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1.  Transplantation Outcomes for Severe Combined Immunodeficiency, 2000–2009 
The New England journal of medicine  2014;371(5):434-446.
The Primary Immune Deficiency Treatment Consortium was formed to analyze the results of hematopoietic-cell transplantation in children with severe combined immunodeficiency (SCID) and other primary immunodeficiencies. Factors associated with a good transplantation outcome need to be identified in order to design safer and more effective curative therapy, particularly for children with SCID diagnosed at birth.
We collected data retrospectively from 240 infants with SCID who had received transplants at 25 centers during a 10-year period (2000 through 2009).
Survival at 5 years, freedom from immunoglobulin substitution, and CD3+ T-cell and IgA recovery were more likely among recipients of grafts from matched sibling donors than among recipients of grafts from alternative donors. However, the survival rate was high regardless of donor type among infants who received transplants at 3.5 months of age or younger (94%) and among older infants without prior infection (90%) or with infection that had resolved (82%). Among actively infected infants without a matched sibling donor, survival was best among recipients of haploidentical T-cell–depleted transplants in the absence of any pretransplantation conditioning. Among survivors, reduced-intensity or myeloablative pre-transplantation conditioning was associated with an increased likelihood of a CD3+ T-cell count of more than 1000 per cubic millimeter, freedom from immunoglobulin substitution, and IgA recovery but did not significantly affect CD4+ T-cell recovery or recovery of phytohemagglutinin-induced T-cell proliferation. The genetic subtype of SCID affected the quality of CD3+ T-cell recovery but not survival.
Transplants from donors other than matched siblings were associated with excellent survival among infants with SCID identified before the onset of infection. All available graft sources are expected to lead to excellent survival among asymptomatic infants. (Funded by the National Institute of Allergy and Infectious Diseases and others.)
PMCID: PMC4183064  PMID: 25075835
2.  Short-read, high-throughput sequencing technology for STR genotyping 
DNA-based methods for human identification principally rely upon genotyping of short tandem repeat (STR) loci. Electrophoretic-based techniques for variable-length classification of STRs are universally utilized, but are limited in that they have relatively low throughput and do not yield nucleotide sequence information. High-throughput sequencing technology may provide a more powerful instrument for human identification, but is not currently validated for forensic casework. Here, we present a systematic method to perform high-throughput genotyping analysis of the Combined DNA Index System (CODIS) STR loci using short-read (150 bp) massively parallel sequencing technology. Open source reference alignment tools were optimized to evaluate PCR-amplified STR loci using a custom designed STR genome reference. Evaluation of this approach demonstrated that the 13 CODIS STR loci and amelogenin (AMEL) locus could be accurately called from individual and mixture samples. Sensitivity analysis showed that as few as 18,500 reads, aligned to an in silico referenced genome, were required to genotype an individual (>99% confidence) for the CODIS loci. The power of this technology was further demonstrated by identification of variant alleles containing single nucleotide polymorphisms (SNPs) and the development of quantitative measurements (reads) for resolving mixed samples.
PMCID: PMC4301848  PMID: 25621315
STR; forensic; next-generation sequencing; high-throughput sequencing; Illumina; Bridge PCR; SNP; genotyping
3.  Trends in Stage-Specific Incidence Rates for Urothelial Carcinoma of the Bladder in the United States: 1988 to 2006 
Cancer  2013;120(1):86-95.
Bladder cancer is notable for a striking heterogeneity of disease-specific risks. Among the approximately 75% of incident cases found to be superficial to the muscularis propria at the time of presentation (non-muscle-invasive bladder cancer), the risk of progression to the lethal phenotype of muscle-invasive disease is strongly associated with stage and grade of disease. Given the suggestion of an increasing percentage of low-risk cases in hospital-based registry data in recent years, the authors hypothesized that population-based data may reveal changes in the stage distribution of early-stage cases.
Surveillance, Epidemiology, and End Results (SEER) data were used to examine trends for the stage-specific incidence of bladder cancer between 1988 and 2006, adjusted for age, race, and sex, using Joinpoint and nonparametric tests.
The adjusted incidence rate of papillary noninvasive (Ta) predominantly low grade (77%) disease was found to increase from 5.52 to 9.09 per 100,000 population (P <.0001), with an average annual percentage change of +3.3. Over the same period, concomitant, albeit smaller, decreases were observed for flat in situ (Tis) and lamina propria-invasive (T1) disease (2.57 to 1.19 and 6.65 to 4.61 per 100,000 population [both P <.0001]; average annual percent change of −5.0 and −1.6, respectively). The trend was most dramatic among patients in the oldest age strata, suggesting a previously unappreciated cohort phenomenon.
The findings of the current study should motivate further epidemiological investigations of differential associations of genetic and environmental factors with different bladder cancer phenotypes as well as further scrutiny of clinical practice guideline recommendations for the growing subgroup of predominantly older patients with lower-risk disease.
PMCID: PMC3964001  PMID: 24122346
bladder cancer; incidence; epidemiology; carcinogenesis; stage migration
4.  Roadmap for the Development of the University of North Carolina at Chapel Hill Genitourinary OncoLogy Database – UNC GOLD 
Urologic oncology  2013;32(1):32.e1-32.e9.
The management of genitourinary malignancies requires a multidisciplinary care team composed of urologists, medical oncologists and radiation oncologists. A genitourinary (GU) oncology clinical database is an invaluable resource for patient care and research. Although electronic medical records provide a single web-based record used for clinical care, billing and scheduling, information is typically stored in a discipline-specific manner and data extraction is often not applicable to a research setting. A GU oncology database may be used for the development of multidisciplinary treatment plans, analysis of disease-specific practice patterns, and identification of patients for research studies. Despite the potential utility, there are many important considerations that must be addressed when developing and implementing a discipline-specific database.
Methods and Materials
The creation of the GU oncology database including prostate, bladder and kidney cancers with the identification of necessary variables was facilitated by meetings of stakeholders in medical oncology, urology, and radiation oncology at the University of North Carolina (UNC) at Chapel Hill with a template data dictionary provided by the Department of Urologic Surgery at Vanderbilt University Medical Center. Utilizing Research Electronic Data Capture (REDCap, version 4.14.5), the UNC Genitourinary OncoLogy Database (UNC GOLD) was designed and implemented.
The process of designing and implementing a discipline-specific clinical database requires many important considerations. The primary consideration is determining the relationship between the database and the Institutional Review Board (IRB) given the potential applications for both clinical and research uses. Several other necessary steps include ensuring information technology security and federal regulation compliance; determination of a core complete data set; creation of standard operating procedures; standardizing entry of free text fields; use of data exports, queries, and de-identification strategies; inclusion of individual investigators’ data; and strategies for prioritizing specific projects and data entry.
A discipline-specific database requires a buy-in from all stakeholders, meticulous development, and data entry resources in order to generate a unique platform for housing information that may be used for clinical care and research with IRB approval. The steps and issues identified in the development of UNC GOLD provide a process map for others interested in developing a GU oncology database.
PMCID: PMC4058502  PMID: 23434424
Urologic Oncology; Clinical Database; Genitourinary Oncology; REDCap; Oncology Database
5.  Beginning a Partnership with PhotoVoice to Explore Environmental Health and Health Inequities in Minority Communities 
Research informs action, but the challenge is its translation into practice. The 2012–2017 National Institute of Environmental Health Sciences Strategic Plan emphasizes partnership with community stakeholders to capture critical missing information about the effects of environment on health and to improve translation of study results, a daunting task for many traditionally-trained researchers. To better understand economic and neighborhood context consistent with these goals as well as existing inequities, we needed access to a highly affected community to inform and participate in our research. Our team therefore undertook a PhotoVoice project as a first step in establishing a participatory partnership and to appreciate the lived experiences of and build trust with youth visiting an urban community center in a high-risk, low-income, African American neighborhood located along a busy, polluted interstate. Ten 8–13 years-olds represented their community’s perspectives through photographs over 14-weeks using structured questioning. Five themes emerged: poor eating habits/inadequate nutrition; safety/violence; family/friends/community support; future hopes/dreams; and garbage/environment. Public viewings of the photos/captions facilitated engagement of other community agencies and multidisciplinary academic faculties to work together to build a sustainable “community collaboratory” that will promote health at the center by providing families knowledge/skills to prevent/minimize environmental exposures via diet/lifestyle changes using community-engaged, citizen scientist and systems thinking approaches.
PMCID: PMC4245604  PMID: 25350008
environmental health; health inequities; community health; PhotoVoice; child/adolescent health; community-based participatory research; community engagement; minority health; health disparities
6.  The Natural History of Children with Severe Combined Immunodeficiency: Baseline Features of the First Fifty Patients of the Primary Immune Deficiency Treatment Consortium Prospective Study 6901 
Journal of clinical immunology  2013;33(7):1156-1164.
The Primary Immune Deficiency Treatment Consortium (PIDTC) consists of 33 centers in North America. We hypothesized that the analysis of uniform data on patients with severe combined immunodeficiency (SCID) enrolled in a prospective protocol will identify variables that contribute to optimal outcomes following treatment. We report baseline clinical, immunologic, and genetic features of the first 50 patients enrolled, and the initial therapies administered, reflecting current practice in the diagnosis and treatment of both typical (n = 37) and atypical forms (n = 13) of SCID.
From August 2010 to May 2012, patients with suspected SCID underwent evaluation and therapy per local center practices. Diagnostic information was reviewed by the PIDTC eligibility review panel, and hematopoietic cell transplantation (HCT) details were obtained from the Center for International Blood and Marrow Transplant Research.
Most patients (92%) had mutations in a known SCID gene. Half of the patients were diagnosed by newborn screening or family history, were younger than those diagnosed by clinical signs (median 15 vs. 181 days; P = <0.0001), and went to HCT at a median of 67 days vs. 214 days of life (P = <0.0001). Most patients (92%) were treated with HCT within 1–2 months of diagnosis. Three patients were treated with gene therapy and 1 with enzyme replacement.
The PIDTC plans to enroll over 250 such patients and analyze short and long-term outcomes for factors beneficial or deleterious to survival, clinical outcome, and T- and B-cell reconstitution, and which biomarkers are predictive of these outcomes.
PMCID: PMC3784642  PMID: 23818196
Severe Combined Immunodeficiency; Hematopoietic Cell Transplantation; Newborn Screening
7.  Prevention and management of complications following robot-assisted radical cystectomy: Lessons learned after >250 consecutive cases 
World journal of urology  2012;31(3):441-446.
An increasing number of case series of robot-assisted radical cystectomy describe complication rates comparable to open series. Conflicting reports describe various pre-operative factors as predictors of post-operative complications. Furthermore, learning curves complicate these predictors and should also be taken into account. Despite these variables, there are a number of considerations, including patient selection, peri-operative care pathway, intra-operative technique and equipment choice that we have found to decrease post-operative complications and improve patient outcomes. In this topic paper, we briefly review the literature surrounding complication rates following robot-assisted radical cystectomy as well as describe our experience after >250 cases, outlining our suggestions for avoidance of surgical complications when building a practice that incorporates this technique.
PMCID: PMC3636191  PMID: 23269587
8.  Microbial Community Profiling of Human Saliva Using Shotgun Metagenomic Sequencing 
PLoS ONE  2014;9(5):e97699.
Human saliva is clinically informative of both oral and general health. Since next generation shotgun sequencing (NGS) is now widely used to identify and quantify bacteria, we investigated the bacterial flora of saliva microbiomes of two healthy volunteers and five datasets from the Human Microbiome Project, along with a control dataset containing short NGS reads from bacterial species representative of the bacterial flora of human saliva. GENIUS, a system designed to identify and quantify bacterial species using unassembled short NGS reads was used to identify the bacterial species comprising the microbiomes of the saliva samples and datasets. Results, achieved within minutes and at greater than 90% accuracy, showed more than 175 bacterial species comprised the bacterial flora of human saliva, including bacteria known to be commensal human flora but also Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae, and Gamma proteobacteria. Basic Local Alignment Search Tool (BLASTn) analysis in parallel, reported ca. five times more species than those actually comprising the in silico sample. Both GENIUSand BLAST analyses of saliva samples identified major genera comprising the bacterial flora of saliva, but GENIUS provided a more precise description of species composition, identifying to strain in most cases and delivered results at least 10,000 times faster. Therefore, GENIUS offers a facile and accurate system for identification and quantification of bacterial species and/or strains in metagenomic samples.
PMCID: PMC4028220  PMID: 24846174
9.  One year follow-up of a pragmatic multi-centre randomised controlled trial of a group-based fatigue management programme (FACETS) for people with multiple sclerosis 
BMC Neurology  2014;14:109.
Fatigue is one of the most common and debilitating symptoms of multiple sclerosis (MS). The aim was to evaluate the effectiveness at 1-year follow-up of a manualised group-based programme (‘FACETS’) for managing MS-fatigue.
One-year follow-up of a pragmatic multi-centre randomised controlled trial. People with MS and significant fatigue were randomised to FACETS plus current local practice (FACETS) or current local practice alone (CLP), using concealed computer-generated randomisation. Participant blinding was not possible. Primary outcome measures were fatigue severity (Global Fatigue Severity subscale of the Fatigue Assessment Instrument), self-efficacy (MS-Fatigue Self-Efficacy) and disease-specific quality of life (MS Impact Scale).
Between May 2008 and November 2009, 164 participants were randomised. Primary outcome data were available at 1 year for 131 (80%). The benefits demonstrated at 4-months in the FACETS arm for fatigue severity and self-efficacy largely persisted, with a slight reduction in standardised effect sizes (SES) (−0.29, p = 0.06 and 0.34, p = 0.09, respectively). There was a significant difference on the MS Impact Scale favouring FACETS that had not been present at 4-months (SES −0.24, p = 0.046). No adverse events were reported.
Improvements in fatigue severity and self-efficacy at 4-months follow-up following attendance of FACETS were mostly sustained at 1 year with additional improvements in MS impact. The FACETS programme provides modest long-term benefits to people with MS-fatigue.
Trial registration
PMCID: PMC4046846  PMID: 24886398
Randomised controlled trial; Multiple sclerosis; Fatigue; Intervention; Energy effectiveness; Cognitive behavioural; Group
10.  Early Hematopoietic Stem Cell Transplant is Associated with Favorable Outcomes in Children with MDS 
Pediatric blood & cancer  2012;60(4):705-710.
Although hematopoietic stem cell transplantation (HSCT) is the treatment of choice for childhood myelodysplastic syndrome (MDS), there is no consensus regarding patient or disease characteristics that predict outcomes.
We reviewed 37 consecutive pediatric MDS patients who received myeloablative HSCT between 1990 and 2010 at a single center.
Twenty had primary MDS and 17 had secondary MDS. Diagnostic cytogenetics included monosomy 7 (n=21), trisomy 8 (n=7) or normal/other (n=8). According to the modified WHO MDS classification, thirty had refractory cytopenia and 7 had refractory anemia with excess blasts. IPSS scores were: low risk (n=1), intermediate-1 (n=15), and intermediate-2 (n=21). OS and DFS at 10-years in the entire cohort was 53% and 45%. Relapse at 10-years was 26% and 1-year TRM was 25%. In multivariate analysis, factors associated with improved 3-year DFS were not receiving pre-HSCT chemotherapy (RR=0.30, 95% CI 0.10–0.88; p=0.03) and a shorter interval (<140 days) from time of diagnosis to transplant (RR=0.27, 95% CI 0.09–0.80; p=0.02). 3-year DFS in patients who did not receive pre-HSCT chemotherapy and those who had a shorter interval to transplant (n=16) was 80%.
These results suggest that children with MDS should be referred for allogeneic HSCT soon after diagnosis and that pre-HSCT chemotherapy does not appear to improve outcomes.
PMCID: PMC3668778  PMID: 23152304
11.  Survival Differences between Adolescent / Young Adults and Children with B-Precursor Acute Lymphoblastic Leukemia following Allogeneic Hematopoietic Cell Transplantation 
Risk adapted therapy has been the cornerstone of treatment for pediatric B-precursor acute lymphoblastic leukemia (B-ALL). Recently, age (>13 years at diagnosis) has been identified as a very high-risk feature for chemotherapy treated pediatric B-ALL patients. Whether age at time of transplant is associated with poor outcomes in adolescents and young adults (AYA) is unknown. We hypothesized AYA receiving allogeneic hematopoietic cell transplantation (allo-HCT) would have greater relapse and inferior survival. We reviewed the outcomes in 136 consecutive patients (ages 0 to 30 years) with B-ALL who received myeloablative allo-HCT at our institution. Fifty-eight percent (n=79) were children <13 years of age and 42% (n=57) were AYA 13 to 30 years of age. Overall survival at 5-years was significantly lower in the AYA group [HR 1.74, 95% CI: 1.04–2.95; p=0.03]. In addition, AYA patients had a greater risk of transplant related mortality (TRM) at 1-year [HR 2.23, 95% CI: 1.01–4.90, p=0.05] but no difference in relapse [RR 0.85, 95% CI 0.41–1.76; p=0.66]. Based on this analysis, AYA patients undergoing allo-HCT for B-ALL have significantly inferior survival and greater TRM compared to children <13 years but no difference in relapse suggesting allo-HCT may overcome relapse in AYA. Further improvements in peri-transplant care are needed to limit complications in AYA patients.
PMCID: PMC3530019  PMID: 22960388
ALL; adolescent and young adult; transplantation
12.  Human Parainfluenza Virus Infection following Hematopoietic Stem Cell Transplantation: Risk Factors, Management, Mortality, and Changes over Time 
Human parainfluenza viruses (HPIV) are uncommon, yet high-risk pathogens after hematopoietic stem cell transplantation (HCT). We evaluated 5178 pediatric and adult patients undergoing HCT between 1974 and 2010 to determine the incidence, risk factors, response to treatment, and outcome of HPIV infection as well as any change in frequency or character of HPIV infection over time. HPIV was identified in 173 patients (3.3%); type 3 was most common (66%). HPIV involved the upper respiratory tract (URTI) (57%), lower respiratory tract (LRTI) (9%), and both (34%) areas of the respiratory tract, at a median of 62 days after transplant. In more recent years, HPIV has occurred later after HCT, while the proportion with nosocomial infection and mortality decreased. Over the last decade, HPIV was more common in older patients and in those receiving reduced intensity conditioning (RIC). RIC was a significant risk factor for later (beyond day +30) HPIV infections and this association was strongest in patients with URTI. HCT using a matched unrelated donor (MUD), mismatched related donor (MMRD), age 10-19 years, and graft-versus-host disease (GVHD) were all risk factors for HPIV infections. LRTI, early (<30 days) infections, age 10-19 years, MMRD, steroid use, and coinfection with other pathogens were risk factors for mortality. The survival of patients with LRTI, especially very early infections, was poor regardless of ribavirin treatment. HPIV incidence remains low, but may have delayed onset associated with RIC regimens and improving survival. Effective prophylaxis and treatment for HPIV are needed.
PMCID: PMC3443286  PMID: 22531491
Human parainfluenza virus; Infection; Respiratory Virus; HCT (hematopoietic cell transplantation); Reduced Intensity Conditioning
13.  Enterococcal Bacteremia Is Associated With Increased Risk of Mortality in Recipients of Allogeneic Hematopoietic Stem Cell Transplantation 
Enterococcal bloodstream infections are associated with an increased risk of mortality during the first year after hematopoietic stem cell transplantation, especially in patients with vancomycin-resistant enterococci (VRE) strains. Colonization with VRE and delayed engraftment are significant risk factors for VRE bacteremia.
Background. Enterococci are an important cause of healthcare-associated infections. We retrospectively analyzed risk factors and outcome of vancomycin-resistant enterococci (VRE) and vancomycin-sensitive enterococci (VSE) infections.
Methods. Seven hundred fifty-two patients who received hematopoietic stem cell transplants from 2004 through 2008 at the University of Minnesota were included.
Results. Ninety-three patients had enterococcal bloodstream infection (BSI) during the first year after transplant. Vancomycin resistance was observed in 66% and 31% of isolates in adults and children, respectively. Cumulative incidence of VRE and VSE bacteremia was 6.6% (95% confidence interval [CI], 4.8%–8.4%) and 5.7% (95% CI, 4.0%–7.4%), respectively. Colonization with VRE before or after transplant was a risk factor for VRE bacteremia (odds ratio [OR], 3.3 [95% CI, 1.3–8.3] and 7.0 [95% CI, 4.0–14.8], respectively). Delay in engraftment increased the incidence of VRE bacteremia from 4.5% (95% CI, 2.9–6.6) if engrafted before day 21 and to 15% (95% CI, 3.2%–38%) if engrafted between days 36 and 42. In adults, mortality 30 days after infection was 38% for both VRE (95% CI, 25%–54%) and VSE cases (95% CI, 21%–62%). The hazard ratio for all-cause mortality up to 1 year after transplant was 4.2 (95% CI, 3.1–6.9) and 2.7 (95% CI, 1.4–5.1) for patients with VRE and VSE BSIs, respectively, compared to patients without enterococcal BSI. In pediatric patients, mortality 30 days after VRE and VSE bacteremia was 20% (95% CI, 5.4%–59%) and 4.5% (95% CI, .6%–28%), respectively.
Conclusion. High rates of vancomycin resistance and association of enterococcal infections with significant mortality warrant further efforts to optimize prevention and management of these infections.
PMCID: PMC3657510  PMID: 22693346
14.  Anterior cruciate ligament- specialized post-operative return-to-sports (ACL-SPORTS) training: a randomized control trial 
Anterior cruciate ligament reconstruction (ACLR) is standard practice for athletes that wish to return to high-level activities; however functional outcomes after ACLR are poor. Quadriceps strength weakness, abnormal movement patterns and below normal knee function is reported in the months and years after ACLR. Second ACL injuries are common with even worse outcomes than primary ACLR. Modifiable limb-to-limb asymmetries have been identified in individuals who re-injure after primary ACLR, suggesting a neuromuscular training program is needed to improve post-operative outcomes. Pre-operative perturbation training, a neuromuscular training program, has been successful at improving limb symmetry prior to surgery, though benefits are not lasting after surgery. Implementing perturbation training after surgery may be successful in addressing post-operative deficits that contribute to poor functional outcomes and second ACL injury risk.
80 athletes that have undergone a unilateral ACLR and wish to return to level 1 or 2 activities will be recruited for this study and randomized to one of two treatment groups. A standard care group will receive prevention exercises, quadriceps strengthening and agility exercises, while the perturbation group will receive the same exercise program with the addition of perturbation training. The primary outcomes measures will include gait biomechanics, clinical and functional measures, and knee joint loading. Return to sport rates, return to pre-injury level of activity rates, and second injury rates will be secondary measures.
The results of this ACL-Specialized Post-Operative Return To Sports (ACL-SPORTS) Training program will help clinicians to better determine an effective post-operative treatment program that will improve modifiable impairments that influence outcomes after ACLR.
Trial registration
Randomized Control Trial NIH 5R01AR048212-07. NCT01773317
PMCID: PMC3617067  PMID: 23522373
Anterior cruciate ligament reconstruction; Neuromuscular training; Return to Sport
15.  Lower Leukemia Relapse in Pediatric Patients with Pulmonary Cytolytic Thrombi Following Allogeneic Transplant 
Bone marrow transplantation  2010;46(3):368-371.
Pulmonary cytolytic thrombi (PCT) is an uncommon complication after hematopoietic cell transplantation. Although the pathogenesis is unknown, patients typically respond to systemic corticosteroid treatment. Considering corticosteroids may impair graft versus leukemia reactions, we reviewed the records of 324 pediatric patients who received a transplant for leukemia and compared the outcomes of those with PCT (n=14) to those without PCT (n=310). PCT patients had a significantly more acute and chronic GVHD. Though 3 year non-relapse mortality and overall survival were similar, there was significantly less relapse in patients with PCT compared to those without PCT, regardless of the presence or absence of aGVHD (0% vs. 34% vs. 18%, p<0.01). In multivariate analysis, grade II–IV aGVHD (p=0.02), cGVHD (p=0.01) and development of PCT (p<0.01) were independently associated with less relapse. These data suggest that patients with PCT are at greater risk for GVHD, but a lower risk of leukemia relapse.
PMCID: PMC3556271  PMID: 20548337
Pulmonary Cytolytic Thrombi; Stem Cell Transplantation; Leukemia; Relapse
16.  Variable sequences outside the SAM-binding core critically influence the conformational dynamics of the SAM-III/SMK box riboswitch 
Journal of molecular biology  2011;409(5):786-799.
The SMK box (SAM-III) translational riboswitches were identified in S-adenosyl-L-methionine (SAM) synthetase metK genes in members of the Lactobacillales. This riboswitch switches between two alternative conformations in response to the intracellular SAM concentration and controls metK expression at the level of translation initiation. We previously reported the crystal structure of the SAM-bound SMK box riboswitch. In this study we combined SHAPE chemical probing with mutagenesis to probe the ligand-induced conformational switching mechanism. We revealed that while the majority of the apo SMK box RNA molecules exist in an alternatively base paired (ON) conformation, a subset of them pre-organize into a SAM-bound-like (READY) conformation, which upon SAM exposure is selectively stabilized into the SAM-bound (OFF) conformation through an induced-fit mechanism. Mutagenesis showed that the ON state is only slightly more stable than the READY state, as several single-nucleotide substitutions in a hypervariable region outside the SAM-binding core can alter the folding landscape to favor the READY state. Such SMK variants display a “constitutively-OFF” behavior both in vitro and in vivo. Time-resolved and temperature-dependent SHAPE analyses revealed adaptation of the SMK box RNA to its mesothermal working environment. The latter analysis revealed that the SAM-bound SMK box RNA follows a two-step folding/unfolding process.
PMCID: PMC3479645  PMID: 21549712
17.  Crystal structures of the SAM-III/SMK riboswitch reveal the SAM-dependent translation inhibition mechanism 
Nature structural & molecular biology  2008;15(10):1076-1083.
Three distinct classes of S-adenosyl-l-methionine (SAM)-responsive riboswitches have been identified that regulate bacterial gene expression at the levels of transcription attenuation or translation inhibition. The SMK box (SAM-III) translational riboswitch has been identified in the SAM synthetase gene in members of the Lactobacillales. Here we report the 2.2-Å crystal structure of the Enterococcus faecalis SMK box riboswitch. The Y-shaped riboswitch organizes its conserved nucleotides around a three-way junction for SAM recognition. The Shine-Dalgarno sequence, which is sequestered by base-pairing with the anti–Shine-Dalgarno sequence in response to SAM binding, also directly participates in SAM recognition. The riboswitch makes extensive interactions with the adenosine and sulfonium moieties of SAM but does not appear to recognize the tail of the methionine moiety. We captured a structural snapshot of the SMK box riboswitch sampling the near-cognate ligand S-adenosyl-l-homocysteine (SAH) in which SAH was found to adopt an alternative conformation and fails to make several key interactions.
PMCID: PMC3467307  PMID: 18806797
18.  Early Lymphocyte Recovery and Outcomes after Umbilical Cord Blood Transplantation (UCBT) for Hematologic Malignancies 
Rapid lymphocyte recovery after bone marrow or peripheral blood transplantation is associated with improved survival. However, the impact of early lymphocyte recovery has not been examined after umbilical cord blood transplant (UCBT). We evaluated lymphocyte recovery in 360 consecutive patients with hematologic malignancy that underwent UCBT between 2001 and 2007. Uniform myeloablative (MA), reduced intensity conditioning (RIC) and graft vs. host disease prophylaxis regimens were used. In multivariate analysis, an ALC >200 ×106/L at day 30 (n=73) after MA conditioning was associated with superior 2-year overall survival (OS) (73% vs. 61%; p=0.02) [RR: 2.29; 95% CI: 1.15 – 4.56], progression-free survival (PFS) (68% vs. 54%; p=0.05) [RR: 1.96; 95% CI: 0.99 – 3.86] and less transplant related mortality (TRM) (8% vs. 28%, p<0.01) [RR: 4.38; 95% CI: 1.65 – 11.60] compared to ≤200×106/L (n=43). Similarly, an ALC >200 ×106/L at day 42 (n=105) after RIC was associated with superior 2-year OS (59% vs. 41%, p<0.01) [RR: 2.10; 95% CI: 1.3 – 3.41] and PFS (46% vs. 36%, p=0.05) [RR: 1.58; 95% CI: 1.01 – 2.49] compared to ≤200 ×106/L (n=55). There was no significant relationship between ALC and relapse. Rapid lymphocyte recovery early after UCBT predicts better survival in patients with hematologic malignancies.
PMCID: PMC3412271  PMID: 20831896
ALL; AML; absolute lymphocyte count; allogeneic hematopoietic cell transplantation; umbilical cord blood; reduced intensity conditioning
19.  Vitamin D status among long-term survivors of hematopoietic cell transplantation 
Bone marrow transplantation  2011;46(11):1472-1479.
Little is known about serum vitamin D levels following hematopoietic cell transplantation (HCT). Patients are instructed to avoid sun exposure due to an increased risk of skin cancers. Altered gastrointestinal absorptive capacity as a result of GVHD, bile acid or pancreatic enzyme insufficiency, or bacterial overgrowth may lead to difficulty absorbing the fat soluble vitamin D. This study was undertaken to determine the prevalence of serum 25-hydroxyvitamin D (25(OH)D) deficiency, and factors associated with 25(OH)D deficiency, among children and adults who were at least one year following HCT. A total of 95 participants (54 males, 41 females) completed a questionnaire on usual diet and lifestyle, and provided a blood sample for 25(OH)D determinations between November 2008 and July 2009. The majority of participants had serum 25(OH)D levels ≥75 nmol/L (n=62, 65%), 23 had insufficient levels (50–75 nmol/L), and 10 participants were deficient (<50 nmol/L). The majority of participants reported regular vitamin D supplement use (n=58, 61%). Prednisone use was significantly inversely associated with serum 25(OH)D concentrations. Total vitamin D intake was the strongest single predictor of 25(OH)D concentrations. These findings suggest that 400–600 IU vitamin D/day appear to be required to achieve optimal serum 25(OH)D concentrations following HCT.
PMCID: PMC3131431  PMID: 21243026
hematopoietic cell transplantation; vitamin D; serum 25(OH)D; cancer survivors; diet; dietary supplements
20.  Tuning Riboswitch Regulation through Conformational Selection 
Journal of molecular biology  2010;405(4):926-938.
The SMK box riboswitch, which represents one of three known classes of S-adenosylmethionine (SAM)-responsive riboswitches, regulates gene expression in bacteria at the level of translation initiation. In contrast to most riboswitches, which contain separate domains responsible for ligand recognition and gene regulation, the ligand-binding and regulatory domains of the SMK box riboswitch are coincident. This property was exploited to allow the first atomic-level characterization of a functionally intact riboswitch in both the ligand-bound and ligand-free states. NMR spectroscopy revealed distinct mutually exclusive RNA conformations that are differentially populated in the presence or absence of the effector metabolite. Isothermal titration calorimetry and in vivo reporter assay results revealed the thermodynamic and functional consequences of this conformational equilibrium. We present a comprehensive model of the structural, thermodynamic, and functional properties of this compact RNA regulatory element.
PMCID: PMC3019289  PMID: 21075119
RNA; NMR spectroscopy; isothermal titration calorimetry; gene regulation; pre-existing equilibrium; riboswitch
21.  The SAM-responsive SMK box is a reversible riboswitch 
Molecular microbiology  2010;78(6):1393-1402.
The SMK (SAM-III) box is an S-adenosylmethionine (SAM)-responsive riboswitch found in the 5′ untranslated region of metK genes, encoding SAM synthetase, in many members of the Lactobacillales. SAM binding causes a structural rearrangement in the RNA that sequesters the Shine-Dalgarno (SD) sequence by pairing with a complementary anti-SD (ASD) sequence; sequestration of the SD sequence inhibits binding of the 30S ribosomal subunit and prevents translation initiation. We observed a slight increase in the half-life of the metK transcript in vivo when Enterococcus faecalis cells were depleted for SAM, but no significant change in overall transcript abundance, consistent with the model that this riboswitch regulates at the level of translation initiation. The half-life of the SAM-SMK box RNA complex in vitro is shorter than that of the metK transcript in vivo, raising the possibility of reversible binding of SAM. We used a fluorescence assay to directly visualize reversible switching between the SAM-free and SAM-bound conformations. We propose that the SMK box riboswitch can make multiple SAM-dependent regulatory decisions during the lifetime of the transcript in vivo, acting as a reversible switch that allows the cell to respond rapidly to fluctuations in SAM pools by modulating expression of the SAM synthetase gene.
PMCID: PMC3064258  PMID: 21143313
riboswitch; RNA; translational regulation; bacteria; gene expression
22.  Randomised Double-Blind Trial of Combination Antibiotic Therapy in Rheumatoid Arthritis 
Objective. A combination of intravenous clindamycin and oral tetracycline has been used for many years as a treatment for active rheumatoid arthritis (RA), despite the absence of good evidence for its efficacy. A single-blind pilot study of this therapy suggested that a double-blind placebo-controlled trial was warranted. Methods. Patients with active RA were randomised in a 2 : 1 ratio to receive active treatment or placebo for 25 weeks. The active treatment consisted of intravenous clindamycin in a reducing regime, and oral tetracycline twice daily three times a week. 50 patients were to be recruited. The primary outcome measure was the proportion of patients achieving an ACR20 response. Results. An interim statistical analysis was performed after 20 patients had completed the study. Two patients in the active group achieved an ACR20 response, with none in the placebo group (NS). There was a better ESR20 response in the placebo group (P = .02). There were no other significant differences between the groups. The results indicated that it was unlikely that a significant difference in ACR20 response would emerge if the remaining 30 patients were recruited. The trial was therefore halted. Conclusion. This antibiotic regime is unlikely to be a valuable therapy for active rheumatoid arthritis.
PMCID: PMC3134171  PMID: 21760803
23.  Alternative Hematopoietic Stem Cell Sources for Transplantation: Place of Umbilical Cord Blood 
British journal of haematology  2009;147(2):246-261.
Umbilical cord blood has rapidly become a valuable alternative stem cell source for allogeneic hematopoietic stem cell transplantation. Extensive research over the last 20 years has established the safety and efficacy of umbilical cord blood transplantation in both children and adults with a variety of malignant and non-malignant diseases. This research has clearly shown that this stem cell source has several unique characteristics resulting in distinct advantages and disadvantages when compared to transplantation with unrelated bone marrow or peripheral blood stem cells. This article reviews the most recent literature comparing the outcomes after umbilical cord blood transplantation with other alternative stem cell sources.
PMCID: PMC2782564  PMID: 19796274
stem cell transplantation; umbilical cord blood; alternative stem cell sources
24.  Phase II Trial of Oral Aminopterin for Adults and Children with Refractory Acute Leukemia 
To determine the antileukemic activity of weekly oral aminopterin in patients with refractory acute leukemia; to describe the pharmacodynamic properties of aminopterin; and to contrast the intracellular metabolism of aminopterin and methotrexate by patients’ blasts in vitro.
Experimental Design
Forty-six patients were enrolled in three strata: children with acute lymphoblastic leukemia (ALL), adults with ALL, and patients with acute myeloid leukemia (AML).Aminopterin was given weekly, in two doses of 2mg/m2, 12 hours apart. Limited sampling pharmacokinetic analysis was done during the first week of therapy. Accumulation of [3H]aminopterin and [3H]methotrexate by leukemic blasts was studied in vitro.
Six of 22 children with ALL (27%; 95% confidence interval, 8–47%) had clinically significant responses. None of those with AML and only two of 11 adults with ALL had responses meeting protocol definitions, although peripheral blast counts tended to decrease with therapy in all groups. Mucosal toxicity was minimal, even with limited use of leucovorin rescue. Complete bioavailability of aminopterin was confirmed, with a mean area under the curve of 0.52 ± 0.03 µmol hour/L after oral dosing. No relationship between aminopterin pharmacokinetics and response was seen. In vitro, aminopterin showed more consistent metabolism by leukemic blasts to polyglutamates than methotrexate. Lineage-specific differences in the pattern of intracellular antifolylpolyglutamates were observed.
Weekly oral aminopterin has significant activity among children with refractory ALL. With greater cellular accumulation and metabolism, more reliable bioavailability than methotrexate, and tolerable toxicity at this dose and schedule, aminopterin deserves further study as a potent alternative to methotrexate.
PMCID: PMC2906753  PMID: 16299240
25.  Finasteride in the treatment of patients with benign prostatic hyperplasia: a review 
Benign prostatic hyperplasia (BPH) is a complex and progressive disease common in aging men. While associated with bothersome lower urinary tract symptoms, it may also result in additional serious complications such as refractory hematuria, acute urinary retention, and BPH-related surgery. Medical therapy has been offered as an approach to halt this progression and perhaps reverse the pathophysiology of BPH. While alpha-blockers provide rapid relief in the form of improved flow rate, their effects may not reduce the overall risk of BPH-related complications. 5α-reductase inhibitors were therefore introduced to affect the underlying disease process by inhibiting the enzyme which converts testosterone to dihydrotesterone, the primary androgen involved in normal and abnormal prostate growth. Through this inhibition, prostate size is decreased, thereby reducing the risk of acute urinary retention and BPH-related surgery while providing symptom control. These effects are most pronounced in men with enlarged prostates (>25 mL) who are at the greatest risk of disease progression. This article reviews the literature for finasteride used in the treatment of BPH and provides evidence for its efficacy, safety and tolerability, applicability for combination therapy, and considerations of its effects on prostate cancer risk.
PMCID: PMC2710385  PMID: 19707263
finasteride; 5α-reductase inhibitor; prostatic hyperplasia

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