Single cell sequencing

Ganz T, Fainstein N, Theotokis P, Elgavish S, Vardi-Yaakov O, Lachish M, Sofer L, Zveik O, Grigoriadis N, Ben-Hur T. Targeting CNS myeloid infiltrates provides neuroprotection in a progressive multiple sclerosis model [Internet]. Brain Behav ImmunBrain, behavior, and immunity 2024;122:497-509.Available from: https://pubmed.ncbi.nlm.nih.gov/39179123/ PubMed
Demyelination and axonal injury in chronic-progressive Multiple Sclerosis (MS) are presumed to be driven by a neurotoxic bystander effect of meningeal-based myeloid infiltrates. There is an unmet clinical need to attenuate disease progression in such forms of CNS-compartmentalized MS. The failure of systemic immune suppressive treatments has highlighted the need for neuroprotective and repair-inducing strategies. Here, we examined whether direct targeting of CNS myeloid cells and modulating their toxicity may prevent irreversible tissue injury in chronic immune-mediated demyelinating disease. To that end, we utilized the experimental autoimmune encephalomyelitis (EAE) model in Biozzi mice, a clinically relevant MS model. We continuously delivered intracerebroventricularly (ICV) a retinoic acid receptor alpha agonist (RARα), as a potent regulator of myeloid cells, in the chronic phase of EAE. We assessed disease severity and performed pathological evaluations, functional analyses of immune cells, and single-cell RNA sequencing on isolated spinal CD11b+ cells. Although initiating treatment in the chronic phase of the disease, the RARα agonist successfully improved clinical outcomes and prevented axonal loss. ICV RARα agonist treatment inhibited pro-inflammatory pathways and shifted CNS myeloid cells toward neuroprotective phenotypes without affecting peripheral infiltrating myeloid cell phenotypes, or peripheral immunity. The treatment regulated cell-death pathways across multiple myeloid cell populations and suppressed apoptosis, resulting in paradoxically marked increased neuroinflammatory infiltrates, consisting mainly of microglia and CNS / border-associated macrophages. This work establishes the notion of bystander neurotoxicity by CNS immune infiltrates in chronic demyelinating disease. Furthermore, it shows that targeting compartmentalized neuroinflammation by selective regulation of CNS myeloid cell toxicity and survival reduces irreversible tissue injury, and may serve as a novel disease-modifying approach.
Paldor M, Levkovitch-Siany O, Eidelshtein D, Adar R, Enk CD, Marmary Y, Elgavish S, Nevo Y, Benyamini H, Plaschkes I, Klein S, Mali A, Rose-John S, Peled A, Galun E, Axelrod JH. Single-cell transcriptomics reveals a senescence-associated IL-6/CCR6 axis driving radiodermatitis [Internet]. EMBO Mol Med 2022;14:e15653.Available from: https://pubmed.ncbi.nlm.nih.gov/35785521/ PubMed
Irradiation-induced alopecia and dermatitis (IRIAD) are two of the most visually recognized complications of radiotherapy, of which the molecular and cellular basis remains largely unclear. By combining scRNA-seq analysis of whole skin-derived irradiated cells with genetic ablation and molecular inhibition studies, we show that senescence-associated IL-6 and IL-1 signaling, together with IL-17 upregulation and CCR6(+) -mediated immune cell migration, are crucial drivers of IRIAD. Bioinformatics analysis colocalized irradiation-induced IL-6 signaling with senescence pathway upregulation largely within epidermal hair follicles, basal keratinocytes, and dermal fibroblasts. Loss of cytokine signaling by genetic ablation in IL-6(-/-) or IL-1R(-/-) mice, or by molecular blockade, strongly ameliorated IRIAD, as did deficiency of CCL20/CCR6-mediated immune cell migration in CCR6(-/-) mice. Moreover, IL-6 deficiency strongly reduced IL-17, IL-22, CCL20, and CCR6 upregulation, whereas CCR6 deficiency reciprocally diminished IL-6, IL-17, CCL3, and MHC upregulation, suggesting that proximity-dependent cellular cross talk promotes IRIAD. Therapeutically, topical application of Janus kinase blockers or inhibition of T-cell activation by cyclosporine effectively reduced IRIAD, suggesting the potential of targeted approaches for the treatment of dermal side effects in radiotherapy patients.
Rosenberg N, Van Haele M, Lanton T, Brashi N, Bromberg Z, Adler H, Giladi H, Peled A, Goldenberg DS, Axelrod JH, Simerzin A, Chai C, Paldor M, Markezana A, Yaish D, Shemulian Z, Gross D, Barnoy S, Gefen M, Amran O, Claerhout S, Fernandez-Vaquero M, Garcia-Beccaria M, Heide D, Shoshkes-Carmel M, Schmidt Arras D, Elgavish S, Nevo Y, Benyamini H, Tirnitz-Parker JEE, Sanchez A, Herrera B, Safadi R, Kaestner KH, Rose-John S, Roskams T, Heikenwalder M, Galun E. Combined hepatocellular-cholangiocarcinoma derives from liver progenitor cells and depends on senescence and IL6 trans-signaling [Internet]. J Hepatol 2022;Available from: https://pubmed.ncbi.nlm.nih.gov/35988690/ PubMed
BACKGROUND AND AIMS: Primary liver cancers include: Hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (CCA) and combined HCC-CCA tumors (cHCC-CCA). It has been suggested, but not unequivocally proven, that hepatic progenitor cells (HPCs) can contribute to hepatocarcinogenesis. We aimed to determine whether HPCs contribute to HCC, cHCC-CCA or both types of tumors. METHOD: To trace progenitor cells during hepatocarcinogenesis, we generated Mdr2-KO mice that harbor an YFP reporter gene driven by the Foxl1 promoter which is expressed specifically in progenitor cells. These mice (Mdr2-KO(Foxl1-CRE;RosaYFP)) develop chronic inflammation and HCCs by the age of 14-16 months, followed by cHCC-CCA tumors at the age of 18 months, as we have first observed. RESULTS: In this Mdr2-KO(Foxl1-CRE;RosaYFP) mouse model, liver progenitor cells are the source of cHCC-CCA tumors, but not the source of HCC. Ablating the progenitors, caused reduction of cHCC-CCA tumors but did not affect HCCs. RNA-seq revealed enrichment of the IL6 signaling pathway in cHCC-CCA tumors compared to HCC tumors. ScRNA-seq analysis revealed that IL6 is expressed from immune and parenchymal cells in senescence, and that IL6 is part of the senescence-associated secretory phenotype (SASP). Administration of anti-IL6 Ab to Mdr2-KO(Foxl1-CRE;RosaYFP) mice, inhibited the development of cHCC-CCA tumors. By blocking IL6 trans-signaling, cHCC-CCA tumors decreased in number and size, indicating that cHCC-CCA is dependent on IL6 trans-signaling. Furthermore, the administration of a senolytic agent inhibited IL6 and the development of cHCC-CCA tumors. CONCLUSION: Our results demonstrate that cHCC-CCA, but not HCC tumors, originate from HPCs, and that IL6, which derives in part from cells in senescence, plays an important role in this process via IL6 trans-signaling. These findings could enhance new therapeutic approaches for cHCC-CCA liver cancer. LAY SUMMARY: Combined hepatocellular carcinoma - cholangiocarcinoma is the third prevalent liver cancer. We show that the source of this tumor is the liver tissue stem cells and that, this tumor type is dependent on an inflammatory signaling of IL6 and can be inhibited by blocking IL6 signaling or using a senolytic agent.
Schlesinger Y, Yosefov-Levi O, Kolodkin-Gal D, Granit RZ, Peters L, Kalifa R, Xia L, Nasereddin A, Shiff I, Amran O, Nevo Y, Elgavish S, Atlan K, Zamir G, Parnas O. Single-cell transcriptomes of pancreatic preinvasive lesions and cancer reveal acinar metaplastic cells' heterogeneity [Internet]. Nat Commun 2020;11:4516.Available from: https://pubmed.ncbi.nlm.nih.gov/32908137/ PubMed
Acinar metaplasia is an initial step in a series of events that can lead to pancreatic cancer. Here we perform single-cell RNA-sequencing of mouse pancreas during the progression from preinvasive stages to tumor formation. Using a reporter gene, we identify metaplastic cells that originated from acinar cells and express two transcription factors, Onecut2 and Foxq1. Further analyses of metaplastic acinar cell heterogeneity define six acinar metaplastic cell types and states, including stomach-specific cell types. Localization of metaplastic cell types and mixture of different metaplastic cell types in the same pre-malignant lesion is shown. Finally, single-cell transcriptome analyses of tumor-associated stromal, immune, endothelial and fibroblast cells identify signals that may support tumor development, as well as the recruitment and education of immune cells. Our findings are consistent with the early, premalignant formation of an immunosuppressive environment mediated by interactions between acinar metaplastic cells and other cells in the microenvironment.