Biology subjects

Zhao, Y.

Publications and source records attributed to Zhao, Y..

At least 469 records · Page 26Linked to original sources

bioRxiv2024

Growth-induced physiological hypoxia correlates with growth deceleration during normal development

Growth deceleration is a universal feature of growth during development: most organs and tissues slow down their growth rate much before growth termination. Using transcriptomics analysis, we show that during their two-day period of growth deceleration, wing imaginal discs of Drosophila undergo a progressive metabolic shift away from oxidative phosphorylation and towards glycolysis. We then develop an ultra-sensitive reporter HIF-1 activity, which reveals that imaginal discs become increasingly hypoxic during development in normoxic conditions, suggesting that limiting oxygen supply could underlie growth deceleration. Growth is energetically expensive and thus expected to contribute, indirectly, to oxygen consumption. Indeed, excess TOR signalling, a key stimulator of growth, triggers hypoxia locally and systemically, highlighting the need to rein in growth when oxygen becomes limiting. This is achieved by a negative feedback loop whereby the classic TOR-inhibitory function of HIF-1 is deployed in response to developmental hypoxia. The absence of Sima/HIF-1 leads to cellular stress, which is alleviated by reduced TOR signalling. Conversely, a small increase in oxygen supply reduces the stress induced by excess TOR activity. We conclude that mild hypoxia is a normal feature of organ development and that Sima/HIF-1 prevents growth-induced oxygen demand from exceeding supply.

developmental biology↗

bioRxiv2024

Quantifying Contributions from TopologicalCycles in the Brain Network towards Cognition

This study proposes a novel metric called Homological Vertex Importance Profile (H-VIP), utilizing topological data analysis tool persistent homology, to analyze human brain structural and functional connectomes. Persistent homology is a useful tool for identifying topological features such as cycles and cavities within a network. The salience of persistent homology lies in the fact that it offers a global view of the network as a whole. However, it falls short in precisely determining the relative relevance of the vertices of the network that contribute to these topological features. Our aim is to quantify the contribution of each individual vertex in the formation of homological cycles and provide insight into local connectivity. Our proposed H-VIP metric captures, quantifies, and compresses connectivity information from vertices even at multiple degrees of separation and projects back onto each vertex. Using this metric, we analyze two independent datasets: structural connectomes from the Human Connectome Project and functional connectomes from the Alzheimers Disease Neuroimaging Initiative. Our findings indicate a positive correlation between various cognitive measures and H-VIP, in both anatomical and functional brain networks. Our study also demonstrates that the connectivity in the frontal lobe has a higher correlation with cognitive performance compared to the whole brain network. Furthermore, the H-VIP provides us with a metric to easily locate, quantify, and visualize potentially impaired connectivity for each subject and may have applications in the context of personalized medicine for neurological diseases and disorders.

bioinformatics↗

bioRxiv2024

Transcription network of SLC7A11 (xCT) in colon cancer provides clinical targets for metabolic regulation and cell proliferation

Colorectal cancer (CRC) represents the third leading cause of cancer-related deaths. Knowledge covering diverse cellular and molecular data from individual patients has become valuable for diagnosis, prognosis, and treatment selection. Here, we present in-depth comparative RNA-seq analysis of 32 CRC patients pairing tumor and healthy tissues (total of 73 samples). Strict thresholds for differential expression genes (DEG) analysis revealed an interconnection between nutrients, metabolic program, and cell cycle pathways. Among the upregulated DEGs, we focused on the Xc- system, composed of the proteins from SLC7A11 (xCT) and SLC3A2 genes, along with several interacting genes. To assess the oncogenic potency of the Xc- system in a cellular setting, we applied a knowledge-based approach, analyzing gene perturbations from CRISPR screens. The study focused on a set of 27 co-dependent genes that were strongly correlated with the fitness of SLC7A11 and SLC3A2 across many cell types. Alterations in these genes in 13 large-scale studies (e.g., by mutations and copy number variation) were found to enhance overall survival and progression-free survival in CRC patients. In agreement, the overexpression of these genes in cancer cells drives cancer progression by allowing effective management of the redox level, induction of stress response mechanisms, and most notably, enhanced activity of ion/amino acid transporters, and enzymes acting in de novo nucleotide synthesis. We also highlight the positive correlation between the Xc- system gene expression level, patient responsiveness to different chemotherapy treatments, and immune cell infiltration (e.g., myeloid-derived suppressor cells) in CRC tumors as a measure for their immunosuppressive activity. This study illustrates that knowledge-based interpretation by synthesizing multiple layers of data leads to functional and mechanistic insights into the role of SLC7A11 and its associated genes in CRC tumorigenesis and therapeutics.

cancer biology↗

bioRxiv2024

Medial amygdalar tau is associated with anxiety symptoms in preclinical Alzheimer's disease

BACKGROUNDWhile the amygdala receives early tau deposition in Alzheimers disease (AD) and is involved in social and emotional processing, the relationship between amygdalar tau and early neuropsychiatric symptoms in AD is unknown. We sought to determine whether focal tau binding in the amygdala and abnormal amygdalar connectivity were detectable in a preclinical AD cohort and identify relationships between these and self-reported mood symptoms. METHODSWe examined n=598 individuals (n=347 amyloid-positive (58% female), n=251 amyloid-negative (62% female); subset into tau PET and fMRI cohorts) from the A4 Study. In our tau PET cohort, we used amygdalar segmentations to examine representative nuclei from three functional divisions of the amygdala. We analyzed between-group differences in division-specific tau binding in the amygdala in preclinical AD. We conducted seed-based functional connectivity analyses from each division in the fMRI cohort. Finally, we conducted exploratory post-hoc correlation analyses between neuroimaging biomarkers of interest and anxiety and depression scores. RESULTSAmyloid-positive individuals demonstrated increased tau binding in medial and lateral amygdala (F(4, 442)=14.61, p=0.00045; F(4, 442)=5.83, p=0.024, respectively). Across amygdalar divisions, amyloid-positive individuals had relatively increased regional connectivity from amygdala to other temporal regions, insula, and orbitofrontal cortex. There was an interaction by amyloid group between tau binding in the medial and lateral amygdala and anxiety. Medial amygdala to retrosplenial connectivity negatively correlated with anxiety symptoms (rs=-0.103, p=0.015). CONCLUSIONSOur findings suggest that preclinical tau deposition in the amygdala may result in meaningful changes in functional connectivity which may predispose patients to mood symptoms.

neuroscience↗

bioRxiv2024

Systemic mRNA transport depends on m5C methylation, nuclear mRNA export factors and developmental phase changes

In grafted plants mRNAs can be transported from shoot to root, however, how their mobility is regulated remains poorly understood. Recent work has shown that m5C methylation plays an essential role in systemic mRNA mobility in vegetative plants, but its role at later developmental stages remains unclear. To address this, we examined the mobility of three mobile mRNAs, TCTP1, HSC70.1 and GRP7 in mutants deficient in m5C mRNA methylation. By comparing vegetative and flowering stages, we found that in contrast to GRP7, the reduced mobility of TCTP1 and HSC70.1 observed in the vegetative growth phase is restored upon flowering, indicating that m5C-dependent regulation of RNA transport is developmentally controlled. We further identified two RNA-binding proteins, the nuclear mRNA export factors ALY2 and ALY4, as phloem mobile. ALY2 and ALY4 deficient plants show a similar developmental effect on mRNA mobility as m5C mRNA methylation mutants, suggesting that they contribute to the regulation of systemic mRNA transport. Notably, combined perturbation of m5C methylation and ALY2 or ALY4 results in reduced mRNA mobility even in flowering plants. Together, our findings reveal an unexpected developmental layer of control over mRNA transport and identify the nuclear mRNA export factors ALY2 and ALY4 as potential regulators of long-distance RNA movement. SIGNIFICANCE STATEMENTmRNA m5C methylation is essential for shoot-to-root mRNA transport during plant growth; however, whether and how mRNA mobility is regulated, and whether it changes during development remains unclear. We show that TCTP1 and HSC70.1 mRNA transport is reduced in vegetatively growing m5C-deficient mutants but remains unaffected upon flowering, and identify ALY2 and ALY4 proteins, two nuclear export factors, as additional regulators of long-distance mRNA transport, providing new layer of mRNA transport.

plant biology↗

bioRxiv2024

Skeleton-forming responses of reef-building corals under ocean acidification

Ocean acidification is increasing in frequency and is considered one of the most important causes of severe damage to global coral reefs. Therefore, there is an urgent need to study the impact of acid stress on the growth patterns of major reef-building corals. Here, we studied the skeleton forming strategies of four widely distributed coral species in a simulated acidified habitat with a pH of 7.6-7.8. We reconstructed and visualized the skeleton building process, quantified elemental calcium loss, and determined gene expression changes. The results suggest that different reef-building corals have diverse growing strategies in acidified seawater. A unique cavity-like forming process starts from the inside of the skeletons of Acropora muricata, which sacrifices skeleton density to protect its polyp-canal system. The forming patterns in Pocillopora damicornis, Montipora capricornis, and M. foliosa were characterized by osteoporosis, exhibiting disordered skeletal structures, insufficient synthesis of adhesion proteins, and low bone mass, correspondingly. In addition, we found that skeletal areas near coral polyps suffered less and had later acidified damage than other skeletal areas in the colony. These results help to understand the skeleton-forming strategies of several major coral species under acid stress, thereby laying a foundation for coral reef protection and restoration under increasing ocean acidification.

ecology↗

bioRxiv2024

Association between mosaic loss of chromosome Y and pulmonary fibrosis susceptibility and severity

Background Pulmonary fibrosis (PF) is a rare lung disease with diverse pathogenesis and multiple interconnected underlying biological mechanisms. Mosaic loss of chromosome Y (mLOY) is one of the most common forms of acquired chromosome abnormality in men, which has been reported to be associated with increased risk of various chronic progressive diseases including fibrotic diseases. However, the exact role of mLOY in the development of PF remains elusive and to be elucidated. MethodsWe adopted three complementary approaches to explore the role of mLOY in the pathogenesis of PF. We used copy number on chromosome Y to estimate mLOY comparing patients in PROFILE and gnomAD cohorts and between cases and control patients from the GE100KGP cohort. Correlation of mLOY with demographic and clinical variables was tested using patients from PROFILE cohort. Lung single-cell transcriptomic data were analysed to assess the cell types implicated in mLOY. We performed Mendelian randomisation to examine the causal relationship between mLOY, IPF, and telomere length. ResultsThe genetic analysis suggests that mLOY is found in PF from both case cohorts but when compared with an age matched population the effect is minimal (P = 0.0032). mLOY is related to age (P = 0.00021) and shorter telomere length (P = 0.0081) rather than PF severity or progression. Single-cell analysis indicates that mLOY appears to be found primarily in immune cells and appears to be related to presence and severity of fibrosis. Mendelian randomisation demonstrates that mLOY is not on the causal pathway for IPF, but partial evidence supports that telomere shortening is on the causal pathway for mLOY. ConclusionOur study confirms the existence of mLOY in PF patients and suggests that mLOY is not a major driver of IPF. The combined evidence suggests a triangulation model where telomere shortening leads to both IPF and mLOY.

genomics↗

bioRxiv2024

New isolates refine the ecophysiology of the Roseobacter CHAB-I-5 lineage

The CHAB-I-5 cluster is a pelagic lineage that can comprise a significant proportion of all roseobacters in surface oceans and have predicted roles in biogeochemical cycling via heterotrophy, aerobic anoxygenic photosynthesis (AAnP), CO oxidation, DMSP degradation, and other metabolisms. Though cultures of CHAB-I-5 have been reported, none have been explored and the best known representative, strain SB2, was lost from culture after obtaining the genome sequence. We have isolated two new CHAB-I-5 representatives, strains US3C007 and FZCC0083, and assembled complete, circularized genomes with 98.7% and 92.5% average nucleotide identities with the SB2 genome. Comparison of these three with 49 other unique CHAB-I-5 metagenome-assembled and single-cell genomes indicated that the cluster represents a genus with two species, and we identified subtle differences in genomic content between the two species subclusters. Metagenomic recruitment from over fourteen hundred samples expanded their known global distribution and highlighted both isolated strains as representative members of the clade. FZCC0083 grew over twice as fast as US3C007 and over a wider range of temperatures. The axenic culture of US3C007 occurs as pleomorphic cells with most exhibiting a coccobacillus/vibrioid shape. We propose the name Thalassovivens spotae, gen nov., sp. nov. for the type strain US3C007T.

microbiology↗

bioRxiv2024

SEIR: a novel multi-locus GWAS method that provides higher statistical power for fast identifying variant-phenotype associations

Multi-locus genome-wide association study (GWAS) methods have considered the joint effects of multiple variants to more accurately unravel the genetic basis of complex traits. Here, we developed a novel multi-locus GWAS method named Selector-Embedded Iterative Regression (SEIR), which integrates the embedded selector with fast single-marker scanning in an iterative manner. SEIR has excellent adaptability and flexibility under various genetic architectures for qualitative and quantitative traits. Reliability of SEIR was experimentally supported by integrating GWAS with 3D epigenomics in a real trait. Conclusively, SEIR exhibits higher statistical power for fast identifying putative variants compared to other single- and multi-locus methods.

genetics↗

bioRxiv2024

Causal network perturbation analysis identifies known and novel type-2 diabetes driver genes

The molecular pathogenesis of type 2 diabetes mellitus (T2DM) involves environmental and genetic factors that remain poorly understood. Increased insulin resistance leads to pancreatic {beta}-islet cell exhaustion and failure, leading to more severe T2DM. As such, targeting {beta}-cell dysfunction is an attractive pathway for T2DM treatment. Single-cell RNA sequencing can help identify differentially expressed genes (DEGs) that may contribute to disease-associated pathophysiology, but cannot capture the full spectrum of disease pathophysiology, as some genes that are not differentially expressed may still play important roles in disease progression or mechanisms. As such, we investigated single-cell gene expression changes in {beta}-cells from healthy (C57BL/6J) and diabetic (NZO/HlLtJ) mice fed with normal or high-fat, high-sugar diet (HFHS) across the spectrum of T2DM development (prediabetic, mild or severely diabetic) using an innovative integration of the causal network perturbation assessment (ssNPA) framework with meta-cell transcriptome analysis to identify driver genes for T2DM. By generating a reference causal network and conducting in silico perturbations, we identified three classes of genes implicated in T2DM pathophysiology: (1) DEGs that were not perturbed (e.g, Igf2bp2 strongly linked to {beta} cell dysfunction and glucose regulation), (2) perturbed non-DEGs (e.g., Glp1r a therapeutic target of modern diabetes drugs) that were perturbed, and (3) DEGs that were perturbed (e.g., Pdx1 a master {beta} cell transcription factor), and validated some of the targets using the KOMP database. Together, these results show that each analytic layer captures complementary mechanisms underlying T2DM severity, and their synthesis provides a more complete view of the disease pathophysiology.

bioinformatics↗

bioRxiv2024

Rtf1 HMD domain facilitates global histone H2B monoubiquitination and regulates morphogenesis and virulence in the meningitis-causing pathogen Cryptococcus neoformans

Rtf1 is generally considered to be a subunit of the Paf1 complex (Paf1C), which is a multifunctional protein complex involved in histone modification and RNA biosynthesis at multiple stages. Rtf1 is stably associated with the Paf1C in Saccharomyces cerevisiae, but not in other species including humans. Little is known about its function in human fungal pathogens. Here, we show that Rtf1 is required for facilitating H2B monoubiquitination (H2Bub1), and regulates fungal morphogenesis and pathogenicity in the meningitis-causing fungal pathogen Cryptococcus neoformans. Rtf1 is not tightly associated with the Paf1C, and its histone modification domain (HMD) is sufficient to promote H2Bub1 and the expression of genes related to fungal mating and filamentation. Moreover, Rtf1 HMD fully restores fungal morphogenesis and pathogenicity; however, it fails to restore defects of thermal tolerance and melanin production in the rtf1{Delta} strain background. The present study establishes a role for cryptococcal Rtf1 as a Paf1C-independent regulator in regulating fungal morphogenesis and pathogenicity, and highlights the function of HMD in facilitating global H2Bub1 in C. neoformans.

molecular biology↗

bioRxiv2024

Improvement in Outcomes and Prevention of Multiple Organ Dysfunction Syndrome After Cardiac Arrest and Successful Cardiopulmonary Resuscitation by Systemic Administration of Bumetanide in Male Mice

BACKGROUNDCardiac arrest (CA) and successful cardiopulmonary resuscitation (CPR) cause post-CA brain injury (PCABI) and extracerebral multiple organ dysfunction (EMOD), leading to low survival and disability in resuscitated patients. The pathogenesis of PCABI is still poorly understood, and no therapeutic-related factors have been identified to improve survival and neurological outcomes to date. Bumetanide is a promising pharmaceutical intervention for some neurological disorders that have some common pathophysiology with PCABI, and it also exhibit systemic protective effects on vital organs under pathological conditions. This study aims to investigate the protective effects of bumetanide on PCABI and EMOD after CA/CPR, and uncover the pathogenesis and biomarkers of PCABI at protein level. METHODSWe generated a hyperkalemia-induced asystole CA/CPR mouse model with bumetanide/vehicle treatment after resuscitation. Survival, neurological outcome, functional outcome, key pathophysiological process underlying PCABI, and injury level of EMOD were evaluated. Proteomics analysis of cerebral cortex was performed for investigating mechanisms of PCABI. RESULTSBumetanide significantly improved outcomes after CA/CPR and reduced the main pathophysiological processes of PCABI, including seizures, neurodegeneration, neuroinflammation, decreased cerebral blood flow, blood-brain barrier disruption, and oxidative stress. CA/CPR-induced injury in heart, lung, liver, kidney, spleen, adrenal gland, spinal cord, pennis, and urinary bladder were also alleviated by bumetanide. Proteomic study and experimental verification identified LCN2/NGAL is a potential biomarker for early neuroprognostication and has association with PCABI severity. CONCLUSIONSSystemic administration of bumetanide improved outcomes and prevented multiple organ dysfunction after CA/CPR. LCN2/NGAL is a novel biomarker for early neuroprognostication at 24 hours after CA/CPR. Clinical PerspectiveO_LIWhat Is New? O_LIPost-resuscitation bumetanide treatment could improve outcomes and prevent brain injury and extracerebral multiple organ dysfunction after hyperkalemia-induced asystole cardiac arrest in mice. C_LIO_LINeuronal subpopulations in cerebral cortex were selectively vulnerable, and all major organs had obvious tissue damage with inflammatory cell infiltration and tissue edema after resuscitation. C_LIO_LIThis the first study to identify the pathogenesis and biomarkers of post-cardiac arrest brain injury with proteomic studies, and LCN2/NGAL had a strong and graded association with pathogenesis of PCABI, which could be a marker for monitoring and neuroprognostication. C_LI C_LIO_LIWhat Are the Clinical Implications? O_LIBumetanide may be a novel pharmacological therapy to improve survival and neurological outcomes in post-resuscitation care, and cerebral-specific quantification of LCN2/NGAL could be used for early neuroprognostication at 24 hours after cardiac arrest. C_LIO_LIExtracerebral multiple organ injury is common and severe after resuscitation, which needs to be given more attention in clinical management. C_LI C_LI

physiology↗

bioRxiv2024

Reproducible single cell annotation of programs underlying T-cell subsets, activation states, and functions

T-cells recognize antigens and induce specialized gene expression programs (GEPs) enabling functions including proliferation, cytotoxicity, and cytokine production. Traditionally, different classes of helper T-cells express mutually exclusive responses - for example, Th1, Th2, and Th17 programs. However, new single-cell RNA sequencing (scRNA-Seq) experiments have revealed a continuum of T-cell states without discrete clusters corresponding to these subsets, implying the need for new analytical frameworks. Here, we advance the characterization of T-cells with T-CellAnnoTator (TCAT), a pipeline that simultaneously quantifies pre-defined GEPs capturing activation states and cellular subsets. From 1,700,000 T-cells from 700 individuals across 38 tissues and five diverse disease contexts, we discover 46 reproducible GEPs reflecting the known core functions of T-cells including proliferation, cytotoxicity, exhaustion, and T helper effector states. We experimentally characterize several novel activation programs and apply TCAT to describe T-cell activation and exhaustion in Covid-19 and cancer, providing insight into T-cell function in these diseases.

genomics↗

bioRxiv2024

Ancient cyanobacterial proto-circadian clock adapted to short day-night cycles ~ 0.95 billion years ago

In the early history, the Earth rotation was much faster; however, how ancient organisms adapted to the day-night cycles of that time remains unclear. We resurrected the ancestor KaiABC (anKaiABC) genes circa 0.95 billion years (Ga) ago when the daily-night cycling period was [~] 18 h. Compared with its contemporary counterpart KaiC, the anKaiC protein shows subtle structural differences, and the activities of kinase, phosphatase activities, and adenosine triphosphatase (ATPase) of anKaiC are lower. The anKaiAB proteins are less effective in regulating KaiC/anKaiC phosphorylation status. The anKaiABC system does not sustain an endogenous oscillation but it can be entrained by an 18-h light/dark cycle. The strain expressing anKaiABC shows better adaptation under 9-h light/9-h dark cycles (LD9:9) which mimic the 18-h day-night cycles. These findings suggest that the ancient cyanobacterial proto-circadian system may not be endogenous, but it conferred the capability to adapt to daily cycles [~] 0.95 Ga ago.

evolutionary biology↗

bioRxiv2024

Super homotypic targeting by exosome surface engineering

Homotypic targeting is the inherent ability of cells for preferential interaction with cells of similar or identical types, a phenomenon commonly seen in cell adhesion, tissue formation, and immune responses. Unfortunately, its full potential remains largely untapped. Here we introduce an approach to drastically boost the homotypic targeting capabilities of cells via exosomes (nanoscale extracellular vesicles secreted by cells). By engineering exosome surfaces with lanthanides, we amplify specific cell-exosome interactions by more than 25-fold, significantly accelerating the selective capture of exosomes by cells of the same lineage. This substantial enhancement in cellular homophilicity opens up an entirely new class of applications, two of which we showcase here with unprecedented performance: using cells to detect specific exosomes and using exosomes to detect specific cells. The concept of "super homotypic targeting" offers enormous potential to transform cancer diagnostics, immunotherapy, targeted drug delivery, tissue engineering, and vaccine development.

cell biology↗

bioRxiv2024

High-resolution detection of copy number alterations in single cells with HiScanner

Improvements in single-cell whole-genome sequencing (scWGS) assays have enabled detailed characterization of somatic copy number alterations (CNAs) at the single-cell level. Yet, current computational methods are mostly designed for detecting chromosome-scale changes in cancer samples with low sequencing coverage. Here, we introduce HiScanner (High-resolution Single-Cell Allelic copy Number callER), which combines read depth, B-allele frequency, and haplotype phasing to identify CNAs with high resolution. In simulated data, HiScanner consistently outperforms state-of-the-art methods across various CNA types and sizes. When applied to high-coverage scWGS data from 65 cells across 11 neurotypical human brains, HiScanner shows a superior ability to detect smaller CNAs, uncovering distinct CNA patterns between neurons and oligodendrocytes. We also generated low-coverage scWGS data from 179 cells sampled from the same meningioma patient at two time points. For this serial dataset, integration of CNAs with point mutations revealed evolutionary trajectories of tumor cells. These findings show that HiScanner enables accurate characterization of frequency, clonality, and distribution of CNAs at the single-cell level in both non-neoplastic and neoplastic cells.

genomics↗

bioRxiv2024

Damaging mutations in LXRα uncouple lipogenesis from hepatotoxicity and implicate hepatic cholesterol sensing in human liver health

The nuclear receptor Liver X Receptor- (LXR) activates lipogenic gene expression in hepatocytes. Its inhibition has therefore been proposed as a strategy to treat metabolic-dysfunction-associated steatotic liver disease (MASLD). In order to understand the impact of reducing LXR activity on human health we first examined the association between the carriage of rare loss of function mutations in NR1H3 (encoding LXR) and metabolic and hepatic phenotypes. We identified 63 rare predicted damaging variants in the ligand binding domain of LXR in 454,787 participants in UK Biobank. On functional characterisation, 42 of these were found to be severely impaired. Consistent with loss of the lipogenic actions of LXR, carriers of damaging mutations in LXR had reduced serum triglycerides ({beta}=-0.13 s.d. {+/-}0.03, P=2.7x10-5, N(carriers)=971). Surprisingly, these carriers also had elevated concentrations of serum liver enzymes (e.g. ALT: {beta}=0.17s.d. {+/-}0.03, P=1.1x10-8, N(carriers)=972) with a 35% increased risk of clinically significant elevations in ALT (OR=1.32, 95%CI:1.15-1.53, P=1.2x10-4, N(carriers)=972), suggestive of hepatotoxicity. We generated a knock-in mouse carrying one of the most severely damaging mutations (Nr1h3 p.W441R) which we demonstrated to have dominant negative properties. Homozygous knock-in mice rapidly developed severe hepatitis and fibrotic liver injury following exposure to western diet despite markedly reduced steatosis, liver triglycerides and lipogenic gene expression. This phenotype was completely rescued by viral over-expression of wildtype LXR specifically in hepatocytes, indicating a cell-autonomous effect of the mutant on hepatocyte health. While homozygous LXR knockout mice showed some evidence of hepatocyte injury under similar dietary conditions, the phenotype of the LXRW441R/W441R mouse was much more severe, suggesting that dominant negative mutations that actively co-repress target genes can result in pathological impacts significantly more severe than those seen with simple absence of the receptor. In summary, our results show that loss of function mutations in LXR occur in at least 1/450 people and are associated with evidence of liver dysfunction. These findings implicate LXR in the maintenance of human liver health, identify a new murine model of rapidly progressive fibrotic liver disease and caution against LXR antagonism as a therapeutic strategy for MASLD.

genetics↗

bioRxiv2024

Moving towards precision TMS? Evaluating individual differences and reproducibility of personalized stimulation targets in UK Biobank

ObjectivePersonalized transcranial magnetic stimulation (TMS) targeting, guided by functional connectivity (FC), shows potential in treating depression. The present study aims to map individual FC peak location using UK Biobank, to evaluate individual differences and reproducibility of FC-based targets. MethodsWe analyzed UK Biobank resting-state fMRI (rfMRI) of 35,423 participants, identifying individual FC peak locations on the dorsolateral prefrontal cortex (DLPFC) that functionally connected to the subcallosal cingulate, amygdala, and ventromedial prefrontal cortex, respectively. Euclidean distance between each participants individual peak and group-average peak was calculated. With follow-up rfMRI of 1341 participants, within-subject FC peak location changes were calculated. We also compared common TMS targets and random locations for their median distance to individual peaks in a permutation test. ResultsSeed-based FC analyses revealed large differences in the individual FC peak location on DLPFC: the mean distance from the individual peaks to group-average peak ranged from 14.24 to 29.92mm; 70% to 94% of participants were >10mm away from the group-average peak and potentially located outside of the TMS effective area with common TMS coils. Similar variability was observed in within-subject peak locations across two fMRI assessments. Common TMS targets and the group-average FC peak showed no significant difference in median distances to individual FC peaks when compared to random locations. ConclusionsFC peak location shows wide inter- and intra-individual variability. We emphasize a role for individualized TMS neuronavigation targeting but emphasize the need for more reliable biomarker studies.

neuroscience↗