Epigenetics and Cancer

Paro, Renato; Grossniklaus, Ueli; Santoro, Raffaella; Wutz, Anton

doi:10.1007/978-3-030-68670-3_8

Cited by 3 publications

(2 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These diverse modalities can capture several aspects of a biological system, such as nucleic acid and protein sequences (Neidle (2008)), gene expression (Raghavachari and Garcia-Reyero (2018)) and the biomolecular structure and its activity (Vergoten and Theophanides (2012)). Other modalities include the epigenetic state and methylation information (Paro et al (2021)) of the genome, metabolites, and anatomic and phenotypic data.…”

Section: Introductionmentioning

confidence: 99%

Navigating the Multiverse: A Hitchhiker’s Guide to Selecting Harmonisation Methods for Multimodal Biomedical Data

Magateshvaren Saras,

Mitra,

Tyagi

2024

Preprint

View full text Add to dashboard Cite

Introduction: The application of machine learning (ML) techniques in classification and prediction tasks has greatly advanced our comprehension of biological systems. There is a notable shift in the trend towards integration methods that specifically target the simultaneous analysis of multiple modes or types of data, showcasing superior results compared to individual analyses. Despite the availability of diverse ML architectures for researchers interested in embracing a multimodal approach, the current literature lacks a comprehensive taxonomy that includes the pros and cons of these methods to guide the entire process. Closing this gap is imperative, necessitating the creation of a robust framework. This framework should not only categorise the diverse ML architectures suitable for multimodal analysis but also offer insights into their respective advantages and limitations. Additionally, such a framework can act as a guide for selecting an appropriate workflow for multimodal analysis. This comprehensive taxonomy would furnish a clear guidance and aid in informed decision-making within the progressively intricate realm of biomedical and clinical data analysis, and is imperative for advancing personalised medicine. Objective: The aims of the work are to comprehensively study and describe the harmonisation processes that are performed and reported in the literature and present a working guide that would enable planning and selecting an appropriate integrative model. Methods: A systematic review of publications that report the multimodal harmonisation of biomedical and clinical data has been performed. Results: We present harmonisation as a dual process of representation and integration, each with multiple methods and categories. The taxonomy of the various representation and integration methods are classified into six broad categories and detailed with the advantages, disadvantages and examples. A guide flowchart that describes the step-by-step processes that are needed to adopt a multimodal approach is also presented along with examples and references. Conclusions: This review provides a thorough taxonomy of methods for harmonising multimodal data and introduces a foundational 10-step guide for newcomers to implement a multimodal workflow.

show abstract

Section: Introductionmentioning

confidence: 99%

Navigating the Multiverse: A Hitchhiker’s Guide to Selecting Harmonisation Methods for Multimodal Biomedical Data

Magateshvaren Saras,

Mitra,

Tyagi

2024

Preprint

View full text Add to dashboard Cite

show abstract

“…Other molecular processes during seed formation, such as the derepression of transposable elements (TEs; Fultz et al 2015 ; Martínez and Köhler 2017 ) and gene regulation mediated by small RNAs (sRNAs; Lu et al 2012 ; Ng et al 2012 ), likely act in the endosperm to determine the success or failure of particular cross combinations. Of particular interest are sRNAs; these RNA forms are involved in plant development, reproduction, and genome reprogramming ( Haig 2013 ; Benkovics and Timmermans 2014 ; Borges and Martienssen 2015 ; Martínez and Köhler 2017 ; Satyaki and Gehring 2019 ; Paro et al 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Endosperm and Seed Transcriptomes Reveal Possible Roles for Small RNA Pathways in Wild Tomato Hybrid Seed Failure

Florez-Rueda

Fiscalini

Roth

et al. 2021

Genome Biology and Evolution

Self Cite

View full text Add to dashboard Cite

Crosses between the wild tomato species Solanum peruvianum and S. chilense result in hybrid seed failure (HSF), characterized by endosperm misdevelopment and embryo arrest. We previously showed that genomic imprinting, the parent-of-origin–dependent expression of alleles, is perturbed in hybrid endosperm, with many of the normally paternally expressed genes losing their imprinted status. Here, we report transcriptome-based analyses of gene and small RNA (sRNA) expression levels. We identified 2,295 genes and 387 sRNA clusters as differentially expressed when comparing reciprocal hybrid seed to seeds and endosperms from the two within-species crosses. Our analyses uncovered a pattern of overdominance in endosperm gene expression in both hybrid cross directions, in marked contrast to the patterns of sRNA expression in whole seeds. Intriguingly, patterns of increased gene expression resemble the previously reported increased maternal expression proportions in hybrid endosperms. We identified physical clusters of sRNAs; differentially expressed sRNAs exhibit reduced transcript abundance in hybrid seeds of both cross directions. Moreover, sRNAs map to genes coding for key proteins involved in epigenetic regulation of gene expression, suggesting a regulatory feedback mechanism. We describe examples of genes that appear to be targets of sRNA-mediated gene silencing; in these cases, reduced sRNA abundance is concomitant with increased gene expression in hybrid seeds. Our analyses also show that S. peruvianum dominance impacts gene and sRNA expression in hybrid seeds. Overall, our study indicates roles for sRNA-mediated epigenetic regulation in HSF between closely related wild tomato species.

show abstract

Cell biologist’s perspective: frontiers in the development of PROTAC-HDAC degraders

Sobko¹

2022

JSRT

View full text Add to dashboard Cite

This “Minireview and Perspective” article describes histone deacetylases (HDACs), as promising specific molecular targets to treat a variety of disease states by downregulating the expression of associated proteins with the use of a new generation of bioengineered compounds called protein targeting chimeras (PROTACs). We present the classification of HDACs, discuss their functions as key epigenetic regulators of gene expression, describe their roles in the biology of aging, describe histone- and nonhistone substrates of HDACs and their functions, and briefly introduce the concept of histone-modifying multiprotein complexes. Insight into the biological functions of specific HDACs comes from genetic knockout studies of individual genes encoding deacetylases. Initially discovered and newly developed HDAC inhibitors are powerful tools to investigate the functions of HDACs in cells and organs, that have also been successfully used in numerous preclinical and clinical studies, as promising drug candidates. We focus on the molecular and cellular mechanisms of their action, and introduce PROTACs, which are bivalent degrader molecules that have been recently developed to target HDACs. We then discuss recent studies focused on designing and testing several classes of selective and nonselective HDAC degraders in terms of their molecular and cellular mechanisms of action. Finally, we present open questions and new perspectives in developing the next generation of HDAC-degraders.

show abstract

Epigenetics and Cancer

Cited by 3 publications

References 32 publications

Navigating the Multiverse: A Hitchhiker’s Guide to Selecting Harmonisation Methods for Multimodal Biomedical Data

Navigating the Multiverse: A Hitchhiker’s Guide to Selecting Harmonisation Methods for Multimodal Biomedical Data

Endosperm and Seed Transcriptomes Reveal Possible Roles for Small RNA Pathways in Wild Tomato Hybrid Seed Failure

Cell biologist’s perspective: frontiers in the development of PROTAC-HDAC degraders

Contact Info

Product

Resources

About