Biology subjects

Das, S.

Publications and source records attributed to Das, S..

At least 379 records · Page 21Linked to original sources

bioRxiv2019

Rif1 functions in a tissue-specific manner to control replication timing through its PP1-binding motif

Replication initiation in eukaryotic cells occurs asynchronously throughout S phase, yielding early and late replicating regions of the genome, a process known as replication timing (RT). RT changes during development to ensure accurate genome duplication and maintain genome stability. To understand the relative contributions that cell lineage, cell cycle, and replication initiation regulators have on RT, we utilized the powerful developmental systems available in Drosophila melanogaster. We generated and compared RT profiles from mitotic cells of different tissues and from mitotic and endocycling cells of the same tissue. Our results demonstrate that cell lineage has the largest effect on RT, whereas switching from a mitotic to an endoreplicative cell cycle has little to no effect on RT. Additionally, we demonstrate that the RT differences we observed in all cases are largely independent of transcriptional differences. We also employed a genetic approach in these same cell types to understand the relative contribution the eukaryotic RT control factor, Rif1, has on RT control. Our results demonstrate that Rif1 can function in a tissue-specific manner to control RT. Importantly, the Protein Phosphatase 1 (PP1) binding motif of Rif1 is essential for Rif1 to regulate RT. Together, our data support a model in which the RT program is primarily driven by cell lineage and is further refined by Rif1/PP1 to ultimately generate tissue-specific RT programs.

developmental biology↗

bioRxiv2019

Acetobacteraceae in the honey bee gut comprise two distant clades with diverging metabolism and ecological niches

Various bacteria of the family Acetobacteraceae are associated with the gut environment of insects. Honey bees harbor two distinct Acetobacteraceae in their gut, Alpha2.1 and Alpha2.2. While Alpha2.1 seems to be a gut specialist, Alpha2.2 is also found in the diet (e.g. royal jelly), the hypopharyngeal glands, and the larvae of honey bees. Here, we combined amplicon and genome sequencing to better understand functional differences associated with the ecology of Alpha2.1 and Alpha2.2. We find that the two phylotypes are differentially distributed along the worker and queen bee gut. Phylogenetic analysis shows that Alpha2.2 is nested within the acetic acid bacteria and consists of two separate sub-lineages, whereas Alpha2.1 belongs to a basal lineage with an unusual GC content for Acetobacteraceae. Gene content analysis revealed major differences in the central carbon and respiratory metabolism between the two phylotypes. While Alpha2.2 encodes two periplasmic dehydrogenases to carry out oxidative fermentation, Alpha2.1 lacks this capability, but instead harbors a diverse set of cytoplasmic dehydrogenases. These differences are accompanied by the loss of the TCA cycle in Alpha2.2, but not in Alpha2.1. We speculate that Alpha2.2 has specialized for fast-resource utilization through incomplete carbohydrate oxidation, giving it an advantage in sugar-rich environments such as royal jelly. On the contrary, the broader metabolic range of Alpha2.1 may provide an advantage in the worker bee hindgut, where competition with other bacteria and flexibility in resource utilization may be relevant for persistence. Our results show that bacteria belonging to the same family may utilize vastly different strategies to colonize niches associated with the animal gut.

genomics↗

bioRxiv2019

Histone chaperone Nucleophosmin regulates transcription of key genes involved in oral tumorigenesis.

Nucleophosmin (NPM1) is a multifunctional histone chaperone that can activate RNA Polymerase II-driven chromatin transcription. Acetylation of NPM1 by acetyltransferase p300 has been shown to further enhance its transcription activation potential. Moreover, its total and acetylated pools are increased in oral squamous cell carcinoma. However, the role of NPM1 or its acetylated form (AcNPM1) in transcriptional regulation in cells is not fully elucidated. Using ChIP-seq analyses, we show that AcNPM1 co-occupies marks of active transcription at promoters and DNase I hypersensitive sites at enhancers. Moreover, NPM1 interacts with proteins involved in transcription, including RNA Pol II, general transcription factors, mediator subunits, histone acetyltransferase complexes, and chromatin remodelers. Moreover, its histone chaperone also contributes to transcriptional activation. We further show that AcNPM1 regulates key genes required for proliferation, migration and invasion potential of oral cancer cells and knockdown of NPM1 mitigates these processes in cells as well as orthotopic tumors in mice. Collectively, these results establish that AcNPM1 functions as a coactivator and regulates the expression of key genes involved in oral tumorigenesis.

biochemistry↗

bioRxiv2019

Elucidating the regulation of glucose tolerance through the interaction between the reaction product and active site pocket residues of a β-glucosidase from Halothermothrix orenii

{beta}-glucosidase catalyzes the hydrolysis of {beta}-1,4 linkage between two glucose molecules in cello-oligosaccharides and is prone to inhibition by the reaction product glucose. Relieving the glucose inhibition of {beta}-glucosidase is a significant challenge. Towards the goal of understanding how glucose interacts with {beta}-glucosidase, we expressed in Escherichia coli, the Hore_15280 gene encoding a {beta}-glucosidase in Halothermothrix orenii. Our results show that the enzyme is glucose tolerant, and its activity stimulated in the presence of up to 0.5 M glucose. NMR analyses show the unexpected interactions between glucose and the {beta}-glucosidase at lower concentrations of glucose that however does not lead to enzyme inhibition. We identified non-conserved residues at the aglycone-binding and the gatekeeper site and show that increased hydrophobicity at the pocket entrance and a reduction in steric hindrances are critical towards enhanced substrate accessibility and significant improvement in activity. Analysis of structures and in combination with molecular dynamics simulations show that glucose increases the accessibility of the substrate by enhancing the structural flexibility of the active site pocket and may explain the stimulation in specific activity up to 0.5 M glucose. Such novel regulation of {beta}-glucosidase activity by its reaction product may offer novel ways of engineering glucose tolerance.

biochemistry↗

bioRxiv2019

Batch cultivation of non-transgenic males suitable for SIT programs

The field performance of Sterile Insect Technique (SIT) is improved by sex-sorting and releasing only the sterile males. This can be accomplished by resource-intensive separation of males from females by morphology. Alternatively, sex-ratio biasing genetic constructs can be used to selectively kill one sex without the need for manual or automated sorting, but the resulting genetically engineered (GE) control agents would be subject to additional governmental regulation. Here we describe and demonstrate a method for the batch production of non-GE males that is applicable for sex-selective production of males suitable for genetic biocontrol programs. This method could be applied to generate the heterogametic sex (XY, or WZ) in any organism with chromosomal sex determination. We observed up to 100% sex-selection with batch cultures of more than 103 individuals. Using a stringent transgene detection assay, we demonstrate the potential of mass rearing of transgene free males.

synthetic biology↗

bioRxiv2019

Liver X Receptor regulates Th17 and RORγt+ Treg cells by distinct mechanisms

The gastrointestinal microenvironment, dominated by dietary compounds and the commensal bacteria, is a major driver of intestinal CD4+ T helper (Th) cell differentiation. Dietary compounds can be sensed by nuclear receptors (NRs) that consequently exerts pleiotropic effects including immune modulation. However, how NRs regulate distinct intestinal Th subsets remain poorly understood. Here, we found that under homeostatic condition Liver X receptor (LXR), a sensor of cholesterol metabolites, controls ROR{gamma}t+ Treg and Th17 cells in the intestine draining mesenteric lymph node (MLN). Mechanistically, while lack of LXR signaling in CD11c+ myeloid cells led to an increase in ROR{gamma}t+ Treg, modulation of MLN Th17 was independent of LXR signaling in either immune or epithelial cells. Of note, LXR modulated only the Th17 cells, but not ROR{gamma}t+ Treg in the MLN and horizontal transfer of microbiota between LXR-/- and WT mice was sufficient to partially increase the MLN Th17 in WT mice. While LXR deficiency increased the abundance of Ruminococcaceae and Lachnospiraceae bacterial families compared to the WT littermates, microbiota ablation including ablation of SFB was not sufficient to dampen LXR-mediated expansion of MLN Th17. Altogether, our results suggest that LXR modulates ROR{gamma}t+ Treg and Th17 cells in the MLN through distinct mechanisms.

immunology↗

bioRxiv2019

Computational approach to identifying universal macrophage biomarker

Macrophages are a type of white blood cell, of the immune system, that engulfs and digests cellular debris, cancer cells, and anything else that does not have the type of proteins specific to healthy body cells on its surface. Understanding gene expression dynamics in macrophages are crucial for studying human diseases. Recent advances in high-throughput technologies have enabled the collection of immense amounts of biological data. A reliable marker of macrophage is essential to study their function. Traditional approaches use a number of markers that may have tissue specific expression patterns. To identify universal biomarker of macrophage, we used a previously published computational approach called BECC (Boolean Equivalent Correlated Clusters) that was originally used to identify universal cell cycle genes. We performed BECC analysis on a seed gene CD14, a known macrophage marker. FCER1G and TYROBP were among the top candidates which were validated as strong candidates for universal biomarkers for macrophages in human and mouse tissues. To our knowledge, such a finding is first of its kind.\n\nCONTRIBUTIONS TO THE FIELDWe have developed a computational approach to identify universal biomarkers of different entities in a biological system. We applied this approach to study macrophages and identified universal biomarkers of this particular cell type. FCER1G and TYROBP were among the top candidates which were validated as strong candidates for universal biomarkers for macrophages in human and mouse tissues. The expression patterns of TYROBP and FCER1G are found to be more homogeneous compared to currently used biomarkers such as ITGAM, EMR1 (F4/80), and CD68. Further, we demonstrated that this homogeneity extends to all the tissues currently profiled in the public domain in multiple species including human and mouse. FCER1G and TYROBP expression patterns were also found to be extremely specific to macrophages found in various tissues. They are strongly co-expressed together. We believe that these two genes are the most reliable candidates of universal biomarker for macrophages.

immunology↗

bioRxiv2019

\"Viscotaxis\" - Directed Migration of Mesenchymal Stem Cells in Response to Loss Modulus Gradient

Directed cell migration in response to chemical and mechanical gradients plays a crucial role in physiological and pathological conditions. One such mechanical cues that is known to influences cell migration is the gradient of substrate elastic modulus (E). However, the elastic modulus alone cannot fully define the material properties of the cellular microenvironment, which often has both elastic and viscous characteristics. In this study, we investigated the influence of the gradient of viscous nature, as defined by loss modulus, G\", on cell migration. We cultured human mesenchymal stem cells (hMSCs) on a collagen-coated polyacrylamide gel with constant elastic property, as defined by the storage modulus G, but with the gradient of loss modulus G\". We found hMSCs to migrate from high to low loss modulus. We have termed this, thus far unreported, directional cellular migration as \"Viscotaxis\". We have confirmed uniform collagen density and constant storage modulus of the gel by fluorescence microscopy and atomic force microscopy to eliminate the possibilities of haptotaxis and durotaxis. We hypothesize that material creep in the high loss modulus region hinders the building up of the cellular traction, leading to a force asymmetry that drives the observed viscotaxis. To verify our hypothesis, we estimated the cellular traction on gels with high and low loss moduli. We indeed found that cells apply higher traction force on more elastic materials i.e. materials with low loss modulus. On the disruption of actomyosin contractility with myosin inhibitor blebbistatin and ROCK inhibitor Y27632, directional migration was lost. Further, we showed that cells can maintain a stable morphology on a low loss modulus substrate but due to its inability to build up stable cellular traction on a substrate with high loss modulus, the cell spreading remains in a dynamic state. Our findings in this paper highlight the importance of considering the viscous modulus while preparing stiffness-based substrates for the field of tissue engineering.

biophysics↗

bioRxiv2019

The GTEx Consortium atlas of genetic regulatory effects across human tissues

The Genotype-Tissue Expression (GTEx) project was established to characterize genetic effects on the transcriptome across human tissues, and to link these regulatory mechanisms to trait and disease associations. Here, we present analyses of the v8 data, based on 17,382 RNA-sequencing samples from 54 tissues of 948 post-mortem donors. We comprehensively characterize genetic associations for gene expression and splicing in cis and trans, showing that regulatory associations are found for almost all genes, and describe the underlying molecular mechanisms and their contribution to allelic heterogeneity and pleiotropy of complex traits. Leveraging the large diversity of tissues, we provide insights into the tissue-specificity of genetic effects, and show that cell type composition is a key factor in understanding gene regulatory mechanisms in human tissues.

genetics↗

bioRxiv2019

Prevalence of RFC1-Mediated Spinocerebellar Ataxia in a United States Ataxia Cohort

ObjectiveRepeat expansions in RFC1 and DAB1 have recently been identified as causing cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS) and spinocerebellar ataxia 37 (SCA37), respectively. We evaluated the prevalence of these repeat-expansions in an undiagnosed ataxia cohort from the United States.\n\nMethodsA cohort of 596 patients with undiagnosed familial or sporadic cerebellar ataxia were evaluated at a tertiary referral ataxia center and excluded for common genetic causes of cerebellar ataxia. Patients were then screened for the presence of pathogenic repeat expansions in RFC1 (AAGGG) and DAB1 (ATTTC) using fluorescent repeat primed polymerase chain reaction (RP-PCR). Two additional undiagnosed ataxia cohorts from different centers, totaling 96 and 13 patients respectively, were subsequently screened for RFC1 resulting in a combined 705 subjects tested.\n\nResultsIn the initial cohort, 42 samples were identified with one expanded allele in the RFC1 gene (7.0%), and 9 had two expanded alleles (1.5%). For the additional cohorts, we found 12 heterozygous samples (12.5%) and 7 biallelic samples (7.3%) in the larger cohort, and 1 heterozygous sample (7.7%) and 3 biallelic samples (23%) in the second. In total, 19 patients were identified with biallelic repeat expansions in RFC1 (2.7%). Of these 19 patients, 6 (32%) had a clinical diagnosis of CANVAS, 10 had cerebellar ataxia with neuropathy (53%), and 3 had spinocerebellar ataxia (16%). No patients were identified with expansions in the DAB1 gene.\n\nConclusionIn a large undiagnosed ataxia cohort from the United States, biallelic pathogenic repeat expansion in RFC1 was observed in 2.7%. Testing should be strongly considered in ataxia patients, especially those with CANVAS or neuropathy.

genetics↗

bioRxiv2019

Diversity analysis and metagenomic insights into the Antibiotic Resistance and Metal Resistances among Hot Spring Bacteriobiome- insinuating inherent environmental baseline levels of Antibiotic and Metal tolerance

Mechanisms of occurrence and expressions of antibiotic resistance genes (ARGs) in thermophilic bacteria are still unknown owing to limited research and data. The evolution and proliferation of ARGs in the thermophilic bacteria is unclear and needs a comprehensive study. In this research, comparative profiling of antibiotic resistance genes and metal tolerance genes among the thermophilic bacteria has been done by culture-independent functional metagenomic methods. Metagenomic analysis showed the dominance of Proteobacteria, Actinobacteria. Firmicutes and Bacteroidetes in these hot springs. ARG analysis through shotgun gene sequencing was found to be negative in case of thermophilic bacteria. However, few of genes were detected but they were showing maximum similarity with mesophilic bacteria. Concurrently, metal resistance genes were also detected in the metagenome sequence of hot springs. Detection of metal resistance gene and absence of ARGs investigated by whole genome sequencing, in the reference genome sequence of thermophilic Geobacillus also conveyed the same message. This evolutionary selection of metal resistance over antibiotic genes may have been necessary to survive in the geological craters which are full of different metals from earth sediments rather than antibiotics. Furthermore, the selection could be environment driven depending on the susceptibility of ARGs in thermophilic environment as it reduces the chances of horizontal gene transfer. With these findings this article highlights many theories and culminates different scopes to study these aspects in thermophiles.

microbiology↗

bioRxiv2019

Design principles of a minimal auxin response system

Auxin controls numerous growth processes in land plants through a gene expression system that modulates ARF transcription factor activity1-3. Gene duplications in families encoding auxin response components have generated tremendous complexity in most land plants, and neofunctionalization enabled various unique response outputs during development2-4. However, it is unclear what fundamental biochemical principles underlie this complex response system. By studying the minimal system in Marchantia polymorpha, we derive an intuitive and simple model where a single auxin-dependent A-ARF activates gene expression. It is antagonized by an auxin-independent B-ARF that represses common target genes. Expression patterns of both ARF proteins define developmental zones where auxin response is permitted, quantitatively tuned, or prevented. This fundamental design likely represents the ancestral system, and formed the basis for inflated, complex systems.

plant biology↗

bioRxiv2019

Neuronal activity triggers uptake of hematopoietic extracellular vesicles in vivo

Communication with the hematopoietic system is a vital component of regulating brain function in health and disease. Traditionally, the major routes considered for this neuroimmune communication are either by individual molecules such as cytokines carried by blood, by neural transmission, or in more severe pathologies, by entry of peripheral immune cells into the brain. In addition, functional mRNA from peripheral blood can be directly transferred to neurons via extracellular vesicles (EVs) but the parameters that determine their uptake are unknown. We show that transfer of EVs from blood is triggered by neuronal activity in vivo. Importantly, this transfer occurs not only in pathological stimulation but also by neuronal activation caused by the physiological stimulus of novel object recognition. This discovery suggests a continuous role of EVs under pathological conditions as well as during routine cognitive tasks in the healthy brain.

neuroscience↗

bioRxiv2019

Quantitative assessment of fecal contamination in multiple environmental sample types in urban communities in Dhaka, Bangladesh using SaniPath microbial approach

Rapid urbanization has led to a growing sanitation crisis in urban areas of Bangladesh and potential exposure to fecal contamination in the urban environment due to inadequate sanitation and poor fecal sludge management. Limited data are available on environmental fecal contamination associated with different exposure pathways in urban Dhaka. We conducted a cross-sectional study to explore the magnitude of fecal contamination in the environment in low-income, high-income, and transient/floating neighborhoods in urban Dhaka. Ten samples were collected from each of 10 environmental compartments in 10 different neighborhoods (4 low-income, 4 high-income and 2 transient/floating neighborhoods). These 1,000 samples were analyzed with the IDEXX-Quanti-Tray technique to determine most-probable-number (MPN) of E. coli. Samples of open drains (6.91 log10 MPN/100 mL), surface water (5.28 log10 MPN/100 mL), floodwater (4.60 log10 MPN/100 mL), produce (3.19 log10 MPN/serving), soil (2.29 log10 MPN/gram), and street food (1.79 log10 MPN/gram) had the highest mean log10 E. coli contamination compared to other samples. The contamination concentrations did not differ between low-income and high-income neighborhoods for shared latrine swabs, open drains, municipal water, produce, and street foodsamples. E. coli contamination were significantly higher (p <0.05) in low-income neighborhoods compared to high-income for soil (0.91 log10 MPN/gram, 95% CI, 0.39, 1.43), bathing water (0.98 log10 MPN/100 mL, 95% CI, 0.41, 1.54), non-municipal water (0.64 log10 MPN/100 mL, 95% CI, 0.24, 1.04), surface water (1.92 log10 MPN/100 mL, 95% CI, 1.44, 2.40), and floodwater (0.48 log10 MPN/100 mL, 95% CI, 0.03, 0.92) samples. E. coli contamination were significantly higher (p<0.05) in low-income neighborhoods compared to transient/floating neighborhoods for drain water, bathing water, non-municipal water and surface water. Future studies should examine behavior that brings people into contact with the environment and assess the extent of exposure to fecal contamination in the environment through multiple pathways and associated risks.

microbiology↗

bioRxiv2019

Disaggregated Level Child Morbidity in Bangladesh: An Application of Small Area Estimation Method

Acute respiratory infection (ARI) and diarrhoea are two major causes of child morbidity and mortality in Bangladesh. National and regional level prevalence of ARI and diarrhoea are calculated from nationwide surveys; however, prevalence at micro-level administrative units (say, district and sub-district) is not possible due to lack of sufficient data. In such case, small area estimation (SAE) methods can be applied by combining a survey data with a census data. Using a SAE method for dichotomous response variable, this study aims to estimate the proportions of under-5 children experienced with ARI and diarrhoea separately as well as either ARI or diarrhoea within a period of two-week preceding the survey. The ARI and diarrhoea information extracted from Bangladesh Demographic and Health Survey 2011 are used to develop a random effect logistic model for each of the indicators, and then the prevalence is estimated adapting the World Bank SAE approach for the dichotomous response variable using the 5% data of the Census 2011. The estimated prevalence of each indicator significantly varied by district and sub-district (1.4-11.3% for diarrhoea, 2.2-11.8% for ARI and 4.3-16.5% for ARI/diarrhoea at sub-district level). In a number of districts and sub-district, the proportions are found double the national level. District and sub-district levels spatial distributions of the indicators might help the policy makers to identify the vulnerable disaggregated and remote hotspots. Particularly, aid industries can provide effective interventions at the highly vulnerable spots to overcome the gaps between micro and macro level administrative units.

scientific communication and education↗

bioRxiv2019

NEIL2 plays a critical role in limiting inflammation and preserving genomic integrity in H. pylori-infected gastric epithelial cells

The accumulation of Helicobacter pylori infection-induced oxidative DNA damage in gastric epithelial cells is a risk factor for developing gastric cancer (GC); however, the underlying mechanisms remain poorly understood. Here we report that the suppression of NEIL2, an oxidized base-specific mammalian DNA glycosylase, is one such mechanism via which H. pylori infection may fuel the accumulation of DNA damage during the initiation and progression of GC. Using a combination of cultured cell lines and primary cells, we show that expression of NEIL2 is significantly down-regulated after H. pylori infection; such down-regulation was also seen in human gastric biopsies. The H. pylori infection-induced down-regulation of NEIL2 is specific, as Campylobacter jejuni has no such effect. Using gastric organoids isolated from the murine stomach in co-culture studies with live bacteria mimicking the infected stomach lining, we found that H. pylori infection was associated with IL-8 production; this response was more pronounced in Neil2 knockout (KO) mouse cells compared to wild type (WT) cells, suggesting that NEIL2 suppresses inflammation under physiological conditions. Interestingly, DNA damage was significantly higher in Neil2 KO mice compared to WT mice. H. pylori-infected Neil2 KO mice showed higher inflammation and more epithelial cell damage. Computational analysis of gene expression profiles of repair genes in gastric specimens showed the reduction of Neil2 level is linked to the GC progression. Taken together, our data suggest that down-regulation of NEIL2 is a plausible mechanism by which H. pylori infection derails DNA damage repair, amplifies the inflammatory response and initiates GCs.

microbiology↗

bioRxiv2019

Detection and identification of bacterial spp. from culture negative surgical site infection patients using molecular tool.

Surgical site infection (SSI) is the most common post operative infections, that sometimes cause postoperative morbidity, mortality and increase in hospital costs. Managing surgical site infections, with negative culture report in routine diagnosis is a common dilemma in microbiology. The present study was carried out to know the presence and frequencies of various bacteria in wound aspirates/ swabs of some culture negative surgical site infection patients attending a tertiary care hospital of eastern India with molecular methods. Ninety seven (97) patients with post-operative SSI whose wound swabs/ aspirate were negative in the conventional aerobic culture after 48 hrs of incubation were taken for finding the presence and identification of any bacteria in sample with 16S rRNA gene specific broad PCR and submitted to NCBI. Of the 97 patients, 16S rRNA based broad range PCR assay could able to identify the presence of bacterial pathogen in 53(54.63%) cases, out of which 29 isolates were of viable but non-culturable bacteria(VBNC), 07 were of obligatory anaerobes and 13 were of unculturable bacteria, 04 were with polybacterial infections. Some measures should be taken in the microbiology laboratory along with conventional culture, for better patient care such as, culture plates should be allowed to incubate for an additional 3 - 4 days that will allow the growth any fastidious bacteria, anaerobic culture system should be developed along with aerobic system, and molecular diagnosis by 16S broad range PCR should be performed routinely.

microbiology↗

bioRxiv2019

Defining the microenvironment landscape of bladder cancer using highly multiplexed spatial genomic and proteomic analysis

Muscle-invasive bladder cancer (MIBC) is an aggressive disease with limited therapeutic options. PD-1 pathway targeting immunotherapies have been approved to treat advanced bladder cancer, but most patients exhibit primary resistance, suggesting that immune evasion mechanisms exist. The PPAR{gamma} pathway has been identified as a potential therapeutic target in MIBC that is associated with reduced CD8+ T-cell infiltration and increased resistance to immunotherapies. We comprehensively profiled the tumor microenvironment (TME) in formalin-fixed, paraffin-embedded (FFPE) tissues from a cohort of PPAR{gamma}high (n=13) and PPRAR{gamma}low (n=12) MIBC, integrating bulk gene expression, targeted mutation sequencing, immunohistochemistry and multiplex spatial profiling of RNA and protein expression on the GeoMx Digital Spatial Profiling (DSP) platform. Molecular subtyping was consistent between traditional methods and GeoMx profiling, and, in this cohort, we observed little evidence of spatial heterogeneity in tumor subtyping. The previously characterized T-cell exclusion phenotype of PPAR{gamma}high MIBC was recapitulated on the GeoMx platform and was further extended to show that this is a general phenomenon across immune cell types, supporting potential combination of PPAR{gamma} inhibition with ICIs. Furthermore, we found that while immune cells were excluded from PPAR{gamma}high tumors, the stromal compartment from these tumors was not significantly different than those PPAR{gamma}low tumors. By preserving spatial relationships during the GeoMx analysis, we also identify a novel association between lower immune cell expression in the tumors and higher expression of {beta}-catenin in the stroma, and differential expression of other WNT pathway members associated with PPAR{gamma} activity.\n\nOne Sentence SummaryA new method for capturing tumor-immune signaling in FFPE tissues explores how the PPARG signaling axis is associated with immune cell exclusion in bladder cancer.

cancer biology↗