An Overview of Parasite Diversity
Eric S. Loker, Bruce V. Hofkin in Parasitology, 2023
For instance, the power of sequencing techniques like RNA-Seq allows one to rapidly profile the mRNA molecules being made within a biological sample (referred to as the transcriptome), thereby gaining a picture of what genes are being expressed. Many studies have now examined the transcriptome in different parasite life cycle stages, different tissues or organs within a parasite like a helminth, or even from single parasite cells. All provide distinctive insights into how the genome is used. Figure 2.35 is of a “heat map” that measures for a long list of parasite genes the extent to which each is expressed in different life cycle stages of S. mansoni. Note the distinctive patterns of gene expression for the six different life cycle stages shown. Increasingly detailed transcriptional profiles of individual organs of S. mansoni are available highlighting, for example, the different suites of genes produced in testes of male, or ovaries of female worms, including from worms that are paired or not. As another example, studies of different life cycle stages of the gut-inhabiting apicomplexan Cryptosporidium (sporozoites, epicellular forms and oocysts) reveal that the epicellular/intracellular stages of the parasite produce many more transcripts than found in oocysts, many of which are related to active biosynthesis for these rapidly growing stages.
Genetic testing for personalised medicine and limitations of the current medical practise in public health
Ben Y.F. Fong, Martin C.S. Wong in The Routledge Handbook of Public Health and the Community, 2021
In addition, a cohort research project on asthma, namely Unbiased BIOmarkers in PREDiction of respiratory disease outcomes (U-BIOPRED), has demonstrated that the use of the transcriptomic approach could lead to accurate diagnosis of different sub-types of asthma (Kuo et al., 2017). Different sub-types of asthma are treated differently, as they trigger different immunological responses in patients that can lead to similar phenotypes of asthmatic episodes. Together, these studies point to the direction that transcriptomic technologies allow for differentiation of subtypes of asthma and for designing effective treatment plans.
Will Systems Biology Transform Clinical Decision Support?
Paul Cerrato, John Halamka in Reinventing Clinical Decision Support, 2020
Transcriptome. Advances in transcriptomics are likewise providing insights into the pathophysiology of asthma. The transcriptome refers to RNA strands in our cells. Body proteins that carry out essential biological functions are created through a 3-step process: DNA provides the basic building blocks—the genes. These genes then go through the process of transcription, in which they are “converted” into RNA, which in turn undergoes the process of translation, which results in the generation of body proteins, including enzymes. As Bunyavanich and Shadt explain, “Transcriptomics offers a complementary and synergistic approach to GWAS for studying disease, as RNA reflects the more dynamic processes at play in a given tissue or tissues that underlie pathophysiology.”18 RNA sequencing has identified gene transcripts linked to eosinophilic esophagitis, a form of allergic inflammation of the esophagus, which are consistent with GWAS of patients with eosinophilic esophagitis. The GWAS also reveal relevant genetic variants on chromosome 5 (5q22). Similarly, RNA sequencing of airway biopsies has found several specific expressed genes, including SLC26A4, POSTN, and BCL2.
Emerging drug targets for triple-negative breast cancer: a guided tour of the preclinical landscape
Published in Expert Opinion on Therapeutic Targets, 2022
Xuemei Xie, Jangsoon Lee, Toshiaki Iwase, Megumi Kai, Naoto T Ueno
One of the key challenges is the intratumoral heterogenicity of TNBC, whose TME is a complex entity composed of different stromal and immune cells and soluble factors. In the past decades, next-generation technology platforms and transcriptomic and computational screening methods have become a new standard for discovering novel targets for cancer treatment. However, most transcriptome analysis techniques, including the use of gene expression microarrays, serial analysis of gene expression, massively parallel signature sequencing, RNA sequencing (RNA-seq), and the detection flux of RNA seq, are based on data from the bulk cell population of a given tissue. Thus, these analyses may overlook genes that are differentially expressed by individual cells in the tissue. Indeed, different responses to treatment have been observed in clinics due to the extensive intratumoral heterogenicity of TNBC, namely, the existence of different gene expression patterns in different clusters of the same tumor [189–191]. Ideally, then, efforts to identify promising therapeutic targets in TNBC should produce results at the single-cell or single-tumor-component level.
Stargardt disease and progress in therapeutic strategies
Published in Ophthalmic Genetics, 2022
Di Huang, Rachael C. Heath Jeffery, May Thandar Aung-Htut, Samuel McLenachan, Sue Fletcher, Steve D. Wilton, Fred K. Chen
Alternative splicing has been considered to contribute to extensive transcriptomic and proteomic complexity by generating multiple transcripts from a defined genomic repertoires, and underlies significant phenotypic difference (119,120). It was estimated that in the retina, 13% of novel mRNA junctions were expressed at levels similar to, or higher than the reference transcripts (121). However, this complexity comes at a cost (122). It is now evident that missense, nonsense or even silent mutations can cause disease through effects on splicing, rather than directly through amino acid changes that impair protein function (123), and for certain genes these types of mutation can be found in as many as 50% of the cases (123). To characterize the functional consequences of ABCA4 splice variants, series of in vitro splice assays, including midigene assays (124), patient-derived fibroblast-based assays (16), assays employing the induced pluripotent stem cell (iPSC) (125–128) and iPSC-derived retinal cells (127,129,130) etc., have been developed successively.
Use of omic technologies in early life gastrointestinal health and disease: from bench to bedside
Published in Expert Review of Proteomics, 2021
Lauren C Beck, Claire L Granger, Andrea C Masi, Christopher J Stewart
Given the importance of identifying underlying mechanisms and biomarkers for many GI pediatric diseases, gene expression studies represent yet another crucial field. Transcriptomics is the comprehensive study of all RNA transcripts transcribed by the genome, usually in a specific cell, at a given developmental stage, or under a specific set of conditions [40]. This includes both coding and non-coding RNA transcripts. Transcriptome profiling studies, therefore, are a very powerful way of dissecting specific transcriptional signatures of disease by allowing the identification of differentially expressed genes between healthy and diseased patients. The transcriptome of a patient can be captured using similar methods to those used for screening genetic content, for example, by RNA-microarrays or RNA-sequencing [41]. RNA-sequencing offers a more comprehensive analysis of the transcriptome than microarray experiments and does not require a priori knowledge [41].
Related Knowledge Centers
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