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So J, Strobel O, Wann J, Kim K, Paul A, Acri DJ, Dabin LC, Peng G, Kim J, Roh HC. Robust single nucleus RNA sequencing reveals depot-specific cell population dynamics in adipose tissue remodeling during obesity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.08.588525. [PMID: 38645263 PMCID: PMC11030456 DOI: 10.1101/2024.04.08.588525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Single nucleus RNA sequencing (snRNA-seq), an alternative to single cell RNA sequencing (scRNA-seq), encounters technical challenges in obtaining high-quality nuclei and RNA, persistently hindering its applications. Here, we present a robust technique for isolating nuclei across various tissue types, remarkably enhancing snRNA-seq data quality. Employing this approach, we comprehensively characterize the depot-dependent cellular dynamics of various cell types underlying adipose tissue remodeling during obesity. By integrating bulk nuclear RNA-seq from adipocyte nuclei of different sizes, we identify distinct adipocyte subpopulations categorized by size and functionality. These subpopulations follow two divergent trajectories, adaptive and pathological, with their prevalence varying by depot. Specifically, we identify a key molecular feature of dysfunctional hypertrophic adipocytes, a global shutdown in gene expression, along with elevated stress and inflammatory responses. Furthermore, our differential gene expression analysis reveals distinct contributions of adipocyte subpopulations to the overall pathophysiology of adipose tissue. Our study establishes a robust snRNA-seq method, providing novel insights into the biological processes involved in adipose tissue remodeling during obesity, with broader applicability across diverse biological systems.
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Affiliation(s)
- Jisun So
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Olivia Strobel
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jamie Wann
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Kyungchan Kim
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Avishek Paul
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Dominic J. Acri
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Luke C. Dabin
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Gang Peng
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jungsu Kim
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Hyun Cheol Roh
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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Huang X, Jiang J, Shen J, Xu Z, Gu F, Pei J, Zhang L, Tang P, Yin P. The Influences of Cryopreservation Methods on RNA, Protein, Microstructure and Cell Viability of Skeletal Muscle Tissue. Biopreserv Biobank 2024; 22:225-234. [PMID: 37594856 DOI: 10.1089/bio.2023.0005] [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] [Indexed: 08/20/2023] Open
Abstract
Background: Different experiments require different sample storage methods. The commonly used preservation methods in biobank practice cannot fully meet the multifarious requirements of experimental techniques. Programmable controlled slow freezing (PCSF) can maintain the viability of tissue. In this study, we hypothesized that PCSF-preserved samples have potential advantages in matching subsequent experiments compared with existing methods. Methods: We compared the differences on skeletal muscle tissue RNA integrity, protein integrity, microstructure integrity, and cell viability between four existing cryopreservation methods: liquid nitrogen (LN2) snap-freezing, LN2-cooled isopentane snap-freezing, RNAlater®-based freezing, and PCSF. RNA integrity was evaluated using agarose gel electrophoresis and RNA integrity number. Freezing-related microstructural damage in the muscle tissue was evaluated using ice crystal diameter and muscle fiber cross-sectional area. Protein integrity was evaluated using immunofluorescence staining. Cell viability was evaluated using trypan blue staining after primary muscle cell isolation. Results: PCSF preserved RNA integrity better than LN2 and isopentane, with a statistically significant difference. RNAlater preserved RNA integrity best. PCSF best controlled ice crystal size in myofibers, with a significant difference compared with LN2. The PCSF method best preserved the integrity of protein epitopes according to the mean fluorescence intensity results, with a significant difference. Cell viability was best preserved in the PCSF method compared with the other three methods, with a significant difference. Conclusion: PCSF protected the RNA integrity, microstructural integrity, protein integrity, and cell viability of skeletal muscle tissue. The application of PCSF in biobank practice is recommended as a multi-experiment-compatible cryopreservation method.
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Affiliation(s)
- Xiang Huang
- Medical School of Chinese PLA, Chinese PLA General Hospital, Beijing, People's Republic of China
- Department of Orthopedics, Chinese PLA General Hospital, Beijing, People's Republic of China
- National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, People's Republic of China
| | - Jingjing Jiang
- Medical Innovation Research Division of Chinese PLA General Hospital, Clinical Biobank Center, Beijing, People's Republic of China
| | - Junmin Shen
- Department of Orthopedics, Chinese PLA General Hospital, Beijing, People's Republic of China
- National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, People's Republic of China
- School of Medicine, Nankai University, Tianjin, People's Republic of China
| | - Ziying Xu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, People's Republic of China
| | - Fangyan Gu
- Medical Innovation Research Division of Chinese PLA General Hospital, Clinical Biobank Center, Beijing, People's Republic of China
| | - Jinlian Pei
- Medical Innovation Research Division of Chinese PLA General Hospital, Clinical Biobank Center, Beijing, People's Republic of China
| | - Licheng Zhang
- Department of Orthopedics, Chinese PLA General Hospital, Beijing, People's Republic of China
- National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, People's Republic of China
| | - Peifu Tang
- Department of Orthopedics, Chinese PLA General Hospital, Beijing, People's Republic of China
- National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, People's Republic of China
| | - Pengbin Yin
- Department of Orthopedics, Chinese PLA General Hospital, Beijing, People's Republic of China
- National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, People's Republic of China
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Hahn N, Bens M, Kempfer M, Reißig C, Schmidl L, Geis C. Protecting RNA quality for spatial transcriptomics while improving immunofluorescent staining quality. Front Neurosci 2023; 17:1198154. [PMID: 37274189 PMCID: PMC10234422 DOI: 10.3389/fnins.2023.1198154] [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: 03/31/2023] [Accepted: 05/03/2023] [Indexed: 06/06/2023] Open
Abstract
In comparison to bulk sequencing or single cell sequencing, spatial transcriptomics preserves the spatial information in tissue slices and can even be mapped to immunofluorescent stainings, allowing translation of gene expression information into their spatial context. This enables to unravel complex interactions of neighboring cells or to link cell morphology to transcriptome data. The 10× Genomics Visium platform offers to combine spatial transcriptomics with immunofluorescent staining of cryo-sectioned tissue slices. We applied this technique to fresh frozen mouse brain slices and developed a protocol that still protects RNA quality while improving buffers for immunofluorescent staining. We investigated the impact of various parameters, including fixation time and buffer composition, on RNA quality and antibody binding. Here, we propose an improved version of the manufacturer protocol, which does not alter RNA quality and facilitates the use of multiple additional antibodies that were not compatible with the manufacturer protocol before. Finally, we discuss the influence of various staining parameters, which contribute to the development of application specific staining protocols.
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Affiliation(s)
- Nina Hahn
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
| | - Martin Bens
- Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), Jena, Germany
| | - Marin Kempfer
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena, Germany
| | - Christin Reißig
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena, Germany
| | - Lars Schmidl
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena, Germany
| | - Christian Geis
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
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Zhang X, Hu C, Huang C, Wei Y, Li X, Hu M, Li H, Wu J, Czajkowsky DM, Guo Y, Shao Z. Robust Acquisition of Spatial Transcriptional Programs in Tissues With Immunofluorescence-Guided Laser Capture Microdissection. Front Cell Dev Biol 2022; 10:853188. [PMID: 35399504 PMCID: PMC8990165 DOI: 10.3389/fcell.2022.853188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/24/2022] [Indexed: 12/22/2022] Open
Abstract
The functioning of tissues is fundamentally dependent upon not only the phenotypes of the constituent cells but also their spatial organization in the tissue, as local interactions precipitate intra-cellular events that often lead to changes in expression. However, our understanding of these processes in tissues, whether healthy or diseased, is limited at present owing to the difficulty in acquiring comprehensive transcriptional programs of spatially- and phenotypically-defined cells in situ. Here we present a robust method based on immunofluorescence-guided laser capture microdissection (immuno-LCM-RNAseq) to acquire finely resolved transcriptional programs with as few as tens of cells from snap-frozen or RNAlater-treated clinical tissues sufficient to resolve even isoforms. The protocol is optimized to protect the RNA with a small molecule inhibitor, the ribonucleoside vanadyl complex (RVC), which thereby enables the typical time-consuming immunostaining and laser capture steps of this procedure during which RNA is usually severely degraded in existing approaches. The efficacy of this approach is exemplified by the characterization of differentially expressed genes between the mouse small intestine lacteal cells at the tip versus the main capillary body, including those that function in sensing and responding to local environmental cues to stimulate intra-cellular signalling. With the extensive repertoire of specific antibodies that are presently available, our method provides an unprecedented capability for the analysis of transcriptional networks and signalling pathways during development, pathogenesis, and aging of specific cell types within native tissues.
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Affiliation(s)
- Xiaodan Zhang
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chuansheng Hu
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chen Huang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Wei
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaowei Li
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Miaomiao Hu
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Hua Li
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Ji Wu
- Bio-X Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Daniel M. Czajkowsky
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Daniel M. Czajkowsky, ; Yan Guo, ; Zhifeng Shao,
| | - Yan Guo
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Daniel M. Czajkowsky, ; Yan Guo, ; Zhifeng Shao,
| | - Zhifeng Shao
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Daniel M. Czajkowsky, ; Yan Guo, ; Zhifeng Shao,
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Genomics and metatranscriptomics of biogeochemical cycling and degradation of lignin-derived aromatic compounds in thermal swamp sediment. THE ISME JOURNAL 2021; 15:879-893. [PMID: 33139871 PMCID: PMC8027834 DOI: 10.1038/s41396-020-00820-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/13/2020] [Accepted: 10/21/2020] [Indexed: 01/30/2023]
Abstract
Thermal swamps are unique ecosystems where geothermally warmed waters mix with decomposing woody biomass, hosting novel biogeochemical-cycling and lignin-degrading microbial consortia. Assembly of shotgun metagenome libraries resolved 351 distinct genomes from hot-spring (30-45 °C) and mesophilic (17 °C) sediments. Annotation of 39 refined draft genomes revealed metabolism consistent with oligotrophy, including pathways for degradation of aromatic compounds, such as syringate, vanillate, p-hydroxybenzoate, and phenol. Thermotolerant Burkholderiales, including Rubrivivax ssp., were implicated in diverse biogeochemical and aromatic transformations, highlighting their broad metabolic capacity. Lignin catabolism was further investigated using metatranscriptomics of sediment incubated with milled or Kraft lignin at 45 °C. Aromatic compounds were depleted from lignin-amended sediment over 148 h. The metatranscriptomic data revealed upregulation of des/lig genes predicted to specify the catabolism of syringate, vanillate, and phenolic oligomers in the sphingomonads Altererythrobacter ssp. and Novosphingobium ssp., as well as in the Burkholderiales genus, Rubrivivax. This study demonstrates how temperature structures biogeochemical cycling populations in a unique ecosystem, and combines community-level metagenomics with targeted metatranscriptomics to identify pathways with potential for bio-refinement of lignin-derived aromatic compounds. In addition, the diverse aromatic catabolic pathways of Altererythrobacter ssp. may serve as a source of thermotolerant enzymes for lignin valorization.
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Mistry RM, Singh PK, Mancini MG, Stossi F, Mancini MA. Single Cell Analysis Of Transcriptionally Active Alleles By Single Molecule FISH. J Vis Exp 2020:10.3791/61680. [PMID: 33016938 PMCID: PMC8549401 DOI: 10.3791/61680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Gene transcription is an essential process in cell biology, and allows cells to interpret and respond to internal and external cues. Traditional bulk population methods (Northern blot, PCR, and RNAseq) that measure mRNA levels lack the ability to provide information on cell-to-cell variation in responses. Precise single cell and allelic visualization and quantification is possible via single molecule RNA fluorescence in situ hybridization (smFISH). RNA-FISH is performed by hybridizing target RNAs with labeled oligonucleotide probes. These can be imaged in medium/high throughput modalities, and, through image analysis pipelines, provide quantitative data on both mature and nascent RNAs, all at the single cell level. The fixation, permeabilization, hybridization and imaging steps have been optimized in the lab over many years using the model system described herein, which results in successful and robust single cell analysis of smFISH labeling. The main goal with sample preparation and processing is to produce high quality images characterized by a high signal-to-noise ratio to reduce false positives and provide data that are more accurate. Here, we present a protocol describing the pipeline from sample preparation to data analysis in conjunction with suggestions and optimization steps to tailor to specific samples.
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Affiliation(s)
- Ragini M Mistry
- GCC Center for Advanced Microscopy and Image Informatics; Department of Molecular and Cellular Biology, Baylor College of Medicine
| | - Pankaj K Singh
- GCC Center for Advanced Microscopy and Image Informatics; Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University
| | - Maureen G Mancini
- GCC Center for Advanced Microscopy and Image Informatics; Department of Molecular and Cellular Biology, Baylor College of Medicine
| | - Fabio Stossi
- GCC Center for Advanced Microscopy and Image Informatics; Department of Molecular and Cellular Biology, Baylor College of Medicine;
| | - Michael A Mancini
- GCC Center for Advanced Microscopy and Image Informatics; Department of Molecular and Cellular Biology, Baylor College of Medicine; Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University; Department of Pharmacology and Chemical Biology, Baylor College of Medicine
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