Genetic variation within the human papillomavirus type 16 genome is associated with oropharyngeal cancer prognosis

PURPOSE

A significant barrier to adoption of de-escalated treatment protocols for human papillomavirus-driven oropharyngeal cancer (HPV-OPC) is that few predictors of poor prognosis exist. We conducted the first large whole-genome sequencing (WGS) study to characterize the genetic variation of the HPV type 16 (HPV16) genome and to evaluate its association with HPV-OPC patient survival.

PATIENTS AND METHODS

A total of 460 OPC tumor specimens from two large United States medical centers (1980-2017) underwent HPV16 whole-genome sequencing. Site-specific variable positions [single nucleotide polymorphisms (SNPs)] across the HPV16 genome were identified. Cox proportional hazards model estimated hazard ratios (HRs) and 95% confidence intervals (CIs) for overall survival by HPV16 SNPs. Harrell C-index and time-dependent positive predictive value (PPV) curves and areas under the PPV curves were used to evaluate the predictive accuracy of HPV16 SNPs for overall survival.

RESULTS

A total of 384 OPC tumor specimens (83.48%) passed quality control filters with sufficient depth and coverage of HPV16 genome sequencing to be analyzed. Some 284 HPV16 SNPs with a minor allele frequency ≥1% were identified. Eight HPV16 SNPs were significantly associated with worse survival after false discovery rate correction (individual prevalence: 1.0%-5.5%; combined prevalence: 15.10%); E1 gene position 1053 [HR for overall survival (HRos): 3.75, 95% CI 1.77-7.95; Pfdr = 0.0099]; L2 gene positions 4410 (HRos: 5.32, 95% CI 1.91-14.81; Pfdr = 0.0120), 4539 (HRos: 6.54, 95% CI 2.03-21.08; Pfdr = 0.0117); 5050 (HRos: 6.53, 95% CI 2.34-18.24; Pfdr = 0.0030), and 5254 (HRos: 7.76, 95% CI 2.41-24.98; Pfdr = 0.0030); and L1 gene positions 5962 (HRos: 4.40, 95% CI 1.88-10.31; Pfdr = 0.0110) and 6025 (HRos: 5.71, 95% CI 2.43-13.41; Pfdr = 0.0008) and position 7173 within the upstream regulatory region (HRos: 9.90, 95% CI 3.05-32.12; Pfdr = 0.0007). Median survival time for patients with ≥1 high-risk HPV16 SNPs was 3.96 years compared with 18.67 years for patients without a high-risk SNP; log-rank test P < 0.001. HPV16 SNPs significantly improved the predictive accuracy for overall survival above traditional factors (age, smoking, stage, treatment); increase in C-index was 0.069 (95% CI 0.019-0.119, P < 0.001); increase in area under the PPV curve for predicting 5-year survival was 0.068 (95% CI 0.015-0.111, P = 0.008).

CONCLUSIONS

HPV16 genetic variation is associated with HPV-OPC prognosis and can improve prognostic accuracy.

Children and young people with inflammatory bowel disease attend less school than their healthy peers

OBJECTIVE

Chronic diseases, such as inflammatory bowel disease (IBD), can impact negatively on education and social development. Examining the impact of IBD on school/college attendance for children and young people (CYP) is vital to provide targeted support to patients, families and schools.

METHODS

We performed a cross-sectional survey to determine the school/college attendance rates, the reasons for absence related to IBD and facilitators or barriers to school/college attendance. In a subset of patients followed up locally, we performed a detailed review of hospital attendance data to assess healthcare burden.

RESULTS

Two hundred and thirty-one questionnaires were given to CYP with IBD aged 5-17 years. Response rate was 74% (final sample 169). The median school/college attendance rate was 92.5%, significantly lower than all children in England (95.2%). 39.6% of children with IBD were persistently absent, defined nationally as missing 10% or more of school. Only five children (3%) had a 100% attendance record. Increasing age and use of monoclonal therapy were predictors of poor school attendance. Concerns about feeling unwell at school/college, access to toilets, keeping up with work and teachers' understanding of IBD are the main issues for CYP with IBD. There was a significant negative correlation between number of days in hospital and school attendance.

CONCLUSION

IBD has a significant impact on school/college attendance, with hospital attendance, disease burden and school difficulties being major factors. Employing strategies to minimise healthcare burden and developing a partnership between health and education to support children with IBD will serve to facilitate school/college attendance.

Factors Contributing to Non-Exclusive Breastfeeding in Primigravid Mothers

Aims We aimed to examine the factors contributing to non-exclusive breastfeeding in primigravid mothers in a large Irish tertiary maternity hospital. Methods This was a retrospective cohort study carried out at the Rotunda Hospital, Dublin, Ireland. Maternal demographics, antenatal, perinatal, delivery-related information and neonatal outcomes were collected and analysed. Results 569 eligible mothers were delivered during the study period. Out of the 416 mothers intending to breastfeed, 278 (67%) mothers were exclusively breastfeeding at discharge. On univariate analysis, a higher body mass index, unemployment, an Asian background, gestational diabetes, antenatal steroids, low birth weight and hypernatremia were all associated with non-exclusive breastfeeding (all p<0.05). On logistic regression, only gestational diabetes, a birthweight < 2500 grams and hypernatremia remained significantly associated with non-exclusive breastfeeding on discharge. Conclusion Addressing barriers to breast feeding through antenatal and early neonatal education, counselling and support, by qualified healthcare personnel may increase the number of infants exclusively breastfeeding on discharge.

A probabilistic intake model to estimate the impact of reformulation by the food industry among Irish consumers

This project quantified the impact that voluntary reformulation efforts of the food industry had on the Irish population's nutrient intake. Nutrient composition data on reformulated products were collected from 14 major food companies for two years, 2005 and 2012. Probabilistic intake assessments were performed using the Irish national food consumption surveys as dietary intake data. The nutrient data were weighted by market shares replacing existing food composition data for these products. The reformulation efforts assessed, significantly reduced mean energy intakes by up to 12 kcal/d (adults), 15 kcal/d (teens), 19 kcal/d (children) and 9 kcal/d (pre-schoolers). Mean daily fat intakes were reduced by up to 1.3 g/d, 1.3 g/d, 0.9 g/d and 0.6 g/d, saturated fat intakes by up to 1.7 g/d, 2.3 g/d, 1.8 g/d and 1 g/d, sugar intakes by up to 1 g/d, 2 g/d, 3.5 g/d and 1 g/d and sodium intakes by up to 0.6 g/d, 0.5 g/d, 0.2 g/d, 0.3 g/d for adults, teenagers, children and pre-school children, respectively. This model enables to assess the impact of industry reformulation amongst Irish consumers' nutrient intakes, using consumption, food composition and market share data.

Crohn's disease in adolescence: presentation and treatment

Crohn's disease is a chronic inflammatory bowel condition that affects more than 115,000 people in the UK. This article focuses on Crohn's disease in adolescents. Management of the condition in this group should address adolescent-specific characteristics and treatment goals. Key elements include optimising growth, pubertal development and social functioning, including education. The condition can affect an individual's mental and emotional wellbeing significantly, as well as their physical health. As adolescence is a time of great change, the additional burden of a chronic illness can prove difficult to manage. The authors provide information on the presentation of Crohn's disease in adolescence and insights into the particular issues encountered by this group.

Personalizing, not patronizing: the case for patient autonomy by unbiased presentation of management options in stage I testicular cancer

Testicular cancer (TC) is the most common neoplasm in males aged 15-40 years. The majority of patients have no evidence of metastases at diagnosis and thus have clinical stage I (CSI) disease [Oldenburg J, Fossa SD, Nuver J et al. Testicular seminoma and non-seminoma: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up. Ann Oncol 2013; 24(Suppl 6): vi125-vi132; de Wit R, Fizazi K. Controversies in the management of clinical stage I testis cancer. J Clin Oncol 2006; 24: 5482-5492.]. Management of CSI TC is controversial and options include surveillance and active treatment. Different forms of adjuvant therapy exist, including either one or two cycles of carboplatin chemotherapy or radiotherapy for seminoma and either one or two cycles of cisplatin-based chemotherapy or retroperitoneal lymph node dissection for non-seminoma. Long-term disease-specific survival is ∼99% with any of these approaches, including surveillance. While surveillance allows most patients to avoid additional treatment, adjuvant therapy markedly lowers the relapse rate. Weighing the net benefits of surveillance against those of adjuvant treatment depends on prioritizing competing aims such as avoiding unnecessary treatment, avoiding more burdensome treatment with salvage chemotherapy and minimizing the anxiety, stress and life disruption associated with relapse. Unbiased information about the advantages and disadvantages of surveillance and adjuvant treatment is a prerequisite for informed consent by the patient. In a clinical scenario like CSI TC, where different disease-management options produce indistinguishable long-term survival rates, patient values, priorities and preferences should be taken into account. In this review, we provide an overview about risk factors for relapse, potential benefits and harms of adjuvant chemotherapy and active surveillance and a rationale for involving patients in individualized decision making about their treatment rather than adopting a uniform recommendation for all.

EuroFlow standardization of flow cytometer instrument settings and immunophenotyping protocols

The EU-supported EuroFlow Consortium aimed at innovation and standardization of immunophenotyping for diagnosis and classification of hematological malignancies by introducing 8-color flow cytometry with fully standardized laboratory procedures and antibody panels in order to achieve maximally comparable results among different laboratories. This required the selection of optimal combinations of compatible fluorochromes and the design and evaluation of adequate standard operating procedures (SOPs) for instrument setup, fluorescence compensation and sample preparation. Additionally, we developed software tools for the evaluation of individual antibody reagents and antibody panels. Each section describes what has been evaluated experimentally versus adopted based on existing data and experience. Multicentric evaluation demonstrated high levels of reproducibility based on strict implementation of the EuroFlow SOPs and antibody panels. Overall, the 6 years of extensive collaborative experiments and the analysis of hundreds of cell samples of patients and healthy controls in the EuroFlow centers have provided for the first time laboratory protocols and software tools for fully standardized 8-color flow cytometric immunophenotyping of normal and malignant leukocytes in bone marrow and blood; this has yielded highly comparable data sets, which can be integrated in a single database.

EuroFlow antibody panels for standardized n-dimensional flow cytometric immunophenotyping of normal, reactive and malignant leukocytes

Most consensus leukemia & lymphoma antibody panels consist of lists of markers based on expert opinions, but they have not been validated. Here we present the validated EuroFlow 8-color antibody panels for immunophenotyping of hematological malignancies. The single-tube screening panels and multi-tube classification panels fit into the EuroFlow diagnostic algorithm with entries defined by clinical and laboratory parameters. The panels were constructed in 2-7 sequential design-evaluation-redesign rounds, using novel Infinicyt software tools for multivariate data analysis. Two groups of markers are combined in each 8-color tube: (i) backbone markers to identify distinct cell populations in a sample, and (ii) markers for characterization of specific cell populations. In multi-tube panels, the backbone markers were optimally placed at the same fluorochrome position in every tube, to provide identical multidimensional localization of the target cell population(s). The characterization markers were positioned according to the diagnostic utility of the combined markers. Each proposed antibody combination was tested against reference databases of normal and malignant cells from healthy subjects and WHO-based disease entities, respectively. The EuroFlow studies resulted in validated and flexible 8-color antibody panels for multidimensional identification and characterization of normal and aberrant cells, optimally suited for immunophenotypic screening and classification of hematological malignancies.

Depletion of RUNX1/ETO in t(8;21) AML cells leads to genome-wide changes in chromatin structure and transcription factor binding

The t(8;21) translocation fuses the DNA-binding domain of the hematopoietic master regulator RUNX1 to the ETO protein. The resultant RUNX1/ETO fusion protein is a leukemia-initiating transcription factor that interferes with RUNX1 function. The result of this interference is a block in differentiation and, finally, the development of acute myeloid leukemia (AML). To obtain insights into RUNX1/ETO-dependant alterations of the epigenetic landscape, we measured genome-wide RUNX1- and RUNX1/ETO-bound regions in t(8;21) cells and assessed to what extent the effects of RUNX1/ETO on the epigenome depend on its continued expression in established leukemic cells. To this end, we determined dynamic alterations of histone acetylation, RNA Polymerase II binding and RUNX1 occupancy in the presence or absence of RUNX1/ETO using a knockdown approach. Combined global assessments of chromatin accessibility and kinetic gene expression data show that RUNX1/ETO controls the expression of important regulators of hematopoietic differentiation and self-renewal. We show that selective removal of RUNX1/ETO leads to a widespread reversal of epigenetic reprogramming and a genome-wide redistribution of RUNX1 binding, resulting in the inhibition of leukemic proliferation and self-renewal, and the induction of differentiation. This demonstrates that RUNX1/ETO represents a pivotal therapeutic target in AML.

Standardization of flow cytometry in myelodysplastic syndromes: a report from an international consortium and the European LeukemiaNet Working Group

Flow cytometry (FC) is increasingly recognized as an important tool in the diagnosis and prognosis of myelodysplastic syndromes (MDS). However, validation of current assays and agreement upon the techniques are prerequisites for its widespread acceptance and application in clinical practice. Therefore, a working group was initiated (Amsterdam, 2008) to discuss and propose standards for FC in MDS. In 2009 and 2010, representatives from 23, mainly European, institutes participated in the second and third European LeukemiaNet (ELN) MDS workshops. In the present report, minimal requirements to analyze dysplasia are refined. The proposed core markers should enable a categorization of FC results in cytopenic patients as 'normal', 'suggestive of', or 'diagnostic of' MDS. An FC report should include a description of validated FC abnormalities such as aberrant marker expression on myeloid progenitors and, furthermore, dysgranulopoiesis and/or dysmonocytopoiesis, if at least two abnormalities are evidenced. The working group is dedicated to initiate further studies to establish robust diagnostic and prognostic FC panels in MDS. An ultimate goal is to refine and improve diagnosis and prognostic scoring systems. Finally, the working group stresses that FC should be part of an integrated diagnosis rather than a separate technique.

Prevention of febrile neutropenia: use of prophylactic antibiotics

Febrile neutropenia (FN) causes significant morbidity and mortality in patients receiving cytotoxic chemotherapy and can lead to reduced chemotherapy dose intensity and increased overall treatment costs. Antibiotic prophylaxis reduces the incidence of FN. Recent research and meta-analyses confirm that prophylactic fluoroquinolones decrease FN and infection-related mortality in patients with acute leukaemia and those receiving high-dose chemotherapy. Fluoroquinolone prophylaxis also lowers the incidence of FN and all-cause mortality following the first cycle of myelosuppressive chemotherapy for solid tumours. Levofloxacin has been the agent studied most thoroughly in this context. Although there is no convincing evidence that colonisation of individuals with resistant organisms due to antibiotic prophylaxis increases FN or mortality, such concerns must be taken seriously and the use of prophylaxis should be limited responsibly for patients with the greatest chance of benefit. Fluoroquinolone prophylaxis is well tolerated and cost-effective and should be offered to patients receiving chemotherapy for haematological malignancies and high-dose chemotherapy for solid tumours in which prolonged (>7 days) neutropenia is expected. It should also be considered for those receiving chemotherapy for solid tumours and lymphomas during the first cycle of chemotherapy when grade 4 neutropenia is anticipated.

Pemetrexed in advanced non-small cell lung cancer: A randomized trial of 500 mg/m2 vs 900 mg/m2 in 588 patients who progressed after platinum-containing chemotherapy

LBA7727

Introduction: The mild toxicity profile of pemetrexed (P), seen in a phase III trial of P 500 mg/m2 vs docetaxel 75 mg/m2 in vitamin-supplemented patients (pts), suggests higher doses of P can be given in pts with previously treated advanced non-small cell lung cancer (NSCLC) without significant toxicity. We conducted a phase III trial to determine if a higher dose of P (900 mg/m2) could improve survival vs the standard P dose in pts with NSCLC. Methods: Pts with stage III/IV NSCLC, previously treated with platinum-based chemotherapy, were randomized to P 500 or 900 mg/m2 iv q3week. After the second planned interim analysis, the Data Safety Monitoring Board recommended discontinuation of enrollment due to low probability of demonstrating a survival advantage and a greater incidence of some toxicities on the P 900 arm. Patients were allowed to continue treatment at the P 500 dose. Results: 588 randomized pts were evaluated for efficacy and 581 pts, who received =1 dose, for safety. Safety data for pts who transitioned from P 900 to P 500 were analyzed separately. The treatment arms were balanced regarding baseline characteristics and prior treatment. Both arms had: ∼67% males, median age 62 yrs, 87% pts with an ECOG PS of 0 or 1, and 77% pts with stage IV disease. Key results are shown in the table . There was no statistical difference between arms for any efficacy measure. In general, the incidence of adverse events (AEs) was comparable or numerically higher in the P 900 arm. Some AEs (all grades) reported a >5% difference between the P 900 (N=240) and P 500 arms: fatigue (41.7% vs 32.8%), anemia (32.9% vs 22.1%), vomiting (20.0% vs 13.1%), stomatitis (17.9% vs 10.0%), diarrhea (15.4% vs 10.0%), and thrombocytopenia (11.3% vs 5.5%). Conclusion: P 900 offers no advantage over P 500 mg/m2 as second-line therapy for pts with advanced NSCLC. Certain toxicities were somewhat more pronounced in the P 900 group.

No significant financial relationships to disclose.

[Table: see text]

Expression microarray analysis of papillary thyroid carcinoma and benign thyroid tissue: emphasis on the follicular variant and potential markers of malignancy

The most common sub-variant of papillary thyroid carcinoma (PTC) is the so-called follicular variant (FVPTC), which is a particularly problematic lesion and can be challenging from a diagnostic viewpoint even in resected lesions. Although fine needle aspiration cytology is very useful in the diagnosis of PTC, its accuracy and utility would be greatly facilitated by the development of specific markers for PTC and its common variants. We used the recently developed Applied Biosystems 1700 microarray system to interrogate a series of 11 benign thyroid lesions and conditions and 14 samples of PTC (six with classic morphology and eight with follicular variant morphology). TaqMan(R) reverse transcriptase-polymerase chain reaction was used to validate the expression portfolios of 50 selected transcripts. Our data corroborates potential biomarkers previously identified in the literature, such as LGALS3, S100A11, LYN, BAX, and cluster of differentiation 44 (CD44). However, we have also identified numerous transcripts never previously implicated in thyroid carcinogenesis, and many of which are not represented on other microarray platforms. Diminished expression of metallothioneins featured strongly among these and suggests a possible role for this family as tumour suppressors in PTC. Fifteen transcripts were significantly associated with FVPTC morphology. Surprisingly, these genes were associated with an extremely narrow repertoire of functions, including the major histocompatibility complex and cathepsin families.

Intravenous immunoglobulin for resistant Clostridium difficile infection

Clostridium difficile (CD)-associated diarrhoea and colitis may relapse in up to 20% of treated patients. We present a patient who failed to respond over a 6-month period to treatment either singly or in combination with metronidazole, vancomycin, rifampicin, cholestyramine and probiotics. Her diarrhoea rapidly resolved after a 3-day course of intravenous immunoglobulin. This treatment may compensate for a failed immune response to CD toxin and should be considered for relapsing CD-associated diarrhoea where there is no response to conventional treatment strategies.

The development of gemcitabine and carboplatin in the treatment of non-small-cell lung cancer

Gemcitabine plus carboplatin is a widely used regimen for the treatment of advanced non-small-cell lung cancer (NSCLC). This two drug combination is effective, with a favorable safety profile, and is well tolerated in the outpatient setting. Gemcitabine/carboplatin prolongs survival compared with gemcitabine alone, but with greater hematological toxicity. The combination regimen appears to be superior to or equally effective as other regimens including mitomycin, ifosfamide and cisplatin (MIC), cisplatin/vinblastine, gemcitabine/paclitaxel, paclitaxel/carboplatin and gemcitabine/cisplatin. Gemcitabine combined with carboplatin is associated with more hematological toxicity, but the incidence of non-hematological toxicity is often significantly lower. Gemcitabine/carboplatin also improves patient quality of life, supporting its use in treating patients with advanced NSCLC in the outpatient setting.

Determinants of isocyanate exposures in auto body repair and refinishing shops

As part of the Survey of Painters and Repairers of Auto bodies by Yale (SPRAY), the determinants of isocyanate exposure in auto body repair shops were evaluated. Measurements (n = 380) of hexamethylene diisocyanate-based monomer and polyisocyanate and isophorone diisocyanate-based polyisocyanate were collected from 33 auto body shops. The median total reactive isocyanate concentrations expressed as mass concentration of the NCO functional group were: 206 microg NCO/m3 for spray operations; 0.93 microg NCO/m3 for samples collected in the vicinity of spray operations done on the shop floor (near spray); 0.05 microg NCO/m3 for office or other shop areas adjacent to spray areas (workplace background); 0.17 microg NCO/m3 for paint mixing and gun cleaning operations (mixing); 0.27 microg NCO/m3 for sanding operations. Exposure determinants for the sample NCO mass load were identified using linear regression, tobit regression and logistic regression models. For spray samples in a spray booth the significant determinants were the number of milliliters of NCO applied, the gallons of clear coat used by the shop each month and the type of spray booth used (custom built crossdraft, prefabricated crossdraft or downdraft/semi-downdraft). For near spray (bystander) samples, outdoor temperature >65 degrees F (18 degrees C) and shop size >5000 feet2 (465 m2) were significant determinants of exposure levels. For workplace background samples the shop annual income was the most important determinant. For sanding samples, the shop annual income and outdoor temperature >65 degrees F (18 degrees C) were the most significant determinants. Identification of these key exposure determinants will be useful in targeting exposure evaluation and control efforts to reduce isocyanate exposures.

Effect of high levels of intense sweetener intake in insulin dependent diabetics on the ratio of dietary sugar to fat: a case–control study

OBJECTIVE

To examine the influence of intense sweetener consumption on nutrient intakes in insulin dependent diabetics compared to controls.

DESIGN

Case-control food consumption survey.

SETTING

Dietary data were collected from individuals in Ireland between 1998 and 1999.

SUBJECTS

Diabetics were recruited through diabetic outpatient departments of St. James's Hospital Dublin. Controls were friends of the patients or staff/students of Trinity College and University College Dublin. Of the 171 diabetics contacted, 122 agreed to participate (70% response rate) and 119 completed the study.

INTERVENTIONS

In all, 3-day food diaries were used to collect the food consumption data.

MAIN OUTCOME MEASURES

Fat--sugar seesaw, intense sweetness.

RESULTS

Patients had significantly higher % energy from starch, lower % energy from sugars and a high intake of fibre compared to controls. In both groups, there was an inverse relationship between % energy from fat and % en from sugar, with the diabetics at the lower level of sugar intake. A score of intense sweetness intakes was computed and across tertiles of this score, there were no significant effects on macronutrient intakes.

CONCLUSION

The fat-sugar seesaw present in the diabetic group was at a lower level compared to the control group. A high intake of intense sweeteners does not have a detrimental effect on macronutrient and micronutrient intakes.

Lung cancer. 4: chemotherapy for non-small cell lung cancer: the end of the beginning

The development of chemotherapy for NSCLC over the last 20 years is reviewed, particularly with regard to its palliative effects. New "fourth generation" agents designed to inhibit specific biological pathways thought to be crucial to tumour growth give cause for optimism in the future treatment of NSCLC.