Biology subjects

Williams, J. L.

Publications and source records attributed to Williams, J. L..

15 recordsLinked to original sources

bioRxiv2026

The BHMT-TET1 axis regulates glycolytic metabolism in oligodendrocytes and increases myelin in the EAE mouse model of multiple sclerosis

The inability of oligodendrocyte progenitor cells (OPCs) to mature into myelin-making oligodendrocytes (OLs) is a major contributor to disease and disability in multiple sclerosis (MS). Oligodendrocyte maturation is a tightly controlled process with a strong reliance on epigenetic regulation involving DNA methylation and hydroxymethylation. We have previously shown that one carbon metabolism is dysregulated in MS, specifically the methyl donor betaine is depleted in the MS brain. Betaine donates methyl groups to betaine homocysteine methyltransferase (BHMT) in the methionine cycle to increase S-adenosylmethionine (SAM) for epigenetic methylation processes. In the present study we tested the effects of activating the BHMT methylation pathway on preventing MS pathology. We describe a novel mechanism mediated by BHMT and the Ten-eleven translocator enzyme (TET1) that converts 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC). We show that this pathway supports oligodendrocyte metabolism to enhance myelin and reduce clinical disability in the experimental autoimmune encephalomyelitis (EAE) mouse model of MS. ChIP-seq studies show that BHMT is enriched at genes involved in OPC metabolism and proximal ligation assays (PLAs) demonstrate that BHMT interacts with TET1 on chromatin. This interaction regulates gene expression programs that support a shift in OPC metabolism to glycolysis during neuroinflammatory processes. These data highlight the critical role of methionine metabolism in supporting myelination and have important implications for the development of new therapeutic strategies for MS and other neurodegenerative diseases.

neuroscience↗

bioRxiv2026

Eco-evolutionary dynamics are shaped by competition in experimental range expansions

Most theory and empirical research on range expansion assumes populations spread into empty landscapes with abundant resources, however expanding populations are likely to compete with residents. In mathematical models, interspecific competition can lead to pushed wave dynamics, where expansions are driven mainly by individuals dispersing from the core, leading to steeper wavefronts and increased genetic diversity at the edge. These predictions are yet to be tested empirically, and the role of interspecific competition in mediating evolution during range expansion is unclear. We used an experimental system with two duckweed species to ask if interspecific competition leads to pushed-like dynamics and to assess how competition alters evolution during range expansion. We found that competition with a resident reduced expansion speed and absolute variance among replicate expansions, suggesting competition makes expansion speed more predictable. Interspecific competition also changed the relative frequencies of genotypes at the leading edge. While competition was associated with some features of pushed waves, genotype diversity did not vary between treatments. Our results demonstrate that demographic and evolutionary patterns associated with pushed waves may not be universal, and that incorporating selective pressures into future research on eco-evolutionary dynamics of range expansion is key to understanding spreading populations in nature.

ecology↗

bioRxiv2026

Earlier flowering explains only a small part of experimental drought's effects on wildflower's population growth

Flowering times are shifting with climate change, but whether these changes will affect population dynamics of long-lived plants remains largely unknown. We combined eight years of demographic censuses and a four-year phenological survey to examine the effects of experimental drought and irrigation on flowering phenology and population growth in a perennial wildflower using integral projection models. Drought advanced flowering and earlier-flowering plants produced more seeds regardless of treatment. However, when decomposing rainfall treatment effects on population growth rates into effects of phenology and direct, non-phenological effects, direct effects on both growth and reproduction were much larger than phenology-driven changes in seed production for either treatment. Our results highlight how phenological shifts may only marginally impact population dynamics in perennial plants and demonstrate that assessing flowering phenologys consequences for persistence under climate change must also account for direct demographic effects of the climate driver itself.

ecology↗

bioRxiv2025

NMR Spectroscopy for the Validation of AlphaFold2 Structures

The introduction of AlphaFold has fundamentally changed our ability to predict the structure of proteins from their primary sequence of amino acids. As machine learning (ML) and artificial intelligence (AI) based protein prediction continues to advance, we examine the potential of hybrid techniques that combine experiment and computation that may yield more accurate structures than AI alone with significantly reduced experimental burden. We have developed heuristics comparing N-edited NOESY spectra and AlphaFold predicted structures that seek to determine whether the predicted structure reasonably describes the structure of the protein which generated the NOESY. These heuristics are fundamentally different than those used before in that they concentrate on interresidue contacts and not specific HH pairs. We present a large collection of data connecting entries across the BMRB, PDB and AlphaFold Database that includes experimentally derived structures and corresponding spectra, establishing it as a means to develop and test hybrid methods utilizing AlphaFold and NMR spectra to perform structure determination. These data test the new heuristics ability to identify inaccurate AlphaFold structures. A support vector machine was developed to test the consistency of NMR data with predicted structure and we show its application to the structure of an unsolved engineered protein, LoTOP.

biophysics↗

bioRxiv2024

Uncovering genetic linkages in the rhizosphere contributing to adaptation

Microorganisms recruited to the rhizosphere from the surrounding soil can benefit the fitness of their host. Variation in plant genetics is associated with variation in rhizosphere microbial community composition leading to changes in fitness and crop productivity. However, what impact the abiotic environment has on connections between microbes and host genetics, and whether those connections in turn impact crop performance in realistic agricultural scenarios remains unclear. We assessed agronomic performance and 16S and ITS amplicon-based rhizosphere bacterial and fungal community composition on a large diverse barley population grown in seven field trials across four locations and two years. Within adapted regions, we observed consistent rhizosphere compositions across diverse soils, whereas in an unadapted environment, distinct microbial communities were recruited, indicating environmental specificity in microbial assembly. A Genome-wide association study (GWAS) identified 864 associations of barley genetic markers with bacterial or fungal taxa abundance. A total of 108 microbe-associated quantitative trait loci (QTL) co-localized with agronomic traits, suggesting pleiotropy or genetic linkage. Associated taxa varied considerably across field trial environments, whereas the mapped host QTL were more consistent. Members of the nitrogen cycling bacterial phylum, Nitrospirota were the most extensively associated. This phylum had 25 marker associations across five of the field trial location-years in the GWAS. These included a locus on chromosome 2H that associated with Nitrospirota bacteria and grain protein in two location-years, and the Leohumicola fungal genus and grain protein in a third trial. These findings support the genetic manipulation of rhizosphere microbiomes to enhance crop adaptation, whether with consistent or environment-specific microbial taxa. Such breeding advances will support phenotyping and selection strategies to improve crop resilience and productivity across variable environments.

plant biology↗

bioRxiv2024

BATF2 is a regulator of interferon-gamma signaling in astrocytes during neuroinflammation

Astrocytic interferon (IFN){gamma} signaling is associated with a reduction in neuroinflammation. We have previously shown that the benefits of astrocytic IFN{gamma} arise from a variety of mechanisms; however, downstream effectors responsible for regulating this protection are unknown. We address this by identifying a specific transcription factor that may play a key role in modulating the consequences of IFN{gamma} signaling. RNA-sequencing of primary human astrocytes treated with IFN{gamma} revealed basic leucine zipper ATF-like transcription factor (BATF)2 as a highly expressed interferon-specific gene. Primarily studied in the periphery, BATF2 has been shown to exert both inflammatory and protective functions; however, its function in the central nervous system (CNS) is unknown. Here, we demonstrate that human spinal cord astrocytes upregulate BATF2 transcript and protein in an IFN{gamma}-specific manner. Additionally, we found that BATF2 prevents overexpression of interferon regulatory factor (IRF)1 and IRF1 targets such as Caspase-1, which are known downstream pro-inflammatory mediators. We also show that Batf2-/- mice exhibit exacerbated clinical disease severity in a murine model of CNS autoimmunity, characterized by an increase in both CNS immune cell infiltration and demyelination. Batf2-/- mice also exhibit increased astrocyte-specific expression of IRF1 and Caspase-1, suggesting an amplified interferon response in vivo. Further, we demonstrate that BATF2 is expressed primarily in astrocytes in MS lesions and that this expression is co-localized with IRF1. Collectively, our results further support a protective role for IFN{gamma} and implicate BATF2 as a key suppressor of overactive immune signaling in astrocytes during neuroinflammation.

neuroscience↗

bioRxiv2024

A novel PSMB8 isoform associated with multiple sclerosis lesions induces P-body formation

Multiple sclerosis (MS) is an inflammatory and demyelinating disease of the central nervous system (CNS). Current therapies primarily target the inflammatory component of the disease and are highly effective in early stages of MS while limited therapies have an effect in the more chronic progressive stages of MS where resident glia have a larger role. MS lesions tend to be inflammatory even after the initial peripheral immune cell invasion has subsided and this inflammation is known to cause alternative splicing events. We used qPCR of normal-appearing white matter and white matter lesions from postmortem MS tissue, in vitro studies, and immunostaining in MS tissue to investigate the alternative splicing of one gene known to be important during recovery in an animal model of MS, PSMB8. We found a novel, intron-retained isoform which has not been annotated, upregulated specifically in MS patient white matter lesions. We found that this novel isoform activates the nonsense-mediated decay pathway in primary human astrocytes, the most populous glial cell in the CNS, and is then degraded. Overexpression of this isoform in astrocytes leads to an increased number of processing bodies in vitro, the primary site of mRNA decay. Finally, we demonstrated that MS white matter lesions have a higher burden of processing bodies compared to normal-appearing white matter, predominantly in GFAP-positive astrocytes. The increase in alternative splicing of the PSMB8 gene, the stress that this alternative splicing causes, and the observation that processing bodies are increased in white matter lesions suggests that the lesion microenvironment may lead to increased alternative splicing of many genes. This alternative splicing may blunt the protective or reparative responses of resident glia in and around white matter lesions in MS patients.

molecular biology↗

bioRxiv2023

Astrocyte interferon-gamma signaling dampens inflammation during chronic central nervous system autoimmunity via PD-L1

Multiple sclerosis (MS) is an inflammatory and neurodegenerative disease of the central nervous system (CNS). Infiltrating inflammatory immune cells perpetuate demyelination and axonal damage in the CNS and significantly contribute to pathology and clinical deficits. While the cytokine interferon (IFN){gamma} is classically described as deleterious in acute CNS autoimmunity, we and others have shown astrocytic IFN{gamma} signaling also has a neuroprotective role. Here, we performed RNA sequencing and ingenuity pathway analysis on IFN{gamma}-treated astrocytes and found that PD-L1 was prominently expressed. Using a PD-1/PD-L1 antagonist, we determined that apoptosis was reduced in leukocytes exposed to IFN{gamma}-treated astrocytes in vitro. To further elucidate the role of astrocytic IFN{gamma} signaling on the PD-1/PD-L1 axis in vivo, we induced the experimental autoimmune encephalomyelitis (EAE) model of MS in Aldh1l1-CreERT2, Ifngr1fl/fl mice. Mice with conditional astrocytic deletion of IFN{gamma} receptor exhibited a reduction in PD-L1 expression which corresponded to increased infiltrating leukocytes, particularly from the myeloid lineage, and exacerbated clinical disease. PD-1 agonism reduced EAE severity and CNS-infiltrating leukocytes. Importantly, PD-1 is expressed by myeloid cells surrounding MS lesions. These data support that IFN{gamma} signaling in astrocytes diminishes inflammation during chronic autoimmunity via upregulation of PD-L1, suggesting potential therapeutic benefit for MS patients.

neuroscience↗

bioRxiv2021

Targeting interferon-{lambda} signaling promotes recovery from central nervous system autoimmunity

Type III interferons (IFNLs) are newly discovered cytokines, acting at epithelial and other barriers, that exert immunomodulatory functions in addition to their primary roles in antiviral defense. Here we define a role for IFNLs in maintaining autoreactive T cell effector function and limiting recovery in a murine model of multiple sclerosis (MS), experimental autoimmune encephalomyelitis (EAE). Genetic or antibody-based neutralization of the IFNL receptor (IFNLR) resulted in lack of disease maintenance during EAE, with loss of CNS Th1 effector responses and limited axonal injury. Phenotypic effects of IFNLR signaling were traced to increased antigen presenting cell (APC) function, with associated increase in T cell production of IFN{gamma} and GM-CSF. Consistent with this, IFNL levels within lesions of CNS tissues derived from MS patients were elevated compared to MS normal appearing white matter (NAWM). Furthermore, expression of IFNLR was selectively elevated in MS active lesions compared to inactive lesions or NAWM. These findings suggest IFNL signaling as a potential therapeutic target to prevent chronic autoimmune neuroinflammation.

immunology↗

bioRxiv2019

Regional astrocyte interferon-γ signaling regulates immunoproteasome-mediated protection during chronic autoimmunity

In early autoimmune neuroinflammation, interferon (IFN){gamma} and its upregulation of the immunoproteasome (iP) is pathologic. However, during chronic multiple sclerosis (MS), IFN{gamma} has protective properties and, the role of the iP remains to be fully elucidated. Here, we demonstrated that IFN{gamma} signaling in regional astrocytes induces the iP and protects the CNS during autoimmunity. In MS tissue, iP expression was enhanced in spinal cord compared to brainstem lesions, which correlated with a decrease in oxidative stress. In vitro, IFN{gamma} stimulation enhanced iP expression, reduced reactive oxygen species burden, and decreased oxidatively damaged and poly-ubiquitinated protein accumulation preferentially in human spinal cord astrocytes, which was abrogated with the use of the iP inhibitor, ONX 0914. During the chronic phase of an MS animal model, experimental autoimmune encephalomyelitis (EAE), ONX 0914 treatment exacerbated disease and led to increased oxidative stress and poly-ubiquitinated protein build-up. Finally, mice with astrocyte-specific loss of the IFN{gamma} receptor exhibited worsened chronic EAE associated with reduced iP expression, enhanced lesion size and oxidative stress and poly-ubiquitinated protein accumulation in astrocytes. Taken together, our data reveal a protective role for IFN{gamma} in chronic neuroinflammation and identify a novel function of the iP in astrocytes during CNS autoimmunity.

neuroscience↗

bioRxiv2019

Loss of the Krppel-like factor 4 tumor suppressor is associated with epithelial-mesenchymal transition in colorectal cancer

Colorectal cancer (CRC) is the third leading cancer-related cause of death due to its propensity to metastasize. Epithelial-mesenchymal transition (EMT) is a multistep process important for invasion and metastasis of CRC. Kruppel-like factor 4 (KLF4) is a zinc finger transcription factor highly expressed in differentiated cells of the intestinal epithelium. KLF4 has been shown to play a tumor suppressor role during CRC tumorigenesis - its loss accelerates development and progression of cancer. The present study examines the relationship between KLF4 and markers of EMT in CRC.\n\nMethodsImmunofluorescence staining for KLF4 and EMT markers was performed on archived patient samples after colorectal cancer resection and on colonic tissues of mice with colitis-associated cancer.\n\nResultsWe found that KLF4 expression is lost in tumor sections obtained from CRC patients and in those of mouse colon following azoxymethane and dextran sodium sulfate (AOM/DSS) treatment when compared to their respective normal appearing mucosa. Importantly, in CRC patient tumor sections we observed a negative correlation between KLF4 levels and mesenchymal markers including TWIST, {beta}-catenin, claudin-1, N-cadherin, and vimentin. Similarly, in tumor tissues from AOM/DSS-treated mice KLF4 levels were negatively correlated with mesenchymal markers including SNAI2, {beta}-catenin, and vimentin and positively correlated with the epithelial marker E-cadherin.\n\nConclusionThese findings suggest that the loss of KLF4 expression is a potentially significant indicator of EMT in CRC.

cancer biology↗

bioRxiv2019

Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation

We present high quality, phased genome assemblies representative of taurine and indicine cattle, subspecies that differ markedly in productivity-related traits and environmental adaptation. We report a new haplotype-aware scaffolding and polishing pipeline using contigs generated by the trio binning method to produce haplotype-resolved, chromosome-level genome assemblies of Angus (taurine) and Brahman (indicine) cattle breeds. These assemblies were used to identify structural and copy number variants that differentiate the subspecies and we found variant detection was sensitive to the specific reference genome chosen. Six gene families with immune related functions are expanded in the indicine lineage. Assembly of the genomes of both subspecies from a single individual enabled transcripts to be phased to detect allele-specific expression, and to study genome-wide selective sweeps. An indicus-specific extra copy of fatty acid desaturase is under positive selection and may contribute to indicine adaptation to heat and drought.

genomics↗

bioRxiv2018

FALCON-Phase: Integrating PacBio and Hi-C data for phased diploid genomes

Haplotype-resolved genome assemblies are important for understanding how combinations of variants impact phenotypes. These assemblies can be created in various ways, such as use of tissues that contain single-haplotype (haploid) genomes, or by co-sequencing of parental genomes, but these approaches can be impractical in many situations. We present FALCON-Phase, which integrates long-read sequencing data and ultra-long-range Hi-C chromatin interaction data of a diploid individual to create high-quality, phased diploid genome assemblies. The method was evaluated by application to three datasets, including human, cattle, and zebra finch, for which high-quality, fully haplotype resolved assemblies were available for benchmarking. Phasing algorithm accuracy was affected by heterozygosity of the individual sequenced, with higher accuracy for cattle and zebra finch (>97%) compared to human (82%). In addition, scaffolding with the same Hi-C chromatin contact data resulted in phased chromosome-scale scaffolds.

genomics↗

bioRxiv2018

Complete assembly of parental haplotypes with trio binning

Reference genome projects have historically selected inbred individuals to minimize heterozygosity and simplify assembly. We challenge this dogma and present a new approach designed specifically for heterozygous genomes. \"Trio binning\" uses short reads from two parental genomes to partition long reads from an offspring into haplotype-specific sets prior to assembly. Each haplotype is then assembled independently, resulting in a complete diploid reconstruction. On a benchmark human trio, this method achieved high accuracy and recovered complex structural variants missed by alternative approaches. To demonstrate its effectiveness on a heterozygous genome, we sequenced an F1 cross between cattle subspecies Bos taurus taurus and Bos taurus indicus, and completely assembled both parental haplotypes with NG50 haplotig sizes >20 Mbp and 99.998% accuracy, surpassing the quality of current cattle reference genomes. We propose trio binning as a new best practice for diploid genome assembly that will enable new studies of haplotype variation and inheritance.

genomics↗

bioRxiv2017

A Model for Genome-First Care: Returning Secondary Genomic Findings to Participants and Their Healthcare Providers in a Large Research Cohort

BackgroundResearch cohorts with linked genomic data exist, or are being developed, at many research centers. Within any such \"sequenced cohort\" of more than 100 participants, it is likely that there are participants with previously undisclosed risk for life-threatening monogenic diseases that could be identified with targeted analysis of their existing data. Identification of such disease-associated findings are not usually primary to the enrollment research goals. At Geisinger Health System, MyCode(R) Community Health Initiative (MyCode) participants represent one such large sequenced cohort. Since 2013, MyCode participants in discovery research have been consented for secondary analysis of their existing research genomic sequences to allow delivery of medically actionable findings to them and their healthcare providers. This return of genomic results program was developed to manage an anticipated 3.5% of MyCode participants who will receive clinically confirmed genomic variants from an approved gene list out of more than 150,000 total participants. Risk-associated DNA sequences alone without any clinical parameter, prompt \"genome-first\" follow-up encounters.\n\nMethodsThis article describes our process for generating clinical grade results from research-based genomic sequencing data, delivering results to patients and their providers, facilitating targeted clinical evaluations of patients and promoting cascade testing of at-risk relatives. We also summarize our early data about the results generated during this process and our ability to contact patients and their providers to disclose the information.\n\nResultsThis process has been used to generate 343 results on 339 patients. 93% of patients with a result have been successfully contacted about their results as evidenced by direct interaction about their result with the research team or a healthcare provider. 222 healthcare providers have been notified of a result on one or more patient through this result delivery process.\n\nConclusionsHere we describe the existing GHS model to deliver genomic data into the electronic medical record and the clinical interactions that are prompted and supported. Elements of this genome-first care model can be applied in other healthcare settings and in national efforts, such as \"All of Us\", that wish to establish programs for returning genomic results to research participants.

genomics↗