Metabolism of tumor cell in tumor micro environment assist immune escape.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e15181-e15181 ◽  
Author(s):  
Ning He ◽  
Jianfei Wang ◽  
Lingyu Wang ◽  
Ge Jin ◽  
Rongbo Lin ◽  
...  
Keyword(s):  
T Cells ◽  
Endothelial Cells ◽  
Tumor Cell ◽  
Single Cell ◽  
Immune Cells ◽  
Immune Cell ◽  
Immune Escape ◽  
Immune Surveillance ◽  
Glutathione Metabolism ◽  
Cancer Pathogenesis

e15181 Background: Tumor cell’s metabolism has been identified assisting immune evasion in tumor micro environment (TME), and it is very different from that of immune cells. Previous studies mostly focus on bulk or cell lines transcriptome; we aim to find the specific metabolic model of tumor cell based on vast single cell RNA-seq data. Methods: Public transcriptome of 7186 cells (SMART-Seq2) from 33 melanoma tumors in Benjamin’s study were collected from Single Cell Portal of Broad Institute, and metabolic genes were obtained from Human Metabolome Database (HMDB). Raw count data was preprocessed and analyzed using Seurat R package. Statistical analysis and data visualization were all carried out using R software. Results: Metabolic signature genes of malignant cells (Mals), CD8+ T cells, CD4+ T cells, B cells, natural killer (NK) cells, macrophages, cancer associated fibroblasts (CAFs), and endothelial cells (Endos) were extracted using Seurat. Mals, CAFs, Endos and macrophages shared similar metabolism patterns (high-level glycolysis, pyruvate metabolism, purine metabolism and specific proteoglycans profile compared to immune cells, p < 0.01). Glutathione metabolism activity in Mal was higher than that in immune cell, especially GPX1, GPX4 and GSTO1 genes were highly expressed in Mal ( fc > 2, p < 0.01). Compared to immune cells, genes participate in glycolysis, PFKL, ADH5, ENO2, G6PC3, PGM1, ALDH1B1, PFKM, ALDH7A1, GAPDHS, TPI1, PGK1, LDHA, GPI, PKM, LDHB, ENO1, ALDOA and GAPDH were highly expressed in Mals, CAFs and Endos ( fc > 2, p < 0.01). Noteworthily, LGALS1, an inducer of T-cell apoptosis, was highly expressed in Mals and CAF ( fc > 2, p < 0.01). Otherwise, proteoglycans (PGs) in cancer, which contribute to cancer pathogenesis, exhibited high variation from immune cells. Conclusions: We firstly highlight the differential metabolism between tumor and immune cells in TME. Mals, CAFs, endothelial cells and macrophages can assist in evading immune surveillance through reshaping their metabolic patterns at cell level. This study is helpful for exploring new target of metabolic based anti-cancer immunotherapy.

Single Cell Profiling Reveals Unique CXCL13 Positive T Cell Subsets in the Tumor Microenvironment of Lymphocyte Rich Classic Hodgkin Lymphoma

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 32-33
Author(s):  
Tomohiro Aoki ◽  
Lauren C. Chong ◽  
Katsuyoshi Takata ◽  
Katy Milne ◽  
Elizabeth Chavez ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
B Cells ◽  
Single Cell ◽  
Immune Cells ◽  
Research Funding ◽  
Immune Cell ◽  
Expression Patterns ◽  
The Other ◽  
Tfh Cells

Introduction: Classic Hodgkin lymphoma (CHL) features a unique crosstalk between malignant cells and different types of normal immune cells in the tumor-microenvironment (TME). On the basis of histomorphologic and immunophenotypic features of the malignant Hodgkin and Reed-Sternberg (HRS) cells and infiltrating immune cells, four histological subtypes of CHL are recognized: Nodular sclerosing (NS), Mixed cellularity, Lymphocyte-rich (LR) and Lymphocyte-depleted CHL. Recently, our group described the high abundance of various types of immunosuppressive CD4+ T cells including LAG3+ and/or CTLA4+ cells in the TME of CHL using single cell RNA sequencing (scRNAseq). However, the TME of LR-CHL has not been well characterized due to the rarity of the disease. In this study, we aimed at characterizing the immune cell profile of LR-CHL at single cell resolution. METHODS: We performed scRNAseq on cell suspensions collected from lymph nodes of 28 primary CHL patients, including 11 NS, 9 MC and 8 LR samples, with 5 reactive lymph nodes (RLN) serving as normal controls. We merged the expression data from all cells (CHL and RLN) and performed batch correction and normalization. We also performed single- and multi-color immunohistochemistry (IHC) on tissue microarray (TMA) slides from the same patients. In addition, an independent validation cohort of 31 pre-treatment LR-CHL samples assembled on a TMA, were also evaluated by IHC. Results: A total of 23 phenotypic cell clusters were identified using unsupervised clustering (PhenoGraph). We assigned each cluster to a cell type based on the expression of genes described in published transcriptome data of sorted immune cells and known canonical markers. While most immune cell phenotypes were present in all pathological subtypes, we observed a lower abundance of regulatory T cells (Tregs) in LR-CHL in comparison to the other CHL subtypes. Conversely, we found that B cells were enriched in LR-CHL when compared to the other subtypes and specifically, all four naïve B-cell clusters were quantitatively dominated by cells derived from the LR-CHL samples. T follicular helper (TFH) cells support antibody response and differentiation of B cells. Our data show the preferential enrichment of TFH in LR-CHL as compared to other CHL subtypes, but TFH cells were still less frequent compared to RLN. Of note, Chemokine C-X-C motif ligand 13 (CXCL13) was identified as the most up-regulated gene in LR compared to RLN. CXCL13, which is a ligand of C-X-C motif receptor 5 (CXCR5) is well known as a B-cell attractant via the CXCR5-CXCL13 axis. Analyzing co-expression patterns on the single cell level revealed that the majority of CXCL13+ T cells co-expressed PD-1 and ICOS, which is known as a universal TFH marker, but co-expression of CXCR5, another common TFH marker, was variable. Notably, classical TFH cells co-expressing CXCR5 and PD-1 were significantly enriched in RLN, whereas PD-1+ CXCL13+ CXCR5- CD4+ T cells were significantly enriched in LR-CHL. These co-expression patterns were validated using flow cytometry. Moreover, the expression of CXCR5 on naïve B cells in the TME was increased in LR-CHL compared to the other CHL subtypes We next sought to understand the spatial relationship between CXCL13+ T cells and malignant HRS cells. IHC of all cases revealed that CXCL13+ T cells were significantly enriched in the LR-CHL TME compared to other subtypes of CHL, and 46% of the LR-CHL cases showed CXCL13+ T cell rosettes closely surrounding HRS cells. Since PD-1+ T cell rosettes are known as a specific feature of LR-CHL, we confirmed co-expression of PD-1 in the rosetting cells by IHC in these cases. Conclusions: Our results reveal a unique TME composition in LR-CHL. LR-CHL seems to be distinctly characterized among the CHL subtypes by enrichment of CXCR5+ naïve B cells and CD4+ CXCL13+ PD-1+ T cells, indicating the importance of the CXCR5-CXCL13 axis in the pathogenesis of LR-CHL. Figure Disclosures Savage: BeiGene: Other: Steering Committee; Merck, BMS, Seattle Genetics, Gilead, AstraZeneca, AbbVie: Honoraria; Roche (institutional): Research Funding; Merck, BMS, Seattle Genetics, Gilead, AstraZeneca, AbbVie, Servier: Consultancy. Scott:Janssen: Consultancy, Research Funding; Celgene: Consultancy; NanoString: Patents & Royalties: Named inventor on a patent licensed to NanoString, Research Funding; NIH: Consultancy, Other: Co-inventor on a patent related to the MCL35 assay filed at the National Institutes of Health, United States of America.; Roche/Genentech: Research Funding; Abbvie: Consultancy; AstraZeneca: Consultancy. Steidl:AbbVie: Consultancy; Roche: Consultancy; Curis Inc: Consultancy; Juno Therapeutics: Consultancy; Bayer: Consultancy; Seattle Genetics: Consultancy; Bristol-Myers Squibb: Research Funding.

scholarly journals Global immune characterization of HBV/HCV-related hepatocellular carcinoma identifies macrophage and T-cell subsets associated with disease progression

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Guohe Song ◽  
Yang Shi ◽  
Meiying Zhang ◽  
Shyamal Goswami ◽  
Saifullah Afridi ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
T Cells ◽  
T Cell ◽  
Single Cell ◽  
Immune Cells ◽  
Immune Cell ◽  
T Cell Subsets ◽  
M2 Macrophage ◽  
Advanced Hcc ◽  
Immune Cell Subsets

AbstractDiverse immune cells in the tumor microenvironment form a complex ecosystem, but our knowledge of their heterogeneity and dynamics within hepatocellular carcinoma (HCC) still remains limited. To assess the plasticity and phenotypes of immune cells within HBV/HCV-related HCC microenvironment at single-cell level, we performed single-cell RNA sequencing on 41,698 immune cells from seven pairs of HBV/HCV-related HCC tumors and non-tumor liver tissues. We combined bio-informatic analyses, flow cytometry, and multiplex immunohistochemistry to assess the heterogeneity of different immune cell subsets in functional characteristics, transcriptional regulation, phenotypic switching, and interactions. We identified 29 immune cell subsets of myeloid cells, NK cells, and lymphocytes with unique transcriptomic profiles in HCC. A highly complex immunological network was shaped by diverse immune cell subsets that can transit among different states and mutually interact. Notably, we identified a subset of M2 macrophage with high expression of CCL18 and transcription factor CREM that was enriched in advanced HCC patients, and potentially participated in tumor progression. We also detected a new subset of activated CD8+ T cells highly expressing XCL1 that correlated with better patient survival rates. Meanwhile, distinct transcriptomic signatures, cytotoxic phenotypes, and evolution trajectory of effector CD8+ T cells from early-stage to advanced HCC were also identified. Our study provides insight into the immune microenvironment in HBV/HCV-related HCC and highlights novel macrophage and T-cell subsets that could be further exploited in future immunotherapy.

scholarly journals Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data with ImmClassifier

2020 ◽  
Author(s):  
Xuan Liu ◽  
Sara J.C. Gosline ◽  
Lance T. Pflieger ◽  
Pierre Wallet ◽  
Archana Iyer ◽  
...  
Keyword(s):  
T Cells ◽  
Single Cell ◽  
Immune Cells ◽  
Immune Cell ◽  
Cell Types ◽  
Effector Memory ◽  
Immune Cell Population ◽  
Fine Grained ◽  
Knowledge Based ◽  
Comparable Performance

AbstractSingle-cell RNA sequencing is an emerging strategy for characterizing the immune cell population in diverse environments including blood, tumor or healthy tissues. While this has traditionally been done with flow or mass cytometry targeting protein expression, scRNA-Seq has several established and potential advantages in that it can profile immune cells and non-immune cells (e.g. cancer cells) in the same sample, identify cell types that lack precise markers for flow cytometry, or identify a potentially larger number of immune cell types and activation states than is achievable in a single flow assay. However, scRNA-Seq is currently limited due to the need to identify the types of each immune cell from its transcriptional profile, which is not only time-consuming but also requires a significant knowledge of immunology. While recently developed algorithms accurately annotate coarse cell types (e.g. T cells vs macrophages), making fine distinctions has turned out to be a difficult challenge. To address this, we developed a machine learning classifier called ImmClassifier that leverages a hierarchical ontology of cell type. We demonstrate that ImmClassifier outperforms other tools (+20% recall, +14% precision) in distinguishing fine-grained cell types (e.g. CD8+ effector memory T cells) with comparable performance on coarse ones. Thus, ImmClassifier can be used to explore more deeply the heterogeneity of the immune system in scRNA-Seq experiments.

scholarly journals OTME-23. Single-cell transcriptomic and epigenomic immune landscape of isocitrate dehydrogenase stratified human gliomas

2021 ◽  
Vol 3 (Supplement_2) ◽  
pp. ii18-ii18
Author(s):  
Pravesh Gupta ◽  
Minghao Dang ◽  
Dapeng Hao ◽  
Krishna Bojja ◽  
Tuan M Tran ◽  
...  
Keyword(s):  
T Cells ◽  
Antigen Presentation ◽  
Single Cell ◽  
Immune Cells ◽  
Isocitrate Dehydrogenase ◽  
Zinc Finger Protein ◽  
Immune Cell ◽  
Hepatitis A Virus ◽  
Cancer Center ◽  
Human Gliomas

Abstract The brain tumor immune microenvironment (TIME) continuously evolves during glioma progression, but a comprehensive characterization of the glioma-centric immune cell repertoire beyond a priori cell states is uncharted. In this study, we performed single-cell RNA-sequencing (scRNA-seq) and single cell- Assay for Transposase-Accessible Chromatin using sequencing (sc-ATAC-seq) on ~100,000 tumor-associated immune cells from seventeen isocitrate dehydrogenase (IDH) mutation classified primary and recurrent human gliomas and non-glioma brains (NGBs). Our analyses revealed sixty-two transcriptionally distinct myeloid and lymphoid cell states within and across glioma subtypes and we noted microglial attrition with increasing disease severity concomitant with invading monocyte-derived cells and lymphocytes. Specifically, certain microglial and monocyte-derived subpopulations were associated with antigen presentation gene modules, akin to cross-presenting dendritic cells (DCs). We identified cytotoxic T cells with poly-functional cytolytic states mostly in recurrent IDH-wt gliomas. Furthermore, ligand-receptor interactome analyses showed a preponderance of antigen presentation and phagocytosis over the checkpoint axis in IDH-wt compared to IDH-mut gliomas. Additionally, our sc-ATAC-seq analyses revealed differences in regulatory networks in NGBs, IDH-mut and IDH-wt glioma associated immune cells. In particular, we noted abundant usage of inflammatory transcription factors (TFs) as exemplified by Nuclear factor kappa B and Activator Protein-1 TF family in IDH-wt microglia when compared with microglia from IDH-mut and NGBs. Unique features such as amplification of 11- Zinc Finger Protein accessibility were restricted to monocyte derived cells and were not observed in microglia. Finally, sc-ATAC-seq profiles of CD8+ exhausted T cells from IDH-wt showed strong enhancer accessibility on Cytotoxic T-lymphocyte-associated protein 4, Layilin and Hepatitis A Virus Cellular Receptor 2 but no enrichment on PDCD1 (gene encoding Programmed cell death protein 1) was seen. In summary, our study provides unprecedented granular detail of transcriptionally defined glioma- specific immune contexture that can be exploited for immunotherapy applications. This study in K.B. laboratory was supported by the generous philanthropic contributions to The University of Texas (UT) MD Anderson Cancer Center (MDACC) Moon Shots Program™, Marnie Rose Foundation, NIH grants: R21 CA222992 and R01CA225963. This study was partly supported by the UT MDACC start-up research fund to L.W. and CPRIT Single Core grant RP180684 to N. E. N.

IMMU-43. IMMUNE CONTEXTURE OF ISOCITRATE DEHYDROGENASE STRATIFIED HUMAN GLIOMAS REVEALED BY SINGLE-CELL TRANSCRIPTOMICS AND ACCESSIBLE CHROMATIN

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi102-vi102
Author(s):  
Pravesh Gupta ◽  
Minghao Dang ◽  
Dapeng Hao Hao ◽  
Krishna Bojja ◽  
Tuan M Tran ◽  
...  
Keyword(s):  
T Cells ◽  
Antigen Presentation ◽  
Single Cell ◽  
Immune Cells ◽  
Isocitrate Dehydrogenase ◽  
Zinc Finger Protein ◽  
Immune Cell ◽  
Human Gliomas ◽  
Immune Contexture ◽  
Accessible Chromatin

Abstract The immune cell composition of isocitrate dehydrogenase wild type (IDH-wt) glioma patients significantly differs compared to IDH-mutant (IDH-mut) yet a detailed and unbiased understanding of their transcriptomic and epigenetic landscapes remains elusive. To this end, we performed single-cell RNA-sequencing (scRNA-seq) and single-cell Assay for Transposase-Accessible Chromatin using sequencing (sc-ATAC-seq) on ~100,000 tumor-associated immune cells from seventeen IDH mutation classified primary and recurrent human gliomas and non-glioma brains (NGBs). Our analyses revealed sixty-two transcriptionally distinct myeloid and lymphoid cell states within and across glioma subtypes and we noted microglial attrition with increasing disease severity concomitant with invading monocyte-derived cells (MDCs) and lymphocytes. Specifically, certain microglial and monocyte-derived subpopulations were associated with antigen presentation gene modules, akin to cross-presenting dendritic cells. As tissue macrophages exhibit multifaceted polarization in response to microenvironmental cues, we clarify the existence of microglia/macrophage functional states beyond M1/M2 paradigms exemplified by the presence of palmitic-, oleic- acid, and glucocorticoid responsive polarized states. We identified cytotoxic T cells with poly-functional cytolytic states mostly in recurrent IDH-wt gliomas. Furthermore, ligand-receptor interactome analyses showed a preponderance of antigen presentation/phagocytosis over the checkpoint axis in IDH-wt compared to IDH-mut gliomas. Additionally, our sc-ATAC-seq analyses revealed differences in regulatory networks in NGBs, IDH-mut, and IDH-wt glioma-associated immune cells. In particular, we noted reduced microglial usage of an iron recycling SPIC transcription factor and Interferon Regulatory Factors (IRFs); IRF1 and IRF2 in IDH-wt relative to IDH-mut and NGBs. Unique features such as amplification of 11-Zinc Finger Protein accessibility were restricted to MDCs. Finally, sc-ATAC-seq profiles of CD8+ exhausted T cells from IDH-wt showed strong enhancer accessibility on CTLA-4, Layilin, and TIM-3 but no enrichment on PD1 was seen. In summary, our study provides unprecedented granular detail of transcriptionally and epigenomically defined glioma-specific immune contexture that can be exploited for immunotherapy applications.

scholarly journals Single-Cell RNA Sequencing of Peripheral Blood Reveals Immune Cell Signatures in Alzheimer’s Disease

2021 ◽  
Vol 12 ◽  
Author(s):  
Hui Xu ◽  
Jianping Jia
Keyword(s):  
Immune Response ◽  
T Cells ◽  
Single Cell ◽  
Immune Cells ◽  
Peripheral Blood ◽  
Immune Cell ◽  
Adaptive Immune Response ◽  
Immune Repertoire ◽  
Adaptive Immune ◽  
Peripheral Immune Cells

The peripheral immune system is thought to affect the pathology of the central nervous system in Alzheimer’s disease (AD). However, current knowledge is inadequate for understanding the characteristics of peripheral immune cells in AD. This study aimed to explore the molecular basis of peripheral immune cells and the features of adaptive immune repertoire at a single cell level. We profiled 36,849 peripheral blood mononuclear cells from AD patients with amyloid-positive status and normal controls with amyloid-negative status by 5’ single-cell transcriptome and immune repertoire sequencing using the cell ranger standard analysis procedure. We revealed five immune cell subsets: CD4+ T cells, CD8+ T cells, B cells, natural killer cells, and monocytes–macrophages cells, and disentangled the characteristic alterations of cell subset proportion and gene expression patterns in AD. Thirty-one cell type-specific key genes, comprising abundant human leukocyte antigen genes, and multiple immune-related pathways were identified by protein–protein interaction network and pathway enrichment analysis. We also found high-frequency amplification clonotypes in T and B cells and decreased diversity in T cells in AD. As clone amplification suggested the activation of an adaptive immune response against specific antigens, we speculated that the peripheral adaptive immune response, especially mediated by T cells, may have a role in the pathogenesis of AD. This finding may also contribute to further research regarding disease mechanism and the development of immune-related biomarkers or therapy.

scholarly journals Single-cell characterization of subsolid and solid lesions in the lung adenocarcinoma spectrum

2020 ◽  
Author(s):  
J. Yanagawa ◽  
L.M. Tran ◽  
E. Fung ◽  
W.D. Wallace ◽  
A.E. Prosper ◽  
...  
Keyword(s):  
T Cells ◽  
Lung Adenocarcinoma ◽  
Single Cell ◽  
Natural Killer ◽  
Immune Cells ◽  
Immune Surveillance ◽  
Pulmonary Nodules ◽  
Alveolar Type ◽  
Solid Lesions

SummaryDetermining the clinical significance of CT scan-detected subsolid pulmonary nodules requires an understanding of the molecular and cellular features that may foreshadow disease progression. We studied the alterations at the transcriptome level in both immune and non-immune cells, utilizing single-cell RNA sequencing, to compare the microenvironment of subsolid, solid, and non-involved lung tissues from surgical resection specimens. This evaluation of early spectrum lung adenocarcinoma reveals a significant decrease in the cytolytic activities of natural killer and natural killer T cells, accompanied by a reduction of effector T cells as well as an increase of CD4+ regulatory T cells in subsolid lesions. Characterization of non-immune cells revealed that both cancer-associated alveolar type 2 cells and fibroblasts contribute to the deregulation of the extracellular matrix, potentially affecting immune infiltration in subsolid lesions through ligand-receptor interactions. These findings suggest a decrement of immune surveillance in subsolid lesions.

scholarly journals Single-cell Map of Diverse Immune Phenotypes Driven by the Tumor Microenvironment

2017 ◽  
Author(s):  
Elham Azizi ◽  
Ambrose J. Carr ◽  
George Plitas ◽  
Andrew E. Cornish ◽  
Catherine Konopacki ◽  
...  
Keyword(s):  
T Cells ◽  
Tumor Microenvironment ◽  
Single Cell ◽  
Cancer Progression ◽  
Immune Cells ◽  
Immune Cell ◽  
Phenotypic Diversity ◽  
Macrophage Polarization ◽  
Sequencing Data ◽  
Significant Similarity

SUMMARYKnowledge of immune cell phenotypes in the tumor microenvironment is essential for understanding mechanisms of cancer progression and immunotherapy response. We created an immune map of breast cancer using single-cell RNA-seq data from 45,000 immune cells from eight breast carcinomas, as well as matched normal breast tissue, blood, and lymph node. We developed a preprocessing pipeline, SEQC, and a Bayesian clustering and normalization method, Biscuit, to address computational challenges inherent to single-cell data. Despite significant similarity between normal and tumor tissue-resident immune cells, we observed continuous tumor-specific phenotypic expansions driven by environmental cues. Analysis of paired single-cell RNA and T cell receptor (TCR) sequencing data from 27,000 additional T cells revealed the combinatorial impact of TCR utilization on phenotypic diversity. Our results support a model of continuous activation in T cells and do not comport with the macrophage polarization model in cancer, with important implications for characterizing tumor-infiltrating immune cells.

scholarly journals Multiparameter Single Cell Analysis to Identify Immune Cell States That May Contribute to Successful Treatment Discontinuation in Patients with Chronic Myeloid Leukemia

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 2999-2999
Author(s):  
Kibeom Jang ◽  
Neil P. Shah
Keyword(s):  
T Cells ◽  
Single Cell ◽  
Cd4 T Cells ◽  
Immune Cell ◽  
Immune Surveillance ◽  
Treatment Discontinuation ◽  
Group 3 ◽  
Memory Cd4 T Cells ◽  
Tki Discontinuation ◽  
Group 1

Abstract Background: Recently, numerous clinical trials have demonstrated that approximately half of CML patients who have achieved deep and durable remissions on TKI therapy can enjoy prolonged treatment-free remissions. A major question in the field concerns why treatment interruption is not universally successful. Two non-mutually exclusive theories have been proposed to explain successful discontinuation: CML stem cell exhaustion, and immune surveillance. Identification of mediators of CML stem cell exhaustion or successful immune surveillance could lead to adjunctive therapeutic approaches. We set out to determine potential immune mediators of disease control through interrogation of clinical samples using emerging technologies. Results: Consenting patients who discontinued TKI at our institution were grouped into three categories based upon BCR-ABL1 transcript kinetics following treatment discontinuation. Group 1 is characterized by stable undetectable or minimally detectable BCR-ABL1 transcripts. Group 2 exhibited molecular relapse, defined as loss of major molecular response (MMR) requiring treatment re-initiation, typically within the first 3-9 months of treatment discontinuation. Group 3 displays kinetics that are particularly intriguing, whereby the transcript level rises substantially upon treatment cessation, but remains below the MMR threshold despite remaining off TKI therapy. We hypothesize that disease control in group 3, and a subset of patients in Group 1, is mediated by the immune system. To investigate the immune system difference between these groups, we performed single cell immune profiling in the pre- (~ 1 week) and post- (~ 3 months) discontinuation PBMC samples obtained from 15 patients through CyTOF and 10x single cell RNA sequencing. Group 1 consist of 5 patients, group 2 consist of 8 patients, and group 3 consist of 2 patients, respectively. There were no meaningful differences in the immune cell composition prior to TKI discontinuation. Assessment of the immune phenotype 3 months after discontinuation in each group by CyTOF revealed an increase in the CD4+ T cell population in group 3 following TKI discontinuation. Specifically, memory CD4+ T cells and CD38+/HLA-DR+ activated CD4+ T cells were increased in group 3. While patients in groups 1 and 2 showed only decrease or moderate change in memory CD4+ T cells and activated CD4+ T cells, group 3 showed 53% increase of memory CD4+ T cells (21% to 32%) and 640% increase of activated CD4+ T cells (0.4% to 3.3%) following TKI discontinuation. While CD45RA-/CD4+ T cells were increased in abundance, the CD45RA- population was unchanged in CD8+ T cells. 10x single cell RNA sequencing of these samples is ongoing and will be presented. Conclusions: We have conducted multiparameter single cell immune profiling in CML patients with sustained deep molecular remission, loss of MMR, or maintenance of MMR despite a sustained rise in BCR-ABL1 transcript level. Our results suggest that an increase in memory and activated CD4+ T cells following TKI discontinuation may correlate with successful immune surveillance of CML. Assessment of a larger cohort of samples is required to confirm our findings. Disclosures Shah: ARIAD: Research Funding; Bristol-Myers Squibb: Research Funding.

scholarly journals The ratio of exhausted to resident infiltrating lymphocytes is prognostic for colorectal cancer patient outcome

2020 ◽  
Author(s):  
Momeneh Foroutan ◽  
Ramyar Molania ◽  
Aline Pfefferle ◽  
Corina Behrenbruch ◽  
Axel Kallies ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
T Cells ◽  
Nk Cells ◽  
Single Cell ◽  
Immune Cells ◽  
Immune Cell ◽  
Colorectal Cancer Patient ◽  
Colon Adenocarcinoma ◽  
Rna Seq ◽  
Infiltrating Lymphocytes

AbstractImmunotherapy success in colorectal cancer (CRC) is mainly limited to patients whose tumours exhibit high microsatellite instability (MSI). However, there is variability in treatment outcomes within this group, which is in part driven by the frequency and characteristics of tumour infiltrating immune cells. Indeed, the presence of specific infiltrating immune cell subsets has been shown to correlate with immunotherapy responses and is in many cases prognostic of treatment outcome. Tumour-infiltrating lymphocytes (TILs) can undergo distinct differentiation programs such as acquire features of tissue-residency or exhaustion, a process during which T cells upregulate inhibitory receptors such as PD-1 and loose functionality. While residency and exhaustion programs of CD8 T cells are relatively well-studied, these programs have only recently been appreciated in CD4 T cells and remain largely unknown in tumour-infiltrating natural killer (NK) cells. In this study, we use single cell RNA-seq data to identify signatures of residency and exhaustion in CRC infiltrating lymphocytes, including CD8, CD4 and NK cells. We then test these signatures in independent single cell data from tumour and normal tissue infiltrating immune cells. Further, we use versions of these signatures adapted for bulk RNA-seq data to identify a list of tumour intrinsic mutations associated with residency and exhaustion from TCGA data. Finally, using two independent transcriptomic data sets from patients with colon adenocarcinoma, we show that combinations of these signatures, in particular NK signatures, as well as tumour-associated signatures, such as TGF-β signalling, are associated with distinct survival outcomes in colorectal cancer patients.

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