Differential gene expression of tumor-infiltrating CD4+ T cells in advanced versus early stage colorectal cancer and identification of a gene signature of poor prognosis

ABSTRACT Tumor-infiltrating lymphocytes (TILs) play indispensable roles in the progression and response to treatment of solid tumors. However, the prognostic significance of CD4+ TILs is not fully disclosed in cancers generally and in CRC in particular, mainly due to the existence of different functional subsets of CD4+ T cells. We performed transcriptomic profiling of CD4+ TILs isolated from CRC patients in order to identify differentially expressed genes and their functional pathways in early versus advanced disease stages. We found that in advanced stages, genes related to immune and inflammatory responses, in particular Th1-mediated immune response and cytotoxicity-mediated genes, were downregulated; while epigenetic-mediated silencing genes were upregulated. Interestingly, we identified genes, which were steadily upregulated or downregulated in CD4+ TILs with CRC progression from stage I to IV. Additionally, of the top 200 deregulated genes, 43 upregulated and 64 downregulated genes showed similar deregulation trends in the cancer genome atlas CRC dataset. From these 97 deregulated genes, we identified a “poor prognosis CD4 gene signature (ppCD4sig)”. Patients with high ppCD4sig score showed shorter disease-specific survival (DSS) and progression-free interval (PFI). The ppCD4sig was an independent prognostic indicator for DSS (HR = 1.73, 95% CI 1.32–2.27, P = 0.0001) and PFI (HR = 1.75, 95% CI 1.3–2.35, P = 0.0016). Additionally, patients at advanced stages and at a younger age (<55 years) were more likely to have a high ppCD4sig score. Altogether, our data provide novel insights and a unique prognostic gene signature of CD4+ TILs in the CRC microenvironment.

[1]  S. M. Toor,et al.  DNA methylation in the promoters of PD-L1, MMP9, ARG1, galectin-9, TIM-3, VISTA and TGF-β genes in HLA-DR– myeloid cells, compared with HLA-DR+ antigen-presenting cells , 2020, Epigenetics.

[2]  S. M. Toor,et al.  Expression of immune checkpoints and T cell exhaustion markers in early and advanced stages of colorectal cancer , 2020, Cancer Immunology, Immunotherapy.

[3]  Bin Zhang,et al.  T Cell Dysfunction and Exhaustion in Cancer , 2020, Frontiers in Cell and Developmental Biology.

[4]  S. M. Toor,et al.  Transcriptomic profiling disclosed the role of DNA methylation and histone modifications in tumor-infiltrating myeloid-derived suppressor cell subsets in colorectal cancer , 2020, Clinical Epigenetics.

[5]  Aibin He,et al.  Distinct epigenetic features of tumor-reactive CD8+ T cells in colorectal cancer patients revealed by genome-wide DNA methylation analysis , 2019, Genome Biology.

[6]  S. M. Toor,et al.  Immune Checkpoints in Circulating and Tumor-Infiltrating CD4+ T Cell Subsets in Colorectal Cancer Patients , 2019, Front. Immunol..

[7]  Wenjun Chang,et al.  Tumor-Infiltrating Immune Cells Act as a Marker for Prognosis in Colorectal Cancer , 2019, Front. Immunol..

[8]  G. Cui.  TH9, TH17, and TH22 Cell Subsets and Their Main Cytokine Products in the Pathogenesis of Colorectal Cancer , 2019, Front. Oncol..

[9]  N. Alajez,et al.  Integrated Transcriptome and Pathway Analyses Revealed Multiple Activated Pathways in Breast Cancer , 2019, Front. Oncol..

[10]  H. Nagano,et al.  Intratumoural-infiltrating CD4 + and FOXP3 + T cells as strong positive predictive markers for the prognosis of resectable colorectal cancer , 2019, British Journal of Cancer.

[11]  S. Henikoff,et al.  Chromatin Bottlenecks in Cancer. , 2019, Trends in cancer.

[12]  E. Timperi,et al.  Wnt3a/β-Catenin Signaling Conditions Differentiation of Partially Exhausted T-effector Cells in Human Cancers , 2018, Cancer Immunology Research.

[13]  X. Shu,et al.  Gene expression in triple-negative breast cancer in relation to survival , 2018, Breast Cancer Research and Treatment.

[14]  Y. Bignon,et al.  Global analysis of H3K27me3 as an epigenetic marker in prostate cancer progression , 2017, BMC Cancer.

[15]  H. Asamura,et al.  Prognostic value of tumor-infiltrating lymphocytes differs depending on histological type and smoking habit in completely resected non-small-cell lung cancer. , 2016, Annals of oncology : official journal of the European Society for Medical Oncology.

[16]  E. Batlle,et al.  Targeting the Microenvironment in Advanced Colorectal Cancer. , 2016, Trends in cancer.

[17]  Jeffrey J Delrow,et al.  Tumor-Specific T Cell Dysfunction Is a Dynamic Antigen-Driven Differentiation Program Initiated Early during Tumorigenesis. , 2016, Immunity.

[18]  M. Hattori,et al.  Two FOXP3+CD4+ T cell subpopulations distinctly control the prognosis of colorectal cancers , 2016, Nature Medicine.

[19]  H. Zarour.  Reversing T-cell Dysfunction and Exhaustion in Cancer , 2016, Clinical Cancer Research.

[20]  Ying Yang,et al.  TOX3 protein expression is correlated with pathological characteristics in breast cancer , 2016, Oncology letters.

[21]  R. Palmqvist,et al.  The infiltration, and prognostic importance, of Th1 lymphocytes vary in molecular subgroups of colorectal cancer , 2015, The journal of pathology. Clinical research.

[22]  L. Terracciano,et al.  Dual role of tumour-infiltrating T helper 17 cells in human colorectal cancer , 2015, Gut.

[23]  F. Gao,et al.  Th22 cell accumulation is associated with colorectal cancer development. , 2015, World journal of gastroenterology.

[24]  Tae-Young Roh,et al.  Polycomb group protein-mediated histone modifications during cell differentiation. , 2015, Epigenomics.

[25]  M. Koch,et al.  Tumor-specific cytotoxic T lymphocyte activity determines colorectal cancer patient prognosis. , 2015, The Journal of clinical investigation.

[26]  J. Kaye,et al.  TOX3 is expressed in mammary ER+ epithelial cells and regulates ER target genes in luminal breast cancer , 2015, BMC Cancer.

[27]  Yanfang Jiang,et al.  The frequency of Th17 and Th22 cells in patients with colorectal cancer at pre-operation and post-operation , 2015, Immunological investigations.

[28]  Z. Du,et al.  Prognostic Value of Tumor-Infiltrating FoxP3+ T Cells in Gastrointestinal Cancers: A Meta Analysis , 2014, PloS one.

[29]  GuyLaurent,et al.  Epigenetics of prostate cancer: distribution of histone H3K27me3 biomarkers in peri-tumoral tissue. , 2014 .

[30]  D. Quail,et al.  Microenvironmental regulation of tumor progression and metastasis , 2014 .

[31]  F. Pallone,et al.  Role of TH17 cytokines in the control of colorectal cancer , 2013, Oncoimmunology.

[32]  Kebin Liu,et al.  Epigenetics and Colorectal Cancer Pathogenesis , 2013, Cancers.

[33]  J. Hong,et al.  Re-Evaluation of PD-1 Expression by T Cells as a Marker for Immune Exhaustion during SIV Infection , 2013, PloS one.

[34]  Y. Bignon,et al.  Histone lysine trimethylation or acetylation can be modulated by phytoestrogen, estrogen or anti-HDAC in breast cancer cell lines. , 2013, Epigenomics.

[35]  A. Goel,et al.  Epigenetics of colorectal cancer. , 2012, Gastroenterology.

[36]  B. Nelson,et al.  Tumor-infiltrating B cells and T cells , 2012, Oncoimmunology.

[37]  T. Hagemann,et al.  The tumor microenvironment at a glance , 2012, Journal of Cell Science.

[38]  U. Güth,et al.  Differential pattern and prognostic significance of CD4+, FOXP3+ and IL-17+ tumor infiltrating lymphocytes in ductal and lobular breast cancers , 2012, BMC Cancer.

[39]  S. Gill,et al.  Presentation and outcomes of patients aged 30 years and younger with colorectal cancer: a 20-year retrospective review , 2011, Medical oncology.

[40]  Shung-Haur Yang,et al.  Differences in clinicopathological characteristics of colorectal cancer between younger and elderly patients: an analysis of 322 patients from a single institution. , 2011, American journal of surgery.

[41]  Susan M. Bridges,et al.  Comparison of Four ChIP-Seq Analytical Algorithms Using Rice Endosperm H3K27 Trimethylation Profiling Data , 2011, PloS one.

[42]  E John Wherry,et al.  T cell exhaustion , 2011 .

[43]  G. D. de Bock,et al.  The prognostic influence of tumour-infiltrating lymphocytes in cancer: a systematic review with meta-analysis , 2011, British Journal of Cancer.

[44]  P. Pauwels,et al.  Immune Cells in Colorectal Cancer: Prognostic Relevance and Role of MSI , 2011, Cancer Microenvironment.

[45]  Zlatko Trajanoski,et al.  Histopathologic-based prognostic factors of colorectal cancers are associated with the state of the local immune reaction. , 2011, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[46]  J. Galon,et al.  Clinical impact of different classes of infiltrating T cytotoxic and helper cells (Th1, th2, treg, th17) in patients with colorectal cancer. , 2011, Cancer research.

[47]  Guy Sauvageau,et al.  Polycomb group proteins: multi-faceted regulators of somatic stem cells and cancer. , 2010, Cell stem cell.

[48]  T. Kerppola.  Polycomb group complexes--many combinations, many functions. , 2009, Trends in cell biology.

[49]  M. Koch,et al.  Antigen-specific Tregs control T cell responses against a limited repertoire of tumor antigens in patients with colorectal carcinoma. , 2009, The Journal of clinical investigation.

[50]  H. Spits,et al.  Identification of a human helper T cell population that has abundant production of interleukin 22 and is distinct from TH-17, TH1 and TH2 cells , 2009, Nature Immunology.

[51]  N. Zeps,et al.  Tumor-infiltrating FOXP3+ T regulatory cells show strong prognostic significance in colorectal cancer. , 2009, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[52]  R. Perez,et al.  Peritumoral Inflammatory Infiltrate is not a Prognostic Factor in Distal Rectal Cancer Following Neoadjuvant Chemoradiation Therapy , 2007, Journal of Gastrointestinal Surgery.

[53]  A. Chang,et al.  Cutting Edge: Th17 and Regulatory T Cell Dynamics and the Regulation by IL-2 in the Tumor Microenvironment1 , 2007, The Journal of Immunology.

[54]  Markus Essler,et al.  IL-22-Mediated Tumor Growth Reduction Correlates with Inhibition of ERK1/2 and AKT Phosphorylation and Induction of Cell Cycle Arrest in the G2-M Phase , 2006, The Journal of Immunology.

[55]  M. Koch,et al.  Tumor Infiltrating T Lymphocytes in Colorectal Cancer: Tumor-Selective Activation and Cytotoxic Activity In Situ , 2006, Annals of surgery.

[56]  Z. Trajanoski,et al.  Type, Density, and Location of Immune Cells Within Human Colorectal Tumors Predict Clinical Outcome , 2006, Science.

[57]  C. Sohn,et al.  Heparanase: a new metastasis-associated antigen recognized in breast cancer patients by spontaneously induced memory T lymphocytes. , 2006, Cancer research.

[58]  Z. Trajanoski,et al.  Effector memory T cells, early metastasis, and survival in colorectal cancer. , 2005, The New England journal of medicine.

[59]  D. McMillan,et al.  The relationship between T-lymphocyte subset infiltration and survival in patients with prostate cancer , 2004, British Journal of Cancer.