Somatic mutations in miRNA genes in lung cancer – potential functional consequences of non-coding sequence variants

AbstractA growing body of evidence indicates that miRNAs may either drive or suppress oncogenesis. However, little is known about somatic mutations in miRNA genes. To determine the frequency and potential consequences of miRNA gene mutations, we analyzed whole exome sequencing datasets of ∼500 lung adenocarcinoma (LUAD) and ∼500 lung squamous cell carcinoma (LUSC) samples generated in the TCGA. Altogether, we identified >1000 mutations affecting ∼500 different miRNA genes and showed that half of all cancers had at least one such mutation. Mutations occurred in most crucial parts of miRNA precursors, including mature miRNA and seed sequences. We showed that seed mutations strongly affected miRNA:target interactions, drastically changing the pool of predicted targets. Mutations may also affect miRNA biogenesis by changing the structure of miRNA precursors, DROSHA and DICER cleavage sites, and regulatory sequence/structure motifs. We identified 10 significantly overmutated hotspot miRNA genes, including themiR-379gene in LUAD enriched in mutations in the mature miRNA and regulatory sequences. The occurrence of mutations in the hotspot miRNA genes was also shown experimentally. We present a comprehensive analysis of somatic mutations in miRNA genes and show that some of these genes are mutational hotspots, suggesting their potential role in cancer.

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Somatic Mutations in miRNA Genes in Lung Cancer—Potential Functional Consequences of Non-Coding Sequence Variants

Cancers ◽

10.3390/cancers11060793 ◽

2019 ◽

Vol 11 (6) ◽

pp. 793 ◽

Cited By ~ 10

Author(s):

Paulina Galka-Marciniak ◽

Martyna Olga Urbanek-Trzeciak ◽

Paulina Maria Nawrocka ◽

Agata Dutkiewicz ◽

Maciej Giefing ◽

...

Keyword(s):

Somatic Mutations ◽

Mirna Gene ◽

Lung Squamous Cell Carcinoma ◽

The Cancer Genome Atlas ◽

Mirna Biogenesis ◽

Regulatory Sequence ◽

Regulatory Sequences ◽

Sequence Variants ◽

Mirna Genes ◽

Mutational Hotspots

A growing body of evidence indicates that miRNAs may either drive or suppress oncogenesis. However, little is known about somatic mutations in miRNA genes. To determine the frequency and potential consequences of miRNA gene mutations, we analyzed whole exome sequencing datasets of 569 lung adenocarcinoma (LUAD) and 597 lung squamous cell carcinoma (LUSC) samples generated in The Cancer Genome Atlas (TCGA) project. Altogether, we identified 1091 somatic sequence variants affecting 522 different miRNA genes and showed that half of all cancers had at least one such somatic variant/mutation. These sequence variants occurred in most crucial parts of miRNA precursors, including mature miRNA and seed sequences. Due to our findings, we hypothesize that seed mutations may affect miRNA:target interactions, drastically changing the pool of predicted targets. Mutations may also affect miRNA biogenesis by changing the structure of miRNA precursors, DROSHA and DICER cleavage sites, and regulatory sequence/structure motifs. We identified 10 significantly overmutated hotspot miRNA genes, including the miR-379 gene in LUAD enriched in mutations in the mature miRNA and regulatory sequences. The occurrence of mutations in the hotspot miRNA genes was also shown experimentally. We present a comprehensive analysis of somatic variants in miRNA genes and show that some of these genes are mutational hotspots, suggesting their potential role in cancer.

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Two pathogenic mutations located within the 5'-regulatory sequence of the GJB1 gene affecting initiation of transcription and translation.

Acta Biochimica Polonica ◽

10.18388/abp.2011_2247 ◽

2011 ◽

Vol 58 (3) ◽

Cited By ~ 9

Author(s):

Dagmara Kabzińska ◽

Katarzyna Kotruchow ◽

Barbara Ryniewicz ◽

Andrzej Kochański

Keyword(s):

Genetic Disorders ◽

Gene Mutations ◽

European Population ◽

Regulatory Sequence ◽

Regulatory Sequences ◽

Entry Site ◽

Charcot Marie Tooth ◽

Charcot Marie Tooth Disease ◽

Pathogenic Mutations ◽

Initiation Of Translation

In contrast to mutations in the coding sequences of a genes involved in the pathogenesis of Charcot-Marie-Tooth disease (CMT), little is known about CMT phenotypes resulting from a DNA variants located in regulatory sequences of a given " CMT gene". Charcot-Marie-Tooth type X1 disease (CMTX1) is caused by mutations in the GJB1 gene coding for an ion channel known as connexin, with a molecular mass of 32 kDa (Cx32). Only 0.01% of the GJB1 gene mutations have been reported in its 5' regulatory sequence. Pathogenic mutations occured in the internal ribosome entry site (IRES) are extremely rarely reported in human genetic disorders. To the best of our knowledge, in this study we report for the first time in an Eastern European population, two CMTX1 families in which two pathogenic mutations in the 5' regulatory sequence of the GJB1 gene (c.-529T>C and -459C>T) have been found. The two mutations identified in our study disturb the 5' UTR sequence in two different ways, by affecting the transcription factor SOX10 binding site (c.-529T>C) and by the disrupting IRES element of GJB1 gene (c.-459C>T). These regions are responsible for transcription (SOX10) and initiation of translation (IRES), respectively. On the basis of our findings that, in contrast to the most DNA sequence variants reported in untranslated regulatory regions of genes, the c.-459C>T and c.-529T>C mutations remain pathogenic in the context of different ethnic background.

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High-Resolution Comparative Genomic Hybridization of Mirna Genes In Therapy-Related AML Identifies a Somatic Deletion of MiR-223

Blood ◽

10.1182/blood.v116.21.2759.2759 ◽

2010 ◽

Vol 116 (21) ◽

pp. 2759-2759

Author(s):

Giridharan Ramsingh ◽

Angela Matson ◽

Matthew J. Walter ◽

Daniel C. Link

Keyword(s):

Gene Expression ◽

High Resolution ◽

Copy Number ◽

Genomic Dna ◽

Mirna Gene ◽

Gene Mutations ◽

Epigenetic Silencing ◽

Comparative Genomic ◽

Copy Number Alterations ◽

Mirna Genes

Abstract Abstract 2759 MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression and diverse cellular processes. Expression profiling of miRNAs has identified dysregulated miRNAs in many cancers, including acute myeloid leukemia (AML). However, the mechanism for altered miRNA gene expression and the frequency of miRNA gene mutations in AML is largely unknown. We performed next-generation sequencing and high-resolution comparative genomic hybridization (CGH) to determine the frequency of miRNA gene mutations in 30 patients with therapy-related AML (t-AML). The sequencing is completed, and final analysis is underway. Herein, we report the results of the CGH. We designed custom CGH arrays for all 835 miRNA genes in miRBase (version 14) and 44 genes involved in miRNA processing. Average probe spacing was 30 bp for miRNA genes and 80 bp for miRNA processing genes and 10 kb flanking regions were interrogated for all genes. In each case, genomic DNA from leukemic blasts was compared with DNA from a skin biopsy from that patient. The median age of the 30 patients with t-AML was 49.2 years (25-77) with M:F ratio 13:17. The mean blast % was 81% (31-100). Consistent with previous reports, many of these patients had an abnormal karyotype with abnormalities of chromosome 5 and 7, 13% and 17% respectively. As expected, CGH analysis confirmed copy number alterations already identified by cytogenetics. In addition, we identified a single t-AML sample (from a male patient) that carried a small (435 kb) hemizygous deletion of miR-223 on chromosome × that was not apparent by cytogenetics. Quantitative PCR of genomic DNA confirmed the loss of the miR-223 gene, and real time RT-PCR demonstrated loss of miR-223 expression. Of note, miR-223 has been implicated in the regulation of granulopoiesis, and mice lacking miR-223 display a myeloproliferative phenotype (Johnnidis, Nature 2008). We screened an additional 27 AML patients for miR-223 expression and identified 3 other samples with miR-223 expression 2 standard deviations below the normal (based on CD34+ cells from healthy donors). No copy number alterations in miR-223 were detected in these patients, suggesting epigenetic silencing of miR-223. Consistent with this possibility, one of these patients carried a t(8;21), which has been shown to epigenetically silence miR-223 (Fazi, Cancer Cell 2007). The mechanism by which miR-223 is silenced in the other two AML samples is under investigation. In summary, cytogenetically silent deletions of miRNA genes are uncommon in t-AML. Loss of miR-223 expression can occur through somatic mutation or epigenetic silencing and is likely to contribute to leukemic transformation in a subset of patients with AML. Disclosures: No relevant conflicts of interest to declare.

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Abstract 057: Cellular and Genetic Causes of Idiopathic Hyperaldosteronism

Hypertension ◽

10.1161/hyp.70.suppl_1.057 ◽

2017 ◽

Vol 70 (suppl_1) ◽

Author(s):

Kei Omata ◽

Fumitoshi Satoh ◽

Ryo Morimoto ◽

Sadayoshi Ito ◽

Yuto Yamazaki ◽

...

Keyword(s):

Somatic Mutations ◽

Clinical Manifestations ◽

Gene Mutations ◽

Median Number ◽

Zona Glomerulosa ◽

Potential Contribution ◽

Unilateral Adrenalectomy ◽

Aldosterone Synthase ◽

Formalin Fixed Paraffin Embedded ◽

Idiopathic Hyperaldosteronism

Background: Primary aldosteronism (PA) affects ~10% of hypertensive patients and has unilateral and bilateral forms (30%:70%). Unilateral PA is caused by aldosterone-producing adenomas (APA), which express CYP11B2 (aldosterone synthase) and frequently harbor somatic mutations in aldosterone regulating genes ( KCNJ5>>CACNA1D ). We recently demonstrated that adrenals from normotensive patients present with pockets of cell expressing aldosterone synthase (CYP11B2). These aldosterone-producing foci (APF) have somatic gene mutations similar to those found in APA ( CACNA1D >> KCNJ5 ). Bilateral PA, which is typically treated by mineralocorticoid receptor (MR) blockade rather than surgery, is termed idiopathic hyperaldosteronism (IHA). Its pathobiology is largely unknown but has been thought to be due to zona glomerulosa (ZG) hyperplasia. Methods: We studied 11 IHA patients (7 males, 4 females) who had unilateral adrenalectomy. Immunohistochemistry for CYP11B2 and next generation sequencing (NGS) targeting genes found in APA were performed on formalin fixed paraffin embedded adrenal tissue. Results were compared to previously described cohorts of 53 age-matched normotensive patients (29 males, 24 females) which were evaluated similarly. Results: CYP11B2 expression was absent from intervening ZG cells in 8/11 (73%) IHA adrenals, but all adrenals harbored at least one APF. The median number and size of APF per case were significantly larger in IHA than normotensive controls (6.1 vs 0 APF/cm 2 of adrenal cortex and 0.25 vs. 0.16 mm 2 , respectively; p<0.0001 and p<0.006). In this IHA cohort, NGS identified CACNA1D and KCNJ5 somatic mutations in 44/71 (62%) and 1/71 (1%) of APF, respectively. Interpretations. Diffuse CYP11B2 expression in adrenal ZG cells was only observed in 3/11 IHA cases, arguing against ZG hyperplasia as the major underlying pathobiology. Rather, we demonstrated increased and enlarged APF in IHA adrenals compared to normotensive controls, supporting potential contribution to the clinical manifestations of hyperaldosteronism. The frequent occurrence of aldosterone-dysregulating CACNA1D somatic mutations in APF support CACNA1D as a potential therapeutic target in IHA to complement current MR blockade approaches.

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Analysis, identification and visualization of subgroups in genomics

Briefings in Bioinformatics ◽

10.1093/bib/bbaa217 ◽

2020 ◽

Author(s):

Gunnar Völkel ◽

Simon Laban ◽

Axel Fürstberger ◽

Silke D Kühlwein ◽

Nensi Ikonomi ◽

...

Keyword(s):

Large Scale ◽

Somatic Mutations ◽

Target Selection ◽

Gene Mutations ◽

Use Case ◽

The Past ◽

Wide Availability ◽

Approaches To Study ◽

User Friendly ◽

Personalized Intervention

Abstract Motivation Cancer is a complex and heterogeneous disease involving multiple somatic mutations that accumulate during its progression. In the past years, the wide availability of genomic data from patients’ samples opened new perspectives in the analysis of gene mutations and alterations. Hence, visualizing and further identifying genes mutated in massive sets of patients are nowadays a critical task that sheds light on more personalized intervention approaches. Results Here, we extensively review existing tools for visualization and analysis of alteration data. We compare different approaches to study mutual exclusivity and sample coverage in large-scale omics data. We complement our review with the standalone software AVAtar (‘analysis and visualization of alteration data’) that integrates diverse aspects known from different tools into a comprehensive platform. AVAtar supplements customizable alteration plots by a multi-objective evolutionary algorithm for subset identification and provides an innovative and user-friendly interface for the evaluation of concurrent solutions. A use case from personalized medicine demonstrates its unique features showing an application on vaccination target selection. Availability AVAtar is available at: https://github.com/sysbio-bioinf/avatar Contact [email protected], phone: +49 (0) 731 500 24 500, fax: +49 (0) 731 500 24 502

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Molecular and Other Novel Advances in Treatment of Metastatic Epithelial and Medullary Thyroid Cancers

Journal of Oncology ◽

10.1155/2010/398564 ◽

2010 ◽

Vol 2010 ◽

pp. 1-7 ◽

Cited By ~ 6

Author(s):

David Tai ◽

Donald Poon

Keyword(s):

Tumor Suppressor Genes ◽

Somatic Mutations ◽

Gene Mutations ◽

C Cells ◽

Therapeutic Approaches ◽

Thyroid Cancers ◽

Medullary Thyroid ◽

Genetic Abnormalities ◽

Pathologic Findings ◽

Inherited Mutations

An understanding of the mutations of the proto-oncogenes and tumor suppressor genes that occur in thyroid cancers should eventually explain the diverse clinical characteristics of these tumors and also direct therapy. Some insights have already emerged in the last decade; some abnormalities in tumor genes are consistently associated with specific clinical and pathologic findings. These genetic abnormalities usually represent somatic mutations in tumors of follicular epithelial origin, as opposed to inherited mutations in medullary thyroid cancers of parafollicular C cells origin because most thyroid tumors are sporadic and not familial. This is different from the multiple endocrine neoplasia syndromes in which the primary tumorigenic gene mutations are inherited. This improved understanding of the molecular basis of these diseases has led to the development of novel targeted therapeutic approaches which will be discussed in this paper.

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Clonal haematopoiesis in chronic ischaemic heart failure: prognostic role of clone size for DNMT3A- and TET2-driver gene mutations

European Heart Journal ◽

10.1093/eurheartj/ehaa845 ◽

2020 ◽

Cited By ~ 1

Author(s):

Birgit Assmus ◽

Sebastian Cremer ◽

Klara Kirschbaum ◽

David Culmann ◽

Katharina Kiefer ◽

...

Keyword(s):

Heart Failure ◽

Somatic Mutations ◽

Prognostic Significance ◽

Gene Mutations ◽

Amplicon Sequencing ◽

Driver Mutations ◽

Driver Gene ◽

Roc Curve Analysis ◽

Driver Genes ◽

Clone Size

Abstract Aims Somatic mutations of the epigenetic regulators DNMT3A and TET2 causing clonal expansion of haematopoietic cells (clonal haematopoiesis; CH) were shown to be associated with poor prognosis in chronic ischaemic heart failure (CHF). The aim of our analysis was to define a threshold of variant allele frequency (VAF) for the prognostic significance of CH in CHF. Methods and results We analysed bone marrow and peripheral blood-derived cells from 419 patients with CHF by error-corrected amplicon sequencing. Cut-off VAFs were optimized by maximizing sensitivity plus specificity from a time-dependent receiver operating characteristic (ROC) curve analysis from censored data. 56.2% of patients were carriers of a DNMT3A- (N = 173) or a TET2- (N = 113) mutation with a VAF >0.5%, with 59 patients harbouring mutations in both genes. Survival ROC analyses revealed an optimized cut-off value of 0.73% for TET2- and 1.15% for DNMT3A-CH-driver mutations. Five-year-mortality was 18% in patients without any detected DNMT3A- or TET2 mutation (VAF < 0.5%), 29% with only one DNMT3A- or TET2-CH-driver mutations above the respective cut-off level and 42% in patients harbouring both DNMT3A- and TET2-CH-driver mutations above the respective cut-off levels. In carriers of a DNMT3A mutation with VAF ≥ 1.15%, 5-year mortality was 31%, compared with 18% mortality in those with VAF < 1.15% (P = 0.048). Likewise, in patients with TET2 mutations, 5-year mortality was 32% with VAF ≥ 0.73%, compared with 19% mortality with VAF < 0.73% (P = 0.029). Conclusion The present study defines novel threshold levels for clone size caused by acquired somatic mutations in the CH-driver genes DNMT3A and TET2 that are associated with worse outcome in patients with CHF.

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Pan-cancer analysis of somatic mutations in miRNA genes

EBioMedicine ◽

10.1016/j.ebiom.2020.103051 ◽

2020 ◽

Vol 61 ◽

pp. 103051 ◽

Cited By ~ 1

Author(s):

Martyna O. Urbanek-Trzeciak ◽

Paulina Galka-Marciniak ◽

Paulina M. Nawrocka ◽

Ewelina Kowal ◽

Sylwia Szwec ◽

...

Keyword(s):

Somatic Mutations ◽

Mirna Genes ◽

Pan Cancer

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Transcriptional repression of microRNA genes by PML-RARA increases expression of key cancer proteins in acute promyelocytic leukemia

Blood ◽

10.1182/blood-2008-05-158139 ◽

2009 ◽

Vol 113 (2) ◽

pp. 412-421 ◽

Cited By ~ 77

Author(s):

Anne Saumet ◽

Guillaume Vetter ◽

Manuella Bouttier ◽

Elodie Portales-Casamar ◽

Wyeth W. Wasserman ◽

...

Keyword(s):

Retinoic Acid ◽

Acute Promyelocytic Leukemia ◽

Transcriptional Repression ◽

Promyelocytic Leukemia ◽

Mirna Biogenesis ◽

Cell Physiology ◽

Small Noncoding Rnas ◽

Mirna Genes ◽

All Trans Retinoic Acid ◽

Key Aspects

Abstract Micro(mi)RNAs are small noncoding RNAs that orchestrate many key aspects of cell physiology and their deregulation is often linked to distinct diseases including cancer. Here, we studied the contribution of miRNAs in a well-characterized human myeloid leukemia, acute promyelocytic leukemia (APL), targeted by retinoic acid and trioxide arsenic therapy. We identified several miRNAs transcriptionally repressed by the APL-associated PML-RAR oncogene which are released after treatment with all-trans retinoic acid. These coregulated miRNAs were found to control, in a coordinated manner, crucial pathways linked to leukemogenesis, such as HOX proteins and cell adhesion molecules whose expressions are thereby repressed by the chemotherapy. Thus, APL appears linked to transcriptional perturbation of miRNA genes, and clinical protocols able to successfully eradicate cancer cells may do so by restoring miRNA expression. The identification of abnormal miRNA biogenesis in cancer may therefore provide novel biomarkers and therapeutic targets in myeloid leukemias.

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Genomic Instability Signature of Palindromic Non-Coding Somatic Mutations in Bladder Cancer

Cancers ◽

10.3390/cancers12102882 ◽

2020 ◽

Vol 12 (10) ◽

pp. 2882

Author(s):

Sophie Vacher ◽

Voreak Suybeng ◽

Elodie Girard ◽

Julien Masliah Planchon ◽

Grégory Thomson ◽

...

Keyword(s):

Bladder Cancer ◽

Cancer Patients ◽

Genomic Instability ◽

Somatic Mutations ◽

Bladder Tumors ◽

Protein Coding ◽

Core Motif ◽

Expression Levels ◽

Mutational Hotspots ◽

Palindromic Sequences

Numerous pan-genomic studies identified alterations in protein-coding genes and signaling pathways involved in bladder carcinogenesis, while non-coding somatic alterations remain weakly explored. The goal of this study was to identify clinical biomarkers in non-coding regions for bladder cancer patients. We have previously identified in bladder tumors two non-coding mutational hotspots occurring at high frequencies (≥30%). These mutations are located close to the GPR126 and PLEKHS1 genes, at the guanine or the cytosine of a TGAACA core motif flanked, on both sides, by a stretch of palindromic sequences. Here, we hypothesize that such a pattern of recurrent non-coding mutations could be a signature of somatic genomic instability specifically involved in bladder cancer. We analyzed 26 additional mutable non-coding sites with the same core motif in a cohort of 103 bladder cancers composed of 44 NMIBC cases and 59 MIBC cases using high-resolution melting (HRM) and Sanger sequencing. Five bladder cancers were additionally analyzed for protein-coding gene mutations using a targeted NGS panel composed of 571 genes. Expression levels of three members of the APOBEC3 family genes were assessed using real-time quantitative RT-PCR. Non-coding somatic mutations were observed for at least one TGAACA core motif locus in 62.1% (64/103) of bladder tumor samples. These non-coding mutations co-occurred in the bladder tumors but were absent in prostate tumor, HPV-positive Head and Neck Squamous Cell Carcinoma, and high microsatellite instability (MSI-H) colorectal tumor series. This signature of palindromic non-coding somatic mutations, specific to bladder tumors, was not associated with patients’ outcome and was more frequent in females. Interestingly, this signature was associated with high tumor mutational burden (TMB) and high expression levels of APOBEC3B and interferon inducible genes. We identified a new type of somatic genomic instability targeting the TGAACA core motif loci flanked by palindromic sequences in bladder cancer. This mutational signature is a promising candidate clinical biomarker for the early detection of relapse and a major low-cost alternative to the TMB to monitor the response to immunotherapy for bladder cancer patients.

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