Biology subjects

Washington, M.

Publications and source records attributed to Washington, M..

6 recordsLinked to original sources

bioRxiv2026

Genomic Consequences of Altered Flood Regimes: Gene Flow and Adaptation in a Threatened Floodplain Plant

Floodplains are highly dynamic ecotones where species persistence depends on synchrony between natural flow regimes and life-history. Artificial river engineering has profoundly altered these systems by reducing the frequency and magnitude of spring floods while increasing the unpredictability of flood timing and intensity during summer. These hydrological changes have disrupted historical patterns of dispersal, growth, reproduction, and competitive success among floodplain specialists. Effective conservation in these ecosystems therefore requires understanding how human-altered flow regimes have reshaped floodplain specialists' demography, genetic diversity, genetic connectivity, functional variation, and adaptive potential. Here, we address this challenge in Boltonia decurrens, a federally threatened floodplain plant endemic to the Illinois River Valley, by integrating a chromosome-scale reference genome, whole-genome resequencing, and common-garden adaptive trait measurements from 424 individuals across 17 populations. Demographic analyses revealed a severe recent bottleneck and a subsequent rebound. Population structure was clinal with downstream-dominant gene flow, indicating that regional population connectivity predominates over longer-distance gene flow. A subset of populations showed elevated genetic isolation with increased inbreeding and homozygous deleterious burden, revealing a genomic cost of disrupted floodplain connectivity. Common-garden observations and GWAS showed extensive within-population phenotypic and genetic variation in flowering time, flowering stem height, and year of first flowering (1st vs. 2nd year), which are hypothesized to buffer populations and to be selectively maintained under human-altered flow regimes. Finally, landscape-genomic approaches detected a divergent haplotype block separating northern and southern populations, suggesting that adaptive divergence can persist even in a system shaped by recurrent disturbance and ongoing gene flow.

evolutionary biology↗

bioRxiv2026

Spatial atlas highlights contribution of C. difficile in early-stage colorectal cancer

Background and AimsIntratumoral heterogeneity with respect to both host and microbial components has emerged as an important contributor to colorectal cancer (CRC) biology. Although the overall taxonomy and abundance of the CRC tumor microbiome have become well characterized, much less is known about bacterial niches within the tumor microenvironment (TME). Escherichia coli and Fusobacterium nucleatum are highly prevalent and abundant species linked to CRC. Less abundant organisms, like Clostridioides difficile and Enterocloster aldenensis, are emerging as potentially important CRC-associated bacteria. Additionally, many studies are confounded by preoperative oral antibiotics or the inclusion of late-stage cancers, both of which may alter the gut microbiome. To better understand the spatial relationships between bacteria and CRC, we generated a molecular atlas based on surgically resected tissue specimens collected from a unique cohort of early-stage CRC patients in whom oral antibiotics were not administered preoperatively. MethodsFrom 20 CRC specimens, we performed matched histopathological analysis, fluorescence in situ hybridization (FISH), whole exome sequencing (WES), 16S rRNA amplicon bacterial DNA sequencing, codetection by indexing (CODEX) multiplex immunofluorescence, and spatial transcriptomics of 756 regions among the specimens. We used 16S rRNA amplicon sequencing data to design and experimentally validate custom bacterial probes that were applied to the spatial transcriptomics. Human colonic organoids were used to validate the relationship between Clostridioides difficile toxin B (TcdB) and an E-twenty-six family transcription factor, ELF3. ResultsWe identified eight intratumoral bacterial niches consisting of a variety of bacterial species, and each niche was associated with unique tumor features. We further defined tumor gene expression patterns correlating with individual bacterial species and show that C. difficile has a disproportionate impact on the tumor transcriptome given its relatively low abundance. Specifically, TcdB induces nuclear localization of ELF3, increased cytosolic {beta}-catenin protein, and upregulated WNT signaling. ConclusionOur study integrates multi-omics to identify bacterial species with biological and spatial relevance in CRC regardless of abundance. These findings will enable further studies to define diagnostic and therapeutic targets for bacteria-associated CRC.

Cancer Biology↗

bioRxiv2025

Effects of sexual dimorphism and estrous cycle on C. difficile infections prophylaxis in two rodent models

Clostridioides difficile infection (CDI) is responsible for the majority of identifiable hospital-related antibiotic-associated diarrhea. Susceptibility to CDI and severity of disease varies depending on a variety of factors such as aggressive use of broad-spectrum antibiotics, age, and immune status. Epidemiological studies have consistently shown that female patients are more at risk for CDI than their male counterparts. C. difficile is spread by spores which can persist in the environment and in the intestines of patients. Spores do not cause disease but germinate in the antibiotic-altered gut of patients to generate toxin producing vegetative cells. The germination of C. difficile spores is mediated by the composition of bile salts in the gut with taurocholate facilitating germination and chenodeoxycholate inhibiting it.

microbiology↗

bioRxiv2023

Effects of sexual dimorphism and estrous cycle on C. difficile infections in rodent models

Clostridioides difficile infection (CDI) is responsible for the majority of identifiable antibiotic-associated diarrhea. Women are more susceptible to CDI than men. In this study, we show that female mice developed more severe CDI than males. Furthermore, females in estrus developed only mild CDI 1-2 days later, while females in proestrus developed deadly disease. Mirroring the delayed effect of the estrous cycle, pre-infection prolactin levels formed a complex network with immunoglobulins and cytokines that affected early CDI severity one day after challenge. Similarly, pre-infection progesterone and luteinizing hormone formed a network that affected CDI two days after challenge. As expected, immune effectors early in the infection formed a hormone-independent network that concurrently correlated with CDI severity. Interestingly, early infection follicular stimulating hormone levels created a network that affected the CDI recovery phase. In summary, murine sexual hormones affect CDI progression by affecting the immune system both before and during disease progression.

microbiology↗

bioRxiv2017

Somatic inactivating PTPRJ mutations and dysregulated pathways identified in canine melanoma by integrated comparative genomic analysis

Canine malignant melanoma, a significant cause of mortality in domestic dogs, is a powerful comparative model for human melanoma, but little is known about its genetic etiology. We mapped the genomic landscape of canine melanoma through multi-platform analysis of 37 tumors (31 mucosal, 3 acral, 2 cutaneous, and 1 uveal) and 17 matching constitutional samples including long- and short-insert whole genome sequencing, RNA sequencing, array comparative genomic hybridization, single nucleotide polymorphism array, and targeted Sanger sequencing analyses. We identified novel predominantly truncating mutations in the putative tumor suppressor gene PTPRJ in 19% of cases. No BRAF mutations were detected, but activating RAS mutations (24% of cases) occurred in conserved hotspots in all cutaneous and acral and 13% of mucosal subtypes. MDM2 amplifications (24%) and TP53 mutations (19%) were mutually exclusive. Additional low-frequency recurrent alterations were observed amidst low point mutation rates, an absence of ultraviolet light mutational signatures, and an abundance of copy number and structural alterations. Mutations that modulate cell proliferation and cell cycle control were common and highlight therapeutic axes such as MEK and MDM2 inhibition. This mutational landscape resembles that seen in BRAF wild-type and sun-shielded human melanoma subtypes. Overall, these data inform biological comparisons between canine and human melanoma while suggesting actionable targets in both species.\n\nAUTHOR SUMMARYMelanoma, an aggressive cancer arising from transformed melanocytes, commonly occurs in pet dogs. Unlike human melanoma, which most often occurs in sun-exposed cutaneous skin, canine melanoma typically arises in sun-shielded oral mucosa. Clinical features of canine melanoma resemble those of human melanoma, particularly the less common sun-shielded human subtypes. However, whereas the genomic basis of diverse human melanoma subtypes is well understood, canine melanoma genomics remain poorly defined. Similarly, although diverse new treatments for human melanoma based on a biologic disease understanding have recently shown dramatic improvements in outcomes for these patients, treatments for canine melanoma are limited and outcomes remain universally poor. Detailing the genomic basis of canine melanoma thus provides untapped potential for improving the lives of pet dogs while also helping to establish canine melanoma as a comparative model system for informing human melanoma biology and treatment. In order to better define the genomic landscape of canine melanoma, we performed multi-platform characterization of 37 tumors. Our integrated analysis confirms that these tumors commonly contain mutations in canine orthologs of human cancer genes such as RAS, MDM2, and TP53 as well mutational patterns that share important similarities with human melanoma subtypes. We have also found a new putative cancer gene, PTPRJ, frequently mutated in canine melanoma. These data will guide additional biologic and therapeutic studies in canine melanoma while framing the utility of comparative studies of canine and human cancers more broadly.

cancer biology↗

bioRxiv2017

Ponatinib shows potent antitumor activity in small cell carcinoma of the ovary hypercalcemic type (SCCOHT) through multi-kinase inhibition

Structured AbstractPurpose: Subunits of the SWI/SNF chromatin-remodeling complex are tumor suppressors inactivated in [~]20% of all cancers. Yet, few targeted treatments for SWI/SNF-mutant cancers exist. Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare, aggressive ovarian cancer in young women that is universally driven by loss of the SWI/SNF ATPase subunits, SMARCA4 and SMARCA2. Given poor two-year survival rates for these women, a great need exists for effective targeted therapies.\n\nExperimental Design: To identify underlying therapeutic vulnerabilities in SCCOHT, we conducted high-throughput siRNA and drug screens. Complementary proteomics approaches comprehensively profiled kinases inhibited by ponatinib. Ponatinib was tested for efficacy in two PDX models and one cell line xenograft model of SCCOHT.\n\nResults: FGFRs and PDGFRs were overlapping hits between screens and the receptor tyrosine kinase (RTK) family was enriched in the siRNA screen hits. Evaluation of eleven RTK inhibitors in three SCCOHT cell lines identified ponatinib, an inhibitor of multiple RTKs, as the most effective clinically approved agent. Proteomics approaches confirmed inhibition of known targets of ponatinib and more than 20 non-canonical ponatinib targets. Ponatinib also delayed tumor doubling time 4-fold in SCCOHT-1 xenografts and reducing final tumor volumes in two SCCOHT patient-derived xenograft (PDX) models by 58.6% and 42.5%.\n\nConclusion: Ponatinib is an effective agent for SCCOHT in both in vitro and in vivo preclinical models through its inhibition of multiple kinases. Clinical investigation of this FDA-approved oncology drug in SCCOHT is warranted.\n\nAdditional InformationThis work was supported by research funds from the Canadian Cancer Society Research Institute 34 (#703458, D.G.H.), the National Institutes of Health (R01 CA195670-01, B.E.W., D.G.H., and 35 J.M.T., and T32 HL007106-39 to E.M.C), the Terry Fox Research Institute Initiative New Frontiers Program in Cancer (#1021, D.G.H.), the British Columbia Cancer Foundation (D.G.H.), the VGH & UBC Foundation (D.G.H.), the Anne Rita Monahan Foundation (P.R.), the Marsha Rivkin Center for Ovarian Cancer Research (J.M.T.), the Ovarian Cancer Alliance of Arizona (J.M.T.), the Small Cell Ovarian Cancer Foundation (P.R., J.D.L., B.V., and J.M.T.), and philanthropic support to the TGen Foundation (J.M.T.).\n\nCOI disclosure statement: The authors declare no potential conflicts of interest.

cancer biology↗