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Integrated Analysis of Gene Correlation Reveals Disordered Relationship Between Metabolism and Immunity in Tumor Microenvironmen

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Integrated Analysis of Gene Correlation Reveals Disordered Relationship Between Metabolism and Immunity in Tumor Microenvironmen bioRxiv preprint doi: https://doi.org/10.1101/2020.03.08.982850; this version posted March 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Integrated analysis of gene correlation reveals disordered relationship between metabolism and immunity in tumor microenvironment Zixi Chen1, Jinfen Wei1, Yuchen Yuan1, Ying Cui1, Yanyu Zhang2, Yumin Hu2, Hongli Du1# 1School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; 2Sun Yet-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060 Guangdong, China #Corresponding Author Hongli Du School of Biology and Biological Engineering South China University of Technology Guangzhou 510006, China Tel: +86-020-3938 0667 Fax: +86-020-3938 0667 E-mail: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.08.982850; this version posted March 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Abstract: 2 Background: Metabolism reprogramming and immune evasion are the 3 most fundamental hallmarks for cancer survival. The complex 4 interactions between metabolism and immune systems in tumors and 5 their microenvironment is complicated. Researching on the correlation 6 changes between metabolic and immune related-genes in normal and 7 tumor tissues would help to reveal these complex interactions. 8 Methods: In this study, the mRNA profiles across 11 cancer types was 9 obtained from The Cancer Genome Atlas (TCGA). Then, the spearman’s 10 correlation coefficient was calculated between metabolic and immune 11 related-genes for each sample group. 12 Results: Our results showed that the number of correlated gene pairs was 13 reduced significantly in tumor tissues compared with those of normal 14 tissue, especially in KIRC, KIRP and STAD. Functional enrichment 15 analysis for the universal (the pairs appeared in more than 2 cancer types) 16 and specific (the pairs only in one specific cancer type) gene pairs across 17 cancer types revealed top pathways which appeared in tumor and normal 18 samples, such as phosphatidylinositol signaling system and inositol 19 phosphate metabolism. Thereinto, the pairs in normal tissues missing in 20 tumors may indicate they are important factors affecting immune system, 21 such as, DGKs and PIP4ks. The correlation analysis between immune 22 checkpoint and metabolism genes also showed a reduced correlation in 2 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.08.982850; this version posted March 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 23 tumor and had the tissue specificity, such as, FUT8 was strongly 24 correlated with PDCD1 in the HC of STAD and they had a weaker 25 correlation in other normal tissues and tumor types. 26 Conclusions: Our study provides a novel strategy for investigating 27 interaction of tumor immune and metabolism in microenvironment and 28 offers some key points for exploring new targets including metabolic 29 targets and immunomodulator of immune checkpoints . 30 31 Keywords: spearman correlation, metabolism, immunity, pan-cancer, 32 immune checkpoints 3 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.08.982850; this version posted March 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 33 Background 34 Recently, inflammation and immune evasion are considered as hallmarks 35 of cancer progression, highlighting the direct involvement of immune [1, 2] 36 cells . The study on immunology has made great progress in cancer 37 treatment, and the role of immune cells in cancer progression is [3, 4] 38 well-recognized . Cancer immunotherapy has subverted the traditional 39 concept of treatment, such as immune checkpoint inhibitors, cancer 40 vaccines and chimeric antigen receptor redirected T (CAR-T) cell [5-8] 41 therapy . 42 The research progresses on cancer has indicated that metabolic [9] 43 reprogramming is another hallmark of cancer . Cells that are common to 44 many cancers that do not produce enough energy due to lack of oxygen, 45 carbohydrate or protein use altered metabolic pathways to ensure their 46 survival. Thus, malignant cells acquire the molecular materials and 47 energy necessary to sustain proliferation through unusual metabolic 48 pathways. The tendency of malignant cells to utilize glucose via the 49 process of glycolysis irrespective of the oxygen availability is known as [10, 11] 50 "aerobic glycolysis" which was pointed by Otto Warburg . 51 Though metabolic reprogramming and evasion of immune surveillance 52 are distinct processes, recent evidence has accumulated to show that 53 specific metabolic signatures as an important regulator in both innate and [12] 54 adaptive immunity in human cancer . The immune response is 4 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.08.982850; this version posted March 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 55 associated with dramatic modifications in tumor microenvironment (TME) 56 metabolism, including depletion of nutrients, increased oxygen 57 consumption, and the generation of reactive nitrogen and oxygen [13] 58 intermediates . For example, the bile metabolism of bile acids in gut [14] 59 microbiome can influence the NKT cell–driven killing ability . 60 Similarly, depletion in amino acid and nutrient depletion were reported [15] 61 for T cells functions on anti-tumor effect . Besides, the crosstalk [16, 17] 62 between immune cells and other cells could influence the immunity . 63 Taken together, the findings of immune cells function have been showed 64 altered by the TME extensively in cancers. 65 The metabolism and immunity are fundamentally linked among the 66 malignant cell, immune cell and the microenvironment cells around them. 67 Thus, there is a renewed interest to exploit the link between these two 68 cancer-related processes in order to develop potent anticancer 69 therapeutics. The correlation between genes expression level can reflect [18-20] 70 the relation between biological processes . Up to now, some [21, 22] [23, 24] 71 researchers have excavated and studied metabolic and immune 72 related genes separately based on TCGA database, however, few studies 73 has been done on the expression relationship between metabolic and 74 immune related genes in tumor samples. Thus, there is an interest to 75 exploit the link between these two cancer-related processes in order to 76 develop potent anticancer therapeutics. In this study, we analyzed 11 5 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.08.982850; this version posted March 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 77 different cancers from the TCGA database, including 5645 cancer and 78 normal samples, describing the co-expression relationship between 79 metabolic and immune genes in pan-cancer. Our findings will provide a 80 comprehensive data basis for further studies of metabolic and immune 81 associations in tumor tissue. 82 83 84 85 86 87 88 89 Methods 90 Data obtaining and preprocessing 91 The mRNA expression data and clinical information data were obtained 92 from The Cancer Genome Atlas (TCGA) program through the NCI's [25] 93 Genomic Data Commons (GDC) website (https://gdc.cancer.gov/) . 94 5645 samples across 11 cancers were included in this research. Samples 95 of colon adenocarcinoma (COAD) and rectum adenocarcinoma (READ) 96 were mixed into colorectal carcinoma (CRC), thus left 10 cancer types in 97 the following study. According to the clinical information, each cancer 6 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.08.982850; this version posted March 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 98 was first classified into 5 groups: healthy control (HC) and tumor samples 99 from stage 1 to stage 4. Then stage 1 and stage 2 were merged into early 100 stage, while stage 3 and stage 4 were merged into advanced stage, the 101 sample details was presented in Supplement Table 1. 102 The list of all human cellular metabolism genes was downloaded from [26] 103 ccmGDB . The immune-related gene list was obtained from the 104 Reactome database, these genes were grouped according to three 105 pathways in Reactome Pathway Browser(http://www.reactome.org/): 106 adaptive immunity, innate immunity and cytokine signaling pathway in [27, 28] 107 immune system . The genes were listed in Supplement Table 2. [29-31] 108 For the RNA-seq data, raw read counts were used to calculate TPM . [32] 109 Annotation file from GENCODE (https://www.gencodegenes.org/) 110 was used to calculate the length of each gene, which was needed in the 111 calculation of TPM.
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