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1.  In Memoriam: Robert C. Moellering, Jr. 
doi:10.1128/AAC.03199-14
PMCID: PMC4068561  PMID: 24798286
2.  Genomic Characterisation of Small Cell Lung Cancer Patient-Derived Xenografts Generated from Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration Specimens 
PLoS ONE  2014;9(9):e106862.
Patient-derived xenograft (PDX) models generated from surgical specimens are gaining popularity as preclinical models of cancer. However, establishment of PDX lines from small cell lung cancer (SCLC) patients is difficult due to very limited amount of available biopsy material. We asked whether SCLC cells obtained from endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) could generate PDX lines that maintained the phenotypic and genetic characteristics of the primary tumor. Following successful EBUS-TBNA sampling for diagnostic purposes, we obtained an extra sample for cytologic analysis and implantation into the flanks of immunodeficient mice. Animals were monitored for engraftment for up to 6 months. Histopathologic and immunohistochemical analysis, and targeted next-generation re-sequencing, were then performed in both the primary sample and the derivative PDX line. A total of 12 patients were enrolled in the study. EBUS-TBNA aspirates yielded large numbers of viable tumor cells sufficient to inject between 18,750 and 1,487,000 cells per flank, and to yield microgram quantities of high-quality DNA. Of these, samples from 10 patients generated xenografts (engraftment rate 83%) with a mean latency of 104 days (range 63–188). All but one maintained a typical SCLC phenotype that closely matched the original sample. Identical mutations that are characteristic of SCLC were identified in both the primary sample and xenograft line. EBUS-TBNA has the potential to be a powerful tool in the development of new targeting strategies for SCLC patients by providing large numbers of viable tumor cells suitable for both xenografting and complex genomic analysis.
doi:10.1371/journal.pone.0106862
PMCID: PMC4156408  PMID: 25191746
3.  An Experimental Evaluation of the Force Requirements for Robotic Mastoidectomy 
Hypothesis
During robotic milling of the temporal bone, forces on the cutting burr may be lowered by choice of cutting parameters.
Background
Robotic bone removal systems are used in orthopedic procedures but they are currently not accurate enough for safe use in otologic surgery. We propose the use of a bone attached milling robot to achieve the required accuracy and speed. To design such a robot and plan its milling trajectories, it is necessary to predict the forces that the robot must exert and withstand under likely cutting conditions.
Materials and Methods
We measured forces during bone removal for several surgical burr types, drill angles, depths of cut, cutting velocities, and bone types (cortical/surface bone and mastoid) on human temporal bone specimens.
Results
Lower forces were observed for 5 mm diameter burrs compared to 3 mm burrs for a given bone removal rate. Higher linear cutting velocities and greater cutting depths independently resulted in higher forces. For combinations of velocities and depths that resulted in the same overall bone removal rate, lower forces were observed in parameter sets that combined higher cutting velocities and shallower depths. Lower mean forces and higher variability were observed in the mastoid compared with cortical/surface bone.
Conclusion
Forces during robotic milling of the temporal bone can be predicted from the parameter sets tested in this study. This information can be used to guide the design of a sufficiently rigid and powerful bone-attached milling robot and to plan efficient milling trajectories. To reduce the time of the surgical intervention without creating very large forces, high linear cutting velocities may be combined with shallow depths of cut. Faster and deeper cuts may be used in mastoid bone compared to cortical bone for a chosen force threshold.
doi:10.1097/MAO.0b013e318291c76b
PMCID: PMC3761064  PMID: 23787968
4.  Peptidoglycan Cross-Linking in Glycopeptide-Resistant Actinomycetales 
Synthesis of peptidoglycan precursors ending in d-lactate (d-Lac) is thought to be responsible for glycopeptide resistance in members of the order Actinomycetales that produce these drugs and in related soil bacteria. More recently, the peptidoglycan of several members of the order Actinomycetales was shown to be cross-linked by l,d-transpeptidases that use tetrapeptide acyl donors devoid of the target of glycopeptides. To evaluate the contribution of these resistance mechanisms, we have determined the peptidoglycan structure of Streptomyces coelicolor A(3)2, which harbors a vanHAX gene cluster for the production of precursors ending in d-Lac, and Nonomuraea sp. strain ATCC 39727, which is devoid of vanHAX and produces the glycopeptide A40296. Vancomycin retained residual activity against S. coelicolor A(3)2 despite efficient incorporation of d-Lac into cytoplasmic precursors. This was due to a d,d-transpeptidase-catalyzed reaction that generated a stem pentapeptide recognized by glycopeptides by the exchange of d-Lac for d-Ala and Gly. The contribution of l,d-transpeptidases to resistance was limited by the supply of tetrapeptide acyl donors, which are essential for the formation of peptidoglycan cross-links by these enzymes. In the absence of a cytoplasmic metallo-d,d-carboxypeptidase, the tetrapeptide substrate was generated by hydrolysis of the C-terminal d-Lac residue of the stem pentadepsipeptide in the periplasm in competition with the exchange reaction catalyzed by d,d-transpeptidases. In Nonomuraea sp. strain ATCC 39727, the contribution of l,d-transpeptidases to glycopeptide resistance was limited by the incomplete conversion of pentapeptides into tetrapeptides despite the production of a cytoplasmic metallo-d,d-carboxypeptidase. Since the level of drug production exceeds the level of resistance, we propose that l,d-transpeptidases merely act as a tolerance mechanism in this bacterium.
doi:10.1128/AAC.02329-13
PMCID: PMC3957865  PMID: 24395229
5.  A Case of Spontaneous Systemic Immunity to Melanoma Associated with Cure after Amputation For Extensive Regional Recurrence 
Purpose
Survival after amputation for melanoma is short; however, rare long-term survivors are reported. The mechanism for durable systemic tumor control in patients with regional failure is not known. To explore whether systemic tumor immunity may be implicated, tumor and circulating immune responses were examined in a patient who survived disease-free 14 years after hip disarticulation.
Methods
A 71 year-old female with extensive regional metastases of melanoma in the left lower extremity underwent amputation for palliative reasons. Tumor was collected at surgery, and blood was collected during follow-up. Tumor sections were evaluated for lymphocytic infiltration and NY-ESO-1 expression by immunohistochemistry. Cellular immune responses to defined tumor antigens were evaluated by ELIspot assay, and antibody responses to a panel of tumor antigens were assayed by ELISA.
Results
The patient's tumor had minimal lymphocytic infiltrate (Immunotype A). NY-ESO-1 was strongly expressed by the melanoma cells. Circulating T cell responses to NY-ESO-1 peptides were observed 6 and 12 years postoperatively, and antibodies to NY-ESO-1 were detected 2-6 years after surgery.
Conclusion
The patient described in this report experienced relentless regional tumor progression, with intravascular metastases, then 14-year systemic disease-free survival after palliative resection, without evidence of melanoma recurrence before death from other causes. Her immune response to NY-ESO-1 likely failed to control established regional metastases because T cells were unable to infiltrate them. It is possible, however, that among other factors, the host immune response may have contributed to systemic protection.
doi:10.1007/s00262-013-1433-7
PMCID: PMC4082724  PMID: 23666534
Melanoma; amputation for melanoma; NY-ESO-1; tumor immunity; antibody; T-cell
6.  Design of a Bone-Attached Parallel Robot for Percutaneous Cochlear Implantation 
Access to the cochlea requires drilling in close proximity to bone-embedded nerves, blood vessels, and other structures, the violation of which can result in complications for the patient. It has recently been shown that microstereotactic frames can enable an image-guided percutaneous approach, removing reliance on human experience and hand–eye coordination, and reducing trauma. However, constructing current microstereotactic frames disrupts the clinical workflow, requiring multiday intrasurgical manufacturing delays, or an on-call machine shop in or near the hospital. In this paper, we describe a new kind of microsterotactic frame that obviates these delay and infrastructure issues by being repositionable. Inspired by the prior success of bone-attached parallel robots in knee and spinal procedures, we present an automated image-guided microstereotactic frame. Experiments demonstrate a mean accuracy at the cochlea of 0.20 ± 0.07 mm in phantom testing with trajectories taken from a human clinical dataset. We also describe a cadaver experiment evaluating the entire image-guided surgery pipeline, where we achieved an accuracy of 0.38 mm at the cochlea.
doi:10.1109/TBME.2011.2162512
PMCID: PMC4104131  PMID: 21788181
Bone-attached robot; cochlear implant; Gough–Stewart platform; microtable; minimally invasive surgery (MIS); parallel robot
7.  Serum Amyloid A Promotes Lung Neutrophilia by Increasing IL-17A Levels in the Mucosa and γδ T Cells 
Rationale: Neutrophilic inflammation is an important pathologic feature of chronic obstructive pulmonary disease (COPD) and infectious exacerbations of COPD. Serum amyloid A (SAA) promotes neutrophilic inflammation by its interaction with lung mucosal ALX/FPR2 receptors. However, little is known about how this endogenous mediator regulates IL-17A immunity.
Objectives: To determine whether SAA causes neutrophilic inflammation by IL-17A–dependent mechanisms.
Methods: The relationship between SAA and neutrophils was investigated in lung sections from patients with COPD and a chronic mouse model of SAA exposure. A neutralizing antibody to IL-17A was used to block SAA responses in vivo, and a cell-sorting strategy was used to identify cellular sources.
Measurements and Main Results: SAA mRNA expression was positively associated with tissue neutrophils in COPD (P < 0.05). SAA predominately promoted expression of the TH17 polarizing cytokine IL-6, which was opposed by 15-epi-lipoxin A4, a counter-regulatory mediator, and ALX/FPR2 ligand. SAA-induced inflammation was markedly reduced by a neutralizing antibody to IL-17A in vivo. Cellular sources of IL-17A induced by SAA include CD4+ T cells, γδ T cells, and an Epcam+CD45− population enriched for epithelial cells. SAA promotes expression of IL-17A in γδ T cells and this innate cell proportionally expressed higher levels of IL-17A transcript than CD4+ T cells or epithelial cells.
Conclusions: The SAA–IL-17A axis represents an important innate defense network that may underlie persistent neutrophilic airway inflammation in COPD and modulating the ALX/FPR2 receptor represents a novel approach to targeting aberrant IL-17A–mediated lung immunity.
doi:10.1164/rccm.201211-2139OC
PMCID: PMC3778755  PMID: 23627303
inflammation; neutrophils; chronic obstructive pulmonary disease; innate immunity
8.  Serine/Threonine Protein Phosphatase-Mediated Control of the Peptidoglycan Cross-Linking l,d-Transpeptidase Pathway in Enterococcus faecium 
mBio  2014;5(4):e01446-14.
ABSTRACT
The last step of peptidoglycan polymerization involves two families of unrelated transpeptidases that are the essential targets of β-lactam antibiotics. d,d-transpeptidases of the penicillin-binding protein (PBP) family are active-site serine enzymes that use pentapeptide precursors and are the main or exclusive cross-linking enzymes in nearly all bacteria. However, peptidoglycan cross-linking is performed mainly by active-site cysteine l,d-transpeptidases that use tetrapeptides in Mycobacterium tuberculosis, Clostridium difficile, and β-lactam-resistant mutants of Enterococcus faecium. We have investigated reprogramming of the E. faecium peptidoglycan assembly pathway by a switch from pentapeptide to tetrapeptide precursors and bypass of PBPs by l,d-transpeptidase Ldtfm. Mutational alterations of two signal transduction systems were necessary and sufficient for activation of the l,d-transpeptidation pathway, which is essentially cryptic in wild-type strains. The first one is a classical two-component regulatory system, DdcRS, that controls the activity of Ldtfm at the substrate level. As previously described, loss of DdcS phosphatase activity leads to production of the d,d-carboxypeptidase DdcY and conversion of the pentapeptide into the tetrapeptide substrate of Ldtfm. Here we show that full bypass of PBPs by Ldtfm also requires increased Ser/Thr protein phosphorylation resulting from impaired activity of phosphoprotein phosphatase StpA. This enzyme negatively controlled the level of protein phosphorylation both by direct dephosphorylation of target proteins and by dephosphorylation of its cognate kinase Stk. In combination with production of DdcY, increased protein phosphorylation by this eukaryotic-enzyme-like Ser/Thr protein kinase was sufficient for activation of the l,d-transpeptidation pathway in the absence of mutational alteration of peptidoglycan synthesis enzymes.
IMPORTANCE
The mechanism of acquisition of high-level ampicillin resistance involving bypass of the penicillin-binding proteins (PBPs) by l,d-transpeptidase Ldtfm was incompletely understood, as production of tetrapeptide precursors following transcriptional activation of the ddc locus by the DdcRS two-component regulatory system was necessary but not sufficient for full activation of the l,d-transpeptidation pathway. Here, we identified the release of a negative control of Ser/Thr protein phosphorylation mediated by phosphatase StpA as the additional factor essential for ampicillin resistance. Thus, bypass of PBPs by Ldtfm requires the modification of signal transduction regulatory systems without any gain of function by mutational alteration of peptidoglycan biosynthetic enzymes. In contrast, previously characterized mechanisms of antibiotic resistance involve horizontal gene transfer and mutational alteration of drug targets. Activation of the l,d-transpeptidation pathway reported in this study is an unprecedented mechanism of emergence of a new metabolic pathway since it involved the recruitment of preexisting functions following modifications of regulatory circuits.
doi:10.1128/mBio.01446-14
PMCID: PMC4161250  PMID: 25006233
9.  A Manually Operated, Advance Off-Stylet Insertion Tool for Minimally Invasive Cochlear Implantation Surgery 
The current technique for cochlear implantation (CI) surgery requires a mastoidectomy to gain access to the cochlea for electrode array insertion. It has been shown that microstereotactic frames can enable an image-guided, minimally invasive approach to CI surgery called percutaneous cochlear implantation (PCI) that uses a single drill hole for electrode array insertion, avoiding a more invasive mastoidectomy. Current clinical methods for electrode array insertion are not compatible with PCI surgery because they require a mastoidectomy to access the cochlea; thus, we have developed a manually operated electrode array insertion tool that can be deployed through a PCI drill hole. The tool can be adjusted using a preoperative CT scan for accurate execution of the advance off-stylet (AOS) insertion technique and requires less skill to operate than is currently required to implant electrode arrays. We performed three cadaver insertion experiments using the AOS technique and determined that all insertions were successful using CT and microdissection.
doi:10.1109/TBME.2012.2210220
PMCID: PMC4081037  PMID: 22851233
Advance off-stylet (AOS); cochlear implant; image-guided surgery; minimally invasive surgery; percutaneous cochlear implantation (PCI)
10.  Obesity and diabetes cause cognitive dysfunction in the absence of accelerated β-amyloid deposition in a novel murine model of mixed or vascular dementia 
Mid-life obesity and type 2 diabetes mellitus (T2DM) confer a modest, increased risk for Alzheimer’s disease (AD), though the underlying mechanisms are unknown. We have created a novel mouse model that recapitulates features of T2DM and AD by crossing morbidly obese and diabetic db/db mice with APPΔNL/ΔNLx PS1P264L/P264L knock-in mice. These mice (db/AD) retain many features of the parental lines (e.g. extreme obesity, diabetes, and parenchymal deposition of β-amyloid (Aβ)). The combination of the two diseases led to additional pathologies-perhaps most striking of which was the presence of severe cerebrovascular pathology, including aneurysms and small strokes. Cortical Aβ deposition was not significantly increased in the diabetic mice, though overall expression of presenilin was elevated. Surprisingly, Aβ was not deposited in the vasculature or removed to the plasma, and there was no stimulation of activity or expression of major Aβ-clearing enzymes (neprilysin, insulin degrading enzyme, or endothelin-converting enzyme). The db/AD mice displayed marked cognitive impairment in the Morris Water Maze, compared to either db/db or APPΔNLx PS1P264L mice. We conclude that the diabetes and/or obesity in these mice leads to a destabilization of the vasculature, leading to strokes and that this, in turn, leads to a profound cognitive impairment and that this is unlikely to be directly dependent on Aβ deposition. This model of mixed or vascular dementia provides an exciting new avenue of research into the mechanisms underlying the obesity-related risk for age-related dementia, and will provide a useful tool for the future development of therapeutics.
doi:10.1186/2051-5960-2-64
PMCID: PMC4229778  PMID: 24916066
Dementia; Diabetes; Obesity; Stroke; Alzheimer’s disease
11.  NEPRILYSIN REGULATES PULMONARY ARTERY SMOOTH MUSCLE CELL PHENOTYPE THROUGH A PDGF RECEPTOR DEPENDENT MECHANISM 
Hypertension  2013;61(4):921-930.
Reduced neprilysin (NEP), a cell surface metallopeptidase, which cleaves and inactivates pro-inflammatory and vasoactive peptides, predisposes the lung vasculature to exaggerated remodeling in response to hypoxia. We hypothesize that loss of NEP in pulmonary artery smooth muscle cells (PASMCs) results in increased migration and proliferation.
PASMCs isolated from NEP−/− mice exhibited enhanced migration and proliferation in response to serum and PDGF, which was attenuated by NEP replacement. Inhibition of NEP by overexpression of a peptidase dead mutant or knockdown by siRNA in NEP+/+ cells increased migration and proliferation. Loss of NEP led to an increase in Src kinase activity and phosphorylation of PTEN resulting in activation of the PDGF receptor (PDGFR). Knockdown of Src kinase with siRNA or inhibition with PP2 a src kinase inhibitor decreased PDGFRY751 phosphorylation and attenuated migration and proliferation in NEP−/− SMCs.
NEP substrates, endothelin-1(ET-1) or fibroblast growth factor-2 (FGF2), increased activation of Src and PDGFR in NEP+/+ cells, which was decreased by an ETAR antagonist, neutralizing antibody to FGF2 and Src inhibitor.
Similar to the observations in PASMCs levels of p-PDGFR, p-Src and p-PTEN were elevated in NEP−/− lungs. ETAR antagonist also attenuated the enhanced responses in NEP−/−PASMCs and lungs. Taken together our results suggest a novel mechanism for regulation of PDGFR signaling by NEP substrates involving Src and PTEN. Strategies that increase lung NEP activity/expression or target key downstream effectors, like Src, PTEN or PDGFR, may be of therapeutic benefit in pulmonary vascular disease.
doi:10.1161/HYPERTENSIONAHA.111.199588
PMCID: PMC3667616  PMID: 23381789
Neprilysin; smooth muscle cell; migration; PDGFR; Src; PTEN
12.  Putting PhDs to Work: Career Planning for Today's Scientist 
CBE Life Sciences Education  2014;13(1):49-53.
The authors examined individual development plan (IDP) awareness and use, the benefits of creating an IDP, and ways to facilitate IDP use by administering surveys to postdoctoral researchers, mentors, and administrators.
Individual development plans (IDPs) have been promoted nationally as a tool to help research trainees explore career opportunities and set career goals. Despite the interest in IDPs from a policy perspective, there is little information about how they have been used. The authors examined IDP awareness and use, the benefits of creating an IDP, and ways to facilitate its use by administering a survey to current or former postdoctoral researchers via the National Postdoctoral Association (NPA) and University of Alabama at Birmingham email lists; individuals belonging to Federation of American Societies for Experimental Biology member societies who mentored postdocs; and postdoctoral administrators at member institutions of the Association of American Medical Colleges and the NPA. Although most postdoctoral administrators (>80%) were familiar with IDPs, less than 50% of postdocs and only 20% of mentors were aware of IDPs. For those postdocs and mentors who reported creating an IDP, the process helped postdocs to identify the skills and abilities necessary for career success and facilitated communication between postdocs and their mentors. Despite the fact that creating an IDP benefits postdocs and mentors, IDP use will likely remain low unless institutions and research mentors encourage trainees to engage in this process.
doi:10.1187/cbe-13-04-0085
PMCID: PMC3940462  PMID: 24591503
14.  Lymphotoxin α1β2 Expression on B Cells Is Required for Follicular Dendritic Cell Activation During the Germinal Center Response 
European journal of immunology  2012;43(2):348-359.
Summary
CD19-deficient mice were used as a model to study FDC activation because these mice have normal numbers of FDC-containing primary follicles, but lack the ability to activate FDC or form GC. It was hypothesized that CD19 expression is necessary for B cell activation and upregulation of membrane-lymphotoxin (mLT) expression, which promotes FDC activation. Using VCAM-1 and FcγRII/III as FDC activation markers, it was determined that the adoptive transfer of CD19+ wild-type B cells into CD19-deficient hosts rescued GC formation and FDC activation, demonstrating that CD19 expression on B cells is required for FDC activation. In contrast, CD19+ donor B cells lacking mLT were unable to induce VCAM-1 expression on FDC and FcγRII/III upregulation was impaired. VCAM-1 expression on FDC, but not FcγRII/III, was rescued when CD19-deficient B cells expressing transgenic mLT were cotransferred into recipient mice with CD19+, mLT-deficient B cells, suggesting that FDC activation requires the CD19-dependent upregulation of mLT on activated B cells. Collectively, these data demonstrate that activated B cells are responsible for the initiation of FDC activation resulting in a microenvironment supportive of GC development and maintenance.
doi:10.1002/eji.201242471
PMCID: PMC3753018  PMID: 23112125
Follicular Dendritic Cell; Germinal Center; CD19; Membrane Lymphotoxin
15.  Structural Analysis of Muscles Elevating the Hyolaryngeal Complex 
Dysphagia  2012;27(4):445-451.
A critical event of pharyngeal swallowing is the elevation of the hyolaryngeal complex to open the upper esophageal sphincter. Current swallowing theory assigns this function to the submental and thyrohyoid muscles. However, the attachments of the long pharyngeal muscles indicate that they could contribute to this function, yet their role is uninvestigated in humans. In addition, there is evidence the posterior digastric and stylohyoid contribute to hyoid elevation. A cadaver model was used to document the structural properties of muscles. These properties were used to model muscle groups as force vectors and analyze their potential for hyolaryngeal elevation. Vector magnitude was determined using physiological cross-sectional areas (PCSAs) of muscles calculated from structural properties of muscle taken from 12 hemisected cadaver specimens. Vector direction (lines of action) was calculated from the three-dimensional coordinates of muscle attachment sites. Unit force vectors in the superior direction of submental, suprahyoid (which includes the submental muscles), long pharyngeal, and thyrohyoid muscles were derived and compared by an analysis of variance (ANOVA) to document each muscle’s potential contribution to hyolaryngeal elevation. An ANOVA with Tukey HSD post hoc analysis of unit force vectors showed no statistically significant difference between the submental (0.92 ± 0.24 cm2) and long pharyngeal (0.73 ± 0.20 cm2) muscles. Both demonstrated greater potential to elevate the hyolaryngeal complex than the thyrohyoid (0.49 ± 0.18 cm2), with P < 0.01 and P < 0.05, respectively. The suprahyoid muscles (1.52 ± 0.35 cm2) demonstrated the greatest potential to elevate the hyolaryngeal complex: greater than both the long pharyngeal muscles (P < 0.01) and the thyrohyoid (P < 0.01). The submental and thyrohyoid muscles by convention are thought to elevate the hyolaryngeal complex. This study demonstrates that structurally the long pharyngeal muscles have similar potential to contribute to this critical function, with the suprahyoid muscles having the greatest potential. If verified by functional data, these findings would amend current swallowing theory.
doi:10.1007/s00455-011-9392-7
PMCID: PMC3350616  PMID: 22278076
Deglutition; Laryngeal elevation; Physiological cross-sectional area; Structural properties; Hyolaryngeal complex; Deglutition disorders
16.  Impact of Oncology Drug Shortages on Patient Therapy: Unplanned Treatment Changes 
Journal of Oncology Practice  2013;9(4):e122-e128.
Drug shortages have substantial economic costs and mandate treatment changes that may affect efficacy and toxicity.
Purpose:
Cancer drug shortages have increased considerably over the past 5 years, but quantitative analyses of the scope and effects are limited. We assessed the effects of drug shortages on outpatient medication use in a single New York City university hospital.
Methods:
We examined pharmacy records for drug shortages, as defined by the American Society of Health-System Pharmacists. We assessed outpatient records for all patients with cancer treated with infusional antineoplastic medications from April 2010 to September 2010 and April 2011 to September 2011.
Results:
Twelve medications were in shortage in 2010 and 22 in 2011. Drugs in shortage were used for 170 patients (50.8%) in 2010 and 241 patients (63.6%) in 2011 (P < .001). Of 235 patients treated in August-September 2011, there were 23(9.8%) documented therapy changes due to shortages, compared with zero changes in August-September 2010 (P < .001). Among patients treated in August-September 2010, 24 (11.4%) received paclitaxel and 19 (9.0%) received docetaxel. Among patients treated in August-September 2011, 11 (4.7%) received paclitaxel and 38 (16.2%) received docetaxel, a 69% decrease for paclitaxel and 80% increase for docetaxel from 1 year prior (P = .009, and P = .024, respectively). The estimated cost of a single treatment with paclitaxel for one patient with body-surface area 1.75 was $47.59 versus $858.39 for docetaxel, a 1,704% increase. Surveyed physicians frequently reported lower level evidence (30.4%) and increased risk of toxicity (34.8%) with alternative therapy in drug shortage cases.
Conclusion:
Oncology drug shortages affected the majority of patients in our center and increased at an alarming rate. Drug shortages have substantial economic costs and mandate treatment changes that may affect efficacy and toxicity.
doi:10.1200/JOP.2012.000799
PMCID: PMC3710178  PMID: 23942928
17.  Trends and Significance of VRE Colonization in the ICU: A Meta-Analysis of Published Studies 
PLoS ONE  2013;8(9):e75658.
Background
The burden and significance of vancomycin-resistant enterococci (VRE) colonization in the ICU is not clearly understood.
Methods
We searched PubMed and EMBASE up to May 2013 for studies reporting the prevalence of VRE upon admission to the ICU and performed a meta-analysis to assess rates and trends of VRE colonization. We calculated the prevalence of VRE on admission and the acquisition (colonization and/or infection) rates to estimate time trends and the impact of colonization on ensuing VRE infections.
Findings
Across 37 studies (62,959 patients at risk), the estimated prevalence of VRE on admission to the ICU was 8.8% (7.1-10.6). Estimates were more consistent when cultures were obtained within 24 hours from admission. The VRE acquisition rate was 8.8% (95% CI 6.9-11.0) across 26 evaluable studies (35,364 patients at risk). Across US studies, VRE acquisition rate was 10.2% (95% CI 7.7-13.0) and demonstrated significant decline in annual trends. We used the US estimate of colonization on admission [12.3% (10.5-14.3)] to evaluate the impact of VRE colonization on admission in overall VRE prevalence. We demonstrated that VRE colonization on admission is a major determinant of the overall VRE burden in the ICU. Importantly, among colonized patients (including admitted and/or acquired cases) the VRE infection rates vary widely from 0-45% (with the risk of VRE bacteremia being reported from 0-16%) and <2% among those without a proven colonization.
Conclusion
In summary, up to 10.6% of patients admitted in the ICU are colonized with VRE on admission and a similar percentage will acquire VRE during their ICU stay. Importantly, colonization on admission is a major determinant of VRE dynamics in the ICU and the risk of VRE-related infections is close related to colonization.
doi:10.1371/journal.pone.0075658
PMCID: PMC3785502  PMID: 24086603
18.  Influenza Vaccine Effectiveness against Hospitalisation with Confirmed Influenza in the 2010–11 Seasons: A Test-negative Observational Study 
PLoS ONE  2013;8(7):e68760.
Immunisation programs are designed to reduce serious morbidity and mortality from influenza, but most evidence supporting the effectiveness of this intervention has focused on disease in the community or in primary care settings. We aimed to examine the effectiveness of influenza vaccination against hospitalisation with confirmed influenza. We compared influenza vaccination status in patients hospitalised with PCR-confirmed influenza with patients hospitalised with influenza-negative respiratory infections in an Australian sentinel surveillance system. Vaccine effectiveness was estimated from the odds ratio of vaccination in cases and controls. We performed both simple multivariate regression and a stratified analysis based on propensity score of vaccination. Vaccination status was ascertained in 333 of 598 patients with confirmed influenza and 785 of 1384 test-negative patients. Overall estimated crude vaccine effectiveness was 57% (41%, 68%). After adjusting for age, chronic comorbidities and pregnancy status, the estimated vaccine effectiveness was 37% (95% CI: 12%, 55%). In an analysis accounting for a propensity score for vaccination, the estimated vaccine effectiveness was 48.3% (95% CI: 30.0, 61.8%). Influenza vaccination was moderately protective against hospitalisation with influenza in the 2010 and 2011 seasons.
doi:10.1371/journal.pone.0068760
PMCID: PMC3712933  PMID: 23874754
19.  Kinetic Features of L,D-Transpeptidase Inactivation Critical for β-Lactam Antibacterial Activity 
PLoS ONE  2013;8(7):e67831.
Active-site serine D,D-transpeptidases belonging to the penicillin-binding protein family (PBPs) have been considered for a long time as essential for peptidoglycan cross-linking in all bacteria. However, bypass of the PBPs by an L,D-transpeptidase (Ldtfm) conveys high-level resistance to β-lactams of the penam class in Enterococcus faecium with a minimal inhibitory concentration (MIC) of ampicillin >2,000 µg/ml. Unexpectedly, Ldtfm does not confer resistance to β-lactams of the carbapenem class (imipenem MIC = 0.5 µg/ml) whereas cephems display residual activity (ceftriaxone MIC = 128 µg/ml). Mass spectrometry, fluorescence kinetics, and NMR chemical shift perturbation experiments were performed to explore the basis for this specificity and identify β-lactam features that are critical for efficient L,D-transpeptidase inactivation. We show that imipenem, ceftriaxone, and ampicillin acylate Ldtfm by formation of a thioester bond between the active-site cysteine and the β-lactam-ring carbonyl. However, slow acylation and slow acylenzyme hydrolysis resulted in partial Ldtfm inactivation by ampicillin and ceftriaxone. For ampicillin, Ldtfm acylation was followed by rupture of the C5–C6 bond of the β-lactam ring and formation of a secondary acylenzyme prone to hydrolysis. The saturable step of the catalytic cycle was the reversible formation of a tetrahedral intermediate (oxyanion) without significant accumulation of a non-covalent complex. In agreement, a derivative of Ldtfm blocked in acylation bound ertapenem (a carbapenem), ceftriaxone, and ampicillin with similar low affinities. Thus, oxyanion and acylenzyme stabilization are both critical for rapid L,D-transpeptidase inactivation and antibacterial activity. These results pave the way for optimization of the β-lactam scaffold for L,D-transpeptidase-inactivation.
doi:10.1371/journal.pone.0067831
PMCID: PMC3701632  PMID: 23861815
20.  Early Insights into the Interactions of Different β-Lactam Antibiotics and β-Lactamase Inhibitors against Soluble Forms of Acinetobacter baumannii PBP1a and Acinetobacter sp. PBP3 
Antimicrobial Agents and Chemotherapy  2012;56(11):5687-5692.
Acinetobacter baumannii is an increasingly problematic pathogen in United States hospitals. Antibiotics that can treat A. baumannii are becoming more limited. Little is known about the contributions of penicillin binding proteins (PBPs), the target of β-lactam antibiotics, to β-lactam–sulbactam susceptibility and β-lactam resistance in A. baumannii. Decreased expression of PBPs as well as loss of binding of β-lactams to PBPs was previously shown to promote β-lactam resistance in A. baumannii. Using an in vitro assay with a reporter β-lactam, Bocillin, we determined that the 50% inhibitory concentrations (IC50s) for PBP1a from A. baumannii and PBP3 from Acinetobacter sp. ranged from 1 to 5 μM for a series of β-lactams. In contrast, PBP3 demonstrated a narrower range of IC50s against β-lactamase inhibitors than PBP1a (ranges, 4 to 5 versus 8 to 144 μM, respectively). A molecular model with ampicillin and sulbactam positioned in the active site of PBP3 reveals that both compounds interact similarly with residues Thr526, Thr528, and Ser390. Accepting that many interactions with cell wall targets are possible with the ampicillin-sulbactam combination, the low IC50s of ampicillin and sulbactam for PBP3 may contribute to understanding why this combination is effective against A. baumannii. Unraveling the contribution of PBPs to β-lactam susceptibility and resistance brings us one step closer to identifying which PBPs are the best targets for novel β-lactams.
doi:10.1128/AAC.01027-12
PMCID: PMC3486531  PMID: 22908165
21.  Photodynamic and Antibiotic Therapy Impair the Pathogenesis of Enterococcus faecium in a Whole Animal Insect Model 
PLoS ONE  2013;8(2):e55926.
Enterococcus faecium has emerged as one of the most important pathogens in healthcare-associated infections worldwide due to its intrinsic and acquired resistance to many antibiotics, including vancomycin. Antimicrobial photodynamic therapy (aPDT) is an alternative therapeutic platform that is currently under investigation for the control and treatment of infections. PDT is based on the use of photoactive dye molecules, widely known as photosensitizer (PS). PS, upon irradiation with visible light, produces reactive oxygen species that can destroy lipids and proteins causing cell death. We employed Galleria mellonella (the greater wax moth) caterpillar fatally infected with E. faecium to develop an invertebrate host model system that can be used to study the antimicrobial PDT (alone or combined with antibiotics). In the establishment of infection by E. faecium in G. mellonella, we found that the G. mellonella death rate was dependent on the number of bacterial cells injected into the insect hemocoel and all E. faecium strains tested were capable of infecting and killing G. mellonella. Antibiotic treatment with ampicillin, gentamicin or the combination of ampicillin and gentamicin prolonged caterpillar survival infected by E. faecium (P = 0.0003, P = 0.0001 and P = 0.0001, respectively). In the study of antimicrobial PDT, we verified that methylene blue (MB) injected into the insect followed by whole body illumination prolonged the caterpillar survival (P = 0.0192). Interestingly, combination therapy of larvae infected with vancomycin-resistant E. faecium, with antimicrobial PDT followed by vancomycin, significantly prolonged the survival of the caterpillars when compared to either antimicrobial PDT (P = 0.0095) or vancomycin treatment alone (P = 0.0025), suggesting that the aPDT made the vancomycin resistant E. faecium strain more susceptible to vancomycin action. In summary, G. mellonella provides an invertebrate model host to study the antimicrobial PDT and to explore combinatorial aPDT-based treatments.
doi:10.1371/journal.pone.0055926
PMCID: PMC3573038  PMID: 23457486
22.  The vaccine-site microenvironment induced by injection of incomplete Freund's adjuvant, with or without melanoma peptides 
Cancer vaccines have not been optimized. They depend on adjuvants to create an immunogenic microenvironment for antigen presentation. However, remarkably little is understood about cellular and molecular changes induced by these adjuvants in the vaccine microenvironment. We hypothesized that vaccination induces dendritic cell activation in the dermal vaccination microenvironment but that regulatory processes may also limit the effectiveness of repeated vaccination. We evaluated biopsies from immunization sites in two clinical trials of melanoma patients. In one study (Mel38), patients received one injection with an adjuvant mixture alone, comprised of incomplete Freund's adjuvant (IFA) plus granulocyte-macrophage colony stimulating factor (GM-CSF). In a second study, patients received multiple vaccinations with melanoma peptide antigens plus IFA. Single injections with adjuvant alone induced dermal inflammatory infiltrates consisting of B cells, T cells, mature dendritic cells (DC) and vessels resembling high endothelial venules (HEV). These cellular aggregates usually lacked organization and were transient. In contrast, multiple repeated vaccinations with peptides in adjuvant induced more organized and persistent lymphoid aggregates containing separate B and T cell areas, mature DC, HEV-like vessels, and lymphoid chemokines. Within these structures, there are proliferating CD4+ and CD8+ T lymphocytes, as well as FoxP3+CD4+ lymphocytes, suggesting a complex interplay of lymphoid expansion and regulation within the dermal immunization microenvironment. Further study of the physiology of the vaccine site microenvironment promises to identify opportunities for enhancing cancer vaccine efficacy by modulating immune activation and regulation at the site of vaccination.
doi:10.1097/CJI.0b013e31823731a4
PMCID: PMC3282210  PMID: 22130163
cancer vaccines; immunotherapy; melanoma; histology; dendritic cells; T-lymphocytes; chemokines
23.  Kinetic Analysis of Enterococcus faecium l,d-Transpeptidase Inactivation by Carbapenems 
Bypass of classical penicillin-binding proteins by the l,d-transpeptidase of Enterococcus faecium (Ldtfm) leads to high-level ampicillin resistance in E. faecium mutants, whereas carbapenems remain the lone highly active β-lactams. Kinetics of Ldtfm inactivation was determined for four commercial carbapenems and a derivative obtained by introducing a minimal ethyl group at position 2. We show that the bulky side chains of commercial carbapenems have both positive and negative effects in preventing hydrolysis of the acyl enzyme and impairing drug binding.
doi:10.1128/AAC.06398-11
PMCID: PMC3370759  PMID: 22450984
24.  Phase I and pharmacokinetic study of COL-3 in patients with recurrent high-grade gliomas 
Journal of neuro-oncology  2011;105(2):375-381.
COL-3 is a chemically modified tetracycline that targets multiple aspects of matrix metalloproteinase regulation. This phase I clinical trial was conducted to determine the maximum tolerated dose (MTD) of COL-3 in adults with recurrent high-grade glioma, to describe the effects of enzyme-inducing antiseizure drugs (EIADs) on its pharmacokinetics, and to obtain preliminary evidence of activity. Adults with recurrent high-grade glioma were stratified by EIAD use. COL-3 was given orally daily without interruption until disease progression or treatment-related dose-limiting toxicity (DLT). Three patients in each EIAD group were evaluated at each dose level beginning with 25 mg/m2/day and escalated by 25 mg/m2/day. Toxicity, response, and pharmacokinetics were assessed. Thirty-three patients were evaluated. The MTD was 75 mg/m2/day in the −EIAD patients while one was not determined in +EIAD patients. The common toxicities observed were anemia, ataxia, diarrhea, hypokalemia, CNS hemorrhage, and myalgia. One partial response was observed. −EIAD patients tended to have a higher steady-state trough concentration that was apparent only at the 100 mg/m2/day dose level (P = 0.01). This study suggests that: (a) EIAD use does affect the pharmacokinetics of COL-3 at higher doses; and (b) there was not enough suggestion of single-agent activity to warrant further study in recurrent high-grade gliomas.
doi:10.1007/s11060-011-0602-9
PMCID: PMC3197967  PMID: 21547395
COL-3; Anticonvulsants; Pharmacokinetics; Gliomas
25.  Cysteine 904 Is Required for Maximal Insulin Degrading Enzyme Activity and Polyanion Activation 
PLoS ONE  2012;7(10):e46790.
Cysteine residues in insulin degrading enzyme have been reported as non-critical for its activity. We found that converting the twelve cysteine residues in rat insulin degrading enzyme (IDE) to serines resulted in a cysteine-free form of the enzyme with reduced activity and decreased activation by polyanions. Mutation of each cysteine residue individually revealed cysteine 904 as the key residue required for maximal activity and polyanion activation, although other cysteines affect polyanion binding to a lesser extent. Based on the structure of IDE, Asn 575 was identified as a potential hydrogen bond partner for Cys904 and mutation of this residue also reduced activity and decreased polyanion activation. The oligomerization state of IDE did not correlate with its activity, with the dimer being the predominant form in all the samples examined. These data suggest that there are several conformational states of the dimer that affect activity and polyanion activation.
doi:10.1371/journal.pone.0046790
PMCID: PMC3471918  PMID: 23077523

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