publications
2022
- JCMAnalysis of Yes-Associated Protein-1 (YAP1) Target Gene Signature to Predict Progressive Breast CancerGomathi Venkatasubramanian, Devaki A. Kelkar, Susmita Mandal, Mohit Kumar Jolly, and Madhura KulkarniJournal of Clinical Medicine
Breast cancers are treated according to the ER/PR or HER2 expression and show better survival outcomes with targeted therapy. Triple-negative breast cancers (TNBCs) with a lack of expression of ER/PR and HER2 are treated with systemic therapy with unpredictable responses and outcomes. It is essential to investigate novel markers to identify targeted therapies for TNBC. One such marker is YAP1, a transcription co-activator protein that shows association with poor prognosis of breast cancer. YAP1 transcriptionally regulates the expression of genes that drive the oncogenic phenotypes. Here, we assess a potential YAP target gene signature to predict a progressive subset of breast tumors from METABRIC and TCGA datasets. YAP1 target genes were shortlisted based on expression correlation and concordance with YAP1 expression and significant association with survival outcomes of patients. Hierarchical clustering was performed for the shortlisted genes. The utility of the clustered genes was assessed by survival analysis to identify a recurring subset. Expression of the shortlisted target genes showed significant association with survival outcomes of HER2-positive and TNBC subset in both datasets. The shortlisted genes were verified using an independent dataset. Further validation using IHC can prove the utility of this potential prognostic signature to identify a recurrent subset of HER2-positive and TNBC subtypes.
- CancersIn Silico Analysis of Ion Channels and Their Correlation with Epithelial to Mesenchymal Transition in Breast CancerK.T. Shreya Parthasarthy, Susmita Mandal, Smrita Singh, Seetaramanjaneyulu Gundimeda, Mohit Kumar Jolly, Akhilesh Pandey, and Jyoti SharmaCancers
Uncontrolled growth of breast cells due to altered gene expression is a key feature of breast cancer. Alterations in the expression of ion channels lead to variations in cellular activities, thus contributing to attributes of cancer hallmarks. Changes in the expression levels of ion channels were observed as a consequence of EMT. Additionally, ion channels were reported in the activation of EMT and maintenance of a mesenchymal phenotype. Here, to identify altered ion channels in breast cancer patients, differential gene expression and weighted gene co-expression network analyses were performed using transcriptomic data. Protein–protein interactions network analysis was carried out to determine the ion channels interacting with hub EMT-related genes in breast cancer. Thirty-two ion channels were found interacting with twenty-six hub EMT-related genes. The identified ion channels were further correlated with EMT scores, indicating mesenchymal phenotype. Further, the pathway map was generated to represent a snapshot of deregulated cellular processes by altered ion channels and EMT-related genes. Kaplan–Meier five-year survival analysis and Cox regressions indicated the expression of CACNA1B, ANO6, TRPV3, VDAC1 and VDAC2 to be potentially associated with poor survival. Deregulated ion channels correlate with EMT-related genes and have a crucial role in breast cancer-associated tumorigenesis. Most likely, they are potential candidates for the determination of prognosis in patients with breast cancer.
- biomQuantifying the Patterns of Metabolic Plasticity and Heterogeneity along the Epithelial–Hybrid–Mesenchymal Spectrum in CancerSrinath Muralidharan, Sarthak Sahoo, Aryamaan Saha, Sanjay Chandran, Sauma Surva Majumdar, Susmita Mandal, Herbert Levine, and Mohit Kumar JollyBiomolecules
Cancer metastasis is the leading cause of cancer-related mortality and the process of the epithelial-to-mesenchymal transition (EMT) is crucial for cancer metastasis. Both partial and complete EMT have been reported to influence the metabolic plasticity of cancer cells in terms of switching among the oxidative phosphorylation, fatty acid oxidation and glycolysis pathways. However, a comprehensive analysis of these major metabolic pathways and their associations with EMT across different cancers is lacking. Here, we analyse more than 180 cancer cell datasets and show the diverse associations of these metabolic pathways with the EMT status of cancer cells. Our bulk data analysis shows that EMT generally positively correlates with glycolysis but negatively with oxidative phosphorylation and fatty acid metabolism. These correlations are also consistent at the level of their molecular master regulators, namely AMPK and HIF1α. Yet, these associations are shown to not be universal. The analysis of single-cell data for EMT induction shows dynamic changes along the different axes of metabolic pathways, consistent with general trends seen in bulk samples. Further, assessing the association of EMT and metabolic activity with patient survival shows that a higher extent of EMT and glycolysis predicts a worse prognosis in many cancers. Together, our results reveal the underlying patterns of metabolic plasticity and heterogeneity as cancer cells traverse through the epithelial–hybrid–mesenchymal spectrum of states.
2021
- biomTranscriptomic-Based Quantification of the Epithelial-Hybrid-Mesenchymal Spectrum across Biological ContextsSusmita Mandal, Tanishq Tejaswi, Rohini Janivara, Syamanthak Srikrishnan, Pradipti Thakur, Sarthak Sahoo, Priyanka Chakraborty, Sukhwinder Singh Sohal, Herbert Levine, Jason T George, and Mohit Kumar JollyBiomolecules
Epithelial-mesenchymal plasticity (EMP) underlies embryonic development, wound healing, and cancer metastasis and fibrosis. Cancer cells exhibiting EMP often have more aggressive behavior, characterized by drug resistance, and tumor-initiating and immuno-evasive traits. Thus, the EMP status of cancer cells can be a critical indicator of patient prognosis. Here, we compare three distinct transcriptomic-based metrics—each derived using a different gene list and algorithm—that quantify the EMP spectrum. Our results for over 80 cancer-related RNA-seq datasets reveal a high degree of concordance among these metrics in quantifying the extent of EMP. Moreover, each metric, despite being trained on cancer expression profiles, recapitulates the expected changes in EMP scores for non-cancer contexts such as lung fibrosis and cellular reprogramming into induced pluripotent stem cells. Thus, we offer a scoring platform to quantify the extent of EMP in vitro and in vivo for diverse biological applications including cancer.
- iScienceSemicoordinated allelic-bursting shape dynamic random monoallelic expression in pregastrulation embryosHemant C. Naik, Kishore Hari, Deepshikha Chandel, Susmita Mandal, Mohit Kumar Jolly, and Srimonta GayeniScience
Recently, allele-specific single-cell RNA-seq analysis has demonstrated widespread dynamic random monoallelic expression of autosomal genes (aRME) in different cell types. However, the prevalence of dynamic aRME during pregastrulation remains unknown. Here, we show that dynamic aRME is widespread in different lineages of pregastrulation embryos. Additionally, the origin of dynamic aRME remains elusive. It is believed that independent transcriptional bursting from each allele leads to dynamic aRME. Here, we show that allelic burst is not perfectly independent; instead it happens in a semicoordinated fashion. Importantly, we show that semicoordinated allelic bursting of genes, particularly with low burst frequency, leads to frequent asynchronous allelic bursting, thereby contributing to dynamic aRME. Furthermore, we found that coordination of allelic bursting is lineage specific and genes regulating the development have a higher degree of coordination. Altogether, our study provides significant insights into the prevalence and origin of dynamic aRME and their developmental relevance during early development.
- JCMAn Integrative Systems Biology Approach Identifies Molecular Signatures Associated with Gallbladder Cancer PathogenesisNabanita Roy, Mrinmoy Kshattry, Susmita Mandal, Mohit Kumar Jolly, Dhruba Kumar Bhattacharyya, and Pankaj BarahJournal of Clinical Medicine
Gallbladder cancer (GBC) has a lower incidence rate among the population relative to other cancer types but is a major contributor to the total number of biliary tract system cancer cases. GBC is distinguished from other malignancies by its high mortality, marked geographical variation and poor prognosis. To date no systemic targeted therapy is available for GBC. The main objective of this study is to determine the molecular signatures correlated with GBC development using integrative systems level approaches. We performed analysis of publicly available transcriptomic data to identify differentially regulated genes and pathways. Differential co-expression network analysis and transcriptional regulatory network analysis was performed to identify hub genes and hub transcription factors (TFs) associated with GBC pathogenesis and progression. Subsequently, we assessed the epithelial-mesenchymal transition (EMT) status of the hub genes using a combination of three scoring methods. The identified hub genes including, CDC6, MAPK15, CCNB2, BIRC7, L3MBTL1 were found to be regulators of cell cycle components which suggested their potential role in GBC pathogenesis and progression.
- NAR CancerA mechanistic model captures the emergence and implications of non-genetic heterogeneity and reversible drug resistance in ER+ breast cancer cellsSarthak Sahoo, Ashutosh Mishra, Harsimran Kaur, Kishore Hari, Srinath Muralidharan, Susmita Mandal, and Mohit Kumar JollyNAR Cancer
Resistance to anti-estrogen therapy is an unsolved clinical challenge in successfully treating ER+ breast cancer patients. Recent studies have demonstrated the role of non-genetic (i.e. phenotypic) adaptations in tolerating drug treatments; however, the mechanisms and dynamics of such non-genetic adaptation remain elusive. Here, we investigate coupled dynamics of epithelial–mesenchymal transition (EMT) in breast cancer cells and emergence of reversible drug resistance. Our mechanism-based model for underlying regulatory network reveals that these two axes can drive one another, thus enabling non-genetic heterogeneity in a cell population by allowing for six co-existing phenotypes: epithelial-sensitive, mesenchymal-resistant, hybrid E/M-sensitive, hybrid E/M-resistant, mesenchymal-sensitive and epithelial-resistant, with the first two ones being most dominant. Next, in a population dynamics framework, we exemplify the implications of phenotypic plasticity (both drug-induced and intrinsic stochastic switching) and/or non-genetic heterogeneity in promoting population survival in a mixture of sensitive and resistant cells, even in the absence of any cell–cell cooperation. Finally, we propose the potential therapeutic use of mesenchymal–epithelial transition inducers besides canonical anti-estrogen therapy to limit the emergence of reversible drug resistance. Our results offer mechanistic insights into empirical observations on EMT and drug resistance and illustrate how such dynamical insights can be exploited for better therapeutic designs.
- CancersEpithelial-to-Mesenchymal Transition Enhances Cancer Cell Sensitivity to Cytotoxic Effects of Cold Atmospheric Plasmas in Breast and Bladder Cancer SystemsPeiyu Wang, Renwu Zhou, Patrick Thomas, Liqian Zhao, Rusen Zhou, Susmita Mandal, Mohit Kumar Jolly, Derek J. Richard, Bernd H.A. Rehm, Kostya Ostrikov, Xiaofeng Dai, Elizabeth D. Williams, and Erik W ThompsonCancers
Cold atmospheric plasma (CAP) and plasma-activated medium (PAM) are known to selectively kill cancer cells, however the efficacy of CAP in cancer cells following epithelial-mesenchymal transition (EMT), a process which endows cancer cells with increased stemness, metastatic potential, and resistance to conventional therapies, has not been previously examined. We have used several established models of EMT to show that PAM is significantly more active in cancer cells exhibiting EMT than their epithelial counterparts. We further show that this enhancement correlated with increased levels of reactive oxygen species (ROS) in the mesenchymally-shifted cell lines.
- Comp & Sys OncoInvestigating epithelial-mesenchymal heterogeneity of tumors and circulating tumor cells with transcriptomic analysis and biophysical modelingFederico Bocci, Susmita Mandal, Tanishq Tejaswi, and Mohit Kumar JollyComputational and Systems Oncology
Cellular heterogeneity along the epithelial-mesenchymal plasticity (EMP) spectrum is a paramount feature observed in tumors and circulating tumor cells (CTCs). High-throughput techniques now offer unprecedented details on this variability at a single-cell resolution. Yet, there is no current consensus about how EMP in tumors propagates to that in CTCs. To investigate the relationship between EMP-associated heterogeneity of tumors and that of CTCs, we integrated transcriptomic analysis and biophysical modeling. We apply three epithelial-mesenchymal transition (EMT) scoring metrics to multiple tumor samples and CTC datasets from several cancer types. Moreover, we develop a biophysical model that couples EMT-associated phenotypic switching in a primary tumor with cell migration. Finally, we integrate EMT transcriptomic analysis and in silico modeling to evaluate the predictive power of several measurements of tumor aggressiveness, including tumor EMT score, CTC EMT score, fraction of CTC clusters found in circulation, and CTC cluster size distribution. Analysis of high-throughput datasets reveals a pronounced heterogeneity without a well-defined relation between EMT traits in tumors and CTCs. Moreover, mathematical modeling predicts different phases where CTCs can be less, equally, or more mesenchymal than primary tumor depending on the dynamics of phenotypic transition and cell migration. Consistently, various datasets of CTC cluster size distribution from different cancer types are fitted onto different regimes of the model. By further constraining the model with experimental measurements of tumor EMT score, CTC EMT score, and fraction of CTC cluster in bloodstream, we show that none of these assays alone can provide sufficient information to predict the other variables. In conclusion, we propose that the relationship between EMT progression in tumors and CTCs can be variable, and in general, predicting one from the other may not be as straightforward as tacitly assumed.
2020
- Stem Cell RepSingle-Cell Analysis Reveals Partial Reactivation of X Chromosome instead of Chromosome-wide Dampening in Naive Human Pluripotent Stem CellsSusmita Mandal, Deepshikha Chandel, Harman Kaur, Sudeshna Majumdar, Maniteja Arava, and Srimonta GayenStem Cell Reports
Recently, a unique form of X chromosome dosage compensation has been demonstrated in human preimplantation embryos, which happens through the dampening of X-linked gene expression from both X chromosomes. Subsequently, X chromosome dampening has also been demonstrated in female human pluripotent stem cells (hPSCs) during the transition from primed to naive state. However, the existence of dampened X chromosomes in both embryos and hPSCs remains controversial. Specifically, in preimplantation embryos it has been shown that there is inactivation of X chromosome instead of dampening. Here, we performed allelic analysis of X-linked genes at the single-cell level in hPSCs and found that there is partial reactivation of the inactive X chromosome instead of chromosome-wide dampening upon conversion from primed to naive state. In addition, our analysis suggests that the reduced X-linked gene expression in naive hPSCs might be the consequence of erasure of active X chromosome upregulation.