Biology subjects

Michael, M.

Publications and source records attributed to Michael, M..

9 recordsLinked to original sources

bioRxiv2026

Hypoxia versus immune depletion - immune profiling and treatment cessation provide mechanistic insights and considerations for translation in Leigh syndrome

Genetic mitochondrial diseases (GMDs) are major challenges to human health accounting for a significant fraction of heritable neurologic diseases, myopathies, and inborn errors of metabolism. Leigh syndrome (LS) is the most common clinical presentation of GMD in pediatric patients. LS is a severe and complex disease for which effective clinical therapies are currently lacking. Preclinical therapies identified in the Ndufs4(-/-) mouse model of LS include immune-targeting interventions and chronic mild hypoxia (11% oxygen). Immune-targeting interventions include rapamycin and high-dose pexidartinib, the latter appearing to fully suppress disease. The mechanisms underlying the benefits of hypoxia remain unclear, and the relationship between hypoxia and immune interventions have not been assessed. Here, we report the immune profile of brainstem of the Ndufs4(-/-) mouse model prior to and after disease onset and the impact of pexidartinib treatment. We provide evidence that macrophages/monocytes drive pathology, consistent with recent genetic studies. We additionally find that pre-disease onset animals lack signs of inflammation, and that the elimination of leukocytes fully suppresses the molecular signature of disease. Finally, using distinct post-developmental periods of treatment, we find pexidartinib and rapamycin provide benefits which persist long beyond treatment cessation, while cessation of hypoxia results in rapid disease onset and an acceleration of disease progression. These findings are consistent with hypoxia acting upstream of immune cell activation and have major implications for the therapeutic translation of both hypoxia and immune targeting interventions. Our findings establish hypoxia-cessation as a novel method for synchronizing inflammatory disease onset in the Ndufs4(-/-) model which will be useful in future mechanistic studies.

pathology↗

bioRxiv2026

Precision measurement of non-conscious avoidance reactions using 3D tracking: Validation across olfaction and vision

One of our sensory systems key functions is to detect threats in the environment. Sensory information eliciting negative emotions, such as fear or disgust, triggers instinctive avoidance reactions. This core survival mechanism is believed to be expressed as subtle non-conscious postural reactions, even when participants are instructed to stand still. Such avoidance behavior has mainly been studied using indirect measures that make participants aware of their posture (e.g. force-plate based methods) or measures that depend on explicit cognitive tasks, like moving a joystick to indicate an urge to approach or avoid the stimulus; experimental tasks with limited ecological validity and generalizability. Therefore, despite the importance of this basic survival strategy, its underlying mechanisms are still poorly understood. Here, we used a novel 3D-camera-based method allowing direct but implicit measures of postural reactions with high precision. Participants are aware that they are being filmed but, crucially, are not informed that distance measures are obtained. We assessed this ecologically valid measure of approach/avoidance responses in two different sensory modalities: olfaction and vision. Participants were standing upright while exposed to either olfactory or visual stimuli and verbally rating their perceived valence in each trial. In response to subjectively unpleasant odors and images, participants moved away from the stimulus source, as compared to pleasant stimuli. These results demonstrate a putative modality-independent early proxy for avoidance behavior in response to perceived negative valence. Considering its face validity and general applicability, this novel experimental method presents new possibilities for assessing non-conscious approach-avoidance responses in humans.

neuroscience↗

bioRxiv2025

Mammalian PABPC4 is non-essential, but has roles in growth, post-natal survival and haematopoiesis.

Cytoplasmic poly(A)-binding proteins (PABPCs) are multifunctional RNA-binding proteins which play crucial roles in mRNA translation and stability. In mammals, two family members, PABPC1 and PABPC4 appear widely expressed, but the consequences of their loss of function in vivo remain unknown, despite PABPC4 being implicated in a variety of human diseases. We address this knowledge gap using a series of Pabpc4 knock-out mice. Unexpectedly, we reveal that mammalian PABPC4 is not essential for development, contrary to findings in non-mammalian vertebrates. However, its loss affects birth weight, post-natal growth trajectories and survival, although these were not tightly associated. Growth to adulthood was impacted in a sexually dimorphic manner. Viable Pabpc4-deficient mice allowed us to interrogate roles of Pabpc4 that may affect human health. Anaemia represents a large global health burden, and work in a red blood cell (RBC) model suggested a potential role in haemoglobin synthesis. Surprisingly in vivo, we find that Pabpc4 loss did not reduce haemoglobin levels but caused microcytic RBCs and altered RBC distribution width. Moreover, conditional genetic approaches established that this was not a red blood cell intrinsic effect. Taken together, this work provides unprecedented insights into the in vivo functions of mammalian PABPC4, and caution against inferring mammalian PABPC function from work in cell-based models and/or non-mammalian species. The generated mouse lines also form a valuable resource with which to further investigate the roles of PABPC4 in health and disease. Significance StatementRNA-binding protein (RBP)-mediated post-transcriptional regulation is essential for life and life-long health. Cytoplasmic poly(A)-binding proteins are family of RBPs that regulate multiple aspects of cytoplasmic mRNA fate. PABPC4 is an understudied family member, genetically associated with a wide range of human diseases. By creating a series of Pabpc4 knock-out mice, we surprisingly find it is not essential but is required for normal post-natal survival and growth and normal red blood cell development. Our results emphasise the importance of whole organism studies for understanding mammalian PABP function, uncovering differences between function inferred from other vertebrate species and prior cell-based work. The generated mice also provide a valuable resource for exploring its potential broad roles in human disease.

molecular biology↗

bioRxiv2025

Multi-omic dereplication of antibiotic production by diffusion chamber isolated bacteria from Australian soils

Soil bacteria are a major source of clinically useful antibiotics, yet the majority of soil-dwelling microorganisms remain uncultivable by standard laboratory methods. To access this untapped microbial diversity, we employed microbial diffusion chambers to isolate bacteria from ten Australian soil samples. A total of 1,218 bacterial isolates were recovered, representing a diverse collection spanning 61 genera from 32 families, covering the major known phyla of soil bacteria. Antibiotic activity screening revealed that 16% of isolates inhibited the growth of at least one of E. coli or S. aureus, with 120 isolates displaying activity against multidrug-resistant pathogens including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecium (VRE). Mass spectrometry-based dereplication using GNPS identified known antibiotics in 33% of bioactive strains, including actinomycin D, nonactins, and valinomycin. Genomic analysis confirmed the presence of corresponding biosynthetic gene clusters (BGCs), while targeted analysis of selected strains uncovered production of additional antibiotics such as nigericin and streptothricin that were not initially detected by mass spectrometry. Our results demonstrate that diffusion chambers enhance bacterial recovery from soil and show the benefits of a combined pipeline including bioactivity screening, mass spectrometry, and genomics for effective antibiotic dereplication and discovery. Impact StatementThis study delivers a significant advance in natural product discovery by demonstrating that microbial diffusion chambers can dramatically improve the recovery of diverse soil bacteria with antibiotic-producing potential from Australian soil samples. By integrating in situ cultivation with high-throughput screening, mass spectrometry-based dereplication and genome mining, this study yielded more than 1,200 bacterial isolates--including many with activity against multidrug-resistant pathogens--and confirms the production of both known and previously undetected antibiotics. The discovery of streptothricin production via genomics, despite its absence from mass spectrometry data, underscores the power of a multi-layered dereplication strategy. This work not only validates the utility of diffusion chambers for unlocking the "rare biosphere" of uncultivable microbes but also highlights critical methodological refinements to diversify antibiotic-producing strains beyond Streptomyces. The findings will inform and accelerate future efforts to discover urgently needed antibiotics from environmental microbiomes. Data SummaryThe whole-genome sequences were deposited in the National Center for Biotechnology Information National Library of Medicine under BioProject accession number PRJNA1272227.

microbiology↗

bioRxiv2023

Human Gut Microbial Sulfonolipids are linked to Inflammatory Bowel Diseases through Toll-Like Receptor 4 Signaling

The trillions of microorganisms inhabiting the human gut are intricately linked to human health. At the species abundance level, correlational studies have connected specific bacterial taxa to various diseases. While the abundances of these bacteria in the gut serve as good indicators for disease progression, understanding the functional metabolites they produce is critical to decipher how these microbes influence human health. Here, we report a unique biosynthetic enzyme-guided disease correlation approach to uncover microbial functional metabolites as potential molecular mechanisms in human health. We directly connect the expression of gut microbial sulfonolipid (SoL) biosynthetic enzymes to inflammatory bowel disease (IBD) in patients, revealing a negative correlation. This correlation is then corroborated by targeted metabolomics, identifying that SoLs abundance is significantly decreased in IBD patient samples. We experimentally validate our analysis in a mouse model of IBD, showing that SoLs production is indeed decreased while inflammatory markers are increased in diseased mice. In support of this connection, we apply bioactive molecular networking to show that SoLs consistently contribute to the immunoregulatory activity of SoL-producing human microbes. We further reveal that sulfobacins A and B, two representative SoLs, primarily target Toll-like receptor 4 (TLR4) to mediate immunomodulatory activity through blocking TLR4s natural ligand lipopolysaccharide (LPS) binding to myeloid differentiation factor 2, leading to significant suppression of LPS-induced inflammation and macrophage M1 polarization. Together, these results suggest that SoLs mediate a protective effect against IBD through TLR4 signaling and showcase a widely applicable biosynthetic enzyme-guided disease correlation approach to directly link the biosynthesis of gut microbial functional metabolites to human health.

biochemistry↗

bioRxiv2022

The global chromatin compaction pathway silences transcription during meiotic prophase in C. elegans

Abstract/SummaryWhile it has been appreciated for decades that prophase-arrested oocytes are transcriptionally silenced on a global level, the molecular pathways that promote silencing have remained elusive. Previous work in C. elegans has shown that both topoisomerase II (TOP-2) and condensin II collaborate with the H3K9me heterochromatin pathway to silence gene expression in the germline during L1 starvation, and that the PIE-1 protein silences the genome in the P-lineage of early embryos. Here, we show that all three of these silencing systems, TOP-2/condensin II, H3K9me, and PIE-1, are required for transcriptional repression in oocytes. We find that H3K9me3 marks increase dramatically on chromatin during silencing, and that silencing is under cell cycle control. We also find that PIE-1 localizes to the nucleolus just prior to silencing, and that nucleolar dissolution during silencing is dependent on TOP-2/condensin II. Our data identify both the molecular components and the trigger for genome silencing in oocytes and establish a link between PIE-1 nucleolar residency and its ability to repress transcription.

developmental biology↗

bioRxiv2021

Members of the CUGBP Elav-Like Family of RNA-Binding Proteins are Expressed in Distinct Populations of Primary Sensory Neurons

Primary sensory Dorsal Root Ganglia (DRG) neurons are diverse, with distinct populations that respond to specific stimuli. Previously, we observed that functionally distinct populations of DRG neurons express mRNA transcript variants with different 3 untranslated regions (3UTRs). 3UTRs harbor binding sites for interaction with RNA-binding proteins (RBPs) for transporting mRNAs to subcellular domains, modulating transcript stability and regulating the rate of translation. In the current study, analysis of publicly available single-cell RNA-Sequencing (scRNA-Seq) data generated from adult mice revealed that 17 3UTR-binding RBPs were enriched in specific populations of DRG neurons. This included 4 members of the CUGBP Elav-Like Family (CELF): CELF2 and CELF4 were enriched in peptidergic, CELF6 in both peptidergic and nonpeptidergic and CELF3 in tyrosine hydroxylase-expressing neurons. Immunofluorescence studies confirmed that 60% of CELF4+ neurons are small diameter C fibers and 33% medium diameter myelinated (likely A{delta}) fibers and showed that CELF4 is distributed to peripheral termini. Co-expression analyses using transcriptomic data and immunofluorescence revealed that CELF4 is enriched in nociceptive neurons that express GFRA3, CGRP and the capsaicin receptor TRPV1. Re-analysis of published transcriptomic data from macaque DRG revealed a highly similar distribution of CELF members, and re-analysis of single-nucleus RNA sequencing data derived mouse and rat DRG after sciatic injury revealed differential expression of CELFs in specific populations of sensory neurons. We propose that CELF RNA-binding proteins may regulate the fate of mRNAs in populations of nociceptors, and may play a role in pain and/or neuronal regeneration following nerve injury.

neuroscience↗

bioRxiv2021

Targeting of TP53-independent cell cycle checkpoints overcomes FOLFOX resistance in Metastatic Colorectal Cancer

Patients with colorectal cancer (CRC) frequently develop liver metastases during the course of their disease. A substantial proportion of them receive neoadjuvant FOLFOX (5-Fluorouracil, Oxaliplatin, Leucovorin) prior to surgery in an attempt to enable successful surgical removal of their metastases and to reduce the risk of recurrence. Yet, the majority of patients progress during treatment or recur following surgery, and molecular mechanisms that contribute to FOLFOX resistance remain poorly understood. Here, using a combination of phenotypic, transcriptomic and genomic analyses of both tumor samples derived from patients with metastatic CRC and matching patient-derived tumor organoids (PDTOs), we characterize a novel FOLFOX resistance mechanism and identify inhibitors that target this mechanism to resensitize metastatic organoids to FOLFOX. Resistant PDTOs, identified after in vitro exposure to FOLFOX, exhibited elevated expression of E2F pathway, S phase, G2/M and spindle assembly checkpoints (SAC) genes. Similar molecular features were detected in CRLM from patients with progressive disease while under neoadjuvant FOLFOX treatment, highlighting the relevance of this finding. FOLFOX resistant PDTOs displayed inactivating mutations of TP53 and exhibited transcriptional features of P53 pathway downregulation. We found that they accumulated in early S-phase and underwent significant DNA damage during FOLFOX exposure, thereafter arresting in G2/M while they repaired their DNA after FOLFOX withdrawal. In parallel, results of a large kinase inhibitor screen indicated that drugs targeting regulators of the DNA damage response, G2M checkpoint and SAC had cytotoxic effects on PDTOs generated from patients whose disease progressed during treatment with FOLFOX. Corroborating this finding, CHK1 and WEE1 inhibitors were found to synergize with FOLFOX and sensitize previously resistant PDTOs. Additionally, targeting the SAC master regulator MPS1 using empesertib after exposure to FOLFOX, when cells accumulate in G2M, was also very effective to kill FOLFOX-resistant PDTOs. Our results indicate that targeted and timely inhibition of specific cell cycle checkpoints shows great potential to improve response rates to FOLFOX in patients with metastatic CRC, for whom therapeutic alternatives remain extremely limited.

cancer biology↗

bioRxiv2018

Neuropathy and neural plasticity in the subcutaneous white adipose depot.

The difficulty in obtaining as well as maintaining weight loss, together with the loss of metabolic control in conditions like diabetes and cardiovascular disease, may represent pathological situations of inadequate neural communication between the brain and peripheral organs and tissues. Innervation of adipose tissues by peripheral nerves provides a means of communication between the master metabolic regulator in the brain (chiefly the hypothalamus), and energy-expending and energy-storing cells in the body (primarily adipocytes). Although chemical and surgical denervation studies have clearly demonstrated how crucial adipose tissue neural innervation is for maintaining proper metabolic health, we have uncovered that adipose tissue becomes neuropathic in various conditions of metabolic dysregulation. Here, utilizing both human and mouse adipose tissues, we present evidence of adipose tissue neuropathy, or loss of innervation, under pathophysiological conditions such as obesity, diabetes, and aging, all of which are concomitant with insult to the adipose organ and metabolic dysfunction. Neuropathy is indicated by loss of nerve fiber protein expression, reduction in synaptic markers, and less neurotrophic factor expression in adipose tissue. Aging-related adipose neuropathy particularly results in loss of innervation around the tissue vasculature. These findings underscore that peripheral neuropathy is not restricted to classic tissues like the skin of distal extremities, and that loss of innervation to adipose may trigger or exacerbate metabolic diseases. In addition, we have demonstrated stimulation of adipose tissue neural plasticity with exercise, cold exposure or neurotrophic factor treatment, which may ameliorate adipose neuropathy and be a potential therapeutic option to re-innervate adipose and restore metabolic health.

neuroscience↗