Biology subjects

Green, T. D.

Publications and source records attributed to Green, T. D..

6 recordsLinked to original sources

bioRxiv2025

Identifying tissue states by spatial protein patterns related to chemotherapy response in triple-negative breast cancer

Triple-negative breast cancer (TNBC) is an aggressive malignancy with limited targeted therapies and variable responses to conventional chemotherapy, influenced by intratumoral heterogeneity and complex tumor microenvironment (TME) interactions. Understanding spatiotemporal cellular interplay and tissue organization is crucial for advancing tumor biology and improving patient stratification. Spatially resolved proteomics, such as Imaging Mass Cytometry (IMC), offers a powerful approach to dissect the TME. We present an end-to-end computational pipeline for robust quantitative analysis of large-scale IMC datasets, addressing the challenge of batch effects through image-level contrast adjustment. Applying this framework to 813 tissue regions encompassing over 4 million cells from 63 TNBC patients, we revealed distinct spatial arrangements of cell types between chemotherapy responders and non-responders. Non-responders showed reduced cytotoxic T-cell infiltration into tumor regions and increased spatial co-localization between fibroblasts and macrophages, a pattern that persisted and intensified after chemotherapy treatment. To integrate these complex spatial-molecular relationships, we used graph neural networks (GNNs) to predict treatment response from pre-treatment samples with AUROC=0.71. Interpretability analysis identified B7H4, CD11b, CD366, and FOXP3 as the most predictive protein markers, with fibroblasts, cancer cells, and CD8+ T cells being the most informative cell types. This study introduces a scalable analytical framework for spatial proteomics with interpretable predictions, suggesting features of tissue state that could guide treatment decisions in TNBC and further our understanding of the spatial determinants of therapeutic response.

cancer biology↗

bioRxiv2025

Deletion of Murine Endothelial Bag3 Alters the Cellular Proteome Among Organs of Origin

BAG3 (Bcl-2 associated athanogene 3) is a multifunctional protein with pleiotropic effects in multiple cell types. Despite our knowledge of its role in cardiovascular disease, its specific role in endothelial cells (ECs) is unknown. The purpose of this study was to identify differences in the EC proteome of multiple tissues before and after cell specific deletion of Bag3. We hypothesized that BAG3 loss would uniquely alter the baseline proteome landscape of ECs in each tissue. Cdh5(PAC)-CreERT2;Bag3f/f mice received tamoxifen (KO; n=18) or vehicle (WT; n=18) and tissues (brain, heart, lung, and peripheral skeletal muscle-skm) were collected for FACS sorting of ECs from equal numbers of male and female mice at >22 weeks of age, followed by LC-MS/MS label-free proteomics. Initial comparisons of the WT proteomes between tissues revealed differential abundance of EC proteins (p<0.05), including: 379 brain v heart; 325 brain v lung; 501 brain v skm; 354 heart v lung; 107 heart v skm; and 442 lung v skm. Additionally, the EC mitochondrial proteome was unique to each tissue of origin, with significantly (p<0.05) higher proportions dedicated to complexes I, III, IV and V, in heart compared to the other tissues. KO demonstrated the largest effect on skm ECs, increasing 30 proteins (Mybpc2 L2FC=4.81; PFKM L2FC=3.02) and decreasing 65 (CDC42 L2FC=-2.44; Prpf8 L2FC=-2.24). Overall, these results demonstrate that the EC proteome of different tissues is unique and that the loss of BAG3 in these cells differentially alters a small proportion of the EC specific proteome.

physiology↗

bioRxiv2025

The MEK inhibitor trametinib incurs mitochondrial injury and induces innate immune responses in the mouse heart

Trametinib (Trm) is a highly selective MEK inhibitor that potently and persistently abrogates ERK1/2 activation. Trm initially was used to treat BRAF V600E-mutated melanoma but its FDA-approved indications are expanding rapidly. Trm generally is well tolerated but it can cause dose-limiting cardiomyopathy and heart failure. Here we characterize a mouse model of Trm cardiotoxicity using complementary in vitro approaches to show that Trm induces mitochondrial dysfunction in cardiomyocytes and some cancer cell types. In vivo, Trm caused contractile dysfunction within 3 days and heart failure within 2 weeks. High resolution respirometry using isolated cardiac mitochondria revealed that Trm compromises oxidative metabolism, in part through blunted activity of Electron Transport System Complexes. Trm-mediated mitochondrial injury led to the release of mitochondrial Damage-Associated Molecular Patterns including mitochondrial DNA in both mice and humans, triggering activation of canonical innate immune pathways including cGAS-STING. In multiple rodent and human cardiomyocyte platforms, Trm diminished mitochondrial respiratory capacity at nanomolar concentrations but this lesion was reversed by expression of a phosphomimetic STAT3-S727 construct. We also found that Trm induced mitochondrial dysfunction in some but not all cancer cell lines, identifying a previously unrecognized effect that could contribute to Trms anti-cancer efficacy.

physiology↗

bioRxiv2024

Mitochondria inside acute myeloid leukemia cells hydrolyze ATP to resist chemotherapy

Despite early optimism, therapeutics targeting oxidative phosphorylation (OxPhos) have faced clinical setbacks, stemming from their inability to distinguish healthy from cancerous mitochondria. Herein, we describe an actionable bioenergetic mechanism unique to cancerous mitochondria inside acute myeloid leukemia (AML) cells. Unlike healthy cells which couple respiration to the synthesis of ATP, AML mitochondria were discovered to support inner membrane polarization by consuming ATP. Because matrix ATP consumption allows cells to survive bioenergetic stress, we hypothesized that AML cells may resist cell death induced by OxPhos damaging chemotherapy by reversing the ATP synthase reaction. In support of this, targeted inhibition of BCL-2 with venetoclax abolished OxPhos flux without impacting mitochondrial membrane potential. In surviving AML cells, sustained polarization of the mitochondrial inner membrane was dependent on matrix ATP consumption. Mitochondrial ATP consumption was further enhanced in AML cells made refractory to venetoclax, consequential to downregulations in both the proton-pumping respiratory complexes, as well as the endogenous F1-ATPase inhibitor ATP5IF1. In treatment-naive AML, ATP5IF1 knockdown was sufficient to drive venetoclax resistance, while ATP5IF1 overexpression impaired F1-ATPase activity and heightened sensitivity to venetoclax. Collectively, our data identify matrix ATP consumption as a cancer-cell intrinsic bioenergetic vulnerability actionable in the context of mitochondrial damaging chemotherapy.

cancer biology↗

bioRxiv2022

scPerturb: Information Resource for Harmonized Single-Cell Perturbation Data

Recent biotechnological advances led to growing numbers of single-cell perturbation studies, which reveal molecular and phenotypic responses to large numbers of perturbations. However, analysis across diverse datasets is typically hampered by differences in format, naming conventions, and data filtering. In order to facilitate development and benchmarking of computational methods in systems biology, we collect a set of 44 publicly available single-cell perturbation-response datasets with molecular readouts, including transcriptomics, proteomics and epigenomics. We apply uniform pre-processing and quality control pipelines and harmonize feature annotations. The resulting information resource enables efficient development and testing of computational analysis methods, and facilitates direct comparison and integration across datasets. In addition, we introduce E-statistics for perturbation effect quantification and significance testing, and demonstrate E-distance as a general distance measure for single cell data. Using these datasets, we illustrate the application of E-statistics for quantifying perturbation similarity and efficacy. The data and a package for computing E-statistics is publicly available at scperturb.org. This work provides an information resource and guide for researchers working with single-cell perturbation data, highlights conceptual considerations for new experiments, and makes concrete recommendations for optimal cell counts and read depth.

systems biology↗

bioRxiv2019

Effects of fasting induced carbohydrate depletion on murine ischemic skeletal muscle function.

Stored muscle carbohydrate supply and energetic efficiency constrain muscle functional capacity during exercise and are influenced by common physiological variables (e.g. age, diet, and physical activity level). Whether these constraints affect overall functional capacity or the timing of muscle energetic failure during acute ischemia is not known. We interrogated skeletal muscle contractile properties in two anatomically distinct hindlimb muscles that have well characterized differences in energetic efficiency (locomotory-extensor digitorum longus (EDL) and postural-soleus muscles) under conditions of reduced carbohydrate supply. 180 mins of acute ischemia resulted in complete energetic failure in all muscles tested, indicated by: loss of force production, substantial reductions in total adenosine nucleotide pool intermediates, and increased adenosine nucleotide degradation product - inosine monophosphate (IMP). These changes occurred in the absence of apparent myofiber structural damage assessed histologically by both transverse section and whole mount. Restriction of the available intracellular carbohydrate pool by fasting (~50% decrease in skeletal muscle) did not significantly alter the timing to muscle functional impairment or affect the overall force/work capacities of either muscle type. Fasting did cause rapid development of passive tension in both muscle types, which may have implications for optimal timing of reperfusion or administration of precision therapeutics.

physiology↗