TCGA Pan-Cancer Genomic Analysis of Alternative Lengthening of Telomeres (ALT) Related Genes

Telomere maintenance mechanisms (TMM) are used by cancer cells to avoid apoptosis, 85–90% reactivate telomerase, while 10–15% use the alternative lengthening of telomeres (ALT). Due to anti-telomerase-based treatments, some tumors switch from a telomerase-dependent mechanism to ALT; in fact, the co-existence between both mechanisms has been observed in some cancers. Although different elements in the ALT pathway are uncovered, some molecular mechanisms are still poorly understood. Therefore, with the aim to identify potential molecular markers for the study of ALT, we combined in silico approaches in a 411 telomere maintenance gene set. As a consequence, we conducted a genomic analysis of these genes in 31 Pan-Cancer Atlas studies from The Cancer Genome Atlas and found 325,936 genomic alterations; from which, we identified 20 genes highly mutated in the cancer studies. Finally, we made a protein-protein interaction network and enrichment analysis to observe the main pathways of these genes and discuss their role in ALT-related processes, like homologous recombination and homology directed repair. Overall, due to the lack of understanding of the molecular mechanisms of ALT cancers, we proposed a group of genes, which after ex vivo validations, could represent new potential therapeutic markers in the study of ALT.

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TCGA Pan-Cancer genomic analysis of Alternative Lengthening of Telomeres (ALT) related genes

10.1101/2020.04.27.063610 ◽

2020 ◽

Author(s):

Isaac Armendáriz-Castillo ◽

Andrés López-Cortés ◽

Jennyfer García-Cárdenas ◽

Patricia Guevara-Ramírez ◽

Paola E. Leone ◽

...

Keyword(s):

Homologous Recombination ◽

Molecular Mechanisms ◽

Ex Vivo ◽

Genomic Analysis ◽

Interaction Network ◽

Telomere Maintenance ◽

The Cancer Genome Atlas ◽

Alternative Lengthening Of Telomeres ◽

Alternative Lengthening ◽

Pan Cancer

AbstractTelomere maintenance mechanisms (TMM) are used by cancer cells to avoid apoptosis, 85-90% reactivate telomerase, while 10-15% use the alternative lengthening of telomeres (ALT). Due to anti-telomerase-based treatments, some tumors have the ability to switch from a telomerase-dependent mechanism to ALT, in fact, the co-existence between telomerase and the ALT pathway have been observed in a variety of cancer types. Despite different elements in the ALT pathway have been uncovered, the molecular mechanism and other factors are still poorly understood, which difficult the detection and treatment of ALT-positive cells, which are known to present poor prognosis. Therefore, with the aim to identify potential molecular markers to be used in the study of ALT, we combined simplistic in silico approaches in 411 telomere maintenance (TM) genes which have been previously validated or predicted to be involved in the ALT pathway. In consequence, we conducted a genomic analysis of these genes in 31 Pan-Cancer Atlas studies (n=9,282) from The Cancer Genome Atlas in the cBioPortal and found 325,936 genomic alterations, being mRNA high and low the top alterations with 65,.8% and 10.7% respectively. Moreover, we analyzed the highest frequency means of genomics alterations, identified and proposed 20 genes, which are highly mutated and up and down regulated in the cancer studies and could be used for future analysis in the study of ALT. Finally, we made a protein-protein interaction network and enrichment analysis to obtain an insight into the main pathways these genes are involved. We could observe their role in main processes related to the ALT mechanism like homologous recombination, homology directed repair (HDR), HDR through homologous recombination and telomere maintenance and organization.. Overall, due to the lack of understanding of the molecular mechanisms and detection of ALT-positive cancers, we identified and proposed more molecular targets that can be used for expression analysis and additional ex vivo assays to validate them as new potential therapeutic markers in the study of the ALT mechanism.

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Identification of Key Proteins in the Alternative Lengthening of Telomeres Associated Promyelocytic Leukemia Nuclear Bodies

10.20944/preprints202110.0001.v1 ◽

2021 ◽

Author(s):

Isaac Armendáriz-Castillo ◽

Katherine Hidalgo-Fernández ◽

Andy Pérez-Villa ◽

Jennyfer García-Cárdenas ◽

Andrés López-Cortés ◽

...

Keyword(s):

Molecular Mechanisms ◽

Ex Vivo ◽

Promyelocytic Leukemia ◽

Nuclear Bodies ◽

The Cancer Genome Atlas ◽

Functional Enrichment ◽

Alternative Lengthening Of Telomeres ◽

Pml Nuclear Bodies ◽

Alternative Lengthening

One of the hallmarks of the Alternative Lengthening of Telomeres (ALT) is the association with Promyelocytic Leukemia (PML) Nuclear Bodies, known as APBs. In the last years, APBs have been described as the main place where telomeric extension occurs in ALT positive cancer cell lines. A different set of proteins have been associated with APBs function, however, the molecular mechanisms behind their assembly, colocalization, and clustering of telomeres, among others, remain unclear. To improve the understanding of APBs in the ALT pathway, we integrated multi-omics analyses to evaluate genomic, transcriptomic and proteomic alterations, and functional interactions of 71 APBs-related genes/proteins in 32 PanCancer Atlas studies from The Cancer Genome Atlas Consortium (TCGA). As a result, we identified 13 key proteins which showed distinctive mutations, interactions, and functional enrichment patterns across all the cancer types and proposed this set of proteins as candidates for future ex vivo and in vivo analyses that will validate these proteins to improve the understanding of the ALT pathway, fill the current research gap about APBs function and their role in ALT, and be considered as potential therapeutic targets for the diagnosis and treatment of ALT positive cancers in the future.

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High Expression of UBB, RAC1, and ITGB1 Predicts Worse Prognosis among Nonsmoking Patients with Lung Adenocarcinoma through Bioinformatics Analysis

BioMed Research International ◽

10.1155/2020/2071593 ◽

2020 ◽

Vol 2020 ◽

pp. 1-14

Author(s):

Huan Deng ◽

Yichao Huang ◽

Li Wang ◽

Ming Chen

Keyword(s):

Extracellular Matrix ◽

Lung Adenocarcinoma ◽

Molecular Mechanisms ◽

Interaction Network ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

The Cancer Genome Atlas ◽

Prognostic Indicators ◽

Hub Genes ◽

Go Enrichment

Purpose. The molecular mechanism underlying the tumorigenesis and progression of lung adenocarcinoma (LUAD) in nonsmoking patients remains unclear. This study was conducted to select crucial therapeutic and prognostic biomarkers for nonsmoking patients with LUAD. Methods. Microarray datasets from the Gene Expression Omnibus (GSE32863 and GSE75037) were analyzed for differentially expressed genes (DEGs). Gene Ontology (GO) enrichment analysis of DEGs was performed, and protein-protein interaction network was then constructed using the Search Tool for the Retrieval of Interacting Genes and Cytoscape. Hub genes were then identified by the rank of degree. Overall survival (OS) analyses of hub genes were performed among nonsmoking patients with LUAD in Kaplan-Meier plotter. The Cancer Genome Atlas (TCGA) and The Human Protein Atlas (THPA) databases were applied to verify hub genes. In addition, we performed Gene Set Enrichment Analysis (GSEA) of hub genes. Results. We identified 1283 DEGs, including 743 downregulated and 540 upregulated genes. GO enrichment analyses showed that DEGs were significantly enriched in collagen-containing extracellular matrix and extracellular matrix organization. Moreover, 19 hub genes were identified, and 12 hub genes were closely associated with OS. Although no obvious difference was detected in ITGB1, the downregulation of UBB and upregulation of RAC1 were observed in LUAD tissues of nonsmoking patients. Immunohistochemistry in THPA database confirmed that UBB and ITGB1 were downregulated, while RAC1 was upregulated in LUAD. GSEA suggested that ribosome, B cell receptor signaling pathway, and cell cycle were associated with UBB, RAC1, and ITGB1 expression, respectively. Conclusions. Our study provides insights into the underlying molecular mechanisms of the carcinogenesis and progression of LUAD in nonsmoking patients and demonstrated UBB, RAC1, and ITGB1 as therapeutic and prognostic indicators for nonsmoking LUAD. This is the first study to report the crucial role of UBB in nonsmoking LUAD.

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Alternative Lengthening of Telomeres is not synonymous with mutations in ATRX/DAXX

10.1101/2020.05.05.076125 ◽

2020 ◽

Author(s):

Alexandre de Nonneville ◽

Roger R. Reddel

Keyword(s):

Large Scale ◽

Telomere Maintenance ◽

Whole Genome Sequence ◽

Structural Variations ◽

Alternative Lengthening Of Telomeres ◽

Maintenance Mechanism ◽

Alternative Lengthening ◽

Different Types ◽

Promoter Mutations ◽

Pan Cancer

AbstractThe PCAWG Consortium has recently released an unprecedented set of tumor whole genome sequence (WGS) data from 2,658 cancer patients across 38 different primary tumor sites1. WGS is able to document the quantity and distribution of telomeric repeats2. In one of the papers analyzing the PCAWG dataset, Sieverling et al.3 confirmed previous data4 indicating that tumors with truncating ATRX or DAXX alterations, referred to as ATRX/DAXXtrunc, have an aberrant telomere variant repeat (TVR) distribution. By regarding these mutations, vs. TERT modifications (TERTmod; i.e. promoter mutations +/− amplifications +/− structural variations), as indicators of Alternative Lengthening of Telomeres (ALT) vs. telomerase, they built a random forest classifier for ALT-probability, and then associated genomic characteristics with the putative Telomere Maintenance Mechanism (TMM)3. However, we show here that equating ATRX/DAXXtrunc and TERTmod with ALT and telomerase, respectively, results in TMM predictions which correlate poorly with TMM assay data. ATRX/DAXXtrunc mutations are heterogeneously distributed in ALT-positive (ALT+) tumors of different types, as are TERTmod in telomerase-positive tumors4. Although these mutations are strongly associated with TMM, most tumors do not harbor them, making them an inadequate basis for building a classifier in a large-scale pan-cancer study4–7. Here, we provide a new analysis of the PCAWG data, based on C-circle assay (CCA)8 that is available for a subset of these tumors4,9,10. We show that the Sieverling et al. score overestimates the proportion of ALT associated with ATRX/DAXXtrunc and misclassifies ALT tumors when these mutations are absent. We also show some TVR correlate with ATRX/DAXXtrunc mutations, regardless of TMM. Finally, we propose a new classifier to identify ALT tumors in the PCAWG cohort.

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Alternative lengthening of telomeres in childhood neuroblastoma from genome to proteome

Nature Communications ◽

10.1038/s41467-021-21247-8 ◽

2021 ◽

Vol 12 (1) ◽

Cited By ~ 1

Author(s):

Sabine A. Hartlieb ◽

Lina Sieverling ◽

Michal Nadler-Holly ◽

Matthias Ziehm ◽

Umut H. Toprak ◽

...

Keyword(s):

High Frequency ◽

Clinical Course ◽

Population Based ◽

Telomeric Repeat ◽

Telomere Maintenance ◽

Study Cohort ◽

Alternative Lengthening Of Telomeres ◽

Course Of Disease ◽

Low Protein ◽

Alternative Lengthening

AbstractTelomere maintenance by telomerase activation or alternative lengthening of telomeres (ALT) is a major determinant of poor outcome in neuroblastoma. Here, we screen for ALT in primary and relapsed neuroblastomas (n = 760) and characterize its features using multi-omics profiling. ALT-positive tumors are molecularly distinct from other neuroblastoma subtypes and enriched in a population-based clinical sequencing study cohort for relapsed cases. They display reduced ATRX/DAXX complex abundance, due to either ATRX mutations (55%) or low protein expression. The heterochromatic histone mark H3K9me3 recognized by ATRX is enriched at the telomeres of ALT-positive tumors. Notably, we find a high frequency of telomeric repeat loci with a neuroblastoma ALT-specific hotspot on chr1q42.2 and loss of the adjacent chromosomal segment forming a neo-telomere. ALT-positive neuroblastomas proliferate slowly, which is reflected by a protracted clinical course of disease. Nevertheless, children with an ALT-positive neuroblastoma have dismal outcome.

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TRPV4 is a Prognostic Biomarker That Correlates With the Immunosuppressive Microenvironment and Chemoresistance of Anti-Cancer Drugs

10.21203/rs.3.rs-383566/v1 ◽

2021 ◽

Author(s):

kai wang ◽

Jun xing Feng ◽

Zhi ling Zheng ◽

Ying ze Chai ◽

Hui jun Yu ◽

...

Keyword(s):

Ovarian Cancer ◽

Transient Receptor Potential ◽

Immune Cell ◽

Colon Adenocarcinoma ◽

Enrichment Analysis ◽

Receptor Potential ◽

Gene Set Enrichment Analysis ◽

The Cancer Genome Atlas ◽

Free Interval ◽

Pan Cancer

Abstract Background: Transient receptor potential cation channel subfamily V member 4 (TRPV4) has been reported to regulate tumor progression in many tumor types. However, its association with the tumor immune microenvironment remains unclear.Methods: TRPV4 expression was assessed using data from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) database. The clinical features and prognostic roles of TRPV4 were assessed using TCGA cohort. Gene set enrichment analysis (GSEA) of TRPV4 was conducted using the R package clusterProfiler. We analyzed the association between TRPV4 and immune cell infiltration scores of TCGA samples downloaded from published articles and the TIMER2 database.Results: TRPV4 was highly expressed and associated with worse overall survival (OS), disease-specific survival (DSS), disease-free interval (DFI), and progression-free interval (PFI) in colon adenocarcinoma (COAD) and ovarian cancer. Furthermore, TRPV4 expression was closely associated with immune regulation-related pathways. Moreover, tumor-associated macrophage (TAM) infiltration levels were positively correlated with TRPV4 expression in TCGA pan-cancer samples. Immunosuppressive genes such as PD-L1, PD-1, CTLA4, LAG3, TIGIT, TGFB1, and TGFBR1 were positively correlated with TRPV4 expression in most tumors.Conclusions: Our results suggest that TRPV4 is an oncogene and a prognostic marker in COAD and ovarian cancer. High TRPV4 expression is associated with tumor immunosuppressive status and may contribute to TAM infiltration based on TCGA data from pan-cancer samples.

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Analysis of Expression Profiles of mRNA and lncRNA in Oviduct During Estrus Phase of Sheep (Ovis Aries) with Two Fecundity (FecB Gene) Genotypes

10.21203/rs.3.rs-119198/v1 ◽

2021 ◽

Author(s):

Weihao Chen ◽

Zhifeng Li ◽

Wei Sun ◽

Mingxing Chu

Keyword(s):

Embryo Development ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Interaction Network ◽

Enrichment Analysis ◽

Ovis Aries ◽

Functional Enrichment ◽

Saga Complex ◽

Rna Seq ◽

Estrus Phase

Abstract Background:In sheep, FecB is the essential biomarker of the fertility, previous researches have provided a detailed insight on the regulation involved estrus phase and FecB in the reproductive-related tissues including hypothalamus, pituitary, and ovary. However, as the host of embryo development and connection between the ovary and the uterus, little is known about the interaction between mRNAs and lncRNAs in sheep oviduct. In the present study, RNA-Seq was performed to identify the transcriptomic profiles of mRNAs and lncRNAs in oviduct during estrus phase of sheep with FecBBB/++ genotypes.Results:In total, 21,863 lncRNAs and 43,674 mRNAs were identified, 57 DE lncRNAs and 637 DE mRNAs were revealed in the comparisons between follicular phase and luteal phase, 26 DE lncRNAs and 421 DE lncRNAs were revealed in the comparisons between FecB BB genotype and FecB ++ genotype. Functional enrichment analysis suggested that GO and KEGG terms related to reproduction such as SAGA complex, ATP-binding cassette (ABC), Nestin, and Hippo signalling pathway. DE-interaction network suggested that LNC_018420 maybe the key regulators related to embryo development in sheep oviduct.Conclusion:This was the first study to reveal the transcriptomic profiles of mRNAs and lncRNAs in the oviduct of FecB BB/++ sheep at estrus phase using RNA-Seq. Our findings can provide new understanding on the molecular mechanisms of mRNAs and lncRNAs underlying sheep embryo development and also opening new lines of investigation in sheep reproduction.

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Gene Prioritization through Consensus Strategy, Enrichment Methodologies Analysis, and Networking for Osteosarcoma Pathogenesis

International Journal of Molecular Sciences ◽

10.3390/ijms21031053 ◽

2020 ◽

Vol 21 (3) ◽

pp. 1053 ◽

Cited By ~ 4

Author(s):

Alejandro Cabrera-Andrade ◽

Andrés López-Cortés ◽

Gabriela Jaramillo-Koupermann ◽

César Paz-y-Miño ◽

Yunierkis Pérez-Castillo ◽

...

Keyword(s):

Molecular Mechanisms ◽

Bone Cancer ◽

Interaction Network ◽

Enrichment Analysis ◽

Protein Protein Interaction ◽

Pathogenic Genes ◽

Total List ◽

Consensus Strategy ◽

Primary Bone ◽

Molecular Etiology

Osteosarcoma is the most common subtype of primary bone cancer, affecting mostly adolescents. In recent years, several studies have focused on elucidating the molecular mechanisms of this sarcoma; however, its molecular etiology has still not been determined with precision. Therefore, we applied a consensus strategy with the use of several bioinformatics tools to prioritize genes involved in its pathogenesis. Subsequently, we assessed the physical interactions of the previously selected genes and applied a communality analysis to this protein–protein interaction network. The consensus strategy prioritized a total list of 553 genes. Our enrichment analysis validates several studies that describe the signaling pathways PI3K/AKT and MAPK/ERK as pathogenic. The gene ontology described TP53 as a principal signal transducer that chiefly mediates processes associated with cell cycle and DNA damage response It is interesting to note that the communality analysis clusters several members involved in metastasis events, such as MMP2 and MMP9, and genes associated with DNA repair complexes, like ATM, ATR, CHEK1, and RAD51. In this study, we have identified well-known pathogenic genes for osteosarcoma and prioritized genes that need to be further explored.

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Nuclear receptors regulate alternative lengthening of telomeres through a novel noncanonical FANCD2 pathway

Science Advances ◽

10.1126/sciadv.aax6366 ◽

2019 ◽

Vol 5 (10) ◽

pp. eaax6366 ◽

Cited By ~ 8

Author(s):

Mafei Xu ◽

Jun Qin ◽

Leiming Wang ◽

Hui-Ju Lee ◽

Chung-Yang Kao ◽

...

Keyword(s):

Nuclear Receptors ◽

Direct Interaction ◽

Telomere Maintenance ◽

Telomeric Dna ◽

Core Complex ◽

Alternative Lengthening Of Telomeres ◽

Independent Manner ◽

Replication Complex ◽

Alternative Lengthening ◽

Key Steps

Alternative lengthening of telomeres (ALT) is known to use homologous recombination (HR) to replicate telomeric DNA in a telomerase-independent manner. However, the detailed process remains largely undefined. It was reported that nuclear receptors COUP-TFII and TR4 are recruited to the enriched GGGTCA variant repeats embedded within ALT telomeres, implicating nuclear receptors in regulating ALT activity. Here, we identified a function of nuclear receptors in ALT telomere maintenance that involves a direct interaction between COUP-TFII/TR4 and FANCD2, the key protein in the Fanconi anemia (FA) DNA repair pathway. The COUP-TFII/TR4-FANCD2 complex actively induces the DNA damage response by recruiting endonuclease MUS81 and promoting the loading of the PCNA-POLD3 replication complex in ALT telomeres. Furthermore, the COUP-TFII/TR4-mediated ALT telomere pathway does not require the FA core complex or the monoubiquitylation of FANCD2, key steps in the canonical FA pathway. Thus, our findings reveal that COUP-TFII/TR4 regulates ALT telomere maintenance through a novel noncanonical FANCD2 pathway.

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