Darrin V. Bann

Nucleolar Trafficking of the Mouse Mammary Tumor Virus Gag Protein Induced by Interaction with Ribosomal Protein L9

ABSTRACT The mouse mammary tumor virus (MMTV) Gag protein directs the assembly in the cytoplasm of immature viral capsids, which subsequently bud from the plasma membranes of infected cells. MMTV Gag localizes to discrete cytoplasmic foci in mouse mammary epithelial cells, consistent with the formation of cytosolic capsids. Unexpectedly, we also observed an accumulation of Gag in the nucleoli of infected cells derived from mammary gland tumors. To detect Gag-interacting proteins that might influence its subcellular localization, a yeast two-hybrid screen was performed. Ribosomal protein L9 (RPL9 or L9), an essential component of the large ribosomal subunit and a putative tumor suppressor, was identified as a Gag binding partner. Overexpression of L9 in cells expressing the MMTV(C3H) provirus resulted in specific, robust accumulation of Gag in nucleoli. Förster resonance energy transfer (FRET) and coimmunoprecipitation analyses demonstrated that Gag and L9 interact within the nucleolus, and the CA domain was the major site of interaction. In addition, the isolated NC domain of Gag localized to the nucleolus, suggesting that it contains a nucleolar localization signal (NoLS). To determine whether L9 plays a role in virus assembly, small interfering RNA (siRNA)-mediated knockdown was performed. Although Gag expression was not reduced with L9 knockdown, virus production was significantly impaired. Thus, our data support the hypothesis that efficient MMTV particle assembly is dependent upon the interaction of Gag and L9 in the nucleoli of infected cells.

Application of live-cell RNA imaging techniques to the study of retroviral RNA trafficking.

Retroviruses produce full-length RNA that serves both as a genomic RNA (gRNA), which is encapsidated into virus particles, and as an mRNA, which directs the synthesis of viral structural proteins. However, we are only beginning to understand the cellular and viral factors that influence trafficking of retroviral RNA and the selection of the RNA for encapsidation or translation. Live cell imaging studies of retroviral RNA trafficking have provided important insight into many aspects of the retrovirus life cycle including transcription dynamics, nuclear export of viral RNA, translational regulation, membrane targeting, and condensation of the gRNA during virion assembly. Here, we review cutting-edge techniques to visualize single RNA molecules in live cells and discuss the application of these systems to studying retroviral RNA trafficking.

Alterations in the MA and NC Domains Modulate Phosphoinositide-Dependent Plasma Membrane Localization of the Rous Sarcoma Virus Gag Protein

ABSTRACT Retroviral Gag proteins direct virus particle assembly from the plasma membrane (PM). Phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P2] plays a role in PM targeting of several retroviral Gag proteins. Here we report that depletion of intracellular PI(4,5)P2 and phosphatidylinositol-(3,4,5)-triphosphate [PI(3,4,5)P3] levels impaired Rous sarcoma virus (RSV) Gag PM localization. Gag mutants deficient in nuclear trafficking were less sensitive to reduction of intracellular PI(4,5)P2 and PI(3,4,5)P3, suggesting a possible connection between Gag nuclear trafficking and phosphoinositide-dependent PM targeting.

Nuclear trafficking of retroviral RNAs and Gag proteins during late steps of replication.

Retroviruses exploit nuclear trafficking machinery at several distinct stages in their replication cycles. In this review, we will focus primarily on nucleocytoplasmic trafficking events that occur after the completion of reverse transcription and proviral integration. First, we will discuss nuclear export of unspliced viral RNA transcripts, which serves two essential roles: as the mRNA template for the translation of viral structural proteins and as the genome for encapsidation into virions. These full-length viral RNAs must overcome the cell’s quality control measures to leave the nucleus by co-opting host factors or encoding viral proteins to mediate nuclear export of unspliced viral RNAs. Next, we will summarize the most recent findings on the mechanisms of Gag nuclear trafficking and discuss potential roles for nuclear localization of Gag proteins in retrovirus replication.

The Effects of Race and Ethnicity on Thyroid Cancer Incidence

IMPORTANCE The incidence of thyroid cancer has increased over the past 30 years. Thyroid cancer is less common in blacks than in persons of white descent, and it has been most common in Asians/Pacific Islanders until recently. OBJECTIVE To determine whether the incidence of thyroid cancer is increasing at disproportionate rates for different races and ethnicities. DESIGN, SETTING, AND PARTICIPANTS Retrospective review. Study participants were individuals with thyroid cancer in the US National Cancer Institutes Surveillance, Epidemiology, and End Results (SEER) 13 database from 1992 through 2010. The SEER 13 registry consists of records from Atlanta (Georgia), Connecticut, Detroit (Michigan), Hawaii, Iowa, New Mexico, San Francisco-Oakland (California), Seattle-Puget Sound (Washington), Utah, Los Angeles (California), San Jose-Monterey (California), rural Georgia, and the Alaska Native Tumor Registry. MAIN OUTCOMES AND MEASURES The SEER*Stat Joinpoint Regression Program was used to determine the average annual percentage change in thyroid cancer incidence for different races and ethnicities from 1992 through 2010. Trends in thyroid cancer incidence were compared between groups using comparability testing. RESULTS During the study period, the average annual percentage change for thyroid cancer was 5.3% (95% CI, 4.8%-5.7%) per year. Stratification of the study population by race revealed that whites experienced the largest increase in age-adjusted thyroid cancer incidence (5.6% per year), followed by blacks (4.8% per year), American Indian/Alaskan natives (3.2% per year), and Asians/Pacific Islanders (2.3% per year). Joinpoint regression comparability testing showed that the increase in disease incidence was not significantly different between whites and blacks (P = .25). However, the increase in incidence for Asians/Pacific Islanders was significantly lower than that for whites and blacks (P < .05). Stratification of the study population by ethnicity revealed that non-Hispanics experienced a larger increase in incidence (5.5% per year) than Hispanics (3.3% per year). CONCLUSIONS AND RELEVANCE The incidence of thyroid cancer continues to increase in all races and ethnicities. No significant difference was observed between the increase in incidence for whites and blacks. However, the increase in incidence for non-Hispanics was significantly larger than that for Hispanics. The increase in incidence of thyroid cancer was greater in whites than in Asians/Pacific Islanders, so whites now have a higher incidence of thyroid cancer than persons of Asian/Pacific Islander descent.

Increasing Incidence of Thyroid Cancer in the Commonwealth of Pennsylvania

IMPORTANCE The incidence of thyroid cancer in the United States has increased rapidly and Pennsylvania is the state with the highest rate of thyroid cancer in the country, although the factors driving this increase are unknown. Moreover, it remains unclear whether the increase in thyroid cancer represents a true increase in disease or is the result of overdiagnosis. OBJECTIVE To compare the increase in thyroid cancer incidence and tumor characteristics in Pennsylvania with the rest of the United States and gain insight into the factors influencing the increased incidence of thyroid cancer. DESIGN, SETTING, AND PARTICIPANTS In a population-based study, data on thyroid cancer from the Surveillance Epidemiology and End Results 9 (SEER-9) registry and the Pennsylvania Cancer Registry (PCR) from 1985 through 2009 were collected and reviewed for information regarding sex, race, histologic type of thyroid cancer, staging, and tumor size at diagnosis. International Classification of Diseases for Oncology, Third Edition code C739 (thyroid carcinoma) was used to identify 110,615 records in the SEER-9 registry and 29,030 records in the PCR. MAIN OUTCOMES AND MEASURES Average annual percent change (AAPC) in thyroid cancer incidence across various demographic groups in Pennsylvania. RESULTS The AAPC for thyroid cancer in Pennsylvania was 7.1% per year (95% CI, 6.3%-7.9%) vs 4.2% (95% CI, 3.7%-4.7%) per year in the remainder of the United States, and trends in incidence were significantly different (P < .001). Females experienced a higher AAPC (7.6% per year; 95% CI, 6.9%-8.3%) compared with males (6.1% per year; 95% CI, 4.9%-7.2%) (P < .01), and trend analysis revealed that thyroid cancer may be increasing more rapidly among black females (8.6% per year; 95% CI, 5.4%-11.9%) than among white females (7.6% per year; 95% CI, 6.8%-8.4) (P = .60; but despite the similarity in AAPC between the 2 groups, the joinpoint models fit to the data were not parallel [P < .005]). The rate of tumors with regional (7.0% per year; 95% CI, 5.8%-8.1%) or distant (1.1% per year; 95% CI, 0.3%-1.8%) spread (P < .05) and tumors that were 2 to 4 cm (7.1% per year; 95% CI, 5.2%-9.0%) (P < .05) or larger than 4 cm (6.4% per year; 95% CI, 4.5%-8.2%) (P < .05) at diagnosis also increased. CONCLUSIONS AND RELEVANCE The incidence of thyroid cancer is rising at a faster rate in Pennsylvania than in the rest of the nation, as is the rate of tumors that are larger and higher stage at diagnosis. These findings suggest that rising disease burden has contributed to the increased incidence of thyroid cancer. Etiologic factors promoting the rise in thyroid cancer in Pennsylvania must be investigated and may provide insight into the drivers of the national increase in thyroid cancer.

Trends in the Incidence of Oropharyngeal Cancers in the United States.

Objective The incidence of oropharyngeal squamous cell carcinoma (SCCa) has increased in the United States despite a decrease in tobacco usage, and it may be driven by an increase in oral human papilloma virus (HPV) infection. We studied the incidence of tongue base and tonsillar SCCa over time to understand the changing epidemiology of oropharyngeal SCCa. Setting Large national tumor registry. Subjects and Methods We studied patients diagnosed with oropharyngeal SCCa in SEER data (Surveillance, Epidemiology, and End Results) from 1973 to 2009. Age-adjusted incidence rates standardized to the 2000 US population were computed, with stratifications for age, sex, race, and stage. Results The sample included 10,061 tongue base and 11,515 tonsillar oropharyngeal cancers. When stratified by age, the incidence of oropharyngeal SCCa in patients ≤55 years of age more than doubled over 30 years. While the incidence rate in females remained stable, the rate in males more than doubled, from 2 per 100,000 persons in 1973 to >4 per 100,000 persons in 2009. The age-adjusted incidence of oropharyngeal SCCa in patients of black race/ethnicity remained consistently elevated, but the incidence in patients of white race/ethnicity rose from 1.3 per 100,000 persons to >2.5 per 100,000 persons, surpassing the incidence in black patients starting in 2002. Conclusion The observation that the incidence of oropharyngeal SCCa is increasing among younger white males, despite a reduction in tobacco usage in the United States, is consistent with HPV as the source. Primary and secondary prevention strategies may be warranted in this population.

Novel Immunotherapeutic Approaches for Head and Neck Squamous Cell Carcinoma

The immune system plays a key role in preventing tumor formation by recognizing and destroying malignant cells. For over a century, researchers have attempted to harness the immune response as a cancer treatment, although this approach has only recently achieved clinical success. Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide and is associated with cigarette smoking, alcohol consumption, betel nut use, and human papillomavirus infection. Unfortunately, worldwide mortality from HNSCC remains high, partially due to limits on therapy secondary to the significant morbidity associated with current treatments. Therefore, immunotherapeutic approaches to HNSCC treatment are attractive for their potential to reduce morbidity while improving survival. However, the application of immunotherapies to this disease has been challenging because HNSCC is profoundly immunosuppressive, resulting in decreased absolute lymphocyte counts, impaired natural killer cell function, reduced antigen-presenting cell function, and a tumor-permissive cytokine profile. Despite these challenges, numerous clinical trials testing the safety and efficacy of immunotherapeutic approaches to HNSCC treatment are currently underway, many of which have produced promising results. This review will summarize immunotherapeutic approaches to HNSCC that are currently undergoing clinical trials.

Age and stage as determinants of treatment for oral cavity and oropharyngeal cancers in the elderly

BACKGROUND We investigate treatment selection for oral cavity and oropharyngeal (OC&OP) cancers to understand factors that influence treatment selection. METHODS We studied 7023 patients, ⩾66 years, diagnosed with a first primary OC&OP cancer using SEER-Medicare data. Multinomial logistic regression was to model treatment selection, controlling for other factors. RESULTS Most patients with OC cancer were treated with surgery alone (56.5%); most patients with OP cancer were treated with chemotherapy and radiation (28.9%). Age, stage and site were the most important predictors of treatment selection. As age increased from 70 to 81 (the interquartile range), treatment shifted toward surgery alone (OR=1.26; CI: 1.08-1.46) and no treatment (OR=1.5, 95% CI: 1.25-1.80), and away from combined surgery, radiation and treatments involving chemotherapy. CONCLUSIONS Age, stage, and site are the most important determinants of treatment selection for patients with OC&OP cancers. Increasing age and stage drive treatment toward non-surgical options and no treatment at all.

An Integrative Framework For Detecting Structural Variations In Cancer Genomes

Structural variants can contribute to oncogenesis through a variety of mechanisms, yet, despite their importance, the identification of structural variants in cancer genomes remains challenging. Here, we present an integrative framework for comprehensively identifying structural variation in cancer genomes. For the first time, we apply next-generation optical mapping, high-throughput chromosome conformation capture (Hi-C), and whole genome sequencing to systematically detect SVs in a variety of cancer cells. Using this approach, we identify and characterize structural variants in up to 29 commonly used normal and cancer cell lines. We find that each method has unique strengths in identifying different classes of structural variants and at different scales, suggesting that integrative approaches are likely the only way to comprehensively identify structural variants in the genome. Studying the impact of the structural variants in cancer cell lines, we identify widespread structural variation events affecting the functions of non-coding sequences in the genome, including the deletion of distal regulatory sequences, alteration of DNA replication timing, and the creation of novel 3D chromatin structural domains. These results underscore the importance of comprehensive structural variant identification and indicate that non-coding structural variation may be an underappreciated mutational process in cancer genomes.