Biology subjects

Wells, C.

Publications and source records attributed to Wells, C..

At least 19 recordsLinked to original sources

bioRxiv2026

GenomeProt: User friendly proteogenomics for canonical and non-canonical proteoform characterisation

Quantifying the diversity of RNAs and proteins produced by cells is fundamental to the biological and clinical sciences. However, many RNAs and proteins remain uncharacterised, especially proteins translated from alternate RNA isoforms; untranslated regions of mRNAs and non-coding RNAs, as well as the effects of DNA variation on protein sequences. Proteogenomics aims to characterise the complete proteome by integrating genomics and/or transcriptomics with proteomics, but current tools have limitations in useability, analysis features and visualisation of resulting data. To address these gaps, we developed GenomeProt, a user-friendly GUI-based tool for integrative proteogenomic analysis. We demonstrate its utility by integrating long-read RNA sequencing with mass-spectrometry-based proteomics to pinpoint proteoform expression generated by alternative splicing; discover novel, unannotated proteins in human brain samples; and quantify variant-containing peptides associated with treatment resistance in a melanoma xenograft model. GenomeProt brings the discovery power of proteogenomics to biologists, illuminating the hidden proteome.

bioinformatics↗

bioRxiv2025

Non-native crustacean predators conditionally trigger inducible defense behaviors in blue mussel

Climate change is driving the poleward expansion of many species, including the Atlantic blue crab (Callinectes sapidus), whose northern range now extends into the Gulf of Maine. As a recently arrived predator, the blue crab may pose a threat to native prey communities already impacted by the earlier introduction of the European green crab (Carcinus maenas). This study investigates the defensive capacity of native blue mussels (Mytilus edulis) in response to 45 h of exposure to chemical cues of blue versus green crabs. Mussels were hypothesized to invest more energy in defensive behaviors in response to green crab cues, owing to a longer shared ecological history in the Gulf of Maine. The results support this hypothesis: female blue mussels exposed to green crab cues spawned, and small mussels exhibited increased relocation behavior. In contrast, exposure to blue crab cues did not alter mussel reproductive, movement, or attachment behaviors. Notably, neither treatment significantly affected mussel attachment as measured by byssal thread quantity and tenacity, suggesting that this behavior may not be a primary defense mechanism against crab predators in this context, contrary to previous findings. These findings underscore the importance of understanding species- and size-specific interactions as expanding ranges and species introductions continue to reshape predator-prey dynamics across coastal ecosystems.

ecology↗

bioRxiv2025

Isolation of Extracellular Vesicles from Minimal Volume Ascites Fluid Using Strong Anion Exchange Magnetic Beads

Ovarian cancer (OC) remains a leading cause of gynecologic cancer mortality due to late-stage diagnosis and limited early detection strategies. Ascites fluid, a pathological hallmark of OC, is a rich source of tumor-derived extracellular vesicles (EVs) that reflect the tumor microenvironment and hold promise for biomarker discovery. However, isolating EVs from minimal ascites volumes (<100 {micro}L) poses technical challenges using conventional methods like ultracentrifugation or size-exclusion chromatography (SEC). This study explores the application of strong anion exchange (SAX) magnetic beads (Mag-Net) for efficient EV isolation from as little as 2 {micro}L of ascites fluid from both murine models and a human patient with mucinous borderline tumor. We demonstrate that SAX achieves robust EV capture at 10{micro}l of input volume, enabling comprehensive proteomic profiling and single-EV surface-enhanced Raman spectroscopy (SERS) with a >2-fold increase in proteomic depth compared to raw ascites. Notably, this study was able to identify 1000 proteins not previously annotated in Vesiclepedia for OC-derived EVs, alongside distinct SERS signatures, highlighting the potential for multiomic analysis. Comparative analysis with UC revealed enhanced proteomic depth obtained with SAX beads, albeit we also observed differential detection of canonical markers (e.g., CD9, CD81) between input volumes of ascites fluid. These findings establish SAX as a scalable, low-input platform for EV-based biomarker discovery, paving the way for improved early detection and molecular insights into OC progression.

biochemistry↗

bioRxiv2025

Pentilludin reduces rat amphetamine and remifentail self-administration with good pharmacologic and toxicologic profiles

Pentilludin is a novel, potent (690 nM) irreversible inhibitor of actions of the receptor type protein tyrosine phosphatase D (PTPRD). Pentilludin displays no in vitro activities in Ames or micronucleus tests, at hERG channels or at targets for currently-licensed drugs. Rats treated with pentilludin doses up to 100 mg/kg/day for two weeks have not been found to display behavioral, hematologic or serum chemistry abnormalities. Treatment with 20 mg/kg sc pentilludin prior to every other M-W-F self-administration session substantially reduces self-administration of amphetamine and more modestly reduces self-administration of remifentanil. Pentilludin provides a novel means for reducing self-administration of psychostimulant and, modestly, opiate drugs in ways that could enhance abstinence in humans.

pharmacology and toxicology↗

bioRxiv2025

The effect of acute and prolonged acidosis on a panel of carcinoma cell lines.

Due to cancer cell metabolism and disorganized tissue structure, the tumour microenvironment is associated with several pathophysiological conditions, including hypoxia, nutrient deprivation, accumulation of waste products, and acidification of the tumour microenvironment (tumour acidosis). Despite the belief that tumour acidosis drives tumorigenesis, it is still not clear how cancer cells respond to acidosis in the absence of other pathophysiological conditions. Here, we investigate how both acute and prolonged acidosis (pH 6.8) affects different epithelial features of a panel of carcinoma cell lines. We find that acute acidosis in all cell lines investigated represses the cell growth and causes a disturbance of adherens junctions and apical-basal polarity, reminiscent of epithelial-to-mesenchymal transition (EMT). However, we do not find that acute acidosis has a general effect on adhesion and migration in our panel of cell lines. Exposing our panel of carcinoma cell lines to acidosis for more than six weeks did not lead to adaptations restoring cell growth. On the contrary, prolonged acidosis caused one cell line (A431) to halt proliferation. Another cell line (A549) reacted to prolonged acidosis by gradually inducing the expression of ZEB2, which caused a partial EMT. In the rest of the cell lines, we did not find any noticeable effect of prolonged acidosis. Lastly, all cell lines quickly restored their original phenotype and growth rate when returned to media with normal pH (pH 7.5).

cancer biology↗

bioRxiv2025

Trophic and temporal dynamics of macrophage biology in human inner ear organogenesis

Recent single-cell transcriptomic approaches are uncovering the breadth and depth of cell diversity within the mammalian inner ear. Macrophages, detected from gestational week 7 in the human inner ear, persist into adulthood, and yet remain poorly understood in terms of their origin and function. Using self-generated and public scRNA-seq data, we identify seven distinct macrophage subtypes spanning fetal weeks 7.5 to 16.4 and adulthood. Each macrophage subtype is linked to specific developmental stages and displays a unique gene expression profile. These findings corroborate earlier histological evidence of resident and non-resident macrophages in both the developing and adult human cochlea. We also show that the human inner ear is seeded by macrophages from both embryonic and more definitive sources, corroborating studies in mouse. By analyzing ligand-receptor interactions, we highlight potential macrophage contributions to inner ear organogenesis. This research provides new insights into the diverse roles of human inner ear macrophages.

bioinformatics↗

bioRxiv2025

Hepatic Yap1 activates systemic catabolism and muscle loss during organ repair: evidence for a liver-derived common mechanism with cancer cachexia.

Recovery from critical injury concomitant with restoration of functional organ mass invokes a systemic catabolic response leading to muscle and fat loss, known as cachexia. We interrogated this process using mouse models of organ repair, including liver regeneration after hepatectomy, Yap1-mediated hepatomegaly, and pneumonectomy. Both hepatectomy and Yap1 induced systemic catabolism. Muscle and adipose wasting scaled with degree of liver growth, with 10-25% reduction of muscle mass and 50-80% of fat mass. In contrast, non-regenerative lung injury did not induce tissue wasting. Liver growth elevated resting energy expenditure. Tracer studies demonstrated redistribution of muscle-derived cholesterol and amino acids to regenerating liver. Gene expression changes in livers and muscles showed high concordance between the liver growth models and cancer cachexia models, including pancreatic adenocarcinoma cachexia. We propose that cachexia is a normal and essential reparative process in organ repair and regeneration and further, that cancer cachexia is a pathological exacerbation of an adaptive process mediated by activation of Yap1 in the liver.

physiology↗

bioRxiv2025

Caribbean octocoral communities: finding the forest for the trees?

Octocorals have increased in abundance on many Caribbean coral reefs, and at some sites "octocoral forest" may be a better community descriptor than "coral reef." Implicit to the concept of a forest is that structural elements, trees, colonies, etc., alter the environment in ways that affect the structural elements themselves and the organisms that inhabit the forest. At what density do the structural elements create the emergent properties of a "forest?" Communities traditionally characterized as hardgrounds and coral reefs around Puerto Rico and St John, US Virgin Islands, varied in density of octocoral colonies from a few to >100 colonies m-2in surveys conducted in 2021 and 2022. Canopy cover was correlated with the density of colonies. Among the quadrats with the highest octocoral density there was no significant correlation between numbers of colonies and canopy cover. Frontal area, a measure related to the communitys effect on water flow, as well as the volume occupied by colonies followed patterns similar to canopy cover. Vertical profiles of flow velocity were measured from the substratum to 3 m above the bottom on a reef on St John where octocoral population density ranged from 0 to 16 colonies m-2. Profiles of orbital velocity exhibited perturbations which were more pronounced in locations with > 12 colonies m-2. Using the effect on flow as a criterion, 4 of the 8 surveyed sites would function as forests. Understanding the density at which emergent properties appear is critical to understanding the bio-physical interactions affecting the community.

ecology↗

bioRxiv2024

The genome assembly of the westslope cutthroat trout, Oncorhynchus lewisi, reveals interspecific chromosomal rearrangements with the rainbow trout

Cutthroat trout (Oncorhynchus clarkii) are popular among anglers throughout their native range along the West Coast and interior of North America. As they colonized the interior of North America, cutthroat trout diverged into several genetically distinct groups. Many of these groups are now threatened by habitat destruction, hybridization with rainbow trout (O. mykiss), and competition from introduced species. These groups were previously classified as subspecies, but recent research suggests they may represent distinct species. In this study, we produced a chromosomal-level genome assembly and a genetic map for one of the species in the cutthroat trout species complex, the westslope cutthroat trout (O. lewisi--formerly O. clarki lewisi). We also constructed haplotype-resolved assemblies from a westslope cutthroat-rainbow trout F1 hybrid. We used the new genome assemblies to identify major interspecific chromosomal rearrangements between the two sister species, including fusions, fissions, and inversions. These genome assemblies and chromosome data provide valuable insights regarding genetic variation within cutthroat trout and in hybrids between rainbow and cutthroat trout. Article SummaryWestslope cutthroat trout inhabit bodies of water in several states and provinces near the Rocky Mountains and are well-known among anglers. In this study, we produced the first publicly available genome assemblies and a high-density genetic map for this species. These are research tools that allow detailed genetic analyses, including identifying differences among the genomes of related species. These comparisons allow researchers to understand the evolution of these species better and may provide insight into why successful interbreeding is possible among cutthroat and rainbow trout.

genomics↗

bioRxiv2024

Efficient generation of human dendritic cells from iPSC by introducing a feeder-free expansion step for hematopoietic progenitors

Dendritic cells (DCs) are rare innate immune cells that are essential regulators of anti-tumour, anti-viral and vaccine responses by the adaptive immune system. Conventional dendritic cells, particularly the cDC1 subset, are most desired for DC-based immunotherapies, however, it can be difficult to isolate sufficient numbers of primary cells from patients. The most common alternate sources of DC are ex vivo, such as monocyte-derived or DC expanded from cord blood hematopoietic progenitors. Induced pluripotent stem cells (iPSC) offer a promising solution, providing an opportunity for in vitro generating DCs that are suitable for patient-derived or off-the-shelf batch-manufactured cells. Here, we developed an in vitro protocol designed to maximise the yield of iPSC-derived DC progenitors, with the specific goal of generating DC1-like cells. The iPSC-DCs subsets generated by our method could be partitioned by cell surface phenotypes of cDC1, cDC2 and DC3, but they were most transcriptionally similar to monocyte-derived DC (MoDC). Stimulated iPSC-DCs generated pro-inflammatory cytokines, expressed migratory chemokine receptors including CCR7 which indicates capacity to traffic through lymphatic endothelium, and upregulated co-stimulatory molecules, indicating their potential for productive interactions with T-cells. This method offers a promising step towards an expandable source of allogeneic human dendritic cells for future applications.

cell biology↗

bioRxiv2024

Australian researchers' perceptions and experiences with stem cell registration.

The recently issued ISSCR standards in stem cell research recommend registration of human pluripotent stem cell lines (hPSCs). Registration is an important part of establishing stem cell provenance and connecting cell lines to data derived on those lines. In this study, we sought to understand common barriers to registration, by conducting interviews with forty-eight Australian stem cell stakeholders, including researchers, clinicians, and industry professionals. Australian stem cell researchers do not routinely register their lines, and of those Australian lines captured by an international registry, only a third have completed the registration process. Most registered Australian cell lines miss information about their ethical provenance or key pluripotency characteristics. Incomplete registration is poorly aligned with the goals of open science that registries are founded on, and users themselves expressed concerns about the quality of the partial information provided to the resource. Registration was considered a publication hurdle, and this impacted on user perceptions of usefulness of registration, and lowered the likelihood that they would engage with registries to find resources. Although the Australian community represents a small fraction of registry users, the results of this study may suggest ways for journals, registries, and the stem cell community to improve registration compliance. HighlightsResearchers who perceive registration as a publication hurdle are unlikely to complete the registration process. Incomplete registration promotes misunderstandings about the goals and quality of a registry. Full registration of pluripotent stem cell lines is an important step in verifying cell line provenance. Greater public awareness of registration, combined with requirements for full registration by journals will support the community adopt ISSCR recommendations to register lines.

scientific communication and education↗

bioRxiv2023

Discovery of NRG1-VII: a novel myeloid-derived class of NRG1 isoforms

The growth factor Neuregulin-1 (NRG1) has pleiotropic roles in proliferation and differentiation of the stem cell niche in different tissues. It has been implicated in gut, brain and muscle development and repair. Six isoform classes of NRG1 and over 28 protein isoforms have been previously described. Here we report a new class of NRG1, designated NRG1-VII to denote that these NRG1 isoforms arise from a myeloid-specific transcriptional start site (TSS) previously uncharacterized. Long-read sequencing was used to identify eight high-confidence NRG1-VII transcripts. These transcripts presented major structural differences from one another, through the use of cassette exons and alternative stop codons. Expression of NRG1-VII was confirmed in primary human monocytes and tissue resident macrophages and iPSC-derived macrophages. Isoform switching via cassette exon usage and alternate polyadenylation was apparent during monocyte maturation and macrophage differentiation. NRG1-VII is the major class expressed by the myeloid lineage, including tissue-resident macrophages. Analysis of public gene expression data indicates that monocytes and macrophages are a primary source of NRG1, suggesting that NRG1-VII is the most common class of NRG1 in most adult human tissues, except brain. The size and structure of type VII isoforms suggests that they may be more diffusible through tissues than other NRG1 classes. However, the specific roles of type VII variants in tissue homeostasis and repair have not yet been determined.

genomics↗

bioRxiv2023

Targeted Sequencing of Pancreatic Ductal Adenocarcinoma Tissue

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer and the majority of patients present with metastatic disease. Metastatic spread requires a reorganisation of the actin cytoskeleton, a process that is dependent on the Rho family GTPases and their interaction with subsequent downstream effectors. The p21 activated kinases (also known as the PAKs) are effectors of Rho GTPases Cdc42 and Rac and play key roles in cell migration and survival. PAK4 is overexpressed in PDAC and can reciprocally activate the PI3K pathway. Hepatocyte growth factor (HGF), via c-Met, is an established activator of PAK4 and the PI3K pathway and may promote PDAC invasion. Next generation sequencing (NGS) was performed on 31 PDAC tissue using a pre-determined targeted panel to attempt to identify novel mutations in the PAK: PI3K pathway. Targeted NGS identified several recurrent mutations including 5 PAK4 mutations in PDAC tissue.

cancer biology↗

bioRxiv2022

A TYPE 2 INNATE LYMPHOID CELL-INTERLEUKIN 9 CIRCUIT INDUCES PANETH CELL METAPLASIA AND SMALL INTESTINAL REMODELING

Paneth cell metaplasia (PCM) typically arises in the setting of pre-existing gastrointestinal (GI) diseases; however, the mechanistic pathway that induces metaplasia and whether PCM is initiated exclusively by disorders intrinsic to the GI tract has not been delineated. Herein, we describe the development of PCM in a murine model of inducible bcr/abl oncogene-driven chronic myelogenous leukemia (CML) in which metaplasia is causally and temporally linked to the development of leukemia. Mechanistically, CML induced a proinflammatory state within the GI tract that resulted in the production of epithelial-derived IL-33. Binding of IL-33 to ST2 led to the production of IL-9 by type 2 innate lymphoid cells (ILC2s) which was directly responsible for the induction of PCM in the colon and Paneth cell hyperplasia in the ileum. In addition, IL-9 directed remodeling of the small intestines characterized by goblet and tuft cell hyperplasia along with the expansion of mucosal mast cells. Thus, we identify that an extra intestinal disease can trigger an ILC2/IL-9 immune circuit which induces PCM and regulates epithelial cell fate decisions in the GI tract.

immunology↗

bioRxiv2022

The Human Dendritic Cell Atlas: An integrated transcriptional tool to study human dendritic cell biology

Dendritic cells (DCs) are functionally diverse and are present in most adult tissues, however progress in understanding human DC biology is hampered by a relatively small number of these in circulation and by limited access to human tissues. We built a transcriptional atlas of human DCs by combining samples from 14 expression profiling studies derived from 10 laboratories. We identified significant gene expression variation of DC subset-defining markers across tissue-type and upon viral or bacterial stimulation. We further highlight critical gaps between in vitro-derived DC subsets and their in vivo counterparts and provide evidence that monocytes or cord blood progenitor in vitro-differentiated DCs fail to capture the repertoire of primary DC subsets or behaviours. In constructing a reference DC atlas, we provide an important resource for the community wishing to identify and annotate tissue-specific DC subsets from single-cell datasets, or benchmark new in vitro models of DC biology. Key PointsO_LIA reference atlas of human DC that allows benchmarking of in vitro DC models C_LIO_LIMeta-analysis of 14 integrated studies demonstrate that human conventional dendritic cells have distinct tissue-of-origin phenotypes C_LIO_LIUser uploads allow tissue-relevant annotation of human DC subsets from single cell datasets C_LIO_LIKey subset markers are altered by tissue or activation status C_LIO_LIGaps between in vitro-differentiated DC and in vivo counterparts are partially rescued by humanized mouse models, or coculture with NOTCH-ligands. C_LI

immunology↗

bioRxiv2022

Proliferation is a driver of quorum sensing in an in vitro model of tissue resident macrophages

Macrophages coordinate the initial host inflammatory response to tissue infection, as well as mediating the reparative phase, by producing growth factors that promote tissue repair. One model of this functional dichotomy is that peripherally recruited monocyte-derived macrophages drive acute inflammatory responses to infection, whereas tissue-resident macrophages are responsible for tissue repair. Alternatively, inflammation and repair may be inter-dependent molecular programs, such that both recruited and resident cells have equivalent capacity to contribute. Repeated exposure to pathogenic challenge results in innate tolerance, which may also alter the contributions of discrete macrophage populations to inflammation or repair. In this study a village model of tissue resident and recruited macrophages was created using induced pluripotent stem cell-derived macrophages and peripheral blood monocyte-derived macrophages, respectively. Population responses to repeated exposure to lipopolysaccharide were assessed with single-cell RNA sequencing and donors demultiplexed with Vireo. A subset of genes escaped classical tolerance programs in the iPSC, but not monocyte-derived macrophages, and this was associated with differences in their proliferative capacity. This suggests that targeting the proliferative resident macrophages would be most effective to limit inflammatory signaling.

systems biology↗

bioRxiv2022

The whole blood microbiome of Indonesians reveals that environmental differences shape immune gene expression signatures

Pathogens found within local environments are a major cause of morbidity and mortality. This is particularly true in Indonesia, where infectious diseases such as malaria or dengue are a significant part of the disease burden. Unequal investment in medical funding throughout Indonesia, particularly in rural areas, has resulted in under-reporting of cases, making surveillance challenging. Here, we use transcriptome data from 117 healthy individuals living on the islands of Mentawai, Sumba, and the Indonesian side of New Guinea Island to explore which pathogens are present within whole blood. We detect a range of taxa within RNA-sequencing data generated from whole blood and find that two pathogens--Flaviviridae and Plasmodium--are the most predominantly abundant, both of which are most pronounced in the easternmost island within our Indonesian dataset. We also compare the Indonesian data to two other cohorts from Mali and UK and find a distinct microbiome profile for each group. This study provides a framework for RNA-seq as a possible retrospective surveillance tool and an insight to what makes up the transient human blood microbiome.

genomics↗

bioRxiv2021

AD Informer Set: Chemical tools to facilitate Alzheimer's disease drug discovery

IntroductionThe portfolio of novel targets to treat Alzheimers disease (AD) has been enriched by the AMP-AD program. MethodsA cheminformatics-driven effort enabled identification of existing small molecule modulators for many protein targets nominated by AMP-AD and suitable positive control compounds to be included in the set. ResultsWe have built an annotated set of 171 small molecule modulators, including mostly inhibitors, targeting 98 unique proteins that have been nominated by AMP-AD consortium members as novel targets for AD treatment. These small molecules vary in their quality and should be considered chemical tools that can be used in efforts to validate therapeutic hypotheses, but which would require further optimization. A physical copy of the AD Informer Set can be ordered via the AD Knowledge Portal. DiscussionSmall molecule tools that enable target validation are important tools for the translation of novel hypotheses into viable therapeutic strategies for AD.

neuroscience↗