Browsing by Author "Tripathi, Shubham"

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    Analysis of Hierarchical Organization in Gene Expression Networks Reveals Underlying Principles of Collective Tumor Cell Dissemination and Metastatic Aggressiveness of Inflammatory Breast Cancer
    (Frontiers, 2018) Tripathi, Shubham; Jolly, Mohit Kumar; Woodward, Wendy A.; Levine, Herbert; Deem, Michael W.; Bioengineering; Physics and Astronomy
    Clusters of circulating tumor cells (CTCs), despite being rare, may account for more than 90% of metastases. Cells in these clusters do not undergo a complete epithelial-to-mesenchymal transition (EMT), but retain some epithelial traits as compared to individually disseminating tumor cells. Determinants of single cell dissemination versus collective dissemination remain elusive. Inflammatory breast cancer (IBC), a highly aggressive breast cancer subtype that chiefly metastasizes via CTC clusters, is a promising model for studying mechanisms of collective tumor cell dissemination. Previous studies, motivated by a theory that suggests physical systems with hierarchical organization tend to be more adaptable, have found that the expression of metastasis-associated genes is more hierarchically organized in cases of successful metastases. Here, we used the cophenetic correlation coefficient (CCC) to quantify the hierarchical organization in the expression of two distinct gene sets, collective dissemination-associated genes and IBC-associated genes, in cancer cell lines and in tumor samples from breast cancer patients. Hypothesizing that a higher CCC for collective dissemination-associated genes and for IBC-associated genes would be associated with retention of epithelial traits enabling collective dissemination and with worse disease progression in breast cancer patients, we evaluated the correlation of CCC with different phenotypic groups. The CCC of both the abovementioned gene sets, the collective dissemination-associated genes and the IBC-associated genes, was higher in (a) epithelial cell lines as compared to mesenchymal cell lines and (b) tumor samples from IBC patients as compared to samples from non-IBC breast cancer patients. A higher CCC of both gene sets was also correlated with a higher rate of metastatic relapse in breast cancer patients. In contrast, neither the levels of CDH1 gene expression nor gene set enrichment analysis (GSEA) of the abovementioned gene sets could provide similar insights. These results suggest that retention of some epithelial traits in disseminating tumor cells as IBC progresses promotes successful breast cancer metastasis. The CCC provides additional information regarding the organizational complexity of gene expression in comparison to GSEA. We have shown that the CCC may be a useful metric for investigating the collective dissemination phenotype and a prognostic factor for IBC.
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    DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases
    (Oxford University Press, 2022) Tripathi, Shubham; Brahmachari, Sumitabha; Onuchic, José N.; Levine, Herbert; Center for Theoretical Biological Physics
    Multiple RNA polymerases (RNAPs) transcribing a gene have been known to exhibit collective group behavior, causing the transcription elongation rate to increase with the rate of transcription initiation. Such behavior has long been believed to be driven by a physical interaction or ‘push’ between closely spaced RNAPs. However, recent studies have posited that RNAPs separated by longer distances may cooperate by modifying the DNA segment under transcription. Here, we present a theoretical model incorporating the mechanical coupling between RNAP translocation and the DNA torsional response. Using stochastic simulations, we demonstrate DNA supercoiling-mediated long-range cooperation between co-transcribing RNAPs. We find that inhibiting transcription initiation can slow down the already recruited RNAPs, in agreement with recent experimental observations, and predict that the average transcription elongation rate varies non-monotonically with the rate of transcription initiation. We further show that while RNAPs transcribing neighboring genes oriented in tandem can cooperate, those transcribing genes in divergent or convergent orientations can act antagonistically, and that such behavior holds over a large range of intergenic separations. Our model makes testable predictions, revealing how the mechanical interplay between RNAPs and the DNA they transcribe can govern transcriptional dynamics.
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    Hierarchy in gene expression is predictive of risk, progression, and outcome in adult acute myeloid leukemia
    (IOP Publishing, 2015) Tripathi, Shubham; Deem, Michael W.; Bioengineering; Physics and Astronomy
    Cancer progresses with a change in the structure of the gene network in normal cells. We define a measure of organizational hierarchy in gene networks of affected cells in adult acute myeloid leukemia (AML) patients. With a retrospective cohort analysis based on the gene expression profiles of 116 AML patients, we find that the likelihood of future cancer relapse and the level of clinical risk are directly correlated with the level of organization in the cancer related gene network. We also explore the variation of the level of organization in the gene network with cancer progression. We find that this variation is non-monotonic, which implies the fitness landscape in the evolution of AML cancer cells is non-trivial. We further find that the hierarchy in gene expression at the time of diagnosis may be a useful biomarker in AML prognosis.
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    Nucleosomes play a dual role in regulating transcription dynamics
    (National Academy of Sciences, 2024) Brahmachari, Sumitabha; Tripathi, Shubham; Onuchic, José N.; Levine, Herbert; Center for Theoretical Biological Physics
    Transcription has a mechanical component, as the translocation of the transcription machinery or RNA polymerase (RNAP) on DNA or chromatin is dynamically coupled to the chromatin torsion. This posits chromatin mechanics as a possible regulator of eukaryotic transcription, however, the modes and mechanisms of this regulation are elusive. Here, we first take a statistical mechanics approach to model the torsional response of topology-constrained chromatin. Our model recapitulates the experimentally observed weaker torsional stiffness of chromatin compared to bare DNA and proposes structural transitions of nucleosomes into chirally distinct states as the driver of the contrasting torsional mechanics. Coupling chromatin mechanics with RNAP translocation in stochastic simulations, we reveal a complex interplay of DNA supercoiling and nucleosome dynamics in governing RNAP velocity. Nucleosomes play a dual role in controlling the transcription dynamics. The steric barrier aspect of nucleosomes in the gene body counteracts transcription via hindering RNAP motion, whereas the chiral transitions facilitate RNAP motion via driving a low restoring torque upon twisting the DNA. While nucleosomes with low dissociation rates are typically transcriptionally repressive, highly dynamic nucleosomes offer less of a steric barrier and enhance the transcription elongation dynamics of weakly transcribed genes via buffering DNA twist. We use the model to predict transcription-dependent levels of DNA supercoiling in segments of the budding yeast genome that are in accord with available experimental data. The model unveils a paradigm of DNA supercoiling-mediated interaction between genes and makes testable predictions that will guide experimental design.
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    The physics of cell-fate choice
    (2022-07-26) Tripathi, Shubham; Levine, Herbert; Igoshin, Oleg A
    Multicellular organisms are composed of many different cell types. All such cells arise from a single cell--- the zygote--- and acquire the various cell fates seen in adult organisms. The different cell types are characterized by distinct, cell-fate-specific gene expression patterns. Cells of different types can also exhibit varying metabolic states depending on their intrinsic needs and the nutrient microenvironment. Both during development and in adult organisms, cell-fate choice is tightly controlled, and its dysregulation is known to contribute to many pathologies, including cancer. In this thesis, I describe our simulations-based efforts to identify certain general principles underlying cell-fate choice. Throughout, I discuss how such regulation can go awry in a disease like cancer, leading to the emergence of aberrant cell fates. First, I describe a spin glass-based theory of minimal frustration in regulatory networks implicated in cell-fate choice, and show that the minimal frustration property is key to the robust establishment and maintenance of biological cell-fates. The minimal frustration property is also crucial to the success of various systems biology models of cell-fate choice. Next, I present two models concerning noise in cell-fate choice--- a mechanical model of DNA supercoiling-mediated transcriptional noise and a coarse-grained model of noise in partitioning during cell division that can create and maintain a phenotypically heterogeneous population. Finally, I describe a mechanistic model of the key metabolic pathways active in tumors and other fast-proliferating cells. Our model recapitulates tumor cell behavior across contexts and makes useful predictions concerning the ways tumor cells can evade metabolic therapies. Overall, this thesis describes multiple examples of how physical and systems biology-based approaches can be leveraged to understand the key principles underlying cell-fate choice across biological contexts.