Biology subjects

Sardiu, M. E.

Publications and source records attributed to Sardiu, M. E..

8 recordsLinked to original sources

bioRxiv2026

INTEGRATOR: Structural Elucidation of the INO80 Chromatin Remodeler via Experimentally Guided Molecular Simulations

The INO80 chromatin remodeling complex plays a central role in DNA repair, transcription, and replication. Yet, a comprehensive understanding of its structural organization remains incomplete due to the dynamic nature of several of its subunits and the sharing of several subunits with related remodeling complexes. Here, we report a computational model of the three-dimensional structure of the S. cerevisiae INO80 complex using an integrative approach that combines experimental crosslinking mass spectrometry, molecular docking, and molecular dynamics simulations. Our results reveal the spatial and dynamical organization of key modules--ARP8, ARP5, NHP10, and RVB1/2--within the intact complex. The resulting structural model agrees with crosslinking constraints, highlighting the architecture of the previously uncharacterized NHP10 module. This module, including the C-terminal region of the Ino80 scaffolding protein, has remained elusive due to its intrinsic flexibility and lack of high-resolution structural data. To facilitate this integrative modeling workflow and make it broadly accessible, we presented INTEGRATOR: (INTEGRAtive TempOral and stRuctural Analysis of protein modules), a versatile workflow package designed as a tool to elucidate the structure and dynamics of large, flexible macromolecular assemblies using well-established softwares. Our findings demonstrate the power of integrative modeling in resolving the role of the highly disordered NPH10 module in recruiting other dynamic modules into INO80 large protein assemblies and offer a generalizable framework for determining the architecture of similarly complex and heterogeneous molecular machines. This work carries broad implications for understanding the structural basis of chromatin regulation in microbial organisms and the implications for the dysregulation in diseases such as cancer.

biophysics↗

bioRxiv2024

Differential Remodeling of the BRCA1 Interactome by a Unique Minimal Clinical Truncation Mutation

BRCA1, a critical tumor suppressor gene, plays an essential role in maintaining genomic stability through its involvement in DNA double-strand break repair, particularly via homologous recombination. Loss or impairment of BRCA1 function disrupts this repair pathway, resulting in genomic instability and significantly increased susceptibility to breast and ovarian cancers. To elucidate the molecular mechanisms by which BRCA1 mutations contribute to tumorigenesis, we employed quantitative mass spectrometry-based proximity labeling and affinity purification to identify cancer-specific protein-protein interactions (PPIs). Our integrated omics and visualization analysis of interactors revealed that the BRCA1-Y1853ter mutant, through its interaction with BARD1, perturbs the interactome and impacts cellular processes within the cytoplasm and nucleoplasm. Structural data further corroborated these findings, showing enhanced binding between the mutant BRCA1 and specific interactors, suggesting an altered functional profile. Together, these observations raise the hypothesis that the BRCA1-Y1853ter mutant may exhibit gain-of-function characteristics, providing new insights into the molecular and cellular effects of mutations in the BRCA1 C-Terminal (BRCT) domain and their implications for the pathogenesis of breast and ovarian cancers.

cancer biology↗

bioRxiv2024

Distinct regions within SAP25 recruit O-linked glycosylation, DNA demethylation, and ubiquitin ligase and hydrolase activities to the Sin3/HDAC complex

Epigenetic control of gene expression is crucial for maintaining gene regulation. Sin3 is an evolutionarily conserved repressor protein complex mainly associated with histone deacetylase (HDAC) activity. A large number of proteins are part of Sin3/HDAC complexes, and the function of most of these members remains poorly understood. SAP25, a previously identified Sin3A associated protein of 25 kDa, has been proposed to participate in regulating gene expression programs involved in the immune response but the exact mechanism of this regulation is unclear. SAP25 is not expressed in HEK293 cells, which hence serve as a natural knockout system to decipher the molecular functions uniquely carried out by this Sin3/HDAC subunit. Using molecular, proteomic, protein engineering, and interaction network approaches, we show that SAP25 interacts with distinct enzymatic and regulatory protein complexes in addition to Sin3/HDAC. While the O-GlcNAc transferase (OGT) and the TET1 /TET2/TET3 methylcytosine dioxygenases have been previously linked to Sin3/HDAC, in HEK293 cells, these interactions were only observed in the affinity purification in which an exogenously expressed SAP25 was the bait. Additional proteins uniquely recovered from the Halo-SAP25 pull-downs included the SCF E3 ubiquitin ligase complex SKP1/FBXO3/CUL1 and the ubiquitin carboxyl-terminal hydrolase 11 (USP11), which have not been previously associated with Sin3/HDAC. Finally, we use mutational analysis to demonstrate that distinct regions of SAP25 participate in its interaction with USP11, OGT/TETs, and SCF(FBXO3).) These results suggest that SAP25 may function as an adaptor protein to coordinate the assembly of different enzymatic complexes to control Sin3/HDAC-mediated gene expression.

biochemistry↗

bioRxiv2023

VCD-induced menopause mouse model reveals reprogramming of hepatic metabolism

Menopause adversely impacts systemic energy metabolism and increases the risk of metabolic disease(s) including hepatic steatosis, but the mechanisms are largely unknown. Dosing female mice with vinyl cyclohexene dioxide (VCD) selectively causes follicular atresia in ovaries, leading to a murine menopause-like phenotype. In this study, we treated female C57BL6/J mice with VCD (160mg/kg i.p. for 20 consecutive days followed by verification of the lack of estrous cycling) to investigate changes in body composition, energy expenditure (EE), hepatic mitochondrial function, and hepatic steatosis across different dietary conditions. VCD treatment induced ovarian follicular loss and increased follicle-stimulating hormone (FSH) levels in female mice, mimicking a menopause-like phenotype. VCD treatment did not affect body composition, or EE in mice on a low-fat diet or in response to a short-term (1-week) high-fat, high sucrose diet (HFHS). However, the transition to a HFHS lowered cage activity in VCD mice. A chronic HFHS diet (16 weeks) significantly increased weight gain, fat mass, and hepatic steatosis in VCD-treated mice compared to HFHS-fed controls. In the liver, VCD mice showed suppressed hepatic mitochondrial respiration on LFD, while chronic HFHS diet resulted in compensatory increases in hepatic mitochondrial respiration. Also, liver RNA sequencing revealed that VCD promoted global upregulation of hepatic lipid/cholesterol synthesis pathways. Our findings suggest that the VCD- induced menopause model compromises hepatic mitochondrial function and lipid/cholesterol homeostasis that sets the stage for HFHS diet-induced steatosis while also increasing susceptibility to obesity.

physiology↗

bioRxiv2023

PerSEveML: A Web-Based Tool to Identify Persistent Biomarker Structure for Rare Events Using Integrative Machine Learning Approach

Omics datasets often pose a computational challenge due to their high dimensionality, large size, and non-linear structures. Analyzing these datasets becomes especially daunting in the presence of rare events. Machine learning (ML) methods have gained traction for analyzing rare events, yet there remains a limited exploration of bioinformatics tools that integrate ML techniques to comprehend the underlying biology. Expanding upon our previously developed computational framework of an integrative machine learning approach1, we introduce PerSEveML, an interactive web-based that uses crowd-sourced intelligence to predict rare events and determine feature selection structures. PerSEveML provides a comprehensive overview of the integrative approach through evaluation metrics that help users understand the contribution of individual ML methods to the prediction process. Additionally, PerSEveML calculates entropy and rank scores, which visually organize input features into a persistent structure of selected, unselected, and fluctuating categories that help researchers uncover meaningful hypotheses regarding the underlying biology. We have evaluated PerSEveML on three diverse biologically complex data sets with extremely rare events from small to large scale and have demonstrated its ability to generate valid hypotheses. PerSEveML is available at https://biostats-shinyr.kumc.edu/PerSEveML/ and https://github.com/sreejatadutta/PerSEveML.

bioinformatics↗

bioRxiv2021

Perturbation of BRMS1 interactome reveals pathways that impact cell migration

Breast Cancer Metastasis Suppressor 1 (BRMS1) expression is associated with longer patient survival in multiple cancer types. Understanding BRMS1 functionality will provide insights into both mechanism of action and will enhance potential therapeutic development. In this study, we confirmed that the C-terminus of BRMS1 is critical for metastasis suppression and hypothesized that critical protein interactions in this region would explain its function. Phosphorylation status at S237 regulates BRMS1 protein interactions related to a variety of biological processes, phenotypes [cell cycle (e.g., CDKN2A), DNA repair (e.g., BRCA1)], and metastasis [(e.g., TCF2 and POLE2)]. Presence of S237 also directly decreased MDA-MB-231 breast carcinoma migration in vitro and metastases in vivo. The results add significantly to our understanding of how BRMS1 interactions with Sin3/HDAC complexes regulate metastasis and expand insights into BRMS1s molecular role, as they demonstrate that BRMS1 C-terminus involvement in distinct direct protein-protein interactions.

cancer biology↗

bioRxiv2019

A systems chemoproteomic analysis of acyl-CoA signaling networks

Acyl-CoA/protein interactions are required for many functions essential to life including membrane synthesis, oxidative metabolism, and macromolecular acetylation. However, despite their importance, the global scope and selectivity of these protein-metabolite interactions remains undefined. Here we describe the development of CATNIP (CoA/AcetylTraNsferase Interaction Profiling), a chemoproteomic platform for the high-throughput analysis of acyl-CoA/protein interactions in endogenous proteomes. First, we apply CATNIP to identify acetyl-CoA-binding proteins through unbiased clustering of competitive dose-response data. Next, we use this method to profile diverse protein-CoA metabolite interactions, identifying biological processes susceptible to altered acetyl-CoA levels. Finally, we apply systems-level analyses to assess the features of novel protein networks that may interact with acyl-CoAs, and demonstrate a strategy for high-confidence proteomic annotation of acetyl-CoA binding proteins. Overall our studies illustrate the power of integrating chemoproteomics and systems biology, and provide a resource for understanding the roles of acyl-CoA metabolites in biology and disease.

biochemistry↗

bioRxiv2016

A new coactivator complex required for retinoic acid-dependent regulation of embryonic symmetry

Bilateral symmetry is a striking feature of the vertebrate body plan organization. Vertebral precursors, called somites, provide one of the best illustrations of embryonic symmetry. Maintenance of somitogenesis symmetry requires Retinoic acid (RA) and its coactivator Rere/Atrophin2. Here, using a proteomic approach we identify a protein complex, containing Wdr5, Hdac1, Hdac2 and Rere (named WHHERE), which regulates RA signalling and controls embryonic symmetry. We demonstrate that Wdr5, Hdac1 and Hdac2 are required for RA signalling in vitro and in vivo. Mouse mutants for Wdr5 and Hdac1 exhibit asymmetrical somite formation characteristic of RA-deficiency. We also identify the Rere-binding histone methyltransferase Ehmt2/G9a, as a RA coactivator controlling somite symmetry. Upon RA treatment, WHHERE and Ehmt2 become enriched at RA target genes to promote RNA Polymerase II recruitment. Our work identifies a novel protein complex linking key epigenetic regulators acting in the molecular control of embryonic bilateral symmetry.

developmental biology↗