CIG-DB: the database for human or mouse immunoglobulin and T cell receptor genes available for cancer studies

Nakamura, Yoji; Komiyama, Tomoyoshi; Furue, Motoki; Gojobori, Takashi; Akiyama, Yasuto

doi:10.1186/1471-2105-11-398

Cited by 9 publications

(7 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Epitope databases were screened in order to evaluate the predicted neo-antigens (last update Dec 2014). Deposited peptidic epitopes, T-cell assays and MHC ligand assays were downloaded from the Immune Epitope Database [ 65 ], Dana Farber repository [ 66 ], and CIG-DB [ 67 ]. Automatized HTTP-mediated download and HTML processing retrieved all records from the following databases: MHCBN [ 68 ], PeptideDatabase [ 69 ], SYFPEITHI [ 70 ], and TANTIGEN [ 71 ].…”

Section: Methodsmentioning

confidence: 99%

Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy

et al. 2015

View full text Add to dashboard Cite

BackgroundWhile large-scale cancer genomic projects are comprehensively characterizing the mutational spectrum of various cancers, so far little attention has been devoted to either define the antigenicity of these mutations or to characterize the immune responses they elicit. Here we present a strategy to characterize the immunophenotypes and the antigen-ome of human colorectal cancer.ResultsWe apply our strategy to a large colorectal cancer cohort (n = 598) and show that subpopulations of tumor-infiltrating lymphocytes are associated with distinct molecular phenotypes. The characterization of the antigenome shows that a large number of cancer-germline antigens are expressed in all patients. In contrast, neo-antigens are rarely shared between patients, indicating that cancer vaccination requires individualized strategy. Analysis of the genetic basis of the tumors reveals distinct tumor escape mechanisms for the patient subgroups. Hypermutated tumors are depleted of immunosuppressive cells and show upregulation of immunoinhibitory molecules. Non-hypermutated tumors are enriched with immunosuppressive cells, and the expression of immunoinhibitors and MHC molecules is downregulated. Reconstruction of the interaction network of tumor-infiltrating lymphocytes and immunomodulatory molecules followed by a validation with 11 independent cohorts (n = 1,945) identifies BCMA as a novel druggable target. Finally, linear regression modeling identifies major determinants of tumor immunogenicity, which include well-characterized modulators as well as a novel candidate, CCR8, which is then tested in an orthologous immunodeficient mouse model.ConclusionsThe immunophenotypes of the tumors and the cancer antigenome remain widely unexplored, and our findings represent a step toward the development of personalized cancer immunotherapies.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0620-6) contains supplementary material, which is available to authorized users.

show abstract

Section: Methodsmentioning

confidence: 99%

Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy

et al. 2015

View full text Add to dashboard Cite

show abstract

“…The V-quest package [ 16 , 17 ] created and hosted by ImMunoGeneTics is a useful tool for medium-scale TCR-seq data handling and annotation. The new tool for TCR-seq data processing called MiTCR [ 18 ] is a recent and welcome addition, as is CIG-DB [ 19 ], a new repository for TCR and immunoglobulin sequences observed in cancer studies. The field will benefit from further development of these types of community resource.…”

Section: Tcr-seq Methodologymentioning

confidence: 99%

Sequence analysis of T-cell repertoires in health and disease

2013

View full text Add to dashboard Cite

T-cell antigen receptor (TCR) variability enables the cellular immune system to discriminate between self and non-self. High-throughput TCR sequencing (TCR-seq) involves the use of next generation sequencing platforms to generate large numbers of short DNA sequences covering key regions of the TCR coding sequence, which enables quantification of T-cell diversity at unprecedented resolution. TCR-seq studies have provided new insights into the healthy human T-cell repertoire, such as revised estimates of repertoire size and the understanding that TCR specificities are shared among individuals more frequently than previously anticipated. In the context of disease, TCR-seq has been instrumental in characterizing the recovery of the immune repertoire after hematopoietic stem cell transplantation, and the method has been used to develop biomarkers and diagnostics for various infectious and neoplastic diseases. However, T-cell repertoire sequencing is still in its infancy. It is expected that maturation of the field will involve the introduction of improved, standardized tools for data handling, deposition and statistical analysis, as well as the emergence of new and equivalently large-scale technologies for T-cell functional analysis and antigen discovery. In this review, we introduce this nascent field and TCR-seq methodology, we discuss recent insights into healthy and diseased TCR repertoires, and we examine the applications and challenges for TCR-seq in the clinic.

show abstract

“…The SYFPEITHI is a continuously maintained database that is used in epitope prediction and binding motifs analysis and consists of constitutive MHC binders and T-cell epitopes collected from different resources. A number of databases have been established for the discovery of cancer vaccine target, including DFRMLI, 74 CIG-DB, 75 TANTIGEN, 76 and CTDatabase. 77 The DFRMLI is a database of immunological datasets from important databanks that is used for the machine learning applications for training and testing purposes.…”

Section: The Impact Of Bioinformatics On Vaccine Designmentioning

confidence: 99%

Breast cancer vaccination comes to age: impacts of bioinformatics

Parvizpour¹,

Razmara²,

Omidi³

2018

Bioimpacts

View full text Add to dashboard Cite

Introduction: Breast cancer, as one of the major causes of cancer death among women, is the central focus of this study. The recent advances in the development and application of computational tools and bioinformatics in the field of immunotherapy of malignancies such as breast cancer have emerged the new dominion of immunoinformatics, and therefore, next generation of immunomedicines . Methods: Having reviewed the most recent works on the applications of computational tools, we provide comprehensive insights into the breast cancer incidence and its leading causes as well as immunotherapy approaches and the future trends. Furthermore, we discuss the impacts of bioinformatics on different stages of vaccine design for the breast cancer, which can be used to produce much more efficient vaccines through a rationalized time- and cost-effective in silico approaches prior to conducting costly experiments. Results: The tools can be significantly used for designing the immune system-modulating drugs and vaccines based on in silico approaches prior to in vitro and in vivo experimental evaluations. Application of immunoinformatics in the cancer immunotherapy has shown its success in the pre-clinical models. This success returns back to the impacts of several powerful computational approaches developed during the last decade. Conclusion: Despite the invention of a number of vaccines for the cancer immunotherapy, more computational and clinical trials are required to design much more efficient vaccines against various malignancies, including breast cancer.

show abstract

CIG-DB: the database for human or mouse immunoglobulin and T cell receptor genes available for cancer studies

Cited by 9 publications

References 34 publications

Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy

Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy

Sequence analysis of T-cell repertoires in health and disease

Breast cancer vaccination comes to age: impacts of bioinformatics

Contact Info

Product

Resources

About