Investigating inter-chromosomal regulatory relationships through a comprehensive meta-analysis of matched copy number and transcriptomics data sets

Transcriptomic analysis of mRNA and miRNA reveals new insights into the regulatory mechanisms of Anadara granosa responses to heat stress

Temperature fluctuations resulting from climate change and global warming pose significant threats to various species. The blood clam, Anadara granosa, a commercially important marine bivalve, predominantly inhabits intertidal mudflats that are especially susceptible to elevated temperatures. This vulnerability has led to noticeable declines in the survival rates of A. granosa larvae, accompanied by an increase in malformations. Despite these observable trends, there is a lack of comprehensive research on the regulatory mechanisms underlying A. granosa's responses to heat stress. In this study, we examined the survival rates of A. granosa under varying high temperature conditions, selecting 34 °C as heat stress temperature. Enzyme activity assays have shed light on A. granosa's adaptive response to heat stress, revealing its ability to maintain redox balance and transition from aerobic to anaerobic metabolic pathways. Subsequently, mRNA and miRNA transcriptome analyses were conducted, elucidating several key responses of A. granosa to heat stress. These responses include the upregulation of transcription and protein synthesis, downregulation of proteasome activity, and metabolic pattern adjustments. Furthermore, we identified miRNA-mRNA networks implicated in heat stress responses, potentially serving as valuable candidate markers for A. granosa's heat stress response. Notably, we validated the involvement of agr-miR-3199 in A. granosa's heat stress response through its regulation of the target gene Foxj1. These findings not only deepen our understanding of the molecular mechanisms underlying the blood clam's response to heat stress but also offer valuable insights for enhancing heat stress resilience in the blood clam aquaculture industry. Moreover, they contribute to improved cultivation strategies for molluscs in the face of global warming and have significant implications for the conservation of marine resources and the preservation of ecological balance.

Automated Hypothesis Generation to Identify Signals Relevant in the Development of Mammalian Cell and Tissue Bioprocesses, With Validation in a Retinal Culture System

We have developed an accessible software tool (receptoR) to predict potentially active signaling pathways in one or more cell type(s) of interest from publicly available transcriptome data. As proof-of-concept, we applied it to mouse photoreceptors, yielding the previously untested hypothesis that activin signaling pathways are active in these cells. Expression of the type 2 activin receptor (Acvr2a) was experimentally confirmed by both RT-qPCR and immunochemistry, and activation of this signaling pathway with recombinant activin A significantly enhanced the survival of magnetically sorted photoreceptors in culture. Taken together, we demonstrate that our approach can be easily used to mine publicly available transcriptome data and generate hypotheses around receptor expression that can be used to identify novel signaling pathways in specific cell types of interest. We anticipate that receptoR (available at https://www.ucalgary.ca/ungrinlab/receptoR) will enable more efficient use of limited research resources.

A meta-analysis of multiple matched aCGH/expression cancer datasets reveals regulatory relationships and pathway enrichment of potential oncogenes

The copy numbers of genes in cancer samples are often highly disrupted and form a natural amplification/deletion experiment encompassing multiple genes. Matched array comparative genomics and transcriptomics datasets from such samples can be used to predict inter-chromosomal gene regulatory relationships. Previously we published the database METAMATCHED, comprising the results from such an analysis of a large number of publically available cancer datasets. Here we investigate genes in the database which are unusual in that their copy number exhibits consistent heterogeneous disruption in a high proportion of the cancer datasets. We assess the potential relevance of these genes to the pathology of the cancer samples, in light of their predicted regulatory relationships and enriched biological pathways. A network-based method was used to identify enriched pathways from the genes’ inferred targets. The analysis predicts both known and new regulator-target interactions and pathway memberships. We examine examples in detail, in particular the gene POGZ, which is disrupted in many of the cancer datasets and has an unusually large number of predicted targets, from which the network analysis predicts membership of cancer related pathways. The results suggest close involvement in known cancer pathways of genes exhibiting consistent heterogeneous copy number disruption. Further experimental work would clarify their relevance to tumor biology. The results of the analysis presented in the database METAMATCHED, and included here as an R archive file, constitute a large number of predicted regulatory relationships and pathway memberships which we anticipate will be useful in informing such experiments.

Interaction network analysis of YBX1 for identification of therapeutic targets in adenocarcinomas

Human Y-box binding protein-1 (YBX1) is a member of highly conserved cold-shock domain protein family, which is involved in transcriptional as well as translational regulation of many genes. Nuclear localization of YBX1 has been observed in various cancer types and it's overexpression has been linked to adverse clinical outcome and poor therapy response, but no diagnostic or therapeutic correlation has been established so far. This study aimed to identify differentially expressed novel genes among the interactors of YBX1 in different cancer types. Analysis of RNA-Seq data for colorectal, lung, prostate and stomach adenocarcinoma identified 39 unique genes, which are differentially expressed in the four adenocarcinoma types. Gene-enrichment analysis for the differentially expressed genes from individual adenocarcinoma with focus on unique genes resulted in a total of 57 gene sets specific to each adenocarcinoma. Gene ontology for commonly expressed genes suggested the pathways and possible mechanisms through which they affect each adenocarcinoma type considered in the study. Gene regulatory network constructed for the common genes and network topology was analyzed for the central nodes. Here 12 genes were found to play important roles in the network formation; among them, two genes FOXM1 and TOP2A were found to be in central network formation, which makes them a common target for therapeutics. Furthermore, five common differentially expressed genes in all adenocarcinomas were also identified.

Genome-wide association study and scan for signatures of selection point to candidate genes for body temperature maintenance under the cold stress in Siberian cattle populations

Background

Design of new highly productive livestock breeds, well-adapted to local climatic conditions is one of the aims of modern agriculture and breeding. The genetics underlying economically important traits in cattle are widely studied, whereas our knowledge of the genetic mechanisms of adaptation to local environments is still scarce. To address this issue for cold climates we used an integrated approach for detecting genomic intervals related to body temperature maintenance under acute cold stress. Our approach combined genome-wide association studies (GWAS) and scans for signatures of selection applied to a cattle population (Hereford and Kazakh Whiteheaded beef breeds) bred in Siberia. We utilized the GGP HD150K DNA chip containing 139,376 single nucleotide polymorphism markers.

Results

We detected a single candidate region on cattle chromosome (BTA)15 overlapping between the GWAS results and the results of scans for selective sweeps. This region contains two genes, MSANTD4 and GRIA4. Both genes are functional candidates to contribute to the cold-stress resistance phenotype, due to their indirect involvement in the cold shock response (MSANTD4) and body thermoregulation (GRIA4).

Conclusions

Our results point to a novel region on BTA15 which is a candidate region associated with the body temperature maintenance phenotype in Siberian cattle. The results of our research and the follow up studies might be used for the development of cattle breeds better adapted to cold climates of the Russian Federation and other Northern countries with similar climates.

Electronic supplementary material

The online version of this article (10.1186/s12863-019-0725-0) contains supplementary material, which is available to authorized users.