Biology subjects

Leach, S. D.

Publications and source records attributed to Leach, S. D..

7 recordsLinked to original sources

bioRxiv2026

A Genetically Engineered Human Organoid Model Reveals Distinct Genetic and Epigenetic Barriers of Lineage Plasticity in Early PDAC Transformation

The lack of accurate, human-based models recapitulating early-stage pancreatic ductal adenocarcinoma (PDAC) has hindered therapeutic development. Using pluripotent stem cell-derived pancreatic progenitor organoids, we established a human PDAC model that faithfully reproduces the genetic, epigenetic, and transcriptomic trajectory of tumor initiation and progression in vitro, validated against clinical datasets and histopathology. We demonstrate that CDKN2A loss, nearly universal in patients but dispensable in mouse models, is essential for neoplastic transformation when combined with KRAS and TP53 mutations, while SMAD4 loss promotes tumor progression. Multi-omics profiling reveals epigenetic repression of pancreatic lineage program during PDAC initiation, alongside oncogenic AP-1-driven chromatin remodeling. Notably, we identify TET1 suppression as a mechanistic link between oncogenic ERK signaling and the hypermethylation and silencing of essential pancreatic transcription factors. This model captures the genetic and epigenetic determinants of human PDAC, reveals antagonism between oncogenic and lineage restriction programs, and supports TET-based lineage restoration as a promising early intervention strategy for high-risk individuals.

cancer biology↗

bioRxiv2025

Molecular dynamics driving phenotypic divergence among KRAS mutants in pancreatic tumorigenesis

Inflammation in the pancreas drives acinar-to-ductal metaplasia (ADM), a progenitor-like state that can be hijacked by mutant Kras in the formation of pancreatic cancer (PDAC). How these cell fate decisions vary according to KRAS mutation remains poorly understood. To define mutation-specific lineage reversion and tumor initiation, we implement novel Ptf1a-TdTomato mice and multiple KRAS mutants across an array of genetic, pharmacologic, and inflammatory perturbations in vivo. Whereas KRASG12D co-opts injury to enable lineage reversion, enhancer reprogramming, and tumor initiation, KRASG12R/V can initiate but not sustain dedifferentiated and neoplastic transcriptional and epigenetic programs. We find the KRASG12R/V defects consist of a failure to invoke robust EGFR signaling and activate Rac1/Vav1, with constitutive Akt activation in vivo sufficient to rescue the tumorigenic potential of KRASG12R. As the marked heterogeneity among KRAS variants begins early in tumorigenesis, these data are crucial to understanding mutation-specific oncogenic trajectories and directing the implementation of KRAS-directed therapeutics. SIGNIFICANCEDefining how KRAS mutants drive distinct outcomes in human pancreatic cancer is critical for developing allele-specific therapeutic approaches. This study unveils a hierarchy among KRASG12D, KRASG12V, and KRASG12R to drive tumor initiation, owing to heterogeneous activation of EGFR, PI3K/AKT, and RAC1 signaling, thus revealing mutation-specific evolutionary paths in pancreatic tumorigenesis.

cancer biology↗

bioRxiv2024

A common set of structurally distinct endogenous retroviruses predict survival in multiple human tumor types

Accumulating evidence suggests that viral mimicry induction in cancer cells through the expression of human endogenous retroviral elements (ERVs) enhances tumor immunogenicity and improves response to immunotherapy. However, the characterization of ERV expression across multiple tumor types, their clinical relevance, and their role in tumor immunity remain limited. Here, we assessed the prognostic and immune-related consequences of ERV expression across 8 different tumor types from The Cancer Genome Atlas (TCGA). We applied a recently developed tool, Telescope, to quantify the expression of 14,968 ERVs in bulk tumor RNA-sequencing data. Approximately 15-22% of Telescopes ERVs (navg = 2,736) were expressed in each tumor cohort. We identified both tissue-specific and commonly expressed ERVs across cohorts. Over 50% of tissue-specific ERVs were ubiquitously expressed (n = 1,709) across all 8 tumor types. Using patient clinical data, we identified a subset of 94 ERVs whose expression levels were significantly associated with overall survival, of which 42 were favorably prognostic. Prognostic ERVs displayed unique structural characteristics, including more frequent inverted repeats and more stable secondary structures. Patients were classified based on ERV expression, allowing identification of patient cohorts with greater than 6-fold differences in overall survival. We also found that expression of positively prognostic ERVs was associated with enrichment for selected anti-tumor immune response gene expression signatures. This analysis extends previous results identifying patterns of ERV expression in bulk tumor RNA-seq datasets, providing further insight into the role of ERVs in tumor clinicopathology and immunogenicity.

cancer biology↗

bioRxiv2023

Analysis of the Distal Urinary Tract in Larval and Adult Zebrafish Reveals Unrecognized Homology to the Human System

Little is known about the distal excretory component of the urinary tract in Danio rerio (zebrafish). This component is affected by many human diseases and disorders of development. Here, we undertook multi-level analyses to determine the structure and composition of the distal urinary tract in the zebrafish. In silico searches identified uroplakin 1a, 2-like and 3-like genes in the zebrafish genome (orthologues to genes that encode proteins that characterise the urothelium in humans). In situ hybridization demonstrated uroplakin-1a expression in the zebrafish pronephros and cloaca from 96 hours post-fertilisation. H&E sectioning of adult zebrafish demonstrated two mesonephric ducts uniting into a urinary bladder which leads to a distinct urethral opening. Immunohistochemistry identified Uroplakin 1a and 2 expression within the urothelial luminal surface and Gata3 expression in cell layers that match human urothelial expression. Fluorescent dye injections demonstrated urinary bladder function, including urine storage, intermittent micturition, and a urethral orifice separate from the larger anal canal and rectum. Our findings reveal homology between the urinary tracts of zebrafish and humans and offer the former as a model system to study disease. Summary StatementThe excretory components of the distal urinary tract in larval and adult zebrafish have been incompletely evaluated. Here, we demonstrate close homology in urinary tract anatomy between zebrafish and human, including the presence of a distinct adult urinary bladder capable of periodic micturition

evolutionary biology↗

bioRxiv2021

Pancreatic cancer prognosis is predicted by a novel ATAC-array technology for assessing chromatin accessibility

We investigated tumor-cell-intrinsic chromatin accessibility patterns of pancreatic ductal adenocarcinoma (PDAC) by ATAC-seq on EpCAM+ PDAC malignant epithelial cells, sorted from 54 freshly resected human tumors, and discovered a signature of 1092 chromatin loci displaying differential accessibility between patients with disease free survival (DFS) < 1 year and patients with DFS > 1 year. Analyzing transcription factor (TF) binding motifs within these loci, we identified two TFs (ZKSCAN1 and HNF1b) displaying differential nuclear localization between patients with short vs. long DFS. We further developed a novel chromatin accessibility microarray methodology termed "ATAC-Array", an easy-to-use platform obviating the time and cost of next generation sequencing. Applying this novel methodology to the original ATAC-seq libraries as well as independent libraries generated from patient-derived organoids, we validated ATAC-array technology in both the original ATAC-Seq cohort as well as in an independent validation cohort. We conclude that PDAC prognosis can be predicted by ATAC-array, which represents a novel, lowcost, clinically feasible technology for assessing chromatin accessibility profiles.

cancer biology↗

bioRxiv2020

The origins and consequences of UPF1 variants in pancreatic adenosquamous carcinoma

Pancreatic adenosquamous carcinoma (PASC) is a rare and aggressive subtype of pancreatic cancer whose mutational origins are poorly understood. An early study reported somatic mutations in UPF1, which encodes a core component of the nonsense-mediated mRNA decay (NMD) pathway, as a common signature of PASC, but subsequent studies did not observe these lesions in other PASC cohorts. The corresponding controversy about whether UPF1 mutations are important contributors to PASC has been exacerbated by a paucity of functional studies of these lesions. Here, we systematically assessed the potential roles of UPF1 mutations in PASC. We modeled two reported UPF1 mutations to find no consistent effects on pancreatic cancer growth, acquisition of adenosquamous features, UPF1 splicing, UPF1 protein levels, or NMD efficiency. We subsequently discovered that ~40% of UPF1 mutations reportedly present in PASCs are identical to standing genetic variation in the human population, suggesting that they are likely non-pathogenic inherited variation rather than pathogenic mutations. Our data suggest that UPF1 is not a common functional driver of PASC and motivate further attempts to identify unique genetic features defining these malignancies.

cancer biology↗

bioRxiv2019

Tumor microtubes connect pancreatic cancer cells in an Arp2/3 complex-dependent manner

Actin-based tubular connections between cells have been observed in many cell types. Termed "tunneling nanotubes (TNTs)", "membrane nanotubes", "tumor microtubes (TMTs)", or "cytonemes", these protrusions interconnect cells in dynamic networks. Structural features in these protrusions vary between cellular systems, including tubule diameter and presence of microtubules. We find tubular protrusions, which we classify as TMTs, in a pancreatic cancer cell line, DHPC-018. TMTs are present in DHPC-018-derived tumors in mice, as well as in a mouse model of pancreatic cancer and a sub-set of primary human tumors. DHPC-018 TMTs have heterogeneous diameter (0.39 - 5.85 m, median 1.92 m) and contain actin filaments, microtubules, and cytokeratin 19-based intermediate filaments. The actin filaments are cortical within the protrusion, as opposed to TNTs, in which filaments run down the center of the tube. TMTs are dynamic in length, but are long-lived (median > 60 min). Inhibition of actin polymerization, but not microtubules, results in TMT loss. A second class of tubular protrusion, which we term cell-substrate protrusion (CSP), has similar width range and cytoskeletal features but make contact with the substratum as opposed to another cell. Similar to previous work on TNTs, we find two assembly mechanisms for TMTs, which we term "pull-away" and "search-and-capture". Inhibition of the Arp2/3 complex, an actin assembly factor, inhibits TMT assembly by both mechanisms. This work demonstrates that the actin architecture of TMTs is fundamentally different from that of TNTs, as well as demonstrating the role of Arp2/3 complex on TMT assembly.

cell biology↗