Single RNA Sequencing Research Articles

Microglia integration into human midbrain organoids leads to increased neuronal maturation and functionality.

The human brain is a complex, three‐dimensional structure. To better recapitulate brain complexity, recent efforts have focused on the development of human‐specific midbrain organoids. Human iPSC‐derived midbrain organoids consist of differentiated and functional neurons, which contain active synapses, as well as astrocytes and oligodendrocytes. However, the absence of microglia, with their ability to remodel neuronal networks and phagocytose apoptotic cells and debris, represents a major disadvantage for the current midbrain organoid systems. Additionally, neuroinflammation‐related disease modeling is not possible in the absence of microglia. So far, no studies about the effects of human iPSC‐derived microglia on midbrain organoid neural cells have been published. Here we describe an approach to derive microglia from human iPSCs and integrate them into iPSC‐derived midbrain organoids. Using single nuclear RNA Sequencing, we provide a detailed characterization of microglia in midbrain organoids as well as the influence of their presence on the other cells of the organoids. Furthermore, we describe the effects that microglia have on cell death and oxidative stress‐related gene expression. Finally, we show that microglia in midbrain organoids affect synaptic remodeling and increase neuronal excitability. Altogether, we show a more suitable system to further investigate brain development, as well as neurodegenerative diseases and neuroinflammation.

Decoding the Role of Astrocytes in the Entorhinal Cortex in Alzheimer’s Disease Using High-Dimensional Single-Nucleus RNA Sequencing Data and Next-Generation Knowledge Discovery Methodologies: Focus on Drugs and Natural Product Remedies for Dementia

Introduction: Alzheimer’s disease (AD) is a major cause of the development of cognitive decline and dementia. AD and associated dementias (ADRD) are the major contributors to the enormous burden of morbidity and mortality worldwide. To date, there are no robust therapies to alleviate or cure this debilitating disease. Most drug treatments focus on restoring the normal function of neurons and the cells that cause inflammation, such as microglia in the brain. However, the role of astrocytes, the brain’s housekeeping cells, in the development of AD and the initiation of dementia is still not well understood. Objective: To decipher the role of astrocytes in the entorhinal cortex of AD patients using single nuclear RNA sequencing (snRNASeq) datasets from the Single Cell RNA-seq Database for Alzheimer’s Disease (scREAD). The datasets were originally derived from astrocytes, isolated from the entorhinal cortex of AD brain and healthy brain to decipher disease-specific signaling pathways as well as drugs and natural products that reverse AD-specific signatures in astrocytes. Methods: We used snRNASeq datasets from the scREAD database originally derived from astrocytes isolated from the entorhinal cortex of AD and healthy brains from the Gene Expression Omnibus (GEO) (GSE138852 and GSE147528) and analyzed them using next-generation knowledge discovery (NGKD) platforms. scREAD is a user-friendly open-source interface available at https://bmbls.bmi.osumc.edu/scread/that enables more discovery-oriented strategies. snRNASeq data and metadata can also be visualized and downloaded via an interactive web application at adsn.ddnetbio.com. Differentially expressed genes (DEGs) for each snRNASeq dataset were analyzed using iPathwayGuide to compare and derive disease-specific pathways, gene ontologies, and in silico predictions of drugs and natural products that regulate AD -specific signatures in astrocytes. In addition, DEGs were analyzed using the L1000FWD and L1000CDS2 signature search programming interfaces (APIs) to identify additional drugs and natural products that mimic or reverse AD-specific gene signatures in astrocytes. Results: We found that PI3K/AKT signaling, Wnt signaling, neuroactive ligand-receptor interaction pathways, neurodegeneration pathways, etc. were significantly impaired in astrocytes from the entorhinal cortex of AD patients. Biological processes such as glutamate receptor signaling pathway, regulation of synapse organization, cell-cell adhesion via plasma membrane adhesion molecules, and chylomicrons were negatively enriched in the astrocytes from the entorhinal cortex of AD patients. Gene sets involved in cellular components such as postsynaptic membrane, synaptic membrane, postsynapse, and synapse part were negatively enriched (p < 0.01). Moreover, molecular functions such as glutamate receptor activity, neurotransmitter receptor activity, and extracellular ligand-gated ion channels were negatively regulated in the astrocytes of the entorhinal cortex of AD patients (p < 0.01). Moreover, the application of NGKD platforms revealed that antirheumatic drugs, vitamin-E, emetine, narciclasine, cephaeline, trichostatin A, withaferin A, dasatinib, etc. can potentially reverse gene signatures associated with AD. Conclusions: The present study highlights an innovative approach to use NGKD platforms to find unique disease-associated signaling pathways and specific synthetic drugs and natural products that can potentially reverse AD and ADRD-associated gene signatures.

Transcriptional, Electrophysiological, and Metabolic Characterizations of hESC-Derived First and Second Heart Fields Demonstrate a Potential Role of TBX5 in Cardiomyocyte Maturation.

Background: Human embryonic stem cell-derived cardiomyocytes (hESC-CMs) can be used as a source for cell delivery to remuscularize the heart after myocardial infarction. Despite their therapeutic potential, the emergence of ventricular arrhythmias has limited their application. We previously developed a double reporter hESC line to isolate first heart field (FHF: TBX5 + NKX2-5 +) and second heart field (SHF: TBX5 - NKX2-5 + ) CMs. Herein, we explore the role of TBX5 and its effects on underlying gene regulatory networks driving phenotypical and functional differences between these two populations. Methods: We used a combination of tools and techniques for rapid and unsupervised profiling of FHF and SHF populations at the transcriptional, translational, and functional level including single cell RNA (scRNA) and bulk RNA sequencing, atomic force and quantitative phase microscopy, respirometry, and electrophysiology. Results: Gene ontology analysis revealed three biological processes attributed to TBX5 expression: sarcomeric structure, oxidative phosphorylation, and calcium ion handling. Interestingly, migratory pathways were enriched in SHF population. SHF-like CMs display less sarcomeric organization compared to FHF-like CMs, despite prolonged in vitro culture. Atomic force and quantitative phase microscopy showed increased cellular stiffness and decreased mass distribution over time in FHF compared to SHF populations, respectively. Electrophysiological studies showed longer plateau in action potentials recorded from FHF-like CMs, consistent with their increased expression of calcium handling genes. Interestingly, both populations showed nearly identical respiratory profiles with the only significant functional difference being higher ATP generation-linked oxygen consumption rate in FHF-like CMs. Our findings suggest that FHF-like CMs display more mature features given their enhanced sarcomeric alignment, calcium handling, and decreased migratory characteristics. Finally, pseudotime analyses revealed a closer association of the FHF population to human fetal CMs along the developmental trajectory. Conclusion: Our studies reveal that distinguishing FHF and SHF populations based on TBX5 expression leads to a significant impact on their downstream functional properties. FHF CMs display more mature characteristics such as enhanced sarcomeric organization and improved calcium handling, with closer positioning along the differentiation trajectory to human fetal hearts. These data suggest that the FHF CMs may be a more suitable candidate for cardiac regeneration.

Reduced TREM2 activation in microglia of patients with Alzheimer's disease.

Loss‐of‐function variants of triggering receptor expressed on myeloid cells 2 (TREM2) increase the risk of developing Alzheimer's disease (AD). The mechanism through which TREM2 contributes to the disease (TREM2 activation vs inactivation) is largely unknown. Here, we analyzed changes in a gene set downstream of TREM2 to determine whether TREM2 signaling is modified by AD progression. We generated an anti‐human TREM2 agonistic antibody and defined TREM2 activation in terms of the downstream expression changes induced by this antibody in microglia developed from human induced pluripotent stem cells (iPSC). Differentially expressed genes (DEGs) following TREM2 activation were compared with the gene set extracted from microglial single nuclear RNA sequencing data of patients with AD, using gene set enrichment analysis. We isolated an anti‐TREM2‐specific agonistic antibody, Hyb87, from anti‐human TREM2 antibodies generated using binding and agonism assays, which helped us identify 300 upregulated and 251 downregulated DEGs. Pathway enrichment analysis suggested that TREM2 activation may be associated with Th2‐related pathways. TREM2 activation was lower in AD microglia than in microglia from healthy subjects or patients with mild cognitive impairment. TREM2 activation also showed a significant negative correlation with disease progression. Pathway enrichment analysis of DEGs controlled by TREM2 activity indicated that TREM2 activation in AD may lead to anti‐apoptotic signaling, immune response, and cytoskeletal changes in the microglia. We showed that TREM2 activation decreases with AD progression, in support of a protective role of TREM2 activation in AD. In addition, the agonistic anti‐TREM2 antibody can be used to identify TREM2 activation state in AD microglia.

Oxidative Phosphorylation Is Dysregulated Within the Basocortical Circuit in a 6-month old Mouse Model of Down Syndrome and Alzheimer's Disease.

Down syndrome (DS) is the primary genetic cause of intellectual disability (ID), which is due to the triplication of human chromosome 21 (HSA21). In addition to ID, HSA21 trisomy results in a number of neurological and physiological pathologies in individuals with DS, including progressive cognitive dysfunction and learning and memory deficits which worsen with age. Further exacerbating neurological dysfunction associated with DS is the concomitant basal forebrain cholinergic neuron (BFCN) degeneration and onset of Alzheimer’s disease (AD) pathology in early mid-life. Recent single population RNA sequencing (RNA-seq) analysis in the Ts65Dn mouse model of DS, specifically the medial septal cholinergic neurons of the basal forebrain (BF), revealed the mitochondrial oxidative phosphorylation pathway was significantly impacted, with a large subset of genes within this pathway being downregulated. We further queried oxidative phosphorylation pathway dysregulation in Ts65Dn mice by examining genes and encoded proteins within brain regions comprising the basocortical system at the start of BFCN degeneration (6 months of age). In select Ts65Dn mice we demonstrate significant deficits in gene and/or encoded protein levels of Complex I-V of the mitochondrial oxidative phosphorylation pathway in the BF. In the frontal cortex (Fr Ctx) these complexes had concomitant alterations in select gene expression but not of the proteins queried from Complex I-V, suggesting that defects at this time point in the BF are more severe and occur prior to cortical dysfunction within the basocortical circuit. We propose dysregulation within mitochondrial oxidative phosphorylation complexes is an early marker of cognitive decline onset and specifically linked to BFCN degeneration that may propagate pathology throughout cortical memory and executive function circuits in DS and AD.

Profiling Basal Forebrain Cholinergic Neurons Reveals a Molecular Basis for Vulnerability Within the Ts65Dn Model of Down Syndrome and Alzheimer’s Disease

Basal forebrain cholinergic neuron (BFCN) degeneration is a hallmark of Down syndrome (DS) and Alzheimer's disease (AD). Current therapeutics have been unsuccessful in slowing disease progression, likely due to complex pathological interactions and dysregulated pathways that are poorly understood. The Ts65Dn trisomic mouse model recapitulates both cognitive and morphological deficits of DS and AD, including BFCN degeneration. We utilized Ts65Dn mice to understand mechanisms underlying BFCN degeneration to identify novel targets for therapeutic intervention. We performed high-throughput, single population RNA sequencing (RNA-seq) to interrogate transcriptomic changes within medial septal nucleus (MSN) BFCNs, using laser capture microdissection to individually isolate ~500 choline acetyltransferase-immunopositive neurons in Ts65Dn and normal disomic (2N) mice at 6 months of age (MO). Ts65Dn mice had unique MSN BFCN transcriptomic profiles at ~6 MO clearly differentiating them from 2N mice. Leveraging Ingenuity Pathway Analysis and KEGG analysis, we linked differentially expressed gene (DEG) changes within MSN BFCNs to several canonical pathways and aberrant physiological functions. The dysregulated transcriptomic profile of trisomic BFCNs provides key information underscoring selective vulnerability within the septohippocampal circuit. We propose both expected and novel therapeutic targets for DS and AD, including specific DEGs within cholinergic, glutamatergic, GABAergic, and neurotrophin pathways, as well as select targets for repairing oxidative phosphorylation status in neurons. We demonstrate and validate this interrogative quantitative bioinformatic analysis of a key dysregulated neuronal population linking single population transcript changes to an established pathological hallmark associated with cognitive decline for therapeutic development in human DS and AD.

The Cellular Choreography of Osteoblast Angiotropism in Bone Development and Homeostasis.

Interaction between endothelial cells and osteoblasts is essential for bone development and homeostasis. This process is mediated in large part by osteoblast angiotropism, the migration of osteoblasts alongside blood vessels, which is crucial for the homing of osteoblasts to sites of bone formation during embryogenesis and in mature bones during remodeling and repair. Specialized bone endothelial cells that form “type H” capillaries have emerged as key interaction partners of osteoblasts, regulating osteoblast differentiation and maturation and ensuring their migration towards newly forming trabecular bone areas. Recent revolutions in high-resolution imaging methodologies for bone as well as single cell and RNA sequencing technologies have enabled the identification of some of the signaling pathways and molecular interactions that underpin this regulatory relationship. Similarly, the intercellular cross talk between endothelial cells and entombed osteocytes that is essential for bone formation, repair, and maintenance are beginning to be uncovered. This is a relatively new area of research that has, until recently, been hampered by a lack of appropriate analysis tools. Now that these tools are available, greater understanding of the molecular relationships between these key cell types is expected to facilitate identification of new drug targets for diseases of bone formation and remodeling.

MOMC-4. Proteogenomic and metabolomic characterization of glioblastoma

Abstract Glioblastoma (GBM) is the most aggressive nervous system cancer, with median survival under 2 years. Understanding its molecular pathogenesis is crucial for improving diagnosis and treatment. We performed an integrated analysis of genomic, proteomic, post-translational modification and metabolomic data on 99 treatment-naive GBMs. We identified key phosphorylation events (e.g., phosphorylated PTPN11 and PLCG1) as potential switches mediating oncogenic pathway activation as well as potential targets for EGFR-, TP53- and RB1-altered tumors. We detected immune subtypes, driven by the presence of distinct immune cell populations using bulk omics, validated by single nulcei RNA sequencing (snRNA-seq), and they were correlated with specific expression and histone acetylation patterns. Acetylation of histone H2B in classical-like and immune-low GBM was driven largely by BRDs, CREBBP, and EP300. Integrated metabolomic and proteomic data identified specific lipid distributions across subtypes and distinct global metabolic changes in IDH mutated tumors. This work highlights biological relationships which could potentially aid GBM patient stratifications for more effective treatments.

Single Nuclear RNA Sequencing Reveals Activation of Neuroinflammation Within the Pre‐Bötzinger Complex Following Repeated Seizures

Epilepsy is one of the most common neurological diseases in the world. Treatment with anti-epileptic drugs (AEDs) prevents recurrent seizures in ~70% of patients with epilepsy, but the remaining 30% of patients with refractory epilepsies continue to experience seizures. The consequences of repeated seizures include but are not limited to memory impairments and a high risk of post-ictal cardiorespiratory failure, and Sudden Unexpected Death in Epilepsy (SUDEP). Fundamental gaps exist in understanding how repeated seizures disrupt the vital cardiorespiratory control system and neural networks facilitating memory formation in refractory epilepsy. A factor commonly identified in many neurological conditions is neuroinflammation, which may support beneficial health functions but is dysregulated in neurological disease. Key cells within the CNS that mediate beneficial and/or pathological neuroinflammation are resident microglia and astrocytes, which have been shown to be dysfunctional in human epilepsy and alter neuronal function. However, it is not known what mechanistic role they play in contributing to epilepsy-related memory impairment, impairment in cardiorespiratory control, or increased SUDEP risk. Here, we tested the hypothesis that repeated seizures lead to activation of neuroinflammation mediated by microglia and astrocytes in CNS regions of memory and ventilatory control, leading to a progressive decline in neurologic function. Preliminary data in our novel rat model with genetic mutations in Kcnj16, a gene encoding an inwardly-rectifying potassium channel Kir5.1 in Dahl salt-sensitive rat (SSkcnj16-/) show that repeated sound-induced seizures lead to a progressively more severe post-ictal suppression of breathing frequency and heart rate, and impaired memory. Single nuclear RNA sequencing of pre-Bötzinger Complex/nucleus ambiguous cells was performed from rats exposed to 0, 3, 7, or 10 seizures to measure cell type-specific gene expression changes induced by seizures. Bioinformatic analyses of transcriptomic changes in microglia, neuronal, and glial cells within these regions point to activation of specific inflammatory pathways following repeated seizures such as IL-1Beta signaling and Toll-like Receptor signaling. Identifying neuroinflammatory signals/pathways induced by repeated seizures within distinct neural circuits will enhance understanding of pathophysiological consequences of uncontrolled seizures in patients with refractory epilepsy and hold the potential for identifying new therapeutic targets aimed at improving memory and cardiorespiratory function to reduce the risk of SUDEP.

Single nucleus RNA-sequencing defines unexpected diversity of cholinergic neuron types in the adult mouse spinal cord

In vertebrates, motor control relies on cholinergic neurons in the spinal cord that have been extensively studied over the past hundred years, yet the full heterogeneity of these neurons and their different functional roles in the adult remain to be defined. Here, we develop a targeted single nuclear RNA sequencing approach and use it to identify an array of cholinergic interneurons, visceral and skeletal motor neurons. Our data expose markers for distinguishing these classes of cholinergic neurons and their rich diversity. Specifically, visceral motor neurons, which provide autonomic control, can be divided into more than a dozen transcriptomic classes with anatomically restricted localization along the spinal cord. The complexity of the skeletal motor neurons is also reflected in our analysis with alpha, gamma, and a third subtype, possibly corresponding to the elusive beta motor neurons, clearly distinguished. In combination, our data provide a comprehensive transcriptomic description of this important population of neurons that control many aspects of physiology and movement and encompass the cellular substrates for debilitating degenerative disorders.

Evidence-based medicine during the COVID-19 pandemic: a survey among healthcare professionals in India

<h3>Abstract</h3> In vertebrates, motor control relies on cholinergic neurons in the spinal cord that have been extensively studied over the past hundred years, yet the full heterogeneity of these neurons and their different functional roles in the adult remain to be defined. Here, we developed a targeted single nuclear RNA sequencing approach and used it to identify an array of cholinergic interneurons, visceral and skeletal motor neurons. Our data expose markers for distinguishing these classes of cholinergic neurons and their extremely rich diversity. Specifically, visceral motor neurons, which provide autonomic control, could be divided into more than a dozen transcriptomic classes with anatomically restricted localization along the spinal cord. The complexity of the skeletal motor neurons was also reflected in our analysis with alpha, beta, and gamma subtypes clearly distinguished. In combination, our data provide a comprehensive transcriptomic description of this important population of neurons that control many aspects of physiology and movement and encompass the cellular substrates for debilitating degenerative disorders.

Single nuclear RNA sequencing reveals microglia diversity associated with cognitive resilience in the AD‐BXD mouse model of human Alzheimer’s disease

AbstractBackgroundAn individual’s genetic background plays an important role in governing the risk (or resilience) to developing Alzheimer’s disease (AD) dementia. The goal of this study was to identify the molecular pathways and cell‐types conferring individual differences in cognitive resilience to human familial AD (FAD) mutations that drive high amyloid.MethodA large set of genetically diverse mice harboring familial AD mutations (AD‐BXDs) and their non‐transgenic littermates (Ntg‐BXDs) were tested for short‐ and long‐term memory using contextual fear conditioning at 6m (AD‐BXD n=180, Ntg‐BXD n=174) and 14m (AD‐BXD n=121, Ntg‐BXD n=137). A subset of 14 AD mutation carriers that exhibited extreme resilience (n=7) or susceptibility (n=7) to cognitive decline were selected for hippocampal molecular profiling, along with their Ntg‐BXD littermates, at both 6m and 14m. Data from all hippocampi were aggregated and batch‐corrected using Harmony, and Seurat clustering was employed using the top 2000 variable genes. Known marker genes were used to associate clusters with cell‐types. The fraction of nuclei per sample (cluster composition) and within cell‐type differential gene expression were performed to determine changes in cell quantity and molecular profiles as a function of age, AD mutation carrier status, and resiliency to cognitive decline.ResultThere were no clusters that showed significant change in composition as a function of age. However, AD‐BXD individuals had significantly fewer astrocytes and more microglia than their Ntg‐BXD counterparts. We also found that resilient AD‐BXDs had fewer microglia than susceptible individuals, and the number of microglia at 6m was significantly negatively correlated with cognitive decline in AD‐BXD individuals. Additionally, microglia from resilient individuals showed up‐regulation of mitochondrial respiration and protein translation genes, proposing two pathways that dictate resilience in a microglia‐specific manner.ConclusionOur findings further implicate non‐neuronal cell‐types such as microglia in promoting resilience to cognitive decline in AD, and suggest several pathways by which microglia may be altered in resilient compared to susceptible individuals. We believe that by altering these microglia pathways within susceptible individuals, we can improve how non‐neuronal cells interact with CNS neurons to improve AD cognitive resilience.

Myocardial infarction triggers Inflammatory deterioration of vascular niche by accelerating loss of a specific vessel subtype in bone

Abstract Introduction The interface between heart and bone emerges as a key trigger of post-infarction inflammation and progression of chronic heart failure (CHF). However, our knowledge on the underlying mechanisms of this interaction is incomplete. Bone vasculature, specifically so-called H-type (Endomucinhigh) endothelial cells (EC), plays a crucial role in maintenance of the bone integrity and regulation of hematopoietic stem cells (HSC). While previous studies in mice showed the reduction of H-type vessels by aging, the impact of ischemic heart disease is unclear. Therefore, we aimed to investigate the effects of myocardial infarction (MI) and chronic heart failure on the vascular bone cell composition in mice and humans. Methods and results Flow cytometric analysis of harvested bones at the different timepoints after MI induction in mice revealed a gradual loss of H-type endothelial cells in the time-course of developing chronic heart failure (P&amp;lt;0.05 at day 7 and 14 vs. control; P&amp;lt;0.0001 at day 28 vs. control). This results were confirmed in immunostainings of tibia sections showing a significant decrease of H-type vessel length after MI (p&amp;lt;0.05 at day 14 and 28, accordingly). The loss of type-H endothelium was accompanied by a significant expansion of long-term HSC in the bone (P=0.0005 at day 28 post MI vs. control). Importantly, type H ECs were also significantly reduced in the bone of ischemic post-infarct HF patients (n=16) compared with control subjects (n=8; P=0.0003). To gain insights into the mechanisms underlying the changes in the vascular niche, we performed single cells RNA sequencing of human BM ECs. These studies confirmed the decrease in Emcnexpressing ECs in ischemic HF patients, which was accompanied by significantly increased expression of inflammatory genes, including IL1b (P&amp;lt;0.0001). Inflammatory EC phenotypes and IL1b expression in HF could be further confirmed at protein level using cytospin immunostainings. Murine studies further revealed an early induction IL-1b specifically in H-type vessels already at day 1 after MI induction, which preceded the loss of H-type endothelium within the following 4 weeks. By inhibiting IL-1b production using a specific Nlrp3 inflammasome inhibitor (MCC950) we could observe a partial restoration of H-type EC frequencies (P=0.033) and a significant increase in H-type vessel length (p=0.035) at day 28 day after MI. Conclusions Our data show for the first time an impact of myocardial infarction and chronic heart failure on the bone marrow vasculature. These changes seem to be strongly associated with inflammatory response in H-type vessels, which precedes its loss after MI. Specifically, the induction of the inflammatory cytokine IL1b may contribute to the disturbed phenotype. This suggest that inhibition of IL1b (e.g. by canakinumab) be used as a novel strategy to prevent or reverse the deterioration of the vascular bone function in ischemic heart disease. Funding Acknowledgement Type of funding source: None

Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation

The mechanisms by which mutant huntingtin (mHTT) leads to neuronal cell death in Huntington's disease (HD) are not fully understood. To gain new molecular insights, we used single nuclear RNA sequencing (snRNA-seq) and translating ribosome affinity purification (TRAP) to conduct transcriptomic analyses of caudate/putamen (striatal) cell type-specific gene expression changes in human HD and mouse models of HD. In striatal spiny projection neurons, the most vulnerable cell type in HD, we observe a release of mitochondrial RNA (mtRNA) (a potent mitochondrial-derived innate immunogen) and a concomitant upregulation of innate immune signaling in spiny projection neurons. Further, we observe that the released mtRNAs can directly bind to the innate immune sensor protein kinase R (PKR). We highlight the importance of studying cell type-specific gene expression dysregulation in HD pathogenesis and reveal that the activation of innate immune signaling in the most vulnerable HD neurons provides a novel framework to understand the basis of mHTT toxicity and raises new therapeutic opportunities.

Factorized embeddings learns rich and biologically meaningful embedding spaces using factorized tensor decomposition.

MotivationThe recent development of sequencing technologies revolutionized our understanding of the inner workings of the cell as well as the way disease is treated. A single RNA sequencing (RNA-Seq) experiment, however, measures tens of thousands of parameters simultaneously. While the results are information rich, data analysis provides a challenge. Dimensionality reduction methods help with this task by extracting patterns from the data by compressing it into compact vector representations.ResultsWe present the factorized embeddings (FE) model, a self-supervised deep learning algorithm that learns simultaneously, by tensor factorization, gene and sample representation spaces. We ran the model on RNA-Seq data from two large-scale cohorts and observed that the sample representation captures information on single gene and global gene expression patterns. Moreover, we found that the gene representation space was organized such that tissue-specific genes, highly correlated genes as well as genes participating in the same GO terms were grouped. Finally, we compared the vector representation of samples learned by the FE model to other similar models on 49 regression tasks. We report that the representations trained with FE rank first or second in all of the tasks, surpassing, sometimes by a considerable margin, other representations. Availability and implementationA toy example in the form of a Jupyter Notebook as well as the code and trained embeddings for this project can be found at: https://github.com/TrofimovAssya/FactorizedEmbeddings.Supplementary information Supplementary data are available at Bioinformatics online.

Immunological history governs human stem cell memory CD4 heterogeneity via the Wnt signaling pathway

The diversity of the naïve T cell repertoire drives the replenishment potential and capacity of memory T cells to respond to immune challenges. Attrition of the immune system is associated with an increased prevalence of pathologies in aged individuals, but whether stem cell memory T lymphocytes (TSCM) contribute to such attrition is still unclear. Using single cells RNA sequencing and high-dimensional flow cytometry, we demonstrate that TSCM heterogeneity results from differential engagement of Wnt signaling. In humans, aging is associated with the coupled loss of Wnt/β-catenin signature in CD4 TSCM and systemic increase in the levels of Dickkopf-related protein 1, a natural inhibitor of the Wnt/β-catenin pathway. Functional assays support recent thymic emigrants as the precursors of CD4 TSCM. Our data thus hint that reversing TSCM defects by metabolic targeting of the Wnt/β-catenin pathway may be a viable approach to restore and preserve immune homeostasis in the context of immunological history.

TMOD-27. A NEURAL CREST CELL SUBPOPULATION UNDERLIES INTRATUMOR HETEROGENEITY IN MENINGIOMA

Abstract BACKGROUND Meningiomas are the most common primary intracranial tumor, and high grade meningiomas are resistant to most cancer therapies. Intratumor heterogeneity is a recognized source of resistance to treatment in numerous malignancies. Thus, we hypothesized that investigating molecular heterogeneity in meningiomas would elucidate biologic drivers and shed light on tumor evolution and mechanisms of resistance. METHODS We collected 86 spatially distinct samples at the time of resection from 13 meningiomas. Seven meningiomas were WHO grade I (46 samples), three were grade II (22 samples), and three were grade III (18 samples). Seven meningiomas were sampled at the time of salvage surgery (48 samples), and 6 were sampled at the time of initial diagnosis (38 samples). We performed multiplatform molecular profiling of these samples to identify drivers of intratumor heterogeneity, and validated our results using meningioma cells co-cultured with human cerebral organoids and RNA sequencing of paired primary and recurrent meningiomas. RESULTS Using bulk RNA sequencing, DNA methylation profiling and phylogenetic analysis of spatially distinct samples, we discovered significant transcriptomic, epigenomic and genomic heterogeneity in meningioma. In particular, we identified chromosomal structural alterations and differences in immune and neuronal signaling that underlie clonal evolution in high grade tumors. Using MRI-stratified bulk RNA sequencing, single nuclear RNA sequencing, RNA sequencing of paired primary and recurrent meningiomas, and live cell microscopy and single cell RNA sequencing of meningioma cells in co-culture with human cerebral organoids, we revealed a rare meningioma cell subpopulation with strong transcriptional concordance to the neural crest, a multipotent embryonic tissue that forms the meninges in development. CONCLUSIONS These data suggest that misactivation of a developmental cell population underlies intratumor heterogeneity in meningioma and that expression of neural crest and immediate early genes are an important step in meningeal oncogenesis.

6091Chronic heart failure is associated with inflammatory deterioration of the bone marrow vascular niche

Abstract Introduction Inflammation plays a crucial role in many aspects of cardiovascular disease. Particularly, acquired mutations of hematopoietic stem cells (HSC) leading to clonal expansion of inflammatory cells (CHIP) are increased with age and are associated with an enhanced risk of cardiovascular disease. The bone marrow (BM) vascular niche plays a crucial role in maintenance and regulation of HSC functions. Previous studies in mice showed the reduction of a specific Endomucin-high (H-type) endothelial cells (EC) subpopulation by aging. However, the impact of cardiovascular disease is unclear. Therefore, we aimed to investigate the effects of age and heart failure (HF) on the vascular BM cell composition in mice and humans. Methods and results Aging mice showed an age-dependent decrease of type H (Emcn-high) BM ECs (p=0.004), whereas the BM frequencies of type L (Emcn-low) ECs did not significantly differ (P=0.18). Importantly, we also observed a marked reduction of type H EC in chronic ischemic mice (P=0.016 vs. sham) indicating that chronic ischemic HF induces similar alterations of the vascular stem cell niche. Importantly, type H ECs were also significantly reduced in ischemic HF patients (n=16) compared with control subjects (n=8; P=0.0003). To gain insights into the mechanisms underlying the changes in the vascular niche, we performed single cells RNA sequencing of human BM ECs. These studies confirmed the decrease in Emcn-expressing ECs in ischemic HF patients, which was accompanied by significantly increased expression of inflammatory genes, including IL1b (P&lt;0.0001 vs. control). Inflammatory EC phenotypes and IL1b expression in HF could be further confirmed at protein level using cytospin immunostainings. Finally, we comprehensively evaluated phenotype-associated differences in the bone marrow plasma proteomes of healthy individuals (n=19) and patients with chronic ischemic (n=22) and non-ischemic (n=19) HF, using proximity extension assays. Here, we identified 182 proteins significantly differentially regulated in CHF versus CTRL. Among the top upregulated proteins the BM environment of patients with CHF showed a striking enrichment of inflammatory and ECM remodeling components. Conclusions Our data show for the first time an impact of chronic heart failure on the bone marrow vascular niche in humans. These changes seem to be strongly associated with increased inflammatory response and bone matrix remodeling in CHF. Specifically, the induction of the inflammatory cytokine IL1b may contribute to the disturbed phenotype suggesting that inhibition of IL1b (e.g. by canakinumab) may be used as a novel strategy to prevent or reverse the deterioration of the vascular BM niche.

Physiological Response of Pacific Abalone (Haliotis discus hannai) Hepatopancreas to Heat Stress

Pacific abalone Haliotis discus hannai is one of the most economically important marine shellfish and is mainly distributed in the cooler seas of northern China. The molecular reactions that occur in this species under high temperature conditions have not been determined. To understand the molecular mechanisms of this species under heat stress, transcriptomic analysis of the hepatopancreas was performed at 33°C (22°C was used for the control) for 1 h on an Illumina HiSeq 2500 platform (pooling of six animals into single RNA-sequencing libraries). The results showed that 17,852 unigenes were annotated. In all, 8,532 genes were significantly differentially expressed in the test group compared with the control group, including 4,788 upregulated and 3,744 downregulated genes. Enrichment analysis identified some noteworthy GO terms (cellular process and response to stimulus) and pathways (protein processing in the endoplasmic reticulum (ER) and apoptotic signaling pathways), and these were further analyzed. Analysis showed that genes indicative of mitochondrial damage were upregulated; DNA damage formation, and fatty acid and amino acid synthesis increased; fatty acid decomposition reduced; and misfolded proteins accumulated in the ER, and the unfolded protein response and ER-associated degradation were triggered to relieve ER stress. In addition, the apoptotic pathway was activated; however, some genes associated with anti-apoptosis and molecular chaperones were upregulated to maintain homeostasis after heat stress. These data provide an increased understanding of the heat stress mechanisms in Pacific abalone.

Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

BackgroundCancer patients with advanced disease routinely exhaust available clinical regimens and lack actionable genomic medicine results, leaving a large patient population without effective treatments options when their disease inevitably progresses. To address the unmet clinical need for evidence-based therapy assignment when standard clinical approaches have failed, we have developed a probabilistic computational modeling approach which integrates molecular sequencing data with functional assay data to develop patient-specific combination cancer treatments.MethodsTissue taken from a murine model of alveolar rhabdomyosarcoma was used to perform single agent drug screening and DNA/RNA sequencing experiments; results integrated via our computational modeling approach identified a synergistic personalized two-drug combination. Cells derived from the primary murine tumor were allografted into mouse models and used to validate the personalized two-drug combination.Computational modeling of single agent drug screening and RNA sequencing of multiple heterogenous sites from a single patient’s epithelioid sarcoma identified a personalized two-drug combination effective across all tumor regions. The heterogeneity-consensus combination was validated in a xenograft model derived from the patient’s primary tumor.Cell cultures derived from human and canine undifferentiated pleomorphic sarcoma were assayed by drug screen; computational modeling identified a resistance-abrogating two-drug combination common to both cell cultures. This combination was validated in vitro via a cell regrowth assay.ResultsOur computational modeling approach addresses three major challenges in personalized cancer therapy: synergistic drug combination predictions (validated in vitro and in vivo in a genetically engineered murine cancer model), identification of unifying therapeutic targets to overcome intra-tumor heterogeneity (validated in vivo in a human cancer xenograft), and mitigation of cancer cell resistance and rewiring mechanisms (validated in vitro in a human and canine cancer model).ConclusionsThese proof-of-concept studies support the use of an integrative functional approach to personalized combination therapy prediction for the population of high-risk cancer patients lacking viable clinical options and without actionable DNA sequencing-based therapy.