Biology subjects

Sebastian, R.

Publications and source records attributed to Sebastian, R..

6 recordsLinked to original sources

bioRxiv2025

Distinct Synaptic Mechanisms Drive NRXN1 Variant-Mediated Pathogenesis in iPSC-Derived Neuronal Models of Autism and Schizophrenia

Copy number deletions in the 2p16.3/NRXN1 locus confer genome wide risk for autism spectrum disorder (ASD) and schizophrenia (SCZ). Prior work demonstrated that heterozygous NRXN1 deletions decreases synaptic strength and neurotransmitter release probability in human-iPSC derived cortical glutamatergic induced neurons and this synaptic phenotype is replicated in SCZ patient iPSCs with varying NRXN1 genomic deletions. What is unknown, however, is whether similar synaptic impairment exists in ASD patients carrying NRXN1 deletions. Answering this question is important to determine whether all NRXN1 deletion carriers should be treated similarly or individually, based on their genetic backgrounds and deletion breakpoints. Here, using previously uncharacterized ASD patient iPSC lines, we show that ASD-NRXN1 deletions impact cortical synaptic function and plasticity in unique ways compared to SCZ-NRXN1 deletions. Specifically, at a single neuronal level, ASD-NRXN1 deletions alter basal spontaneous synaptic transmission by selectively enhancing excitatory synaptic signaling with no changes at inhibitory synapses while SCZ-NRXN1 deletions reduce both excitatory and inhibitory synaptic transmission. At the neuronal network level, there exists enhanced transmission probability and irregular firing patterns in ASD-NRXN1 deletions. Such changes at the synaptic and network level connectivity patterns influence a critical form of developmental cortical plasticity, synaptic scaling, as ASD-NRXN1 deletions uniquely fail to upscale their synaptic strength in response to chronic neuronal silencing. Together, these findings highlight the disorder-specific consequences of NRXN1 deletions on synaptic function and connectivity, offering mechanistic insights with implications for therapeutic targeting and refinement strategies for NRXN1-associated synaptopathies. HighlightsO_LINovel ASD patient-iPSC-derived E-I culture model to investigate pathogenic NRXN1 deletions on cortical synaptic function and plasticity C_LIO_LIASD-NRXN1 deletions enhance basal synaptic transmission by specifically increasing excitatory neurotransmitter release, opposite of SCZ-NRXN1 deletions C_LIO_LISynaptic scaling homeostasis is impaired in ASD-NRXN1 deletions C_LIO_LISpike train cross-correlation analysis reveals increased transmission probability and irregular firing patterns in ASD-NRXN1 deletions C_LI

neuroscience↗

bioRxiv2024

Microenvironment Shapes Cell State, Plasticity, and Heterogeneity of Small Cell Lung Cancer

Small-cell lung cancer (SCLC) is the most fatal form of lung cancer. Intra-tumoral heterogeneity, marked by neuroendocrine (NE) and non-neuroendocrine (non-NE) cell states, defines SCLC, but the drivers of SCLC plasticity are poorly understood. To map the landscape of SCLC tumor microenvironment (TME), we apply spatially resolved transcriptomics and quantitative mass spectrometry-based proteomics to metastatic SCLC tumors obtained via rapid autopsy. The phenotype and overall composition of non-malignant cells in the tumor microenvironment (TME) exhibits substantial variability, closely mirroring the tumor phenotype, suggesting TME-driven reprogramming of NE cell states. We identify cancer-associated fibroblasts (CAF) as a crucial element of SCLC TME heterogeneity, contributing to immune exclusion, and predicting exceptionally poor prognosis. Together, our work provides a comprehensive map of SCLC tumor and TME ecosystems, emphasizing their pivotal role in SCLCs adaptable nature, opening possibilities for re-programming the intercellular communications that shape SCLC tumor states.

cancer biology↗

bioRxiv2023

Patterning ganglionic eminences in developing human brain organoids using morphogen gradient inducing device

In early neurodevelopment, the central nervous system is established through the coordination of various neural organizers directing tissue patterning and cell differentiation. Better recapitulation of morphogen gradient production and signaling will be crucial for establishing improved developmental models of the brain in vitro. Here, we developed a method by assembling polydimethylsiloxane (PDMS) devices capable of generating a sustained chemical gradient to produce patterned brain organoids, which we termed Morphogen-gradient Induced Brain Organoids (MIBOs). At 3.5 weeks, MIBOs replicated Dorsal-Ventral patterning observed in the Ganglionic Eminence (GE). Analysis of matured MIBOs through single-cell RNA sequencing revealed distinct Dorsal GE derived CALB2+ interneurons (INs), Medium Spiny Neurons (MSNs), and MGE derived cell types. Finally, we demonstrate long term culturing capabilities with MIBOs maintaining stable neural activity in cultures grown up to 5.5 months. MIBOs demonstrate a versatile approach for generating spatially patterned brain organoids for embryonic development and disease modeling. MotivationThe use of small molecules for the guided differentiation of brain organoids has proven to be a useful tool for modeling various aspects of early neurodevelopment. Still, the embryonic brain is patterned through a combination of morphogen gradients stemming from organizer regions. To address this inconsistency, we designed a device capable of mimicking neural organizers by maintaining a steady morphogen gradient. We used this device to expose forebrain organoids to multiple gradient conditions and cataloged the diversity of cell types produced.

neuroscience↗

bioRxiv2022

ATR inhibition augments the efficacy of lurbinectedin in small cell lung cancer

Abstract/SummarySmall cell lung cancer (SCLC) is the most lethal type of lung cancer. Specifically, MYC-driven non-neuroendocrine SCLC are particularly resistant to standard therapies. Lurbinectedin was recently approved for the treatment of relapsed SCLC, but combinatorial approaches are needed to increase the depth and duration of responses to lurbinectedin. Using high-throughput screens, we found inhibitors of ataxia telangiectasia-mutated and rad3-related (ATR) as the most effective agents for augmenting lurbinectedin efficacy. First-in-class ATR inhibitor berzosertib synergized with lurbinectedin in multiple SCLC cell lines, organoid and in-vivo models. Mechanistically, ATR inhibition abrogated S-phase arrest induced by lurbinectedin and forced cell-cycle progression causing mitotic catastrophe and cell death. High CDKN1A/p21 expression was associated with decreased synergy due to G1 arrest, while increased levels of ERCC5/XPG were predictive of increased combination efficacy. Importantly, MYC-driven non-neuroendocrine tumors which were resistant to first-line therapies displayed decreased CDKN1A/p21 expression and increased ERCC5/XPG indicating they were primed for response to lurbinectedin-berzosertib combination. The combination is being assessed in a clinical trial NCT04802174. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/520783v1_ufig1.gif" ALT="Figure 1"> View larger version (63K): org.highwire.dtl.DTLVardef@19acf72org.highwire.dtl.DTLVardef@a9703forg.highwire.dtl.DTLVardef@86592org.highwire.dtl.DTLVardef@1448372_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2022

Single cell transcriptomic profiling of human brain organoids reveals developmental timing- and cell-type-specific vulnerabilities induced by NRXN1 CNVs in schizophrenia

De novo mutations and copy number deletions in NRXN1 (2p16.3) pose a significant risk for schizophrenia (SCZ). It is unclear how NRXN1 deletions impact cortical development in a cell type-specific manner and disease background modulates these phenotypes. Here, we leveraged human pluripotent stem cell-derived forebrain organoid models carrying NRXN1 heterozygous deletions in isogenic and SCZ patient genetic backgrounds and conducted single-cell transcriptomic analysis over the course of brain organoid development from 3 weeks to 3.5 months. Intriguingly, while both deletions similarly impacted molecular pathways associated with ubiquitin-proteasome system, alternative splicing, and synaptic signaling in maturing glutamatergic and GABAergic neurons, SCZ-NRXN1 deletions specifically perturbed developmental trajectories of early neural progenitors and accumulated disease-specific transcriptomic signatures. Using calcium imaging, we found that both deletions led to long-lasting changes in spontaneous and synchronous neuronal networks, implicating synaptic dysfunction. Our study reveals developmental-timing- and cell-type-dependent actions of NRXN1 deletions in unique genetic contexts.

neuroscience↗

bioRxiv2020

SCLC_CellMiner: Integrated Genomics and Therapeutics Predictors of Small Cell Lung Cancer Cell Lines based on their genomic signatures

Model systems are necessary to understand the biology of SCLC and develop new therapies against this recalcitrant disease. Here we provide the first online resource, CellMiner-SCLC (https://discover.nci.nih.gov/SclcCellMinerCDB) incorporating 118 individual SCLC cell lines and extensive omics and drug sensitivity datasets, including high resolution methylome performed for the purpose of the current study. We demonstrate the reproducibility of the cell lines and genomic data across the CCLE, GDSC, CTRP, NCI and UTSW datasets. We validate the SCLC classification based on four master transcription factors: NEUROD1, ASCL1, POU2F3 and YAP1 (NAPY classification) and show transcription networks connecting each them with their downstream and upstream regulators as well as with the NOTCH and HIPPO pathways and the MYC genes (MYC, MYCL1 and MYCN). We find that each of the 4 subsets express specific surface markers for antibody-targeted therapies. The SCLC-Y cell lines differ from the other subsets by expressing the NOTCH pathway and the antigen-presenting machinery (APM), and responding to mTOR and AKT inhibitors. Our analyses suggest the potential value of NOTCH activators, YAP1 inhibitors and immune checkpoint inhibitors in SCLC-Y tumors that can now be independently validated. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/980623v2_ufig1.gif" ALT="Figure 1"> View larger version (65K): org.highwire.dtl.DTLVardef@10930e7org.highwire.dtl.DTLVardef@699d9corg.highwire.dtl.DTLVardef@1ea773corg.highwire.dtl.DTLVardef@3a1589_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LISCLC-CellMiner provides the most extensive SCLC resource in terms of number of cell lines (118 cell lines), extensive omics data (exome, microarray, RNA-seq, copy number, methylomes and microRNA) and drug sensitivity testing. C_LIO_LIWe find evidence of distinct epigenetic profile of SCLC cell lines (global hypomethylation and histone gene methylation), which is consistent with their plasticity. C_LIO_LITranscriptome analyses demonstrate the coherent transcriptional networks associated with the 4 main genomic subgroups (NEUROD1, ASCL1, POU2F3 & YAP1 = NAPY classification) and their connection with the NOTCH and HIPPO signaling pathways. C_LIO_LISCLC-CellMiner provides a conceptual framework for the selection of therapies for SCLC in a personalized fashion allowing putative biomarkers according molecular classifications and molecular characteristics. C_LIO_LISCLC-Y cell lines differ from the other cancer cell lines; their transcriptome resemble NSCLC cell lines. YAP1 cell lines while being the most resistant to standard of care treatments (etoposide, cisplatin and topotecan) respond to mTOR and AKT inhibitors and present native immune predisposition suggesting sensitivity to immune checkpoint inhibitors. C_LI

cancer biology↗