Harshavardhan BV’s research while affiliated with Indian Institute of Science Bangalore and other places

Background Myofibroblastic cancer-associated fibroblasts (CAF) in tumor stroma serves as an independent poor prognostic indicator, supporting higher stemness in oral cancer; however, the underlying biology is not fully comprehended. Here, we have explored the crucial role of Tunica Interna Endothelial Cell Kinase (Tie2/TEK) signaling in transition and maintenance of myofibroblastic phenotype of CAFs, and as possible link with the poor prognosis of head and neck squamous cell carcinoma (HNSCC) patients. Methods Bulk and single cell RNA-sequencing (scRNAseq) methods and in-depth bioinformatic analysis were applied for CAF and cancer cells co-culture for studying molecular relationships. In vitro 3D-spheroid-forming ability, expression of stemness markers, in vivo tumor formation ability in zebrafish embryo and syngeneic mouse allografts formation was conducted to test stemness, upon targeting CAF-specific Tie2 activity by gene silencing or with small molecule inhibitor. Immunohistochemistry analysis was performed to locate the distribution of Tie2 and αSMA in primary tumors of oral carcinoma. Prognosis in HNSCC patient cohort from The Cancer Genome Atlas (TCGA) study was analysed based on single sample gene set enrichment score (ssGSEA) and Kaplan–Meier analysis. Results Autocrine or exogenous TGFβ-induction in CAF led to the recruitment of histone deacetylase 2 (HDAC2) on the promoter of Tie2-antagonist, Angiopoietin-2 (ANGPT2), resulting in its downregulation, leading to phosphorylation of Tie2 (Y992) and subsequent activation of SRC (Y418). This led to SRC/ROCK mediated αSMA-positive stress-fiber formation with gain of myofibroblast phenotype. The CAF-specific Tie2-signaling was responsible for producing embryonic-like cell state in co-cultured cancer cells; with enhanced tumor initiating ability. Tie2 activity in CAF exerted the dynamic gene expression reprogramming, with the upregulation of ‘cell migration’ and downregulation of ‘protein biosynthesis’ related gene-regulatory-network modules in malignant cells. The AUCell scores calculated for gene signatures derived from these modules showed significant concordance in independently reported scRNAseq studies of HNSCC tumors and significant association with poor prognosis in HNSCC patient cohort. Conclusions CAF-specific Tie2 activity may serve as direct stromal-target against cancer cell plasticity leading to poor prognosis of oral cancer patients. Overall, our work has provided wider applicability of Tie2-specific functions in tumor biology, along with its known role in endothelial cell-specific function.

Stem cell differentiation during development is governed by the dynamics of the underlying gene regulatory networks (GRNs). Mutually inhibiting nodes/collection of nodes encompass the GRNs that govern differentiation to two distinct fates. But the properties of GRNs that can allow differentiation into n-terminal phenotypes are not understood. In this study, we examine toggle-n networks, encompassing mutual inhibitions among multiple transcription factors, to derive generalized conclusions regarding the dynamics underlying differentiation into n-terminal phenotypes. We show that in steady-state distributions of gene expression, multiple cell state-specific transcription factors are co-expressed, indicating an obligatory multi-step process of multi-lineage differentiation. Furthermore, we show that cytokine signaling and specific asymmetry of regulatory links can lead to directed differentiation towards a particular cell state. Our findings provide valuable insights into the mechanistic aspects of directed differentiation of stem cells.

In mammalian reproduction, a significant proportion of embryos fail to implant despite a receptive uterus, suggesting that defects in epithelial remodelling at the embryo-uterine interface contribute to implantation failure. The molecular programs enabling such remodelling remain incompletely understood. Here, we identify a conserved transcriptional circuit involving HOXA10 and TWIST2 that regulates epithelial plasticity in the endometrium via partial epithelial-to-mesenchymal transition (pEMT). HOXA10, a transcription factor essential for uterine receptivity, is specifically downregulated in the luminal epithelium at implantation in mice, hamsters, and monkeys. Integrated CUT&RUN and transcriptomic profiling in human endometrial epithelial cells reveal that HOXA10 directly activates epithelial gene networks and represses mesenchymal programs. HOXA10 loss, both in vitro and in vivo , induces a pEMT state with increased cell motility. Mechanistically, HOXA10 represses TWIST2, a core EMT regulator; its derepression promotes mesenchymal gene expression and epithelial cell displacement. TWIST2 knockdown restores epithelial identity and impairs implantation. These findings establish a mutually antagonistic HOXA10-TWIST2 circuit as a key regulator of pEMT and epithelial remodelling during implantation. Graphical Abstract

Dysregulated pH is now recognised as a hallmark of cancer. Recent evidence has revealed that the endosomal pH regulator Na⁺/H⁺ exchanger NHE9 is upregulated in colorectal cancer to impose a pseudo-starvation state associated with invasion, highlighting an underexplored mechanistic link between adaptive endosomal reprogramming and malignant transformation. In this study, we use a model that quantitatively captures the dynamics of the core regulatory network governing epithelial mesenchymal plasticity. The model recapitulated NHE9-induced calcium signalling and the emergence of migratory phenotypes in colorectal cancer cells. Model predictions were compared with patient data and experimental results from RNA sequencing analysis of colorectal cancer cells with stable NHE9 expression. Mathematical analyses identified that tumours leverage elevated NHE9 levels to delay the transition of cells to a mesenchymal state and allow for metastatic progression. Ectopic expression of NHE9 is sufficient to induce loss of epithelial nature but does not fully couple with gain of mesenchymal state, resulting in a hybrid epithelial-mesenchymal population with increased aggressiveness and metastatic competence. Higher NHE9 expression is associated with cancer cell migration, and the effect appears to be independent of hypoxia status. Our data suggests that alterations in endosomal pH, an evolutionarily conserved starvation response, may be hijacked by colorectal cancer cells to drive phenotypic plasticity and invasion. We propose that cancer cells rewire their endosomal pH not only to meet the demands of rapid cell proliferation, but also to enable invasion, metastasis, and cell survival. Endosomal pH may be an attractive therapeutic target for halting tumour progression.

Elucidating the emergent dynamics of cellular differentiation networks is crucial to understanding cell-fate decisions. Toggle switch - a network of mutually repressive lineage-specific transcription factors A and B - enables two phenotypes from a common progenitor: (high A, low B) and (low A, high B). However, the dynamics of networks enabling differentiation of more than two phenotypes from a progenitor cell has not been well-studied. Here, we investigate the dynamics of a four-node network A, B, C, and D inhibiting each other, forming a toggle tetrahedron. Our simulations show that this network is multistable and predominantly allows for the co-existence of six hybrid phenotypes where two of the nodes are expressed relatively high as compared to the remaining two, for instance (high A, high B, low C, low D). Finally, we apply our results to understand naïve CD4+ T cell differentiation into Th1, Th2, Th17 and Treg subsets, suggesting Th1/Th2/Th17/Treg decision-making to be a two-step process.

Epithelial ovarian cancer (EOC) is characterized by resistance to platinum-based therapy, resulting in rapid progression and poor survival. Here, we ask whether drug resistance and invasiveness coevolve to drive metastasis. Selection experiments involving pulsed carboplatin exposure established isogenic chemoresistant variants of lines, which typify high-grade serous ovarian carcinoma (HGSOC), the most aggressive type of EOC. Time-lapse imaging showed enhanced migration of resistant single cells and their collectives. Resistant cell spheroids spread faster on Collagen I substrata than sensitive controls. The resistant OVCAR-3 transcriptome was ontologically enriched for migration and showed overlap with previously reported markers of resistance in EOC patients and other evolved lines. Gene set enrichment predicted transition between epithelial, mesenchymal, and amoeboid states is higher in resistance compared to control lines. Lower matrix adhesion, weak focal adhesion, and highly deformable and translatory dynamics of cell collectives indicated that resistant cancer cells displayed a unique collective amoeboid-like migration. When injected intraperitoneally into immunodeficient mice, resistant cells colonized to a greater extent on parietal mucosae. Ex vivo, suspended resistant cells formed moruloids associated with quicker peritoneal adhesion, clearing human coelomic mesothelial monolayers with higher efficiency. Knockdown in resistant OVCAR-3 cells of two upregulated proteins, E-cadherin and LGALS3BP, had distinct consequences. E-cadherin knockdown partially restored sensitivity to carboplatin but did not affect invasion. In contrast, silencing LGALS3BP decreased invasion but not resistance. Our results suggest that drug resistance and invasiveness could coevolve through the upregulation of distinct trait drivers in EOC.

In mammals, X chromosome dosage is balanced between sexes through the silencing of one X chromosome in females. Recent single-cell RNA sequencing analysis demonstrated that the inactivation of the X chromosome is accompanied by the upregulation of the active X chromosome (Xa) during mouse embryogenesis. Here, we have investigated if the reactivation of inactive-X (Xi) leads to the loss of Xa upregulation in different cellular or developmental contexts. We find that while Xi reactivation and loss of Xa upregulation are tightly coupled in mouse embryonic epiblast and induced pluripotent stem cells, that is not the case in germ cells. Moreover, we demonstrate that partial reactivation of Xi in mouse extra-embryonic endoderm stem cells and human B cells does not result in the loss of Xa upregulation. Finally, we have established a mathematical model for the transcriptional coordination of two X chromosomes. Together, we conclude that the reactivation of Xi is not always synchronized with the loss of Xa upregulation.

Exploring the complexity of the epithelial-to-mesenchymal transition (EMT) unveils a diversity of potential cell fates; however, the exact timing and mechanisms by which early cell states diverge into distinct EMT trajectories remain unclear. Studying these EMT trajectories through single-cell RNA sequencing is challenging due to the necessity of sacrificing cells for each measurement. In this study, we employed optimal-transport analysis to reconstruct the past trajectories of different cell fates during TGF-beta-induced EMT in the MCF10A cell line. Our analysis revealed three distinct trajectories leading to low EMT, partial EMT, and high EMT states. Cells along the partial EMT trajectory showed substantial variations in the EMT signature and exhibited pronounced stemness. Throughout this EMT trajectory, we observed a consistent downregulation of the EED and EZH2 genes. This finding was validated by recent inhibitor screens of EMT regulators and CRISPR screen studies. Moreover, we applied our analysis of early-phase differential gene expression to gene sets associated with stemness and proliferation, pinpointing ITGB4 , LAMA3 , and LAMB3 as genes differentially expressed in the initial stages of the partial versus high EMT trajectories. We also found that CENPF , CKS1B , and MKI67 showed significant upregulation in the high EMT trajectory. While the first group of genes aligns with findings from previous studies, our work uniquely pinpoints the precise timing of these upregulations. Finally, the identification of the latter group of genes sheds light on potential cell cycle targets for modulating EMT trajectories.

Elucidating the emergent dynamics of complex regulatory networks enabling cellular differentiation is crucial to understand embryonic development and suggest strategies for synthetic circuit design. A well-studied network motif often driving cellular decisions is a toggle switch - a set of two mutually inhibitory lineage-specific transcription factors A and B. A toggle switch often enables two possible mutually exclusive states - (high A, low B) and (low A, high B) - from a common progenitor cell. However, the dynamics of networks enabling differentiation of more than two cell types from a progenitor cell is not well-studied. Here, we investigate the dynamics of four master regulators A, B, C and D inhibiting each other, thus forming a toggle tetrahedron. Our simulations show that a toggle tetrahedron predominantly allows for co-existence of six ‘double positive’ or hybrid states where two of the nodes are expressed relatively high as compared to the remaining two - (high A, high B, low C, low D), (high A, low B, high C, low D), (high A, low B, low C, high D), (low A, high B, high C, low D), (low A, low B, high C, high D) and (low A, high B, low C, high D). Stochastic simulations showed state-switching among these phenotypes, indicating phenotypic plasticity. Finally, we apply our results to understand the differentiation of naive CD4 ⁺ T cells into Th1, Th2, Th17 and Treg subsets, suggesting Th1/Th2/Th17/Treg decision-making to be a two-step process. Our results reveal multistable dynamics and establish the stable co-existence of hybrid cell-states, offering a potential explanation for simultaneous differentiation of multipotent naïve CD4+ T cells.