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Rationale: Obesity affects 40% of U.S. adults, is associated with a proinflammatory state, and presents a significant risk factor for the development of severe coronavirus disease (COVID-19). To date, there is limited information on how obesity might affect immune cell responses in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Objectives: To determine the impact of obesity on respiratory tract immunity in COVID-19 across the human lifespan. Methods: We analyzed single-cell transcriptomes from BAL in three ventilated adult cohorts with (n = 24) or without (n = 9) COVID-19 from nasal immune cells in children with (n = 14) or without (n = 19) COVID-19, and from peripheral blood mononuclear cells in an independent adult COVID-19 cohort (n = 42), comparing obese and nonobese subjects. Measurements and Main Results: Surprisingly, we found that obese adult subjects had attenuated lung immune or inflammatory responses in SARS-CoV-2 infection, with decreased expression of IFN-α, IFN-γ, and TNF-α (tumor necrosis factor α) response gene signatures in almost all lung epithelial and immune cell subsets, and lower expression of IFNG and TNF in specific lung immune cells. Peripheral blood immune cells in an independent adult cohort showed a similar but less marked reduction in type-I IFN and IFNγ response genes, as well as decreased serum IFNα, in obese patients with SARS-CoV-2. Nasal immune cells from obese children with COVID-19 also showed reduced enrichment of IFN-α and IFN-γ response genes. Conclusions: These findings show blunted tissue immune responses in obese patients with COVID-19, with implications for treatment stratification, supporting the specific application of inhaled recombinant type-I IFNs in this vulnerable subset.

Objectives Evidence from temporal artery tissue and blood suggests involvement of CD8+ T cells in the pathogenesis of GCA, but their exact role is poorly understood. Therefore, we performed a comprehensive analysis of circulating and lesional CD8+ T cells in GCA patients. Methods Circulating CD8+ T cells were analysed for differentiation status (CD45RO, CCR7), markers of activation (CD69 and CD25) and proliferation (Ki-67) in 14 newly diagnosed GCA patients and 18 healthy controls by flow cytometry. Proliferative capacity of CD8+ T cells upon anti-CD3 and anti-CD3/28 in vitro stimulation was assessed. Single-cell RNA sequencing of peripheral blood mononuclear cells of patients and controls (n = 3 each) was performed for mechanistic insight. Immunohistochemistry was used to detect CD3, CD8, Ki-67, TNF-α and IFN-γ in GCA-affected tissues. Results GCA patients had decreased numbers of circulating effector memory CD8+ T cells but the percentage of Ki-67-expressing effector memory CD8+ T cells was increased. Circulating CD8+ T cells from GCA patients demonstrated reduced T cell receptor activation thresholds and displayed a gene expression profile that is concurrent with increased proliferation. CD8+ T cells were detected in GCA temporal arteries and aorta. These vascular CD8+ T cells expressed IFN-γ but not Ki-67. Conclusion In GCA, circulating effector memory CD8+ T cells demonstrate a proliferation-prone phenotype. The presence of CD8+ T cells in inflamed arteries seems to reflect recruitment of circulating cells rather than local expansion. CD8+ T cells in inflamed tissues produce IFN-γ, which is an important mediator of local inflammatory responses in GCA.

Conventional 2D cultures are commonly used in cancer research though they come with limitations such as the lack of microenvironment or reduced cell heterogeneity. In this study, we investigated in what respect a scaffold-based (Matrigel™) 3D culture technique can ameliorate the limitations of 2D cultures. NGS-based bulk and single-cell sequencing of matched pairs of 2D and 3D models showed an altered transcription of key immune regulatory genes in around 36% of 3D models, indicating the reoccurrence of an immune suppressive phenotype. Changes included the presentation of different HLA surface molecules as well as cellular stressors. We also investigated the 3D tumor organoids in a co-culture setting with tumor-infiltrating lymphocytes (TILs). Of note, lymphocyte-mediated cell killing appeared less effective in clearing 3D models than their 2D counterparts. IFN-γ release, as well as live cell staining and proliferation analysis, pointed toward an elevated resistance of 3D models. In conclusion, we found that the scaffold-based (Matrigel™) 3D culture technique affects the transcriptional profile in a subset of GBM models. Thus, these models allow for depicting clinically relevant aspects of tumor-immune interaction, with the potential to explore immunotherapeutic approaches in an easily accessible in vitro system.

Adipose-derived stem cells (ADSCs) as part of autologous fat grafting have anti-fibrotic and anti-inflammatory effects, but the exact mechanisms of action remain unknown. By simulating the interaction of ADSCs with fibroblasts and endothelial cells (EC) from scleroderma (SSc) skin in silico, we aim to unravel these mechanisms. Publicly available single-cell RNA sequencing data from the stromal vascular fraction of 3 lean patients and biopsies from the skin of 10 control and 12 patients with SSc were obtained from the GEO and analysed using R and Seurat. Differentially expressed genes were used to compare the fibroblast and EC transcriptome between controls and SSc. GO and KEGG functional enrichment was performed. Ligand–receptor interactions of ADSCs with fibroblasts and ECs were explored with LIANA. Pro-inflammatory and extracellular matrix (ECM) interacting fibroblasts were identified in SSc. Arterial, capillary, venous and lymphatic ECs showed a pro-fibrotic and pro-inflammatory transcriptome. Most interactions with both cell types were based on ECM proteins. Differential interactions identified included NTN1, VEGFD, MMP2, FGF2, and FNDC5. The ADSC secretome may disrupt vascular and perivascular inflammation hubs in scleroderma by promoting angiogenesis and especially lymphangiogenesis. Key phenomena observed after fat grafting remain unexplained, including modulation of fibroblast behaviour.

Polycystic ovary syndrome (PCOS) is a common endocrine disorder characterized by hyperandrogenemia of ovarian thecal cell origin, resulting in anovulation/oligo-ovulation and infertility. Our previous studies established that ovarian theca cells isolated and propagated from ovaries of normal ovulatory women and women with PCOS have distinctive molecular and cellular signatures that underlie the increased androgen biosynthesis in PCOS. To evaluate differences between gene expression in single-cells from passaged cultures of theca cells from ovaries of normal ovulatory women and women with PCOS, we performed single-cell RNA sequencing (scRNA-seq). Results from these studies revealed differentially expressed pathways and genes involved in the acquisition of cholesterol, the precursor of steroid hormones, and steroidogenesis. Bulk RNA-seq and microarray studies confirmed the theca cell differential gene expression profiles. The expression profiles appear to be directed largely by increased levels or activity of the transcription factors SREBF1, which regulates genes involved in cholesterol acquisition (LDLR, LIPA, NPC1, CYP11A1, FDX1, and FDXR), and GATA6, which regulates expression of genes encoding steroidogenic enzymes (CYP17A1) in concert with other differentially expressed transcription factors (SP1, NR5A2). This study provides insights into the molecular mechanisms underlying the hyperandrogenemia associated with PCOS and highlights potential targets for molecular diagnosis and therapeutic intervention.

Juvenile idiopathic arthritis (JIA) is the most common chronic rheumatic disease in children. The heterogeneity of the disease can be investigated via single-cell RNA sequencing (scRNA-seq) for its gap in the literature. Firstly, five types of immune cells (plasma cells, naive CD4 T cells, memory-activated CD4 T cells, eosinophils, and neutrophils) were significantly different between normal control (NC) and JIA samples. WGCNA was performed to identify genes that exhibited the highest correlation to differential immune cells. Then, 168 differentially expressed immune cell-related genes (DE-ICRGs) were identified by overlapping 13,706 genes identified by WGCNA and 286 differentially expressed genes (DEGs) between JIA and NC specimens. Next, four key genes, namely SOCS3, JUN, CLEC4C, and NFKBIA, were identified by a protein–protein interaction (PPI) network and three machine learning algorithms. The results of functional enrichment revealed that SOCS3, JUN, and NFKBIA were all associated with hallmark TNF-α signaling via NF-κB. In addition, cells in JIA samples were clustered into four groups (B cell, monocyte, NK cell, and T cell groups) by single-cell data analysis. CLEC4C and JUN exhibited the highest level of expression in B cells; NFKBIA and SOCS3 exhibited the highest level of expression in monocytes. Finally, real-time quantitative PCR (RT-qPCR) revealed that the expression of three key genes was consistent with that determined by differential analysis. Our study revealed four key genes with prognostic value for JIA. Our findings could have potential implications for JIA treatment and investigation.

Amniotic fluid has been proposed as an easily available source of cells for numerous applications in regenerative medicine and tissue engineering. The use of amniotic fluid cells in biomedical applications necessitates their unequivocal characterization; however, the exact cellular composition of amniotic fluid and the precise tissue origins of these cells remain largely unclear. Using cells cultured from the human amniotic fluid of fetuses with spina bifida aperta and of a healthy fetus, we performed single-cell RNA sequencing to characterize the tissue origin and marker expression of cultured amniotic fluid cells at the single-cell level. Our analysis revealed nine different cell types of stromal, epithelial and immune cell phenotypes, and from various fetal tissue origins, demonstrating the heterogeneity of the cultured amniotic fluid cell population at a single-cell resolution. It also identified cell types of neural origin in amniotic fluid from fetuses with spina bifida aperta. Our data provide a comprehensive list of markers for the characterization of the various progenitor and terminally differentiated cell types in cultured amniotic fluid. This study highlights the relevance of single-cell analysis approaches for the characterization of amniotic fluid cells in order to harness their full potential in biomedical research and clinical applications.

Pediatric intestinal failure (IF) is the reduction in gut function to below the minimum necessary for the absorption of macronutrients and/or water and electrolytes, such that intravenous supplementation is required to maintain health and/or growth. The overall goal in treating IF is to achieve intestinal adaptation; however, the underlying mechanisms have not been fully understood. In this study, by performing single-cell RNA sequencing in pediatric IF patients, we found that decreased Kruppel-Like Factor 4 (KLF4) may serve as the hub gene responsible for the functional deficit in mature enterocytes in IF patients, leading to the downregulation of solute carrier (SLC) family transporters (e.g., SLC7A9) and, consequently, nutrient malabsorption. We also found that inducible KLF4 was highly sensitive to the loss of certain enteral nutrients: in a rodent model of total parenteral nutrition mimicking the deprivation of enteral nutrition, the expression of KLF4 dramatically decreased only at the tip of the villus and not at the bottom of crypts. By using IF patient-derived intestinal organoids and Caco-2 cells as in vitro models, we demonstrated that the supplementation of decanoic acid (DA) could significantly induce the expression of KLF4 along with SLC6A4 and SLC7A9, suggesting that DA may function as a potential therapeutic strategy to promote cell maturation and functional improvement. In summary, this study provides new insights into the mechanism of intestinal adaptation depending on KLF4, and proposed potential strategies for nutritional management using DA.

Localized scleroderma (LS) is an autoimmune disease with both inflammatory and fibrotic components causing an abnormal deposition of collagen in the skin and underlying tissue, often leading to disfigurement and disability. Much of its pathophysiology is extrapolated from systemic sclerosis (SSc) since the histopathology findings in the skin are nearly identical. However, LS is critically understudied. Single-cell RNA sequencing (scRNA seq) technology provides a novel way to obtain detailed information at the individual cellular level, overcoming this barrier. Here, we analyzed the affected skin of 14 patients with LS (pediatric and adult) and 14 healthy controls. Fibroblast populations were the focus, since they are the main drivers of fibrosis in SSc. We identified 12 fibroblast subclusters in LS, which overall had an inflammatory gene expression (IFN and HLA-associated genes). A myofibroblast-like cluster (SFRP4/PRSS23) was more prevalent in LS subjects and shared many upregulated genes expressed in SSc-associated myofibroblasts, though it also had strong expression of CXCL9/10/11, known CXCR3 ligands. A CXCL2/IRF1 cluster identified was unique to LS, with a robust inflammatory gene signature, including IL-6, and according to cell communication analysis are influenced by macrophages. In summary, potential disease-propagating fibroblasts and associated gene signatures were identified in LS skin via scRNA seq.

Genetic variation in the mitochondrial genome is linked to important biological functions and various human diseases. Recent progress in single-cell genomics has established single-cell RNA sequencing (scRNAseq) as a popular and powerful technique to profile transcriptomics at the cellular level. While most studies focus on deciphering gene expression, polymorphisms including mitochondrial variants can also be readily inferred from scRNAseq. However, limited attention has been paid to investigate the single-cell landscape of mitochondrial variants, despite the rapid accumulation of scRNAseq data in the community. In addition, a diploid context is assumed for most variant calling tools, which is not appropriate for mitochondrial heteroplasmies. Here, we introduce MitoTrace, an R package for the analysis of mitochondrial genetic variation in bulk and scRNAseq data. We applied MitoTrace to several publicly accessible data sets and demonstrated its ability to robustly recover genetic variants from scRNAseq data. We also validated the applicability of MitoTrace to scRNAseq data from diverse platforms. Overall, MitoTrace is a powerful and user-friendly tool to investigate mitochondrial variants from scRNAseq data.

The revolutionary single-cell RNA sequencing (scRNA-seq) measures the activity of all genes separately in each cell, giving a more accurate picture of how cells differ from each other. This technology will produce a vast amount of information on diseases, such as cancer. There are millions of cancer cells in a tumour. Data analysis requires increasingly more computing capacity and efficient algorithms as the number of cells and samples analysed increases.

Bovine respiratory disease (BRD) is the leading cause of morbidity and mortality in feedlot cattle. Bovine herpesvirus-1 (BHV-1) is one of the main culprits of BRD; however, research on BHV-1 is hampered by the lack of suitable models for infection and drug testing. In this study, we established a novel bovine tracheal organoid culture grown in a basement membrane extract type 2 (BME2) matrix and compared it with the air–liquid interface (ALI) culture system. After differentiation, the matrix-embedded organoids developed beating cilia and demonstrated a transcriptomic profile similar to the ALI culture system. The matrix-embedded organoids were also highly susceptible to BHV-1 infection and immune stimulation by Pam2Cys, an immunomodulator, which resulted in robust cytokine production and tracheal antimicrobial peptide mRNA upregulation. However, treatment of bovine tracheal organoid cultures with Pam2Cys was not sufficient to inhibit viral infection or replication, suggesting a role of the non-epithelial cellular microenvironment in vivo.

Le carcinome séreux de haut grade (CSHG) est le sous-type de cancer de l'ovaire le plus agressif et mortel. Alors qu'une meilleure survie globale des patientes soit associée à une infiltration lymphocytaire, l'immunothérapie par blocage des points de contrôle immunitaires a obtenu des résultats limités, témoignant ainsi l'importance de comprendre le fonctionnement du système immunitaire au sein de ces tumeurs malignes. L’immunologie des tumeurs intègre des cellules immunitaires innées et adaptatives et utilise des médiateurs inflammatoires pour ajuster finement l'ampleur et la durée de la réponse immunitaire. Ainsi, cette thèse a pour objectif de définir l'hétérogénéité des cellules immunitaires intratumorales et périphériques chez les patientes atteintes d'un cancer de l'ovaire mais aussi à explorer les mécanismes de la réponse immunitaire. En combinant des techniques de biologie computationnelle et de séquençage de l'ARN à cellule unique nous avons pu identifier les différents composants du système immunitaire des patientes atteintes d'un cancer de l'ovaire mais aussi valider nos résultats dans une plus large cohorte associant d'autres types de cancer. Dans un premier temps, nous avons étudié l'un des médiateurs de l'inflammation, la voie de signalisation extracellulaire de l'adénosine. Nous avons évalué l'impact de cette voie de signalisation sur la survie des patientes atteintes de CSHG et identifié les cellules du microenvironnement tumoral participant au fonctionnement de cette voie. Ensuite, nous avons concentré notre étude sur la dynamique des lymphocytes T et identifié leurs états cellulaires associés, déduit leur relation développementale et étudié les changements transcriptionnels déclenchés par les interactions entre les cellules dans le microenvironnement immunitaire tumoral. Nous avons démontré que les cellules de type Tfh produisent le médiateur 7α,25 dihydroxycholestérol (7α,25-HC) décrit comme régulant le positionnement des cellules immunitaires dans les organes lymphoïdes secondaires. Ainsi, notre étude suggère que les cellules de type Tfh utilise ce mécanisme pour recruter des lymphocytes T CD8 pré-effecteurs/prédysfonctionnels et des cellules dendritiques plasmacytoïdes dans les tumeurs. Finalement, nos résultats indiquent que les cellules de type Tfh exprimant l'interleukine-21 aident à promouvoir l'immunité antitumorale contre les tumeurs ovariennes en coordonnant l'action des lymphocytes et des cellules dendritiques plasmacytoïdes sensibles au 7α,25-HC. En conclusion, nos travaux de recherche ont permis d’identifier des vulnérabilités dans le microenvironnement immunitaire tumoral pouvant être ciblées dans la thérapie contre le CSHG., High-grade serous ovarian carcinoma (HGSOC) is the most aggressive and lethal subtype of ovarian cancer. Although better overall survival is associated with lymphocytic infiltration, immunotherapy by immune checkpoint blockades achieved modest results, reinforcing the importance of understanding immunity in this malignancy. Cancer immunity integrates innate and adaptive immune cells and makes use of inflammatory mediators to finely tune the magnitude and duration of the immune response. This thesis aims to reveal the heterogeneity of intratumoral and peripheral immune cells in ovarian cancer patients and explore the mechanisms of the immune response. For this purpose, we have used the high-resolution technology of single-cell RNAsequencing and computational biology to immune profile HGSOC patients. Firstly, we explored one of the mediators of inflammation, the immunosuppressive extracellular adenosine (eADO). The ectonucleotidases CD73 and CD39 regulate the eADO signaling pathway, and their expression is prognostic in several cancer types. Since their role in HGSOC was yet largely unexplored, we hypothesized that a transcriptomic meta-analysis of eADO signaling pathway would provide the clinical impact of the pathway in this malignancy. We analyzed the transcriptome of approximately 1200 HGSOC patients to evaluate the effect of CD39 and CD73 on clinical outcomes. While high expression of both ectonucleotidases was associated with worse overall survival in HGSOC, only CD39 was associated with chemoresistance, supporting the evaluation of eADO-targeting agents in HGSOC. Subsequently, we investigated T cell dynamics. Because T cell clones expanded in both tumor and peripheral tissue associated with response to ICB, we hypothesized that the tumor immune microenvironment (TIME) modulates their function and, therefore, analysis of cell-cell interaction would identify the cells participating in this process. Thus, we identified T cell states, inferred their developmental relationship, and studied transcriptional changes triggered by cellcell interactions in the TIME. We demonstrated that exhausted CD8 T cells highly expressed the chemokines CCL4 and XCL1, previously described in the priming of CD8 T cells in secondary lymphoid organs (SLOs). Finally, we proposed that the lipid mediator 7α,25 dihydroxycholesterol (7α,25-HC), only described in SLOs, may also modulate cell-cell interactions in the tumor immune microenvironment. Collectively, our studies propose strategies to modulate TIME in HGSOC targeting the adenosine pathway and oxysterols metabolites.

International audience; BACKGROUND: Intratumor heterogeneity (ITH) is a key feature in clear cell renal cell carcinomas (ccRCCs) that impacts outcomes such as aggressiveness, response to treatments, or recurrence. In particular, it may explain tumor relapse after surgery in clinically low-risk patients who did not benefit from adjuvant therapy. Recently, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool to unravel expression ITH (eITH) and might enable better assessment of clinical outcomes in ccRCC. OBJECTIVE: To explore eITH in ccRCC with a focus on malignant cells (MCs) and assess its relevance to improve prognosis for low-risk patients. DESIGN, SETTING, AND PARTICIPANTS: We performed scRNA-seq on tumor samples from five untreated ccRCC patients ranging from pT1a to pT3b. Data were complemented with a published dataset composed of pairs of matched normal and ccRCC samples. INTERVENTION: Radical or partial nephrectomy on untreated ccRCC patients. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Viability and cell type proportions were determined by flow cytometry. Following scRNA-seq, a functional analysis was performed and tumor progression trajectories were inferred. A deconvolution approach was applied on an external cohort, and Kaplan-Meier survival curves were estimated with respect to the prevalence of malignant clusters. RESULTS AND LIMITATIONS: We analyzed 54 812 cells and identified 35 cell subpopulations. The eITH analysis revealed that each tumor contained various degrees of clonal diversity. The transcriptomic signatures of MCs in one particularly heterogeneous sample were used to design a deconvolution-based strategy that allowed the risk stratification of 310 low-risk ccRCC patients. CONCLUSIONS: We described eITH in ccRCCs, and used this information to establish significant cell population-based prognostic signatures and better discriminate ccRCC patients. This approach has the potential to improve the stratification of clinically low-risk patients and their therapeutic management. PATIENT SUMMARY: We sequenced the RNA content of individual cell subpopulations composed of clear cell renal cell carcinomas and identified specific malignant cells the genetic information of which can be used to predict tumor progression.

Huntington's disease (HD) is caused by a CAG repeat expansion in the huntingtin (HTT) gene. Knock-in mice carrying a CAG repeat-expanded Htt will develop HD phenotypes. Previous studies suggested dysregulated molecular networks in a CAG length genotype- and the age-dependent manner in brain tissues from knock-in mice carrying expanded Htt CAG repeats. Furthermore, a large-scale phenome analysis defined a behavioral signature for HD genotype in knock-in mice carrying expanded Htt CAG repeats. However, an integrated analysis correlating phenotype features with genotypes (CAG repeat expansions) was not conducted previously. In this study, we revealed the landscape of the behavioral features and gene expression correlations based on 445 mRNA samples and 445 microRNA samples, together with behavioral features (396 PhenoCube behaviors and 111 NeuroCube behaviors) in Htt CAG-knock-in mice. We identified 37 behavioral features that were significantly associated with CAG repeat length including the number of steps and hind limb stand duration. The behavioral features were associated with several gene coexpression groups involved in neuronal dysfunctions, which were also supported by the single-cell RNA sequencing data in the striatum and the spatial gene expression in the brain. We also identified 15 chemicals with significant responses for genes with enriched behavioral features, most of them are agonist or antagonist for dopamine receptors and serotonin receptors used for neurology/psychiatry. Our study provides further evidence that abnormal neuronal signal transduction in the striatum plays an important role in causing HD-related phenotypic behaviors and provided rich information for the further pharmacotherapeutic intervention possibility for HD.

We propose DEGAS (Diagnostic Evidence GAuge of Single cells), a novel deep transfer learning framework, to transfer disease information from patients to cells. We call such transferrable information “impressions,” which allow individual cells to be associated with disease attributes like diagnosis, prognosis, and response to therapy. Using simulated data and ten diverse single-cell and patient bulk tissue transcriptomic datasets from glioblastoma multiforme (GBM), Alzheimer’s disease (AD), and multiple myeloma (MM), we demonstrate the feasibility, flexibility, and broad applications of the DEGAS framework. DEGAS analysis on myeloma single-cell transcriptomics identified PHF19high myeloma cells associated with progression. Availability: https://github.com/tsteelejohnson91/DEGAS.

Podocytes are critical components of the glomerular filtration barrier, sitting on the outside of the glomerular basement membrane. Primary and secondary foot processes are characteristic for podocytes, but cell processes that develop in culture were not studied much in the past. Moreover, protocols for diverse visualization methods mostly can only be used for one technique, due to differences in fixation, drying and handling. However, we detected by single-cell RNA sequencing (scRNAseq) analysis that cells reveal high variability in genes involved in cell type-specific morphology, even within one cell culture dish, highlighting the need for a compatible protocol that allows measuring the same cell with different methods. Here, we developed a new serial and correlative approach by using a combination of a wide variety of microscopic and spectroscopic techniques in the same cell for a better understanding of podocyte morphology. In detail, the protocol allowed for the sequential analysis of identical cells with light microscopy (LM), Raman spectroscopy, scanning electron microscopy (SEM) and atomic force microscopy (AFM). Skipping the fixation and drying process, the protocol was also compatible with scanning ion-conductance microscopy (SICM), allowing the determination of podocyte surface topography of nanometer-range in living cells. With the help of nanoGPS Oxyo®, tracking concordant regions of interest of untreated podocytes and podocytes stressed with TGF-β were analyzed with LM, SEM, Raman spectroscopy, AFM and SICM, and revealed significant morphological alterations, including retraction of podocyte process, changes in cell surface morphology and loss of cell-cell contacts, as well as variations in lipid and protein content in TGF-β treated cells. The combination of these consecutive techniques on the same cells provides a comprehensive understanding of podocyte morphology. Additionally, the results can also be used to train automated intelligence networks to predict various outcomes related to podocyte injury in the future.

Das Herz ist das zentrale Kreislauforgan in unserem Körper und jede Abweichung seiner Funktion wirkt sich negativ auf die Homöostase des gesamten Körpers aus. Die Herzfunktion beruht auf der Synergie der Zellen, die das Organ bilden. Die detaillierte zelluläre Zusammensetzung sowie die Funktionalität der einzelnen Zellen müssen noch ermittelt werden, und diese Arbeit ist eine wichtige Ergänzung dieser Bemühungen. Dank der jüngsten Entwicklungen in den Einzelzelltechnologien sind wir nun in der Lage, Transkriptome einzelner Zellen aus komplexem Gewebe in beispiellosem Umfang zu charakterisieren. Im ersten Schritt eines solchen Experiments müssen die Zellen und Zellkerne aus dem Gewebe befreit und vereinzelt werden. Herzgewebe wirft in dieser Hinsicht einzigartige Herausforderungen auf, darunter die Knappheit des gesunden menschlichen Herzgewebes für die Forschung, das Vorhandensein von Kardiomyozyten, die aufgrund ihrer Größe nicht durch Microfluid-basierte Standardinstrumente passen und deren Multinukleation, sowie mögliche Voreingenommenheit verschiedener Methoden zur Gewebedissoziation. Hier präsentiere ich den umfassenden Zellatlas des gesunden erwachsenen menschlichen Herzens. Ich beginne mit der Methodenentwicklung zur Isolierung von einzelnen Zellen und Zellkernen aus Mausherzen. Um den Zellatlas des menschlichen Herzens zu erstellen, analysiere ich einen Datensatz von fast einer halben Million Einzelzellen und Zellkerne aus sechs Herzregionen von vierzehn gesunden Menschen. In diesem Atlas definieren wir 11 Hauptzelltypen und 62 Zellzustände des menschlichen Herzens. Ein tieferer Fokus wird auf das Herzgefäßsystem gelegt und die Zellen der arterio-venösen Achse sowie deren Wechselwirkungen und potenzielle Funktionalität werden definiert. Insgesamt präsentiert diese Dissertation einen komplex Datensatz aus menschlichem Herzgewebe und liefert neue Einblicke in die Biologie des gesunden Herzens mit Implikationen für kardiovaskuläre Erkrankungen. The heart is the central circulatory organ in our bodies and any discrepancies of its function relative to healthy homeostasis negatively impact the whole body. Cardiac function relies on the synergy of all the cells that constitute the organ. The detailed cellular composition as well as the heterogeneity and functionality of the individual cells is yet to be established and this work is a major advance in this effort. Thanks to the recent developments in single cell genomics technologies, we are now able to profile transcriptomes from individual cells of complex tissues at unprecedented scale. In the first step of such an experiment, the single cells and nuclei need to be liberated from the tissue. Heart tissue presents a unique set of challenges in this regard, including the scarcity of healthy human cardiac tissue for research, large cardiomyocytes that do not fit into the standard droplet-based instruments, multinucleation of cardiomyocytes that might skew the proportions of the recovered nuclei as well as potential bias of tissue dissociation methods. Here I present a cell atlas of the free walls, apex and septum of the healthy adult human heart. I start with methods development for the isolation of single cells and single nuclei from mouse heart. Next, I move to the building of the atlas of the human cells and nuclei, where I describe the dataset of close to half a million single cells and nuclei sampled from 14 organ donors, defining 11 major cell types and 62 cell states of the heart. A deeper focus on the cardiac vasculature defined the cells of the arterio-venous axis as well as their interactions and potential functionality. Overall, this thesis presents a joined dataset of single cells and single nuclei from human cardiac tissues and provides new insights into cardiac biology in heath with implications for cardiovascular disease.

Epstein-Barr virus (EBV) causes lifelong infection in over 90% of the world’s population. EBV infection leads to several types of B cell and epithelial cancers due to the viral reprogramming of host-cell growth and gene expression. EBV is associated with 10% of stomach/gastric adenocarcinomas (EBVaGCs), which have distinct molecular, pathological, and immunological characteristics compared to EBV-negative gastric adenocarcinomas (EBVnGCs). Publicly available datasets, such as The Cancer Genome Atlas (TCGA), contain comprehensive transcriptomic, genomic, and epigenomic data for thousands of primary human cancer samples, including EBVaGCs. Additionally, single-cell RNA-sequencing data are becoming available for EBVaGCs. These resources provide a unique opportunity to explore the role of EBV in human carcinogenesis, as well as differences between EBVaGCs and their EBVnGC counterparts. We have constructed a suite of web-based tools called the EBV Gastric Cancer Resource (EBV-GCR), which utilizes TCGA and single-cell RNA-seq data and can be used for research related to EBVaGCs. These web-based tools allow investigators to gain in-depth biological and clinical insights by exploring the effects of EBV on cellular gene expression, associations with patient outcomes, immune landscape features, and differential gene methylation, featuring both whole-tissue and single-cell analyses.

Crohn’s disease is a highly heterogeneous autoimmune disease with a unique inflammatory phenotype of T cells at the lesion site. We aim to further explore the diagnosis of Crohn’s disease and drug prediction of T cell marker gene expression. We obtained single-cell expression profile data from 22 CDs or normal samples and performed cell annotation and cellular communication analysis. Through the intersection of T cell marker genes, differential genes, and WGCNA results, we identified T cell-specific key genes and their immune landscapes and potential pathogenesis, and validated them across multiple datasets and patient tissue samples. We also explored the differentiation characteristics of genes by pseudo-temporal analysis and assessed their diagnostic performance and drug sensitivity by molecular docking. Finally, we extended this study to the prognosis of IBD-associated colon cancer. TNF-centered 5-gene diagnostic model not only has excellent diagnostic efficacy, but is also closely associated with KRAS, P53, and IL6/JAK/STAT3 pathways and physiological processes, such as EMT, coagulation, and apoptosis. In addition, this diagnostic model may have potential synergistic immunotherapeutic effects, with positive correlations with immune checkpoints such as CTLA4, CD86, PDCD1LG2, and CD40. Molecular docking demonstrated that BIRC3 and ANXA1 have strong binding properties to Azathioprine and Glucoocorticoid. Furthermore, the 5-gene model may suggest antagonism to IFX and prognosis for colon cancer associated with inflammatory bowel disease. Single-cell sequencing targeting T cell-related features in patients with Crohn’s disease may aid in new diagnostic decisions, as well as the initial exploration of high-potential therapies.

In recent years, technological developments have enabled the comprehensive transcriptional profiling of thousands of single cells in a single experiment. However, there is still much to be gained from the integration of datasets from different donors, studies, and technological platforms. One major challenge in this regard is the technical variability introduced by handling different batches, known as batch effects, which can obscure biological variations. Assessing batch effects within a dataset has been the focus of various studies seeking to establish reliable criteria for selecting a batch effect removal method. However, these methods do not always perform reliably. This study provides a comprehensive review of both batch effect removal and assessment methods and introduces a novel method for batch effect removal assessment. The performance of the proposed method is evaluated by comparing it to four other batch effect assessment methods using eleven test datasets. The results showed that the proposed method consistently outperformed the other methods, successfully passing all challenges while the other methods failed at least one test. The proposed method was applied to three biological integrated datasets to evaluate its performance on real-world data. The results of the evaluation showed that the proposed method demonstrated the highest correlation with the expert’s assessment of the datasets, indicating that it was able to accurately identify batch effects in the data.

Background RNA sequencing has become the gold standard for transcriptome analysis but has an inherent limitation of challenging quantification of low-abundant transcripts. In contrast to microarray technology, RNA sequencing reads are proportionally divided in function of transcript abundance. Therefore, low-abundant RNAs compete against highly abundant - and sometimes non-informative - RNA species. Results We developed an easy-to-use strategy based on high-affinity RNA-binding oligonucleotides to block reverse transcription and PCR amplification of specific RNA transcripts, thereby substantially reducing their abundance in the final sequencing library. To demonstrate the broad application potential of our method, we applied it to different transcripts and library preparation strategies, including YRNAs in small RNA sequencing of human blood plasma, mitochondrial rRNAs in both 3′ end sequencing and long-read sequencing, and MALAT1 in single-cell 3′ end sequencing. We demonstrate that the blocking strategy is highly efficient, reproducible, specific, and generally results in better transcriptome coverage and complexity. Conclusion Our method does not require modifications of the library preparation procedure apart from simply adding blocking oligonucleotides to the RT reaction and can thus be easily integrated into virtually any RNA sequencing library preparation protocol.

Differentiation of B cells into antibody-secreting cells (ASCs) is a key process to generate protective humoral immunity. A detailed understanding of the cues controlling ASC differentiation is important to devise strategies to modulate antibody formation. Here, we dissected differentiation trajectories of human naive B cells into ASCs using single-cell RNA sequencing. By comparing transcriptomes of B cells at different stages of differentiation from an in vitro model with ex vivo B cells and ASCs, we uncovered a novel pre-ASC population present ex vivo in lymphoid tissues. For the first time, a germinal-center-like population is identified in vitro from human naive B cells and possibly progresses into a memory B cell population through an alternative route of differentiation, thus recapitulating in vivo human GC reactions. Our work allows further detailed characterization of human B cell differentiation into ASCs or memory B cells in both healthy and diseased conditions.

The enteric nervous system (ENS) consists of glial cells (EGCs) and neurons derived from neural crest precursors. EGCs retain capacity for large-scale neurogenesis in culture, and invivo lineage tracing has identified neurons derived from glial cells in response to inflammation. We thus hypothesize that EGCs possess a chromatin structure poised for neurogenesis. We use single-cell multiome sequencing to simultaneously assess transcription and chromatin accessibility in EGCs undergoing spontaneous neurogenesis in culture, as well as small intestine myenteric plexus EGCs. Cultured EGCs maintain open chromatin at genomic loci accessible in neurons, and neurogenesis from EGCs involves dynamic chromatin rearrangements with a net decrease in accessible chromatin. A subset of invivo EGCs, highly enriched within the myenteric ganglia and that persist into adulthood, have a gene expression program and chromatin state consistent with neurogenic potential. These results clarify the mechanisms underlying EGC potential for neuronal fate transition.

Peer reviewed: True, Acknowledgements: We thank Nancy Thornberry and Paul Richards for manuscript comments, Lin Gan (Rochester) for Atoh1-Cre mice, Chris Wright (Vanderbilt) for Ptf1a-Cre mice, Patricia Jensen (NIH) and Nicholas Plummer (NIH) for genotyping advice, members of the Liberles laboratory for experimental advice and assistance, the Boston Children’s Hospital Mouse Gene Manipulation Core (NIH P50 HD105351) for help with generating mice, the Beth Israel Deaconess Medical Center Energy Balance Core (OD028635, P30 DK034854) for help with CLAMS assays, the Harvard Medical School Nikon Imaging Center and Neurobiology Imaging Facility (NINDS P30 NS072030) for help with microscopy, the Biopolymers Facility for help with sequencing, the Immunology Flow Cytometry Core Facility for help with cell sorting, and the Harvard Medical School O2 High Performance Computer Cluster for bioinformatics support. This work was supported by the NIH (DP1AT009497 to SDL, R01DK103703 to SDL, and T32 HL007901 to JAK), and the Food Allergy Science Initiative (to SDL). MH is a fellow of Japan Society for the Promotion for Science. SDL is an investigator of the Howard Hughes Medical Institute., Funder: Food Allergy Initiative; FundRef: http://dx.doi.org/10.13039/100001419, Funder: Japan Society for the Promotion of Science; FundRef: http://dx.doi.org/10.13039/501100001691, Enteroendocrine cells are specialized sensory cells of the gut-brain axis that are sparsely distributed along the intestinal epithelium. The functions of enteroendocrine cells have classically been inferred by the gut hormones they release. However, individual enteroendocrine cells typically produce multiple, sometimes apparently opposing, gut hormones in combination, and some gut hormones are also produced elsewhere in the body. Here, we developed approaches involving intersectional genetics to enable selective access to enteroendocrine cells in vivo in mice. We targeted FlpO expression to the endogenous Villin1 locus (in Vil1-p2a-FlpO knock-in mice) to restrict reporter expression to intestinal epithelium. Combined use of Cre and Flp alleles effectively targeted major transcriptome-defined enteroendocrine cell lineages that produce serotonin, glucagon-like peptide 1, cholecystokinin, somatostatin, or glucose-dependent insulinotropic polypeptide. Chemogenetic activation of different enteroendocrine cell types variably impacted feeding behavior and gut motility. Defining the physiological roles of different enteroendocrine cell types provides an essential framework for understanding sensory biology of the intestine.

Macrophages play an important role in the progression of sporadic acute type A aortic dissection (ATAAD). The aim of this study was to characterize the cellular heterogeneity of macrophages in ATAAD tissues by scRNA-seq. Ascending aortic wall tissue from six ATAAD patients and three heart transplant donors was assessed by scRNA-seq and then analyzed and validated by various bioinformatic algorithms and histopathology experiments. The results revealed that the proportion of macrophages in ATAAD tissues (24.51%) was significantly higher than that in normal tissues (13.69%). Among the six macrophage subclusters, pro-inflammatory macrophages accounted for 14.96% of macrophages in the AD group and 0.18% in the normal group. Chemokine- and inflammation-related genes (CCL2, CCL20, S100A8, and S100A9) were expressed more intensively in macrophages in ATAAD tissue than in those in normal tissue. Additionally, intercellular communication analysis and transcription factor analysis indicated the activation of inflammation and degradation of the extracellular matrix in ATAAD tissue. Finally, immunohistochemistry, immunofluorescence, and Western blot experiments confirmed the overexpression of macrophage marker genes (CD68 and CD163) and matrix metalloproteinases (MMP9 and MMP2) in ATAAD tissue. Collectively, our study provides a preliminary evaluation of the role of macrophages in ATAAD, and the results could aid in the development of therapeutic options in the future.

Checkpoint immunotherapy is capable of unleashing T cells for controlling tumor, whereas it is destroyed by immunosuppressive myeloid cell. Apoprotein E (APOE) refers to a ligand in terms of the members of low-density lipoprotein (LDL) receptor family for mediating Apoprotein B-involving atherogenic lipoprotein clearance. Besides, tumor-infiltration macrophage can express APOE. The present study reported Apoe-/- mice to exhibit higher resistance toward the development of three types of carcinomas as compared with mice with wild type and to have greater responses to αPD-1 (anti-PD-1) immunotherapy. Moreover, treatment by exploiting APOE inhibitor (COG 133TFA, αAPOE) was capable of curbing tumor development and fostering regression if in combination of αPD-1. According to single-cell RNA sequencing (scRNA-seq), Apoe deletion was correlated with the decline of C1QC+ and CCR2+ macrophage within tumor infiltration, and mass spectrometry results noticeably showed down-regulated the number of M2 macrophages as well. Furthermore, APOE expression in cancer patients resistant to αPD-1 treatment significantly exceeded that in the sensitive group. For this reason, APOE is likely to be targeted for modifying tumor macrophage infiltrate and augmenting checkpoint immunotherapy.

As the importance of cell heterogeneity has begun to be emphasized, single-cell sequencing approaches are rapidly adopted to study cell heterogeneity and cellular evolutionary relationships of various cells, including stem cell populations. The hematopoietic stem and progenitor cell (HSPC) compartment contains HSC hematopoietic stem cells (HSCs) and distinct hematopoietic cells with different abilities to self-renew. These cells perform their own functions to maintain different hematopoietic lineages. Undeniably, single-cell sequencing approaches, including single-cell RNA sequencing (scRNA-seq) technologies, empower more opportunities to study the heterogeneity of normal and pathological HSCs. In this review, we discuss how these scRNA-seq technologies contribute to tracing origin and lineage commitment of HSCs, profiling the bone marrow microenvironment and providing high-resolution dissection of malignant hematopoiesis, leading to exciting new findings in HSC biology.

Inferring the cell types in single-cell RNA-sequencing (scRNA-seq) data is of particular importance for understanding the potential cellular mechanisms and phenotypes occurring in complex tissues, such as the tumor-immune microenvironment (TME). The sparsity and noise of scRNA-seq data, combined with the fact that immune cell types often occur on a continuum, make cell typing of TME scRNA-seq data a significant challenge. Several single-label cell typing methods have been put forth to address the limitations of noise and sparsity, but accounting for the often overlapped spectrum of cell types in the immune TME remains an obstacle. To address this, we developed a new scRNA-seq cell-typing method, Cell-typing using variance Adjusted Mahalanobis distances with Multi-Labeling (CAMML). CAMML leverages cell type-specific weighted gene sets to score every cell in a dataset for every potential cell type. This allows cells to be labelled either by their highest scoring cell type as a single label classification or based on a score cut-off to give multi-label classification. For single-label cell typing, CAMML performance is comparable to existing cell typing methods, SingleR and Garnett. For scenarios where cells may exhibit features of multiple cell types (e.g., undifferentiated cells), the multi-label classification supported by CAMML offers important benefits relative to the current state-of-the-art methods. By integrating data across studies, omics platforms, and species, CAMML serves as a robust and adaptable method for overcoming the challenges of scRNA-seq analysis.

Background Dairy cows utilize human-inedible, low-value plant biomass to produce milk, a low-cost product with rich nutrients and high proteins. This process largely relies on rumen microbes that ferment lignocellulose and cellulose to produce volatile fatty acids (VFAs). The VFAs are absorbed and partly metabolized by the stratified squamous rumen epithelium, which is mediated by diverse cell types. Here, we applied a metagenomic binning approach to explore the individual microbes involved in fiber digestion and performed single-cell RNA sequencing on rumen epithelial cells to investigate the cell subtypes contributing to VFA absorption and metabolism. Results The 52 mid-lactating dairy cows in our study (parity = 2.62 ± 0.91) had milk yield of 33.10 ± 6.72 kg. We determined the fiber digestion and fermentation capacities of 186 bacterial genomes using metagenomic binning and identified specific bacterial genomes with strong cellulose/xylan/pectin degradation capabilities that were highly associated with the biosynthesis of VFAs. Furthermore, we constructed a rumen epithelial single-cell map consisting of 18 rumen epithelial cell subtypes based on the transcriptome of 20,728 individual epithelial cells. A systematic survey of the expression profiles of genes encoding candidates for VFA transporters revealed that IGFBP5+ cg-like spinous cells uniquely highly expressed SLC16A1 and SLC4A9, suggesting that this cell type may play important roles in VFA absorption. Potential cross-talk between the microbiome and host cells and their roles in modulating the expression of key genes in the key rumen epithelial cell subtypes were also identified. Conclusions We discovered the key individual microbial genomes and epithelial cell subtypes involved in fiber digestion, VFA uptake and metabolism, respectively, in the rumen. The integration of these data enables us to link microbial genomes and epithelial single cells to the trophic system.

In recent decades, our understanding of the molecular changes involved in neurodegenerative diseases has been transformed. Single-cell RNA sequencing and single-nucleus RNA sequencing technologies have been applied to provide cellular and molecular details of the brain at the single-cell level. This has expanded our knowledge of the central nervous system and provided insights into the molecular vulnerability of brain cell types and underlying mechanisms in neurodegenerative diseases. In this review, we highlight the recent advances and findings related to neurodegenerative diseases using these cutting-edge technologies., At the time of writing this review, N.V.T is funded by a postdoctoral grant, Juan de la Cierva Programme (FJC2018-038085-I), Ministerio de Ciencia, Innovación y Universidades – Spanish State Research Agency. Her research is also supported by the “la Caixa'' Foundation (LCF/PR/GN17/10300004) and the Health Department of the Catalan Government (Health Research and Innovation Strategic Plan (PERIS) 2016–2020 grant #SLT002/16/00201). J.D.G is supported by the Spanish Ministry of Science and Innovation (RYC-2013-13054). All CRG authors acknowledge the support of the Spanish Ministry of Science, Innovation, and Universities to the EMBL partnership, the Centro de Excelencia Severo Ochoa, and the CERCA Programme/Generalitat de Catalunya.

Recent advances in spatially resolved transcriptomics (SRT) have revolutionized biological and medical research and enabled unprecedented insight into the functional organization and cell communication of tissues and organs in situ. Identifying and elucidating gene spatial expression variation (SE analysis) is fundamental to elucidate the SRT landscape. There is an urgent need for public repositories and computational techniques of SRT data in SE analysis alongside technological breakthroughs and large-scale data generation. Increasing efforts to use in silico techniques in SE analysis have been made. However, these attempts are widely scattered among a large number of studies that are not easily accessible or comprehensible by both medical and life scientists. This study provides a survey and a summary of public resources on SE analysis in SRT studies. An updated systematic overview of state-of-the-art computational approaches and tools currently available in SE analysis are presented herein, emphasizing recent advances. Finally, the present study explores the future perspectives and challenges of in silico techniques in SE analysis. This study guides medical and life scientists to look for dedicated resources and more competent tools for characterizing spatial patterns of gene expression., Graphical abstract, This study presented an overview of public repositories and state-of-the-art computational algorithms, approaches, and tools available in SE analysis. Therefore, this study will guide medical and life scientists to look for dedicated resources and more competent tools for characterizing spatial patterns of gene expression.

The mortality rate is high for cancer patients and treatments are only efficient in a fraction of patients. To be able to cure more patients, new treatments need to be invented. Immunotherapy activates the immune system to fight against cancer and one treatment targets immune checkpoints. If more targets are found, more patients can be treated successfully. In this project, interactions between immune and cancer cells that drive tumour growth were investigated in an attempt to find new potential targets. This was achieved by creating a machine learning model that finds genes expressed in cells involved in tumour-driving interactions. Single-cell RNA sequencing and spatial transcriptomic data from breast cancer patients were utilised as well as single-cell RNA sequencing data from healthy patients. The tumour rate was based on the cumulative expression of G2/M genes. The G2/M related genes were excluded from the analysis since these were assumed to be cell cycle genes. The machine learning model was based on a supervised variational autoencoder architecture. By using this kind of architecture, it was possible to compress the input into a low dimensional space of genes, called a latent space, which was able to explain the tumour rate. Optuna hyperparameter optimizer framework was utilised to find the best combination of hyperparameters for the model. The model had a R2 score of 0.93, which indicated that the latent space was able to explain the growth rate 93% accurately. The latent space consisted of 20 variables. To find out which genes that were in this latent space, the correlation between each latent variable and each gene was calculated. The genes that were positively correlated or negatively correlated were assumed to be in the latent space and therefore involved in explaining tumour growth. Furthermore, the correlation between each latent variable and the growth rate was calculated. The up- and downregulated genes in each latent variable were kept and used for finding out the pathways for the different latent variables. Five of these latent variables were involved in immune responses and therefore these were further investigated. The genes in these five latent variables were mapped to cell types. One of these latent variables had upregulated immune response for positively correlated growth, indicating that immune cells were involved in promoting cancer progression. Another latent variable had downregulated immune response for negatively correlated growth. This indicated that if these genes would be upregulated instead, the tumour would be thriving. The genes found in these latent variables were analysed further. CD80, CSF1, CSF1R, IL26, IL7, IL34 and the protein NF-kappa-B were interesting finds and are known immune-modulators. These could possibly be used as markers for pro-tumour immunity. Furthermore, CSF1, CSF1R, IL26, IL34 and the protein NF-kappa-B could potentially be targeted in immunotherapy.

Palmoplantar skin is structurally and functionally unique, but the transcriptional programs driving this specialization are unclear. Here, we use bulk and single-cell RNA sequencing of human palm, sole, and hip skin to describe the distinguishing characteristics of palmoplantar and non-palmoplantar skin while also uncovering differences between palmar and plantar sites. Our approach reveals an altered immune environment in palmoplantar skin, with downregulation of diverse immunological processes and decreased immune cell populations. Further, we identify specific fibroblast populations that appear to orchestrate key differences in cell-cell communication in palm, sole, and hip. Dedicated keratinocyte analysis highlights major differences in basal cell fraction among the three sites and demonstrates the existence of two spinous keratinocyte populations constituting parallel, site-selective epidermal differentiation trajectories. In summary, this deep characterization of highly adapted palmoplantar skin contributes key insights into the fundamental biology of human skin and provides a valuable data resource for further investigation.

Immune checkpoint therapy (ICT) has the power to eradicate cancer, but the mechanisms that determine effective therapy-induced immune responses are not fully understood. Here, using high-dimensional single-cell profiling, we interrogate whether the landscape of T cell states in the peripheral blood predict responses to combinatorial targeting of the OX40 costimulatory and PD-1 inhibitory pathways. Single-cell RNA sequencing and mass cytometry expose systemic and dynamic activation states of therapy-responsive CD4+ and CD8+ T cells in tumor-bearing mice with expression of distinct natural killer (NK) cell receptors, granzymes, and chemokines/chemokine receptors. Moreover, similar NK cell receptor-expressing CD8+ T cells are also detected in the blood of immunotherapy-responsive cancer patients. Targeting the NK cell and chemokine receptors in tumor-bearing mice shows the functional importance of these receptors for therapy-induced anti-tumor immunity. These findings provide a better understanding of ICT and highlight the use and targeting of dynamic biomarkers on T cells to improve cancer immunotherapy.

Memory B cells (Bmem) provide a unique layer of defence against pathogens and are an essential component of the immunological memory acquired by vaccination and infection. Long-lived Bmem are generated upon antigen encounter in the primary immune response. Following the resolution of primary response, a subpopulation of Bmem is retained in the lymph node draining the site of vaccine injection or pathogen entry. In this draining lymph node, resting Bmem occupy the subcapsular sinus (SCS) niche where they scan SCS macrophages for antigen. Booster immunisation reactivates Bmem to become either short-lived plasma cells (PC) or re-enter secondary germinal centers (GC) to increase their B cell receptor affinity and diversity to the immunising antigen. However, it is unclear whether Bmem retained in the draining lymph node after primary immunisation have different cellular phenotypes, transcriptional states, and cell fate potential compared to recirculating Bmem found in the non-draining lymph node. Here, the established SWHEL mouse model was used to track and characterise antigen-specific Bmem in the draining and non-draining lymph nodes. Using intravital two-photon microscopy to probe the cellular dynamics of Bmem under homeostatic conditions in vivo, this study found that recirculating Bmem in the non-draining lymph node have distinct localisation, dynamic, and behaviour compared to Bmem residing in the draining lymph node. Importantly, boosting in the draining lymph node reactivates Bmems that preferentially re-enter the GC, facilitating affinity maturation of the secondary antibody response. In contrast, boosting in the non-draining lymph node preferentially recalls the PC response. These differential memory recall responses are not dependent on persisting primary GC or memory CD4 T cells but can be altered by disrupting the SCS macrophages. Furthermore, transcriptomic profiling by single-cell RNA sequencing revealed that Bmem in the draining and non-draining lymph nodes occupy distinct cell states, suggesting their cell fate potentials may also be molecularly imprinted. This thesis thus highlights an additional layer of control over Bmem fate through their geographical positioning and suggests that the site of booster vaccinations can affect the Bmem cell fate choice and, thereby, the quality and quantity of the resulting secondary antibody response.

Keloide stellen eine abnorme Wundheilungsreaktion dar und zeichnen sich durch ein Wachstum über den Wundrand hinaus aus. Sie gehen mit Symptomen wie Schmerzen, Juckreiz und Bewegungseinschränkung einher und können daher die Lebensqualität betroffener Patient*innen deutlich einschränken. Rezente Studien legen nahe, dass abnorm reagierende Schwann-Zellen zur Pathogenese von Keloiden beitragen. Möglicherweise von zentraler Bedeutung ist dabei CCL2. Dieses Chemokin ist u.a. für die Rekrutierung von M1-Makrophagen, welche eine wichtige Rolle in der Wundheilung spielen, zuständig. In dieser Forschungsarbeit wurden Schwann-Zellen und die CCL2-Expression in Keloiden untersucht und die Ergebnisse mit denen der gesunden Haut, normalen Narben und hypertrophen Narben verglichen. Außerdem wurde die Wirkung von Hydrocortison auf Schwann-Zellen analysiert, um den therapeutischen Nutzen von Steroiden in der Behandlung von Keloiden besser zu verstehen. Die Clusteranalyse der scRNA-seq zeigte ein vermehrtes Vorkommen von Schwann-Zellen im Keloid. Dieses Ergebnis konnte auch mittels Immunfluoreszenzfärbungen bestätigt werden. Diese zeigten zusätzlich, dass die meisten keloidalen Schwann-Zellen nicht mit Axonen assoziiert sind. Mittels scRNA-seq und Immunfluoreszenzfärbungen wurden stark reduzierte CCL2-Expressionslevel im Keloid festgestellt. Die CCL2-Expression der hypertrophen Narbe war in der scRNA-seq deutlich, in den Immunfluoreszenzfärbungen allerdings nur leicht reduziert. Mittels PCR konnte gezeigt werden, dass die CCL2-Expression von Schwann-Zellen durch Hydrocortison runterreguliert wird. Diese Ergebnisse unterstützen die Vermutung, dass Schwann-Zellen an der Pathogenese von Keloiden beteiligt sind. Die Wirkung von Hydrocortison auf Schwann-Zellen sollte mit einem größeren Stichprobenumfang weiter erforscht werden. Keloids represent an abnormal wound healing reaction and are characterized by a growth beyond the margin of the wound. They can cause severe pain, pruritus and movement restriction and can therefore significantly reduce patients’ quality of life. Recent studies suggest that an abnormal reaction of Schwann cells contributes to keloid pathogenesis. CCL2 could represent a crucial step in the development of keloids. This chemokine is responsible for the recruitment of M1-macrophages, which play an important role in wound healing. In this thesis, Schwann cells and CCL2 expression were investigated in keloids and the results were compared with healthy skin, normal scars and hypertrophic scars. In addition, the effect of hydrocortisone on Schwann cells was analyzed to get a better understanding of the therapeutic benefits of steroids in the treatment of keloids. Cluster analysis of scRNA-seq showed an increase in cell number of Schwann cells in keloids. This result could also be confirmed by immunofluorescence staining. These additionally showed that most keloidal Schwann cells are not associated with axons. ScRNA-seq and immunofluorescence staining showed that CCL2 is strongly down-regulated in keloids. CCL2 expression of the hypertrophic scar was significantly reduced in scRNA-seq, but only slightly reduced in immunofluorescence staining. PCR showed that CCL2 expression of Schwann cells is downregulated by hydrocortisone. These results support the assumption that Schwann cells contribute to keloid pathogenesis. The effect of hydrocortisone on Schwann cells should be further investigated with a larger sample size.

Single-cell RNA sequencing, which quantifies cell transcriptomes, has seen widespread adoption, accompanied by proliferation of analysis methods. However, there has been relatively little systematic investigation of its best practices and their underlying assumptions, leading to challenges and discrepancies in interpretation. I present a set of generic, principled strategies for modeling the biological and technical components of sequencing experiments and use case studies to motivate their application to sequencing data.

Sox transcription factors are crucial for vertebrate nervous system development. In zebrafish embryo, sox1 genes are expressed in neural progenitor cells and neurons of ventral spinal cord. Our recent study revealed that the loss of sox1a and sox1b function results in a significant decline of V2 subtype neurons (V2s). Using single-cell RNA sequencing, we analyzed the transcriptome of sox1a lineage progenitors and neurons in the zebrafish spinal cord at four time points during embryonic development, employing the Tg(sox1a:eGFP) line. In addition to previously characterized sox1a-expressing neurons, we discovered the expression of sox1a in late-developing intraspinal serotonergic neurons (ISNs). Developmental trajectory analysis suggests that ISNs arise from lateral floor plate (LFP) progenitor cells. Pharmacological inhibition of the Notch signaling pathway revealed its role in negatively regulating LFP progenitor cell differentiation into ISNs. Our findings highlight the zebrafish LFP as a progenitor domain for ISNs, alongside known Kolmer-Agduhr (KA) and V3 interneurons.

B and T cells are integral parts of the immune system and are implicated in many diseases, e.g. autoimmunity. Towards understanding the biology of B and T cells and subsets thereof, their transcriptomes can be analyzed using single-cell RNA sequencing. In some studies, the V(D)J transcripts encoding the variable regions of the B- and T-cell antigen receptors have been removed before the analyses. However, a systematic analysis of the effects of including versus excluding these genes is currently lacking. We have investigated the effects of these transcripts on unsupervised clustering and down-stream analyses of single-cell RNA sequencing data from B and T cells. We found that exclusion of the B-/T-cell receptor genes prior to unsupervised clustering resulted in clusters that represented biologically meaningful subsets, such as subsets of memory B and memory T cells. Furthermore, pseudo-time and trajectory inference analyses of early B-lineage cells resulted in a developmental pathway from progenitor to immature B cells. In contrast, when the B-/T-cell receptor genes were not removed, with the PCs used for clustering consisting of up to 70% V-genes, this resulted in some clusters being defined exclusively by V-gene segments. These did not represent biologically meaningful subsets; for instance in the early B-lineage cells, these clusters contained cells representing all developmental stages. Thus, in studies of B and T cells, to derive biologically meaningful results, it is imperative to remove the gene sequences that encode B- and T-cell receptors. CC BY-NC 4.0Corresponding author: Inga-Lill Mårtensson, Department of Rheumatology and Inflammation Research, Institute of Medicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden. Tel.:+46(0)703640068; E-mail: lill.martensson@rheuma.gu.seThis work was supported by the Swedish Research Council, grants 2018-03128 and 2021-01150 (ILM) and 2016-01576 (IG); the Swedish Cancer Foundation, grant 19 0464 (ILM); the Swedish Childhood Cancer Fund, grants PR2018-0170 and PR2020-0147 (ILM), and TJ2019-0098 (AC); Assar Gabrielsson’s Foundation, FB21-104 (AC); Patient Association for Rheumatic Diseases, R-94129 (ILM) and R-940945 (IG); ALF (agreement between the Government of Sweden and the County Councils), ALFGBG-719631 (IG); Adlerbertska stiftelsen (TS); and the IngaBritt och Arne Lundbergs Foundation (ILM, IG)

Inflammatory bowel disease (IBD) is an abnormal immune response to the gut microbiome causing chronic debilitating pain in genetically susceptible people. The development of effective therapies for this condition is hampered by a poor understanding of its complex aetiology. Progress in this area will require identification of both the immune and epithelial contributions to disease in susceptible individuals as well as detangling the contributions of different pathways and genes, all in a cell type specific context. This thesis summarizes my research into the gene regulatory architecture of IBD in intestinal epithelial cells. First I assess the utility of intestinal epithelial organoids, a model of the human intestine. This system is well established and has been shown to be comparable to in vivo intestinal tissue in many ways. However, my study revealed DNA methylation (DNAm) is generally lost and becomes more variable the longer organoids are cultured. My findings suggest a major impact of prolonged culturing on global organoid DNAm profiles, highlighting the importance of considering time in culture in organoid experiments. Next I explore DNAm, gene expression and genotype to: define a possible IBD biomarker, explain previously established IBD genotype associations, and identify potential mechanistic candidates for functional follow-up. In both primary epithelial cells and organoids I found widespread differential DNAm with IBD. Of the CpGs differentially DNAm in IBD, changes in the major histocompatibility complex class I (MHC I) signaling pathway are particularly interesting. The MHC I pathway represents a promising candidate mechanism of IBD as it is involved in the communication between cells and the immune system. Finally, I follow up on the association of MHC I and IBD in individual intestinal epithelial cells. As in the bulk expression data, I also see increased expression of MHC I in IBD compared to controls. This is consistent across cell types, but interestingly MHC I activity is higher in villus tip cells compared to crypt cells regardless of diagnosis, suggesting activity could be related to exposure to luminal microbiota. I also show MHC I can be activated successfully in organoids with proinflammatory cytokine stimulation, meaning organoids could be a useful model to study MHC I pathway function in IBD. In this thesis, I demonstrate that organoids are a valuable model of the human gut, and use them to identify MHC I activation as a potential mechanism of pediatric IBD pathogenesis., The work was supported by the EMBL International PhD Programme.

The glucocorticoid stress hormones affect brain function via high-affinity mineralocorticoid receptors (MRs) and lower-affinity glucocorticoid receptors (GRs). MR and GR not only differ in affinity for ligands, but also have distinct, sometimes opposite, actions on neuronal excitability and other cellular and higher-order parameters related to cerebral function. GR and MR messenger RNA (mRNA) levels are often used as a proxy for the responsiveness to glucocorticoids, assuming proportionality between mRNA and protein levels. This may be especially relevant for the MR, which because of its high affinity is already largely occupied at low basal (trough) hormone levels. Here we explore how GR and MR mRNA levels are associated with the expression of a shared target gene, glucocorticoid-induced leucine zipper (GILZ, coded by Tsc22d3) with basal and elevated levels of corticosterone in male mice, using in situ hybridization. Depending on the hippocampal subfield and the corticosterone levels, mRNA levels of MR rather than GR mostly correlated with GILZ mRNA in the hippocampus and hypothalamus at the bulk tissue level. At the individual cell level, these correlations were much weaker. Using publicly available single-cell RNA sequencing data, we again observed that MR and GR mRNA levels were only weakly correlated with target gene expression in glutamatergic and GABAergic neurons. We conclude that MR mRNA levels can be limiting for receptor action, but many other cell-specific and region-specific factors ultimately determine corticosteroid receptor action. Altogether, our results argue for caution while interpreting the consequences of changed receptor expression for the response to glucocorticoids.

A major challenge in single cell gene expression analysis is to discern meaningful cellular heterogeneity from technical or biological noise. To address this challenge, we present Entropy Sorting, a mathematical framework that distinguishes genes indicative of cell identity. ES achieves this in an unsupervised manner by quantifying if observed correlations between features are more likely to have occurred due to random chance versus a dependent relationship, without the need for any user defined significance threshold. On synthetic data we demonstrate the removal of noisy signals to reveal a higher resolution of gene expression patterns than commonly used feature selection methods. We then apply ES to human pre-implantation embryo scRNA-seq data. Previous studies failed to unambiguously identify early inner cell mass (ICM), suggesting that the human embryo may diverge from the mouse paradigm. In contrast, ES resolves the ICM and reveals sequential lineage bifurcations as in the classical model. Entropy sorting thus provides a powerful approach for maximising information extraction from high dimensional datasets such as scRNA-seq data.

Multiple myeloma (MM) has a highly heterogeneous genetic background, which complicates its molecular tracking over time. Nevertheless, each MM patient’s malignant plasma cells (PCs) share unique V(D)J rearranged sequences at immunoglobulin loci, which represent ideal disease biomarkers. Because the tumor-specific V(D)J sequence is highly expressed in bulk RNA in MM patients, we wondered whether it can be identified by single-cell RNA sequencing (scRNA-seq). To this end we analyzed CD138+ cells purified from bone marrow aspirates of 19 samples with PC dyscrasias by both a standard method based on bulk DNA and by an implementation of the standard 10x Genomics protocol to detect expressed V(D)J sequences. A dominant clonotype was easily identified in each sample, accounting on average for 83.65% of V(D)J-rearranged cells. Compared with standard methods, scRNA-seq analysis proved highly concordant and even more effective in identifying clonal productive rearrangements, by-passing limitations related to the misannealing of consensus primers in hypermutated regions. We next validated its accuracy to track 5 clonal cells with absolute sensitivity in a virtual sample containing 3180 polyclonal cells. This shows that single-cell V(D)J analysis may be used to find rare clonal cells, laying the foundations for functional single-cell dissection of minimal residual disease.

Mezenhimski hondrosarkom (MCS) je agresiven podtip hondrosarkoma, ki prizadene predvsem otroke in mladostnike. Pred odkritjem genske fuzije HEY1-NCoA2 v večini MCS, je njegova diagnoza predstavljala izziv zaradi histopatoloških podobnosti s številnimi drugimi primitivnimi sarkomi, ki se predstavljajo z morfologijo majhnih modrih in okroglih malignih celic. S trenutnimi pristopi zdravljenja, je bila mediana preživetja brez napredovanja bolezni ocenjena na 57 mesecev. Dodatni lastnosti MCS sta tudi visoka zunajskeletna pojavnost, in visoka stopnja poznih ponovitev. Kirurška resekcija MCS pa je pokazala izboljšano stopnjo preživetja kot zdravljenje s konvencionalno kemoterapijo. V tej študiji smo odkrili potencialno terapevtsko sredstvo za zdravljenju mezenhimskega hondrosarkoma (MCS), ki ga poganja genska fuzija HEY-NCoA2 in je že na voljo v kliniki, imatinib mezilat. Pokazali smo potencial kombiniranja bioloških in genomskih funkcionalnih asociacijskih omrežij za boljše prepoznavanje nadomestnih tarč, saj se trenutno genske fuzije HEY1-NCoA2 še ne more direktno ciljati. Prikazujemo tudi utemeljitev strategije ponovne uporabe licenčnih zdravil za zdravljenje MCS, potek dela te študije pa bi lahko uporabili za študije drugih redkih rakov, ki jih poganja le ena genska fuzija. Takšna strategija tudi podpira trenutna prizadevanja iskanj boljših načinov zdravljenja redkih rakov, ki večinoma nimajo predkliničnih modelov, so zato premalo raziskani in za katere je razvoj novih zdravil nepraktičen. Poleg tega pa lahko tudi odkrije potencialne rezistence na trenutno uporabljenje kemoterapije, za zadravljenje tovrstnih rakov. Navsezadnje, rezultati našega dela predstavljajo podlago za ponovno klinično oceno učinkovitosti imatiniba za zdravljenje MCS, ki ga poganja HEY1-NCoA2 genska fuzija. Mesenchymal chondrosarcoma (MCS) is an aggressive subtype of chondrosarcoma, mainly affecting children and young adults. Before the discovery of a recurrent HEY1-NCoA2 gene fusion in most MCS patient samples, MCS diagnosis presented a challenge due to histopathological similarities to many other small blue round cell neoplasms of primitive sarcomas. With current treatments, the median event-free survival is 57 months. MCS characteristics are high extraskeletal occurrence and a late recurrence rate. Surgical resection shows improved survival rates compared to treatment with conventional chemotherapy. This study identified a potential therapeutic agent to treat HEY-NCoA2 gene fusion-driven mesenchymal chondrosarcoma (MCS), which is already available in the clinic, imatinib mesylate. Our findings highlighted the potential of combining biological and genome-wide functional association network frameworks to facilitate the identification of proxy druggable targets of MCS since HEY1-NCoA2 gene fusion cannot yet be directly targeted. Therefore we show the rationale to utilize the repurposing of licensed drugs strategy for the treatment of MCS and the workflow of this study could be applied to other rare single fusion-driven tumors. This strategy also supports current efforts for reinvigorating therapy development in underresearched rare cancers, without preclinical models and in which de novo drug development is, in the majority of cases, impractical. Additionally, it can also identify the potential resistance of these tumors to currently used chemotherapy to treat them. Lastly, this work rationally justifies a re-evaluation of licensed multikinase inhibitor imatinib to treat HEY1-NCoA2 fusion-driven MCS in a clinical trial.

Intervertebral disc (IVD) degeneration is characterized by a loss of cellularity, and changes in cell-mediated activity that drives anatomic changes to IVD structure. In this study, we use single cell RNA-sequencing analysis of cells extracted from the degenerating tissues of the rat IVD following lumbar disc puncture. Two control, uninjured IVDs (L2-3, L3-4) and two degenerated, injured IVDs (L4-5, L5-6) from each animal were examined either at two- and eight-week post-operative time points. The cells from these IVDs were extracted and transcriptionally profiled at a single-cell resolution. Unsupervised cluster analysis revealed the presence of 4 known cell types in both non-degenerative and degenerated IVDs based on previously established gene markers: IVD cells, endothelial cells, myeloid cells, and lymphoid cells. As a majority of cells were associated with the IVD cell cluster, sub-clustering was used to further identify the cell populations of the nucleus pulposus, inner and outer annulus fibrosus. The most notable difference between control and degenerated IVDs was the increase of myeloid and lymphoid cells in degenerated samples at 2- and 8- weeks post-surgery. Differential gene expression analysis revealed multiple distinct cell types from the myeloid and lymphoid lineages, most notably macrophages and B lymphocytes and demonstrated a high degree of immune specificity during degeneration. In addition to the heterogenous infiltrating immune cell populations in the degenerating IVD, the increased number of cells in the AF sub-cluster expressing Ngf and Ngfr, encoding for p75NTR, suggest that NGF signaling may be one of the key mediators of the IVD crosstalk between immune and neuronal cell populations. These findings provide the basis for future work to understand the involvement of select subsets of non-resident cells in IVD degeneration.

Glioblastoma (GBM) is an aggressive primary brain tumor with unique immunity predominated by myeloid cells. GBM cells have been implicated to evade immune attack through hijacking myeloid-affiliated transcriptional programs to establish an immunosuppressive microenvironment. However, molecular features of immune-evading GBM cells in heterogeneous GBMs and their interactions with immune cells remain unclear. Herein, we employed single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data to develop an in silico method for delineating GBM immune signature and identifying new molecular subsets for immunotherapy. We identified a new GBM cell subset, termed TC-6, that harbored immune-invading signature and actively interacted with tumor-associated macrophages (TAMs) to orchestrate an immune-suppressive niche. Proinflammatory transcriptional factors STAT1, STAT2, IRF1, IRF2, IRF3, and IRF7 were identified as the core regulons defining TC-6 subsets. Further immune transcriptome analyses revealed three immune subtypes (C1, C2, and C3). C3 subtype GBMs were enriched with TC-6 cells and immunosuppressive TAMs, and exhibited an immunomodulatory signature that associated with reduced efficacy of anti-PD-1 treatment. Interferon-related DNA damage resistance signaling was upregulated in C3 GBMs, predicting shortened survival of GBM patients who received chemo-radiation treatment. Treatment of OSI-930 as a molecular agent targeting c-kit and VEGFR2 tyrosine kinases may compromise the immunomodulatory signature of C3 GBMs and synergize with chemo-radiation therapy. We further developed a simplified 11-gene set for defining C3 GBMs. Our work identified TC-6 subset as an immune-evading hub that creates an immunomodulatory signature of C3 GBMs, gaining insights into the heterogeneity of GBM immune microenvironment and holding promise for optimized anti-GBM immunotherapy.

Human natural killer (NK) cells in lymphoid tissues can be categorized into three subsets: CD56brightCD16+, CD56dimCD16+ and CD69+CXCR6+ lymphoid tissue-resident (lt)NK cells. How the three subsets are functionally and developmentally related is currently unknown. Therefore, we performed single-cell RNA sequencing combined with oligonucleotide-conjugated antibodies against CD56, CXCR6, CD117 and CD34 on fresh bone marrow NK cells. A minor CD56dimGzmK+ subset was identified that shared features with CD56bright and CD56dimGzmK- NK cells based on transcriptome, phenotype (NKG2AhighCD16lowKLRG1highTIGIThigh) and functional analysis in bone marrow and blood, supportive for an intermediate subset. Pseudotime analysis positioned CD56bright, CD56dimGzmK+ and CD56dimGzmK- cells in one differentiation trajectory, while ltNK cells were developmentally separated. Integrative analysis with bone marrow cells from the Human Cell Atlas did not demonstrate a developmental connection between CD34+ progenitor and NK cells, suggesting absence of early NK cell stages in bone marrow. In conclusion, single-cell transcriptomics provide new insights on development and differentiation of human NK cells.

The ability to differentiate human induced pluripotent stem cells (hiPSCs) efficiently into defined cardiac lineages, such as cardiomyocytes and cardiac endothelial cells, is crucial to study human heart development and model cardiovascular diseasesin vitro. The mechanisms underlying the specification of these cell types during human development are not well-understood which limits fine-tuning and broader application of cardiac model systems. Here, we used the expression of ETV2, a master regulator of hematoendothelial specification in mice, to identify functionally distinct subpopulations during the co-differentiation of endothelial cells and cardiomyocytes from hiPSCs. Targeted analysis of single-cell RNA sequencing data revealed differential ETV2 dynamics in the two lineages. A newly created fluorescent reporter line allowed us to identify early lineage-predisposed states and show that a transient ETV2-high state initiates the specification of endothelial cells. We further demonstrated, unexpectedly, that functional cardiomyocytes can originate from progenitors expressing ETV2 at a low level. Our study thus sheds light on thein vitrodifferentiation dynamics of two important cardiac lineages.SIGNIFICANCE STATEMENTIn vitrodifferentiation of cardiac cell types is of great importance for understanding heart development, disease modeling and future regenerative medicine. Currently, underlying molecular mechanisms are incompletely understood, which limits the efficiency and fine-tuning of present differentiation protocols. Here, we investigated the master regulator ETV2 and showed that its upregulation marks the specification of two cardiac cell types during co-differentiation. Using single-cell RNA-seq and a new fluorescent reporter line we identified lineage-predisposed subpopulations in the ETV2+ cells. We thus resolved ETV2 dynamics at the single-cell level in the context ofin vitrohuman cardiac differentiation.