1
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Brazovskaja A, Gomes T, Holtackers R, Wahle P, Körner C, He Z, Schaffer T, Eckel JC, Hänsel R, Santel M, Seimiya M, Denecke T, Dannemann M, Brosch M, Hampe J, Seehofer D, Damm G, Camp JG, Treutlein B. Cell atlas of the regenerating human liver after portal vein embolization. Nat Commun 2024; 15:5827. [PMID: 38992008 DOI: 10.1038/s41467-024-49236-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 05/28/2024] [Indexed: 07/13/2024] Open
Abstract
The liver has the remarkable capacity to regenerate. In the clinic, regeneration is induced by portal vein embolization, which redirects portal blood flow, resulting in liver hypertrophy in locations with increased blood supply, and atrophy of embolized segments. Here, we apply single-cell and single-nucleus transcriptomics on healthy, hypertrophied, and atrophied patient-derived liver samples to explore cell states in the regenerating liver. Our data unveils pervasive upregulation of genes associated with developmental processes, cellular adhesion, and inflammation in post-portal vein embolization liver, disrupted portal-central hepatocyte zonation, and altered cell subtype composition of endothelial and immune cells. Interlineage crosstalk analysis reveals mesenchymal cells as an interaction hub between immune and endothelial cells, and highlights the importance of extracellular matrix proteins in liver regeneration. Moreover, we establish tissue-scale iterative indirect immunofluorescence imaging for high-dimensional spatial analysis of perivascular microenvironments, uncovering changes to tissue architecture in regenerating liver lobules. Altogether, our data is a rich resource revealing cellular and histological changes in human liver regeneration.
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Affiliation(s)
| | - Tomás Gomes
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
| | - Rene Holtackers
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Philipp Wahle
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Christiane Körner
- Department of Hepatobiliary Surgery and Visceral Transplantation, University Hospital, Leipzig University, Leipzig, Germany
| | - Zhisong He
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Theresa Schaffer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Julian Connor Eckel
- Department of Hepatobiliary Surgery and Visceral Transplantation, University Hospital, Leipzig University, Leipzig, Germany
| | - René Hänsel
- Department of Hepatobiliary Surgery and Visceral Transplantation, University Hospital, Leipzig University, Leipzig, Germany
- Institute for Medical Informatics, Statistics and Epidemiology (IMISE), Leipzig University, Leipzig, Germany
| | - Malgorzata Santel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Makiko Seimiya
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Timm Denecke
- Department of Diagnostic and Interventional Radiology, Leipzig University, Leipzig, Germany
| | - Michael Dannemann
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Mario Brosch
- Medical Department 1, University Hospital Dresden, Technical University Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technical University Dresden, Dresden, Germany
| | - Jochen Hampe
- Medical Department 1, University Hospital Dresden, Technical University Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technical University Dresden, Dresden, Germany
| | - Daniel Seehofer
- Department of Hepatobiliary Surgery and Visceral Transplantation, University Hospital, Leipzig University, Leipzig, Germany
| | - Georg Damm
- Department of Hepatobiliary Surgery and Visceral Transplantation, University Hospital, Leipzig University, Leipzig, Germany.
| | - J Gray Camp
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.
| | - Barbara Treutlein
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
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2
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Xu J, Guo P, Hao S, Shangguan S, Shi Q, Volpe G, Huang K, Zuo J, An J, Yuan Y, Cheng M, Deng Q, Zhang X, Lai G, Nan H, Wu B, Shentu X, Wu L, Wei X, Jiang Y, Huang X, Pan F, Song Y, Li R, Wang Z, Liu C, Liu S, Li Y, Yang T, Xu Z, Du W, Li L, Ahmed T, You K, Dai Z, Li L, Qin B, Li Y, Lai L, Qin D, Chen J, Fan R, Li Y, Hou J, Ott M, Sharma AD, Cantz T, Schambach A, Kristiansen K, Hutchins AP, Göttgens B, Maxwell PH, Hui L, Xu X, Liu L, Chen A, Lai Y, Esteban MA. A spatiotemporal atlas of mouse liver homeostasis and regeneration. Nat Genet 2024; 56:953-969. [PMID: 38627598 DOI: 10.1038/s41588-024-01709-7] [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: 01/08/2023] [Accepted: 03/06/2024] [Indexed: 05/09/2024]
Abstract
The mechanism by which mammalian liver cell responses are coordinated during tissue homeostasis and perturbation is poorly understood, representing a major obstacle in our understanding of many diseases. This knowledge gap is caused by the difficulty involved with studying multiple cell types in different states and locations, particularly when these are transient. We have combined Stereo-seq (spatiotemporal enhanced resolution omics-sequencing) with single-cell transcriptomic profiling of 473,290 cells to generate a high-definition spatiotemporal atlas of mouse liver homeostasis and regeneration at the whole-lobe scale. Our integrative study dissects in detail the molecular gradients controlling liver cell function, systematically defining how gene networks are dynamically modulated through intercellular communication to promote regeneration. Among other important regulators, we identified the transcriptional cofactor TBL1XR1 as a rheostat linking inflammation to Wnt/β-catenin signaling for facilitating hepatocyte proliferation. Our data and analytical pipelines lay the foundation for future high-definition tissue-scale atlases of organ physiology and malfunction.
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Affiliation(s)
- Jiangshan Xu
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Pengcheng Guo
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China.
- 3DC STAR, Spatiotemporal Campus at BGI Shenzhen, Shenzhen, China.
| | - Shijie Hao
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shuncheng Shangguan
- BGI Research, Shenzhen, China
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health and Guangzhou Medical University, Guangzhou, China
| | - Quan Shi
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Giacomo Volpe
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - Keke Huang
- Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jing Zuo
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Juan An
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yue Yuan
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Mengnan Cheng
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Qiuting Deng
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiao Zhang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Guangyao Lai
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health and Guangzhou Medical University, Guangzhou, China
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Haitao Nan
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Baihua Wu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Xinyi Shentu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Liang Wu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaoyu Wei
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Yujia Jiang
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Xin Huang
- BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Fengyu Pan
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Yumo Song
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Ronghai Li
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Zhifeng Wang
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Chuanyu Liu
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
- BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan, China
| | - Shiping Liu
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | | | - Tao Yang
- China National GeneBank, BGI Research, Shenzhen, China
- Guangdong Provincial Genomics Data Center, BGI Research, Shenzhen, China
| | - Zhicheng Xu
- China National GeneBank, BGI Research, Shenzhen, China
- Guangdong Provincial Genomics Data Center, BGI Research, Shenzhen, China
| | - Wensi Du
- China National GeneBank, BGI Research, Shenzhen, China
- Guangdong Provincial Genomics Data Center, BGI Research, Shenzhen, China
| | - Ling Li
- China National GeneBank, BGI Research, Shenzhen, China
- Guangdong Provincial Genomics Data Center, BGI Research, Shenzhen, China
| | - Tanveer Ahmed
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Kai You
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zhen Dai
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Li Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Baoming Qin
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yinxiong Li
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Liangxue Lai
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Dajiang Qin
- The Fifth Affiliated Hospital of Guangzhou Medical University-BGI Research Center for Integrative Biology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Junling Chen
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangzhou, China
| | - Rong Fan
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangzhou, China
| | - Yongyin Li
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangzhou, China
| | - Jinlin Hou
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangzhou, China
| | - Michael Ott
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Amar Deep Sharma
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Tobias Cantz
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Axel Schambach
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | | | - Andrew P Hutchins
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Berthold Göttgens
- Department of Haematology and Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Patrick H Maxwell
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Lijian Hui
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Xun Xu
- BGI Research, Hangzhou, China.
- BGI Research, Shenzhen, China.
- BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan, China.
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China.
| | - Longqi Liu
- BGI Research, Hangzhou, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
- BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan, China.
| | - Ao Chen
- BGI Research, Shenzhen, China.
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- BGI Research, Chongqing, China.
- JFL-BGI STOmics Center, BGI-Shenzhen, Chongqing, China.
| | - Yiwei Lai
- BGI Research, Hangzhou, China.
- BGI Research, Shenzhen, China.
- 3DC STAR, Spatiotemporal Campus at BGI Shenzhen, Shenzhen, China.
- BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan, China.
| | - Miguel A Esteban
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China.
- 3DC STAR, Spatiotemporal Campus at BGI Shenzhen, Shenzhen, China.
- Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- The Fifth Affiliated Hospital of Guangzhou Medical University-BGI Research Center for Integrative Biology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.
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3
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Zhou Y, Zhao Y, Carbonaro M, Chen H, Germino M, Adler C, Ni M, Zhu YO, Kim SY, Altarejos J, Li Z, Burczynski ME, Glass DJ, Sleeman MW, Lee AH, Halasz G, Cheng X. Perturbed liver gene zonation in a mouse model of non-alcoholic steatohepatitis. Metabolism 2024; 154:155830. [PMID: 38428673 DOI: 10.1016/j.metabol.2024.155830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 02/23/2024] [Accepted: 02/24/2024] [Indexed: 03/03/2024]
Abstract
Liver zonation characterizes the separation of metabolic pathways along the lobules and is required for optimal hepatic function. Wnt signaling is a master regulator of spatial liver zonation. A perivenous-periportal Wnt activity gradient orchestrates metabolic zonation by activating gene expression in perivenous hepatocytes, while suppressing gene expression in their periportal counterparts. However, the understanding as to the liver gene zonation and zonation regulators in diseases is limited. Non-alcoholic steatohepatitis (NASH) is a chronic liver disease characterized by fat accumulation, inflammation, and fibrosis. Here, we investigated the perturbation of liver gene zonation in a mouse NASH model by combining spatial transcriptomics, bulk RNAseq and in situ hybridization. Wnt-target genes represented a major subset of genes showing altered spatial expression in the NASH liver. The altered Wnt-target gene expression levels and zonation spatial patterns were in line with the up regulation of Wnt regulators and the augmentation of Wnt signaling. Particularly, we found that the Wnt activator Rspo3 expression was restricted to the perivenous zone in control liver but expanded to the periportal zone in NASH liver. AAV8-mediated RSPO3 overexpression in controls resulted in zonation changes, and further amplified the disturbed zonation of Wnt-target genes in NASH, similarly Rspo3 knockdown in Rspo3+/- mice resulted in zonation changes of Wnt-target genes in both chow and HFD mouse. Interestingly, there were no impacts on steatosis, inflammation, or fibrosis NASH pathology from RSPO3 overexpression nor Rspo3 knockdown. In summary, our study demonstrated the alteration of Wnt signaling in a mouse NASH model, leading to perturbed liver zonation.
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Affiliation(s)
- Ye Zhou
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Yuanqi Zhao
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Marisa Carbonaro
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Helen Chen
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Mary Germino
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Christina Adler
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Min Ni
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Yuan O Zhu
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Sun Y Kim
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Judith Altarejos
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Zhe Li
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | | | - David J Glass
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Mark W Sleeman
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Ann-Hwee Lee
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Gabor Halasz
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Xiping Cheng
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America.
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4
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Granath-Panelo M, Kajimura S. Mitochondrial heterogeneity and adaptations to cellular needs. Nat Cell Biol 2024; 26:674-686. [PMID: 38755301 DOI: 10.1038/s41556-024-01410-1] [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: 11/10/2023] [Accepted: 03/21/2024] [Indexed: 05/18/2024]
Abstract
Although it is well described that mitochondria are at the epicentre of the energy demands of a cell, it is becoming important to consider how each cell tailors its mitochondrial composition and functions to suit its particular needs beyond ATP production. Here we provide insight into mitochondrial heterogeneity throughout development as well as in tissues with specific energy demands and discuss how mitochondrial malleability contributes to cell fate determination and tissue remodelling.
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Affiliation(s)
- Melia Granath-Panelo
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, USA.
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Shingo Kajimura
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, USA.
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5
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Fujiwara N, Kimura G, Nakagawa H. Emerging Roles of Spatial Transcriptomics in Liver Research. Semin Liver Dis 2024. [PMID: 38574750 DOI: 10.1055/a-2299-7880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Spatial transcriptomics, leveraging sequencing- and imaging-based techniques, has emerged as a groundbreaking technology for mapping gene expression within the complex architectures of tissues. This approach provides an in-depth understanding of cellular and molecular dynamics across various states of healthy and diseased livers. Through the integration of sophisticated bioinformatics strategies, it enables detailed exploration of cellular heterogeneity, transitions in cell states, and intricate cell-cell interactions with remarkable precision. In liver research, spatial transcriptomics has been particularly revelatory, identifying distinct zonated functions of hepatocytes that are crucial for understanding the metabolic and detoxification processes of the liver. Moreover, this technology has unveiled new insights into the pathogenesis of liver diseases, such as the role of lipid-associated macrophages in steatosis and endothelial cell signals in liver regeneration and repair. In the domain of liver cancer, spatial transcriptomics has proven instrumental in delineating intratumor heterogeneity, identifying supportive microenvironmental niches and revealing the complex interplay between tumor cells and the immune system as well as susceptibility to immune checkpoint inhibitors. In conclusion, spatial transcriptomics represents a significant advance in hepatology, promising to enhance our understanding and treatment of liver diseases.
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Affiliation(s)
- Naoto Fujiwara
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Mie University, Mie, Japan
| | - Genki Kimura
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Mie University, Mie, Japan
| | - Hayato Nakagawa
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Mie University, Mie, Japan
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6
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Taylor BC, Steinthal LH, Dias M, Yalamanchili HK, Ochsner SA, Zapata GE, Mehta NR, McKenna NJ, Young NL, Nuotio-Antar AM. Histone proteoform analysis reveals epigenetic changes in adult mouse brown adipose tissue in response to cold stress. Epigenetics Chromatin 2024; 17:12. [PMID: 38678237 PMCID: PMC11055387 DOI: 10.1186/s13072-024-00536-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/09/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Regulation of the thermogenic response by brown adipose tissue (BAT) is an important component of energy homeostasis with implications for the treatment of obesity and diabetes. Our preliminary analyses of RNA-Seq data uncovered many nodes representing epigenetic modifiers that are altered in BAT in response to chronic thermogenic activation. Thus, we hypothesized that chronic thermogenic activation broadly alters epigenetic modifications of DNA and histones in BAT. RESULTS Motivated to understand how BAT function is regulated epigenetically, we developed a novel method for the first-ever unbiased top-down proteomic quantitation of histone modifications in BAT and validated our results with a multi-omic approach. To test our hypothesis, wildtype male C57BL/6J mice were housed under chronic conditions of thermoneutral temperature (TN, 28°C), mild cold/room temperature (RT, 22°C), or severe cold (SC, 8°C) and BAT was analyzed for DNA methylation and histone modifications. Methylation of promoters and intragenic regions in genomic DNA decrease in response to chronic cold exposure. Integration of DNA methylation and RNA expression datasets suggest a role for epigenetic modification of DNA in regulation of gene expression in response to cold. In response to cold housing, we observe increased bulk acetylation of histones H3.2 and H4, increased histone H3.2 proteoforms with di- and trimethylation of lysine 9 (K9me2 and K9me3), and increased histone H4 proteoforms with acetylation of lysine 16 (K16ac) in BAT. CONCLUSIONS Our results reveal global epigenetically-regulated transcriptional "on" and "off" signals in murine BAT in response to varying degrees of chronic cold stimuli and establish a novel methodology to quantitatively study histones in BAT, allowing for direct comparisons to decipher mechanistic changes during the thermogenic response. Additionally, we make histone PTM and proteoform quantitation, RNA splicing, RRBS, and transcriptional footprint datasets available as a resource for future research.
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Affiliation(s)
- Bethany C Taylor
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Loic H Steinthal
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA
| | - Michelle Dias
- Department of Pediatrics, Division of Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Hari Krishna Yalamanchili
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Division of Neurology, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Scott A Ochsner
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Gladys E Zapata
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA
| | - Nitesh R Mehta
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA
| | - Neil J McKenna
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Nicolas L Young
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA.
| | - Alli M Nuotio-Antar
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA.
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7
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Scheidecker B, Poulain S, Sugimoto M, Kido T, Kawanishi T, Miyajima A, Kim SH, Arakawa H, Kato Y, Nishikawa M, Danoy M, Sakai Y, Leclerc E. Dynamic, IPSC-derived hepatic tissue tri-culture system for the evaluation of liver physiology in vitro. Biofabrication 2024; 16:025037. [PMID: 38447229 DOI: 10.1088/1758-5090/ad30c5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 03/06/2024] [Indexed: 03/08/2024]
Abstract
Availability of hepatic tissue for the investigation of metabolic processes is severely limited. While primary hepatocytes or animal models are widely used in pharmacological applications, a change in methodology towards more sustainable and ethical assays is highly desirable. Stem cell derived hepatic cells are generally regarded as a viable alternative for the above model systems, if current limitations in functionality and maturation can be overcome. By combining microfluidic organ-on-a-chip technology with individually differentiated, multicellular hepatic tissue fractions, we aim to improve overall functionality of hepatocyte-like cells, as well as evaluate cellular composition and interactions with non-parenchymal cell populations towards the formation of mature liver tissue. Utilizing a multi-omic approach, we show the improved maturation profiles of hepatocyte-like cells maintained in a dynamic microenvironment compared to standard tissue culture setups without continuous perfusion. In order to evaluate the resulting tissue, we employ single cell sequencing to distinguish formed subpopulations and spatial localization. While cellular input was strictly defined based on established differentiation protocols of parenchyma, endothelial and stellate cell fractions, resulting hepatic tissue was shown to comprise a complex mixture of epithelial and non-parenchymal fractions with specific local enrichment of phenotypes along the microchannel. Following this approach, we show the importance of passive, paracrine developmental processes in tissue formation. Using such complex tissue models is a crucial first step to develop stem cell-derivedin vitrosystems that can compare functionally with currently used pharmacological and toxicological applications.
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Affiliation(s)
- Benedikt Scheidecker
- CNRS UMI 2820, Institute of Industrial Science, University of Tokyo, 153-8505 Tokyo, Japan
| | - Stéphane Poulain
- Institute of Industrial Science, University of Tokyo, 153-8505 Tokyo, Japan
| | - Masahiro Sugimoto
- Institute for Advanced Biosciences, Keio University, 997-0035 Yamagata, Japan
- Institute of Medical Science, Tokyo Medical University, 160-8402 Tokyo, Japan
| | - Taketomo Kido
- Institute for Quantitative Biosciences, University of Tokyo, 113-0032 Tokyo, Japan
| | - Takumi Kawanishi
- School of Pharmaceutical Sciences, Kanazawa University, 920-1102 Kanazawa, Japan
| | - Atsushi Miyajima
- Institute for Quantitative Biosciences, University of Tokyo, 113-0032 Tokyo, Japan
| | - Soo Hyeon Kim
- Institute of Industrial Science, University of Tokyo, 153-8505 Tokyo, Japan
| | - Hiroshi Arakawa
- School of Pharmaceutical Sciences, Kanazawa University, 920-1102 Kanazawa, Japan
| | - Yukio Kato
- School of Pharmaceutical Sciences, Kanazawa University, 920-1102 Kanazawa, Japan
| | - Masaki Nishikawa
- Department of Chemical System Engineering, University of Tokyo, 113-8654 Tokyo, Japan
| | - Mathieu Danoy
- Department of Chemical System Engineering, University of Tokyo, 113-8654 Tokyo, Japan
| | - Yasuyuki Sakai
- Department of Chemical System Engineering, University of Tokyo, 113-8654 Tokyo, Japan
| | - Eric Leclerc
- CNRS UMI 2820, Institute of Industrial Science, University of Tokyo, 153-8505 Tokyo, Japan
- CNRS UMR 7338, Laboratoire de Biomécanique et Bioingénierie, Université de Technologies de Compiègne, 60203 Compiègne, France
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8
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Murphy WA, Diehl AM, Loop MS, Fu D, Guy CD, Abdelmalek MF, Karachaliou GS, Sjöstedt N, Neuhoff S, Honkakoski P, Brouwer KLR. Alterations in zonal distribution and plasma membrane localization of hepatocyte bile acid transporters in patients with NAFLD. Hepatol Commun 2024; 8:e0377. [PMID: 38381537 PMCID: PMC10871794 DOI: 10.1097/hc9.0000000000000377] [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] [Received: 10/09/2023] [Accepted: 12/16/2023] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND NAFLD is highly prevalent with limited treatment options. Bile acids (BAs) increase in the systemic circulation and liver during NAFLD progression. Changes in plasma membrane localization and zonal distribution of BA transporters can influence transport function and BA homeostasis. However, a thorough characterization of how NAFLD influences these factors is currently lacking. This study aimed to evaluate the impact of NAFLD and the accompanying histologic features on the functional capacity of key hepatocyte BA transporters across zonal regions in human liver biopsies. METHODS A novel machine learning image classification approach was used to quantify relative zonal abundance and plasma membrane localization of BA transporters (bile salt export pump [BSEP], sodium-taurocholate cotransporting polypeptide, organic anion transporting polypeptide [OATP] 1B1 and OATP1B3) in non-diseased (n = 10), NAFL (n = 9), and NASH (n = 11) liver biopsies. Based on these data, membrane-localized zonal abundance (MZA) measures were developed to estimate transporter functional capacity. RESULTS NAFLD diagnosis and histologic scoring were associated with changes in transporter membrane localization and zonation. Increased periportal BSEPMZA (mean proportional difference compared to non-diseased liver of 0.090) and decreased pericentral BSEPMZA (-0.065) were observed with NASH and also in biopsies with higher histologic scores. Compared to Non-diseased Liver, periportal OATP1B3MZA was increased in NAFL (0.041) and NASH (0.047). Grade 2 steatosis (mean proportional difference of 0.043 when compared to grade 0) and grade 1 lobular inflammation (0.043) were associated with increased periportal OATP1B3MZA. CONCLUSIONS These findings provide novel mechanistic insight into specific transporter alterations that impact BA homeostasis in NAFLD. Changes in BSEPMZA likely contribute to altered BA disposition and pericentral microcholestasis previously reported in some patients with NAFLD. BSEPMZA assessment could inform future development and optimization of NASH-related pharmacotherapies.
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Affiliation(s)
- William A. Murphy
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Anna Mae Diehl
- Division of Gastroenterology and Hepatology, Duke University Medical Center, Durham, North Carolina, USA
| | - Matthew Shane Loop
- Department of Health Outcomes Research and Policy, Harrison College of Pharmacy, Auburn University, Auburn, Alabama, USA
| | - Dong Fu
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Cynthia D. Guy
- Department of Pathology, Duke University, Durham, North Carolina, USA
| | - Manal F. Abdelmalek
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Georgia Sofia Karachaliou
- Division of Gastroenterology and Hepatology, Duke University Medical Center, Durham, North Carolina, USA
| | - Noora Sjöstedt
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | | | - Paavo Honkakoski
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Kim L. R. Brouwer
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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9
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Kang SWS, Cunningham RP, Miller CB, Brown LA, Cultraro CM, Harned A, Narayan K, Hernandez J, Jenkins LM, Lobanov A, Cam M, Porat-Shliom N. A spatial map of hepatic mitochondria uncovers functional heterogeneity shaped by nutrient-sensing signaling. Nat Commun 2024; 15:1799. [PMID: 38418824 PMCID: PMC10902380 DOI: 10.1038/s41467-024-45751-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 02/04/2024] [Indexed: 03/02/2024] Open
Abstract
In the liver, mitochondria are exposed to different concentrations of nutrients due to their spatial positioning across the periportal and pericentral axis. How the mitochondria sense and integrate these signals to respond and maintain homeostasis is not known. Here, we combine intravital microscopy, spatial proteomics, and functional assessment to investigate mitochondrial heterogeneity in the context of liver zonation. We find that periportal and pericentral mitochondria are morphologically and functionally distinct; beta-oxidation is elevated in periportal regions, while lipid synthesis is predominant in the pericentral mitochondria. In addition, comparative phosphoproteomics reveals spatially distinct patterns of mitochondrial composition and potential regulation via phosphorylation. Acute pharmacological modulation of nutrient sensing through AMPK and mTOR shifts mitochondrial phenotypes in the periportal and pericentral regions, linking nutrient gradients across the lobule and mitochondrial heterogeneity. This study highlights the role of protein phosphorylation in mitochondrial structure, function, and overall homeostasis in hepatic metabolic zonation. These findings have important implications for liver physiology and disease.
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Affiliation(s)
- Sun Woo Sophie Kang
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Rory P Cunningham
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Colin B Miller
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Lauryn A Brown
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Constance M Cultraro
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Adam Harned
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Research Technology Programs, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kedar Narayan
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Research Technology Programs, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jonathan Hernandez
- Surgical Oncology Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Alexei Lobanov
- CCR Collaborative Bioinformatics Resource (CCBR) National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Maggie Cam
- CCR Collaborative Bioinformatics Resource (CCBR) National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Natalie Porat-Shliom
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA.
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10
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Bravo González-Blas C, Matetovici I, Hillen H, Taskiran II, Vandepoel R, Christiaens V, Sansores-García L, Verboven E, Hulselmans G, Poovathingal S, Demeulemeester J, Psatha N, Mauduit D, Halder G, Aerts S. Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation. Nat Cell Biol 2024; 26:153-167. [PMID: 38182825 PMCID: PMC10791584 DOI: 10.1038/s41556-023-01316-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 11/15/2023] [Indexed: 01/07/2024]
Abstract
In the mammalian liver, hepatocytes exhibit diverse metabolic and functional profiles based on their location within the liver lobule. However, it is unclear whether this spatial variation, called zonation, is governed by a well-defined gene regulatory code. Here, using a combination of single-cell multiomics, spatial omics, massively parallel reporter assays and deep learning, we mapped enhancer-gene regulatory networks across mouse liver cell types. We found that zonation affects gene expression and chromatin accessibility in hepatocytes, among other cell types. These states are driven by the repressors TCF7L1 and TBX3, alongside other core hepatocyte transcription factors, such as HNF4A, CEBPA, FOXA1 and ONECUT1. To examine the architecture of the enhancers driving these cell states, we trained a hierarchical deep learning model called DeepLiver. Our study provides a multimodal understanding of the regulatory code underlying hepatocyte identity and their zonation state that can be used to engineer enhancers with specific activity levels and zonation patterns.
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Affiliation(s)
- Carmen Bravo González-Blas
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Irina Matetovici
- VIB Center for Brain & Disease Research, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
- VIB Tech Watch, VIB Headquarters, Ghent, Belgium
| | - Hanne Hillen
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Ibrahim Ihsan Taskiran
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | - Roel Vandepoel
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | - Valerie Christiaens
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | - Leticia Sansores-García
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Elisabeth Verboven
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | | | - Jonas Demeulemeester
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Nikoleta Psatha
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - David Mauduit
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | - Georg Halder
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Stein Aerts
- VIB Center for Brain & Disease Research, Leuven, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium.
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11
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Benassi B, Bacchetta L, Maccioni O, Pacchierotti F. Epigenetic-based antioxidant effect of an ethanolic extract of Corylus avellana L. on THLE-2 human primary hepatocytes. Nat Prod Res 2023; 37:4162-4168. [PMID: 36735396 DOI: 10.1080/14786419.2023.2174537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/22/2023] [Indexed: 02/04/2023]
Abstract
The ethanolic extract of Corylus avellana L hazelnut, prepared in our laboratories, has been previously characterized by liquid chromatography coupled to high resolution mass spectrometry. We here aimed at testing the antioxidant effect of such extract in H2O2-challenged THLE-2 human primary hepatocytes and verified whether it might be based on microRNA-34b/c expression changes. We here demonstrate that miR-34b/miR-34c undergo significant stimulation (≥2-fold change, p < 0.05) in THLE-2 when treated for 72h with not-toxic hazelnut concentrations (0.04-0.4 mg/ml), when compared with 0.06% ethanol control. When administered with H2O2 (1000-2000 µM, 24h), THLE-2 are significantly protected from oxidative stress if pre-treated with hazelnut, the H2O2-driven cytotoxicity and reactive oxygen species generation being recovered by hazelnut extract, through miR-34b/c stimulation. Although preliminary, our findings pave the way for further preclinical studies aimed at validating the possible health-related application of hazelnut matrix, and/or its metabolites, as powerful epigenetic-based drugs, food supplements or nutraceuticals.
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Affiliation(s)
- Barbara Benassi
- Division of Health Protection Technologies, ENEA-Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Loretta Bacchetta
- Division of Biotechnologies and Agroindustry, ENEA-Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Oliviero Maccioni
- Division of Biotechnologies and Agroindustry, ENEA-Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Francesca Pacchierotti
- Division of Health Protection Technologies, ENEA-Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
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12
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Kang SWS, Cunningham RP, Miller CB, Brown LA, Cultraro CM, Harned A, Narayan K, Hernandez J, Jenkins LM, Lobanov A, Cam M, Porat-Shliom N. A spatial map of hepatic mitochondria uncovers functional heterogeneity shaped by nutrient-sensing signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.13.536717. [PMID: 37333328 PMCID: PMC10274915 DOI: 10.1101/2023.04.13.536717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
In the liver, mitochondria are exposed to different concentrations of nutrients due to their spatial positioning across the periportal (PP) and pericentral (PC) axis. How these mitochondria sense and integrate these signals to respond and maintain homeostasis is not known. Here, we combined intravital microscopy, spatial proteomics, and functional assessment to investigate mitochondrial heterogeneity in the context of liver zonation. We found that PP and PC mitochondria are morphologically and functionally distinct; beta-oxidation was elevated in PP regions, while lipid synthesis was predominant in the PC mitochondria. In addition, comparative phosphoproteomics revealed spatially distinct patterns of mitochondrial composition and potential regulation via phosphorylation. Acute pharmacological modulation of nutrient sensing through AMPK and mTOR shifted mitochondrial phenotypes in the PP and PC regions, linking nutrient gradients across the lobule and mitochondrial heterogeneity. This study highlights the role of protein phosphorylation in mitochondrial structure, function, and overall homeostasis in hepatic metabolic zonation. These findings have important implications for liver physiology and disease.
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Affiliation(s)
- Sun Woo Sophie Kang
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Rory P. Cunningham
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Colin B. Miller
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Lauryn A. Brown
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Constance M. Cultraro
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Adam Harned
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Kedar Narayan
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Jonathan Hernandez
- Surgical Oncology Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Lisa M. Jenkins
- Laboratory of Cell Biology, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Alexei Lobanov
- CCR Collaborative Bioinformatics Resource (CCBR) National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Maggie Cam
- CCR Collaborative Bioinformatics Resource (CCBR) National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Natalie Porat-Shliom
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
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13
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Harrison SP, Siller R, Tanaka Y, Chollet ME, de la Morena-Barrio ME, Xiang Y, Patterson B, Andersen E, Bravo-Pérez C, Kempf H, Åsrud KS, Lunov O, Dejneka A, Mowinckel MC, Stavik B, Sandset PM, Melum E, Baumgarten S, Bonanini F, Kurek D, Mathapati S, Almaas R, Sharma K, Wilson SR, Skottvoll FS, Boger IC, Bogen IL, Nyman TA, Wu JJ, Bezrouk A, Cizkova D, Corral J, Mokry J, Zweigerdt R, Park IH, Sullivan GJ. Scalable production of tissue-like vascularized liver organoids from human PSCs. Exp Mol Med 2023; 55:2005-2024. [PMID: 37653039 PMCID: PMC10545717 DOI: 10.1038/s12276-023-01074-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 04/18/2023] [Accepted: 06/02/2023] [Indexed: 09/02/2023] Open
Abstract
The lack of physiological parity between 2D cell culture and in vivo culture has led to the development of more organotypic models, such as organoids. Organoid models have been developed for a number of tissues, including the liver. Current organoid protocols are characterized by a reliance on extracellular matrices (ECMs), patterning in 2D culture, costly growth factors and a lack of cellular diversity, structure, and organization. Current hepatic organoid models are generally simplistic and composed of hepatocytes or cholangiocytes, rendering them less physiologically relevant compared to native tissue. We have developed an approach that does not require 2D patterning, is ECM independent, and employs small molecules to mimic embryonic liver development that produces large quantities of liver-like organoids. Using single-cell RNA sequencing and immunofluorescence, we demonstrate a liver-like cellular repertoire, a higher order cellular complexity, presenting with vascular luminal structures, and a population of resident macrophages: Kupffer cells. The organoids exhibit key liver functions, including drug metabolism, serum protein production, urea synthesis and coagulation factor production, with preserved post-translational modifications such as N-glycosylation and functionality. The organoids can be transplanted and maintained long term in mice producing human albumin. The organoids exhibit a complex cellular repertoire reflective of the organ and have de novo vascularization and liver-like function. These characteristics are a prerequisite for many applications from cellular therapy, tissue engineering, drug toxicity assessment, and disease modeling to basic developmental biology.
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Affiliation(s)
- Sean P Harrison
- Hybrid Technology Hub-Centre of Excellence, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Department of Pediatric Research, Oslo University Hospital, Oslo, Norway
| | - Richard Siller
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Yoshiaki Tanaka
- Department of Genetics, Yale Stem Cell Center, Child Study Center, Yale School of Medicine, New Haven, USA
- Department of Medicine, Faculty of Medicine, Maisonneuve-Rosemont Hospital Research Center (CRHMR), University of Montreal, Montreal, Canada
| | - Maria Eugenia Chollet
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
- Department of Haematology, Oslo University Hospital, Oslo, Norway
| | - María Eugenia de la Morena-Barrio
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB, CIBERER, Murcia, Spain
| | - Yangfei Xiang
- Department of Genetics, Yale Stem Cell Center, Child Study Center, Yale School of Medicine, New Haven, USA
| | - Benjamin Patterson
- Department of Genetics, Yale Stem Cell Center, Child Study Center, Yale School of Medicine, New Haven, USA
| | - Elisabeth Andersen
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
- Department of Haematology, Oslo University Hospital, Oslo, Norway
| | - Carlos Bravo-Pérez
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB, CIBERER, Murcia, Spain
| | - Henning Kempf
- Department: Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Hannover Medical School, Hannover, Germany
| | - Kathrine S Åsrud
- Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Oleg Lunov
- Department of Optical and Biophysical Systems, Institute of Physics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Alexandr Dejneka
- Department of Optical and Biophysical Systems, Institute of Physics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Marie-Christine Mowinckel
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
- Department of Haematology, Oslo University Hospital, Oslo, Norway
| | - Benedicte Stavik
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
- Department of Haematology, Oslo University Hospital, Oslo, Norway
| | - Per Morten Sandset
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
- Department of Haematology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Espen Melum
- Hybrid Technology Hub-Centre of Excellence, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Department of Haematology, Oslo University Hospital, Oslo, Norway
- Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Section for Gastroenterology, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
- European Reference Network RARE-LIVER, Hamburg, Germany
| | - Saphira Baumgarten
- Hybrid Technology Hub-Centre of Excellence, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Department of Pediatric Research, Oslo University Hospital, Oslo, Norway
| | | | | | - Santosh Mathapati
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Runar Almaas
- Department of Pediatric Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- European Reference Network RARE-LIVER, Hamburg, Germany
| | - Kulbhushan Sharma
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Steven R Wilson
- Hybrid Technology Hub-Centre of Excellence, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, NO-0315, Oslo, Norway
| | - Frøydis S Skottvoll
- Hybrid Technology Hub-Centre of Excellence, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, NO-0315, Oslo, Norway
| | - Ida C Boger
- Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, NO-0315, Oslo, Norway
| | - Inger Lise Bogen
- Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway
| | - Tuula A Nyman
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Jun Jie Wu
- Department of Engineering, Faculty of Science, Durham University, Durham, DH1 3LE, United Kingdom
| | - Ales Bezrouk
- Department of Medical Biophysics, Faculty of Medicine in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Dana Cizkova
- Department of Histology and Embryology, Faculty of Medicine in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Javier Corral
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB, CIBERER, Murcia, Spain
| | - Jaroslav Mokry
- Department of Histology and Embryology, Faculty of Medicine in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Robert Zweigerdt
- Department: Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Hannover Medical School, Hannover, Germany
| | - In-Hyun Park
- Department of Genetics, Yale Stem Cell Center, Child Study Center, Yale School of Medicine, New Haven, USA
| | - Gareth J Sullivan
- Hybrid Technology Hub-Centre of Excellence, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
- Department of Pediatric Research, Oslo University Hospital, Oslo, Norway.
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.
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14
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Jose A, Elwing JM, Kawut SM, Pauciulo MW, Sherman KE, Nichols WC, Fallon MB, McCormack FX. Human liver single nuclear RNA sequencing implicates BMPR2, GDF15, arginine, and estrogen in portopulmonary hypertension. Commun Biol 2023; 6:826. [PMID: 37558836 PMCID: PMC10412637 DOI: 10.1038/s42003-023-05193-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/31/2023] [Indexed: 08/11/2023] Open
Abstract
Portopulmonary hypertension (PoPH) is a type of pulmonary vascular disease due to portal hypertension that exhibits high morbidity and mortality. The mechanisms driving disease are unknown, and transcriptional characteristics unique to the PoPH liver remain unexplored. Here, we apply single nuclear RNA sequencing to compare cirrhotic livers from patients with and without PoPH. We identify characteristics unique to PoPH in cells surrounding the central hepatic vein, including increased growth differentiation factor signaling, enrichment of the arginine biosynthesis pathway, and differential expression of the bone morphogenic protein type II receptor and estrogen receptor type I genes. These results provide insight into the transcriptomic characteristics of the PoPH liver and mechanisms by which PoPH cellular dysfunction might contribute to pulmonary vascular remodeling.
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Affiliation(s)
- Arun Jose
- Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Jean M Elwing
- Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Steven M Kawut
- Department of Medicine, Perelman School at the University of Pennsylvania, Philadelphia, PA, USA
| | - Michael W Pauciulo
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kenneth E Sherman
- Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - William C Nichols
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Francis X McCormack
- Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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15
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Shi X, Hu Z, Gan B, He Y, Zhang L, Chen M, Wang Y, Li X. Multivariate Evaluation of DNA Quality Differences in Different Preanalytical Procedures in Mouse Livers. Biopreserv Biobank 2023; 21:378-387. [PMID: 36067273 DOI: 10.1089/bio.2022.0027] [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: 11/13/2022] Open
Abstract
Successful histogenetic research relies on proper handling of tissue samples to maximize DNA quality. As the largest gland in the body, the liver is particularly sensitive to sample mishandling owing to its enzymatic and transcriptional activity. However, the impact of preanalytical procedures on the quality of extracted liver DNA remains poorly understood. In this study, we assessed the impact of extraction methods, duration of ex vivo liver ischemia, liver storage time, and temperature on extracted DNA quality. Comprehensive parameters such as DNA yields, purity, DNA integrity number, the percentage of double-stranded DNA (%dsDNA), and PCR amplification of the GAPDH gene fragment were assessed to identify the quality of extracted DNA. Our results revealed that these preanalytical processes had little effect on DIN values and PCR efficiency of GAPDH gene fragments for each sample, whereas the DNA yields, purity, and %dsDNAs varied widely across different processes. For liver DNA extraction, RNase is necessary to isolate "pure" DNA, and the presence of RNase could significantly increase the %dsDNA. In addition, significant increases in the yields, purity, and %dsDNA of extracted DNA were observed in the TissueLyser-processed livers compared with the mortar and pestle or shear cell disruption methods. Further investigation revealed that livers experiencing longer periods of ex vivo ischemia resulted in significantly compromised DNA yields, and to obtain sufficient DNA, the ex vivo liver ischemia should be limited to within 30 minutes. Moreover, compared with storage of livers at -80°C, storage of livers in the vapor phase of liquid nitrogen yielded a higher quality of the extracted DNA. Our findings exhibited significant implications for liver-derived DNA quality assessment and management.
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Affiliation(s)
- Xue Shi
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Zhenyue Hu
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Baoyu Gan
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Yinlin He
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Linpei Zhang
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Min Chen
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Yawen Wang
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Xiaojiao Li
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
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16
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Chen F, Schönberger K, Tchorz JS. Distinct hepatocyte identities in liver homeostasis and regeneration. JHEP Rep 2023; 5:100779. [PMID: 37456678 PMCID: PMC10339260 DOI: 10.1016/j.jhepr.2023.100779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 03/27/2023] [Accepted: 04/07/2023] [Indexed: 07/18/2023] Open
Abstract
The process of metabolic liver zonation is spontaneously established by assigning distributed tasks to hepatocytes along the porto-central blood flow. Hepatocytes fulfil critical metabolic functions, while also maintaining hepatocyte mass by replication when needed. Recent technological advances have enabled us to fine-tune our understanding of hepatocyte identity during homeostasis and regeneration. Subsets of hepatocytes have been identified to be more regenerative and some have even been proposed to function like stem cells, challenging the long-standing view that all hepatocytes are similarly capable of regeneration. The latest data show that hepatocyte renewal during homeostasis and regeneration after liver injury is not limited to rare hepatocytes; however, hepatocytes are not exactly the same. Herein, we review the known differences that give individual hepatocytes distinct identities, recent findings demonstrating how these distinct identities correspond to differences in hepatocyte regenerative capacity, and how the plasticity of hepatocyte identity allows for division of labour among hepatocytes. We further discuss how these distinct hepatocyte identities may play a role during liver disease.
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Affiliation(s)
- Feng Chen
- Novartis Institutes for BioMedical Research, Cambridge, MA, United States
| | | | - Jan S. Tchorz
- Novartis Institutes for BioMedical Research, Basel, Switzerland
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17
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Tamargo-Rubio I, Simpson AB, Hoogerland JA, Fu J. Human induced pluripotent stem cell-derived liver-on-a-chip for studying drug metabolism: the challenge of the cytochrome P450 family. Front Pharmacol 2023; 14:1223108. [PMID: 37448965 PMCID: PMC10338083 DOI: 10.3389/fphar.2023.1223108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023] Open
Abstract
The liver is the primary organ responsible for the detoxification and metabolism of drugs. To date, a lack of preclinical models that accurately emulate drug metabolism by the human liver presents a significant challenge in the drug development pipeline, particularly for predicting drug efficacy and toxicity. In recent years, emerging microfluidic-based organ-on-a-chip (OoC) technologies, combined with human induced pluripotent stem cell (hiPSC) technology, present a promising avenue for the complete recapitulation of human organ biology in a patient-specific manner. However, hiPSC-derived organoids and liver-on-a-chip models have so far failed to sufficiently express cytochrome P450 monooxygenase (CYP450) enzymes, the key enzymes involved in first-pass metabolism, which limits the effectiveness and translatability of these models in drug metabolism studies. This review explores the potential of innovative organoid and OoC technologies for studying drug metabolism and discusses their existing drawbacks, such as low expression of CYP450 genes. Finally, we postulate potential approaches for enhancing CYP450 expression in the hope of paving the way toward developing novel, fully representative liver drug-metabolism models.
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Affiliation(s)
- Isabel Tamargo-Rubio
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Anna Bella Simpson
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Joanne A. Hoogerland
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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18
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Ryaboshapkina M, Azzu V. Sample size calculation for a NanoString GeoMx spatial transcriptomics experiment to study predictors of fibrosis progression in non-alcoholic fatty liver disease. Sci Rep 2023; 13:8943. [PMID: 37268815 DOI: 10.1038/s41598-023-36187-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/29/2023] [Indexed: 06/04/2023] Open
Abstract
Sample size calculation for spatial transcriptomics is a novel and understudied research topic. Prior publications focused on powering spatial transcriptomics studies to detect specific cell populations or spatially variable expression patterns on tissue slides. However, power calculations for translational or clinical studies often relate to the difference between patient groups, and this is poorly described in the literature. Here, we present a stepwise process for sample size calculation to identify predictors of fibrosis progression in non-alcoholic fatty liver disease as a case study. We illustrate how to infer study hypothesis from prior bulk RNA-sequencing data, gather input requirements and perform a simulation study to estimate required sample size to evaluate gene expression differences between patients with stable fibrosis and fibrosis progressors with NanoString GeoMx Whole Transcriptome Atlas assay.
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Affiliation(s)
- Maria Ryaboshapkina
- Translational Science and Experimental Medicine, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
| | - Vian Azzu
- Translational Science and Experimental Medicine, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
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19
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Intra-pituitary follicle-stimulating hormone signaling regulates hepatic lipid metabolism in mice. Nat Commun 2023; 14:1098. [PMID: 36841874 PMCID: PMC9968338 DOI: 10.1038/s41467-023-36681-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/09/2023] [Indexed: 02/27/2023] Open
Abstract
Inter-organ communication is a major hallmark of health and is often orchestrated by hormones released by the anterior pituitary gland. Pituitary gonadotropes secrete follicle-stimulating hormone (FSH) and luteinizing hormone (LH) to regulate gonadal function and control fertility. Whether FSH and LH also act on organs other than the gonads is debated. Here, we find that gonadotrope depletion in adult female mice triggers profound hypogonadism, obesity, glucose intolerance, fatty liver, and bone loss. The absence of sex steroids precipitates these phenotypes, with the notable exception of fatty liver, which results from ovary-independent actions of FSH. We uncover paracrine FSH action on pituitary corticotropes as a mechanism to restrain the production of corticosterone and prevent hepatic steatosis. Our data demonstrate that functional communication of two distinct hormone-secreting cell populations in the pituitary regulates hepatic lipid metabolism.
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20
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Martini T, Naef F, Tchorz JS. Spatiotemporal Metabolic Liver Zonation and Consequences on Pathophysiology. ANNUAL REVIEW OF PATHOLOGY 2023; 18:439-466. [PMID: 36693201 DOI: 10.1146/annurev-pathmechdis-031521-024831] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Hepatocytes are the main workers in the hepatic factory, managing metabolism of nutrients and xenobiotics, production and recycling of proteins, and glucose and lipid homeostasis. Division of labor between hepatocytes is critical to coordinate complex complementary or opposing multistep processes, similar to distributed tasks at an assembly line. This so-called metabolic zonation has both spatial and temporal components. Spatial distribution of metabolic function in hepatocytes of different lobular zones is necessary to perform complex sequential multistep metabolic processes and to assign metabolic tasks to the right environment. Moreover, temporal control of metabolic processes is critical to align required metabolic processes to the feeding and fasting cycles. Disruption of this complex spatiotemporal hepatic organization impairs key metabolic processes with both local and systemic consequences. Many metabolic diseases, such as nonalcoholic steatohepatitis and diabetes, are associated with impaired metabolic liver zonation. Recent technological advances shed new light on the spatiotemporal gene expression networks controlling liver function and how their deregulation may be involved in a large variety of diseases. We summarize the current knowledge about spatiotemporal metabolic liver zonation and consequences on liver pathobiology.
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Affiliation(s)
- Tomaz Martini
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland;
| | - Felix Naef
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland;
| | - Jan S Tchorz
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland;
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21
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Murine breast cancers disorganize the liver transcriptome in a zonated manner. Commun Biol 2023; 6:97. [PMID: 36694005 PMCID: PMC9873924 DOI: 10.1038/s42003-023-04479-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 01/12/2023] [Indexed: 01/25/2023] Open
Abstract
The spatially organized gene expression program within the liver specifies hepatocyte functions according to their relative distances to the bloodstream (i.e., zonation), contributing to liver homeostasis. Despite the knowledge that solid cancers remotely disrupt liver homeostasis, it remains unexplored whether solid cancers affect liver zonation. Here, using spatial transcriptomics, we thoroughly investigate the abundance and zonation of hepatic genes in cancer-bearing mice. We find that breast cancers affect liver zonation in various distinct manners depending on biological pathways. Aspartate metabolism and triglyceride catabolic processes retain relatively intact zonation patterns, but the zonation of xenobiotic catabolic process genes exhibits a strong disruption. The acute phase response is induced in zonated manners. Furthermore, we demonstrate that breast cancers activate innate immune cells in particular neutrophils in distinct zonated manners, rather than in a uniform fashion within the liver. Collectively, breast cancers disorganize hepatic transcriptomes in zonated manners, thereby disrupting zonated functions of the liver.
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22
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Impact of Liver Inflammation on Bile Acid Side Chain Shortening and Amidation. Cells 2022; 11:cells11243983. [PMID: 36552746 PMCID: PMC9777420 DOI: 10.3390/cells11243983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Bile acid (BA) synthesis from cholesterol by hepatocytes is inhibited by inflammatory cytokines. Whether liver inflammation also affects BA side chain shortening and conjugation was investigated. In human liver cell lines (IHH, HepG2, and HepaRG), agonists of nuclear receptors including the farnesoid X receptor (FXR), liver X receptor (LXR), and peroxisome proliferator-activated receptors (PPARs) did not affect the expression of BA-related peroxisomal enzymes. In contrast, hepatocyte nuclear factor 4α (HNF4α) inhibition down-regulated acyl-CoA oxidase 2 (ACOX2). ACOX2 was repressed by fibroblast growth factor 19 (FGF19), which was prevented by extracellular signal-regulated kinase (ERK) pathway inhibition. These changes were paralleled by altered BA synthesis (HPLC-MS/MS). Cytokines able to down-regulate cholesterol-7α-hydroxylase (CYP7A1) had little effect on peroxisomal enzymes involved in BA synthesis except for ACOX2 and bile acid-CoA:amino acid N-acyltransferase (BAAT), which were down-regulated, mainly by oncostatin M (OSM). This effect was prevented by Janus kinase (JAK) inhibition, which restored BA side chain shortening and conjugation. The binding of OSM to the extracellular matrix accounted for a persistent effect after culture medium replacement. In silico analysis of four databases (n = 201) and a validation cohort (n = 90) revealed an inverse relationship between liver inflammation and ACOX2/BAAT expression which was associated with changes in HNF4α levels. In conclusion, BA side chain shortening and conjugation are inhibited by inflammatory effectors. However, other mechanisms involved in BA homeostasis counterbalance any significant impact on the serum BA profile.
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23
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Kleino I, Frolovaitė P, Suomi T, Elo LL. Computational solutions for spatial transcriptomics. Comput Struct Biotechnol J 2022; 20:4870-4884. [PMID: 36147664 PMCID: PMC9464853 DOI: 10.1016/j.csbj.2022.08.043] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/18/2022] [Accepted: 08/18/2022] [Indexed: 11/18/2022] Open
Abstract
Transcriptome level expression data connected to the spatial organization of the cells and molecules would allow a comprehensive understanding of how gene expression is connected to the structure and function in the biological systems. The spatial transcriptomics platforms may soon provide such information. However, the current platforms still lack spatial resolution, capture only a fraction of the transcriptome heterogeneity, or lack the throughput for large scale studies. The strengths and weaknesses in current ST platforms and computational solutions need to be taken into account when planning spatial transcriptomics studies. The basis of the computational ST analysis is the solutions developed for single-cell RNA-sequencing data, with advancements taking into account the spatial connectedness of the transcriptomes. The scRNA-seq tools are modified for spatial transcriptomics or new solutions like deep learning-based joint analysis of expression, spatial, and image data are developed to extract biological information in the spatially resolved transcriptomes. The computational ST analysis can reveal remarkable biological insights into spatial patterns of gene expression, cell signaling, and cell type variations in connection with cell type-specific signaling and organization in complex tissues. This review covers the topics that help choosing the platform and computational solutions for spatial transcriptomics research. We focus on the currently available ST methods and platforms and their strengths and limitations. Of the computational solutions, we provide an overview of the analysis steps and tools used in the ST data analysis. The compatibility with the data types and the tools provided by the current ST analysis frameworks are summarized.
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Key Words
- AOI, area of illumination
- BICCN, Brain Initiative Cell Census Network
- BOLORAMIS, barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses
- Baysor, Bayesian Segmentation of Spatial Transcriptomics Data
- BinSpect, Binary Spatial Extraction
- CCC, cell–cell communication
- CCI, cell–cell interactions
- CNV, copy-number variation
- Computational biology
- DSP, digital spatial profiling
- DbiT-Seq, Deterministic Barcoding in Tissue for spatial omics sequencing
- FA, factor analysis
- FFPE, formalin-fixed, paraffin-embedded
- FISH, fluorescence in situ hybridization
- FISSEQ, fluorescence in situ sequencing of RNA
- FOV, Field of view
- GRNs, gene regulation networks
- GSEA, gene set enrichment analysis
- GSVA, gene set variation analysis
- HDST, high definition spatial transcriptomics
- HMRF, hidden Markov random field
- ICG, interaction changed genes
- ISH, in situ hybridization
- ISS, in situ sequencing
- JSTA, Joint cell segmentation and cell type annotation
- KNN, k-nearest neighbor
- LCM, Laser Capture Microdissection
- LCM-seq, laser capture microdissection coupled with RNA sequencing
- LOH, loss of heterozygosity analysis
- MC, Molecular Cartography
- MERFISH, multiplexed error-robust FISH
- NMF (NNMF), Non-negative matrix factorization
- PCA, Principal Component Analysis
- PIXEL-seq, Polony (or DNA cluster)-indexed library-sequencing
- PL-lig, padlock ligation
- QC, quality control
- RNAseq, RNA sequencing
- ROI, region of interest
- SCENIC, Single-Cell rEgulatory Network Inference and Clustering
- SME, Spatial Morphological gene Expression normalization
- SPATA, SPAtial Transcriptomic Analysis
- ST Pipeline, Spatial Transcriptomics Pipeline
- ST, Spatial transcriptomics
- STARmap, spatially-resolved transcript amplicon readout mapping
- Single-cell analysis
- Spatial data analysis frameworks
- Spatial deconvolution
- Spatial transcriptomics
- TIVA, Transcriptome in Vivo Analysis
- TMA, tissue microarray
- TME, tumor micro environment
- UMAP, Uniform Manifold Approximation and Projection for Dimension Reduction
- UMI, unique molecular identifier
- ZipSeq, zipcoded sequencing.
- scRNA-seq, single-cell RNA sequencing
- scvi-tools, single-cell variational inference tools
- seqFISH, sequential fluorescence in situ hybridization
- sequ-smFISH, sequential single-molecule fluorescent in situ hybridization
- smFISH, single molecule FISH
- t-SNE, t-distributed stochastic neighbor embedding
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Affiliation(s)
- Iivari Kleino
- Turku Bioscience Centre, University of Turku and Åbo Akademi University Turku, Turku, Finland
| | - Paulina Frolovaitė
- Turku Bioscience Centre, University of Turku and Åbo Akademi University Turku, Turku, Finland
| | - Tomi Suomi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University Turku, Turku, Finland
| | - Laura L. Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University Turku, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
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24
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Tarnow G, Matrenec R, Oropeza CE, Maienschein-Cline M, McLachlan A. Distinct phenotypic spectra of hepatocellular carcinoma in liver-specific tumor suppressor-deficient hepatitis B virus transgenic mice. Virology 2022; 574:84-95. [PMID: 35961146 DOI: 10.1016/j.virol.2022.08.002] [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: 06/30/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 11/22/2022]
Abstract
The hepatitis B virus (HBV) transgenic mouse model was used to interrogate the origins of HCC heterogeneity. HBV biosynthesis was used as a marker of liver tumor heterogeneity. Principal component and correlation analysis of HBV and cellular transcript levels demonstrated major differences within and between the gene expression profiles of Apc-deficient, Apc-deficient Pten-deficient, and Pten-deficient HCC. Hence, both oncogenic stimuli and zonal hepatocyte properties determine heterogeneous HCC phenotypes. Additionally, Apc-deficient HCC display decreased expression of Apob, Otc and Tet2 relative to Pten-deficient HCC and control liver tissue suggesting their gene products may represent markers of Apc-deficient HCC. A subset of human HCC with mutations in the β-catenin gene (CTNNB1) displayed a gene expression profile similar to that observed in the mouse Apc-deficient HCC indicating this model of liver cancer may be useful for interrogating the molecular properties of these tumors and their potential therapeutic vulnerabilities.
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Affiliation(s)
- Grant Tarnow
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, 909 South Wolcott Avenue, Chicago, IL, 60612, USA
| | - Rachel Matrenec
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, 909 South Wolcott Avenue, Chicago, IL, 60612, USA
| | - Claudia E Oropeza
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, 909 South Wolcott Avenue, Chicago, IL, 60612, USA
| | - Mark Maienschein-Cline
- Research Resources Center, College of Medicine, University of Illinois at Chicago, 835 South Wolcott Avenue, Chicago, IL, 60612, USA
| | - Alan McLachlan
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, 909 South Wolcott Avenue, Chicago, IL, 60612, USA.
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25
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Elmentaite R, Domínguez Conde C, Yang L, Teichmann SA. Single-cell atlases: shared and tissue-specific cell types across human organs. Nat Rev Genet 2022; 23:395-410. [PMID: 35217821 DOI: 10.1038/s41576-022-00449-w] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2022] [Indexed: 12/12/2022]
Abstract
The development of single-cell and spatial transcriptomics methods was instrumental in the conception of the Human Cell Atlas initiative, which aims to generate an integrated map of all cells across the human body. These technology advances are bringing increasing depth and resolution to maps of human organs and tissues, as well as our understanding of individual human cell types. Commonalities as well as tissue-specific features of primary and supportive cell types across human organs are beginning to emerge from these human tissue maps. In this Review, we highlight key biological insights obtained from cross-tissue studies into epithelial, fibroblast, vascular and immune cells based on single-cell gene expression data in humans and contrast it with mechanisms reported in mice.
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Affiliation(s)
- Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Lu Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK.
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26
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Yu S, Gao J, Wang H, Liu L, Liu X, Xu Y, Shi J, Guo W, Zhang S. Significance of Liver Zonation in Hepatocellular Carcinoma. Front Cell Dev Biol 2022; 10:806408. [PMID: 35813194 PMCID: PMC9260020 DOI: 10.3389/fcell.2022.806408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Liver zonation is fundamental to normal liver function, and numerous studies have investigated the microstructure of normal liver lobules. However, only a few studies have explored the zonation signature in hepatocellular carcinoma (HCC). In this study, we investigated the significance of liver zonation in HCC with the help of single-cell RNA sequencing (scRNA-seq) and multicolor immunofluorescence staining. Liver zonation-related genes were extracted from the literature, and a three-gene model was established for HCC prognosis. The model reliability was validated using bulk RNA and single-cell RNA-level data, and the underlying biological mechanism was revealed by a functional enrichment analysis. The results showed that the signaling pathways of high-risk groups were similar to those of perivenous zones in the normal liver, indicating the possible regulating role of hypoxia in HCC zonation. Furthermore, the co-staining results showed that the low-grade tumors lost their zonation features whereas the high-grade tumors lost the expression of zonation-related genes, which supported the results obtained from the sequencing data.
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Affiliation(s)
- Shizhe Yu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering Technology Research Center for Organ Transplantation, Zhengzhou, China
- Open and Key Laboratory for Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
| | - Jie Gao
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering Technology Research Center for Organ Transplantation, Zhengzhou, China
- Open and Key Laboratory for Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
| | - Haoren Wang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Long Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering Technology Research Center for Organ Transplantation, Zhengzhou, China
- Open and Key Laboratory for Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
| | - Xudong Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering Technology Research Center for Organ Transplantation, Zhengzhou, China
- Open and Key Laboratory for Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
| | - Yuantong Xu
- Department of Hepatopancreatobiliary Surgery, The First People’s Hospital of Kunming, Calmette Hospital, Kunming, China
| | - Jihua Shi
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering Technology Research Center for Organ Transplantation, Zhengzhou, China
- Open and Key Laboratory for Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering Technology Research Center for Organ Transplantation, Zhengzhou, China
- Open and Key Laboratory for Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
| | - Shuijun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering Technology Research Center for Organ Transplantation, Zhengzhou, China
- Open and Key Laboratory for Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- *Correspondence: Shuijun Zhang,
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27
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Conrad T, Altmüller J. Single cell- and spatial 'Omics revolutionize physiology. Acta Physiol (Oxf) 2022; 235:e13848. [PMID: 35656634 DOI: 10.1111/apha.13848] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/24/2022] [Accepted: 05/27/2022] [Indexed: 11/29/2022]
Abstract
Single cell multi- 'Omics and Spatial Transcriptomics are prominent technological highlights of recent years, and both fields still witness a ceaseless firework of novel approaches for high resolution profiling of additional omics layers. As all life processes in organs and organisms are based on the functions of their fundamental building blocks, the individual cells and their interactions, these methods are of utmost worth for the study of physiology in health and disease. Recent discoveries on embryonic development, tumor immunology, the detailed cellular composition and function of complex tissues like for example the kidney or the brain, different roles of the same cell type in different organs, the oncogenic program of individual tumor entities, or the architecture of immunopathology in infected tissue are based on single cell and spatial transcriptomics experiments. In this review, we will give a broad overview of technological concepts for single cell and spatial analysis, showing both advantages and limitations, and illustrate their impact with some particularly impressive case studies.
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Affiliation(s)
- Thomas Conrad
- Genomics Technology Platform Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin Germany
| | - Janine Altmüller
- Genomics Technology Platform Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin Germany
- Core Facility Genomics Berlin Institute of Health at Charité ‐ Universitätsmedizin Berlin Berlin Germany
- Center for Molecular Medicine Cologne (CMMC) Cologne Germany
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28
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Dam TV, Toft NI, Grøntved L. Cell-Type Resolved Insights into the Cis-Regulatory Genome of NAFLD. Cells 2022; 11:cells11050870. [PMID: 35269495 PMCID: PMC8909044 DOI: 10.3390/cells11050870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/27/2022] [Accepted: 02/28/2022] [Indexed: 11/20/2022] Open
Abstract
The prevalence of non-alcoholic fatty liver disease (NAFLD) is increasing rapidly, and unmet treatment can result in the development of hepatitis, fibrosis, and liver failure. There are difficulties involved in diagnosing NAFLD early and for this reason there are challenges involved in its treatment. Furthermore, no drugs are currently approved to alleviate complications, a fact which highlights the need for further insight into disease mechanisms. NAFLD pathogenesis is associated with complex cellular changes, including hepatocyte steatosis, immune cell infiltration, endothelial dysfunction, hepatic stellate cell activation, and epithelial ductular reaction. Many of these cellular changes are controlled by dramatic changes in gene expression orchestrated by the cis-regulatory genome and associated transcription factors. Thus, to understand disease mechanisms, we need extensive insights into the gene regulatory mechanisms associated with tissue remodeling. Mapping cis-regulatory regions genome-wide is a step towards this objective and several current and emerging technologies allow detection of accessible chromatin and specific histone modifications in enriched cell populations of the liver, as well as in single cells. Here, we discuss recent insights into the cis-regulatory genome in NAFLD both at the organ-level and in specific cell populations of the liver. Moreover, we highlight emerging technologies that enable single-cell resolved analysis of the cis-regulatory genome of the liver.
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29
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Selective PPARα Modulator Pemafibrate and Sodium-Glucose Cotransporter 2 Inhibitor Tofogliflozin Combination Treatment Improved Histopathology in Experimental Mice Model of Non-Alcoholic Steatohepatitis. Cells 2022; 11:cells11040720. [PMID: 35203369 PMCID: PMC8870369 DOI: 10.3390/cells11040720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/14/2022] Open
Abstract
Ballooning degeneration of hepatocytes is a major distinguishing histological feature of non-alcoholic steatosis (NASH) progression that can lead to cirrhosis and hepatocellular carcinoma (HCC). In this study, we evaluated the effect of the selective PPARα modulator (SPPARMα) pemafibrate (Pema) and sodium-glucose cotransporter 2 (SGLT2) inhibitor tofogliflozin (Tofo) combination treatment on pathological progression in the liver of a mouse model of NASH (STAM) at two time points (onset of NASH progression and HCC survival). At both time points, the Pema and Tofo combination treatment significantly alleviated hyperglycemia and hypertriglyceridemia. The combination treatment significantly reduced ballooning degeneration of hepatocytes. RNA-seq analysis suggested that Pema and Tofo combination treatment resulted in an increase in glyceroneogenesis, triglyceride (TG) uptake, lipolysis and liberated fatty acids re-esterification into TG, lipid droplet (LD) formation, and Cidea/Cidec ratio along with an increased number and reduced size and area of LDs. In addition, combination treatment reduced expression levels of endoplasmic reticulum stress-related genes (Ire1a, Grp78, Xbp1, and Phlda3). Pema and Tofo treatment significantly improved survival rates and reduced the number of tumors in the liver compared to the NASH control group. These results suggest that SPPARMα and SGLT2 inhibitor combination therapy has therapeutic potential to prevent NASH-HCC progression.
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30
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Steinman JB, Salomao MA, Pajvani UB. Zonation in NASH - A key paradigm for understanding pathophysiology and clinical outcomes. Liver Int 2021; 41:2534-2546. [PMID: 34328687 DOI: 10.1111/liv.15025] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 12/11/2022]
Abstract
Non-alcoholic fatty liver disease (NAFLD) exists as a spectrum ranging from simple steatosis to histologically defined hepatocyte injury and inflammatory changes that define steatohepatitis (NASH), and increase risk for fibrosis. Although zonal differences in NASH have not been systematically studied, periportal involvement has been associated with worse metabolic outcomes and more hepatic fibrosis as compared to pericentral disease. These data suggest that hepatic zonation of disease may influence the diversity of clinical presentations. Similarly, several randomized clinical trials suggest a differential response based on zonation of disease, with preferential effects on periportal (cysteamine) or pericentral disease (obeticholic acid, pioglitazone). Intriguingly, morphogenic pathways known to affect zonal development and maintenance - WNT/β-Catenin, Hedgehog, HIPPO/Yap/TAZ and Notch - have been implicated in NASH pathogenesis, and nuclear hormone receptors downstream of potential NASH therapeutics show zonal preferences. In this review, we summarize these data and propose that patient-specific activation of these pathways may explain the variability in clinical presentation, and the zone-specific response observed in clinical trials.
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Affiliation(s)
| | - Marcela A Salomao
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, AZ, USA
| | - Utpal B Pajvani
- Department of Medicine, Columbia University, New York, NY, USA
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31
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Longo SK, Guo MG, Ji AL, Khavari PA. Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics. Nat Rev Genet 2021; 22:627-644. [PMID: 34145435 PMCID: PMC9888017 DOI: 10.1038/s41576-021-00370-8] [Citation(s) in RCA: 364] [Impact Index Per Article: 121.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2021] [Indexed: 02/07/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) identifies cell subpopulations within tissue but does not capture their spatial distribution nor reveal local networks of intercellular communication acting in situ. A suite of recently developed techniques that localize RNA within tissue, including multiplexed in situ hybridization and in situ sequencing (here defined as high-plex RNA imaging) and spatial barcoding, can help address this issue. However, no method currently provides as complete a scope of the transcriptome as does scRNA-seq, underscoring the need for approaches to integrate single-cell and spatial data. Here, we review efforts to integrate scRNA-seq with spatial transcriptomics, including emerging integrative computational methods, and propose ways to effectively combine current methodologies.
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Affiliation(s)
- Sophia K. Longo
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA,Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Margaret G. Guo
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA,Stanford Cancer Institute, Stanford University, Stanford, CA, USA,Program in Biomedical Informatics, Stanford University, Stanford, CA, USA
| | - Andrew L. Ji
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA,Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Paul A. Khavari
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA,Stanford Cancer Institute, Stanford University, Stanford, CA, USA,Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
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32
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Yuan Z, Zhou Q, Cai L, Pan L, Sun W, Qumu S, Yu S, Feng J, Zhao H, Zheng Y, Shi M, Li S, Chen Y, Zhang X, Zhang MQ. SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment. Nat Methods 2021; 18:1223-1232. [PMID: 34608315 DOI: 10.1038/s41592-021-01276-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 08/18/2021] [Indexed: 02/08/2023]
Abstract
Spatial metabolomics can reveal intercellular heterogeneity and tissue organization. Here we report on the spatial single nuclear metabolomics (SEAM) method, a flexible platform combining high-spatial-resolution imaging mass spectrometry and a set of computational algorithms that can display multiscale and multicolor tissue tomography together with identification and clustering of single nuclei by their in situ metabolic fingerprints. We first applied SEAM to a range of wild-type mouse tissues, then delineated a consistent pattern of metabolic zonation in mouse liver. We further studied the spatial metabolic profile in the human fibrotic liver. We discovered subpopulations of hepatocytes with special metabolic features associated with their proximity to the fibrotic niche, and validated this finding by spatial transcriptomics with Geo-seq. These demonstrations highlighted SEAM's ability to explore the spatial metabolic profile and tissue histology at the single-cell level, leading to a deeper understanding of tissue metabolic organization.
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Affiliation(s)
- Zhiyuan Yuan
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, BNRist, Institute of TCM-X, Department of Automation, Tsinghua University, Beijing, China
| | - Qiming Zhou
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, BNRist, School of Life Sciences, Tsinghua University, Beijing, China
| | - Lesi Cai
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Lin Pan
- Institute of Clinical Medicine, China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, China
| | - Weiliang Sun
- Institute of Clinical Medicine, China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, China
| | - Shiwei Qumu
- Department of Pulmonary and Critical Care Medicine, China-Japan Friend Hospital, National Clinical Research Center for Respiratory Diseases, Beijing, China
| | - Si Yu
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiaxin Feng
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Hansen Zhao
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Yongchang Zheng
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Minglei Shi
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, BNRist, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Shao Li
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, BNRist, Institute of TCM-X, Department of Automation, Tsinghua University, Beijing, China
| | - Yang Chen
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, BNRist, Institute of TCM-X, Department of Automation, Tsinghua University, Beijing, China. .,The State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.
| | - Xinrong Zhang
- Department of Chemistry, Tsinghua University, Beijing, China.
| | - Michael Q Zhang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, BNRist, Institute of TCM-X, Department of Automation, Tsinghua University, Beijing, China. .,MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, BNRist, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China. .,Department of Biological Sciences, Center for Systems Biology, The University of Texas, Richardson, TX, USA.
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33
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Campbell SA, Stephan TL, Lotto J, Cullum R, Drissler S, Hoodless PA. Signalling pathways and transcriptional regulators orchestrating liver development and cancer. Development 2021; 148:272023. [PMID: 34478514 DOI: 10.1242/dev.199814] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Liver development is controlled by key signals and transcription factors that drive cell proliferation, migration, differentiation and functional maturation. In the adult liver, cell maturity can be perturbed by genetic and environmental factors that disrupt hepatic identity and function. Developmental signals and fetal genetic programmes are often dysregulated or reactivated, leading to dedifferentiation and disease. Here, we highlight signalling pathways and transcriptional regulators that drive liver cell development and primary liver cancers. We also discuss emerging models derived from pluripotent stem cells, 3D organoids and bioengineering for improved studies of signalling pathways in liver cancer and regenerative medicine.
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Affiliation(s)
| | - Tabea L Stephan
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada.,Program in Cell and Developmental Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jeremy Lotto
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada.,Program in Cell and Developmental Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Rebecca Cullum
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Sibyl Drissler
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada.,Program in Cell and Developmental Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada.,Program in Cell and Developmental Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada.,School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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34
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Gianmoena K, Gasparoni N, Jashari A, Gabrys P, Grgas K, Ghallab A, Nordström K, Gasparoni G, Reinders J, Edlund K, Godoy P, Schriewer A, Hayen H, Hudert CA, Damm G, Seehofer D, Weiss TS, Boor P, Anders HJ, Motrapu M, Jansen P, Schiergens TS, Falk-Paulsen M, Rosenstiel P, Lisowski C, Salido E, Marchan R, Walter J, Hengstler JG, Cadenas C. Epigenomic and transcriptional profiling identifies impaired glyoxylate detoxification in NAFLD as a risk factor for hyperoxaluria. Cell Rep 2021; 36:109526. [PMID: 34433051 DOI: 10.1016/j.celrep.2021.109526] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 05/12/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023] Open
Abstract
Epigenetic modifications (e.g. DNA methylation) in NAFLD and their contribution to disease progression and extrahepatic complications are poorly explored. Here, we use an integrated epigenome and transcriptome analysis of mouse NAFLD hepatocytes and identify alterations in glyoxylate metabolism, a pathway relevant in kidney damage via oxalate release-a harmful waste product and kidney stone-promoting factor. Downregulation and hypermethylation of alanine-glyoxylate aminotransferase (Agxt), which detoxifies glyoxylate, preventing excessive oxalate accumulation, is accompanied by increased oxalate formation after metabolism of the precursor hydroxyproline. Viral-mediated Agxt transfer or inhibiting hydroxyproline catabolism rescues excessive oxalate release. In human steatotic hepatocytes, AGXT is also downregulated and hypermethylated, and in NAFLD adolescents, steatosis severity correlates with urinary oxalate excretion. Thus, this work identifies a reduced capacity of the steatotic liver to detoxify glyoxylate, triggering elevated oxalate, and provides a mechanistic explanation for the increased risk of kidney stones and chronic kidney disease in NAFLD patients.
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Affiliation(s)
- Kathrin Gianmoena
- Department of Toxicology, Leibniz-Research Centre for Working Environment and Human Factors at the TU Dortmund (IfADo), 44139 Dortmund, Germany
| | - Nina Gasparoni
- Department of Genetics, Saarland University, 66123 Saarbrücken, Germany
| | - Adelina Jashari
- Department of Toxicology, Leibniz-Research Centre for Working Environment and Human Factors at the TU Dortmund (IfADo), 44139 Dortmund, Germany
| | - Philipp Gabrys
- Department of Toxicology, Leibniz-Research Centre for Working Environment and Human Factors at the TU Dortmund (IfADo), 44139 Dortmund, Germany
| | - Katharina Grgas
- Department of Toxicology, Leibniz-Research Centre for Working Environment and Human Factors at the TU Dortmund (IfADo), 44139 Dortmund, Germany
| | - Ahmed Ghallab
- Department of Toxicology, Leibniz-Research Centre for Working Environment and Human Factors at the TU Dortmund (IfADo), 44139 Dortmund, Germany; Department of Forensic and Veterinary Toxicology, Faculty of Veterinary Medicine, South Valley University, 83523 Qena, Egypt
| | - Karl Nordström
- Department of Genetics, Saarland University, 66123 Saarbrücken, Germany
| | - Gilles Gasparoni
- Department of Genetics, Saarland University, 66123 Saarbrücken, Germany
| | - Jörg Reinders
- Department of Toxicology, Leibniz-Research Centre for Working Environment and Human Factors at the TU Dortmund (IfADo), 44139 Dortmund, Germany
| | - Karolina Edlund
- Department of Toxicology, Leibniz-Research Centre for Working Environment and Human Factors at the TU Dortmund (IfADo), 44139 Dortmund, Germany
| | - Patricio Godoy
- Department of Toxicology, Leibniz-Research Centre for Working Environment and Human Factors at the TU Dortmund (IfADo), 44139 Dortmund, Germany
| | - Alexander Schriewer
- Department of Analytical Chemistry, Institute of Inorganic and Analytical Chemistry, University of Münster, 48149 Münster, Germany
| | - Heiko Hayen
- Department of Analytical Chemistry, Institute of Inorganic and Analytical Chemistry, University of Münster, 48149 Münster, Germany
| | - Christian A Hudert
- Department of Pediatric Gastroenterology, Hepatology and Metabolic Diseases, Charité-University Medicine Berlin, 13353 Berlin, Germany
| | - Georg Damm
- Department of Hepatobiliary Surgery and Visceral Transplantation, University of Leipzig, 04103 Leipzig, Germany; Department of General-, Visceral- and Transplantation Surgery, Charité University Medicine Berlin, 13353 Berlin, Germany
| | - Daniel Seehofer
- Department of Hepatobiliary Surgery and Visceral Transplantation, University of Leipzig, 04103 Leipzig, Germany; Department of General-, Visceral- and Transplantation Surgery, Charité University Medicine Berlin, 13353 Berlin, Germany
| | - Thomas S Weiss
- University Children Hospital (KUNO), University Hospital Regensburg, 93053 Regensburg, Germany
| | - Peter Boor
- Institute of Pathology and Department of Nephrology, University Clinic of RWTH Aachen, 52074 Aachen, Germany
| | - Hans-Joachim Anders
- Department of Medicine IV, Renal Division, University Hospital, Ludwig-Maximilians-University Munich, 80336 Munich, Germany
| | - Manga Motrapu
- Department of Medicine IV, Renal Division, University Hospital, Ludwig-Maximilians-University Munich, 80336 Munich, Germany
| | - Peter Jansen
- Maastricht Centre for Systems Biology, University of Maastricht, 6229 Maastricht, the Netherlands
| | - Tobias S Schiergens
- Biobank of the Department of General, Visceral and Transplant Surgery, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Maren Falk-Paulsen
- Institute of Clinical Molecular Biology (IKMB), Kiel University and University Hospital Schleswig Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology (IKMB), Kiel University and University Hospital Schleswig Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Clivia Lisowski
- Institute of Experimental Immunology, University Hospital Bonn, Rheinische-Friedrich-Wilhelms University Bonn, 53127 Bonn, Germany
| | - Eduardo Salido
- Hospital Universitario de Canarias, Universidad La Laguna, CIBERER, 38320 Tenerife, Spain
| | - Rosemarie Marchan
- Department of Toxicology, Leibniz-Research Centre for Working Environment and Human Factors at the TU Dortmund (IfADo), 44139 Dortmund, Germany
| | - Jörn Walter
- Department of Genetics, Saarland University, 66123 Saarbrücken, Germany
| | - Jan G Hengstler
- Department of Toxicology, Leibniz-Research Centre for Working Environment and Human Factors at the TU Dortmund (IfADo), 44139 Dortmund, Germany
| | - Cristina Cadenas
- Department of Toxicology, Leibniz-Research Centre for Working Environment and Human Factors at the TU Dortmund (IfADo), 44139 Dortmund, Germany.
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35
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Vvedenskaya O, Rose TD, Knittelfelder O, Palladini A, Wodke JAH, Schuhmann K, Ackerman JM, Wang Y, Has C, Brosch M, Thangapandi VR, Buch S, Züllig T, Hartler J, Köfeler HC, Röcken C, Coskun Ü, Klipp E, von Schoenfels W, Gross J, Schafmayer C, Hampe J, Pauling JK, Shevchenko A. Nonalcoholic fatty liver disease stratification by liver lipidomics. J Lipid Res 2021; 62:100104. [PMID: 34384788 PMCID: PMC8488246 DOI: 10.1016/j.jlr.2021.100104] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/20/2021] [Accepted: 07/30/2021] [Indexed: 02/06/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a common metabolic dysfunction leading to hepatic steatosis. However, NAFLD's global impact on the liver lipidome is poorly understood. Using high-resolution shotgun mass spectrometry, we quantified the molar abundance of 316 species from 22 major lipid classes in liver biopsies of 365 patients, including nonsteatotic patients with normal or excessive weight, patients diagnosed with NAFL (nonalcoholic fatty liver) or NASH (nonalcoholic steatohepatitis), and patients bearing common mutations of NAFLD-related protein factors. We confirmed the progressive accumulation of di- and triacylglycerols and cholesteryl esters in the liver of NAFL and NASH patients, while the bulk composition of glycerophospho- and sphingolipids remained unchanged. Further stratification by biclustering analysis identified sphingomyelin species comprising n24:2 fatty acid moieties as membrane lipid markers of NAFLD. Normalized relative abundance of sphingomyelins SM 43:3;2 and SM 43:1;2 containing n24:2 and n24:0 fatty acid moieties, respectively, showed opposite trends during NAFLD progression and distinguished NAFL and NASH lipidomes from the lipidome of nonsteatotic livers. Together with several glycerophospholipids containing a C22:6 fatty acid moiety, these lipids serve as markers of early and advanced stages of NAFL.
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Affiliation(s)
- Olga Vvedenskaya
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Tim Daniel Rose
- LipiTUM, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Oskar Knittelfelder
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Alessandra Palladini
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum Munich at the University Hospital Carl Gustav Carus, Technische Universität (TU) Dresden, Dresden, Germany; German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | | | - Kai Schuhmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Yuting Wang
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Canan Has
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Mario Brosch
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Germany; Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Veera Raghavan Thangapandi
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Germany; Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Stephan Buch
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Germany; Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Thomas Züllig
- Core Facility Mass Spectrometry, Medical University of Graz, Graz, Austria
| | - Jürgen Hartler
- Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria; Field of Excellence BioHealth, University of Graz, Graz, Austria
| | - Harald C Köfeler
- Core Facility Mass Spectrometry, Medical University of Graz, Graz, Austria
| | - Christoph Röcken
- Department of Pathology, University Hospital Schleswig Holstein, Kiel, Schleswig-Holstein, Germany
| | - Ünal Coskun
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum Munich at the University Hospital Carl Gustav Carus, Technische Universität (TU) Dresden, Dresden, Germany; German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany; Department of Membrane Biochemistry and Lipid Research, University Hospital Carl Gustav Carus of Technische Universität Dresden, Dresden, Germany
| | - Edda Klipp
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Witigo von Schoenfels
- Department of Visceral and Thoracic Surgery, University Hospital Schleswig-Holstein, Kiel Campus, Christian-Albrechts-University Kiel, Kiel, Germany; Christian Albrechts University in Kiel Center of Clinical Anatomy Kiel, Schleswig-Holstein, Germany
| | - Justus Gross
- Department of General, Visceral, Vascular and Transplant Surgery, Rostock University Medical Center, Rostock, Germany
| | - Clemens Schafmayer
- Department of General, Visceral, Vascular and Transplant Surgery, Rostock University Medical Center, Rostock, Germany
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Germany
| | - Josch Konstantin Pauling
- LipiTUM, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany.
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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Thangapandi VR, Knittelfelder O, Brosch M, Patsenker E, Vvedenskaya O, Buch S, Hinz S, Hendricks A, Nati M, Herrmann A, Rekhade DR, Berg T, Matz-Soja M, Huse K, Klipp E, Pauling JK, Wodke JA, Miranda Ackerman J, Bonin MV, Aigner E, Datz C, von Schönfels W, Nehring S, Zeissig S, Röcken C, Dahl A, Chavakis T, Stickel F, Shevchenko A, Schafmayer C, Hampe J, Subramanian P. Loss of hepatic Mboat7 leads to liver fibrosis. Gut 2021; 70:940-950. [PMID: 32591434 PMCID: PMC8040158 DOI: 10.1136/gutjnl-2020-320853] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/22/2020] [Accepted: 05/23/2020] [Indexed: 12/30/2022]
Abstract
OBJECTIVE The rs641738C>T variant located near the membrane-bound O-acyltransferase domain containing 7 (MBOAT7) locus is associated with fibrosis in liver diseases, including non-alcoholic fatty liver disease (NAFLD), alcohol-related liver disease, hepatitis B and C. We aim to understand the mechanism by which the rs641738C>T variant contributes to pathogenesis of NAFLD. DESIGN Mice with hepatocyte-specific deletion of MBOAT7 (Mboat7Δhep) were generated and livers were characterised by histology, flow cytometry, qPCR, RNA sequencing and lipidomics. We analysed the association of rs641738C>T genotype with liver inflammation and fibrosis in 846 NAFLD patients and obtained genotype-specific liver lipidomes from 280 human biopsies. RESULTS Allelic imbalance analysis of heterozygous human liver samples pointed to lower expression of the MBOAT7 transcript on the rs641738C>T haplotype. Mboat7Δhep mice showed spontaneous steatosis characterised by increased hepatic cholesterol ester content after 10 weeks. After 6 weeks on a high fat, methionine-low, choline-deficient diet, mice developed increased hepatic fibrosis as measured by picrosirius staining (p<0.05), hydroxyproline content (p<0.05) and transcriptomics, while the inflammatory cell populations and inflammatory mediators were minimally affected. In a human biopsied NAFLD cohort, MBOAT7 rs641738C>T was associated with fibrosis (p=0.004) independent of the presence of histological inflammation. Liver lipidomes of Mboat7Δhep mice and human rs641738TT carriers with fibrosis showed increased total lysophosphatidylinositol levels. The altered lysophosphatidylinositol and phosphatidylinositol subspecies in MBOAT7Δhep livers and human rs641738TT carriers were similar. CONCLUSION Mboat7 deficiency in mice and human points to an inflammation-independent pathway of liver fibrosis that may be mediated by lipid signalling and a potentially targetable treatment option in NAFLD.
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Affiliation(s)
- Veera Raghavan Thangapandi
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Oskar Knittelfelder
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Sachsen, Germany
| | - Mario Brosch
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Eleonora Patsenker
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - Olga Vvedenskaya
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Sachsen, Germany
| | - Stephan Buch
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Sebastian Hinz
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Alexander Hendricks
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Marina Nati
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
| | - Alexander Herrmann
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Devavrat Ravindra Rekhade
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Thomas Berg
- Division of Hepatology, Department of Oncology, Gastroenterology, Hepatology Pulmonology, and Infectious Diseases, University Hospital Leipzig, Leipzig, Sachsen, Germany
| | - Madlen Matz-Soja
- Division of Hepatology, Department of Oncology, Gastroenterology, Hepatology Pulmonology, and Infectious Diseases, University Hospital Leipzig, Leipzig, Sachsen, Germany
- Rudolf Schönheimer- Institute of Biochemistry, University of Leipzig Faculty of Medicine, Leipzig, Germany
| | - Klaus Huse
- Leibniz Institute for Age Research Fritz-Lipmann Institute, Jena, Thüringen, Germany
| | - Edda Klipp
- Department of Theoretical Biophysics, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Josch K Pauling
- Department of Theoretical Biophysics, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
- LipiTUM, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Bayern, Germany
| | - Judith Ah Wodke
- Department of Theoretical Biophysics, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Malte von Bonin
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
- German Cancer Consortium, Heidelberg, Baden-Württemberg, Germany
| | - Elmar Aigner
- Department of Medicine, Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Christian Datz
- Department of Internal Medicine, Hospital Oberndorf, Teaching Hospital of the Paracelsus Private University of Salzburg, Obendorf, Austria
| | - Witigo von Schönfels
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Sophie Nehring
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Sebastian Zeissig
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Christoph Röcken
- Department of Pathology, University Hospital Schleswig Holstein, Kiel, Schleswig-Holstein, Germany
| | - Andreas Dahl
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Triantafyllos Chavakis
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Sachsen, Germany
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
- German Center for Diabetes Research, Neuherberg, Germany
- Paul Langerhans Institute Dresden, Helmholtz Zentrum München, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
| | - Felix Stickel
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - Andrej Shevchenko
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Sachsen, Germany
| | - Clemens Schafmayer
- Department of General, Visceral, Vascular and Transplantation Surgery, University of Rostock, Rostock, Mecklenburg-Vorpommern, Germany
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Pallavi Subramanian
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
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37
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PPARs in liver physiology. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166097. [PMID: 33524529 DOI: 10.1016/j.bbadis.2021.166097] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 02/07/2023]
Abstract
Peroxisome proliferator-activated receptors (PPARs) are nuclear receptors and transcriptional modulators with crucial functions in hepatic and whole-body energy homeostasis. Besides their well-documented roles in lipid and glucose metabolism, emerging evidence also implicate PPARs in the control of other processes such as inflammatory responses. Recent technological advances, such as single-cell RNA sequencing, have allowed to unravel an unexpected complexity in the regulation of PPAR expression, activity and downstream signaling. Here we provide an overview of the latest advances in the study of PPARs in liver physiology, with a specific focus on formerly neglected aspects of PPAR regulation, such as tissular zonation, cellular heterogeneity, circadian rhythms, sexual dimorphism and species-specific features.
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38
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Ölander M, Wegler C, Flörkemeier I, Treyer A, Handin N, Pedersen JM, Vildhede A, Mateus A, LeCluyse EL, Urdzik J, Artursson P. Hepatocyte size fractionation allows dissection of human liver zonation. J Cell Physiol 2021; 236:5885-5894. [PMID: 33452735 DOI: 10.1002/jcp.30273] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/21/2020] [Accepted: 12/30/2020] [Indexed: 11/08/2022]
Abstract
Human hepatocytes show marked differences in cell size, gene expression, and function throughout the liver lobules, an arrangement termed liver zonation. However, it is not clear if these zonal size differences, and the associated phenotypic differences, are retained in isolated human hepatocytes, the "gold standard" for in vitro studies of human liver function. Here, we therefore explored size differences among isolated human hepatocytes and investigated whether separation by size can be used to study liver zonation in vitro. We used counterflow centrifugal elutriation to separate cells into different size fractions and analyzed them with label-free quantitative proteomics, which revealed an enrichment of 151 and 758 proteins (out of 5163) in small and large hepatocytes, respectively. Further analysis showed that protein abundances in different hepatocyte size fractions recapitulated the in vivo expression patterns of previously described zonal markers and biological processes. We also found that the expression of zone-specific cytochrome P450 enzymes correlated with their metabolic activity in the different fractions. In summary, our results show that differences in hepatocyte size matches zonal expression patterns, and that our size fractionation approach can be used to study zone-specific liver functions in vitro.
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Affiliation(s)
- Magnus Ölander
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - Christine Wegler
- Department of Pharmacy, Uppsala University, Uppsala, Sweden.,DMPK, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | | | - Andrea Treyer
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - Niklas Handin
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | | | - Anna Vildhede
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - André Mateus
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | | | - Jozef Urdzik
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Per Artursson
- Department of Pharmacy, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Maude H, Sanchez-Cabanillas C, Cebola I. Epigenetics of Hepatic Insulin Resistance. Front Endocrinol (Lausanne) 2021; 12:681356. [PMID: 34046015 PMCID: PMC8147868 DOI: 10.3389/fendo.2021.681356] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/20/2021] [Indexed: 01/14/2023] Open
Abstract
Insulin resistance (IR) is largely recognized as a unifying feature that underlies metabolic dysfunction. Both lifestyle and genetic factors contribute to IR. Work from recent years has demonstrated that the epigenome may constitute an interface where different signals may converge to promote IR gene expression programs. Here, we review the current knowledge of the role of epigenetics in hepatic IR, focusing on the roles of DNA methylation and histone post-translational modifications. We discuss the broad epigenetic changes observed in the insulin resistant liver and its associated pathophysiological states and leverage on the wealth of 'omics' studies performed to discuss efforts in pinpointing specific loci that are disrupted by these changes. We envision that future studies, with increased genomic resolution and larger cohorts, will further the identification of biomarkers of early onset hepatic IR and assist the development of targeted interventions. Furthermore, there is growing evidence to suggest that persistent epigenetic marks may be acquired over prolonged exposure to disease or deleterious exposures, highlighting the need for preventative medicine and long-term lifestyle adjustments to avoid irreversible or long-term alterations in gene expression.
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Affiliation(s)
| | | | - Inês Cebola
- *Correspondence: Hannah Maude, ; Inês Cebola,
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40
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Kolbe E, Aleithe S, Rennert C, Spormann L, Ott F, Meierhofer D, Gajowski R, Stöpel C, Hoehme S, Kücken M, Brusch L, Seifert M, von Schoenfels W, Schafmayer C, Brosch M, Hofmann U, Damm G, Seehofer D, Hampe J, Gebhardt R, Matz-Soja M. Mutual Zonated Interactions of Wnt and Hh Signaling Are Orchestrating the Metabolism of the Adult Liver in Mice and Human. Cell Rep 2020; 29:4553-4567.e7. [PMID: 31875560 DOI: 10.1016/j.celrep.2019.11.104] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/14/2019] [Accepted: 11/25/2019] [Indexed: 12/12/2022] Open
Abstract
The Hedgehog (Hh) and Wnt/β-Catenin (Wnt) cascades are morphogen pathways whose pronounced influence on adult liver metabolism has been identified in recent years. How both pathways communicate and control liver metabolic functions are largely unknown. Detecting core components of Wnt and Hh signaling and mathematical modeling showed that both pathways in healthy liver act largely complementary to each other in the pericentral (Wnt) and the periportal zone (Hh) and communicate mainly by mutual repression. The Wnt/Hh module inversely controls the spatiotemporal operation of various liver metabolic pathways, as revealed by transcriptome, proteome, and metabolome analyses. Shifting the balance to Wnt (activation) or Hh (inhibition) causes pericentralization and periportalization of liver functions, respectively. Thus, homeostasis of the Wnt/Hh module is essential for maintaining proper liver metabolism and to avoid the development of certain metabolic diseases. With caution due to minor species-specific differences, these conclusions may hold for human liver as well.
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Affiliation(s)
- Erik Kolbe
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig 04103, Germany
| | - Susanne Aleithe
- Department of Neurology, Leipzig University, Leipzig 04103, Germany
| | - Christiane Rennert
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig 04103, Germany; Department of Hepatobiliary Surgery and Visceral Transplantation, University Hospital, Leipzig University, Leipzig 04103, Germany
| | - Luise Spormann
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig 04103, Germany
| | - Fritzi Ott
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig 04103, Germany
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Mass Spectrometry Faculty, Berlin 14195, Germany
| | - Robert Gajowski
- Max Planck Institute for Molecular Genetics, Mass Spectrometry Faculty, Berlin 14195, Germany
| | - Claus Stöpel
- Institute for Computer Science, Leipzig University, Leipzig 04103, Germany
| | - Stefan Hoehme
- Institute for Computer Science, Leipzig University, Leipzig 04103, Germany
| | - Michael Kücken
- Center for Information Services and High Performance Computing, Technische Universität Dresden, Dresden 01069, Germany
| | - Lutz Brusch
- Center for Information Services and High Performance Computing, Technische Universität Dresden, Dresden 01069, Germany
| | - Michael Seifert
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden 01307, Germany
| | - Witigo von Schoenfels
- Department of General Surgery and Thoracic Surgery, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Clemens Schafmayer
- Department of General Surgery and Thoracic Surgery, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Mario Brosch
- Medical Department 1, University Hospital Dresden, Technical University Dresden, Dresden 01069, Germany
| | - Ute Hofmann
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, University of Tübingen, Stuttgart 70376, Germany
| | - Georg Damm
- Department of Hepatobiliary Surgery and Visceral Transplantation, University Hospital, Leipzig University, Leipzig 04103, Germany
| | - Daniel Seehofer
- Department of Hepatobiliary Surgery and Visceral Transplantation, University Hospital, Leipzig University, Leipzig 04103, Germany
| | - Jochen Hampe
- Medical Department 1, University Hospital Dresden, Technical University Dresden, Dresden 01069, Germany
| | - Rolf Gebhardt
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig 04103, Germany
| | - Madlen Matz-Soja
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig 04103, Germany.
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41
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Ali ES, Rychkov GY, Barritt GJ. Targeting Ca 2+ Signaling in the Initiation, Promotion and Progression of Hepatocellular Carcinoma. Cancers (Basel) 2020; 12:cancers12102755. [PMID: 32987945 PMCID: PMC7600741 DOI: 10.3390/cancers12102755] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Liver cancer (hepatocellular carcinoma) is a significant health burden worldwide. It is often not detected until at an advanced stage when there are few treatment options available. Changes in calcium concentrations within liver cancer cells are essential for regulating their growth, death, and migration (metastasis). Our aim was to review published papers which have identified proteins involved in calcium signaling as potential drug targets for the treatment of liver cancer. About twenty calcium signaling proteins were identified, including those involved in regulating calcium concentrations in the cytoplasm, endoplasmic reticulum and mitochondria. A few of these have turned out to be sites of action of natural products previously known to inhibit liver cancer. More systematic studies are now needed to determine which calcium signaling proteins might be used clinically for treatment of liver cancer, especially advanced stage cancers and those resistant to inhibition by current drugs. Abstract Hepatocellular carcinoma (HCC) is a considerable health burden worldwide and a major contributor to cancer-related deaths. HCC is often not noticed until at an advanced stage where treatment options are limited and current systemic drugs can usually only prolong survival for a short time. Understanding the biology and pathology of HCC is a challenge, due to the cellular and anatomic complexities of the liver. While not yet fully understood, liver cancer stem cells play a central role in the initiation and progression of HCC and in resistance to drugs. There are approximately twenty Ca2+-signaling proteins identified as potential targets for therapeutic treatment at different stages of HCC. These potential targets include inhibition of the self-renewal properties of liver cancer stem cells; HCC initiation and promotion by hepatitis B and C and non-alcoholic fatty liver disease (principally involving reduction of reactive oxygen species); and cell proliferation, tumor growth, migration and metastasis. A few of these Ca2+-signaling pathways have been identified as targets for natural products previously known to reduce HCC. Promising Ca2+-signaling targets include voltage-operated Ca2+ channel proteins (liver cancer stem cells), inositol trisphosphate receptors, store-operated Ca2+ entry, TRP channels, sarco/endoplasmic reticulum (Ca2++Mg2+) ATP-ase and Ca2+/calmodulin-dependent protein kinases. However, none of these Ca2+-signaling targets has been seriously studied any further than laboratory research experiments. The future application of more systematic studies, including genomics, gene expression (RNA-seq), and improved knowledge of the fundamental biology and pathology of HCC will likely reveal new Ca2+-signaling protein targets and consolidate priorities for those already identified.
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Affiliation(s)
- Eunus S. Ali
- Department of Medical Biochemistry, College of Medicine and Public Health, Flinders University, Adelaide 5001, South Australia, Australia;
| | - Grigori Y. Rychkov
- School of Medicine, The University of Adelaide, Adelaide 5005, South Australia, Australia;
- South Australian Health and Medical Research Institute, Adelaide 5005, South Australia, Australia
| | - Greg J. Barritt
- Department of Medical Biochemistry, College of Medicine and Public Health, Flinders University, Adelaide 5001, South Australia, Australia;
- Correspondence: ; Tel.: +61-438-204-426
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42
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Villesen IF, Daniels SJ, Leeming DJ, Karsdal MA, Nielsen MJ. Review article: the signalling and functional role of the extracellular matrix in the development of liver fibrosis. Aliment Pharmacol Ther 2020; 52:85-97. [PMID: 32419162 DOI: 10.1111/apt.15773] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/17/2020] [Accepted: 04/16/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Patients with liver fibrosis show a large heterogeneity, and for that reason effective treatments are still lacking. Emerging data suggest that there is more to fibrosis than previously understood. Opposed to earlier belief of being a passive scaffold for cells to reside in, the extracellular matrix (ECM) is now known to hold both signalling and functional properties important for the development of fibrosis. The interaction between the ECM and the collagen-producing cells determines the course of the disease but is still poorly understood. Exploring the dynamics of this interplay will aid in the development of effective treatments. AIM To summarise and discuss the latest advances in the pathogenesis of liver fibrosis as well as key mediators of early disease progression. METHODS Through literature search using databases including PubMed and Google Scholar, manuscripts published between 1961 and 2019 were included to assess both well-established and recent theories of fibrosis development. Both pre-clinical and clinical studies were included. RESULTS Fibrosis alters the structure of the ECM releasing signalling fragments with the potential to escalate disease severity. In a diseased liver, hepatic stellate cells and other fibroblasts, together with hepatocytes and sinusoidal cells, produce an excessive amount of collagens. The cell-to-collagen interactions are unique in the different liver aetiologies, generating ECM profiles with considerable patient-monitoring potential. CONCLUSIONS The local milieu in the injured area affects the course of fibrosis development in a site-specific manner. Future research should focus on the dissimilarities in the ECM profile between different aetiologies of liver fibrosis.
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Affiliation(s)
- Ida Falk Villesen
- Nordic Bioscience A/S, Herlev, Denmark.,University of Copenhagen, Copenhagen, Denmark
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43
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Ölander M, Wiśniewski JR, Artursson P. Cell-type-resolved proteomic analysis of the human liver. Liver Int 2020; 40:1770-1780. [PMID: 32243721 DOI: 10.1111/liv.14452] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/31/2020] [Accepted: 03/21/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND & AIMS The human liver functions through a complex interplay between parenchymal and non-parenchymal cells. Mass spectrometry-based proteomic analysis of intact tissue has provided an in-depth view of the human liver proteome. However, the predominance of parenchymal cells (hepatocytes) means that the total tissue proteome mainly reflects hepatocyte expression. Here we therefore set out to analyse the proteomes of the major parenchymal and non-parenchymal cell types in the human liver. METHODS We applied quantitative label-free proteomic analysis on the major cell types of the human liver: hepatocytes, liver endothelial cells, Kupffer cells and hepatic stellate cells. RESULTS We identified 9791 proteins, revealing distinct protein expression profiles across cell types, whose in vivo relevance was shown by the presence of cell-type-specific proteins. Analysis of proteins related to the immune system indicated that mechanisms of immune-mediated liver injury include the involvement of several cell types. Furthermore, in-depth investigation of proteins related to the absorption, distribution, metabolism, excretion and toxicity (ADMET) of xenobiotics showed that ADMET-related tasks are not exclusively confined to hepatocytes, and that non-parenchymal cells may contribute to drug transport and metabolism. CONCLUSIONS Overall, the data we provide constitute a unique resource for exploring the proteomes of the major types of human liver cells, which will facilitate an improved understanding of the human liver in health and disease.
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Affiliation(s)
- Magnus Ölander
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - Jacek R Wiśniewski
- Biochemical Proteomics Group, Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Per Artursson
- Department of Pharmacy and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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44
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Oh S, Jo Y, Jung S, Yoon S, Yoo KH. From genome sequencing to the discovery of potential biomarkers in liver disease. BMB Rep 2020. [PMID: 32475383 PMCID: PMC7330805 DOI: 10.5483/bmbrep.2020.53.6.074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Chronic liver disease progresses through several stages, fatty liver, steatohepatitis, cirrhosis, and eventually, it leads to hepatocellular carcinoma (HCC) over a long period of time. Since a large proportion of patients with HCC are accompanied by cirrhosis, it is considered to be an important factor in the diagnosis of liver cancer. This is because cirrhosis leads to an irreversible harmful effect, but the early stages of chronic liver disease could be reversed to a healthy state. Therefore, the discovery of biomarkers that could identify the early stages of chronic liver disease is important to prevent serious liver damage. Biomarker discovery at liver cancer and cirrhosis has enhanced the development of sequencing technology. Next generation sequencing (NGS) is one of the representative technical innovations in the biological field in the recent decades and it is the most important thing to design for research on what type of sequencing methods are suitable and how to handle the analysis steps for data integration. In this review, we comprehensively summarized NGS techniques for identifying genome, transcriptome, DNA methylome and 3D/4D chromatin structure, and introduced framework of processing data set and integrating multi-omics data for uncovering biomarkers.
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Affiliation(s)
- Sumin Oh
- Laboratory of Biomedical Genomics, Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310, Korea
- Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Korea
| | - Yeeun Jo
- Laboratory of Biomedical Genomics, Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310, Korea
| | - Sungju Jung
- Laboratory of Biomedical Genomics, Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310, Korea
| | - Sumin Yoon
- Laboratory of Biomedical Genomics, Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310, Korea
| | - Kyung Hyun Yoo
- Laboratory of Biomedical Genomics, Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310, Korea
- Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Korea
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An in Situ Atlas of Mitochondrial DNA in Mammalian Tissues Reveals High Content in Stem and Proliferative Compartments. THE AMERICAN JOURNAL OF PATHOLOGY 2020; 190:1565-1579. [PMID: 32304697 DOI: 10.1016/j.ajpath.2020.03.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 02/25/2020] [Accepted: 03/19/2020] [Indexed: 02/07/2023]
Abstract
Mitochondria regulate ATP production, metabolism, and cell death. Alterations in mitochondrial DNA (mtDNA) sequence and copy number are implicated in aging and organ dysfunction in diverse inherited and sporadic diseases. Because most measurements of mtDNA use homogenates of complex tissues, little is known about cell-type-specific mtDNA copy number heterogeneity in normal physiology, aging, and disease. Thus, the precise cell types whose loss of mitochondrial activity and altered mtDNA copy number that result in organ dysfunction in aging and disease have often not been clarified. Here, an in situ hybridization approach to generate a single-cell-resolution atlas of mtDNA content in mammalian tissues was validated. In hierarchically organized self-renewing tissues, higher levels of mtDNA were observed in stem/proliferative compartments compared with differentiated compartments. Striking zonal patterns of mtDNA levels in the liver reflected the known oxygen tension gradient. In the kidney, proximal and distal tubules had markedly higher mtDNA levels compared with cells within glomeruli and collecting duct epithelial cells. In mice, decreased mtDNA levels were visualized in renal tubules as a function of aging, which was prevented by calorie restriction. This study provides a novel approach for quantifying species- and cell-type-specific mtDNA copy number and dynamics in any normal or diseased tissue that can be used for monitoring the effects of interventions in animal and human studies.
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Kammer D, Keck M, Grunder T, Maasch A, Thom T, Kleinsteuber M, Groh R. Glyphboard: Visual Exploration of High-Dimensional Data Combining Glyphs with Dimensionality Reduction. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2020; 26:1661-1671. [PMID: 31985425 DOI: 10.1109/tvcg.2020.2969060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Rigorous data science is interdisciplinary at its core. In order to make sense of high-dimensional data, data scientists need to enter into a dialogue with domain experts. We present Glyphboard, a visualization tool that aims to support this dialogue. Glyphboard is a zoomable user interface that combines well-known methods such as dimensionality reduction and glyph-based visualizations in a novel, seamless, and integrated tool. While the dimensionality reduction affords a quick overview over the data, glyph-based visualizations are able to show the most relevant dimensions in the data set at one glance. We contribute an open-source prototype of Glyphboard, a general exchange format for high-dimensional data, and a case study with nine data scientists and domain experts from four exemplary domains in order to evaluate how the different visualization and interaction features of Glyphboard are used.
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Bayoumi A, Grønbæk H, George J, Eslam M. The Epigenetic Drug Discovery Landscape for Metabolic-associated Fatty Liver Disease. Trends Genet 2020; 36:429-441. [PMID: 32396836 DOI: 10.1016/j.tig.2020.03.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/05/2020] [Accepted: 03/09/2020] [Indexed: 02/07/2023]
Abstract
Despite decades of research, effective therapies for metabolic (dysfunction)-associated fatty liver disease (MAFLD) are lacking. An increasing body of evidence suggests that epigenetic dysregulation is frequent in MAFLD, and orchestrates many aspects of its development and progression. Furthermore, the high plasticity of epigenetic modifications in response to environmental cues renders epigenetics a novel area for therapeutic drug discovery. Over recent years, several epigenetics-based drugs and diagnostic biomarkers have entered clinical development and/or obtained regulatory approval. Here, we review recent advances in our understanding of epigenetic regulation and programming during MAFLD, including DNA methylation, histone modifications, chromatin remodelling, transcriptional control, and noncoding (nc)RNAs. We also discuss the potential translational implications and challenges of epigenetics in the context of MAFLD.
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Affiliation(s)
- Ali Bayoumi
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia
| | - Henning Grønbæk
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
| | - Jacob George
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia
| | - Mohammed Eslam
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia.
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Cebola I. Liver gene regulatory networks: Contributing factors to nonalcoholic fatty liver disease. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2020; 12:e1480. [PMID: 32020788 DOI: 10.1002/wsbm.1480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 01/02/2020] [Accepted: 01/03/2020] [Indexed: 12/17/2022]
Abstract
Metabolic diseases such as nonalcoholic fatty liver disease (NAFLD) result from complex interactions between intrinsic and extrinsic factors, including genetics and exposure to obesogenic environments. These risk factors converge in aberrant gene expression patterns in the liver, which are underlined by altered cis-regulatory networks. In homeostasis and in disease states, liver cis-regulatory networks are established by coordinated action of liver-enriched transcription factors (TFs), which define enhancer landscapes, activating broad gene programs with spatiotemporal resolution. Recent advances in DNA sequencing have dramatically expanded our ability to map active transcripts, enhancers and TF cistromes, and to define the 3D chromatin topology that contains these elements. Deployment of these technologies has allowed investigation of the molecular processes that regulate liver development and metabolic homeostasis. Moreover, genomic studies of NAFLD patients and NAFLD models have demonstrated that the liver undergoes pervasive regulatory rewiring in NAFLD, which is reflected by aberrant gene expression profiles. We have therefore achieved an unprecedented level of detail in the understanding of liver cis-regulatory networks, particularly in physiological conditions. Future studies should aim to map active regulatory elements with added levels of resolution, addressing how the chromatin landscapes of different cell lineages contribute to and are altered in NAFLD and NAFLD-associated metabolic states. Such efforts would provide additional clues into the molecular factors that trigger this disease. This article is categorized under: Biological Mechanisms > Metabolism Biological Mechanisms > Regulatory Biology Laboratory Methods and Technologies > Genetic/Genomic Methods.
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Affiliation(s)
- Inês Cebola
- Department of Metabolism, Digestion and Reproduction, Section of Genetics and Genomics, Imperial College London, London, UK
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49
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Wu Y, Feng W, Liu R, Xia T, Liu S. Graphene Oxide Causes Disordered Zonation Due to Differential Intralobular Localization in the Liver. ACS NANO 2020; 14:877-890. [PMID: 31891481 DOI: 10.1021/acsnano.9b08127] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The liver is the primary organ to sequester nanodrugs, representing a substantial hurdle for drug delivery and raising toxicity concerns. However, the mechanistic details underlying the liver sequestration and effects on the liver are still elusive. The difficulty in studying the liver lies in its complexity, which is structured with stringently organized anatomical units called lobules. Graphene oxide (GO) has attracted attention for its applications in biomedicine, especially as a nanocarrier; however, its sequestration and effects in the liver, the major enrichment and metabolic organ, are less understood. Herein, we unveiled the differential distribution of GO in lobules in the liver, with a higher amount surrounding portal triad zones than the central vein zones. Strikingly, liver zonation patterns also changed, as reflected by changes in vital zonated genes involved in hepatocyte integrity and metabolism, leading to compromised hepatic functions. RNA-Seq and DNA methylation sequencing analyses unraveled that GO-induced changes in liver functional zonation could be ascribed to dysregulation of key signaling pathways governing liver zonation at not only mRNA transcriptions but also DNA methylation imprinting patterns, partially through TET-dependent signaling. Together, this study reveals the differential GO distribution pattern in liver lobules and pinpoints the genetic and epigenetic mechanisms in GO-induced liver zonation alterations.
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Affiliation(s)
- Yakun Wu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Wenya Feng
- State Key Laboratory of Environmental Chemistry and Ecotoxicology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Rui Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Tian Xia
- Division of Nanomedicine, Department of Medicine, California NanoSystems Institute , University of California , Los Angeles , California 90095 , United States
| | - Sijin Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
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50
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Lung T, Sakem B, Risch L, Würzner R, Colucci G, Cerny A, Nydegger U. The complement system in liver diseases: Evidence-based approach and therapeutic options. J Transl Autoimmun 2019; 2:100017. [PMID: 32743505 PMCID: PMC7388403 DOI: 10.1016/j.jtauto.2019.100017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 09/05/2019] [Accepted: 09/10/2019] [Indexed: 12/12/2022] Open
Abstract
Complement is usually seen to largely originate from the liver to accomplish its tasks systemically - its return to the production site has long been underestimated. Recent progress in genomics, therapeutic effects on complement, standardised possibilities in medical laboratory tests and involvement of complosome brings the complement system with its three major functions of opsonization, cytolysis and phagocytosis back to liver biology and pathology. The LOINC™ system features 20 entries for the C3 component of complement to anticipate the application of artificial intelligence data banks algorythms of which are fed with patient-specific data connected to standard lab assays for liver function. These advancements now lead to increased vigilance by clinicians. This reassessment article will further elucidate the distribution of synthesis sites to the three germ layer-derived cell systems and the role complement now known to play in embryogenesis, senescence, allotransplantation and autoimmune disease. This establishes the liver as part of the gastro-intestinal system in connection with nosological entities never thought of, such as the microbiota-liver-brain axis. In neurological disease etiology infectious and autoimmune hepatitis play an important role in the context of causative viz reactive complement activation. The mosaic of autoimmunity, i.e. multiple combinations of the many factors producing varying clinical pictures, leads to the manifold facets of liver autoimmunity.
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Affiliation(s)
- Thomas Lung
- Labormedizinisches Zentrum Dr. Risch, Lagerstrasse 30, CH-9470, Buchs, Switzerland
| | - Benjamin Sakem
- Labormedizinisches Zentrum Dr. Risch, Waldeggstrasse 37, CH-3097, Liebefeld bei Bern, Switzerland
| | - Lorenz Risch
- Labormedizinisches Zentrum Dr. Risch, Waldeggstrasse 37, CH-3097, Liebefeld bei Bern, Switzerland
| | - Reinhard Würzner
- Medical University Innsbruck, Division of Hygiene & Medical Microbiology, Department of Hygiene, Microbiology and Public Health, Schöpfstrasse 41, A-6020, Innsbruck, Austria
| | - Giuseppe Colucci
- Clinica Luganese Moncucco, Lugano, Via Moncucco, CH-6900, Lugano, Switzerland
- Faculty of Medicine, University of Basel, Basel, Switzerland
| | - Andreas Cerny
- Epatocentro Ticino, Via Soldino 5, CH-6900, Lugano, Switzerland
| | - Urs Nydegger
- Labormedizinisches Zentrum Dr. Risch, Waldeggstrasse 37, CH-3097, Liebefeld bei Bern, Switzerland
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