Omics in urology: An overview on concepts, current status and future perspectives

Panunzio, Andrea; Tafuri, Alessandro; Princiotta, Alessandro; Gentile, Ilaria; Mazzucato, Giovanni; Trabacchin, Nicolò; Antonelli, Alessandro

doi:10.1177/03915603211022960

Cited by 7 publications

(4 citation statements)

References 77 publications

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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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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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“…Another potential of the lifelong OAB concept could be transition in care, as it has been recently brought to discussion in neurogenic LUT dysfunction among teenagers 14,15 aiming to ensure smooth transitions between different phases of care and optimize treatment outcomes. Additionally, “omics”—which encompass comprehensive studies of cellular biology such as genomics and proteomics—have been increasingly influential in various urological research areas 16 . From a lifelong perspective, they could be instrumental in formulating research questions for longitudinal studies, such as identifying biomarkers for clinical persistence factors or for therapeutic monitoring.…”

Section: Introductionmentioning

confidence: 99%

“…Additionally, "omics"which encompass comprehensive studies of cellular biology such as genomics and proteomics-have been increasingly influential in various urological research areas. 16 From a lifelong perspective, they could be instrumental in formulating research questions for longitudinal studies, such as identifying biomarkers for clinical persistence factors or for therapeutic monitoring.…”

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confidence: 99%

Exploring lifelong overactive bladder: Transitions, evidence, and clinical implications; A modified Delphi process

Bou Kheir,

Verbakel,

Vande Walle

et al. 2024

Neurourology and Urodynamics

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IntroductionOveractive bladder (OAB) is a prevalent urological condition characterized by urinary urgency, with or without urgency urinary incontinence, accompanied by increased daytime frequency and nocturia. However, the current definition of OAB lacks a specified time frame, hindering our understanding of the temporal aspects and transitions that occur within the OAB spectrum.MethodsA modified Delphi study was conducted in three rounds, involving a panel of international experts in functional urology, urogynaecology, geriatrics, transitional medicine, and pediatric urology. The study took place between February 2023 and June 2023 and employed two sequential rounds of online surveys, followed by a final hybrid group discussion session in June 2023.ResultsThe Delphi process resulted in a consensus definition of lifelong OAB as a persistent and continuous condition that may manifest differently from birth and evolve over time, with varying levels of clinical perception. The course of its progression is influenced by transition periods and modifying factors, mainly anatomical, hormonal, and psychosocial/stressors. Three main transition periods were identified: achievement of daytime continence, adulthood to elderly, and transition to frail elderly. The panel also considered the therapeutic and diagnostic implications of lifelong OAB, as well as future research prospects in terms of importance and feasibility.ConclusionsFuture longitudinal research is needed to develop this concept and further identify transitions and temporal dynamics.

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“…Phenomics has been established on the basis of the following development: first, there has been rapid development of multi-omics technologies that include genomics, proteomics, metabolomics, radiomics, epigenomics, transcriptomics and microbiomics (Hasin et al 2017 ; Leon-Mimila et al 2019 ; Olivier et al 2019 ; Panunzio et al 2021 ). Development of numerous new technologies including multi-omics technologies has enabled us to conduct large scale, multi-dimensional determinations on the biological properties of human subjects; second, development of AI and big data science has made it possible to analyze the big data from phenomic studies (Biswas and Chakrabarti 2020 ); third, development of modern biology and medicine has exposed significant relationships among various biological properties of human, indicating the potential and importance of not only determining the properties of individual units of life, including individual organs, tissues, cells and molecules, but also investigating the relationships among the biological properties of these units; fourth, it is required by precision medicine that multi-dimensional data of patients are collected and analyzed (Delude 2015 ; Houle et al 2010 ; Newgard and Attie 2010 ; Nicholson 2021 ; Zhang et al 2021 ); and fifth, cumulative evidence has indicated that the information from genetic studies on patients is far from sufficient for elucidating the mechanisms of diseases and establishing novel strategies for diagnosis and treatment of diseases (Delude 2015 ; Hasin et al 2017 ; Wu et al 2016 ).…”

Section: Introductionmentioning

confidence: 99%

Phenomic Studies on Diseases: Potential and Challenges

Ying

2023

Phenomics

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The rapid development of such research field as multi-omics and artificial intelligence (AI) has made it possible to acquire and analyze the multi-dimensional big data of human phenomes. Increasing evidence has indicated that phenomics can provide a revolutionary strategy and approach for discovering new risk factors, diagnostic biomarkers and precision therapies of diseases, which holds profound advantages over conventional approaches for realizing precision medicine: first, the big data of patients' phenomes can provide remarkably richer information than that of the genomes; second, phenomic studies on diseases may expose the correlations among cross-scale and multi-dimensional phenomic parameters as well as the mechanisms underlying the correlations; and third, phenomics-based studies are big data-driven studies, which can significantly enhance the possibility and efficiency for generating novel discoveries. However, phenomic studies on human diseases are still in early developmental stage, which are facing multiple major challenges and tasks: first, there is significant deficiency in analytical and modeling approaches for analyzing the multi-dimensional data of human phenomes; second, it is crucial to establish universal standards for acquirement and management of phenomic data of patients; third, new methods and devices for acquirement of phenomic data of patients under clinical settings should be developed; fourth, it is of significance to establish the regulatory and ethical guidelines for phenomic studies on diseases; and fifth, it is important to develop effective international cooperation. It is expected that phenomic studies on diseases would profoundly and comprehensively enhance our capacity in prevention, diagnosis and treatment of diseases.

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Omics in urology: An overview on concepts, current status and future perspectives

Cited by 7 publications

References 77 publications

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

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

Exploring lifelong overactive bladder: Transitions, evidence, and clinical implications; A modified Delphi process

Phenomic Studies on Diseases: Potential and Challenges

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