Biology subjects

Collier, P.

Publications and source records attributed to Collier, P..

13 recordsLinked to original sources

bioRxiv2026

Modulator Resolves Transcript-, Allele-, and Condition-associated RNA Modification Differences from Direct RNA Sequencing

Nanopore direct-RNA sequencing (DRS) reports RNA modifications on single molecules, but there is no comprehensive algorithm for processing, aligning, and differentiating base modifications across reads that are often 5'-truncated. Here we present Modulator, which assigns every read, truncated or not, to a fragmentform, defined by a shared transcript 3'-end and the splice-junctions upstream of it. Of note, Modulator builds fragmentforms from genomic alignments without a reference transcriptome, estimates per-base modification stoichiometry within each fragmentform, and classifies each stoichiometry difference as transcript-, allele-, or condition-dependent. In the control HG002 transcriptome, Modulator built 23,746 fragmentforms, with 15,620 candidate novel isoforms that carried poly(A) signals as often as previously annotated transcripts. Also, assigning 5'-truncated reads to fragmentforms nearly doubled the number of testable and differentially modified sites. m6A sites within 100 nucleotides (nt) of a splice junction or within 1 kb of a poly(A) site were less modified in fragmentforms that use that junction or poly(A) site, indicating that local transcript context shapes where m6A is deposited. From the same reads, Modulator called SNPs with 93% precision and no phasing errors against the Genome in a Bottle benchmark. It identified 131 SNPs that create or remove a modifiable nucleotide and 1,358 allele-specific modification differences, most involving SNPs more than 50 nt from the modified site. In cells infected with Zika virus, which remodels gene expression relative to uninfected cells, Modulator identified 1,253 transcript-independent modification stoichiometry changes. Of the m6A changes at sites measured by GLORI, 96% agreed in direction with single-nucleotide-resolution GLORI maps of the same samples. Thus, Modulator accurately separates changes in RNA modification from transcript-associated and allele-associated differences and can improve the utility of nanopore DRS. Availability and Implementation: Modulator is free and open source: https://github.com/Theo-Nelson/Modulator. It is written in Python and runs on Linux OS.

bioinformatics↗

bioRxiv2026

Alternative polyadenylation drives isoform-dependent m6A remodeling during Zika virus infection

Alternative RNA processing generates extensive transcript diversity, yet how transcript architecture influences selective m6A deposition is incompletely understood. Exon-junction-based models explain where m6A is excluded, but a positive determinant of m6A accumulation remains undefined. Here, we leverage Zika virus-induced changes in m6A deposition to uncover determinants of transcript-selective methylation. By integrating GLORI-seq, native METTL3 RNA immunoprecipitation, and nanopore direct RNA sequencing, we generate a single-nucleotide, isoform-resolved map of m6A dynamics during infection. We identify over 2,000 dynamic m6A sites, many arising from changes in transcript architecture, and pinpoint proximal polyadenylation sites as positive determinants of m6A accumulation. The cleavage stimulation factors CSTF2 and CSTF2T drive this remodeling through two routes: redundant induction of intronic polyadenylation, which converts internal exons into terminal exons that expose DRACH motifs to METTL3, and non-redundant, cleavage-independent recruitment of METTL3 near proximal polyadenylation sites, establishing alternative polyadenylation as a key architectural determinant of the m6A landscape.

molecular biology↗

bioRxiv2026

Whole-genome benchmarking reveals context-specific error rates in the Ultima UG100 and Illumina NovaSeqX Platforms.

Whole genome sequencing (WGS) is becoming more common in research and clinical applications, but there is a paucity of comparative data between high-throughput WGS platforms. We benchmarked the Ultima Genomics UG100 system against Illumina NovaSeqX using the Genome in a Bottle (GIAB) WGS reference set sample HG002. Across NIST v4.2.1 benchmark regions, UG100 exhibited higher total variant-calling errors (27x), primarily driven by indel false negatives. Restricting to Ultima Genomics high confidence regions (UG HCR v3.1, 90.3% of GRCh38) reduced the error burden by 89.6%, indicating most errors lie outside these regions. Strong degradation of variant calling performances occurred in homopolymer tracts > 10 bp, and base calling error rates increased sharply after position 200 bp within each read, whereas Illuminas error rates were higher earlier in the read. Coverage dropouts in UG100 data were pronounced in GC-rich regions. Of note, 2.24% of ClinVar Pathogenic and Likely Pathogenic variants and 22.6% of a common catalogue of polymorphic STRs were found to be excluded from UG HCR v3.1, indicating potential impact to clinical applications. These results highlight context-specific genotyping errors of the UG100 and NovaSeqX platforms, and underscore the importance of whole genome benchmarking for adjudicating accuracy of NGS platforms beyond the current HG002 reference set.

genomics↗

bioRxiv2025

Hybrid Scaffolds Decouple Biochemical & Biophysical Regulation of Cell Phenotype

The extracellular matrix changes dramatically during the progression of diseases like cancer. These complex, tissue-specific changes are not adequately replicated by most current biomaterial disease models. Here we demonstrate, for the first time, a biomaterial system allowing combined, independent control over stiffness, composition and 3D collagen architecture. We demonstrate successful perfusion of defined hydrogel formulations into ice-templated collagen scaffolds, controlling the composition of these hybrid scaffolds at constant stiffness. The Youngs moduli of these hybrid scaffolds can also be tuned independently of composition via chemical crosslinking. Encapsulation of human dermal fibroblasts reveals that fibroblast morphology depends on hybrid scaffold composition and on viscoelasticity, highlighting the importance of a system that decouples biophysical from biochemical properties. Finally, we demonstrate application of this system to exert combined control over biochemical and biophysical drivers of cell growth and invasion, focussing on breast cancer as proof-of-concept. We show that collagen fibre patterning enhances breast cancer cell proliferation, also directing the invasion of patient-derived breast cancer cells. These hybrid scaffolds are therefore promising new tools for dissecting the diverse but complementary roles played by the extracellular matrix in regulating cell phenotype, in a range of healthcare applications.

bioengineering↗

bioRxiv2025

Short-term gonadal cultures are sufficient for germline transmission in a songbird

1Primordial germ cells (PGCs) are germline stem cells that develop into sperm or egg cells and are valuable for avian biobanking and the propagation of donor-derived offspring. However, in non-poultry birds the long-term maintenance and self-renewal of PGCs in vitro remains challenging. This limitation hinders biobanking in other avian clades, particularly in the zebra finch and other songbirds that uniquely possess a germline restricted chromosome (GRC). Here, we generated and compared short-term cultures of chicken and zebra finch PGCs from the embryonic gonads or blood, as well as established long-term cultures of chicken PGCs. Using single-cell RNA sequencing, we found that the transcriptome profile of long-term chicken gonadal cultures were exclusively PGCs, whereas the short-term chicken and zebra finch cultures represented a heterogeneous mixture of cell types. The zebra finch culture further included rapidly differentiating PGCs, as well as a germ cell type not previously identified in the embryonic songbird gonad. Although zebra finch short-term gonadal cultures did not yield robust long-term PGC cultures, short-term cultured PGCs were able to integrate into host zebra finch gonads after injection into the dorsal aorta, contribute to gametic populations in adult chimeras, and give rise to phenotypically- and genomically-validated offspring. This study provides a foundation for using short-term gonadal cultures to derive donor and transgenic offspring in songbirds and further explore the unique developmental genetics of PGCs across the avian clade. SummaryBeyond poultry, the long-term culture of self-renewing primordial germ cells (PGCs) remains a challenge. Here, we compare the cell population heterogeneity and reproductive viability of gonadal cultures for the zebra finch, a songbird model of vocal learning, with established chicken PGC protocols. Using single-cell RNA sequencing, we identify the rapid differentiation of zebra finch gonadal germ cells in vitro, including germline identities not previously noted in the embryonic gonad. In comparison, these differentiated cell profiles were also found in zebra finch blood PGC culture conditions, but not identified in short- or long-term chicken PGC cultures. Host embryo injections of these short-term zebra finch gonadal cultures resulted in germline chimeric animals, but at lower rates of gonadal reconstitution compared to chicken. Nonetheless, these cultures allowed for the derivation of zebra finch germline chimeras that yield phenotypically- and genomically-validated offspring from cultured PGCs.

developmental biology↗

bioRxiv2021

Patient-derived gene and protein expression signatures of NGLY1 deficiency

N-Glycanase 1 (NGLY1) deficiency is a rare and complex genetic disorder. Although recent studies have shed light on the molecular underpinnings of NGLY1 deficiency, a systematic characterization of gene and protein expression changes in patient-derived cells has been lacking. Here, we performed RNA-sequencing and mass spectrometry to determine the transcriptomes and proteomes of 66 cell lines representing 4 different cell types derived from 14 NGLY1 deficient patients and 17 controls. While gene and protein expression levels agreed well with each other, expression differences were more pronounced at the protein level. Although NGLY1 protein levels were up to 9.5-fold downregulated in patients compared to parent controls, depending on the genotype, NGLY1 protein was still detectable in all patient-derived lymphoblastoid cell lines. Consistent with the role of NGLY1 as a regulator of the transcription factor Nrf1, we observed a cell type-independent downregulation of proteasomal genes in NGLY1 deficient cells. In contrast, genes involved in ribosomal mRNA processing were upregulated in multiple cell types. In addition, we observed cell type-specific effects. For example, genes and proteins involved in glutathione synthesis, such as the glutamate-cystein ligase subunits GCLC and GCLM, were downregulated specifically in lymphoblastoid cells. We provide a web application that enables access to all results generated in this study at https://apps.embl.de/ngly1browser. This resource will guide future studies of NGLY1 deficiency in directions that are most relevant to patients.

systems biology↗

bioRxiv2021

BRN2 and PTN unveil multiple neurodevelopmental mechanisms in Schizophrenia patient-derived cerebral organoids

Due to an inability to ethically access developing human brain tissue as well as identify prospective cases, early-arising neurodevelopmental and cell-specific signatures of Schizophrenia (Scz) have remained unknown and thus undefined. To overcome these challenges, we utilized Scz patient-derived stem cells to generate 3D cerebral organoids to model neuropathology of Scz during this critical period. We discovered that Scz organoids exhibited ventricular neuropathology resulting in altered progenitor survival and disrupted neurogenesis. This ultimately yielded fewer neurons within developing cortical fields of Scz organoids. Single-cell sequencing revealed that Scz progenitors were specifically depleted of neuronal programming factors leading to a remodeling of cell-lineages, altered differentiation trajectories, and distorted cortical cell-type diversity. While Scz organoids were 99.95% similar in their macromolecular diversity to Ctrls, four GWAS factors (PTN, COMT, PLCL1, and PODXL) and peptide fragments belonging to the POU-domain transcription factor family (e.g. POU3F2/BRN2) were altered. This revealed that Scz organoids principally differed not in their proteomic diversity, but specifically in their total quantity of disease and neurodevelopmental factors at the molecular level. Single-cell sequencing also subsequently identified cell-type specific alterations in neuronal programming factors and growth factors, and specifically replicated the depletion of POU3F2 (BRN2) and PTN in both Scz progenitors and neurons. Consequently, in two mechanistic rescue experiments we identified that the transcription factor POU3F2 (BRN2) and growth factor PTN operate as mechanistic substrates of neurogenesis and cellular survival, respectively, in Scz organoids. This suggests that multiple mechanisms of Scz exist in patient-derived organoids, and that these disparate mechanisms converge upon primordial brain developmental pathways such as neuronal differentiation, survival, and growth factor support, which may amalgamate to elevate intrinsic risk of Scz.

neuroscience↗

bioRxiv2021

Induction of an immortalized songbird cell line allows for gene characterization and knockout by CRISPR-Cas9

The zebra finch is a powerful model for several biological fields, particularly neuroscience and vocal communication. However, this species lacks a robust cell line for molecular biology research and reagent optimization. Here we describe a cell line, CFS414, generated from zebra finch embryonic fibroblasts using the SV40 large and small T antigens. This cell line demonstrates an improvement over previous songbird cell lines through continuous and density-independent growth, allowing for indefinite culture and monoclonal line derivation. Cytogenetic, genomic, and transcriptomic profiling established the provenance of this cell line and identified the expression of genes relevant to ongoing songbird research. Using this cell line, we demonstrated a stress-dependent localization response of the zebra finch song nuclei specialized gene, SAP30L, and disrupted endogenous gene sequences using S.aureus Cas9. The utility of this cell line enhances the molecular potential of the zebra finch and validates cell immortalization strategies in a songbird species.

cell biology↗

bioRxiv2020

Cell-type, single-cell, and spatial signatures of brain-region specific splicing in postnatal development

Alternative RNA splicing varies across brain regions, but the single-cell resolution of such regional variation is unknown. Here we present the first single-cell investigation of differential isoform expression (DIE) between brain regions, by performing single cell long-read transcriptome sequencing in the mouse hippocampus and prefrontal cortex in 45 cell types at postnatal day 7 (www.isoformAtlas.com). Using isoform tests for brain-region specific DIE, which outperform exon-based tests, we detect hundreds of brain-region specific DIE events traceable to specific cell-types. Many DIE events correspond to functionally distinct protein isoforms, some with just a 6-nucleotide exon variant. In most instances, one cell type is responsible for brain-region specific DIE. Cell types indigenous to only one anatomic structure display distinctive DIE, where for example, the choroid plexus epithelium manifest unique transcription start sites. However, for some genes, multiple cell-types are responsible for DIE in bulk data, indicating that regional identity can, although less frequently, override cell-type specificity. We validated our findings with spatial transcriptomics and long-read sequencing, yielding the first spatially resolved splicing map in the postnatal mouse brain (www.isoformAtlas.com). Our methods are highly generalizable. They provide a robust means of quantifying isoform expression with cell-type and spatial resolution, and reveal how the brain integrates molecular and cellular complexity to serve function.

neuroscience↗

bioRxiv2020

Modulation of the tumour promoting functions of cancer associated fibroblasts by phosphodiesterase type 5 inhibition increases the efficacy of chemotherapy in human preclinical models of esophageal adenocarcinoma.

Background and aimsEsophageal adenocarcinoma (EAC) is chemoresistant in the majority of cases. The tumor-promoting biology of cancer associated fibroblasts (CAF) make them a target for novel therapies. Phosphodiesterase type 5 inhibitors (PDE5i) have been shown to regulate the activated fibroblast phenotype in benign disease. We investigated the potential for CAF modulation in EAC using PDE5i to enhance the efficacy of chemotherapy. MethodsEAC fibroblasts were treated with PDE5i and phenotypic effects examined using immunoblotting, immunohistochemistry, gel contraction, transwell invasion, organotypics, single cell RNAseq and shotgun proteomics. The combination of PDE5i with standard-of-care chemotherapy (Epirubicin, 5-Fluorouracil and Cisplatin) was tested for safety and efficacy in validated near-patient model systems (3D tumor growth assays (3D-TGAs) and patient derived xenograft (PDX) mouse models). ResultsPDE5i treatment reduced -SMA expression in CAFs by 50% (p<0.05), associated with a significant reduction in the ability of CAFs to contract collagen-1 gels and induce cancer cell invasion, (p<0.05). RNAseq and proteomic analysis of CAF and EAC cell lines revealed PDE5i specific regulation of pathways related to fibroblast activation and tumor promotion. 3D-TGA assays confirmed the importance of stromal cells to chemoresistance in EAC, which could be attenuated by PDE5i. Chemotherapy+PDE5i in PDX-bearing mice was safe and significantly reduced PDX tumor volume (p<0.05). ConclusionPDE5 is a candidate for clinical trials to alter the fibroblast phenotype in esophageal cancer. We demonstrate the specificity of PDE5i for fibroblasts to prevent transdifferentiation and revert the CAF phenotype. Finally, we confirm the efficacy of PDE5i in combination with chemotherapy in close-to-patient in vitro and in vivo PDX-based model systems.

cancer biology↗

bioRxiv2018

Self-organization controls expression more than abundance of molecular components of transcription and translation in confined cell-free gene expression

Cell-free gene expression using purified components or cell extracts has become an important platform for synthetic biology that is finding a growing numBer of practical applications. Unfortunately, at cell-relevant reactor volumes, cell-free expression suffers from excessive variability (noise) such that protein concentrations may vary by more than an order of magnitude across a population of identically constructed reaction chambers. Consensus opinion holds that variability in expression is due to the stochastic distribution of expression resources (DNA, RNAP, ribosomes, etc.) across the population of reaction chambers. In contrast, here we find that chamber-to-chamber variation in the expression efficiency generates the large variability in protein production. Through analysis and modeling, we show that chambers self-organize into expression centers that control expression efficiency. Chambers that organize into many centers, each having relatively few expression resources, exhibit high expression efficiency. Conversely, chambers that organize into just a few centers where each center has an abundance of resources, exhibit low expression efficiency. A particularly surprising finding is that diluting expression resources reduces the chamber-to-chamber variation in protein production. Chambers with dilute pools of expression resources exhibit higher expression efficiency and lower expression noise than those with more concentrated expression resources. In addition to demonstrating the means to tune expression noise, these results demonstrate that in cell-free systems, self-organization may exert even more influence over expression than the abundance of the molecular components of transcription and translation. These observations in cell-free platform may elucidate how self-organized, membrane-less structures emerge and function in cells.

biophysics↗

bioRxiv2017

Single-cell RNA-sequencing redefines blood cell type classification in mosquitoes

Mosquito blood cells are ancestral immune cells that help control infection by vector-borne pathogens. Despite their importance, little is known about mosquito blood cell biology beyond the ambiguous morphological and functional criteria used for their classification. Here we combined the power of single-cell RNA-sequencing, imaging flow cytometry and single-molecule RNA hybridization to analyze blood cells of the malaria mosquito Anopheles gambiae. By demonstrating that blood cells express nearly half of the mosquito transcriptome, our dataset represents an unprecedented view into their transcriptional machinery. Analyses of differentially expressed genes identified transcriptional signatures of two distinct cell types that challenge the current morphology-based classification of these cells. We further demonstrated an active transfer of a cellular marker between blood cells that confounds their identity. We propose that cell-to-cell exchange is broadly relevant for cell type classification and may account for the remarkable cellular diversity observed in nature.

immunology↗

bioRxiv2017

Whole-body single-cell sequencing of the Platynereis larva reveals a subdivision into apical versus non-apical tissues

Animal bodies comprise a diverse array of tissues and cells. To characterise cellular identities across an entire body, we have compared the transcriptomes of single cells randomly picked from dissociated whole larvae of the marine annelid Platynereis dumerilii1-4. We identify five transcriptionally distinct groups of differentiated cells that are spatially coherent, as revealed by spatial mapping5. Besides somatic musculature, ciliary bands and midgut, we find a group of cells located at the apical tip of the animal, comprising sensory-peptidergic neurons, and another group composed of non-apical neural and epidermal cells covering the rest of the body. These data establish a basic subdivision of the larval body surface into molecularly defined apical versus non-apical tissues, and support the evolutionary conservation of the apical nervous system as a distinct part of the bilaterian brain6.

evolutionary biology↗