Single-cell technologies provide novel insights into liver physiology and pathology
image: (A) scRNA-seq with ST can reveal spatial zonation profiles of gene expression in the normal liver and a detailed cell landscape of the human liver, showing that 50% of liver genes have partitioning rules. Intrahepatic resident immune cells are demonstrated their unique distribution and functions. The receptor tyrosine kinase Tie1 is the key to regulate vascular activity signals and liver regeneration. (B) The most important feature of the CHB process is immune dysregulation, with CD8+T at the center of the process; B cell reduction impairs specific T-cell subsets and decreases the clearance of HBV and the decreased cell population in hepatitis B samples results in poor IFN-α response but activated B-0 subpopulation. (C) TREM2+/CD9+macrophages and PDGFRα+collagen-producing myofibroblasts subpopulations involve in fibrosis process; ACKR1+ and PLVAP+ endothelial cells are found to accumulate in the fibrotic ecotone and participate in immune cell migration; Galectin-9 on Kupffer cells is associated with specific immunity and could be a potential therapeutic target for cirrhosis treatment. (D) ACLF samples show high expression of the genes FGF19, ADCY8, KRT17 and SPP1 secreted by macrophages resulting in reduced LVs and dysfunctional LyECs. The pro-inflammatory monocyte subtype THBS1 may reflect ACLF progression and poor prognosis. (E) HCC with different prognosis shows differential immune cell microenvironment changes, with increasing PD-1+/CD4+T & CD8+T cells and CD8+T diversity suggesting a good prognosis; high heterogeneity in HCC as well as the increasing subtypes of TAMs, exhausted CD8+T/Tregs, CD161+/CD8+T, CCL4+/PD-L1+/TAN, ILCs/ILC2a, CD24+/CD133+/EpCAM+/CD45- cells suggesting a poor prognosis. The Layilin gene is functionally associated with tumor-characteristic CD8+T cells and may serve as a new target for immunotherapy in HCC. ACLF, acute-on-chronic liver failure; ACKR1, atypical chemokine receptor 1; CHB, chronic hepatitis B; EpCAM, epithelial cell adhesion molecule; HBV, hepatitis B virus; HCC, hepatocellular carcinoma; IFN-α, interferon-α; LVs, lymphatic vessels; LyECs, lymphatic vessel endothelial cells; PD-1, programmed cell death-1; PD-L1, programmed cell death-ligand 1; PDGFRα, recombinant human platelet-derived growth factor-α; PLVAP, plasmalemma vesicle-associated protein; scRNA-seq, single-cell transcriptome sequencing; SPP1, secretory phosphoprotein 1; ST, spatial transcriptome technology; TAMs, tumor-associated macrophages; TAN, tumors-associated neutrophil; THBS1, thrombospondin-1; Tie 1, tyrosine kinase with immunoglobulin like and EGF like domains 1; TREM2, triggering receptor expressed on myeloid cells-2.
Credit: Yusheng Jie, Bingliang Lin, Guanzi Chen, Wenli Xu
The liver, the largest glandular organ in the body, plays a crucial role in various metabolic processes and maintains overall body homeostasis. Despite its regenerative capacity, the treatment outcomes for end-stage liver diseases, such as cirrhosis and liver cancer, remain poor. Traditional therapeutic approaches are limited, necessitating liver transplantation, which is not feasible for all patients due to the shortage of available organs. Consequently, there is an urgent need for advanced methodologies to better understand the liver's pathological mechanisms and to develop precise, individualized treatments.
Single-cell sequencing represents a groundbreaking advancement in molecular biology, enabling the analysis of gene expression at the level of individual cells. Unlike traditional whole-tissue RNA sequencing, which can obscure cellular heterogeneity, single-cell RNA sequencing (scRNA-seq) and other single-cell techniques provide a higher resolution and accuracy in identifying distinct cell populations and biomolecular changes. This technology is particularly powerful for identifying rare cell types and understanding their roles in liver disease progression, offering potential targets for immunotherapy.
In our review, we comprehensively summarize various single-cell approaches, including transcriptomic, spatial transcriptomic, immunomic, proteomic, epigenomic, and multiomic technologies. Each method offers unique insights into cellular functions and interactions:
- Transcriptomic Approaches: scRNA-seq enables the detailed characterization of gene expression profiles in individual cells, revealing heterogeneity within cell populations and identifying rare cell types.
- Spatial Transcriptomic: This technique maps gene expression patterns within tissue sections, providing spatial context to the transcriptomic data.
- Immunomic: Single-cell immunomic techniques profile the diversity and functional states of immune cells, crucial for understanding liver immunopathology.
- Proteomic: Single-cell proteomics analyzes protein expression and modifications, essential for understanding cellular functions and signaling pathways.
- Epigenomic: This approach studies the epigenetic modifications at the single-cell level, shedding light on gene regulation mechanisms.
- Multiomic Technologies: Integrating data from different omics layers provides a comprehensive view of cellular states and interactions.
Single-cell technologies have been applied to various aspects of liver physiology and pathology. For example:
- Normal Liver: scRNA-seq has revealed the spatial zonation of gene expression and the unique distribution of intrahepatic immune cells, highlighting the liver's complex cellular architecture.
- Chronic Liver Diseases: In chronic hepatitis B, single-cell approaches have identified immune dysregulation as a key feature, with specific T cell subsets playing central roles. In liver fibrosis, distinct macrophage and fibroblast subpopulations have been implicated, suggesting novel therapeutic targets.
- Liver Cancer: In hepatocellular carcinoma (HCC), single-cell analyses have uncovered differential immune cell microenvironment changes associated with prognosis. The identification of specific immune cell subtypes and markers offers potential for developing targeted immunotherapies.
Recent studies utilizing single-cell technologies have provided novel insights into liver diseases. For instance, the identification of TREM2+/CD9+ macrophages and PDGFRα+ myofibroblasts in liver fibrosis has revealed new cellular targets for antifibrotic therapies. Similarly, the characterization of immune cell dynamics in HCC has highlighted potential biomarkers for prognosis and therapeutic response.
The continuous advancement of single-cell technologies promises to further enhance our understanding of liver biology. Emerging techniques, such as single-cell multiomics and spatially resolved transcriptomics, offer even greater resolution and integration of cellular data. These advancements are expected to drive the development of more precise and personalized therapeutic strategies for liver diseases.
Single-cell technologies have revolutionized our understanding of liver physiology and pathology by providing unprecedented resolution in the analysis of cellular heterogeneity and molecular changes. These approaches offer new insights into the pathophysiological mechanisms of liver diseases, paving the way for precise and individualized treatments. As the field continues to evolve, single-cell analyses will undoubtedly play a crucial role in the future of liver disease research and therapy.
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https://www.xiahepublishing.com/2310-8819/JCTH-2023-00224
The study was recently published in the Journal of Clinical and Translational Hepatology.
The Journal of Clinical and Translational Hepatology (JCTH) is owned by the Second Affiliated Hospital of Chongqing Medical University and published by XIA & HE Publishing Inc. JCTH publishes high quality, peer reviewed studies in the translational and clinical human health sciences of liver diseases. JCTH has established high standards for publication of original research, which are characterized by a study’s novelty, quality, and ethical conduct in the scientific process as well as in the communication of the research findings. Each issue includes articles by leading authorities on topics in hepatology that are germane to the most current challenges in the field. Special features include reports on the latest advances in drug development and technology that are relevant to liver diseases. Regular features of JCTH also include editorials, correspondences and invited commentaries on rapidly progressing areas in hepatology. All articles published by JCTH, both solicited and unsolicited, must pass our rigorous peer review process.
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