Biology subjects

Salem, A.

Publications and source records attributed to Salem, A..

15 recordsLinked to original sources

bioRxiv2026

Clustered structural variant hotspots enable oncogenic addiction and plasticity in osteosarcoma

The genomic landscape of osteosarcoma, the most common bone cancer worldwide, is among the most structurally complex of all human malignancies. The identification of recurrent and functionally consequential patterns has thus remained a challenge. Across 236 whole-genome sequencing osteosarcoma samples, we uncovered five genomic hotspots of clustered structural variation collectively altered in 58% of tumors. Four were associated with amplification of oncogenes ( MYC , CCND3 , CCNE1 , CDK4) , while the fifth mapped largely upstream of TP53 . Hotspot events showed coordinated patterns of co-occurrence and mutual exclusivity with each other and with tumor suppressor alterations, suggesting genomic context-specific selection. We found localized transcriptional dysregulation at hotspot event loci, and single cells harboring these events converged on a neural crest-like program, linking these structural alterations to a less differentiated cell state. These events were also detectable non-invasively through liquid biopsies and displayed ongoing structural evolution throughout disease progression, a finding with potential clinical utility. Our results provide novel insight into how complex rearrangements shape oncogenesis in osteosarcoma, with broader relevance to other cancers characterized by complex genomes.

cancer biology↗

bioRxiv2026

FLIM-FRET as a Molecular Filter for Membrane-Induced Aggregation

Membrane binding is thought to trigger early aggregation of alpha-synuclein (aSyn) in neurons. However, live-cell measurements of membrane-proximal aggregation with high specificity remain challenging. We combine three- channel fluorescence lifetime imaging microscopy (FLIM) with Forster resonance energy transfer (FRET) in a model that uses FRET as a proximity filter. A membrane-tethered donor reports membrane-aSyn separation through lifetime changes, while an aSyn-labeled acceptor reports the aggregation state through its lifetime. We estimate per-cell lifetimes and mixture fractions for membrane-bound and membrane-unbound populations using a hierarchical expectation-maximization (EM) algorithm that pools information across pixels. We validate the estimator using Monte Carlo studies. Using experimental neuronal data, this method resolves changes in membrane-proximal aggregation and aggregate-associated lifetimes. This framework provides quantitative per-cell metrics linking membrane proximity and aggregation for comparative live-cell studies. SIGNIFICANCEMany studies map FRET signals pixel by pixel or average signals over whole cells. Neither approach reliably answers key biological questions: how much membrane-proximal aggregation exists in a given cell, and how does it change across conditions? Here, we combine three-channel FLIM-FRET with a hierarchical analysis that estimates per-cell lifetimes and fractions for bound and unbound populations by pooling information across pixels. This method shifts the focus from noisy images to cell-level metrics that support comparisons across treatments, time points, or genotypes. Simulations and neuronal data show improved accuracy under realistic photon budgets and reveal membrane-proximal aggregation effects that were unattainable otherwise. This approach is broadly applicable and extends beyond alpha-synuclein.

biophysics↗

bioRxiv2025

Distributed neural computation and the evolution of the first brains

The origin of brains in the Precambrian was a landmark in animal evolution, enabling new behavior and life histories. Brains likely evolved from diffuse nerve nets, but we do not know what the first brains looked like or how they were organized. Acoel worms, the likely sister lineage to all other animals with brains, offer a unique window into this transition. Here, we studied the acoel worm Hofstenia miamia, a marine predator that hunts planktonic invertebrates and displays other sophisticated behavior. We found that H. miamia has an unusual diffuse brain: a subepidermal network of dense neuropil exhibiting little regionalization or stereotypy in gross anatomy or distribution of neural cell types. Remarkably, we found that behavior in H. miamia is robust to large, arbitrary amputations of brain regions, suggesting that most regions can perform most computations. More brain tissue improves performance, especially on challenging tasks, but no specific brain region is required. These results lead us to propose that H. miamias brain is composed of computationally pluripotent "tiles" that interact to generate coherent behavior. This architecture suggests a trajectory for nervous system evolution in which early brains may have arisen through the condensation of diffuse nerve nets into unregionalized brains, with regionalization evolving secondarily.

neuroscience↗

bioRxiv2025

Enhanced Wound Healing and Anti-Inflammatory Effects of Vitamin C-Loaded Hyaluronic Acid/Collagen Scaffolds in Preclinical Rat Models

Wound healing is a complex biological process critical for restoring skin integrity after injury. However, chronic wounds present significant clinical challenges due to persistent inflammation, disrupted collagen synthesis, and susceptibility to infection. Bioactive scaffolds have emerged as promising therapeutic strategies to enhance tissue regeneration by modulating cellular behavior and extracellular matrix (ECM) dynamics. This study explores a hyaluronic acid-collagen (HyCol) scaffold enriched with vitamin C (VC), producing (VC-HyCol) to improve wound healing in preclinical rat models. Hyaluronic acid and collagen, key ECM components, provide structural and biochemical support, while vitamin C acts as both a collagen biosynthesis cofactor and an antioxidant to counteract oxidative stress. The scaffold was designed to emulate the native ECM microenvironment, facilitating fibroblast proliferation, keratinocyte migration, and angiogenesis. Physicochemical characterization, biocompatibility assessments, and in vivo wound healing experiments were performed to evaluate its therapeutic efficacy. Results demonstrated that the incorporation of vitamin C significantly enhanced fibroblast activity, reduced inflammatory markers, and accelerated tissue regeneration compared to control groups. Histological and molecular analyses further confirmed enhanced collagen deposition and neovascularization, indicating faster and more organized wound repair. These findings highlight the potential of this multifunctional scaffold as an advanced wound dressing, with significant implications for regenerative medicine and clinical wound management. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC="FIGDIR/small/665568v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@d8d248org.highwire.dtl.DTLVardef@d58e05org.highwire.dtl.DTLVardef@5f210eorg.highwire.dtl.DTLVardef@17354b1_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

EP300 and FCGR2B Emerge as Coordinated Mediators of Chromatin-Driven Immune Evasion in Melanoma Resistance

Primary resistance to anti-PD-1 therapy in metastatic melanoma remains a clinical challenge. This study reanalyzed the GSE168204 dataset to elucidate molecular mechanisms of resistance and response, incorporating batch correction to address limitations in our prior preprint[6]. RNA-seq data from 25 melanoma biopsies (9 responders, 16 non-responders) were analyzed using DESeq2 with surrogate variable analysis[9,10]. We identified 3,247 differentially expressed genes, revealing a "cell cycle shield" signature in non-responders characterized by upregulation of CDK1, CCNB1, E2F1, and HSP90AA1 enriched for proliferation and DNA repair pathways, suggesting immune evasion through rapid tumor growth. Responders exhibited upregulation of EP300, CREBBP, FCGR2B, and histone genes enriched for chromatin organization and systemic lupus erythematosus pathways, indicating immune activation and autoimmune-like transcriptional programs. Notably, batch correction reversed the roles of EP300 and FCGR2B from non-responders to responders[6], highlighting their context-dependent functions in immune engagement. The "cell cycle shield" suggests targeting CDK1 or HSP90AA1 to overcome resistance[13,14], while the SLE signature may serve as a response biomarker reflecting immune activation states[7]. Validation in larger cohorts and experimental models is needed to translate these findings into personalized immunotherapy strategies.

cancer biology↗

bioRxiv2025

High-integrity nanoemulsions formulation of resiquimod (R848) enhances stability and delivery for triple negative breast cancer immunotherapy

Triple-negative breast cancer (TNBC) poses significant clinical challenges due to its high heterogeneity, with multiple subtypes exhibiting distinct molecular characteristics and treatment responses. The development of resistance to chemotherapy and targeted therapies remains a major obstacle, and identifying reliable biomarkers to predict therapeutic response continues to be challenging. This study aims to enhance the delivery of the immunostimulant Toll-like receptor 7/8 (TLR7/8) agonist resiquimod (R848) using a safe and highly integrated nanoemulsions (NEs) formulation, providing effective and reliable immunotherapy. A series of NEs were prepared and optimized with and without the reactive lipophilic compound ricinoleic acid. Neutral and negatively charged NE formulations encapsulating R848 were compared. The physicochemical properties and in vitro delivery of resiquimod into RAW 264.7 macrophages and 4T1 TNBC cell line models were studied. Both R848-loaded NE formulations exhibited prolonged shelf-life stability with minimal protein binding. Incorporating small portions of ricinoleic acid into the formulation (negatively charged NEs) slowed drug release and improved physical properties and overall delivery compared to ricinoleic-free formulations, likely due to its interaction with the drug. Cytotoxicity and cellular uptake studies were conducted on both NE models, showing localization in the macrophage cell membrane and 4T1 cell cytoplasm. Molecular profiling in 4T1 cells revealed R848-NEs modulated key biomarkers (TLR4/7, Cyclin D1, NF-{kappa}B) while potently inducing autophagy (evidenced by LC3II/p62/Beclin-1 alterations) and PD-L1 upregulation. These dual effects--autophagy-mediated tumor suppression and immune checkpoint modulation--suggest therapeutic synergy between R848-NEs and anti-PD-L1 antibodies, presenting a promising combinatorial strategy for TNBC treatment. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=72 SRC="FIGDIR/small/647265v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@d4daceorg.highwire.dtl.DTLVardef@692daforg.highwire.dtl.DTLVardef@13676d7org.highwire.dtl.DTLVardef@b449fc_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Effects of complex whole-body movements on EEG activity: a scoping review

The influence of movements on brain activity has been part of research for decades. Recent advancements in electroencephalography (EEG) coupled with a shift in focus towards the effects of complex whole-body movements provided additional inspirations in this area. Besides the metabolic load, the amount of information to be processed in parallel provides rough indications of its influence on central nervous activity. Accordingly, this scoping review aimed to synthesize studies investigating the acute effects of complex whole-body movements with increased parallel information processing on electrical brain activity. A comprehensive search across five scientific databases resulted in thirteen studies meeting the inclusion criteria. The results showed increased theta and alpha activity in frontal, central and parietal areas in most studies during and after movement. However, in other frequency bands the findings were not consistent. Comparisons between complex movements with varying parallel demands revealed a trend towards higher theta for movements with more parallel actions. Based on a consistent EEG methodology, future research should consider movement complexity not only related to the length of sequences but rather in terms of parallel motor activities as a moderator of brain activity to obtain more consistent results in the context of neural effects of movement exercise.

neuroscience↗

bioRxiv2024

A FRET-Based FLIM Method to Probe Membrane-Induced Alpha-Synuclein Aggregation in Neurons

1Parkinsons disease (PD) involves the aggregation of the protein alpha-synuclein, a process promoted by interactions with intracellular membranes. To study this phenomenon in neurons for the first time, we developed a fluorescence lifetime imaging (FLIM) method using Forster resonance energy transfer and self-quenching reporters, analyzed with a custom-built FLIM microscope. This method offers insights into aggregate formation in PD and can be broadly applied to probe protein-membrane interactions in neurons.

neuroscience↗

bioRxiv2024

Mechanisms of Alpha-Synuclein Seeded Aggregation in Neurons Revealed by Fluorescence Lifetime Imaging

1The brains of Parkinsons disease (PD) patients are characterized by the presence of Lewy body inclusions enriched with fibrillar forms of the presynaptic protein alpha-synuclein (aSyn). Despite related evidence that Lewy pathology spreads across different brain regions as the disease progresses, the underlying mechanism hence the fundamental cause of PD progression is unknown. The propagation of aSyn pathology is thought to potentially occur through the release of aSyn aggregates from diseased neurons, their uptake by neighboring healthy neurons via endocytosis, and subsequent seeding of native aSyn aggregation in the cytosol. A critical aspect of this process is believed to involve the escape of internalized ag-gregates from the endolysosomal compartment, though direct evidence of this mechanism in cultured neuron models remains lacking. In this study, we utilize a custom-built, time-gated fluorescence lifetime imaging microscope (FLIM) to investigate the progression of seeded ag-gregation over time in live cortical neurons. By establishing fluorescence lifetime sensitivity to aSyn aggregation level, we are able to monitor the proteins aggregation state. Through a FLIM analysis of neurons expressing aSyn-mVenus and exposed to aSyn preformed fibrils labeled with the acid-responsive dye pHrodo, we reveal the proteins aggregation state in both the cytosol and the endolysosomal compartment. The results indicate that aSyn seeds undergo partial disassembly prior to escaping the endocytic pathway, and that this escape is closely linked to the aggregation of cytosolic aSyn. In certain neurons, monomeric aSyn is found to translocate from the cytosol into the endolysosomal compartment, where it appar-ently forms aggregates in proximity to retained seeds. Additional analyses reveals zones of neuritic aSyn aggregates that overlaps with regions of microtubule disruption. Collectively, these findings enhance our understanding of aSyn pathology propagation in PD and other synucleinopathies, motivate additional experiments along these lines, and offer a path to guide the development of disease-modifying therapies.

neuroscience↗

bioRxiv2024

Mechanical control of the splicing factor PTBP1 regulates extracellular matrix stiffness-induced cell proliferation and mechanomemory

Cells sense and respond to mechanical cues from their environment. Mechanical cues are important for many biological processes, including embryonic development, ageing, cellular homeostasis, and diseases. Cells translate mechanical cues into cellular biochemical signals that govern cellular behaviour, like cell proliferation or migration, via a process called mechanotransduction. However, this process and the proteins involved remain incompletely understood. Here, we present an unbiased and large-scale approach to identify proteins involved in mechanotransduction. The screen revealed that the splicing factor PTBP1 is a novel mechanotransducer. We show that the nuclear localisation of PTBP1 depends on extracellular matrix stiffness, cell density, and the actomyosin-based contractility of the cell. Furthermore, we demonstrate that PTBP1 promotes the mechanosensitive splicing of the adapter protein Numb and that alternative splicing of Numb is crucial for matrix stiffness-induced cell proliferation and mechanomemory. Our results support the idea that changes in alternative splicing are an integral part of mechanotransduction and provide a mechanism by which matrix stiffness regulates cell proliferation and the formation of a mechanomemory in cells.

cell biology↗

bioRxiv2023

A Multi-Epitope/CXCL11 Prime/Pull Coronavirus Mucosal Vaccine Boosts the Frequency and the Function of Lung-Resident CD4+ and CD8+ Memory T Cells and Protects Against COVID-19-like Symptoms and Death Caused by SARS-CoV-2 infection

The pandemic of the coronavirus disease 2019 (COVID-19) has created the largest global health crisis in almost a century. Following exposure to SARS-CoV-2, the virus particles replicate in the lungs, induce a "cytokine storm" and potentially cause life-threatening inflammatory disease. Low frequencies of function SARS-CoV-2-specific CD4+ and CD8+ T cells in the lungs of COVID-19 patients were associated with severe cases of COVID-19. The apparent low level of T cell-attracting CXCL9, CXCL10, and CXCL11 chemokines in infected lungs may not be sufficient enough to assure the sequestration and/or homing of CD4+ and CD8+ T cells from the circulation into infected lungs. We hypothesize that a Coronavirus vaccine strategy that boosts the frequencies of functional SARS-CoV-2-specific CD4+ and CD8+ T cells in the lungs would lead to better protection against SARS-CoV-2 infection, COVID19-like symptoms, and death. In the present study, we designed and pre-clinically tested the safety, immunogenicity, and protective efficacy of a novel multi-epitope//CXCL11 prime/pull mucosal Coronavirus vaccine. This prime/pull vaccine strategy consists of intranasal delivery of a lung-tropic adeno-associated virus type 9 (AAV-9) vector that incorporates highly conserved human B, CD4+ CD8+ cell epitopes of SARS-CoV-2 (prime) and pulling the primed B and T cells into the lungs using the T cell attracting chemokine, CXCL-11 (pull). We demonstrated that immunization of HLA-DR*0101/HLA-A*0201/hACE2 triple transgenic mice with this multi-epitope//CXCL11 prime/pull Coronavirus mucosal vaccine: (i) Increased the frequencies of CD4+ and CD8+ TEM, TCM, and TRM cells in the lungs; and (ii) reduced COVID19-like symptoms, lowered virus replication, and prevented deaths following challenge with SARS-CoV-2. These findings discuss the importance of bolstering the number and function of lung-resident memory CD4+ and CD8+ T cells for better protection against SARS-CoV-2 infection, COVID-19-like symptoms, and death.

immunology↗

bioRxiv2021

A yeast model of the ALS protein Matrin3 uncovers Hsp90 and its co-chaperone Sti1 as modifiers of misfolding and toxicity

The MATR3 gene encoding the protein Matrin3 is implicated in the pathogenesis of the neurodegenerative disease amyotrophic lateral sclerosis (ALS). Matrin3 forms neuronal cytoplasmic and nuclear inclusions in ALS-affected neurons. Additionally, 13 heterozygous missense mutations in MATR3 are identified in ALS patients. To further explore Matrin3 misfolding and toxicity, we established and characterized a yeast model. We demonstrate that wild type Matrin3 and the ALS-associated variant F115C are toxic and form inclusions in yeast. Our further characterization uncovers substantial modification of Matrin3 toxicity and inclusion formation by Hsp90 and its co-chaperones, specifically Sti1. Thus, our study demonstrates how specific branches of cellular protein quality control regulate the misfolding and toxicity of Matrin3. Summary StatementWe established and characterized a yeast model expressing human Matrin3, a protein implicated in the pathogenesis of amyotrophic lateral sclerosis (ALS). Using this yeast model and mammalian neuronal cells, we showed that Matrin3 mislocalizes and forms inclusions, is cytotoxic, and increases sensitivity to cellular stress. We also uncovered that Hsp90 and particularly its co-chaperone Sti1 alter Matrin3 toxicity.

molecular biology↗

bioRxiv2021

Variation in mechanical and structural properties of enamel in primate molars

Mechanical properties of enamel are known to vary across molar crowns in some primates, but the association of this variation with phylogeny, structural properties and tribological behaviour is not well understood. In this study, 20 molars from a range of primate taxa (n=15) were studied using nanoindentation, micro-CT scanning, and SEM imaging. After micro-CT scanning, teeth were sectioned in the lingual-buccal plane through the mesial cusps. Five positions (buccal lateral, buccal cuspal, occlusal middle, lingual cuspal, lingual lateral) were studied in three locations (inner, middle, outer enamel regions). The results show middle enamel had the highest hardness and elastic modulus values in all positions. Non-functional molar sides (lingual in lower molars and buccal in upper molars) had higher hardness values than their functional counterparts. Increase in prism size was associated with a decrease in hardness in some tooth positions, and mineral density showed a significant relationship with elastic modulus values. Variation in enamel structure variation (e.g., enamel Schmelzmuster, Hunter-Schreger band thickness), may also be crucial in explaining variation in mechanical properties, with decussation zones associated with higher mechanical properties values. Primate enamel is not a homogeneous material, with variation in mechanical and structural properties across the crown likely associated with functional differences and variation in force distribution. Overall structural and mechanical patterns were similar in the primate species studied despite substantial differences in diet, suggesting these properties are potentially evolutionary conserved.

evolutionary biology↗

bioRxiv2019

The metronomic combination of paclitaxel with cholinergic agonists inhibits triple negative breast tumor progression. Participation of M2 receptor subtype

Triple negative tumors are more aggressive than other breast cancer subtypes and there is a lack of specific therapeutic targets on them. Since muscarinic receptors have been linked to tumor progression, we investigated the effect of metronomic therapy employing a traditional anti-cancer drug, paclitaxel plus muscarinic agonists at low doses on this type of tumor. We observed that MDA-MB231 tumor cells express muscarinic receptors, while they are absent in the non-tumorigenic MCF-10A cell line, which was used as control. The addition of carbachol or arecaidine propargyl ester, a non-selective or a selective subtype 2 muscarinic (M2) receptor agonist respectively, plus paclitaxel reduces cell viability involving a down-regulation in the expression of ATP "binding cassette" G2 drug transporter and epidermal growth factor receptor. We also detected an inhibition of tumor cell migration and anti-angiogenic effects produced by those drug combinations in vitro and in vivo (in NUDE mice) respectively. Our findings provide substantial evidence about M2 receptors as therapeutic target for the treatment of triple negative tumors.

pharmacology and toxicology↗

bioRxiv2019

Mapping the Immune Landscape of Clear Cell Renal Cell Carcinoma by Single-Cell RNA-seq

The immune cells within the tumor microenvironment are considered key determinants of response to cancer immunotherapy. Immune checkpoint blockade (ICB) has transformed the treatment of clear cell renal cell carcinoma (ccRCC), although the role of specific immune cell states remains unclear. To characterize the tumor microenvironment (TME) of ccRCC, we applied single-cell RNA sequencing (scRNA-seq) along with paired T cell receptor sequencing to map the transcriptomic heterogeneity of 24,904 individual CD45+ lymphoid and myeloid cells in matched tumor and blood from patients with ccRCC. We identified multiple distinct immune cell phenotypes for B and T (CD4 and CD8) lymphocytes, natural kill (NK) cells, and myeloid cells. Evaluation of T cell receptor (TCR) sequences revealed limited shared clonotypes between patients, whereas tumor-infiltrating T cell clonotypes were frequently found in peripheral blood, albeit in lower abundance. We further show that the circulating CD4+ T cell clonality is far less diverse than peripheral CD8+. Evaluation of myeloid subsets revealed unique gene programs defining monocytes, dendritic cells and tumor-associated macrophages. In summary, here we have leveraged scRNA-seq to refine our understanding of the relative abundance, diversity and complexity of the immune landscape of ccRCC. This report represents the first characterization of ccRCC immune landscape using scRNA-seq. With further characterization and functional validation, these findings may identify novel sub-populations of immune cells amenable to therapeutic intervention.\n\nOne Sentence SummarySingle-cell RNA-sequencing reveals unique lymphoid and myeloid gene programs with putative functions in clear cell renal cancer patients

immunology↗