Tales from the EMR: Does a 21st-Century Data Warehouse Facilitate Clinical Research for Pancreatic Cancer?

Background: The importance of an electronic medical record has been highlighted for both clinical care and research. In the current era, data warehouses and repositories have been established to serve the dual function of patient care and investigation. Purpose: The aim of this study was to compare a newly developed institutional clinical data warehouse, linked with the hospital information system (HIS), to a prospectively-maintained departmental database. Methods: A novel HIS-linked institutional clinical data warehouse was queried for 9 primary and secondary ICD-9-CM discharge diagnosis codes for pancreatic cancer. The database captured inpatient and outpatient clinical and billing information from a pool of over 2 million patients evaluated at an academic medical institution and its affiliates since 1995. A cohort was identified; following Institutional Review Board approval, demographic and clinical data was obtained. This data was compared to a manually-entered and prospectively-maintained surgical oncology database of the same institution, tracking 394 patients since 1999. Duplicated patients, and those unique to either dataset, were flagged. Patients with diagnosis dates prior to 1999 were excluded to allow comparison over the same time period. For validation purposes, a 10% random sample of remaining patients unique to each dataset underwent manual review of medical records including clinic notes, admission/discharge notes, diagnostic imaging, and pathology reports. Results: 1107 patients were identified from the HIS-linked dataset with pancreatic neoplasm-associated diagnosis codes dating from 1999 to 2009. Of these, 254 (22.9%) were captured in both datasets, while 853 (77.1%) were only in the HIS-linked dataset. Manual review of the 10% subset of the HIS-only group demonstrated that 55.6% of patients were without identifiable pancreatic pathology, suggesting miscoding, while 31.7% had diagnoses consistent with pancreatic neoplasm, and 12.7% had pseudocyst or pancreatitis. Of the 394 patients tracked by surgical oncology, 254 (64.5%) were captured in both datasets, while 140 (35.5%) had not been captured in the HIS-linked dataset. Manual review of the 10% subset of the non-captured patients demonstrated 93.3% with pancreatic neoplasm and 6.7% with pseudocyst or pancreatitis. Lastly, a review of the 10% subset of the 254 patient overlap demonstrated that 87.5% of patients were with pancreatic neoplasm, 8.3% with pseudocyst or pancreatitis, and 4.2% without pancreatic pathology. Conclusions: While technological advances provide a powerful means to automate institutional-level cohort identification and data collection, a high degree of misclassification may be present if queries are based solely on ICD-9-CM discharge codes. For that reason, careful validation and data cleaning are critical steps prior to research use. These results also suggest cautious interpretation of national-level administrative data utilizing ICD-9-CM diagnosis codes. Our findings suggest that the current state-of-the-art data warehouses continue to require clinical correlation and validation through traditional retrospective mechanisms

Constitutive Gs activation using a single-construct tetracycline-inducible expression system in embryonic stem cells and mice

Abstract Introduction The controlled expression of many genes, including G-protein coupled receptors (GPCRs), is important for delineating gene functions in complex model systems. Binary systems for inducible regulation of transgene expression are widely used in mice. One system is the tTA/TRE expression system, composed of a tetracycline-dependent DNA binding factor and a separate tetracycline operon. However, the requirement for two separate transgenes (one for each tTA or TRE component) makes this system less amenable to models requiring directed cell targeting, increases the risk of multiple transgene integration sites, and requires extensive screening for appropriately-functioning clones. Methods We developed a single, polycistronic tetracycline-inducible expression platform to control the expression of multiple cistrons in mammalian cells. This platform has three basic constructs: regulator, responder, and destination vectors. The modular platform is compatible with both the TetOff (tTA) and TetOn (rtTA) systems. The modular Gateway recombineering-compatible components facilitate rapidly generating vectors to genetically modify mammalian cells. We apply this system to use the elongation factor 1α (EF1α) promoter to drive doxycycline-regulated expression of both the fluorescent marker mCherry and an engineered Gs-coupled GPCR "Rs1" separated by a 2A ribosomal skip site. Results We show that our combined expression construct drives expression of both the mCherry and Rs1 transgenes in a doxycycline-dependent manner. We successfully target the expression construct into the Rosa26 locus of mouse embryonic stem (ES) cells. Rs1 expression in mouse ES cells increases cAMP accumulation via both basal and ligand-induced Gs mechanisms and is associated with increased embryoid body size. Heterozygous mice carrying the Rs1 expression construct showed normal growth and weight, and developed small increases in bone formation that could be observed in the calvaria. Conclusions Our results demonstrate the feasibility of a single-vector strategy that combines both the tTA and TRE tetracycline-regulated components for use in cells and mouse models. Although the EF1α promoter is useful for driving expression in pluripotent cells, a single copy of the EF1α promoter did not drive high levels of mCherry and Rs1 expression in the differentiated tissues of adult mice. These findings indicate that promoter selection is an important factor when developing transgene expression models

Is pancreatic cancer palliatable? A national study

Background: Pancreatic cancer is frequently diagnosed at advanced stages where potentially curative resection is no longer possible. Palliative procedures can be performed; however, results on a national level are unknown. This study examines pancreatic cancer patients who underwent potentially palliative procedures including gastric bypass, biliary bypass surgery, celiac block, biliary stent, gastrostomy or jejunostomy, and examines post-intervention complications and 30-day mortality. Methods: SEER-Medicare 1991-2005 was used to identify patients with Stage 3-4 pancreatic cancer. Complication rates were calculated including post-op infection, myocardial infarction, aspiration pneumonia, DVT/PE, pulmonary compromise, gastric bleed, acute renal failure, and reoperation. Kaplan-Meier survival analysis was performed. Finally, Cox proportional hazards modeling was used to control for the effects of age, sex, race, stage, and resection. Results: Of 22,314 pancreatic cancer patients, 858 (3.9%) patients were Stage 3, and 11,149 (50.0%) stage 4. Post-procedure median survival for all patients is approximately two months, with longest survival for biliary bypass patients (3.2mo, 95% CI(2.9-3.7), and lowest survival for jejunostomy 1.3 mo (1.2-1.5) and gastrostomy 1.5 mo (1.4-1.8). Post-procedure 30-day mortality was highest for gastrostomy patients at 41.5%; followed by jejunostomy (39.1%), celiac plexus block (30.0%), gastric bypass (23.8%), biliary bypass (17.8%), and biliary stent (21.2%). The rate of complications averaged 40%, with highest rate for gastrostomy (47.4%) and gastric bypass (45.3%) and lowest for celiac plexus block (29.3%). Stage 4 disease was an independent predictor of death for patients undergoing five out of six procedures. Conclusion: We found that morbidity and mortality of palliative procedures in unresectable pancreatic cancer is high, especially in stage 4 patients. Further studies need to be conducted to identify patients who will have sufficient expected post-procedure survival to benefit from these palliative interventions

Frequent mutation of receptor protein tyrosine phosphatases provides a mechanism for STAT3 hyperactivation in head and neck cancer

The underpinnings of STAT3 hyperphosphorylation resulting in enhanced signaling and cancer progression are incompletely understood. Loss-of-function mutations of enzymes that dephosphorylate STAT3, such as receptor protein tyrosine phosphatases, which are encoded by the PTPR gene family, represent a plausible mechanism of STAT3 hyperactivation. We analyzed whole exome sequencing (n = 374) and reverse-phase protein array data (n = 212) from head and neck squamous cell carcinomas (HNSCCs). PTPR mutations are most common and are associated with significantly increased phospho-STAT3 expression in HNSCC tumors. Expression of receptor-like protein tyrosine phosphatase T (PTPRT) mutant proteins induces STAT3 phosphorylation and cell survival, consistent with a “driver” phenotype. Computational modeling reveals functional consequences of PTPRT mutations on phospho-tyrosine–substrate interactions. A high mutation rate (30%) of PTPRs was found in HNSCC and 14 other solid tumors, suggesting that PTPR alterations, in particular PTPRT mutations, may define a subset of patients where STAT3 pathway inhibitors hold particular promise as effective therapeutic agents.Fil: Lui, Vivian Wai Yan. University of Pittsburgh; Estados UnidosFil: Peyser, Noah D.. University of Pittsburgh; Estados UnidosFil: Ng, Patrick Kwok-Shing. University Of Texas Md Anderson Cancer Center;Fil: Hritz, Jozef. University of Pittsburgh at Johnstown; Estados Unidos. University of Pittsburgh; Estados Unidos. Masaryk University; República ChecaFil: Zeng, Yan. University of Pittsburgh at Johnstown; Estados Unidos. University of Pittsburgh; Estados UnidosFil: Lu, Yiling. University Of Texas Md Anderson Cancer Center;Fil: Li, Hua. University of Pittsburgh; Estados Unidos. University of Pittsburgh at Johnstown; Estados UnidosFil: Wang, Lin. University of Pittsburgh; Estados Unidos. University of Pittsburgh at Johnstown; Estados UnidosFil: Gilbert, Breean R.. University of Pittsburgh; Estados Unidos. University of Pittsburgh at Johnstown; Estados UnidosFil: General, Ignacio. University of Pittsburgh; Estados Unidos. University of Pittsburgh at Johnstown; Estados UnidosFil: Bahar, Ivet. University of Pittsburgh at Johnstown; Estados Unidos. University of Pittsburgh; Estados UnidosFil: Ju, Zhenlin. University Of Texas Md Anderson Cancer Center;Fil: Wang, Zhenghe. Case Western Reserve University; Estados UnidosFil: Pendleton, Kelsey P.. University of Pittsburgh; Estados Unidos. University of Pittsburgh at Johnstown; Estados UnidosFil: Xiao, Xiao. University of Pittsburgh at Johnstown; Estados Unidos. University of Pittsburgh; Estados UnidosFil: Du, Yu. University of Pittsburgh at Johnstown; Estados Unidos. University of Pittsburgh; Estados UnidosFil: Vries, John K.. University of Pittsburgh; Estados Unidos. University of Pittsburgh at Johnstown; Estados UnidosFil: Hammerman, Peter S.. Harvard Medical School; Estados UnidosFil: Garraway, Levi A.. Harvard Medical School; Estados UnidosFil: Mills, Gordon B.. University Of Texas Md Anderson Cancer Center;Fil: Johnson, Daniel E.. University of Pittsburgh at Johnstown; Estados Unidos. University of Pittsburgh; Estados UnidosFil: Grandis, Jennifer R.. University of Pittsburgh; Estados Unidos. University of Pittsburgh at Johnstown; Estados Unido

Towards the prediction of antimicrobial efficacy for hydrogen bonded, self-associating amphiphiles

Herein, we report 50 structurally related supramolecular self-associating amphiphilic (SSA) salts and related compounds. These SSAs are shown to act as antimicrobial agents, active against model Gram-positive (Methicillin-Resistant Staphylococcus aureus) and/or Gram-negative (Escherichia coli) bacteria of clinical interest. Through a combination of solution state, gas phase, solid state and in silico measurements we determine 14 different physicochemical parameters for each of these 50 structurally related compounds. These parameter sets are then used to identify molecular structure – physicochemical property – antimicrobial activity relationships for our model Gram-negative and Gram-positive bacteria, while simultaneously providing insight towards the elucidation of SSA mode of antimicrobial action

DHODH modulates transcriptional elongation in the neural crest and melanoma

Melanoma is a tumour of transformed melanocytes, which are originally derived from the embryonic neural crest. It is unknown to what extent the programs that regulate neural crest development interact with mutations in the BRAF oncogene, which is the most commonly mutated gene in human melanoma1. We have used zebrafish embryos to identify the initiating transcriptional events that occur on activation of human BRAF(V600E) (which encodes an amino acid substitution mutant of BRAF) in the neural crest lineage. Zebrafish embryos that are transgenic for mitfa:BRAF(V600E) and lack p53 (also known as tp53) have a gene signature that is enriched for markers of multipotent neural crest cells, and neural crest progenitors from these embryos fail to terminally differentiate. To determine whether these early transcriptional events are important for melanoma pathogenesis, we performed a chemical genetic screen to identify small-molecule suppressors of the neural crest lineage, which were then tested for their effects on melanoma. One class of compound, inhibitors of dihydroorotate dehydrogenase (DHODH), for example leflunomide, led to an almost complete abrogation of neural crest development in zebrafish and to a reduction in the self-renewal of mammalian neural crest stem cells. Leflunomide exerts these effects by inhibiting the transcriptional elongation of genes that are required for neural crest development and melanoma growth. When used alone or in combination with a specific inhibitor of the BRAF(V600E) oncogene, DHODH inhibition led to a marked decrease in melanoma growth both in vitro and in mouse xenograft studies. Taken together, these studies highlight developmental pathways in neural crest cells that have a direct bearing on melanoma formation

Revisiting the SAR of the antischistosomal aryl hydantoin (Ro 13-3978)

The aryl hydantoin 1 (Ro 13-3978) was identified in the early 1980s as a promising antischistosomal lead compound. However, this series of aryl hydantoins produced antiandrogenic side effects in the host, a not unexpected outcome given their close structural similarity to the antiandrogenic drug nilutamide. Building on the known SAR of this compound series, we now describe a number of analogs of 1 designed to maximize structural diversity guided by incorporation of substructures and functional groups known to diminish ligand-androgen receptor interactions. These analogs had calculated polar surface area (PSA), measured LogD7.4, aqueous kinetic solubility, and estimated plasma protein binding values in ranges predictive of good ADME profiles. The principal SAR insight was that the hydantoin core of 1 is required for high antischistosomal activity. We identified several compounds with high antischistosomal efficacy that were less antiandrogenic than 1. These data provide direction for the ongoing optimization of antischistosomal hydantoins

Towards the use of (pseudo) nucleobase substituted amphiphiles as DNA nucleotide mimics and antimicrobial agents

Here we present the synthesis of complementary (pseudo) nucleobase appended Supramolecular Self-associating Amphiphilic (SSA) salts and, establish the potential for this molecular construct to produce a new class of DNA inspired synthetic structures/materials. The anionic component of this class of amphiphile contains multiple hydrogen bond donating and accepting functionalities, meaning that these systems can access multiple self-associative hydrogen bonding modes simultaneously. Herein, we characterise the self-associative properties of these DNA inspired amphiphiles in the solid state, solution state and gas phase. Finally, we investigate the potential of these amphiphilic salts to act as antimicrobial agents against model Gram-positive (methicillin resistant Staphylococcus aureus – MRSA) and Gram-negative (Escherichia coli – E. coli) bacteria

Pan-viral serology implicates enteroviruses in acute flaccid myelitis.

Since 2012, the United States of America has experienced a biennial spike in pediatric acute flaccid myelitis (AFM)1-6. Epidemiologic evidence suggests non-polio enteroviruses (EVs) are a potential etiology, yet EV RNA is rarely detected in cerebrospinal fluid (CSF)2. CSF from children with AFM (n = 42) and other pediatric neurologic disease controls (n = 58) were investigated for intrathecal antiviral antibodies, using a phage display library expressing 481,966 overlapping peptides derived from all known vertebrate and arboviruses (VirScan). Metagenomic next-generation sequencing (mNGS) of AFM CSF RNA (n = 20 cases) was also performed, both unbiased sequencing and with targeted enrichment for EVs. Using VirScan, the viral family significantly enriched by the CSF of AFM cases relative to controls was Picornaviridae, with the most enriched Picornaviridae peptides belonging to the genus Enterovirus (n = 29/42 cases versus 4/58 controls). EV VP1 ELISA confirmed this finding (n = 22/26 cases versus 7/50 controls). mNGS did not detect additional EV RNA. Despite rare detection of EV RNA, pan-viral serology frequently identified high levels of CSF EV-specific antibodies in AFM compared with controls, providing further evidence for a causal role of non-polio EVs in AFM

Ionicity-dependent proton-coupled electron transfer of supramolecular self-assembled electroactive heterocycles

Herein, we investigate the electrochemical properties of a class of Supramolecular Self-associated Amphiphilic salts (SSAs). We show that varying ionic strength of an SSA solution can cause a switching of the thermodynamics and kinetics of electron transfer. The effect of self-assembly on proton-coupled electron transfer has implications for the understanding of electron transfer kinetics in aqueous organic redox flow batteries, especially at high concentration where organic–organic intermolecular interactions become dominant even for highly soluble organic species