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HLA class I alterations in breast carcinoma are associated with a high frequency of the loss of heterozygosity at chromosomes 6 and 15

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Abstract

HLA class I (HLA-I) molecules play a crucial role in the presentation of tumor antigenic peptides to CD8+ T cells. Tumor HLA-I loss provides a route of immune escape from T cell-mediated killing. We analyzed HLA-I expression in 98 cryopreserved breast cancer tissues using a broad panel of anti-HLA-I antibodies. Genomic HLA-I typing was performed using DNA obtained from autologous normal breast tissue. Analysis of the loss of heterozygosity (LOH) in the HLA-I region of chromosome 6 (LOH-6) and in the β2-microglobulin (B2M) region of chromosome 15 (LOH-15) was done by microsatellite amplification of DNA isolated from microdissected tumor areas. B2M gene sequencing was done using this DNA form HLA-I-negative tumors. Immunohistological analysis revealed various types of HLA-I alterations in 79 tumors (81%), including total HLA-I loss in 53 cases (54%) and partial loss in 16 samples (14%). In 19 cases (19%), HLA-I expression was positive. Using microsatellite analysis, we detected LOH in 36 cases out of 92 evaluated (39%), including 15 samples with only LOH-6, 14 with LOH-15, and seven tumors with LOH-6 and LOH-15 at the same time. Remarkably, we detected LOH-6 in eight tumors with positive HLA-I immunolabeling. We did not find any B2M mutations in HLA-I-negative breast tumors. In conclusion, LOH at chromosomes 6 and 15 has a high incidence in breast cancer and occurs in tumors with different HLA-I immunophenotypes. This common molecular mechanism of HLA-I alterations may reduce the ability of cytotoxic T lymphocytes  to kill tumor cells and negatively influence the clinical success of cancer immunotherapy.

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Abbreviations

HLA:

Human leukocite antigens

MHC:

Major histocompatibility antigens

LOH:

Loss of heterozygosity

Β2Μ:

Beta-2-microglobilin

FFPE:

Formalin fixed paraffin embedded

IDC:

Infiltrating ductal carcinoma

ILC:

Infiltrating lobular carcinoma

TNM:

Tumor-node-metastasis

ER:

Estrogen receptor

PgR:

Progesterone receptor

SSO:

Sequence-specific oligonucleotide analysis

STR:

Short tandem repeat

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Acknowledgements

We would like to thank Antonia Martín Casares for the technical support in HLA typing and Amanda Rocío González-Ramírez for the statistical analysis of the obtained results.

Funding

This work was supported by the grants from Spanish Institute of Health Carlos III (ISCIII, Instituto Carlos III) co-financed by European Union (FEDER-Fondo Europeo de Desarrollo Regional) (PI12/02031, PI08/1265, PI11/01022, PI11/01386, RETIC RD 06/020, RD09/0076/00165, PT13/0010/0039, PI14/01978, PI16/00752, PI17/00197), the Junta de Andalucía in Spain (Groups CTS-143), and Beckman-Coulter. This study is part of the doctoral thesis of Maria A. Garrido.

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Authors and Affiliations

  1. Servicio de Radiología, UGC de Radiología, Hospital Universitario Virgen de las Nieves, Granada, Spain

    María A. Garrido

  2. Servicio de Análisis Clínicos e Inmunología, UGC de Laboratorio Clinico, Hospital Universitario Virgen de las Nieves, Granada, Spain

    Teresa Rodriguez, Svitlana Zinchenko, Isabel Maleno, Francisco Ruiz-Cabello & Federico Garrido

  3. Instituto de Investigación Biosanitaria ibs. Granada, Granada, Spain

    Francisco Ruiz-Cabello, Nicolás Olea, Federico Garrido & Natalia Aptsiauri

  4. Departamento de Bioquímica, Biología Molecular III e Inmunología, Facultad de Medicina, Universidad de Granada, Granada, Spain

    Francisco Ruiz-Cabello, Federico Garrido & Natalia Aptsiauri

  5. Servicio de Anatomía Patológica, Hospital Juan Canalejo, A Coruña, Spain

    Ángel Concha

  6. Servicio de Radiología, UGC de Radiología, Hospital del Campus, Granada, Spain

    Nicolás Olea

Authors
  1. María A. Garrido
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  2. Teresa Rodriguez
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  3. Svitlana Zinchenko
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  4. Isabel Maleno
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  5. Francisco Ruiz-Cabello
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  6. Ángel Concha
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  7. Nicolás Olea
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  8. Federico Garrido
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  9. Natalia Aptsiauri
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Corresponding authors

Correspondence to Federico Garrido or Natalia Aptsiauri.

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Ethical approval

All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.

The study protocol was approved by the ethical committee of the Virgen de las Nieves University Hospital and Instituto de Investigación Biosanitaria “ibs. Granada” (Comité de Ética de la Investigación de Centro de Granada (CEI Granada), number 2014-22/12). Signed informed consent approved by the Ethics Committee of our institution was obtained from all the patients.

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The authors declare that they have no competing interests.

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Garrido, M.A., Rodriguez, T., Zinchenko, S. et al. HLA class I alterations in breast carcinoma are associated with a high frequency of the loss of heterozygosity at chromosomes 6 and 15. Immunogenetics 70, 647–659 (2018). https://doi.org/10.1007/s00251-018-1074-2

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