Epstein-Barr Virus-Positive Cancers Show Altered B-Cell Clonality

Epstein-Barr virus (EBV) is convincingly associated with gastric cancer, nasopharyngeal carcinoma, and certain lymphomas, but its role in other cancer types remains controversial. To test the hypothesis that there are additional cancer types with high prevalence of EBV, we determined EBV viral expression in all the Cancer Genome Atlas Project (TCGA) mRNA sequencing (mRNA-seq) samples (n 10,396) from 32 different tumor types. We found that EBV was present in gastric adenocarcinoma and lymphoma, as expected, and was also present in 5% of samples in 10 additional tumor types. For most samples, EBV transcript levels were low, which suggests that EBV was likely present due to infected infiltrating B cells. In order to determine if there was a difference in the B-cell populations, we assembled B-cell receptors for each sample and found B-cell receptor abundance (P 1.4 1020) and diversity (P 8.3 1027) were significantly higher in EBV-positive samples. Moreover, diversity was independent of B-cell abundance, suggesting that the presence of EBV was associated with an increased and altered B-cell population. IMPORTANCE Around 20% of human cancers are associated with viruses. Epstein-Barr virus (EBV) contributes to gastric cancer, nasopharyngeal carcinoma, and certain lymphomas, but its role in other cancer types remains controversial. We assessed the prevalence of EBV in RNA-seq from 32 tumor types in the Cancer Genome Atlas Project (TCGA) and found EBV to be present in 5% of samples in 12 tumor types. EBV infects epithelial cells and B cells and in B cells causes proliferation. We hypothesized that the low expression of EBV in most of the tumor types was due to infiltration of B cells into the tumor. The increase in B-cell abundance and diversity in subjects where EBV was detected in the tumors strengthens this hypothesis. Overall, we found that EBV was associated with an increased and altered immune response. This result is not evidence of causality, but a potential novel biomarker for tumor immune status

Virus expression detection reveals RNA-sequencing contamination in TCGA

Background: Contamination of reagents and cross contamination across samples is a long-recognized issue in molecular biology laboratories. While often innocuous, contamination can lead to inaccurate results. Cantalupo et al., for example, found HeLa-derived human papillomavirus 18 (H-HPV18) in several of The Cancer Genome Atlas (TCGA) RNA-sequencing samples. This work motivated us to assess a greater number of samples and determine the origin of possible contaminations using viral sequences. To detect viruses with high specificity, we developed the publicly available workflow, VirDetect, that detects virus and laboratory vector sequences in RNA-seq samples. We applied VirDetect to 9143 RNA-seq samples sequenced at one TCGA sequencing center (28/33 cancer types) over 5 years. Results: We confirmed that H-HPV18 was present in many samples and determined that viral transcripts from H-HPV18 significantly co-occurred with those from xenotropic mouse leukemia virus-related virus (XMRV). Using laboratory metadata and viral transcription, we determined that the likely contaminant was a pool of cell lines known as the "common reference", which was sequenced alongside TCGA RNA-seq samples as a control to monitor quality across technology transitions (i.e. microarray to GAII to HiSeq), and to link RNA-seq to previous generation microarrays that standardly used the "common reference". One of the cell lines in the pool was a laboratory isolate of MCF-7, which we discovered was infected with XMRV; another constituent of the pool was likely HeLa cells. Conclusions: Altogether, this indicates a multi-step contamination process. First, MCF-7 was infected with an XMRV. Second, this infected cell line was added to a pool of cell lines, which contained HeLa. Finally, RNA from this pool of cell lines contaminated several TCGA tumor samples most-likely during library construction. Thus, these human tumors with H-HPV or XMRV reads were likely not infected with H-HPV 18 or XMRV

Prognostic value of B cells in cutaneous melanoma

Background: Measures of the adaptive immune response have prognostic and predictive associations in melanoma and other cancer types. Specifically, intratumoral T cell density and function have considerable prognostic and predictive value in skin cutaneous melanoma (SKCM). Less is known about the significance of tumor-infiltrating B cells in SKCM. Our goal was to understand the prognostic and predictive value of B cell phenotypic subsets in SKCM using RNA sequencing. Methods: We used our previously published algorithm, V'DJer, to assemble B cell receptor (BCR) repertoires and estimate diversity from short-read RNA sequencing (RNA-seq). We applied machine learning-based cellular phenotype classifiers to measure relative similarity of bulk tumor sample gene expression profiles and different B cell phenotypes. We assessed these aspects of B cell biology in 473 SKCM from the Cancer Genome Atlas Project (TCGA) as well as in RNA-seq data corresponding to tumor samples procured from patients who received CTLA-4 and PD-1 inhibitors for metastatic SKCM. Results: We found that the BCR repertoire was associated with different clinical factors, such as tumor tissue site and sex. However, increased clonality of the BCR repertoire was favorably prognostic in SKCM and was prognostic even after first conditioning on various clinical factors. Mutation burden was not correlated with any BCR measurement, and no specific mutation had an altered BCR repertoire. Lack of an assembled BCR in pre-treatment tumor tissues was associated with a lack of anti-tumor response to a CTLA-4 inhibitor in metastatic SKCM. Conclusions: These findings suggest an important prognostic and predictive role for B cell characteristics in SKCM. This has implications for melanoma immunobiology and potential development of immunogenomics features to predict survival and response to immunotherapy

Reply to P. de Paoli et al

Weare grateful for the correspondence provided by De Paoli and Carbone1 regarding our recently published Comments and Controversies piece focused on HIV-associated cancers. Their letter provides an important extension of some of the main points articulated in our article. Indeed, we wish to acknowledge our correspondents’ own excellent review also highlighting the complexity and heterogeneity of cancers occurring in the HIV-infected populatio

Moving forward in HIV-associated cancer

Cancer has been linked to HIV since the earliest days of the epidemic. The unusually frequent occurrence of Kaposi sarcoma (KS) among men who have sex with men (MSM) in 1981 was a sentinel observation leading to the inclusion of KS in the first AIDS case definition.1,2 More than three decades later, major research investments have led to striking advances in understanding HIV pathogenesis, with antiretroviral therapy (ART) reducing AIDS complications and allowing HIV-infected individuals to experience life expectancy approaching that of persons without HIV

Chlamydia trachomatis Seroprevalence and Ultrasound-Diagnosed Uterine Fibroids in a Large Population of Young African-American Women

Reproductive tract infections have long been hypothesized to increase the risk of uterine fibroids. Few studies have been conducted, even for the common infection genital Chlamydia trachomatis (gCT), and only with self-reported gCT data. Our investigation used micro-immunofluorescence serology for gCT to characterize past exposure. We used cross-sectional enrollment data from a prospective fibroid study carried out in the Detroit, Michigan, area; ultrasound examinations systematically screened for fibroids. Participants were African-American women aged 23–34 years (recruited in 2010–2012). Age- and multivariable-adjusted logistic regression models were used to estimate odds ratios. A total of 1,587 women (94% of participants) had unequivocal gCT serology results; 22% had fibroids. Those who were seropositive for gCT were less likely to have fibroids (age-adjusted odds ratio = 0.68, 95% confidence interval: 0.54, 0.87; multivariable-adjusted odds ratio = 0.80, 95% confidence interval: 0.62, 1.03). Inverse associations were similar across categories of fibroid size, number, and total volume. Participant groups likely to have had multiple or severe infections (multiple serovar groups, more sex partners, clinically diagnosed chlamydia) all showed statistically significantly reduced odds of fibroids. A protective association of gCT with fibroids was unexpected but plausible. gCT infection might increase immune surveillance and eliminate early lesions. Further investigation on the relationship between fibroid development and reproductive tract infections is neede

Oral shedding of herpesviruses in HIV-infected patients with varying degrees of immune status

Objective: Herpesvirus shedding in the oral cavity was analyzed to determine if presence in the oral compartment correlates with systemic changes in HIV-associated immune deficiency as measured by CD4 + cell counts, plasma HIV viral load and presence of AIDS-defining events. Design: A5254 is a multicenter, cross-sectional, single-visit study to evaluate oral complications of HIV/AIDS and determine the association between clinical appearance, herpesvirus shedding, and immune status as ascertained by CD4 + cell count and HIV viral load. In total, 307 HIV-infected individuals were evaluated and throat wash collected. Methods: Fisher's exact test and Kruskal-Wallis test were used to assess the association between presence of herpesviruses and the state of immunodeficiency as stratified by a combination of CD4 + cell count and HIV viral load. Relationship between pathogens and HIV viral load in plasma was modeled by logistic regression. Results: The presence of cytomegalovirus (CMV) and herpes simplex virus-1 in throat wash was associated with decreased CD4 + cell counts. By contrast, Kaposi sarcoma-associated herpesvirus and Epstein-Barr virus were similarly detectable across all levels of CD4 + cell counts. One unit increase in log 10 (HIV viral load) was associated with 1.31 times higher odds of detecting CMV in throat wash when controlling for oral candidiasis, CD4 + cell count, and sites (95% confidence interval 1.04-1.65, P=0.02). Conclusion: Oral CMV shedding was significantly higher in highly immunocompromised HIV + participants. Our finding supports the recommendations to start antiretroviral therapy independent of CD4 + cell count as this may have the added benefit to lower the risk of herpesvirus transmission among persons infected with HIV and their partners

Source and purity of dengue-viral preparations impact requirement for enhancing antibody to induce elevated IL-1β secretion: A primary human monocyte model

Dengue virus is a major global health threat and can lead to life-threatening hemorrhagic complications due to immune activation and cytokine production. Cross-reactive antibodies to an earlier dengue virus infection are a recognized risk factor for severe disease. These antibodies bind heterologous dengue serotypes and enhance infection into Fc-receptorbearing cells, a process known as antibody-dependent enhancement of infection. One crucial cytokine seen elevated in severe dengue patients is IL-1β, a potent inflammatory cytokine matured by the inflammasome. We used a highly-physiologic system by studying antibody-dependent enhancement of IL-1β in primary human monocytes with anti-dengue human monoclonal antibodies isolated from patients. Antibody-enhancement increased viral replication in primary human monocytes inoculated with supernatant harvested from Vero cells infected with dengue virus serotype 2 (DENV-2) 16681. Surprisingly, IL-1β secretion induced by infectious supernatant harvested from two independent Vero cell lines was not enhanced by antibody. Secretion of multiple other inflammatory cytokines was also independent of antibody signaling. However, IL-1β secretion did require NLRP3 and caspase- 1 activity. Immunodepletion of dengue virions from the infectious supernatant confirmed that virus was not the main IL-1β-inducing agent, suggesting that a supernatant component(s) not associated with the virion induced IL-1β production. We excluded RNA, DNA, contaminating LPS, viral NS1 protein, complement, and cytokines. In contrast, purified Vero-derived DENV-2 16681 exhibited antibody-enhancement of both infection and IL-1β induction. Furthermore, C6/36 mosquito cells did not produce such an inflammatory component, as crude supernatant harvested from insect cells infected with DENV-2 16681 induced antibody-dependent IL-1β secretion. This study indicates that Vero cells infected with DENV-2 16681 may produce inflammatory components during dengue virus propagation that mask the virus-specific immune response. Thus, the choice of host cell and viral purity should be carefully considered, while insect-derived virus represents a systemthat elicits antibody- dependent cytokine responses to dengue virus with fewer confounding issues

Prevalence, incidence, and distribution of human papillomavirus types in female sex workers in Kenya

Female sex workers (FSWs) have a notably high risk of acquiring human papillomavirus (HPV) infections. Relatively few studies address the type-specific prevalence and incidence of HPV among FSWs in sub-Saharan Africa. FSWs (n = 348) attending the Korogocho clinic in Nairobi, Kenya participated from August 2009 to March 2011. HPV DNA was detected using the SPF10-LiPA25 PCR assay. Baseline prevalence of HPV infection and cervical dysplasia were calculated, stratified by HIV-serostatus. Incidence rate (IR) of infection was calculated as number of new infections from baseline over person-months among 160 HPV-negative participants with complete 12-month follow-up. Baseline HPV prevalence was 23.6% for any HPV and 20.4% for high-risk HPV (hrHPV) types. Most prevalent types were HPV52 (10.1%), HPV35 (2.3%), and HPV51 (2.3%). A quarter (24%) of participants were HIV-positive. HPV prevalence was higher in HIV-positive (32.1%) than HIV-negative (20.8%) participants. hrHPV prevalence was higher in HIV-positive (27.4%) than HIV-negative (18.2%) women. During follow-up, HPV IR was 31.4 (95% CI: 23.8–41.5) for any HPV and 24.2 (95% CI: 17.9–32.8) for hrHPV types. HPV52 had the highest IR (6.0; 95% CI: 6.5–10.3). Overall HPV and hrHPV prevalence were lower than expected, but both prevalence and incidence were higher in HIV-positive than in HIV-negative women

Incomplete viral suppression and mortality in HIV patients after antiretroviral therapy initiation

Objective: To determine whether there is a threshold of detectable HIV RNA under 1000 copies/ml after antiretroviral therapy initiation associated with 10-year all-cause mortality. Design: This study included nearly 8000 patients from a US-based multicenter clinical cohort who started antiretroviral therapy between 1 January 1998 and 31 December 2013. Viral load was assessed 6 months after initiation of therapy. Patients were followed from 6 months after therapy initiation (between 1 July 1998 and 30 June 2014) until death, and data were administratively censored after 10 years or on 31 December 2014. Methods: We used nonparametric multiple imputation to account for left-censored viral load measurements, Cox proportional hazards models to estimate all-cause mortality hazard ratios, Nelson-Aalen cumulative hazard estimates to construct risk curves, and inverse probability of exposure weights to standardize estimated hazard ratios and risk curves to the total study population. Results: Plots of standardized hazard ratio estimates and 95% confidence intervals indicated there was no demonstrable viral load threshold between 30 and 500 copies/ml associated with a marked increase in 10-year mortality. The standardized 10-year risk of mortality among patients with viral loads between 400 and 999 copies/ml 6 months after starting treatment was comparable with the risk of mortality among patients with viral loads between 1000 and 4 million copies/ml (20 vs. 23%). Conclusion: Incomplete suppression of plasma HIV RNA 6 months after starting therapy is associated with substantial 10-year all-cause mortality risk, highlighting the importance of rapid viral load suppression after therapy initiation