Gastric cancer was the world’s third leading cause of cancer mortality in 2012, responsible for 723,000 deaths1. The vast majority of gastric cancers are adenocarcinomas, which can be further subdivided into intestinal and diffuse types according to the Lauren classification2. An alternative system, proposed by the World Health Organization, divides gastric cancer into papillary, tubular, mucinous (colloid) and poorly cohesive carcinomas3. These classification systems have little clinical utility, making the development of robust classifiers that can guide patient therapy an urgent priority.

The majority of gastric cancers are associated with infectious agents, including the bacterium Helicobacter pylori4 and Epstein–Barr virus (EBV). The distribution of histological subtypes of gastric cancer and the frequencies of H. pylori and EBV associated gastric cancer vary across the globe5. A small minority of gastric cancer cases are associated with germline mutation in E-cadherin (CDH1)6 or mismatch repair genes7 (Lynch syndrome), whereas sporadic mismatch repair-deficient gastric cancers have epigenetic silencing of MLH1 in the context of a CpG island methylator phenotype (CIMP)8. Molecular profiling of gastric cancer has been performed using gene expression or DNA sequencing9–12, but has not led to a clear biologic classification scheme. The goals of this study by The Cancer Genome Atlas (TCGA) were to develop a robust molecular classification of gastric cancer and to identify dysregulated pathways and candidate drivers of distinct classes of gastric cancer.

/pdf/comprehensive-molecular-characterization-of-gastric-3jzhmi95fs.pdf

Comprehensive molecular characterization of gastric adenocarcinoma

The clinical relevance of T cells in the control of a diverse set of human cancers is now beyond doubt. However, the nature of the antigens that allow the immune system to distinguish cancer cells from noncancer cells has long remained obscure. Recent technological innovations have made it possible to dissect the immune response to patient-specific neoantigens that arise as a consequence of tumor-specific mutations, and emerging data suggest that recognition of such neoantigens is a major factor in the activity of clinical immunotherapies. These observations indicate that neoantigen load may form a biomarker in cancer immunotherapy and provide an incentive for the development of novel therapeutic approaches that selectively enhance T cell reactivity against this class of antigens.

http://science.sciencemag.org/content/sci/348/6230/69.full.pdf

Neoantigens in cancer immunotherapy

The Cancer Genome Atlas profiled 279 head and neck squamous cell carcinomas (HNSCCs) to provide a comprehensive landscape of somatic genomic alterations Here we show that human-papillomavirus-associated tumours are dominated by helical domain mutations of the oncogene PIK3CA, novel alterations involving loss of TRAF3, and amplification of the cell cycle gene E2F1 Smoking-related HNSCCs demonstrate near universal loss-of-function TP53 mutations and CDKN2A inactivation with frequent copy number alterations including amplification of 3q26/28 and 11q13/22 A subgroup of oral cavity tumours with favourable clinical outcomes displayed infrequent copy number alterations in conjunction with activating mutations of HRAS or PIK3CA, coupled with inactivating mutations of CASP8, NOTCH1 and TP53 Other distinct subgroups contained loss-of-function alterations of the chromatin modifier NSD1, WNT pathway genes AJUBA and FAT1, and activation of oxidative stress factor NFE2L2, mainly in laryngeal tumours Therapeutic candidate alterations were identified in most HNSCCs

/pdf/comprehensive-genomic-characterization-of-head-and-neck-1o705nnerz.pdf

Comprehensive genomic characterization of head and neck squamous cell carcinomas

Most tumor cells express antigens that can mediate recognition by host CD8(+) T cells. Cancers that are detected clinically must have evaded antitumor immune responses to grow progressively. Recent work has suggested two broad categories of tumor escape based on cellular and molecular characteristics of the tumor microenvironment. One major subset shows a T cell-inflamed phenotype consisting of infiltrating T cells, a broad chemokine profile and a type I interferon signature indicative of innate immune activation. These tumors appear to resist immune attack through the dominant inhibitory effects of immune system-suppressive pathways. The other major phenotype lacks this T cell-inflamed phenotype and appears to resist immune attack through immune system exclusion or ignorance. These two major phenotypes of tumor microenvironment may require distinct immunotherapeutic interventions for maximal therapeutic effect.

http://www.therenegadecell.com/wiki/images/7/7c/Gajewski_T_-_Innate_and_Adaptive_Immune_Cells.pdf

Innate and adaptive immune cells in the tumor microenvironment

After a century of controversy, the notion that the immune system regulates cancer development is experiencing a new resurgence. An overwhelming amount of data from animal models--together with compelling data from human patients--indicate that a functional cancer immunosurveillance process indeed exists that acts as an extrinsic tumor suppressor. However, it has also become clear that the immune system can facilitate tumor progression, at least in part, by sculpting the immunogenic phenotype of tumors as they develop. The recognition that immunity plays a dual role in the complex interactions between tumors and the host prompted a refinement of the cancer immunosurveillance hypothesis into one termed "cancer immunoediting." In this review, we summarize the history of the cancer immunosurveillance controversy and discuss its resolution and evolution into the three Es of cancer immunoediting--elimination, equilibrium, and escape.

The three Es of cancer immunoediting.

Implications for immunosurveillance of altered hla class i phenotypes in human tumours

https://www.cell.com/trends/immunology/pdf/0167-5699(93)90264-L.pdf

Natural history of HLA expression during tumour development

Oncogenic transformation in human and experimental animals is not necessarily followed by the appearance of a tumor mass. The immune system of the host can recognize tumor antigens by the presentation of small antigenic peptides to the receptor of cytotoxic T-lymphocytes (CTLs) and reject the nascent tumor. However, cancer cells can sometimes escape these specific T-cell immune responses in the course of somatic (genetic and phenotypic) clonal evolution. Among the tumor immune escape mechanisms described to date, the alterations in the expression of major histocompatibility complex (MHC) molecules play a crucial step in tumor development due to the role of MHC antigens in antigen presentation to T-lymphocytes and the regulation of natural killer cell (NK) cell function. In this work, we have (1) updated information on the mechanisms that allow CTLs to recognize tumor antigens after antigen processing by transformed cells, (2) described the altered MHC class I phenotypes that are commonly found in human tumors, (3) summarized the molecular mechanisms responsible for MHC class I alteration in human tumors, (4) provided evidence that these altered human leukocyte antigens (HLA) class I phenotypes are detectable as result of a T-cell immunoselection of HLA class I-deficient variants by an immunecompetent host, and (5) presented data indicating the MHC class I phenotype and the immunogenicity of experimental metastatic tumors change drastically when tumors develop in immunodeficient mice.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcp.10290

MHC class I antigens, immune surveillance, and tumor immune escape.

https://www.repositoriosalud.es/bitstream/10668/2236/1/GarridoF_TheUrgentNeedToRecoverMHC.pdf

The urgent need to recover MHC class I in cancers for effective immunotherapy

Publisher Summary The chapter presents that the primary and metastatic tumor cell growth results from the development of sophisticated molecular and biological mechanisms that allow tumor cells to escape immune surveillance. These escape mechanisms are selected by the cancer cells after a period of interaction with the immune system. Among these mechanisms, the MHC class I phenotypic alteration that occurs in tumor cells plays a leading role in the tumor–host scenario since these are crucial molecules for antigen presentation to T cells and modulation of NK activity. This chapter discusses the major HLA class I phenotypic alterations found in human tumors, with special attention paid to the molecular mechanisms responsible for their generation. The chapter also describes the HLA class I alterations that are detected in tumors derived from different tissues of the body, such as the bladder, breast, colon and rectum, larynx, lung, kidney, melanocytes, pancreas, and prostate. The issue of nonclassical HLA class I molecule expression in tumor cell lines and tumor tissues and its possible role in immune escape is also discussed, as are the implications of these findings for T cell-based immunotherapy. The chapter concludes with the experimental data supporting the hypothesis that the MHC class I-negative tumor variants are selected in vivo by cytotoxic lymphocyte (CTL) responses against MHC class I-positive tumor cells.

Federico Garrido

Papers

Implications for immunosurveillance of altered hla class i phenotypes in human tumours

Natural history of HLA expression during tumour development

MHC class I antigens, immune surveillance, and tumor immune escape.

The urgent need to recover MHC class I in cancers for effective immunotherapy

MHC antigens and tumor escape from immune surveillance.