Biology subjects

Ma, K.

Publications and source records attributed to Ma, K..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Genome-wide maps of transcription factor footprints identify noncoding variants rewiring gene regulatory networks with varTFBridge

Genome-wide association studies have identified millions of noncoding loci linked to human traits, yet how these variants alter gene regulation remains a major challenge, particularly for rare variants where whole-genome sequencing cohorts and high-resolution functional annotations remain limited. Here we show that single-molecule deaminase footprinting (FOODIE) in K562 cells captures up to 103-fold heritability enrichment for erythroid traits despite covering 0.12% of the genome. We introduce varTFBridge, integrating FOODIE footprinting with AlphaGenome variant effect prediction to identify causal noncoding variants altering transcription factor (TF)-mediated regulation. Applied to 490,640 UK Biobank genomes across 13 erythrocyte traits, varTFBridge prioritises 113 high-confidence regulatory variants (104 common, 9 rare), encompassing 2,173 linkages along the variant-TF binding- gene-trait cascade across 64 TFs and 108 genes. varTFBridge recapitulates rs112233623 and resolves its mechanism: GATA1/TAL1 co-binding disruption at a CCND3 enhancer altering red blood cell count and volume.

bioinformatics↗

bioRxiv2026

A long-read human pangenome initiative for comprehensive interpretation of nuclear-embedded mitochondrial DNA

Nuclear-embedded mitochondrial DNA segments (NUMT) preserve a record of ongoing mitochondrial-to-nuclear DNA transfer during evolution, with important implications for disease mechanisms and genome organization. Here, we developed a Pangenome Graph-based NUMT Detection (PG-NUMT) approach to improve NUMT detection sensitivity by 2.52-fold compared to short-read based approaches and comprehensively resolved seven concatenated mega-NUMTs with a maximum length of 127.7 kbp. We generated a high-resolution human NUMT map comprising 774 fixed, 280 polymorphic, and 123 pericentromeric NUMTs, alongside 74 superpopulation-stratified NUMTs. Both fixed and polymorphic NUMTs are hypermethylated and enriched within segmental duplications, whereas fixed NUMTs preferentially localize to intergenic regions and avoid transposable elements. Interestingly, NUMTs derived from the 3-end of the mtDNA D-loop are less frequently fixed in human genomes and exhibit potential cis-regulatory activity in the nuclear genome. These observations suggest that selective pressures shape the genomic features of fixed NUMTs. Seven NUMTs associated with gene expression or alternative splicing were further identified, suggesting potential modulatory functions of common NUMTs. Using 20 complete non-human primate genomes, we identified variable NUMT insertion rates across primate lineages (1.5-18.7 insertions per million years), with particularly high rates in the Pan lineage. Notably, we uncovered two NUMT-derived variable number tandem repeats (VNTRs), establishing NUMTs as a novel source of VNTRs. In summary, the integrated analysis enhances our understanding of NUMT genomic architecture, population dynamics, and evolutionary implications in human and non-human primates, establishing NUMTs as dynamic genomic components of biomedical relevance.

genomics↗

bioRxiv2026

The genetic repertoire of the deep sea: from sequence to structure and function

The deep sea as the largest and maybe most hostile environment on Earth is still underexplored especially regarding its genetic repertoire. Yet, previous work has revealed significant habitat-specific deep-sea biodiversity. Here, we present an integrated deep-sea genetic dataset comprising 502 million nonredundant genes from 2,138 samples and 2.4 million predicted structures, and used it to link specific protein structures with genetic variants associated with life in the deep sea and to assess their biotechnology potential. Combining global sequence analysis with biophysical and biochemical measurements revealed unprecedented sequence diversity, yet substantial structural conservation of proteins. Especially proteins involved in replication, recombination, and repair were identified to be under rapid evolution and with specialized properties. Among these, a structurally divergent helicase exhibited advantages in controlling nanopore sequencing speed. Thus, our work positions the deep sea as a unique evolutionary engine that generates and hosts genetic diversity and bridges genetic knowledge with biotechnology.

bioinformatics↗

bioRxiv2026

CCycDB: an integrative knowledgebase to fingerprint microbially mediated carbon cycling processes

Microorganisms play essential roles in mediating biogeochemical cycling of carbon across Earths ecosystems. Understanding the processes and underlying mechanisms for microbially mediated carbon cycling is therefore critical for advancing global ecology and climate change research. To comprehensively depict these complex biogeochemical processes, we developed CCycDB, a knowledge-based functional gene database, to accurately fingerprint microbially-mediated carbon cycling pathways and gene families, particularly from shotgun metagenomes. The CCycDB database comprises 4,676 gene families classified into six major functional categories, further structured into 45 level-1 and 188 level-2 sub-categories, encompassing a total of 10,991,724 high-quality reference sequences. Validation using both synthetic and real-world datasets demonstrated that CCycDB outperforms existing orthology databases in terms of accuracy, coverage and specificity. By directly targeting carbon-cycling functional gene families, CCycDB provided promising routines to reconstruct both functional gene and taxonomic profiles associated with microbially mediated carbon cycling. Application of CCycDB to shotgun metagenomes from diverse and complex ecosystems revealed pronounced habitat-specific differences in carbon cycling processes and their associated microbial taxa. Collectively, CCycDB provides a powerful and reliable tool for profiling carbon cycling processes from both functional and taxonomic perspectives in complex ecosystems. CCycDB is accessible at https://ccycdb.github.io/. Impact StatementThe microbially mediated carbon cycling processes are the most complex biogeochemical processes in the Earths biosphere, playing profound regulatory roles on global climate changes. A key bottleneck in linking microbial communities to global change is the lack of integrated tools for comprehensive carbon cycle profiling. Here, we present CCycDB, a tool that serves a dual purpose--first being a reference database that obtains functional gene and taxonomic profiles and functioning as a customized routine for efficiently aligning sequences and querying associated functional information. CCycDB enables researchers to accurately link microbial community dynamics to carbon cycling and transforming pathways, thereby advancing integrated global change studies with microbes and ecological research via complex metagenomic datasets.

microbiology↗

bioRxiv2026

Iron Deficiency Drives Sarcopenia in the Elderly: HIF-1α-Mediated Fibro-Adipogenic Progenitor Differentiation Induces Fat Infiltration and Impairs Muscle Function

Abnormal iron metabolism is closely linked to sarcopenia; however, the specific iron metabolism features of fat-infiltrating sarcopenia remain poorly understood. Proteomic sequencing revealed that in skeletal muscle with severe fat infiltration, the expression of iron utilization-related proteins was significantly downregulated, whereas that of iron uptake and storage proteins was markedly upregulated, thereby presenting an abnormal iron deficiency (ID) phenotype. Nevertheless, the mechanism by which ID drives intramuscular fat infiltration has not been fully elucidated. Using clinical samples, aged murine ID models, and in vitro cell assays, this study is the first to demonstrate that ID stabilizes hypoxia-inducible factor-1 (HIF-1), promoting aberrant adipogenic differentiation of fibro-adipogenic progenitors (FAPs), disrupting the homeostatic balance between satellite cells (SCs) and FAPs, exacerbating skeletal muscle fat infiltration, and impairing muscle repair capacity. Notably, treatment with the HIF-1 inhibitor PX478 reversed these pathological alterations and improved muscle function. Collectively, our findings identify the ID-HIF-1-FAPs axis as a key driver of intramuscular fat infiltration, offering a novel therapeutic target for the clinical management of fat-infiltrating sarcopenia.

cell biology↗

bioRxiv2026

Joint Segmental Duplication Co-option Drives Human-specific Transcriptional Readthrough and Expression Fine-tuning of NPEPPS-TBC1D3

Segmental duplication (SD) is a major driver of functional changes in evolution and disease. Many genes embedded within SDs, such as NPEPPS and TBC1D3, display substantial copy number variation (CNV) across individuals. Yet, the precise identification of the functional copies and their transcriptional outputs remains largely unstudied. Focusing on NPEPPS and TBC1D3, we illustrate human-specific expression fine-tuning mechanisms associated with readthrough transcripts. We identified a human-specific NPEPPS-TBC1D3 digenic genomic structure that originated from a joint SD pair and became fixed across populations. Experiments demonstrate that this structure generates NPEPPS-TBC1D3 readthrough transcripts, which are the predominant isoforms of TBC1D3 expression in various cell types, fine-tuning its protein level. Furthermore, a human-specific hypomethylation signal within an upstream CpG island of NPEPPS precisely pinpoints the expressed TBC1D3 paralog. Moreover, we reveal transcriptional readthrough events are [~]3-fold enriched for joint-SD-associated transcriptional readthrough (JSDTR) and identify 109 JSDTR gene pairs, including neurodevelopmentally important pairs and clinically interesting SERF1A/B-SMN1/2. Taken together, our findings comprehensively describe an example of how a joint SD event shaped evolution and suggest that JSDTR is a broad mechanism for the emergence of new functions.

genetics↗

bioRxiv2026

Novel circadian clock activators display anti-obesity efficacy via suppression of adipocyte development and hypertrophy

The circadian clock exerts temporal coordination of metabolic processes to maintain homeostasis, and its disruption predisposes to the development of obesity and insulin resistance. Despite the established genetic basis of clock modulation in adipocyte development, whether it can be targeted for anti-obesity interventions remains to be explored. Here we report the novel actions of clock-activating molecules, chlorhexidine and a new derivative CM002, on inhibiting adipocyte development and hypertrophy that results in anti-obesity efficacy in vivo. Both chlorhexidine and CM002 were sufficient to activate clock in adipocytes with induction of core clock components and shortening of clock period length. Consistent with their clock-activating properties, these compounds suppressed the distinct lineage commitment and terminal differentiation stages of adipogenic precursor cells mediated via activation of the Wnt signaling pathway. Furthermore, CM002 attenuated lipid storage and adipocyte hypertrophy by suppressing the lipogenic and adipogenic program in a clock-dependent manner. Most importantly, CM002 administration in mice with diet-induced obesity was sufficient to induce clock activation in adipose depots, leading to robust suppression of adipogenic factors and lipogenic enzymes with marked effect on reducing fat mass and promoting insulin sensitivity. Collectively, our findings uncovered the anti-adipogenic properties of novel small molecule clock activators with demonstrated anti-obesity efficacy. These compounds provide novel chemical probes to dissect clock function in metabolic regulations with translational potential toward development of first-in-class clock-targeting drugs for anti-obesity therapy. HighlightsO_LIDiscovery of the anti-adipogenic properties of the clock activator chlorhexidine C_LIO_LIIdentification of a new clock-activating molecule CM002 C_LIO_LICM002 inhibits the lineage commitment and terminal differentiation of adipocytes C_LIO_LIClock activation by CM002 suppresses lipid storage in mature adipocytes C_LIO_LICM002 displays anti-obesity efficacy in diet-induced obesity model C_LI

physiology↗

bioRxiv2025

NanoporeDB: A Structural Resource Of Multimeric Protein Nanopores In Single-Molecule Sensing

Protein nanopores are essential molecular gateways in biology and have inspired transformative technologies in biosensing and single-molecule sequencing. While this technology has transformed genomics and biosensing, the discovery of novel nanopore scaffolds remains limited due to the scarcity of experimentally resolved pore structures. Here, we present NanoporeDB, an open-access structural resource comprising over 6,600 high-confidence multimeric models across four representative pore types. Candidate proteins were systematically mined from large-scale datasets, including the AlphaFold Protein Structure Database, UniRef90, and MGnify90, and assembled using AlphaFold-Multimer and AlphaFold3. We performed membrane embedding, pore axis annotation, and constriction profiling to enable functional interpretation. NanoporeDB features an interactive web interface with 3D visualization and quantitative metrics such as insertion depth, tilt angle, and pore geometry. This resource provides a structural foundation for advancing nanopore-based molecular sensing, precision diagnostics, and synthetic biology.

bioinformatics↗

bioRxiv2025

Engineering magnetically guided bacteriophages for precision antimicrobial therapy and targeted biofilm eradication

Viruses, including bacteriophages, rely on passive diffusion to reach their hosts, limiting the efficacy of virus-based therapies and leading to off-target accumulation with systemic effects. Here, we present a strategy to confer controllable motility to bacteriophages by incorporating iron nanoparticles (FeNPs) into their head structures while preserving infectivity. Cryo-electron microscopy (Cryo-EM) and transmission electron microscopy-energy dispersive spectroscopy (TEM-EDS) confirmed the FeNP presence in the phages head. FeNP-tagged phages can be magnetically enriched and isolated from bacterial prey cultures, eliminating the need for ultracentrifugation. Under magnetic guidance, these engineered phages exhibit rapid and directed movement through complex microenvironments, including mazes and polymer barriers, enabling precise bacterial targeting and biofilm eradication in a microfluidic system. In an in vivo wound infection model, magnetically guided phages successfully navigated from the peritoneum to the biofilms on the wound, thus selectively eliminating biofilms while minimizing systemic exposure to other organs. Hence, our approach confers viral mobility, thus enhancing the precision and efficacy of bacteriophage-based biotechnological and therapeutic applications.

microbiology↗

bioRxiv2025

Disrupted Regional Dynamics of Structure-Function Connectivity Coupling in Euthymic Bipolar Disorder

BackgroundBipolar disorder (BD) is characterized by persistent disturbances in emotional regulation and cognitive function, even during euthymia, yet its neural mechanisms remain unclear. Given evidence of structural and dynamic functional connectivity (dFC) abnormalities in BD, investigating dynamic structure-function connectivity coupling (SC-FC coupling) may provide insights into the pathophysiology of the disorder. MethodsDiffusion tensor imaging and resting-state fMRI data were collected from 61 euthymic BD-I patients and 54 healthy controls (HC). Structural connectivity was derived using probabilistic tractography, and dFC was estimated with a sliding-window approach. SC-FC coupling was quantified as the extent to which structural features predicted dFC using multivariate linear regression. Abnormal SC-FC coupling in BD was assessed at both the network and regional levels, relative to HC. Over time, SC-FC coupling was categorized into high- and low-coupling states, and dynamic state analyses of dwell time, occurrence rate, and transition probabilities were performed in the affected brain regions. ResultsNetwork-level analyses indicated that BD exhibits lower SC-FC coupling in subcortical regions compared with HC. Regional analyses revealed significantly reduced dynamic SC-FC coupling in two thalamic subregions (medial posterior and rostral temporal) and in the right primary somatosensory cortex in BD compared to HC. Dynamic analyses further demonstrated thalamic instability: BD showed shorter dwell times in high-coupling states, increased occurrence of low-coupling states, and more frequent high-to-low coupling transitions than HC. These abnormalities suggest that BD is characterized by disrupted structure-function integration and unstable thalamocortical dynamics. ConclusionOur findings reveal regional abnormalities in SC-FC coupling dynamics in BD, indicating persistent dysfunction of structure-function integration during euthymia. Dynamic coupling measures may provide preliminary insights into potential biomarkers for disease monitoring.

neuroscience↗

bioRxiv2025

Clock Modulation by Naringenin via RORα Suppresses Lipogenesis and Promotes Adipose Tissue Browning

The circadian clock orchestrates adipocyte development and lipid remodeling, with its disruption leading to the development of obesity and insulin resistance. Here we demonstrate that the flavonoid compound naringenin displays clock modulatory activity via ROR that suppresses adipocyte lipid storage while promoting browning. In adipogenic progenitors, naringenin activates ROR with induction of clock gene expression to promote circadian clock oscillation with protective effect against cytokine-induced dampening. The clock-enhancing properties of naringenin suppressed lipogenesis in mature adipocytes together with induction of browning characteristics. The inhibitory effect of naringenin on lipogenesis was dependent on clock modulation as it was abolished in ROR-deficient adipocytes. We further show that naringenin administration in vivo up-regulated ROR expression with clock gene induction together with browning of subcutaneous beige fat depot, resulting reduced fat mass and body weight. Naringenin treatment in vivo also lowered plasma glucose and free fatty acid levels, with markedly enhanced insulin signaling in adipose depots and skeletal muscle. Collectively, our findings uncover a new clock-activating mechanism of action in mediating the metabolic benefits of naringenin, suggesting its potential as a natural supplement for anti-obesity and metabolic disease interventions.

cell biology↗

bioRxiv2025

Integrated phenotypic screening and chemical proteomics identifies ETF1 ligands that modulate viral translation and replication

Emerging and re-emerging viruses pose a significant threat to global health. Although direct-acting antivirals have shown success, their efficacy is limited by the rapid emergence of drug-resistant viral variants. Hence, there is an urgent need for additional broad spectrum antiviral therapeutic strategies. Here, we identify by phenotypic screening a set of stereochemically defined photoreactive small molecules (photo-stereoprobes) that stereoselectively suppress SARS-CoV-2 replication in human lung epithelial cells. Structure-activity relationship-guided chemical proteomics identified the eukaryotic translation termination factor 1 (ETF1) as a target of the photo-stereoprobes, and this interaction was recapitulated with recombinant purified ETF1. We found that the photo-stereoprobes modulate programmed ribosomal frameshifting mechanisms essential for SARS-CoV-2 infection without causing ETF1 degradation, thus distinguishing the photo-stereoprobes from other known ETF1-directed small molecules. We finally show that the photo-stereoprobes also inhibit the replication of additional viruses with non-canonical ribosomal frameshifting mechanisms. Our findings thus identify a mechanistically distinct class of ETF1 ligands that implicate host translation termination processes as a potential target for antiviral development. SIGNIFICANCE STATEMENTThe identification of broad-spectrum antivirals that target host proteins is a desirable strategy to combat emerging viral infections given the rapid escape potential of viruses and the need to develop new countermeasures for clinically significant pathogens. Here, we integrate phenotypic screening and chemical proteomics to identify photo-stereoprobe small molecules that inhibit the replication of multiple viruses. We show that these compounds bind the protein eukaryotic peptide chain release factor subunit 1 (ETF1) and modulate programmed ribosomal frameshifting. Unlike previously described ligands for ETF1, which lead to proteasomal destruction of the protein, we did not find that the photo-stereoprobes altered ETF1 content in cells. Our findings thus point to an opportunity to pharmacologically modulate a host protein implicated in programmed ribosomal frameshifting as a strategy to combat infection of viruses from different families.

microbiology↗

bioRxiv2025

A complete and near-perfect rhesus macaque reference genome: lessons from subtelomeric repeats and sequencing bias

A truly complete, telomere-to-telomere (T2T), and error-free reference genome remains a foundational resource--and long-standing goal--for unbiased comparative and functional genomics. While recent T2T assemblies of humans and other primates have made substantial progress, most still contain thousands of base-level errors, particularly within highly repetitive regions. Here, we present T2T-MMU8v2.0, a near-perfect T2T assembly of the rhesus macaque (Macaca mulatta), representing the highest base-level accuracy reported in a primate genome to date. By employing an optimized ONT-only assembly strategy, we identify subtelomeric satellite-rich regions as the principal bottleneck to improving assembly quality, owing to technological biases in long-read platforms and limitations in current hybrid assembly frameworks. We discover 268 previously unannotated repeat families and resolve [~]8 Mbp of SATR satellite arrays, with over 99-fold enrichment in historically misassembled subtelomeric regions. These satellites form four distinct genomic architectures, each with unique SATR satellite composition, segmental duplication organization, and epigenetic signatures, distinct from the subtelomeric architectures observed in hominid genomes. Notably, in contrast to the largely gene-poor subtelomeric regions in African hominids, the SATR architectures in macaques harbor 58 actively transcribed genes, supported by open chromatin and expression data, suggesting gene innovation within these repetitive regions. Functionally, T2T-MMU8v2.0 improves read mappability and accuracy across sequencing platforms, and results in a 19% improvement of transcription start site enrichment scores and 5,821 additional chromatin accessibility peaks on average, thereby enhancing variant detection, regulatory annotation, and transcriptomic resolution in population genetics or single-nucleus studies. Together, this work establishes a new benchmark for genomics, offers a roadmap for resolving complex repetitive regions, and reveals previously unrecognized features of subtelomeric genome structure and evolution.

genomics↗

bioRxiv2025

Interpretable spatial multi-omics data integration and dimension reduction with SpaMV

Spatial multi-omics technologies have revolutionized our understanding of biological systems by providing spatially resolved molecular profiles from multiple perspectives. Existing spatial multi-omics integration methods often assume that data from different modalities share a common underlying distribution, aiming to project them into a single unified latent space. This assumption, however, can obscure the unique insights offered by each modality, thereby limiting the full potential of multi-omics analyses. To address this limitation, we present the Spatial Multi-View (SpaMV) representation learning algorithm, which captures both the shared information across modalities and the distinct, modality-specific information, enabling a more comprehensive and interpretable representation of spatial multi-omics data. Through extensive evaluation on both simulated and real-world datasets, SpaMV demonstrates superior spatial domain clustering performance and provides users with more interpretable dimension reduction for downstream analysis. Moreover, SpaMV effectively annotates cell types within clusters of a mouse thymus dataset, highlighting its effectiveness in interpretable dimensionality reduction.

bioinformatics↗

bioRxiv2025

Measure Sodium Transport in Cells with NMR

Sodium ions (Na+) are fundamental to numerous physiological functions, such as maintaining electrolyte balance, enabling nerve impulse transmission, and facilitating muscle contraction. Dysregulation of Na+ transport across cell membranes is implicated in a range of health issues, including metabolic syndromes, neurological conditions, and cardiovascular diseases. However, current methods for assessing cellular Na+ activity often face limitations; they can be invasive or fail to capture dynamic changes. In this study, we introduce a non-invasive 23Na nuclear magnetic resonance (NMR) methodology designed to directly quantify the transport rate of sodium ions in living cells. Our technique integrates relaxation exchange spectroscopy (REXSY) with a multi-site exchange model, enabling the investigation of Na+ transport dynamics on a timescale of sub-seconds. A key advantage is its ability to differentiate between intracellular and extracellular Na+ pools based on the endogenous NMR relaxation difference, thereby avoiding the need for potentially disruptive exogenous reagents. Experiments conducted on human cell lines successfully demonstrated the techniques capacity to distinguish between various physiological states, such as when ion channels are pharmacologically blocked or activated. The resulting measurements of Na+ transport rates and intracellular Na+ fractions show a clear correlation with cellular metabolic activity, offering valuable quantitative markers for monitoring transmembrane ion dynamics in vitro.

cell biology↗

bioRxiv2025

Insight into the structure and interactions of the M. tuberculosis Mce-associated membrane proteins Mam1A-1D

Tuberculosis (TB) is a major infectious disease caused by Mycobacterium tuberculosis (Mtb), leading to more than a million human deaths every year. Mammalian cell entry complexes (Mce1-4) play an essential role in the survival of Mtb during the latent stage by mediating the import of lipids, including fatty acids and cholesterol, from the host. The proper functioning of Mce-complexes requires additional proteins such as Mce-associated membrane (Mam) proteins and lipid uptake coordinator (LucA), thus making them potential candidates for the development of anti-TB drugs. Four Mam (Mam1A-1D) proteins are coded from the mce1 operon and two from the mce3 (Mam3A-3B) and mce4 (Mam4A-4B) operons. In addition, five orphaned mam (Omam) proteins have been identified, which are not part of the mce operons but are functionally relevant for the Mce complexes. Analysis of the sequences of Mam/Omam proteins suggests that they share many common secondary and tertiary structural elements despite the low sequence identity between them. Here, we have characterized a recombinantly produced Mam1A variant by small-angle X-ray and neutron scattering. The studies indicate that Mam1A is tetrameric in solution with two disulfide bridges necessary for the stability of Mam1A. Similarly, a disulfide bridge has also been identified in Mam1C. Furthermore, through coexpression and copurification, we demonstrate that Mam1A-1D and LucA interact to form stable Mam1ABCD as well as Mam1ABCD-LucA complexes. The results obtained pave the way for further understanding how the Mam1ABCD and Mam1ABCD-LucA complexes are organized and interact with the Mce complexes, leading to their stabilization.

biochemistry↗

bioRxiv2025

Microbial biofilm matrix restricts phagocytic cells motility in a 3D-microfluidics phagocyte migration model

Understanding how immune cells navigate complex microbial environments requires models that integrate biophysical and biological realism. However, the microscale mechanisms underlying phagocyte migration on pathogenic biofilms remain poorly understood, and there remains a lack of experimental models for study of 3D-interactions between host cells and biofilms. Here, we present a multiscale microfluidic secondary-infection-on-a-chip incorporating human-cell-based model or an ex vivo perfused porcine skin system, to study macrophage migration across bacterial biofilms under controlled flow and spatial confinement. Using Pseudomonas aeruginosa as model pathogen, we demonstrated that biofilm matrix components, specifically the exopolysaccharide Psl, physically impede macrophage motility and directional persistence. Exopolysaccharide-deficient mutants allowed near-normal macrophage migration. Persistent random walk (PRW) simulation modeling recapitulated these motility dynamics, revealing altered migration coefficients within biofilm matrices. Consistent with cell-based model, biofilms impede macrophages on the skin tissue. Hence, our results establish an experimental and modelling framework for studying physical constraints in host-pathogen interactions, providing new insights into mechanical and spatial barriers that shape immune responses to biofilm infections.

microbiology↗

bioRxiv2025

ProteoAutoNet: high-throughput co-eluted protein analysis with robotics and a multi-database search strategy

Co-fractionation mass spectrometry (CF-MS) enables large-scale profiling of endogenous protein-protein interactions. Protein complexes identified by CF-MS using different databases are typically integrated. However, this integration uses varying cutoffs, leading to inconsistencies in protein complex identification. Here, we present ProteoAutoNet, a robotic experimental platform integrating multi-database search strategy into machine learning models, for high-throughput CF-MS analysis. This workflow increases the throughput of sample processing from protein complex to peptide by about two times. We then applied this workflow to map protein interaction networks in thyroid cancer cell lines, identifying significantly upregulated proteasome and prefoldin complexes in lung metastatic follicular thyroid carcinoma cell line FTC238 compared to normal thyroid cell line Nthy-ori 3-1. Notably, we identified a novel protein interaction network comprising PFAS, TGM2, and HK1 that was significantly upregulated in the papillary thyroid carcinoma cell line TPC-1. ProteoAutoNet provides an improved approach for investigating protein-protein interactions and uncovering novel networks, driving advancements in high-throughput proteomics research.

biochemistry↗