Biology subjects

Colgan, W. N.

Publications and source records attributed to Colgan, W. N..

8 recordsLinked to original sources

bioRxiv2026

Pycea: a scverse toolkit for single-cell lineage tracing analysis

Lineage tracing enables reconstruction of cellular histories in development, regeneration, and disease, but integrating lineage data into single-cell analysis workflows remains challenging. We introduce Pycea, a Python toolkit for lineage analysis and visualization, and TreeData, an extension of AnnData that stores lineage trees alongside cellular measurements. TreeData is compatible with Scanpy and other scverse tools, enabling integrated analysis without converting between formats. Pycea provides scalable methods for tree visualization, clade identification, distance comparisons, ancestral state inference, and lineage statistics. This software is open source and available at https://github.com/YosefLab/pycea.

bioinformatics↗

bioRxiv2026

Folate deficiency disrupts key metabolic transitions within the developing neural ectoderm

Despite long-standing epidemiological associations, the mechanism linking folate availability to gestational neural tube defects remains unclear, partly because measuring and interpreting metabolic activity in dynamic biological systems remains challenging. Here, we apply a deep-learning-based graph-guided variational autoencoder (MeRN; Metabolic Representation Network) to infer single-cell metabolic activity and states from scRNA-seq data of mouse embryogenesis. By analyzing folate-deficient embryogenesis from E7.0 to E9.0, we identify a transient state within the nascent neural lineage that is acutely sensitive to folate availability, leading to an interconnected disruption between key bioenergetic pathways and de novo purine biosynthesis. Moreover, metabolically induced growth defects lead to permanent morphological disruptions along the dorsal-ventral axis, which we confirm by generating whole-embryo fate maps using a prime-editing-based lineage recorder (PEtracer). Collectively, our results establish a highly scalable framework for interpreting dynamic changes in embryonic metabolism and elucidating the mechanistic bases underlying environmentally linked congenital disorders.

genomics↗

bioRxiv2026

Dissecting context-dependent cancer vulnerabilities using Perturb-seq

Background CRISPR-mediated viability assays in diverse cancer cell lines have informed cancer biology and precision medicine, but cell fitness is not the only cancer-relevant phenotype. Gene expression profiling provides insight into cellular stress, inflammation, and differential state, while still identifying activation of cell-death pathways. Perturb-seq allows scalable functional genomics screening of expression phenotypes at single-cell resolution, however existing datasets cover only a small number of work-horse cell lines. Results We produced a proof-of-concept Perturb-seq dataset targeting 100 genes in 16 diverse cancer cell lines. In the process, we established methods to address single-cell technical artifacts, identified Cas9-mediated chromosomal aberrations and assessed screen quality. Even with a limited library, we observed common signatures of deleting essential genes as well as context-specific responses based on intrinsic genomic properties of the models. For example, we inferred a previously undescribed relationship between dependence on the ER-golgi transport gene immediate early response 3 interacting protein 1 (IER3IP1) and oxidative stress, demonstrating the potential of integrated Perturb-seq for hypothesis generation. Conclusions We established a framework for building a comprehensive map of post-perturbational transcriptional phenotypes using parallel Perturb-seq experiments across multiple cell lines. We demonstrated that integrated Perturb-seq experiments spanning diverse contexts enable hypotheses about gene function specific to tissue types or cancer subtypes - suggesting large-scale, genome-wide datasets would offer invaluable insight into the highly context-dependent nature of cancer biology.

cancer biology↗

bioRxiv2026

Comprehensive Lineage Tracing Maps the Landscape of Cell Fate Decisions in Mouse Embryogenesis

A comprehensive cell fate map of mammalian embryogenesis has remained out of reach due to the scale, cellular diversity, and non-deterministic nature of development in utero. Here, we use PEtracer to continuously install heritable genetic marks as cells divide, reconstructing lineage trees that resolve [~]75% of cell divisions across >1.5 million cells from 16 mouse embryos collected at half-day intervals from E7.5-E10.0. We pair these trees with deep transcriptional profiling to chart the landscape of cell fate decisions during gastrulation and early organogenesis. Using these data, we quantify cell fate biases, restriction timing, progenitor pool sizes, and lineage relationships across the embryo, revealing strikingly reproducible lineage architecture across replicate embryos despite the regulative flexibility of mammalian development. We further show how lineage, spatial position, and signaling jointly determine fate outcomes and timing, with their relative influence varying by tissue. This dataset provides a quantitative framework for understanding cell fate specification and a lineage-resolved reference for generating and contextualizing developmental hypotheses at organismal scale.

developmental biology↗

bioRxiv2025

Atlas of Lysosomal Aging Reveals a Molecular Clock of Storage Disorder-Associated Metabolites

Lysosomal dysfunction is a well-recognized feature of aging, yet its systematic molecular investigation remains limited. Here, we employ a suite of tools for rapid lysosomal isolation to construct a multi-tissue atlas of the metabolite changes that murine lysosomes undergo during aging. Aged lysosomes in brain, heart, muscle and adipose accumulate glycerophosphodiesters and cystine, metabolites that are causally linked to juvenile lysosomal storage disorders like Batten disease. Levels of these metabolites increase linearly with age, preceding organismal decline. Caloric restriction, a lifespan-extending intervention, mitigates these changes in the heart but not the brain. Our findings link lysosomal storage disorders to aging-related dysfunction, uncover a metabolic lysosomal "aging clock," and open avenues for the mechanistic investigation of how lysosomal functions deteriorate during aging and in age-associated diseases. One-Sentence SummaryAging in mice is tracked by a lysosomal "clock", where glycerophosphodiesters and cystine - metabolites causally linked to juvenile lysosomal storage disorders - gradually accumulate in lysosomes of the brain, heart, skeletal muscle and adipose tissue.

cell biology↗

bioRxiv2025

High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer

Charting the spatiotemporal dynamics of cell fate determination in development and disease is a long-standing objective in biology. Here we present the design, development, and extensive validation of PEtracer, a prime editing-based, evolving lineage tracing technology compatible with both single-cell sequencing and multimodal imaging methodologies to jointly profile cell state and lineage in dissociated cells or while preserving cellular context in tissues with high spatial resolution. Using PEtracer coupled with MERFISH spatial transcriptomic profiling in a syngeneic mouse model of tumor metastasis, we reconstruct the growth of individually-seeded tumors in vivo and uncover distinct modules of cell-intrinsic and cell-extrinsic factors that coordinate tumor growth. More generally, PEtracer enables systematic characterization of cell state and lineage relationships in intact tissues over biologically-relevant temporal and spatial scales.

molecular biology↗

bioRxiv2024

Spatiotemporal lineage tracing reveals the dynamic spatial architecture of tumor growth and metastasis

Tumour progression is driven by dynamic interactions between cancer cells and their surrounding microenvironment. Investigating the spatiotemporal evolution of tumours can provide crucial insights into how intrinsic changes within cancer cells and extrinsic alterations in the microenvironment cooperate to drive different stages of tumour progression. Here, we integrate high-resolution spatial transcriptomics and evolving lineage tracing technologies to elucidate how tumour expansion, plasticity, and metastasis co-evolve with microenvironmental remodelling in a Kras;p53-driven mouse model of lung adenocarcinoma. We find that rapid subclonal expansion contributes to a hypoxic, immunosuppressive, and fibrotic microenvironment that is associated with the emergence of pro-metastatic cancer cell states. Furthermore, metastases arise from spatially-confined subclones of primary tumours and remodel the distant metastatic niche into a fibrotic, collagen-rich microenvironment. Together, we present a comprehensive dataset integrating spatial assays and lineage tracing to elucidate how sequential changes in cancer cell state and microenvironmental structures cooperate to promote tumour progression.

cancer biology↗

bioRxiv2020

Phosphate dysregulation via the XPR1:KIDINS220 protein complex is a therapeutic vulnerability in ovarian cancer

Clinical outcomes for patients with ovarian and uterine cancers have not improved greatly in the past twenty years. To identify ovarian and uterine cancer vulnerabilities, we analyzed genome-scale CRISPR/ Cas9 loss-of-function screens across 739 human cancer cell lines. We found that many ovarian cancer cell lines overexpress the phosphate importer SLC34A2, which renders them sensitive to loss of the phosphate exporter XPR1. We extensively validated the XPR1 vulnerability in cancer cell lines and found that the XPR1 dependency was retained in vivo. Overexpression of SLC34A2 is frequently observed in tumor samples and is regulated by PAX8 -a transcription factor required for ovarian cancer survival. XPR1 overexpression and copy number amplifications are also frequently observed. Mechanistically, SLC34A2 overexpression and impaired phosphate efflux leads to the accumulation of intracellular phosphate and cell death. We further show that proper localization and phosphate efflux by XPR1 requires a novel binding partner, KIDINS220. Loss of either XPR1 or KIDINS220 results in acidic vacuolar structures which precede cell death. These data point to the XPR1:KIDINS220 complex - and phosphate dysregulation more broadly -as a therapeutic vulnerability in ovarian cancer.

cancer biology↗