publications

2025

1. Nature

   OncoMark: a high-throughput neural multi-task learning framework for comprehensive cancer hallmark quantification

   Shreyansh Priyadarshi, Camellia Mazumder, Bhavesh Neekhra, and 4 more authors

   Nature Communications Biology, 2025

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   Quantifying the biological processes that drive cancer progression remains a key challenge in oncology. Although the hallmarks of cancer provide a foundational framework for understanding tumor behavior, existing diagnostic tools rarely measure these hallmarks directly. Here we present a neural multi-task learning-based framework that estimates hallmark activity using gene expression data from tumor biopsies. The model was trained on transcriptomic profiles from 941 tumors spanning 14 tissue types and tested on five independent datasets. It predicts the activity of ten cancer hallmarks simultaneously and with high accuracy. Additional validation on large-scale datasets including normal and cancer samples confirmed its sensitivity and specificity. Predicted hallmark activity was associated with clinical staging, suggesting biological relevance. A web-based tool was developed to facilitate integration into research and clinical workflows. This approach enables efficient analysis of transcriptomic data to inform understanding of tumor biology and support individualized treatment strategies.

   @article{shreyansh2025oncomark,
     title = {OncoMark: a high-throughput neural multi-task learning framework for comprehensive cancer hallmark quantification},
     author = {Priyadarshi, Shreyansh and Mazumder, Camellia and Neekhra, Bhavesh and Biswas, Sayan and Chowdhury, Debojyoti and Gupta, Debayan and Haldar, Shubhasis},
     year = {2025},
     journal = {Nature Communications Biology},
     doi = {https://doi.org/10.1038/s42003-025-08727-z},
     metatype = {Published}
   }

2024

1. Nature

   Pan-cancer analyses suggest kindlin-associated global mechanochemical alterations

   Debojyoti Chowdhury*, Ayush Mistry*, Debashruti Maity, and 5 more authors

   Nature Communications Biology, 2024

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   Kindlins serve as mechanosensitive adapters, transducing extracellular mechanical cues to intracellular biochemical signals and thus, their perturbations potentially lead to cancer progressions. Despite the kindlin involvement in tumor development, understanding their genetic and mechanochemical characteristics across different cancers remains elusive. Here, we thoroughly examined genetic alterations in kindlins across more than 10,000 patients with 33 cancer types. Our findings reveal cancer-specific alterations, particularly prevalent in advanced tumor stage and during metastatic onset. We observed a significant co-alteration between kindlins and mechanochemical proteome in various tumors through the activation of cancer-related pathways and adverse survival outcomes. Leveraging normal mode analysis, we predicted structural consequences of cancer-specific kindlin mutations, highlighting potential impacts on stability and downstream signaling pathways. Our study unraveled alterations in epithelial–mesenchymal transition markers associated with kindlin activity. This comprehensive analysis provides a resource for guiding future mechanistic investigations and therapeutic strategies targeting the roles of kindlins in cancer treatment.

   @article{shreyansh2024kindlin,
     title = {Pan-cancer analyses suggest kindlin-associated global mechanochemical alterations},
     author = {Chowdhury*, Debojyoti and Mistry*, Ayush and Maity, Debashruti and Bhatia, Riti and Priyadarshi, Shreyansh and Wadan, Simran and Chakraborty, Soham and Haldar, Shubhasis},
     year = {2024},
     journal = {Nature Communications Biology},
     doi = {https://doi.org/10.1038/s42003-024-06044-5},
     metatype = {Published}
   }

2. bioRxiv

   Comprehensive Enumeration of Cancer Stem-like Cell Heterogeneity Using Deep Neural Network

   Debojyoti Chowdhury*, Shreyansh Priyadarshi*, Sayan Biswas, and 3 more authors

   bioarXiv (preprint), 2024

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   Cancer stem cells (CSCs), a distinct subpopulation within tumors, are pivotal in driving treatment resistance and tumor recurrence, posing substantial challenges to conventional therapeutic strategies. Precise quantification and profiling of these cells are essential for improving cancer treatment outcomes. We present ACSCeND, an advanced deep neural network model accompanied by a robust workflow, specifically developed to quantify cellular compositions from bulk RNA-seq data, enabling accurate CSC profiling. By integrating bulk RNA-seq data with insights derived from single-cell RNA-seq datasets, ACSCeND effectively captures the diversity and hierarchical organization of tumor-resident cell states, alongside cell-specific gene expression profiles (GEPs). Compared to current tissue deconvolution models, ACSCeND exhibits superior performance, achieving significantly higher Concordance Correlation Coefficient (CCC) values and lower Root Mean Square Error (RMSE) across various pseudobulk and real-world bulk tissue samples. Application of ACSCeND to TCGA and PRECOG datasets reveals a strong association between CSC abundance and poorer disease-free survival outcomes, underscoring the clinical relevance of CSCs in cancer progression. Furthermore, cell-specific GEPs for distinct CSC states unveil novel molecular signatures and illuminate the origins of CSC-driven tumor heterogeneity. In summary, ACSCeND provides a powerful, scalable platform for high-throughput quantification of cellular compositions and distinct potency states within normal tissues as well as highly heterogeneous tissues, such as tumors.

   @article{shreyansh2024stem,
     title = {Comprehensive Enumeration of Cancer Stem-like Cell Heterogeneity Using Deep Neural Network},
     author = {Chowdhury*, Debojyoti and Priyadarshi*, Shreyansh and Biswas, Sayan and Neekhra, Bhavesh and Gupta, Debayan and Haldar, Shubhasis},
     year = {2024},
     journal = {bioarXiv (preprint)},
     doi = {https://doi.org/10.1101/2024.11.26.625418},
     metatype = {Under Review}
   }