Pan-cancer analysis identified inflamed microenvironment associated multi-omics signatures

AbstractBackgroundImmunotherapy has revolutionized cancer therapy. However, responses are not universal. The inflamed tumor microenvironment has been reported to correlate with response in tumor patients. However, how different tumors shape their tumor microenvironment remains a critical unsolved problem. A deeper insight into the molecular characteristics of inflamed tumor microenvironment may be needed.Materials and methodsHere, based on single-cell RNA sequencing technology and TCGA pan-cancer cohort, we investigated multi-omics molecular features of tumor microenvironment phenotypes. Based on single-cell RNA-seq analysis, we classified pan-cancer tumor samples into inflamed or non-inflamed tumor and identified molecular features of these tumors. Analysis of integrating identified gene signatures with a drug-genomic perturbation database identified multiple drugs which may be helpful for converting non-inflamed tumors to inflamed tumors.ResultsOur results revealed several inflamed/non-inflamed tumor microenvironments-specific molecular characteristics. For example, inflamed tumors highly expressed miR-650 and lncRNA including MIR155HG and LINC00426, these tumors showed activated cytokines-related signaling pathways. Interestingly, non-inflamed tumors tended to express several genes related to neurogenesis. Multi-omics analysis demonstrated the neuro phenotype transformation may be induced by hypomethylated promoters of these genes and down-regulated miR-650. Drug discovery analysis revealed histone deacetylase inhibitors may be a potential choice for helping favorable tumor microenvironment phenotype transformation and aiding current immunotherapy.ConclusionOur results provide a comprehensive molecular-level understanding of tumor cell-immune cell interaction and may have profound clinical implications.

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IMMU-02. GENOMIC AND TRANSCRIPTOMIC CORRELATES OF IMMUNOTHERAPY RESPONSE WITHIN THE TUMOR MICROENVIRONMENT OF LEPTOMENINGEAL METASTASES

Neuro-Oncology ◽

10.1093/neuonc/noab196.362 ◽

2021 ◽

Vol 23 (Supplement_6) ◽

pp. vi92-vi92

Author(s):

Christopher Alvarez-Breckenridge ◽

Sanjay Prakadan ◽

Samuel Markson ◽

Albert Kim ◽

Naema Nayyar ◽

...

Keyword(s):

Tumor Microenvironment ◽

Single Cell ◽

T Cell Activation ◽

Antigen Processing ◽

Cell Activation ◽

Immune Cell ◽

Checkpoint Inhibitors ◽

Leptomeningeal Disease ◽

Ifn Gamma ◽

Molecular Features

Abstract Leptomeningeal disease (LMD) is a devastating complication of solid tumor malignancies, with dire prognosis and no effective systemic treatment options. Over the past decade, the incidence of LMD has steadily increased due to therapeutics that have extended the survival of cancer patients, highlighting the need for new interventions. To examine the efficacy of immune checkpoint inhibitors (ICI) in patients with LMD, we completed two phase II clinical trials utilizing either Pembrolizumab alone or the combination of Ipilimumab and Nivolumab. We investigated the cellular and molecular features underpinning observed patient trajectories in these trials by applying single-cell RNA and cell-free DNA profiling to longitudinal cerebrospinal fluid (CSF) draws from enrolled patients. We isolated and sequenced 34,742 cells from both the malignant and immune compartment within CSF. Amongst the 19 patients included in the cohort, there were 13 pre-treatment and 24 post-treatment samples, and 9 patients were sampled across multiple timepoints. We detected dynamic changes in immune cell recruitment into the CSF and activation within 30 days of ICI, including increased effector T cell activation and IFN-gamma response pathways within T cells. Moreover, the overall level of IFN-gamma response and antigen processing within 30 days of ICI in malignant cells correlated with survival past clinical trial primary endpoint. Lastly, we observed evidence of longitudinal outgrowth of distinct immunogenic clones over the course of ICI. Overall, our study describes the liquid LMD tumor microenvironment prior to and following ICI treatment and provides unique insights into the compartmental and temporal variation during the course of ICI. Moreover, our findings demonstrate the clinical utility of cell- free and single-cell genomic measurements for LMD research.

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Pan-cancer analysis reveals tumor-associated macrophage communication in the tumor microenvironment

Experimental Hematology and Oncology ◽

10.1186/s40164-021-00226-1 ◽

2021 ◽

Vol 10 (1) ◽

Author(s):

Linbang Wang ◽

Tao He ◽

Jingkun Liu ◽

Jiaojiao Tai ◽

Bing Wang ◽

...

Keyword(s):

Tumor Microenvironment ◽

Tumor Cell ◽

Hub Genes ◽

Tumor Associated Macrophage ◽

Molecular Features ◽

Receptor Interactions ◽

Tumor Types ◽

Pan Cancer

Abstract Background Tumor-associated macrophages (TAMs) are abundant in the tumor microenvironment (TME). However, their contribution to the immunosuppressive status of the TME remains unclear. Methods We integrated single-cell sequencing and transcriptome data from different tumor types to uncover the molecular features of TAMs. In vitro experiments and prospective clinical tests confirmed the results of these analysis. Results We first detected intra- and inter-tumoral heterogeneities between TAM subpopulations and their functions, with CD86+ TAMs playing a crucial role in tumor progression. Next, we focused on the ligand-receptor interactions between TAMs and tumor cells in different TME phenotypes and discovered that aberrant expressions of six hub genes, including FLI1, are involved in this process. A TAM-tumor cell co-culture experiment proved that FLI1 was involved in tumor cell invasion, and FLI1 also showed a unique pattern in patients. Finally, TAMs were discovered to communicate with immune and stromal cells. Conclusion We determined the role of TAMs in the TME by focusing on their communication pattern with other TME components. Additionally, the screening of hub genes revealed potential therapeutic targets.

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Single-cell RNA Sequencing Reveals Immunosuppressive Myeloid Cell Diversity and Restricted Cytotoxic Effector Cell Trafficking and Activation During Malignant Progression in Glioma

10.1101/2021.09.24.461735 ◽

2021 ◽

Author(s):

Sakthi Rajendran ◽

Clayton Peterson ◽

Alessandro Canella ◽

Yang Hu ◽

Amy Gross ◽

...

Keyword(s):

T Cells ◽

Tumor Microenvironment ◽

Single Cell ◽

Immune Cell ◽

Myeloid Cell ◽

Malignant Progression ◽

Low Grade ◽

Cell Trafficking ◽

High Grade ◽

Single Cell Rna Sequencing

Low grade gliomas (LGG) account for about two-thirds of all glioma diagnoses in adolescents and young adults (AYA) and malignant progression of these patients leads to dismal outcomes. Recent studies have shown the importance of the dynamic tumor microenvironment in high-grade gliomas (HGG), yet its role is still poorly understood in low-grade glioma malignant progression. Here, we investigated the heterogeneity of the immune microenvironment using a platelet-derived growth factor (PDGF)-driven RCAS (replication-competent ASLV long terminal repeat with a splice acceptor) glioma model that recapitulates the malignant progression of low to high-grade glioma in humans and also provides a model system to characterize immune cell trafficking and evolution. To illuminate changes in the immune cell landscape during tumor progression, we performed single-cell RNA sequencing on immune cells isolated from animals bearing no tumor (NT), LGG and HGG, with a particular focus on the myeloid cell compartment, which is known to mediate glioma immunosuppression. LGGs demonstrated significantly increased infiltrating T cells, CD4 T cells, CD8 T cells, B cells, and natural killer cells in the tumor microenvironment, whereas HGGs significantly abrogated this infiltration. Our study identified two distinct macrophage clusters in the tumor microenvironment; one cluster appeared to be bone marrow-derived while another was defined by overexpression of Trem2, a marker of tumor associated macrophages. Our data demonstrates that these two distinct macrophage clusters show an immune-activated phenotype (Stat1, Tnf, Cxcl9 and Cxcl10) in LGG which evolves to an immunosuppressive state (Lgals3, Apoc1 and Id2) in HGG that restricts T cell recruitment and activation. We identified CD74 and macrophage migration inhibition factor (MIF) as potential targets for these distinct macrophage populations. Interestingly, these results were mirrored by our analysis of the TCGA dataset, which demonstrated a statistically significant association between CD74 overexpression and decreased overall survival in AYA patients with grade II gliomas. Targeting immunosuppressive myeloid cells and intra-tumoral macrophages within this therapeutic window may ameliorate mechanisms associated with immunosuppression before and during malignant progression.

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Patient-derived micro-organospheres recapitulate tumor microenvironment and heterogeneity for precision oncology.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.3076 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. 3076-3076

Author(s):

Shengli Ding ◽

Zhaohui Wang ◽

Marcos Negrete Obando ◽

Grecia rivera Palomino ◽

Tomer Rotstein ◽

...

Keyword(s):

Drug Discovery ◽

Tumor Microenvironment ◽

Single Cell ◽

Stromal Cells ◽

Mononuclear Cells ◽

Immune Cell ◽

Tumor Biology ◽

Cell Types ◽

Precision Oncology ◽

Original Tumor

3076 Background: Preclinical models that can recapitulate patients’ intra-tumoral heterogeneity and microenvironment are crucial for tumor biology research and drug discovery. In particular, the ability to retain immune and other stromal cells in the microenvironment is vital for the development of immuno-oncology assays. However, current patient-derived organoid (PDO) models are largely devoid of immune components. Methods: We first developed an automated microfluidic and membrane platform that can generate tens of thousands of micro-organospheres from resected or biopsied clinical tumor specimens within an hour. We next characterized growth rate and drug response of micro-organospheres. Finally, extensive single-cell RNA-seq profiling were performed on both micro-organospheres and original tumor samples from lung, ovarian, kidney, and breast cancer patients. Results: Micro-organospheres derived from clinical tumor samples preserved all original tumor and stromal cells, including fibroblasts and all immune cell types. Single-cell analysis revealed that unsupervised clustering of tumor and non-tumor cells were identical between original tumors and the derived micro-organospheres. Quantification showed similar cell composition and percentages for all cell types and also preserved functional intra-tumoral heterogeneity.. An automated, end-to-end, high-throughput drug screening pipeline demonstrated that matched peripheral blood mononuclear cells (PBMCs) from the same patient added to micro-organospheres can be used to assess the efficacy of immunotherapy moieties. Conclusions: Micro-organospheres are a rapid and scalable platform to preserve patient tumor microenvironment and heterogeneity. This platform will be useful for precision oncology, drug discovery, and immunotherapy development. Funding sources: NIH U01 CA217514, U01 CA214300, Duke Woo Center for Big Data and Precision Health

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Applications of Single-Cell Omics to Dissect Tumor Microenvironment

Frontiers in Genetics ◽

10.3389/fgene.2020.548719 ◽

2020 ◽

Vol 11 ◽

Author(s):

Tingting Guo ◽

Weimin Li ◽

Xuyu Cai

Keyword(s):

Tumor Microenvironment ◽

Single Cell ◽

Immune Cells ◽

Immune Cell ◽

Cell Types ◽

Immune Checkpoint Blockade ◽

Lineage Tracing ◽

Great Success ◽

Novel Technologies ◽

Single Cell Sequencing

The recent technical and computational advances in single-cell sequencing technologies have significantly broaden our toolkit to study tumor microenvironment (TME) directly from human specimens. The TME is the complex and dynamic ecosystem composed of multiple cell types, including tumor cells, immune cells, stromal cells, endothelial cells, and other non-cellular components such as the extracellular matrix and secreted signaling molecules. The great success on immune checkpoint blockade therapy has highlighted the importance of TME on anti-tumor immunity and has made it a prime target for further immunotherapy strategies. Applications of single-cell transcriptomics on studying TME has yielded unprecedented resolution of the cellular and molecular complexity of the TME, accelerating our understanding of the heterogeneity, plasticity, and complex cross-interaction between different cell types within the TME. In this review, we discuss the recent advances by single-cell sequencing on understanding the diversity of TME and its functional impact on tumor progression and immunotherapy response driven by single-cell sequencing. We primarily focus on the major immune cell types infiltrated in the human TME, including T cells, dendritic cells, and macrophages. We further discuss the limitations of the existing methodologies and the prospects on future studies utilizing single-cell multi-omics technologies. Since immune cells undergo continuous activation and differentiation within the TME in response to various environmental cues, we highlight the importance of integrating multimodal datasets to enable retrospective lineage tracing and epigenetic profiling of the tumor infiltrating immune cells. These novel technologies enable better characterization of the developmental lineages and differentiation states that are critical for the understanding of the underlying mechanisms driving the functional diversity of immune cells within the TME. We envision that with the continued accumulation of single-cell omics datasets, single-cell sequencing will become an indispensable aspect of the immune-oncology experimental toolkit. It will continue to drive the scientific innovations in precision immunotherapy and will be ultimately adopted by routine clinical practice in the foreseeable future.

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A pan-cancer blueprint of the heterogeneous tumor microenvironment revealed by single-cell profiling

Cell Research ◽

10.1038/s41422-020-0355-0 ◽

2020 ◽

Vol 30 (9) ◽

pp. 745-762 ◽

Cited By ~ 9

Author(s):

Junbin Qian ◽

Siel Olbrecht ◽

Bram Boeckx ◽

Hanne Vos ◽

Damya Laoui ◽

...

Keyword(s):

Tumor Microenvironment ◽

Single Cell ◽

Single Cell Profiling ◽

Pan Cancer ◽

Heterogeneous Tumor

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SCISSOR™: a single-cell inferred site-specific omics resource for tumor microenvironment association study

NAR Cancer ◽

10.1093/narcan/zcab037 ◽

2021 ◽

Vol 3 (3) ◽

Author(s):

Xiang Cui ◽

Fei Qin ◽

Xuanxuan Yu ◽

Feifei Xiao ◽

Guoshuai Cai

Keyword(s):

Tumor Microenvironment ◽

Single Cell ◽

Clinical Outcomes ◽

Large Scale ◽

Cell Types ◽

Cell Interaction ◽

Specific Cell ◽

Dynamic Visualization ◽

Tissue Specific ◽

Cell Composition

Abstract Tumor tissues are heterogeneous with different cell types in tumor microenvironment, which play an important role in tumorigenesis and tumor progression. Several computational algorithms and tools have been developed to infer the cell composition from bulk transcriptome profiles. However, they ignore the tissue specificity and thus a new resource for tissue-specific cell transcriptomic reference is needed for inferring cell composition in tumor microenvironment and exploring their association with clinical outcomes and tumor omics. In this study, we developed SCISSOR™ (https://thecailab.com/scissor/), an online open resource to fulfill that demand by integrating five orthogonal omics data of >6031 large-scale bulk samples, patient clinical outcomes and 451 917 high-granularity tissue-specific single-cell transcriptomic profiles of 16 cancer types. SCISSOR™ provides five major analysis modules that enable flexible modeling with adjustable parameters and dynamic visualization approaches. SCISSOR™ is valuable as a new resource for promoting tumor heterogeneity and tumor–tumor microenvironment cell interaction research, by delineating cells in the tissue-specific tumor microenvironment and characterizing their associations with tumor omics and clinical outcomes.

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Single cell transcriptomics reveals the effect of PD-L1/TGF-β blockade on the tumor microenvironment

10.1101/2020.11.13.382358 ◽

2020 ◽

Author(s):

Yoong Wearn Lim ◽

Garry L. Coles ◽

Savreet K. Sandhu ◽

David S. Johnson ◽

Adam S. Adler ◽

...

Keyword(s):

T Cell ◽

Tumor Microenvironment ◽

Single Cell ◽

Immune Cell ◽

Single Cells ◽

Cell Infiltration ◽

Cytotoxic Lymphocytes ◽

T Cell Infiltration ◽

Anti Tumor Activity

AbstractBackgroundThe anti-tumor activity of anti-PD-1/PD-L1 therapies correlates with T cell infiltration in tumors. Thus, a major goal in oncology is to find strategies that enhance T cell infiltration and efficacy of anti-PD-1/PD-L1 therapy. TGF-β has been shown to contribute to T cell exclusion and anti-TGF-β improves anti-PD-L1 efficacy in vivo. However, TGF-β inhibition has frequently been shown to induce toxicity in the clinic, and the clinical efficacy of combination PD-L1 and TGF-β blockade has not yet been proven. To identify strategies to overcome resistance to PD-L1 blockade, the transcriptional programs associated with PD-L1 and/or TGF-β blockade in the tumor microenvironment should be further elucidated.ResultsFor the first time, we used single-cell RNA sequencing to characterize the transcriptomic effects of PD-L1 and/or TGF-β blockade on nearly 30,000 single cells in the tumor and surrounding microenvironment. Combination treatment led to upregulation of immune response genes, including multiple chemokine genes such as CCL5, in CD45+ cells, and down-regulation of extracellular matrix genes in CD45-cells. Analysis of publicly available tumor transcriptome profiles showed that the chemokine CCL5 was strongly associated with immune cell infiltration in various human cancers. Further investigation with in vivo models showed that intratumorally administered CCL5 enhanced cytotoxic lymphocytes and the anti-tumor activity of anti-PD-L1.ConclusionsTaken together, our data could be leveraged translationally to improve anti-PD-L1 plus anti-TGF-β combination therapy, for example through companion biomarkers, and/or to identify novel targets that could be modulated to overcome resistance.

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Multiomics characteristics of neurogenesis-related gene are dysregulated in tumor immune microenvironment

npj Genomic Medicine ◽

10.1038/s41525-021-00202-y ◽

2021 ◽

Vol 6 (1) ◽

Author(s):

Ben Wang ◽

Hai Mou ◽

Mengmeng Liu ◽

Zhujie Ran ◽

Xin Li ◽

...

Keyword(s):

Tumor Microenvironment ◽

Single Cell ◽

Large Scale ◽

Neural System ◽

Molecular Characteristics ◽

Tumor Microenvironments ◽

Expression Of Genes ◽

Immune Molecule ◽

Methylome Analysis ◽

Immune Exclusion

AbstractThe success of immunotherapy was overshadowed by its low response rate, and the hot or cold tumor microenvironment was reported to be responsible for it. However, due to the lack of an appropriate method, it is still a huge challenge for researchers to understand the molecular differences between hot and cold tumor microenvironments. Further research is needed to gain deeper insight into the molecular characteristics of the hot/cold tumor microenvironment. A large-scale clinical cohort and single-cell RNA-seq technology were used to identify the molecular characteristics of inflamed or noninflamed tumors. With single-cell RNA sequencing technology, we provided a novel method to dissect the tumor microenvironment into a hot/cold tumor microenvironment to help us understand the molecular differences between hot and cold tumor microenvironments. Compared with cold tumors, hot tumors highly expressed B cell-related genes, such as MS4A1 and CXCR5, neurogenesis-related miRNA such as MIR650, and immune molecule-related lncRNA such as MIR155HG and LINC00426. In cold tumors, the expression of genes related to multiple biological processes, such as the neural system, was significantly upregulated, and methylome analysis indicated that the promoter methylation level of genes related to neurogenesis was significantly reduced. Finally, we investigated the pan-cancer prognostic value of the cold/hot microenvironment and performed pharmacogenomic analysis to predict potential drugs that may have the potential to convert the cold microenvironment into a hot microenvironment. Our study reveals the multiomics characteristics of cold/hot microenvironments. These molecular characteristics may contribute to the understanding of immune exclusion and the development of microenvironment-targeted therapy.

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Single-cell analyses of renal cell cancers reveal insights into tumor microenvironment, cell of origin, and therapy response

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2103240118 ◽

2021 ◽

Vol 118 (24) ◽

pp. e2103240118

Author(s):

Yuping Zhang ◽

Sathiya P. Narayanan ◽

Rahul Mannan ◽

Gregory Raskind ◽

Xiaoming Wang ◽

...

Keyword(s):

Tumor Microenvironment ◽

Single Cell ◽

Renal Cell ◽

Immune Cell ◽

Checkpoint Inhibitors ◽

Wide Spectrum ◽

Response To Therapy ◽

Cell Infiltration ◽

Immune Cell Infiltration ◽

Cell Of Origin

Diverse subtypes of renal cell carcinomas (RCCs) display a wide spectrum of histomorphologies, proteogenomic alterations, immune cell infiltration patterns, and clinical behavior. Delineating the cells of origin for different RCC subtypes will provide mechanistic insights into their diverse pathobiology. Here, we employed single-cell RNA sequencing (scRNA-seq) to develop benign and malignant renal cell atlases. Using a random forest model trained on this cell atlas, we predicted the putative cell of origin for more than 10 RCC subtypes. scRNA-seq also revealed several attributes of the tumor microenvironment in the most common subtype of kidney cancer, clear cell RCC (ccRCC). We elucidated an active role for tumor epithelia in promoting immune cell infiltration, potentially explaining why ccRCC responds to immune checkpoint inhibitors, despite having a low neoantigen burden. In addition, we characterized an association between high endothelial cell types and lack of response to immunotherapy in ccRCC. Taken together, these single-cell analyses of benign kidney and RCC provide insight into the putative cell of origin for RCC subtypes and highlight the important role of the tumor microenvironment in influencing ccRCC biology and response to therapy.

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