A systematic review of randomized control trials looking at functional improvement of rotator cuff partial thickness tears following platelet-rich-plasma injection: a comparison of glenohumeral joint vs. subacromial bursa vs. intratendinous injection locations

Background

Prior research has demonstrated that platelet-rich plasma (PRP) has shown promising results in the treatment of knee osteoarthritis, lateral epicondylitis, and rotator cuff disease. However, there is a lack of standardization with PRP regarding its use for partial thickness rotator cuff tears (PTRCTs). The primary objective of this review is to assess the location of PRP injections in the shoulder, and how it corresponds to shoulder functional outcomes in PTRCTs.

Methods

Data sources included randomized controlled trials (RCTs) conducted between January 2010 and September 2021 with the terms PRP, partial thickness rotator cuff tears, intra-articular injections, subacromial injections, and intratendinous injections. Major inclusion criteria: partial thickness rotator cuff tears only, functional outcome scores pre-injection and post-injection, minimum 2-month follow-up time, and nonsurgical PRP injections only. Major exclusion criteria: PRP used as an adjunct therapy, full-thickness rotator cuff tears, and surgical intervention before treatment.

Results

A total of 8 RCTs were included which utilized PRP injected into the shoulder for PTRCTs. Studies were grouped by the location of the injection with the following breakdown: 1 glenohumeral joint, 4 subacromial bursa, and 3 intratendinous as the site of injection of PRP. Intra-articular PRP showed a 46.2% improvement (P < .05) in the Disabilities of the Arm, Shoulder, and Hand score at 12-month follow-up, however PRP compared to physical therapy had no statistical difference. For subacromial injections, one study showed no statistical difference between hyaluronic acid and PRP vs PRP, but both groups showed improvement compared to normal saline at 3, 6, and 12 months (P < .05). For intratendinous injections, PRP was found to be superior in the Shoulder Pain and Disability Index scores at 66.1% improvement (P < .05) at 3 months and 71.6% at 6 months (P < .05) after two PRP injections when compared to dry needling. Another study showed a statistically significant difference in ASES score when combining LP-PRP injection intratendinous and subacromial bursa when compared to corticosteroid at 3 months. Furthermore, at 6-month follow-up, the PRP group showed significant improvement in the Oxford Shoulder Score compared to a subacromial bursa corticosteroid group 53.8% vs 31.7% (P < .01).

Conclusion

Based on our review of current literature, there is inconclusive evidence of the ideal location to inject PRP when partial rotator cuff tear is present. Despite PRP showing improved functional outcomes in patients diagnosed with PTRCT regardless of the injection site, more research is needed to figure out the optimal concentration of PRP, frequency of injection, and who are ideal candidates when utilizing PRP for PTRCTs.

Femoral stem taper geometry and porous coating in cementless direct anterior primary total hip arthroplasty

Objective

This study aims to compare the clinical outcomes and complications between a fully coated, dual-tapered hip stem versus a proximally coated, triple-tapered hip stem in patients undergoing cementless direct anterior (DA) primary total hip arthroplasty (THA).

Methods

A retrospective analysis was conducted on patients who underwent primary THA with either a fully coated, dual-tapered hip stem or a proximally coated, triple-tapered stem with at least a 1-year follow up. Exclusion criteria included any patients that did not receive either femoral stem, those undergoing bilateral THA, those with a surgical approach other than DA, those with an indication other than osteoarthritis, avascular necrosis (AVN), or femoral neck fracture, and those that had a cemented femoral component. Complications and clinical outcomes were assessed. Statistical analyses were conducted to identify significant differences between the groups.

Results

A total of 95 patients were included in the study. The average ages for the dual-tapered and triple-tapered stem cohorts were 63.6 and 59.5, respectively (p = 0.168). At 1-year follow-up, no significant differences were seen between the groups in terms of ambulatory status, ROM, and patient satisfaction (p = 0.414, p = 0.106, and p = 0.126). 6 (18 %) of the patients receiving the dual-tapered, fully coated hip stem had at least one complication while 8 (13 %) of the triple-tapered, proximally coated hip stem patients did (p = 0.550).

Conclusion

Both hip stem cohorts demonstrated comparable clinical outcomes and complication rates in patients undergoing primary DA THA and we believe that either hip stem may be a reasonable choice for patients. Future studies with larger sample sizes and longer follow-up periods are warranted to validate these findings.

National Analysis of Recent Trends in Organ Donation and Transplantation in the United States: Toward Optimizing Care Delivery and Patient Outcomes

INTRODUCTION

In 2021, over 100 000 people were awaiting solid organ transplantation, yet only 44 634 transplants were performed. The aim of this study is to evaluate trends in donor availability, waitlist additions, and transplants performed in the United States from 2001 to 2021.

METHODS

This was a retrospective analysis to evaluate trends in donor availability, waitlist additions, and solid organ transplants for the 4 most common organs requiring transplants (kidney, liver, heart, and lung) between 2001 and 2021 according to OPTN data.

RESULTS

Between 2001 and 2021, the overall number of transplants performed, donors available, and waitlist additions increased by 71%, 61%, and 54%, respectively. The number of kidney transplant waitlist additions significantly increased compared to other organs (P < .001). For each kidney transplant performed, there was a 2.25 increase in waitlist additions throughout the study period (P < .001). For each liver and heart transplant performed, there was a .92 and .80 increase in waitlist additions, respectively (P < .001). Lung transplants increased the most by 138% and there was an increase in waitlist additions for every transplant by 1.0 (P < .001).

CONCLUSION

There was an absolute increase in the annual number of transplants, donor recruitment, and patients added to the waitlist between 2001 and 2021. Kidney transplant waitlist additions are increasing at a rate outpacing the rates of donor recruitment and transplantation.

Nationwide Analysis of Biomechanics of Motor Vehicle Collisions Involving Passenger Vehicle and Associated Outcomes: Towards Improving Vehicle Safety Standards and Regulations

BACKGROUND

Motor vehicle collisions (MVCs) pose significant mortality and economic burden on the United States. Biomechanics research may guide future vehicle innovation. The objective of this study is to investigate the biomechanics of two-vehicle MVCs involving passenger vehicle (PV) to evaluate associated injury patterns and outcomes including mortality.

METHODS

A retrospective cohort study of cases from the Crash Injury Research Engineering Network database was performed to evaluate the biomechanics (angle of impact, seatbelt use, and airbag deployment) of two-vehicle MVCs involving at least one PV from 2005-2015.

RESULTS

Out of 629 MVCs evaluated, lateral collisions were most common (49.5%), followed by head-on (41.3%) and rear-end (9.2%) collisions. Thoracic injuries accounted for 30.1%, 31.4%, and 31.1% of injuries in lateral, head-on, and rear-end collisions, respectively, and were the most common body region injured for all collision types. Seatbelt use was associated with shorter ICU stay (10.9 vs 19.1 days, P = .036) and mortality (Cramer's V = .224, P < .001), but a greater average number of injuries (10.2 injuries vs 8.6 injuries, P = .011).

CONCLUSION

Passenger vehicle are commonly involved in MVCs nationwide and efforts are needed to prevent occupant injuries and fatalities. The incorporation of energy-absorbing material into common points of contact within the vehicle interior may decrease the severity of these injuries. Seatbelt use remains a protective factor against MVC-fatalities but is associated with collateral injuries and should be a focus of further innovation.

Analysis of Biomechanics of Motor Vehicle Collisions for Passenger Cars: Implications for Passenger Vehicle Safety and Future Car Design Innovations

INTRODUCTION

Investigating biomechanics of injury patterns from motor vehicle collisions (MVCs) informs improvements in vehicle safety. This study aims to investigate two-vehicle MVCs involving a passenger car and specific injury patterns associated with sources of injury, collision biomechanics, vehicle properties, and patient outcomes.

METHODS

Retrospective cohort study conducted to evaluate the biomechanics of specific injury patterns seen in MVCs involving passenger cars using the Crash Injury Research Engineering Network database between the years 2005 and 2015.

RESULTS

A total of 631 MVC cases were included from 2005 to 2015. The majority of cases involved injuries to the head or neck, the thorax, and the abdomen (80.5%). Head/neck injuries from the steering wheel were associated with significantly higher injury severity score compared to those from seatbelts (26.11 versus 18.28, P < 0.001) and airbags (26.11 versus 20.10, P = 0.006), as well as a >6-fold higher fatality rate (P = 0.019). Thoracic injuries caused by the center console were twice as likely to be fatal than those caused by the seatbelt (P = 0.09).

CONCLUSIONS

Occupants suffering injuries to the head/neck, the thorax, and the abdomen had higher injury severity score and fatality rates compared to other body regions, demonstrating that manufacturing and safety guidelines should focus on minimizing these injury patterns. Head/neck injuries caused by the steering wheel were associated with worse outcomes compared to those caused by seatbelts and airbags, further emphasizing the benefits of these critical safety features. Integration of innovative safety features like center-mounted airbags may improve occupant safety.

National analysis of whole blood and component versus component transfusions in civilian trauma patients who underwent a thoracotomy or laparotomy: Toward improving patient outcomes and quality of care

BACKGROUND

This study aimed to investigate the associations of whole blood and component versus component transfusions with in-hospital mortality, complication rates, intensive care unit length of stay, and packed red blood cells transfusion volumes in adult civilian trauma patients.

METHODS

We performed a retrospective cohort study of the American College of Surgeons Trauma Quality Program Participant Use File 2016 to 2019 dataset. Adult civilian trauma patients (aged >18 years) sustaining injuries of at least moderate severity who received whole blood and component or component within 4 hours of arrival and underwent thoracotomy or laparotomy were included. Multivariable regression analysis was used to compare outcomes between whole blood and component and component groups.

RESULTS

A total of 37,384 patients met eligibility criteria, of which 218 received whole blood and component and 37,166 received component. There was no significant difference in in-hospital mortality between whole blood and component and component groups for those who underwent thoracotomy (adjusted odds ratio = 0.408, P = .413) or laparotomy (adjusted odds ratio = 1.046, P = .857). Thoracotomy patients who received whole blood and component had no difference in 4-hour or 24-hour pack red blood cell volumes (3336 mL vs 3106 mL, P = .754; 3 658mL vs 3,636mL, P = .982), intensive care unit length of stay (10.68 days vs 8.63 days, P = .542), or complications rates compared to those who received component. Laparotomy patients who received whole blood and component had no difference in 4 hour or 24-hour packed red blood cell volumes (2,758 mL vs 2,721mL, P = .927; 3,538 mL vs 3,385 mL, P = .754), intensive care unit length of stay (11.78 days vs 9.90 days, P = .177), or complications rates compared to those who received component.

CONCLUSION

Study findings have indicated that a combined resuscitation with whole blood and component transfusion in adult civilian trauma patients is a viable alternative to component transfusion alone.

Nationwide analysis of proximity of America College of Surgeons--verified and state-designated trauma centers to the nearest highway exit and associated prehospital motor vehicle collision fatalities

BACKGROUND

Motor vehicle collisions remain a leading cause of trauma-related deaths. We aim to investigate the relationship between the proximity of trauma centers to the nearest highway exit and prehospital motor vehicle collision fatalities at the county level nationwide.

METHODS

This was a cross-sectional study evaluating the association between the distance of trauma centers to the nearest highway exit and prehospital motor vehicle collision fatalities between the years 2014 and 2019. Prehospital motor vehicle collision fatalities were obtained from National Highway Traffic Safety Administration. Mapping software was used to determine the distance of trauma center to the nearest highway exit and transport time. Linear regression analysis was performed.

RESULTS

A total of 2,019 American College of Surgeons-verified and/or state-designated trauma centers were included (211 Level 1, 356 Level 2, 491 Level 3, and 961 Level 4 trauma centers). Prehospital motor vehicle collision fatalities were positively correlated with the distance of trauma center to the nearest highway exit for counties with trauma centers located ≤5 miles from the nearest highway exit (r = 0.328; P < .001). In the 612 counties with a 10% increase in prehospital motor vehicle collision fatalities from 2014 to 2019, prehospital motor vehicle collision fatalities were also positively correlated with distance to the nearest highway exit (r = 0.302; P < .001). The counties with more dispersed distributions of trauma centers were significantly associated with motor vehicle collision fatalities (Spearman's rank coefficient = 0.456; 95% confidence interval, 0.163-0.675; P = .003).

CONCLUSION

Shorter distances between trauma centers and the nearest highway exit are associated with fewer prehospital motor vehicle collision fatalities for counties with trauma centers ≤5 miles of the nearest highway exit. Further enhancement of existing highway infrastructure and standardization of emergency medical services transport protocols are needed to address the burden of prehospital motor vehicle collision fatalities in the United States.

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.

Trends of Cancer Screenings, Diagnoses, and Mortalities During the COVID-19 Pandemic: Implications and Future Recommendations

Introduction

The impact of the COVID-19 pandemic on cancer screenings and care has yet to be determined. This study aims to investigate the screening, diagnosis, and mortality rates of the top five leading causes of cancer mortality in the United States from 2019 to 2021 to determine the potential impact of the COVID-19 pandemic on cancer care.

Methods

A retrospective cohort study investigating the impact of the COVID-19 pandemic on screening, diagnoses, and mortality rates of the top five leading causes of cancer death (lung/bronchus, colon/rectum, pancreas, breast, and prostate), as determined by the National Institute of Health (NIH) utilizing The United States Healthcare Cost Institute and American Cancer Society databases from 2019 to 2021.

Results

Screenings decreased by 24.98% for colorectal cancer and 16.01% for breast cancer from 2019 to 2020. Compared to 2019, there was a .29% increase in lung/bronchus, 19.72% increase in colorectal, 1.46% increase in pancreatic, 2.89% increase in breast, and 144.50% increase in prostate cancer diagnoses in 2020 (all P < .01). There was an increase in the total number of deaths from colorectal, pancreatic, breast, and prostate cancers from 2019 to 2021.

Conclusion

There was a decrease in the screening rates for breast and colorectal cancer, along with an increase in the estimated incidence and mortality rate among the five leading causes of cancer deaths from 2019 to 2021. The findings suggest that the COVID-19 pandemic is associated with impaired cancer screening, diagnosis, and care, and further emphasizes the need for proactive screening and follow-up to prevent subsequent cancer morbidity and mortality.

AGENT ORANGE-INDUCED Anaplastic Large-Cell Lymphoma (ALCL) with Cutaneous Involvement

Anaplastic large-cell lymphoma (ALCL) is a CD30 + lymphoproliferative disorder that may manifest with skin involvement.1 We present a rare case of Agent Orange-induced ALCL with cutaneous involvement of the hand, surgical excision, and follow-up treatment.

Comparative analysis of the lateral and posterolateral trajectories for fixation of the sacroiliac joint-a cadaveric study

Background

A number of minimally invasive sacroiliac (SI) joint fusion solutions for placing implants exist, with reduced post-operative pain and improved outcomes compared to open procedures. The objective of this study was to compare two MIS SI joint fusion approaches that place implants directly across the joint by comparing the ilium and sacrum bone characteristics and SI joint separation along the implant trajectories.

Methods

Nine cadaveric specimens (n = 9) were CT scanned and the left and right ilium and sacrum were segmented. The bone density, bone volume fraction, and SI joint gap distance were calculated along lateral and posterolateral trajectories and compared using analysis of variance between the two orientations.

Results

Iliac bone density, indicated by the mean Hounsfield Unit, was significantly greater for each lateral trajectory compared to posterolateral. The volume of cortical bone in the ilium was greater for the middle lateral trajectory compared to all others and for the top and bottom lateral trajectories compared to both posterolateral trajectories. Cortical density was greater in the ilium for all lateral trajectories compared to posterolateral. The bone fraction was significantly greater in all lateral trajectories compared to posterolateral in the ilium. No differences in cortical volume, cortical density, or cancellous density were found between trajectories in the sacrum. The ilium was significantly greater in density compared with the sacrum when compared irrespective of trajectory (p < 0.001). The posterolateral trajectories had a significantly larger SI joint gap than the lateral trajectories (p < 0.001).

Conclusion

Use of the lateral approach for minimally invasive SI fusion allows the implant to interact with bone across a significantly smaller joint space. This interaction with increased cortical bone volume and density may afford better fixation with a lower risk of pull-out or implant loosening when compared to the posterolateral approach.

Adenosine stress CMR perfusion imaging of the temporal evolution of perfusion defects in a porcine model of progressive obstructive coronary artery occlusion

Adenosine stress CMR perfusion imaging can quantify absolute perfusion and myocardial perfusion reserve (MPR) in coronary artery disease (CAD) with higher spatial resolution than positron emission tomography, the only clinically available technique for quantitative myocardial perfusion imaging. While porcine models of CAD are excellent for studying perfusion abnormalities in chronic CAD, to date there are a limited number of studies that use quantitative perfusion for evaluation. Therefore, we developed an adenosine stress CMR protocol to evaluate the temporal evolution of perfusion defects in a porcine model of progressive obstructive CAD. 10 Yucatan minipigs underwent placement of an ameroid occluder around the left circumflex artery (LCX) to induce a progressive chronic coronary obstruction. Four animals underwent a hemodynamic dose range experiment to determine the adenosine dose inducing maximal hyperemia. Each animal had a CMR examination, including stress/rest spiral quantitative perfusion imaging at baseline and 1, 3, and 6 weeks. Late gadolinium enhancement images determined the presence of myocardial infarction, if any existed. Pixelwise quantitative perfusion maps were generated using Fermi deconvolution. The results were statistically analyzed with a repeated mixed measures model to block for physiological variation between the animals. Five animals developed myocardial infarction by 3 weeks, while three developed ischemia without an infarction. The perfusion defects were located in the inferolateral myocardium in the perfusion territory of the LCX. Stress perfusion values were higher in remote segments than both the infarcted and ischemic segments (p < 0.01). MPR values were significantly greater in the remote segments than infarcted and ischemic segments (p < 0.01). While the MPR decreased in all segments, the MPR recovered by the sixth week in the remote regions. We developed a model of progressive CAD and evaluated the temporal evolution of the development of quantitative perfusion defects. This model will serve as a platform for understanding the development of perfusion abnormalities in chronic occlusive CAD.

A consideration for the utility of the post-operative Oswestry Disability Index for measuring outcomes after sacroiliac joint fusion

Sacroiliac joint (SIJ) dysfunction and its surgical treatment remain a controversial topic in spine surgery. Determining success after SIJ fusion may be difficult due to preexisting back pain, lumbar fusion (LF), and functional disability. We examine the utility of Oswestry Disability Index (ODI) as a measure of clinical outcomes after minimally invasive SIJ fusion. A retrospective review of 24 patients with at least 12- months follow-up. Patients were divided into two groups based on presence of previous LF. Their post-operative ODI was compared with overall satisfaction, pain reduction, and return to work status. No difference in demographics was found in patients with and without prior LF with 92% of patients reporting lower post-operative pain and 96% being satisfied. Presence of LF did not show any statistically significant differences in pain or satisfaction. However, patient with prior LF reported lower ODI than those without LF at 1-year post-operatively (P=0.015). Postoperative ODI may give a falsely pessimistic impression of outcomes in SIJ fusion patients with prior LF, and its use and limitations should be carefully considered in future studies.

TET2 binds the androgen receptor and loss is associated with prostate cancer

Genetic alterations associated with prostate cancer (PCa) may be identified by sequencing metastatic tumour genomes to identify molecular markers at this lethal stage of disease. Previously, we characterized somatic alterations in metastatic tumours in the methylcytosine dioxygenase ten-eleven translocation 2 (TET2), which is altered in 5-15% of myeloid, kidney, colon and PCas. Genome-wide association studies previously identified non-coding risk variants associated with PCa and melanoma. We perform fine-mapping of PCa risk across TET2 using genotypes from the PEGASUS case-control cohort and identify six new risk variants in introns 1 and 2. Oligonucleotides containing two risk variants are bound by the transcription factor octamer-binding protein 1 (Oct1/POU2F1) and TET2 and Oct1 expression are positively correlated in prostate tumours. TET2 is expressed in normal prostate tissue and reduced in a subset of tumours from the Cancer Genome Atlas (TCGA). Small interfering RNA-mediated TET2 knockdown (KD) increases LNCaP cell proliferation, migration and wound healing, verifying loss drives a cancer phenotype. Endogenous TET2 bound the androgen receptor (AR) and AR-coactivator proteins in LNCaP cell extracts, and TET2 KD increases prostate-specific antigen (KLK3/PSA) expression. Published data reveal TET2 binding sites and hydroxymethylcytosine proximal to KLK3. A gene co-expression network identified using TCGA prostate tumour RNA-sequencing identifies co-regulated cancer genes associated with 2-oxoglutarate (2-OG) and succinate metabolism, including TET2, lysine demethylase (KDM) KDM6A, BRCA1-associated BAP1, and citric acid cycle enzymes IDH1/2, SDHA/B, and FH. The co-expression signature is conserved across 31 TCGA cancers suggesting a putative role for TET2 as an energy sensor (of 2-OG) that modifies aspects of androgen-AR signalling. Decreased TET2 mRNA expression in TCGA PCa tumours is strongly associated with reduced patient survival, indicating reduced expression in tumours may be an informative biomarker of disease progression and perhaps metastatic disease.

Abstract LB-337: Synergistic effects of twelve common genetic polymorphisms and smoking habits on absolute risk of bladder cancer

Smoking is the strongest established risk factor for bladder cancer and recent studies have identified multiple common susceptibility loci for this disease. Evaluation of gene-smoking interactions on absolute risk of bladder cancer could be important for understanding both the public health and biological significance of the combined effect of these factors. However, previous studies of gene-environment interactions focused on relative rather than absolute risk measures and thus did not address this important question. The aim of our analyses was to estimate absolute risk of bladder cancer in relation to smoking habits and 12 known susceptibility variants for this disease, and to evaluate if smoking risk differences (RD) vary by levels of a polygenic risk score derived from these variants, using additive tests for interaction. Analyses were based on data from 4,098 cases and 5,995 controls of European background in eight studies participating in the NCI bladder cancer genome-wide association study (GWAS). Absolute risks were estimated based on US incidence and mortality data. The main outcome measures were 30-year cumulative absolute risk of bladder cancer and RDs for males aged 50 years in relation to smoking habits and the polygenic risk score. RDs for ever compared to never smokers were significantly larger (P-additive interaction &lt; 0.05) for subjects carrying risk alleles for seven out of 12 known susceptibility variants. Polymorphisms in two detoxification enzymes, NAT2 and UGT1A6, provided the strongest evidence of additive interactions (P-additive interaction of 0.0002 and 0.0003, respectively), supporting the presence of biological interactions between smoking and these variants. The 30-year risk of bladder cancer in never, former and current smokers was 0.7%, 1.6% and 3.7%, respectively, for subjects in the bottom quartile of the polygenic risk score, compared to 2.0%, 5.1% and 8.0% for subjects in the top quartile. This translates into a significantly larger number of projected cases, which could be avoided by smoking prevention in subjects at higher compared to lower genetic risk (P-additive (2df)=4.6x10-9 for top to bottom quartile of the polygenic risk score). In conclusion, our analyses provide strong evidence for synergistic effects of smoking and known susceptibility loci for bladder cancer on the absolute risk of the disease. This indicates that targeting intense smoking prevention efforts to individuals at elevated genetic risk for bladder cancer could improve the public health impact of such efforts. However, genetic susceptibility for other smoking-related diseases, as well as practical and ethical considerations, would need to be taken into account before any recommendations could be made. (MGC, NR are Co-first authors; N.C. and DTS are Co-last authors)

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-337. doi:1538-7445.AM2012-LB-337

Risk alleles for chronic hepatitis B are associated with decreased mRNA expression of HLA-DPA1 and HLA-DPB1 in normal human liver

A genome-wide association study identified single nucleotide polymorphisms (SNPs) rs3077 and rs9277535 located in the 3' untranslated regions of human leukocyte antigen (HLA) class II genes HLA-DPA1 and HLA-DPB1, respectively, as the independent variants most strongly associated with chronic hepatitis B. We examined whether these SNPs are associated with mRNA expression of HLA-DPA1 and HLA-DPB1. We identified gene expression-associated SNPs (eSNPs) in normal liver samples obtained from 651 individuals of European ancestry by integrating genotype (~650 000 SNPs) and gene expression (>39 000 transcripts) data from each sample. We used the Kruskal-Wallis test to determine associations between gene expression and genotype. To confirm findings, we measured allelic expression imbalance (AEI) of complementary DNA compared with DNA in liver specimens from subjects who were heterozygous for rs3077 and rs9277535. On a genome-wide basis, rs3077 was the SNP most strongly associated with HLA-DPA1 expression (p=10(-48)), and rs9277535 was strongly associated with HLA-DPB1 expression (p=10(-15)). Consistent with these gene expression associations, we observed AEI for both rs3077 (p=3.0 × 10(-7); 17 samples) and rs9277535 (p=0.001; 17 samples). We conclude that the variants previously associated with chronic hepatitis B are also strongly associated with mRNA expression of HLA-DPA1 and HLA-DPB1, suggesting that expression of these genes is important in control of HBV.

Worldwide genetic structure in 37 genes important in telomere biology

Telomeres form the ends of eukaryotic chromosomes and are vital in maintaining genetic integrity. Telomere dysfunction is associated with cancer and several chronic diseases. Patterns of genetic variation across individuals can provide keys to further understanding the evolutionary history of genes. We investigated patterns of differentiation and population structure of 37 telomere maintenance genes among 53 worldwide populations. Data from 898 unrelated individuals were obtained from the genome-wide scan of the Human Genome Diversity Panel (HGDP) and from 270 unrelated individuals from the International HapMap Project at 716 single-nucleotide polymorphism (SNP) loci. We additionally compared this gene set to HGDP data at 1396 SNPs in 174 innate immunity genes. The majority of the telomere biology genes had low to moderate haplotype diversity (45-85%), high ancestral allele frequencies (>60%) and low differentiation (FST<0.10). Heterozygosity and differentiation were significantly lower in telomere biology genes compared with the innate immunity genes. There was evidence of evolutionary selection in ACD, TERF2IP, NOLA2, POT1 and TNKS in this data set, which was consistent in HapMap 3. TERT had higher than expected levels of haplotype diversity, likely attributable to a lack of linkage disequilibrium, and a potential cancer-associated SNP in this gene, rs2736100, varied substantially in genotype frequency across major continental regions. It is possible that the genes under selection could influence telomere biology diseases. As a group, there appears to be less diversity and differentiation in telomere biology genes than in genes with different functions, possibly due to their critical role in telomere maintenance and chromosomal stability.

Comprehensive analysis of hormone and genetic variation in 36 genes related to steroid hormone metabolism in pre- and postmenopausal women from the breast and prostate cancer cohort consortium (BPC3)

CONTEXT

Sex steroids play a central role in breast cancer development.

OBJECTIVE

This study aimed to relate polymorphic variants in 36 candidate genes in the sex steroid pathway to serum concentrations of sex steroid hormones and SHBG.

DESIGN

Data on 700 genetic polymorphisms were combined with existing hormone assays and data on breast cancer incidence, within the European Prospective Investigation into Cancer and Nutrition (EPIC) and the Nurses' Health Study (NHS) cohorts; significant findings were reanalyzed in the Multiethnic Cohort (MEC).

SETTING AND PARTICIPANTS

We analyzed data from a pooled sample of 3852 pre- and postmenopausal Caucasian women from EPIC and NHS and 454 postmenopausal women from MEC.

MAIN OUTCOME MEASURES

Outcome measures were SHBG, testosterone, dehydroepiandrosterone (DHEAS), androstenedione, estrone (E1), and estradiol (E2) as well as breast cancer risk.

RESULTS

Globally significant associations were found among pre- and postmenopausal women combined between levels of SHBG and the SHBG gene and between DHEAS and the FSHR and AKR1C3 genes. Among postmenopausal women, serum E1 and E2 were significantly associated with the genes CYP19 and FSHR, and E1 was associated with ESR1. None of the variants related to serum hormone levels showed any significant association with breast cancer risk.

CONCLUSIONS

We confirmed associations between serum levels of SHBG and the SHBG gene and of E1 and E2 and the CYP19 and ESR1 genes. Novel associations were observed between FSHR and DHEAS, E1, and E2 and between AKR1C3 and DHEAS.

Vitamin d pathway genes, diet, and risk of renal cell carcinoma

Mediated by binding to the high-affinity vitamin D receptor (VDR), vitamin D forms a heterodimer complex with the retinoid-X-receptor (RXR). Variation in both genes has been shown to modify renal cell carcinoma (RCC) risk. Therefore, we investigated whether VDR and RXRA polymorphisms modify associations between RCC risk and frequency of dietary intake of vitamin D and calcium rich foods, and occupational ultraviolet exposure among 777 RCC case and 1035 controls from Central and Eastern Europe. A positive association was observed in this population between increasing dietary intake frequency of yogurt, while an inverse association was observed with egg intake frequency. RXRA polymorphisms, located 3' of the coding sequence, modified associations between specific vitamin D rich foods and RCC risk, while RXRA polymorphisms, located in introns 1 and 4, modified associations with specific calcium rich foods. Results suggest that variants in the RXRA gene modified the associations observed between RCC risk and calcium and vitamin D intake.

Association between genetic variants in VEGF, ERCC3 and occupational benzene haematotoxicity

INTRODUCTION

Benzene is an established human haematotoxin, with substantial interindividual variation in benzene-induced toxicity.

METHODS

To further examine if genetic variation contributes to benzene haematotoxicity, we analysed 1023 tagSNPs in 121 gene regions important for benzene metabolism, haematopoiesis, leukaemia and lymphoma among 250 workers exposed to benzene and 140 unexposed controls in a cross-sectional study carried out in China. Linear regression was used to analyse the relationship between genetic polymorphisms and total white blood cell (WBC) count and its subtypes, adjusting for potential confounders and occupational exposure to benzene and toluene among exposed workers. The minp test assessed the association on the gene region level. The false discovery rate method was used to control for multiple comparisons.

RESULTS

VEGF (minp = 0.0030) and ERCC3 (minp = 0.0042) were the most significantly associated gene regions with altered WBC counts among benzene-exposed workers, after accounting for multiple comparisons. Highly significant changes were also found for WBC subtype counts, including granulocytes, CD4+ T cells and lymphocytes for VEGF and granulocytes and NK cells for ERCC3. Further, in workers exposed to <1 ppm, a SNP in VEGF was associated with changes in WBC and granulocyte counts, and SNPs in ERCC3 were associated with changes in WBC, NK cell and granulocyte counts.

DISCUSSION

Our findings suggest that genetic variation in VEGF, which plays an important role in blood vessel growth, and ERCC3, which is a member of the DNA repair pathway and is responsible for repairing bulky DNA adducts formed by chemicals, may contribute to individual susceptibility to benzene-induced haematotoxicity at relatively low levels of benzene exposure.

Polymorphisms in Th1-type cell-mediated response genes and risk of gastric cancer

Helicobacter pylori infection, the dominant risk factor for gastric cancers, has been shown to elicit T helper type 1 (Th1) polarized immunological responses. We conducted a population-based study of 305 gastric cancer cases and 427 age- and gender-matched controls in Warsaw, Poland, to evaluate the association with several variants in genes responsible for Th1-cell-mediated response. Genotyping was performed on genomic DNA by TaqMan(TM) assays to determine TNFA (-308 G>A, -417 G>A, -555 G>A, -1036 C>T, -1042 C>A, -1210 T>C), IL1A (-889 C>T), IFNGR2 (Ex7-128 T>C, Ex2-34 C>G and Ex2-16 A>G) and IL12A (IVS2-798 T>A, IVS2-701 C>A and Ex7+277 G>A) polymorphisms. We used unconditional logistic regression to estimate odds ratios (ORs) and 95% confidence intervals (CIs), adjusting for sex, age, education and smoking status. Out of six single nucleotide polymorphisms (SNPs) tested in TNFA, gastric cancer risk was significantly associated with the TNFA (-308 G>A) polymorphism, with ORs of 1.4 (95% CI: 1.0-2.0) for the G/A and 2.5 (95% CI: 1.3-4.9) for the A/A genotype carriers, when compared with the more frequent genotype (G/G) (P-trend < 0.001). Among the three tested SNPs in the IFNGR2 gene, only the Ex7-128C>T polymorphism was associated with increased risk, with ORs of 1.5 (95% CI: 1.0-2.3) for T/C and 1.7 (95% CI: 1.1-2.7) for C/C carriers when compared with T/T carriers (P-trend = 0.01). Subjects carrying both IFNGR2 Ex7-128 C/C and TNFA -308 A/A genotypes had the highest risk (OR = 5.5, 95% CI: 1.5-19.4), although the interaction was not statistically significant. IL1A (-889 C>T) and the three examined IL12A variants were unrelated to gastric cancer risk. Our findings suggest that two Th1-related polymorphisms (TNFA -308 A>G and IFNGR2 Ex7-128 C>T) may increase the risk of gastric cancer.

Sequence analysis of the mannose-binding lectin (MBL2) gene reveals a high degree of heterozygosity with evidence of selection

Human mannose-binding protein (MBL) is a component of innate immunity. To capture the common genetic variants of MBL2, we resequenced a 10.0 kb region that includes MBL2 in 102 individuals representing four major US ethnic groups. In all, 87 polymorphic sites were observed, indicating a high level of heterozygosity (total pi=18.3 x 10(-4)). Estimates of linkage disequilibrium across MBL2 indicate that it is divided into two blocks, with a probable recombination hot spot in the 3' end. Three non-synonymous SNPs in exon 1 of the encoding MBL2 gene and three upstream SNPs form common 'secretor haplotypes' that can predict circulating levels. Common variants have been associated with increased susceptibility to infection and autoimmune diseases. The high frequencies of B, C and D alleles in certain populations suggest a possible selective advantage for heterozygosity. There is limited diversity of haplotype structure; the 'secretor haplotypes' lie on a restricted number of extended haplotypes, which could include additional linked SNPs, which might also have possible functional implications. There is evidence for gene conversion in the region between the two blocks, in the last exon. Our data should form the basis for conducting MBL2 candidate gene association studies using a locus-wide approach.

Candidate genes for anorexia nervosa in the 1p33-36 linkage region: serotonin 1D and delta opioid receptor loci exhibit significant association to anorexia nervosa

Serotonergic and opioidergic neurotransmitter system alterations have been observed in people with eating disorders; the genes for the serotonin 1D receptor (HTR1D) and the opioid delta receptor (OPRD1) are found on chr1p36.3-34.3, a region identified by our group in a linkage analysis of anorexia nervosa (AN). These candidate genes were evaluated for sequence variation and for linkage and association of this sequence variation to AN in family and case : control data sets. Resequencing of the HTR1D locus and a portion of the OPRD1 locus identified novel SNPs and confirmed existing SNPs. Genotype assay development and genotyping of nine SNPs (four at HTR1D and five at OPRD1) was performed on 191 unrelated individuals fulfilling DSM-IV criteria (w/o amenorrhea criterion) for AN, 442 relatives of AN probands and 98 psychiatrically screened controls. Linkage analysis of these candidate gene SNPs with 33 microsatellite markers in families including relative pairs concordantly affected with restricting AN (N=37) substantially increased the evidence for linkage of this region to restricting AN to an NPL score of 3.91. Statistically significant genotypic, allelic, and haplotypic association to AN in the case : control design was observed at HTR1D and OPRD1 with effect sizes for individual SNPs of 2.63 (95% CI=1.21-5.75) for HTR1D and 1.61 (95% CI=1.11-2.44) for OPRD1. Using genotype data on parents and AN probands, three SNPs at HTR1D were found to exhibit significant transmission disequilibrium (P&<0.05). The combined statistical genetic evidence suggests that HTR1D and OPRD1 or linked genes may be involved in the etiology of AN.

Candidate gene analysis of the Price Foundation anorexia nervosa affected relative pair dataset

The eating disorders are severe psychiatric illnesses with significant morbidity and mortality that exhibit statistically significant familial risk and heritability, providing support for a molecular genetic approach toward defining etiological factors. An emerging candidate gene literature has concentrated on serotinergic and dopaminergic candidates. With the financial support of the Price Foundation, a group of investigators initiated an international multi-center collaboration (Price Foundation Collaborative Group) in 1995 to study the genetics of anorexia and bulimia nervosa by collecting and analyzing phenotypes and genotypes of individuals and their relatives affected with eating disorders. The first sample of families collected by this collaborative group, known as the Price Foundation Anorexia Nervosa Affected Relative Pair (AN-ARP) dataset, was ascertained on an proband affected with Anorexia Nervosa (AN), with relative pairs affected with the eating disorders AN, Bulimia Nervosa or Eating Disorders Not Otherwise Specified [1]. Biognosis U.S., Inc. was founded to identify and characterize candidate susceptibility genes for anorexia and bulimia nervosa phenotypes in the Price Foundation eating disorder datasets. During 2000-2001, Biognosis U.S., Inc. developed and implemented a research program with a focus on the analysis of candidate genes nominated by neurochemical characteristics of eating disorder patients [2], serotonergic and dopaminergic candidate gene polymorphisms [3], neuroendocrine regulation of appetite [4], and by a positional hypothesis from a linkage analysis of the AN-ARP dataset [5]. This report reviews the anorexia nervosa candidate gene literature through 2001, the candidate gene research program implemented at Biognosis U.S., Inc. and selected candidate gene findings in the AN-ARP dataset derived from that research program.

Localization of membrane permeabilization and receptor binding sites on the VP4 hemagglutinin of rotavirus: implications for cell entry

The surface of rotavirus is decorated with 60 spike-like projections, each composed of a dimer of VP4, the viral hemagglutinin. Trypsin cleavage of VP4 generates two fragments, VP8*, which binds sialic acid (SA), and VP5*, containing an integrin binding motif and a hydrophobic region that permeabilizes membranes and is homologous to fusion domains. Although the mechanism for cell entry by this non-enveloped virus is unclear, it is known that trypsin cleavage enhances viral infectivity and facilitates viral entry. We used electron cryo-microscopy and difference map analysis to localize the binding sites for two neutralizing monoclonal antibodies, 7A12 and 2G4, which are directed against the SA-binding site within VP8* and the membrane permeabilization domain within VP5*, respectively. Fab 7A12 binds at the tips of the dimeric heads of VP4, and 2G4 binds in the cleft between the two heads of the spike. When these binding results are combined with secondary structure analysis, we predict that the VP4 heads are composed primarily of beta-sheets in VP8* and that VP5* forms the body and base primarily in beta-structure and alpha-helical conformations, respectively. Based on these results and those of others, a model is proposed for cell entry in which VP8* and VP5* mediate receptor binding and membrane permeabilization, and uncoating occurs during transfer across the lipid bilayer, thereby generating the transcriptionally active particle.

Nosocomial bloodstream infections in patients with implantable left ventricular assist devices

BACKGROUND

Implantable left ventricular assist devices (LVAD) are used as a bridge to transplantation but are associated with a high risk of infection including nosocomial bloodstream infections (BSI).

METHODS

We retrospectively reviewed the medical records of all patients with implantable LVAD at the Cleveland Clinic with 72 hours or longer of LVAD support from January 1992 through June 2000, to determine the attack rate, incidence, and impact of nosocomial BSI in patients with LVAD. A nosocomial BSI was defined using Centers for Disease Control and Prevention definition. An LVAD-related BSI was defined as one where the same pathogen is cultured from the device and the blood with no other obvious source. Two hundred fourteen patients were included in the study (17,831 LVAD-days).

RESULTS

One hundred forty BSI were identified in 104 patients for an attack rate of 49% and incidence of 7.9 BSI per 1000 LVAD-days. Thirty-eight percent of the BSI were LVAD associated. The most common pathogens causing BSI were coagulase-negative staphylococci (n = 33), Staphylococcus aureus, and Candida spp. (19 each), and Pseudomonas aeruginosa (16 each). A Cox proportional hazard model found BSI in patients with LVAD to be significantly associated with death (hazard ratio = 4.02, p < 0.001). Fungemia had the highest hazard ratio (10.9), followed by gram-negative bacteremia (5.1), and gram-positive bacteremia (2.2).

CONCLUSIONS

Patients with implantable LVAD have a high incidence of BSI, which are associated with a significantly increased mortality. Strategies for prevention of infection in LVAD recipients should focus on the drive line exit site until technical advances can achieve a totally implantable device.

The pathobiology of pulmonary hypertension. Endothelium

Dysfunctional endothelial cells have a central and critical role in the initiation and progression of severe pulmonary hypertension. The elucidation of the mechanisms involved in the control of endothelial cell proliferation and cell death in the pulmonary vasculature, therefore, is fundamentally important in the pathogenesis of severe pulmonary hypertension and of great interest for a better understanding of endothelial cell biology. Because the intravascular growth of endothelial cells resulting in tumorlets is unique to severe pulmonary hypertension, this phenomenon can teach researchers about the factors involved in the formation and maintenance of the normal endothelial cell monolayer. Clearly, in severe pulmonary hypertension, the "law of the endothelial cell monolayer" has been broken. The ultimate level of such a control is at the altered gene expression pattern that is conducive to endothelial cell growth and disruption of pulmonary blood flow. Secondary pulmonary hypertension certainly also is associated with proliferated pulmonary endothelial cells and plexiform lesions that are histologically indistinguishable from those in PPH. What is then the difference in the mechanisms of endothelial cell proliferation between primary and secondary pulmonary hypertension? The authors believe that PPH is a disease caused by somatic mutations in key angiogenesis- or apoptosis-related genes such as the TGF-beta receptor-2 and Bax. The loss of these important cell growth control mechanisms allows for the clonal expansion of endothelial cells from a single cell that has acquired a selective growth advantage. On the other hand, the proliferated endothelial cells in secondary pulmonary hypertension are polyclonal. It follows from this finding that local (vascular) factor(s) (such as increased shear stress), rather than mutations, play a major role in triggering endothelial cell proliferation. In PPH and secondary pulmonary hypertension, the researcher can postulate that the pulmonary vascular bed contains progenitor-like cells with the capacity of dysregulated growth. The main difference in the pathogenesis of primary and secondary pulmonary endothelial cell proliferation therefore may be the initial mechanism involved in the recruitment of an endothelial progenitor-like cell. In PPH, anorexigen-associated, and familial PPH, the proliferation of endothelial cells occurs from a mutated single cell, whereas in secondary pulmonary hypertension, several progenitor-like cells would be activated to grow. The abnormal endothelial cells in both forms of severe pulmonary hypertension expand because of the expression of angiogenesis-related molecules such as VEGF, VEGFR-2, HIF-1 alpha, and HIF-beta. Also important for the expansion of these cells is the down-regulation of expression of apoptosis-related mediators such as TGF-beta receptor-2 or Bax. The success of any therapy for severe pulmonary hypertension requires that the underlying process of endothelial cell proliferation could be controlled or reversed.

Transmembrane alpha-helices in the gap junction membrane channel: systematic search of packing models based on the pair potential function

Recent progress in the field of electron cryo-microscopy and image analysis has shown that there is an overwhelming need to interpret medium resolution (5 to 10 A) three-dimensional maps. Traditional methods of fitting amino acid residues into electron density using molecular modeling programs must be supplemented with further analysis. We have used a potential of mean force (PMF) method, derived from Boltzmann statistics in protein structure, to generate models for the packing of alpha-helices, using pairwise potentials between amino acid residues. The approach was tested using the three-dimensional map of a recombinant cardiac gap junction membrane channel provided by electron cryo-crystallography (Unger et al., 1997; 1999a, 1999b) which had a resolution of 7.5 A in the membrane plane and 21 A in the vertical direction. The dodecameric channel was formed by the end-to-end docking of two hexamers, each of which displayed 24 rods of density in the membrane interior, which was consistent with an alpha-helical conformation for the four transmembrane domains of each connexin subunit. Based on the three-dimensional map and the amino acid sequence for the 4 transmembrane domains determined by hydropathy analysis, we used the modeling utility SymServ (Macke et al., 1998) to build hexameric connexons with 24 transmembrane alpha-helices. Canonical alpha-helices were aligned to the axes of the rods of density and translated along the density so that the center of masses coincided. The PMF function was used to evaluate 162,000 conformations for each of the 24 possible alpha-helical packing models. Since the different packing models yielded different energy distributions, the pair potential function appears to be a promising tool for evaluating the packing of alpha-helices in membrane proteins. The analysis will be refined by energy calculations based on the expectations that the outer boundary of the channel will be formed by hydrophobic residues in contact with the lipids.

The structure of pariacoto virus reveals a dodecahedral cage of duplex RNA

The 3.0 A resolution crystal structure of Pariacoto virus (PaV) reveals extensive interactions between portions of the viral RNA genome and the icosahedral capsid. Under the protein shell of the T = 3 quasi equivalent capsid lies a dodecahedral cage composed of RNA duplex that accounts for approximately 35% of the single-stranded RNA genome. The highly basic N-terminal regions (residues 7-54) of the subunits, forming pentamers (A subunits) are clearly visible in the density map and make numerous interactions with the RNA cage. The C-terminal segments (residues 394-401) of the A subunits lie in channels near the quasi three-fold axes. Electron cryo-microscopy and image reconstruction of PaV particles clearly show the dodecahedral RNA cage.

Structure of native and expanded sobemoviruses by electron cryo-microscopy and image reconstruction

Rice yellow mottle virus (RYMV) and southern bean mosaic virus, cowpea strain (SCPMV) are members of the Sobemovirus genus of RNA-containing viruses. We used electron cryo-microscopy (cryo-EM) and icosahedral image analysis to examine the native structures of these two viruses at 25 A resolution. Both viruses have a single tightly packed capsid layer with 180 subunits assembled on a T=3 icosahedral lattice. Distinctive crown-like pentamers emanate from the 12 5-fold axes of symmetry. The exterior face of SCPMV displays deep valleys along the 2-fold axes and protrusions at the quasi-3-fold axes. While having a similar topography, the surface of RYMV is comparatively smooth. Two concentric shells of density reside beneath the capsid layer of RYMV and SCPMV, which we interpret as ordered regions of genomic RNA. In the presence of divalent cations, SCPMV particles swell and fracture, whereas the expanded form of RYMV is stable. We previously proposed that the cell-to-cell movement of RYMV in xylem involves chelation of Ca(2+) from pit membranes of infected cells, thereby stabilizing the capsid shells and allowing a pathway for spread of RYMV through destabilized membranes. In the context of this model, we propose that the expanded form of RYMV is an intermediate in the in vivo assembly of virions.

3D domain swapping modulates the stability of members of an icosahedral virus group

BACKGROUND

Rice yellow mottle virus (RYMV) is a major pathogen that dramatically reduces rice production in many African countries. RYMV belongs to the genus sobemovirus, one group of plant viruses with icosahedral capsids and single-stranded, positive-sense RNA genomes.

RESULTS

The structure of RYMV was determined and refined to 2.8 A resolution by X-ray crystallography. The capsid contains 180 copies of the coat protein subunit arranged with T = 3 icosahedral symmetry. Each subunit adopts a jelly-roll beta sandwich fold. The RYMV capsid structure is similar to those of other sobemoviruses. When compared with these viruses, however, the betaA arm of the RYMV C subunit, which is a molecular switch that regulates quasi-equivalent subunit interactions, is swapped with the 2-fold-related betaA arm to a similar, noncovalent bonding environment. This exchange of identical structural elements across a symmetry axis is categorized as 3D domain swapping and produces long-range interactions throughout the icosahedral surface lattice. Biochemical analysis supports the notion that 3D domain swapping increases the stability of RYMV.

CONCLUSIONS

The quasi-equivalent interactions between the RYMV proteins are regulated by the N-terminal ordered residues of the betaA arm, which functions as a molecular switch. Comparative analysis suggests that this molecular switch can also modulate the stability of the viral capsids.

Recombinant tobacco mosaic virus movement protein is an RNA-binding, alpha-helical membrane protein

The 30-kDa movement protein (MP) is essential for cell-cell spread of tobacco mosaic virus in planta. To explore the structural properties of MP, the full-length recombinant MP gene was expressed in Escherichia coli, and one-step purification from solubilized inclusion bodies was accomplished by using anion exchange chromatography. Soluble MP was maintained at >4 mg/ml without aggregation and displayed approximately 70% alpha-helical conformation in the presence of urea and SDS. A trypsin-resistant core domain of the MP had tightly folded tertiary structure, whereas 18 aa at the C terminus of the monomer were rapidly removed by trypsin. Two hydrophobic regions within the core were highly resistant to proteolysis. Based on results of CD spectroscopy, trypsin treatment, and MS, we propose a topological model in which MP has two putative alpha-helical transmembrane domains and a protease-sensitive carboxyl terminus.

Large conformational changes in the maturation of a simple RNA virus, nudaurelia capensis omega virus (NomegaV)

An assembly intermediate of a small, non-enveloped RNA virus has been discovered that exhibits striking differences from the mature virion. Virus-like particles (VLPs) of Nudaurelia capensis omega virus (NomegaV), a T=4 icosahedral virus infecting Lepidoptera insects, were produced in insect cells using a baculovirus vector expressing the coat protein. A procapsid form was discovered when NomegaV VLPs were purified at neutral pH conditions. These VLPs were fragile and did not undergo the autoproteolytic maturation that occurs in the infectious virus. Electron cryo-microscopy (cryoEM) and image analysis showed that, compared with the native virion, the VLPs were 16% larger in diameter, more rounded, porous, and contained an additional internal domain. Upon lowering the pH to 5.0, the VLP capsids became structurally indistinguishable from the authentic virion and the subunits autoproteolyzed. The NomegaV protein subunit coordinates, which were previously determined crystallographically, were modelled into the 28 A resolution cryoEM map of the procapsid. The resulting pseudo-atomic model of the NomegaV procapsid demonstrated the large rearrangements in quaternary and tertiary structure needed for the maturation of the VLPs and presumably of the virus. Based on this model, we propose that electrostatically driven rearrangements of interior helical regions are responsible for the large conformational change. These results are surprising because large structural rearrangements have not been found in the maturation of any other small RNA viruses. However, similarities of this conformational change to the maturational processes of more complex DNA viruses (e.g. bacteriophages and herpesvirus) and to the swelling of simple plant viruses suggest that structural changes in icosahedral viruses, which are integral to their function, have similar strategies and perhaps mechanisms.

Class I and class II MHC bind self peptide sets that are strikingly different in their evolutionary characteristics

Comparison of peptides eluted from human class I and class II major histocompatibility complex (MHC) molecules and the proteins from which they are derived (source proteins) revealed that class I MHC bind peptides derived from proteins that are highly conserved, hydrophilic, and universally expressed, while the peptides themselves are hydrophobic and even more conserved than their source proteins. In contrast, source proteins for class II-bound peptides were not significantly more conserved than a random sample of proteins. Class II-bound peptides were generally more conserved than their source proteins but were significantly less conserved than class I-bound peptides. The characteristics of class I-bound peptides can probably be explained by the selectivity of processing and transport of peptides for binding by class I, while the relative lack of selectivity of peptide binding for class II may explain the high incidence of autoimmune diseases associated with alleles of these molecules.

Projection structure of a plant vacuole membrane aquaporin by electron cryo-crystallography

The water channel protein alpha-TIP is a member of the major intrinsic protein (MIP) membrane channel family. This aquaporin is found abundantly in vacuolar membranes of cotyledons (seed storage organs) and is synthesized during seed maturation. The water channel activity of alpha-TIP can be regulated by phosphorylation, and the protein may function in seed desiccation, cytoplasmic osmoregulation, and/or seed rehydration. Alpha-TIP was purified from seed meal of the common bean (Phaseolus vulgaris) by membrane fractionation, solubilization in diheptanoylphosphocholine and anion-exchange chromatography. Upon detergent removal and reconstitution into lipid bilayers, alpha-TIP crystallized as helical tubes. Electron cryo-crystallography of flattened tubes demonstrated that the crystals exhibit plane group p2 symmetry and c222 pseudosymmetry. Since the 2D crystals with p2 symmetry are derived from helical tubes, we infer that the unit of crystallization on the helical lattice is a dimer of tetramers. A projection density map at a resolution of 7.7 A revealed that alpha-TIP assembles as a 60 A x 60 A square tetramer. Each subunit is formed by a heart-shaped ring comprised of density peaks which we interpret as alpha-helices. The similarity of this structure to mammalian plasma membrane MIP-family proteins suggests that the molecular design of functionally analogous and genetically homologous aquaporins is maintained between the plant and animal kingdoms.

Expression, two-dimensional crystallization, and electron cryo-crystallography of recombinant gap junction membrane channels

We used electron cryo-microscopy and image analysis to examine frozen-hydrated, two-dimensional (2D) crystals of a recombinant, 30-kDa C-terminal truncation mutant of the cardiac gap junction channel formed by 43-kDa alpha(1) connexin. To our knowledge this is the first example of a structural analysis of a membrane protein that has been accomplished using microgram amounts of starting material. The recombinant alpha(1) connexin was expressed in a stably transfected line of baby hamster kidney cells and spontaneously assembled gap junction plaques. Detergent treatment with Tween 20 and 1,2-diheptanoyl-sn-phosphocholine resulted in well-ordered 2D crystals. A three-dimensional density (3D) map with an in-plane resolution of approximately 7.5 A revealed that each hexameric connexon was formed by 24 closely packed rods of density, consistent with an alpha-helical conformation for the four transmembrane domains of each connexin subunit. In the extracellular gap the aqueous channel was bounded by a continuous wall of protein that formed a tight electrical and chemical seal to exclude exchange of substances with the extracellular milieu.

Chronic fatigue syndrome

The chronic fatigue syndrome is an illness of unknown etiology characterized by severe fatigue, myalgias, lymphadenopathy, arthralgias, chills, fevers, and postexertional malaise. Recognizing chronic fatigue syndrome is primarily a method of exclusion with no definitive diagnostic test or physical findings. As research continues to delve into the many possible etiologic agents for chronic fatigue syndrome--infectious, immunologic, neurologic, or psychiatric alone or in combination--the answer remains elusive. What is known is that chronic fatigue syndrome is a heterogeneous disorder very possibly involving an interaction of biological systems. Therefore, chronic fatigue syndrome may describe a large subset of patients, each exhibiting unique symptoms and serologic profiles dependent on the nature of the onset of illness and the genetic profile of individual patients.

Electron cryo-crystallography of a recombinant cardiac gap junction channel

Gap junctions in the heart play an important functional role by electrically coupling cells, thereby organizing the pattern of current flow to allow co-ordinated muscle contraction. Cardiac gap junctions are therefore intimately involved in normal conduction as well as the genesis of potentially lethal arrhythmias. We recently utilized electron cryo-microscopy and image analysis to examine frozen-hydrated 2D crystals of a recombinant, C-terminal truncated form of connexin 43 (Cx43; alpha 1), the principal cardiac gap junction protein. The projection map at 7 A resolution revealed that each 30 kDa connexin subunit has a transmembrane alpha-helix that lines the aqueous pore and a second alpha-helix in close contact with the membrane lipids. The distribution of densities allowed us to propose a model in which the two apposing connexons that form the channel are staggered by approximately 30 degrees. We are now recording images of tilted, frozen-hydrated 2D crystals, and a preliminary 3D map has been computed at an in-plane resolution of approximately 7.5 A and a vertical resolution of approximately 25 A. As predicted by our model, the two apposing connexons that form the channel are staggered with respect to each other for certain connexin molecular boundaries within the hexamer. Within the membrane interior each connexin subunit displays four rods of density, which are consistent with an alpha-helical conformation for the four transmembrane domains. Preliminary studies of BHK hamster cells that express the truncated Cx43 designated alpha 1 Cx263T demonstrate that oleamide, a sleep inducing lipid, blocks in vivo dye transfer, suggesting that oleamide causes closure of alpha 1 Cx263T channels. The comparison of the 3D structures in the presence and absence of oleamide may provide an opportunity to explore the conformational changes that are associated with oleamide-induced blockage of dye transfer. The structural details revealed by our analysis will be essential for delineating the molecular basis for intercellular current flow in the heart, as well as the general molecular design and functional properties of this important class of channel proteins.

Three-dimensional structure of a recombinant gap junction membrane channel

Gap junction membrane channels mediate electrical and metabolic coupling between adjacent cells. The structure of a recombinant cardiac gap junction channel was determined by electron crystallography at resolutions of 7.5 angstroms in the membrane plane and 21 angstroms in the vertical direction. The dodecameric channel was formed by the end-to-end docking of two hexamers, each of which displayed 24 rods of density in the membrane interior, which is consistent with an alpha-helical conformation for the four transmembrane domains of each connexin subunit. The transmembrane alpha-helical rods contrasted with the double-layered appearance of the extracellular domains. Although not indicative for a particular type of secondary structure, the protein density that formed the extracellular vestibule provided a tight seal to exclude the exchange of substances with the extracellular milieu.

Natural selection at major histocompatibility complex loci of vertebrates

The loci of the vertebrate major histocompatibility complex encode cell-surface glycoproteins that present peptides to T cells. Certain of these loci are highly polymorphic, and the mechanisms responsible for this polymorphism have been intensely debated. Four independent lines of evidence support the hypothesis that MHC polymorphisms are selectively maintained: (a) The distribution of allelic frequencies does not fit the neutral expectation. (b) The rate of nonsynonymous nucleotide substitution significantly exceeds the rate of synonymous substitution in the codons encoding the peptide-binding region of the molecule. (c) Polymorphisms have been maintained for long periods of time ("trans-species polymorphism"). (d) Introns have been homogenized relative to exons over evolutionary time, suggesting that balancing selection acts to maintain diversity in the latter, in contrast to the former.

Coevolution of the mammalian chemokines and their receptors

A phylogeny of mammalian chemokines revealed two major clusters, corresponding to the CC and CXC chemokines; the C chemokines appeared to be more closely related to the former. In a phylogeny of chemokine receptors, there were also two major clusters: one containing CC chemokine receptors plus other receptors of unknown function and another containing CXC receptors and other receptors of unknown function. However, within the CC receptors, there was not a close correspondence between the phylogenies of chemokines and their receptors. The CC chemokines contained two major subfamilies: (1) the MIP subfamily (including MIP-1alpha, MIP-1beta, and RANTES); and (2) the MCP subfamily (including MCP-1,-2,-3, and -4 and eotaxin). Receptors having preferred ligands in the MCP subfamily did not constitute a monophyletic group but rather evolved twice independently. Reconstruction of ancestral amino acid sequences suggested that these two groups of MCP receptors did not convergently evolve any amino acid residues; rather, they convergently lost sequence features found in the third and fourth extracellular domains of known receptors for MIP-subfamily chemokines.

Evolution of the mammalian MHC: natural selection, recombination, and convergent evolution

The genes that encode molecules involved in antigen presentation within the class I and class II regions of the mammalian major histocompatibility complex (MHC) include several that are highly polymorphic. There is evidence that this polymorphism is maintained by positive selection, most likely overdominant selection, relating to their role in presenting foreign peptides to T cells. This selection can maintain allelic lineages for much longer periods of time than neutral polymorphisms are expected to last, but sharing of polymorphic amino acid motifs among species of different mammalian orders is due to independent (or convergent) evolution rather than common ancestry. It has been suggested that interallelic recombination (gene conversion) plays a role in enhancing polymorphism, but there is evidence of striking differences among loci with respect to the rate at which such recombination has contributed to current polymorphism. Recent attempts to interpret linkage relationships in the MHC region as evidence of ancient genomic duplications are not supported by phylogenetic analysis. Rather, natural selection may have played a role in the linkage of other genes to those of the MHC.