Biology subjects

Shaikh, R.

Publications and source records attributed to Shaikh, R..

7 recordsLinked to original sources

bioRxiv2026

Integrative Multiomics Analysis of the Angiogenesis-EMT Interface in Head and Neck Squamous Cell Carcinoma

Angiogenesis and epithelial-mesenchymal transition (EMT) are key hallmarks that contribute to the progression of oral squamous cell carcinoma (OSCC), but whether the two programs vary simultaneously across tumors and how much of this reflects tumor composition remain unclear. We scored predefined, non-overlapping 20-gene angiogenesis and EMT signatures with a rank-based method in 342 primary oral cavity tumors from The Cancer Genome Atlas (TCGA-OSCC). The two programs were strongly correlated (Spearman rho = 0.809, P = 2.7 x 10^-80), and 2,396 bridge genes were associated with both programs across the transcriptome. The bridge genes were enriched in pathways associated with focal adhesion and extracellular matrix-receptor interaction. In the cellular case, fibroblast and endothelial marker scores were prominent and correlated with the program scores. The coupling was attenuated but remained positive after joint adjustment for tumor purity and stromal and immune scores (partial rho = 0.406) and with an epithelial-restricted EMT score (rho = 0.710). Further correlation was performed with a partial EMT (pEMT), which shows a significant positive correlation (rho = 0.59) and an inverse correlation with tumor purity (rho = -0.70). 146 final gene candidates were found using multi-omic evidence and candidate-level testing on the external cohort GSE30784; after adjusting for inferred cell fractions, 101 of these candidates supported the dual program. For thorough characterization, three candidates with an emphasis on OSMR, MICAL2, and LHFPL2 were chosen. Additional CPTAC data were used to confirm protein-level support, which was strongest for MICAL2. No significant connection was seen between the Interface score and overall survival (hazard ratio per 1-SD increase, 0.92; 95% CI, 0.78-1.08). These results describe a coordinated angiogenesis-EMT transcriptional state in OSCC that is attenuated but retained after accounting for tumor composition, and nominate candidate genes for experimental study.

bioinformatics↗

bioRxiv2026

Enhancer Activity-informed Gap GEne Regulatory Network (EAGER) to model Drosophila gap gene expression on the entire anterior-posterior (A-P) axis

Across metazoa, morphogen gradients differentially regulate gene expression and activate a spatially distinct program to specify body axis development. The Drosophila gap gene network, initiated by maternal morphogen Bicoid, is one of the most well-studied systems. Several regulatory interactions act synergistically to produce distinct gap gene expression patterns along the anterior-posterior (AP) axis of the blastoderm stage Drosophila embryo to ensure the proper segmentation of the larval and, eventually, adult stage fly. Several mathematical models have been proposed to summarize the interconnectivity of gap gene regulatory elements and predict expression in mutant systems. However, these models have not successfully predicted the gap gene expression profile over the entire AP axis. Here, we present an Enhancer Activity-informed Gap GEne Regulatory network (EAGER) model that incorporates enhancer activity-driven differential regulation along the AP axis, which successfully summarizes gap gene expression patterns over the entire AP axis. We validated the predictions of EAGER on Kr mutants and performed a comprehensive parametric sensitivity and identifiability analysis to evaluate the robustness of the EAGER model fits and predictions. We also propose a reduced version of the model, rEAGER, which identifies a minimal set of regulatory interactions and successfully summarizes the gap gene interactions over the entire AP axis. Our results suggest that the expression driven by individual enhancers must be accounted for in models of developmental pattern formation.

developmental biology↗

bioRxiv2025

MIDOE: Maximally-informed Design of Experiment to infer experimentally inaccessible transcription factors dynamics

1The TGF-{beta}/Smad signaling pathway regulates growth, development, and homeostasis of tissues across the animal kingdom. The pathway is activated when transforming growth factor -{beta} (TGF-{beta}) binds to its cognate transmembrane receptors to activate Smad2 by phosphorylation. The activated phosphor-Smad2 (PSmad2) undergoes a series of biochemical interactions with transcriptional activator Smad4 to form several oligomers, including the transcription factor (PSmad2)2/Smad4, which regulates target gene expression. Quantitative live cell imaging and mathematical modeling have been used to estimate the dynamics of (PSmad2)2/Smad4. However, due to the emergent nature of Smad2-Smad4 interactions, deconvolving the dynamics of the (PSmad2)2/Smad4 is challenging. We show that the Smad model is sloppy, has large parameter uncertainties (O[~]1015), and the eigenvalues of the Fisher Information Matrix span over several decades. As such, well-fit parameter sets generate highly under-constrained predictions. To overcome this, we employ Profile Log-Likelihood to guide maximally informed design of experiments (MIDOE) and infer the dynamics of (PSmad2)2/Smad4. We generate these experiments computationally and validate that MIDOE can optimally constrain model predictions. We demonstrate that such careful analysis would not only improve the predictive power of models in systems biology but also reduce the time and expense of performing non-optimal experiments.

systems biology↗

bioRxiv2024

Elucidating the role of multiple feedback loops in regulating stem cell decisions

Stem cell decisions are regulated by a complex network of gene regulatory pathways that determine the reproductive health of the tissue. The Drosophila ovarian germline is a well-characterized model system which facilitates visualizing stem cell behavior in its native environment to attain a systems-level understanding of the stem cell dynamics. The asymmetric division of the Germline Stem Cells (GSCs) forms two daughter cells-a self-renewed GSC and a differentiated Cystoblast (CB). The highly conserved Bone Morphogenetic Protein (BMP) pathway ensures growth and maintenance of the GSCs, but is downregulated in the CBs, to allow for differentiation. BMP signal transduction upregulates dad and represses Fused, both of which are negative regulators of the BMP pathway. Moreover, these regulatory mechanisms operate on a system of two cells which remain connected during a portion of the cell cycle. We developed a biologically-informed mathematical model of multi-compartment GSC division to investigate the dynamic roles Dad and Fused play in determining cell fate. We found that Dad optimally controls the BMP signal transduction to enable GSC homeostasis and differentiation. In dadKO mutants, GSCs were more likely to divide symmetrically. Our work identifies the synergistic role of Dad and Fused rendering robustness to stem cell division.

systems biology↗

bioRxiv2024

Spatiotemporal dynamics of NF-κB/Dorsal inhibitor IκBα/Cactus in Drosophila blastoderm embryos

The NF-{kappa}B signaling pathway is a key regulatory network in mammals that controls many cellular processes, including immunity and inflammation. Of particular note is the relationship between NF-{kappa}B and its inhibitor I{kappa}B, which sequesters NF-{kappa}B to the cytoplasm of cells until needed. It is also known that I{kappa}B can enter nuclei, disrupt NF-{kappa}B binding to DNA, and shuttle it out to again sequester NF-{kappa}B in the cytoplasm. In Drosophila melanogaster, a homologous system between the proteins Dorsal (homologous to NF-{kappa}B) and Cactus (homologous to I{kappa}B) is important in embryo development, specifically in establishment of the Dorsal nuclear concentration gradient. Previous work suggests Cactus also enters the nucleus; mathematical models of the Dorsal gradient fail to accurately predict the normal range of the gradient without nuclear Cactus. However, direct, in vivo visualization of Cactus spatiotemporal dynamics, including its localization to the nuclei, has been difficult to gather. Previously, imaging Cactus in live embryos was complicated by rapid protein turnover, preventing fluorescent protein fusions from fully maturing. To address this, we used the CRISPR/Cas9 system to tag Cactus with the recently developed "LlamaTag" (LT), a genetically encodable nanobody from llamas that dynamically binds to GFP in vivo. We then employed standard confocal imaging, as well as advanced optical techniques such as raster image correlation spectroscopy (RICS) and fluorescent recovery after photobleaching (FRAP) to investigate the spatiotemporal distribution of Cactus-LlamaTag in Drosophila embryos at the blastoderm stage. Our results demonstrate that Cactus can be found in the nuclei of early embryos, consistent with its role as a transcription factor regulator. Moreover, by using the data from FRAP and RICS, we were able to estimate biophysical parameters of Cactus dynamics in vivo, including its nuclear transport rate constants and fraction bound to GFP. These data were further used to constrain a mathematical model that allowed us to infer experimentally inaccessible biophysical parameters, such as the concentration of Cact protein and the dissociation constant of LT and GFP. Our study provides new insights into the regulation of the NF-{kappa}B pathway in early Drosophila embryos and highlights the power of advanced optical techniques for investigating complex biological dynamics.

developmental biology↗

bioRxiv2024

Optimal Performance Objectives in the Highly Conserved Bone Morphogenetic Protein Signaling Pathway

Throughout development, complex networks of cell signaling pathways drive cellular decision-making across different tissues and contexts. The transforming growth factor {beta} (TGF-{beta}) pathways, including the BMP/Smad pathway, play crucial roles in these cellular responses. However, as the Smad pathway is used reiteratively throughout the life cycle of all animals, its systems-level behavior varies from one context to another, despite the pathway connectivity remaining nearly constant. For instance, some cellular systems require a rapid response, while others require high noise filtering. In this paper, we examine how the BMP- Smad pathway balances trade-offs among three such systems-level behaviors, or "Performance Objectives (POs)": response speed, noise amplification, and the sensitivity of pathway output to receptor input. Using a Smad pathway model fit to human cell data, we show that varying non-conserved parameters (NCPs) such as protein concentrations, the Smad pathway can be tuned to emphasize any of the three POs and that the concentration of nuclear phosphatase has the greatest effect on tuning the POs. However, due to competition among the POs, the pathway cannot simultaneously optimize all three, but at best must balance trade-offs among the POs. We applied the multi-objective optimization concept of the Pareto Front, a widely used concept in economics to identify optimal trade-offs among various requirements. We show that the BMP pathway efficiently balances competing POs across species and is largely Pareto optimal. Our findings reveal that varying the concentration of NCPs allows the Smad signaling pathway to generate a diverse range of POs. This insight identifies how signaling pathways can be optimally tuned for each context.

systems biology↗

bioRxiv2020

Infrared fiber optic spectroscopy detects bovine articular cartilage degeneration

Articular cartilage (AC) is a soft connective tissue that covers the ends of articulating bones. Joint injuries may lead to degeneration of cartilage tissue and initiate development of post-traumatic osteoarthritis (OA). Arthroscopic surgeries can be used to treat joint injuries, but arthroscopic evaluation of cartilage quality is subjective. Therefore, new methods are needed for objective assessment of cartilage degeneration. Fourier transform infrared (FTIR) spectroscopy can be used to assess tissue composition based on the fundamental molecular vibrations. When combined with fiber optics and attenuated total reflectance (ATR) crystal, the measurements can be done flexibly without any sample processing. We hypothesize that Fourier transform infrared attenuated total reflection (FTIR-ATR) spectroscopy can detect enzymatically and mechanically induced changes similar to changes occurring during progression of OA. Fresh bovine patellar cartilage plugs (n = 60) were extracted and degraded enzymatically and mechanically. Adjacent untreated control samples (n = 60) were utilized as controls. Enzymatic degradation was implemented by 90-min and 24-hour collagenase as well as 30-min trypsin treatments. Mechanical damage was induced by: 1) dropping a weight impactor on the cartilage plugs, and 2) abrading the cartilage surface with a rotating sandpaper. Fiber optic FTIR-ATR spectroscopic measurements were conducted for control and degraded samples, and spectral changes were assessed with random forest (RF), partial least squares discriminant analysis (PLS-DA), and support vector machine (SVM) classifiers. RF (accuracy 93.1 % to 79.2 %), PLS-DA (accuracy 95.8% to 81.9%), and SVM (accuracy 91.7% to 80.6%) all had excellent classification performance for detecting the different enzymatic and mechanical damage on cartilage matrix. The results suggest that fiber optic FTIR-ATR spectroscopy is a viable way to detect minor degeneration of AC.

biophysics↗