A mutations were present in 20%. Average TMB per MB varied from 8.2/8.6 (females/males) in oral cavity cancers to 26.5/27.7 (females/males) in cancer of the lip. Mean TMB was typically higher in the presence of damaging LOF/DNE TP53 mutations or CDKN2A mutations, but not TP53 GOF mutations. Based on ACMG, for tumors with TP53 and CDKN2A wild type (WT) TMB was 8.03, for those with CDKN2Amut-only 9.82, for TP53mut-only 10.56, and TP53 mut/CDKN2A mut 17.6 (p < 0.001). For disruptive TP53mut (Poeta algorithm), mean TMB for WT/WT was 8.67, for TP53mut 11.31, CDKN2Amut 17.9 and TP53mut/CDKN2A mut 15.83 (p < 0.001). Conclusions: Mutation of TP53 and/or CDKN2A is associated with increased mean TMB relative to WT; mean TMB was highest for tumors bearing damaging mutations in both genes. GOF TP53 mutation was not clearly associated with increased TMB. As TMB is evaluated as a predictive biomarker in the immunotherapy of HNSCC, specific TP53/CDKN2A mutational status should also be evaluated.

Mutation Spectrum in Patients with Wiskott-Aldrich Syndrome and X-linked Thrombocytopenia: Identification of Twelve Different Mutations in the WASP Gene

1996 ◽  
Vol 75 (04) ◽  
pp. 546-550 ◽  
Author(s):  
Marianne Schwartz ◽  
Albert Békássy ◽  
Mikael Donnér ◽  
Thomas Hertel ◽  
Stefan Hreidarson ◽  
...  
Keyword(s):  
Base Pair ◽  
Hot Spot ◽  
Missense Mutations ◽  
Nucleotide Substitutions ◽  
Exon 2 ◽  
Wiskott Aldrich Syndrome ◽  
Base Pair Deletion ◽  
Reliable Diagnosis ◽  
Wasp Gene ◽  
Detection Of Mutations

SummaryTwelve different mutations in the WASP gene were found in twelve unrelated families with Wiskott-Aldrich syndrome (WAS) or X-linked thrombocytopenia (XLT). Four frameshift, one splice, one nonsense mutation, and one 18-base-pair deletion were detected in seven patients with WAS. Only missense mutations were found in five patients diagnosed as having XLT. One of the nucleotide substitutions in exon 2 (codon 86) results in an Arg to Cys replacement. Two other nucleotide substitutions in this codon, R86L and R86H, have been reported previously, both giving rise to typical WAS symptoms, indicating a mutational hot spot in this codon. The finding of mutations in the WASP gene in both WAS and XLT gives further evidence of these syndromes being allelic. The relatively small size of the WASP gene facilitates the detection of mutations and a reliable diagnosis of both carriers and affected fetuses in families with WAS or XLT.

scholarly journals Alterations in ZnT1 expression and function lead to impaired intracellular zinc homeostasis in cancer

2019 ◽  
Vol 5 (1) ◽  
Author(s):  
Adrian Israel Lehvy ◽  
Guy Horev ◽  
Yarden Golan ◽  
Fabian Glaser ◽  
Yael Shammai ◽  
...  
Keyword(s):  
Malignant Tumors ◽  
Zinc Homeostasis ◽  
Healthy Population ◽  
Missense Mutations ◽  
Protein Alignment ◽  
Loss Of Function ◽  
Intracellular Zinc ◽  
Dismal Prognosis ◽  
Zinc Levels ◽  
And Function

Abstract Zinc is vital for the structure and function of ~3000 human proteins and hence plays key physiological roles. Consequently, impaired zinc homeostasis is associated with various human diseases including cancer. Intracellular zinc levels are tightly regulated by two families of zinc transporters: ZIPs and ZnTs; ZIPs import zinc into the cytosol from the extracellular milieu, or from the lumen of organelles into the cytoplasm. In contrast, the vast majority of ZnTs compartmentalize zinc within organelles, whereas the ubiquitously expressed ZnT1 is the sole zinc exporter. Herein, we explored the hypothesis that qualitative and quantitative alterations in ZnT1 activity impair cellular zinc homeostasis in cancer. Towards this end, we first used bioinformatics to analyze inactivating mutations in ZIPs and ZNTs, catalogued in the COSMIC and gnomAD databases, representing tumor specimens and healthy population controls, respectively. ZnT1, ZnT10, ZIP8, and ZIP10 showed extremely high rates of loss of function mutations in cancer as compared to healthy controls. Analysis of the putative functional impact of missense mutations in ZnT1-ZnT10 and ZIP1-ZIP14, using homologous protein alignment and structural predictions, revealed that ZnT1 displays a markedly increased frequency of predicted functionally deleterious mutations in malignant tumors, as compared to a healthy population. Furthermore, examination of ZnT1 expression in 30 cancer types in the TCGA database revealed five tumor types with significant ZnT1 overexpression, which predicted dismal prognosis for cancer patient survival. Novel functional zinc transport assays, which allowed for the indirect measurement of cytosolic zinc levels, established that wild type ZnT1 overexpression results in low intracellular zinc levels. In contrast, overexpression of predicted deleterious ZnT1 missense mutations did not reduce intracellular zinc levels, validating eight missense mutations as loss of function (LoF) mutations. Thus, alterations in ZnT1 expression and LoF mutations in ZnT1 provide a molecular mechanism for impaired zinc homeostasis in cancer formation and/or progression.

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