AID-associated gene-regulatory network in cancer

Activation-induced cytidine deaminase (AID) is critically involved in class switch recombination and somatic hypermutation of Ig loci resulting in diversification of antibodies repertoire and production of high affinity antibodies and as such represents a physiological tool to introduce DNA alterations. These processes take place within germinal centers (GC). Expression and activity of AID is considered to be restricted to B lymphocytes and because of its mutagenic and recombinogenic potential is tightly regulated on different levels to minimize the risk of unwanted DNA damage. However, chronic inflammation and, probably, combination of other notyet-identified factors, are able to create a microenvironment sufficient for triggering an aberrant AID expression in B cells and, importantly, in non-B-cells. Under these circumstances, AID may target also non-Ig genes, including cancer- related genes as oncogenes, tumour suppressor genes and genomic stability genes. Despite ongoing progress, complete understanding of the impact of AID expression in human non-B cells on the abnormal cell state associated with an increased rate of genomic alterations as point mutations, small insertions or deletions, and/or recurrent chromosomal translocations during solid tumor development and progression is still lacking. To address the role of just one particular module associated with AID among diverse oncogenic pathways contributing to heterogeneity of human cancers, we aim to perform a systematic analysis of AID expression in various types of solid tumors and attempt to estimate the functional consequence. To build up the AID expression pattern, we propose to use a combination of data-driven approach based on the analysis of genomewide microarray data sets and dissecting AID-associated pathways into the meaningful modules, and knowledge-driven approach based on the real-time PCR gene expression profiling using pre-designed gene signature, which composition is selected on the basis of the scientific literature. Being part of the research plan, expression patterns of other APOBEC family members will be investigated and aligned with the one for AID. Furthermore, we attempt to delineate the AID-associated DNA alterations and estimate their potential impact to pathology of solid tumors under investigation. A strong advantage of the current proposal is the excess to the well- characterized clinical specimens. Therefore, conceptualization of obtained data might be used not only for basic research, but presumably for therapeutic target proposal and building of prognostic and/or predictive AID-driven tumor-associated multigene expression signatures.

Accumulated knowledge on dysregulated cellular checkpoints associated with cancer development and systematic studies using genomic analysis tools have suggested many new classes of cancer-causing and/or cancer-promoting genes. Revolutionized impact gave the discovery of activation-induced cytidine deaminase, AID, with its remarkable ability to edit DNA and thus introduce point mutations or other types of DNA damagers. Under physiological conditions, AID functions as "good", health protecting factor being THE molecule responsible for the diversity of antibody repertoire directed against infectious agents by targeting immunoglobulin genes and driving somatic hypermutations and class switch recombination events. These reactions take place in GC-like structures within secondary lymphoid tissues in activated B cells. However, chronic inflammatory processes as well as other not-yet-identified factors are able to create a microenvironment sufficient for triggering an aberrant AID expression in B cells allocated outside of lymphoid organs and, importantly, in non-B cells including epithelial cells. Under these circumstances, AID may target cancer-related genes genome-wide, increase the risk of unwanted DNA damage and thus act as extremely "bad" factor. The complexity is multiplied by identification of other ten functionally related molecules which now compose the AID/APOBEC gene family. To what extent may aberrant AID/APOBEC expression/activity contribute to multifactorial processes of tumour development and progression? To give light, in the current project we developed and successfully applied two innovative approaches. Firstly, the microscopy-based imaging platform was used for automated scanning of large-scale tissue sections of patients with colorectal cancer metastases in the liver and subsequent computerized quantitative analyses of immune cells at metastatic area, named immunological imprint. We reported for the first time that B cells and, strikingly, functionally active, AID-positive ectopic lymphoid structures were accumulated at the tumour - liver border within the metastatic margin of 1 mm only. Furthermore, the data suggest that as more B lymphocytes are present at the border as better the prognosis for the patient. Taken together, we nominate the magnitude of B lymphocytes, including those organized in ectopic follicles, as novel prognostic marker which is superior to any clinicopathological parameter. Findings emphasize anti-tumoral role of B cell-driven mechanism(s) and thus indicate a new way of thinking about potential treatment strategies for patients with metastatic colorectal cancer. Secondly, we applied the multigene signature-based gene profiling approach combined with statistical modelling and bioinformatics to test whether AID/APOBECs could be part of mechanism(s) contributing to the etiology of solid tumours including ovarian cancer. We herein defined the multigene-based model which is eligible as prognostic for patients with advanced stage of serous ovarian carcinoma and delineated novel key AID/APOBEC-associated aspects of ovarian cancer biology. Our data deliver a proposal for ovarian cancer patient stratification and risk assessment and propose the established algorithm to be used in other malignant disorders. Furthermore, the results of our study strongly suggest that AID might be a critical factor in the epithelial cell plasticity program triggered during metastasising process.