Biology subjects

Kamali-Moghaddam, M.

Publications and source records attributed to Kamali-Moghaddam, M..

6 recordsLinked to original sources

bioRxiv2025

Spatial mapping of proteins and their activity states in cancer models by multiplex in situ PLA

Improved methods are needed to gain insights in how proteins exert their myriad roles in cells and organs. Multiplex in situ proximity ligation assay (misPLA), described herein, can provide a window into the functional states of proteins in cells and tissues by applying pairs of antibody-oligonucleotide conjugates to generate amplifiable DNA circles upon proximal binding. The analysis reveals interactions and modifications among sets of proteins, read out by recording the identity and location of the resulting localized DNA amplification products. We applied misPLA to both primary and cultured cells and to formalin-fixated paraffin-embedded (FFPE) tissues, to map dynamic changes in protein localizations, phosphorylations and interactions across surface markers, MAPK, immune-checkpoints, T- and B-cell receptors, and adhesion panels. Comparisons of single-plex versus nine-plex assays confirmed that misPLA maintains sensitivity and specificity while increasing throughput and spatial context. Across breast cancer, lymphomas and chronic myeloid leukemia (CML) misPLA uncovered shared and disease-specific signaling patterns, underscoring convergence of oncogenic networks. By preserving tissue architecture and enabling high-content functional spatial proteomics at single-cell resolution, misPLA offers a versatile platform for dissecting signaling heterogeneity, pathway crosstalk, and therapeutic responses, with broad applications in cell biology, biomarker discovery and in precision oncology.

molecular biology↗

bioRxiv2025

Seven blood biomarkers are associated with TGF-β and VHL-HIF signaling in patients with clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is an aggressive kidney cancer subtype frequently associated with poor prognosis. Most ccRCC cases are asymptomatic in early stages and symptomatic mostly in advanced stages. Furthermore, the heterogeneity of ccRCC presents a challenge to design new treatments. In this study, using proximity extension assay (PEA), we analyzed blood samples from 134 patients with ccRCC and from 111 age- and gender-matched healthy donors. We identified a panel of seven proteins (ANXA1, ESM1, FGFBP1, MDK, METAP2, SDC1, and TFPI2) that are associated with clinicopathological parameters and patient survival. These biomarkers can differentiate patients with ccRCC from the control individuals with high diagnostic sensitivity and specificity. Moreover, by studying protein expression in solid tumors from the same ccRCC patients, we revealed associations between the panel biomarkers and proteins in the TGF-{beta} and VHL-HIF signaling pathways. We found that most tumor promoting biomarkers were positively associated with TGF-{beta} signaling and HIF-2, and negatively associated with pVHL and HIF-1. We also found that most tumor suppressing biomarkers were positively associated with pVHL and HIF-1 and negatively associated with TGF-{beta} signaling and HIF-2. For ccRCC patients, the blood protein biomarkers that were connected to poor prognosis and TGF-{beta}/HIF-2 signaling, as identified in this study, are potentially important assets in personalized medicine.

cancer biology↗

bioRxiv2024

Beyond Basic Characterization and Omics: Immunomodulatory Roles of Platelet-Derived Extracellular Vesicles Unveiled by Functional Testing

Renowned for their role in hemostasis and thrombosis, platelets are also increasingly recognized for their contribution in innate immunity, immunothrombosis and inflammatory diseases. Platelets express a wide range of receptors, which allows them to reach a variety of activation endpoints and grants them immunomodulatory functions. Activated platelets release extracellular vesicles (PEVs), whose formation and molecular cargo has been shown to depend on receptor-mediated activation and environmental cues. This study compares the immunomodulatory profiles of PEVs generated via activation of platelets by different receptors, glycoprotein VI, C-type lectin-like receptor 2, and combining all thrombin-collagen receptors. Functional assays in vivo in zebrafish and in vitro in human macrophages respectively highlighted distinct homing and secretory responses triggered by the PEVs. In contrast, omics analyses of protein and miRNA cargo combined with physicochemical particle characterization found only subtle differences between the PEV types, which were insufficient to explain their different functional immunomodulatory profiles. Constitutively released PEVs, formed in the absence of an exogenous activator, displayed a disparate activation profile from the receptor induced PEVs. Our findings underscore that PEVs are tunable through receptor-mediated activation. To truly comprehend their role(s) in mediating platelet functions among immune cells, conducting functional assays is imperative. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/570750v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@75a9dborg.highwire.dtl.DTLVardef@e2787corg.highwire.dtl.DTLVardef@543525org.highwire.dtl.DTLVardef@6d1362_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2023

GABA, glucose and insulin orchestrate CD4+ T cells effector functions

Metabolic programs of immune cells are closely linked to their effector functions. Physiological molecules including glucose, insulin and {gamma}-aminobutyric acid (GABA) provide environmental cues and guidance, although how they coordinate to regulate the cells is still being unraveled. Here, we demonstrate that GABA-mediated reduction of metabolic activity and release of inflammatory molecules, including IFN{gamma} and IL-10, was abolished in human CD4+ T cells when the glucose concentration was elevated above normal levels. Insulin enhanced the GABAA receptors-mediated currents and Ca2+ influx. GABA decreased, whereas insulin sustained glycolysis but in a SGLT (Na+-glucose transporter)-dependent manner. In high glucose (16.7 mM), the SGLTs antagonist phlorizin alone or together with GABA restored the inhibition of IFN{gamma} and IL-10 release. This study exposes concerted effects of GABA, glucose and insulin on CD4+ T cells metabolic activity and release of inflammatory molecules, and identifies a role for SGLTs in CD4+ T cells function.

physiology↗

bioRxiv2022

Magnetic Bead Based Proximity Extension Assay for Sensitive Protein and Extracellular Vesicles Detection

During the early stages of disease development, protein biomarkers can leak into the blood creating opportunities for early diagnosis of disease with minimally invasive sampling. These proteins biomarkers however are often masked by the presence of more abundant functional blood proteins, making specific detection a challenge with most current immunoassays. We we report on the development of a magnetic bead based solid-phase PEA (SP-PEA) for sensitive detection of proteins in plasma and serum samples. Antibody functionalized magnetic beads are used to capture the target of interest. Following capture, non-specifically bound proteins are washed off before PEA probes are added for detection of the bound proteins. Compared to hoogenous PEA, SP-PEA admits the use of larger sample volumes to increase available target molecules, higher concentration of detection reagents for more efficient formation of detection complexes and washes for removal of nonspecific background. We compared SP-PEA to solution phase PEA for the detection of cytokines: interlukin-6, interlukin-2, interlukin-4, interlukin-10 and Tumor Necrosis Factor-alpha, and we demonstrated an increased sensitivity by 15 to 60 fold in buffer and chicken serum. We further expanded SP-PEA to detect extracellular vesicles (EVs) through combinations of proteins on the surface of specific EV populations.

biochemistry↗

bioRxiv2019

Depression, GABA and age correlate with the plasma levels of inflammatory markers.

Immunomodulation is increasingly being recognised as a part of mental diseases. Here, we examined if levels of immunological protein markers altered with depression, age or by the inhibitory neurotransmitter gamma-aminobutyric acid (GABA). Analysis of plasma samples from patients with major depressive episode and control blood donors (CBD) revealed expression of 67 inflammatory markers. Thirteen of these markers had augmented levels in patients as compared to CBD. and 21 markers correlated with age of the patients, whereas 10 markers correlated with the age of CBD. Interestingly, CST5 and CDCP1 showed the strongest correlation with age in the patients and in the CBD, respectively. IL-18 was the only marker that correlated with the MADRS-S scores of the patients. Neuronal growth factors (NGFs) were significantly enhanced in plasma from the patients and so was the average plasma GABA concentration. GABA modulated release of seven cytokines in CD3+ stimulated peripheral blood mononuclear cells (PBMC) from the patients. The study reveals significant changes in plasma composition of small molecules during depression and identifies potential peripheral biomarkers of the disease.

pathology↗