151
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Richard JLC, Eichhorn PJA. Deciphering the roles of lncRNAs in breast development and disease. Oncotarget 2018; 9:20179-20212. [PMID: 29732012 PMCID: PMC5929455 DOI: 10.18632/oncotarget.24591] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 02/21/2018] [Indexed: 02/06/2023] Open
Abstract
Breast cancer is the second leading cause of cancer related deaths in women. It is therefore important to understand the mechanisms underlying breast cancer development as well as raises the need for enhanced, non-invasive strategies for novel prognostic and diagnostic methods. The emergence of long non-coding RNAs (lncRNAs) as potential key players in neoplastic disease has received considerable attention over the past few years. This relatively new class of molecular regulators has been shown from ongoing research to act as critical players for key biological processes. Deregulated expression levels of lncRNAs have been observed in a number of cancers including breast cancer. Furthermore, lncRNAs have been linked to breast cancer initiation, progression, metastases and to limit sensitivity to certain targeted therapeutics. In this review we provide an update on the lncRNAs associated with breast cancer and mammary gland development and illustrate the versatility of such lncRNAs in gene control, differentiation and development both in normal physiological conditions and in diseased states. We also highlight the therapeutic and diagnostic potential of lncRNAs in cancer.
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Affiliation(s)
- John Lalith Charles Richard
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
- Current Address: Genome Institute of Singapore, Agency for Science Technology and Research, 138672, Singapore
| | - Pieter Johan Adam Eichhorn
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
- School of Pharmacy, Curtin University, Perth, 6845, Australia
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152
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Sonea L, Buse M, Gulei D, Onaciu A, Simon I, Braicu C, Berindan-Neagoe I. Decoding the Emerging Patterns Exhibited in Non-coding RNAs Characteristic of Lung Cancer with Regard to their Clinical Significance. Curr Genomics 2018; 19:258-278. [PMID: 29755289 PMCID: PMC5930448 DOI: 10.2174/1389202918666171005100124] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 07/14/2017] [Accepted: 09/21/2017] [Indexed: 12/17/2022] Open
Abstract
Lung cancer continues to be the leading topic concerning global mortality rate caused by can-cer; it needs to be further investigated to reduce these dramatic unfavorable statistic data. Non-coding RNAs (ncRNAs) have been shown to be important cellular regulatory factors and the alteration of their expression levels has become correlated to extensive number of pathologies. Specifically, their expres-sion profiles are correlated with development and progression of lung cancer, generating great interest for further investigation. This review focuses on the complex role of non-coding RNAs, namely miR-NAs, piwi-interacting RNAs, small nucleolar RNAs, long non-coding RNAs and circular RNAs in the process of developing novel biomarkers for diagnostic and prognostic factors that can then be utilized for personalized therapies toward this devastating disease. To support the concept of personalized medi-cine, we will focus on the roles of miRNAs in lung cancer tumorigenesis, their use as diagnostic and prognostic biomarkers and their application for patient therapy.
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Affiliation(s)
- Laura Sonea
- MEDFUTURE - Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihail Buse
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Diana Gulei
- MEDFUTURE - Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Anca Onaciu
- MEDFUTURE - Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ioan Simon
- Surgery Department IV, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Surgery Department, Romanian Railway (CF) University Hospital, Cluj-Napoca, Romania
| | - Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ioana Berindan-Neagoe
- MEDFUTURE - Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Functional Genomics and Experimental Pathology, "Prof. Dr. Ion Chiricuta" The Oncology Institute, Republicii Street, No. 34-36, 401015, Cluj-Napoca, Romania
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153
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Genetic diagnosis of a Chinese multiple endocrine neoplasia type 2A family through whole genome sequencing. J Biosci 2018; 42:209-218. [PMID: 28569245 DOI: 10.1007/s12038-017-9686-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Approximately 98% of patients with multiple endocrine neoplasia type 2A (MEN 2A) have an identifiable RET mutation. Prophylactic or early total thyroidectomy or pheochromocytoma/parathyroid removal in patients can be preventative or curative and has become standard management. The general strategy for RET screening on family members at risk is to sequence the most commonly affected exons and, if negative, to extend sequencing to additional exons. However, different families with MEN 2A due to the same RET mutation often have significant variability in the clinical exhibition of disease and aggressiveness of the MTC, which implies additional genetic loci exsit beyond RET coding region. Whole genome sequencing (WGS) greatly expands the breadth of screening from genes associated with a particular disease to the whole genome and, potentially, all the information that the genome contains about diseases or traits. This is presumably due to additive effect of disease modifying factors. In this study, we performed WGS on a typical Chinese MEN 2A proband and identified the pathogenic RET p.C634R mutation. We also identified several neutral variants within RET and pheochromocytoma-related genes. Moreover, we found several interesting structural variants including genetic deletions (RSPO1, OVCH2 and AP3S1, etc.) and fusion transcripts (FSIP1-BAZ2A, etc.).
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154
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Nabissi M, Morelli MB, Arcella A, Cardinali C, Santoni M, Bernardini G, Santoni A, Santoni G, Amantini C. Post-transcriptional regulation of 5'-untranslated regions of human Transient Receptor Potential Vanilloid type-1 (TRPV-1) channels: role in the survival of glioma patients. Oncotarget 2018; 7:81541-81554. [PMID: 27829230 PMCID: PMC5348411 DOI: 10.18632/oncotarget.13132] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/14/2016] [Indexed: 01/02/2023] Open
Abstract
The Transient Receptor Potential Vanilloid type-1 (TRPV1) channel is a non-selective cation channel belonging to the Transient Receptor Potential family; variation of its expression has been correlated to glioma progression. In human, TRPV1 transcripts display a remarkable homogeneity differing only for the 5'-untranslated region (5'UTR) sequence that generates four variants encoding the same protein. Herein, we investigated the role of the 5'UTR sequences in TRPV1 transcripts stability, regulation of translation, expression in glioma cells and tissues. In addition, the expression of 5'UTR TRPV1 variants as prognostic factor in the survival of glioblastoma patients was evaluated. The expression level for each 5'UTR and their stability was evaluated by RT-PCR analysis. The effect of rapamycin and interferon-gamma in 5'UTR-regulating TRPV1 translation was determined by western blot analysis in glioma cell lines. We demonstrated that the 5'UTR influences the stability and translation efficacy of TRPV1 transcripts, and that TRPV1 variant three (TRPV1v3) was the most stable and the only variant expressed in GBM samples and in glioma stem-like cells. Furthermore, we found that TRPV1v3 expression levels correlate with patient's survival, suggesting that it may represent a potential prognostic marker for patients with glioma.
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Affiliation(s)
- Massimo Nabissi
- School of Pharmacy, Experimental Medicine Section, University of Camerino, Camerino (MC), Italy
| | | | | | - Claudio Cardinali
- Department of Molecular Medicine, Sapienza University, Rome (RM), Italy
| | - Matteo Santoni
- Department of Medical Oncology, AOU Ospedali Riuniti, Polytechnic University of the Marche Region, Ancona (AN), Italy
| | - Giovanni Bernardini
- Department of Molecular Medicine, Sapienza University, Rome (RM), Italy.,I.N.M. Neuromed, Pozzilli, Isernia (IS), Italy
| | - Angela Santoni
- Department of Molecular Medicine, Sapienza University, Rome (RM), Italy.,I.N.M. Neuromed, Pozzilli, Isernia (IS), Italy
| | - Giorgio Santoni
- School of Pharmacy, Experimental Medicine Section, University of Camerino, Camerino (MC), Italy
| | - Consuelo Amantini
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), Italy
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155
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Signaling Pathways Driving Aberrant Splicing in Cancer Cells. Genes (Basel) 2017; 9:genes9010009. [PMID: 29286307 PMCID: PMC5793162 DOI: 10.3390/genes9010009] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/07/2017] [Accepted: 12/18/2017] [Indexed: 12/17/2022] Open
Abstract
Aberrant profiles of pre-mRNA splicing are frequently observed in cancer. At the molecular level, an altered profile results from a complex interplay between chromatin modifications, the transcriptional elongation rate of RNA polymerase, and effective binding of the spliceosome to the generated transcripts. Key players in this interplay are regulatory splicing factors (SFs) that bind to gene-specific splice-regulatory sequence elements. Although mutations in genes of some SFs were described, a major driver of aberrant splicing profiles is oncogenic signal transduction pathways. Signaling can affect either the transcriptional expression levels of SFs or the post-translational modification of SF proteins, and both modulate the ratio of nuclear versus cytoplasmic SFs in a given cell. Here, we will review currently known mechanisms by which cancer cell signaling, including the mitogen-activated protein kinases (MAPK), phosphatidylinositol 3 (PI3)-kinase pathway (PI3K) and wingless (Wnt) pathways but also signals from the tumor microenvironment, modulate the activity or subcellular localization of the Ser/Arg rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs) families of SFs.
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156
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Bhargava S, Patil V, Shah RA, Somasundaram K. IGF2 mRNA binding protein 3 (IMP3) mediated regulation of transcriptome and translatome in glioma cells. Cancer Biol Ther 2017; 19:42-52. [PMID: 28485999 DOI: 10.1080/15384047.2017.1323601] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
RNA binding proteins mediate global regulation at the level of transcriptome and translatome of a cell. We studied the global level expression changes regulated by IMP3 in transcriptome and translatome by performing microarray using total cellular RNA and heavy polysome derived RNA of IMP3 silenced glioma cells respectively. Differentially regulated transcripts at the transcriptome level (n = 2388) and at the level of translatome (n = 479) were identified. Further, these transcripts were classified as direct and indirect targets on the basis of presence of IMP3 binding site. Additional investigation revealed that direct targets at transcriptome level were found to be associated with processes related to cell cycle, whereas direct targets at the translatome level participated in apoptosis related pathways. Probable mechanism of indirect regulation at both the levels is also investigated. Collectively, our study reveals multi-level gene expression regulation imposed by IMP3 in glioma cells.
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Affiliation(s)
- Shruti Bhargava
- a Department of Microbiology and Cell Biology , Indian Institute of Science , Bangalore , India
| | - Vikas Patil
- a Department of Microbiology and Cell Biology , Indian Institute of Science , Bangalore , India
| | - Riyaz Ahmad Shah
- a Department of Microbiology and Cell Biology , Indian Institute of Science , Bangalore , India
| | - Kumaravel Somasundaram
- a Department of Microbiology and Cell Biology , Indian Institute of Science , Bangalore , India
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157
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Cimadamore A, Gasparrini S, Mazzucchelli R, Doria A, Cheng L, Lopez-Beltran A, Santoni M, Scarpelli M, Montironi R. Long Non-coding RNAs in Prostate Cancer with Emphasis on Second Chromosome Locus Associated with Prostate-1 Expression. Front Oncol 2017; 7:305. [PMID: 29312884 PMCID: PMC5732923 DOI: 10.3389/fonc.2017.00305] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/27/2017] [Indexed: 12/18/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a class of RNA with transcripts longer than 200 nucleotides that lack functional open reading frames. They play various roles in human carcinoma, such as dysregulating gene expression in prostate cancer (PCa), which results in cancer initiation, development, and progression. The non-coding RNA SChLAP1 (second chromosome locus associated with prostate-1) is highly expressed in approximately 25% of PCas with higher prevalence in metastatic compared to localized PCa. Its expression is detectable non-invasively in PCa patient urine samples. Experimental data suggest that targeting SChLAP1 may represent a novel therapeutic application in PCa. This contribution focuses on the role of lncRNAs SChLAP1 expression in PCa diagnosis and prognosis.
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Affiliation(s)
- Alessia Cimadamore
- Section of Pathological Anatomy, School of Medicine, Polytechnic University of the Marche Region, United Hospitals, Ancona, Italy
| | - Silvia Gasparrini
- Section of Pathological Anatomy, School of Medicine, Polytechnic University of the Marche Region, United Hospitals, Ancona, Italy
| | - Roberta Mazzucchelli
- Section of Pathological Anatomy, School of Medicine, Polytechnic University of the Marche Region, United Hospitals, Ancona, Italy
| | - Andrea Doria
- Section of Pathological Anatomy, School of Medicine, Polytechnic University of the Marche Region, United Hospitals, Ancona, Italy
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Antonio Lopez-Beltran
- Department of Pathology and Surgery, Faculty of Medicine, Universidad de Córdoba, Córdoba, Spain
| | | | - Marina Scarpelli
- Section of Pathological Anatomy, School of Medicine, Polytechnic University of the Marche Region, United Hospitals, Ancona, Italy
| | - Rodolfo Montironi
- Section of Pathological Anatomy, School of Medicine, Polytechnic University of the Marche Region, United Hospitals, Ancona, Italy
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158
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Wu SZ, Ye H, Yang XG, Lu ZL, Qu Q, Qu J. Case-control pharmacogenetic study of HCN1/HCN2 variants and genetic generalized epilepsies. Clin Exp Pharmacol Physiol 2017; 45:226-233. [PMID: 29047147 DOI: 10.1111/1440-1681.12877] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/06/2017] [Accepted: 10/12/2017] [Indexed: 11/27/2022]
Abstract
Epilepsy is a common complex neurological disorder, and some forms are resistant to drug treatment. The HCN1/HCN2 genes encode hyperpolarization-activated cyclic nucleotide-gated channels, which play important roles in the electrophysiology of neurons. We investigated the association between HCN1/HCN2 variants and drug resistance or the risk of genetic generalized epilepsies (GGEs). We used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry to assess nine variants of HCN1/HCN2 in 284 healthy participants and 483 GGEs (279 drug-responsive, 204 drug-resistant). Frequencies of HCN2 rs7255568 and rs3752158 G alleles differed in GGEs and in controls (P = .039, P = .027, respectively). The frequency of HCN2 haplotype (CAC) was higher in patients than controls (P = .046). The frequency of the HCN1 rs10462087 CC+CT genotype was lower in patients with childhood absence epilepsy (CAE) than controls (P = .047). Rs7255568 was associated with the risk of CAE (P = .028) and juvenile myoclonic epilepsy (JME) (P = .02). Rs3752158 was associated with the risk of generalized tonic-clonic seizures, JME, and febrile seizures (all P < .05). The frequency of the HCN2 haplotype (CAC) was higher in patients with JME (P = .015) and in those with febrile seizures (P = .024) than in controls. No significant association was found between HCN1/HCN2 alleles, genotypes or haplotypes, and drug resistance in patients. After Bonferroni's multiple comparisons correction, only the HCN2 rs3752158 C allele and GC+CC genotype frequencies in patients with JME were higher than those in controls (19.2% vs 11.6%, odds ratio (OR) = 1.71, 95% CI = 1.18-2.32), P = .004 < 0.05/9; 36% vs 22.2%, OR = 1.62(1.18-2.23), P = .003 < 0.05/9). Our study suggests that HCN2 rs3752158 is involved in the susceptibility to JME.
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Affiliation(s)
- Shu-Zhi Wu
- Department of Neurology, The Third Clinical Institute Affiliated to Wenzhou Medical University & Wenzhou People's Hospital, Wenzhou, China
| | - Hua Ye
- Department of Neurology, The Third Clinical Institute Affiliated to Wenzhou Medical University & Wenzhou People's Hospital, Wenzhou, China
| | - Xiao-Guo Yang
- Department of Neurology, The Third Clinical Institute Affiliated to Wenzhou Medical University & Wenzhou People's Hospital, Wenzhou, China
| | - Zhi-Li Lu
- Department of Pathology, Hunan Cancer Hospital, Central South University, Changsha, China
| | - Qiang Qu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Jian Qu
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacy, Central South University, Changsha, China
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159
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Jacob R, Zander S, Gutschner T. The Dark Side of the Epitranscriptome: Chemical Modifications in Long Non-Coding RNAs. Int J Mol Sci 2017; 18:ijms18112387. [PMID: 29125541 PMCID: PMC5713356 DOI: 10.3390/ijms18112387] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 11/05/2017] [Accepted: 11/06/2017] [Indexed: 12/20/2022] Open
Abstract
The broad application of next-generation sequencing technologies in conjunction with improved bioinformatics has helped to illuminate the complexity of the transcriptome, both in terms of quantity and variety. In humans, 70–90% of the genome is transcribed, but only ~2% carries the blueprint for proteins. Hence, there is a huge class of non-translated transcripts, called long non-coding RNAs (lncRNAs), which have received much attention in the past decade. Several studies have shown that lncRNAs are involved in a plethora of cellular signaling pathways and actively regulate gene expression via a broad selection of molecular mechanisms. Only recently, sequencing-based, transcriptome-wide studies have characterized different types of post-transcriptional chemical modifications of RNAs. These modifications have been shown to affect the fate of RNA and further expand the variety of the transcriptome. However, our understanding of their biological function, especially in the context of lncRNAs, is still in its infancy. In this review, we will focus on three epitranscriptomic marks, namely pseudouridine (Ψ), N6-methyladenosine (m6A) and 5-methylcytosine (m5C). We will introduce writers, readers, and erasers of these modifications, and we will present methods for their detection. Finally, we will provide insights into the distribution and function of these chemical modifications in selected, cancer-related lncRNAs.
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Affiliation(s)
- Roland Jacob
- Faculty of Medicine, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany.
| | - Sindy Zander
- Faculty of Medicine, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany.
| | - Tony Gutschner
- Faculty of Medicine, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany.
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160
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Lambert CA, Garbacki N, Colige AC. Chemotherapy induces alternative transcription and splicing: Facts and hopes for cancer treatment. Int J Biochem Cell Biol 2017; 91:84-97. [DOI: 10.1016/j.biocel.2017.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 04/04/2017] [Accepted: 04/15/2017] [Indexed: 01/14/2023]
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161
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Sulima SO, Hofman IJF, De Keersmaecker K, Dinman JD. How Ribosomes Translate Cancer. Cancer Discov 2017; 7:1069-1087. [PMID: 28923911 PMCID: PMC5630089 DOI: 10.1158/2159-8290.cd-17-0550] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 07/18/2017] [Accepted: 07/31/2017] [Indexed: 12/13/2022]
Abstract
A wealth of novel findings, including congenital ribosomal mutations in ribosomopathies and somatic ribosomal mutations in various cancers, have significantly increased our understanding of the relevance of ribosomes in oncogenesis. Here, we explore the growing list of mechanisms by which the ribosome is involved in carcinogenesis-from the hijacking of ribosomes by oncogenic factors and dysregulated translational control, to the effects of mutations in ribosomal components on cellular metabolism. Of clinical importance, the recent success of RNA polymerase inhibitors highlights the dependence on "onco-ribosomes" as an Achilles' heel of cancer cells and a promising target for further therapeutic intervention.Significance: The recent discovery of somatic mutations in ribosomal proteins in several cancers has strengthened the link between ribosome defects and cancer progression, while also raising the question of which cellular mechanisms such defects exploit. Here, we discuss the emerging molecular mechanisms by which ribosomes support oncogenesis, and how this understanding is driving the design of novel therapeutic strategies. Cancer Discov; 7(10); 1069-87. ©2017 AACR.
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Affiliation(s)
- Sergey O Sulima
- Department of Oncology, KU Leuven, University of Leuven, LKI, Leuven Cancer Institute, Leuven, Belgium
| | - Isabel J F Hofman
- Department of Oncology, KU Leuven, University of Leuven, LKI, Leuven Cancer Institute, Leuven, Belgium
| | - Kim De Keersmaecker
- Department of Oncology, KU Leuven, University of Leuven, LKI, Leuven Cancer Institute, Leuven, Belgium.
| | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland.
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162
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Caudron-Herger M, Diederichs S. Mitochondrial mutations in human cancer: Curation of translation. RNA Biol 2017; 15:62-69. [PMID: 28873329 DOI: 10.1080/15476286.2017.1373239] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
As a genetic disease, cancer is caused by the activation of oncogenes and the inhibition of tumor suppressor genes via genetic and epigenetic mechanisms. Given the important role of energy metabolism in tumors, we analyzed the cancer-derived mutations occurring in the DNA of the mitochondrion. Mutations in the mitochondrial DNA (mtDNA) compared to nuclear DNA are 62% decreased relative to the coding length per chromosome. We find that the majority of these mutations affects highly conserved nucleotides - significantly exceeding the conservation of the mtDNA - and are devoid of single nucleotide polymorphisms (SNPs). Surprisingly, the leading resources for tumor genetics information universally use the standard genetic code for translation of nucleotide into amino acid sequences in their online resources. However, the nuclear and mitochondrial genetic codes differ for four codons and the usage of incomplete STOP codons. Hence, we analyze and curate the consequences for all mutations in the mtDNA and comprehensively reclassify missense, nonsense and synonymous mutations accordingly. In total, 10% of the mutations are incorrectly translated leading to significant changes in the distribution of mutation types with tripling of nonsense and 69% loss of nonstop extension mutations. Lastly, we provide a curated dataset of coding and non-coding mitochondrial mutations in cancer merged, standardized, duplicate-free and aggregated from two databases as a resource including orthogonal data on their high conservation and SNPs. This study generally highlights the need to universally regard the important differences between the standard and mitochondrial genetic code in life science research.
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Affiliation(s)
- Maϊwen Caudron-Herger
- a Division of RNA Biology & Cancer , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Sven Diederichs
- a Division of RNA Biology & Cancer , German Cancer Research Center (DKFZ) , Heidelberg , Germany.,b Faculty of Medicine , University of Freiburg , Freiburg , Germany.,c German Cancer Consortium (DKTK) , Freiburg , Germany.,d Division of Cancer Research, Dept. of Thoracic Surgery , Medical Center - University of Freiburg , Freiburg , Germany
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163
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Alternative splicing discriminates molecular subtypes and has prognostic impact in diffuse large B-cell lymphoma. Blood Cancer J 2017; 7:e596. [PMID: 28841210 PMCID: PMC5596382 DOI: 10.1038/bcj.2017.71] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 06/13/2017] [Accepted: 06/16/2017] [Indexed: 02/08/2023] Open
Abstract
Effect of alternative splicing (AS) on diffuse large B-cell lymphoma (DLBCL) pathogenesis and survival has not been systematically addressed. Here, we compared differentially expressed genes and exons in association with survival after chemoimmunotherapy, and between germinal center B-cell like (GCB) and activated B-cell like (ABC) DLBCLs. Genome-wide exon array-based screen was performed from samples of 38 clinically high-risk patients who were treated in a Nordic phase II study with dose-dense chemoimmunotherapy and central nervous system prophylaxis. The exon expression profile separated the patients according to molecular subgroups and survival better than the gene expression profile. Pathway analyses revealed enrichment of AS genes in inflammation and adhesion-related processes, and in signal transduction, such as phosphatidylinositol signaling system and adenosine triphosphate binding cassette transporters. Altogether, 49% of AS-related exons were protein coding, and domain prediction showed 28% of such exons to include a functional domain, such as transmembrane helix domain or phosphorylation sites. Validation in an independent cohort of 92 DLBCL samples subjected to RNA-sequencing confirmed differential exon usage of selected genes and association of AS with molecular subtypes and survival. The results indicate that AS events are able to discriminate GCB and ABC DLBCLs and have prognostic impact in DLBCL.
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164
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Prevalence of high-risk human papillomavirus infection and cancer gene mutations in nonmalignant tonsils. Oral Oncol 2017; 73:77-82. [PMID: 28939080 DOI: 10.1016/j.oraloncology.2017.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 08/11/2017] [Accepted: 08/14/2017] [Indexed: 02/01/2023]
Abstract
OBJECTIVES To analyze the prevalence of high-risk HPV (human papillomavirus) and genetic alterations in nonmalignant tonsils. METHODS We collected benign fresh tonsillar tissue specimens from 477 patients undergoing tonsillectomy because of chronic tonsillitis or tonsillar hypertrophy in 2012 (Group A, n=237) and in 2015 (Group B, n=240). Luminex xMAP technique served to detect E6/E7 DNA from 16 different high-risk HPV types. Tonsillar DNA and peripheral blood leukocyte DNA from the infected individuals were analyzed using Nimblegen SeqCap EZ Comprehensive Cancer Design panel. The panel targets 578 different genes that are relevant in carcinogenesis. HPV negative tonsillar specimens from age- and gender matched individuals were used as controls. All specimens harboring high-risk HPV were analyzed using fluorescence in situ hybridization (FISH). RESULTS Five of 477 (1.0%) patients tested positive for the following HPV types: HPV16 (two cases), HPV52 (one case), HPV66 (one case), HPV52 and HPV68 (coinfection, one case). FISH analyses showed that the appearance of HPV in specimens infected with HPV 16 was episomal. Benign tonsils infected with high-risk HPV harbored mutations in EP300, NF1, PIK3CA, and RB1 which are considered relevant in the development of HPV-associated head and neck squamous cell carcinoma (SCC). CONCLUSIONS The prevalence of high-risk HPV in nonmalignant tonsils is low. High-risk HPV positive tonsils harbored mutations in genes that are commonly altered in HPV-associated head and neck SCC. The role of these mutations in tonsillar carcinogenesis is an interesting target for future research.
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165
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Istas G, Declerck K, Pudenz M, Szic KSV, Lendinez-Tortajada V, Leon-Latre M, Heyninck K, Haegeman G, Casasnovas JA, Tellez-Plaza M, Gerhauser C, Heiss C, Rodriguez-Mateos A, Berghe WV. Identification of differentially methylated BRCA1 and CRISP2 DNA regions as blood surrogate markers for cardiovascular disease. Sci Rep 2017; 7:5120. [PMID: 28698603 PMCID: PMC5506022 DOI: 10.1038/s41598-017-03434-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 05/08/2017] [Indexed: 02/07/2023] Open
Abstract
Genome-wide Illumina InfiniumMethylation 450 K DNA methylation analysis was performed on blood samples from clinical atherosclerosis patients (n = 8) and healthy donors (n = 8) in the LVAD study (NCT02174133, NCT01799005). Multiple differentially methylated regions (DMR) could be identified in atherosclerosis patients, related to epigenetic control of cell adhesion, chemotaxis, cytoskeletal reorganisations, cell proliferation, cell death, estrogen receptor pathways and phagocytic immune responses. Furthermore, a subset of 34 DMRs related to impaired oxidative stress, DNA repair, and inflammatory pathways could be replicated in an independent cohort study of donor-matched healthy and atherosclerotic human aorta tissue (n = 15) and human carotid plaque samples (n = 19). Upon integrated network analysis, BRCA1 and CRISP2 DMRs were identified as most central disease-associated DNA methylation biomarkers. Differentially methylated BRCA1 and CRISP2 regions were verified by MassARRAY Epityper and pyrosequencing assays and could be further replicated in blood, aorta tissue and carotid plaque material of atherosclerosis patients. Moreover, methylation changes at BRCA1 and CRISP2 specific CpG sites were consistently associated with subclinical atherosclerosis measures (coronary calcium score and carotid intima media thickness) in an independent sample cohort of middle-aged men with subclinical cardiovascular disease in the Aragon Workers’ Health Study (n = 24). Altogether, BRCA1 and CRISP2 DMRs hold promise as novel blood surrogate markers for early risk stratification and CVD prevention.
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Affiliation(s)
- Geoffrey Istas
- Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty, Düsseldorf University, Düsseldorf, Germany.,Division of Diabetes and Nutritional Sciences, Faculty of Life Sciences and Medicine, King's College, London, UK
| | - Ken Declerck
- Laboratory of Protein chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Antwerp University, Antwerp (Wilrijk), Belgium
| | - Maria Pudenz
- Workgroup Cancer Chemoprevention and Epigenomics, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Katarzyna Szarc Vel Szic
- Division of Hematology, Oncology and Stem Cell Transplantation, Center for Translational Cell Research, The University Medical Center Freiburg, Freiburg, Germany
| | - Veronica Lendinez-Tortajada
- Genomic and Genetic Diagnosis Unit, Institute for Biomedical Research Hospital Clinic de Valencia, Valencia, Spain
| | | | - Karen Heyninck
- Laboratory of Eukaryotic Gene Expression and Signal Transduction LEGEST, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Guy Haegeman
- Laboratory of Eukaryotic Gene Expression and Signal Transduction LEGEST, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Jose A Casasnovas
- IIS de Aragon, Zaragoza, Spain.,Instituto Aragonés de Ciencias de Salud, Zaragoza, Spain.,Universidad de Zaragoza, Zaragoza, Spain
| | - Maria Tellez-Plaza
- Workgroup Cardiometabolic and Renal Risk, Institute for Biomedical Research Hospital Clinic de Valencia, Valencia, Spain
| | - Clarissa Gerhauser
- Workgroup Cancer Chemoprevention and Epigenomics, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Heiss
- Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty, Düsseldorf University, Düsseldorf, Germany
| | - Ana Rodriguez-Mateos
- Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty, Düsseldorf University, Düsseldorf, Germany.,Division of Diabetes and Nutritional Sciences, Faculty of Life Sciences and Medicine, King's College, London, UK
| | - Wim Vanden Berghe
- Laboratory of Protein chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Antwerp University, Antwerp (Wilrijk), Belgium. .,Laboratory of Eukaryotic Gene Expression and Signal Transduction LEGEST, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium.
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166
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Lin Z, Cai YJ, Chen RC, Chen BC, Zhao L, Xu SH, Wang XD, Song M, Wu JM, Wang YQ, Zhou MT, Shi KQ. A microRNA expression profile for vascular invasion can predict overall survival in hepatocellular carcinoma. Clin Chim Acta 2017; 469:171-179. [DOI: 10.1016/j.cca.2017.03.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/21/2017] [Accepted: 03/28/2017] [Indexed: 12/11/2022]
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167
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Lacerda R, Menezes J, Romão L. More than just scanning: the importance of cap-independent mRNA translation initiation for cellular stress response and cancer. Cell Mol Life Sci 2017; 74:1659-1680. [PMID: 27913822 PMCID: PMC11107732 DOI: 10.1007/s00018-016-2428-2] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 11/24/2016] [Accepted: 11/29/2016] [Indexed: 12/11/2022]
Abstract
The scanning model for eukaryotic mRNA translation initiation states that the small ribosomal subunit, along with initiation factors, binds at the cap structure at the 5' end of the mRNA and scans the 5' untranslated region (5'UTR) until an initiation codon is found. However, under conditions that impair canonical cap-dependent translation, the synthesis of some proteins is kept by alternative mechanisms that are required for cell survival and stress recovery. Alternative modes of translation initiation include cap- and/or scanning-independent mechanisms of ribosomal recruitment. In most cap-independent translation initiation events there is a direct recruitment of the 40S ribosome into a position upstream, or directly at, the initiation codon via a specific internal ribosome entry site (IRES) element in the 5'UTR. Yet, in some cellular mRNAs, a different translation initiation mechanism that is neither cap- nor IRES-dependent seems to occur through a special RNA structure called cap-independent translational enhancer (CITE). Recent evidence uncovered a distinct mechanism through which mRNAs containing N 6-methyladenosine (m6A) residues in their 5'UTR directly bind eukaryotic initiation factor 3 (eIF3) and the 40S ribosomal subunit in order to initiate translation in the absence of the cap-binding proteins. This review focuses on the important role of cap-independent translation mechanisms in human cells and how these alternative mechanisms can either act individually or cooperate with other cis-acting RNA regulons to orchestrate specific translational responses triggered upon several cellular stress states, and diseases such as cancer. Elucidation of these non-canonical mechanisms reveals the complexity of translational control and points out their potential as prospective novel therapeutic targets.
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Affiliation(s)
- Rafaela Lacerda
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
- Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Juliane Menezes
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
- Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Luísa Romão
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
- Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal.
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168
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Faulty RNA splicing: consequences and therapeutic opportunities in brain and muscle disorders. Hum Genet 2017; 136:1215-1235. [DOI: 10.1007/s00439-017-1802-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/13/2017] [Indexed: 12/12/2022]
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169
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Juul M, Bertl J, Guo Q, Nielsen MM, Świtnicki M, Hornshøj H, Madsen T, Hobolth A, Pedersen JS. Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate. eLife 2017; 6. [PMID: 28362259 PMCID: PMC5440169 DOI: 10.7554/elife.21778] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 03/14/2017] [Indexed: 02/06/2023] Open
Abstract
Non-coding mutations may drive cancer development. Statistical detection of non-coding driver regions is challenged by a varying mutation rate and uncertainty of functional impact. Here, we develop a statistically founded non-coding driver-detection method, ncdDetect, which includes sample-specific mutational signatures, long-range mutation rate variation, and position-specific impact measures. Using ncdDetect, we screened non-coding regulatory regions of protein-coding genes across a pan-cancer set of whole-genomes (n = 505), which top-ranked known drivers and identified new candidates. For individual candidates, presence of non-coding mutations associates with altered expression or decreased patient survival across an independent pan-cancer sample set (n = 5454). This includes an antigen-presenting gene (CD1A), where 5'UTR mutations correlate significantly with decreased survival in melanoma. Additionally, mutations in a base-excision-repair gene (SMUG1) correlate with a C-to-T mutational-signature. Overall, we find that a rich model of mutational heterogeneity facilitates non-coding driver identification and integrative analysis points to candidates of potential clinical relevance.
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Affiliation(s)
- Malene Juul
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Johanna Bertl
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Qianyun Guo
- Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
| | - Morten Muhlig Nielsen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Michał Świtnicki
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Henrik Hornshøj
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Tobias Madsen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Asger Hobolth
- Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
| | - Jakob Skou Pedersen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark.,Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
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170
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Demidowich AP, Jun JY, Yanovski JA. Polymorphisms and mutations in the melanocortin-3 receptor and their relation to human obesity. Biochim Biophys Acta Mol Basis Dis 2017; 1863:2468-2476. [PMID: 28363697 DOI: 10.1016/j.bbadis.2017.03.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 03/23/2017] [Accepted: 03/27/2017] [Indexed: 12/18/2022]
Abstract
Inactivating mutations in the melanocortin 3 receptor (Mc3r) have been described as causing obesity in mice, but the physiologic effects of MC3R mutations in humans have been less clear. Here we review the MC3R polymorphisms and mutations identified in humans, and the in vitro, murine, and human cohort studies examining their putative effects. Some, but not all, studies suggest that the common human MC3R variant T6K+V81I, as well as several other rare, function-altering mutations, are associated with greater adiposity and hyperleptinemia with altered energy partitioning. In vitro, the T6K+V81I variant appears to decrease MC3R expression and therefore cAMP generation in response to ligand binding. Knockin mouse studies confirm that the T6K+V81I variant increases feeding efficiency and the avidity with which adipocytes derived from bone or adipose tissue stem cells store triglycerides. Other MC3R mutations occur too infrequently in the human population to make definitive conclusions regarding their clinical effects. This article is part of a Special Issue entitled: Melanocortin Receptors - edited by Ya-Xiong Tao.
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Affiliation(s)
- Andrew P Demidowich
- Section on Growth and Obesity, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Joo Yun Jun
- Section on Growth and Obesity, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Jack A Yanovski
- Section on Growth and Obesity, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States.
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171
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Zhao H, Shen J, Hodges TR, Song R, Fuller GN, Heimberger AB. Serum microRNA profiling in patients with glioblastoma: a survival analysis. Mol Cancer 2017; 16:59. [PMID: 28284220 PMCID: PMC5346242 DOI: 10.1186/s12943-017-0628-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/28/2017] [Indexed: 01/23/2023] Open
Abstract
Because circulating microRNAs (miRNAs) have drawn a great deal of attention as promising novel cancer diagnostics and prognostic biomarkers, we sought to identify serum miRNAs significantly associated with outcome in glioblastoma patients. To do this, we performed global miRNA profiling in serum samples from 106 primary glioblastoma patients. The study subjects were randomly divided into two sets: set one (n = 40) and set two (n = 66). Using a Cox regression model, 3 serum miRNAs (miR-106a-5p, miR-182, and miR-145-5p) and 5 serum miRNAs (miR-222-3p, miR-182, miR-20a-5p, miR-106a-5p, and miR-145-5p) were identified significantly associated with 2-year patient overall survival and disease-free survival (P < 0.05) in both sets and the combined set. We then created the miRNA risk scores to assess the total impact of the significant serum miRNAs on survival. The high risk scores were associated with poor patient survival (overall survival: HR = 1.92, 95% CI: 1.19, 10.23, and disease-free survival: HR = 2.03, 95%CI: 1.24, 4.28), and were independent of other clinicopathological factors. Our results suggest that serum miRNAs could serve as prognostic predictors of glioblastoma.
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Affiliation(s)
- Hua Zhao
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, 1155 Pressler Street, Houston, TX, 77030, USA.
| | - Jie Shen
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, 1155 Pressler Street, Houston, TX, 77030, USA
| | - Tiffany R Hodges
- Department of Neuro-Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Renduo Song
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, 1155 Pressler Street, Houston, TX, 77030, USA
| | - Gregory N Fuller
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Amy B Heimberger
- Department of Neuro-Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
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172
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Winkler M, Gärtner S, Wrensch F, Krawczak M, Sauermann U, Pöhlmann S. Rhesus macaque IFITM3 gene polymorphisms and SIV infection. PLoS One 2017; 12:e0172847. [PMID: 28257482 PMCID: PMC5336200 DOI: 10.1371/journal.pone.0172847] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 02/10/2017] [Indexed: 01/01/2023] Open
Abstract
Interferon-induced transmembrane proteins (IFITMs) have been recognized as important antiviral effectors of the innate immune system, both in cell culture and in infected humans. In particular, polymorphisms of the human IFITM3 gene have been shown to affect disease severity and progression in influenza A virus (FLUAV) and human immunodeficiency virus (HIV) infection, respectively. Rhesus macaques (Macaca mulatta) are commonly used to model human infections and the experimental inoculation of these animals with simian immunodeficiency virus (SIV) is one of the best models for HIV/AIDS in humans. However, information on the role of IFITM3 in SIV infection of rhesus macaques is currently lacking. We show that rhesus macaque (rh) IFITM3 inhibits SIV and FLUAV entry in cell culture, although with moderately reduced efficiency as compared to its human counterpart. We further report the identification of 16 polymorphisms in the rhIFITM3 gene, three of which were exonic and synonymous while the remainder was located in non-coding regions. Employing previously characterized samples from two cohorts of SIV-infected rhesus macaques, we investigated the relationship between these rhIFITM3 polymorphisms and both AIDS-free survival time and virus load. In cohort 1, several intronic polymorphisms were significantly associated with virus load or survival. However, an association with both parameters was not observed and significance was lost in most cases when animals were stratified for the presence of MHC allele Mamu-A1*001. Moreover, no significant genotype-phenotype associations were detected in cohort 2. These results suggest that, although IFITM3 can inhibit SIV infection in cell culture, genetic variation in rhIFITM3 might have only a minor impact on the course of SIV infection in experimentally infected animals.
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Affiliation(s)
- Michael Winkler
- Infection Biology Unit, Deutsches Primatenzentrum, Leibniz Institute for Primate Research, Göttingen, Germany
- * E-mail: (MW); (SP)
| | - Sabine Gärtner
- Infection Biology Unit, Deutsches Primatenzentrum, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Florian Wrensch
- Infection Biology Unit, Deutsches Primatenzentrum, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University, Kiel, Germany
| | - Ulrike Sauermann
- Infection Models Unit, Deutsches Primatenzentrum, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, Deutsches Primatenzentrum, Leibniz Institute for Primate Research, Göttingen, Germany
- * E-mail: (MW); (SP)
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173
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Racimo F, Gokhman D, Fumagalli M, Ko A, Hansen T, Moltke I, Albrechtsen A, Carmel L, Huerta-Sánchez E, Nielsen R. Archaic Adaptive Introgression in TBX15/WARS2. Mol Biol Evol 2017; 34:509-524. [PMID: 28007980 PMCID: PMC5430617 DOI: 10.1093/molbev/msw283] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A recent study conducted the first genome-wide scan for selection in Inuit from Greenland using single nucleotide polymorphism chip data. Here, we report that selection in the region with the second most extreme signal of positive selection in Greenlandic Inuit favored a deeply divergent haplotype that is closely related to the sequence in the Denisovan genome, and was likely introgressed from an archaic population. The region contains two genes, WARS2 and TBX15, and has previously been associated with adipose tissue differentiation and body-fat distribution in humans. We show that the adaptively introgressed allele has been under selection in a much larger geographic region than just Greenland. Furthermore, it is associated with changes in expression of WARS2 and TBX15 in multiple tissues including the adrenal gland and subcutaneous adipose tissue, and with regional DNA methylation changes in TBX15.
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Affiliation(s)
- Fernando Racimo
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA
| | - David Gokhman
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | - Matteo Fumagalli
- Department of Genetics, Evolution, and Environment, University College London, London, United Kingdom
| | - Amy Ko
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Anders Albrechtsen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liran Carmel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | | | - Rasmus Nielsen
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA
- Department of Statistics, University of California Berkeley, Berkeley, CA
- Museum of Natural History, University of Copenhagen, Copenhagen, Denmark
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174
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Yan Y, Xu Z, Li Z, Sun L, Gong Z. An Insight into the Increasing Role of LncRNAs in the Pathogenesis of Gliomas. Front Mol Neurosci 2017; 10:53. [PMID: 28293170 PMCID: PMC5328963 DOI: 10.3389/fnmol.2017.00053] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 02/15/2017] [Indexed: 02/05/2023] Open
Abstract
Long non-coding RNAs (LncRNAs) are essential epigenetic regulators with critical roles in tumor initiation and malignant progression. However, the roles and mechanisms of aberrantly expressed lncRNAs in the pathogenesis of gliomas are not fully understood. With the development of deep sequencing analyses, an extensive amount of functional non-coding RNAs has been discovered in glioma tissues and cell lines. Additionally, the contributions of several lncRNAs, such as Hox transcript antisense intergenic RNA, H19 and Colorectal neoplasia differentially expressed, previously reported to be involved in other pathogenesis and processes to the oncogenesis of glioblastoma are currently addressed. Thus, lncRNAs detected in tumor tissues could serve as candidate diagnostic biomarkers and therapeutic targets for gliomas. To understand the potential function of lncRNAs in gliomas, in this review, we briefly describe the profile of lncRNAs in human glioma research and therapy. Then, we discuss the individual lncRNA that has been under intensive investigation in glioma research, and the focus is its mechanism and clinical implication.
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Affiliation(s)
- Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South UniversityChangsha, China; Institute of Hospital Pharmacy, Central South UniversityChangsha, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University Changsha, China
| | - Zhi Li
- Center for Molecular Medicine, Xiangya Hospital, Key Laboratory of Molecular Radiation Oncology of Hunan Province, Central South University Changsha, China
| | - Lunquan Sun
- Center for Molecular Medicine, Xiangya Hospital, Key Laboratory of Molecular Radiation Oncology of Hunan Province, Central South University Changsha, China
| | - Zhicheng Gong
- Department of Pharmacy, Xiangya Hospital, Central South UniversityChangsha, China; Institute of Hospital Pharmacy, Central South UniversityChangsha, China
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175
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Bhatia P, Singh A, Hegde A, Jain R, Bansal D. Systematic evaluation of paediatric cohort with iron refractory iron deficiency anaemia (IRIDA) phenotype reveals multipleTMPRSS6gene variations. Br J Haematol 2017; 177:311-318. [DOI: 10.1111/bjh.14554] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 11/23/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Prateek Bhatia
- Paediatric Haematology-Oncology Unit; Department of Paediatrics; Advanced Paediatric Centre; Post Graduate Institute of Medical Education and Research; Chandigarh India
| | - Aditya Singh
- Paediatric Haematology-Oncology Unit; Department of Paediatrics; Advanced Paediatric Centre; Post Graduate Institute of Medical Education and Research; Chandigarh India
| | - Avani Hegde
- Paediatric Haematology-Oncology Unit; Department of Paediatrics; Advanced Paediatric Centre; Post Graduate Institute of Medical Education and Research; Chandigarh India
| | - Richa Jain
- Paediatric Haematology-Oncology Unit; Department of Paediatrics; Advanced Paediatric Centre; Post Graduate Institute of Medical Education and Research; Chandigarh India
| | - Deepak Bansal
- Paediatric Haematology-Oncology Unit; Department of Paediatrics; Advanced Paediatric Centre; Post Graduate Institute of Medical Education and Research; Chandigarh India
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176
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Activating mutations and translocations in the guanine exchange factor VAV1 in peripheral T-cell lymphomas. Proc Natl Acad Sci U S A 2017; 114:764-769. [PMID: 28062691 DOI: 10.1073/pnas.1608839114] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Peripheral T-cell lymphomas (PTCLs) are a heterogeneous group of non-Hodgkin lymphomas frequently associated with poor prognosis and for which genetic mechanisms of transformation remain incompletely understood. Using RNA sequencing and targeted sequencing, here we identify a recurrent in-frame deletion (VAV1 Δ778-786) generated by a focal deletion-driven alternative splicing mechanism as well as novel VAV1 gene fusions (VAV1-THAP4, VAV1-MYO1F, and VAV1-S100A7) in PTCL. Mechanistically these genetic lesions result in increased activation of VAV1 catalytic-dependent (MAPK, JNK) and non-catalytic-dependent (nuclear factor of activated T cells, NFAT) VAV1 effector pathways. These results support a driver oncogenic role for VAV1 signaling in the pathogenesis of PTCL.
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177
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Abstract
The functional capacity of cells is defined by the transcriptome. Many recent studies have identified variations in the transcriptome of tumors due to alternative splicing changes, as well as mutations in splicing factors and regulatory signals in most tumor types. Some of these alterations have been linked to tumor progression, metastasis, therapy resistance, and other oncogenic processes. Here, we describe the different mechanisms that drive splicing changes in tumors and their impact in cancer. Motivated by the current evidence, we propose a model whereby a subset of the splicing patterns contributes to the definition of specific tumor phenotypes, and may hold potential for the development of novel clinical biomarkers and therapeutic approaches.
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Affiliation(s)
- Babita Singh
- a Pompeu Fabra University, PRBB , Barcelona , Spain
| | - Eduardo Eyras
- a Pompeu Fabra University, PRBB , Barcelona , Spain.,b ICREA , Barcelona , Spain
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178
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Pölönen P, Levonen AL. Insights into the role of NRF2 in cancer provided by cancer genomics. CURRENT OPINION IN TOXICOLOGY 2016. [DOI: 10.1016/j.cotox.2016.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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179
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Floris I, Kraft JD, Altosaar I. Roles of MicroRNA across Prenatal and Postnatal Periods. Int J Mol Sci 2016; 17:ijms17121994. [PMID: 27916805 PMCID: PMC5187794 DOI: 10.3390/ijms17121994] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 11/11/2016] [Accepted: 11/17/2016] [Indexed: 12/20/2022] Open
Abstract
Communication between mother and offspring in mammals starts at implantation via the maternal-placental-fetal axis, and continues postpartum via milk targeted to the intestinal mucosa. MicroRNAs (miRNAs), short, noncoding single-stranded RNAs, of about 22 nucleotides in length, are actively involved in many developmental and physiological processes. Here we highlight the role of miRNA in the dynamic signaling that guides infant development, starting from implantation of conceptus and persisting through the prenatal and postnatal periods. miRNAs in body fluids, particularly in amniotic fluid, umbilical cord blood, and breast milk may offer new opportunities to investigate physiological and/or pathological molecular mechanisms that portend to open novel research avenues for the identification of noninvasive biomarkers.
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Affiliation(s)
- Ilaria Floris
- Biochemistry, Microbiology & Immunology Department, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H8M5, Canada.
| | - Jamie D Kraft
- Biochemistry, Microbiology & Immunology Department, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H8M5, Canada.
| | - Illimar Altosaar
- Biochemistry, Microbiology & Immunology Department, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H8M5, Canada.
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180
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Li J, Lian Y, Yan C, Cai Z, Ding J, Ma Z, Peng P, Wang K. Long non-coding RNA FOXP4-AS1 is an unfavourable prognostic factor and regulates proliferation and apoptosis in colorectal cancer. Cell Prolif 2016; 50. [PMID: 27790757 DOI: 10.1111/cpr.12312] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/22/2016] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVES Despite improvements in diagnosis and treatment, colorectal cancer (CRC) remains the third most common malignancy, and fourth-leading cause of cancer-related death worldwide, and has a particularly high incidence in Western countries. Recent studies have suggested that long non-coding RNAs (lncRNAs) compose a novel class of regulators of cancer biological processes, such as proliferation, apoptosis and metastasis. Here, we report that lncRNA FOXP4-AS1 acts as a functional oncogene in CRC pathogenesis. Moreover, we have attempted to investigate the effects of FOXP4-AS1 on tumour progression, both in vitro and in vivo. MATERIALS AND METHODS In this study, bioinformatic analyses and qPCR were performed to investigate FOXP4-AS1 expression in CRC tissue samples and CRC cell lines. We inhibited FOXP4-AS1 expression via FOXP4-AS1-specific siRNA transfection. Cell proliferation was assessed using cell viability and colony formation assays, as well as by flow cytometry and ethynyl deoxyuridine (Edu) analyses. Apoptosis was assessed using flow cytometry. Animal tumour xenografts were generated, and immunohistochemistry (IHC) was performed to evaluate effects of FOXP4-AS1 on CRC tumour growth in vivo. RESULTS We found that FOXP4-AS1 was up-regulated in CRC tissues and cell lines and that its overexpression positively correlated with advanced pathological stages and larger tumour size. Additionally, we found that FOXP4-AS1 knockdown inhibited cell proliferation and induced apoptosis. Furthermore, FOXP4-AS1 knockdown induced marked increase in number of cells in G0/G1 phase and reduction in number of cells in S phase, in DLD-1, HT-29 and HCT116 cell lines. Consistent with these findings, FOXP4-AS1 silencing inhibited tumour growth in vivo. CONCLUSION These findings suggest that FOXP4-AS1 plays a crucial role in CRC progression and may be a new biomarker in patients with CRC.
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Affiliation(s)
- Juan Li
- The Second Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yifan Lian
- The Second Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Changsheng Yan
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zeling Cai
- Department of General Surgery, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jie Ding
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhonghua Ma
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Peng Peng
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Keming Wang
- The Second Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
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181
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Lam G, Xian RR, Li Y, Burns KH, Beemon KL. Lack of TERT Promoter Mutations in Human B-Cell Non-Hodgkin Lymphoma. Genes (Basel) 2016; 7:genes7110093. [PMID: 27792139 PMCID: PMC5126779 DOI: 10.3390/genes7110093] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/21/2016] [Accepted: 10/13/2016] [Indexed: 11/23/2022] Open
Abstract
Non-Hodgkin lymphomas (NHL) are a heterogeneous group of immune cell neoplasms that comprise molecularly distinct lymphoma subtypes. Recent work has identified high frequency promoter point mutations in the telomerase reverse transcriptase (TERT) gene of different cancer types, including melanoma, glioma, liver and bladder cancer. TERT promoter mutations appear to correlate with increased TERT expression and telomerase activity in these cancers. In contrast, breast, pancreatic, and prostate cancer rarely demonstrate mutations in this region of the gene. TERT promoter mutation prevalence in NHL has not been thoroughly tested thus far. We screened 105 B-cell lymphoid malignancies encompassing nine NHL subtypes and acute lymphoblastic leukemia, for TERT promoter mutations. Our results suggest that TERT promoter mutations are rare or absent in most NHL. Thus, the classical TERT promoter mutations may not play a major oncogenic role in TERT expression and telomerase activation in NHL.
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Affiliation(s)
- Gary Lam
- Department of Biology, Johns Hopkins University, Baltimore, MD 21210, USA.
| | - Rena R Xian
- Department of Pathology, Johns Hopkins Medical Institutes, Baltimore, MD 212105, USA.
- Department of Pathology, University of California Los Angeles, Los Angeles, CA 90095, USA.
| | - Yingying Li
- Department of Biology, Johns Hopkins University, Baltimore, MD 21210, USA.
| | - Kathleen H Burns
- Department of Pathology, Johns Hopkins Medical Institutes, Baltimore, MD 212105, USA.
| | - Karen L Beemon
- Department of Biology, Johns Hopkins University, Baltimore, MD 21210, USA.
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182
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Long noncoding RNAs in the progression, metastasis, and prognosis of osteosarcoma. Cell Death Dis 2016; 7:e2389. [PMID: 27685633 PMCID: PMC5059871 DOI: 10.1038/cddis.2016.272] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 07/27/2016] [Accepted: 08/01/2016] [Indexed: 01/01/2023]
Abstract
Long noncoding RNAs (lncRNAs) are a class of non-protein-coding molecules longer than 200 nucleotides that are involved in the development and progression of many types of tumors. Numerous lncRNAs regulate cell proliferation, metastasis, and chemotherapeutic drug resistance. Osteosarcoma is one of the main bone tumor subtypes that poses a serious threat to adolescent health. We summarized how lncRNAs regulate osteosarcoma progression, invasion, and drug resistance, as well as how lncRNAs can function as biomarkers or independent prognostic indicators with respect to osteosarcoma therapy.
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183
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Hasche D, Stephan S, Savelyeva L, Westermann F, Rösl F, Vinzón SE. Establishment of an Immortalized Skin Keratinocyte Cell Line Derived from the Animal Model Mastomys coucha. PLoS One 2016; 11:e0161283. [PMID: 27533138 PMCID: PMC4988767 DOI: 10.1371/journal.pone.0161283] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/02/2016] [Indexed: 11/18/2022] Open
Abstract
In the present report we describe the establishment of a spontaneous immortalized skin keratinocyte cell line derived from the skin of the multimammate rodent Mastomys coucha. These animals are used in preclinical studies for a variety of human diseases such as infections with nematodes, bacteria and papillomaviruses, especially regarding cutaneous manifestations such as non-melanoma skin cancer. Here we characterize the cells in terms of their origin and cytogenetic features. Searching for genomic signatures, a spontaneous mutation in the splicing donor sequence of Trp53 (G to A transition at the first position of intron 7) could be detected. This point mutation leads to alternative splicing and to a premature stop codon, resulting in a truncated and, in turn, undetectable form of p53, probably contributing to the process of immortalization. Mastomys coucha-derived skin keratinocytes can be used as an in vitro system to investigate molecular and immunological aspects of infectious agent interactions with their host cells.
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Affiliation(s)
- Daniel Hasche
- Division of Viral Transformation Mechanisms (F030), German Cancer Research Center, Heidelberg, Germany
| | - Sonja Stephan
- Division of Viral Transformation Mechanisms (F030), German Cancer Research Center, Heidelberg, Germany
| | - Larissa Savelyeva
- Division of Neuroblastoma Genomics (B087), German Cancer Research Center, Heidelberg, Germany
| | - Frank Westermann
- Division of Neuroblastoma Genomics (B087), German Cancer Research Center, Heidelberg, Germany
| | - Frank Rösl
- Division of Viral Transformation Mechanisms (F030), German Cancer Research Center, Heidelberg, Germany
- * E-mail: ; (SEV); (FR)
| | - Sabrina E. Vinzón
- Division of Viral Transformation Mechanisms (F030), German Cancer Research Center, Heidelberg, Germany
- * E-mail: ; (SEV); (FR)
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184
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Diederichs S, Bartsch L, Berkmann JC, Fröse K, Heitmann J, Hoppe C, Iggena D, Jazmati D, Karschnia P, Linsenmeier M, Maulhardt T, Möhrmann L, Morstein J, Paffenholz SV, Röpenack P, Rückert T, Sandig L, Schell M, Steinmann A, Voss G, Wasmuth J, Weinberger ME, Wullenkord R. The dark matter of the cancer genome: aberrations in regulatory elements, untranslated regions, splice sites, non-coding RNA and synonymous mutations. EMBO Mol Med 2016; 8:442-57. [PMID: 26992833 PMCID: PMC5126213 DOI: 10.15252/emmm.201506055] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Cancer is a disease of the genome caused by oncogene activation and tumor suppressor gene inhibition. Deep sequencing studies including large consortia such as TCGA and ICGC identified numerous tumor‐specific mutations not only in protein‐coding sequences but also in non‐coding sequences. Although 98% of the genome is not translated into proteins, most studies have neglected the information hidden in this “dark matter” of the genome. Malignancy‐driving mutations can occur in all genetic elements outside the coding region, namely in enhancer, silencer, insulator, and promoter as well as in 5′‐UTR and 3′‐UTR. Intron or splice site mutations can alter the splicing pattern. Moreover, cancer genomes contain mutations within non‐coding RNA, such as microRNA, lncRNA, and lincRNA. A synonymous mutation changes the coding region in the DNA and RNA but not the protein sequence. Importantly, oncogenes such as TERT or miR‐21 as well as tumor suppressor genes such as TP53/p53,APC,BRCA1, or RB1 can be affected by these alterations. In summary, coding‐independent mutations can affect gene regulation from transcription, splicing, mRNA stability to translation, and hence, this largely neglected area needs functional studies to elucidate the mechanisms underlying tumorigenesis. This review will focus on the important role and novel mechanisms of these non‐coding or allegedly silent mutations in tumorigenesis.
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Affiliation(s)
- Sven Diederichs
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany Division of RNA Biology & Cancer (B150), German Cancer Research Center (DKFZ), Heidelberg, Germany German Cancer Consortium (DKTK), Freiburg, Germany
| | - Lorenz Bartsch
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Julia C Berkmann
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Karin Fröse
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Jana Heitmann
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Caroline Hoppe
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Deetje Iggena
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Danny Jazmati
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Philipp Karschnia
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Miriam Linsenmeier
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Thomas Maulhardt
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Lino Möhrmann
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Johannes Morstein
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Stella V Paffenholz
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Paula Röpenack
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Timo Rückert
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Ludger Sandig
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Maximilian Schell
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Anna Steinmann
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Gjendine Voss
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Jacqueline Wasmuth
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Maria E Weinberger
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Ramona Wullenkord
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
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