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Friend or Foe? New Perspectives on Hepatic Immune Cells at Single Cell Resolution
Time:2023-01-30 22:47:24  


Friend or Foe? New Perspectives on Hepatic Immune Cells at Single Cell Resolution

The liver performs many crucial functions, such as gluconeogenesis, glycogen storage, lipolysis, detoxification, bile secretion, urea, and hormone synthesis. It also plays a central role in maintaining homeostasis and regulating the immune system (1, 2).  Given this, it is unsurprising that liver problems cause many serious diseases (2). In 2020, liver cancer was estimated to be the second most deadly, and the sixth most common diagnosed cancer, with more than 900,000 global cases annually (3), which is expected to rise to 1,000,000 by 2025 (4).

Constituting approximately 90% of all cases, hepatocellular carcinoma (HCC) is the most common type of liver cancer (4). Risk factors include hepatitis B virus (HBV) and hepatitis C virus (HCV) infections, chronic alcohol consumption and non-alcoholic fatty liver disease (NAFLD), which is also associated with metabolic disorders such as diabetes and obesity (4, 5). NAFLD is defined by steatosis, an abnormal accumulation of lipids in the liver that can further progress into non-alcoholic steatohepatitis (NASH) (5-7). In recent years, NASH, which develops in the context of chronic inflammation, increased hepatic damage, fibrosis, and steatosis, has become a leading risk factor for end-stage liver diseases such as HCC (6, 8).

Understanding the underlying mechanisms triggering disease development and progression, from etiologies to diseased conditions may allow us to identify new diagnostic biomarkers and to develop new treatment strategies. Here, we review recent studies addressing these important questions using single cell sequencing technologies.


Figure 1. Number of publications focusing on liver research and applying single cell sequencing technologies. 'PubMed Advanced Search Builder' search query: “Liver” AND “scRNA-seq” OR “single-cell sequencing”, December 28, 2022 (10).

Using single cell sequencing to identify new cell populations in human livers

To better understand cellular interactions in healthy and diseased livers, MacParland and colleagues (1) mapped liver cell populations using single cell sequencing, an approach that pictured the human liver cell composition at a much higher resolution than previous approaches.

Using donor liver graft lysates, they analyzed the expression profiles of 8444 single cells (parenchymal and non-parenchymal) and found 20 distinct cell populations - not only hepatocytes, hepatic stellate cells (HSCs) and cholangiocytes, but also different immune cell subtypes such as B cell, T cell and macrophage clusters (1). In particular, the authors found two distinct Kupffer cell clusters (liver-resident macrophages) that showed different inflammatory and non-inflammatory properties.  This could help explain how different immune cell populations contribute to liver functions, such as its regenerative capacity, but also to liver pathologies under diseased conditions (1).

Together, MacParland et al. provide valuable insights to better understand the cellular mechanisms within human livers and especially, the diverse role of macrophages that could be used to develop more precise treatment options for various liver diseases (1).


Figure 2. Single cell sequencing revealed the presence of two liver resident macrophage populations with non-inflammatory or inflammatory properties (image modified from MacParland et al. (1);

Understanding the role of immune cells in healthy and diseased livers

In their study, Pfister and colleagues (9) investigate how immunotherapy affects HCC development in the context of a pre-existing NASH condition as that might affect treatment efficacy. Thus, identifying target biomarkers is crucial for precise and effective treatment.

The data obtained in this study showed that there was an elevated number of exhausted and effector-like CD8 PD1 T cells in mouse NASH models (9). However, anti-PD1 treatment could not reduce the tumor burden but instead promoted liver fibrosis. In contrast, CD8 T cell depletion hampered tumor growth and diminished HCC development in NASH mice, suggesting that CD8 T cells might play a role in NASH-HCC transition. In-line with those findings, combined anti-PD1/CD8 or anti-PD1/TNF treatment was shown to reduce inflammation and disease progression, indicating that anti-PD1 alone might promote T cell-mediated inflammation and tissue damage. Finally, Pfister et al. compared their murine data with human patient samples and found that CD8 T cells from patients with NAFLD/NASH had similar expression profiles as those from NASH mice. Interestingly, patients with HBV- or HCV-related HCC showed a better immunotherapy response than patients with a non-viral condition, further highlighting the importance of context-specific treatment strategies (9).

In summary, Pfister et al. show that patient stratification in consideration of etiologies and specific biomarkers will be crucial to develop personalized treatments and that the understanding of the underlying mechanisms will provide valuable information to allow for effective, patient-centered therapies (9).


Figure 3. Single cell sequencing data from T lymphocytes from murine NASH models (A) and human patient data (B) (image modified from Pfister et al. (9);

The human liver is a complex organ that is composed of many different cell types and holds essential functions. Especially in diseased tissues, clear vision is needed to discover novel biomarkers and new drug targets to develop effective treatment strategies. Single cell sequencing lets you see the heterogeneity of tissue samples more clearly, and so to better understand underlying mechanisms and cellular interactions orchestrating these crucial functions. Singleron’s GEXSCOPE® Single Cell V(D)J and sCircle® Single Cell Full Length Immunoreceptor Library kits let you gain detailed insights into processes such as BCR/TCR diversity and other immune-regulatory mechanisms that will help to promote your research.

To learn more about how single cell multi-omics can accelerate your research to enable precision medicine, visit



  1. MacParland SA, Liu JC, Ma XZ, Innes BT, Bartczak AM, Gage BK, Manuel J, Khuu N, Echeverri J, Linares I, Gupta R, Cheng ML, Liu LY, Camat D, Chung SW, Seliga RK, Shao Z, Lee E, Ogawa S, Ogawa M, Wilson MD, Fish JE, Selzner M, Ghanekar A, Grant D, Greig P, Sapisochin G, Selzner N, Winegarden N, Adeyi O, Keller G, Bader GD, McGilvray ID. Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations. Nat Commun. 9, 4384 (2018). doi: 10.1038/s41467-018-06318-7.
  2. Tanaka M, Itoh T, Tanimizu N, Miyajima A. Liver stem/progenitor cells: their characteristics and regulatory mechanisms. J Biochem. (2011) doi: 10.1093/jb/mvr001.
  3. Ferlay J, Ervik M, Lam F, Colombet M, Mery L, Piñeros M, Znaor A, Soerjomataram I, Bray F (2020). Global Cancer Observatory: Cancer Today. Lyon, France: International Agency for Research on Cancer. Available from:, accessed [17 11 2022].
  4. Llovet JM, Kelley RK, Villanueva A, Singal AG, Pikarsky E, Roayaie S, Lencioni R, Koike K, Zucman-Rossi J, Finn RS. Hepatocellular carcinoma. Nat Rev Dis Primers. (2021) doi: 10.1038/s41572-020-00240-3.
  5. Huby T, Gautier EL. Immune cell-mediated features of non-alcoholic steatohepatitis. Nat Rev Immunol. (2022) doi: 10.1038/s41577-021-00639-3.
  6. Xiong X, Kuang H, Ansari S, Liu T, Gong J, Wang S, Zhao XY, Ji Y, Li C, Guo L, Zhou L, Chen Z, Leon-Mimila P, Chung MT, Kurabayashi K, Opp J, Campos-Pérez F, Villamil-Ramírez H, Canizales-Quinteros S, Lyons R, Lumeng CN, Zhou B, Qi L, Huertas-Vazquez A, Lusis AJ, Xu XZS, Li S, Yu Y, Li JZ, Lin JD. Landscape of Intercellular Crosstalk in Healthy and NASH Liver Revealed by Single-Cell Secretome Gene Analysis. Mol Cell. (2019) doi: 10.1016/j.molcel.2019.07.028.
  7. Deng CJ, Lo TH, Chan KY, Li X, Wu MY, Xiang Z, Wong CM. Role of B Lymphocytes in the Pathogenesis of NAFLD: A 2022 Update. Int J Mol Sci. (2022) doi: 10.3390/ijms232012376.
  8. Sutti S, Albano E. Adaptive immunity: an emerging player in the progression of NAFLD. Nat Rev Gastroenterol Hepatol. (2020) doi: 10.1038/s41575-019-0210-2.
  9. Pfister D, Núñez NG, Pinyol R, et al., NASH limits anti-tumour surveillance in immunotherapy-treated HCC. Nature 592, 450-456 (2021). doi: 10.1038/s41586-021-03362-0.
  10. PubMed [Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; 2004 – [cited 2022 Dec. 28]. Available from:
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