Investigation of Cervical Tumor Biopsies for Chromosomal Loss of Heterozygosity (LOH) and Microsatellite Instability (MSI) at the HLA II Locus in HIV-1/HPV Co-infected Women

Ramadhani Chambuso; Evelyn Kaambo; Lynette Denny; Clive M Gray; Anna-Lise Williamson; Monika Migdalska-Sęk; Gloudi Agenbag; George Rebello; Raj Ramesar

doi:10.3389/fonc.2019.00951

Investigation of Cervical Tumor Biopsies for Chromosomal Loss of Heterozygosity (LOH) and Microsatellite Instability (MSI) at the HLA II Locus in HIV-1/HPV Co-infected Women

Front Oncol. 2019 Oct 15:9:951. doi: 10.3389/fonc.2019.00951. eCollection 2019.

Authors

Ramadhani Chambuso^{1

2}, Evelyn Kaambo^{3

4}, Lynette Denny^{5

6}, Clive M Gray^{7

8}, Anna-Lise Williamson^{3

5

7}, Monika Migdalska-Sęk⁹, Gloudi Agenbag^{1

7}, George Rebello¹, Raj Ramesar^{1

7}

Affiliations

¹ MRC Unit for Genomic and Precision Medicine, Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
² Department of Gynaecology, Morogoro Regional Referral Hospital, Morogoro, Tanzania.
³ Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
⁴ Department of Biochemistry and Medical Microbiology, University of Namibia School of Medicine, Windhoek, Namibia.
⁵ South African Medical Research Council, Clinical Gynaecological Cancer Research Centre, University of Cape Town, Cape Town, South Africa.
⁶ Department of Obstetrics and Gynaecology, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.
⁷ Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
⁸ Division of Immunology, Department of Pathology and National Health Laboratory Service, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa.
⁹ Department of Biomedicine and Genetics, Medical University of Lodz, Lodz, Poland.

Abstract

Background: A subgroup of women who are co-infected with human immunodeficiency virus type 1 (HIV-1) and human papillomavirus (HPV) progress rapidly to cervical disease regardless of high CD4 counts. Chromosomal loss of heterozygosity (LOH) and microsatellite instability (MSI) are early frequent genetic alterations occurring in solid tumors. Loss of an allele or part of a chromosome can have multiple functional effects on immune response genes, oncogenes, DNA damage-repair genes, and tumor-suppressor genes. To characterize the genetic alterations that may influence rapid tumor progression in some HIV-1-positive women, the extent of LOH and MSI at the HLA II locus on chromosome 6p in cervical tumor biopsy DNA samples with regard to HIV-1/HPV co-infection in South African women was investigated. Methods: A total of 164 women with cervical disease were recruited for this study, of which 74 were HIV-1-positive and 90 were HIV-1-seronegative. DNA from cervical tumors and matched buccal swabs were used for analyses. Six fluorescently-labeled oligonucleotide primer pairs in a multiplex PCR amplification were used to study LOH and MSI. Pearson chi-squared test for homogeneity of proportions using an exact p value, a two-proportion Z-score test, ROC curves and a logistic regression model were used for statistical analyses. All p-values were corrected for false discovery rate (FDR) using the Benjamini-Hochberg test and the adjusted p-values (q-values) were reported. All tests were significant when both p and q < 0.05. Results: Tumor DNA from HIV-1/HPV co-infected women demonstrated a higher frequency of LOH/MSI at the HLA II locus on chromosome 6p21.21 than tumor DNA from HIV-1-seronegative women (D6S2447, 74.2 vs. 42.6%; p = 0.001, q = 0.003), D6S2881 at 6p21.31 (78.3 vs. 42.9%; p = 0.002, q = 0.004), D6S2666 at 6p21.32 (79 vs. 57.1%; p = 0.035, q = 0.052), and D6S2746, at 6p21.33 (64.3 vs. 29.4%; p < 0.001, q < 0.001), respectively. Conclusions: HPV infection alone can induce LOH/MSI at the HLA II locus in cervical tumor DNA, whereas HIV-1 co-infection exacerbates it, suggesting that this may accelerate cervical disease progression in a subgroup of HIV-1-positive women.

Keywords: HIV-1/HPV co-infection; HLA II locus; cervical cancer; genetic alterations; host molecular genetics; loss of heterozygosity; microsatellite instability.