Biology subjects

Soliymani, R.

Publications and source records attributed to Soliymani, R..

6 recordsLinked to original sources

bioRxiv2026

Conjunctive Targeting Links Drug Synergy to Emergent Proteome Structural States

Combinatorial therapies are widely used in the treatment of acute myeloid leukemia (AML) to address disease heterogeneity, adaptive resistance, and rewired signaling and metabolic states. Yet drug prioritization remains largely guided by clinical or phenotypic evidence, while the molecular mechanisms underlying effective drug combinations remain incompletely defined. To narrow this gap, we developed Combinatorial high-ratio Partial proteolysis with reference PRoteome Analysis (CoPPRA), a structural proteomics workflow based on limited proteolysis of cell lysates that profiles drug-associated changes in regional protein accessibility at peptide-level resolution. Here, we applied CoPPRA to ruxolitinib and ulixertinib, individually and in combination, in AML-related cell lysates. Our findings extend conjunctive targeting (CT), a recently proposed mechanism of combinatorial drug action in which combined exposure produces protein targeting patterns not observed with either drug alone. Previously identified through combination-associated changes in protein solubility/stability, CT is examined here at peptide-level resolution through regional differences in proteolytic accessibility. The ruxolitinib-ulixertinib combination produced broad peptide-level accessibility changes, including a subset meeting the predefined criteria for CT. CT candidates predominantly exhibited regional accessibility changes, with altered peptide regions occurring against comparatively small changes across the remaining quantified peptides from the same proteins. MAP2K1 and ATP6V1G1 showed pronounced differences between overlapping peptide sequences, highlighting localized variation in combination-associated accessibility, including an ATP6V1G1 peptide mapping to an annotated helical region. Combination-associated increases in peptide signals were also observed in PIK3R1, BRD4, and PTPN11, linking regional accessibility changes to signaling and transcriptional regulators relevant to AML. Functional enrichment and network analyses further implicated nucleotide and glucose metabolism, ficolin-1-rich granules, ribosome-associated processes, and phagocytic vesicles. These results extend conjunctive targeting from protein-level solubility/stability changes to regional differences in proteolytic accessibility, showing that combination-associated effects can be concentrated within specific peptide regions rather than distributed uniformly across proteins. More broadly, CoPPRA provides a peptide-resolved approach for investigating the molecular features of combinatorial drug action and prioritizing protein regions for subsequent mechanistic validation.

biochemistry↗

bioRxiv2024

Exploring Mechanisms of Action in Combinatorial Therapy through Stability/Solubility Alterations: Advancing AML Treatment

Acute myeloid leukemia (AML) remains a formidable clinical challenge due to genetic heterogeneity, high relapse rates, and toxicities associated with conventional chemotherapies. Rationally designed drug combinations offer improved efficacy, yet their selection is often empirical and lacks molecular mechanistic understanding. Here, we present CoPISA workflow (Proteome Integral Solubility/Stability Alteration Analysis for Combinations), a high-throughput proteomics workflow that captures protein solubility/stability alterations unique to combinatorial drug treatments, revealing mechanisms unattainable through single-drug analyses. Applying CoPISA to two rationally designed AML drug pairs, LY3009120-sapanisertib (LS) and ruxolitinib-ulixertinib (RU), we mapped primary (lysate) and secondary (living cell) protein target landscapes. Notably, our analysis uncovered an emergent mechanistic principle, "conjunctional targeting" (i.e., conjunctional inhibition), wherein cooperative drug actions induce treatment-specific targets not achievable individually, analogous to an AND-gate logic model. LS-specific AND-gate proteins converged on SUMOylation, chromatin condensation, and VEGF-linked adhesion, while RU-specific targets disrupted DNA-damage checkpoints, mitochondrial bioenergetics, and RNA-splicing machinery, collectively implicating synthetic-lethal vulnerabilities. Additionally, the post-translational modifications (PTMs) profiling of differential soluble proteins confirms several combination-induced modifications (e.g., acetylation, dimethylation, phosphorylation) on key AML proteins, such as NPM1. Network interrogation of AML-associated proteins showed that a high percentage of targeted proteins are unique to the combinations, including frequently mutated drivers DNMT3A, NPM1, and TP53. CoPISA exposes how drug pairs enact multi-axis pressure on AML cells through conjunctional targeting, a mechanistic layer beyond classical synergy. By pinpointing combination-exclusive protein targets and signaling pathways, CoPISA provides a blueprint for precision-guided regimen design in AML and other heterogeneous cancers. Data are available via ProteomeXchange with identifier PXD066812.

biochemistry↗

bioRxiv2024

CX3CR1 modulates migration of resident microglia towards brain injury

Microglia are innate immune cells of the central nervous system (CNS). They extend their processes towards and migrate towards injuries in vivo. However, whether the fractalkine receptor (CX3CR1) influences microglial migration remains unknown. Label-free proteomic profiling predicted changes in RHO-signaling activity that hint at dysregulated cytoskeleton signaling in Cx3cr1-deficient murine cortex tissue. To further investigate microglial migration, we carried out 4-hour interval two-photon in vivo imaging for 72 hours after a laser lesion in the cortex. Cx3cr1-deficient microglia showed enhanced migration towards the lesion. Additionally, length and velocity of microglial fine processes extending towards the lesion were increased in Cx3cr1-deficient microglia. Migration remained unchanged in Ccr2-deficient mice, indicating that monocyte-derived macrophages/microglia did not contribute to microglia accumulation around the lesion. These results demonstrate microglia migration towards CNS injury and suggest CX3CR1 as a modulator of this. Manipulating microglia migration via CX3CR1 therefore is a potential target for treatment of CNS-injury.

neuroscience↗

bioRxiv2024

USP14 regulates pS129 α-synuclein levels and oxidative stress in human SH-SY5Y dopaminergic cells

Ubiquitin specific protease-14 (USP14) is critical for controlling protein homeostasis disturbed in human disorders like Parkinso[n]s disease (PD). Here we investigated the role of USP14 in regulating proteasome and autophagy pathways, and their influence on -synuclein (-syn) degradation. Data showed that -syn and phosphorylated serine129 -syn (pS129 -syn) were elevated in USP14 gene-deleted SH-SY5Y dopaminergic cells with concomitant reduction in proteasome activity. Inhibition of proteasomes using MG132 particularly elevated pS129 -syn in these cells, but the levels were not influenced by inhibiting autophagy using chloroquine. In contrast, autophagy and the CLEAR (Coordinated Lysosomal Expression and Regulation) pathways were elevated in USP14 lacking cells with an upregulation of the transcription factor TFEB. USP14-ablated cells also exhibited increases in reactive oxidative species (ROS) and elongation of mitochondria. The addition of N-Acetylcysteine amide (NACA) to counteract oxidative stress, reduced pS129 -syn and -syn levels in USP14 deficient cells. Phospho-proteomic analyses revealed that USP14 is phosphorylated at S143 affecting its function and structure as shown by molecular modeling, and protein interaction studies. Re-expression of wild-type and the phospho-mimetic S143D-USP14 mutant decreased ROS, pS129 -syn, and -syn in USP14 lacking cells. These results demonstrate that pS129 -syn levels are sensitive to oxidative stress in SH-SY5Y dopaminergic cells. USP14 by stimulating the proteasome activity and reducing oxidative stress is a promising factor for targeting -syn and its pathogenic variants in PD.

neuroscience↗

bioRxiv2024

Menopause-associated proteomic and lipidomic alterations in high-density lipoprotein: Perimenopause is characterized by smaller triacylglycerols-enriched particles.

High-density lipoprotein particles (HDL) possess anti-inflammatory, anti-thrombotic, cytoprotective, and anti-oxidative properties, thus protecting against cardiovascular diseases. Menopause is associated with changes in serum metabolome and HDL size distribution. We analyzed the protein and lipid composition of the HDL particles from pre-, peri-, and postmenopausal women (N=216) with nuclear magnetic resonance and mass spectrometry to get a deeper insight into the composition of HDL in different stages of menopause. Both particle size and composition differed; in perimenopause, the proportion of small HDL particles (8.7 nm on average) was higher, and the proportion of large HDL particles (12.1 nm on average) was lower than in pre- or postmenopause. In perimenopause, each particle size class was enriched with triacylglycerols, and the calculated lipid class ratio of triacylglycerol/cholesteryl ester was the highest within perimenopausal HDL particles. This potentially affects the HDL interaction with lipid-modifying enzymes. We also observed directionally opposite associations for HDL cholesteryl ester and unesterified cholesterol with systemic estradiol and follicle-stimulating hormone levels, especially regarding S-sized HDL particles, but not the hormone associations with HDL triacylglycerols. Perimenopausal HDL also exhibited a lower proportion of apolipoproteins (apoA-I, apoA-II, apoC-I, apoC-III, apoD and apoE) per particle than premenopausal or postmenopausal HDL. In summary, we found that premenopausal and postmenopausal HDL particles were compositionally similar and differed from perimenopausal ones. We suggest that menopause, and especially the unbalanced hormonal state in perimenopause, are reflected in the lipid and protein compositions of the HDL, which, in turn, may affect the functions of the HDL particle.

molecular biology↗

bioRxiv2019

Epicardial therapy with atrial appendage micrografts salvages myocardium after infarction

Ischemic heart disease remains the leading cause of mortality and morbidity worldwide despite improved possibilities in medical care. Alongside interventional therapies, such as coronary artery bypass grafting, adjuvant tissue-engineered and cell-based treatments can provide regenerative improvement. Unfortunately, most of these advanced approaches require multiple lengthy and costly preparation stages without delivering significant clinical benefits.\n\nWe evaluated the effect of epicardially delivered minute pieces of atrial appendage tissue material, defined as atrial appendage micrografts (AAMs), in mouse myocardial infarction model. An extracellular matrix patch was used to cover and fix the AAMs onto the surface of the infarcted heart. The matrix-covered AAMs salvaged the heart from infarction-induced loss of functional myocardium and attenuated scarring. Site-selective proteomics of injured ischemic and uninjured distal myocardium from AAM-treated and untreated tissue sections revealed an increased expression of several cardiac regeneration-associated proteins (i.e. periostin, transglutaminases and glutathione peroxidases) as well as activation of pathways responsible for angio- and cardiogenesis in relation to AAMs therapy.\n\nEpicardial delivery of AAMs encased in an extracellular matrix patch scaffold salvages functional cardiac tissue from ischemic injury and restricts fibrosis after myocardial infarction. Our results support the use of AAMs as tissue-based therapy adjuvants for salvaging the ischemic myocardium.

bioinformatics↗