4.6 Article

Characterization and evaluation of gene fusions as a measure of genetic instability and disease prognosis in prostate cancer

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

FusionGDB 2.0: fusion gene annotation updates aided by deep learning

Pora Kim et al.

Summary: The study introduces FusionGDB 2.0, a database with updated functional annotations of fusion genes, which is crucial for understanding genomic breakage context and developing therapeutic strategies. FusionGDB 2.0 provides comprehensive information on human fusion genes and their characteristics, making it a valuable resource for diverse human genomic studies.

NUCLEIC ACIDS RESEARCH (2022)

Article Oncology

Comprehensive Evaluation of Machine Learning Models and Gene Expression Signatures for Prostate Cancer Prognosis Using Large Population Cohorts

Ruidong Li et al.

Summary: This study systematically evaluated the performance of machine learning algorithms and gene expression signatures for prostate cancer prognosis. Survival analysis models outperformed binary classification models, with Cox-Ridge and Cox-PLS methods being the most robust. These findings can assist clinical decision-making.

CANCER RESEARCH (2022)

Review Biochemistry & Molecular Biology

The Expression of Proto-Oncogene ETS-Related Gene (ERG) Plays a Central Role in the Oncogenic Mechanism Involved in the Development and Progression of Prostate Cancer

Ealia Khosh Kish et al.

Summary: The ERG gene is consistently overexpressed in prostate cancer and is mainly due to the fusion of ERG and TMPRSS2 genes. ERG enhances tumor growth by promoting inflammatory and angiogenic responses and is involved in the epithelial-mesenchymal transition, increasing the metastatic ability of prostate cancer.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)

Article Biotechnology & Applied Microbiology

Accurate and efficient detection of gene fusions from RNA sequencing data

Sebastian Uhrig et al.

GENOME RESEARCH (2021)

Article Biochemistry & Molecular Biology

The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets

Damian Szklarczyk et al.

Summary: The STRING database integrates various associations between proteins, including physical interactions and functional associations, by collecting evidence from sources such as literature, databases, computational predictions, and systematic transfers. STRING aims for wide coverage and provides extensive user interface features and querying methods for experimental data.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

Pten-NOLC1 fusion promotes cancers involving MET and EGFR signalings

Jian-Hua Luo et al.

Summary: The fusion gene Pten-NOLC1, derived from Pten gene, is a driver for human cancers as it promotes cancer proliferation, growth, invasion, and metastasis. Its presence in primary cancer samples and cancer cell lines from different organs suggests its significance in oncogenesis.

ONCOGENE (2021)

Article Oncology

Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries

Hyuna Sung et al.

Summary: The global cancer burden in 2020 saw an estimated 19.3 million new cancer cases and almost 10.0 million cancer deaths. Female breast cancer surpassed lung cancer as the most commonly diagnosed cancer, while lung cancer remained the leading cause of cancer death. These trends are expected to rise in 2040, with transitioning countries experiencing a larger increase compared to transitioned countries due to demographic changes and risk factors associated with globalization and a growing economy. Efforts to improve cancer prevention measures and provision of cancer care in transitioning countries will be crucial for global cancer control.

CA-A CANCER JOURNAL FOR CLINICIANS (2021)

Article Multidisciplinary Sciences

Genetic fusions favor tumorigenesis through degron loss in oncogenes

Jing Liu et al.

Summary: Genetic fusions affecting degrons can alter protein stability and increase oncogene stability. Recurrent fusions such as BCR-ABL, CCDC6-RET, and PML-RARA disrupt protein stability by exchanging internal degrons. Additionally, fusions like EGFR or RAF1 can be stabilized by losing a C-terminal degron.

NATURE COMMUNICATIONS (2021)

Article Medicine, General & Internal

Prostate cancer

Richard J. Rebello et al.

Summary: Prostate cancer is a prevalent disease among men, with key genetic alterations including gene fusions, oncogene amplification, and mutations in androgen receptors. Treatment options range from active surveillance to surgery and radiotherapy for localized disease.

NATURE REVIEWS DISEASE PRIMERS (2021)

Review Oncology

Grading Evolution and Contemporary Prognostic Biomarkers of Clinically Significant Prostate Cancer

Konrad Sopyllo et al.

Summary: Prostate cancer treatment decisions are based on clinical stage and histological diagnosis, including Gleason grading. PSA is best suited as a marker of cancer relapse. Gleason grading remains the strongest prognostic parameter in localized prostate adenocarcinoma.

CANCERS (2021)

Article Oncology

Transcriptional landscape of PTEN loss in primary prostate cancer

Eddie Luidy Imada et al.

Summary: In this study, a transcriptional signature of PTEN loss in prostate cancer was identified, showing activation of immune systems and cell-cycle genes. The study also discovered potential novel lncRNAs associated with PTEN loss and prostate cancer progression, expanding the understanding of the molecular landscape in PCa. The findings suggest that PTEN loss in prostate cancer leads to increased immune system activation, contrary to observations in other cancers, which could have implications for the development of biomarkers and therapy choices.

BMC CANCER (2021)

Article Pathology

Diagnostic Utility of Gene Fusion Panel to Detect Gene Fusions in Fresh and Formalin-Fixed, Paraffin-Embedded Cancer Specimens

Lisa Haley et al.

Summary: The study demonstrates the high sensitivity and specificity of NanoString fusion assays in a clinical diagnostics laboratory, which is crucial for diagnosing leukemias/lymphomas and solid tumors.

JOURNAL OF MOLECULAR DIAGNOSTICS (2021)

Article Multidisciplinary Sciences

Detection of fusion gene transcripts in the blood samples of prostate cancer patients

Yan-Ping Yu et al.

Summary: Prostate cancer patients have various fusion transcripts in their blood samples, with high positivity rates for MAN2A1-FER, SLC45A2-AMACR, and Pten-NOLC1, and low positivity rates for CCNH-C5orf30 and mTOR-TP53BP1. Overall, 89.8% of patients tested positive for at least one fusion transcript in their blood samples.

SCIENTIFIC REPORTS (2021)

Review Oncology

Emerging Role of Chimeric RNAs in Cell Plasticity and Adaptive Evolution of Cancer Cells

Sumit Mukherjee et al.

Summary: Chimeric RNAs play a crucial role in cancer, generating phenotypic diversity and potentially impacting cancer cell survival and proliferation. Due to their association with oncogenic processes, chimeric RNAs are considered biomarkers for cancer diagnosis and could contribute to the development of drug resistance in cancer cells. Understanding the functional impact of chimeric RNAs in cancer cells from an evolutionary perspective could offer new insights for developing more effective and personalized therapies for cancer patients.

CANCERS (2021)

Article Oncology

Re-Evaluate Fusion Genes in Prostate Cancer

Ting Wei et al.

Summary: The majority of reported fusion genes cannot be validated in TCGA samples, ETS family and androgen response genes are significantly enriched in prostate cancer-specific fusion genes. Transcription activity is significantly repressed, and DNA methylation is significantly increased in samples carrying ERG fusion.

CANCER INFORMATICS (2021)

Article Biochemistry & Molecular Biology

snoDB: an interactive database of human snoRNA sequences, abundance and interactions

Philia Bouchard-Bourelle et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Biochemistry & Molecular Biology

ChimerDB 4.0: an updated and expanded database of fusion genes

Ye Eun Jang et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Biochemistry & Molecular Biology

ChiTaRS 5.0: the comprehensive database of chimeric transcripts matched with druggable fusions and 3D chromatin maps

Deepak Balamurali et al.

NUCLEIC ACIDS RESEARCH (2020)

Review Biochemistry & Molecular Biology

A guide to naming human non-coding RNA genes

Ruth L. Seal et al.

EMBO JOURNAL (2020)

Article Multidisciplinary Sciences

Landscape analysis of adjacent gene rearrangements reveals BCL2L14-ETV6 gene fusions in more aggressive triple-negative breast cancer

Sanghoon Lee et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Urology & Nephrology

ProstaTrend-A Multivariable Prognostic RNA Expression Score for Aggressive Prostate Cancer

Markus Kreuz et al.

EUROPEAN UROLOGY (2020)

Article Urology & Nephrology

Multifocal Primary Prostate Cancer Exhibits High Degree of Genomic Heterogeneity

Marthe Lovf et al.

EUROPEAN UROLOGY (2019)

Article Biochemistry & Molecular Biology

TumorFusions: an integrative resource for cancer-associated transcript fusions

Xin Hu et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemistry & Molecular Biology

Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer

David A. Quigley et al.

Article Multidisciplinary Sciences

Systematic analysis reveals molecular characteristics of ERG-negative prostate cancer

Qingyu Xiao et al.

SCIENTIFIC REPORTS (2018)

Review Oncology

Predictive significance of TMRPSS2-ERG fusion in prostate cancer: a meta-analysis

Chunjiao Song et al.

CANCER CELL INTERNATIONAL (2018)

Review Andrology

Surrogate endpoints in early prostate cancer research

Scott Williams

TRANSLATIONAL ANDROLOGY AND UROLOGY (2018)

Article Oncology

Significance of the TMPRSS2:ERG gene fusion in prostate cancer

Zhu Wang et al.

MOLECULAR MEDICINE REPORTS (2017)

Article Oncology

Novel transcription-induced fusion RNAs in prostate cancer

Sen Zhao et al.

ONCOTARGET (2017)

Article Public, Environmental & Occupational Health

TMPRSS2:ERG Gene Fusions in Prostate Cancer of West African Men and a Meta-Analysis of Racial Differences

Cindy Ke Zhou et al.

AMERICAN JOURNAL OF EPIDEMIOLOGY (2017)

Article Oncology

SLC45A3-ELK4 functions as a long non-coding chimeric RNA

Fujun Qin et al.

CANCER LETTERS (2017)

Article Biochemistry & Molecular Biology

Discovering and understanding oncogenic gene fusions through data intensive computational approaches

Natasha S. Latysheva et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

The Molecular Taxonomy of Primary Prostate Cancer

Adam Abeshouse et al.

Article Multidisciplinary Sciences

Tissue-based map of the human proteome

Mathias Uhlen et al.

SCIENCE (2015)

Article Biochemistry & Molecular Biology

The Molecular Signatures Database Hallmark Gene Set Collection

Arthur Liberzon et al.

CELL SYSTEMS (2015)

Article Pharmacology & Pharmacy

Therapeutic Targeting of Cancers with Loss of PTEN Function

Lloye M. Dillon et al.

CURRENT DRUG TARGETS (2014)

Review Oncology

ETS fusion genes in prostate cancer

Delila Gasi Tandefelt et al.

ENDOCRINE-RELATED CANCER (2014)

Article Biochemical Research Methods

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin et al.

BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

Atlas of Genetics and Cytogenetics in Oncology and Haematology in 2013

Jean-Loup Huret et al.

NUCLEIC ACIDS RESEARCH (2013)

Letter Biotechnology & Applied Microbiology

Towards a knowledge-based Human Protein Atlas

Mathias Uhlen et al.

NATURE BIOTECHNOLOGY (2010)

Article Multidisciplinary Sciences

Transcriptome sequencing to detect gene fusions in cancer

Christopher A. Maher et al.

NATURE (2009)

Article Endocrinology & Metabolism

Prostein expression is highly restricted to normal and malignant prostate tissues

M Kalos et al.

PROSTATE (2004)

Review Cell Biology

The ETS-domain transcription factor family

AD Sharrocks

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2001)

Article Biochemistry & Molecular Biology

A bacterial artificial chromosome library for sequencing the complete human genome

K Osoegawa et al.

GENOME RESEARCH (2001)