Epigenetic machinery is functionally conserved in cephalopods

Epigenetic regulatory mechanisms are divergent across the animal kingdom, yet little is known about the epigenome in non-model organisms. Unique features of cephalopods make them attractive for investigating behavioral, sensory, developmental and regenerative processes, but using molecular approaches in such studies is hindered by the lack of knowledge about genome organization and gene regulation in these animals. We combined bioinformatic and molecular analysis of Octopus bimaculoides to identify gene expression signatures for 12 adult tissues and a hatchling, and investigate the presence and pattern of DNA methylation and histone methylation marks across tissues. This revealed a dynamic gene expression profile encoding several epigenetic regulators, including DNA methylation maintenance factors that were highly conserved and functional in cephalopods, as shown by detection of 5-methyl-cytosine in multiple tissues of octopus, squid and bobtail squid. WGBS of octopus brain and RRBS from a hatchling revealed that less than 10% of CpGs are methylated, highlighting a non-random distribution in the genome of all tissues, with enrichment in the bodies of a subset of 14,000 genes and absence from transposons. Each DNA methylation pattern encompassed genes with distinct functions and, strikingly, many of these genes showed similar expression levels across tissues. In contrast to the static pattern of DNA methylation, the histone marks H3K27me3, H3K9me3 and H3K4me3 were detected at different levels in diverse cephalopod tissues. This suggests the methylome and histone code cooperate to regulate tissue specific gene expression in a way that may be unique to cephalopods.

Gelsolin and dCryAB act downstream of muscle identity genes and contribute to preventing muscle splitting and branching in Drosophila

A combinatorial code of identity transcription factors (iTFs) specifies the diversity of muscle types in Drosophila. We previously showed that two iTFs, Lms and Ap, play critical role in the identity of a subset of larval body wall muscles, the lateral transverse (LT) muscles. Intriguingly, a small portion of ap and lms mutants displays an increased number of LT muscles, a phenotype that recalls pathological split muscle fibers in human. However, genes acting downstream of Ap and Lms to prevent these aberrant muscle feature are not known. Here, we applied a cell type specific translational profiling (TRAP) to identify gene expression signatures underlying identity of muscle subsets including the LT muscles. We found that Gelsolin (Gel) and dCryAB, both encoding actin-interacting proteins, displayed LT muscle prevailing expression positively regulated by, the LT iTFs. Loss of dCryAB function resulted in LTs with irregular shape and occasional branched ends also observed in ap and lms mutant contexts. In contrast, enlarged and then split LTs with a greater number of myonuclei formed in Gel mutants while Gel gain of function resulted in unfused myoblasts, collectively indicating that Gel regulates LTs size and prevents splitting by limiting myoblast fusion. Thus, dCryAB and Gel act downstream of Lms and Ap and contribute to preventing LT muscle branching and splitting. Our findings offer first clues to still unknown mechanisms of pathological muscle splitting commonly detected in human dystrophic muscles and causing muscle weakness.

Gerea: Prediction Of Gene Expression Regulators From Transcriptome Profiling Data To Transition Networks

Background: Mammalian genes are regulated at the transcriptional and post-transcriptional levels. These mechanisms may involve the direct promotion or inhibition of transcription via a regulator or post-transcriptional regulation through factors such as micro (mi)RNAs. Objective: This study aimed to construct gene regulation relationships modulated by causality inference-based miRNA-(transition factor)-(target gene) networks and analyze gene expression data to identify gene expression regulators. Methods: Mouse gene expression regulation relationships were manually curated from literature using a text mining method which was then employed to generate miRNA-(transition factor)-(target gene) networks. An algorithm was then introduced to identify gene expression regulators from transcriptome profiling data by applying enrichment analysis to these networks. Results: A total of 22,271 mouse gene expression regulation relationships were curated for 4,018 genes and 242 miRNAs. GEREA software was developed to perform the integrated analyses. We applied the algorithm to transcriptome data for synthetic miR-155 oligo-treated mouse CD4+ T-cells and confirmed that miR-155 is an important network regulator. The software was also tested on publicly available transcriptional profiling data for Salmonella infection, resulting in the identification of miR-125b as an important regulator. Conclusion: The causality inference-based miRNA-(transition factor)-(target gene) networks serve as a novel resource for gene expression regulation research, and GEREA is an effective and useful adjunct to the currently available methods. The regulatory networks and the algorithm implemented in the GEREA software package are available under a free academic license at website : http://www.thua45.cn/gerea.

Transcriptome-wide association study uncovers the role of essential genes in anthracycline-induced cardiotoxicity

Anthracyclines are highly effective chemotherapeutic agents; however, their clinical utility is limited by severe anthracycline-induced cardiotoxicity (ACT). Genome-wide association studies (GWAS) have uncovered several genetic variants associated with ACT, but the impact of these findings requires further elucidation. We conducted a transcriptome-wide association study (TWAS) using our previous GWAS summary statistics (n = 280 patients) to identify gene expression-related associations with ACT. We identified a genetic association between decreased expression of GDF5 and ACT (Z-score = −4.30, P = 1.70 × 10−5), which was replicated in an independent cohort (n = 845 patients, P = 3.54 × 10−3). Additionally, cell viability of GDF5-silenced human cardiac myocytes was significantly decreased in response to anthracycline treatment. Subsequent gene set enrichment and pathway analyses of the TWAS data revealed that genes essential for survival, cardioprotection and response to anthracyclines, as well as genes involved in ribosomal, spliceosomal and cardiomyopathy pathways are important for the development of ACT.

AB0108 USING RNA SEQUENCING TO IDENTIFY GENE EXPRESSION SIGNATURES ASSOCIATED WITH RESPONSE TO ABATACEPT IN PATIENTS WITH RHEUMATOID ARTHRITIS

Background:Rheumatoid arthritis (RA) is a common chronic autoimmune disease. Abatacept (CTLA4-immunoglobulin) is one of the biological disease-modifying antirheumatic drug (bDMARD) for RA patients with indequate response to methotrexate. Recently, Yokoyama-Kokuryo et al. compared gene expression levels between abatacept responders and non-responders in RA patients using a microarray and found that type I IFN score and expression levels of nine genes may be used as a biomarker to predict response to abatacept. However, little study used RNA sequencing (RNA-seq) to identify whole blood gene expression signatures to predict therapeutic response to abatacept.Objectives:The aim of this study is to identify gene expression signatures to predict therapeutic responses to abatacept in RA patients using RNA-seq.Methods:This study is a single-center, prospective study. We used a PAX gene Blood RNA kit to collect whole blood at baseline and 4 weeks after abatacept treatment from RA patients. We also measured DAS28, physician global assessment, HAQ, ESR, CRP at baseline and 12 week to calculate EULAR response at 12 week. Patients with good EULAR response were defined as responders and those with moderate or no EULAR response were defined as non-responders.Results:We finally conducted RNA-seq for whole blood from 7 RA patients initiating abatacept therapy. Of the 7 RA patients, one was non-responder and 6 were responders. We first use DESeq2 to analyze the differentially expressed genes of non-responder and responder before taking the drug. We used hierarchical clustering and PCA to evaluate the overall similarity of the samples, and group the patient data, and find that the nonresponder can be distinguished from responders. Subsequently, we analyzed the differentially expressed genes of the two groups of non-responder and responder patients before taking the drug. Before treatment, we found that 72 genes had a higher expression in the non-responder, and 23 genes had a higher expression level in responders. Figure 1 showed the top 20 DEG Heatmap between the non-responder and responders.Using these two sets of genes for GO analysis, we found that most of the pathways in the non-responder are related to immune response and cytokine production, and most of the pathways in the responders are related to antigen processing and MHC class II.Figure 1.Top 20 DEG Heatmap between non-responder and respondersConclusion:The study showed that most of the pathways in RA patients with no EULAR response to abatacept are related to immune response and cytokine production; while most of the pathways in RA patients with moderate/good response to abatacept are related to antigen processing and MHC class II.References:[1]Yokoyama-Kokuyo W, Yamazaki H, Takeuchi T, et al. Identification of molecules associated with response to abatacept in patients with rheumatoid arthritis. Arthritis Research & Therapy. 2020;22:46.Disclosure of Interests:Hsin-Hua Chen Grant/research support from: This is an investigator-sponsored trial with Bristol-Myers Squibb who provides funding support., Wen-Cheng Chao: None declared, Jing-Rong Wang: None declared, Tai-Ming Ko: None declared

High-throughput transcriptomic analysis of human primary hepatocyte spheroids exposed to per- and polyfluoroalkyl substances (PFAS) as a platform for relative potency characterization

Per- and poly-fluoroalkyl substances (PFAS) are widely found in the environment because of their extensive use and persistence. Although several PFAS are well studied, most lack toxicity data to inform human health hazard and risk assessment. This study focussed on four model PFAS: perfluorooctanoic acid (PFOA; 8 carbon), perfluorobutane sulfonate (PFBS; 4 carbon), perfluorooctane sulfonate (PFOS; 8 carbon), and perfluorodecane sulfonate (PFDS; 10 carbon). Human primary liver cell spheroids (pooled from 10 donors) were exposed to 10 concentrations of each PFAS and analyzed at four time-points. The approach aimed to: (1) identify gene expression changes mediated by the PFAS; (2) identify similarities in biological responses; (3) compare PFAS potency through benchmark concentration analysis; and (4) derive bioactivity exposure ratios (ratio of the concentration at which biological responses occur, relative to daily human exposure). All PFAS induced transcriptional changes in cholesterol biosynthesis and lipid metabolism pathways, and predicted PPARα activation. PFOS exhibited the most transcriptional activity and had a highly similar gene expression profile to PFDS. PFBS induced the least transcriptional changes and the highest benchmark concentration (i.e., was the least potent). The data indicate that these PFAS may have common molecular targets and toxicities, but that PFOS and PFDS are the most similar. The transcriptomic bioactivity exposure ratios derived here for PFOA and PFOS were comparable to those derived using rodent apical endpoints in risk assessments. These data provide a baseline level of toxicity for comparison with other known PFAS using this testing strategy.

Elucidating Anthracnose Resistance Mechanisms in Sorghum—A Review

Sorghum (Sorghum bicolor) is the fifth most cultivated cereal crop in the world, traditionally providing food, feed, and fodder, but more recently also fermentable sugars for the production of renewable fuels and chemicals. The hemibiotrophic fungal pathogen Colletotrichum sublineola, the causal agent of anthracnose disease in sorghum, is prevalent in the warm and humid climates where much of the sorghum is cultivated and poses a serious threat to sorghum production. The use of anthracnose-resistant sorghum germplasm is the most environmentally and economically sustainable way to protect sorghum against this pathogen. Even though multiple anthracnose resistance loci have been mapped in diverse sorghum germplasm in recent years, the diversity in C. sublineola pathotypes at the local and regional levels means that these resistance genes are not equally effective in different areas of cultivation. This review summarizes the genetic and cytological data underlying sorghum’s defense response and describes recent developments that will enable a better understanding of the interactions between sorghum and C. sublineola at the molecular level. This includes releases of the sorghum genome and the draft genome of C. sublineola, the use of next-generation sequencing technologies to identify gene expression networks activated in response to infection, and improvements in methodologies to validate resistance genes, notably virus-induced and transgenic gene silencing approaches.

Physiological System Dysregulation in Gene Expression Correlates Negatively with Age

We attempted to identify gene expression systems that dysregulate with age in human peripheral blood samples across five public datasets. Dysregulation of gene ontology (GO)-defined systems was measured using the Mahalanobis distance (DM), a measure of multivariant aberrance. We expected many weak positive DM-age correlations, indicating loss of homeostatic control. Out of the 5180 GO terms tested, we found 230 systems that replicated in at least three datasets. Surprisingly, all 230 systems showed negative DM-age correlations, in contrast to findings with clinical biomarkers. These systems were mostly metabolic functions related to small molecules and nitrogen compounds, transport functions, biosynthetic processes and response to stress functions. These results suggest a loss of responsiveness in these gene expression systems during the aging process, and contrast to some previous literature showing increased gene expression heterogeneity with age.

Genetic Underpinnings of Host Manipulation by Ophiocordyceps as Revealed by Comparative Transcriptomics

Ant-infecting Ophiocordyceps fungi are globally distributed, host manipulating, specialist parasites that drive aberrant behaviors in infected ants, at a lethal cost to the host. An apparent increase in activity and wandering behaviors precedes a final summiting and biting behavior onto vegetation, which positions the manipulated ant in a site beneficial for fungal growth and transmission. We investigated the genetic underpinnings of host manipulation by: (i) producing a high-quality hybrid assembly and annotation of the Ophiocordyceps camponoti-floridani genome, (ii) conducting laboratory infections coupled with RNAseq of O. camponoti-floridani and its host, Camponotus floridanus, and (iii) comparing these data to RNAseq data of Ophiocordyceps kimflemingiae and Camponotus castaneus as a powerful method to identify gene expression patterns that suggest shared behavioral manipulation mechanisms across Ophiocordyceps-ant species interactions. We propose differentially expressed genes tied to ant neurobiology, odor response, circadian rhythms, and foraging behavior may result by activity of putative fungal effectors such as enterotoxins, aflatrem, and mechanisms disrupting feeding behaviors in the ant.