Whole Transcriptome Profiling: An RNA‐Seq Primer and Implications for Pharmacogenomics Research

Sá, Ana Caroline Costa; Sadée, Wolfgang

doi:10.1111/cts.12511

Cited by 9 publications

(4 citation statements)

References 90 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, gene polymorphisms, differences in gene methylation due to age, sex, and environmental factors are all considered contributing factors. 35 , 36 We observed variability in the magnitude (frequency of CD69 + cells in bulk PBMCs, number of DEGs per subject) and the specificity of the response (pathways). Stimulating PBMC in vitro with specific antigen (SPZ) and isolating antigen-specific cells prior to processing samples for transcriptomics reduced the individual variability.…”

Section: Discussionmentioning

confidence: 88%

Human transcriptional signature of protection after Plasmodium falciparum immunization and infectious challenge via mosquito bites

Mura,

Misganaw,

Gautam

et al. 2023

Human Vaccines & Immunotherapeutics

View full text Add to dashboard Cite

The identification of immune correlates of protection against infectious pathogens will accelerate the design and optimization of recombinant and subunit vaccines. Systematic analyses such as immunoprofiling including serological, cellular, and molecular assessments supported by computational tools are key to not only identify correlates of protection but also biomarkers of disease susceptibility. The current study expands our previous cellular and serological profiling of vaccine-induced responses to a whole parasite malaria vaccine. The irradiated sporozoite model was chosen as it is considered the most effective vaccine against malaria. In contrast to whole blood transcriptomics analysis, we stimulated peripheral blood mononuclear cells (PBMC) with sporozoites and enriched for antigen-specific cells prior to conducting transcriptomics analysis. By focusing on transcriptional events triggered by antigen-specific stimulation, we were able to uncover quantitative and qualitative differences between protected and non-protected individuals to controlled human malaria infections and identified differentially expressed genes associated with sporozoite-specific responses. Further analyses including pathway and gene set enrichment analysis revealed that vaccination with irradiated sporozoites induced a transcriptomic profile associated with Th1-responses, Interferon-signaling, antigen-presentation, and inflammation. Analyzing longitudinal time points not only post-vaccination but also post-controlled human malaria infection further revealed that the transcriptomic profile of protected vs non-protected individuals was not static but continued to diverge over time. The results lay the foundation for comparing protective immune signatures induced by various vaccine platforms to uncover immune correlates of protection that are common across platforms.

show abstract

Section: Discussionmentioning

confidence: 88%

Human transcriptional signature of protection after Plasmodium falciparum immunization and infectious challenge via mosquito bites

Mura,

Misganaw,

Gautam

et al. 2023

Human Vaccines & Immunotherapeutics

View full text Add to dashboard Cite

show abstract

“…It is widely known that natural products are characterized by their structural diversity; therefore, the molecular mechanisms of natural products are highly complex [ 35 , 36 ]. RNA-seq is a novel technology that objectively evaluates the molecular mechanisms of drugs at the omics level; observing the change of molecule landscape and biological functions after drug treatment is made possible through RNA-seq [ 37 , 38 ]. In this study, RNA-seq was performed to explore the molecular mechanisms underlying T4O.…”

Section: Discussionmentioning

confidence: 99%

Terpinen-4-ol inhibits the proliferation and mobility of pancreatic cancer cells by downregulating Rho-associated coiled-coil containing protein kinase 2

et al. 2022

View full text Add to dashboard Cite

Terpinen-4-ol (T4O), a compound isolated from the seeds of turmeric, has exhibited anti-malignancy, anti-aging, and anti-inflammatory properties in previous studies. However, the specific effects and molecular mechanisms of T4O on pancreatic cancer (PC) cells remain largely unknown. In this study, we demonstrated that T4O markedly suppressed PC cell proliferation and colony formation in vitro and induced apoptosis. Similarly, T4O significantly inhibited the migration and invasion of PC cells in vitro . Through RNA sequencing, 858 differentially expressed genes (DEGs) were identified, which were enriched in the Rhodopsin (RHO)/ Ras homolog family member A (RHOA) signaling pathway. Rho-associated coiled-coil containing protein kinase 2 (ROCK2), a DEG enriched in the RHO/RHOA signaling pathway, was considered as a key target of T4O in PC cells; it was significantly reduced after T4O treatment, highly expressed in PC tissues, and negatively associated with patient outcome. Overexpression of ROCK2 significantly reduced the inhibitory effects of T4O on PC cell proliferation and mobility. Moreover, T4O inhibited cell proliferation in vivo and decreased the Ki-67, cell nuclear antigen, EMT markers, and ROCK2 expression. In conclusion, we consider that T4O can suppress the malignant biological behavior of PC by reducing the expression of ROCK2, thus contributing to PC therapy.

show abstract

“…The fragments are amplified and then sequenced with millions of short reads (Nagalakshmi et al, 2008). The major advantages of RNA-seq over that of microarray technology is that both low and high abundance RNA transcripts can be detected efficiently, as well as the ability to detect new transcription start sites, new RNA splice sites, new exons, and even new genes (Sá, Sadee, & Johnson, 2018). A number of other new technologies that can be used to analyze different components of the transcriptome, such as sequencing newly synthesized RNA, sequencing mRNA bound to ribosomes, or measuring the rate of RNA degradation, are listed in Table 2. RNA-seq is used in two main ways.…”

Section: Technologies In Transcriptome Researchmentioning

confidence: 99%

Omics technologies for kidney disease research

Wang

Yang

Fan

et al. 2020

The Anatomical Record

View full text Add to dashboard Cite

show abstract

Whole Transcriptome Profiling: An RNA‐Seq Primer and Implications for Pharmacogenomics Research

Cited by 9 publications

References 90 publications

Human transcriptional signature of protection after Plasmodium falciparum immunization and infectious challenge via mosquito bites

Human transcriptional signature of protection after Plasmodium falciparum immunization and infectious challenge via mosquito bites

Terpinen-4-ol inhibits the proliferation and mobility of pancreatic cancer cells by downregulating Rho-associated coiled-coil containing protein kinase 2

Omics technologies for kidney disease research

Contact Info

Product

Resources

About