Biology subjects

Schmidt, M. A.

Publications and source records attributed to Schmidt, M. A..

6 recordsLinked to original sources

bioRxiv2025

Sex-Stratified Transcriptomic Meta-Analysis of Alzheimer's Disease Reveal Brain Region and Sex Specific Dysregulation

ObjectiveAlzheimer disease (AD) is a neurodegenerative disorder leading to cognitive decline. Despite growing recognition of sex differences in epidemiology, symptomatology, and clinical outcomes of AD, the molecular mechanisms underlying these variations remain poorly defined. We performed transcriptome association studies of AD aiming to identify sex-specific and sex-dependent transcriptomic profiles that could provide insights into the molecular mechanisms underlying sex differences in AD pathogenesis. MethodsWe conducted a meta-analysis of bulk-RNAseq data derived from human postmortem brain studies. Specifically, we analyzed gene expression differences between individuals diagnosed with AD and non-cognitively impaired (NCI) individuals across two key brain regions: the prefrontal cortex and the temporal lobe. We performed stratified differential expression analyses separately in males and females, alongside combined analyses across sexes. Additionally, we assessed the data in relation to known AD genes, proteomic studies, and drug repurposing opportunities. ResultsBeyond the genes commonly dysregulated across both sexes, our meta-analyses identified multiple differentially expressed genes (DEGs) between AD and NCI that are either altered in only one sex or show different effects between sexes. Some genes are known AD genes from genetic studies, but others are novel. Correlation with proteomic data suggests that these transcriptional differences have functional significance, potentially contributing to the biological mechanisms underlying sex differences observed in AD. Finally, we identify drug compounds that are potential candidates for treatment. InterpretationOur findings enhance our understanding of sex-related differences in disease etiology and progression, and underscore the importance of incorporating sex as a critical variable in transcriptomic studies of AD. These insights help pave the way for more precise, personalized medicine approaches that account for sex-specific molecular mechanisms.

molecular biology↗

bioRxiv2024

Potential Benefits of Ketone Therapy as a Novel Immunometabolic Treatment for Schizophrenia

RationaleCurrent treatment options for patients with schizophrenia-spectrum disorders (SSD) remain unsatisfactory, leaving patients with persistent negative and cognitive symptoms and metabolic side effects. Therapeutic ketosis was recently hypothesized to target the bio-energetic pathophysiology of SSD. However, neuro-inflammation plays an important role in the pathobiology of SSD as well. Ideally, novel treatments would target both the bio-energetic, and the inflammatory aspects of SSD. In this study, we aimed to investigate the effects of ketone bodies on neuro-inflammation in an acute inflammation mouse model. Methods8-week-old male C57BL/6 N mice (n=11) were treated with either ketone ester (KE) or vehicle for 3 days. On day 3, a single intraperitoneal injection of lipopolysaccharide (LPS) or phosphate buffered saline (PBS) was administered. Mice were euthanized 24 h after LPS/PBS injection. Whole brain gene expression analysis using RT-PCR was done for Tnf-a, Il-6 and Il-1b. ResultsLPS caused a potent transcriptional upregulation of Tnf-a, Il-6 and Il-1b in the vehicle-treated mouse brain compared to PBS-injected controls. KE strongly and significantly attenuated the increased transcription of pro-inflammatory cytokines (Tnf-a, Il-6 and Il-1b) in the brain upon LPS injection compared to vehicle. ConclusionsKE potently dampened neuro-inflammation in this acute inflammation mouse model. Ketone therapy holds great promise as a treatment for SSD patients by simultaneously targeting two main pathophysiological disease pathways. We encourage more research into the immunometabolic potential of therapeutic ketosis in SSD. HighlightsO_LIA brain bio-energetic deficit and neuro-inflammation are involved in schizophrenia C_LIO_LIKetone therapy is being investigated as a bio-energetic treatment of schizophrenia C_LIO_LIKetone ester inhibits neuro-inflammation in an acute inflammation mouse mode C_LIO_LITherapeutic ketosis could target both pathophysiological pathways in SSD C_LIO_LIThe Immunometabolic potential of ketone therapy for SSD warrants further attention C_LI

neuroscience↗

bioRxiv2024

Pharmacogenomics Guided Spaceflight: the intersection between space-flown drugs and space genes

Ten years ago, it was predicted that the multi-omics revolution would also revolutionize space pharmacogenomics. Current barriers related to the findable, accessible, interoperable, and reproducible use of space-flown pharmaceutical data have contributed to a lack of progress beyond application of earth-based principles. To directly tackle these challenges, we have produced a novel database of all the drugs flown into space, compiled from publicly available ontological and spaceflight-related datasets, to exemplify analyses for describing significant spaceflight-related targets. By focusing on mechanisms perturbed by spaceflight, we have provided a novel avenue for identifying the most relevant changes within the drug absorption, distribution, metabolism, and excretion pathways. We suggest a set of space genes, by necessity limited to available tissue types, that can be expanded and modified based on future tissue-specific and mechanistic-specific high-throughput assays. In sum, we provide the justification and a definitive starting point for pharmacogenomics guided spaceflight as a foundation of precision medicine, which will enable long-term human habitation of the Moon, Mars, and beyond. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=147 SRC="FIGDIR/small/575951v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@48f739org.highwire.dtl.DTLVardef@5ecdb0org.highwire.dtl.DTLVardef@121c93org.highwire.dtl.DTLVardef@1122b3f_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2023

Collection of Biospecimens from the Inspiration4 Mission Establishes the Standards for the Space Omics and Medical Atlas (SOMA)

The SpaceX Inspiration4 mission provided a unique opportunity to study the impact of spaceflight on the human body. Biospecimen samples were collected from the crew at different stages of the mission, including before (L-92, L-44, L-3 days), during (FD1, FD2, FD3), and after (R+1, R+45, R+82, R+194 days) spaceflight, creating a longitudinal sample set. The collection process included samples such as venous blood, capillary dried blood spot cards, saliva, urine, stool, body swabs, capsule swabs, SpaceX Dragon capsule HEPA filter, and skin biopsies, which were processed to obtain aliquots of serum, plasma, extracellular vesicles, and peripheral blood mononuclear cells. All samples were then processed in clinical and research laboratories for optimal isolation and testing of DNA, RNA, proteins, metabolites, and other biomolecules. This paper describes the complete set of collected biospecimens, their processing steps, and long-term biobanking methods, which enable future molecular assays and testing. As such, this study details a robust framework for obtaining and preserving high-quality human, microbial, and environmental samples for aerospace medicine in the Space Omics and Medical Atlas (SOMA) initiative, which can also aid future experiments in human spaceflight and space biology.

molecular biology↗

bioRxiv2023

DEGAP: Dynamic Elongation of a Genome Assembly Path

Genome assembly remains to be a major task in genomic research. Despite the development over the past decades of different assembler software programs and algorithms, it is still a great challenge to assemble a complete genome with no gaps. With the latest DNA Circular Consensus Sequencing (CCS) technology, several assembler programs now can build a genome from raw sequencing data to contigs, however, some complex sequence regions remain as unresolved gaps. Here, we present a novel gap-filling software DEGAP that can resolve gap regions in genomes by utilizing the dual advantages of accuracy and length of high-fidelity (HiFi) reads. DEGAP optimizes HiFi reads by identifying the differences between reads and provides GapFiller or CtgLinker modes to eliminate or shorten gaps in genomes. DEGAP adopts a cyclic elongation strategy that automatically and dynamically adjusts parameters according to the complexity of the sequences and selects the optimal extension path. DEGAP has already been successfully applied to decipher complex genomic regions in several projects and may be widely employed to generate more gap-free genomes.

bioinformatics↗

bioRxiv2021

A novel adhesive complex at the base of intestinal microcilli

Intestinal epithelial cells form dense arrays of microvilli at the apical membrane to enhance their functional capacity. Microvilli contain a protocadherin-based intermicrovillar adhesion complex localized at their tips which regulates microvillar length and packaging. Here, we identify a second adhesive complex in microvilli of intestinal epithelial cells. This complex is localized at the basal region of microvilli and consists of the adhesion molecule TMIGD1, the phosphoprotein EBP50 and the F-actin - plasma membrane cross-linking protein ezrin. Ternary complex formation requires unmasking of the EBP50 PDZ domains by ezrin binding and is strongly enhanced upon mutating Ser162 located in PDZ domain 2 of EBP50. Dephosphorylation of EBP50 at S162 is mediated by PP1, a serine/threonine phosphatase localized at the microvillar base and involved in ezrin phosphocycling. Importantly, the binding of EBP50 to TMIGD1 enhances the dynamic turnover of EBP50 at microvilli in a Ser162 phosphorylation-dependent manner. We identify an adhesive complex at the microvillar base and propose a potential mechanism that regulates microvillar dynamics in enterocytes.

cell biology↗