Biology subjects

Saba, A.

Publications and source records attributed to Saba, A..

6 recordsLinked to original sources

bioRxiv2025

Single-cell phenomics through integrated imaging and molecular profiling

Single-cell technologies such as transcriptomics, microscopy, and flow cytometry have revolutionized the study of cellular identity and function. While each of these technologies is powerful on its own, their full potential lies in their integration, enabling multimodal profiling of the same cell and revealing how distinct modalities influence one another. Here, we introduce IRIS (Interconnected Robotic Imaging and Single cell transcriptomics), a deterministic single-cell platform technology that seamlessly couples high-resolution microscopy with droplet-based single-cell RNA sequencing. IRIS enables precise cell positioning, multimode imaging across brightfield and fluorescent channels, and subsequent molecular capture from the same cell, directly linking high-resolution morphological features to matched transcriptomes. We validate IRIS by recovering cell cycle progression states and transcriptional programmes associated with canonical morphologies and demonstrate its discovery power by molecularly resolving two nuclear-ER architectures within naive CD8+ T cells, each defined by distinct gene expression profiles and functional markers. IRIS establishes an integrative single-cell phenomics framework, opening new avenues for dissecting how cellular form relates to molecular state and function.

immunology↗

bioRxiv2025

Toll-like Receptor 4 Contributes to PCOS-like Metabolic and Reproductive Pathogenesis

Polycystic ovary syndrome (PCOS) is a reproductive disorder with heterogeneous symptoms and severity. Despite extensive research documenting chronic immune dysfunction as a hallmark of PCOS, the specific molecular mechanisms driving immune activation and its connection to the syndromes diverse symptoms remain poorly understood. Emerging evidence suggests that gut-derived bacterial endotoxins, particularly lipopolysaccharide (LPS), may breach the intestinal barriers in PCOS patients and trigger systemic inflammation through Toll-like receptor 4 (TLR4), a pattern recognition receptor of the innate immune system. This study investigated whether TLR4 serves as a critical mechanistic driver of PCOS pathogenesis by examining the effect of genetic TLR4 knockout (TLR4-/-) in a letrozole (LET)-induced mouse model of PCOS. Our results demonstrate that TLR4 deficiency reduces many PCOS-like symptoms, including elevated luteinizing hormone, anovulation, and metabolic dysfunction. TLR4 knockout also preserved estrous cycling and fertility, improved glucose tolerance, maintained gut barrier integrity, and reduced inflammatory markers in LET-treated females. These findings establish TLR4 as a key mediator orchestrating PCOSs multi-system pathology, positioning TLR4 as a critical convergence point rather than affecting individual symptoms in isolation. This novel work reveals that TLR4-mediated inflammation drives multiple PCOS pathologies, opening avenues for targeted anti-inflammatory treatments in women with this disorder. Significance StatementPolycystic ovary syndrome (PCOS) affects up to 15% of reproductive-age women worldwide. This study reveals that TLR4, an innate immune receptor, is key to the pathophysiology of PCOS-like symptoms in female mice. When TLR4 was genetically deleted, mice treated with letrozole to induce PCOS-like symptoms maintained normal weight, glucose regulation, estrous cycling, and fertility. The improvements coincided with preserved gut barrier breakdown and reduced inflammation. These findings identify TLR4 as a key mediator between gut health, immune activation, and PCOS pathophysiology, suggesting that targeting TLR4 could offer new therapeutic approaches for this common but poorly understood syndrome affecting millions of women.

immunology↗

bioRxiv2025

CNS-Tau Specific Antibodies Illuminate Disease Signatures Across Tauopathies

BackgroundAlternative splicing of the MAPT gene produces distinct tau isoforms in the central and peripheral nervous systems (CNS and PNS), yet their respective biological and pathological roles remain poorly understood. Recent studies suggest that CNS-tau may play a key role in amyloid-{beta} associated neurodegeneration in Alzheimers disease (AD), but the absence of isoform-specific tools has limited both mechanistic insight and biomarker development. We aimed to develop and validate CNS-tau-specific monoclonal antibodies and assess their utility in neuropathology and fluid-based biomarker assays across AD and primary tauopathies. MethodsWe generated six recombinant rabbit monoclonal antibodies targeting a CNS-tau-specific sequence encoded by exons 4 and 5. Specificity and affinity were evaluated via biolayer interferometry, immunoblotting, and tau-expressing HEK293 models. The lead clone, LL-T-1-1, was tested in postmortem brain sections from AD (n = 23), progressive supranuclear palsy (PSP, n = 3), and corticobasal degeneration (CBD, n = 3). A second clone, LL-T-1-5, was optimized for use in plasma assays via an ultrasensitive nanoneedle platform, LoD < 1 pg/ml. ResultsLL-T-1-1 showed nanomolar affinity for CNS-tau and no cross-reactivity with PNS-tau. It selectively labeled dystrophic neurites in AD and all hallmark tau lesions in PSP and CBD without antigen retrieval. LL-T-1-5-based plasma assays revealed CNS-tau levels significantly correlated with cognitive scores (MMSE and QDRS) and differentiated impaired from unimpaired individuals. ConclusionsCNS-tau-specific antibodies LL-T-1-1 and LL-T-1-5 provide new tools for neuropathology and fluid biomarker development across tauopathies.

neuroscience↗

bioRxiv2024

The pathogenicity of PSEN2 variants is tied to Aβ production and homology to PSEN1

INTRODUCTIONThough recognized as a potential cause of Autosomal Dominant Alzheimers Disease, the pathogenicity of many PSEN2 variants remains uncertain. We compared A{beta} production across all missense PSEN2 variants in the Alzforum database and, when possible, to corresponding PSEN1 variants. METHODSWe expressed 74 PSEN2 variants, 21 of which had homologous PSEN1 variants with the same amino acid substitution, in HEK293 cells lacking PSN1/2. A{beta} production was compared to age at symptom onset (AAO) and between homologous PSEN1/2 variants. RESULTSA{beta}42/40 and A{beta}37/42 ratios were associated with AAO across PSEN2 variants, strongly driven by PSEN2 variants with PSEN1 homologs. PSEN2 AAO was 18.3 years later compared to PSEN1 homologs. A{beta} ratios from PSEN1/2 homologs were highly correlated, suggesting a similar mechanism of {gamma}-secretase dysfunction. DISCUSSIONThe existence of a PSEN1 homolog and patterns of A{beta} production are important considerations in assessing the pathogenicity of previously-reported and new PSEN2 variants.

neuroscience↗

bioRxiv2024

Identification of Fibrinogen as a Plasma Protein Binding Partner for Lecanemab Biosimilar IgG: Implications for Alzheimer's Disease Therapy

ObjectiveRecombinant monoclonal therapeutic antibodies like lecanemab, which target amyloid beta in Alzheimers disease, offer a promising approach for modifying the disease progression. Due to its relatively short half-life, Lecanemab, administered as a bi-monthly infusion (typically 10mg/kg) has a relatively brief half-life. Interaction with abundant plasma proteins binder in the bloodstream can affect pharmacokinetics of drugs, including their half-life. In this study we investigated potential plasma protein binding interaction to lecanemab using lecanemab biosimilar. MethodsLecanemab biosimilar used in this study was based on publicly available sequences. ELISA and Western blotting were used to assess lecanemab biosimilar immunoreactivity in the fractions human plasma sample obtained through size exclusion chromatography. The binding of lecanemab biosimilar to candidate binders was confirmed by Western blotting, ELISA, and surface plasmon resonance analysis. ResultsUsing a combination of equilibrium dialysis, ELISA, and Western blotting in human plasma, we first describe the presence of likely plasma protein binding partner to lecanemab biosimilar, and then identify fibrinogen as one of them. Utilizing surface plasmon resonance, we confirmed that lecanemab biosimilar does bind to fibrinogen, although with lower affinity than to monomeric amyloid beta. InterpretationIn the context of lecanemab therapy, these results imply that fibrinogen levels could impact the levels of free antibodies in the bloodstream and that fibrinogen might serve as a reservoir for lecanemab. More broadly, these results indicate that plasma protein binding may be an important consideration when clinically utilizing therapeutic antibodies in neurodegenerative disease.

neuroscience↗

bioRxiv2019

Therapeutically Exploring Persister Metabolism In Bacteria

Bacterial persisters are rare phenotypic variants that are temporarily tolerant to high concentrations of antibiotics. We have previously discovered that persisters are mostly derived from stationary-phase cells with high redox activities that are maintained by endogenous protein and RNA degradation. This intracellular degradation resulted in self-inflicted damage that transiently repressed the cellular functions targeted by antibiotics. Leveraging this knowledge, we developed an assay integrating a degradable fluorescent protein system and a small library, containing FDA-approved drugs and antibiotics, to detect chemicals that target persister metabolism. We identified several metabolic inhibitors, including anti-psychotic drugs, that can reduce Escherichia coli persistence. These chemical inhibitors also reduce Pseudomonas aeruginosa persistence, potentially verifying the existence of similar mechanisms in a medically relevant organism.

microbiology↗