reString: an open-source Python software to perform automatic functional enrichment retrieval, results aggregation and data visualization

Bisphenol A induces lipid metabolism disorder and impairs hepatopancreas of Sesarmops sinensis

Bisphenol A (BPA) is a chemical that disrupts the endocrine system and may have negative implications on the lipid metabolism of organisms. To ascertain BPA implications on lipid metabolism in the hepatopancreas of Sesarmops sinensis, we exposed S. sinensis to different concentrations of BPA for 14 days. The outcomes manifested that BPA may stimulate hepatopancreas injury and lipid deposition in the hepatopancreas of S. sinensis and lead to the increase of hepatosomatic index (HSI). Transcriptome analysis showed that lipid metabolism-related pathways were significantly enriched in KEGG pathways. BPA exposure also caused disorders in lipid metabolism by altering fatty acid composition and lipid metabolites. The up-regulation of lipid synthesis genes and the alteration of lipid transport genes may be important reasons for the disorder of lipid metabolism. Furthermore, these outcomes provide a fresh point of reference for comprehending the ecotoxicological impacts of BPA on aquatic organisms.

The transcriptome profiling of diseased mouse aortas discloses a dysregulation of the sympathetic neurotransmission in atherosclerosis

Previous reports suggest an association between the development of atherosclerosis and alterations in the aortic sympathetic nervous system, but there is no agreement on whether atherosclerotic plaques are accompanied by increased or decreased sympathetic innervation in the arterial wall. In the present study, the aortic transcriptional profile of mice with different predisposition to atherosclerosis was investigated to clarify how the expression of genes involved in sympathetic neurotransmission varied. Eight-week-old C57Bl/6J control mice, Apoe knockout mice (EKO), EKO mice overexpressing human apoA-I (EKO/hA-I) and double Apoe/Apoa1 knockout mice (DKO) mice were fed either a standard rodent diet or a Western-type diet for 22 weeks. Atherosclerosis was quantified, and the aortic transcriptome was analyzed by RNAseq. Western-type diet administration deeply modified the aortic transcriptome. In the genetically modified atherosclerosis-prone mouse lines, an upregulated expression of genes associated with the immunomodulatory response was observed, paralleled by a downregulated expression of the genes related to sympathetic nervous system. Functional enrichment analysis indicated that the presence of advanced atherosclerosis was accompanied by reduced neuronal generation, modulation of synapse chemical transmission, and catecholamine biosynthesis, supporting a relationship between atherosclerosis, dyslipidemia, and sympathetic neurotransmission.

Autism-linked NLGN3 is a key regulator of gonadotropin-releasing hormone deficiency

Gonadotropin-releasing hormone (GnRH) deficiency (GD) is a disorder characterized by absent or delayed puberty, with largely unknown genetic causes. The purpose of this study was to obtain and exploit gene expression profiles of GnRH neurons during development to unveil novel biological mechanisms and genetic determinants underlying GD. Here, we combined bioinformatic analyses of immortalized and primary embryonic GnRH neuron transcriptomes with exome sequencing from GD patients to identify candidate genes implicated in the pathogenesis of GD. Among differentially expressed and filtered transcripts, we found loss-of-function (LoF) variants of the autism-linked neuroligin 3 (NLGN3) gene in two unrelated patients co-presenting with GD and neurodevelopmental traits. We demonstrated that NLGN3 is upregulated in maturing GnRH neurons and that NLGN3 wild-type, but not mutant, protein promotes neuritogenesis when overexpressed in developing GnRH cells. Our data represent proof of principle that this complementary approach can identify new candidate GD genes and demonstrate that LoF NLGN3 variants can contribute to GD. This novel genotype-phenotype correlation implies common genetic mechanisms underlying neurodevelopmental disorders, such as GD and autistic spectrum disorder.

DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update)

DAVID is a popular bioinformatics resource system including a web server and web service for functional annotation and enrichment analyses of gene lists. It consists of a comprehensive knowledgebase and a set of functional analysis tools. Here, we report all updates made in 2021. The DAVID Gene system was rebuilt to gain coverage of more organisms, which increased the taxonomy coverage from 17 399 to 55 464. All existing annotation types have been updated, if available, based on the new DAVID Gene system. Compared with the last version, the number of gene-term records for most annotation types within the updated Knowledgebase have significantly increased. Moreover, we have incorporated new annotations in the Knowledgebase including small molecule-gene interactions from PubChem, drug-gene interactions from DrugBank, tissue expression information from the Human Protein Atlas, disease information from DisGeNET, and pathways from WikiPathways and PathBank. Eight of ten subgroups split from Uniprot Keyword annotation were assigned to specific types. Finally, we added a species parameter for uploading a list of gene symbols to minimize the ambiguity between species, which increases the efficiency of the list upload and eliminates confusion for users. These current updates have significantly expanded the Knowledgebase and enhanced the discovery power of DAVID.

Lack of ApoA-I in ApoEKO Mice Causes Skin Xanthomas, Worsening of Inflammation, and Increased Coronary Atherosclerosis in the Absence of Hyperlipidemia

Background:

HDL (high-density lipoprotein) and its major protein component, apoA-I (apolipoprotein A-I), play a unique role in cholesterol homeostasis and immunity. ApoA-I deficiency in hyperlipidemic, atheroprone mice was shown to drive cholesterol accumulation and inflammatory cell activation/proliferation. The present study was aimed at investigating the impact of apoA-I deficiency on lipid deposition and local/systemic inflammation in normolipidemic conditions.

Methods:

ApoE deficient mice, apoE/apoA-I double deficient (DKO) mice, DKO mice overexpressing human apoA-I, and C57Bl/6J control mice were fed normal laboratory diet until 30 weeks of age. Plasma lipids were quantified, atherosclerosis development at the aortic sinus and coronary arteries was measured, skin ultrastructure was evaluated by electron microscopy. Blood and lymphoid organs were characterized through histological, immunocytofluorimetric, and whole transcriptome analyses.

Results:

DKO were characterized by almost complete HDL deficiency and by plasma total cholesterol levels comparable to control mice. Only DKO showed xanthoma formation and severe inflammation in the skin-draining lymph nodes, whose transcriptome analysis revealed a dramatic impairment in energy metabolism and fatty acid oxidation pathways. An increased presence of CD4⁺ T effector memory cells was detected in blood, spleen, and skin-draining lymph nodes of DKO. A worsening of atherosclerosis at the aortic sinus and coronary arteries was also observed in DKO versus apoE deficient. Human apoA-I overexpression in the DKO background was able to rescue the skin phenotype and halt atherosclerosis development.

Conclusions:

HDL deficiency, in the absence of hyperlipidemia, is associated with severe alterations of skin morphology, aortic and coronary atherosclerosis, local and systemic inflammation.

An overview of technologies for MS-based proteomics-centric multi-omics

INTRODUCTION

Mass spectrometry-based proteomics reveals dynamic molecular signatures underlying phenotypes reflecting normal and perturbed conditions in living systems. Although valuable on its own, the proteome has only one level of moleclar information, with the genome, epigenome, transcriptome, and metabolome, all providing complementary information. Multi-omic analysis integrating information from one or more of these other domains with proteomic information provides a more complete picture of molecular contributors to dynamic biological systems.

AREAS COVERED

Here, we discuss the improvements to mass spectrometry-based technologies, focused on peptide-based, bottom-up approaches that have enabled deep, quantitative characterization of complex proteomes. These advances are facilitating the integration of proteomics data with other 'omic information, providing a more complete picture of living systems. We also describe the current state of bioinformatics software and approaches for integrating proteomics and other 'omics data, critical for enabling new discoveries driven by multi-omics.

EXPERT COMMENTARY

Multi-omics, centered on the integration of proteomics information with other 'omic information, has tremendous promise for biological and biomedical studies. Continued advances in approaches for generating deep, reliable proteomic data and bioinformatics tools aimed at integrating data across 'omic domains will ensure the discoveries offered by these multi-omic studies continue to increase.