A new transcript in the TCRB locus unveils the human ortholog of the mouse pre-Dß1 promoter

Introduction

While most transcripts arising from the human T Cell Receptor locus reflect fully rearranged genes, several germline transcripts have been identified. We describe a new germline transcript arising from the human TCRB locus.

Methods

cDNA sequencing, promoter, and gene expression analyses were used to characterize the new transcript.

Results

The new germline transcript encoded by the human TCRB locus consists of a new exon of 103 bp, which we named TRBX1 (X1), spliced with the first exon of gene segments Cß1 or Cß2. X1 is located upstream of gene segment Dß1 and is therefore deleted from a V‐DJ rearranged TCRB locus. The X1‐Cß transcripts do not appear to code for a protein. We define their transcription start and minimal promoter. These transcripts are found in populations of mature T lymphocytes from blood or tissues and in T cell clones with a monoallelic TCRB rearrangement. In immature thymocytes, they are already detectable in CD1a⁻CD34⁺CD4⁻CD8⁻ cells, therefore before completion of the TCRB rearrangements.

Conclusions

The X1 promoter appears to be the ortholog of the mouse pre‐Dß1 promoter (PDß1). Like PDß1, its activation is regulated by Eß in T cells and might facilitate the TCRB rearrangement process by contributing to the accessibility of the Dß1 locus.

Identification of a naturally processed HLA-A*02:01-restricted CTL epitope from the human tumor-associated antigen Nectin-4

Nectin-4 is a tumor antigen present on the surface of breast, ovarian and lung carcinoma cells. It is rarely present in normal adult tissues and is therefore a candidate target for cancer immunotherapy. Here, we identified a Nectin-4 antigenic peptide that is naturally presented to T cells by HLA-A2 molecules. We first screened the 502 nonamer peptides of Nectin-4 (510 amino acids) for binding to and off-rate from eight different HLA class I molecules. We then combined biochemical, cellular and algorithmic assays to select 5 Nectin-4 peptides that bound to HLA-A*02:01 molecules. Cytolytic T lymphocytes were obtained from healthy donors, that specifically lyzed HLA-A2(+) cells pulsed with 2 out of the 5 peptides, indicating the presence of anti-Nectin-4 CD8(+) T lymphocytes in the human T cell repertoire. Finally, an HLA-A2-restricted cytolytic T cell clone derived from a breast cancer patient recognized peptide Nectin-4145-153 (VLVPPLPSL) and lyzed HLA-A2(+) Nectin-4(+) breast carcinoma cells. These results indicate that peptide Nectin-4145-153 is naturally processed for recognition by T cells on HLA-A2 molecules. It could be used to monitor antitumor T cell responses or to immunize breast cancer patients.

Abstract P4-04-08: Presence of tumor-specific cytolytic T cells in human primary breast carcinoma: Consequences for immunotherapy

Background: Immunotherapy through stimulatory antibodies targeting the CTLA-4 or PD-1 pathways has a clear clinical efficacy in a fraction of patients with various cancers. It is likely that the main immune effectors of these therapies are CD8+ cytolytic T lymphocytes (CTL) recognizing tumor-specific antigens. The antigenicity of human tumors has been demonstrated with studies conducted mostly on melanomas. However the genetic mechanisms leading to antigenicity, notably point mutations in the tumor cells, apply to all cancer types. Thus primary breast carcinoma cells do certainly bear tumor-specific antigens, even though the extent of this antigenicity is unknown. Most melanomas, which are highly antigenic tumors, are also immunogenic, i.e. they stimulate spontaneous anti-tumor CTL responses. This immunogenicity, of which the presence of tumor-infiltrating T cells (TILs) is probably a surrogate marker, might be a predictive marker for clinical benefit to immunostimulatory antibodies. Whether primary breast carcinomas are immunogenic is not known, mainly due the absence of autologous tumor cell lines to analyze patients' T cells. However even in the absence of T-cell aimed immunotherapy the amounts of TILs have been positively correlated with patients' survival. Here we wished to obtain evidence for the presence of tumor-specific CD8+ T cells in TILs from primary breast carcinomas.

Methods: From each tumor we isolated TILs and derived a random set of ±100 CD8+ clones maintained in culture by stimulation with anti-CD3 antibodies, thus irrespective of their antigenic specificity. We screened these clones for recognition of tumor-specific antigens present on the autologous tumor. In the absence of autologous tumor lines we restricted our analysis to mutated antigens selected on the basis of tumor exome sequencing and gene expression profiling. Indels and non-synonymous base substitutions were selected to synthesize candidate mutated peptides.

Results: Thus far we have analyzed two hormone receptor-positive HER2-negative primary carcinomas. For one patient we screened 144 T cell clones for recognition of 40 candidate mutated peptides, without any positive result. For the other patient, 6 out of 98 T cell clones recognized 4 out of 119 candidate mutated peptides. Two peptides were recognized by two different T cell clones, i.e. with different T cell receptor sequences. These 4 'antigenic' mutations appear to be passenger, i.e. the four genes have a low published mutation frequency.

Conclusions: We conclude that some human primary breast carcinomas are immunogenic, as one tumor contained at least 6% of tumor-specific T cells among the CD8+ TILs. It suggests that the corresponding patient could benefit from the currently used immunostimulatory antibodies. More work is required to understand the reasons for the negative results in the first patient. We are pursuing the work on 2 HER2-positive and 2 triple-negative tumors, in which TILs are better correlated with prognosis. Our results warrant more investigations on the activation or inhibition of tumor-specific T cells at early stages of human breast cancer development.

Citation Format: Schröder DJ, Bricard O, Hames G, Remy N, Carrasco J, Canon J-L, Berlière M, Galant C, Coulie PG. Presence of tumor-specific cytolytic T cells in human primary breast carcinoma: Consequences for immunotherapy. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P4-04-08.

DNA methylation profiling reveals a predominant immune component in breast cancers

Breast cancer is a molecularly, biologically and clinically heterogeneous group of disorders. Understanding this diversity is essential to improving diagnosis and optimizing treatment. Both genetic and acquired epigenetic abnormalities participate in cancer, but the involvement of the epigenome in breast cancer and its contribution to the complexity of the disease are still poorly understood. By means of DNA methylation profiling of 248 breast tissues, we have highlighted the existence of previously unrecognized breast cancer groups that go beyond the currently known 'expression subtypes'. Interestingly, we showed that DNA methylation profiling can reflect the cell type composition of the tumour microenvironment, and in particular a T lymphocyte infiltration of the tumours. Further, we highlighted a set of immune genes having high prognostic value in specific tumour categories. The immune component uncovered here by DNA methylation profiles provides a new perspective for the importance of the microenvironment in breast cancer, holding implications for better management of breast cancer patients.

Identification of a tumor-specific shared antigen derived from an Eph receptor and presented to CD4 T cells on HLA class II molecules

We obtained a lytic CD4 T-cell clone that recognized an antigen presented by HLA-DRB1*1101 on the tumor cells of a melanoma patient who enjoyed an unusually favorable clinical evolution. The antigen appeared to be shared between several melanoma cell lines. To identify the encoding gene, we used a new method, based on the cotransfection into human embryonal kidney cell line 293 of a cDNA library from the tumor together with a cDNA clone encoding the class II transactivator, which induces the expression of HLA class II molecules. The product of the gene coding for the antigenic peptide is EphA3, a member of the Eph family of tyrosine kinase receptors, which mediate the repulsion of neural cells by cells carrying the ligand Ephrins on their surface. EphA3 is expressed at a high level in the retina and fetal brain, at a lower level in several normal tissues, and not at all in hematopoietic cells, the only cells that constitutively express HLA class II molecules. It is overexpressed in several types of tumors, including melanoma, lung carcinoma, and sarcoma. On the basis of this pattern of expression, EphA3 may be a source of tumor-specific antigens recognized on tumor cells that express HLA class II molecules. Anti-EphA3 T cells may have participated in a tumor rejection response in the patient, because the cells of metastases collected several years later than the metastasis used to characterize the antigen had lost expression of HLA-DR or EphA3, therefore escaping recognition by these lymphocytes.

Genes encoding tumor-specific antigens are expressed in human myeloma cells

Genes of the MAGE, BAGE, GAGE, and LAGE-1/NY-ESO-1 families encode antigenic peptides that are presented by HLA class I molecules and that are recognized on human tumors by autologous cytolytic T lymphocytes. These genes are expressed in many solid tumor types but not in normal tissues, except male germline cells. Because the latter cells are devoid of HLA molecules, the derived antigens are strictly tumor-specific and should constitute safe immunogens for cancer immunotherapy. We detected a significant expression of these genes in a high proportion of bone marrow samples from patients with advanced multiple myeloma. This observation provides a basis for clinical trials aimed at inducing a cellular immune response directed at malignant plasma cells in advanced myeloma patients.