Screening Genes Related with Tumor Immunity in Pancreatic Cancer with the WGCN Analysis

LI Huiyue; WANG Muzhen; YU Ye; TIAN Xuemei

doi:10.6054/j.jscnun.2021093

Journal of South China Normal University (Natural Science Edition) > 2021 > 53(6): 61-67. > DOI: 10.6054/j.jscnun.2021093

LI Huiyue, WANG Muzhen, YU Ye, TIAN Xuemei. Screening Genes Related with Tumor Immunity in Pancreatic Cancer with the WGCN Analysis[J]. Journal of South China Normal University (Natural Science Edition), 2021, 53(6): 61-67. DOI: 10.6054/j.jscnun.2021093

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Screening Genes Related with Tumor Immunity in Pancreatic Cancer with the WGCN Analysis

College of Life Sciences, South China Normal University, Guangzhou 510631, China

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Received Date: July 11, 2021
Available Online: January 09, 2022

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Abstract

Abstract

The immune infiltrating cells of pancreatic cancer are analyzed to find immunotherapy targets for pancreatic cancer. The weighted gene co-expression network (WGCN) analysis and the CIBERSORT algorithm were used to analyze the gene expression data of pancreatic cancer in the TCGA database to identify the gene modules related to the level of B cell immune infiltration. Nine hub genes (CD79B, MYC, BANK1, TIMELESS, CD19, ATF3, ITGAL, IKZF3 and RRAGB) were identified with the co-expression network and the PPI interaction network analysis. The Timer, Kaplan-Meier and differentially expressed gene analyses showed that ITGAL was highly expressed in B cells and significantly upregulated in pancreatic cancer tissues, and the high expression of ITGAL in pancreatic cancer was significantly correlated with good prognosis.
- pancreatic cancer,
- immune infiltration,
- WGCNA,
- CIBERSORT,
- B cells

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[1]	TAO J, YANG G, ZHOU W, et al. Targeting hypoxic tumor microenvironment in pancreatic cancer[J]. Journal of Hematology & Oncology, 2021, 14(1): 1-25. doi: 10.1186/s13045-020-01030-w
[2]	SUI H, MA N, WANG Y, et al. Anti-PD-1/PD-L1 therapy for non-small-cell lung cancer: toward personalized medicine and combination strategies[J]. Journal of Immunology Research, 2018(2): 1-17. http://downloads.hindawi.com/journals/jir/2018/6984948.pdf
[3]	TOPALIAN S, DRAKE C, PARDOLL D. Immune checkpoint blockade: a common denominator approach to cancer therapy[J]. Cancer Cell, 2015, 27(4): 450-461. doi: 10.1016/j.ccell.2015.03.001
[4]	TUMEH P C, HARVIEW C L, YEARLEY J H, et, al. PD-1 blockade induces responses by inhibiting adaptive immune resistance[J]. Nature, 2014, 515(7528): 568-571. doi: 10.1038/nature13954
[5]	WU T, DAI Y. Tumor microenvironment and therapeutic response[J]. Cancer Letters, 2017, 387(2): 61-68.
[6]	UDALL M, RIZZO M, KENNY J, et al. PD-L1 diagnostic tests: a systematic literature review of scoring algorithms and test-validation metrics[J]. Diagnostic Pathology, 2018, 13(1): 1-11. http://www.onacademic.com/detail/journal_1000040329081810_b9bd.html
[7]	BREMBES R M, Al-SHIBLI K M D, DONNEM T, et al. The role of tumor-infiltrating immune cells and chronic inflammation at the tumor site on cancer development, progression, and prognosis: emphasis on non-small cell lung cancer[J]. Journal of Thoracic Oncology, 2011, 6(4): 824-833. doi: 10.1097/JTO.0b013e3182037b76
[8]	LANGFELDER P, HORVATH S, LANGFELDER P, et al. WGCNA: an R package for weighted correlation network analysis[J]. BMC Bioinformatics, 2009, 9(559): 1-13. http://pdfs.semanticscholar.org/1ebe/33188f74b65fddd8679f5dbc8d243293bd80.pdf
[9]	LIU H, SUN Y, TIAN H, et al. Characterization of long non-coding RNA and messenger RNA profiles in laryngeal cancer by weighted gene co-expression network analysis[J]. Aging, 2019, 11(22): 10074-10099. doi: 10.18632/aging.102419
[10]	NEWMAN A M, LIU C L, GREEN M R, et al. Robust enumeration of cell subsets from tissue expression profiles[J]. Nature Methods, 2015, 12(5): 453-457. doi: 10.1038/nmeth.3337
[11]	ZHOU Y, ZHOU B, PACHE L, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets[J]. Nature Communications, 2019, 10(1): 1-10. doi: 10.1038/s41467-018-07882-8
[12]	SZKLARCZYK D, GABLE A L, LYON D, et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets[J]. Nucleic Acids Research, 2019, 47(D1): D607-D613. doi: 10.1093/nar/gky1131
[13]	SHANNON P, MARKIEL A, OZIER O, et al. CYTOSCAPE: a software environment for integrated models of biomolecular interaction networks[J]. Genome Research, 2003, 13(11): 2498-2504. doi: 10.1101/gr.1239303
[14]	LI T, FAN J, WANG B, et al. TIMER: a web server for comprehensive analysis of tumor-infiltrating immune cells[J]. Cancer Research, 2017, 77(21): e108-e110. doi: 10.1158/0008-5472.CAN-17-0307
[15]	LI B, SEVERSON E, PIGNON J C, et al. Comprehensive analyses of tumor immunity: implications for cancer immunotherapy[J]. Genome Biology, 2016, 17(1): 174-190. doi: 10.1186/s13059-016-1028-7
[16]	GAUTIER L, COPE L, BOLSTAD B M, et al. Affy-analysis of Affymetrix GeneChip data at the probe level[J]. Bioinformatics, 2004, 20(3): 307-315. doi: 10.1093/bioinformatics/btg405
[17]	GOEL M K, KHANNA P, KISHORE J. Understanding survival analysis: Kaplan-Meier estimate[J]. International Journal of Ayurveda Research, 2010, 1(4): 274-278. doi: 10.4103/0974-7788.76794
[18]	RHODES D R, KALYANA-SUNDARAM S, MAHAVISNO V, et al. Oncomine 3.0: genes, pathways, and networks in a collection of 18, 000 cancer gene expression profiles[J]. Neoplasia, 2007, 9(2): 166-180. doi: 10.1593/neo.07112
[19]	KUNK P R, BAUER T W, SLINGLUFF C L, et al. From bench to bedside a comprehensive review of pancreatic cancer immuno therapy[J]. Journal for Immunotherapy of Cancer, 2016, 4: 1-12. doi: 10.1186/s40425-015-0105-x
[20]	CHEN W, ZHANG W, WU R, et al. Identification of biomarkers associated with histological grade and prognosis of gastric cancer by coexpression network analysis[J]. Oncology Letters, 2019, 18(5): 5499-5507.
[21]	YAO Q, SONG Z, WANG B, et al. Identifying key genes and functionally enriched pathways in sjgren's syndrome by weighted gene co-expression network analysis[J]. Frontiers in Genetics, 2019, 10(11): 1142-1152. http://www.ncbi.nlm.nih.gov/pubmed/31798636
[22]	CABRITA R, LAUSS M, SANNA A, et al. Tertiary lymphoid structures improve immunotherapy and survival in melanoma[J]. Nature, 2020, 577(7791): 561-565. doi: 10.1038/s41586-019-1914-8
[23]	HELMINK B A, REDDY S M, GAO J, et al. B cells and tertiary lymphoid structures promote immunotherapy response[J]. Nature, 2020, 577(7791): 1-7. http://www.nature.com/articles/s41586-019-1922-8/
[24]	BLEIJS D A, BINNERTS M E, VLIET S, et al. Low-affinity LFA-1/ICAM-3 interactions augment LFA-1/ICAM-1-mediated T cell adhesion and signaling by redistribution of LFA-1[J]. Journal of Cell Science, 2000, 113(3): 391-400. doi: 10.1242/jcs.113.3.391
[25]	CARRASCO Y R, FLEIRE S J, CAMERON T, et al. LFA-1/ICAM-1 interaction lowers the threshold of B cell activation by facilitating B cell adhesion and synapse formation[J]. Immunity, 2004, 20(5): 589-599. doi: 10.1016/S1074-7613(04)00105-0
[26]	LIU Y X, ZHANG F, YAO Q M, et al. Expression of CD11a in lymphocyte subpopulation in immune thrombocytopenia[J]. International Journal of Clinical & Experimental Pathology, 2015, 8(12): 15642-15651. http://europepmc.org/articles/PMC4730046?pdf=render
[27]	TEMPIA-CALIERA A A, HORVATH L Z, ZIMMERMANN A, et al. Adhesion molecules in human pancreatic cancer[J]. Journal of Surgical Oncology, 2010, 79(2): 93-100.
[28]	JENKINSON C, ELLIOTT V, MENON U, et al. Evaluation in pre-diagnosis samples discounts ICAM-1 and TIMP-1 as biomarkers for earlier diagnosis of pancreatic cancer[J]. Journal of Proteomics, 2015, 113(1): 400-402. http://core.ac.uk/download/pdf/21623553.pdf

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Screening Genes Related with Tumor Immunity in Pancreatic Cancer with the WGCN Analysis

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