1
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Liu X, Wang H, Gao J. scIALM: A method for sparse scRNA-seq expression matrix imputation using the Inexact Augmented Lagrange Multiplier with low error. Comput Struct Biotechnol J 2024; 23:549-558. [PMID: 38274995 PMCID: PMC10809077 DOI: 10.1016/j.csbj.2023.12.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/27/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) is a high-throughput sequencing technology that quantifies gene expression profiles of specific cell populations at the single-cell level, providing a foundation for studying cellular heterogeneity and patient pathological characteristics. It is effective for developmental, fertility, and disease studies. However, the cell-gene expression matrix of single-cell sequencing data is often sparse and contains numerous zero values. Some of the zero values derive from noise, where dropout noise has a large impact on downstream analysis. In this paper, we propose a method named scIALM for imputation recovery of sparse single-cell RNA data expression matrices, which employs the Inexact Augmented Lagrange Multiplier method to use sparse but clean (accurate) data to recover unknown entries in the matrix. We perform experimental analysis on four datasets, calling the expression matrix after Quality Control (QC) as the original matrix, and comparing the performance of scIALM with six other methods using mean squared error (MSE), mean absolute error (MAE), Pearson correlation coefficient (PCC), and cosine similarity (CS). Our results demonstrate that scIALM accurately recovers the original data of the matrix with an error of 10e-4, and the mean value of the four metrics reaches 4.5072 (MSE), 0.765 (MAE), 0.8701 (PCC), 0.8896 (CS). In addition, at 10%-50% random masking noise, scIALM is the least sensitive to the masking ratio. For downstream analysis, this study uses adjusted rand index (ARI) and normalized mutual information (NMI) to evaluate the clustering effect, and the results are improved on three datasets containing real cluster labels.
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Affiliation(s)
- Xiaohong Liu
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Han Wang
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jingyang Gao
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
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2
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Li D, Mei Q, Li G. scQA: A dual-perspective cell type identification model for single cell transcriptome data. Comput Struct Biotechnol J 2024; 23:520-536. [PMID: 38235363 PMCID: PMC10791572 DOI: 10.1016/j.csbj.2023.12.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 01/19/2024] Open
Abstract
Single-cell RNA sequencing technologies have been pivotal in advancing the development of algorithms for clustering heterogeneous cell populations. Existing methods for utilizing scRNA-seq data to identify cell types tend to neglect the beneficial impact of dropout events and perform clustering focusing solely on quantitative perspective. Here, we introduce a novel method named scQA, notable for its ability to concurrently identify cell types and cell type-specific key genes from both qualitative and quantitative perspectives. In contrast to other methods, scQA not only identifies cell types but also extracts key genes associated with these cell types, enabling bidirectional clustering for scRNA-seq data. Through an iterative process, our approach aims to minimize the number of landmarks to approximately a dozen while maximizing the inclusion of quasi-trend-preserved genes with dropouts both qualitatively and quantitatively. It then clusters cells by employing an ingenious label propagation strategy, obviating the requirement for a predetermined number of cell types. Validated on 20 publicly available scRNA-seq datasets, scQA consistently outperforms other salient tools. Furthermore, we confirm the effectiveness and potential biological significance of the identified key genes through both external and internal validation. In conclusion, scQA emerges as a valuable tool for investigating cell heterogeneity due to its distinctive fusion of qualitative and quantitative facets, along with bidirectional clustering capabilities. Furthermore, it can be seamlessly integrated into border scRNA-seq analyses. The source codes are publicly available at https://github.com/LD-Lyndee/scQA.
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Affiliation(s)
- Di Li
- Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao 266237, China
| | - Qinglin Mei
- MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Guojun Li
- Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao 266237, China
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3
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Grobecker P, Sakoparnig T, van Nimwegen E. Identifying cell states in single-cell RNA-seq data at statistically maximal resolution. PLoS Comput Biol 2024; 20:e1012224. [PMID: 38995959 DOI: 10.1371/journal.pcbi.1012224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 06/04/2024] [Indexed: 07/14/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has become a popular experimental method to study variation of gene expression within a population of cells. However, obtaining an accurate picture of the diversity of distinct gene expression states that are present in a given dataset is highly challenging because the sparsity of the scRNA-seq data and its inhomogeneous measurement noise properties. Although a vast number of different methods is applied in the literature for clustering cells into subsets with 'similar' expression profiles, these methods generally lack rigorously specified objectives, involve multiple complex layers of normalization, filtering, feature selection, dimensionality-reduction, employ ad hoc measures of distance or similarity between cells, often ignore the known measurement noise properties of scRNA-seq measurements, and include a large number of tunable parameters. Consequently, it is virtually impossible to assign concrete biophysical meaning to the clusterings that result from these methods. Here we address the following problem: Given raw unique molecule identifier (UMI) counts of an scRNA-seq dataset, partition the cells into subsets such that the gene expression states of the cells in each subset are statistically indistinguishable, and each subset corresponds to a distinct gene expression state. That is, we aim to partition cells so as to maximally reduce the complexity of the dataset without removing any of its meaningful structure. We show that, given the known measurement noise structure of scRNA-seq data, this problem is mathematically well-defined and derive its unique solution from first principles. We have implemented this solution in a tool called Cellstates which operates directly on the raw data and automatically determines the optimal partition and cluster number, with zero tunable parameters. We show that, on synthetic datasets, Cellstates almost perfectly recovers optimal partitions. On real data, Cellstates robustly identifies subtle substructure within groups of cells that are traditionally annotated as a common cell type. Moreover, we show that the diversity of gene expression states that Cellstates identifies systematically depends on the tissue of origin and not on technical features of the experiments such as the total number of cells and total UMI count per cell. In addition to the Cellstates tool we also provide a small toolbox of software to place the identified cellstates into a hierarchical tree of higher-order clusters, to identify the most important differentially expressed genes at each branch of this hierarchy, and to visualize these results.
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Affiliation(s)
- Pascal Grobecker
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Thomas Sakoparnig
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Erik van Nimwegen
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
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4
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Schäfer F, Tomar A, Sato S, Teperino R, Imhof A, Lahiri S. Enhanced in situ spatial proteomics by effective combination of MALDI imaging and LC-MS/MS. Mol Cell Proteomics 2024:100811. [PMID: 38996918 DOI: 10.1016/j.mcpro.2024.100811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 06/13/2024] [Accepted: 07/08/2024] [Indexed: 07/14/2024] Open
Abstract
Highly specialized cells are fundamental for proper functioning of complex organs. Variations in cell-type specific gene expression and protein composition have been linked to a variety of diseases. Investigation of the distinctive molecular makeup of these cells within tissues is therefore critical in biomedical research. Although several technologies have emerged as valuable tools to address this cellular heterogeneity, most workflows lack sufficient in situ resolution and are associated with high cost and extremely long analysis times. Here, we present a combination of experimental and computational approaches that allows a more comprehensive investigation of molecular heterogeneity within tissues than by either shotgun LC-MS/MS or MALDI imaging alone. We applied our pipeline on mouse brain, which contains a wide variety of cell types that not only perform unique functions but also exhibit varying sensitivities to insults. We explored the distinct neuronal populations within the hippocampus, a brain region crucial for learning and memory that is involved in various neurological disorders. As an example, we identified the groups of proteins distinguishing the neuronal populations of dentate gyrus (DG) and the cornu ammonis (CA) in the same brain section. Most of the annotated proteins matched the regional enrichment of their transcripts, thereby validating the method. As the method is highly reproducible, the identification of individual masses through the combination of MALDI-IMS and LC-MS/MS methods can be used for the much faster and more precise interpretation of MALDI-IMS measurements only. This greatly speeds up spatial proteomic analyses and allows the detection of local protein variations within the same population of cells. The method's general applicability has the potential to be used to investigate different biological conditions and tissues and a much higher throughput than other techniques making it a promising approach for clinical routine applications.
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Affiliation(s)
- Frederike Schäfer
- Biomedical Center Munich, Department of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany; Biomedical Center Munich, Protein Analysis Unit, Faculty of Medicine, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany; Institute for Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD) - Neuherberg, Germany
| | - Archana Tomar
- Institute for Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD) - Neuherberg, Germany
| | - Shogo Sato
- Center for Biological Clocks Research, Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Raffaele Teperino
- Institute for Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD) - Neuherberg, Germany
| | - Axel Imhof
- Biomedical Center Munich, Department of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany; Biomedical Center Munich, Protein Analysis Unit, Faculty of Medicine, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany.
| | - Shibojyoti Lahiri
- Biomedical Center Munich, Department of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany; Biomedical Center Munich, Protein Analysis Unit, Faculty of Medicine, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany.
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5
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Zacharjasz J, Sztachera M, Smuszkiewicz M, Piwecka M. Micromanaging the neuroendocrine system - A review on miR-7 and the other physiologically relevant miRNAs in the hypothalamic-pituitary axis. FEBS Lett 2024; 598:1557-1575. [PMID: 38858179 DOI: 10.1002/1873-3468.14948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/12/2024]
Abstract
The hypothalamic-pituitary axis is central to the functioning of the neuroendocrine system and essential for regulating physiological and behavioral homeostasis and coordinating fundamental body functions. The expanding line of evidence shows the indispensable role of the microRNA pathway in regulating the gene expression profile in the developing and adult hypothalamus and pituitary gland. Experiments provoking a depletion of miRNA maturation in the context of the hypothalamic-pituitary axis brought into focus a prominent involvement of miRNAs in neuroendocrine functions. There are also a few individual miRNAs and miRNA families that have been studied in depth revealing their crucial role in mediating the regulation of fundamental processes such as temporal precision of puberty timing, hormone production, fertility and reproduction capacity, and energy balance. Among these miRNAs, miR-7 was shown to be hypothalamus-enriched and the top one highly expressed in the pituitary gland, where it has a profound impact on gene expression regulation. Here, we review miRNA profiles, knockout phenotypes, and miRNA interaction (targets) in the hypothalamic-pituitary axis that advance our understanding of the roles of miRNAs in mammalian neurosecretion and related physiology.
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Affiliation(s)
- Julian Zacharjasz
- Department of Non-coding RNAs, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Marta Sztachera
- Department of Non-coding RNAs, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Michał Smuszkiewicz
- Department of Non-coding RNAs, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Monika Piwecka
- Department of Non-coding RNAs, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
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6
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Dardente H, Lomet D, Robert V, Lasserre O, Gonzalez AA, Mialhe X, Beltramo M. Photoperiod, but not progesterone, has a strong impact upon the transcriptome of the medio-basal hypothalamus in female goats and ewes. Mol Cell Endocrinol 2024; 588:112216. [PMID: 38556161 DOI: 10.1016/j.mce.2024.112216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 03/11/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024]
Abstract
Photoperiod is the main environmental driver of seasonal responses in organisms living at temperate and polar latitudes. Other external cues such as food and temperature, and internal cues including hormones, intervene to fine-tune phasing of physiological functions to the solar year. In mammals, the medio-basal hypothalamus (MBH) is the key integrator of these cues, which orchestrates a wide array of seasonal functions, including breeding. Here, using RNAseq and RT-qPCR, we demonstrate that molecular components of the photoperiodic response previously identified in ewes are broadly conserved in does (female goats, Capra hircus), with a common core of ∼50 genes. This core group can be defined as the "MBH seasonal trancriptome", which includes key players of the pars tuberalis-tanycytes neuroendocrine retrograde pathway that governs intra-MBH photoperiodic switches of triiodothyronine (T3) production (Tshb, Eya3, Dio2 and SlcO1c1), the two histone methyltransferases Suv39H2 and Ezh2 and the secreted protein Vmo1. Prior data in ewes revealed that T3 and estradiol (E2), both key hormones for the proper timing of seasonal breeding, differentially impact the MBH seasonal transcriptome, and identified cellular and molecular targets through which these hormones might act. In contrast, information regarding the potential impact of progesterone (P4) upon the MBH transcriptome was nonexistent. Here, we demonstrate that P4 has no discernible transcriptional impact in either does or ewes. Taken together, our data show that does and ewes possess a common core set of photoperiod-responsive genes in the MBH and conclusively demonstrate that P4 is not a key regulator of the MBH transcriptome.
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Affiliation(s)
- Hugues Dardente
- INRAE, CNRS, Université de Tours, PRC, 37380, Nouzilly, France.
| | - Didier Lomet
- INRAE, CNRS, Université de Tours, PRC, 37380, Nouzilly, France
| | - Vincent Robert
- INRAE, CNRS, Université de Tours, PRC, 37380, Nouzilly, France
| | | | - Anne-Alicia Gonzalez
- MGX-Montpellier GenomiX, Univ. Montpellier, CNRS, INSERM, 34094, Montpellier, France
| | - Xavier Mialhe
- MGX-Montpellier GenomiX, Univ. Montpellier, CNRS, INSERM, 34094, Montpellier, France
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7
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Chen S, Xing L, Xie Z, Zhao M, Yu H, Gan J, Zhao H, Ma Z, Li H. Single-cell transcriptomic reveals a cell atlas and diversity of chicken amygdala responded to social hierarchy. iScience 2024; 27:109880. [PMID: 38952686 PMCID: PMC11215297 DOI: 10.1016/j.isci.2024.109880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/29/2024] [Accepted: 04/29/2024] [Indexed: 07/03/2024] Open
Abstract
Amygdala serves as a highly cellular, heterogeneous brain region containing excitatory and inhibitory neurons and is involved in the dopamine and serotoninergic neuron systems. An increasing number of studies have revealed the underpinned mechanism mediating social hierarchy in mammal and vertebrate, however, there are rare studies conducted on how amygdala on social hierarchy in poultry. In this study, we conducted food competition tests and determined the social hierarchy of the rooster. We performed cross-species analysis with mammalian amygdala, and found that cell types of human and rhesus monkeys were more closely related and that of chickens were more distant. We identified 26 clusters and divided them into 10 main clusters, of which GABAergic and glutamatergic neurons were associated with social behaviors. In conclusion, our results provide to serve the developmental studies of the amygdala neuron system and new insights into the underpinned mechanism of social hierarchy in roosters.
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Affiliation(s)
- Siyu Chen
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528250, China
| | - Limin Xing
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528250, China
| | - Zhijiang Xie
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528250, China
| | - Mengqiao Zhao
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528250, China
| | - Hui Yu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528250, China
| | - Jiankang Gan
- Guangdong Tinoo’s FOODS Group Co., Ltd, Qingyuan 511500, China
| | - Haiquan Zhao
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528250, China
| | - Zheng Ma
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528250, China
| | - Hua Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528250, China
- Guangdong Tinoo’s FOODS Group Co., Ltd, Qingyuan 511500, China
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8
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Leal H, Carvalhas-Almeida C, Álvaro AR, Cavadas C. Modeling hypothalamic pathophysiology in vitro for metabolic, circadian, and sleep disorders. Trends Endocrinol Metab 2024; 35:505-517. [PMID: 38307813 DOI: 10.1016/j.tem.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/04/2024]
Abstract
The hypothalamus, a small and intricate brain structure, orchestrates numerous neuroendocrine functions through specialized neurons and nuclei. Disruption of this complex circuitry can result in various diseases, including metabolic, circadian, and sleep disorders. Advances in in vitro models and their integration with new technologies have significantly benefited research on hypothalamic function and pathophysiology. We explore existing in vitro hypothalamic models and address their challenges and limitations as well as translational findings. We also highlight how collaborative efforts among multidisciplinary teams are essential to develop relevant and translational experimental models capable of replicating intricate neural circuits and neuroendocrine pathways, thereby advancing our understanding of therapeutic targets and drug discovery in hypothalamus-related disorders.
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Affiliation(s)
- Helena Leal
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal; Center for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Catarina Carvalhas-Almeida
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal; Center for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Ana Rita Álvaro
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal; Center for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
| | - Cláudia Cavadas
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal; Center for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal.
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9
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Littleton SH, Trang KB, Volpe CM, Cook K, DeBruyne N, Maguire JA, Weidekamp MA, Hodge KM, Boehm K, Lu S, Chesi A, Bradfield JP, Pippin JA, Anderson SA, Wells AD, Pahl MC, Grant SFA. Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3' UTR of FAIM2. CELL GENOMICS 2024; 4:100556. [PMID: 38697123 PMCID: PMC11099382 DOI: 10.1016/j.xgen.2024.100556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 03/21/2024] [Accepted: 04/08/2024] [Indexed: 05/04/2024]
Abstract
The ch12q13 locus is among the most significant childhood obesity loci identified in genome-wide association studies. This locus resides in a non-coding region within FAIM2; thus, the underlying causal variant(s) presumably influence disease susceptibility via cis-regulation. We implicated rs7132908 as a putative causal variant by leveraging our in-house 3D genomic data and public domain datasets. Using a luciferase reporter assay, we observed allele-specific cis-regulatory activity of the immediate region harboring rs7132908. We generated isogenic human embryonic stem cell lines homozygous for either rs7132908 allele to assess changes in gene expression and chromatin accessibility throughout a differentiation to hypothalamic neurons, a key cell type known to regulate feeding behavior. The rs7132908 obesity risk allele influenced expression of FAIM2 and other genes and decreased the proportion of neurons produced by differentiation. We have functionally validated rs7132908 as a causal obesity variant that temporally regulates nearby effector genes and influences neurodevelopment and survival.
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Affiliation(s)
- Sheridan H Littleton
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Khanh B Trang
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Christina M Volpe
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kieona Cook
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Psychiatry, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nicole DeBruyne
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jean Ann Maguire
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mary Ann Weidekamp
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kenyaita M Hodge
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Keith Boehm
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sumei Lu
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alessandra Chesi
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan P Bradfield
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Quantinuum Research LLC, San Diego, CA 92101, USA
| | - James A Pippin
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Stewart A Anderson
- Department of Child and Adolescent Psychiatry, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew C Pahl
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Struan F A Grant
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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10
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Qiu Y, Yang L, Jiang H, Zou Q. scTPC: a novel semisupervised deep clustering model for scRNA-seq data. BIOINFORMATICS (OXFORD, ENGLAND) 2024; 40:btae293. [PMID: 38684178 DOI: 10.1093/bioinformatics/btae293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/14/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
MOTIVATION Continuous advancements in single-cell RNA sequencing (scRNA-seq) technology have enabled researchers to further explore the study of cell heterogeneity, trajectory inference, identification of rare cell types, and neurology. Accurate scRNA-seq data clustering is crucial in single-cell sequencing data analysis. However, the high dimensionality, sparsity, and presence of "false" zero values in the data can pose challenges to clustering. Furthermore, current unsupervised clustering algorithms have not effectively leveraged prior biological knowledge, making cell clustering even more challenging. RESULTS This study investigates a semisupervised clustering model called scTPC, which integrates the triplet constraint, pairwise constraint, and cross-entropy constraint based on deep learning. Specifically, the model begins by pretraining a denoising autoencoder based on a zero-inflated negative binomial distribution. Deep clustering is then performed in the learned latent feature space using triplet constraints and pairwise constraints generated from partial labeled cells. Finally, to address imbalanced cell-type datasets, a weighted cross-entropy loss is introduced to optimize the model. A series of experimental results on 10 real scRNA-seq datasets and five simulated datasets demonstrate that scTPC achieves accurate clustering with a well-designed framework. AVAILABILITY AND IMPLEMENTATION scTPC is a Python-based algorithm, and the code is available from https://github.com/LF-Yang/Code or https://zenodo.org/records/10951780.
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Affiliation(s)
- Yushan Qiu
- School of Mathematical Sciences, Shenzhen University, Shenzhen, Guangdong 518000, China
| | - Lingfei Yang
- School of Mathematical Sciences, Shenzhen University, Shenzhen, Guangdong 518000, China
| | - Hao Jiang
- School of Mathematics, Renmin University of China, Haidian District, Beijing 100872, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610056, China
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11
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Leon S, Simon V, Lee TH, Steuernagel L, Clark S, Biglari N, Lesté-Lasserre T, Dupuy N, Cannich A, Bellocchio L, Zizzari P, Allard C, Gonzales D, Le Feuvre Y, Lhuillier E, Brochard A, Nicolas JC, Teillon J, Nikolski M, Marsicano G, Fioramonti X, Brüning JC, Cota D, Quarta C. Single cell tracing of Pomc neurons reveals recruitment of 'Ghost' subtypes with atypical identity in a mouse model of obesity. Nat Commun 2024; 15:3443. [PMID: 38658557 PMCID: PMC11043070 DOI: 10.1038/s41467-024-47877-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 04/09/2024] [Indexed: 04/26/2024] Open
Abstract
The hypothalamus contains a remarkable diversity of neurons that orchestrate behavioural and metabolic outputs in a highly plastic manner. Neuronal diversity is key to enabling hypothalamic functions and, according to the neuroscience dogma, it is predetermined during embryonic life. Here, by combining lineage tracing of hypothalamic pro-opiomelanocortin (Pomc) neurons with single-cell profiling approaches in adult male mice, we uncovered subpopulations of 'Ghost' neurons endowed with atypical molecular and functional identity. Compared to 'classical' Pomc neurons, Ghost neurons exhibit negligible Pomc expression and are 'invisible' to available neuroanatomical approaches and promoter-based reporter mice for studying Pomc biology. Ghost neuron numbers augment in diet-induced obese mice, independent of neurogenesis or cell death, but weight loss can reverse this shift. Our work challenges the notion of fixed, developmentally programmed neuronal identities in the mature hypothalamus and highlight the ability of specialised neurons to reversibly adapt their functional identity to adult-onset obesogenic stimuli.
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Affiliation(s)
- Stéphane Leon
- University of Bordeaux, INSERM, Neurocentre Magendie, U1215, F-33000, Bordeaux, France
| | - Vincent Simon
- University of Bordeaux, INSERM, Neurocentre Magendie, U1215, F-33000, Bordeaux, France
| | - Thomas H Lee
- University of Bordeaux, INSERM, Neurocentre Magendie, U1215, F-33000, Bordeaux, France
| | - Lukas Steuernagel
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Cologne, Germany
| | - Samantha Clark
- University of Bordeaux, INSERM, Neurocentre Magendie, U1215, F-33000, Bordeaux, France
| | - Nasim Biglari
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Cologne, Germany
| | | | - Nathalie Dupuy
- University of Bordeaux, INSERM, Neurocentre Magendie, U1215, F-33000, Bordeaux, France
| | - Astrid Cannich
- University of Bordeaux, INSERM, Neurocentre Magendie, U1215, F-33000, Bordeaux, France
| | - Luigi Bellocchio
- University of Bordeaux, INSERM, Neurocentre Magendie, U1215, F-33000, Bordeaux, France
| | - Philippe Zizzari
- University of Bordeaux, INSERM, Neurocentre Magendie, U1215, F-33000, Bordeaux, France
| | - Camille Allard
- University of Bordeaux, INSERM, Neurocentre Magendie, U1215, F-33000, Bordeaux, France
| | - Delphine Gonzales
- University of Bordeaux, INSERM, Neurocentre Magendie, U1215, F-33000, Bordeaux, France
| | - Yves Le Feuvre
- University of Bordeaux, INSERM, Neurocentre Magendie, U1215, F-33000, Bordeaux, France
| | - Emeline Lhuillier
- University of Toulouse III Paul Sabatier, INSERM, Institut des Maladies Métaboliques et Cardiovasculaires, U1297, 31400, France; GeT-Santé, Plateforme Génome et Transcriptome, GenoToul, Toulouse, France
| | - Alexandre Brochard
- University of Bordeaux, INSERM, Neurocentre Magendie, U1215, F-33000, Bordeaux, France
| | - Jean Charles Nicolas
- University of Bordeaux, INSERM, Neurocentre Magendie, U1215, F-33000, Bordeaux, France
| | - Jérémie Teillon
- University of Bordeaux, CNRS, INSERM, BIC, US4, UAR 3420, F-33000, Bordeaux, France
| | - Macha Nikolski
- University of Bordeaux, Bordeaux Bioinformatics Center, Bordeaux, France
- University of Bordeaux, CNRS, IBGC UMR 5095, Bordeaux, France
| | - Giovanni Marsicano
- University of Bordeaux, INSERM, Neurocentre Magendie, U1215, F-33000, Bordeaux, France
| | - Xavier Fioramonti
- University of Bordeaux, INRAE, Bordeaux INP, NutriNeuro, UMR 1286, F-33000, Bordeaux, France
| | - Jens C Brüning
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Cologne, Germany
- Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Cologne, Germany
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- National Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Daniela Cota
- University of Bordeaux, INSERM, Neurocentre Magendie, U1215, F-33000, Bordeaux, France
| | - Carmelo Quarta
- University of Bordeaux, INSERM, Neurocentre Magendie, U1215, F-33000, Bordeaux, France.
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12
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Xie G, Qin Y, Wu N, Han X, Li J. Single-Nucleus Transcriptome Profiling from the Hippocampus of a PTSD Mouse Model and CBD-Treated Cohorts. Genes (Basel) 2024; 15:519. [PMID: 38674453 PMCID: PMC11050643 DOI: 10.3390/genes15040519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Post-traumatic stress disorder (PTSD) is the most common psychiatric disorder after a catastrophic event; however, the efficacious treatment options remain insufficient. Increasing evidence suggests that cannabidiol (CBD) exhibits optimal therapeutic effects for treating PTSD. To elucidate the cell-type-specific transcriptomic pathology of PTSD and the mechanisms of CBD against this disease, we conducted single-nucleus RNA sequencing (snRNA-seq) in the hippocampus of PTSD-modeled mice and CBD-treated cohorts. We constructed a mouse model by adding electric foot shocks following exposure to single prolonged stress (SPS+S) and tested the freezing time, anxiety-like behavior, and cognitive behavior. CBD was administrated before every behavioral test. The PTSD-modeled mice displayed behaviors resembling those of PTSD in all behavioral tests, and CBD treatment alleviated all of these PTSD-like behaviors (n = 8/group). Three mice with representative behavioral phenotypes were selected from each group for snRNA-seq 15 days after the SPS+S. We primarily focused on the excitatory neurons (ExNs) and inhibitory neurons (InNs), which accounted for 68.4% of the total cell annotations. A total of 88 differentially upregulated genes and 305 differentially downregulated genes were found in the PTSD mice, which were found to exhibit significant alterations in pathways and biological processes associated with fear response, synaptic communication, protein synthesis, oxidative phosphorylation, and oxidative stress response. A total of 63 overlapping genes in InNs were identified as key genes for CBD in the treatment of PTSD. Subsequent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the anti-PTSD effect of CBD was related to the regulation of protein synthesis, oxidative phosphorylation, oxidative stress response, and fear response. Furthermore, gene set enrichment analysis (GSEA) revealed that CBD also enhanced retrograde endocannabinoid signaling in ExNs, which was found to be suppressed in the PTSD group. Our research may provide a potential explanation for the pathogenesis of PTSD and facilitate the discovery of novel therapeutic targets for drug development. Moreover, it may shed light on the therapeutic mechanisms of CBD.
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Affiliation(s)
| | | | | | - Xiao Han
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Key Laboratory of Neuropsychopharmacology, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China; (G.X.); (Y.Q.); (N.W.); (J.L.)
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13
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Lavoie O, Turmel A, Mattoon P, Desrosiers WJ, Plamondon J, Michael NJ, Caron A. Hypothalamic GABAergic Neurons Expressing Cellular Retinoic Acid Binding Protein 1 (CRABP1) Are Sensitive to Metabolic Status and Liraglutide in Male Mice. Neuroendocrinology 2024; 114:681-697. [PMID: 38631315 PMCID: PMC11232952 DOI: 10.1159/000538716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/29/2024] [Indexed: 04/19/2024]
Abstract
INTRODUCTION Owing to their privileged anatomical location, neurons of the arcuate nucleus of the hypothalamus (ARC) play critical roles in sensing and responding to metabolic signals such as leptin and glucagon-like peptide 1 (GLP-1). In addition to the well-known proopiomelanocortin (POMC)- and agouti-related peptide (AgRP)-expressing neurons, subpopulations of GABAergic neurons are emerging as key regulators of energy balance. However, the precise identity of these metabolic neurons is still elusive. Here, we identified and characterized the molecular signature of a novel population of GABAergic neurons of the ARC expressing Cellular retinoic acid binding protein 1 (Crabp1). METHODS Using a combination of immunohistochemistry and in situ hybridization techniques, we investigated the expression of Crabp1 across the mouse brain and characterized the molecular identity of Crabp1ARC neurons. We also determined whether Crabp1ARC neurons are sensitive to fasting, leptin, and GLP1R agonism by assessing cFOS immunoreactivity as a marker of neuronal activity. RESULTS Crabp1ARC neurons represent a novel GABAergic neuronal population robustly enriched in the ARC and are distinct from the prototypical melanocortin neurons. Crabp1ARC neurons overlap with three subpopulations of yet uncharacterized ARC neurons expressing Htr3b, Tbx19, and Tmem215. Notably, Crabp1ARC neurons express receptors for metabolic hormones and their activity is modulated by the nutritional state and GLP1R agonism. CONCLUSION Crabp1ARC neurons represent a novel heterogeneous population of GABAergic neurons sensitive to metabolic status.
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Affiliation(s)
- Olivier Lavoie
- Faculty of Pharmacy, Université Laval, Quebec City, Québec, Canada
- Quebec Heart and Lung Institute, Quebec City, Québec, Canada
| | - Audrey Turmel
- Faculty of Pharmacy, Université Laval, Quebec City, Québec, Canada
- Quebec Heart and Lung Institute, Quebec City, Québec, Canada
| | - Paige Mattoon
- Quebec Heart and Lung Institute, Quebec City, Québec, Canada
| | | | - Julie Plamondon
- Quebec Heart and Lung Institute, Quebec City, Québec, Canada
| | - Natalie Jane Michael
- Faculty of Pharmacy, Université Laval, Quebec City, Québec, Canada
- Quebec Heart and Lung Institute, Quebec City, Québec, Canada
| | - Alexandre Caron
- Faculty of Pharmacy, Université Laval, Quebec City, Québec, Canada
- Quebec Heart and Lung Institute, Quebec City, Québec, Canada
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14
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Qu R, Cheng X, Sefik E, Stanley Iii JS, Landa B, Strino F, Platt S, Garritano J, Odell ID, Coifman R, Flavell RA, Myung P, Kluger Y. Gene trajectory inference for single-cell data by optimal transport metrics. Nat Biotechnol 2024:10.1038/s41587-024-02186-3. [PMID: 38580861 DOI: 10.1038/s41587-024-02186-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/26/2024] [Indexed: 04/07/2024]
Abstract
Single-cell RNA sequencing has been widely used to investigate cell state transitions and gene dynamics of biological processes. Current strategies to infer the sequential dynamics of genes in a process typically rely on constructing cell pseudotime through cell trajectory inference. However, the presence of concurrent gene processes in the same group of cells and technical noise can obscure the true progression of the processes studied. To address this challenge, we present GeneTrajectory, an approach that identifies trajectories of genes rather than trajectories of cells. Specifically, optimal transport distances are calculated between gene distributions across the cell-cell graph to extract gene programs and define their gene pseudotemporal order. Here we demonstrate that GeneTrajectory accurately extracts progressive gene dynamics in myeloid lineage maturation. Moreover, we show that GeneTrajectory deconvolves key gene programs underlying mouse skin hair follicle dermal condensate differentiation that could not be resolved by cell trajectory approaches. GeneTrajectory facilitates the discovery of gene programs that control the changes and activities of biological processes.
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Affiliation(s)
- Rihao Qu
- Computational Biology & Bioinformatics Program, Yale University, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Xiuyuan Cheng
- Department of Mathematics, Duke University, Durham, NC, USA
| | - Esen Sefik
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Boris Landa
- Program in Applied Mathematics, Yale University, New Haven, CT, USA
| | | | - Sarah Platt
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
| | - James Garritano
- Program in Applied Mathematics, Yale University, New Haven, CT, USA
| | - Ian D Odell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
| | - Ronald Coifman
- Program in Applied Mathematics, Yale University, New Haven, CT, USA
- Department of Mathematics, Yale University, New Haven, CT, USA
- Department of Electrical Engineering, Yale University, New Haven, CT, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Peggy Myung
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
| | - Yuval Kluger
- Computational Biology & Bioinformatics Program, Yale University, New Haven, CT, USA.
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
- Program in Applied Mathematics, Yale University, New Haven, CT, USA.
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15
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Benevento M, Alpár A, Gundacker A, Afjehi L, Balueva K, Hevesi Z, Hanics J, Rehman S, Pollak DD, Lubec G, Wulff P, Prevot V, Horvath TL, Harkany T. A brainstem-hypothalamus neuronal circuit reduces feeding upon heat exposure. Nature 2024; 628:826-834. [PMID: 38538787 PMCID: PMC11041654 DOI: 10.1038/s41586-024-07232-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/22/2024] [Indexed: 04/06/2024]
Abstract
Empirical evidence suggests that heat exposure reduces food intake. However, the neurocircuit architecture and the signalling mechanisms that form an associative interface between sensory and metabolic modalities remain unknown, despite primary thermoceptive neurons in the pontine parabrachial nucleus becoming well characterized1. Tanycytes are a specialized cell type along the wall of the third ventricle2 that bidirectionally transport hormones and signalling molecules between the brain's parenchyma and ventricular system3-8. Here we show that tanycytes are activated upon acute thermal challenge and are necessary to reduce food intake afterwards. Virus-mediated gene manipulation and circuit mapping showed that thermosensing glutamatergic neurons of the parabrachial nucleus innervate tanycytes either directly or through second-order hypothalamic neurons. Heat-dependent Fos expression in tanycytes suggested their ability to produce signalling molecules, including vascular endothelial growth factor A (VEGFA). Instead of discharging VEGFA into the cerebrospinal fluid for a systemic effect, VEGFA was released along the parenchymal processes of tanycytes in the arcuate nucleus. VEGFA then increased the spike threshold of Flt1-expressing dopamine and agouti-related peptide (Agrp)-containing neurons, thus priming net anorexigenic output. Indeed, both acute heat and the chemogenetic activation of glutamatergic parabrachial neurons at thermoneutrality reduced food intake for hours, in a manner that is sensitive to both Vegfa loss-of-function and blockage of vesicle-associated membrane protein 2 (VAMP2)-dependent exocytosis from tanycytes. Overall, we define a multimodal neurocircuit in which tanycytes link parabrachial sensory relay to the long-term enforcement of a metabolic code.
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Affiliation(s)
- Marco Benevento
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Alán Alpár
- Department of Anatomy, Histology, and Embryology, Semmelweis University, Budapest, Hungary
- SE NAP Research Group of Experimental Neuroanatomy and Developmental Biology, Semmelweis University, Budapest, Hungary
| | - Anna Gundacker
- Department of Neurophysiology and Neuropharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Leila Afjehi
- Programme Proteomics, Paracelsus Medizinische Privatuniversität, Salzburg, Austria
| | - Kira Balueva
- Institute of Physiology, Christian Albrechts University, Kiel, Germany
| | - Zsofia Hevesi
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - János Hanics
- Department of Anatomy, Histology, and Embryology, Semmelweis University, Budapest, Hungary
- SE NAP Research Group of Experimental Neuroanatomy and Developmental Biology, Semmelweis University, Budapest, Hungary
| | - Sabah Rehman
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Daniela D Pollak
- Department of Neurophysiology and Neuropharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Gert Lubec
- Programme Proteomics, Paracelsus Medizinische Privatuniversität, Salzburg, Austria
| | - Peer Wulff
- Institute of Physiology, Christian Albrechts University, Kiel, Germany
| | - Vincent Prevot
- University of Lille, INSERM, CHU Lille, Development and Plasticity of the Neuroendocrine Brain, Lille Neuroscience and Cognition, UMR S1172, EGID, Lille, France
| | - Tamas L Horvath
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Tibor Harkany
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria.
- Department of Neuroscience, Karolinska Institutet, Solna, Sweden.
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16
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An S, Shi J, Liu R, Chen Y, Wang J, Hu S, Xia X, Dong G, Bo X, He Z, Ying X. scDAC: deep adaptive clustering of single-cell transcriptomic data with coupled autoencoder and Dirichlet process mixture model. BIOINFORMATICS (OXFORD, ENGLAND) 2024; 40:btae198. [PMID: 38603616 DOI: 10.1093/bioinformatics/btae198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 03/20/2024] [Accepted: 04/10/2024] [Indexed: 04/13/2024]
Abstract
MOTIVATION Clustering analysis for single-cell RNA sequencing (scRNA-seq) data is an important step in revealing cellular heterogeneity. Many clustering methods have been proposed to discover heterogenous cell types from scRNA-seq data. However, adaptive clustering with accurate cluster number reflecting intrinsic biology nature from large-scale scRNA-seq data remains quite challenging. RESULTS Here, we propose a single-cell Deep Adaptive Clustering (scDAC) model by coupling the Autoencoder (AE) and the Dirichlet Process Mixture Model (DPMM). By jointly optimizing the model parameters of AE and DPMM, scDAC achieves adaptive clustering with accurate cluster numbers on scRNA-seq data. We verify the performance of scDAC on five subsampled datasets with different numbers of cell types and compare it with 15 widely used clustering methods across nine scRNA-seq datasets. Our results demonstrate that scDAC can adaptively find accurate numbers of cell types or subtypes and outperforms other methods. Moreover, the performance of scDAC is robust to hyperparameter changes. AVAILABILITY AND IMPLEMENTATION The scDAC is implemented in Python. The source code is available at https://github.com/labomics/scDAC.
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Affiliation(s)
- Sijing An
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Jinhui Shi
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Runyan Liu
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Yaowen Chen
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Jing Wang
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Shuofeng Hu
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Xinyu Xia
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Guohua Dong
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Xiaochen Bo
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Zhen He
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Xiaomin Ying
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing 100850, China
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17
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Huang Y, Wang A, Zhou W, Li B, Zhang L, Rudolf AM, Jin Z, Hambly C, Wang G, Speakman JR. Maternal dietary fat during lactation shapes single nucleus transcriptomic profile of postnatal offspring hypothalamus in a sexually dimorphic manner in mice. Nat Commun 2024; 15:2382. [PMID: 38493217 PMCID: PMC10944494 DOI: 10.1038/s41467-024-46589-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 03/01/2024] [Indexed: 03/18/2024] Open
Abstract
Maternal overnutrition during lactation predisposes offspring to develop metabolic diseases and exacerbates the relevant syndromes in males more than females in later life. The hypothalamus is a heterogenous brain region that regulates energy balance. Here we combined metabolic trait quantification of mother and offspring mice under low and high fat diet (HFD) feeding during lactation, with single nucleus transcriptomic profiling of their offspring hypothalamus at peak lacation to understand the cellular and molecular alterations in response to maternal dietary pertubation. We found significant expansion in neuronal subpopulations including histaminergic (Hdc), arginine vasopressin/retinoic acid receptor-related orphan receptor β (Avp/Rorb) and agouti-related peptide/neuropeptide Y (AgRP/Npy) in male offspring when their mothers were fed HFD, and increased Npy-astrocyte interactions in offspring responding to maternal overnutrition. Our study provides a comprehensive offspring hypothalamus map at the peak lactation and reveals how the cellular subpopulations respond to maternal dietary fat in a sex-specific manner during development.
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Affiliation(s)
- Yi Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Broad Institute of MIT and Harvard, Metabolism Program, Cambridge, MA, 02142, USA
| | - Anyongqi Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Wenjiang Zhou
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Centre for Evolutionary Biology, Fudan University, Shanghai, 200438, China
| | - Baoguo Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Linshan Zhang
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Centre for Evolutionary Biology, Fudan University, Shanghai, 200438, China
| | - Agata M Rudolf
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zengguang Jin
- Shenzhen Key Laboratory of Metabolic Health, Center for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Catherine Hambly
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3FX, UK
| | - Guanlin Wang
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Centre for Evolutionary Biology, Fudan University, Shanghai, 200438, China.
| | - John R Speakman
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- Shenzhen Key Laboratory of Metabolic Health, Center for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3FX, UK.
- China Medical University, Shenyang, Liaoning, 110122, China.
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18
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Elliott A, Walters RK, Pirinen M, Kurki M, Junna N, Goldstein JI, Reeve MP, Siirtola H, Lemmelä SM, Turley P, Lahtela E, Mehtonen J, Reis K, Elnahas AG, Reigo A, Palta P, Esko T, Mägi R, Palotie A, Daly MJ, Widén E. Distinct and shared genetic architectures of gestational diabetes mellitus and type 2 diabetes. Nat Genet 2024; 56:377-382. [PMID: 38182742 PMCID: PMC10937370 DOI: 10.1038/s41588-023-01607-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 11/07/2023] [Indexed: 01/07/2024]
Abstract
Gestational diabetes mellitus (GDM) is a common metabolic disorder affecting more than 16 million pregnancies annually worldwide1,2. GDM is related to an increased lifetime risk of type 2 diabetes (T2D)1-3, with over a third of women developing T2D within 15 years of their GDM diagnosis. The diseases are hypothesized to share a genetic predisposition1-7, but few studies have sought to uncover the genetic underpinnings of GDM. Most studies have evaluated the impact of T2D loci only8-10, and the three prior genome-wide association studies of GDM11-13 have identified only five loci, limiting the power to assess to what extent variants or biological pathways are specific to GDM. We conducted the largest genome-wide association study of GDM to date in 12,332 cases and 131,109 parous female controls in the FinnGen study and identified 13 GDM-associated loci, including nine new loci. Genetic features distinct from T2D were identified both at the locus and genomic scale. Our results suggest that the genetics of GDM risk falls into the following two distinct categories: one part conventional T2D polygenic risk and one part predominantly influencing mechanisms disrupted in pregnancy. Loci with GDM-predominant effects map to genes related to islet cells, central glucose homeostasis, steroidogenesis and placental expression.
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Grants
- R00 AG062787 NIA NIH HHS
- R01 MH101244 NIMH NIH HHS
- A.E. was a research Scholar supported by Sarnoff Cardiovascular Research Foundation
- U.S. Department of Health & Human Services | National Institutes of Health (NIH)
- Academy of Finland (Suomen Akatemia)
- U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)
- The FinnGen project is funded by two grants from Business Finland (HUS 4685/31/2016 and UH 4386/31/2016) and by eleven industry partners (AbbVie Inc, AstraZeneca UK Ltd, Biogen MA Inc, Celgene Corporation, Celgene International II Sàrl, Genentech Inc, Merck Sharp & Dohme Corp, Pfizer Inc., GlaxoSmithKline, Sanofi, Maze Therapeutics Inc., Janssen Biotech Inc).
- EstBB GWAS analysis is supported by research funding from the Estonian Research Council: Team grant PRG1291 and PRG1911.
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Affiliation(s)
- Amanda Elliott
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Raymond K Walters
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Matti Pirinen
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Mitja Kurki
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Nella Junna
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Jacqueline I Goldstein
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mary Pat Reeve
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Harri Siirtola
- TAUCHI Research Center, Faculty of Information Technology and Communication Sciences (ITC), Tampere University, Tampere, Finland
| | - Susanna M Lemmelä
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Patrick Turley
- Center for Economic and Social Research, University of Southern California, Los Angeles, CA, USA
- Department of Economics, University of Southern California, Los Angeles, CA, USA
| | - Elisa Lahtela
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Juha Mehtonen
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Kadri Reis
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Anu Reigo
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Priit Palta
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Tõnu Esko
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Reedik Mägi
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Aarno Palotie
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland.
| | - Elisabeth Widén
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland.
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19
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Liu Y, Zhao ZD, Xie G, Chen R, Zhang Y. A molecularly defined NAcSh D1 subtype controls feeding and energy homeostasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.27.530275. [PMID: 36909586 PMCID: PMC10002697 DOI: 10.1101/2023.02.27.530275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Orchestrating complex behavioral states, such as approach and consumption of food, is critical for survival. In addition to hypothalamus neuronal circuits, the nucleus accumbens (NAc) also plays an important role in controlling appetite and satiety in responses to changing external stimuli. However, the specific neuronal subtypes of NAc involved as well as how the humoral and neuronal signals coordinate to regulate feeding remain incompletely understood. Here, we deciphered the spatial diversity of neuron subtypes of the NAc shell (NAcSh) and defined a dopamine receptor D1(Drd1)- and Serpinb2-expressing subtype located in NAcSh encoding food consumption. Chemogenetics- and optogenetics-mediated regulation of Serpinb2 + neurons bidirectionally regulates food seeking and consumption specifically. Circuitry stimulation revealed the NAcSh Serpinb2 →LH LepR projection controls refeeding and can overcome leptin-mediated feeding suppression. Furthermore, NAcSh Serpinb2 + neuron ablation reduces food intake and upregulates energy expenditure resulting in body weight loss. Together, our study reveals a neural circuit consisted of molecularly distinct neuronal subtype that bidirectionally regulates energy homeostasis, which can serve as a potential therapeutic target for eating disorders.
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Affiliation(s)
- Yiqiong Liu
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
| | - Zheng-dong Zhao
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
| | - Guoguang Xie
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
| | - Renchao Chen
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Harvard Stem Cell Institute, WAB-149G, 200 Longwood Avenue, Boston, Massachusetts 02115, USA
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20
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Aranda S, Muntané G, Vilella E. Coexpression network analysis of the adult brain sheds light on the pathogenic mechanism of DDR1 in schizophrenia and bipolar disorder. Transl Psychiatry 2024; 14:112. [PMID: 38395959 PMCID: PMC10891045 DOI: 10.1038/s41398-024-02823-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
DDR1 has been linked to schizophrenia (SCZ) and bipolar disorder (BD) in association studies. DDR1 encodes 58 distinct transcripts, which can be translated into five isoforms (DDR1a-e) and are expressed in the brain. However, the transcripts expressed in each brain cell type, their functions and their involvement in SCZ and BD remain unknown. Here, to infer the processes in which DDR1 transcripts are involved, we used transcriptomic data from the human brain dorsolateral prefrontal cortex of healthy controls (N = 936) and performed weighted gene coexpression network analysis followed by enrichment analyses. Then, to explore the involvement of DDR1 transcripts in SCZ (N = 563) and BD (N = 222), we studied the association of coexpression modules with disease and performed differential expression and transcript significance analyses. Some DDR1 transcripts were distributed across five coexpression modules identified in healthy controls (MHC). MHC1 and MHC2 were enriched in the cell cycle and proliferation of astrocytes and OPCs; MHC3 and MHC4 were enriched in oligodendrocyte differentiation and myelination; and MHC5 was enriched in neurons and synaptic transmission. Most of the DDR1 transcripts associated with SCZ and BD pertained to MHC1 and MHC2. Altogether, our results suggest that DDR1 expression might be altered in SCZ and BD via the proliferation of astrocytes and OPCs, suggesting that these processes are relevant in psychiatric disorders.
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Affiliation(s)
- Selena Aranda
- Institut d'Investigació Sanitària Pere Virgili-CERCA, Reus, Spain
- Hospital Universitari Institut Pere Mata, Reus, Spain
- Universitat Rovira i Virgili, Reus, Spain
- Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM)-Instituto de Salud Carlos III, Madrid, Spain
| | - Gerard Muntané
- Institut d'Investigació Sanitària Pere Virgili-CERCA, Reus, Spain
- Hospital Universitari Institut Pere Mata, Reus, Spain
- Universitat Rovira i Virgili, Reus, Spain
- Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM)-Instituto de Salud Carlos III, Madrid, Spain
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Elisabet Vilella
- Institut d'Investigació Sanitària Pere Virgili-CERCA, Reus, Spain.
- Hospital Universitari Institut Pere Mata, Reus, Spain.
- Universitat Rovira i Virgili, Reus, Spain.
- Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM)-Instituto de Salud Carlos III, Madrid, Spain.
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21
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Lei Y, Liang X, Sun Y, Yao T, Gong H, Chen Z, Gao Y, Wang H, Wang R, Huang Y, Yang T, Yu M, Liu L, Yi CX, Wu QF, Kong X, Xu X, Liu S, Zhang Z, Liu T. Region-specific transcriptomic responses to obesity and diabetes in macaque hypothalamus. Cell Metab 2024; 36:438-453.e6. [PMID: 38325338 DOI: 10.1016/j.cmet.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 10/27/2023] [Accepted: 01/05/2024] [Indexed: 02/09/2024]
Abstract
The hypothalamus plays a crucial role in the progression of obesity and diabetes; however, its structural complexity and cellular heterogeneity impede targeted treatments. Here, we profiled the single-cell and spatial transcriptome of the hypothalamus in obese and sporadic type 2 diabetic macaques, revealing primate-specific distributions of clusters and genes as well as spatial region, cell-type-, and gene-feature-specific changes. The infundibular (INF) and paraventricular nuclei (PVN) are most susceptible to metabolic disruption, with the PVN being more sensitive to diabetes. In the INF, obesity results in reduced synaptic plasticity and energy sensing capability, whereas diabetes involves molecular reprogramming associated with impaired tanycytic barriers, activated microglia, and neuronal inflammatory response. In the PVN, cellular metabolism and neural activity are suppressed in diabetic macaques. Spatial transcriptomic data reveal microglia's preference for the parenchyma over the third ventricle in diabetes. Our findings provide a comprehensive view of molecular changes associated with obesity and diabetes.
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Affiliation(s)
- Ying Lei
- BGI-Research, Hangzhou 310012, China; BGI-Research, Shenzhen 518103, China
| | - Xian Liang
- State Key Laboratory of Genetic Engineering, Department of Endocrinology and Metabolism, Human Phenome Institute, Institute of Metabolism and Integrative Biology, and School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yunong Sun
- BGI-Research, Hangzhou 310012, China; BGI-Research, Shenzhen 518103, China
| | - Ting Yao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University School of Medicine, Xi'an, Shanxi 710063, China
| | - Hongyu Gong
- School of Life Sciences, Institues of Biomedical Sciences, Inner Mongolia University, Hohhot 010000, China
| | - Zhenhua Chen
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuanqing Gao
- Jiangsu Provincial Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Hui Wang
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ru Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Yunqi Huang
- BGI-Research, Hangzhou 310012, China; BGI-Research, Shenzhen 518103, China
| | - Tao Yang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Miao Yu
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Longqi Liu
- BGI-Research, Hangzhou 310012, China; BGI-Research, Shenzhen 518103, China
| | - Chun-Xia Yi
- Department of Endocrinology and Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, the Netherlands
| | - Qing-Feng Wu
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xingxing Kong
- School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Xun Xu
- BGI-Research, Hangzhou 310012, China; BGI-Research, Shenzhen 518103, China.
| | - Shiping Liu
- BGI-Research, Hangzhou 310012, China; BGI-Research, Shenzhen 518103, China.
| | - Zhi Zhang
- State Key Laboratory of Genetic Engineering, Department of Endocrinology and Metabolism, Human Phenome Institute, Institute of Metabolism and Integrative Biology, and School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Tiemin Liu
- State Key Laboratory of Genetic Engineering, Department of Endocrinology and Metabolism, Human Phenome Institute, Institute of Metabolism and Integrative Biology, and School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; School of Life Sciences, Fudan University, Shanghai 200438, China; School of Life Sciences, Institues of Biomedical Sciences, Inner Mongolia University, Hohhot 010000, China.
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22
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Tan D, Yang C, Wang J, Su Y, Zheng C. scAMAC: self-supervised clustering of scRNA-seq data based on adaptive multi-scale autoencoder. Brief Bioinform 2024; 25:bbae068. [PMID: 38426327 PMCID: PMC10905526 DOI: 10.1093/bib/bbae068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/15/2024] [Accepted: 01/26/2024] [Indexed: 03/02/2024] Open
Abstract
Cluster assignment is vital to analyzing single-cell RNA sequencing (scRNA-seq) data to understand high-level biological processes. Deep learning-based clustering methods have recently been widely used in scRNA-seq data analysis. However, existing deep models often overlook the interconnections and interactions among network layers, leading to the loss of structural information within the network layers. Herein, we develop a new self-supervised clustering method based on an adaptive multi-scale autoencoder, called scAMAC. The self-supervised clustering network utilizes the Multi-Scale Attention mechanism to fuse the feature information from the encoder, hidden and decoder layers of the multi-scale autoencoder, which enables the exploration of cellular correlations within the same scale and captures deep features across different scales. The self-supervised clustering network calculates the membership matrix using the fused latent features and optimizes the clustering network based on the membership matrix. scAMAC employs an adaptive feedback mechanism to supervise the parameter updates of the multi-scale autoencoder, obtaining a more effective representation of cell features. scAMAC not only enables cell clustering but also performs data reconstruction through the decoding layer. Through extensive experiments, we demonstrate that scAMAC is superior to several advanced clustering and imputation methods in both data clustering and reconstruction. In addition, scAMAC is beneficial for downstream analysis, such as cell trajectory inference. Our scAMAC model codes are freely available at https://github.com/yancy2024/scAMAC.
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Affiliation(s)
- Dayu Tan
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 230601 Hefei, China
| | - Cheng Yang
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 230601 Hefei, China
| | - Jing Wang
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 230601 Hefei, China
| | - Yansen Su
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 230601 Hefei, China
| | - Chunhou Zheng
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 230601 Hefei, China
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23
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Jörgensen SK, Karnošová A, Mazzaferro S, Rowley O, Chen HJC, Robbins SJ, Christofides S, Merkle FT, Maletínská L, Petrik D. An analogue of the Prolactin Releasing Peptide reduces obesity and promotes adult neurogenesis. EMBO Rep 2024; 25:351-377. [PMID: 38177913 PMCID: PMC10897398 DOI: 10.1038/s44319-023-00016-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 11/02/2023] [Accepted: 11/17/2023] [Indexed: 01/06/2024] Open
Abstract
Hypothalamic Adult Neurogenesis (hAN) has been implicated in regulating energy homeostasis. Adult-generated neurons and adult Neural Stem Cells (aNSCs) in the hypothalamus control food intake and body weight. Conversely, diet-induced obesity (DIO) by high fat diets (HFD) exerts adverse influence on hAN. However, the effects of anti-obesity compounds on hAN are not known. To address this, we administered a lipidized analogue of an anti-obesity neuropeptide, Prolactin Releasing Peptide (PrRP), so-called LiPR, to mice. In the HFD context, LiPR rescued the survival of adult-born hypothalamic neurons and increased the number of aNSCs by reducing their activation. LiPR also rescued the reduction of immature hippocampal neurons and modulated calcium dynamics in iPSC-derived human neurons. In addition, some of these neurogenic effects were exerted by another anti-obesity compound, Liraglutide. These results show for the first time that anti-obesity neuropeptides influence adult neurogenesis and suggest that the neurogenic process can serve as a target of anti-obesity pharmacotherapy.
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Affiliation(s)
| | - Alena Karnošová
- First Faculty of Medicine, Charles University, Prague, 12108, Czech Republic
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, 16610, Czech Republic
| | - Simone Mazzaferro
- Wellcome-MRC Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
- Wellcome-MRC Stem Cell Institute, Cambridge, CB2 0AW, UK
| | - Oliver Rowley
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Hsiao-Jou Cortina Chen
- Wellcome-MRC Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
- Wellcome-MRC Stem Cell Institute, Cambridge, CB2 0AW, UK
| | - Sarah J Robbins
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | | | - Florian T Merkle
- Wellcome-MRC Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
- Wellcome-MRC Stem Cell Institute, Cambridge, CB2 0AW, UK
| | - Lenka Maletínská
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, 16610, Czech Republic
| | - David Petrik
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK.
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24
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Kim HJ, Saikia JM, Monte KMA, Ha E, Romaus-Sanjurjo D, Sanchez JJ, Moore AX, Hernaiz-Llorens M, Chavez-Martinez CL, Agba CK, Li H, Zhang J, Lusk DT, Cervantes KM, Zheng B. Deep scRNA sequencing reveals a broadly applicable Regeneration Classifier and implicates antioxidant response in corticospinal axon regeneration. Neuron 2023; 111:3953-3969.e5. [PMID: 37848024 PMCID: PMC10843387 DOI: 10.1016/j.neuron.2023.09.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/26/2023] [Accepted: 09/15/2023] [Indexed: 10/19/2023]
Abstract
Despite substantial progress in understanding the biology of axon regeneration in the CNS, our ability to promote regeneration of the clinically important corticospinal tract (CST) after spinal cord injury remains limited. To understand regenerative heterogeneity, we conducted patch-based single-cell RNA sequencing on rare regenerating CST neurons at high depth following PTEN and SOCS3 deletion. Supervised classification with Garnett gave rise to a Regeneration Classifier, which can be broadly applied to predict the regenerative potential of diverse neuronal types across developmental stages or after injury. Network analyses highlighted the importance of antioxidant response and mitochondrial biogenesis. Conditional gene deletion validated a role for NFE2L2 (or NRF2), a master regulator of antioxidant response, in CST regeneration. Our data demonstrate a universal transcriptomic signature underlying the regenerative potential of vastly different neuronal populations and illustrate that deep sequencing of only hundreds of phenotypically identified neurons has the power to advance regenerative biology.
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Affiliation(s)
- Hugo J Kim
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Junmi M Saikia
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA; Neurosciences Graduate Program, University of California San Diego, La Jolla, CA, USA USA
| | - Katlyn Marie A Monte
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Eunmi Ha
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Daniel Romaus-Sanjurjo
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Joshua J Sanchez
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Andrea X Moore
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Marc Hernaiz-Llorens
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Carmine L Chavez-Martinez
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA; Graduate program in Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Chimuanya K Agba
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA; Neurosciences Graduate Program, University of California San Diego, La Jolla, CA, USA USA
| | - Haoyue Li
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Joseph Zhang
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Daniel T Lusk
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kayla M Cervantes
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Binhai Zheng
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA; VA San Diego Research Service, San Diego, CA, USA.
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25
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Goggin SM, Zunder ER. A hyperparameter-randomized ensemble approach for robust clustering across diverse datasets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.571953. [PMID: 38187667 PMCID: PMC10769222 DOI: 10.1101/2023.12.18.571953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Clustering analysis is widely used to group objects by similarity, but for complex datasets such as those produced by single-cell analysis, the currently available clustering methods are limited by accuracy, robustness, ease of use, and interpretability. To address these limitations, we developed an ensemble clustering method with hyperparameter randomization that outperforms other methods across a broad range of single-cell and synthetic datasets, without the need for manual hyperparameter selection. In addition to hard cluster labels, it also outputs soft cluster memberships to characterize continuum-like regions and per cell overlap scores to quantify the uncertainty in cluster assignment. We demonstrate the improved clustering interpretability from these features by tracing the intermediate stages between handwritten digits in the MNIST dataset, and between tanycyte subpopulations in the hypothalamus. This approach improves the quality of clustering and subsequent downstream analyses for single-cell datasets, and may also prove useful in other fields of data analysis.
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Affiliation(s)
- Sarah M. Goggin
- Neuroscience Graduate Program, School of Medicine, University of Virginia, Charlottesville, VA 22902
| | - Eli R. Zunder
- Neuroscience Graduate Program, School of Medicine, University of Virginia, Charlottesville, VA 22902
- Department of Biomedical Engineering, School of Engineering, University of Virginia, Charlottesville, VA 22902
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26
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Junaid M, Choe HK, Kondoh K, Lee EJ, Lim SB. Unveiling Hypothalamic Molecular Signatures via Retrograde Viral Tracing and Single-Cell Transcriptomics. Sci Data 2023; 10:861. [PMID: 38049462 PMCID: PMC10696032 DOI: 10.1038/s41597-023-02789-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/24/2023] [Indexed: 12/06/2023] Open
Abstract
Despite the importance of hypothalamic neurocircuits in regulating homeostatic and survival-related behaviors, our understanding of the intrinsic molecular identities of neural components involved in these complex multi-synaptic interactions remains limited. In this study, we constructed a Cre recombinase-dependent pseudorabies virus (PRVs) capable of crossing synapses, coupled with transcriptome analysis of single upstream neurons post-infection. By utilizing this retrograde nuclear Connect-seq (nuConnect-seq) approach, we generated a single nuclei RNA-seq (snRNA-seq) dataset of 1,533 cells derived from the hypothalamus of CRH-IRES-Cre (CRH-Cre) mice. To ensure the technical validity of our nuConnect-seq dataset, we employed a label transfer technique against an integrated reference dataset of postnatal mouse hypothalamus comprising 152,524 QC-passed cells. The uniqueness of our approach lies in the integration of diverse datasets for validation, providing a more nuanced diversity of hypothalamic cell types. The presented validated dataset may deepen our understanding of hypothalamic neurocircuits and underscore the essential role of comprehensive integrated transcriptomic data for technical validity.
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Affiliation(s)
- Muhammad Junaid
- Department of Biochemistry & Molecular Biology, Ajou University School of Medicine, Suwon, 16499, Korea
| | - Han Kyoung Choe
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Korea
| | - Kunio Kondoh
- Division of Endocrinology and Metabolism, Department of Homeostatic Regulation, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi, 444-8585, Japan
| | - Eun Jeong Lee
- Department of Brain Science, Ajou University School of Medicine, Suwon, 16499, Korea.
| | - Su Bin Lim
- Department of Biochemistry & Molecular Biology, Ajou University School of Medicine, Suwon, 16499, Korea.
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27
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Zhang M, Pan X, Jung W, Halpern AR, Eichhorn SW, Lei Z, Cohen L, Smith KA, Tasic B, Yao Z, Zeng H, Zhuang X. Molecularly defined and spatially resolved cell atlas of the whole mouse brain. Nature 2023; 624:343-354. [PMID: 38092912 PMCID: PMC10719103 DOI: 10.1038/s41586-023-06808-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 10/31/2023] [Indexed: 12/17/2023]
Abstract
In mammalian brains, millions to billions of cells form complex interaction networks to enable a wide range of functions. The enormous diversity and intricate organization of cells have impeded our understanding of the molecular and cellular basis of brain function. Recent advances in spatially resolved single-cell transcriptomics have enabled systematic mapping of the spatial organization of molecularly defined cell types in complex tissues1-3, including several brain regions (for example, refs. 1-11). However, a comprehensive cell atlas of the whole brain is still missing. Here we imaged a panel of more than 1,100 genes in approximately 10 million cells across the entire adult mouse brains using multiplexed error-robust fluorescence in situ hybridization12 and performed spatially resolved, single-cell expression profiling at the whole-transcriptome scale by integrating multiplexed error-robust fluorescence in situ hybridization and single-cell RNA sequencing data. Using this approach, we generated a comprehensive cell atlas of more than 5,000 transcriptionally distinct cell clusters, belonging to more than 300 major cell types, in the whole mouse brain with high molecular and spatial resolution. Registration of this atlas to the mouse brain common coordinate framework allowed systematic quantifications of the cell-type composition and organization in individual brain regions. We further identified spatial modules characterized by distinct cell-type compositions and spatial gradients featuring gradual changes of cells. Finally, this high-resolution spatial map of cells, each with a transcriptome-wide expression profile, allowed us to infer cell-type-specific interactions between hundreds of cell-type pairs and predict molecular (ligand-receptor) basis and functional implications of these cell-cell interactions. These results provide rich insights into the molecular and cellular architecture of the brain and a foundation for functional investigations of neural circuits and their dysfunction in health and disease.
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Affiliation(s)
- Meng Zhang
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Physics, Harvard University, Cambridge, MA, USA
| | - Xingjie Pan
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Physics, Harvard University, Cambridge, MA, USA
| | - Won Jung
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Physics, Harvard University, Cambridge, MA, USA
| | - Aaron R Halpern
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Physics, Harvard University, Cambridge, MA, USA
| | - Stephen W Eichhorn
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Physics, Harvard University, Cambridge, MA, USA
| | - Zhiyun Lei
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Physics, Harvard University, Cambridge, MA, USA
| | - Limor Cohen
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Physics, Harvard University, Cambridge, MA, USA
| | | | | | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Department of Physics, Harvard University, Cambridge, MA, USA.
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Ripoll-Sánchez L, Watteyne J, Sun H, Fernandez R, Taylor SR, Weinreb A, Bentley BL, Hammarlund M, Miller DM, Hobert O, Beets I, Vértes PE, Schafer WR. The neuropeptidergic connectome of C. elegans. Neuron 2023; 111:3570-3589.e5. [PMID: 37935195 PMCID: PMC7615469 DOI: 10.1016/j.neuron.2023.09.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 08/02/2023] [Accepted: 09/29/2023] [Indexed: 11/09/2023]
Abstract
Efforts are ongoing to map synaptic wiring diagrams, or connectomes, to understand the neural basis of brain function. However, chemical synapses represent only one type of functionally important neuronal connection; in particular, extrasynaptic, "wireless" signaling by neuropeptides is widespread and plays essential roles in all nervous systems. By integrating single-cell anatomical and gene-expression datasets with biochemical analysis of receptor-ligand interactions, we have generated a draft connectome of neuropeptide signaling in the C. elegans nervous system. This network is characterized by high connection density, extended signaling cascades, autocrine foci, and a decentralized topology, with a large, highly interconnected core containing three constituent communities sharing similar patterns of input connectivity. Intriguingly, several key network hubs are little-studied neurons that appear specialized for peptidergic neuromodulation. We anticipate that the C. elegans neuropeptidergic connectome will serve as a prototype to understand how networks of neuromodulatory signaling are organized.
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Affiliation(s)
- Lidia Ripoll-Sánchez
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK; Department of Psychiatry, Cambridge University, Cambridge, UK
| | - Jan Watteyne
- Department of Biology, KU Leuven, Leuven, Belgium
| | - HaoSheng Sun
- Department of Biological Sciences/HHMI, Columbia University, New York, NY, USA; Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert Fernandez
- Department of Biological Sciences/HHMI, Columbia University, New York, NY, USA
| | - Seth R Taylor
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Alexis Weinreb
- Departments of Genetics and Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Barry L Bentley
- Cardiff School of Technologies, Cardiff Metropolitan University, Cardiff, UK
| | - Marc Hammarlund
- Departments of Genetics and Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - David M Miller
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Oliver Hobert
- Department of Biological Sciences/HHMI, Columbia University, New York, NY, USA
| | - Isabel Beets
- Department of Biology, KU Leuven, Leuven, Belgium
| | - Petra E Vértes
- Department of Psychiatry, Cambridge University, Cambridge, UK
| | - William R Schafer
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK; Department of Biology, KU Leuven, Leuven, Belgium.
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29
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Herb BR, Glover HJ, Bhaduri A, Colantuoni C, Bale TL, Siletti K, Hodge R, Lein E, Kriegstein AR, Doege CA, Ament SA. Single-cell genomics reveals region-specific developmental trajectories underlying neuronal diversity in the human hypothalamus. SCIENCE ADVANCES 2023; 9:eadf6251. [PMID: 37939194 PMCID: PMC10631741 DOI: 10.1126/sciadv.adf6251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 10/24/2023] [Indexed: 11/10/2023]
Abstract
The development and diversity of neuronal subtypes in the human hypothalamus has been insufficiently characterized. To address this, we integrated transcriptomic data from 241,096 cells (126,840 newly generated) in the prenatal and adult human hypothalamus to reveal a temporal trajectory from proliferative stem cell populations to mature hypothalamic cell types. Iterative clustering of the adult neurons identified 108 robust transcriptionally distinct neuronal subtypes representing 10 hypothalamic nuclei. Pseudotime trajectories provided insights into the genes driving formation of these nuclei. Comparisons to single-cell transcriptomic data from the mouse hypothalamus suggested extensive conservation of neuronal subtypes despite certain differences in species-enriched gene expression. The uniqueness of hypothalamic neuronal lineages was examined developmentally by comparing excitatory lineages present in cortex and inhibitory lineages in ganglionic eminence, revealing both distinct and shared drivers of neuronal maturation across the human forebrain. These results provide a comprehensive transcriptomic view of human hypothalamus development through gestation and adulthood at cellular resolution.
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Affiliation(s)
- Brian R. Herb
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, USA
- UM-MIND, University of Maryland School of Medicine, Baltimore, MD, USA
- Kahlert Institute for Addiction Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Hannah J. Glover
- Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Aparna Bhaduri
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Carlo Colantuoni
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tracy L. Bale
- Department of Psychiatry, University of Colorado School of Medicine, Aurora, CO, USA
| | - Kimberly Siletti
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Rebecca Hodge
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Arnold R. Kriegstein
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
| | - Claudia A. Doege
- Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Seth A. Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- UM-MIND, University of Maryland School of Medicine, Baltimore, MD, USA
- Kahlert Institute for Addiction Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
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30
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Louden ED, Dougherty MP, Chorich LP, Eroglu A, Layman LC. Investigation of subfertility in the female Nsmf knockout mouse. F&S SCIENCE 2023; 4:286-293. [PMID: 37516276 DOI: 10.1016/j.xfss.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 07/31/2023]
Abstract
OBJECTIVE To study if a pituitary or ovarian defect contributes to subfertility of the female Nsmf knockout (KO) mouse, an animal model of the hypogonadotropic hypogonadism gene NSMF. DESIGN Analysis of hypothalamic, pituitary and ovarian gene expression at baseline, serum gonadotropin levels before and after gonadotropin-releasing hormone (GnRH) stimulation, ovarian response and implantation after superovulation, gonadotropin effects after ovariectomy, and ovarian NSMF protein expression. SETTING University research laboratory. PATIENTS None; mice were used. INTERVENTIONS Gonadotropin-releasing hormone stimulation, superovulation, and ovariectomy in separate experiments. MAIN OUTCOME MEASURES Gene expression in the hypothalamus, pituitary, and ovary; ovarian response and implantation after superovulation; serum gonadotropins after GnRH stimulation and ovariectomy; Western blot to measure ovarian NSMF expression. RESULTS We found increased hypothalamic Kiss1, Gnrh1, and Jak2 mRNA expression in female Nsmf KO vs. wild type (WT) mice. However, pituitary gonadotropin, and GnRH receptor gene expression was not affected, and serum gonadotropin levels were normal. Gonadotropins increased after ovariectomy for both groups. Baseline Kiss1, Fshr, Prkaca, Prkar1a, and Gdf9 ovarian mRNA expression was increased and Cyp19a1 expression was decreased in Nsmf KO mice, while superovulated Nsmf KO mice had reduced ovarian Kiss1r, Prkar1a, and Fshr mRNA expression, 50% less oocytes, and normal implantation. Western blot demonstrated NSMF protein expression in the ovary of WT mice. CONCLUSIONS Altered hypothalamic and ovarian gene expression was demonstrated in female Nsmf KO mice. It is possible that increased hypothalamic Gnrh1 and Kiss1 mRNA expression could compensate for reduced NSMF enabling a normal pituitary gonadotropin response. Impaired superovulation response, altered ovarian gene expression, and decreased number of oocytes indicate ovarian dysfunction, but a uterine factor cannot be excluded. These findings provide an anatomic basis for future mechanistic studies of subfertility in female Nsmf KO mice.
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Affiliation(s)
- Erica D Louden
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology
| | - Michael P Dougherty
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology
| | - Lynn P Chorich
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology
| | - Ali Eroglu
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology; Department of Neuroscience and Regenerative Medicine
| | - Lawrence C Layman
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology; Department of Neuroscience and Regenerative Medicine; Department of Physiology, Medical College of Georgia at Augusta University, Augusta, Georgia.
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31
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Fong H, Zheng J, Kurrasch D. The structural and functional complexity of the integrative hypothalamus. Science 2023; 382:388-394. [PMID: 37883552 DOI: 10.1126/science.adh8488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023]
Abstract
The hypothalamus ("hypo" meaning below, and "thalamus" meaning bed) consists of regulatory circuits that support basic life functions that ensure survival. Sitting at the interface between peripheral, environmental, and neural inputs, the hypothalamus integrates these sensory inputs to influence a range of physiologies and behaviors. Unlike the neocortex, in which a stereotyped cytoarchitecture mediates complex functions across a comparatively small number of neuronal fates, the hypothalamus comprises upwards of thousands of distinct cell types that form redundant yet functionally discrete circuits. With single-cell RNA sequencing studies revealing further cellular heterogeneity and modern photonic tools enabling high-resolution dissection of complex circuitry, a new era of hypothalamic mapping has begun. Here, we provide a general overview of mammalian hypothalamic organization, development, and connectivity to help welcome newcomers into this exciting field.
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Affiliation(s)
- Harmony Fong
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Jing Zheng
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Deborah Kurrasch
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
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32
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Li B, Li J, Fan Y, Zhao Z, Li L, Okano H, Ouchi T. Dissecting calvarial bones and sutures at single-cell resolution. Biol Rev Camb Philos Soc 2023; 98:1749-1767. [PMID: 37171117 DOI: 10.1111/brv.12975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/13/2023]
Abstract
Cranial bones constitute a protective shield for the vulnerable brain tissue, bound together as a rigid entity by unique immovable joints known as sutures. Cranial sutures serve as major growth centres for calvarial morphogenesis and have been identified as a niche for mesenchymal stem cells (MSCs) and/or skeletal stem cells (SSCs) in the craniofacial skeleton. Despite the established dogma of cranial bone and suture biology, technological advancements now allow us to investigate these tissues and structures at unprecedented resolution and embrace multiple novel biological insights. For instance, a decrease or imbalance of representation of SSCs within sutures might underlie craniosynostosis; dural sinuses enable neuroimmune crosstalk and are newly defined as immune hubs; skull bone marrow acts as a myeloid cell reservoir for the meninges and central nervous system (CNS) parenchyma in mediating immune surveillance, etc. In this review, we revisit a growing body of recent studies that explored cranial bone and suture biology using cutting-edge techniques and have expanded our current understanding of this research field, especially from the perspective of development, homeostasis, injury repair, resident MSCs/SSCs, immunosurveillance at the brain's border, and beyond.
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Affiliation(s)
- Bo Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jingya Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yi Fan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Zhihe Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Longjiang Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 1608582, Japan
- Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science, Wako-shi, Saitama, 3510198, Japan
| | - Takehito Ouchi
- Department of Physiology, Tokyo Dental College, 2-9-18 Kanda-Misaki-cho, Chiyoda-ku, Tokyo, 1010061, Japan
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33
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Higgs MJ, Webberley AE, Allan AJ, Talat M, John RM, Isles AR. The parenting hub of the hypothalamus is a focus of imprinted gene action. PLoS Genet 2023; 19:e1010961. [PMID: 37856383 PMCID: PMC10586610 DOI: 10.1371/journal.pgen.1010961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 09/07/2023] [Indexed: 10/21/2023] Open
Abstract
Imprinted genes are subject to germline epigenetic modification resulting in parental-specific allelic silencing. Although genomic imprinting is thought to be important for maternal behaviour, this idea is based on serendipitous findings from a small number of imprinted genes. Here, we undertook an unbiased systems biology approach, taking advantage of the recent delineation of specific neuronal populations responsible for controlling parental care, to test whether imprinted genes significantly converge to regulate parenting behaviour. Using single-cell RNA sequencing datasets, we identified a specific enrichment of imprinted gene expression in a recognised "parenting hub", the galanin-expressing neurons of the preoptic area. We tested the validity of linking enriched expression in these neurons to function by focusing on MAGE family member L2 (Magel2), an imprinted gene not previously linked to parenting behaviour. We confirmed expression of Magel2 in the preoptic area galanin expressing neurons. We then examined the parenting behaviour of Magel2-null(+/p) mice. Magel2-null mothers, fathers and virgin females demonstrated deficits in pup retrieval, nest building and pup-directed motivation, identifying a central role for this gene in parenting. Finally, we show that Magel2-null mothers and fathers have a significant reduction in POA galanin expressing cells, which in turn contributes to a reduced c-Fos response in the POA upon exposure to pups. Our findings identify a novel imprinted gene that impacts parenting behaviour and, moreover, demonstrates the utility of using single-cell RNA sequencing data to predict gene function from expression and in doing so here, have identified a purposeful role for genomic imprinting in mediating parental behaviour.
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Affiliation(s)
- Matthew J. Higgs
- Behavioural Genetics Group, Centre for Neuropsychiatric, Genetics and Genomics, Neuroscience and Mental Health Innovation Institute, Cardiff University, Cardiff, United Kingdom
| | - Anna E. Webberley
- Behavioural Genetics Group, Centre for Neuropsychiatric, Genetics and Genomics, Neuroscience and Mental Health Innovation Institute, Cardiff University, Cardiff, United Kingdom
| | | | - Moaz Talat
- The Mary Lyon Centre, MRC Harwell, Didcot, United Kingdom
| | - Rosalind M. John
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Anthony R. Isles
- Behavioural Genetics Group, Centre for Neuropsychiatric, Genetics and Genomics, Neuroscience and Mental Health Innovation Institute, Cardiff University, Cardiff, United Kingdom
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34
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Gazestani V, Kamath T, Nadaf NM, Dougalis A, Burris SJ, Rooney B, Junkkari A, Vanderburg C, Pelkonen A, Gomez-Budia M, Välimäki NN, Rauramaa T, Therrien M, Koivisto AM, Tegtmeyer M, Herukka SK, Abdulraouf A, Marsh SE, Hiltunen M, Nehme R, Malm T, Stevens B, Leinonen V, Macosko EZ. Early Alzheimer's disease pathology in human cortex involves transient cell states. Cell 2023; 186:4438-4453.e23. [PMID: 37774681 PMCID: PMC11107481 DOI: 10.1016/j.cell.2023.08.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/31/2023] [Accepted: 08/03/2023] [Indexed: 10/01/2023]
Abstract
Cellular perturbations underlying Alzheimer's disease (AD) are primarily studied in human postmortem samples and model organisms. Here, we generated a single-nucleus atlas from a rare cohort of cortical biopsies from living individuals with varying degrees of AD pathology. We next performed a systematic cross-disease and cross-species integrative analysis to identify a set of cell states that are specific to early AD pathology. These changes-which we refer to as the early cortical amyloid response-were prominent in neurons, wherein we identified a transitional hyperactive state preceding the loss of excitatory neurons, which we confirmed by acute slice physiology on independent biopsy specimens. Microglia overexpressing neuroinflammatory-related processes also expanded as AD pathology increased. Finally, both oligodendrocytes and pyramidal neurons upregulated genes associated with β-amyloid production and processing during this early hyperactive phase. Our integrative analysis provides an organizing framework for targeting circuit dysfunction, neuroinflammation, and amyloid production early in AD pathogenesis.
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Affiliation(s)
- Vahid Gazestani
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tushar Kamath
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Graduate Program in Biophysics and Harvard/MIT MD-PhD Program, Harvard University, Cambridge, MA 02139, USA
| | - Naeem M Nadaf
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Antonios Dougalis
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - S J Burris
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Brendan Rooney
- Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
| | - Antti Junkkari
- Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland; Department of Neurosurgery, Kuopio University Hospital, Kuopio, Finland
| | | | - Anssi Pelkonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Mireia Gomez-Budia
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Nelli-Noora Välimäki
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Tuomas Rauramaa
- Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland; Department of Pathology, Kuopio University Hospital, Kuopio, Finland
| | | | - Anne M Koivisto
- Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA; Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland; Department of Neurology, Kuopio University Hospital, Kuopio, Finland; Department of Neurosciences, University of Helsinki, Helsinki, Finland; Department of Geriatrics, Helsinki University Hospital, Helsinki, Finland
| | | | - Sanna-Kaisa Herukka
- Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland; Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | | | - Samuel E Marsh
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Mikko Hiltunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Ralda Nehme
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tarja Malm
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Beth Stevens
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute (HHMI), Boston, MA 02115, USA
| | - Ville Leinonen
- Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland; Department of Neurosurgery, Kuopio University Hospital, Kuopio, Finland
| | - Evan Z Macosko
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Massachusetts General Hospital, Department of Psychiatry, Boston, MA 02114, USA.
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35
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Lu Z, Zhang M, Lee J, Sziraki A, Anderson S, Zhang Z, Xu Z, Jiang W, Ge S, Nelson PT, Zhou W, Cao J. Tracking cell-type-specific temporal dynamics in human and mouse brains. Cell 2023; 186:4345-4364.e24. [PMID: 37774676 PMCID: PMC10545416 DOI: 10.1016/j.cell.2023.08.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 05/28/2023] [Accepted: 08/30/2023] [Indexed: 10/01/2023]
Abstract
Progenitor cells are critical in preserving organismal homeostasis, yet their diversity and dynamics in the aged brain remain underexplored. We introduced TrackerSci, a single-cell genomic method that combines newborn cell labeling and combinatorial indexing to characterize the transcriptome and chromatin landscape of proliferating progenitor cells in vivo. Using TrackerSci, we investigated the dynamics of newborn cells in mouse brains across various ages and in a mouse model of Alzheimer's disease. Our dataset revealed diverse progenitor cell types in the brain and their epigenetic signatures. We further quantified aging-associated shifts in cell-type-specific proliferation and differentiation and deciphered the associated molecular programs. Extending our study to the progenitor cells in the aged human brain, we identified conserved genetic signatures across species and pinpointed region-specific cellular dynamics, such as the reduced oligodendrogenesis in the cerebellum. We anticipate that TrackerSci will be broadly applicable to unveil cell-type-specific temporal dynamics in diverse systems.
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Affiliation(s)
- Ziyu Lu
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA; The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Melissa Zhang
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Jasper Lee
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Andras Sziraki
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA; The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Sonya Anderson
- Department of Pathology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Zehao Zhang
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA; The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Zihan Xu
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA; The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Weirong Jiang
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Shaoyu Ge
- Department of Neurobiology & Behavior, SUNY at Stony Brook, Stony Brook, NY, USA
| | - Peter T Nelson
- Department of Pathology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Wei Zhou
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA.
| | - Junyue Cao
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA.
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Sarrafha L, Neavin DR, Parfitt GM, Kruglikov IA, Whitney K, Reyes R, Coccia E, Kareva T, Goldman C, Tipon R, Croft G, Crary JF, Powell JE, Blanchard J, Ahfeldt T. Novel human pluripotent stem cell-derived hypothalamus organoids demonstrate cellular diversity. iScience 2023; 26:107525. [PMID: 37646018 PMCID: PMC10460991 DOI: 10.1016/j.isci.2023.107525] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/19/2023] [Accepted: 07/31/2023] [Indexed: 09/01/2023] Open
Abstract
The hypothalamus is a region of the brain that plays an important role in regulating body functions and behaviors. There is a growing interest in human pluripotent stem cells (hPSCs) for modeling diseases that affect the hypothalamus. Here, we established an hPSC-derived hypothalamus organoid differentiation protocol to model the cellular diversity of this brain region. Using an hPSC line with a tyrosine hydroxylase (TH)-TdTomato reporter for dopaminergic neurons (DNs) and other TH-expressing cells, we interrogated DN-specific pathways and functions in electrophysiologically active hypothalamus organoids. Single-cell RNA sequencing (scRNA-seq) revealed diverse neuronal and non-neuronal cell types in mature hypothalamus organoids. We identified several molecularly distinct hypothalamic DN subtypes that demonstrated different developmental maturities. Our in vitro 3D hypothalamus differentiation protocol can be used to study the development of this critical brain structure and can be applied to disease modeling to generate novel therapeutic approaches for disorders centered around the hypothalamus.
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Affiliation(s)
- Lily Sarrafha
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Department of Neurology, Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY 10029, USA
| | - Drew R. Neavin
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Gustavo M. Parfitt
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY 10029, USA
| | | | - Kristen Whitney
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Molecular, and Cell-Based Medicine, Mount Sinai, New York, NY 10029, USA
| | - Ricardo Reyes
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Department of Neurology, Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY 10029, USA
| | - Elena Coccia
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Department of Neurology, Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY 10029, USA
| | - Tatyana Kareva
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Department of Neurology, Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY 10029, USA
| | - Camille Goldman
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Department of Neurology, Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY 10029, USA
| | - Regine Tipon
- New York Stem Cell Foundation, New York, NY 10019, USA
| | - Gist Croft
- New York Stem Cell Foundation, New York, NY 10019, USA
| | - John F. Crary
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Molecular, and Cell-Based Medicine, Mount Sinai, New York, NY 10029, USA
- Windreich Department of Artificial Intelligence and Human Health, Mount Sinai, New York, NY 10029, USA
| | - Joseph E. Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- UNSW Cellular Genomics Futures Institute, University of New South Wales, Kensington, Sydney, NSW 2052, Australia
| | - Joel Blanchard
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY 10029, USA
| | - Tim Ahfeldt
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Department of Neurology, Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY 10029, USA
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Lemcke R, Egebjerg C, Berendtsen NT, Egerod KL, Thomsen AR, Pers TH, Christensen JP, Kornum BR. Molecular consequences of peripheral Influenza A infection on cell populations in the murine hypothalamus. eLife 2023; 12:RP87515. [PMID: 37698546 PMCID: PMC10497288 DOI: 10.7554/elife.87515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023] Open
Abstract
Infection with Influenza A virus (IAV) causes the well-known symptoms of the flu, including fever, loss of appetite, and excessive sleepiness. These responses, mediated by the brain, will normally disappear once the virus is cleared from the system, but a severe respiratory virus infection may cause long-lasting neurological disturbances. These include encephalitis lethargica and narcolepsy. The mechanisms behind such long lasting changes are unknown. The hypothalamus is a central regulator of the homeostatic response during a viral challenge. To gain insight into the neuronal and non-neuronal molecular changes during an IAV infection, we intranasally infected mice with an H1N1 virus and extracted the brain at different time points. Using single-nucleus RNA sequencing (snRNA-seq) of the hypothalamus, we identify transcriptional effects in all identified cell populations. The snRNA-seq data showed the most pronounced transcriptional response at 3 days past infection, with a strong downregulation of genes across all cell types. General immune processes were mainly impacted in microglia, the brain resident immune cells, where we found increased numbers of cells expressing pro-inflammatory gene networks. In addition, we found that most neuronal cell populations downregulated genes contributing to the energy homeostasis in mitochondria and protein translation in the cytosol, indicating potential reduced cellular and neuronal activity. This might be a preventive mechanism in neuronal cells to avoid intracellular viral replication and attack by phagocytosing cells. The change of microglia gene activity suggest that this is complemented by a shift in microglia activity to provide increased surveillance of their surroundings.
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Affiliation(s)
- René Lemcke
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Christine Egebjerg
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Nicolai T Berendtsen
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Kristoffer L Egerod
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Allan R Thomsen
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Tune H Pers
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Jan P Christensen
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Birgitte R Kornum
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
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38
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He X, Qian K, Wang Z, Zeng S, Li H, Li WV. scAce: an adaptive embedding and clustering method for single-cell gene expression data. Bioinformatics 2023; 39:btad546. [PMID: 37672035 PMCID: PMC10500084 DOI: 10.1093/bioinformatics/btad546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/01/2023] [Accepted: 09/05/2023] [Indexed: 09/07/2023] Open
Abstract
MOTIVATION Since the development of single-cell RNA sequencing (scRNA-seq) technologies, clustering analysis of single-cell gene expression data has been an essential tool for distinguishing cell types and identifying novel cell types. Even though many methods have been available for scRNA-seq clustering analysis, the majority of them are constrained by the requirement on predetermined cluster numbers or the dependence on selected initial cluster assignment. RESULTS In this article, we propose an adaptive embedding and clustering method named scAce, which constructs a variational autoencoder to simultaneously learn cell embeddings and cluster assignments. In the scAce method, we develop an adaptive cluster merging approach which achieves improved clustering results without the need to estimate the number of clusters in advance. In addition, scAce provides an option to perform clustering enhancement, which can update and enhance cluster assignments based on previous clustering results from other methods. Based on computational analysis of both simulated and real datasets, we demonstrate that scAce outperforms state-of-the-art clustering methods for scRNA-seq data, and achieves better clustering accuracy and robustness. AVAILABILITY AND IMPLEMENTATION The scAce package is implemented in python 3.8 and is freely available from https://github.com/sldyns/scAce.
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Affiliation(s)
- Xinwei He
- School of Mathematics and Physics, China University of Geosciences, Wuhan 430074, China
| | - Kun Qian
- School of Mathematics and Physics, China University of Geosciences, Wuhan 430074, China
| | - Ziqian Wang
- School of Mathematics and Physics, China University of Geosciences, Wuhan 430074, China
| | - Shirou Zeng
- School of Mathematics and Physics, China University of Geosciences, Wuhan 430074, China
| | - Hongwei Li
- School of Mathematics and Physics, China University of Geosciences, Wuhan 430074, China
| | - Wei Vivian Li
- Department of Statistics, University of California, Riverside, Riverside 92521, United States
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Wang S, Zhang Y, Zhang Y, Wu W, Ye L, Li Y, Su J, Pang S. scASGC: An adaptive simplified graph convolution model for clustering single-cell RNA-seq data. Comput Biol Med 2023; 163:107152. [PMID: 37364529 DOI: 10.1016/j.compbiomed.2023.107152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/24/2023] [Accepted: 06/07/2023] [Indexed: 06/28/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) is now a successful technique for identifying cellular heterogeneity, revealing novel cell subpopulations, and forecasting developmental trajectories. A crucial component of the processing of scRNA-seq data is the precise identification of cell subpopulations. Although many unsupervised clustering methods have been developed to cluster cell subpopulations, the performance of these methods is vulnerable to dropouts and high dimensionality. In addition, most existing methods are time-consuming and fail to adequately account for potential associations between cells. In the manuscript, we present an unsupervised clustering method based on an adaptive simplified graph convolution model called scASGC. The proposed method builds plausible cell graphs, aggregates neighbor information using a simplified graph convolution model, and adaptively determines the most optimal number of convolution layers for various graphs. Experiments on 12 public datasets show that scASGC outperforms both classical and state-of-the-art clustering methods. In addition, in a study of mouse intestinal muscle containing 15,983 cells, we identified distinct marker genes based on the clustering results of scASGC. The source code of scASGC is available at https://github.com/ZzzOctopus/scASGC.
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Affiliation(s)
- Shudong Wang
- College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao, 266580, China.
| | - Yu Zhang
- College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao, 266580, China.
| | - Yulin Zhang
- College of Mathematics and Systems Science, Shandong University of Science and Technology, Qingdao, 266590, China.
| | - Wenhao Wu
- College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao, 266580, China.
| | - Lan Ye
- Cancer Center, the Second Hospital of Shandong University, Jinan, 250033, China.
| | - YunYin Li
- College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao, 266580, China.
| | - Jionglong Su
- School of AI and Advanced Computing, XJTLU Entrepreneur College (Taicang), Xi'an Jiaotong-Liverpool University, Suzhou, 215123, China.
| | - Shanchen Pang
- College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao, 266580, China.
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40
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Rumpler É, Göcz B, Skrapits K, Sárvári M, Takács S, Farkas I, Póliska S, Papp M, Solymosi N, Hrabovszky E. Development of a versatile LCM-Seq method for spatial transcriptomics of fluorescently tagged cholinergic neuron populations. J Biol Chem 2023; 299:105121. [PMID: 37536628 PMCID: PMC10477691 DOI: 10.1016/j.jbc.2023.105121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/29/2023] [Accepted: 07/20/2023] [Indexed: 08/05/2023] Open
Abstract
Single-cell transcriptomics are powerful tools to define neuronal cell types based on co-expressed gene clusters. Limited RNA input in these technologies necessarily compromises transcriptome coverage and accuracy of differential expression analysis. We propose that bulk RNA-Seq of neuronal pools defined by spatial position offers an alternative strategy to overcome these technical limitations. We report a laser-capture microdissection (LCM)-Seq method which allows deep transcriptome profiling of fluorescently tagged neuron populations isolated with LCM from histological sections of transgenic mice. Mild formaldehyde fixation of ZsGreen marker protein, LCM sampling of ∼300 pooled neurons, followed by RNA isolation, library preparation and RNA-Seq with methods optimized for nanogram amounts of moderately degraded RNA enabled us to detect ∼15,000 different transcripts in fluorescently labeled cholinergic neuron populations. The LCM-Seq approach showed excellent accuracy in quantitative studies, allowing us to detect 2891 transcripts expressed differentially between the spatially defined and clinically relevant cholinergic neuron populations of the dorsal caudate-putamen and medial septum. In summary, the LCM-Seq method we report in this study is a versatile, sensitive, and accurate bulk sequencing approach to study the transcriptome profile and differential gene expression of fluorescently tagged neuronal populations isolated from transgenic mice with high spatial precision.
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Affiliation(s)
- Éva Rumpler
- Laboratory of Reproductive Neurobiology, Institute of Experimental Medicine, Budapest, Hungary.
| | - Balázs Göcz
- Laboratory of Reproductive Neurobiology, Institute of Experimental Medicine, Budapest, Hungary; János Szentágothai Doctoral School of Neurosciences, Semmelweis University, Budapest, Hungary.
| | - Katalin Skrapits
- Laboratory of Reproductive Neurobiology, Institute of Experimental Medicine, Budapest, Hungary
| | - Miklós Sárvári
- Laboratory of Reproductive Neurobiology, Institute of Experimental Medicine, Budapest, Hungary
| | - Szabolcs Takács
- Laboratory of Reproductive Neurobiology, Institute of Experimental Medicine, Budapest, Hungary
| | - Imre Farkas
- Laboratory of Reproductive Neurobiology, Institute of Experimental Medicine, Budapest, Hungary
| | - Szilárd Póliska
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
| | - Márton Papp
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, Hungary
| | - Norbert Solymosi
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, Hungary; Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Erik Hrabovszky
- Laboratory of Reproductive Neurobiology, Institute of Experimental Medicine, Budapest, Hungary.
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Liu Q, Wang D, Zhou L, Li J, Wang G. MTGDC: A Multi-Scale Tensor Graph Diffusion Clustering for Single-Cell RNA Sequencing Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:3056-3067. [PMID: 37418411 DOI: 10.1109/tcbb.2023.3293112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a new technology that focuses on the expression levels for each cell to study cell heterogeneity. Thus, new computational methods matching scRNA-seq are designed to detect cell types among various cell groups. Herein, we propose a Multi-scale Tensor Graph Diffusion Clustering (MTGDC) for single-cell RNA sequencing data. It has the following mechanisms: 1) To mine potential similarity distributions among cells, we design a multi-scale affinity learning method to construct a fully connected graph between cells; 2) For each affinity matrix, we propose an efficient tensor graph diffusion learning framework to learn high-order information among multi-scale affinity matrices. First, the tensor graph is explicitly introduced to measure cell-cell edges with local high-order relationship information. To further preserve more global topology structure information in the tensor graph, MTGDC implicitly considers the propagation of information via a data diffusion process by designing a simple and efficient tensor graph diffusion update algorithm. 3) Finally, we mix together the multi-scale tensor graphs to obtain the fusion high-order affinity matrix and apply it to spectral clustering. Experiments and case studies showed that MTGDC had obvious advantages over the state-of-art algorithms in robustness, accuracy, visualization, and speed.
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42
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Brivio E, Kos A, Ulivi AF, Karamihalev S, Ressle A, Stoffel R, Hirsch D, Stelzer G, Schmidt MV, Lopez JP, Chen A. Sex shapes cell-type-specific transcriptional signatures of stress exposure in the mouse hypothalamus. Cell Rep 2023; 42:112874. [PMID: 37516966 DOI: 10.1016/j.celrep.2023.112874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 05/19/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023] Open
Abstract
Stress-related psychiatric disorders and the stress system show prominent differences between males and females, as well as strongly divergent transcriptional changes. Despite several proposed mechanisms, we still lack the understanding of the molecular processes at play. Here, we explore the contribution of cell types to transcriptional sex dimorphism using single-cell RNA sequencing. We identify cell-type-specific signatures of acute restraint stress in the paraventricular nucleus of the hypothalamus, a central hub of the stress response, in male and female mice. Further, we show that a history of chronic mild stress alters these signatures in a sex-specific way, and we identify oligodendrocytes as a major target for these sex-specific effects. This dataset, which we provide as an online interactive app, offers the transcriptomes of thousands of individual cells as a molecular resource for an in-depth dissection of the interplay between cell types and sex on the mechanisms of the stress response.
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Affiliation(s)
- Elena Brivio
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, 80804 Munich, Germany; International Max Planck Research School for Translational Psychiatry (IMPRS-TP), 80804 Munich, Germany; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Brain Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Aron Kos
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | | | - Stoyo Karamihalev
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, 80804 Munich, Germany; International Max Planck Research School for Translational Psychiatry (IMPRS-TP), 80804 Munich, Germany
| | - Andrea Ressle
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Rainer Stoffel
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Dana Hirsch
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gil Stelzer
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Mathias V Schmidt
- Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Juan Pablo Lopez
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, 80804 Munich, Germany; Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden.
| | - Alon Chen
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, 80804 Munich, Germany; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Brain Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
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43
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Bouâouda H, Jha PK. Orexin and MCH neurons: regulators of sleep and metabolism. Front Neurosci 2023; 17:1230428. [PMID: 37674517 PMCID: PMC10478345 DOI: 10.3389/fnins.2023.1230428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023] Open
Abstract
Sleep-wake and fasting-feeding are tightly coupled behavioral states that require coordination between several brain regions. The mammalian lateral hypothalamus (LH) is a functionally and anatomically complex brain region harboring heterogeneous cell populations that regulate sleep, feeding, and energy metabolism. Significant attempts were made to understand the cellular and circuit bases of LH actions. Rapid advancements in genetic and electrophysiological manipulation help to understand the role of discrete LH cell populations. The opposing action of LH orexin/hypocretin and melanin-concentrating hormone (MCH) neurons on metabolic sensing and sleep-wake regulation make them the candidate to explore in detail. This review surveys the molecular, genetic, and neuronal components of orexin and MCH signaling in the regulation of sleep and metabolism.
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Affiliation(s)
- Hanan Bouâouda
- Pharmacology Institute, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Pawan Kumar Jha
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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44
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Littleton SH, Trang KB, Volpe CM, Cook K, DeBruyne N, Ann Maguire J, Ann Weidekamp M, Boehm K, Chesi A, Pippin JA, Anderson SA, Wells AD, Pahl MC, Grant SF. Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3' UTR of FAIM2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.553157. [PMID: 37662342 PMCID: PMC10473629 DOI: 10.1101/2023.08.21.553157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The ch12q13 obesity locus is among the most significant childhood obesity loci identified in genome-wide association studies. This locus resides in a non-coding region within FAIM2; thus, the underlying causal variant(s) presumably influence disease susceptibility via an influence on cis-regulation within the genomic region. We implicated rs7132908 as a putative causal variant at this locus leveraging a combination of our inhouse 3D genomic data, public domain datasets, and several computational approaches. Using a luciferase reporter assay in human primary astrocytes, we observed allele-specific cis-regulatory activity of the immediate region harboring rs7132908. Motivated by this finding, we went on to generate isogenic human embryonic stem cell lines homozygous for either rs7132908 allele with CRISPR-Cas9 homology-directed repair to assess changes in gene expression due to genotype and chromatin accessibility throughout a differentiation to hypothalamic neurons, a key cell type known to regulate feeding behavior. We observed that the rs7132908 obesity risk allele influenced the expression of FAIM2 along with other genes, decreased the proportion of neurons produced during differentiation, up-regulated cell death gene sets, and conversely down-regulated neuron differentiation gene sets. We have therefore functionally validated rs7132908 as a causal obesity variant which temporally regulates nearby effector genes at the ch12q13 locus and influences neurodevelopment and survival.
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Affiliation(s)
- Sheridan H. Littleton
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Khanh B. Trang
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Christina M. Volpe
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kieona Cook
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Psychiatry, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nicole DeBruyne
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jean Ann Maguire
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mary Ann Weidekamp
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Keith Boehm
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alessandra Chesi
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James A. Pippin
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Stewart A. Anderson
- Department of Child and Adolescent Psychiatry, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew D. Wells
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew C. Pahl
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Struan F.A. Grant
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
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45
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Imoesi PI, Olarte-Sánchez CM, Croce L, Blaner WS, Morgan PJ, Heisler L, McCaffery P. Control by the brain of vitamin A homeostasis. iScience 2023; 26:107373. [PMID: 37599827 PMCID: PMC10432198 DOI: 10.1016/j.isci.2023.107373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/16/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023] Open
Abstract
Vitamin A is a micronutrient essential for vertebrate animals maintained in homeostatic balance in the body; however, little is known about the control of this balance. This study investigated whether the hypothalamus, a key integrative brain region, regulates vitamin A levels in the liver and circulation. Vitamin A in the form of retinol or retinoic acid was stereotactically injected into the 3rd ventricle of the rat brain. Alternatively, retinoids in the mouse hypothalamus were altered through retinol-binding protein 4 (Rbp4) gene knockdown. This led to rapid change in the liver proteins controlling vitamin A homeostasis as well as vitamin A itself in liver and the circulation. Prolonged disruption of Rbp4 in the region of the arcuate nucleus of the mouse hypothalamus altered retinol levels in the liver. This supports the concept that the brain may sense retinoids and influence whole-body vitamin A homeostasis with a possible "vitaminostatic" role.
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Affiliation(s)
- Peter I. Imoesi
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Cristian M. Olarte-Sánchez
- Rowett Institute, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Lorenzo Croce
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - William S. Blaner
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY 10032, USA
| | - Peter J. Morgan
- Rowett Institute, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Lora Heisler
- Rowett Institute, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Peter McCaffery
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
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46
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Cappelletti C, Henriksen SP, Geut H, Rozemuller AJM, van de Berg WDJ, Pihlstrøm L, Toft M. Transcriptomic profiling of Parkinson's disease brains reveals disease stage specific gene expression changes. Acta Neuropathol 2023; 146:227-244. [PMID: 37347276 PMCID: PMC10329075 DOI: 10.1007/s00401-023-02597-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 05/02/2023] [Accepted: 06/06/2023] [Indexed: 06/23/2023]
Abstract
Parkinson´s disease (PD) is a progressive neurodegenerative disorder characterized by both motor and non-motor symptoms. Aggravation of symptoms is mirrored by accumulation of protein aggregates mainly composed by alpha-synuclein in different brain regions, called Lewy bodies (LB). Previous studies have identified several molecular mechanisms as autophagy and inflammation playing a role in PD pathogenesis. Increased insights into mechanisms involved in early disease stages and driving the progression of the LB pathology are required for the development of disease-modifying strategies. Here, we aimed to elucidate disease stage-specific transcriptomic changes in brain tissue of well-characterized PD and control donors. We collected frontal cortex samples from 84 donors and sequenced both the coding and non-coding RNAs. We categorized our samples into groups based on their degree of LB pathology aiming to recapitulate a central aspect of disease progression. Using an analytical pipeline that corrected for sex, age at death, RNA quality, cell composition and unknown sources of variation, we found major disease stage-specific transcriptomic changes. Gene expression changes were most pronounced in donors at the disease stage when microscopic LB changes first occur in the sampled brain region. Additionally, we identified disease stage-specific enrichment of brain specific pathways and immune mechanisms. On the contrary, we showed that mitochondrial mechanisms are enriched throughout the disease course. Our data-driven approach also suggests a role for several poorly characterized lncRNAs in disease development and progression of PD. Finally, by combining genetic and epigenetic information, we highlighted two genes (MAP4K4 and PHYHIP) as candidate genes for future functional studies. Together our results indicate that transcriptomic dysregulation and associated functional changes are highly disease stage-specific, which has major implications for the study of neurodegenerative disorders.
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Affiliation(s)
- Chiara Cappelletti
- Department of Mechanical, Electronics and Chemical Engineering, Faculty of Technology, Art and Design, OsloMet-Oslo Metropolitan University, Oslo, Norway
- Department of Research, Innovation and Education, Oslo University Hospital, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | | | - Hanneke Geut
- Amsterdam UMC, Section Clinical Neuroanatomy and Biobanking, Department of Anatomy and Neurosciences, Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, Netherlands
- Netherlands Brain Bank, Netherlands Institute of Neurosciences, Amsterdam, Netherlands
| | - Annemieke J M Rozemuller
- Department of Pathology, Amsterdam UMC, Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, Netherlands
| | - Wilma D J van de Berg
- Amsterdam UMC, Section Clinical Neuroanatomy and Biobanking, Department of Anatomy and Neurosciences, Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, Netherlands
| | - Lasse Pihlstrøm
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Mathias Toft
- Department of Neurology, Oslo University Hospital, Oslo, Norway.
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
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47
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Jin K, Yao Z, van Velthoven CTJ, Kaplan ES, Glattfelder K, Barlow ST, Boyer G, Carey D, Casper T, Chakka AB, Chakrabarty R, Clark M, Departee M, Desierto M, Gary A, Gloe J, Goldy J, Guilford N, Guzman J, Hirschstein D, Lee C, Liang E, Pham T, Reding M, Ronellenfitch K, Ruiz A, Sevigny J, Shapovalova N, Shulga L, Sulc J, Torkelson A, Tung H, Levi B, Sunkin SM, Dee N, Esposito L, Smith K, Tasic B, Zeng H. Cell-type specific molecular signatures of aging revealed in a brain-wide transcriptomic cell-type atlas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.26.550355. [PMID: 38168182 PMCID: PMC10760145 DOI: 10.1101/2023.07.26.550355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Biological aging can be defined as a gradual loss of homeostasis across various aspects of molecular and cellular function. Aging is a complex and dynamic process which influences distinct cell types in a myriad of ways. The cellular architecture of the mammalian brain is heterogeneous and diverse, making it challenging to identify precise areas and cell types of the brain that are more susceptible to aging than others. Here, we present a high-resolution single-cell RNA sequencing dataset containing ~1.2 million high-quality single-cell transcriptomic profiles of brain cells from young adult and aged mice across both sexes, including areas spanning the forebrain, midbrain, and hindbrain. We find age-associated gene expression signatures across nearly all 130+ neuronal and non-neuronal cell subclasses we identified. We detect the greatest gene expression changes in non-neuronal cell types, suggesting that different cell types in the brain vary in their susceptibility to aging. We identify specific, age-enriched clusters within specific glial, vascular, and immune cell types from both cortical and subcortical regions of the brain, and specific gene expression changes associated with cell senescence, inflammation, decrease in new myelination, and decreased vasculature integrity. We also identify genes with expression changes across multiple cell subclasses, pointing to certain mechanisms of aging that may occur across wide regions or broad cell types of the brain. Finally, we discover the greatest gene expression changes in cell types localized to the third ventricle of the hypothalamus, including tanycytes, ependymal cells, and Tbx3+ neurons found in the arcuate nucleus that are part of the neuronal circuits regulating food intake and energy homeostasis. These findings suggest that the area surrounding the third ventricle in the hypothalamus may be a hub for aging in the mouse brain. Overall, we reveal a dynamic landscape of cell-type-specific transcriptomic changes in the brain associated with normal aging that will serve as a foundation for the investigation of functional changes in the aging process and the interaction of aging and diseases.
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Affiliation(s)
- Kelly Jin
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | - Daniel Carey
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Max Departee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jessica Gloe
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | - Josh Sevigny
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Boaz Levi
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
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48
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Cai J, Chen J, Ortiz-Guzman J, Huang J, Arenkiel BR, Wang Y, Zhang Y, Shi Y, Tong Q, Zhan C. AgRP neurons are not indispensable for body weight maintenance in adult mice. Cell Rep 2023; 42:112789. [PMID: 37422762 PMCID: PMC10909125 DOI: 10.1016/j.celrep.2023.112789] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/16/2023] [Accepted: 06/23/2023] [Indexed: 07/11/2023] Open
Abstract
In addition to their role in promoting feeding and obesity development, hypothalamic arcuate agouti-related protein/neuropeptide Y (AgRP/NPY) neurons are widely perceived to be indispensable for maintaining normal feeding and body weight in adults, and consistently, acute inhibition of AgRP neurons is known to reduce short-term food intake. Here, we adopted complementary methods to achieve nearly complete ablation of arcuate AgRP/NPY neurons in adult mice and report that lesioning arcuate AgRP/NPY neurons in adult mice causes no apparent alterations in ad libitum feeding or body weight. Consistent with previous studies, loss of AgRP/NPY neurons blunts fasting refeeding. Thus, our studies show that AgRP/NPY neurons are not required for maintaining ad libitum feeding or body weight homeostasis in adult mice.
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Affiliation(s)
- Jing Cai
- Brown Institute of Molecular Medicine at McGovern Medical School and Neuroscience Program of MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jing Chen
- School of Sport Science, Beijing Sport University, Beijing 100084, China
| | - Joshua Ortiz-Guzman
- Duncan Institute of Neurological Research and Department of Neuroscience and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jessica Huang
- Brown Institute of Molecular Medicine at McGovern Medical School and Neuroscience Program of MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Benjamin R Arenkiel
- Duncan Institute of Neurological Research and Department of Neuroscience and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yuchen Wang
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Hematology, The First Affiliated Hospital of USTC, CAS Key Laboratory of Brain Function and Disease, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Yan Zhang
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yuyan Shi
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Hematology, The First Affiliated Hospital of USTC, CAS Key Laboratory of Brain Function and Disease, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Qingchun Tong
- Brown Institute of Molecular Medicine at McGovern Medical School and Neuroscience Program of MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Cheng Zhan
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Hematology, The First Affiliated Hospital of USTC, CAS Key Laboratory of Brain Function and Disease, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.
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49
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Qian T, Wang H, Wang P, Geng L, Mei L, Osakada T, Wang L, Tang Y, Kania A, Grinevich V, Stoop R, Lin D, Luo M, Li Y. A genetically encoded sensor measures temporal oxytocin release from different neuronal compartments. Nat Biotechnol 2023; 41:944-957. [PMID: 36593404 PMCID: PMC11182738 DOI: 10.1038/s41587-022-01561-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 10/12/2022] [Indexed: 01/03/2023]
Abstract
Oxytocin (OT), a peptide hormone and neuromodulator, is involved in diverse physiological and pathophysiological processes in the central nervous system and the periphery. However, the regulation and functional sequences of spatial OT release in the brain remain poorly understood. We describe a genetically encoded G-protein-coupled receptor activation-based (GRAB) OT sensor called GRABOT1.0. In contrast to previous methods, GRABOT1.0 enables imaging of OT release ex vivo and in vivo with suitable sensitivity, specificity and spatiotemporal resolution. Using this sensor, we visualize stimulation-induced OT release from specific neuronal compartments in mouse brain slices and discover that N-type calcium channels predominantly mediate axonal OT release, whereas L-type calcium channels mediate somatodendritic OT release. We identify differences in the fusion machinery of OT release for axon terminals versus somata and dendrites. Finally, we measure OT dynamics in various brain regions in mice during male courtship behavior. Thus, GRABOT1.0 provides insights into the role of compartmental OT release in physiological and behavioral functions.
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Affiliation(s)
- Tongrui Qian
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Huan Wang
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Peng Wang
- Medical Center for Human Reproduction, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Lan Geng
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Long Mei
- Neuroscience Institute, Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA
| | - Takuya Osakada
- Neuroscience Institute, Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA
| | - Lei Wang
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Peking University, Beijing, China
| | - Yan Tang
- Center for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital Center (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Alan Kania
- Department of Neuropeptide Research in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Valery Grinevich
- Department of Neuropeptide Research in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Ron Stoop
- Center for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital Center (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Dayu Lin
- Neuroscience Institute, Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA
| | - Minmin Luo
- National Institute of Biological Sciences (NIBS), Beijing, China
- Chinese Institute for Brain Research, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research (TIMBR), Tsinghua University, Beijing, China
| | - Yulong Li
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China.
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China.
- Chinese Institute for Brain Research, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
- National Biomedical Imaging Center, Peking University, Beijing, China.
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50
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Wu SR, Butts JC, Caudill MS, Revelli JP, Dhindsa RS, Durham MA, Zoghbi HY. Atoh1 drives the heterogeneity of the pontine nuclei neurons and promotes their differentiation. SCIENCE ADVANCES 2023; 9:eadg1671. [PMID: 37390208 PMCID: PMC10313176 DOI: 10.1126/sciadv.adg1671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 05/26/2023] [Indexed: 07/02/2023]
Abstract
Pontine nuclei (PN) neurons mediate the communication between the cerebral cortex andthe cerebellum to refine skilled motor functions. Prior studies showed that PN neurons fall into two subtypes based on their anatomic location and region-specific connectivity, but the extent of their heterogeneity and its molecular drivers remain unknown. Atoh1 encodes a transcription factor that is expressed in the PN precursors. We previously showed that partial loss of Atoh1 function in mice results in delayed PN development and impaired motor learning. In this study, we performed single-cell RNA sequencing to elucidate the cell state-specific functions of Atoh1 during PN development and found that Atoh1 regulates cell cycle exit, differentiation, migration, and survival of PN neurons. Our data revealed six previously not known PN subtypes that are molecularly and spatially distinct. We found that the PN subtypes exhibit differential vulnerability to partial loss of Atoh1 function, providing insights into the prominence of PN phenotypes in patients with ATOH1 missense mutations.
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Affiliation(s)
- Sih-Rong Wu
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
| | - Jessica C. Butts
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX, USA
| | - Matthew S. Caudill
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
| | - Jean-Pierre Revelli
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ryan S. Dhindsa
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Mark A. Durham
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
- Medical Student Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Huda Y. Zoghbi
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
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