Single Nucleus Research Articles

Abstract P3079: Integrating Existing Cardiac Single-cell RNA Sequencing Datasets To Uncover The Role Of B-cells In Heart Disease

Introduction: The role of B-cells in human heart failure remains unclear. To address this knowledge gap, we analyzed publicly available datasets of scRNAseq and snRNAseq from patients with various forms of cardiomyopathy. Methods and Results: We used two public datasets including single cells or single nuclei RNAseq data collected from the myocardium of patients with arrhythmogenic right ventricular cardiomyopathy (ARVC), dilated cardiomyopathy (DCM), idiopathic cardiac diseases (ICD), or healthy controls. The first dataset comprised 30 healthy controls and 22 non-ischemic DCM; the second contained 18 controls and 61 with DCM, ARVC, or ICD. Data were normalized and scaled, a UMAP plot was generated, and cells were classified using ScType. B-cells were merged into a single matrix, and the final dataset contained 1100 cells from 32 healthy controls, 59 DCM, and 8 ARVC patients. Four different B-cell clusters were identified. The top 100 biomarkers from each cluster were used to identify B-cell subtypes. Cluster 1 was identified as transitional splenic B-cells; Cluster 2 as plasma cells; Cluster 3 as follicular splenic B-cells; Cluster 4, present only in DCM, as immature B cells. Ingenuity Pathway Analysis (IPA) of the genes enriched in each cluster highlighted that different B cell clusters displayed distinct biological activity, ranging from phagosome formation to B cell receptor signaling and cytokine production. Differentially expressed gene analysis comparing healthy controls to DCM and ARVC showed both similar and disease-specific gene expression patterns in the various B cell clusters. For instance, cluster 2 showed upregulation of oxidative phosphorylation in both DCM and ARVC. On the other hand, DCM cluster 2 showed downregulation of CD40 signaling, while in ARVC the same cluster showed downregulation of IL-6 signaling (Z score >2, p<0.05). Discussion: Our findings suggest that human heart failure is associated with perturbations in B cell gene expression, with both shared and disease-specific features. This data supports the notion that B cells likely play a role in human cardiomyopathy. Further, this data suggests that B-cells play distinct roles in disparate forms of cardiac disease.

Abstract P1097: Foxk1 Is A Regulator Of Cardiomyocyte Proliferation And Heart Regeneration

While the adult mammalian heart has limited regenerative potential, the neonatal mouse heart has a remarkable regenerative capacity. Our goal focused on defining new factors and mechanisms that could enhance repair and regeneration in the adult mouse heart. FOXK1 is a transcription factor that regulates cell cycle kinetics, myogenic stem cell proliferation and skeletal muscle regeneration. During development, its expression is restricted to progenitors, somites and the heart. However, its role in neonatal heart regeneration is unknown and warrants investigation. Here, we describe a novel role for FOXK1 as a regulator of cardiomyocyte (CM) proliferation and regeneration. Using computational analysis of single nucleus RNAseq datasets of neonatal CMs, we determined that FOXK1 was expressed in CMs. qPCR analysis of P1 hearts from control or Foxk1 null mice demonstrated that the absence of FOXK1 led to the dysregulation of Ccne1 and p21 expression, suggesting that FOXK1 could play a role in cell cycle kinetics in the neonatal heart. Control or Foxk1 null mice were pulsed with EdU which demonstrated that the absence of FOXK1 led to a decrease in CM proliferation in vivo. We then engineered a transgenic mouse model that overexpressed FOXK1 using the muscle creatine kinase ( MCK-Foxk1 ) promoter and isolated and cultured control or MCK-Foxk1 CMs (72 hrs), and determined that overexpression of FOXK1 led to a significant increase in CM proliferation. Furthermore, EdU pulsing studies in adult control or MCK-Foxk1 mice demonstrated a significant increase in EdU incorporation in adult CMs of MCK-Foxk1 unperturbed mice compared to control. We then performed LAD ligation surgeries in control and MCK-Foxk1 adult mice. Echocardiography 2 months following LAD ligations showed a significant increase in both ejection fraction and fractional shortening in MCK-Foxk1 mice compared to controls. Single nucleus RNAseq analysis of control and MCK-Foxk1 adult hearts highlighted two distinct CM populations by UMAP analysis, with the latter demonstrating a higher expression of myoblast proliferative pathways. These results identify FOXK1 as a regulator of CM proliferation and heart regeneration by employing both knockout and transgenic mouse models.

Abstract P1073: The Mir-200 Family Modulates Expression Of Tbx5 , Gata 4, And Pitx2 During Early Cardiac Development.

Congenital heart defects (CHDs) may be caused by mutations in genes that drive cardiac development. Cardiac development is also regulated at the transcription level. MicroRNAs (miRs) target the transcripts of genes in numerous cardiac cell types during embryonic development. We and others have shown that the miR-200 family modulates the transcripts of cardiogenic transcription factors (TFs) Tbx5 , Gata4 , and Pitx2 ( TGP ). However, relationship between these miRs and cardiogenic TFs during cardiac development is poorly understood. To this relationship, we cultured cardiomyocytes (CMs) with reduced miR-200 expression and found increased expression of Tbx5, Gata4, and Pitx2, providing evidence for targeting in cell-autonomous role. In vivo, the miR-200 family members, miR-200a and -200c , are highly expressed in the developing heart (e14.5) and reduced in adults (2mo) (Ct Value- 200a: 24.3 ± 0.59 v 38.3 ± 0.21; 200c: 25.0 ± 0.64 v 32.5 ± 0.16). Using our miR-200 family inhibitor mice models ( I-200 ), we have found these miRs are required for cardiac development. I-200 embryos are found with a membranous ventral septal defect and poor ventricle wall development, which is lethal by e16.5. At e14.5, I-200 hearts have a significant increase in expression fold change of Tbx5 (5.98 ± 1.51 p ≤ 0.05), Gata4 (3.29 ± 0.61 p ≤ 0.05), and Pitx2 (4.67 ± 0.23 p ≤ 0.05) compared to Wild-Type. With further investigation we discovered the miR-200 family is required for CMs differentiation. I-200 CMs have increased expression of cardiac progenitor markers Nkx2.5 and Mef2c compared to Wild-Type. As these cardiogenic transcription factors target DNA elements required for the maintenance of the CM transcriptome and identity, our data suggests the miR-200 family acts in this process. Concurrent single nuclei multiomics sequencing revealed changes in CM transcription and open chromatin to provided corresponding evidence to support this conclusion. Conclusions: The miR-200 family is a modulator of cardiogenic TFs expression and activity during development. Future directions will determine the role of miR- 200 in adult cardiac disease, such as ischemic injury. Our work provides new insights into gene dosage, modulated by miRs, that is required and necessary during cardiac development.

Abstract P1098: Molecular Maturation Of Engrafted Human Pluripotent Stem Cell-derived Cardiomyocytes

The transplantation of human pluripotent stem cell derived cardiomyocytes (hPSC-CMs) represents an attractive strategy to regenerate myocardium lost following injury and mitigate the pathological remodeling that ultimately leads to heart failure. However, in vitro hPSC-CMs have an immature phenotype that likely contributes to the transient arrhythmias observed during the initial weeks following hPSC-CM transplantation in large-animal models, hindering safe translation into the clinic. We hypothesized that maturational changes in hPSC-CMs in vivo facilitate the improved electrophysiological behavior of graft tissue observed at later time-points. Because the changing phenotype of hPSC-CM graft tissue remains largely unexplored, we used single nucleus RNA sequencing to evaluate the transcriptional dynamics and cell population heterogeneity of hPSC-CMs prior to transplantation and at 2- and 8-weeks following transplantation in a guinea pig cardiac cryoinjury model (n=3). We used methods based on the sorting of nuclei labeled by a genetically-encoded fluorescent reporter to enrich the proportion of human nuclei sequenced from the graft site and created a comprehensive atlas (> 20,000 cells) of host and graft cells present at the implantation site at both time-points. We identified an upregulation of genes involved in intracellular calcium handling, AMPK, and cAMP signaling pathways, as well as a metabolic shift in engrafted hPSC-CMs that we speculate supports their growth and enhanced electrophysiological function. Our study includes a comprehensive description of the temporal changes in hPSC-CM graft tissue at the single-cell resolution and provides unique insights into how these cells adapt to the injured heart environment and mature in vivo.

Revealing Temperature-Dependent Oxidation Dynamics of Ni Nanoparticles via Ambient Pressure Transmission Electron Microscopy.

Understanding the oxidation mechanism of metal nanoparticles under ambient pressure is extremely important to make the best use of them in a variety of applications. Through ambient pressure transmission electron microscopy, we in situ investigated the dynamic oxidation processes of Ni nanoparticles at different temperatures under atmospheric pressure, and a temperature-dependent oxidation behavior was revealed. At a relatively low temperature (e.g., 600 °C), the oxidation of Ni nanoparticles underwent a classic Kirkendall process, accompanied by the formation of oxide shells. In contrast, at a higher temperature (e.g., 800 °C), the oxidation began with a single crystal nucleus at the metal surface and then proceeded along the metal/oxide interface without voids formed during the whole process. Through our experiments and density functional theory calculations, a temperature-dependent oxidation mechanism based on Ni nanoparticles was proposed, which was derived from the discrepancy of gas adsorption and diffusion rates under different temperatures.

Human Alzheimer’s disease reactive astrocytes exhibit a loss of homeostastic gene expression

Astrocytes are one of the brain’s major cell types and are responsible for maintaining neuronal homeostasis via regulating the extracellular environment, providing metabolic support, and modulating synaptic activity. In neurodegenerative diseases, such as Alzheimer’s disease, astrocytes can take on a hypertrophic appearance. These reactive astrocytes are canonically associated with increases in cytoskeletal proteins, such as glial fibrillary acidic protein and vimentin. However, the molecular alterations that characterize astrocytes in human disease tissues have not been extensively studied with single cell resolution. Using single nucleus RNA sequencing data from normal, pathologic aging, and Alzheimer’s disease brains, we identified the transcriptomic changes associated with reactive astrocytes. Deep learning-based clustering algorithms denoised expression data for 17,012 genes and clustered 15,529 astrocyte nuclei, identifying protoplasmic, gray matter and fibrous, white matter astrocyte clusters. RNA trajectory analyses revealed a spectrum of reactivity within protoplasmic astrocytes characterized by a modest increase of reactive genes and a marked decrease in homeostatic genes. Amyloid but not tau pathology correlated with astrocyte reactivity. To identify reactivity-associated genes, linear regressions of gene expression versus reactivity were used to identify the top 52 upregulated and 144 downregulated genes. Gene Ontology analysis revealed that upregulated genes were associated with cellular growth, responses to metal ions, inflammation, and proteostasis. Downregulated genes were involved in cellular interactions, neuronal development, ERBB signaling, and synapse regulation. Transcription factors were significantly enriched among the downregulated genes. Using co-immunofluorescence staining of Alzheimer’s disease brain tissues, we confirmed pathologic downregulation of ERBB4 and transcription factor NFIA in reactive astrocytes. Our findings reveal that protoplasmic, gray matter astrocytes in Alzheimer’s disease exist within a spectrum of reactivity that is marked by a strong loss of normal function.

MEKiAUTO: A multicenter phase 1 study of combination therapy with the MEK inhibitor, cobimetinib, immune checkpoint blockade, atezolizumab, and the autophagy inhibitor hydroxychloroquine (HCQ) in KRAS-mutated advanced malignancies.

45 Background: Autophagy, a catabolic cell survival process, is upregulated when cancer cells undergo MEK inhibition (MEKi) in preclinical models of pancreas adenocarcinoma (PDAC), and may function as a pathway of resistance. Simultaneous inhibition of the MEK and autophagy pathway in preclinical PDAC models has demonstrated anti-tumor and immune modulating effects. MEKiAUTO evaluated the tolerability and safety of combination cobimetinib, HCQ, and atezolizumab at three dose levels (DL), in advanced KRAS-mutated malignancies. Methods: This multicenter phase I study used the time-to-event continual reassessment method (TITE-CRM) with the primary objective of estimating the maximum tolerated dose (MTD) of the combination of cobimetinib (DL1 and DL2: 40mg; DL3: 60mg PO daily; on days 1-21); HCQ (DL1-DL3: 600mg PO BID), without (DL1) or with (DL2 and DL3) atezolizumab (840mg IV on days 1 and 15) every 28 days, in patients with advanced KRAS-mutated malignancies who had received at least one prior line of therapy (N=18). The secondary objective was to evaluate safety. Exploratory analysis included interrogating the MEK, autophagy, and key molecular pathways. Results: A total of 14 patients with PDAC were enrolled at Columbia University and Brown University between 02/24/20 through 03/15/22. The median age was 58, 57% were female. Of the 10 evaluable patients for dose limiting toxicity ((DLT); >80% drug adherence and ≥4 week of follow-up), 4 experienced a DLT (3 out of 8 at DL1 and 1 out of 2 at DL2). The estimated MTD is dose level 1 with an estimated probability of DLT 0.37. Grade 3 or higher treatment-related adverse events occurred in 7 of 14 (50%) patients with elevation in AST and ALT (14%), acute kidney injury, hypokalemia, anemia, rash, and CPK increase (7% each). One grade 5 multi-organ failure and acute kidney injury occurred at DL1 possibly related to cobimetinib. Clinical benefit was observed in 5 of 14 (36%) patients, all of whom experienced stable disease as best response. The median PFS and OS for overall population was 7.7 weeks (95%CI: 6-NA) and 20.7 weeks (95%CI: 15.6-46.1). Patients with KRASG12R (N=7) had a trend toward longer OS (mOS: 20.9 vs 16.4 weeks) than patients with KRASnon-G12R mutations (N=7). Correlative analysis on paired tumor specimens using single nucleus RNAseq, multiplex immunofluorescence, and pathway analysis will discuss putative mechanisms of resistance. Conclusions: Combination cobimetinib, HCQ and atezolizumab had limited tolerability and efficacy in advanced KRAS-mutated PDAC. Patients with KRASG12R had a trend towards improved OS versus KRASnon-G12R mutations. Correlative analysis for pharmacodynamic and resistance mechanisms will be discussed. Funding: Roche-Genentech. Clinical trial information: NCT04214418 .

A Simple, Quick, and Partially Automated Protocol for the Isolation of Single Nuclei from Frozen Mammalian Tissues for Single Nucleus Sequencing.

Single-cell and single-nucleus RNA sequencing have become common laboratory applications due to the wealth of transcriptomic information that they provide. Single nucleus RNA sequencing, particularly, is useful for investigating gene expression in difficult-to-dissociate tissues. Furthermore, this approach is also compatible with frozen (archival) material. Here, we describe a protocol to isolate high-quality single nuclei from frozen mammalian tissues for downstream single nucleus RNA sequencing in a partially-automated manner using commercially available instruments and reagents. Specifically, a robotic dissociator is used to automate and standardize tissue homogenization, followed by an optimized chemical gradient to filter the nuclei. Lastly, we accurately and automatically count the nuclei using an automated fluorescent cell counter. The performance of this protocol is demonstrated on mouse brain, rat kidney, and cynomolgus liver and spleen tissue. This protocol is straightforward, rapid, and readily adaptable to various mammalian tissues without requiring extensive optimization and provides good quality nuclei for downstream single nuclei RNA sequencing.

Transcriptomic analysis of paired healthy human skeletal muscles to identify modulators of disease severity in DMD.

Muscle damage and fibro-fatty replacement of skeletal muscles is a main pathologic feature of Duchenne muscular dystrophy (DMD) with more proximal muscles affected earlier and more distal affected later in the disease course, suggesting that different skeletal muscle groups possess distinctive characteristics that influence their susceptibility to disease. To explore transcriptomic factors driving differential gene expression and modulating DMD skeletal muscle severity, we characterized the transcriptome of vastus lateralis (VL), a more proximal and susceptible muscle, relative to tibialis anterior (TA), a more distal and protected muscle, in 15 healthy individuals using bulk RNA sequencing to identify gene expression differences that may mediate their relative susceptibility to damage with loss of dystrophin. Matching single nuclei RNA sequencing data was generated for 3 of the healthy individuals, to infer cell composition in the bulk RNA sequencing dataset and to improve mapping of differentially expressed genes to their cell source of expression. A total of 3,410 differentially expressed genes were identified and mapped to cell type using single nuclei RNA sequencing of muscle, including long non-coding RNAs and protein coding genes. There was an enrichment of genes involved in calcium release from the sarcoplasmic reticulum, particularly in the myofibers and these myofiber genes were higher in the VL. There was an enrichment of genes in "Collagen-Containing Extracellular Matrix" expressed by fibroblasts, endothelial, smooth muscle and pericytes, with most genes higher in the TA, as well as genes in "Regulation Of Apoptotic Process" expressed across all cell types. Previously reported genetic modifiers were also enriched within the differentially expressed genes. We also identify 6 genes with differential isoform usage between the VL and TA. Lastly, we integrate our findings with DMD RNA sequencing data from the TA, and identify "Collagen-Containing Extracellular Matrix" and "Negative Regulation Of Apoptotic Process" as differentially expressed between DMD compared to healthy. Collectively, these findings propose novel candidate mechanisms that may mediate differential muscle susceptibility in muscular dystrophies and provide new insight into potential therapeutic targets.

Dopamine release and negative valence gated by inhibitory neurons in the laterodorsal tegmental nucleus

GABAergic neurons in the laterodorsal tegmental nucleus (LDTGABA) encode aversion by directly inhibiting mesolimbic dopamine (DA). Yet, the detailed cellular and circuit mechanisms by which these cells relay unpleasant stimuli to DA neurons and regulate behavioral output remain largely unclear. Here, we show that LDTGABA neurons bidirectionally respond to rewarding and aversive stimuli in mice. Activation of LDTGABA neurons promotes aversion and reduces DA release in the lateral nucleus accumbens. Furthermore, we identified two molecularly distinct LDTGABA cell populations. Somatostatin-expressing (Sst+) LDTGABA neurons indirectly regulate the mesolimbic DA system by disinhibiting excitatory hypothalamic neurons. In contrast, Reelin-expressing LDTGABA neurons directly inhibit downstream DA neurons. The identification of separate GABAergic subpopulations in a single brainstem nucleus that relay unpleasant stimuli to the mesolimbic DA system through direct and indirect projections is critical for establishing a circuit-level understanding of how negative valence is encoded in the mammalian brain.

Discrimination of early HCC using single cell nucleus image and visualization of feature distribution in whole slide images.

Among hepatocellular carcinoma (HCC), early HCC such as well-differentiated hepatocellular carcinoma is more difficult to distinguish from non-cancer than other cancers. In particular, very well-differentiated hepatocellular carcinoma is even more difficult to distinguish, and it is difficult for pathologists to distinguish between cancer and non-cancer from a single nucleus image. If a function to distinguish cancer with a single cell nucleus image is realized, it may be possible to find new features related to nuclei that are useful for differentiating early HCC. The function will also be very helpful in needle biopsy where the area that can be observed is limited.In this study, we investigated the potential to discriminate cancer/non-cancer from an image of a single hepatocyte nucleus using CNN. The results indicated that discrimination was achievable with a correct rate of around 70%.The probability of cancer/non-cancer was visualized on WSI. The visualization results indicated a difference between cancerous and non-cancerous areas in 71% of the cases, which will help pathologists distinguish region of interest. Grouping sections with similar features also proved useful in improving accuracy and visualization results.

Revealing the polar lipidome, pigment profiles, and antioxidant activity of the giant unicellular green alga, Acetabularia acetabulum.

Marine algae are one of the most important sources of high-value compounds such as polar lipids, omega-3 fatty acids, photosynthetic pigments, or secondary metabolites with interesting features for different niche markets. Acetabularia acetabulum is a macroscopic green single-celled alga, with a single nucleus hosted in the rhizoid. This alga is one of the most studied dasycladalean species and represents an important model system in cell biology studies. However, its lipidome and pigment profile have been overlooked. Total lipid extracts were analyzed using hydrophilic interaction liquid chromatography-high resolution mass spectrometry (HILIC-HRMS), tandem mass spectrometry (MS/MS), and high-performance liquid chromatography (HPLC). The antioxidant capacity of lipid extracts was tested using DPPH and ABTS assays. Lipidomics identified 16 polar lipid classes, corresponding to glycolipids, betaine lipids, phospholipids, and sphingolipids, with a total of 191 lipid species, some of them recognized by their bioactivities. The most abundant polar lipids were glycolipids. Lipid classes less studied in algae were identified, such as diacylglyceryl-carboxyhydroxymethylcholine (DGCC) or hexosylceramide (HexCer). The pigment profile of A. acetabulum comprised carotenoids (17.19%), namely cis-neoxanthin, violaxanthin, lutein and β,β-carotene, and chlorophylls a and b (82.81%). A. acetabulum lipid extracts showed high antioxidant activity promoting a 50% inhibition (IC50 ) with concentrations of 57.91 ± 1.20 μg · mL-1 (438.18 ± 8.95 μmol Trolox · g-1 lipid) in DPPH and 20.55 ± 0.60 μg · mL-1 in ABTS assays (918.56 ± 27.55 μmol Trolox · g-1 lipid). This study demonstrates the potential of A. acetabulum as a source of natural bioactive molecules and antioxidant compounds.

Localization of the Drosophila pioneer factor GAF to subnuclear foci is driven by DNA binding and required to silence satellite repeat expression

The eukaryotic genome is organized to enable the precise regulation of gene expression. This organization is established as the embryo transitions from a fertilized gamete to a totipotent zygote. To understand the factors and processes that drive genomic organization, we focused on the pioneer factor GAGA factor (GAF) that is required for early development in Drosophila. GAF transcriptionally activates the zygotic genome and is localized to subnuclear foci. This non-uniform distribution is driven by binding to highly abundant GA repeats. At GA repeats, GAF is necessary to form heterochromatin and silence transcription. Thus, GAF is required to establish both active and silent regions. We propose that foci formation enables GAF to have opposing transcriptional roles within a single nucleus. Our data support a model in which the subnuclear concentration of transcription factors acts to organize the nucleus into functionally distinct domains essential for the robust regulation of gene expression.

New hypotheses of cell type diversity and novelty from orthology-driven comparative single cell and nuclei transcriptomics in echinoderms.

Cell types are the building blocks of metazoan biodiversity and offer a powerful perspective for inferring evolutionary phenomena. With the development of single-cell transcriptomic techniques, new definitions of cell types are emerging. This allows a conceptual reassessment of traditional definitions of novel cell types and their evolution. Research in echinoderms, particularly sea star and sea urchin embryos has contributed significantly to understanding the evolution of novel cell types, through the examination of skeletogenic mesenchyme and pigment cells, which are found in sea urchin larvae, but not sea star larvae. This paper outlines the development of a gene expression atlas for the bat sea star, Patiria miniata, using single nuclear RNA sequencing (snRNA-seq) of embryonic stages. The atlas revealed 23 cell clusters covering all expected cell types from the endoderm, mesoderm, and ectoderm germ layers. In particular, four distinct neural clusters, an immune-like cluster, and distinct right and left coelom clusters were revealed as distinct cell states. A comparison with Strongylocentrotus purpuratus embryo single-cell transcriptomes was performed using 1:1 orthologs to anchor and then compare gene expression patterns. The equivalent of S. purpuratus piwil3+ Cells were not detected in P. miniata, while the Left Coelom of P. miniata has no equivalent cell cluster in S. purpuratus. These differences may reflect changes in developmental timing between these species. While considered novel morphologically, the Pigment Cells of S. purpuratus map to clusters containing Immune-like Mesenchyme and Neural cells of P. miniata, while the Skeletogenic Mesenchyme of S. purpuratus are revealed as orthologous to the Right Coelom cluster of P. miniata. These results suggest a new interpretation of the evolution of these well-studied cell types and a reflection on the definition of novel cell types.

Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury

Physical exercise represents a potentially inexpensive, accessible, and optimizable rehabilitation approach to traumatic brain injury (TBI) recovery. However, little is known about the impact of post-injury exercise on the neurometabolic, transcriptional, and cognitive outcomes following a TBI. In the current study, we examined TBI outcomes in adolescent male and female mice following a controlled cortical impact (CCI) injury. Mice underwent a 10-day regimen of sedentary, low-, moderate-, or high-intensity treadmill exercise and were assessed for cognitive function, histopathology, mitochondrial function, and oxidative stress. Among male mice, low-moderate exercise improved cognitive recovery, and reduced cortical lesion volume and oxidative stress, whereas high-intensity exercise impaired both cognitive recovery and mitochondrial function. On the other hand, among female mice, exercise had an intermediate effect on cognitive recovery but significantly improved brain mitochondrial function. Moreover, single nuclei RNA sequencing of perilesional brain tissue revealed neuronal plasticity-related differential gene expression that was largely limited to the low-intensity exercise injured males. Taken together, these data build on previous reports of the neuroprotective capacity of exercise in a TBI model, and reveal that this rehabilitation strategy impacts neurometabolic, functional, and transcriptional outcome measures in an intensity- and sex-dependent manner.

Opposing gene regulatory programs governing myofiber development and maturation revealed at single nucleus resolution

Skeletal muscle fibers express distinct gene programs during development and maturation, but the underlying gene regulatory networks that confer stage-specific myofiber properties remain unknown. To decipher these distinctive gene programs and how they respond to neural activity, we generated a combined multi-omic single-nucleus RNA-seq and ATAC-seq atlas of mouse skeletal muscle development at multiple stages of embryonic, fetal, and postnatal life. We found that Myogenin, Klf5, and Tead4 form a transcriptional complex that synergistically activates the expression of muscle genes in developing myofibers. During myofiber maturation, the transcription factor Maf acts as a transcriptional switch to activate the mature fast muscle gene program. In skeletal muscles of mutant mice lacking voltage-gated L-type Ca2+ channels (Cav1.1), Maf expression and myofiber maturation are impaired. These findings provide a transcriptional atlas of muscle development and reveal genetic links between myofiber formation, maturation, and contraction.

Single Cell Multiomics Identifies Cells and Genetic Networks Underlying Alveolar Capillary Dysplasia.

Rationale: Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a lethal developmental disorder of lung morphogenesis caused by insufficiency of FOXF1 (forkhead box F1) transcription factor function. The cellular and transcriptional mechanisms by which FOXF1 deficiency disrupts human lung formation are unknown. Objectives: To identify cell types, gene networks, and cell-cell interactions underlying the pathogenesis of ACDMPV. Methods: We used single-nucleus RNA and assay for transposase-accessible chromatin sequencing, immunofluorescence confocal microscopy, and RNA in situ hybridization to identify cell types and molecular networks influenced by FOXF1 in ACDMPV lungs. Measurements and Main Results: Pathogenic single-nucleotide variants and copy-number variant deletions involving the FOXF1 gene locus in all subjects with ACDMPV (n = 6) were accompanied by marked changes in lung structure, including deficient alveolar development and a paucity of pulmonary microvasculature. Single-nucleus RNA and assay for transposase-accessible chromatin sequencing identified alterations in cell number and gene expression in endothelial cells (ECs), pericytes, fibroblasts, and epithelial cells in ACDMPV lungs. Distinct cell-autonomous roles for FOXF1 in capillary ECs and pericytes were identified. Pathogenic variants involving the FOXF1 gene locus disrupt gene expression in EC progenitors, inhibiting the differentiation or survival of capillary 2 ECs and cell-cell interactions necessary for both pulmonary vasculogenesis and alveolar type 1 cell differentiation. Loss of the pulmonary microvasculature was associated with increased VEGFA (vascular endothelial growth factor A) signaling and marked expansion of systemic bronchial ECs expressing COL15A1 (collagen type XV α 1 chain). Conclusions: Distinct FOXF1 gene regulatory networks were identified in subsets of pulmonary endothelial and fibroblast progenitors, providing both cellular and molecular targets for the development of therapies for ACDMPV and other diffuse lung diseases of infancy.

Anatomical and molecular characterization of parvalbumin-cholecystokinin co-expressing inhibitory interneurons: implications for neuropsychiatric conditions.

Inhibitory interneurons are crucial to brain function and their dysfunction is implicated in neuropsychiatric conditions. Emerging evidence indicates that cholecystokinin (CCK)-expressing interneurons (CCK+) are highly heterogenous. We find that a large subset of parvalbumin-expressing (PV+) interneurons express CCK strongly;between 40 and 56% of PV+ interneurons in mouse hippocampal CA1express CCK. Primate interneurons also exhibit substantial PV/CCK co-expression. Mouse PV+/CCK+ and PV+/CCK- cells show distinguishable electrophysiological and molecular characteristics. Analysis of single nuclei RNA-seq and ATAC-seq data shows that PV+/CCK+ cells are a subset of PV+ cells, not of synuclein gamma positive (SNCG+) cells, and that they strongly express oxidative phosphorylation (OXPHOS) genes. We find that mitochondrial complex I and IV-associated OXPHOS gene expression isstrongly correlated with CCK expression in PV+ interneurons at both the transcriptomic and protein levels. Both PV+ interneurons and dysregulation of OXPHOS processes are implicated in neuropsychiatric conditions, including autism spectrum (ASD) disorder and schizophrenia(SCZ). Analysis of human brain samples from patients with these conditions shows alterations in OXPHOS gene expression. Together these data reveal important molecular characteristics of PV-CCK co-expressing interneurons and support their implication in neuropsychiatric conditions.

Developmental dynamics of the single nucleus regulatory landscape of pig hippocampus.

The hippocampus is a brain region associated with memory, learning and spatial navigation, its aging-related dysfunction is a common sign of Alzheimer's disease. Pig is a good model for human neurodegenerative disease, but our understanding of the regulatory program of the pig hippocampus and its cross-species conservation in humans remains limited. Here, we profiled chromatin accessibility in 33,409 high-quality nuclei and gene expression in 8,122 high-quality nuclei of the pig hippocampus at four postnatal stages. We identified 510,908 accessible chromatin regions (ACRs) in 12 major cell types, among which progenitor cells such as neuroblasts and oligodendrocyte progenitor cells showed a dynamic decrease from early to later developmental stages. We revealed significant enrichment of transposable elements in cell type-specific ACRs, particularly in neuroblasts. We identified oligodendrocytes as the most prominent cell type with the greatest number of genes that showed significant changes during the development. We identified ACRs and key transcription factors underlying the trajectory of neurogenesis (such as POU3F3 and EGR1) and oligodendrocyte differentiation (RXRA and FOXO6). We examined 27 Alzheimer's disease-related genes in our data and found that 15 showed cell type-specific activity (TREM2, RIN3 and CLU), and 15 genes displayed age-associated dynamic activity (BIN1, RABEP1 and APOE). We intersected our data with human genome-wide association study results to detect neurological disease-associated cell types. The present study provides a single nucleus-accessible chromatin landscape of the pig hippocampus at different developmental stages and is helpful for the exploration of pigs as a biomedical model in human neurodegenerative diseases.

Cytopathology of benign sebaceous salivary gland neoplasia: Comparison of two analogous yet dissimilar entities.

Benign sebaceous salivary gland (SG) neoplasms represent approximately 0.2% of all salivary gland neoplasms. Not only are fine needle aspiration (FNA) biopsy findings of sebaceous adenoma (SA) and sebaceous lymphadenoma (SLA) limited, but their findings are also rarely compared with one another. Our cytopathology files were searched for examples of benign sebaceous SG neoplasms with concomitant histopathological verification. FNA biopsy and cell collection were performed using standard technique. One case each of parotid SA and parotid SLA showed markedly dissimilar cytomorphology. The SA case was composed of a repetitive population of profusely multivacuolated polygonal cells with single and multiple nuclei, and was specifically recognised cytologically as a sebaceous neoplasm due to its characteristic cytoplasmic vacuolisation. The SLA case, however, was characterised by smears filled primarily with lymphocytes and only scant widely scattered basaloid cell clusters. A non-specific diagnosis of basaloid neoplasm was rendered. In retrospect, recognition of sebaceous differentiation was limited to rare cell groups. Though nominally, epidemiologically, and to a degree histopathologically analogous, the cytopathology of SA and SLA are markedly dissimilar, reflecting the dominant cell component in each. With FNA biopsy, a specific interpretation is more likely for SA than SLA due to the overwhelming obscuring lymphoid population in the latter.