scholarly journals Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Young Seok Ju ◽  
Ludmil B Alexandrov ◽  
Moritz Gerstung ◽  
Inigo Martincorena ◽  
Serena Nik-Zainal ◽  
...  
Keyword(s):  
Human Cancer ◽  
Missense Mutations ◽  
Mtdna Mutations ◽  
Dna Mutations ◽  
Mtdna Sequence ◽  
Sequencing Studies ◽  
Functional Consequences ◽  
Somatic Alterations ◽  
Mtdna Replication ◽  
Tumor Types

Recent sequencing studies have extensively explored the somatic alterations present in the nuclear genomes of cancers. Although mitochondria control energy metabolism and apoptosis, the origins and impact of cancer-associated mutations in mtDNA are unclear. In this study, we analyzed somatic alterations in mtDNA from 1675 tumors. We identified 1907 somatic substitutions, which exhibited dramatic replicative strand bias, predominantly C > T and A > G on the mitochondrial heavy strand. This strand-asymmetric signature differs from those found in nuclear cancer genomes but matches the inferred germline process shaping primate mtDNA sequence content. A number of mtDNA mutations showed considerable heterogeneity across tumor types. Missense mutations were selectively neutral and often gradually drifted towards homoplasmy over time. In contrast, mutations resulting in protein truncation undergo negative selection and were almost exclusively heteroplasmic. Our findings indicate that the endogenous mutational mechanism has far greater impact than any other external mutagens in mitochondria and is fundamentally linked to mtDNA replication.

scholarly journals Concerted action of two novel tRNA mtDNA point mutations in chronic progressive external ophthalmoplegia

2008 ◽  
Vol 28 (2) ◽  
pp. 89-96 ◽  
Author(s):  
Cornelia Kornblum ◽  
Gábor Zsurka ◽  
Rudolf J. Wiesner ◽  
Rolf Schröder ◽  
Wolfram S. Kunz
Keyword(s):  
Skeletal Muscle ◽  
Northern Blot ◽  
Phenotypic Expression ◽  
Point Mutations ◽  
Skeletal Muscle Fibre ◽  
Progressive External Ophthalmoplegia ◽  
Chronic Progressive External Ophthalmoplegia ◽  
Mtdna Mutations ◽  
Mtdna Sequence ◽  
Functional Consequences

CPEO (chronic progressive external ophthalmoplegia) is a common mitochondrial disease phenotype in adults which is due to mtDNA (mitochondrial DNA) point mutations in a subset of patients. Attributing pathogenicity to novel tRNA mtDNA mutations still poses a challenge, particularly when several mtDNA sequence variants are present. In the present study we report a CPEO patient for whom sequencing of the mitochondrial genome revealed three novel tRNA mtDNA mutations: G5835A, del4315A, T1658C in tRNATyr, tRNAIle and tRNAVal genes. In skeletal muscle, the tRNAVal and tRNAIle mutations were homoplasmic, whereas the tRNATyr mutation was heteroplasmic. To address the pathogenic relevance, we performed two types of functional tests: (i) single skeletal muscle fibre analysis comparing G5835A mutation loads and biochemical phenotypes of corresponding fibres, and (ii) Northern-blot analyses of mitochondrial tRNATyr, tRNAIle and tRNAVal. We demonstrated that both the G5835A tRNATyr and del4315A tRNAIle mutation have serious functional consequences. Single-fibre analyses displayed a high threshold of the tRNATyr mutation load for biochemical phenotypic expression at the single-cell level, indicating a rather mild pathogenic effect. In contrast, skeletal muscle tissue showed a severe decrease in respiratory-chain activities, a reduced overall COX (cytochrome c oxidase) staining intensity and abundant COX-negative fibres. Northern-blot analyses showed a dramatic reduction of tRNATyr and tRNAIle levels in muscle, with impaired charging of tRNAIle, whereas tRNAVal levels were only slightly decreased, with amino-acylation unaffected. Our findings suggest that the heteroplasmic tRNATyr and homoplasmic tRNAIle mutation act together, resulting in a concerted effect on the biochemical and histological phenotype. Thus homoplasmic mutations may influence the functional consequences of pathogenic heteroplasmic mtDNA mutations.

scholarly journals Author response: Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer

2014 ◽  
Author(s):  
Young Seok Ju ◽  
Ludmil B Alexandrov ◽  
Moritz Gerstung ◽  
Inigo Martincorena ◽  
Serena Nik-Zainal ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Human Cancer ◽  
Author Response ◽  
Mitochondrial Dna Mutations ◽  
Dna Mutations ◽  
Functional Consequences

scholarly journals AI-Driver: an ensemble method for identifying driver mutations in personal cancer genomes

2020 ◽  
Vol 2 (4) ◽  
Author(s):  
Haoxuan Wang ◽  
Tao Wang ◽  
Xiaolu Zhao ◽  
Honghu Wu ◽  
Mingcong You ◽  
...  
Keyword(s):  
Human Cancer ◽  
Ensemble Method ◽  
Driver Mutations ◽  
Missense Mutations ◽  
Gene Level ◽  
Cancer Genomes ◽  
Sequencing Studies ◽  
Stable Performance ◽  
Overall Performance ◽  
Improved Methods

Abstract The current challenge in cancer research is to increase the resolution of driver prediction from gene-level to mutation-level, which is more closely aligned with the goal of precision cancer medicine. Improved methods to distinguish drivers from passengers are urgently needed to dig out driver mutations from increasing exome sequencing studies. Here, we developed an ensemble method, AI-Driver (AI-based driver classifier, https://github.com/hatchetProject/AI-Driver), to predict the driver status of somatic missense mutations based on 23 pathogenicity features. AI-Driver has the best overall performance compared with any individual tool and two cancer-specific driver predicting methods. We demonstrate the superior and stable performance of our model using four independent benchmarks. We provide pre-computed AI-Driver scores for all possible human missense variants (http://aidriver.maolab.org/) to identify driver mutations in the sea of somatic mutations discovered by personal cancer sequencing. We believe that AI-Driver together with pre-computed database will play vital important roles in the human cancer studies, such as identification of driver mutation in personal cancer genomes, discovery of targeting sites for cancer therapeutic treatments and prediction of tumor biomarkers for early diagnosis by liquid biopsy.

scholarly journals Mammalian SWI/SNF chromatin remodeling complexes and cancer: Mechanistic insights gained from human genomics

2015 ◽  
Vol 1 (5) ◽  
pp. e1500447 ◽  
Author(s):  
Cigall Kadoch ◽  
Gerald R. Crabtree
Keyword(s):  
Chromatin Remodeling ◽  
Human Cancer ◽  
Human Genomics ◽  
Chromatin Remodelers ◽  
Fundamental Process ◽  
Sequencing Studies ◽  
Genes Encoding ◽  
Chromatin Remodeling Complexes ◽  
Tumor Types ◽  
Oncogenic Function

Over the past 4 years, nearly 100 exome sequencing studies have revealed the high frequency of mutations in the genes encoding the subunits of ATP-dependent chromatin remodelers in human cancer. Most of these mutations are within the genes encoding subunits of the BAF (Brg/Brahma-associated factors) or mSWI/SNF complex, which is one of two dozen predicted ATP-dependent chromatin remodeling complexes in mammals. Considering BAF complexes as a single entity, the 15 subunits encoded by 29 genes are mutated in >20% of human cancer, across a broad range of tumor types. These observations demonstrate that there is little redundancy in the oncogenic function of BAF complexes with the other remodeling complexes, underscoring their unique roles. Several important conclusions emerge from these genomic data: specific subunits appear to be mutated in specific cancers, highlighting tissue-specific protective roles; mutations can function as tumor suppressors or oncogenes; mutations can be homozygous or, more commonly, heterozygous, implying their dosage-sensitive roles in an unknown yet fundamental process used to suppress the genesis of cancer. These new human genetic findings paired with biochemical studies are challenging old ideas on how chromatin remodeling complexes function, generating new hypotheses with respect to their normal and oncogenic mechanisms and highlighting potential avenues for therapeutic intervention in human cancer.

Do mitochondrial DNA mutations play the key role in chronification of sterile inflammation? Special focus on atherosclerosis

2020 ◽  
Vol 26 ◽  
Author(s):  
Alexander N. Orekhov ◽  
Elena V. Gerasimova ◽  
Vasily N. Sukhorukov ◽  
Anastasia V. Poznyak ◽  
Nikita G. Nikiforov
Keyword(s):  
Innate Immunity ◽  
Mitochondrial Dna ◽  
Low Density Lipoprotein ◽  
Atherosclerotic Lesion ◽  
Density Lipoprotein ◽  
Sterile Inflammation ◽  
Special Focus ◽  
Mitochondrial Dysfunctions ◽  
Mtdna Mutations ◽  
Dna Mutations

Background: The elucidation of mechanisms implicated in the chronification of inflammation is able to shed the light on the pathogenesis of disorders that are responsible for the majority of the incidence of disease and deaths, and also causes of ageing. Atherosclerosis is an example of the most significant inflammatory pathology. The inflammatory response of innate immunity is implicated in the development of atherosclerosis arising locally or focally. Modified low-density lipoprotein (LDL) was regarded as the trigger for this response. No atherosclerotic changes in the arterial wall occur due to the quick decrease in inflammation rate. Nonetheless, the atherosclerotic lesion formation can be a result of the chronification of local inflammation, which, in turn, is caused by alteration of the response of innate immunity. Objective: In this review, we discussed potential mechanisms of the altered response of the immunity in atherosclerosis with a particular emphasis on mitochondrial dysfunctions. Conclusion: A few mitochondrial dysfunctions can be caused by the mitochondrial DNA (mtDNA) mutations. Moreover, mtDNA mutations were found to affect the development of defective mitophagy. Modern investigations have demonstrated the controlling mitophagy function in the response of the immune system. Therefore, we hypothesized that impaired mitophagy, as a consequence of mutations in mtDNA, can raise a disturbed innate immunity response resulting in the chronification of inflammation in atherosclerosis.

scholarly journals Prediction of Functional Consequences of Missense Mutations in ANO4 Gene

2021 ◽  
Vol 22 (5) ◽  
pp. 2732
Author(s):  
Nadine Reichhart ◽  
Vladimir M. Milenkovic ◽  
Christian H. Wetzel ◽  
Olaf Strauß
Keyword(s):  
Transmembrane Protein ◽  
Functional Characterization ◽  
Missense Mutations ◽  
Mutant Proteins ◽  
Functional Consequences ◽  
New Perspective ◽  
The Stability ◽  
Dynamics Simulations ◽  
And Function

The anoctamin (TMEM16) family of transmembrane protein consists of ten members in vertebrates, which act as Ca2+-dependent ion channels and/or Ca2+-dependent scramblases. ANO4 which is primarily expressed in the CNS and certain endocrine glands, has been associated with various neuronal disorders. Therefore, we focused our study on prioritizing missense mutations that are assumed to alter the structure and stability of ANO4 protein. We employed a wide array of evolution and structure based in silico prediction methods to identify potentially deleterious missense mutations in the ANO4 gene. Identified pathogenic mutations were then mapped to the modeled human ANO4 structure and the effects of missense mutations were studied on the atomic level using molecular dynamics simulations. Our data show that the G80A and A500T mutations significantly alter the stability of the mutant proteins, thus providing new perspective on the role of missense mutations in ANO4 gene. Results obtained in this study may help to identify disease associated mutations which affect ANO4 protein structure and function and might facilitate future functional characterization of ANO4.

scholarly journals FBXW7 mutations reduce binding of NOTCH1, leading to cleaved NOTCH1 accumulation and target gene activation in CLL

Blood ◽  
2019 ◽  
Vol 133 (8) ◽  
pp. 830-839 ◽  
Author(s):  
Viola Close ◽  
William Close ◽  
Sabrina Julia Kugler ◽  
Michaela Reichenzeller ◽  
Deyan Yordanov Yosifov ◽  
...  
Keyword(s):  
Target Gene ◽  
Hypoxia Inducible Factor ◽  
Gene Activation ◽  
Lymphocytic Leukemia ◽  
Negative Regulator ◽  
Missense Mutations ◽  
Protein Levels ◽  
In Silico Modeling ◽  
Functional Consequences ◽  
Wd40 Domain

Abstract NOTCH1 is mutated in 10% of chronic lymphocytic leukemia (CLL) patients and is associated with poor outcome. However, NOTCH1 activation is identified in approximately one-half of CLL cases even in the absence of NOTCH1 mutations. Hence, there appear to be additional factors responsible for the impairment of NOTCH1 degradation. E3-ubiquitin ligase F-box and WD40 repeat domain containing-7 (FBXW7), a negative regulator of NOTCH1, is mutated in 2% to 6% of CLL patients. The functional consequences of these mutations in CLL are unknown. We found heterozygous FBXW7 mutations in 36 of 905 (4%) untreated CLL patients. The majority were missense mutations (78%) that mostly affected the WD40 substrate binding domain; 10% of mutations occurred in the first exon of the α-isoform. To identify target proteins of FBXW7 in CLL, we truncated the WD40 domain in CLL cell line HG-3 via clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein-9 (Cas9). Homozygous truncation of FBXW7 resulted in an increase of activated NOTCH1 intracellular domain (NICD) and c-MYC protein levels as well as elevated hypoxia-inducible factor 1-α activity. In silico modeling predicted that novel mutations G423V and W425C in the FBXW7-WD40 domain change the binding of protein substrates. This differential binding was confirmed via coimmunoprecipitation of overexpressed FBXW7 and NOTCH1. In primary CLL cells harboring FBXW7 mutations, activated NICD levels were increased and remained stable upon translation inhibition. FBXW7 mutations coincided with an increase in NOTCH1 target gene expression and explain a proportion of patients characterized by dysregulated NOTCH1 signaling.

scholarly journals Functional consequences of the first reported mutations of the proto-oncogene PTTG1IP/PBF

2017 ◽  
Vol 24 (9) ◽  
pp. 459-474 ◽  
Author(s):  
W Imruetaicharoenchoke ◽  
A Fletcher ◽  
W Lu ◽  
R J Watkins ◽  
B Modasia ◽  
...  
Keyword(s):  
Colony Formation ◽  
Human Cancer ◽  
Soft Agar ◽  
Cellular Migration ◽  
3T3 Fibroblasts ◽  
Wide Range ◽  
Functional Consequences ◽  
Altered Cell ◽  
Proliferation Assays ◽  
Nih 3T3

Pituitary tumor-transforming gene 1-binding factor (PTTG1IP; PBF) is a multifunctional glycoprotein, which is overexpressed in a wide range of tumours, and significantly associated with poorer oncological outcomes, such as early tumour recurrence, distant metastasis, extramural vascular invasion and decreased disease-specific survival. PBF transforms NIH 3T3 fibroblasts and induces tumours in nude mice, while mice harbouring transgenic thyroidal PBF expression show hyperplasia and macrofollicular lesions. Our assumption that PBF becomes an oncogene purely through increased expression has been challenged by the recent report of mutations in PBF within the Catalogue of Somatic Mutations in Cancer (COSMIC) database. We therefore sought to determine whether the first 10 PBF missense substitutions in human cancer might be oncogenic. Anisomycin half-life studies revealed that most mutations were associated with reduced protein stability compared to wild-type (WT) PBF. Proliferation assays narrowed our interest to two mutational events which significantly altered cell turnover: C51R and R140W. C51R was mainly confined to the endoplasmic reticulum while R140W was apparent in the Golgi apparatus. Both C51R and R140W lost the capacity to induce cellular migration and significantly reduced cell invasion. Colony formation and soft agar assays demonstrated that, in contrast to WT PBF, both mutants were unable to elicit significant colony formation or anchorage-independent growth. However, C51R and R140W retained the ability to repress radioiodide uptake, a functional hallmark of PBF. Our data reveal new insight into PBF function and confirm that, rather than being oncogenic, mutations in PBF are likely to be passenger effects, with overexpression of PBF the more important aetiological event in human cancer.

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