Biology subjects

Lin, L.

Publications and source records attributed to Lin, L..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Essential function reflected in the phylodynamics of a multigene family: the pir genes of malaria parasites

The genomes of malaria parasites (Plasmodium spp.) encode many gene families, which are intimately associated with host interactions and disease in these important pathogens. The largest malaria gene family is the Plasmodium interspersed repeat (pir) genes, present in rodent, primate and most human malaria parasites, which are suggested to have originated from one highly conserved gene, which we call pirC1. The precise function(s) of pir is unknown but to determine their potentially multifarious roles we must understand the evolutionary dynamics of pir repertoire to discriminate among the many genes. Here we estimate the global phylogeny for pir genes in 14 Plasmodium species and one Hepatocystis species. We reveal that pirC1 is not the common ancestor but is one of several orthologous genes conserved in multiple species amidst the rapid turnover of species-specific paralogs. We show that the PIRC1 protein is nonetheless essential for blood stage growth of P. berghei, P. chabaudi and P. knowlesi, as parasites lacking the pirC1 gene could not be generated or had severely reduced growth rates. As this effect was observed both in vivo and in vitro, the role of pirC1 is not related to host immune interaction. Rather, P. berghei and P. knowlesi PIRC1 are secreted from the parasite, pointing to a role in parasite interaction with the host cell or nutrient uptake by blood stages. The phylodynamics of pir genes indicate that old orthologs, like pirC1, and younger within-species paralogs could have fundamentally different roles, and emphasize the need to distinguish between them in future. This study is the first to provide evidence for the existence of an essential pir gene and provides a robust rationale for further experimental approaches to pir gene functions. SIGNFICANCEThe genomes of malaria parasites (Plasmodium) contain many different gene families, of which the pir family is the largest, with more than 1000 members in some species. The PIR proteins are likely important for parasite fitness but their precise functions remain unknown - roles in adherence of infected red blood cells to blood vessels, virulence and immune evasion of have been suggested. How, and why, this highly diverse gene family evolved is a significant question both for understanding malaria physiology and pathogenesis. Here we present a comprehensive pir phylogeny, identifying the origins of gene diversity during Plasmodium evolution and a select group of highly conserved genes. We show that one conserved pir gene (pirC1) encodes a protein that is essential for optimal growth of multiple malaria parasites during the asexual blood stage, both in the host and in vitro. This indicates that pirC1 function relates to interaction with the host cell or nutrient acquisition, and not to immune evasion or sequestration, (although this might still be the function of other pir genes). This study provides a robust rationale for the hitherto baffling diversity of pir genes, and shows why it is important to distinguish old orthologs from young paralogs in future studies on pir gene function.

microbiology↗

bioRxiv2026

BiOmics: A Foundational Agent for Grounded and Autonomous Multi-omics Interpretation

While AI has automated bioinformatic workflows, biological interpretation remains fragmented and often disconnected from mechanistic insights. Existing AI is bifurcated between statistical "black-box" models that lack logical grounding and simple agents restricted to shallow knowledge retrieval. To bridge this divide, we introduce BiOmics, a foundational agent that synthesizes multi-omics data with adaptive knowledge for biological interpretation. BiOmics introduces a novel dual-track architecture comprising a harmonized explicit reasoning space for grounded logic and a unified latent embedding space for high-dimensional association mapping. This architecture enables a transformative "Retrieving-Reasoning-Predicting" paradigm for purposeful, cross-scale inference traversing the biological hierarchy, from molecular variants to disease phenotypes. Empirical evaluations demonstrate that BiOmics surpasses state-of-the-art AI agents and specialized algorithms, markedly augmenting the granularity and depth of biological insights. Specifically, BiOmics exhibits unique superiority in uncovering indirect pathogenic variants, achieving reference-free cell annotation, and prioritizing drug repurposing candidates tailored to specific datasets. BiOmics further enriches the interpretive landscape of biological entities, leveraging its reasoning-grounded knowledge graph to uncover deep functional contexts. Ultimately, BiOmics provides a versatile engineering foundation to transition AI for Science from descriptive "data fitting" to autonomous, knowledge-driven interpretation.

bioinformatics↗

bioRxiv2026

A micropeptide component of the OGDH complex modulates ATP production in the TCA cycle

Since its elucidation, the tricarboxylic acid (TCA) cycle has been regarded as a fully defined enzymatic pathway. Here, we report the discovery of a previously unrecognized micropeptide component of this central metabolic system. Through analyzing ribosome profiling data from the mouse sORFs.org database, we discovered APPM (ATP production-promoting micropeptide), a 29-amino acid peptide encoded by a non-canonical small open reading frame within the mouse Ctsb gene. APPM localizes to the mitochondrial matrix and inner membrane, where it directly binds to the E1 subunit (OGDH) of the -ketoglutarate dehydrogenase complex (OGDHc). This interaction modulates OGDHc enzymatic activity, thereby regulating NADH and ATP production. We identified tyrosine-13 as the critical residue mediating the APPM-OGDH interaction and functional activation. Exogenous APPM administration increased ATP levels in vivo and, in a mouse model of heart failure, restored cardiac function, outperforming the reference drug trimetazidine. Collectively, our findings identify APPM as the first micropeptide regulator of the OGDH complex, expanding the known repertoire of the TCA cycle and presenting a potential therapeutic strategy for bioenergetic disorders.

molecular biology↗

bioRxiv2025

Unraveling Candidatus Dermatophostum as a Novel Genus of Polyphosphate-Accumulating Organisms for High-Strength Wastewater Treatment

Dermatophilaceae polyphosphate-accumulating organisms (PAOs), formerly classified as Tetrasphaera PAOs, play pivotal roles in enhanced biological phosphorus removal (EBPR). However, their phylogenetic diversity, ecological preferences, and metabolic traits remain poorly characterized, and a robust marker gene for their classification is lacking. Here, we performed an extensive phylogenomic and metabolic analysis of Dermatophilaceae PAOs utilizing 46 newly recovered metagenome-assembled genomes (MAGs) from a laboratory-scale EBPR reactor treating high-strength wastewater and full-scale wastewater treatment plants. These analyses revealed a previously uncharacterized PAO genus, named Candidatus Dermatophostum, which is adapted to high-phosphorus environments. Its representative species, Ca. D. ammonifactor, was enriched in the EBPR reactor and its PAO phenotype was confirmed by polyphosphate staining and fluorescence in situ hybridization. Genomic, transcriptomic, and protein structure analyses revealed its specialized metabolic capabilities for phosphate metabolism, glycogen synthesis and dissimilatory nitrate reduction to ammonium. Moreover, Ca. Dermatophostum was found to be widely distributed across WWPTs worldwide, underscoring both its ecological importance and its potential role in mitigating nitrous oxide (N2O) emissions. Finally, we propose a ppk1-based classification framework that resolves Dermatophilaceae PAOs into six distinct clades, consistent with whole-genome phylogeny, and demonstrates that ppk1 can serve as a reliable marker gene for tracking these populations. Together, these findings expand the ecological and functional understanding of Dermatophilaceae PAOs and highlight their promise for advancing sustainable wastewater treatment and resource recovery.

microbiology↗

bioRxiv2025

Aspartate Transaminases Are Dispensable for Pancreatic Development and Pancreatic Cancer Progression

Pancreatic ductal adenocarcinoma (PDA) is the third leading cause of cancer-related deaths in the United States. This is due in part to the limited availability of effective treatment options for patients, highlighting a significant need for new targets and approaches. Deregulated metabolism is a hallmark feature of PDA that has gained attention as a promising inroad for therapy. The aspartate transaminases (glutamate oxaloacetate transaminases, cytosolic GOT1 and mitochondrial GOT2) have several important metabolic functions, including maintaining energy and redox balance and generating aspartate, an essential building block in protein and nucleotide biosynthesis. Previous studies of GOT proteins in preclinical tumor transplant models have yielded conflicting results regarding the requirement of GOT1 and GOT2 for PDA tumor growth. To assess the role of GOT proteins in tumor development and tumor maintenance, we generated conditional knockout mice for Got1 and Got2 and crossed these into pancreas-specific models. Whereas loss of either Got does not impact pancreas development, double Got1 and Got2 knockout results in markedly reduced pancreas size and cellularity without overtly impacting endocrine or exocrine function. In genetically engineered cancer models, single Got loss does not impact lesion formation, tumor size, animal survival, or the composition of the tumor microenvironment. Identical results were also observed in orthotopic allograft mouse models. Together, these findings add to a growing body of work illustrating the adaptability of metabolism in cancer. They also emphasize the importance of model selection, the use of multiple independent models, and the in vivo context when studying the role of metabolic programs in cancer.

cancer biology↗

bioRxiv2025

A near-complete lamprey genome illuminates ancestral vertebrate innovations

The origin of vertebrates is characterized by a suite of phenotypic innovations, yet the underlying genetic mechanisms remain poorly understood. As a living representative of jawless vertebrates, the lamprey serves as a pivotal model for investigating the genomic basis of early vertebrate evolutioin. Here, we report a near telomere-to-telomere (T2T) genome assembly of the reissner lamprey (Lethenteron reissneri), generated from sperm DNA that is not subject to programmed genome rearrangement. The 1.25 Gb assembly resolves over 97% of chromosome sequences into single contigs, enabling reconstruction of previously inaccessible genomic regions. Centromeres display highly diversified, lamprey-specific repeat units and structural architectures, whereas telomeres contain both conserved and lineage-specific satellite repeats. Deep transcriptomic profiling across representative organs and developmental stages substantially improved genome annotation. Comparative genomic analyses revealed a major expansion of 1,562 gene families at the base of the vertebrate lineage, and they are significantly enriched for functions related to neural development, skeletal formation, and cardiac function, echoing the known phenotypic innovations in vertebrates. Notably, the CDH2 gene family underwent vertebrate-specific copy number expansion and acquired conserved cis-regulatory elements (CREs), highlighting its potential role in shaping the early vertebrate circulatory system. Histological analyses and functional knockout experiments demonstrated that one CDH2 paralog (CDH2_H) is essential for lamprey heart development and chamber formation, playing a critical role in the emergence of the closed circulatory system in early vertebrates. This high-quality lamprey genome provides a foundational resource for dissecting the genetic basis of key innovations that shaped vertebrate evolution.

genomics↗

bioRxiv2025

TagF coordinates spike-loading as an intermediate checkpoint in Type VI Secretion System assembly

Diderm bacteria use contact-dependent Type VI secretion systems (T6SS) to gain a competitive advantage within bacterial communities and during infection. Whereas the structural core assembly of T6SS is well characterized, the role of diverse accessory proteins during assembly remains under investigation. One well-conserved accessory protein is TagF, a post-translational inhibitor of T6SS dynamics, which was previously characterized in the context of a kinase-phosphatase signaling relay. Here, we identify a subset of T6SS clusters in which TagF occurs in a distinct regulatory context and without known binding partners. Investigating the role of TagF in the constitutively active Acinetobacter baylyi T6SS, we show that though TagF can suppress assembly dynamics, it primarily acts as an assembly coordinator. Using structured illumination microscopy, we show that TagF coordinates the transition from baseplate assembly to sheath elongation by preventing premature and nonproductive sheath assembly in absence of the VgrG spike. Direct interactions with the conserved T6SS tube protein Hcp suggested that TagF blocks sheath elongation by binding and disrupting Hcp hexamers and thus preventing tube formation. Finally, we show that TagF activity depends on crosstalk with TagZ, a previously uncharacterized membrane-associated accessory protein that recruits TagF to the cell periphery, and demonstrate that this interaction can be specifically disrupted by expression of an artificial TagF-binding protein. Together, our findings establish a novel role of TagF as a checkpoint protein that controls for spike-insertion into the baseplate to ensure effective T6SS assembly.

microbiology↗

bioRxiv2025

Screening of Oyster Peptides for Anti-Muscle Atrophy Based on Machine Learning and Computer Simulation: Guided by Antioxidant Pathways

Muscle atrophy poses a serious threat to human health, with its primary pathogenic mechanisms closely linked to oxidative stress. This study focuses on the potential of oyster peptides in alleviating dexamethasone (DEX)-induced skeletal muscle atrophy and their underlying antioxidant mechanisms. Utilizing efficient integrated machine learning and computer simulation methods, a systematic screening of active peptides and mechanistic research was conducted. The results revealed that oyster peptides at concentrations of 25-50 g/mL significantly improved the decline in cell viability and myotube atrophy induced by DEX, while downregulating the expression of muscle atrophy markers Atrogin-1 and MuRF1. Through LC-MS/MS, 220 high-activity peptide sequences were identified. Following the replication and extension of the iAnOxPep integrated learning model, 15 potential antioxidant peptides were selected. Among them, the short peptide AWPGPQ demonstrated the strongest binding affinity with Keap1 and PPAR{gamma} targets. Molecular dynamics simulations confirmed its stability, suggesting that AWPGPQ may exert its dual effects--antioxidant and anti-muscle atrophy--by modulating the Keap1-Nrf2 and PPAR{gamma} signaling pathways. This study established a systematic and efficient strategy for screening natural active peptides, providing theoretical support and technical pathways for the discovery of multifunctional short peptide candidates, with significant theoretical value and application prospects.

molecular biology↗

bioRxiv2025

Benchmarking Perturbation Tools for the Noncoding Genome

Deciphering the functionality of the noncoding genome which includes important cis-regulatory elements (CREs) and transcribed noncoding RNA genes remains technically challenging. Here, using massively parallel genetic screening, we systematically benchmark the performance of five representative loss-of-function perturbation tools, including single guide RNA (gRNA) mediated SpCas9 cleavage or CRISPR interference, and paired gRNA (pgRNA) involved dual-SpCas9, Big Papi (paired SpCas9 and SaCas9) or dual-enAsCas12a fragment deletion methods, in decoding the roles of the noncoding genome. For targeting CREs such as enhancer, dual-SpCas9 outperforms other methods with superior efficiency of destroying functional genomic regions. For perturbing noncoding RNA genes, in addition to dual-SpCas9, other RNA-targeting methods such as RNA interference are recommended to discriminate transcript-dependent or -independent roles. A deep learning model DeepDC with associated web server is built to facilitate optimal dual-SpCas9 pgRNA design for efficiently deleting a genomic fragment. Together, our work provides practical guidance on selecting appropriate loss-of-function tools to resolve the functional complexity of the noncoding genome.

genetics↗

bioRxiv2025

Ultra-mild bisulfite outperforms EM-seq for 5-methylcytosine detection with low input DNA

We present Ultra-Mild Bisulfite Sequencing (UMBS-seq), a method for 5-methylcytosine (5mC) detection that minimizes DNA degradation and background noise. UMBS-seq outperforms conventional bisulfite and enzymatic methyl-sequencing (EM-seq) methods in library yield, complexity, and conversion efficiency when applied to low-input DNA samples. In particular, its effectiveness with low-input cell-free DNA (cfDNA) and hybridization-based target capture highlight its potential for clinical applications, including 5mC biomarker detection and early disease diagnosis.

genomics↗

bioRxiv2025

Birds that don't exist: niche pre-emption as a constraint on morphological evolution in the Passeroidea

Understanding why some viable body forms never evolve can reveal how ecological and evolutionary forces shape biodiversity. We investigate this question in the Passeroidea, a large group of songbirds, by analyzing their morphological trait space using topological data analysis and ancestral state reconstruction. We identify a long-standing morphological gap densely surrounded by extant species but unoccupied throughout passeroid diversification. The gap patterns deviate from neutral expectations and show no evidence of past occupation, rendering neutral evolution and extinction unlikely. Similar morphologies exist in other bird lineages, ruling out intrinsic constraints or niche absence. Geographic distributions and traits of passeroids versus non-passeroid gap occupants point to competitive exclusion as the plausible explanation: early-colonizing territorial specialists outside the Passeroidea may have preemptively occupied key habitats, limiting evolutionary opportunities for later-arriving lineages. We demonstrate how historical contingency can shape macroevolutionary outcomes, and introduce a generalizable framework for investigating structural gaps in trait evolution.

ecology↗

bioRxiv2025

Aspartate transaminases are required for blood development

Red blood cells (RBCs) have a limited lifespan of approximately 120 days. This necessitates continuous RBC production, resulting in [~]200 billion new RBCs made per day to maintain oxygen delivery. Despite this enormous biosynthetic demand, the metabolic pathways supporting erythropoiesis are poorly understood. We profiled metabolites across four independent models of elevated erythropoiesis and a consistent increase in aspartate levels emerged when compared to controls. This suggested a potential role for aspartate metabolism in RBC production. To test this, we deleted the aspartate aminotransferases Got1 or Got2 globally or in an erythroid-specific manner. Loss of either enzyme resulted in anemia, with Got2 deficiency producing a more severe phenotype. Individual loss of either Got or dual Got deletion led to an erythroid defect, where early progenitors accumulated. In human and mouse models of erythropoiesis, GOT1 and GOT2 loss had opposing impacts on aspartate despite exhibiting similar anemic phenotypes, suggesting an aspartate-independent function for these enzymes. GOT1 and GOT2 are also components of the malate-aspartate shuttle (MAS), which regulates NAD(H) homeostasis. However, conditional deletion of another MAS enzyme, Mdh1, did not cause anemia, and alleviating NADH reductive stress in GOT2-deficient cells with cytoplasmic bacterial NADH oxidase (LbNOX) failed to restore erythropoiesis. Instead, transcriptomic and epigenetic analyses revealed dysregulation of chromatin histone modifications in GOT-deficient erythroid cells, implicating epigenetic dysfunction as a driver of defective erythropoiesis. Collectively, these findings identify a previously unrecognized role for GOT1 and GOT2 as a central link between metabolism and epigenetic regulation during erythroid development. These insights may inform the development of new therapeutic strategies for anemia.

biochemistry↗

bioRxiv2025

Mechanistically Informed Machine Learning Links Non-Canonical TCA Cycle Activity to Warburg Metabolism and Hallmarks of Malignancy

Cancer cells undergo extensive metabolic rewiring to support growth, survival, and phenotypic plasticity. A non-canonical variant of the tricarboxylic acid (TCA) cycle, characterized by mitochondrial-to-cytosolic citrate export, has emerged as critical for embryonic stem cell differentiation. However, its role in cancer remains poorly understood. Here, we present a two-step computational framework to systematically analyze the activity of this non-canonical TCA cycle across over 500 cancer cell lines and investigate its role in shaping hallmarks of malignancy. First, we applied constraint-based modeling to infer cycle activity, defining two complementary metrics: Cycle Propensity, measuring the likelihood of its engagement in each cell line, and Cycle Flux Intensity, quantifying average flux through the reaction identified as rate-limiting. We identified distinct tumor-specific patterns of pathway utilization. Notably, cells with high Cycle Propensity preferentially rerouted cytosolic citrate via aconitase 1 (ACO1) and isocitrate dehydrogenase 1 (IDH1), promoting -ketoglutarate (KG) and NADPH production. Elevated engagement of this cycle strongly correlated with Warburg-like metabolic shifts, including decreased oxygen consumption and increased lactate secretion. In the second step, to uncover non-metabolic transcriptional signatures associated with non-canonical TCA cycle activity, we performed machine learning-based feature selection using ElasticNet and Random Forest, identifying robust gene signatures predictive of cycle activity. Over-representation analysis revealed enrichment in genes involved in invasiveness, angiogenesis, stemness, and key oncogenic pathways. Analysis of DepMap gene dependency data revealed that TCA cycle activity correlates with differential vulnerability to perturbation of these oncogenic pathways, reinforcing the functional relevance of identified transcriptional signatures. To further interpret the predictive models, SHapley Additive exPlanations (SHAP) was applied to prioritize genes contributing most to non-canonical cycle activity, suggesting novel candidates for experimental investigation. Overall, our framework enables comprehensive analysis of non-canonical TCA cycle dynamics and uncovers potential links between metabolic plasticity and malignant phenotypes.

cancer biology↗

bioRxiv2025

Multi-omic analysis of photoreceptor alterations during early-onset retinal degeneration in Mfrp-/- mice

Loss-of-function mutations in the membrane frizzled-related protein (MFRP) gene are associated with autosomal recessive ocular disorders such as nanophthalmos, posterior microphthalmia, and retinitis pigmentosa, yet the molecular mechanisms underlying MFRP-related retinal degeneration remain poorly defined. To investigate these mechanisms, we generated and characterized Mfrp-/- mice and conducted an integrated multi-omic analysis to map the onset and progression of transcriptional changes during retinal degeneration. Using longitudinal in vivo imaging, histological and immunohistochemical analysis, qRT-PCR, single-nucleus RNA sequencing (snRNA-seq), snATAC seq (single-nucleus Assay for Transposase-Accessible Chromatin using sequencing) and spatial transcriptomics (GeoMx DSP), we identified early and progressive photoreceptor loss in Mfrp-/- mice, beginning by 28d. Retinal thinning and autofluorescent deposits in Mfrp-/- mice were accompanied by decreased expression of rod and cone opsins. Transcriptomic profiling by snRNA-seq revealed distinct, photoreceptor-specific gene expression changes, including early upregulation of inflammatory and stress-related genes and later downregulation of genes involved in chromatin remodeling, synaptic function, and neurodevelopment. Spatial transcriptomic analysis of the outer nuclear layer (ONL) revealed disruptions in mitochondrial function, mTORC1 signaling, and G protein-coupled receptor pathways. These findings define a temporally and spatially coordinated program of degeneration triggered by Mfrp loss and demonstrate that Mfrp is required for the maintenance of photoreceptor integrity and gene regulatory homeostasis during retinal development. Our work establishes Mfrp-/- mice as a robust model for dissecting photoreceptor vulnerability and provides a transcriptomic atlas of disease progression with potential relevance for therapeutic development in MFRP-associated retinal dystrophies.

genomics↗

bioRxiv2025

Signatures of digital Polycomb regulation in functional iPSC heterogeneity between individuals

Induced pluripotent stem cells (iPSCs) show substantial heterogeneity between individuals in their capacity to differentiate into various cell types, hindering their translational application. To explore the causes of this variability, we analysed a panel of ten human iPSC lines, evaluating their differentiation efficiency for two different fates, profiling their transcriptome and chromatin state. Using a machine learning approach, we related chromatin state variability with transcriptional differences. We found that regulation of the Polycomb-mediated histone modification H3K27me3 at specific gene loci exhibited the most consistent differences among iPSC lines, frequently displaying a digital ON/OFF pattern, consistent with a mathematical model based on Polycomb read-write feedback. Notably, altered gene expression patterns of Polycomb-regulated genes were largely propagated into an intermediate state in the differentiation trajectory. Finally, we uncovered a subset of Polycomb-regulated genes with heterogeneous expression and chromatin signatures that were highly predictive of iPSC differentiation efficiencies for two cell types.

systems biology↗

bioRxiv2025

AAV NRF2 Gene Therapy Preserves Retinal Structure and Function in Rodent Models of Oxidative Damage

Dry age-related macular degeneration is the most frequent cause of visual impairment in individuals over age 50 in developed countries. It is characterized by subretinal deposits of oxidized proteins and lipids and results in progressive loss of high acuity vision. One major risk factor is smoking, which causes oxidative stress in many tissues, including the eye. We previously showed that an adeno-associated viral vector expressing human NRF2 (AAV8/Best1-Nrf2), a transcription factor that regulates responses to oxidative damage, slowed degeneration in mouse models of another blinding disorder, retinitis pigmentosa, which also includes oxidative stress. Here, our AAV8/Best1-Nrf2 vector was tested in a model of oxidative stress wherein sodium iodate was injected systemically, as this is often used to model dry age-related macular degeneration. Sodium iodate causes acute oxidative damage to supporting cells of the retina, the retinal pigment epithelial cells, and ultimately leads to photoreceptor death. Subretinal injection of AAV8/Best1-Nrf2 led to protection of the retinal pigment epithelium and photoreceptors, as well as preservation of visual function, in rat and mouse sodium iodate models. AAV8/Best1-Nrf2 may serve as an effective gene-agnostic therapy for diseases with oxidative stress, including dry age-related macular degeneration. ETOCOxidative stress occurs in diseases that lead to vision loss, including age-related macular degeneration (AMD). AMD is commonly modeled by injection of sodium iodate (S.I.), an oxidizing agent. AAV-mediated delivery of Nrf2, a transcription factor that regulates oxidative stress, protects the eye from S.I. damage in rat and mouse models. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/663952v1_ufig1.gif" ALT="Figure 1"> View larger version (67K): org.highwire.dtl.DTLVardef@357e57org.highwire.dtl.DTLVardef@1f9986dorg.highwire.dtl.DTLVardef@186537corg.highwire.dtl.DTLVardef@1d31aad_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2025

Organism-wide spatiotemporal profiling of gene expression utilizing a X-CreERT2/Ai9 tracing system

This study utilizes a novel inducible X-CreERT2/Ai9 system to comprehensively delineate the spatial expression landscape of Fermt2, which encodes a key focal adhesion protein Kindlin-2, across organs in mice. We can confirm all known Kindlin-2-expressing cells and identify any previously unknown Kindlin-2-expressing cells and those that do not express Kindlin-2 in all tissues/organs in mice. We have developed this cost-effective, rapid, and high-fidelity system and implemented its first whole-organism application for comprehensive gene expression profiling. This work not only provides unprecedented insights into roles of Kindlin-2 in diverse physiologies and pathologies, but also establishes the inducible X-CreERT2/Ai9 system as a powerful paradigm-shifting platform for organism-wide pan-organ spatiotemporal expression profiling of any target genes encoding any proteins and micro-RNAs. By enabling high-resolution mapping of drug target expression, this system may lay critical groundwork for elucidating previously unknown adverse and beneficial effects of targeted therapies, offering transformative potential for precision medicine.

biochemistry↗

bioRxiv2025

Neuronal SEL1L-HRD1 ERAD regulates one-carbon metabolism and is essential for motor function and survival

Hypomorphic variants in the SEL1L-HRD1 ER-associated degradation (ERAD) complex have been linked to severe neurological syndromes in children, including neurodevelopmental delay, intellectual disability, motor dysfunction, and early death. Despite this association, its physiological importance and underlying mechanisms in neurons remain poorly understood. Here, we show that neuronal SEL1L-HRD1 ERAD is essential for maintaining one-carbon metabolism, motor function, and overall viability. Neuron-specific deletion of Sel1L in mice (Sel1LSynCre) resulted in growth retardation, severe motor impairments, and early mortality by 9 weeks of age--mirroring core clinical features observed in affected patients--despite preserved neuronal numbers and only modest ER stress. Multi-omics analyses, including single-nucleus RNA sequencing and metabolomics, revealed significant dysregulation of one-carbon metabolism in ERAD-deficient brains. This included activation of the serine, folate, and methionine pathways, accompanied by elevated levels of S-adenosylmethionine and related metabolites, likely resulted from induction of the integrated stress response (ISR). Together, these findings uncover a previously unappreciated role for neuronal SEL1L-HRD1 ERAD in coordinating ER protein quality control with metabolic adaptation, providing new insight into the molecular basis of ERAD-related neurodevelopmental disease. SummaryUsing a neuron-specific Sel1L knockout mouse model, we demonstrate that Sel1L deficiency activates integrated stress responses, rewires one-carbon metabolism, and impairs motor function and survival.

cell biology↗