Biology subjects

Kottapalli, S.

Publications and source records attributed to Kottapalli, S..

11 recordsLinked to original sources

bioRxiv2026

IL-1β/IL-6 signaling circuit in the tumor microenvironment drives prostate cancer development

Despite considerable progress in elucidating mechanisms leading to castration-resistant prostate cancer (CRPC), insight into the early stages of prostate cancer initiation and progression remains limited. Genomic drivers of prostate cancer initiation have been defined through patient tumor sequencing, but the subsequent events responsible for local tissue invasion are poorly understood. Here we leverage a well-studied genetically engineered mouse prostate cancer model (Hi-Myc) that, based on robust and reproducible kinetics for transitioning from pre-invasive prostatic intraepithelial neoplasia (PIN) to invasive prostate adenocarcinoma (PCa), provides an ideal system to systematically address this question using single-cell analysis. Surprisingly, the transcriptomic profiles of early PIN lesions are indistinguishable from those of late-stage, highly invasive tumor cells, suggesting that MYC activation at the PIN stage establishes a transcriptional program that is fully capable of driving invasion but is restrained by the local tumor microenvironment (TME). Indeed, we find that progression to PCa is associated with progressive infiltration of IL-1{beta}+ tumor-infiltrating macrophages at the PIN stage that, based on immunodepletion and cytokine neutralization experiments, are required for the PIN-to-PCa transition. Mechanistically, IL-1{beta} from macrophages acts directly on prostate fibroblasts, leading to the release of IL-6, which drives invasion by activating IL-6R in tumor cells. Collectively, these findings identify a pro-tumorigenic IL-1{beta}/IL-6 signaling circuit mediated through local macrophages and fibroblasts that unleashes the full oncogenic potential of a cancer driver (MYC) activated at the PIN stage. We also find evidence of this circuit in other (non-MYC-driven) prostate cancer models as well as human prostate and lung adenocarcinoma, with implications for TME-specific targeted therapeutics in early-stage disease.

cancer biology↗

bioRxiv2025

Macrophage-to-Myofibroblast Transition (MMT)- an adverse response to polypropylene mesh implanted for pelvic organ prolapse repair surgery in a non-human primate model

Surgical repair of pelvic organ prolapse (POP) is often augmented by polypropylene mesh to provide mechanical support to the vagina and improve anatomical outcomes as compared to native tissue repair. However, POP repair surgeries utilizing PPM have complications (most often pain or mesh exposure into the vagina) in over 10% of cases. Previous work has demonstrated that tensioning of meshes with certain geometries (diamond and hexagon pores), results in both planar (pore collapse) and nonplanar (wrinkles) deformations, significantly altering textile properties and impacting the host response. To further investigate the impact of mesh deformation on the host response, we implanted mesh in a validated non-human primate model via sacrocolpopexy with stable flat (square pores, N=20) versus deformed geometries (mesh loaded on the diamond prior to implantation resulting in collapsed pores and wrinkles, N=20). To investigate the impact of tension independent of deformation, we implanted on and off tension (10N, N=10 in each group). We hypothesized that more stable geometries trigger a healing response that achieves homeostasis while deformed mesh, by increasing the amount of material in contact with the host, triggers a maladaptive remodeling response with the formation of myofibroblasts. After twelve weeks, we found that mesh deformations and the absence of tension increase the amount of mesh per area on the vagina (mesh burden) and reproduced clinical complications (mesh exposure and vaginal thinning). Interestingly, MMT cells, or myofibroblasts co-expressing a macrophage marker (CD68), were seen to significantly increase in response to mesh burden, as well as respond hyper-locally to the mesh fiber interface. We observed decreased collagen density and more immature matrix deposited in conditions with higher MMT cell presence, showing more disorganization in deposited matrix with increased mesh burden, and the loss of tension. TGF-{beta}1, in both active and latent forms, increased with increasing mesh burden, and highest expression was observed in conditions precipitating the highest percentage of MMT cells, a possible mechanism of transdifferentiation. This study showed the importance of PPM mesh properties on mesh burden following tensioning, impact on MMT transdifferentiation, and the downstream effect of these changes on the host response and healing outcomes.

bioengineering↗

bioRxiv2025

Lineage recording in monoclonal gastruloids reveals heritable modes of early development

Mammalian stem cells possess a remarkable capacity for self-organization, a property that underlies increasingly sophisticated in vitro models of early development. However, even under carefully controlled conditions, stem cell-derived models exhibit substantial "inter-individual" heterogeneity. Focusing on gastruloids, a powerful model of the early posterior embryo1, we sought to investigate the origins of this heterogeneity. To this end, we developed a scalable protocol for generating gastruloids that are monoclonal, i.e. derived from a single mouse embryonic stem cell (mESC). Single cell transcriptional profiling of monoclonal gastruloids revealed extensive inter-individual heterogeneity, with some hardly progressing, others resembling conventional gastruloids but biased towards mesodermal or neural lineages, and yet others bearing cell types rare or absent from conventional polyclonal gastruloids. To investigate this further, we leveraged DNA Typewriter2 to record the cell lineage relationships among the mESCs from which monoclonal gastruloids originate. Early in the expansion of "founder" mESCsprior to induction of the resulting aggregates to form gastruloidswe observe clear examples of fate bias or fate restriction, i.e. sister clades that exhibit markedly different cell type compositions. In a separate experiment with DNA Typewriter, we reconstructed a monophyletic "tree of trees", composed of [~]50,000 cells derived from [~]100 gastruloids, all descended from a single "founder of founders" stem cell. From these data, we find that founder mESCs that are more closely related are more likely to give rise to monoclonal gastruloids with similar cell type compositions. Our results suggest that fluctuations in the intrinsic states of mESCs are heritable, and shape their descendants fates across many cell divisions. Our study also showcases how DNA Typewriter can be used to reconstruct high-resolution, monophyletic cell lineage trees in stem cell models of early development.

developmental biology↗

bioRxiv2024

Optics-free reconstruction of 2D images via DNA barcode proximity graphs

Spatial genomics technologies include imaging- and sequencing-based methods. Sequencing-based spatial methods typically require surfaces coated with coordinate-associated DNA barcodes, but the physical registration of these barcodes to spatial coordinates is challenging, necessitating either high density printing of oligonucleotides or in situ sequencing/probing of randomly deposited, DNA-barcode-bearing beads. As a consequence, the surface areas available to sequencing-based spatial genomic methods are constrained by the time, labor, cost and instrumentation required to either print or decode a coordinate-tagged surface. To address this challenge, we developed SCOPE (Spatial reConstruction via Oligonucleotide Proximity Encoding), an optics-free, DNA microscopy-inspired method. With SCOPE, the relative positions of DNA-barcoded beads within a 2D shape, 2D image or 3D volume are inferred from the ex situ sequencing of chimeric molecules formed from diffusing "sender" and tethered "receiver" oligonucleotides. To demonstrate the potential of this approach, we applied SCOPE to reconstruct 2D shapes, 2D images or 3D volumes defined by 104-106 x 20-100 {micro}m DNA barcoded beads, including an asymmetric "swoosh" resembling the Nike logo (44 mm2), a "color" Snellen eye chart (704 mm2) and the surface topology of 3D molds of a teddy bear, star, butterfly or block letter (75-100 mm3). Each of the resulting "DNA barcode proximity graphs" was computationally reconstructed in an automated fashion, across fields of view and at resolutions that were determined by sequencing depth, bead size and diffusion kinetics, rather than by microarray or microscope instrument time. Because the ground truth shapes are known, these datasets may be particularly useful for the further development of computational algorithms by this nascent field.

genomics↗

bioRxiv2023

Breast Cancer Macrophage Heterogeneity and Self-renewal are Determined by Spatial Localization

Tumor-infiltrating macrophages support critical steps in tumor progression, and their accumulation in the tumor microenvironment (TME) is associated with adverse outcomes and therapeutic resistance across human cancers. In the TME, macrophages adopt diverse phenotypic alterations, giving rise to heterogeneous immune activation states and induction of cell cycle. While the transcriptional profiles of these activation states are well-annotated across human cancers, the underlying signals that regulate macrophage heterogeneity and accumulation remain incompletely understood. Here, we leveraged a novel ex vivo organotypic TME (oTME) model of breast cancer, in vivo murine models, and human samples to map the determinants of functional heterogeneity of TME macrophages. We identified a subset of F4/80highSca-1+ self-renewing macrophages maintained by type-I interferon (IFN) signaling and requiring physical contact with cancer-associated fibroblasts. We discovered that the contact-dependent self-renewal of TME macrophages is mediated via Notch4, and its inhibition abrogated tumor growth of breast and ovarian carcinomas in vivo, as well as lung dissemination in a PDX model of triple-negative breast cancer (TNBC). Through spatial multi-omic profiling of protein markers and transcriptomes, we found that the localization of macrophages further dictates functionally distinct but reversible phenotypes, regardless of their ontogeny. Whereas immune-stimulatory macrophages (CD11C+CD86+) populated the tumor epithelial nests, the stroma-associated macrophages (SAMs) were proliferative, immunosuppressive (Sca-1+CD206+PD-L1+), resistant to CSF-1R depletion, and associated with worse patient outcomes. Notably, following cessation of CSF-1R depletion, macrophages rebounded primarily to the SAM phenotype, which was associated with accelerated growth of mammary tumors. Our work reveals the spatial determinants of macrophage heterogeneity in breast cancer and highlights the disruption of macrophage self-renewal as a potential new therapeutic strategy.

cancer biology↗

bioRxiv2023

Optimization of extraction, Structural characterization of immunomodulatory acidic polysaccharide from Euphorbia caducifolia

Heating confluence method in combination with response surface methodology (RSM) was performed to optimize polysaccharides extraction from Euphorbia caducifolia Haines. The Box-Behnken Design was used to optimize the extraction conditions with three parameters such as temperature (A), Solid to liquid ratio (B), and time (C). The percentage yields obtained were fitted to a 2nd order polynomial equation using multiple regression analysis. From the regression equation, the optimal polysaccharides extraction parameters for 2.3% of yield are Temperature-120{degrees}C, Solid to liquid ratio-75 g/L, and Time-2 h. Further, crude polysaccharide was purified and disclosed GlaUA, Rha, Glc, Gal, Xyl and Ara (1:2.5:4:3.6:3.7:3.3) ratio of poysaccharide. Thermogram of the EC polysaccharide showed typical natural polysaccharide behavior, and hydrophilic nature of polysaccharide attributed to endothermic water loss. Furthermore, purified polysaccharides exhibited strong in vitro free radical scavenging activities, reducing ability, and immunomodulatory activity by the effective production of pro-inflammatory cytokines with RAW 264.7 cells.

biochemistry↗

bioRxiv2023

Unusual starch grains from the Euphorbia caducifolia Haines

Nature has chosen the starch as a universal form for storing carbohydrate. In granule form, it is semi-crystalline, water-insoluble, dense and a ubiquitous constituent. Structure of the starch granules depends on their biological source and varies from part to part of the sources. In sequence to that, starch granules from the latex of Euphorbia caducifolia was isolated and characterized under different conditions to reveal its uniqueness in the structure. A flat dumbbell-shaped starch was notified with distinctive "maltese cross" under various microscopes. These starches are found to be high amylose contents, which resist water solubility, swelling index, and turbidity of the starches. X-Ray Diffraction studies states the presence C type pattern of crystallinity whereas typical polysaccharide spectrum was observed with ATR studies. Gelatinization of the starches remarked them as highly thermal stable and retrogradation studies failed to detect realignment of the heat disrupted amylose and amylopectin. Lintnerization of starch granules reveals the high complexity of the structure. Thus, latex starch granules from the E caducifolia are considered to be unusual because of their highly complex structure, shape and properties.

biochemistry↗

bioRxiv2023

ATR-FTIR spectra of polysaccharide isolated from Euphorbia caducifolia and its chemical modifications: A study of Principal component analysis

Polysaccharides are the carbohydrates composed of same or different types of saccharides in an organized manner with glycosidic bonds. These are useful for various industrial applications mainly in food and pharmaceutical companies. Modifications of the polysaccharides change its structure and lead to the physical as well as functional differences. Mostly, chemical methods are used to modify its structure to study the structure-activity relationship in interest towards its physical properties like solubility and biological activities among various types of molecular modifications. In this study, a polysaccharide isolated from stems of Euphorbia caducifolia and modified its structure chemically by substituting different groups by sulfonation, carboxymethylation, acetylation and phosphorylation with various degree of substitutions. Molecular modifications of the polysaccharides showed the impact on water solubility as a physiochemical property. Thus, ATR-FTIR spectroscopy was employed along with a chemometric analysis, i.e., Principal components analysis (PCA) to understand and identify the chemical moieties differed from the unmodified polysaccharide. From PCA analysis, PC1 and PC2 components suffice to differentiate the modified polysaccharides with its native form.

biochemistry↗

bioRxiv2023

Purification and characterization of a novel anti-tumour galactose binding lectin from Euphorbia caducifolia latex

A galactose specific lectin was isolated from the latex of Euphorbia caducifolia to investigate the therapeutical aspects protein. Protein was purified from latex serum with two different affinity matrices and confirmed to contain 8 isoforms called isolectin with a molecular weight of 32 and 32.5 kDa. Preliminary studies state the specificity towards galactose, but its affinity with lactose is more favourable even at low concentrations. Circular spectrometry suggests the predominance {beta} conformation is high in comparison to others as like most of the other latex lectins. Haemagglutination activity of the protein with different thermal and pH ranges shows maximum activity at pH 6-8 and 60-70{degrees}C. In therapeutically, it is noticed that the galactose specific lectin showed mitogenicity with human macrophages and anti-cancer properties on human cervical cancer cells.

biochemistry↗

bioRxiv2022

Integrated Single-Cell Genotyping and Chromatin Accessibility Charts JAK2V617F Human Hematopoietic Differentiation

In normal somatic tissue differentiation, changes in chromatin accessibility govern priming and commitment of precursors towards cellular fates. In turn, somatic mutations can disrupt differentiation topologies leading to abnormal clonal outgrowth. However, defining the impact of somatic mutations on the epigenome in human samples is challenging due to admixed mutated and wildtype cells. To chart how somatic mutations disrupt epigenetic landscapes in human clonal outgrowths, we developed Genotyping of Targeted loci with single-cell Chromatin Accessibility (GoT-ChA). This high-throughput, broadly accessible platform links genotypes to chromatin accessibility at single-cell resolution, across thousands of cells within a single assay. We applied GoT-ChA to CD34+ cells from myeloproliferative neoplasm (MPN) patients with JAK2V617F-mutated hematopoiesis, where the JAK2 mutation is known to perturb hematopoietic differentiation. Differential accessibility analysis between wildtype and JAK2V617F mutant progenitors revealed both cell-intrinsic and cell state-specific shifts within mutant hematopoietic precursors. An early subset of mutant hematopoietic stem and progenitor cells (HSPCs) exhibited a cell-intrinsic pro-inflammatory signature characterized by increased NF-{kappa}B and JUN/FOS transcription factor motif accessibility. In addition, mutant HSPCs showed increased myeloid/erythroid epigenetic priming, preceding increased erythroid and megakaryocytic cellular output. Erythroid progenitors displayed aberrant regulation of the {gamma}-globin locus, providing an intrinsic epigenetic basis for the dysregulated fetal hemoglobin expression observed in MPNs. In contrast, megakaryocytic progenitors exhibited a more specialized inflammatory chromatin landscape relative to early HSPCs, with increased accessibility of pro-fibrotic JUN/FOS transcription factors. Notably, analysis of myelofibrosis patients treated with JAK inhibitors revealed an overall loss of mutant-specific phenotypes without modifying clonal burden, consistent with clinical responses. Finally, expansion of the multi-modality capability of GoT-ChA to integrate mitochondrial genome profiling and cell surface protein expression measurement enabled genotyping imputation and discovery of aberrant cellular phenotypes. Collectively, we show that the JAK2V617F mutation leads to epigenetic rewiring in a cell-intrinsic and cell type-specific manner. We envision that GoT-ChA will thus serve as a foundation for broad future explorations to uncover the critical link between mutated somatic genotypes and epigenetic alterations across clonal populations in malignant and non-malignant contexts.

cancer biology↗

bioRxiv2018

Deconvoluting Virome-Wide Antiviral Antibody Profiling Data

The ability to comprehensively characterize exposures and immune responses to viral infections will be critical to better understanding human health and disease. We previously described the VirScan system, a phage-display based technology for profiling antibody binding to a comprehensive library of peptides designed to represent the human virome. The previous VirScan analytical approach did not fully account for disproportionate representation of viruses in the library or for antibody cross-reactivity among sequences shared by related viruses. Here we present the AntiViral Antibody Response Deconvolution Algorithm ( AVARDA), a multi-module software package for analyzing VirScan datasets. AVARDA provides a probabilistic assessment of infection at species-level resolution by considering alignment of all library peptides to each other and to all human viruses. We employed AVARDA to analyze VirScan data from a cohort of encephalitis patients with either known viral infections or undiagnosed etiologies. By comparing acute and convalescent sera, AVARDA successfully confirmed or detected antibody responses to human herpesviruses 1, 3, 4, 5, and 6, thereby improving the rate of diagnosing viral encephalitis in this cohort by 62.5%. We further assessed AVARDAs utility in the setting of an epidemiological study, demonstrating its ability to determine infections acquired in a child followed prospectively from infancy. We consider ways in which AVARDAs conceptual framework may be further developed in the future and describe how its analyses may be extended beyond investigations of viral infection. AVARDA, in combination with VirScan and other pan-pathogen serological techniques, is likely to find broad utility in the epidemiology and diagnosis of infectious diseases.

bioinformatics↗