Biology subjects

Sood, C.

Publications and source records attributed to Sood, C..

3 recordsLinked to original sources

bioRxiv2025

A live tumor fragment platform to assess immunotherapy response in core needle biopsies while addressing challenges of tumor heterogeneity

BackgroundImmune checkpoint inhibitors (ICIs) have revolutionized cancer treatment, providing durable and even curative responses. However, most patients do not respond and current biomarkers (eg, programmed death ligand (PD-L1), mismatch repair deficiency (dMMR)/high microsatellite instability (MSI) and tumor mutational burden) lack predictive accuracy. Ex vivo profiling of patient-derived tumor fragments shows promise as a predictive biomarker but relies on substantial surgical tissue to mitigate intra-specimen heterogeneity. Innovations are needed that address these challenges, particularly where limited tissue is available in core needle biopsies (CNBs). MethodsLive tumor fragments (LTFs) were generated from 59 human tumor resections and 31 CNBs from patients enrolled in observational clinical trials (ClinicalTrials.gov identifiers: NCT05478538, NCT05520099, NCT06349642) to assess cytokine induction following ICI treatment. LTFs were encapsulated in hydrogel and cultured ex vivo for up to 72 hours. A sequential treatment strategy that applies control and treatment within the same well was used with response to ICI or CD3/CD28 assessed using a multiplex secretome assay. Viability was assessed using established metabolic assays and dynamic optical coherence microscopy. ResultsLTFs maintained viability and retained T cells responsive to stimulation throughout ex vivo culture. Multiplex immunofluorescence and immunohistochemistry showed key components of the tumor microenvironment, including relative proportions of CD4+ and CD8+ immune cell populations, were preserved. Specimens positive for PD-L1 or dMMR/MSI-high were enriched for cytokine upregulation, including T-cell response cytokines IFN{gamma} and CXCL10, after PD-1 treatment. To demonstrate clinical applicability of the sequential treatment strategy, CNBs from patients with lung, gastrointestinal or kidney cancer were profiled and differential cytokine induction in response to ICI treatment was observed. ConclusionsThe novel ex vivo platform presented is capable of detecting T-cell response to ICI treatment by using a sequential treatment strategy. This approach addresses challenges associated with cross-well heterogeneity in tissue composition and requires half as much tissue as a cross-well comparison, mitigating tissue limitations typically associated with non-surgical biopsies. Importantly, the platform is compatible with established functional assays as well as non-destructive spatial imaging, enabling researchers to characterize response to ICI longitudinally. Ongoing trials will enable clinicians to assess platform performance in predicting response to immunotherapy.

cancer biology↗

bioRxiv2024

Notch controls early temporal factor expression to control timing of Mushroom body neuroblast apoptosis

The neurogenic period, where neural stem cells (NSCs) proliferate to produce molecularly distinct progeny in the developing brain, is a critical time of growth in many organisms. Proper brain development is crucial for survival and requires strict regulation of NSC divisions along a set developmental timeline. In Drosophila NSCs known as neuroblasts (NBs), cell intrinsic programs integrate with extrinsic cues to control periods of rapid growth through temporal patterning genes. Without regulation, NSCs can under proliferate leading to diseases like microcephaly and autism spectrum disorders, or over proliferate leading to macrocephaly and tumors. We know programs to control timing of proliferation and elimination of NSCs exist, but many elements of temporal cassettes are still unclear. What genes may be upstream to regulate known temporal programs to control when certain progeny are produced have not been fully identified, leaving a gap in our understanding. To address these questions, we carried out a large-scale RNAi screen aimed at identifying genes required for NSC elimination. We identified Notch and its ligand, Delta. When Notch pathway activity is reduced in NSCs, we found premature elimination of an important subset of neuroblasts called the mushroom body neuroblasts (MBNBs). These MBNBs produce the neurons responsible for formation of the evolutionarily conserved structure called the mushroom body (MB), which is involved in olfactory based learning and memory. MBNBs with reduced Notch pathway activity also experienced defects in MB structure. Furthermore, we determined that temporal patterning is disrupted primarily through loss of early temporal factor expression. In this work, we find that cell signaling pathways that involve the receptor Notch and its ligand. Delta function to regulate NB proliferation in Drosophila melanogaster by regulating early temporal factor expression.

developmental biology↗

bioRxiv2023

Delta-dependent Notch activation closes the early neuroblast temporal program to promote lineage progression and neurogenesis termination in Drosophila

Neuroblasts in Drosophila divide asymmetrically, sequentially expressing a series of intrinsic factors to generate a diversity of neuron types. These intrinsic factors known as temporal factors dictate timing of neuroblast transitions in response to steroid hormone signaling and specify early versus late temporal fates in neuroblast neuron progeny. After completing their temporal programs, neuroblasts differentiate or die, finalizing both neuron number and type within each neuroblast lineage. From a screen aimed at identifying genes required to terminate neuroblast divisions, we identified Notch and Notch pathway components. When Notch is knocked down, neuroblasts maintain early temporal factor expression longer, delay late temporal factor expression, and continue dividing into adulthood. We find that Delta, expressed in cortex glia, neuroblasts, and after division, their GMC progeny, regulates neuroblast Notch activity. We also find that Delta in neuroblasts is expressed high early, low late, and is controlled by the intrinsic temporal program: early factor Imp promotes Delta, late factors Syp/E93 reduce Delta. Thus, in addition to systemic steroid hormone cues, forward lineage progression is controlled by local cell-cell signaling between neuroblasts and their cortex glia/GMC neighbors: Delta transactivates Notch in neuroblasts bringing the early temporal program and early temporal factor expression to a close.

developmental biology↗