Human Immunodeficiency Virus/Human Papillomavirus co-infection and host molecular genetics of cervical carcinoma

A subgroup of women who are co-infected with human immunodeficiency virus type 1 (HIV1) and human papillomavirus (HPV) progress relatively rapidly to cervical disease regardless of the number of absolute CD4 count. During infection, viral peptides are recognized by the host immune system. It is reasonable to propose that the development of viral-associated cancers, like cervical cancer, requires interference with specific immune-response genes. This thesis investigates this proposition with consideration of host molecular genetic alterations and variations of the human leukocyte antigen class II (HLA II) genes as one of the groups of immune-response genes that are involved in directing CD4 T-cell responses during infection, in the instance of cervical cancer progression in HIV-1/HPV co-infected women. Study I, reviewed the available literature on host molecular genetics and HIV-1/HPV coinfection on cervical cancer progression. This study suggests that the dual pro-oncogenic effects of HPV oncoproteins E6/E7 and the HIV-1 oncoprotein Tat, may exacerbate and accelerate the rate of cervical disease progression in a subgroup of HIV-1-positive women. Additionally, HIV-1-positive cervical cancer has three important carcinogenesis steps: firstly, HPV integration into the host genome, secondly, dual pro-oncogenic effects of HPV oncoproteins E6/E7, and the HIV-1 Tat oncoprotein in the host genome and, thirdly, the accumulation of repeated, unrepaired genetic mutations and genetic alterations within the host chromosomal DNA. Genetic variations or mutations that affect the following host gene categories were suggested to be responsible for cervical cancer susceptibility and disease progression; (i) genes for the immune-response against oncogenic HPV infection, (ii) oncogenes, (iii) tumour-suppressor genes, (iv) apoptosis-related genes, (v) DNA damagerepair genes, and (vi) cell cycle-regulatory genes. However, studies II, III and IV are linked together and listed according to the specific objectives of this thesis. Study II, characterized the distribution of HPV genotypes within cervical tumour biopsies from a cohort of 181 HPV-unvaccinated South African women and studied the relationships with HIV-1 infection, age of patients, absolute CD4 count, CD4 percentage and the stage of cervical disease, and identified the predictive power of these variables for cervical disease stage. Distribution of HPV genotypes was related to the stage of cervical disease in HIV-1-positive women. Older age was a significant predictor for invasive cervical cancer (ICC) in both HIV-1-seronegative (p28% CD4 cells (both p350 cells/µl compared to 30% (12/40) who possessed absolute CD4 count ≤ 350 cells/µl (both p< 0.001, q< 0.001). Study III, was the first case-control study to investigate the association of HIV-1/HPV coinfection with specific host HLA II-DRB1 and -DQB1 alleles in cervical cancer. Two hundred and fifty-six (256) women of the same ethnicity were recruited, comprising 56 cases and 200 age-matched controls. A total of 624 HLA-DRB1 and -DQB1 class II genotypes were studied. HLA II-DQB1*03:01 and -DQB1*06:02 alleles were associated with cervical cancer in HIV-1/HPV co-infected women (p=0.001 and p< 0.0001, respectively) while HLA II-DRB1*13:01 and -DQB1*03:19 were rare or absent in women with cervical disease when compared to the control population (p=0.012 and 0.011, respectively). Study IV, aimed to investigate the host genetic alterations that may be involved in rapid tumour progression in HIV-1/HPV co-infected women. The frequency of loss of heterozygosity (LOH) and microsatellite instability (MSI) at the HLA II locus on chromosome 6p was analysed in cervical tumour biopsy DNA, with regard to HIV-1/HPV co-infection in 164 women. Seventy-four women were HIV-1-positive and ninety women were HIV-1-seronegative. Tumour DNA from HIV-1/HPV co-infected women demonstrated a higher frequency of LOH/MSI at the HLA II locus at 6p21.21 than tumour DNA from HIV1-seronegative women (D6S2447, 74.2% versus 42.6%; p=0.001, q=0.003), D6S2881 at 6p21.31 (78.3% versus 42.9%; p=0.002, q=0.004), D6S1666 at 6p21.32 (79% versus 57.1%; p=0.035, q=0.052), and D6S2746, at 6p21.33 (64.3% versus 29.4%; p< 0.001, q< 0.001), respectively. This thesis provides novel insights and adds to the existing knowledge on the relationships between HIV-1/HPV co-infection, CD4 immune status, host HLA II allele variations and genetic alterations at chromosome 6p in association or likely protection to cervical disease in the studied cohort of South African women. Identification of host molecular genetic susceptibility to disease with regard to viral infection is important for individualized molecular targeted prevention of cervical cancer

A Scoring Model and Protocol to Adapt Universal Screening for Lynch Syndrome to Identify Germline Pathogenic Variants by Next Generation Sequencing from Colorectal Cancer Patients and Cascade Screening

Identification of germline pathogenic variants (PV) predisposing to Lynch syndrome (LS) is an important step for effective use of cascade screening of extended at-risk lineages, leading to reduced morbidity and mortality due to colorectal cancer (CRC). As a general rule, however, next generation sequencing (NGS, either of gene panels or whole exomes) is relatively expensive and unaffordable for general clinical use. In resource-poor settings, performing NGS testing on an entire cohort of CRC patients, even if limited to those under 50 or 60 years of age, still places an enormous burden on limited resources. Although family history can be a good indicator for LS testing, identifying at-risk family members and offering cascade screening may not benefit many patients/probands without an obvious family history. This article presents a novel program called Modified Ascertainment and follow-up Program (MAP) with a scoring model for LS ascertainment and molecular screening by NGS with diagnosis confirmation of PV and cascade screening. The goal is to improve LS ascertainment in light of the growing burden of early-onset CRC, particularly in low- and middle-income countries. Through MAP, judiciously applied molecular genetics will improve identification of PV predisposing to LS and cascade screening

Vaginal microbiomes associated with aerobic vaginitis and bacterial vaginosis

A healthy vaginal microbiota is considered to be significant for maintaining vaginal health and preventing infections. However, certain vaginal bacterial commensal species serve an important first line of defense of the body. Any disruption of this microbial barrier might result in a number of urogenital conditions including aerobic vaginitis (AV) and bacterial vaginosis (BV). The health of the vagina is closely associated with inhabitant microbiota. Furthermore, these microbes maintain a low vaginal pH, prevent the acquisition of pathogens, stimulate or moderate the local innate immune system, and further protect against complications during pregnancies. Therefore, this review will focus on vaginal microbial “health” in the lower reproductive tract of women and on the physiological characteristics that determine the well-being of reproductive health. In addition, we explore the distinct versus shared characteristics of BV and AV, which are commonly associated with increased risk for preterm delivery

Genetic insights: High germline variant rate in an indigenous African cohort with early-onset colorectal cancer

IntroductionThe increase in incidence of colorectal cancer in young patients of African ancestry coupled with increased aggressiveness has warranted investigation of the heritable nature of these cancers. Only a limited number of published reports of hereditary colorectal cancer in indigenous African populations have been reported and no systematic screening of these groups has been performed previously. We aimed to investigate causative germline variants and to establish the incidence of pathogenic/likely pathogenic germline variants in the known colorectal cancer genes in indigenous African colorectal cancer patients using a next-generation sequencing (NGS) multigene panel.Materials and methodsPatients were selected from two hospitals in Cape Town and Johannesburg, South Africa. Patients with unresolved molecular diagnosis with an age of onset below or at 60 years were selected. Germline DNA samples were analyzed using a 14-gene NGS panel on the Ion Torrent platform. Variant calling and annotation were performed, and variants were classified according to the American College of Medical Genetics and Genomics guidelines. Observed variants were verified by Sanger sequencing and/or long-range PCR.ResultsOut of 107 patients, 25 (23.4%) presented with a pathogenic/likely pathogenic germline variant (PGV). Fourteen PGVs in at least one mismatch repair (MMR) gene were identified and verified in 12 patients (11.2%). Of these MMR gene variants, five were novel. The remaining 10 PGVs were in the APC, BMPR1A, MUTYH, POLD1, and TP53 genes.ConclusionThe high incidence of PGVs associated with early-onset colorectal cancer in indigenous African patients has important implications for hereditary colorectal cancer risk management. These findings pave the way for personalized genetic screening programs and cascade testing in South Africa. The next step would involve further screening of the unresolved cases using tools to detect copy number variation, methylation, and whole exome sequencing

A Scoring Model and Protocol to Adapt Universal Screening for Lynch Syndrome to Identify Germline Pathogenic Variants by Next Generation Sequencing from Colorectal Cancer Patients and Cascade Screening

Identification of germline pathogenic variants (PV) predisposing to Lynch syndrome (LS) is an important step for effective use of cascade screening of extended at-risk lineages, leading to reduced morbidity and mortality due to colorectal cancer (CRC). As a general rule, however, next generation sequencing (NGS, either of gene panels or whole exomes) is relatively expensive and unaffordable for general clinical use. In resource-poor settings, performing NGS testing on an entire cohort of CRC patients, even if limited to those under 50 or 60 years of age, still places an enormous burden on limited resources. Although family history can be a good indicator for LS testing, identifying at-risk family members and offering cascade screening may not benefit many patients/probands without an obvious family history. This article presents a novel program called Modified Ascertainment and follow-up Program (MAP) with a scoring model for LS ascertainment and molecular screening by NGS with diagnosis confirmation of PV and cascade screening. The goal is to improve LS ascertainment in light of the growing burden of early-onset CRC, particularly in low- and middle-income countries. Through MAP, judiciously applied molecular genetics will improve identification of PV predisposing to LS and cascade screening

Common bacterial isolates, clinical outcome and TB meningitis in children admitted at Morogoro Regional Referral Hospital, Tanzania

Background: Bacterial meningitis is still one of the major causes of deaths, disabilities, and mental retardation in children in Morogoro region. To study the current meningitis burden, we evaluated the common bacterial isolates and clinical outcome of the disease in the region. Methods: We conducted a hospital-based prospective study on 1352 children aged between 7 days and 12 years admitted in pediatric wards at Morogoro Regional Referral Hospital for 7 months. Cerebrospinal fluid (CSF) for laboratory microbiological examination was collected by lumbar puncture in 72 children with signs and symptoms of meningitis. Latex agglutination test was used to confirm the bacterial colonies in the culture. Chi-square test was used for relative risk with 95% confidence intervals; statistical analysis and tests were considered statistically significant when P < 0.05. Results: Among 72 CSF samples, 23 (31.9%) were positive for Streptococcus pneumoniae, 6 (8.3%) for Haemophilus influenzae, 5 (6.9%) for Group B Streptococcus, 3 (4.2%) for Escherichia coli, and 1 (1.4%) was positive for Mycobacterium tuberculosis. Furthermore, 34 CSF samples showed no bacteria growth in the culture media. In addition, 39 children (54.2%) did not respond to the treatment, whereas 79.5% (n = 39) of them died, while 20.5% (n = 39) of them were referred to a tertiary hospital. Nevertheless, the incidence of meningitis infection was 5.3% (n = 1352) among the admitted children. Conclusions: S. pneumoniae was the major laboratory-confirmed bacterial isolate associated with meningitis in children. We report for the first time the presence of tuberculous meningitis in Morogoro region. Ziehl–Neelsen staining for acid-fast bacilli should be mandatory for any case clinically suspected for meningitis

Immunogenomic Biomarkers and Validation in Lynch Syndrome

Lynch syndrome (LS) is an inherited disorder in which affected individuals have a significantly higher-than-average risk of developing colorectal and non-colorectal cancers, often before the age of 50 years. In LS, mutations in DNA repair genes lead to a dysfunctional post-replication repair system. As a result, the unrepaired errors in coding regions of the genome produce novel proteins, called neoantigens. Neoantigens are recognised by the immune system as foreign and trigger an immune response. Due to the invasive nature of cancer screening tests, universal cancer screening guidelines unique for LS (primarily colonoscopy) are poorly adhered to by LS variant heterozygotes (LSVH). Currently, it is unclear whether immunogenomic components produced as a result of neoantigen formation can be used as novel biomarkers in LS. We hypothesise that: (i) LSVH produce measurable and dynamic immunogenomic components in blood, and (ii) these quantifiable immunogenomic components correlate with cancer onset and stage. Here, we discuss the feasibility to: (a) identify personalised novel immunogenomic biomarkers and (b) validate these biomarkers in various clinical scenarios in LSVH

Immunogenomic Biomarkers and Validation in Lynch Syndrome

Lynch syndrome (LS) is an inherited disorder in which affected individuals have a significantly higher-than-average risk of developing colorectal and non-colorectal cancers, often before the age of 50 years. In LS, mutations in DNA repair genes lead to a dysfunctional post-replication repair system. As a result, the unrepaired errors in coding regions of the genome produce novel proteins, called neoantigens. Neoantigens are recognised by the immune system as foreign and trigger an immune response. Due to the invasive nature of cancer screening tests, universal cancer screening guidelines unique for LS (primarily colonoscopy) are poorly adhered to by LS variant heterozygotes (LSVH). Currently, it is unclear whether immunogenomic components produced as a result of neoantigen formation can be used as novel biomarkers in LS. We hypothesise that: (i) LSVH produce measurable and dynamic immunogenomic components in blood, and (ii) these quantifiable immunogenomic components correlate with cancer onset and stage. Here, we discuss the feasibility to: (a) identify personalised novel immunogenomic biomarkers and (b) validate these biomarkers in various clinical scenarios in LSVH

Vaginal Microbiomes Associated With Aerobic Vaginitis and Bacterial Vaginosis

A healthy vaginal microbiota is considered to be significant for maintaining vaginal health and preventing infections. However, certain vaginal bacterial commensal species serve an important first line of defense of the body. Any disruption of this microbial barrier might result in a number of urogenital conditions including aerobic vaginitis (AV) and bacterial vaginosis (BV). The health of the vagina is closely associated with inhabitant microbiota. Furthermore, these microbes maintain a low vaginal pH, prevent the acquisition of pathogens, stimulate or moderate the local innate immune system, and further protect against complications during pregnancies. Therefore, this review will focus on vaginal microbial “health” in the lower reproductive tract of women and on the physiological characteristics that determine the well-being of reproductive health. In addition, we explore the distinct versus shared characteristics of BV and AV, which are commonly associated with increased risk for preterm delivery