Next-generation characterization of the Cancer Cell Line Encyclopedia

Nature, Journal Year: 2019, Volume and Issue: 569(7757), P. 503 - 508

Published: May 1, 2019

Language: Английский

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Single-Cell RNA-Seq Technologies and Related Computational Data Analysis

Frontiers in Genetics, Journal Year: 2019, Volume and Issue: 10

Published: April 5, 2019

Single-cell RNA sequencing (scRNA-seq) technologies allow the dissection of gene expression at single-cell resolution, which greatly revolutionizes transcriptomic studies. A number scRNA-seq protocols have been developed, and these methods possess their unique features with distinct advantages disadvantages. Due to technical limitations biological factors, data are noisier more complex than bulk RNA-seq data. The high variability raises computational challenges in analysis. Currently, although an increasing bioinformatics proposed for analyzing interpreting data, novel algorithms required ensure accuracy reproducibility results. In this review, we provide overview currently available isolation technologies, discuss diverse analyses including quality control, read mapping, quantification, batch effect correction, normalization, imputation, dimensionality reduction, feature selection, cell clustering, trajectory inference, differential calling, alternative splicing, allelic regulatory network reconstruction. Further, outline prospective development applications technologies.

Language: Английский

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Roles and mechanisms of alternative splicing in cancer — implications for care

Nature Reviews Clinical Oncology, Journal Year: 2020, Volume and Issue: 17(8), P. 457 - 474

Published: April 17, 2020

Language: Английский

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Selective degradation of splicing factor CAPERα by anticancer sulfonamides

Nature Chemical Biology, Journal Year: 2017, Volume and Issue: 13(6), P. 675 - 680

Published: April 24, 2017

Language: Английский

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Electrochemical biosensors for the detection of lung cancer biomarkers: A review

Talanta, Journal Year: 2019, Volume and Issue: 206, P. 120251 - 120251

Published: Aug. 10, 2019

Language: Английский

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EMT and stemness: flexible processes tuned by alternative splicing in development and cancer progression

Molecular Cancer, Journal Year: 2017, Volume and Issue: 16(1)

Published: Jan. 13, 2017

Epithelial-to-mesenchymal transition (EMT) is associated with metastasis formation as well generation and maintenance of cancer stem cells. In this way, EMT contributes to tumor invasion, heterogeneity chemoresistance. Morphological functional changes involved in these processes require robust reprogramming gene expression, which only partially accomplished at the transcriptional level. Alternative splicing another essential layer expression regulation that expands cell proteome. This step post-transcriptional tightly controls identity between epithelial mesenchymal states during differentiation. Importantly, dysregulation factor function cancer-specific isoform frequently occurs human tumors, suggesting importance alternative for biology. review, we briefly discuss role programs development, differentiation progression. Next, focus on selected examples key factors are regulated post-transcriptionally through mechanisms. Lastly, describe relevant oncogenic splice-variants directly orchestrate biology EMT, may be envisioned novel targets therapeutic intervention.

Language: Английский

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Metals and Mechanisms of Carcinogenesis

The Annual Review of Pharmacology and Toxicology, Journal Year: 2019, Volume and Issue: 59(1), P. 537 - 554

Published: Jan. 6, 2019

Metal exposure is pervasive and not limited to sporadic poisoning events or toxic waste sites. Hundreds of millions people around the globe are affected by chronic metal exposure, which associated with serious health concerns, including cancer, as demonstrated in a variety studies at molecular, systemic, epidemiologic levels. Metal-induced toxicity carcinogenicity sophisticated complex nature. This review provides broad context holistic view currently available on mechanisms metal-induced carcinogenesis. Specifically, we focus five most prevalent carcinogenic metals, arsenic, nickel, cadmium, chromium, beryllium, their potential drive carcinogenesis humans. A comprehensive understanding behind development cancer can provide valuable insights for therapeutic intervention involving molecular targets

Language: Английский

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Transcriptome Profiling in Human Diseases: New Advances and Perspectives

International Journal of Molecular Sciences, Journal Year: 2017, Volume and Issue: 18(8), P. 1652 - 1652

Published: July 29, 2017

In the last decades, transcriptome profiling has been one of most utilized approaches to investigate human diseases at molecular level. Through expression studies, many biomarkers and therapeutic targets have found for several pathologies. This number is continuously increasing thanks total RNA sequencing. Indeed, this new technology completely revolutionized analysis allowing quantification gene levels allele-specific in a single experiment, as well identify novel genes, splice isoforms, fusion transcripts, world non-coding an unprecedented sequencing also employed important projects, like ENCODE (Encyclopedia regulatory elements) TCGA (The Cancer Genome Atlas), provide snapshot dozens cell lines thousands primary tumor specimens. Moreover, these studies paved way development data integration order facilitate management disease markers use clinics. scenario, ongoing clinical trials utilize through strategies instrument diagnosis numerous

Language: Английский

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The Landscape of Isoform Switches in Human Cancers

Molecular Cancer Research, Journal Year: 2017, Volume and Issue: 15(9), P. 1206 - 1220

Published: June 6, 2017

Alternative usage of transcript isoforms from the same gene has been hypothesized as an important feature in cancers. However, differential transcripts between conditions (isoform switching) not comprehensively characterized and across cancer types. To this end, we developed methods for identification visualization isoform switches with predicted functional consequences. Using these methods, switching RNA-seq data >5,500 patients covering 12 solid Isoform potential consequences were common, affecting approximately 19% multiple genes. Among these, leading to loss DNA sequence encoding protein domains more frequent than expected, particularly pancancer switches. We identified several powerful biomarkers: 31 highly predictive patient survival independent Our constitute resource researchers, available through interactive web tools. Moreover, our R package, enable systematic analysis other datasets.Implications: This study indicates that are common dysfunctional cells, which turn means expression should be analyzed at level. Visual Overview: http://mcr.aacrjournals.org/content/molcanres/15/9/1206/F1.large.jpg.Mol Cancer Res; 15(9); 1206-20. ©2017 AACR.

Language: Английский

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Phase Separation as a Missing Mechanism for Interpretation of Disease Mutations

Cell, Journal Year: 2020, Volume and Issue: 183(7), P. 1742 - 1756

Published: Dec. 1, 2020

Language: Английский

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