Biology subjects

Koh, A.

Publications and source records attributed to Koh, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Distinct genetic requirements underlie LITE-1-dependent photosensation and avoidance of high concentration of diacetyl in C. elegans

The eyeless nematode C. elegans can detect and respond to aversive blue and ultraviolet light using the gustatory receptor homolog LITE-1. In addition to its role in phototransduction, LITE-1 also functions as a chemoreceptor for the odorants diacetyl and 2,3-pentanedione. However, whether these different sensory modalities rely on the same downstream signalling components is unknown. In this study, we provide behavioural evidence that unlike its LITE-1-dependent photosensory function which relies on cGMP signalling components, its chemosensory function remains intact in mutants with disrupted cGMP signalling.

neuroscience↗

bioRxiv2026

A Neuronally Active Bacterial Siderophore Manipulates Host Behavior and Longevity

Aging populations face a growing burden of neurodegenerative disease and behavioral decline. The microbiota is increasingly implicated in host physiology, highlighting an urgent need to understand how gut microbes modulate brain function and late life health. Here, we develop a high-throughput microbe-host screening platform to systematically dissect how bacterial genes shape organismal behavior. Using the Escherichia coli Keio library of 3,985 distinct non-essential single-gene deletion mutants in combination with Caenorhabditis elegans, we quantitatively profiled 768 behavioral features per bacterial clone and uncovered a coherent module of bacterial genes involved in iron homeostasis that robustly reprogrammed host behavior. Bacterial omics analyses revealed that alterations in iron homeostasis amplify siderophore production in a TCA cycle-dependent manner, and loss of enterobactin biosynthesis abolished the bacteria-induced changes in worm movement. Transcriptional, molecular and functional studies demonstrated that bacterial enterobactin activates host neuromuscular responses to shape both lifespan and healthspan in a manner dependent on the mitochondrial unfolded protein response. Thermal proteome profiling identified mitochondrial glutaryl-CoA dehydrogenase and the electron-transfer flavoproteins A and B as enterobactin-binding targets that control mitochondrial function. Finally, genetic manipulation of neuronal mitochondrial and cytosolic reactive oxygen species via superoxide dismutase and catalase revealed that redox state modulates enterobactin-driven changes in movement and lifespan through the secretin-family GPCR neuropeptide receptor PDFR-1. Together, these findings establish microbial enterobactin as a non-canonical neurotransmitter regulating neuronal mitochondrial function, behavior and aging, defining a gut bacteria-brain axis with broad implications for maintaining late-life health.

animal behavior and cognition↗

bioRxiv2026

Continuous negative autoregulation fine-tunes dosage-sensitive transcription factor expression to maintain post-mitotic neuron identity

How post-mitotic neurons maintain precise transcription factor (TF) levels throughout life remains a fundamental open question. Here, we challenge the prevailing model of positive autoregulation by demonstrating that UNC-3 (Collier/EBF1-4), a dosage-sensitive TF continuously required for cholinergic motor neuron identity in C. elegans, negatively regulates its own expression. Using genetics, biochemistry, and inducible protein depletion, we show this self-repression occurs directly at the transcriptional level and persists beyond development. CRISPR/Cas9 disruption of negative autoregulation causes motor neuron identity and locomotion defects, establishing its functional necessity. Mechanistically, the UNC-3 DNA-binding domain is required and sufficient for self-repression, with an AlphaFold2 screen implicating chromatin factors as interaction partners. Critically, UNC-3 self-repression is continuously counterbalanced by positive input from the HOX cofactor CEH-20/PBX, revealing a dynamic "balancing act" between opposing regulatory inputs that stabilize TF dosage over time. Mutations in the unc-3 ortholog EBF3 cause a neurodevelopmental syndrome, and disease-associated variants disrupt UNC-3 self-repression, revealing a key molecular mechanism underlying the disorder. We propose that negative autoregulation continuously counteracted by positive input represents a broadly applicable principle for maintaining dosage-sensitive TF expression to secure post-mitotic cell identity.

developmental biology↗

bioRxiv2026

Membrane-targeting antimicrobials trigger lysis in Bacillus subtilis by disturbing the MreB-dependent regulation of peptidoglycan hydrolases

Membrane-targeting antimicrobials are generally assumed to kill bacteria through bacteriolysis induced by the permeabilisation of the cytoplasmic membrane. This model relies on the notion that bacteriolysis is the direct cellular manifestation of the membrane-disruptive (membranolytic) activity of an antibacterial compound. However, it underappreciates the key role of peptidoglycan hydrolases in bacteriolysis. Using the Gram-positive model organism Bacillus subtilis, we demonstrate that the bacteriolytic activity of membrane-targeting antimicrobials arises from the misregulation of peptidoglycan hydrolases, regardless of whether they induce large membrane pores or trigger more subtle membrane disturbances such as depolarisation. Contrary to previous models, the autolysis of B. subtilis induced by membrane depolarising compounds does not depend on pH changes associated with the cell surface. Instead, the autolytic process is triggered by membrane depolarisation-dependent dissociation of the bacterial actin homolog MreB, a key spatial coordinator of cell wall synthesis in rod-shaped bacteria, from the cytoplasmic membrane. These findings provide valuable insights into the cellular pathways involved in autolysis, highlight the challenges in distinguishing between direct and indirect cellular effects of membrane-targeting antibiotics, and improve our understanding of antibiotic-induced bacteriolysis.

microbiology↗

bioRxiv2026

Species and strain diversity in Staphylococcus drive divergent host responses in human skin

The skin microbiome regulates key skin processes, yet the functional diversity of a dominant genus, Staphylococcus, remains poorly resolved at the strain level for multiple species across its pathogenic and commensal continuum. It is likely that Staphylococcus effects on skin are diverse at these finest taxonomic resolutions, but current skin models lack the physiological relevance and scalability needed to profile this diversity. Using an organotypic 3D human skin model (reconstructed human epidermis, RHE), we profiled skin responses to 187 Staphylococcus strains across seven dominant species. Canonically pathogenic species (e.g., S. aureus) induced broad inflammatory responses, whereas prototypical commensal species (e.g., S. hominis) elicited more nuanced effects on innate immune and skin barrier responses. Strikingly, S. epidermidis displayed pronounced strain-level heterogeneity, with subsets inducing either commensal or pathogen-like responses despite lacking canonical virulence factors, suggesting pleiotropic effects. Comparative genomics, dual-transcriptomics, untargeted metabolomics, and growth phenotyping revealed species- and strain-specific traits underlying these differential effects on RHE, including the presence of select cell surface proteins and differential arginine metabolism. Together, our study provides the first high-throughput, species- and strain-resolved analysis of skin-Staphylococcus interactions, offering mechanistic insights and a platform for microbiome-based strategies to modulate skin inflammation and diseases. One-line summaryHigh-throughput profiling of Staphylococcus in a human skin model shows that species- and strain-level diversity underlies a continuum of host barrier and immune responses.

microbiology↗

bioRxiv2025

Identifying Optimal Machine Learning Approaches for Microbiome-Metabolomics Integration with Stable Feature Selection

Microbiome research is often limited by methodological inconsistencies that reduce reproducibility and functional insight. Traditional taxonomy-based profiling is limited by sparse data, variable resolution, and reliance on gDNA sequencing which provides only indirect links to microbial function. Multi-omics integration offers a framework for linking community composition to functional outputs, but progress has been hindered by the lack of standardized frameworks and inconsistent use of machine learning. In particular, feature selection stability, which is central to biomarker discovery and experimental validation, remains underexplored. Here, we systematically benchmarked three widely used algorithms (Elastic Net, Random Forest, XGBoost) across seven multi-omics integration strategies and single-omics models. Additionally, we evaluated the impact of transforming metabolomics and taxonomic abundance data. Using human gut microbiome datasets that integrate metagenomic taxonomic profiles with metabolomics, we evaluated models for 9 binary and 8 continuous outcomes across 20 train/test splits per dataset. We further assessed the effect of feature reduction on both predictive accuracy and feature selection stability. Nonlinear learners were most consistently competitive: continuous outcomes favored metabolomics-dominant models, whereas binary outcomes favored stacked multi-omics models. Random Forest and XGBoost also yielded greater feature selection stability, particularly for full dimensional metabolomics data. Together, these findings demonstrate how integration strategy, algorithm choice, and data preprocessing jointly shape predictive performance and feature selection reproducibility in multi-omics microbiome modeling.

bioinformatics↗

bioRxiv2025

Multi-selective RAS(ON) Inhibition Targets Oncogenic RAS Mutations and Overcomes RAS/MAPK-Mediated Resistance to FLT3 and BCL2 Inhibitors in Acute Myeloid Leukemia

Aberrant activation of the RAS/MAPK signaling limits the clinical efficacy of several targeted therapies in acute myeloid leukemia (AML). In FLT3-mutant AML, the selection of clones harboring heterogeneous RAS mutations drives resistance to FLT3 inhibitors (FLT3i). RAS activation is also associated with resistance to other AML targeted therapies, including the BCL2 inhibitor venetoclax. Despite the critical need to inhibit RAS/MAPK signaling in AML, no targeted therapies have demonstrated clinical benefit in RAS-driven AML. To address this unmet need, we investigated the preclinical activity of RMC-7977, a multi-selective inhibitor of GTP-bound active [RAS(ON)] isoforms of mutant and wild-type RAS in AML models. RMC-7977 exhibited potent antiproliferative and pro-apoptotic activity across AML cell lines with MAPK-activating signaling mutations. In cell line models with acquired FLT3i resistance due to secondary RAS mutations, treatment with RMC-7977 restored sensitivity to FLT3i. Similarly, RMC-7977 effectively reversed resistance to venetoclax in RAS-addicted cell line models with both RAS wild-type and mutant genetic backgrounds. In murine patient-derived xenograft models of RAS-mutant AML, RMC-7977 was well tolerated and significantly suppressed leukemic burden in combination with gilteritinib or venetoclax. Our findings strongly support clinical investigation of broad-spectrum RAS(ON) inhibition in AML to treat and potentially prevent drug resistance due to activated RAS signaling.

cancer biology↗

bioRxiv2025

The C. elegans gustatory receptor homolog LITE-1 is a chemoreceptor required for diacetyl avoidance

The nematode C. elegans does not have eyes but can respond to aversive UV and blue light stimulation and even distinguish colours. The gustatory receptor homolog LITE-1 was identified in forward genetic screens for worms that failed to respond to blue light stimulation. When LITE-1 is expressed in body-wall muscles, it causes contraction in response to blue light suggesting that LITE-1 is both necessary and sufficient for blue light response. Here we show that in addition to light avoidance, LITE-1 is also required for worms avoidance of high concentrations of diacetyl, an odorant that is attractive at low concentrations. Like blue light, diacetyl causes muscle contraction in transgenic worms engineered to express LITE-1 in body-wall muscles. These data are consistent with a direct chemoreceptor function for LITE-1 which would make it a multimodal sensor of aversive stimuli.

neuroscience↗

bioRxiv2025

RAS pathway activation drives clonal selection and monocytic differentiation in FLT3 and BCL2 inhibitor resistance

Despite efficacy of FLT3 and BCL2 inhibition in acute myeloid leukemia (AML), relapse limits survival. Mutation status and AML monocytic differentiation are implicated in resistance. On-treatment tumor evolution may select for genetically distinct clones or shifts in differentiation not resolvable by bulk sequencing. We performed multiomic single cell (SC) DNA/protein and RNA/protein profiling of patients treated on a clinical trial of the BCL2 inhibitor venetoclax and the FLT3 inhibitor gilteritinib (Ven/Git) to characterize immunophenotypic, transcriptional, and genetic clonal evolution on therapy. We found that while Ven/Gilt effectively eliminated FLT3 mutant clones, it selected for RAS mutations, RAS pathway activation and RAS-associated monocytic differentiation. In an in vitro model of monocytic differentiation associated with heightened RAS pathway activation, we demonstrated that MEK inhibition re-sensitized to Ven/Gilt. These data indicate RAS signaling is central to FLT3 and BCL2 inhibitor resistance, is tightly coupled to monocytic differentiation and can be overcome by RAS pathway inhibition. COIC.C.S. has provided educational talks for Astellas Pharma, served on advisory boards for Genentech/Abbvie and received research funding from Abbvie. B.C., Y.S. and J.H. are employees of Abbvie. M.S. and H.H. are or were previously employees of Genentech. FundingThis work was supported in part by Abbvie. C.C.S. is a Leukemia & Lymphoma Society Scholar in Clinical Research and a Damon Runyon-Richard Lumsden Foundation Clinical Investigator supported (in part) by the Damon Runyon Cancer Research Foundation (CI-99-18). Statement of SignificanceMutational and non-mutational RAS signaling activation drives clonal selection, monocytic differentiation and treatment resistance to FLT3 and BCL2 inhibition in AML. MEK inhibition can resensitize resistant AML cells, suggesting therapeutic potential for combined FLT3, BCL2 and RAS pathway inhibition in AML.

cancer biology↗

bioRxiv2024

The last resort antibiotic daptomycin exhibits two independent antibacterial mechanisms of action

Daptomycin is a lipopeptide antibiotic, commonly used as last resort treatment against multidrug resistant Gram-positive pathogens. Despite its clinical success, the mechanism through which daptomycin exerts its antibacterial properties has remained controversial. Much of the debate is focused around daptomycins ability to depolarise the cytoplasmic membrane, potential formation of large membrane pores, and its more recently discovered capability to inhibit cell wall synthesis and disturb membrane lipid domain organisation through interactions with cell wall precursor lipids. Here we show that, rather than representing different facets of a single underlying activity, daptomycin exhibits two independent antibacterial mechanisms of action: (i) targeting of cell wall precursor lipids that leads to cell wall synthesis inhibition and (ii) membrane depolarisation that does not rely on interactions with cell wall precursor lipids. This dual mechanism of action provides an explanation for the frequently disagreeing findings obtained through in vivo and in vitro studies and explains why resistance development towards daptomycin is slow and multifactorial. In a broader context, this demonstrates that dual mechanism antibiotics can be clinically successful and exhibit favourable characteristics in terms of real-world, clinically relevant resistance development.

microbiology↗

bioRxiv2024

Bacterial genome encoded ParMs

ParMs generally exist on low copy number plasmids where they contribute to plasmid segregation and stable inheritance. We carried out bioinformatics analysis, which indicated that ParM genes are not only confined to plasmids but are also occasionally found on genomes. Here we report the discovery and characterization of two chromosome encoded ParMs (cParMs) from the genomes of Desulfitobacterium hafniense (Dh-cParM1) and Clostridium botulinum (Cb-cParM). Both cParMs form filaments, exhibit nucleotide hydrolysis, and possess characteristic ParM subunit structures. Dh-cParM1 forms single and tightly coupled double filaments and is highly conserved on the chromosomes of five of six Desulfitobacterium species. Interestingly, these bacteria have not been reported to harbour plasmids. Cb-cParM possesses unique properties. Its filaments were stable after nucleotide hydrolysis and Pi release, and its ParR, (Cb-cParR) did not affect the initial stage of Cb-cParM polymerization but displayed properties of a depolymerization factor for mature filaments. These results indicate functional, polymerizing ParMs can be encoded on genomes, suggesting that ParM roles may extend to other functions beyond plasmid segregation.

microbiology↗

bioRxiv2024

Extensively acquired antimicrobial resistant bacteria restructure the individual microbial community in post-antibiotic conditions

In recent years, the overuse of antibiotics has led to the emergence of antimicrobial resistant (AMR) bacteria. To evaluate the spread of AMR bacteria, the reservoir of AMR genes (resistome) has traditionally been identified from environmental samples, hospital environments, and human populations; however, the functional role of AMR bacteria in the human gut microbiome and their persistency within individuals has not been fully investigated. Here, we performed a strain-resolved in-depth analysis of the resistome changes by reconstructing a large number of metagenome-assembled genomes (MAGs) of antibiotics- treated individuals gut microbiome. Interestingly, we identified two bacterial populations with different resistome profiles, extensively acquired antimicrobial resistant bacteria (EARB) and sporadically acquired antimicrobial resistant bacteria (SARB), and found that EARB showed broader drug resistance and a significant functional role in shaping individual microbiome composition after antibiotic treatment. Furthermore, longitudinal strain analysis revealed that EARB bacteria were inherently carried by individuals and can reemerge through strain switching in the human gut microbiome. Our data on the presence of AMR bacteria in the human gut microbiome provides a new avenue for controlling the spread of AMR bacteria in the human community.

genomics↗

bioRxiv2024

MICOS Complex Loss Governs Age-Associated Murine Mitochondrial Architecture and Metabolism in the Liver, While Sam50 Dictates Diet Changes

Background & AimsAging is associated with a significant decline in mitochondrial function in the liver, leading to an increased risk of liver disease. This study examines age-related changes in the mitochondrial structure of human and murine livers using a combination of Serial Block-Face Scanning Electron Microscopy (SBF-SEM) and mass spectrometry approaches. MethodsThis study integrates mitochondrial structure analysis in a murine model with an analysis of liver architecture, lipogenesis, and genetically regulated gene expression in human cohorts. We explored the Mitochondrial Contact Site and Cristae Organizing System (MICOS) complex using SBF-SEM, three-dimensional reconstruction with Amira software, and mass spectrometry techniques. ResultsAging leads to a reduction in mitochondrial size and complexity, resulting in changes in the metabolomic and lipidomic profiles of murine liver cells that are comparable to those observed in aged human samples. We find that genetically modeled expression of MICOS complex genes OPA1 and CHCHD3 is associated with chronic liver disease phenotypes within a large biobank population. Furthermore, we observed dysregulated mitochondrial calcium handling and increased oxidative stress due to the disruption of the MICOS complex. ConclusionOur study highlights the age-associated decline in mitochondrial complexity and metabolic regulation within the aging murine liver and the human population. We have identified that these changes are partially attributable to the age-related loss of the MICOS complex. Impact and implicationsThis study offers new insights into the changes to mitochondrial ultrastructure that occur during aging. Using SBF-SEM, the quantification of young and aged murine mitochondrial structure was performed, which had previously been an underexplored avenue for measuring mitochondrial changes. The discovery of mitochondrial ultrastructural changes, in conjunction with measurements of age-associated metabolic alterations and gene association data, provides a model for how changes in MICOS expression may modulate age-related impairment of hepatic mitochondria. These results provide a new model by which changes in MICOS protein expression may both cause and be a potential therapeutic target for age-related impairment in hepatic function. HighlightsDecreased modeled expression of CHCHD3 in individuals of European genetic ancestry is linked to liver transplant and cirrhosis, while decreased modeled expression of OPA1 in individuals of African genetic ancestry is associated with chronic liver disease and cirrhosis. Aging alters liver lipid accumulation, MICOS mRNA levels, and disease markers. Aging reduces the volume and complexity of murine liver ultrastructure. Aging and diet significantly alter the MICOS complex in mice. Knockdown of Mic60 and Chchd6 lowers Ca2+ uptake, retention, and induces oxidative stress in HepG2 cells. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/599846v3_ufig1.gif" ALT="Figure 1000"> View larger version (47K): org.highwire.dtl.DTLVardef@1cdd61corg.highwire.dtl.DTLVardef@a3fb74org.highwire.dtl.DTLVardef@1d1ad36org.highwire.dtl.DTLVardef@c2e55f_HPS_FORMAT_FIGEXP M_FIG C_FIG Liver aging causes metabolic, lipidomic, and mitochondrial structural alterations, reflecting age-dependent losses in the MICOS complex. Key components of the MICOS complex (MIC60, CHCHD3 and CHCHD6) are illustrated.

physiology↗

bioRxiv2024

The MICOS Complex Regulates Mitochondrial Structure and Oxidative Stress During Age-Dependent Structural Deficits in the Kidney

Due to aging, the efficiency of kidney function begins to decrease. Dysfunction in mitochondria and their cristae is a hallmark of aging. Therefore, age-related decline in kidney function could be attributed to changes in mitochondrial ultrastructure, increased reactive oxygen species, and alterations in metabolism and lipid composition. We sought to understand how mitochondrial ultrastructure is altered over time in tubular kidney cells. A serial block facing-scanning electron microscope and manual segmentation using the Amira software were employed to visualize murine kidney samples during the aging process at 3 months (young) and 2 years (old). We found that 2-year mitochondria are more fragmented with many uniquely shaped mitochondria observed across aging, concomitant with shifts in ROS, metabolomics, and lipid homeostasis. Furthermore, we demonstrate that the mitochondrial contact site and cristae organizing system (MICOS) complex is impaired in the kidney during aging. Disruption of the MICOS complex resulted in altered mitochondrial metabolic function and increased ROS levels. We found significant, detrimental structural changes in the mitochondria of aged kidney tubules, suggesting a potential mechanism underlying the increased frequency of kidney disease with aging. We hypothesize that disruption of the MICOS complex exacerbates mitochondrial dysfunction, creating a vicious cycle of mitochondrial degradation and oxidative stress, which impacts kidney health. Impact and ImplicationsDue to aging, the efficiency of kidney function begins to decrease, and the risk of kidney diseases may increase; however, the specific regulators of mitochondrial age-related changes are poorly understood. This study demonstrates that the MICOS complex may be a target for mitigating age-related mitochondrial changes. The MICOS complex is associated with oxidative stress and calcium dysregulation, which also arise in many kidney pathologies. HighlightsO_LIAging alters the MICOS mRNA levels and disease markers. C_LIO_LIAging reduces cristae architecture, mitochondrial volume and complexity in murine kidney ultrastructure C_LIO_LIReducing MIC60 and CHCHD6 lowers Ca2+ uptake and retention and induces oxidative stress in HEK cells. C_LIO_LIMetabolomic Profiling revealed that NAD+ and amino acid metabolism were altered in aged kidneys. C_LIO_LIMICOS deficiency alters the reduced basal, ATP-linked, maximal capacity and spare capacity. C_LIO_LIDecreased modeled expression of CHCHD6 in individuals of European genetic ancestry is linked to chronic kidney disease, whereas decreased modeled expression of OPA1 in individuals of African genetic ancestry is associated with chronic kidney disease. C_LI Graphical AbstractKidney aging causes a decline in the MICOS complex, concomitant with metabolic, lipidomic, and mitochondrial structural alterations. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/598108v3_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@1a868f0org.highwire.dtl.DTLVardef@1817bfborg.highwire.dtl.DTLVardef@1f2a1a3org.highwire.dtl.DTLVardef@520692_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2024

Untargeted Plasma Metabolomics Unveils Distinct Metabolite Profiles in Parkinson Disease Subtypes: A Focus on idiopathic REM Sleep Behavior Disorders

BackgroundParkinsons disease (PD) is characterized by diverse clinical presentations and etiological complexities, with rapid eye movement (REM) sleep behavior disorder (RBD) serving as a prodromal marker. While extensive unbiased metabolic profiling of plasma samples from PD subjects has been conducted to identify novel PD metabolic biomarkers, comprehensive metabolic profiling of PD subtypes based on RBD status remains limited. MethodsWe conducted a comprehensive metabolic profiling of PD subtypes at disease onset, considering the presence or absence of RBD, utilizing an untargeted metabolomics approach. Plasma samples were collected from subjects with PD with and without RBD at the initial stages of disease, idiopathic RBD, and healthy controls to elucidate similarities and differences among PD subtypes. Based on ordination analysis and metabolome-wide association study (Wilcoxon rank-sum tests and generalized fold changes), we identified specific groups of metabolites enriched in the PD_Only group and RBD groups (iRBD & PD_RBD+), with few metabolites shared between groups. Furthermore, pathway enrichment analysis (hypergeometric tests) identified specific groups enriched with metabolites from specific origins and associated biospecimens, as well as disease-associated metabolites. Finally, we evaluated the biomarker potential of the identified disease metabolites by ROC curves and proposed logistic regression models of key biomarkers and clinical parameters for predicting disease status. ResultsMetabolomic analysis revealed distinct metabolic profiles between PD subtypes with and without RBD. Our analysis confirmed previously reported PD metabolic markers, such as a reduction in caffeine and urate, as well as an increase in cortisol, secondary bile acids, and p-cresol sulfate. However, our stratified analyses based on the presence of RBD discriminated RBD-associated metabolites from those associated with PD_Only (without RBD). PD patients with RBD exhibited enrichment of gut microbial-origin metabolites, including secondary bile acids and p-cresol sulfate, compared to PD patients without RBD. Conversely, metabolites associated with neuro-psychiatric diseases were enriched in PD patients without RBD. ConclusionsOur study elucidates the heterogeneous nature of PD subtypes, particularly differentiated with the presence of RBD. The metabolic features of PD with RBD subtype supports the "body-first" concept of PD pathogenesis originating from the gut.

systems biology↗

bioRxiv2024

Single Nucleotide Polymorphism (SNP) and Antibody-based Cell Sorting (SNACS): A tool for demultiplexing single-cell DNA sequencing data

MotivationRecently, single-cell DNA sequencing (scDNA-seq) and multi-modal profiling with the addition of cell-surface antibodies (scDAb-seq) have provided key insights into cancer heterogeneity. Scaling these technologies across large patient cohorts, however, is cost and time prohibitive. Multiplexing, in which cells from unique patients are pooled into a single experiment, offers a possible solution. While multiplexing methods exist for scRNAseq, accurate demultiplexing in scDNAseq remains an unmet need. ResultsHere, we introduce SNACS: Single-Nucleotide Polymorphism (SNP) and Antibody-based Cell Sorting. SNACS relies on a combination of patient-level cell-surface identifiers and natural variation in genetic polymorphisms to demultiplex scDNAseq data. We demonstrated the performance of SNACS on a dataset consisting of multi-sample experiments from patients with leukemia where we knew truth from single-sample experiments from the same patients. Using SNACS, accuracy ranged from 0.948 - 0.991 vs 0.552 - 0.934 using demultiplexing methods from the single-cell literature. Availability ImplementationSNACS is available at https://github.com/olshena/SNACS. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC="FIGDIR/small/579345v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@1e52aaorg.highwire.dtl.DTLVardef@c51d1dorg.highwire.dtl.DTLVardef@fa68a6org.highwire.dtl.DTLVardef@1ec6bd1_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2023

Quantitative Assessment of Morphological Changes in Lipid Droplets and Lipid-Mito Interactions with Aging in Brown Adipose

The physical characteristics of brown adipose tissue (BAT) are defined by the presence of multilocular lipid droplets (LD) within the brown adipocytes and a high abundance of iron-containing mitochondria, which give it its characteristic color. Normal mitochondrial function is, in part, regulated by organelle-to-organelle contacts. Particularly, the contact sites that mediate mitochondria-LD interactions are thought to have various physiological roles, such as the synthesis and metabolism of lipids. Aging is associated with mitochondrial dysfunction, and previous studies show that there are changes in mitochondrial structure and proteins that modulate organelle contact sites. However, how mitochondria-LD interactions change with aging has yet to be fully clarified. Therefore, we sought to define age-related changes in LD morphology and mitochondria-lipid interactions in BAT. We examined the three-dimensional morphology of mitochondria and LDs in young (3-month) and aged (2-year) murine BAT using serial block face-scanning electron microscopy and the Amira program for segmentation, analysis, and quantification. Analysis showed reductions in LD volume, area, and perimeter in aged samples compared to young samples. Additionally, we observed changes in LD appearance and type in aged samples compared to young samples. Notably, we found differences in mitochondrial interactions with LDs, which could implicate that these contacts may be important for energetics in aging. Upon further investigation, we also found changes in mitochondrial and cristae structure for mitochondria interacting with LD lipids. Overall, these data define the nature of LD morphology and organelle-organelle contacts during aging and provide insight into LD contact site changes that interconnect biogerontology and mitochondrial functionality, metabolism, and bioactivity in aged BAT. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/559135v2_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@e5b7org.highwire.dtl.DTLVardef@e965e5org.highwire.dtl.DTLVardef@120c7e9org.highwire.dtl.DTLVardef@124bfb5_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract Workflow highlighting the process of murine interscapular BAT extraction, processing and imaging serial block facing-scanning electron microscopy and using Amira software for 3D reconstruction of LDs and mitochondrial lipid contact sites to elucidate their structure across aging. C_FIG

biophysics↗

bioRxiv2023

Multiomic Single Cell Sequencing Identifies Stemlike Nature of Mixed Phenotype Acute Leukemia and Provides Novel Risk Stratification

Mixed phenotype acute leukemia (MPAL) is a leukemia whose biologic drivers are poorly understood, therapeutic strategy remains unclear, and prognosis is poor. We performed multiomic single cell (SC) profiling of 14 newly diagnosed adult MPAL patients to characterize the immunophenotypic, genetic, and transcriptional landscapes of MPAL. We show that neither genetic profile nor transcriptome reliably correlate with specific MPAL immunophenotypes. However, progressive acquisition of mutations is associated with increased expression of immunophenotypic markers of immaturity. Using SC transcriptional profiling, we find that MPAL blasts express a stem cell-like transcriptional profile distinct from other acute leukemias and indicative of high differentiation potential. Further, patients with the highest differentiation potential demonstrated inferior survival in our dataset. A gene set score, MPAL95, derived from genes highly enriched in this cohort, is applicable to bulk RNA sequencing data and was predictive of survival in an independent patient cohort, suggesting utility for clinical risk stratification.

cancer biology↗