Biology subjects

Ali, D.

Publications and source records attributed to Ali, D..

3 recordsLinked to original sources

bioRxiv2026

High-Throughput Single-Cell Spectroscopy Using Phasor Analysis of Spectral Flow Cytometry

Phasor analysis is a well-established tool in hyperspectral and lifetime microscopy, providing a powerful, fit-free approach for interpreting complex fluorescence. However, its application has remained largely restricted to imaging-based modalities. Spectral flow cytometry (SFC) enables acquisition of full emission spectra from large numbers of independent single-cell events, offering superior statistical power compared to microscopy, albeit at the expense of spatial and temporal information. Here, we present the first implementation of spectral phasor analysis for SFC (phSFC), establishing a unified analytical framework that preserves interpretative continuity with hyperspectral microscopy while extending phasor-based analysis to high-throughput, single-cell measurements. Using the membrane-sensitive probe LAURDAN as a benchmark, we demonstrate that SFC reproduces phasor signatures of membrane order previously reported by hyperspectral confocal microscopy (HSI). We performed comparative analyses using multilamellar lipid vesicles (MLVs) prepared from known physical order compositions. Both modalities, SFC and HSI, accurately resolved MLVs with fluid, gel and liquid-ordered and liquid-disorder membrane phases, capturing cholesterol-dependent spectral shifts, including trajectories associated with mixtures of the different lipid phase behavior. Although absolute phasor coordinates differed between modalities due to distinct spectral sampling and detector configurations, the relative organization of membrane physical states was preserved. Notably, SFC produced more compact phasor distributions, consistent with larger sample size and enhanced statistical robustness. To further extend phSFC, we first evaluated its capacity to resolve membrane changes in live cultured cells following cholesterol depletion, establishing consistency between HSI and SFC measurements. We then applied phSFC to detect membrane dynamics in primary leukocytes isolated from bronchoalveolar lavage of mice with inflammation-associated lung pathology. LAURDAN fluorescence in the presence of autofluorescence and antibody-derived signals is quantified and discussed with simple solution by n-harmonic phasor analysis unmixing. Together, these results establish SFC as a robust and complementary extension of LAURDAN phasor analysis, bridging HSI and high-throughput flow cytometry measurements.

biophysics↗

bioRxiv2025

The Dynamic Nature of Genetic Risk for Schizophrenia Within Genes Regulated by FOXP1 During Neurodevelopment

FOXP1 (Forkhead-box protein P1) is a crucial transcription factor in neural development and is associated with schizophrenia (SCZ). FOXP1-regulated genes may contribute to genetic risk of SCZ and this may vary across different stages of neurodevelopment. We analyzed transcriptomic data from mouse and human models of FOXP1 loss-of-function across prenatal and postnatal developmental stages, including neural stem cells from embryonic mice (E14.5) and human brain organoids (equivalent to second trimester), and cortical tissues from different mouse postnatal stages P0, P7, and P47. P0 in mice corresponds to the third trimester in humans, while P7 and P47 represent early childhood and adolescence, respectively. The effect of FOXP1 disruption on gene expression in cortical tissues/cells was assayed using RNA-seq, including time-course and pairwise gene expression analysis. Linkage disequilibrium score regression assessed if FOXP1-regulated genes were enriched for SCZ heritability. Gene-set enrichment analysis investigated if FOXP1-regulated genes were enriched for SCZ-associated genes reported as differentially expressed in single cortical cell studies. SynGO analysis mapped FOXP1-regulated genes to synaptic locations and functions. FOXP1-regulated genes are enriched for SCZ heritability, with significant results for E14.5, P7 and P47 but not P0. The P7 gene-set showed the strongest enrichment for SCZ-associated genes from single cortical cell studies. FOXP1-regulated genes at both P7 and P47 were involved in multiple synaptic functions and were mainly enriched within glutamatergic excitatory neurons, with P47 also showing enrichment within GABAergic inhibitory neurons across regions of the postnatal cortex. Prenatal FOXP1-regulated genes were enriched in progenitor cells and also mapped to the synapse. Genetic risk for SCZ within FOXP1-regulated genes follows a dynamic trajectory across developmental stages, showing stronger effects at timepoints that map to early childhood, followed by adolescence and second trimester. Author SummarySchizophrenia is a complex disorder caused by many genes. While existing treatments can help manage some positive symptoms, such as hallucinations and delusions, they are not effective in treating other life-limiting symptom areas. As a result, individuals with schizophrenia continue to face significant challenges, including disability, unemployment, homelessness, and social isolation. Genome-wide association studies of schizophrenia have been effective at identifying individual SNPs and genes that contribute to these phenotypes but have struggled to immediately uncover the bigger picture of the underlying biology of the disorder. Here we take an individual gene associated with schizophrenia risk, FOXP1, which is an important regulator of brain development. Using functional genomics data from models where FOXP1 has been disrupted, we identified sets of genes regulated by FOXP1 across different developmental stages, focusing on the cortical region of the brain. Our findings reveal that FOXP1-regulated genes are most strongly associated with schizophrenia during early childhood and adolescence. These genes are associated with synaptic components, including presynaptic and postsynaptic structures. By integrating developmental timing, cell type specificity, and functional pathways, this study provides valuable insights into the molecular mechanisms underlying schizophrenia.

genomics↗

bioRxiv2023

Direct targets of MEF2C are enriched for genes associated with schizophrenia and cognitive function and are involved in neurogenesis and mitochondrial function

Myocyte Enhancer Factor 2C (MEF2C) is a transcription factor that plays a crucial role in neurogenesis and synapse development. Genetic studies have identified MEF2C as a gene that influences cognition and risk for neuropsychiatric disorders, including autism spectrum disorder (ASD) and schizophrenia (SCZ). Here, we investigated the involvement of MEF2C in these phenotypes using human-derived neural stem cells (NSCs) and induced neurons (iNs), which represented early and late neurodevelopmental stages. For these cellular models, MEF2C function had previously been disrupted, either by direct or indirect mutation, and gene expression assayed using RNA-seq. We integrated these RNA-seq data with MEF2C ChIP-seq data to identify dysregulated direct target genes of MEF2C in the NSCs and iNs models. Several MEF2C direct target gene-sets were enriched for SNP-based heritability for intelligence, educational attainment and SCZ, as well as being enriched for genes containing rare de novo mutations reported in ASD and/or developmental disorders. These gene-sets are enriched in both excitatory and inhibitory neurons in the hippocampus and cortex and are involved in a wide range of biological processes including neurogenesis, metabolic processes, protein modifications, as well as mitochondrial function and energy production. We observed a trans expression quantitative trait locus (eQTL) effect of a single SNP at MEF2C (rs6893807, which is associated with IQ) on the expression of a target gene, BNIP3L. BNIP3L is a prioritized risk gene from the largest genome-wide association study of SCZ and has a function in mitophagy in mitochondria. Overall, our analysis reveals that either direct or indirect disruption of MEF2C dysregulates sets of genes that contain multiple alleles associated with SCZ risk and cognitive function and implicates neurogenesis and mitochondrial function in the etiology of these phenotypes. Author SummarySchizophrenia is a complex disorder caused by many genes. Current drugs for schizophrenia are only partially effective and do not treat cognitive deficits, which are key factors for explaining disability, leading to unemployment, homelessness and social isolation. Genome-wide association studies of schizophrenia and cognitive function have been effective at identifying individual SNPs and genes that contribute to these phenotypes but have struggled to immediately uncover the bigger picture of the underlying biology of the disorder. Here we take an individual gene associated with schizophrenia and cognitive function called MEF2C, which on its own is a very important regulator of brain development. We use functional genomics data from studies where MEF2C has been mutated to identify sets of other genes that are influenced by MEF2C in developing and mature neurons. We show that several of these gene-sets are enriched for common variants associated with schizophrenia and cognitive function, and for rare variants that increase risk of various neurodevelopmental disorders. These gene-sets are involved in neurogenesis and mitochondrial function, providing evidence that these biological processes may be important in the context of the molecular mechanisms that underpin schizophrenia and cognitive function.

genetics↗