Biology subjects

Elias, J.

Publications and source records attributed to Elias, J..

8 recordsLinked to original sources

bioRxiv2025

Beta2* Nicotinic Receptors Tune Prefrontal Behavior Through Distinct Neuronal Populations

Beta2 subunit-containing nicotinic acetylcholine receptors (beta2*nAChRs) are highly expressed in the prefrontal cortex (PFC) and critically regulate behavioral and cognitive domains that are disrupted in neuropsychiatric disorders. Despite their therapeutic potential, the cell-type- and circuit-specific functions of beta2* nAChRs remain poorly defined, partially due to the lack of selective pharmacological tools. Here, we delineate the cellular expression patterns and behavioral roles of beta2* nAChRs expressed in a general vs. highly specific neuronal populations of the mouse PFC. Using fluorescence in situ hybridization (FISH), we mapped beta2 nicotinic subunit expression across cortical layers and major neuronal classes. We then employed CRISPR-mediated knockdown (KD) to reduce beta2* nAChRs expression selectively in two distinct PFC neuronal populations and, for comparison, in a striatal population. The KD of beta2* nAChRs in a mixed population of excitatory and inhibitory neurons in deep PFC layers resulted in a mild impairment of social and exploratory behaviors. In contrast, KD in a highly selective population of superficial-layer interneurons expressing the serotonin receptor 5HT3a induced a robust hypersocial phenotype, accompanied by changes in exploratory behavior. Notably, KD of beta2* nAChRs in a rare NPY-expressing striatal population slightly affected similar behavioral domains, but in the opposite direction to PFC manipulations. Together, these findings reveal opposing, cell-type- and region-specific contributions of beta2* nAChRs to behavioral regulations, highlighting the necessity of circuit-resolved targeting strategies to improve the precision and efficacy of therapeutic intervention for neuropsychiatric disorders.

neuroscience↗

bioRxiv2024

The N-terminus of YY1 regulates DNA and RNA binding affinity for both the zinc-fingers and an unexpected nucleic acid binding domain

Transcription factors (TFs) play central roles in dictating cellular identity and function by regulating gene expression programs. Beyond their well-folded DNA binding domains (DBDs) which recognize cognate DNA elements in the genome, TFs are enriched for intrinsically disordered regions (IDRs), which have a host of proposed functions including facilitating protein-protein interactions, aiding in binding site search, and binding RNA. Defining intrinsic regulatory properties of TFs requires further mechanistic investigation. We chose to investigate the DNA and RNA binding properties of Yin Yang 1 (YY1), a ubiquitously expressed TF directly involved in transcriptional activation, repression and genome architecture. Through systematic in vitro nucleic acid binding experiments we resolve conflicting literature defining the RNA binding interface of YY1, demonstrating that there are two RNA binding domains within YY1: its canonical 4 zinc finger DBD and a previously unannotated nucleic acid binding domain, which we term the REPO-NAB. Furthermore, we discover surprising autoinhibitory properties that the N-terminus of the protein imparts on each of these binding domains. Our results provide a new example of IDR-mediated regulation within TFs and enables future mechanistically precise functional investigations.

molecular biology↗

bioRxiv2024

Confounding factors in targeted degradation of short-lived proteins

Targeted protein degradation has recently emerged as a novel option in drug discovery. Natural protein half-life is expected to affect the efficacy of degrading agents, but to what extent it influences target protein degradation has not been systematically explored. Using mathematical modelling of protein degradation, we demonstrate that the natural half-life of a target protein has a dramatic effect on the level of protein degradation induced by a degrader agent which can pose significant hurdles to screening efforts. Moreover, we show that upon screening for degraders of short-lived proteins, agents that stall protein synthesis, such as GSPT1 degraders and generally cytotoxic compounds, deceptively appear as protein degrading agents. This is exemplified by the disappearance of short-lived proteins such as MCL1 and MDM2 upon GSPT1 degradation and upon treatment with cytotoxic agents such as doxorubicin. These findings have implications for target selection as well as for the type of control experiments required to conclude that a novel agent works as a bona fide targeted protein degrader.

cancer biology↗

bioRxiv2023

SARS-CoV-2 Nsp1 regulates translation start site fidelity to promote infection

A better mechanistic understanding of virus-host interactions can help reveal vulnerabilities and identify opportunities for therapeutic interventions. Of particular interest are essential interactions that enable production of viral proteins, as those could target an early step in the virus lifecycle. Here, we use subcellular proteomics, ribosome profiling analyses and reporter assays to detect changes in polysome composition and protein synthesis during SARS-CoV-2 (CoV2) infection. We identify specific translation factors and molecular chaperones whose inhibition impairs infectious particle production without major toxicity to the host. We find that CoV2 non-structural protein Nsp1 selectively enhances virus translation through functional interactions with initiation factor EIF1A. When EIF1A is depleted, more ribosomes initiate translation from an upstream CUG start codon, inhibiting translation of non-structural genes and reducing viral titers. Together, our work describes multiple dependencies of CoV2 on host biosynthetic networks and identifies druggable targets for potential antiviral development.

microbiology↗

bioRxiv2021

Re-evaluating the role of nucleosomal bivalency in early development

Nucleosomes, composed of DNA and histone proteins, represent the fundamental repeating unit of the eukaryotic genome1; posttranslational modifications of these histone proteins influence the activity of the associated genomic regions to regulate cell identity2-4. Traditionally, trimethylation of histone 3-lysine 4 (H3K4me3) is associated with transcriptional initiation5-10, whereas trimethylation of H3K27 (H3K27me3) is considered transcriptionally repressive11-15. The apparent juxtaposition of these opposing marks, termed "bivalent domains"16-18, was proposed to specifically demarcate of small set transcriptionally-poised lineage-commitment genes that resolve to one constituent modification through differentiation, thereby determining transcriptional status19-22. Since then, many thousands of studies have canonized the bivalency model as a chromatin hallmark of development in many cell types. However, these conclusions are largely based on chromatin immunoprecipitations (ChIP) with significant methodological problems hampering their interpretation. Absent direct quantitative measurements, it has been difficult to evaluate the strength of the bivalency model. Here, we present reICeChIP, a calibrated sequential ChIP method to quantitatively measure H3K4me3/H3K27me3 bivalency genome-wide, addressing the limitations of prior measurements. With reICeChIP, we profile bivalency through the differentiation paradigm that first established this model16,18: from naive mouse embryonic stem cells (mESCs) into neuronal progenitor cells (NPCs). Our results cast doubt on every aspect of the bivalency model; in this context, we find that bivalency is widespread, does not resolve with differentiation, and is neither sensitive nor specific for identifying poised developmental genes or gene expression status more broadly. Our findings caution against interpreting bivalent domains as specific markers of developmentally poised genes.

molecular biology↗

bioRxiv2021

Succinate Dehydrogenase (SDH)-subunit C regulates muscle oxygen consumption and fatigability in an animal model of pulmonary emphysema.

Patients with pulmonary emphysema often develop locomotor muscle dysfunction, which is independently associated with disability and higher mortality in that population. Muscle dysfunction entails reduced force-generation capacity which partially depends on fibers oxidative potential, yet very little mechanistic research has focused on muscle respiration in pulmonary emphysema. Using a recently established animal model of pulmonary emphysema-driven skeletal muscle dysfunction, we found downregulation of succinate dehydrogenase (SDH) subunit C in association with lower oxygen consumption and fatigue-tolerance in locomotor muscles. Reduced SDH activity has been previously observed in muscles from patients with pulmonary emphysema and we found that SDHC is required to support respiration in cultured muscle cells. Moreover, in-vivo gain of SDH function in emphysema animals muscles resulted in better oxygen consumption rate (OCR) and fatigue tolerance. These changes correlated with a larger number of relatively more oxidative type 2-A and 2X fibers, and a reduced amount of 2B fibers. Our data suggests that SDHC is a key regulator of respiration and fatigability in pulmonary emphysema-driven skeletal muscles, which could be impactful to develop strategies aimed at attenuating this comorbidity.

physiology↗

bioRxiv2020

Inter-annual stability and age-dependent changes in plasma testosterone levels in a longitudinally monitored free-living passerine bird

While seasonal trends in the testosterone-driven hormonal regulation of resource allocation are known from cohort population samples, data on the inter-annual individual stability of blood plasma testosterone levels in wild birds are lacking, and our understanding of age-dependent changes is limited. We assessed plasma testosterone levels in 105 samples originating from 49 repeatedly captured free-living great tits (Parus major) to investigate their relative long-term stability and lifetime changes. Furthermore, we examined the inter-annual stability of selected condition-related traits (carotenoid- and melanin-based plumage ornamentation, ptilochronological feather growth rate, body mass, and haematological heterophil/lymphocyte ratio) and their relationships to testosterone levels. We show that testosterone levels in both sexes are inter-annually repeatable, both in their absolute values and individual ranks (indicating the maintenance of relative status in a population), yet with higher stability in females. Despite this stability, in males we found a quadratic dependence of testosterone levels on age, with a peak in midlife. In contrast, female testosterone levels showed no lifetime trend. The inter-annual stability of condition-related traits was mostly moderate and unrelated to plasma testosterone concentrations. However, males with elevated testosterone had significantly higher carotenoid-pigmented yellow plumage brightness, presumably serving as a sexually selected trait. Showing inter-annual stability in testosterone levels, this research opens the way to further understanding of the causes of variation in fitness-related traits. Based on a unique longitudinal dataset, this study demonstrates that male plasma testosterone undergoes age-related changes that may regulate resource allocation. Our results thus demonstrate that male birds undergo hormonal senescence similar to mammals.

zoology↗

bioRxiv2019

Strategies for understanding dynamic, personalized profiles of host-derived proteins and microbes from human stool

Measuring host proteins through noninvasive stool-based assays opens new avenues for characterizing states of gastrointestinal health. However, the extent to which these proteins vary over time and between healthy subjects is poorly characterized. Here, we characterize technical and biological sources of variability in mass spectrometry-based measurements of host proteins in stool. We identify the proteins that most vary over time within an individual, and among different individuals. Finally, we examine and compare temporal and inter-individual variation in host protein and bacterial taxonomic profiles of the same fecal specimens. To address these issues, five self-reported healthy individuals were each sampled eight times over four weeks. First, we demonstrate that mass spectrometry-based identification and label-free quantification of stool proteins exhibit non-significant variability (p>0.05) between both technical and preparative replicates for a subset of 78 proteins, supporting the utility of this method for biomarker measurement. Second, although 13 human stool proteins varied significantly in relative abundance over time within individuals, 58 proteins varied significantly (at least four-fold) between subjects. The average pair-wise difference between individuals was greater than the average within-subject difference for both the proteome and microbiome datasets (p<0.0001). Fecal host proteins, like the traditional fecal protein marker, calprotectin, unambiguously pointed to innate and adaptive immune responses. For example, one subjects fecal protein profile suggested a sub-clinical inflammatory state. From these data, we conclude that host-centric protein measurements in stool reveal a wide range of variation during states of apparent health, and add a valuable complementary insight into host-microbiota relationships. IMPORTANCEHuman proteins in stool hold untapped potential for characterizing gastrointestinal health. To fully harness this potential and create a baseline of healthy stool protein abundances and identifications, it will be important to establish the extent to which these proteins might vary in the absence of disease. This study quantifies the major sources of variation in stool protein abundance data. We assessed technical, preparative, temporal, and inter-subject variability of human protein abundances in stool and found that among these sources, differences between subjects accounted for the greatest amount of variation, followed by temporal differences, and then technical factors. Our paired microbiome analysis found matching patterns of temporal and inter-subject variability. By characterizing multiple variance parameters in host stool protein abundances, our analysis helps to contextualize a wide range of future disease-focused stool studies as well as elucidate host-microbe interactions.

molecular biology↗