Multimodal Biomarkers That Predict the Presence of Gleason Pattern 4: Potential Impact for Active Surveillance

PURPOSE

Latent grade group ≥2 prostate cancer can impact the performance of active surveillance protocols. To date, molecular biomarkers for active surveillance have relied solely on RNA or protein. We trained and independently validated multimodal (mRNA abundance, DNA methylation, and/or DNA copy number) biomarkers that more accurately separate grade group 1 from grade group ≥2 cancers.

MATERIALS AND METHODS

Low- and intermediate-risk prostate cancer patients were assigned to training (n=333) and validation (n=202) cohorts. We profiled the abundance of 342 mRNAs, 100 DNA copy number alteration loci, and 14 hypermethylation sites at 2 locations per tumor. Using the training cohort with cross-validation, we evaluated methods for training classifiers of pathological grade group ≥2 in centrally reviewed radical prostatectomies. We trained 2 distinct classifiers, PRONTO-e and PRONTO-m, and validated them in an independent radical prostatectomy cohort.

RESULTS

PRONTO-e comprises 353 mRNA and copy number alteration features. PRONTO-m includes 94 clinical, mRNAs, copy number alterations, and methylation features at 14 and 12 loci, respectively. In independent validation, PRONTO-e and PRONTO-m predicted grade group ≥2 with respective true-positive rates of 0.81 and 0.76, and false-positive rates of 0.43 and 0.26. Both classifiers were resistant to sampling error and identified more upgrading cases than a well-validated presurgical risk calculator, CAPRA (Cancer of the Prostate Risk Assessment; P < .001).

CONCLUSIONS

Two grade group classifiers with superior accuracy were developed by incorporating RNA and DNA features and validated in an independent cohort. Upon further validation in biopsy samples, classifiers with these performance characteristics could refine selection of men for active surveillance, extending their treatment-free survival and intervals between surveillance.

Incorporation of automated buffer exchange empowers high-throughput protein and plasmid purification for downstream uses

The continued acceleration of time-to-market product development and rising demand for biotherapeutics have hastened the need for higher throughput within the biopharmaceutical industry. Automated liquid handlers (ALH) are increasingly popular due to flexible programming that enables processing of multiple samples with an array of functions. This flexibility is useful in streamlining research that requires chromatographic procedures to achieve product purity for downstream analysis. However, purification of biologics often requires additional off-deck buffer exchange steps due to undesirable elution conditions such as high acid or high salt content. Expanding the capability of ALHs to perform purification in sequence with buffer exchange would, therefore, increase workflow efficiency by eliminating the need for manual intervention, thus expediting sample preparation. Here we demonstrate two different automated purifications using pipet-based dispersive solid-phase extraction (dSPE). The first is an affinity purification of His-tagged proteins from bacterial lysate. The second is an anion-exchange purification of plasmid DNA. Both methods are followed by buffer exchange performed by an ALH. Percent recoveries for the three purified recombinant proteins ranged from 51 ± 1.2 to 86 ± 10%. The yields were inversely correlated to starting sample load and protein molecular weight. Yields for plasmid purification ranged between 11.4 ± 0.8 and 13.7 ± 0.9 µg, with the largest plasmid providing the highest yield. Both programs were rapid, with protein purification taking <80 min and plasmid purification <60 min. Our results demonstrate that high-quality, ready-to-use biologics can be obtained rapidly from a crude sample after two separate chromatographic processes without manual intervention.

Automated multi-attribute method sample preparation using high-throughput buffer exchange tips

RATIONALE

The multi-attribute method (MAM) has become a valuable mass spectrometry (MS)-based tool that can identify and quantify the site-specific product attributes and purity information for biotherapeutics such as monoclonal antibodies (mAbs) and fusion molecules in recent years. As we expand the use of the MAM at various stages of drug development, it is critical to enhance the sample preparation throughput without additional chemical modifications and variability.

METHODS

In this study, a fully automated MAM sample preparation protocol is presented, where rapid desalting in less than 15 minutes is achieved using miniaturized size-exclusion chromatography columns in pipette tips on an automated liquid handler. The peptide samples were analyzed using an electrospray ionization (ESI) orbitrap mass spectrometer coupled to an ultra-high-performance liquid chromatography (UHPLC) system with a dual column switching system.

RESULTS

No significant change was observed in product attributes and their quantities compared with manual, low-artifact sample preparation. The sample recovery using the buffer exchange tips was greatly enhanced over the manual spin cartridges while still demonstrating excellent reproducibility for a wide variety of starting sample concentrations. Unlike a plate desalting system, the individual columns provide flexibility in the number of samples prepared at a time and sample locations within plates.

CONCLUSIONS

This automated protocol enables the preparation of up to 96 samples with less "at-bench" time than the manual preparation of a smaller batch of samples, thereby greatly facilitating support of process development and the use of the MAM in quality control.

Purification, Characterization, and Structural Studies of a Sulfatase from Pedobacter yulinensis

Sulfatases are ubiquitous enzymes that hydrolyze sulfate from sulfated organic substrates such as carbohydrates, steroids, and flavones. These enzymes can be exploited in the field of biotechnology to analyze sulfated metabolites in humans, such as steroids and drugs of abuse. Because genomic data far outstrip biochemical characterization, the analysis of sulfatases from published sequences can lead to the discovery of new and unique activities advantageous for biotechnological applications. We expressed and characterized a putative sulfatase (PyuS) from the bacterium Pedobacter yulinensis. PyuS contains the (C/S)XPXR sulfatase motif, where the Cys or Ser is post-translationally converted into a formylglycine residue (FGly). His-tagged PyuS was co-expressed in Escherichia coli with a formylglycine-generating enzyme (FGE) from Mycobacterium tuberculosis and purified. We obtained several crystal structures of PyuS, and the FGly modification was detected at the active site. The enzyme has sulfatase activity on aromatic sulfated substrates as well as phosphatase activity on some aromatic phosphates; however, PyuS did not have detectable activity on 17α-estradiol sulfate, cortisol 21-sulfate, or boldenone sulfate.

Enhancing the multi-attribute method through an automated and high-throughput sample preparation

The multi-attribute method (MAM), a recent advance in the application of liquid chromatography-mass spectrometry within the pharmaceutical industry, enables the simultaneous monitoring of multiple product quality attributes in a single analytical method. While MAM is coupled with automated data processing and reporting, the sample preparation, based on proteolytic peptide mapping, remains cumbersome and low throughput. The standard sample preparation for MAM relies on protein denaturation, reduction, and alkylation prior to proteolytic digestion, but often a desalting step is required to maintain enzymatic activity. While most of the sample preparation can be automated on a standard robotic liquid handling system, a streamlined approach for protein desalting and temperature modulation is required for a viable, fully automated digestion. In this work, for the first time, a complete tip-based MAM sample preparation is automated on a single robotic liquid handling system, leveraging a deck layout that integrates both heating and cooling functionalities. The fully automated method documented herein achieves a high-throughput sample preparation for MAM, while maintaining superior method performance.

Abbreviations: MAM: multi-attribute method; PQAs: product quality attributes; CE: capillary electrophoresis; IEX: ion-exchange chromatography; HILIC-FLR: hydrophilic interaction liquid chromatography coupled to a fluorescence detector; RP-LC/UV: reversed-phase liquid chromatography coupled to a UV detector; MS: mass spectrometry; NPD: new peak detection; GdnHCl: guanidine hydrochloride; TIC: total ion current; pAb: polyclonal antibody; IgG: immunoglobulin G; DTT: dithiothreitol; IAA: iodoacetic acid; TFA: trifluoroacetic acid; A280: absorbance at 280 nm wavelength; 96MPH: 96-channel multi-probe head; CPAC: Cold Plate Air Cooled; HHS: Hamilton Heater Shaker; DWP: Deep-Well Plate; PCR: Polymerase Chain Reaction; NTR: Nested Tip Rack; Met: methionine; Trp: tryptophan; N-term pQ: N-terminal glutamine cyclization; Lys: lysine; PAM: peptidylglycine α-amidating monooxygenase; G0F: asialo-, agalacto-, bi-antennary, core substituted with fucose; G1F: asialo-, mono-galactosylated bi-antennary, core substituted with fucose; G2F: asialo-, bi-galactosylated bi-antennary, core substituted with fucose; G0: asialo-, agalacto-, bi-antennary; Man5: oligomannose 5; Man8: oligomannose 8; TriF: asialo-, tri-galactosylated tri-antennary, core substituted with fucose.

Factors Compromising Glucuronidase Performance in Urine Drug Testing Potentially Resulting in False Negatives

Next generation β-glucuronidases can effectively cleave glucuronides in urine at room temperature. However, during the discovery studies, additional challenges were identified for urine drug testing across biologically relevant pH extremes and patient urine specimens. Different enzymes were evaluated across clinical urine specimens and commercially available urine control matrices. Each enzyme shows distinct substrate preferences, pH optima, and variability across clinical specimens. These results demonstrate how reliance on a single glucuronidated substrate as the internal hydrolysis control cannot ensure performance across a broader panel of analytes. Moreover, sample specific urine properties compromise β-glucuronidases to varying levels, more pronounced for some enzymes, and thereby lower the recovery of some drug analytes in an enzyme-specific manner. A minimum of 3-fold dilution of urine with buffer yields measurable improvements in achieving target pH and reducing the impact of endogenous compounds on enzyme performance. After subjecting the enzymes to pH extremes and compromising chemicals, one particular β-glucuronidase was identified that addressed many of these challenges and greatly lower the risk of failed hydrolyses. In summary, we present strategies to evaluate glucuronidases that aid in higher accuracy urine drug tests with lower potential for false negatives.

Variants of glycosyl hydrolase family 2 β-glucuronidases have increased activity on recalcitrant substrates

Glucuronidated drug metabolites can be quantified from urine samples by first hydrolyzing conjugates with β-glucuronidase (β-GUS) and then separating free drug molecules by liquid chromatography and mass spectrometry detection (LC-MS). To improve the activity and specificity of various β-GUS, we designed enzyme chimeras and generated site-saturation variants based on structural analyses, then screened them for improved activity on drug metabolites important to clinical and forensic drug-testing laboratories. Often, an increase of activity on one substrate of interest was countered by loss of activity against another, and there was no strong correlation of activity on standard β-glucuronidase substrates to activity on recalcitrant drug glucuronides. However, we discovered a chimera of two enzymes from different species of Aspergillus that displays a 27 % increase in activity on morphine-3-glucuronide than the parent proteins. Furthermore, mutations in the M-loop, which is a loop near the active site, resulted in numerous variants with dramatically increased rates of hydrolysis on drug glucuronides. Specifically, the M-loop variant Q451D/A452E of a β-GUS from Brachyspira pilosicoli has a 50-fold and 25-fold increase in activity on the recalcitrant substrates codeine-6-glucuronide and dihydrocodeine-6-glucuronide, respectively, compared to the parent enzyme.

Parallel sample processing using dispersive INtip micro-purification on programmable multichannel pipettes

Automation gives researchers the ability to process and screen orders of magnitude higher numbers of samples than manual experimentation. Current biomacromolecule separation methodologies suffer from necessary manual intervention, making their translation to high-throughput automation difficult. Herein, we present the first characterization of biomacromolecule affinity purification via dispersive solid-phase extraction in a pipette tip (INtip). We use commercially available resin and compare efficiency with batch and spin column methodologies. Moreover, we measure the kinetics of binding and evaluate resin binding capacities. INtip technology is effective on, and scalable for, an automated platform (INTEGRA ASSIST). The results suggest that high-throughput biomolecular workflows will benefit from the integration of INtip separations.

Automating Complex, Multistep Processes on a Single Robotic Platform to Generate Reproducible Phosphoproteomic Data

Mass spectrometry-based phosphoproteomics holds promise for advancing drug treatment and disease diagnosis; however, its clinical translation has thus far been limited. This is in part due to an unstandardized and segmented sample preparation process that involves cell lysis, protein digestion, peptide desalting, and phosphopeptide enrichment. Automating this entire sample preparation process will be key in facilitating standardization and clinical translation of phosphoproteomics. While peptide desalting and phosphopeptide enrichment steps have been individually automated, integrating these two extractions and, further, the entire process requires more advanced robotic platforms as well as automation-friendly extraction tools. Here we describe a fully automated peptide desalting and phosphopeptide enrichment method using IMCStips on a Hamilton STAR. Using our established automated method, we identified more than 10,000 phosphopeptides from 200 µg of HCT116 cell lysate without fractionation with >85% phosphopeptide specificities. Compared with titania-based Spin Tip products, the automated IMCStips-based method gave 50% higher phosphopeptide identifications. The method reproducibility was further assessed using multiple reaction monitoring (MRM) to show >50% phosphopeptide recoveries after the automated phosphopeptide extraction with coefficients of variation (CVs) of <20% over a 3-week period. The established automated method is a step toward standardization of the sample preparation of phosphopeptide samples and could be further expanded upon to create a fully automated "cells to phosphopeptides" method.

Relating gastric scintigraphy and symptoms to motility capsule transit and pressure findings in suspected gastroparesis

BACKGROUND

Wireless motility capsule (WMC) findings are incompletely defined in suspected gastroparesis. We aimed to characterize regional WMC transit and contractility in relation to scintigraphy, etiology, and symptoms in patients undergoing gastric emptying testing.

METHODS

A total of 209 patients with gastroparesis symptoms at NIDDK Gastroparesis Consortium centers underwent gastric scintigraphy and WMCs on separate days to measure regional transit and contractility. Validated questionnaires quantified symptoms.

KEY RESULTS

Solid scintigraphy and liquid scintigraphy were delayed in 68.8% and 34.8% of patients; WMC gastric emptying times (GET) were delayed in 40.3% and showed 52.8% agreement with scintigraphy; 15.5% and 33.5% had delayed small bowel (SBTT) and colon transit (CTT) times. Transit was delayed in ≥2 regions in 23.3%. Rapid transit was rarely observed. Diabetics had slower GET but more rapid SBTT versus idiopathics (P ≤ .02). GET delays related to greater scintigraphic retention, slower SBTT, and fewer gastric contractions (P ≤ .04). Overall gastroparesis symptoms and nausea/vomiting, early satiety/fullness, bloating/distention, and upper abdominal pain subscores showed no relation to WMC transit. Upper and lower abdominal pain scores (P ≤ .03) were greater with increased colon contractions. Constipation correlated with slower CTT and higher colon contractions (P = .03). Diarrhea scores were higher with delayed SBTT and CTT (P ≤ .04).

CONCLUSIONS & INFERENCES

Wireless motility capsules define gastric emptying delays similar but not identical to scintigraphy that are more severe in diabetics and relate to reduced gastric contractility. Extragastric transit delays occur in >40% with suspected gastroparesis. Gastroparesis symptoms show little association with WMC profiles, although lower symptoms relate to small bowel or colon abnormalities.

Safety and pharmacodynamics of intranasal GSK2245035, a TLR7 agonist for allergic rhinitis: A randomized trial

BACKGROUND

Toll-like receptor 7 (TLR7) stimulation in the airways may reduce responses to aeroallergens by induction of type 1 interferons (IFNs). GSK2245035 is a novel selective TLR7 agonist in pharmaceutical development.

OBJECTIVE

Assessment of safety, pharmacodynamics and nasal allergic reactivity following repeated weekly intranasal (i.n.) GSK2245035.

METHODS

This randomized, double-blind, placebo-controlled study (TL7116958) was conducted over two pollen seasons (2013-2014) and follow-up study (204509) conducted 1 year later. Participants with allergic rhinitis (n=42) were randomized to receive eight weekly doses of i.n. GSK2245035 (20 ng [2014 Cohort; n=14] or 80 ng [2013 Cohort; n=14]) or placebo (n=14). Adverse events (AEs) including cytokine release syndrome AEs (CytoRS-AEs) and nasal symptoms were assessed. Nasal and serum IFN-inducible protein 10 (IP-10) were measured after doses 1 and 8, then 1 (follow-up visit [FUV] 1) and 3 (FUV2) weeks after final dose. Nasal allergen challenges (NACs) and allergic biomarker assessment (nasal, serum) were conducted at baseline, FUV1, FUV2 and at a FUV 1 year after final dose (FUV3; 2014 Cohort only). A Bayesian framework enabled probability statements for mean effect sizes.

RESULTS

GSK2245035 induced CytoRS-AEs (most commonly headache, median duration <1 day) in 93% of participants at 80 ng, while AE incidence at 20 ng was similar to placebo. There was no evidence of nasal inflammation. Dose-related increases in nasal and serum IP-10 were observed 24 hours after doses 1 and 8 (>95% certainty). Both doses showed a trend in reducing total nasal symptom score 15 minutes post-NAC at FUV1 and FUV2, but there was no reduction evident at FUV3. Nasal levels of selected allergic biomarkers demonstrated trends for reductions at FUV1, FUV2 and FUV3.

CONCLUSIONS AND CLINICAL RELEVANCE

Weekly i.n. GSK2245035 20 ng was well tolerated and reduced allergic reactivity to nasal challenge for 3 weeks post-treatment.

Polymer-Protein Core-Shell Nanoparticles for Enhanced Antigen Immunogenicity

Nanoengineered vaccine platforms can be modeled after viruses and other pathogens with highly organized and repetitive structures that trigger the host immune system. Here we demonstrated a pyridine-grafted poly(ε-caprolactone)-based polymer-protein core-shell nanoparticles (PPCS-NPs) platform can effectively trigger the host immune system and lead to significantly higher antibody titers.

Ras oncogene-independent activation of RALB signaling is a targetable mechanism of escape from NRAS(V12) oncogene addiction in acute myeloid leukemia

Somatic mutations that lead to constitutive activation of NRAS and KRAS proto-oncogenes are among the most common in human cancer and frequently occur in acute myeloid leukemia (AML). An inducible NRAS(V12)-driven AML mouse model has established a critical role for continued NRAS(V12) expression in leukemia maintenance. In this model genetic suppression of NRAS(V12) expression results in rapid leukemia remission, but some mice undergo spontaneous relapse with NRAS(V12)-independent (NRI) AMLs providing an opportunity to identify mechanisms that bypass the requirement for Ras oncogene activity and drive leukemia relapse. We found that relapsed NRI AMLs are devoid of NRAS(V12) expression and signaling through the major oncogenic Ras effector pathways, phosphatidylinositol-3-kinase and mitogen-activated protein kinase, but express higher levels of an alternate Ras effector, Ralb, and exhibit NRI phosphorylation of the RALB effector TBK1, implicating RALB signaling in AML relapse. Functional studies confirmed that inhibiting CDK5-mediated RALB activation with a clinically relevant experimental drug, dinaciclib, led to potent RALB-dependent antileukemic effects in human AML cell lines, induced apoptosis in patient-derived AML samples in vitro and led to a 2-log reduction in the leukemic burden in patient-derived xenograft mice. Furthermore, dinaciclib potently suppressed the clonogenic potential of relapsed NRI AMLs in vitro and prevented the development of relapsed AML in vivo. Our findings demonstrate that Ras oncogene-independent activation of RALB signaling is a therapeutically targetable mechanism of escape from NRAS oncogene addiction in AML.

Abstract P1-14-05: Three distinct HER2 subtypes identified by BluePrint 80-gene functional subtyping predict treatment-specific response in the prospective neo-adjuvant NBRST registry

Background

Ideally classification by subtype predicts treatment response and overall outcome. BluePrint 80-gene functional molecular subtype is based on mRNA expression (as is intrinsic subtype) associated with intact translation to protein (unlike intrinsic subtype). BluePrint (BP) classifies patients into Luminal, Her2 or Basal-type. Presently subtype is approximated using conventional immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) ("conventional subtype") or assigned by gene expression profiling. The main objective of the prospective neo-adjuvant NBRST study is to compare drug sensitivity as defined by pathological Complete Response (pCR), using 80-gene functional subtype vs. conventional IHC/FISH subtyping. NBRST enrolled over 1,000 US patients between June 2011 and December 2014. In this analysis we present the results for IHC/FISH Her2-positive patients.

Methods

Here we report findings in the 260 NBRST patients who had IHC/FISH Her2+ breast cancer, according to ASCO CAP guidelines at the time of diagnosis. Treatment, including chemotherapy and HER2-targeted agents, was at the discretion of the physician adhering to NCCN approved or other peer-reviewed, established regimens over the course of the study. pCR was defined as T0/isN0. Fisher's exact test was used to compare pCR rates among IHC/FISH and functional subtypes and treatment groups.

Results

The 260 IHC/FISH Her2+ patients had median age 53 (range 23-81) and included T1-4, N0-3 tumors. Of 169 ER+/Her2+ tumors 49% were re-classified as BP Luminal, 43% as BP HER2, and 8% as BP Basal. The median ER% of ER+/Her2+/BP Luminal tumors was 93% (range 3-100), compared to 79% in ER+/Her2+/BP HER2 (range 1-91) and 8% in ER+/Her2+/BP Basal-type (range 2-99).The overall pCR rate in ER+/Her2+/BP Luminal was 17% (4% with chemo/trastuzumab; 39% chemo/trastuzumab/pertuzumab, p&lt;0.0001) and statistically inferior (p&lt;0.0001) to the 59% pCR rate in ER+/Her2+/BP HER2. Of 91 ER-/Her2+ tumors 74% were classified as BP HER2, 25% were re-classified BP Basal and &lt;1% was BP Luminal. NCT pCR rates for ER-/Her2+/BP HER2 was 67% (64% with chemo/trastuzumab; 77% chemo/trastuzumab/pertuzumab, p=0.40) and significantly superior (p=0.026) to the 39% pCR rate in ER-/Her2+/BP Basal (p=0.026).

Conclusions

In the NBRST study, BP 80-gene functional subtype (based on mRNA expression and translation): 1. Re-classifies over half of all IHC/FISH ER+/Her2+ patients; 2. Predicts treatment response or resistance in Her2+ patients not segregated by conventional IHC/FISH classification and 3. Identifies ER+/Her2+ tumors that are sensitive to chemo/trastuzumab/pertuzumab but resistant to chemo/trastuzumab.

Citation Format: Whitworth P, Beitsch P, Baron P, Beatty J, Pellicane JV, Murray MK, Dul CL, Mislowsky AM, Nash CH, Richards PD, Lee LA, Stork-Sloots L, de Snoo F, Untch S, Gittleman M, Akbari S, Rotkis MC. Three distinct HER2 subtypes identified by BluePrint 80-gene functional subtyping predict treatment-specific response in the prospective neo-adjuvant NBRST registry. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P1-14-05.

Abstract P4-14-29: One-third of HER2 positive patients have 80-gene luminal subtype that is resistant to chemo-trastuzumab but sensitive to chemo-trastuzumab-pertuzumab: Critical implications for the adjuvant setting from the NBRST phase 4 neoadjuvant study

Background

The phase 4 Neo-adjuvant Breast Registry Symphony Trial (NBRST) enrolled over 1,000 US patients between June 2011 and December 2014. The aim of NBRST study is to compare chemo-sensitivity as defined by pathological Complete Response (pCR) using the 80-gene BluePrint (BP) functional subtype profile vs. conventional IHC/FISH subtyping. Treatment was at the discretion of the physician utilizing standard NCCN regimens. Pertuzumab, a monoclonal antibody, inhibits the dimerization of HER2 with other HER receptors. Pertuzumab received US FDA approval for the neo-adjuvant treatment of HER2-positive breast cancer in September 2013. Essentially all patients with HER2 positive cancers were treated with chemotherapy + trastuzumab and after this date pertuzumab was added, creating 2 distinct groups of Her2-treated patients.

The aim of the current analysis is to compare the pCR rate of chemo-trastuzumab (c-t) vs chemo-trastuzumab plus pertuzumab (c-t-p) by conventional and 80-gene BP functional subtype. 80-gene BP functional subtype was derived by supervised cluster analysis for concordant mRNA and protein expression.

Methods

The current analysis includes women from the NBRST study, with histologically proven breast cancer, who received neo-adjuvant treatment, had 80-gene subtyping and provided written informed consent. Pathological assessment of HER2 was performed according to ASCO CAP guidelines at the time of diagnosis. 80-gene BluePrint (BP) classifies patients into Luminal, HER2 or Basal-type. pCR is defined as T0/isN0. All pCRs were verified with a de-identified copy of the surgical pathology report. Fisher's exact test was used to compare pCR rates within different subgroups.

Results

286 IHC/FISH HER2+ patients received c-t (175) or c-t-p (111). Of these 80-gene BP subtype classified 53% as HER2-type, 33% as Luminal-type and 14% as Basal-type. 64% were ER positive.

The pCR rates and p-values within different subgroups of clinical HER2+ patients are provided in the table below.

 c-tc-t-p (n)pCR ratep-valueTotal (n=286)41%57%0.01BP HER2 (153)58%73%0.06 BP Luminal (93) 6% 39% 0.0002BP Basal (40)45%1.0IHC/FISH HER2+/ER+ (183)31%53%0.003IHC/FISH HER2+/ER- (103)59%64%0.68

Conclusions

One-third of ASCO/CAP Her2+ patients had 80-gene BP Luminal subtype and demonstrated resistance to c-t (pCR 6%). Addition of Pertuzumab overcame resistance in this group (pCR 39%). This finding in the neoadjuvant setting suggests a substantial potential benefit in the adjuvant setting and thus an urgent need to consider treatment in at-risk patients as well as confirmatory tissue analysis from independently reported trials.

Citation Format: Beitsch P, Whitworth P, Baron P, Beatty J, Pellicane JV, Murray MK, Dul C, Mislowsky AM, Nash CH, Richards PD, Lee LA, Stork-Sloots L, de Snoo F, Untch S, Gittleman M, Akbari S, Rotkis MC. One-third of HER2 positive patients have 80-gene luminal subtype that is resistant to chemo-trastuzumab but sensitive to chemo-trastuzumab-pertuzumab: Critical implications for the adjuvant setting from the NBRST phase 4 neoadjuvant study. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P4-14-29.

Changes of snoring sound after relocation pharyngoplasty for obstructive sleep apnoea: the surgery reduces mean intensity in snoring which correlates well with apnoea-hypopnoea index

OBJECTIVE

To investigate objective changes of snoring after surgery in patients with obstructive sleep apnoea (OSA) and correlate these with changes in the apnoea-hypopnoea index (AHI).

DESIGN

Prospective case series.

SETTING

A novel measurement, Snore Map, was used to analyse full-night snore sounds in terms of the maximal/mean intensity, peak/mean frequency, snoring index and energy type (Snore Map type, 0-4). Snore sound was classified into three bands according to frequency energy spectrum: B1 (40-300 Hz), B2 (301-850 Hz) and B3 (851-2000 Hz).

PARTICIPANTS

Thirty-four male and two female OSA patients (mean age, 39 years; mean AHI, 53.1/h; mean body mass index, 26.8 kg/m(2) ) with favourable anatomic structure were consecutively enrolled.

MAIN OUTCOME MEASURES

Parameters of polysomnographies and Snore Maps at baseline and six months after operation were compared. Statistical significance was set at P < 0.05.

RESULTS

Thirty-two patients completed this study. The mean reduction in the total-snoring index was insignificant but there were significant decreases in total mean intensity, total peak frequency, total mean frequency and Snore Map type after surgery. There were also significant decreases in the mean intensity in all three bands, the snoring index in B2/B3 and the mean frequency in B1 postoperatively. Changes in the total mean intensity, total mean frequency, B2 mean intensity and B3 snoring index positively correlated with change in the AHI.

CONCLUSIONS

Relocation pharyngoplasty significantly decreases both the snoring sound intensity and snoring frequency. These reductions are directly proportional to the improvement of OSA.

Synthesis of self-assembled IL-1Ra-presenting nanoparticles for the treatment of osteoarthritis

Osteoarthritis is a progressive joint disease that results in degradation of cartilage in load-bearing joints. Pain and inflammation in the joint are the hallmarks of this condition, which further exacerbate the cartilage destruction and health of the patient. It is hence imperative to treat the joint inflammation at the earliest. Interleukin 1 (IL-1) blockade by IL-1 receptor antagonist (IL-1Ra) has shown promise in the clinic but this therapy suffers from rapid clearance, high doses, and frequent intervention. Use of carrier particles that result in longer residence time has been proposed. Here we have synthesized a new class of nanoparticles presenting IL-1Ra on the surface and with tunable size from 300 to 700 nm. These IL-1Ra-poly(2-hydroxyethyl methacrylate)-pyridine nanoparticles are cytocompatible and stable in serum-containing solutions for several days. Our results further demonstrate that these nanoparticles are capable of blocking IL-1β signaling in an NF-κB inducible reporter cell line. These engineered nanoparticles are promising for localized intra-articular delivery in joint space to reduce inflammation in osteoarthritis and other inflammatory diseases. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 595-599, 2016.

Nanoengineered particles for enhanced intra-articular retention and delivery of proteins

Localized intra-articular delivery of anti-inflammatory proteins can reduce inflammation in osteoarthritis but poses a challenge because of raid clearance within few hours of injection. A new class of polymer is developed that forms self-assembled nanoparticles ranging from 300 to 900 nm and demonstrates particle size dependent prolonged retention in intra-articular joint spaces compared to bolus protein over a period of 14 d.

Plant virus incorporated hydrogels as scaffolds for tissue engineering possess low immunogenicity in vivo

Viruses are no longer recognized purely for being ubiquitous pathogens, but have served as building blocks for material chemistry and nanotechnology. Thousands of coat protein subunits of a viral particle can be modified chemically and/or genetically. We have previously shown that the three-dimensional porous hydrogels can easily be functionalized by Tobacco mosaic virus (TMV), a rod-like plant virus, using its mutant, RGD-TMV. RGD-TMV hosted bioadhesive peptide (RGD) in the hydrogel, which was shown to enhance cell attachment and promote osteogenic differentiation of cultured stem cell. To translate this technology to potential clinical applications, we sought to study the biocompatibility of the hydrogel. In this paper, the hydrogels were implanted in vivo and assessed for their immunogenicity, toxicity, and biodegradability. Immune response for TMV substantially decreased when incorporated in the hydrogel implants. The implanted TMV hydrogels exhibited no apparent toxicity and were degradable in mice. The results highlighted the feasibility of using TMV incorporated hydrogels as scaffolding materials for regenerative medicine in terms of biocompatibility and biodegradability.

RGD-conjugated rod-like viral nanoparticles on 2D scaffold improve bone differentiation of mesenchymal stem cells

Viral nanoparticles have uniform and well-defined nano-structures and can be produced in large quantities. Several plant viral nanoparticles have been tested in biomedical applications due to the lack of mammalian cell infectivity. We are particularly interested in using Tobacco mosaic virus (TMV), which has been demonstrated to enhance bone tissue regeneration, as a tunable nanoscale building block for biomaterials development. Unmodified TMV particles have been shown to accelerate osteogenic differentiation of adult stem cells by synergistically upregulating bone morphogenetic protein 2 (BMP2) and integrin-binding bone sialoprotein (IBSP) expression with dexamethasone. However, their lack of affinity to mammalian cell surface resulted in low initial cell adhesion. In this study, to increase cell binding capacity of TMV based material the chemical functionalization of TMV with arginine-glycine-aspartic acid (RGD) peptide was explored. An azide-derivatized RGD peptide was "clicked" to tyrosine residues on TMV outer surface via an efficient copper(I) catalyzed azide-alkyne cycloaddition (CuAAC) reaction. The ligand spacing is calculated to be 2-4 nm, which could offer a polyvalent ligand clustering effect for enhanced cell receptor signaling, further promoting the proliferation and osteogenic differentiation of bone marrow-derived mesenchymal stem cells (BMSCs).

Porous alginate hydrogel functionalized with virus as three-dimensional scaffolds for bone differentiation

In regenerative medicine, a synthetic extracellular matrix is crucial for supporting stem cells during its differentiation process to integrate into surrounding tissues. Hydrogels are used extensively in biomaterials as synthetic matrices to support the cells. However, to mimic the biological niche of a functional tissue, various chemical functionalities are necessary. We present here, a method of functionalizing a highly porous hydrogel with functional groups by mixing the hydrogel with a plant virus, tobacco mosaic virus (TMV), and its mutant. The implication of this process resides with the three important features of TMV: its well-defined genetic/chemical modularity, its multivalency (TMV capsid is composed of 2130 copies of identical subunits), and its well-defined structural features. Previous studies utilizing the native TMV on two-dimensional supports accelerated mesenchymal stem cell differentiation, and surfaces modified with genetically modified viral particles further enhanced cell attachment and differentiation. Herein we demonstrate that functionalization of a porous alginate scaffold can be achieved by the addition of viral particles with minimal processing and downstream purifications, and the cell attachment and differentiation within the macroporous scaffold can be effectively manipulated by altering the peptide or small molecule displayed on the viral particles.

In vivo virus-based macrofluorogenic probes target azide-labeled surface glycans in MCF-7 breast cancer cells

Chemical addressability of viral particles has played a pivotal role in adapting these biogenic macromolecules for various applications ranging from medicine to inorganic catalysis. Cowpea mosaic virus possesses multiple features that are advantageous for the next generation of virus-based nanotechnology: consistent multimeric assemblies dictated by its genetic code, facile large scale production, and lack of observable toxicity in humans. Herein, the chemistry of the viral particles is extended with the use of Cu-free strain-promoted azide-alkyne cycloaddition reaction, or SPAAC reaction. The elimination of Cu, its cocatalyst and reducing agent, simplifies the reaction scheme to a more straightforward approach, which can be directly applied to living systems. As a proof of concept, the viral particles modified with the azadibenzylcyclooctyne functional groups are utilized to trigger and amplify a weak fluorescent signal (azidocoumarin) in live cell cultures to visualize the non-natural sugars. Future adaptations of this platform may be developed to enhance biosensing applications.

Thermally controlled release of anticancer drug from self-assembled γ-substituted amphiphilic poly(ε-caprolactone) micellar nanoparticles

A thermo-responsive poly{γ-2-[2-(2-methoxyethoxy)ethoxy]ethoxy-ε-caprolactone}-b-poly(γ-octyloxy-ε-caprolactone) (PMEEECL-b-POCTCL) diblock copolymer was synthesized by ring-opening polymerization using tin octanoate (Sn(Oct)(2)) catalyst and a fluorescent dansyl initiator. The PMEEECL-b-POCTCL had a lower critical solution temperature (LCST) of 38 °C, and it was employed to prepare thermally responsive micelles. Nile Red and Doxorubicin (DOX) were loaded into the micelles, and the micellar stability and drug carrying ability were investigated. The size and the morphology of the cargo-loaded micelles were determined by DLS, AFM, and TEM. The Nile-Red-loaded polymeric micelles were found to be stable in the presence of both fetal bovine serum and bovine serum albumin over a 72 h period and displayed thermo-responsive in vitro drug release. The blank micelles showed a low cytotoxicity. As comparison, the micelles loaded with DOX showed a much higher in vitro cytotoxicity against MCF-7 human breast cancer cell line when the incubation temperature was elevated above the LCST. Confocal laser scanning microscopy was used to study the cellular uptake and showed that the DOX-loaded micelles were internalized into the cells via an endocytosis pathway.

Visualizing cell extracellular matrix (ECM) deposited by cells cultured on aligned bacteriophage M13 thin films

Topographical features ranging from micro- to nanometers can affect cell orientation and migratory pathways, which are important factors in tissue engineering and tumor migration. In our previous study, a convective assembly of bacteriophage M13 resulted in thin films which could be used to control the alignment of cells. However, several questions regarding its underlying reasons to dictate cell alignment remained unanswered. Here, we further study the nanometer topographical features generated by the bacteriophage M13 crystalline film, which results in the alignment of the cells and extracellular matrix (ECM) proteins. Sequential imaging analyses at micro- and nanoscale levels of aligned cells and fibrillar matrix proteins were documented using scanning electron microscopy and immunofluorescence microscopy. As a result, we observed baby hamster kidney cells with higher degree of alignment on the ordered M13 substrates than NIH-3T3 fibroblasts, a difference which could be attributed to the intrinsic nature of the cells' production of ECM proteins. The results from this study provide a crucial insight into the topographical features of a biological thin film, which can be utilized to control the orientation of cells and surrounding ECM proteins.

Altering the landscape of viruses and bionanoparticles

In recent years, protein-based nanoparticles or bionanoparticles (BNPs), have been used as primary building blocks to generate ornate nanomaterials for a wide-range of applications. Over the past fifty years, numerous BNPs have been chemically modified or genetically engineered to function as smart drug/gene delivery vehicles, advanced vaccine vehicles, and isolated reaction vessels for inorganic, metallic, and semi-conductive depositions. These studies have contributed invaluable insights to the expansive capabilities of these simple, yet highly robust, nanosized building materials. Here we highlight some of the recent progress in the chemical modifications of BNPs and hopefully inspire the development of many new materials in the near future.

Chemoselective modification of turnip yellow mosaic virus by Cu(I) catalyzed azide-alkyne 1,3-dipolar cycloaddition reaction and its application in cell binding

Turnip yellow mosaic virus (TYMV) is an icosahedral plant virus with a diameter of 28-30 nm that can be isolated in gram quantities from turnip or Chinese cabbage inexpensively. In this study, TYMV combined with spatially addressable surface chemistries was selected as a prototype bionanoparticle for modulating patterns of cell adhesion, morphology, and proliferation. We exploited the chemical reactivity of TYMV using the mild conditions of Cu(I) catalyzed azide-alkyne cycloaddition (CuAAC) reaction, the best example of "click" chemistry. Oligo-ethylene glycol (OEG) short chain, coumarintriazole, and RGD-containing peptide were grafted on the surface of TYMV via carbodiimide activation and CuAAC reaction. The bioconjugation to intact viral particles was confirmed by MS, TEM, FPLC, and SDS-PAGE with fluorescence visualization analysis. Therefore, this method is a generally useful means of incorporating various types of functionalities onto the TYMV surface. Further studies were done to learn the behavior of NIH-3T3 fibroblast cells on the modified or unmodified TYMV surfaces. OEG-modified TYMV surfaces retarded cell attachment and growth, while cell adhesion, spreading, and proliferation were dramatically enhanced on RGD-modified TYMV surfaces. Compared with RGD immobilized 3-aminopropyltriethoxysilane-coated glass surface, the cells are more ready to spread fully and proliferate on TYMV-RGD coated surface, which thus provides a more cell-friendly environment with nanometer-scale surface features. This illustrates the potential application of plant virus based materials in tissue engineering, drug delivery, and biosensing.

Cutaneous lupus in infancy and childhood

Cutaneous lupus may occur in infancy as transient lesions associated with and probably caused by maternal autoantibodies, or later in childhood, associated with the endogenous development of autoimmunity. In this review, clinical findings, diagnosis, management, and pathogenesis of neonatal lupus are discussed, and the management of cutaneous lupus in children is detailed.

Comparison of the reliability and validity of outcome instruments for cutaneous dermatomyositis

BACKGROUND

Reliable and validated measures of skin disease severity are needed for cutaneous dermatomyositis (DM). Cutaneous Dermatomyositis Disease Area and Severity Index (CDASI), Dermatomyositis Skin Severity Index (DSSI) and Cutaneous Assessment Tool (CAT) skin indices have been developed as outcome instruments.

OBJECTIVES

We sought to demonstrate reliability and validity of the CDASI, and to compare the CDASI with other potential tools for use in measuring disease severity in cutaneous dermatomyositis.

PATIENTS AND METHODS

CDASI has four activity and two damage measures, with scores from 0 to 148. DSSI assesses activity based on body surface area and severity on a scale of 0-72. CAT uses 21 activity and damage items, for a range of 0-175 for activity and 0-33 for damage. Ten dermatologists used the instruments to score the same 12-16 patients in one session. Global validation measures were administered to physicians and patients.

RESULTS

Global validation measures correlated with the three outcome instruments (P < 0.0001). CAT displayed lower inter- and intrarater reliability relative to the CDASI. All scales correlate better with physician than patient global skin measures.

CONCLUSIONS

It appears that the CDASI may be a useful outcome measure for studies of cutaneous DM. Further testing to compare responsiveness of all three measures is necessary.

Biological templated synthesis of water-soluble conductive polymeric nanowires

One-dimensional (1D) conductive nanowire is one of the most important components for the development of nanosized electronic devices, sensors, and energy storage units. Great progresses have been made to prepare the 1D-conducting polymeric nanofibers by the low concentration process or the synthesis with hard or soft templates. However, it still remains as a great challenge to prepare polymeric nanofibers with narrow dispersity, high aspect ratio, and good processibility. With the rod-like tobacco mosaic virus as the template, 1D-conducting polyaniline and polypyrrole nanowires can be readily prepared via a hierarchical assembly process. This synthesis discloses a unique way to produce composite fibrillar materials with controlled morphology and great processibility, which can promote many potential applications including electronics, optics, sensing, and biomedical engineering.

Assembly of tobacco mosaic virus into fibrous and macroscopic bundled arrays mediated by surface aniline polymerization

One-dimensional (1D) polyaniline/tobacco mosaic virus (TMV) composite nanofibers and macroscopic bundles of such fibers were generated via a self-assembly process of TMV assisted by in-situ polymerization of polyaniline on the surface of TMV. At near-neutral reaction pH, branched polyaniline formed on the surface of TMV preventing lateral association. Therefore, long 1D nanofibers were observed with high aspect ratios and excellent processibility. At a lower pH, transmission electron microscopy (TEM) analysis revealed that initially long nanofibers were formed which resulted in bundled structures upon long-time reaction, presumably mediated by the hydrophobic interaction because of the polyaniline on the surface of TMV. In-situ time-resolved small-angle X-ray scattering study of TMV at different reaction conditions supported this mechanism. This novel strategy to assemble TMV into 1D and 3D supramolecular composites could be utilized in the fabrication of advanced materials for potential applications including electronics, optics, sensing, and biomedical engineering.

Quantitative imaging and sigmoidoscopy to assess distribution of rectal microbicide surrogates

Understanding the distribution of microbicide and human immunodeficiency virus (HIV) within the gastrointestinal tract is critical to development of rectal HIV microbicides. A hydroxyethylcellulose-based microbicide surrogate or viscosity-matched semen surrogate, labeled with gadolinium-DTPA (diethylene triamine pentaacetic acid) and 99mTechnetium-sulfur colloid, was administered to three subjects under varying experimental conditions to evaluate effects of enema, coital simulation, and microbicide or semen simulant over 5 h duration. Quantitative assessment used single photon emission computed tomography (SPECT)/computed tomography (CT) and magnetic resonance imaging (MRI) imaging, and sigmoidoscopic sampling. Over 4 h, radiolabel migrated cephalad in all studies by a median (interquartile range) of 50% (29-102%; P<0.001), as far as the splenic flexure (approximately 60 cm) in 12% of studies. There was a correlation in concentration profile between endoscopic sampling and SPECT assessments. HIV-sized particles migrate retrograde, 60 cm in some studies, 4 h after simulated ejaculation in our model. SPECT/CT, MRI, and endoscopy can be used quantitatively to facilitate rational development of microbicides for rectal use.

Childhood asthma and human leukocyte antigen type

Little is known about the relationship between human leukocyte antigen (HLA) class II genes and family history of asthma or atopy in relation to the incidence of childhood asthma. The objective of the study was to determine whether specific HLA class II genes (e.g., DRB1*03) are associated with asthma and whether such association explains the influences of family history of asthma or atopy on asthma incidence. A stratified random sample of 340 children who had HLA data available from the Rochester Family Measles Study cohort (n= 876) and a convenience sample of healthy children aged 5-12 years were the participants. We conducted comprehensive medical record reviews to determine asthma status of these children. The associations between the presence of specific HLA alleles and development of asthma and the role of family history of asthma or atopy in the association were evaluated by fitting Cox models. The cumulative incidence of asthma by 12 years of age among children who carry HLA DRB1*03 was 33%, compared to 24.2% among those who did not carry this allele. Adjusting for family history of asthma or atopy, gender, low birth weight, season of birth, HLA DRB1*04, and HLA DQB1*0302, the hazards ratio for HLA DRB1*03 carriers was 1.8 (95% confidence interval: 1.1-2.9, P= 0.020). We concluded that the HLA DRB1*03 allele is associated with asthma. However, the HLA class II gene does not explain the influences of family history of asthma or atopy on development of asthma. The mechanism underlying the association between asthma and HLA genes needs to be elucidated.

Adaptations of nanoscale viruses and other protein cages for medical applications

Nanosized materials (5-100 nm) with multiple functionalities (cell targeting, drug delivery, and bio-imaging) have emerged over the recent years as promising therapeutic agents. Liposomal carriers, amphiphilic co-polymers, silica-based particles, colloidal systems, and dendrimer clusters are among the many available nanoscale scaffolds that have been explored for medical applications such as gene delivery, bio-imaging, and drug delivery. On the other hand, viruses, ferritin, and other protein cages for ages have self-organized in the nanometer range with biologically relevant functionalities. These bio-inspired systems form monodispersed units that are highly amendable through genetic and chemical modifications. In this review the expansion of these protein-based nanosystems, termed bionanoparticles (BNPs), beyond their native functionalities, and their application as building materials for nanomedicine will be discussed. The recent developments of biology-inspired systems with potential medical applications will be outlined, with particular emphasis on adaptations of protein-based nanostructures for gene delivery, bio-imaging, drug encapsulation, and vaccine development. Notable systems already streamlined for medical applications are recombinant virus-like particles derived from human papillomaviruses as multivalent vaccine carriers to immunize patients against genital infections, and vaccinia viruses to treat patients with established cancers.

SLAP: design software for optimization of fluorescence analysis systems

Initial results of a comprehensive design software that optimizes parameters for fluorescence analysis of a user-defined fluorophore are presented. SLAP (spectral LED aggregation program) automatically selects configurations of LEDs that, in a fluorescence analysis system, maximize the emission signal (useful output) as a function of the excitation signal (interference), optics, photodetection modality, and sample characteristics. Initial results draw on an extensive database of blue, blue-green, green and purple LEDs characterized across a range of nominal and overdrive operating conditions. Overdrive conditions enable spectral shifts of the LED excitation bands to enhance the overall flexibility of SLAP optimization. Representative results show a 70.1% improvement in collected signal for GFPuv fluorophores when compared to conventional LED-based fluorescence operated under nominal operating conditions.

Myc target transcriptomes

The c-Myc oncogenic transcription factor plays a central role in many human cancers through the regulation of gene expression. Although the molecular mechanisms by which c-Myc and its obligate partner, Max, regulate gene expression are becoming better defined, genes or transcriptomes that c-Myc regulate are just emerging from a variety of different experimental approaches. Studies of individual c-Myc target genes and their functional implications are now complemented by large surveys of c-Myc target genes through the use of subtraction cloning, DNA microarray analysis, serial analysis of gene expression (SAGE), chromatin immunoprecipitation, and genome marking methods. To fully appreciate the differences between physiological c-Myc function in normal cells and deregulated c-Myc function in tumors, the challenge now is to determine how the authenticated transcriptomes effect the various phenotypes induced by c-Myc and to define how c-Myc transcriptomes are altered by the Mad family of proteins.

Field test results of an automated exposure assessment tool, the local positioning system (LPS)

A user-friendly environmental monitoring system that collects real time data has been developed. Flash card memory logs exposure data from multiple sensors along with corresponding times and positions. Optional use of telemetry repeaters and a reference station allows central monitoring of data to assess exposure and to initiate intervention when safe levels are exceeded. A software analysis package allows researchers to identify exposure hot spots and direct control efforts, with the ultimate goal being to reduce injury and disease. Preliminary field test results document position accuracy and system performance in harsh environments.