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Biology subjects

Doherty, S.

Publications and source records attributed to Doherty, S..

7 recordsLinked to original sources
bioRxiv2025

Investigation of region-specific effects of pepsin-digested decellularized meniscus on human adipose-derived stromal cells within alginate hydrogels

Meniscus tears are one of the most common musculoskeletal injuries, but treatment options remain limited. The meniscus can be divided into distinct inner and outer regions based on differences in the tissue structure and composition. Recognizing that the extracellular matrix (ECM) provides cell-instructive cues that can direct cell differentiation, the current study investigated the effects of incorporating region-specific ECM derived from decellularized meniscus on the viability, growth, and lineage-specific differentiation of human adipose-derived stromal cells (ASCs) encapsulated in alginate beads. The first phase of research focused on validating a novel decellularization protocol for porcine meniscus, which demonstrated the effective removal of cellular content while preserving key ECM constituents including glycosaminoglycans (GAGs) in both the inner and outer meniscus regions. Subsequently, the decellularized inner meniscus (DIM) and decellularized outer meniscus (DOM) were digested with pepsin and combined with a propriety alginate formulation to enable rapid cell encapsulation under mild conditions. Viability staining confirmed that encapsulated human ASCs remained highly viable over 28 days in culture in proliferation or chondrogenic differentiation media. Under both media conditions, the ASC density was significantly higher in the alginate beads incorporating DIM or DOM as compared to alginate alone controls at 28 days. In addition, gene expression analysis and immunofluorescence staining supported that the incorporation of the pepsin-digested ECM within the alginate enhanced fibrochondrogenic marker expression in the samples cultured in chondrogenic differentiation medium. Qualitatively, more intense staining for collagen types I and II were observed within the beads incorporating DOM as compared to DIM, supporting that the formulations had varying effects. Overall, these studies provide new insight supporting that region-specific meniscus ECM can be harnessed to direct cell phenotype and function towards the goal of developing tissue-specific bioinks for tissue-engineering applications.

bioengineering↗
bioRxiv2025

In vivo screening reveals cell-intrinsic mediators of solid tumor resistance to CAR T cell-therapy

Chimeric antigen receptor (CAR) T cell therapy has transformed the treatment of hematologic cancers, but has shown limited efficacy in solid tumors, including pancreatic ductal adenocarcinoma (PDAC). The cellular and molecular factors that influence CAR T cell therapy response remain largely unknown. By integrating modular in vivo CRISPR screens with single cell genomics and immunocompetent orthotopic models of PDAC, we uncover oxidative and proteotoxic stress pathways as previously unknown tumor-intrinsic modulators of CAR T cell therapy response. Disruption of stress-regulatory genes, particularly Keap1 and Slc33a1, sensitizes PDAC tumors to CAR T cell killing in vivo. Mechanistically, hyperactivation of the Nrf2 pathway by genetic ablation of the Keap1 tumor suppressor or endogenous engineering of a clinically observed Keap1 mutation enhances tumor susceptibility to CAR T cell therapy. Thus, tumor-intrinsic molecular stress phenotypes accompanying malignant tumor progression can induce unexpected cell state-specific vulnerabilities to cell-based immunotherapies. These findings provide a mechanistic molecular foundation to improve the efficacy of CAR T cell therapy in solid malignancies and to better stratify cancer patients by tumor genotype. Statement of significanceCAR T cell therapy remains an unsolved challenge for pancreatic cancer. Factors that influence CAR-T cell therapy response remain largely unknown, in part due to lack of robust and scalable experimental models. By integrating in vivo genetic screens with single cell genomics in an orthotopic, immunocompetent model of pancreatic cancer, we uncover cell-intrinsic stress states as key regulators of CAR T cell response.

cancer biology↗
bioRxiv2025

The dispersal of domestic cats from Northern Africa and their introduction to Europe over the last two millennia

The domestic cat (Felis catus) descends from the African wildcat subspecies Felis lybica lybica. Its global distribution alongside humans testifies to its successful adaptation to anthropogenic environments. Uncertainty remains regarding whether domestic cats originated in the Levant, Egypt or elsewhere in its natural range, and on the timing and circumstances of their dispersal into Europe. By analysing 87 ancient and modern cat genomes, we demonstrate that domestic cats did not spread to Europe with Neolithic farmers, as previously thought. Conversely, our results suggest that they were introduced to Europe over the last 2,000 years, most likely from North Africa. We also demonstrate that a separate earlier (1st millennium BCE) introduction of wildcats from Northwest Africa originated the present-day wild population in Sardinia.

evolutionary biology↗
bioRxiv2025

Leopard Cats Occupied Human Settlements in China for 3,500 years before the Arrival of Domestic cats in 600-900 CE around the Tang Dynasty

The earliest cats in human settlements in China were not domestic cats (Felis catus), but native leopard cats (Prionailurus bengalensis). To trace when and how domestic cats arrived in East Asia, we analyzed 22 feline bones from 14 sites across China spanning 5,000 years. Nuclear and mitochondrial genomes revealed that leopard cats began occupying anthropogenic scenes around 5,400 years ago and last appeared in 150 CE. Following several centuries gap of archeological feline remains, the first known domestic cat (706-883 CE) in China was identified in Shaanxi during the Tang Dynasty. Genomic analysis suggested a white or partially white coat and a link to a contemporaneous domestic cat from Kazakhstan, indicating a likely dispersal route via the Silk Road. The two felids once independently occupied ancient anthropogenic environments in China but followed divergent paths and reached different destinations in human-animal interactions.

evolutionary biology↗
bioRxiv2024

Absence of c-Maf and IL-10 enables Type I IFN enhancement of innate responses to low-dose LPS in alveolar macrophages

Alveolar macrophages (AMs) are lower-airway resident myeloid cells and are among the first to respond to inhaled pathogens. Here, we interrogate AM innate sensing to Pathogen Associated Molecular Patterns (PAMPs) and determine AMs have decreased responses to low- dose LPS compared to other macrophages, as measured by TNF, IL-6, Ifnb, and Ifit3. We find the reduced response to low-dose LPS correlates with minimal TLR4 and CD14 surface expression, despite sufficient internal expression of TLR4. Additionally, we find that AMs do not produce IL-10 in response to a variety of PAMPs due to low expression of transcription factor c- Maf and that lack of IL-10 production contributes to an enhancement of pro-inflammatory responses by Type I IFN. Our findings demonstrate that AMs have cell-intrinsic dampened responses to LPS, which is enhanced by type I IFN exposure. These data implicate conditions where AMs may have reduced or enhanced sentinel responses to bacterial infections. HIGHLIGHTSO_LIAlveolar macrophages (AMs) do not produce TNF or IL-6 in response to low-dose LPS due to minimal surface expression of TLR4 and CD14 C_LIO_LILack of AM IL-10 production is dependent on low c-Maf expression C_LIO_LIExogenous c-Maf expression increases AM IL-10 production C_LIO_LIIFN{beta} enhances AM TNF and IL-6 responses to low-dose LPS and this is dependent on a lack of IL-10 C_LI

immunology↗
bioRxiv2022

Predicting predator-prey interactions in terrestrial endotherms using random forest

Species interactions play a fundamental role in ecosystems. However, few ecological communities have complete data describing such interactions, which is an obstacle to understanding how ecosystems function and respond to perturbations. Because it is often impractical to collect empirical data for all interactions in a community, various methods have been developed to infer interactions. Machine learning is increasingly being used for making interaction predictions, with random forest being one of the most frequently used of these methods. However, performance of random forest in inferring predator-prey interactions in terrestrial vertebrates and its sensitivity to training data quality remain untested. We examined predator-prey interactions in two diverse, primarily terrestrial vertebrate classes: birds and mammals. Combining data from a global interaction dataset and a specific community (Simpson Desert, Australia), we tested how well random forest predicted predator-prey interactions for mammals and birds using species ecomorphological and phylogenetic traits. We also tested how variation in training data quality--manipulated by removing records and switching interaction records to non-interactions--affected model performance. We found that random forest could predict predator-prey interactions for birds and mammals using ecomorphological or phylogenetic traits, correctly predicting up to 88% and 67% of interactions and non-interactions in the global and community-specific datasets, respectively. These predictions were accurate even when there were no records in the training data for focal species. In contrast, false non-interactions for focal predators in training data strongly degraded model performance. Our results demonstrate that random forest can identify predator-prey interactions for birds and mammals that have few or no interaction records. Furthermore, our study provides guidance on how to prepare training data to optimise machine-learning classifiers for predicting species interactions, which could help ecologists (i) address knowledge gaps and explore network-related questions in data-poor situations, and (ii) predict interactions for range-expanding species.

ecology↗