单细胞转录组学和表观基因组学指出CD58-CD2相互作用控制原发性黑色素瘤的生长和免疫。

IF 20.1 1区 医学 Q1 ONCOLOGY
Antonia Stubenvoll, Maria Schmidt, Johanna Moeller, Max Alexander Lingner Chango, Carolyn Schultz, Olga Antoniadou, Henry Loeffler-Wirth, Stephan Bernhart, Florian Große, Beatrice Thier, Annette Paschen, Ulf Anderegg, Jan C. Simon, Mirjana Ziemer, Clara T. Schoeder, Hans Binder, Manfred Kunz
{"title":"单细胞转录组学和表观基因组学指出CD58-CD2相互作用控制原发性黑色素瘤的生长和免疫。","authors":"Antonia Stubenvoll,&nbsp;Maria Schmidt,&nbsp;Johanna Moeller,&nbsp;Max Alexander Lingner Chango,&nbsp;Carolyn Schultz,&nbsp;Olga Antoniadou,&nbsp;Henry Loeffler-Wirth,&nbsp;Stephan Bernhart,&nbsp;Florian Große,&nbsp;Beatrice Thier,&nbsp;Annette Paschen,&nbsp;Ulf Anderegg,&nbsp;Jan C. Simon,&nbsp;Mirjana Ziemer,&nbsp;Clara T. Schoeder,&nbsp;Hans Binder,&nbsp;Manfred Kunz","doi":"10.1002/cac2.12651","DOIUrl":null,"url":null,"abstract":"<p>Immunotherapy is currently one of the most promising treatment options for malignant melanoma [<span>1</span>]. To uncover new immunological targets for future treatment approaches, single-cell transcriptomic and epigenomic analyses were performed on human primary melanoma (MM) and melanocytic nevus (Nev) samples (Figure 1A). The detailed methods of this study are described in the Supplementary Material.</p><p>MM and Nev biopsies (Supplementary Figure S1; Supplementary Table S1) were analyzed by single-cell RNA sequencing (scRNA-seq) and single-cell Assay for Transposase-Accessible Chromatin sequencing (scATAC-seq) (Supplementary Figure S2; Supplementary Tables S2 and S3). Using Uniform Manifold Approximation and Projection (UMAP), 28 distinct cellular clusters were identified and annotated based on scRNA-seq data from a previous report and manual curation (Figure 1B; Supplementary Figure S3A) [<span>2</span>]. Examples of gene expression patterns for individual cell types are provided in Supplementary Table S4. Lesional T lymphocytes were quantified using scRNA-seq data and anti-CD3 immunofluorescence staining, which revealed three distinct immune states: hot (&gt;25 % T cells), intermediate (&gt;6-25 % T cells), and cold (0-6 % T cells) (Supplementary Table S5).</p><p>Based on a previous study examining melanoma cell differentiation statuses, the melanoma cell cluster was divided into 8 distinct subclusters (Supplementary Figure S3B, C) [<span>3</span>]. Unsupervised clustering further refined these findings, predicting 11 cellular subclusters of melanoma cells (Figure 1C, Supplementary Table S6) [<span>3</span>].</p><p>To investigate the molecular mechanisms underlying melanoma cell dedifferentiation, RNA velocity and latent time (LT) analyses were performed (Supplementary Material and Methods). These analyses measure developmental processes based on the gene expression patterns of spliced and unspliced genes [<span>4</span>], with LT more directly reflecting transcriptional dynamics. As shown in Figure 1C, RNA velocity arrows indicate a trajectory from the melanoma subcluster of undifferentiated, neural crest (nc)-like cells on the left toward the more differentiated Mel_trans-melan_c7 and Mel_trans-melan_c8 subclusters at the right edge. LT analysis (Figure 1C) and the latent time heatmap (Figure 1D) revealed an opposing trajectory toward a more dedifferentiated state, exemplified by the Mel_trans subcluster. Here, melanoma cell dedifferentiation was linked to gene sets enriched in antigen presentation and the induction of T cell receptor signaling (Figure 1D). This aligns with the known association between high immune cell infiltrates and dedifferentiated tumors. Notably, Serpin Family E Member 2 <i>(SERPINE2)</i> has been identified as a mediator of melanoma metastasis and tumor progression [<span>5</span>].</p><p>Next, we performed regulon analysis (https://github.com/aertslab/pySCENIC) of the melanoma cell clusters, which refers to a group of genes regulated by the same transcription factor [<span>6</span>]. We identified a number of regulons associated with nc-like and more dedifferentiated melanoma cells, such as Retinoid X Receptor Gamma (<i>RXRG</i>), SRY-Box Transcription Factor 2 (<i>SOX2</i>), CAMP Responsive Element Binding Protein 5 (<i>CREB5</i>), BTB Domain And CNC Homolog (<i>BACH1</i>), and Transcription Factor 12 (<i>TCF12</i>), as well as those associated with more differentiated melanocytic cells, such as Melanocyte Inducing Transcription Factor (<i>MITF</i>), SOX10, Paired Box 3 (<i>PAX3</i>), TEA Domain Transcription Factor 1 (<i>TEAD1</i>), and <i>SOX4</i> (Supplementary Figure S4). In line with this, it is known that BACH1 activates the expression of genes involved in cell motility and metastasis and plays an essential role in both innate and adaptive immune responses [<span>7</span>]. Taken together, melanoma cell dedifferentiation processes may be defined by an activated immune response and by specific transcriptional mechanisms.</p><p>Next, we focused on melanoma-immune cell interactions by analyzing ligand-receptor interactions with an emphasis on cytotoxic T cells, using the LIANA software (https://saezlab.github.io/liana/) (Figure 1E; Supplementary Tables S7 and S8). For a more focused analysis, we removed HLA and collagen genes from the subsequent analysis. As shown in Figure 1E, CD2 on cytotoxic T cells was a major interaction partner for several molecules in melanoma cells, especially CD58 and CD59. This interaction was most prominent in hot tumors. A recent study using a CRISPR/Cas knockout screen provided evidence that the CD58-CD2 interaction may indeed be a major mechanism of melanoma immune control [<span>8</span>]. Our data suggest that CD58 and CD59, both interacting with CD2, may control the T cell-melanoma cell interaction. In contrast, the most prominent interaction in cold tumors was between Fibronectin1 (FN1) and Integrin Subunit Beta 1 (ITGB1). Fibronectin-integrin β1 interaction is known to antagonize integrin β3 and thus might have an inactivating effect on integrin downstream signaling [<span>9</span>].</p><p>Immunofluorescence staining for CD58, CD59 and CD2 expression in melanoma/nevus samples (Supplementary Figure S5; Supplementary Table S9) showed higher numbers of CD2<sup>+</sup> immune cells in the vicinity of melanoma cells in hot/intermediate tumors compared to cold tumors/nevi. However, nevi do express both CD58 and CD2. Moreover, CD58 expression was higher in hot/intermediate samples and increased with increasing LT (Supplementary Figure S5).</p><p>Using data from The Cancer Genome Atlas (TCGA) melanoma cohort (https://www.genome.gov/Funded-Programs-Projects/Cancer-Genome-Atlas), we demonstrated that high CD58, together with high CD2 expression, significantly improved the prognosis of melanoma patients (Figure 1F, Supplementary Figure S6). Similarly, CD2 expression was associated with overall survival in a recently published melanoma immunotherapy study, making it a possible target for immunotherapy (Supplementary Figure S6).</p><p>Next, we used isolated tumor-infiltrating lymphocytes (TILs) enriched in tumor-reactive CD8<sup>+</sup> T cells from tumor tissue of a melanoma patient. As shown in Figure 1G and Supplementary Figure S7, T cell activation, as determined by intracellular Interferon γ (IFN-γ) expression, was reduced by blockade of CD58, but not of CD59, on autologous melanoma cells. Moreover, melanoma cell killing in the presence of T cells could be inhibited by the addition of the anti-CD58 antibody (Figure 1G).</p><p>Soluble recombinant extracellular domains of CD58, CD59 and CD2 were then used to measure the binding affinity of CD2 to CD58 and CD59, respectively (Figure 1H). These analyses showed high binding activity of CD2 to CD58, but none to CD59, which further supports an activating role of CD58-CD2, but not CD59-CD2. Overall, in addition to its known inactivating capacity on the membrane attack complex, CD59 appears to require a specific conformation to be active in the CD2 immune context, which may explain its inactivity in our settings.</p><p>Finally, scATAC-seq data of six MM and one Nev sample were analyzed in T cell populations (Figure 1I; Supplementary Tables S10 and S11). Among the top ten open chromatin regions in T cells from immune hot samples were <i>CD3D</i>, Interferon Gamma (<i>IFNG)</i>, <i>CD28</i>, <i>CD2</i>, <i>CD3G</i>, and Granzyme A (<i>GZMA</i>). In line with this, <i>CD2</i> expression was most prominent in the T cell and NK cell clusters of the scATAC-seq UMAP and scRNA-seq UMAP (Supplementary Figure S8). By analyzing chromatin accessible networks (CAN), an open chromatin region was observed immediately upstream of the <i>CD2</i> gene (Figure 1I), which harbored a binding motif for various transcription factors, including <i>CAMP</i> Responsive Element Binding Protein 1 (<i>CREB1</i>), Zinc Finger Protein 143 (<i>ZNF143</i>), MYB Proto-Oncogene Like 2 (<i>MYBL2</i>), Recombination Signal Binding Protein For Immunoglobulin Kappa J Region (<i>RBPJ</i>), Jun Proto-Oncogene, AP-1 Transcription Factor Subunit (<i>JUN</i>), JunB Proto-Oncogene (<i>JUNB</i>), and FOS Like 2, AP-1 Transcription Factor Subunit (<i>FOSL2</i>) (Figure 1J, Supplementary Figure S8, Supplementary Figure S9). RBPJ might play an important role in this setting since it has been associated with T cell immune response in hepatocellular carcinoma and may thus be a target in immunotherapy [<span>10</span>].</p><p>Taken together, a detailed map of melanoma single-cell differentiation steps in MM and Nev lesions is presented, supporting a developmental trajectory of different melanoma cellular subpopulations towards a high immune phenotype. The CD58-CD2 interaction appears to play a prominent role in the melanoma immune response, which may be exploited in future clinical trials.</p><p><b>Antonia Stubenvoll</b>: Conceptualization; data curation; formal analysis; investigation; methodology; visualization, and writing original draft. <b>Maria Schmidt</b>: Conceptualization; data curation; formal analysis; investigation; methodology; software, and writing original draft. <b>Johanna Moeller</b>: Investigation; formal analysis, and methodology. <b>Max Alexander Lingner Chango</b>: Data curation; formal analysis, and investigation. <b>Henry Loeffler-Wirth</b>: Investigation; methodology; data curation; formal analysis; validation, and visualization. <b>Stephan Bernhart</b>: Investigation; methodology; data curation; formal analysis; validation and visualization. <b>Florian Große</b>: Data curation; formal analysis; investigation; methodology; software and writing original draft. <b>Carolyn Schultz</b>: Data curation; investigation; validation, and visualization. <b>Olga Antoniadou</b>: Investigation; validation, and visualization. <b>Beatrice Thier</b>: Investigation; formal analysis; investigation, and methodology. <b>Annette Paschen</b>: Investigation; formal analysis; investigation; methodology, and supervision. <b>Ulf Anderegg</b>: Investigation; formal analysis; investigation; methodology, and supervision. <b>Jan C. Simon</b>: Resources; supervision; validation; writing; review, and editing. <b>Mirjana. Ziemer</b>: Resources; investigation; writing; review, and editing. <b>Clara T. Schoeder</b>: Data curation; conceptualization; investigation; validation; visualization, and supervision. <b>Hans Binder</b>: Data curation; formal analysis; software; writing; review, and editing. <b>Manfred Kunz</b>: Conceptualization; data curation; funding acquisition; investigation; project administration; resources; supervision; writing; review, and editing. All authors reviewed and approved the final version of the manuscript.</p><p>Manfred Kunz has received honoraria from the Speakers Bureau of Roche Pharma and travel support from Novartis Pharma GmbH and Bristol-Myers Squibb GmbH. Jan Christoph Simon has received speaker's fees from Bristol-Myers Squibb, Roche Pharma AG, Novartis and MSD Sharp &amp; Dohme as well as financial support for congress attendance from Bristol-Myers Squibb, MSD Sharp &amp; Dohme and Novartis. Mirjana Ziemer has received speaker's fees from Bristol-Myers Squibb, MSD Sharp &amp; Dohme GmbH, Pfizer Pharma GmbH and Sanofi-Aventis Deutschland GmbH and received financial support for congress participation from Bristol-Myers Squibb and serves as a member of expert panels on cutaneous adverse reactions for Pfizer INC. Clara Tabea Schoeder has received research support from Navigo Protein GmbH, Halle (Saale), Germany.</p><p>This work was supported by the Deutsche Forschungsgemeinschaft (DFG) (German Research Foundation; grant numbers: KU 1320/10-1 and HO 6586/1-1, and SFB1430, project 424228829) and the Sächsische Aufbaubank (grant number: 10071450).</p><p>Single-cell transcriptomic analyses were approved by the local Ethics committee of the Medical Faculty (AZ 023-16-01022016). Biopsies were taken after informed consent of the patients.</p>","PeriodicalId":9495,"journal":{"name":"Cancer Communications","volume":"45 4","pages":"465-470"},"PeriodicalIF":20.1000,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cac2.12651","citationCount":"0","resultStr":"{\"title\":\"Single-cell transcriptomics and epigenomics point to CD58-CD2 interaction in controlling primary melanoma growth and immunity\",\"authors\":\"Antonia Stubenvoll,&nbsp;Maria Schmidt,&nbsp;Johanna Moeller,&nbsp;Max Alexander Lingner Chango,&nbsp;Carolyn Schultz,&nbsp;Olga Antoniadou,&nbsp;Henry Loeffler-Wirth,&nbsp;Stephan Bernhart,&nbsp;Florian Große,&nbsp;Beatrice Thier,&nbsp;Annette Paschen,&nbsp;Ulf Anderegg,&nbsp;Jan C. Simon,&nbsp;Mirjana Ziemer,&nbsp;Clara T. Schoeder,&nbsp;Hans Binder,&nbsp;Manfred Kunz\",\"doi\":\"10.1002/cac2.12651\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>Immunotherapy is currently one of the most promising treatment options for malignant melanoma [<span>1</span>]. To uncover new immunological targets for future treatment approaches, single-cell transcriptomic and epigenomic analyses were performed on human primary melanoma (MM) and melanocytic nevus (Nev) samples (Figure 1A). The detailed methods of this study are described in the Supplementary Material.</p><p>MM and Nev biopsies (Supplementary Figure S1; Supplementary Table S1) were analyzed by single-cell RNA sequencing (scRNA-seq) and single-cell Assay for Transposase-Accessible Chromatin sequencing (scATAC-seq) (Supplementary Figure S2; Supplementary Tables S2 and S3). Using Uniform Manifold Approximation and Projection (UMAP), 28 distinct cellular clusters were identified and annotated based on scRNA-seq data from a previous report and manual curation (Figure 1B; Supplementary Figure S3A) [<span>2</span>]. Examples of gene expression patterns for individual cell types are provided in Supplementary Table S4. Lesional T lymphocytes were quantified using scRNA-seq data and anti-CD3 immunofluorescence staining, which revealed three distinct immune states: hot (&gt;25 % T cells), intermediate (&gt;6-25 % T cells), and cold (0-6 % T cells) (Supplementary Table S5).</p><p>Based on a previous study examining melanoma cell differentiation statuses, the melanoma cell cluster was divided into 8 distinct subclusters (Supplementary Figure S3B, C) [<span>3</span>]. Unsupervised clustering further refined these findings, predicting 11 cellular subclusters of melanoma cells (Figure 1C, Supplementary Table S6) [<span>3</span>].</p><p>To investigate the molecular mechanisms underlying melanoma cell dedifferentiation, RNA velocity and latent time (LT) analyses were performed (Supplementary Material and Methods). These analyses measure developmental processes based on the gene expression patterns of spliced and unspliced genes [<span>4</span>], with LT more directly reflecting transcriptional dynamics. As shown in Figure 1C, RNA velocity arrows indicate a trajectory from the melanoma subcluster of undifferentiated, neural crest (nc)-like cells on the left toward the more differentiated Mel_trans-melan_c7 and Mel_trans-melan_c8 subclusters at the right edge. LT analysis (Figure 1C) and the latent time heatmap (Figure 1D) revealed an opposing trajectory toward a more dedifferentiated state, exemplified by the Mel_trans subcluster. Here, melanoma cell dedifferentiation was linked to gene sets enriched in antigen presentation and the induction of T cell receptor signaling (Figure 1D). This aligns with the known association between high immune cell infiltrates and dedifferentiated tumors. Notably, Serpin Family E Member 2 <i>(SERPINE2)</i> has been identified as a mediator of melanoma metastasis and tumor progression [<span>5</span>].</p><p>Next, we performed regulon analysis (https://github.com/aertslab/pySCENIC) of the melanoma cell clusters, which refers to a group of genes regulated by the same transcription factor [<span>6</span>]. We identified a number of regulons associated with nc-like and more dedifferentiated melanoma cells, such as Retinoid X Receptor Gamma (<i>RXRG</i>), SRY-Box Transcription Factor 2 (<i>SOX2</i>), CAMP Responsive Element Binding Protein 5 (<i>CREB5</i>), BTB Domain And CNC Homolog (<i>BACH1</i>), and Transcription Factor 12 (<i>TCF12</i>), as well as those associated with more differentiated melanocytic cells, such as Melanocyte Inducing Transcription Factor (<i>MITF</i>), SOX10, Paired Box 3 (<i>PAX3</i>), TEA Domain Transcription Factor 1 (<i>TEAD1</i>), and <i>SOX4</i> (Supplementary Figure S4). In line with this, it is known that BACH1 activates the expression of genes involved in cell motility and metastasis and plays an essential role in both innate and adaptive immune responses [<span>7</span>]. Taken together, melanoma cell dedifferentiation processes may be defined by an activated immune response and by specific transcriptional mechanisms.</p><p>Next, we focused on melanoma-immune cell interactions by analyzing ligand-receptor interactions with an emphasis on cytotoxic T cells, using the LIANA software (https://saezlab.github.io/liana/) (Figure 1E; Supplementary Tables S7 and S8). For a more focused analysis, we removed HLA and collagen genes from the subsequent analysis. As shown in Figure 1E, CD2 on cytotoxic T cells was a major interaction partner for several molecules in melanoma cells, especially CD58 and CD59. This interaction was most prominent in hot tumors. A recent study using a CRISPR/Cas knockout screen provided evidence that the CD58-CD2 interaction may indeed be a major mechanism of melanoma immune control [<span>8</span>]. Our data suggest that CD58 and CD59, both interacting with CD2, may control the T cell-melanoma cell interaction. In contrast, the most prominent interaction in cold tumors was between Fibronectin1 (FN1) and Integrin Subunit Beta 1 (ITGB1). Fibronectin-integrin β1 interaction is known to antagonize integrin β3 and thus might have an inactivating effect on integrin downstream signaling [<span>9</span>].</p><p>Immunofluorescence staining for CD58, CD59 and CD2 expression in melanoma/nevus samples (Supplementary Figure S5; Supplementary Table S9) showed higher numbers of CD2<sup>+</sup> immune cells in the vicinity of melanoma cells in hot/intermediate tumors compared to cold tumors/nevi. However, nevi do express both CD58 and CD2. Moreover, CD58 expression was higher in hot/intermediate samples and increased with increasing LT (Supplementary Figure S5).</p><p>Using data from The Cancer Genome Atlas (TCGA) melanoma cohort (https://www.genome.gov/Funded-Programs-Projects/Cancer-Genome-Atlas), we demonstrated that high CD58, together with high CD2 expression, significantly improved the prognosis of melanoma patients (Figure 1F, Supplementary Figure S6). Similarly, CD2 expression was associated with overall survival in a recently published melanoma immunotherapy study, making it a possible target for immunotherapy (Supplementary Figure S6).</p><p>Next, we used isolated tumor-infiltrating lymphocytes (TILs) enriched in tumor-reactive CD8<sup>+</sup> T cells from tumor tissue of a melanoma patient. As shown in Figure 1G and Supplementary Figure S7, T cell activation, as determined by intracellular Interferon γ (IFN-γ) expression, was reduced by blockade of CD58, but not of CD59, on autologous melanoma cells. Moreover, melanoma cell killing in the presence of T cells could be inhibited by the addition of the anti-CD58 antibody (Figure 1G).</p><p>Soluble recombinant extracellular domains of CD58, CD59 and CD2 were then used to measure the binding affinity of CD2 to CD58 and CD59, respectively (Figure 1H). These analyses showed high binding activity of CD2 to CD58, but none to CD59, which further supports an activating role of CD58-CD2, but not CD59-CD2. Overall, in addition to its known inactivating capacity on the membrane attack complex, CD59 appears to require a specific conformation to be active in the CD2 immune context, which may explain its inactivity in our settings.</p><p>Finally, scATAC-seq data of six MM and one Nev sample were analyzed in T cell populations (Figure 1I; Supplementary Tables S10 and S11). Among the top ten open chromatin regions in T cells from immune hot samples were <i>CD3D</i>, Interferon Gamma (<i>IFNG)</i>, <i>CD28</i>, <i>CD2</i>, <i>CD3G</i>, and Granzyme A (<i>GZMA</i>). In line with this, <i>CD2</i> expression was most prominent in the T cell and NK cell clusters of the scATAC-seq UMAP and scRNA-seq UMAP (Supplementary Figure S8). By analyzing chromatin accessible networks (CAN), an open chromatin region was observed immediately upstream of the <i>CD2</i> gene (Figure 1I), which harbored a binding motif for various transcription factors, including <i>CAMP</i> Responsive Element Binding Protein 1 (<i>CREB1</i>), Zinc Finger Protein 143 (<i>ZNF143</i>), MYB Proto-Oncogene Like 2 (<i>MYBL2</i>), Recombination Signal Binding Protein For Immunoglobulin Kappa J Region (<i>RBPJ</i>), Jun Proto-Oncogene, AP-1 Transcription Factor Subunit (<i>JUN</i>), JunB Proto-Oncogene (<i>JUNB</i>), and FOS Like 2, AP-1 Transcription Factor Subunit (<i>FOSL2</i>) (Figure 1J, Supplementary Figure S8, Supplementary Figure S9). RBPJ might play an important role in this setting since it has been associated with T cell immune response in hepatocellular carcinoma and may thus be a target in immunotherapy [<span>10</span>].</p><p>Taken together, a detailed map of melanoma single-cell differentiation steps in MM and Nev lesions is presented, supporting a developmental trajectory of different melanoma cellular subpopulations towards a high immune phenotype. The CD58-CD2 interaction appears to play a prominent role in the melanoma immune response, which may be exploited in future clinical trials.</p><p><b>Antonia Stubenvoll</b>: Conceptualization; data curation; formal analysis; investigation; methodology; visualization, and writing original draft. <b>Maria Schmidt</b>: Conceptualization; data curation; formal analysis; investigation; methodology; software, and writing original draft. <b>Johanna Moeller</b>: Investigation; formal analysis, and methodology. <b>Max Alexander Lingner Chango</b>: Data curation; formal analysis, and investigation. <b>Henry Loeffler-Wirth</b>: Investigation; methodology; data curation; formal analysis; validation, and visualization. <b>Stephan Bernhart</b>: Investigation; methodology; data curation; formal analysis; validation and visualization. <b>Florian Große</b>: Data curation; formal analysis; investigation; methodology; software and writing original draft. <b>Carolyn Schultz</b>: Data curation; investigation; validation, and visualization. <b>Olga Antoniadou</b>: Investigation; validation, and visualization. <b>Beatrice Thier</b>: Investigation; formal analysis; investigation, and methodology. <b>Annette Paschen</b>: Investigation; formal analysis; investigation; methodology, and supervision. <b>Ulf Anderegg</b>: Investigation; formal analysis; investigation; methodology, and supervision. <b>Jan C. Simon</b>: Resources; supervision; validation; writing; review, and editing. <b>Mirjana. Ziemer</b>: Resources; investigation; writing; review, and editing. <b>Clara T. Schoeder</b>: Data curation; conceptualization; investigation; validation; visualization, and supervision. <b>Hans Binder</b>: Data curation; formal analysis; software; writing; review, and editing. <b>Manfred Kunz</b>: Conceptualization; data curation; funding acquisition; investigation; project administration; resources; supervision; writing; review, and editing. All authors reviewed and approved the final version of the manuscript.</p><p>Manfred Kunz has received honoraria from the Speakers Bureau of Roche Pharma and travel support from Novartis Pharma GmbH and Bristol-Myers Squibb GmbH. Jan Christoph Simon has received speaker's fees from Bristol-Myers Squibb, Roche Pharma AG, Novartis and MSD Sharp &amp; Dohme as well as financial support for congress attendance from Bristol-Myers Squibb, MSD Sharp &amp; Dohme and Novartis. Mirjana Ziemer has received speaker's fees from Bristol-Myers Squibb, MSD Sharp &amp; Dohme GmbH, Pfizer Pharma GmbH and Sanofi-Aventis Deutschland GmbH and received financial support for congress participation from Bristol-Myers Squibb and serves as a member of expert panels on cutaneous adverse reactions for Pfizer INC. Clara Tabea Schoeder has received research support from Navigo Protein GmbH, Halle (Saale), Germany.</p><p>This work was supported by the Deutsche Forschungsgemeinschaft (DFG) (German Research Foundation; grant numbers: KU 1320/10-1 and HO 6586/1-1, and SFB1430, project 424228829) and the Sächsische Aufbaubank (grant number: 10071450).</p><p>Single-cell transcriptomic analyses were approved by the local Ethics committee of the Medical Faculty (AZ 023-16-01022016). 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摘要

免疫疗法是目前最有希望的恶性黑色素瘤治疗方案之一。为了发现未来治疗方法的新免疫靶点,对人类原发性黑色素瘤(MM)和黑素细胞痣(Nev)样本进行了单细胞转录组学和表观基因组学分析(图1A)。本研究的详细方法见补充资料。MM和Nev活检(补充图S1;通过单细胞RNA测序(scRNA-seq)和单细胞转座酶可及染色质测序(scATAC-seq)分析(补充图S2;补充表S2和S3)。使用统一流形近似和投影(UMAP),基于先前报告和人工整理的scRNA-seq数据,识别和注释了28个不同的细胞簇(图1B;补充图S3A) [2]个别细胞类型的基因表达模式示例见补充表S4。使用scRNA-seq数据和抗cd3免疫荧光染色对病变T淋巴细胞进行定量,结果显示三种不同的免疫状态:热(&gt; 25% T细胞)、中(&gt;6- 25% T细胞)和冷(0- 6% T细胞)(补充表S5)。根据先前对黑色素瘤细胞分化状态的研究,将黑色素瘤细胞簇分为8个不同的亚簇(Supplementary Figure S3B, C)[3]。无监督聚类进一步完善了这些发现,预测了黑色素瘤细胞的11个细胞亚簇(图1C,补充表S6)[3]。为了研究黑色素瘤细胞去分化的分子机制,进行了RNA速度和潜伏时间(LT)分析(补充材料和方法)。这些分析基于剪接和未剪接基因[4]的基因表达模式来衡量发育过程,而LT更直接地反映了转录动力学。如图1C所示,RNA速度箭头显示了从左侧未分化的神经嵴(nc)样细胞的黑色素瘤亚簇到右侧边缘分化程度更高的Mel_trans-melan_c7和Mel_trans-melan_c8亚簇的轨迹。LT分析(图1C)和潜在时间热图(图1D)显示了一个相反的轨迹,趋向于更加去分化的状态,Mel_trans亚簇就是一个例子。在这里,黑色素瘤细胞去分化与富含抗原呈递和诱导T细胞受体信号传导的基因集有关(图1D)。这与已知的高免疫细胞浸润与去分化肿瘤之间的关联一致。值得注意的是,Serpin家族E成员2 (SERPINE2)已被确定为黑色素瘤转移和肿瘤进展的中介。接下来,我们对黑色素瘤细胞簇进行了调控分析(https://github.com/aertslab/pySCENIC),这是指由相同转录因子[6]调控的一组基因。我们发现了许多与nc样和更多去分化黑色素瘤细胞相关的调控因子,如类维生素a X受体γ (RXRG)、SRY-Box转录因子2 (SOX2)、CAMP响应元件结合蛋白5 (CREB5)、BTB结构域和CNC同源物(BACH1)和转录因子12 (TCF12),以及与更多分化的黑素细胞相关的调控因子,如黑素细胞诱导转录因子(MITF)、SOX10、配对盒3 (PAX3)、TEA结构域转录因子1 (TEAD1)和SOX4(补充图S4)。与此相一致,我们知道BACH1激活参与细胞运动和转移的基因表达,在先天和适应性免疫反应[7]中都起着重要作用。综上所述,黑色素瘤细胞去分化过程可能由激活的免疫反应和特定的转录机制来定义。接下来,我们使用LIANA软件(https://saezlab.github.io/liana/),通过分析配体与受体的相互作用,重点分析细胞毒性T细胞,专注于黑色素瘤与免疫细胞的相互作用(图1E;补充表S7和S8)。为了进行更集中的分析,我们从随后的分析中删除了HLA和胶原蛋白基因。如图1E所示,细胞毒性T细胞上的CD2是黑色素瘤细胞中几种分子的主要相互作用伙伴,尤其是CD58和CD59。这种相互作用在高温肿瘤中最为突出。最近一项使用CRISPR/Cas敲除筛选的研究提供了证据,证明CD58-CD2相互作用可能确实是黑色素瘤免疫控制[8]的主要机制。我们的数据表明,CD58和CD59都与CD2相互作用,可能控制T细胞-黑色素瘤细胞相互作用。相比之下,冷肿瘤中最突出的相互作用是纤维连接蛋白1 (FN1)和整合素亚单位β 1 (ITGB1)之间的相互作用。已知纤维连接蛋白-整合素β1相互作用可拮抗整合素β3,因此可能对整合素下游信号通路[9]具有失活作用。 免疫荧光染色检测黑色素瘤/痣样本中CD58、CD59和CD2的表达(补充图S5;补充表S9)显示,与冷肿瘤/痣相比,热/中度肿瘤中黑色素瘤细胞附近的CD2+免疫细胞数量更高。然而,痣确实同时表达CD58和CD2。此外,CD58在热/中间样品中的表达更高,并随着LT的增加而增加(补充图S5)。利用癌症基因组图谱(TCGA)黑色素瘤队列(https://www.genome.gov/Funded-Programs-Projects/Cancer-Genome-Atlas)的数据,我们证明高CD58和高CD2表达可显著改善黑色素瘤患者的预后(图1F,补充图S6)。同样,在最近发表的一项黑色素瘤免疫治疗研究中,CD2表达与总生存率相关,使其成为免疫治疗的可能靶点(补充图S6)。接下来,我们使用从黑色素瘤患者的肿瘤组织中分离的肿瘤浸润淋巴细胞(til)富集肿瘤反应性CD8+ T细胞。如图1G和补充图S7所示,通过细胞内干扰素γ (IFN-γ)表达来确定的T细胞活化,通过阻断CD58而非CD59来降低自体黑色素瘤细胞的活化。此外,在T细胞存在下,黑色素瘤细胞的杀伤可以通过添加抗cd58抗体来抑制(图1G)。然后利用CD58、CD59和CD2的可溶性重组细胞外结构域分别测定CD2与CD58和CD59的结合亲和力(图1H)。这些分析显示CD2与CD58的结合活性高,而与CD59的结合活性低,这进一步支持了CD58-CD2的激活作用,而不是CD59-CD2。总的来说,除了已知的在膜攻击复合体上的失活能力外,CD59似乎需要一个特定的构象才能在CD2免疫环境中活跃,这可能解释了它在我们的环境中的失活。最后,在T细胞群中分析6个MM和1个Nev样本的scATAC-seq数据(图1I;补充表S10和S11)。免疫热样品中T细胞的十大开放染色质区域包括CD3D、干扰素γ (IFNG)、CD28、CD2、CD3G和颗粒酶A (GZMA)。与此相一致的是,CD2在scATAC-seq UMAP和scRNA-seq UMAP的T细胞和NK细胞簇中表达最为突出(Supplementary Figure S8)。通过分析染色质可及网络(CAN),我们发现CD2基因上游有一个开放的染色质区域(图1I),该区域含有多种转录因子的结合基元,包括CAMP响应元件结合蛋白1 (CREB1)、锌指蛋白143 (ZNF143)、MYB原癌基因样2 (MYBL2)、免疫球蛋白Kappa J区重组信号结合蛋白(RBPJ)、Jun原癌基因、AP-1转录因子亚基(Jun)、JunB原癌基因(JunB)和FOS Like 2, AP-1转录因子亚基(FOSL2)(图1J,补充图S8,补充图S9)。RBPJ可能在这种情况下发挥重要作用,因为它与肝细胞癌中的T细胞免疫反应有关,因此可能是免疫治疗的靶点。综上所述,本文提供了MM和Nev病变中黑色素瘤单细胞分化步骤的详细图谱,支持了不同黑色素瘤细胞亚群向高免疫表型的发展轨迹。CD58-CD2相互作用似乎在黑色素瘤免疫反应中发挥着重要作用,这可能在未来的临床试验中得到利用。Antonia Stubenvoll:概念化;数据管理;正式的分析;调查;方法;可视化,并撰写原稿。Maria Schmidt:概念化;数据管理;正式的分析;调查;方法;软件,并撰写原稿。约翰娜·莫勒:调查;形式分析和方法论。Max Alexander Lingner Chango:数据策展;正式的分析和调查。Henry Loeffler-Wirth:调查;方法;数据管理;正式的分析;验证和可视化。Stephan Bernhart:调查;方法;数据管理;正式的分析;验证和可视化。弗洛里安·格罗ße:数据管理;正式的分析;调查;方法;软件编写和撰写初稿。卡罗琳·舒尔茨:数据管理;调查;验证和可视化。Olga Antoniadou:调查;验证和可视化。Beatrice Thier:调查;正式的分析;调查和方法论。安妮特·帕申:调查;正式的分析;调查;方法和监督。Ulf Anderegg:调查;正式的分析;调查;方法和监督。Jan C. Simon:资源;监督;验证;写作;审阅和编辑。米里亚。除:资源;调查;写作;审阅和编辑。Clara T. Schoeder:数据管理;概念化;调查;验证;可视化和监督。 汉斯·宾德:数据管理;正式的分析;软件;写作;审阅和编辑。Manfred Kunz:概念化;数据管理;资金收购;调查;项目管理;资源;监督;写作;审阅和编辑。所有作者都审阅并批准了手稿的最终版本。Manfred Kunz曾获得Roche Pharma演讲局的荣誉,以及Novartis Pharma GmbH和Bristol-Myers Squibb GmbH的差旅支持。Jan Christoph Simon获得了百时美施贵宝、罗氏制药、诺华制药和默沙东夏普公司的演讲费。此外,百时美施贵宝(Bristol-Myers Squibb)、默沙东(MSD Sharp &amp;Dohme和诺华。Mirjana Ziemer获得了百时美施贵宝(Bristol-Myers Squibb)、默沙普(MSD Sharp &amp;Dohme GmbH, Pfizer Pharma GmbH和Sanofi-Aventis Deutschland GmbH,并获得Bristol-Myers Squibb的国会资助,并担任Pfizer INC.皮肤不良反应专家小组成员。Clara Tabea Schoeder获得了德国Halle (Saale) Navigo Protein GmbH的研究支持。这项工作得到了德国研究基金会(DFG)的支持;基金编号:KU 1320/10-1和HO 6586/1-1, SFB1430,项目编号:424228829)和Sächsische Aufbaubank(基金编号:10071450)。单细胞转录组分析经当地医学院伦理委员会批准(AZ 023-16-01022016)。经患者知情同意后进行活检。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Single-cell transcriptomics and epigenomics point to CD58-CD2 interaction in controlling primary melanoma growth and immunity

Single-cell transcriptomics and epigenomics point to CD58-CD2 interaction in controlling primary melanoma growth and immunity

Immunotherapy is currently one of the most promising treatment options for malignant melanoma [1]. To uncover new immunological targets for future treatment approaches, single-cell transcriptomic and epigenomic analyses were performed on human primary melanoma (MM) and melanocytic nevus (Nev) samples (Figure 1A). The detailed methods of this study are described in the Supplementary Material.

MM and Nev biopsies (Supplementary Figure S1; Supplementary Table S1) were analyzed by single-cell RNA sequencing (scRNA-seq) and single-cell Assay for Transposase-Accessible Chromatin sequencing (scATAC-seq) (Supplementary Figure S2; Supplementary Tables S2 and S3). Using Uniform Manifold Approximation and Projection (UMAP), 28 distinct cellular clusters were identified and annotated based on scRNA-seq data from a previous report and manual curation (Figure 1B; Supplementary Figure S3A) [2]. Examples of gene expression patterns for individual cell types are provided in Supplementary Table S4. Lesional T lymphocytes were quantified using scRNA-seq data and anti-CD3 immunofluorescence staining, which revealed three distinct immune states: hot (>25 % T cells), intermediate (>6-25 % T cells), and cold (0-6 % T cells) (Supplementary Table S5).

Based on a previous study examining melanoma cell differentiation statuses, the melanoma cell cluster was divided into 8 distinct subclusters (Supplementary Figure S3B, C) [3]. Unsupervised clustering further refined these findings, predicting 11 cellular subclusters of melanoma cells (Figure 1C, Supplementary Table S6) [3].

To investigate the molecular mechanisms underlying melanoma cell dedifferentiation, RNA velocity and latent time (LT) analyses were performed (Supplementary Material and Methods). These analyses measure developmental processes based on the gene expression patterns of spliced and unspliced genes [4], with LT more directly reflecting transcriptional dynamics. As shown in Figure 1C, RNA velocity arrows indicate a trajectory from the melanoma subcluster of undifferentiated, neural crest (nc)-like cells on the left toward the more differentiated Mel_trans-melan_c7 and Mel_trans-melan_c8 subclusters at the right edge. LT analysis (Figure 1C) and the latent time heatmap (Figure 1D) revealed an opposing trajectory toward a more dedifferentiated state, exemplified by the Mel_trans subcluster. Here, melanoma cell dedifferentiation was linked to gene sets enriched in antigen presentation and the induction of T cell receptor signaling (Figure 1D). This aligns with the known association between high immune cell infiltrates and dedifferentiated tumors. Notably, Serpin Family E Member 2 (SERPINE2) has been identified as a mediator of melanoma metastasis and tumor progression [5].

Next, we performed regulon analysis (https://github.com/aertslab/pySCENIC) of the melanoma cell clusters, which refers to a group of genes regulated by the same transcription factor [6]. We identified a number of regulons associated with nc-like and more dedifferentiated melanoma cells, such as Retinoid X Receptor Gamma (RXRG), SRY-Box Transcription Factor 2 (SOX2), CAMP Responsive Element Binding Protein 5 (CREB5), BTB Domain And CNC Homolog (BACH1), and Transcription Factor 12 (TCF12), as well as those associated with more differentiated melanocytic cells, such as Melanocyte Inducing Transcription Factor (MITF), SOX10, Paired Box 3 (PAX3), TEA Domain Transcription Factor 1 (TEAD1), and SOX4 (Supplementary Figure S4). In line with this, it is known that BACH1 activates the expression of genes involved in cell motility and metastasis and plays an essential role in both innate and adaptive immune responses [7]. Taken together, melanoma cell dedifferentiation processes may be defined by an activated immune response and by specific transcriptional mechanisms.

Next, we focused on melanoma-immune cell interactions by analyzing ligand-receptor interactions with an emphasis on cytotoxic T cells, using the LIANA software (https://saezlab.github.io/liana/) (Figure 1E; Supplementary Tables S7 and S8). For a more focused analysis, we removed HLA and collagen genes from the subsequent analysis. As shown in Figure 1E, CD2 on cytotoxic T cells was a major interaction partner for several molecules in melanoma cells, especially CD58 and CD59. This interaction was most prominent in hot tumors. A recent study using a CRISPR/Cas knockout screen provided evidence that the CD58-CD2 interaction may indeed be a major mechanism of melanoma immune control [8]. Our data suggest that CD58 and CD59, both interacting with CD2, may control the T cell-melanoma cell interaction. In contrast, the most prominent interaction in cold tumors was between Fibronectin1 (FN1) and Integrin Subunit Beta 1 (ITGB1). Fibronectin-integrin β1 interaction is known to antagonize integrin β3 and thus might have an inactivating effect on integrin downstream signaling [9].

Immunofluorescence staining for CD58, CD59 and CD2 expression in melanoma/nevus samples (Supplementary Figure S5; Supplementary Table S9) showed higher numbers of CD2+ immune cells in the vicinity of melanoma cells in hot/intermediate tumors compared to cold tumors/nevi. However, nevi do express both CD58 and CD2. Moreover, CD58 expression was higher in hot/intermediate samples and increased with increasing LT (Supplementary Figure S5).

Using data from The Cancer Genome Atlas (TCGA) melanoma cohort (https://www.genome.gov/Funded-Programs-Projects/Cancer-Genome-Atlas), we demonstrated that high CD58, together with high CD2 expression, significantly improved the prognosis of melanoma patients (Figure 1F, Supplementary Figure S6). Similarly, CD2 expression was associated with overall survival in a recently published melanoma immunotherapy study, making it a possible target for immunotherapy (Supplementary Figure S6).

Next, we used isolated tumor-infiltrating lymphocytes (TILs) enriched in tumor-reactive CD8+ T cells from tumor tissue of a melanoma patient. As shown in Figure 1G and Supplementary Figure S7, T cell activation, as determined by intracellular Interferon γ (IFN-γ) expression, was reduced by blockade of CD58, but not of CD59, on autologous melanoma cells. Moreover, melanoma cell killing in the presence of T cells could be inhibited by the addition of the anti-CD58 antibody (Figure 1G).

Soluble recombinant extracellular domains of CD58, CD59 and CD2 were then used to measure the binding affinity of CD2 to CD58 and CD59, respectively (Figure 1H). These analyses showed high binding activity of CD2 to CD58, but none to CD59, which further supports an activating role of CD58-CD2, but not CD59-CD2. Overall, in addition to its known inactivating capacity on the membrane attack complex, CD59 appears to require a specific conformation to be active in the CD2 immune context, which may explain its inactivity in our settings.

Finally, scATAC-seq data of six MM and one Nev sample were analyzed in T cell populations (Figure 1I; Supplementary Tables S10 and S11). Among the top ten open chromatin regions in T cells from immune hot samples were CD3D, Interferon Gamma (IFNG)CD28, CD2, CD3G, and Granzyme A (GZMA). In line with this, CD2 expression was most prominent in the T cell and NK cell clusters of the scATAC-seq UMAP and scRNA-seq UMAP (Supplementary Figure S8). By analyzing chromatin accessible networks (CAN), an open chromatin region was observed immediately upstream of the CD2 gene (Figure 1I), which harbored a binding motif for various transcription factors, including CAMP Responsive Element Binding Protein 1 (CREB1), Zinc Finger Protein 143 (ZNF143), MYB Proto-Oncogene Like 2 (MYBL2), Recombination Signal Binding Protein For Immunoglobulin Kappa J Region (RBPJ), Jun Proto-Oncogene, AP-1 Transcription Factor Subunit (JUN), JunB Proto-Oncogene (JUNB), and FOS Like 2, AP-1 Transcription Factor Subunit (FOSL2) (Figure 1J, Supplementary Figure S8, Supplementary Figure S9). RBPJ might play an important role in this setting since it has been associated with T cell immune response in hepatocellular carcinoma and may thus be a target in immunotherapy [10].

Taken together, a detailed map of melanoma single-cell differentiation steps in MM and Nev lesions is presented, supporting a developmental trajectory of different melanoma cellular subpopulations towards a high immune phenotype. The CD58-CD2 interaction appears to play a prominent role in the melanoma immune response, which may be exploited in future clinical trials.

Antonia Stubenvoll: Conceptualization; data curation; formal analysis; investigation; methodology; visualization, and writing original draft. Maria Schmidt: Conceptualization; data curation; formal analysis; investigation; methodology; software, and writing original draft. Johanna Moeller: Investigation; formal analysis, and methodology. Max Alexander Lingner Chango: Data curation; formal analysis, and investigation. Henry Loeffler-Wirth: Investigation; methodology; data curation; formal analysis; validation, and visualization. Stephan Bernhart: Investigation; methodology; data curation; formal analysis; validation and visualization. Florian Große: Data curation; formal analysis; investigation; methodology; software and writing original draft. Carolyn Schultz: Data curation; investigation; validation, and visualization. Olga Antoniadou: Investigation; validation, and visualization. Beatrice Thier: Investigation; formal analysis; investigation, and methodology. Annette Paschen: Investigation; formal analysis; investigation; methodology, and supervision. Ulf Anderegg: Investigation; formal analysis; investigation; methodology, and supervision. Jan C. Simon: Resources; supervision; validation; writing; review, and editing. Mirjana. Ziemer: Resources; investigation; writing; review, and editing. Clara T. Schoeder: Data curation; conceptualization; investigation; validation; visualization, and supervision. Hans Binder: Data curation; formal analysis; software; writing; review, and editing. Manfred Kunz: Conceptualization; data curation; funding acquisition; investigation; project administration; resources; supervision; writing; review, and editing. All authors reviewed and approved the final version of the manuscript.

Manfred Kunz has received honoraria from the Speakers Bureau of Roche Pharma and travel support from Novartis Pharma GmbH and Bristol-Myers Squibb GmbH. Jan Christoph Simon has received speaker's fees from Bristol-Myers Squibb, Roche Pharma AG, Novartis and MSD Sharp & Dohme as well as financial support for congress attendance from Bristol-Myers Squibb, MSD Sharp & Dohme and Novartis. Mirjana Ziemer has received speaker's fees from Bristol-Myers Squibb, MSD Sharp & Dohme GmbH, Pfizer Pharma GmbH and Sanofi-Aventis Deutschland GmbH and received financial support for congress participation from Bristol-Myers Squibb and serves as a member of expert panels on cutaneous adverse reactions for Pfizer INC. Clara Tabea Schoeder has received research support from Navigo Protein GmbH, Halle (Saale), Germany.

This work was supported by the Deutsche Forschungsgemeinschaft (DFG) (German Research Foundation; grant numbers: KU 1320/10-1 and HO 6586/1-1, and SFB1430, project 424228829) and the Sächsische Aufbaubank (grant number: 10071450).

Single-cell transcriptomic analyses were approved by the local Ethics committee of the Medical Faculty (AZ 023-16-01022016). Biopsies were taken after informed consent of the patients.

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来源期刊
Cancer Communications
Cancer Communications Biochemistry, Genetics and Molecular Biology-Cancer Research
CiteScore
25.50
自引率
4.30%
发文量
153
审稿时长
4 weeks
期刊介绍: Cancer Communications is an open access, peer-reviewed online journal that encompasses basic, clinical, and translational cancer research. The journal welcomes submissions concerning clinical trials, epidemiology, molecular and cellular biology, and genetics.
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