An overview of advances in multi-omics analysis in prostate cancer

Zhang, Enchong; Zhang, Mo; Shi, Changlong; Sun, Li; Shan, Liping; Zhang, Hui; Song, Yi

doi:10.1016/j.lfs.2020.118376

Cited by 19 publications

(19 citation statements)

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“…Single-omics analysis plays a key role in the diagnosis and therapy of diseases in modern society. However, with the development of research technologies and needs, single-omics is not sufficiently comprehensive; one type of omics change can't represent the overall status of the disease, only 10–20% of transcriptome changes are associated with proteomic data ( 186 ). Abnormal gene expression is also a risk factor leading to tumor cell formation.…”

Section: Discussionmentioning

confidence: 99%

Advances in Multi-Omics Applications in HBV-Associated Hepatocellular Carcinoma

Cui

et al. 2021

Front. Med.

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Hepatitis B virus (HBV) specifically infects liver cells, leading to progressive liver cirrhosis and significantly increasing the risk of hepatocellular carcinoma (HCC). The maturity of sequencing technology, improvement in bioinformatics data analysis and progress of omics technologies had improved research efficiency. The occurrence and progression of HCC are affected by multisystem and multilevel pathological changes. With the application of single-omics technologies, including genomics, transcriptomics, metabolomics and proteomics in tissue and body fluid samples, and even the novel development of multi-omics analysis on a single-cell platform, HBV-associated HCC changes can be better analyzed. The review summarizes the application of single omics and combined analysis of multi-omics data in HBV-associated HCC and proposes the importance of multi-omics analysis in the type of HCC, which provide the possibility for the precise diagnosis and therapy of HBV-associated HCC.

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Section: Discussionmentioning

confidence: 99%

Advances in Multi-Omics Applications in HBV-Associated Hepatocellular Carcinoma

Cui

et al. 2021

Front. Med.

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“…For patients uncomfortable with active surveillance, or who display clinical criteria of higher risk disease, potentially curative treatment options include radical prostatectomy (the surgical removal of the prostate gland) or radiation therapy, albeit these modalities come with common side effects that seriously affect patients’ quality of life, including incontinence and loss of erectile function [ 5 ]. The increasing implementation of prostate-specific antigen (PSA) testing in the Western world over the past three decades has led to many more cases being detected but this also contributed significantly to overtreatment of men with PCa [ 6 ]. PSA is also upregulated in non-cancerous disease states, such as prostatitis, enlarged prostate (benign prostatic hyperplasia) and infection.…”

Section: Prostate Cancer Heterogeneitymentioning

confidence: 99%

Unravelling Prostate Cancer Heterogeneity Using Spatial Approaches to Lipidomics and Transcriptomics

Mutuku

Spotbeen

Trim

et al. 2022

Cancers

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Due to advances in the detection and management of prostate cancer over the past 20 years, most cases of localised disease are now potentially curable by surgery or radiotherapy, or amenable to active surveillance without treatment. However, this has given rise to a new dilemma for disease management; the inability to distinguish indolent from lethal, aggressive forms of prostate cancer, leading to substantial overtreatment of some patients and delayed intervention for others. Driving this uncertainty is the critical deficit of novel targets for systemic therapy and of validated biomarkers that can inform treatment decision-making and to select and monitor therapy. In part, this lack of progress reflects the inherent challenge of undertaking target and biomarker discovery in clinical prostate tumours, which are cellularly heterogeneous and multifocal, necessitating the use of spatial analytical approaches. In this review, the principles of mass spectrometry-based lipid imaging and complementary gene-based spatial omics technologies, their application to prostate cancer and recent advancements in these technologies are considered. We put in perspective studies that describe spatially-resolved lipid maps and metabolic genes that are associated with prostate tumours compared to benign tissue and increased risk of disease progression, with the aim of evaluating the future implementation of spatial lipidomics and complementary transcriptomics for prognostication, target identification and treatment decision-making for prostate cancer.

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“…Detailed transcriptomic profiles of cells or tissues are now mostly generated by next-generation sequencing techniques. They can focus on mRNAs but may include non-coding RNAs, such as miRNAs, lncRNAs or circular RNAs (circRNAs) [ 146 , 147 , 148 , 149 ]. RNA modifications, such as N6-methyladenosine methylation, are also being examined at a large scale due to their impact on stability and splicing [ 150 ].…”

Section: Transcriptomementioning

confidence: 99%

From Omics to Multi-Omics Approaches for In-Depth Analysis of the Molecular Mechanisms of Prostate Cancer

Nevedomskaya

Haendler

2022

IJMS

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Cancer arises following alterations at different cellular levels, including genetic and epigenetic modifications, transcription and translation dysregulation, as well as metabolic variations. High-throughput omics technologies that allow one to identify and quantify processes involved in these changes are now available and have been instrumental in generating a wealth of steadily increasing data from patient tumors, liquid biopsies, and from tumor models. Extensive investigation and integration of these data have led to new biological insights into the origin and development of multiple cancer types and helped to unravel the molecular networks underlying this complex pathology. The comprehensive and quantitative analysis of a molecule class in a biological sample is named omics and large-scale omics studies addressing different prostate cancer stages have been performed in recent years. Prostate tumors represent the second leading cancer type and a prevalent cause of cancer death in men worldwide. It is a very heterogenous disease so that evaluating inter- and intra-tumor differences will be essential for a precise insight into disease development and plasticity, but also for the development of personalized therapies. There is ample evidence for the key role of the androgen receptor, a steroid hormone-activated transcription factor, in driving early and late stages of the disease, and this led to the development and approval of drugs addressing diverse targets along this pathway. Early genomic and transcriptomic studies have allowed one to determine the genes involved in prostate cancer and regulated by androgen signaling or other tumor-relevant signaling pathways. More recently, they have been supplemented by epigenomic, cistromic, proteomic and metabolomic analyses, thus, increasing our knowledge on the intricate mechanisms involved, the various levels of regulation and their interplay. The comprehensive investigation of these omics approaches and their integration into multi-omics analyses have led to a much deeper understanding of the molecular pathways involved in prostate cancer progression, and in response and resistance to therapies. This brings the hope that novel vulnerabilities will be identified, that existing therapies will be more beneficial by targeting the patient population likely to respond best, and that bespoke treatments with increased efficacy will be available soon.

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An overview of advances in multi-omics analysis in prostate cancer

Cited by 19 publications

References 100 publications

Advances in Multi-Omics Applications in HBV-Associated Hepatocellular Carcinoma

Advances in Multi-Omics Applications in HBV-Associated Hepatocellular Carcinoma

Unravelling Prostate Cancer Heterogeneity Using Spatial Approaches to Lipidomics and Transcriptomics

From Omics to Multi-Omics Approaches for In-Depth Analysis of the Molecular Mechanisms of Prostate Cancer

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