Biology subjects

Thomas, T.

Publications and source records attributed to Thomas, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Persistent Malignant Stem Cells Drive Relapse After Transplantation in the Myelodysplastic Neoplasms

The myelodysplastic neoplasms (MDS) are initiated in hematopoietic stem cells (HSCs). Allogeneic transplantation is the only curative treatment, but relapse remains common. To detect rare MDS HSCs, we developed an ultra-low-input DNA sequencing assay and applied it to a multicenter post-transplant cohort. HSC mutation detection preceded relapse by a mean of 98 days and strongly predicted relapse (95.7% vs. 30.3%; hazard ratio, 8.8; P=1.5e-7). Mutations detected only in unfractionated marrow did not predict relapse. We developed methods to measure donor-host HSC chimerism, improving relapse prediction sensitivity. Single-cell protein, DNA, and RNA analyses with mitochondrial lineage tracing confirmed MDS cell enrichment within immunophenotypically- and transcriptionally-defined HSCs, identifying shared ribosomal gene downregulation and candidate mechanisms of venetoclax sensitivity. Venetoclax/azacytidine depleted detectable MDS HSCs in longitudinally evaluated patients. These findings establish that HSC mutation detection predicts post-transplant relapse, provide a rationale for preemptive intervention, and define shared biological features of transplant-resistant MDS HSCs.

cancer biology↗

bioRxiv2026

Ocean depth modifies host-microbiome ecology and evolution

A major unsolved question in ecology and evolution is how similar free-living and symbiotic microbial communities are. In marine systems, depth homogenises free-living communities due to stronger dispersal and weaker environmental filtering compared to surface waters. We show that symbiotic communities of marine sponges follow a different pattern, with a subset of sponge species mirroring the increased similarity with depth seen in their free-living counterparts, while others remain highly host-specific both in shallow and deep waters. Moreover, in deep waters, more phylogenetically similar hosts harbor more similar microbiomes, yet host-symbiont cophylogeny nearly vanishes. This reveals two contrasting eco-evolutionary assembly rules: in more constant environments like the deep sea, community assembly is driven by host and environmental filtering with minimal signature of coevolution, whereas in variable environments, like shallow waters, host-symbiont coevolution is strong and key to maintain host-specific microbiomes.

microbiology↗

bioRxiv2026

Mechanistical and structural basis of Kv channel inhibition by 4 aminopyridine

Inhibition of Kv channels by 4-aminopyridine (4AP) improves motor function in multiple sclerosis by enhancing neuronal excitability. The mechanism of inhibition and the structural basis of 4AP binding to Kv channels remain unclear. Here, we determined the structure of the Shaker V369I-I372L-S376T (ILT) mutant bound to 4AP at 3.3 [A], demonstrating that 4AP binds to the closed state of the channel. This structure is inconsistent with an open channel block mechanism. Electrophysiology experiments show that 4AP binds even when intracellular pore access is constitutively blocked, suggesting that 4AP enters the pore through membrane-facing fenestrations. MD simulations and mutational analysis agree with the proposed fenestration pathway and suggest that 4AP binds in its neutral form. These results support a mechanism where 4AP binds to a partially activated closed state that prevents complete activation of Kv channels, explaining its pharmacological activity.

biophysics↗

bioRxiv2026

Proteomic and Kinetic Analyses Reveal Discordant Apolipoprotein Turnover and Support a Revised Model of Human Lipoprotein(a) Metabolism

Objective: Lipoprotein(a) [Lp(a)] is a causal risk factor for atherosclerotic cardiovascular disease composed of apolipoprotein(a) [APO(a)] covalently linked to apolipoprotein B100 (APOB). Although plasma Lp(a) concentrations are largely genetically determined, the mechanisms governing Lp(a) metabolism after particle assembly remain poorly understood. We sought to define the Lp(a) proteome and determine the metabolic behavior of APO(a) and APOB within circulating Lp(a) particles using integrated proteomic, kinetic, and imaging approaches. Approach and Results: Sixteen healthy adults underwent stable isotope tracer studies with 2H3-L-leucine and 2H5-glycerol. Lp(a) particles were isolated by APO(a)-specific immunoprecipitation for high-resolution liquid chromatography-mass spectrometry and kinetic analyses, and extracellular vesicles (EVs) were characterized by imaging flow cytometry and super-resolution microscopy. Proteomic analysis identified 92 proteins associated with immuno-isolated Lp(a), enriched in pathways related to immunity, coagulation, and atherogenesis. Lp(a)-APO(a) exhibited a mean fractional clearance rate of 0.04 pools/day, whereas Lp(a)-APOB cleared approximately sevenfold faster (0.25 pools/day), independent of plasma Lp(a) concentration or APO(a) isoform size. Both APO(a) and APOB were detected on circulating EVs, suggesting that EVs may contribute to post-secretory Lp(a) particle remodeling. Conclusion: These integrated human studies demonstrate marked discordance between APO(a) and APOB turnover within circulating Lp(a) particles, challenging the prevailing assumption that both apolipoproteins behave as a single metabolic unit after Lp(a) assembly and supporting a revised model of human Lp(a) metabolism.

physiology↗

bioRxiv2026

Cis-regulatory variation and transcription factor binding contribute to allelic genotype-by-environment interactions for gene expression in maize

Genotype-by-environment interactions (GxE), or differences in how genotypes perform across varying environments, are a pervasive source of phenotypic variation and underlie differences in local adaptation. Though GxE is well characterized across kingdoms of life, less is known about what causes GxE interactions, particularly at the molecular level. In this study, we use allele-specific gene expression estimates in a maize (Zea mays L.) B73 x Mo17 hybrid to isolate cis-regulatory effects on gene expression for each of the two parental alleles. The hybrid was grown in two environments, and expression differences between the parental alleles were used to characterize allele-by-environment (AxE) interactions and study the influence of gene-proximal sequence variation on transcript abundance AxE. We tested the hypothesis that gene-proximal sequence variation can cause GxE in gene expression by modifying transcription factor binding. Our results show that sequence variation in gene promoter regions has a small but consistent enrichment in genes that show transcriptional AxE. Further, we demonstrate that differential transcription factor binding potential caused by sequence variation is also enriched in AxE genes. Predictive models trained on sequence and transcription factor binding variation show that while these features contain some information about whether a gene will show transcriptional AxE, they alone are not sufficient to reliably distinguish AxE genes. These findings support the hypothesis that gene expression GxE can be caused by sequence variation that modifies transcription factor binding, while also reinforcing the complex and context-specific nature of GxE interactions.

genomics↗

bioRxiv2026

Comparative genomics of Dolichospermum circinale strains with differential paralytic shellfish toxin profiles

The cyanobacterium Dolichospermum circinale is a known producer of the neurotoxin saxitoxin and its analogues, collectively known as the paralytic shellfish toxins (PSTs). PSTs vary in potency, and the reported toxin profiles of D. circinale blooms vary in the quantities of individual PSTs, with the regulation of these profiles being poorly understood. In this study, we present the genomes of four D. circinale strains (ACBU01, ACMB03, ACMB13 and FSS-124) with unique PST profiles and perform genome-wide comparisons and specific analysis of the PST-producing biosynthetic gene cluster (sxt) to understand the variability in PST quotas. A reassessment of the previously published D. circinale AWQC131C genome was also performed to collate genomic variation between all strains. Analysis at the nucleotide and amino acid sequence level revealed that toxic strains maintain high genome-wide similarities, corroborated by the analysis of the pan- and variable genomes of each strain. Specifically, the sxt gene sequences were 99-100% identical across all strains. Novel tailoring (sxtSUL, sxtDIOX) and transport (sxtM4) genes were identified within the sxt cluster that were not reported previously in D. circinale. Taken together, these results indicate that the genetic machinery involved in PST production is conserved in this species, suggesting that the regulation of PST biosynthesis in D. circinale does not occur at the genomic level.

microbiology↗

bioRxiv2026

Coral Probiotics Buffer Adjacent Ecosystem-Level Responses to Extreme Marine Heatwave

Probiotics can enhance coral thermal tolerance, yet their ecosystem-level effects remain unknown. Here, we present the first long-term in-situ test of whether coral-targeted probiotics influence adjacent cryptobenthic reef communities during a record marine heatwave. Probiotics were applied to Pocillopora favosa and Acropora spp. coral colonies for 18 months, spanning the fourth global bleaching event. Cryptobenthic communities were assessed using biomimetic monitoring structures integrating biodiversity surveys, molecular profiling, microbial network analyses, and metabolic assays. Before the heatwave, probiotic and control patches were comparable across structural, microbial, and functional metrics. Following thermal stress, control patches exhibited pronounced losses of cryptobenthic invertebrate abundance and taxonomic breadth, microbial network fragmentation, and net carbonate dissolution. In contrast, probiotic-treated patches retained higher biodiversity, cohesive microbial interaction architectures, and positive calcification. These findings demonstrate that coral-targeted probiotics can scale from host-level intervention to buffer adjacent ecosystem-level responses to extreme marine heatwaves under accelerating climate change. TeaserA coral-targeted probiotic strategy enhances multi-trophic resilience under heat stress.

microbiology↗

bioRxiv2026

An eco-evolutionary theory of host-associated microbiomes

Host-associated microbiomes often display host specificity and heritability, yet the evolutionary processes under which such structured communities first emerge are still unclear. In particular, the conditions by which intergenerational (i.e. vertical) transmission of microbes can evolve and generate host-specific microbiomes are still unresolved. Here, we present an eco-evolutionary theory of microbiome assembly under minimal assumptions of microbial dynamics (i.e. neutrally driven by environmental fluctuations) and host control. We consider the adaptive evolution of microbial and host traits, including microbiome size and vertical transmission. We show that environmental fluctuations can generate enough among-host microbial variation to enable host-level selection favouring beneficial microbiome configurations. Vertical transmission can then evolve and, even when weak, allow microbiome specificity to be inherited and amplified across generations despite continuous influx from the external environment. Selection is most effective at intermediate levels of environmental fluctuation and host lifespan, revealing fundamental trade-offs between stochastic assembly, inheritance, and dispersal of microbes. The resulting microbiomes are dense, host-specific, and heritable, yet retain high intraspecific variability and lack strict phylosymbiosis. Simulated patterns of microbial dominance, diversity, and host-microbiome dissimilarity closely match those observed in nature, as evidenced using marine sponge microbiomes. Our results provide a mechanistic theory for the early evolution of host-associated microbiomes, showing that beneficial and species-specific communities can arise through selection and inheritance prior to the evolution of dedicated host-control mechanisms.

evolutionary biology↗

bioRxiv2025

The Closed State of the Shaker Potassium Channel and the Mechanism of Voltage Activation

To understand the process of voltage activation in Kv channels, we determined the cryo-EM structure of the Shaker channel ILT mutant (V369I, I372L, S376T), known to partially decouple the gating charge movement of the voltage sensing domain (VSD) and the opening of the pore domain (PD). The structure captures a previously unobserved intermediate state in which the VSD is only partially activated while the PD remains closed. Combined with computational modeling based on AlphaFold2 predictions and molecular dynamics simulations, it is shown that VSD activation does not mechanically pull the gate open, but instead induces a dynamic shift in the population equilibrium of the VSD-PD linker, providing the basis for electromechanical coupling between the two domains.

biophysics↗

bioRxiv2025

Towards key principles of host-associated microbiome assembly

Symbiotic relationships between microbes and host organisms frequently involve the assembly of complex microbial communities (microbiomes) within hosts. Patterns at the community level influence life-history traits, the evolutionary trajectories of both microbes and their hosts, and are often critical for maintaining host health. These community-level patterns are dynamically driven by eco-evolutionary mechanisms acting at the individual level, such as microbial dispersal, host selection, and microbe-resource interactions. Critically, we still lack a clear picture of the ways in which these mechanisms interact to shape microbiome assembly. Here, we present a model of assembly to describe how distinct community structures can be characterised by underlying mechanisms. To illustrate the approach, we analyse microbiome data from marine sponges and simulate different structures of host-microbe associations, thereby bridging mechanistic models and empirical patterns. We further apply the model to human microbiome data to explore its relevance across biological systems, proposing that the combined effect of a small set of general mechanisms may govern diverse patterns of microbial diversity and abundance. Our findings advance ecological theory by linking individual-level processes to community-scale patterns, illuminating the key drivers underlying microbiome assembly.

microbiology↗

bioRxiv2025

Molecular Dynamics-Guided Design and Chemoproteomic Profiling of Covalent Kinase Activity Probes

Covalent small molecule activity probes can be powerful tools to interrogate protein function in native cellular environments. The design of family-wide activity probes requires an understanding of the molecular sources of general targeting potential and specificity to enable broad targeting of protein family members. Here, we developed and applied a multifaceted docking and molecular dynamics (MD) simulation pipeline to design and test cell-permeable covalent kinase activity probes from a set of hinge-binding pharmacophores. This computationally-guided approach yielded a new cell-active probe, K60P, which targets around 114 kinases across distinct kinase classes in live cells. Chemoproteomic profiling of this probe and a clinical candidate sharing the same indazole core, KW-2449, identified kinase and non-kinase target profiles that differ from recombinant protein assay profiles, underscoring the utility of native kinase profiling in situ. Biochemical studies with a model target kinase, ABL1, confirmed covalent labeling of the active site lysine across several kinase probes with distinct kinetics, as well as covalent labeling of key tyrosines in trans between ABL1 monomers. Finally, focused proteomics, kinetic modeling, and molecular dynamics simulations revealed that K60P, as well as the comparator probe XO44, preferentially engage with target kinases in their active, DFG-in conformations, which is driven by increasing population of reaction-ready small molecule conformation. These results together establish a computational and kinetic modeling framework for designing covalent activity probes and highlight the balance of target selectivity and kinetic efficiency as a key factor in determining their proteome-wide reactivity. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC="FIGDIR/small/683178v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1ea3e5forg.highwire.dtl.DTLVardef@1a4e999org.highwire.dtl.DTLVardef@1e468c3org.highwire.dtl.DTLVardef@99e04e_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

An end-to-end framework for Cell DIVE multiplexed imaging and spatial immune microenvironment analysis

This paper describes an end-to-end workflow for highly multiplexed fluorescence imaging with the Cell DIVE platform, allowing simultaneous detection of 40+ markers at single-cell resolution. Combining whole-slide multiplexed imaging with a dedicated analysis pipeline provides a powerful approach to investigate immune cell interactions with stromal and vascular networks within human tissue microenvironments. With a focus on spatial investigation of human immune niches, here we provide a complete framework for tissue preparation, autofluorescence reduction, multiplex panel design and whole-slide image analysis. For complete details on the use and execution of this protocol, please refer to Korsunsky et al. (Med, 2022) [1]. HighlightsO_LIComplete workflow for Cell DIVE multiplex imaging and quantitative image analysis. C_LIO_LIHuman FFPE tissue preparation, LED-based reduction of tissue autofluorescence. C_LIO_LIAntibody panel design for 3-40 marker multiplexing, in-house antibody conjugation. C_LIO_LIQuPath and DeepCell based analysis workflows for whole-slide multi-marker images. C_LIO_LIAdaptable code templates to accelerate cell segmentation and spatial niche analysis. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/656440v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1ef708dorg.highwire.dtl.DTLVardef@c6422dorg.highwire.dtl.DTLVardef@22d961org.highwire.dtl.DTLVardef@1ed7479_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Promiscuous endosymbionts in deep-sea corals and crinoids are shaped by nitrogen cycling

Crinoids are commonly associated with corals, but whether they physiologically interact is unclear. Like corals, crinoids host symbiotic microorganisms but little is known about the crinoid microbiome. Here, we reveal the microbiomes of the deep-sea corals Desmophyllum pertusum and Solenosmilia variabilis and, notably, their associated feather star crinoid, Koehlermetra (of the family Thalassometridae) in the Campos Basin, Brazil. We showed that the same endosymbiotic members of the families Endozoicomonadaceae and Nitrosopumilaceae interchangeably inhabit the internal and external structures of the corals and crinoid, indicating promiscuity in symbioses. The metagenome-assembled genome of the novel and dominant Endozoicomonas promiscua sp. nov. suggest that these symbionts may drive dissimilatory nitrate reduction to ammonia, which could be a source of energy for ammonia-oxidizing archaea (AOA) of the family Nitrosopumilaceae. Thus, nitrogen cycling may determine the microorganisms that are hosted by deep-sea corals, which may be provided by their associated crinoids. These findings provide important insight about the complex ecological interactions that could lead to promiscuous symbiosis. TeaserDeep-sea corals and crinoids share symbiotic microbes that cycle nitrogen, potentially supporting each other in the nutrient-poor deep sea.

microbiology↗

bioRxiv2025

CobVar - a comprehensive resource of Vitamin B 12-associated genomic variants

The importance of vitamin B12 (cobalamin) in numerous biological processes, including DNA synthesis and cellular energy production, underscores the need for therapeutic and public health strategies to address B12 insufficiency/deficiency in the population. Genetic variations in pathways influencing cobalamin absorption, transport, and metabolism can affect various direct and indirect measures of vitamin B12 status. To facilitate a structured approach to studying these genetic factors, we aimed to systematically curate and create a user-friendly web database that offers comprehensive data on genetic variants influencing B12 biomarkers. A Pubmed search was performed for 5 B12 traits (total serum/plasma B12, holotranscobalamin (active B12), total transcobalamin, holo haptocorrin, and methylmalonic acid) resulting in 493 research publications, of which 47 relevant publications were reviewed further. The database backend was built using MongoDB and the web interface was coded in PHP, JavaScript, HTML and CSS on an Apache HTTP server. We have manually curated and compiled the Cobalamin Associated Genetic Variant (CobVar) database, comprising a total of 324 genetic variant associations for 5 different vitamin B12 traits involving 222 unique genetic variants and 84 genes identified across several genome-wide association studies (GWAS) and candidate gene studies. About one-third of the total genetic variant associations have been reported in >1 independent studies and 15 variants in >1 ethnic group. FUT2 gene showed the maximum number of associations for total serum/plasma B12 (N=39), followed by MTHFR (N=24) and TCN2 (N=23). The database is accessible online at https://datatools.sjri.res.in/VBG/. CobVar is a vital resource for researchers and nutritionists, offering quick access to the latest developments in B12-related genetic variant research and serves as a valuable tool for advancing personalized treatment. Database URLhttps://datatools.sjri.res.in/VBG/.

genomics↗

bioRxiv2024

Bacterial inoculation manipulates the coral epigenome

Environmental shifts can cause epigenetic modifications in corals, which are associated with changes in gene expression and physiology, though it remains unclear if associated bacteria can also induce such changes. Here, we inoculated nubbins of the coral Pocillopora verrucosa with an opportunistic pathogen, Vibrio coralliilyticus, and/or a coral probiotic, Cobetia sp., and subjected the nubbins to heat stress. We show that pathogen exposure led to distinct DNA methylation changes compared to the control, probiotic, and co-inoculation groups. We also demonstrate that DNA methylation correlates with coral gene expression and highlight genes altered by pathogen inoculation that showed similar responses in their expression and methylation. Notably, the coral probiotic was able to mitigate specific epigenetic changes, which correlated with increased stress resilience and higher coral survival rates. Thus, bacterial-induced changes to the coral epigenome may instigate long-term changes in host resilience.

molecular biology↗

bioRxiv2024

A resource for extracellular vesicles from activated CD4 T cells that relay pro-inflammatory signals

CD4 T helper cells (TH cells) play a vital role in coordinating and amplifying the immune response to specific pathogens. They constitutively produce different kinds of extracellular vesicles (EVs), which mediate cell-to cell communication and play diverse roles in immune regulation and inflammatory processes. Here we provide a resource documenting the composition of activated TH cell EVs and demonstrating their ability to instigate pro-inflammatory response in antigen-presenting cells (APCs). EVs were characterized by lipidomics, proteomics, and NanoFCM. The activated TH cells derived EVs (act-EVs) were found to be enriched in TH cell-specific proteins, transmembrane and cytosolic EV marker proteins, and HLA proteins relative to resting CD4 T cells EVs (rest-EVs). The pro-inflammatory effect of act-EVs vs rest-EVs on donor matched APCs were characterized by chemokine and cytokine profiling and flow cytometry analysis. There was no discernible contrast in endotoxin levels between act-EVs and rest-EVs. Functional distinctions were seen to arise from variations in the content and composition of these EVs. Moreover, we validated our findings with an in-vivo investigation in mice, demonstrating the recruitment of monocytes, dendritic cells (DCs), neutrophils, and NK cells in the spleen, accompanied by the release of pro-inflammatory cytokines in the serum after administering act-EVs. In summary, this study sheds light on the role of TH cell released EVs in modulating the immune response during pro-inflammatory responses and this resource provides a foundation for development of novel therapeutics on EV based scaffolds.

immunology↗

bioRxiv2024

Functional mapping of epigenetic regulators uncovers coordinated tumor suppression by the HBO1 and MLL1 complexes

Epigenetic dysregulation is widespread in cancer. However, the specific epigenetic regulators and the processes they control to drive cancer phenotypes are poorly understood. Here, we employed a novel, scalable and high-throughput in vivo method to perform iterative functional screens of over 250 epigenetic regulatory genes within autochthonous oncogenic KRAS-driven lung tumors. We identified multiple novel epigenetic tumor suppressor and tumor dependency genes. We show that a specific HBO1 complex and the MLL1 complex are among the most impactful tumor suppressive epigenetic regulators in lung. The histone modifications generated by the HBO1 complex are frequently absent or reduced in human lung adenocarcinomas. The HBO1 and MLL1 complexes regulate chromatin accessibility of shared genomic regions, lineage fidelity and the expression of canonical tumor suppressor genes. The HBO1 and MLL1 complexes are epistatic during lung tumorigenesis, and their functional correlation is conserved in human cancer cell lines. Together, these results demonstrate the value of quantitative methods to generate a phenotypic roadmap of epigenetic regulatory genes in tumorigenesis in vivo.

cancer biology↗

bioRxiv2024

Aging limits stemness and tumorigenesis in the lung by reprogramming iron homeostasis

Aging is associated with a decline in the number and fitness of adult stem cells1-4. Aging-associated loss of stemness is posited to suppress tumorigenesis5,6, but this hypothesis has not been tested in vivo. Here, using physiologically aged autochthonous genetically engineered mouse models and primary cells7,8, we demonstrate aging suppresses lung cancer initiation and progression by degrading stemness of the alveolar cell of origin. This phenotype is underpinned by aging-associated induction of the transcription factor NUPR1 and its downstream target lipocalin-2 in the cell of origin in mice and humans, leading to a functional iron insufficiency in the aged cells. Genetic inactivation of the NUPR1--lipocalin-2 axis or iron supplementation rescue stemness and promote tumorigenic potential of aged alveolar cells. Conversely, targeting the NUPR1-- lipocalin-2 axis is detrimental to young alveolar cells via induction of ferroptosis. We find that aging-associated DNA hypomethylation at specific enhancer sites associates with elevated NUPR1 expression, which is recapitulated in young alveolar cells by inhibition of DNA methylation. We uncover that aging drives a functional iron insufficiency, which leads to loss of stemness and tumorigenesis, but promotes resistance to ferroptosis. These findings have significant implications for the therapeutic modulation of cellular iron homeostasis in regenerative medicine and in cancer prevention. Furthermore, our findings are consistent with a model whereby most human cancers initiate in young individuals, revealing a critical window for such cancer prevention efforts.

cancer biology↗