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.

Ligand-dependent kinase activity of MERTK drives efferocytosis in human iPSC-derived macrophages

Removal of apoptotic cells by phagocytes (also called efferocytosis) is a crucial process for tissue homeostasis. Professional phagocytes express a plethora of surface receptors enabling them to sense and engulf apoptotic cells, thus avoiding persistence of dead cells and cellular debris and their consequent effects. Dysregulation of efferocytosis is thought to lead to secondary necrosis and associated inflammation and immune activation. Efferocytosis in primarily murine macrophages and dendritic cells has been shown to require TAM RTKs, with MERTK and AXL being critical for clearance of apoptotic cells. The functional role of human orthologs, especially the exact contribution of each individual receptor is less well studied. Here we show that human macrophages differentiated in vitro from iPSC-derived precursor cells express both AXL and MERTK and engulf apoptotic cells. TAM RTK agonism by the natural ligand growth-arrest specific 6 (GAS6) significantly enhanced such efferocytosis. Using a newly-developed mouse model of kinase-dead MERTK, we demonstrate that MERTK kinase activity is essential for efferocytosis in peritoneal macrophages in vivo. Moreover, human iPSC-derived macrophages treated in vitro with blocking antibodies or small molecule inhibitors recapitulated this observation. Hence, our results highlight a conserved MERTK function between mice and humans, and the critical role of its kinase activity in homeostatic efferocytosis.

Deep Phenotyping of CD11c+ B Cells in Systemic Autoimmunity and Controls

Circulating CD11c⁺ B cells are a key phenomenon in certain types of autoimmunity but have also been described in the context of regular immune responses (i.e., infections, vaccination). Using mass cytometry to profile 46 different markers on individual immune cells, we systematically initially confirmed the presence of increased CD11c⁺ B cells in the blood of systemic lupus erythematosus (SLE) patients. Notably, significant differences in the expression of CD21, CD27, and CD38 became apparent between CD11c⁻ and CD11c⁺ B cells. We observed direct correlation of the frequency of CD21⁻CD27⁻ B cells and CD21⁻CD38⁻ B cells with CD11c⁺ B cells, which were most pronounced in SLE compared to primary Sjögren's syndrome patients (pSS) and healthy donors (HD). Thus, CD11c⁺ B cells resided mainly within memory subsets and were enriched in CD27⁻IgD⁻, CD21⁻CD27⁻, and CD21⁻CD38⁻ B cell phenotypes. CD11c⁺ B cells from all donor groups (SLE, pSS, and HD) showed enhanced CD69, Ki-67, CD45RO, CD45RA, and CD19 expression, whereas the membrane expression of CXCR5 and CD21 were diminished. Notably, SLE CD11c⁺ B cells showed enhanced expression of the checkpoint molecules CD86, PD1, PDL1, CD137, VISTA, and CTLA-4 compared to HD. The substantial increase of CD11c⁺ B cells with a CD21⁻ phenotype co-expressing distinct activation and checkpoint markers, points to a quantitative increased alternate (extrafollicular) B cell activation route possibly related to abnormal immune regulation as seen under the striking inflammatory conditions of SLE which shows a characteristic PD-1/PD-L1 upregulation.

The Knowledge Broker Mentoring Program: Developing capacity for evidence-informed decision making

Background

Evidence-informed decision making (EIDM) is important to ensure that practice is evidence-informed and resources are used efficiently and effectively. However, public health professionals can face barriers to EIDM. Knowledge Brokers can support and champion EIDM within an organization. The National Collaborating Centre for Methods and Tools (NCCMT) developed a Knowledge Broker (KB) Mentoring program, a hands-on mentorship program to develop capacity for evidence-informed decision making.

Objectives

The objectives of the KB Mentoring program are to build individual and organizational capacity for evidence-informed decision making. The program takes place over 20 months and includes an organizational assessment, nine face-to-face workshop days, monthly webinars, completion of a rapid review, and a period post-program to connect with mentors. Participating cohorts are evaluated qualitatively.

Results

To date, two cohorts of five organizations each have completed the program (n = 56 participants). At the individual level, participants reported increased: confidence; EIDM knowledge and skills; and interpersonal connections. At the organizational level, the groups reported conducting rapid reviews, critically appraising evidence, and using evidence in program planning decisions. Additionally, organizations have put in place ongoing supports to build EIDM capacity. Participants noted that they would like more support both before and after the program. This recommendation was put in place for the third cohort, currently in progress.

Conclusions

Participants indicated the KB mentoring program was high quality and increased EIDM capacity and behaviour in their organizations. This innovative program is important across settings and countries as public health continues to face changes to public health practice. In order to scale up the program to diverse geographic settings, an online KB mentoring program is currently in development.

Key messages

Knowledge Broker mentoring supports public health practitioners to use evidence in practice. Knowledge broker mentoring raises the confidence, knowledge, skills, and connections of participants.

Effect of an antimicrobial stewardship programme on antimicrobial utilisation and costs in patients with leukaemia: a retrospective controlled study

OBJECTIVES

To examine the effectiveness of an antimicrobial stewardship programme on utilization and cost of antimicrobials in leukaemia patients in Canada.

METHODS

We conducted a multisite retrospective observational time series study from 2005 to 2013. We implemented academic detailing as the intervention of an antimicrobial stewardship programme in leukaemia units at a hospital, piloted February-July 2010, then fully implemented December 2010-March 2013, with no intervention in August-November 2010. Internal control was the same hospital's allogeneic haematopoietic stem-cell transplantation unit. External control was the combined leukaemia-haematopoietic stem-cell transplantation unit at another hospital. Primary outcome was antimicrobial utilization (antibiotics and antifungals) in defined daily dose per 100 patient-days (PD). Secondary outcomes were antimicrobial cost (Canadian dollars per PD); cost and utilization by drug class; length of stay; 30-day inpatient mortality; and nosocomial Clostridium difficile infection. We used autoregressive integrated moving average models to evaluate the impact of the intervention on outcomes.

RESULTS

The intervention group included 1006 patients before implementation and 335 during full implementation. Correspondingly, internal control had 723 and 264 patients, external control 1395 and 864 patients. Antimicrobial utilization decreased significantly in the intervention group (p <0.01, 278 vs. 247 defined daily dose per 100 PD), increased in external control (p = 0.02, 237.4 vs. 268.9 defined daily dose per 100 PD) and remained stable in internal control (p = 0.66). Antimicrobial cost decreased in the intervention group (p = 0.03; $154.59 per PD vs. $128.93 per PD), increased in external control (p = 0.01; $109.4 per PD vs. $135.97 per PD) but was stable in internal control (p = 0.27). Mortality, length of stay and nosocomial C. difficile rate in intervention group remained stable.

CONCLUSIONS

The antimicrobial stewardship programme reduced antimicrobial use in leukaemia patients without affecting inpatient mortality and length of stay.

Clinical predictors and clinical prediction rules to estimate initial patient risk for infective endocarditis in Staphylococcus aureus bacteraemia: a systematic review and meta-analysis

OBJECTIVES

We conducted a meta-analysis to summarize diagnostic properties of risk factors and clinical prediction rules for diagnosing infective endocarditis (IE) in Staphylococcus aureus bacteraemia (SAB).

METHODS

We searched MEDLINE, Embase, and the Cochrane Database from inception to 6 January 2016 to identify studies evaluating risk factors and clinical prediction rules for IE in SAB patients. Pooled estimates of diagnostic properties for main risk factors were calculated using a bivariate random effects model.

RESULTS

Of 962 articles identified, 30 studies were included. These involved 16 538 SAB patients including 1572 IE cases. Risk factors with positive likelihood ratio (PLR) greater than 5 included embolic events (PLR 12.7, 95% CI 9.2-17.7), pacemakers (PLR 9.7, 95% CI 3.7-21.2), history of previous IE (PLR 8.2, 95% CI 3.1-22.0), prosthetic valves (PLR 5.7, 95% CI 3.2-9.5), and intravenous drug use (PLR 5.2, 95% CI 3.8-6.9). The only clinical factor with negative likelihood ratio (NLR) less than 0.5 was documented clearance of bacteraemia within 72 hours (NLR range 0.32-0.35). Of the nine published clinical prediction rules for ruling out IE, five had an NLR below 0.1.

CONCLUSIONS

SAB patients with high-risk features (embolic events, pacemakers, prosthetic valves, previous IE, or intravenous drug use) should undergo a trans-esophageal echocardiography (TEE) for IE. Clinical prediction rules show promise in safely ruling out endocarditis, but require validation in future studies.

Long-term follow-up of sacrocolpopexy mesh implants at two time intervals at least 1 year apart using 4D transperineal ultrasound

OBJECTIVE

To determine, using four-dimensional (4D) transperineal ultrasound, whether the appearance, position or dimensions of sacrocolpopexy mesh implants or the degree of tissue support change in the long term.

METHODS

Women who had undergone minimally invasive abdominal sacrocolpopexy for pelvic organ prolapse were invited for follow-up assessment at two consecutive visits at least 1 year apart. All participants completed a Pelvic Floor Distress Inventory questionnaire (PFDI-20) and underwent a pelvic examination by one examiner and had 4D ultrasound volumes obtained by a different examiner. Volumes were analyzed offline for mesh position with the woman at rest and on maximal Valsalva maneuver, and for mesh dimensions and characteristics on three-dimensional orthogonal planes and rendered views, with the operator blinded to the clinical data. Findings were compared between the two examinations.

RESULTS

Thirty women attended follow-up assessment at two time points, a median of 22 (range, 12-37) months apart. The median age at the latter visit was 60 (range, 46-72) years, median body mass index was 25.9 (range, 20.8-31.9) kg/m² , median parity was 3 (range, 1-7) and median time from surgery to first and second visit, respectively, was 11.2 (range, 6-26) months and 33.5 (range, 14-56) months. There were no significant differences between the two time points in symptom scores, reported satisfaction from surgery, pelvic examination findings or pelvic organ descent in any compartment according to ultrasound. While mesh dimensions of anterior and posterior arms did not change significantly over time, both arms descended less on Valsalva at the second follow-up compared with at the first (13.2 ± 6.7 mm vs 21.9 ± 10.0 mm and 9.1 ± 5.3 mm vs 16.1 ± 8.1 mm, respectively, both P < 0.001). There were no mesh erosions, but folding remained a consistent finding, occurring in 80% of women in each assessment.

CONCLUSIONS

Characteristics of tissue support and dimensions of sacrocolpopexy mesh implants remained constant over long-term follow-up, with no mesh shrinkage or erosion. Copyright © 2016 ISUOG. Published by John Wiley & Sons Ltd.

Preventive physiotherapy in schools

Discussion of preventive physiotherapy in schools should cover many issues-nearly all specialist fields. These should include anthropometry and ergonomics in relation to furniture design (Oxford, 1971), and in relation to the prevention of postural defects. Consideration of postural defects should also cover screening of ten to eleven year old girls for early detection of scoliosis. Asthma and other chest conditions, as well as general orthopaedic conditions, should also be included.

How do radiologists evaluate osteonecrosis?

OBJECTIVES

Management of patients with osteonecrosis of the hip remains controversial and challenging. Because the prognosis and treatment are determined in large part by the stage and extent of the disease, it is important to use a reliable and efficient method for evaluation and staging. The objective of this study was to determine how musculoskeletal (MSK) radiologists evaluate osteonecrosis and whether this evaluation is adequate.

MATERIALS AND METHODS

A 12-part questionnaire was designed to determine how MSK radiologists evaluate patients with osteonecrosis of the femoral head (ONFH). This was sent to 888 members of the Society of Skeletal Radiology.

RESULTS

One hundred and twenty-one members responded to essentially all questions. Patients were evaluated using plain radiographs and MRI. All agreed that it is clinically important to determine the extent of necrosis and joint involvement, and 115 (95 %) stated that this should be part of the radiologists' evaluation. However, only 55 (46 %) said that in practice they used a specific system of classification, and most of these used the Ficat and Arlet classification, which does not indicate the extent of involvement. One hundred and seven (88 %) respondents included a simple visual estimate of the extent of involvement, and a small number added a specific measurement of lesion size. The majority indicated that they were infrequently consulted about which imaging studies should be obtained.

CONCLUSIONS

Although radiologists recognize the clinical importance of determining the extent of necrosis and joint involvement in patients with ONFH, in practice the methods used to evaluate these patients often do not accomplish this satisfactorily. The use of an effective classification, which includes both stage and extent of involvement, should be stressed, as it will lead to improved treatment of patients with ON. Physicians who order imaging studies for patients with ON should be encouraged to consult routinely with their radiology colleagues regarding which studies to request, as well as on the interpretation of these studies.

Three-dimensional transperineal ultrasound for imaging mesh implants following sacrocolpopexy

OBJECTIVE

To characterize, using three-dimensional (3D) transperineal ultrasound, the appearance, position and dimensions of mesh implants following minimally invasive abdominal sacrocolpopexy.

METHODS

In women who underwent sacrocolpopexy, mesh was evaluated at rest and on maximal Valsalva, on all 3D orthogonal planes and rendered views. Mesh dimensions were obtained by 3D processing in the midsagittal and coronal planes (anterior, posterior and sacral arm) and were analyzed offline, the operator blinded to clinical data.

RESULTS

Overall, 62 women, mean age 58.4 (range, 42-79) years were evaluated at a median of 9 (range, 1-26) months following surgery. The anterior arm of the mesh was caudal to the lowermost point of descent of the anterior compartment in 56 (90.3%) women, was equally positioned in five (8.1%) and was cranial in one. The posterior arm was caudal in 44 (71%) women, was equally positioned in 16 (25.8%) and was cranial in two (3.2%). The Y connection and the sacral arm of the mesh could not be adequately seen because of physical limitations of ultrasound (lower resolution at greater depth), large recurrent rectoceles, echogenic stools or folding of mesh remnants. Folding of the mesh was seen in 46 (74.2%) women, folding of the anterior arm in five (8.1%) and folding of the posterior arm in 23 (37.1%). Folding occurred caudally in 26 (41.9%) women, proximally in 11 (17.7%) and in both areas in nine (14.5%). There were no erosions.

CONCLUSION

Mesh visualization following minimally invasive abdominal sacrocolpopexy procedures using transperineal 3D/four-dimensional (4D) ultrasound is feasible. Studies are needed to evaluate the correlation between ultrasound measures and prolapse recurrence or mesh erosion.

Use of ultrasound in the clinical evaluation of women following colpocleisis

OBJECTIVE

To assess the role of transperineal ultrasound in the postoperative evaluation of patients undergoing colpocleisis.

METHODS

Patients who underwent colpocleisis between July 2009 and January 2011 completed the pelvic floor distress inventory questionnaire (PFDI-20) and underwent pelvic organ prolapse quantification (POP-Q) examination and four-dimensional (4D) transperineal ultrasound. Volumes were analyzed offline for assessment of pelvic organ descent, levator hiatal dimensions, levator avulsion trauma and the location of the colpocleisis scar.

RESULTS

The study included 16 women, of mean ± SD age 75.7 ± 2.9 years, median body mass index 28 (range, 21-32) kg/m2 and median parity 2 (range, 0-5); one woman was nulliparous. Nine (56.2%) women were posthysterectomy. The median interval from surgery to ultrasound examination was 6.5 (range, 2-19) months. Most patients did not have symptoms of prolapse. The median pelvic organ prolapse distress inventory (POPDI-6) score was 37.5 (range, 0-75) and the median postoperative clinical POP-Q stage was 1 (range, 0-2). Ultrasound demonstrated clear visualization in all patients. Ten had avulsion defects (six were bilateral). Ultrasound estimated greater prolapse descent for all compartments when compared with the clinical examination. However, this difference was significant for anterior and posterior descent, but not for apical descent. In two women urethral diverticulum was detected on ultrasound; it was neither symptomatic nor clinically apparent.

CONCLUSIONS

4D transperineal ultrasound seems to be a potentially effective tool for the evaluation of vaginal anatomic and functional changes following colpocleisis surgery. Future investigation of the association between ultrasound findings and patients' subjective symptoms in a larger cohort is warranted.

Quantitative MRI analysis of salivary glands in sickle cell disease

OBJECTIVES

The purpose of this prospective study was to characterize the MR relaxometric features of the major salivary glands in patients with sickle cell disease (SCD).

METHODS

15 patients with SCD (aged 19.8-43.6 years) and 12 controls were imaged with the mixed turbo-spin echo pulse sequence. The major salivary glands were manually segmented and T1, T2 and secular T2 relaxometry histograms were modelled with Gaussian functions.

RESULTS

Shortened T1 relaxation times were seen solely in the submandibular glands of patients with SCD (747.5±54.8 ms vs 807.1±38.3 ms, p<0.001). Slight T2 and secular T2 shortening were seen in the parotid gland; however, this difference was not significant (p=0.07). The sublingual gland showed no changes under MR relaxometry. There was no difference in glandular volumes, and no correlation was demonstrated between history of blood transfusion and salivary gland relaxometry.

CONCLUSIONS

Patients with SCD exhibited changes in quantitative MRI T1 relaxometry histograms of the submandibular glands.

Learning Chronobiology by Improving Wikipedia

Although chronobiology is of growing interest to scientists, physicians, and the general public, access to recent discoveries and historical perspectives is limited. Wikipedia is an online, user-written encyclopedia that could enhance public access to current understanding in chronobiology. However, Wikipedia is lacking important information and is not universally trusted. Here, 46 students in a university course edited Wikipedia to enhance public access to important discoveries in chronobiology. Students worked for an average of 9 h each to evaluate the primary literature and available Wikipedia information, nominated sites for editing, and, after voting, edited the 15 Wikipedia pages they determined to be highest priorities. This assignment ( http://www.nslc.wustl.edu/courses/Bio4030/wikipedia_project.html ) was easy to implement, required relatively short time commitments from the professor and students, and had measurable impacts on Wikipedia and the students. Students created 3 new Wikipedia sites, edited 12 additional sites, and cited 347 peer-reviewed articles. The targeted sites all became top hits in online search engines. Because their writing was and will be read by a worldwide audience, students found the experience rewarding. Students reported significantly increased comfort with reading, critiquing, and summarizing primary literature and benefited from seeing their work edited by other scientists and editors of Wikipedia. We conclude that, in a short project, students can assist in making chronobiology widely accessible and learn from the editorial process.