Perspectives on Bulk-Tissue RNA Sequencing and Single-Cell RNA Sequencing for Cardiac Transcriptomics

Abstract

The heart has been the center of numerous transcriptomic studies in the past decade. Even though our knowledge of the key organ in our cardiovascular system has significantly increased over the last years, it is still not fully understood yet. In recent years, extensive efforts were made to understand the genetic and transcriptomic contribution to cardiac function and failure in more detail. The advent of Next Generation Sequencing (NGS) technologies has brought many discoveries but it is unable to comprehend the finely orchestrated interactions between and within the various cell types of the heart. With the emergence of single-cell sequencing more than 10 years ago, researchers gained a valuable new tool to enable the exploration of new subpopulations of cells, cell-cell interactions, and integration of multi-omic approaches at a single-cell resolution. Despite this innovation, it is essential to make an informed choice regarding the appropriate technique for transcriptomic studies, especially when working with myocardial tissue. Here, we provide a primer for researchers interested in transcriptomics using NGS technologies.

Conundrums of choice of ‘normal’ kidney tissue for single cell studies

“…They range from targeted interrogation of expression of select genes in a few cells to genome wide transcriptome analysis of thousands of cells or nuclei. The assays vary in depth of sequencing, extent of coding region covered, method of isolation of single cell or nuclei and costs per cell (Table 1) and have advantages and disadvantages [11,12,13]. Therefore, identifying the desired outcome will aid in selecting the assay best suited for purpose.…”

Group Heteroscedasticity - A Silent Saboteur of Power and False Discovery in RNA-Seq Differential Expression

“…Traditional bulk RNA sequencing (RNA-Seq) provides a revolutionary way to uncover the transcriptomic landscape of health and disease by measuring the gene expression of thousands of genes simultaneously over tens of thousands of cells using ultra-high-throughput sequencing 68,71 . Naturally, RNA-Seq has emerged as a universal and established technology in modern biology over the last decade or so for unraveling the molecular basis of biological processes 9,8 , as highlighted by increasingly common translational and clinical studies utilizing transcriptome profiling across a variety of disease areas and therapeutic outcomes 37,26,60,69,42,22 . Diverse applications of RNA-Seq include patient stratification, disease subtype identification, biomarker discovery, and mechanism of action study, among others 17,63 .…”

Expanding the concept of serotoninomics: perspectives for serotonin studies in the 20’s of the 21st century

“…The involvement of serotoninomics in biological processes is extensive and it is clear that a lot of research must to be done to further expand its physiological significance and to achieve a more complete understanding about its role in the pathologies in which its balance has been altered (for example, female infertility, andrology, embryology, animal biotechnology, stem cell biology, transplant technology or regenerative medicine, oncofertility and cancer, molecular pharmacology; Horgan and Kenny, 2011 ; Barh et al, 2013 ). Training about recent technological innovations, such as spectral flow cytometry, cryo-electron microscopy, focused ion beam microscopy, correlative microscopy, expansion microscopy, super-resolution microscopy, integration of multi-omic approaches at a single-cell resolution: Bulk-Single-Cell RNA Sequencing, will allow us to gain new perspectives into the function and cell biology and disease, which in turn will enable us to perform better therapeutic interventions ( Hasin et al, 2017 ; Chakraborty et al, 2018 ; Hegenbarth et al, 2022 ). As mentioned by the organizers of the Congress of Innovations in Reproductive Medicine 2030: IVF Technologies (RM2030; November 16–18, 2023, Paris, France): “The progress of medicine depends on new technologies and revolutionary concepts, which are translated into practice to solve long-standing problems for the benefit of patients, as well as fostering communication and debate of cutting-edge ideas among thoughtful selected leaders.”…”