Biology subjects

Sedighi, S.

Publications and source records attributed to Sedighi, S..

7 recordsLinked to original sources

bioRxiv2026

SureQuant IS-PRM Enables Cross-Species Targeted Quantification of Retinoid Metabolism and Signaling Proteins in the Heart

Retinoic acid signaling is critical for cardiac development and homeostasis. Dysregulation of all-trans retinoic acid metabolism contributes to vascular atherogenesis, restenosis, calcification, and heart failure. Therefore, assessment of proteins involved in retinoid metabolism and signaling has gained interest for identifying potential biomarkers and therapeutic targets in cardiovascular disease. However, quantifying these proteins remains challenging due to limitations of antibody-based methods. We developed a targeted proteomics approach using SureQuant internal standard-triggered parallel reaction monitoring mass spectrometry to profile these proteins. We designed a panel of 80 stable isotope-labeled (heavy) peptides representing proteins involved in retinoid signaling and metabolism, with sequences applicable to human samples and conserved across multiple species. Survey experiments using directed data-dependent acquisition on the Orbitrap Fusion Lumos mass spectrometer determined precursor and product ion masses for each heavy peptide, which were programmed into the SureQuant method for continuous monitoring. Upon detection of these heavy internal standards, the instrument transitions to a targeted PRM acquisition mode in which repeated high-resolution MS/MS spectra of both endogenous (light) and heavy peptides are acquired. Using this method, retinoid pathway-associated proteins were quantified to as low as 10 attomoles for selected targets across multiple tissues and developmental stages. Distinct tissue-specific retinoid metabolic networks were identified across lung, liver, retinal cell lines and cardiac tissues. Developmental profiling of mouse and rat hearts revealed remodeling of retinoid pathway proteins from embryonic to postnatal and adult stages, suggesting a functional transition from retinoid-driven cardiac development toward maintenance of retinoid homeostasis in the mature heart.

biochemistry↗

bioRxiv2026

Chromosome 2q31.2 Deletion Impairs Neuronal Plasticity through Integrated Stress Response Activation

Rare genomic deletions disrupt gene networks essential for neural development and synaptic plasticity, yet their mechanistic effects remain poorly understood. Here, we investigated the impact of a chromosome 2q31.2 deletion using induced pluripotent stem cell (iPSC)-derived neural models from an affected individual and a genetically matched parental control. Differentiation into neural precursor cells and glial lineages was maintained, with subtle changes in cytoskeletal and lineage-associated gene expression. Transcriptomic analysis showed activation of oxidative stress, mitochondrial dysfunction, and degeneration-linked pathways, consistent with engagement of the integrated stress response (ISR). Pharmacologic inhibition of the ISR with ISRIB reduced ATF4 expression in neural precursors and mature neurons and increased CREB phosphorylation throughout development. Functionally, ISRIB improved neuronal network activity in cortical organoids, increasing calcium burst amplitude and synchronization after NMDA and AMPA stimulation. These results identify ISR dysregulation as a mechanistic link between chromosome 2q31.2 deletion and impaired neuronal plasticity, highlighting ISR modulation via ISRIB as a potential therapeutic approach.

neuroscience↗

bioRxiv2025

AI-Driven and 3D-Bioprinted New Approach Methodology (NAM) Identifies NEO100 as Potent Ultrasound-Activated Therapeutic for Primary and Metastatic Brain Tumors

Primary and metastatic brain tumors are among the deadliest and treatment-resistant cancers, mainly because of their inherent resistance to chemoradiation and limited drug delivery across the blood-brain barrier (BBB). Identifying molecules that can cross the BBB and serve as sonosensitizers is crucial for developing noninvasive, targeted therapies such as sonodynamic therapy (SDT). To overcome the limitations of traditional low-throughput screening, a New Approach Methodology (NAM) was developed, starting with AI-driven molecular discovery. A positive-unlabeled neural network, trained on over 200 molecular descriptors, was used to predict compounds likely to respond to focused ultrasound (FUS), penetrate the BBB, and mediate therapeutic sonodynamic activity. While AI helps prioritize potent candidates, effective SDT also depends on clinically scalable FUS delivery. Low-intensity FUS enables noninvasive activation of small molecules in the brain and has been validated in several clinical settings. Therefore, AI-guided predictions were combined with ultrasound-based sonodynamic testing using parameters relevant to human therapy. A major challenge in SDT development is the lack of rapid, physiologically relevant tumor models, as traditional 3D organoids take weeks to mature, delaying validation. To address this, a magnetic bioprinting platform was used to produce uniform 3D tumor spheroids within hours, enabling high-throughput screening of SDT. These spheroids replicate key microenvironmental gradients, supporting reliable ultrasound-driven cytotoxicity testing. Through this combined NAM pipeline, AI identified NEO100--an ultrapure, pharmaceutical-grade perillyl alcohol currently in Phase 2a clinical trials--as a promising sonosensitizer candidate. These predictions were validated in rapidly 3D bioprinted tumor models representing glioblastoma, Group 3 pediatric medulloblastoma, meningioma, and breast-to-brain and lung-to-brain metastases. In all tumor types, ultrasound activation significantly increased NEO100s cytotoxicity. Given its established safety profile in humans and ability to cross the BBB, NEO100 demonstrates how integrating AI-based molecular discovery, accelerated 3D bioprinting, and clinically relevant ultrasound parameters can rapidly advance precision sonodynamic therapies for various primary and metastatic brain cancers.

cancer biology↗

bioRxiv2025

Benchmarking of proximity-dependent biotinylation enzymes across cellular compartments and time windows

Proximity-dependent biotinylation has become a powerful approach for mapping protein interactions and subcellular organization in living cells. Although a growing number of engineered biotin ligases have been introduced, their performance has not been systematically evaluated across diverse cellular contexts. Here, we benchmark ten proximity ligases spanning three bacterial lineages using standardized proteomic workflows across multiple labeling durations, subcellular compartments, and two human cell types. While all enzymes efficiently detect proximal associations, they differ in labeling kinetics, background activity, and spatial specificity. TurboID exhibits the highest overall activity but generates substantial background in standard media. miniTurbo and ultraID support rapid, biotin-dependent labeling with low background, making them better suited for dynamic and time-resolved applications. However, miniTurbo showed aberrant mitochondrial localization with two cytoskeletal baits (VASP and PFN1). Across 15 diverse baits, ultraID consistently provides an excellent combination of specificity, efficiency, and spatial compatibility--including unique recovery of Golgi-resident glycosyltransferases. This study serves as a comparative resource, offering guidance for enzyme selection and experimental design in proximity proteomics.

systems biology↗

bioRxiv2024

Inhibition of Cardiac p38 Highlights the Role of the Phosphoproteome in Heart Failure Progression

Heart failure (HF) is a complex condition characterized by the inability of the heart to pump sufficient oxygen to the organs to meet their metabolic needs. Among the altered signal transduction pathways associated with HF pathogenesis, the p38 mitogen-activated protein kinase (p38 MAPK) pathway--activated in response to stress-- has attracted considerable attention for its potential role in HF progression and cardiac hypertrophy. However, the exact mechanisms by which p38 MAPK influences HF remain unclear. Addressing knowledge gaps may provide insight on why p38 inhibition has yielded inconsistent outcomes in clinical trials. Here we investigate the effects of p38 MAPK inhibition via SB203580 on cardiac remodeling in a guinea pig model of HF and sudden cardiac death. Using a well-established HF model with ascending aortic constriction and daily isoproterenol (ACi) administration, we assessed proteomic changes across three groups: sham-operated controls, untreated ACi, and ACi treated with SB203580 (ACiSB). Cardiac function was evaluated by M-mode echocardiography, while proteome and phosphoproteome profiles were analyzed using multiplexed tandem mass tag labeling and LC-MS/MS. Our findings demonstrate that chronic SB203580 treatment offers protection against progressive decline in cardiac function in HF. The proteomic data indicate that SB203580-treatment exerts broad protection of the cardiac phosphoproteome, beyond inhibiting maladaptive p38-dependent phosphorylation, extending to PKA and AMPK networks among others, ultimately protecting the phosphorylation status of critical myofibrillar and Ca2+-handling proteins. Though SB203580 had a more restricted impact on widespread protein changes in HF, its biosignature was consistent with preserved mitochondrial energetics as well as reduced oxidative and inflammatory stress.

molecular biology↗

bioRxiv2024

Computational design and evaluation of optimal bait sets for scalable proximity proteomics

The spatial organization of proteins in eukaryotic cells can be explored by identifying nearby proteins using proximity-dependent biotinylation approaches like BioID. BioID defines the localization of thousands of endogenous proteins in human cells when used on hundreds of bait proteins. However, this high bait number restricts the approachs usage and gives these datasets limited scalability for context-dependent spatial profiling. To make subcellular proteome mapping across different cell types and conditions more practical and cost-effective, we developed a comprehensive benchmarking platform and multiple metrics to assess how well a given bait subset can reproduce an original BioID dataset. We also introduce GENBAIT, which uses a genetic algorithm to optimize bait subset selection, to derive bait subsets predicted to retain the structure and coverage of two large BioID datasets using less than a third of the original baits. This flexible solution is poised to improve the intelligent selection of baits for contextual studies.

bioinformatics↗

bioRxiv2024

Targeting MDSC-HTR2B to Improve Immune Checkpoint Inhibitors in Breast to Brain Metastasis

Myeloid Derived Suppressor Cells (MDSCs) support breast cancer growth via immune suppression and non-immunological mechanisms. Although 15% of patients with breast cancer will develop brain metastasis, there is scant understanding of MDSCs contribution within the breast-to-brain metastatic microenvironment. Utilizing co-culture models mimicking a tumor-neuron-immune microenvironment and patient tissue arrays, we identified serotonergic receptor, HTR2B, on MDSCs to upregulate pNF-{kappa}B and suppress T cell proliferation, resulting in enhanced tumor growth. In vivo murine models of metastatic and intracranial breast tumors treated with FDA-approved, anti-psychotic HTR2B antagonist, clozapine, combined with immunotherapy anti-PD-1 demonstrated a significant increase in survival and increased T cell infiltration. Collectively, these findings reveal a previously unknown role of MDSC-HTR2B in breast-to-brain metastasis, suggesting a novel and immediate therapeutic approach using neurological drugs to treat patients with metastatic breast cancer.

cancer biology↗