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Das, S. S.

Publications and source records attributed to Das, S. S..

4 recordsLinked to original sources

Mechanistically informed adaptive dosing for cancer immunotherapy using AI-guided decision making

Optimizing dose and schedule remains a central challenge in oncology drug development, particularly for immunotherapies where fixed dosing regimens often fail to account for patient specific heterogeneity in tumor-immune dynamics. Here, we present a hybrid quantitative systems pharmacology-reinforcement learning-Monte Carlo Tree Search (QSP-RL-MCTS) framework for personalized immunotherapy dosing that formulates dose selection as a sequential decision-making problem. The approach integrates a mechanistic QSP model of prostate cancer immunotherapy, transcriptomics informed virtual patient populations and data driven AI system comprising reinforcement learning and Monte Carlo tree search. Reinforcement learning is used to learn adaptive generalized dosing policies that optimize treatment outcomes across the population, while Monte Carlo Tree Search provides forward-looking evaluation of RL predicted dosing trajectories to refine patient-specific decisions. On benchmarking against fixed dosing regimens of ipilimumab, the remission rate of the proposed model (95.2%) was comparable to the highest fixed dosing regimen of 10 mg/kg per dose while the median total dose (72 mg/kg) of the proposed model designed regimen was comparable to the lowest fixed dosing regimen of 3 mg/kg per dose. The model is generalizable across different dosing protocols and can be extended to predict optimal dose under different therapeutic scenarios. Analysis of the learned dosing trajectories enables stratification of patients into distinct response groups and identifies drug activity rate as the dominant determinant of long-term treatment outcome. These results demonstrate how mechanistically guided artificial intelligence can transform population-level dose optimization into patient-specific, biologically interpretable treatment strategies for precision immuno-oncology.

systems biology↗

Single-cell DNA methylome and 3D genome atlas of the human subcutaneous adipose tissue

Human subcutaneous adipose tissue (SAT) contains a diverse array of cell-types; however, the epigenomic landscape among the SAT cell-types has remained elusive. Our integrative analysis of single-cell resolution DNA methylation and chromatin conformation profiles (snm3C-seq), coupled with matching RNA expression (snRNA-seq), systematically cataloged the epigenomic, 3D topology, and transcriptomic dynamics across the SAT cell-types. We discovered that the SAT CG methylation (mCG) landscape is characterized by pronounced hyper-methylation in myeloid cells and hypo-methylation in adipocytes and adipose stem and progenitor cells (ASPCs), driving nearly half of the 705,063 detected differentially methylated regions (DMRs). In addition to the enriched cell-type-specific transcription factor binding motifs, we identified TET1 and DNMT3A as plausible candidates for regulating cell-type level mCG profiles. Furthermore, we observed that global mCG profiles closely correspond to SAT lineage, which is also reflected in cell-type-specific chromosome compartmentalization. Adipocytes, in particular, display significantly more short-range chromosomal interactions, facilitating the formation of complex local 3D genomic structures that regulate downstream transcriptomic activity, including those associated with adipogenesis. Finally, we discovered that variants in cell-type level DMRs and A compartments significantly predict and are enriched for variance explained in abdominal obesity. Together, our multimodal study characterizes human SAT epigenomic landscape at the cell-type resolution and links partitioned polygenic risk of abdominal obesity to SAT epigenome.

genomics↗

MicroRNA775 and target Galactosyltransferase (GALT9) module regulates recovery from submergence induced senescence by modulating SAGs in Arabidopsis thaliana

Submergence induced hypoxic condition is one of the abiotic stresses which negatively affects the plant growth and development, and causes early onset of senescence. Hypoxic conditions ateres the expression of a number of non-coding microRNAs (miRNAs), besides protein-coding genes. However, the molecular function of stress-induced miRNA in submergence induced physiological or developmental changes and recovery remains to be understood. The expression of miR775 is highly induced under hypoxic stress conditions. Here, we show that miR775 is a potential post-transcriptional regulator number of targets, including Galactosyltransferase (GALT9). The expression of miR775 and target GALT9 was significantly induced and reduced respectively at 24 hours of submergence. The overexpression of miR775 (miR775-Oe) confers enhanced recovery from submergence stress and reduced accumulation of ROS, in contrast to wild type and endogenous target mimic of miR775 (MIM775) Arabidopsis plants. We observed a similar recovery phenotype in case of target galt9 mutant plants, indicating the role of miR775-GALT9 module in recovery from submergence. Further, we showed that the expression of SENESCENCE ASSOCIATED GENES (SAGs), such as SAG12, SAG29, and ORE1. was increased in MIM775 and reduced in miR775-Oe and galt9 plants. Thus, our results suggest that miR775-GALT9 module plays a crucial role in the recovery from submergence by modulating the expression of SAGs through differential accumulation of ROS.

plant biology↗

Antagonistic activities of Fmn2 and ADF regulate axonal F-actin patch dynamics and the initiation of collateral branching

Interstitial collateral branching of axons is a critical component in the development of functional neural circuits. Axon collateral branches are established through a series of cellular processes initiated by the development of a specialized, focal F-actin network in axons. The formation, maintenance and remodelling of this F-actin patch is critical for the initiation of axonal protrusions that are subsequently consolidated to form a collateral branch. However, the mechanisms regulating F-actin patch dynamics are poorly understood. Fmn2 is a formin family member implicated in multiple neurodevelopmental disorders. We find that Fmn2 regulates the initiation of axon collateral protrusions. Fmn2 localises to the protrusion-initiating axonal F-actin patches and regulates the lifetime and size of these F-actin networks. The F-actin nucleation activity of Fmn2 is necessary for F-actin patch stability but not for initiating patch formation. We show that Fmn2 insulates the F-actin patches from disassembly by the actin-depolymerizing factor, ADF, and promotes long-lived, larger patches that are competent to initiate axonal protrusions. The regulation of axonal branching can contribute to the neurodevelopmental pathologies associated with Fmn2 and the dynamic antagonism between Fmn2 and ADF may represent a general mechanism of formin-dependent protection of Arp2/3-initiated F-actin networks from disassembly.

neuroscience↗