Biology subjects

MacKenzie, T. A.

Publications and source records attributed to MacKenzie, T. A..

4 recordsLinked to original sources

bioRxiv2026

X-SPATIO: An Explanatory Deep Learning Pipeline for the Prediction and Visualization of Spatially Resolved Biomarker Expression in Triple-Negative Breast Cancer

Histopathologic evaluation remains central to cancer diagnosis and treatment planning, yet the molecular programs underlying distinct tissue morphologies are not routinely accessible in clinical workflows. Spatial transcriptomic/proteomic platforms provide region-specific molecular measurements but are limited by cost, throughput, and scalability. Most computational pathology models rely on either bulk tissue-based gene expression or a focused gene/protein expression-panel prediction, thereby obscuring subregion-specific morpho-molecular relationships and limiting spatial interpretation of a wider gene/protein expression network. This limitation is particularly significant in triple-negative breast cancer (TNBC), which exhibits pronounced spatial heterogeneity across tumor, stroma, and immune compartments. We developed X-SPATIO, a spatially compatible computational pipeline designed to directly link hematoxylin and eosin (H&E) morphology with region-matched mRNA and protein expression. The model was trained on H&E-defined regions of interest paired with spatially-resolved transcriptomic and proteomic data obtained from GeoMx Digital Spatial Profiler. Using a multiple-instance learning approach, X-SPATIO captures morpho-molecular associations, generating spatio-morphologic attention maps that indicate predictive tissue regions. X-SPATIO demonstrated strong performance across biologically relevant spatial biomarkers, achieving area under the curve values ranging [0.79, 0.97]. Attention maps revealed spatial patterns consistent with known biology, indicating alignment between learned features and tissue organization. By integrating spatial molecular ground truth with routine histopathology, X-SPATIO enables cost-effective inference of spatial biomarker expression and establishes a foundation for biologically grounded discovery and precision oncology in TNBC.

pathology↗

bioRxiv2026

Differences in T-cell counts and neighborhood patterns in human colorectal adenomas and sessile serrated lesions

BackgroundT-cell responses influence recurrence and survival in colorectal cancer. T-cell subset distributions vary by molecular phenotype and location, shaping cytotoxic or immune-cold tumor immune microenvironments (TiMEs). However, the T-cell contexture and their spatial proximities within preinvasive lesions are not well characterized. MethodsWe analyzed sessile serrated lesions (SSLs), tubulovillous/villous adenomas (TVs), and tubular adenomas (TAs) from three completed studies (N=120). Whole-slide multiplex immunofluorescence was used to quantify eight T-cell subsets (CD4, CD8, Th1, Th17, Treg, Tc1, Tc17, TcTreg). Counts were compared by histology using a generalized linear mixed model with a negative binomial distribution, including an offset for total cell counts and adjusting for age, sex, anatomic location, and lesion size. Nearest-neighbor (NN) analyses assessed proximities of T-cell pairs across lesion types. ResultsTAs and SSLs had higher CD4 and CD8 T-cell counts compared with TVs (q<0.05). SSLs had lower Th17 counts than TAs (q<0.05) and compared with TVs leaned toward fewer Tregs (q=0.07). NN analysis showed that TVs, compared with SSLs and TAs, had increased Treg clustering. In contrast, TA versus SSL comparisons revealed predominant CD4 clustering with Th17, Th1, and CD8 subsets. ConclusionTVs are characterized by lower T-cell infiltration and a greater tendency for regulatory T-cell clustering, consistent with an immune-cold TiME relative to TAs. SSLs and TAs were both more immune-infiltrated than TVs, but SSLs appeared less inflamed and less dominated by regulatory subsets. In contrast, CD4dominant clustering in TAs suggested stronger helper coordination. Preinvasive lesions therefore demonstrate immune and spatial heterogeneity by lesion types.

pathology↗

bioRxiv2024

Gene expression responses of CF airway epithelial cells exposed to elexacaftor/tezacaftor/ivacaftor (ETI) suggest benefits beyond improved CFTR channel function

The combination of elexacaftor/tezacaftor/ivacaftor (ETI, Trikafta) reverses the primary defect in Cystic Fibrosis (CF) by improving CFTR mediated Cl- and HCO3- secretion by airway epithelial cells (AEC), leading to improved lung function and less frequent exacerbations and hospitalizations. However, studies have shown that CFTR modulators like ivacaftor, a component of ETI, has numerous effects on CF cells beyond improved CFTR channel function. Because little is known about the effect of ETI on CF AEC gene expression we exposed primary human AEC to ETI for 48 hours and interrogated the transcriptome by RNA-seq and qPCR. ETI increased defensin gene expression (DEFB1) an observation consistent with reports of decreased bacterial burden in the lungs of people with CF (pwCF). ETI also decreased MMP10 and MMP12 gene expression, suggesting that ETI may reduce proteolytic induced lung destruction in CF. ETI also reduced the expression of the stress response gene heme oxygenase (HMOX1). qPCR analysis confirmed DEFB1, HMOX1, MMP10 and MMP12 gene expression results observed by RNA-seq. Gene pathway analysis revealed that ETI decreased inflammatory signaling, cellular proliferation and MHC Class II antigen presentation. Collectively, these findings suggest that the clinical observation that ETI reduces lung infections in pwCF is related in part to drug induced increases in DEFB1, and that ETI may reduce lung damage by reducing MMP10 and MMP12 gene expression, which is predicted to reduce matrix metalloprotease activity. Moreover, pathway analysis also identified several genes responsible for the ETI induced reduction in inflammation observed in people with CF. New and NoteworthyGene expression responses by CF AEC exposed to ETI suggest that in addition to improving CFTR channel function, ETI is likely to increase resistance to bacterial infection by increasing levels of beta defensin 1 (hBD-1). ETI may also reduce lung damage by suppressing MMP10, and reduce airway inflammation by repressing proinflammatory cytokine secretion by AEC cells.

pharmacology and toxicology↗

bioRxiv2018

Altered Stool Microbiota of Infants with Cystic Fibrosis Shows Reduction in Genera Associated with Immune Programming

Previous work from our group indicated a connection between the gastrointestinal microbiota of infants and children with cystic fibrosis (CF) and airway disease in this population. Here we examine the stool microbiota of infants with CF and from the general population who did not have CF over the first year of life. CF children had reduced gastrointestinal Bacteroides and Bifidobacterium beginning in infancy, even after adjusting for antibiotic treatment. We also identify several metabolic pathways that are enriched or under represented among the microbial communities in the stool of these young patients with CF as compared to children without CF. In vitro studies demonstrated that exposure of the apical face of a polarized Intestinal cell line to Bacteroides thetaiotaomicron significantly reduced production of IL-8 secreted from both the apical and basolateral face of these cells, suggesting a mechanism whereby changes in the intestinal microflora could impact systemic inflammation. This work further establishes a link between gastrointestinal microbiota, systemic inflammation and airway disease, and presents the opportunity for therapeutic probiotic interventions.\n\nSignificance statementThere is a surprising link between gastrointestinal microbial communities and airway disease progression in CF. Here we show that infants with CF [≤]1 year of age show a distinct stool microbiota compared with children of a comparable age from a general population cohort. We detect associations between stool microbes and airway exacerbation events in the cohort of infants with CF, and in vitro studies provide a possible mechanism for this observation. These data argue that current therapeutics do not establish a healthy-like gastrointestinal microbiota in young patients with CF, and we suggest that interventions that direct the gastrointestinal microbiota closer to a healthy state may provide benefit to these patients.

microbiology↗