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Berg K, Gorham J, Lundt F, Seidman J, Brueckner M. Endocardial primary cilia and blood flow are required for regulation of EndoMT during endocardial cushion development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594405. [PMID: 38798559 PMCID: PMC11118576 DOI: 10.1101/2024.05.15.594405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Blood flow is critical for heart valve formation, and cellular mechanosensors are essential to translate flow into transcriptional regulation of development. Here, we identify a role for primary cilia in vivo in the spatial regulation of cushion formation, the first stage of valve development, by regionally controlling endothelial to mesenchymal transition (EndoMT) via modulation of Kruppel-like Factor 4 (Klf4) . We find that high shear stress intracardiac regions decrease endocardial ciliation over cushion development, correlating with KLF4 downregulation and EndoMT progression. Mouse embryos constitutively lacking cilia exhibit a blood-flow dependent accumulation of KLF4 in these regions, independent of upstream left-right abnormalities, resulting in impaired cushion cellularization. snRNA-seq revealed that cilia KO endocardium fails to progress to late-EndoMT, retains endothelial markers and has reduced EndoMT/mesenchymal genes that KLF4 antagonizes. Together, these data identify a mechanosensory role for endocardial primary cilia in cushion development through regional regulation of KLF4.
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2
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Xiao F, Zhang X, Morton SU, Kim SW, Fan Y, Gorham JM, Zhang H, Berkson PJ, Mazumdar N, Cao Y, Chen J, Hagen J, Liu X, Zhou P, Richter F, Shen Y, Ward T, Gelb BD, Seidman JG, Seidman CE, Pu WT. Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease. Nat Genet 2024; 56:420-430. [PMID: 38378865 DOI: 10.1038/s41588-024-01669-y] [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: 07/21/2022] [Accepted: 01/23/2024] [Indexed: 02/22/2024]
Abstract
Rare coding mutations cause ∼45% of congenital heart disease (CHD). Noncoding mutations that perturb cis-regulatory elements (CREs) likely contribute to the remaining cases, but their identification has been problematic. Using a lentiviral massively parallel reporter assay (lentiMPRA) in human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), we functionally evaluated 6,590 noncoding de novo variants (ncDNVs) prioritized from the whole-genome sequencing of 750 CHD trios. A total of 403 ncDNVs substantially affected cardiac CRE activity. A majority increased enhancer activity, often at regions with undetectable reference sequence activity. Of ten DNVs tested by introduction into their native genomic context, four altered the expression of neighboring genes and iPSC-CM transcriptional state. To prioritize future DNVs for functional testing, we used the MPRA data to develop a regression model, EpiCard. Analysis of an independent CHD cohort by EpiCard found enrichment of DNVs. Together, we developed a scalable system to measure the effect of ncDNVs on CRE activity and deployed it to systematically assess the contribution of ncDNVs to CHD.
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Affiliation(s)
- Feng Xiao
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Xiaoran Zhang
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Sarah U Morton
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Seong Won Kim
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Youfei Fan
- Department of Pediatrics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Joshua M Gorham
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Huan Zhang
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paul J Berkson
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Neil Mazumdar
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Yangpo Cao
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Jian Chen
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Jacob Hagen
- Mindich Child Health and Development Institute and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Xujie Liu
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Pingzhu Zhou
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Felix Richter
- Mindich Child Health and Development Institute and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Yufeng Shen
- Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York City, NY, USA
| | - Tarsha Ward
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Bruce D Gelb
- Mindich Child Health and Development Institute and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | | | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Division of Cardiology, Brigham and Women's Hospital, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
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3
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Qiu Y, Sajidah ES, Kondo S, Narimatsu S, Sandira MI, Higashiguchi Y, Nishide G, Taoka A, Hazawa M, Inaba Y, Inoue H, Matsushima A, Okada Y, Nakada M, Ando T, Lim K, Wong RW. An Efficient Method for Isolating and Purifying Nuclei from Mice Brain for Single-Molecule Imaging Using High-Speed Atomic Force Microscopy. Cells 2024; 13:279. [PMID: 38334671 PMCID: PMC10855070 DOI: 10.3390/cells13030279] [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: 12/20/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/10/2024] Open
Abstract
Nuclear pore complexes (NPCs) on the nuclear membrane surface have a crucial function in controlling the movement of small molecules and macromolecules between the cell nucleus and cytoplasm through their intricate core channel resembling a spiderweb with several layers. Currently, there are few methods available to accurately measure the dynamics of nuclear pores on the nuclear membranes at the nanoscale. The limitation of traditional optical imaging is due to diffraction, which prevents achieving the required resolution for observing a diverse array of organelles and proteins within cells. Super-resolution techniques have effectively addressed this constraint by enabling the observation of subcellular components on the nanoscale. Nevertheless, it is crucial to acknowledge that these methods often need the use of fixed samples. This also raises the question of how closely a static image represents the real intracellular dynamic system. High-speed atomic force microscopy (HS-AFM) is a unique technique used in the field of dynamic structural biology, enabling the study of individual molecules in motion close to their native states. Establishing a reliable and repeatable technique for imaging mammalian tissue at the nanoscale using HS-AFM remains challenging due to inadequate sample preparation. This study presents the rapid strainer microfiltration (RSM) protocol for directly preparing high-quality nuclei from the mouse brain. Subsequently, we promptly utilize HS-AFM real-time imaging and cinematography approaches to record the spatiotemporal of nuclear pore nano-dynamics from the mouse brain.
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Affiliation(s)
- Yujia Qiu
- Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan; (Y.Q.); (M.I.S.)
| | - Elma Sakinatus Sajidah
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan (M.H.); (T.A.)
| | - Sota Kondo
- Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan; (Y.Q.); (M.I.S.)
| | - Shinnosuke Narimatsu
- Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan; (Y.Q.); (M.I.S.)
| | - Muhammad Isman Sandira
- Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan; (Y.Q.); (M.I.S.)
| | - Yoshiki Higashiguchi
- Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan; (Y.Q.); (M.I.S.)
| | - Goro Nishide
- Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan; (Y.Q.); (M.I.S.)
| | - Azuma Taoka
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan (M.H.); (T.A.)
| | - Masaharu Hazawa
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan (M.H.); (T.A.)
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan
| | - Yuka Inaba
- Metabolism and Nutrition Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa 920-8641, Japan
| | - Hiroshi Inoue
- Metabolism and Nutrition Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa 920-8641, Japan
| | - Ayami Matsushima
- Laboratory of Structure-Function Biochemistry, Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Yuki Okada
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Mitsutoshi Nakada
- Department of Neurosurgery, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8641, Japan
| | - Toshio Ando
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan (M.H.); (T.A.)
| | - Keesiang Lim
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan (M.H.); (T.A.)
| | - Richard W. Wong
- Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan; (Y.Q.); (M.I.S.)
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan (M.H.); (T.A.)
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan
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4
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Lu C, Wei Y, Abbas M, Agula H, Wang E, Meng Z, Zhang R. Application of Single-Cell Assay for Transposase-Accessible Chromatin with High Throughput Sequencing in Plant Science: Advances, Technical Challenges, and Prospects. Int J Mol Sci 2024; 25:1479. [PMID: 38338756 PMCID: PMC10855595 DOI: 10.3390/ijms25031479] [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: 11/28/2023] [Revised: 01/16/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
The Single-cell Assay for Transposase-Accessible Chromatin with high throughput sequencing (scATAC-seq) has gained increasing popularity in recent years, allowing for chromatin accessibility to be deciphered and gene regulatory networks (GRNs) to be inferred at single-cell resolution. This cutting-edge technology now enables the genome-wide profiling of chromatin accessibility at the cellular level and the capturing of cell-type-specific cis-regulatory elements (CREs) that are masked by cellular heterogeneity in bulk assays. Additionally, it can also facilitate the identification of rare and new cell types based on differences in chromatin accessibility and the charting of cellular developmental trajectories within lineage-related cell clusters. Due to technical challenges and limitations, the data generated from scATAC-seq exhibit unique features, often characterized by high sparsity and noise, even within the same cell type. To address these challenges, various bioinformatic tools have been developed. Furthermore, the application of scATAC-seq in plant science is still in its infancy, with most research focusing on root tissues and model plant species. In this review, we provide an overview of recent progress in scATAC-seq and its application across various fields. We first conduct scATAC-seq in plant science. Next, we highlight the current challenges of scATAC-seq in plant science and major strategies for cell type annotation. Finally, we outline several future directions to exploit scATAC-seq technologies to address critical challenges in plant science, ranging from plant ENCODE(The Encyclopedia of DNA Elements) project construction to GRN inference, to deepen our understanding of the roles of CREs in plant biology.
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Affiliation(s)
- Chao Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.L.); (Y.W.)
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Yunxiao Wei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.L.); (Y.W.)
| | - Mubashir Abbas
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.L.); (Y.W.)
| | - Hasi Agula
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Edwin Wang
- Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Zhigang Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.L.); (Y.W.)
| | - Rui Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.L.); (Y.W.)
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5
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Sweat ME, Cao Y, Zhang X, Burnicka-Turek O, Perez-Cervantes C, Arulsamy K, Lu F, Keating EM, Akerberg BN, Ma Q, Wakimoto H, Gorham JM, Hill LD, Kyoung Song M, Trembley MA, Wang P, Gianeselli M, Prondzynski M, Bortolin RH, Bezzerides VJ, Chen K, Seidman JG, Seidman CE, Moskowitz IP, Pu WT. Tbx5 maintains atrial identity in post-natal cardiomyocytes by regulating an atrial-specific enhancer network. NATURE CARDIOVASCULAR RESEARCH 2023; 2:881-898. [PMID: 38344303 PMCID: PMC10854392 DOI: 10.1038/s44161-023-00334-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 08/21/2023] [Indexed: 02/15/2024]
Abstract
Understanding how the atrial and ventricular heart chambers maintain distinct identities is a prerequisite for treating chamber-specific diseases. Here, we selectively knocked out (KO) the transcription factor Tbx5 in the atrial working myocardium to evaluate its requirement for atrial identity. Atrial Tbx5 inactivation downregulated atrial cardiomyocyte (aCM) selective gene expression. Using concurrent single nucleus transcriptome and open chromatin profiling, genomic accessibility differences were identified between control and Tbx5 KO aCMs, revealing that 69% of the control-enriched ATAC regions were bound by TBX5. Genes associated with these regions were downregulated in KO aCMs, suggesting they function as TBX5-dependent enhancers. Comparing enhancer chromatin looping using H3K27ac HiChIP identified 510 chromatin loops sensitive to TBX5 dosage, and 74.8% of control-enriched loops contained anchors in control-enriched ATAC regions. Together, these data demonstrate TBX5 maintains the atrial gene expression program by binding to and preserving the tissue-specific chromatin architecture of atrial enhancers.
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Affiliation(s)
- Mason E. Sweat
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Yangpo Cao
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Xiaoran Zhang
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Ozanna Burnicka-Turek
- Department of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL
| | - Carlos Perez-Cervantes
- Department of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL
| | - Kulandai Arulsamy
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Fujian Lu
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Erin M. Keating
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Brynn N. Akerberg
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Qing Ma
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Joshua M. Gorham
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Lauren D. Hill
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Mi Kyoung Song
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
| | - Michael A. Trembley
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Peizhe Wang
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Matteo Gianeselli
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | | | - Raul H. Bortolin
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | | | - Kaifu Chen
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Jonathan G. Seidman
- Department of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL
| | - Christine E. Seidman
- Department of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL
| | - Ivan P. Moskowitz
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - William T. Pu
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
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6
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Chen C, Ge Y, Lu L. Opportunities and challenges in the application of single-cell and spatial transcriptomics in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1185377. [PMID: 37636094 PMCID: PMC10453814 DOI: 10.3389/fpls.2023.1185377] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/26/2023] [Indexed: 08/29/2023]
Abstract
Single-cell and spatial transcriptomics have diverted researchers' attention from the multicellular level to the single-cell level and spatial information. Single-cell transcriptomes provide insights into the transcriptome at the single-cell level, whereas spatial transcriptomes help preserve spatial information. Although these two omics technologies are helpful and mature, further research is needed to ensure their widespread applicability in plant studies. Reviewing recent research on plant single-cell or spatial transcriptomics, we compared the different experimental methods used in various plants. The limitations and challenges are clear for both single-cell and spatial transcriptomic analyses, such as the lack of applicability, spatial information, or high resolution. Subsequently, we put forth further applications, such as cross-species analysis of roots at the single-cell level and the idea that single-cell transcriptome analysis needs to be combined with other omics analyses to achieve superiority over individual omics analyses. Overall, the results of this review suggest that combining single-cell transcriptomics, spatial transcriptomics, and spatial element distribution can provide a promising research direction, particularly for plant research.
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Affiliation(s)
- Ce Chen
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yining Ge
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Lingli Lu
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Agricultural Resource and Environment of Zhejiang Province, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
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7
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Jones RE, Gruszczyk AV, Schmidt C, Hammersley DJ, Mach L, Lee M, Wong J, Yang M, Hatipoglu S, Lota AS, Barnett SN, Toscano-Rivalta R, Owen R, Raja S, De Robertis F, Smail H, De-Souza A, Stock U, Kellman P, Griffin J, Dumas ME, Martin JL, Saeb-Parsy K, Vazir A, Cleland JGF, Pennell DJ, Bhudia SK, Halliday BP, Noseda M, Frezza C, Murphy MP, Prasad SK. Assessment of left ventricular tissue mitochondrial bioenergetics in patients with stable coronary artery disease. NATURE CARDIOVASCULAR RESEARCH 2023; 2:733-745. [PMID: 38666037 PMCID: PMC11041759 DOI: 10.1038/s44161-023-00312-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 06/29/2023] [Indexed: 04/28/2024]
Abstract
Recurrent myocardial ischemia can lead to left ventricular (LV) dysfunction in patients with coronary artery disease (CAD). In this observational cohort study, we assessed for chronic metabolomic and transcriptomic adaptations within LV myocardium of patients undergoing coronary artery bypass grafting. During surgery, paired transmural LV biopsies were acquired on the beating heart from regions with and without evidence of inducible ischemia on preoperative stress perfusion cardiovascular magnetic resonance. From 33 patients, 63 biopsies were acquired, compared to analysis of LV samples from 11 donor hearts. The global myocardial adenosine triphosphate (ATP):adenosine diphosphate (ADP) ratio was reduced in patients with CAD as compared to donor LV tissue, with increased expression of oxidative phosphorylation (OXPHOS) genes encoding the electron transport chain complexes across multiple cell types. Paired analyses of biopsies obtained from LV segments with or without inducible ischemia revealed no significant difference in the ATP:ADP ratio, broader metabolic profile or expression of ventricular cardiomyocyte genes implicated in OXPHOS. Differential metabolite analysis suggested dysregulation of several intermediates in patients with reduced LV ejection fraction, including succinate. Overall, our results suggest that viable myocardium in patients with stable CAD has global alterations in bioenergetic and transcriptional profile without large regional differences between areas with or without inducible ischemia.
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Affiliation(s)
- Richard E. Jones
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
- Anglia Ruskin University, Chelmsford, UK
- Essex Cardiothoracic Centre, Basildon, UK
| | - Anja V. Gruszczyk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | | | - Daniel J. Hammersley
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Lukas Mach
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Michael Lee
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Joyce Wong
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Ming Yang
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
- University of Cologne, CECAD, Cologne, Germany
| | - Suzan Hatipoglu
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Amrit S. Lota
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Sam N. Barnett
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Ruth Owen
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, London, UK
| | - Shahzad Raja
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Fabio De Robertis
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Hassiba Smail
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Anthony De-Souza
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Ulrich Stock
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Peter Kellman
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Julian Griffin
- The Rowett Institute, University of Aberdeen, Aberdeen, UK
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Marc-Emmanuel Dumas
- National Heart and Lung Institute, Imperial College London, London, UK
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- European Genomic Institute of Diabetes, INSERM U1283, CNRS 8199, Institut Pasteur de Lille, Lille University Hospital, University of Lille, Lille, France
- McGill Genome Centre, McGill University, Montréal, QC Canada
| | - Jack L. Martin
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Ali Vazir
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | | | - Dudley J. Pennell
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Sunil K. Bhudia
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Brian P. Halliday
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Michela Noseda
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Michael P. Murphy
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Sanjay K. Prasad
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
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8
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Piwecka M, Rajewsky N, Rybak-Wolf A. Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease. Nat Rev Neurol 2023:10.1038/s41582-023-00809-y. [PMID: 37198436 DOI: 10.1038/s41582-023-00809-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2023] [Indexed: 05/19/2023]
Abstract
In the past decade, single-cell technologies have proliferated and improved from their technically challenging beginnings to become common laboratory methods capable of determining the expression of thousands of genes in thousands of cells simultaneously. The field has progressed by taking the CNS as a primary research subject - the cellular complexity and multiplicity of neuronal cell types provide fertile ground for the increasing power of single-cell methods. Current single-cell RNA sequencing methods can quantify gene expression with sufficient accuracy to finely resolve even subtle differences between cell types and states, thus providing a great tool for studying the molecular and cellular repertoire of the CNS and its disorders. However, single-cell RNA sequencing requires the dissociation of tissue samples, which means that the interrelationships between cells are lost. Spatial transcriptomic methods bypass tissue dissociation and retain this spatial information, thereby allowing gene expression to be assessed across thousands of cells within the context of tissue structural organization. Here, we discuss how single-cell and spatially resolved transcriptomics have been contributing to unravelling the pathomechanisms underlying brain disorders. We focus on three areas where we feel these new technologies have provided particularly useful insights: selective neuronal vulnerability, neuroimmune dysfunction and cell-type-specific treatment response. We also discuss the limitations and future directions of single-cell and spatial RNA sequencing technologies.
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Affiliation(s)
- Monika Piwecka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Agnieszka Rybak-Wolf
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Center for Molecular Medicine, Berlin, Germany.
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9
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Safabakhsh S, Ma WF, Miller CL, Laksman Z. Cardiovascular utility of single cell RNA-Seq. Curr Opin Cardiol 2023; 38:193-200. [PMID: 36728943 DOI: 10.1097/hco.0000000000001014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
PURPOSE OF REVIEW Cardiovascular diseases remain the leading causes of morbidity and mortality globally. Single-cell RNA sequencing has the potential to improve diagnostics, risk stratification, and provide novel therapeutic targets that have the potential to improve patient outcomes. RECENT FINDINGS Here, we provide an overview of the basic processes underlying single-cell RNA sequencing, including library preparation, data processing, and downstream analyses. We briefly discuss how the technique has been adapted to related medical disciplines, including hematology and oncology, with short term translational impact. We discuss potential applications of this technology within cardiology as well as recent innovative research within the field. We also discuss future directions to translate this technology to other high impact clinical areas. SUMMARY The use of single-cell RNA sequencing technology has made significant advancements in the field of cardiology, with ongoing growth in terms of applications and uptake. Most of the current research has focused on structural or atherosclerotic heart disease. Future areas that stand to benefit from this technology include cardiac electrophysiology and cardio-oncology.
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Affiliation(s)
- Sina Safabakhsh
- Division of Cardiology
- Centre for Heart Lung Innovation
- Centre for Cardiovascular Innovation, University of British Columbia, Vancouver, BC, Canada
| | - Wei Feng Ma
- Center for Public Health Genomics, Department of Public Health Sciences
- Medical Scientist Training Program, University of Virginia, Charlottesville, Virginia, USA
| | - Clint L Miller
- Center for Public Health Genomics, Department of Public Health Sciences
| | - Zachary Laksman
- Division of Cardiology
- Centre for Heart Lung Innovation
- Centre for Cardiovascular Innovation, University of British Columbia, Vancouver, BC, Canada
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10
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Miranda AMA, Janbandhu V, Maatz H, Kanemaru K, Cranley J, Teichmann SA, Hübner N, Schneider MD, Harvey RP, Noseda M. Single-cell transcriptomics for the assessment of cardiac disease. Nat Rev Cardiol 2023; 20:289-308. [PMID: 36539452 DOI: 10.1038/s41569-022-00805-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/03/2022] [Indexed: 12/24/2022]
Abstract
Cardiovascular disease is the leading cause of death globally. An advanced understanding of cardiovascular disease mechanisms is required to improve therapeutic strategies and patient risk stratification. State-of-the-art, large-scale, single-cell and single-nucleus transcriptomics facilitate the exploration of the cardiac cellular landscape at an unprecedented level, beyond its descriptive features, and can further our understanding of the mechanisms of disease and guide functional studies. In this Review, we provide an overview of the technical challenges in the experimental design of single-cell and single-nucleus transcriptomics studies, as well as a discussion of the type of inferences that can be made from the data derived from these studies. Furthermore, we describe novel findings derived from transcriptomics studies for each major cardiac cell type in both health and disease, and from development to adulthood. This Review also provides a guide to interpreting the exhaustive list of newly identified cardiac cell types and states, and highlights the consensus and discordances in annotation, indicating an urgent need for standardization. We describe advanced applications such as integration of single-cell data with spatial transcriptomics to map genes and cells on tissue and define cellular microenvironments that regulate homeostasis and disease progression. Finally, we discuss current and future translational and clinical implications of novel transcriptomics approaches, and provide an outlook of how these technologies will change the way we diagnose and treat heart disease.
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Affiliation(s)
| | - Vaibhao Janbandhu
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
- School of Clinical Medicine, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Henrike Maatz
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Kazumasa Kanemaru
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - James Cranley
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sarah A Teichmann
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Deptartment of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Norbert Hübner
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Charite-Universitätsmedizin Berlin, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | | | - Richard P Harvey
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
- School of Clinical Medicine, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Michela Noseda
- National Heart and Lung Institute, Imperial College London, London, UK.
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11
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Agarwal R, Wakimoto H, Paulo JA, Zhang Q, Reichart D, Toepfer C, Sharma A, Tai AC, Lun M, Gorham J, DePalma SR, Gygi SP, Seidman J, Seidman CE. Pathogenesis of Cardiomyopathy Caused by Variants in ALPK3, an Essential Pseudokinase in the Cardiomyocyte Nucleus and Sarcomere. Circulation 2022; 146:1674-1693. [PMID: 36321451 PMCID: PMC9698156 DOI: 10.1161/circulationaha.122.059688] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND ALPK3 encodes α-kinase 3, a muscle-specific protein of unknown function. ALPK3 loss-of-function variants cause cardiomyopathy with distinctive clinical manifestations in both children and adults, but the molecular functions of ALPK3 remain poorly understood. METHODS We explored the putative kinase activity of ALPK3 and the consequences of damaging variants using isogenic human induced pluripotent stem cell-derived cardiomyocytes, mice, and human patient tissues. RESULTS Multiple sequence alignment of all human α-kinase domains and their orthologs revealed 4 conserved residues that were variant only in ALPK3, demonstrating evolutionary divergence of the ALPK3 α-kinase domain sequence. Phosphoproteomic evaluation of both ALPK3 kinase domain inhibition and overexpression failed to detect significant changes in catalytic activity, establishing ALPK3 as a pseudokinase. Investigations into alternative functions revealed that ALPK3 colocalized with myomesin proteins (MYOM1, MYOM2) at both the nuclear envelope and the sarcomere M-band. ALPK3 loss-of-function variants caused myomesin proteins to mislocalize and also dysregulated several additional M-band proteins involved in sarcomere protein turnover, which ultimately impaired cardiomyocyte structure and function. CONCLUSIONS ALPK3 is an essential cardiac pseudokinase that inserts in the nuclear envelope and the sarcomere M-band. Loss of ALPK3 causes mislocalization of myomesins, critical force-buffering proteins in cardiomyocytes, and also dysregulates M-band proteins necessary for sarcomere protein turnover. We conclude that ALPK3 cardiomyopathy induces ventricular dilatation caused by insufficient myomesin-mediated force buffering and hypertrophy by impairment of sarcomere proteostasis.
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Affiliation(s)
- Radhika Agarwal
- Department of Genetics (R.A., H.W., Q.Z., D.R., C.T., A.S., A.C.T., M.L., J.G., S.R.D., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
| | - Hiroko Wakimoto
- Department of Genetics (R.A., H.W., Q.Z., D.R., C.T., A.S., A.C.T., M.L., J.G., S.R.D., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
| | - Joao A. Paulo
- Department of Cell Biology (J.A.P., S.P.G.), Harvard Medical School, Boston, MA
| | - Qi Zhang
- Department of Genetics (R.A., H.W., Q.Z., D.R., C.T., A.S., A.C.T., M.L., J.G., S.R.D., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
| | - Daniel Reichart
- Department of Genetics (R.A., H.W., Q.Z., D.R., C.T., A.S., A.C.T., M.L., J.G., S.R.D., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
| | - Christopher Toepfer
- Department of Genetics (R.A., H.W., Q.Z., D.R., C.T., A.S., A.C.T., M.L., J.G., S.R.D., J.G.S., C.E.S.), Harvard Medical School, Boston, MA.,Radcliffe Department of Medicine (C.T.), University of Oxford, United Kingdom.,Wellcome Centre for Human Genetics (C.T.), University of Oxford, United Kingdom
| | - Arun Sharma
- Department of Genetics (R.A., H.W., Q.Z., D.R., C.T., A.S., A.C.T., M.L., J.G., S.R.D., J.G.S., C.E.S.), Harvard Medical School, Boston, MA.,Board of Governors Regenerative Medicine Institute (A.S.), Cedars-Sinai Medical Center, Los Angeles, CA.,Smidt Heart Institute (A.S.), Cedars-Sinai Medical Center, Los Angeles, CA.,Department of Biomedical Sciences (A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
| | - Angela C. Tai
- Department of Genetics (R.A., H.W., Q.Z., D.R., C.T., A.S., A.C.T., M.L., J.G., S.R.D., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
| | - Mingyue Lun
- Department of Genetics (R.A., H.W., Q.Z., D.R., C.T., A.S., A.C.T., M.L., J.G., S.R.D., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
| | - Joshua Gorham
- Department of Genetics (R.A., H.W., Q.Z., D.R., C.T., A.S., A.C.T., M.L., J.G., S.R.D., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
| | - Steven R. DePalma
- Department of Genetics (R.A., H.W., Q.Z., D.R., C.T., A.S., A.C.T., M.L., J.G., S.R.D., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
| | - Steven P. Gygi
- Department of Cell Biology (J.A.P., S.P.G.), Harvard Medical School, Boston, MA
| | - J.G. Seidman
- Department of Genetics (R.A., H.W., Q.Z., D.R., C.T., A.S., A.C.T., M.L., J.G., S.R.D., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
| | - Christine E. Seidman
- Department of Genetics (R.A., H.W., Q.Z., D.R., C.T., A.S., A.C.T., M.L., J.G., S.R.D., J.G.S., C.E.S.), Harvard Medical School, Boston, MA.,Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston, MA (C.E.S.).,Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
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12
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Zhang Q, Kim SW, Gorham JM, DeLaughter D, Ward T, Seidman C, Seidman J. Multiplexed Single-Nucleus RNA Sequencing Using Lipid-Oligo Barcodes. Curr Protoc 2022; 2:e579. [PMID: 36286606 PMCID: PMC9614549 DOI: 10.1002/cpz1.579] [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: 11/06/2022]
Abstract
This protocol describes a robust pipeline for simultaneously analyzing multiple samples by single-nucleus (sn)RNA-seq. cDNA obtained from each single sample are labeled with the same lipid-coupled oligonucleotide barcode (10X Genomics). Nuclei from as many as 12 individual samples can be pooled together and simultaneously processed for cDNA library construction and subsequent DNA sequencing. While previous protocols using lipid-coupled oligonucleotide barcodes were optimized for analysis of samples consisting of viable cells, this protocol is optimized for analyses of quick-frozen cell samples. The protocol ensures efficient recovery of nuclei both by incorporating high sucrose buffered solutions and by including a tracking dye (trypan blue) during nuclei isolation. The protocol also describes a procedure for removing single nuclei 'artifacts' by removing cell debris prior to single nuclear fractionation. This protocol informs the use of computational tools for filtering poorly labeled nuclei and assigning sample identity using barcode unique molecular identifier (UMI) read counts percentages. The computational pipeline is applicable to either cultured or primary, fresh or frozen cells, regardless of their cell types and species. Overall, this protocol reduces batch effects and experimental costs while enhancing sample comparison. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Labeling cells with lipid oligo barcodes and generating multiplexed single-nucleus RNA-seq libraries Basic Protocol 2: Bioinformatic deconvolution of the multiplexed snRNAseq libraries.
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Affiliation(s)
- Qi Zhang
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- These authors contributed equally to this work
| | - Seong Won Kim
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- These authors contributed equally to this work
| | - Joshua M. Gorham
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Daniel DeLaughter
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Tarsha Ward
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Christine Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Cardiovascular Division, Brigham and Women’s Hospital; Boston, MA USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Jonathan Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
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13
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Reichart D, Lindberg EL, Maatz H, Miranda AMA, Viveiros A, Shvetsov N, Gärtner A, Nadelmann ER, Lee M, Kanemaru K, Ruiz-Orera J, Strohmenger V, DeLaughter DM, Patone G, Zhang H, Woehler A, Lippert C, Kim Y, Adami E, Gorham JM, Barnett SN, Brown K, Buchan RJ, Chowdhury RA, Constantinou C, Cranley J, Felkin LE, Fox H, Ghauri A, Gummert J, Kanda M, Li R, Mach L, McDonough B, Samari S, Shahriaran F, Yapp C, Stanasiuk C, Theotokis PI, Theis FJ, van den Bogaerdt A, Wakimoto H, Ware JS, Worth CL, Barton PJR, Lee YA, Teichmann SA, Milting H, Noseda M, Oudit GY, Heinig M, Seidman JG, Hubner N, Seidman CE. Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies. Science 2022; 377:eabo1984. [PMID: 35926050 PMCID: PMC9528698 DOI: 10.1126/science.abo1984] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Pathogenic variants in genes that cause dilated cardiomyopathy (DCM) and arrhythmogenic cardiomyopathy (ACM) convey high risks for the development of heart failure through unknown mechanisms. Using single-nucleus RNA sequencing, we characterized the transcriptome of 880,000 nuclei from 18 control and 61 failing, nonischemic human hearts with pathogenic variants in DCM and ACM genes or idiopathic disease. We performed genotype-stratified analyses of the ventricular cell lineages and transcriptional states. The resultant DCM and ACM ventricular cell atlas demonstrated distinct right and left ventricular responses, highlighting genotype-associated pathways, intercellular interactions, and differential gene expression at single-cell resolution. Together, these data illuminate both shared and distinct cellular and molecular architectures of human heart failure and suggest candidate therapeutic targets.
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Affiliation(s)
- Daniel Reichart
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA.,Department of Medicine I, University Hospital, LMU Munich, 80336 Munich, Germany
| | - Eric L Lindberg
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Henrike Maatz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10785 Berlin, Germany
| | - Antonio M A Miranda
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,British Heart Foundation Centre for Research Excellence and Centre for Regenerative Medicine, Imperial College London, London WC2R 2LS, UK
| | - Anissa Viveiros
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada.,Mazankowski Alberta Heart Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Nikolay Shvetsov
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Anna Gärtner
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, 32545 Bad Oeynhausen, Germany
| | - Emily R Nadelmann
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Lee
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Kazumasa Kanemaru
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Viktoria Strohmenger
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Walter-Brendel-Centre of Experimental Medicine, Ludwig-Maximilian University of Munich, 81377 Munich, Germany
| | - Daniel M DeLaughter
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Bethesda, MD 20815, USA
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Hao Zhang
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada.,Mazankowski Alberta Heart Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Andrew Woehler
- Systems Biology Imaging Platform, Berlin Institute for Medical Systems Biology (BIMSB), Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 10115 Berlin, Germany
| | - Christoph Lippert
- Digital Health-Machine Learning group, Hasso Plattner Institute for Digital Engineering, University of Potsdam, 14482 Potsdam, Germany.,Hasso Plattner Institute for Digital Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yuri Kim
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Eleonora Adami
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Joshua M Gorham
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sam N Barnett
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Kemar Brown
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Cardiac Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rachel J Buchan
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
| | - Rasheda A Chowdhury
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | | | - James Cranley
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Leanne E Felkin
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
| | - Henrik Fox
- Heart and Diabetes Center NRW, Clinic for Thoracic and Cardiovascular Surgery, University Hospital of the Ruhr-University, 32545 Bad Oeynhausen, Germany
| | - Ahla Ghauri
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Jan Gummert
- Heart and Diabetes Center NRW, Clinic for Thoracic and Cardiovascular Surgery, University Hospital of the Ruhr-University, 32545 Bad Oeynhausen, Germany
| | - Masatoshi Kanda
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.,Department of Rheumatology and Clinical Immunology, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan
| | - Ruoyan Li
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Lukas Mach
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
| | - Barbara McDonough
- Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Bethesda, MD 20815, USA
| | - Sara Samari
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Farnoush Shahriaran
- Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), 85764 Neuherberg, Germany
| | - Clarence Yapp
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Caroline Stanasiuk
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, 32545 Bad Oeynhausen, Germany
| | - Pantazis I Theotokis
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK
| | - Fabian J Theis
- Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), 85764 Neuherberg, Germany
| | | | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - James S Ware
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK.,MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK
| | - Catherine L Worth
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Paul J R Barton
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK.,MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK
| | - Young-Ae Lee
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.,Clinic for Pediatric Allergy, Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
| | - Sarah A Teichmann
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.,Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
| | - Hendrik Milting
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, 32545 Bad Oeynhausen, Germany
| | - Michela Noseda
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,British Heart Foundation Centre for Research Excellence and Centre for Regenerative Medicine, Imperial College London, London WC2R 2LS, UK
| | - Gavin Y Oudit
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada.,Mazankowski Alberta Heart Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Matthias Heinig
- Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), 85764 Neuherberg, Germany.,Department of Informatics, Technische Universitaet Muenchen (TUM), 85748 Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Munich Heart Association, Partner Site Munich, 10785 Berlin, Germany
| | | | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10785 Berlin, Germany.,Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Bethesda, MD 20815, USA
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14
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Abstract
The single-cell revolution in the field of genomics is in full bloom, with clever new molecular biology tricks appearing regularly that allow researchers to explore new modalities or scale up their projects to millions of cells and beyond. Techniques abound to measure RNA expression, DNA alterations, protein abundance, chromatin accessibility, and more, all with single-cell resolution and often in combination. Despite such a rapidly changing technology landscape, there are several fundamental principles that are applicable to the majority of experimental workflows to help users avoid pitfalls and exploit the advantages of the chosen platform. In this overview article, we describe a variety of popular single-cell genomics technologies and address some common questions pertaining to study design, sample preparation, quality control, and sequencing strategy. As the majority of relevant publications currently revolve around single-cell RNA-seq, we will prioritize this genomics modality in our discussion. © 2022 Wiley Periodicals LLC.
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Affiliation(s)
- Claire Regan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
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15
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Meng Q, Li Y, Yu Y, Chu K, Smith ZJ. A Drop-in, Focus-Extending Phase Mask Simplifies Microscopic and Microfluidic Imaging Systems for Cost-Effective Point-of-Care Diagnostics. Anal Chem 2022; 94:11000-11007. [PMID: 35895976 DOI: 10.1021/acs.analchem.2c01421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Microscopic imaging and imaging flow cytometry have wide potential in point-of-care assays; however, their narrow depth of focus necessitates precise mechanical or fluidic focus control of a sample in order to acquire high-quality images that can be used for downstream analysis, increasing the cost and complexity of the imaging system. This complexity represents a barrier to miniaturization and translation of point-of-care assays based on microscopic imaging or imaging flow cytometry. To address this challenge, we present a simple drop-in phase mask with a physics-informed, circularly symmetric asphere phase profile that extends the depth of focus by >5-fold while largely preserving the image quality compared to other depth extending methods. We show that such a focus-extended system overcomes manufacturing tolerances in low-cost sample chambers, enlarges the useable field-of-view of low-cost objectives, and permits increased throughput and precision in flow imaging systems without the need for complex flow-focusing. As the image quality is preserved without the need for postacquisition image restoration, our solution is also highly appropriate for on-line applications such as cell sorting.
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Affiliation(s)
- Qi Meng
- Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Yaning Li
- Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Yajun Yu
- Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Kaiqin Chu
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu 215123, China
| | - Zachary J Smith
- Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, Anhui 230027, China
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16
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Axelsson Raja A, Wakimoto H, DeLaughter DM, Reichart D, Gorham J, Conner DA, Lun M, Probst CK, Sakai N, Knipe RS, Montesi SB, Shea B, Adam LP, Leinwand LA, Wan W, Choi ES, Lindberg EL, Patone G, Noseda M, Hübner N, Seidman CE, Tager AM, Seidman JG, Ho CY. Ablation of lysophosphatidic acid receptor 1 attenuates hypertrophic cardiomyopathy in a mouse model. Proc Natl Acad Sci U S A 2022; 119:e2204174119. [PMID: 35787042 PMCID: PMC9282378 DOI: 10.1073/pnas.2204174119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/25/2022] [Indexed: 01/07/2023] Open
Abstract
Myocardial fibrosis is a key pathologic feature of hypertrophic cardiomyopathy (HCM). However, the fibrotic pathways activated by HCM-causing sarcomere protein gene mutations are poorly defined. Because lysophosphatidic acid is a mediator of fibrosis in multiple organs and diseases, we tested the role of the lysophosphatidic acid pathway in HCM. Lysphosphatidic acid receptor 1 (LPAR1), a cell surface receptor, is required for lysophosphatidic acid mediation of fibrosis. We bred HCM mice carrying a pathogenic myosin heavy-chain variant (403+/-) with Lpar1-ablated mice to create mice carrying both genetic changes (403+/- LPAR1 -/-) and assessed development of cardiac hypertrophy and fibrosis. Compared with 403+/- LPAR1WT, 403+/- LPAR1 -/- mice developed significantly less hypertrophy and fibrosis. Single-nucleus RNA sequencing of left ventricular tissue demonstrated that Lpar1 was predominantly expressed by lymphatic endothelial cells (LECs) and cardiac fibroblasts. Lpar1 ablation reduced the population of LECs, confirmed by immunofluorescence staining of the LEC markers Lyve1 and Ccl21a and, by in situ hybridization, for Reln and Ccl21a. Lpar1 ablation also altered the distribution of fibroblast cell states. FB1 and FB2 fibroblasts decreased while FB0 and FB3 fibroblasts increased. Our findings indicate that Lpar1 is expressed predominantly by LECs and fibroblasts in the heart and is required for development of hypertrophy and fibrosis in an HCM mouse model. LPAR1 antagonism, including agents in clinical trials for other fibrotic diseases, may be beneficial for HCM.
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Affiliation(s)
- Anna Axelsson Raja
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Department of Cardiology, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
| | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | | | - Daniel Reichart
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Joshua Gorham
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - David A. Conner
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Mingyue Lun
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Clemens K. Probst
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
- Fibrosis Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - Norihiko Sakai
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
- Fibrosis Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
- Division of Nephrology, Kanazawa University, Kanazawa, 920-1192 Japan
| | - Rachel S. Knipe
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
- Fibrosis Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - Sydney B. Montesi
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - Barry Shea
- Division of Pulmonary, Critical Care and Sleep Medicine, Albert Medical School of Brown University, Providence, RI 02903
| | - Leonard P. Adam
- Research and Development, Bristol-Myers Squibb Company, Princeton, NJ 08540
| | - Leslie A. Leinwand
- Biofrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80302
| | - William Wan
- Biofrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80302
| | - Esther Sue Choi
- Biofrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80302
| | - Eric L. Lindberg
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Michela Noseda
- National Heart and Lung Institute, British Heart Foundation Centre of Regenerative Medicine, British Heart Foundation Centre of Research Excellence, Imperial College London, London SW7 2AZ, United Kingdom
| | - Norbert Hübner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- Charité-Universitätsmedizin, Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Cardiovascular Research, Partner Site Berlin, 13347 Berlin, Germany
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston, MA 02115
- HHMI, Chevy Chase, MD 20815
| | - Andrew M. Tager
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
- Fibrosis Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - J. G. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Carolyn Y. Ho
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston, MA 02115
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17
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Safabakhsh S, Sar F, Martelotto L, Haegert A, Singhera G, Hanson P, Parker J, Collins C, Rohani L, Laksman Z. Isolating Nuclei From Frozen Human Heart Tissue for Single-Nucleus RNA Sequencing. Curr Protoc 2022; 2:e480. [PMID: 35816165 DOI: 10.1002/cpz1.480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Heart disease is the leading cause of global morbidity and mortality. This is in part because, despite an abundance of animal and in vitro models, it has been a challenge to date to study human heart tissue with sufficient depth and resolution to develop disease-modifying therapies for common cardiac conditions. Single-nucleus RNA sequencing (snRNA-seq) has emerged as a powerful tool capable of analyzing cellular function and signaling in health and disease, and has already contributed to significant advances in areas such as oncology and hematology. Employing snRNA-seq technology on flash-frozen human tissue has the potential to unlock novel disease mechanisms and pathways in any organ. Studying the human heart using snRNA-seq is a key priority for the field of cardiovascular sciences; however, progress to date has been slowed by numerous barriers. One key challenge is the fact that the human heart is very resistant to shearing and stress, making tissue dissociation and nuclear isolation difficult. Here, we describe a tissue dissociation method allowing the efficient and cost-effective isolation of high-quality nuclei from flash-frozen human heart tissue collected in surgical operating rooms. Our protocol addresses the challenge of nuclear isolation from human hearts, enables snRNA-seq of the human heart, and paves the way for an improved understanding of the human heart in health and disease. Ultimately, this will be key to uncovering signaling pathways and networks amenable to therapeutic intervention and the development of novel biomarkers and disease-modifying therapies. © 2022 Wiley Periodicals LLC. Basic Protocol: Human heart tissue dissociation and nuclear isolation for snRNA-seq.
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Affiliation(s)
- Sina Safabakhsh
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Funda Sar
- Vancouver Prostate Centre, UBC, Vancouver, British Columbia, Canada
| | | | - Anne Haegert
- Vancouver Prostate Centre, UBC, Vancouver, British Columbia, Canada
| | | | | | - Jeremy Parker
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Colin Collins
- Vancouver Prostate Centre, UBC, Vancouver, British Columbia, Canada
| | - Leili Rohani
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Zachary Laksman
- University of British Columbia, Vancouver, British Columbia, Canada
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18
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Rousselle TV, McDaniels JM, Shetty AC, Bardhi E, Maluf DG, Mas VR. An optimized protocol for single nuclei isolation from clinical biopsies for RNA-seq. Sci Rep 2022; 12:9851. [PMID: 35701599 PMCID: PMC9198012 DOI: 10.1038/s41598-022-14099-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 06/01/2022] [Indexed: 11/10/2022] Open
Abstract
Single nuclei RNA sequencing (snRNA-seq) has evolved as a powerful tool to study complex human diseases. Single cell resolution enables the study of novel cell types, biological processes, cell trajectories, and cell-cell signaling pathways. snRNA-seq largely relies on the dissociation of intact nuclei from human tissues. However, the study of complex tissues using small core biopsies presents many technical challenges. Here, an optimized protocol for single nuclei isolation is presented for frozen and RNAlater preserved human kidney biopsies. The described protocol is fast, low cost, and time effective due to the elimination of cell sorting and ultra-centrifugation. Samples can be processed in 90 min or less. This method is effective for obtaining normal nuclei morphology without signs of structural damage. Using snRNA-seq, 16 distinct kidney cell clusters were recovered from normal and peri-transplant acute kidney injury allograft samples, including immune cell clusters. Quality control measurements demonstrated that these optimizations eliminated cellular debris and allowed for a high yield of high-quality nuclei and RNA for library preparation and sequencing. Cellular disassociation did not induce cellular stress responses, which recapitulated transcriptional patterns associated with standardized methods of nuclei isolation. Future applications of this protocol will allow for thorough investigations of small biobank biopsies, identifying cell-specific injury pathways and driving the discovery of novel diagnostics and therapeutic targets.
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Affiliation(s)
- Thomas V Rousselle
- Department of Surgery, University of Maryland School of Medicine, 670 W Baltimore Street, Baltimore, MD, 21201, USA
| | - Jennifer M McDaniels
- Department of Surgery, University of Maryland School of Medicine, 670 W Baltimore Street, Baltimore, MD, 21201, USA
| | - Amol C Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Elissa Bardhi
- Department of Surgery, University of Maryland School of Medicine, 670 W Baltimore Street, Baltimore, MD, 21201, USA
| | - Daniel G Maluf
- Department of Surgery, University of Maryland School of Medicine, 670 W Baltimore Street, Baltimore, MD, 21201, USA
- Program in Transplantation, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Valeria R Mas
- Department of Surgery, University of Maryland School of Medicine, 670 W Baltimore Street, Baltimore, MD, 21201, USA.
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19
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Lu F, Ma Q, Xie W, Liou CL, Zhang D, Sweat ME, Jardin BD, Naya FJ, Guo Y, Cheng H, Pu WT. CMYA5 establishes cardiac dyad architecture and positioning. Nat Commun 2022; 13:2185. [PMID: 35449169 PMCID: PMC9023524 DOI: 10.1038/s41467-022-29902-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 04/05/2022] [Indexed: 11/18/2022] Open
Abstract
Cardiac excitation-contraction coupling requires dyads, the nanoscopic microdomains formed adjacent to Z-lines by apposition of transverse tubules and junctional sarcoplasmic reticulum. Disruption of dyad architecture and function are common features of diseased cardiomyocytes. However, little is known about the mechanisms that modulate dyad organization during cardiac development, homeostasis, and disease. Here, we use proximity proteomics in intact, living hearts to identify proteins enriched near dyads. Among these proteins is CMYA5, an under-studied striated muscle protein that co-localizes with Z-lines, junctional sarcoplasmic reticulum proteins, and transverse tubules in mature cardiomyocytes. During cardiac development, CMYA5 positioning adjacent to Z-lines precedes junctional sarcoplasmic reticulum positioning or transverse tubule formation. CMYA5 ablation disrupts dyad architecture, dyad positioning at Z-lines, and junctional sarcoplasmic reticulum Ca2+ release, leading to cardiac dysfunction and inability to tolerate pressure overload. These data provide mechanistic insights into cardiomyopathy pathogenesis by demonstrating that CMYA5 anchors junctional sarcoplasmic reticulum to Z-lines, establishes dyad architecture, and regulates dyad Ca2+ release.
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Affiliation(s)
- Fujian Lu
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Qing Ma
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Wenjun Xie
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Institute of Health and Rehabilitation Science, School of Life Science and Technology, Xi'an Jiaotong University, 710049, Xi'an, Shanxi, China
| | - Carter L Liou
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Donghui Zhang
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Science, Hubei University, 430062, Wuhan, Hubei, China
| | - Mason E Sweat
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Blake D Jardin
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Francisco J Naya
- Department of Biology, Program in Cell and Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Yuxuan Guo
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
- Peking University Health Science Center, School of Basic Medical Sciences, The Institute of Cardiovascular Sciences, Key Laboratory of Molecular Cardiovascular Science of Ministry of Education, 100191, Beijing, China
| | - Heping Cheng
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA.
- Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA, 02138, USA.
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20
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Single nucleus RNA-sequencing: how it's done, applications and limitations. Emerg Top Life Sci 2021; 5:687-690. [PMID: 34515767 DOI: 10.1042/etls20210074] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/10/2021] [Accepted: 08/24/2021] [Indexed: 11/17/2022]
Abstract
Single nuclei RNA-sequencing (sNuc-Seq) is a methodology which uses isolated nuclei instead of whole cells to profile gene expression. By using droplet microfluidic technologies, users are able to profile thousands of single transcriptomes at high throughput from their chosen tissue. This article aims to introduce sNuc-Seq as a method and its utility in multiple tissue types. Furthermore, we discuss the risks associated with the use of nuclei, which must be considered before committing to a methodology.
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