A phase 2 trial of zanidatamab in HER2-overexpressed advanced endometrial carcinoma and carcinosarcoma (ZW25-IST-2)

OBJECTIVE

HER2 overexpression is associated with decreased overall survival in metastatic endometrial cancer. Trastuzumab with chemotherapy has demonstrated efficacy for first-line management of advanced HER2+ endometrial carcinoma, but HER2-directed therapy in the recurrent setting is limited. Zanidatamab (ZW25), a humanized, bispecific antibody that simultaneously binds the 2 distinct HER2 epitopes bound by trastuzumab and pertuzumab, has demonstrated safety and activity in HER2+ tumors. Here, we report the results of a phase 2, open-label study evaluating the efficacy and safety of zanidatamab in patients with HER2+ metastatic endometrial carcinoma/carcinosarcoma who received prior treatment.

METHODS

We enrolled 16 patients with HER2+ endometrial carcinoma/carcinosarcoma after progression on ≤2 lines of therapy on a single-arm phase 2 study of zanidatamab. The primary endpoint was overall response rate (ORR; complete or partial response) by Response Evaluation Criteria in Solid Tumors version 1.1. HER2 immunohistochemistry and fluorescence in situ hybridization (FISH) were performed on pretreatment samples. Intratumor HER2 genetic heterogeneity was assessed.

RESULTS

This study did not meet its primary efficacy endpoint. Although a clinical benefit rate of 37.5% was observed by 24 weeks, only 1 patient achieved a partial response (ORR, 6.2%). Eight patients had HER2 intratumor heterogeneity or lacked HER2 amplification by FISH. Decreased HER2 expression on repeat pretreatment samples was observed in 3 (75%) of 4 patients evaluated.

CONCLUSIONS

We observed a low response rate to zanidatamab in recurrent HER2+ endometrial carcinoma/carcinosarcoma, which may be driven by downregulation of HER2 expression. Repeat HER2 testing should be considered prior to second-line HER2-directed therapy.

CLINICALTRIALS

govidentifier: NCT04513665.

Durvalumab with or without tremelimumab in patients with persistent or recurrent endometrial cancer or endometrial carcinosarcoma: A randomized open-label phase 2 study

INTRODUCTION

Our understanding of the biologic heterogeneity of endometrial cancer has improved, but which patients benefit from single-agent versus combination immune checkpoint blockade remains unclear.

METHODS

We conducted a single-center, randomized, open-label, phase 2 study of durvalumab 1500 mg (Arm 1) versus durvalumab 1500 mg plus tremelimumab 75 mg every 4 weeks (Arm 2) in patients with endometrial carcinoma. The primary endpoints were overall response rate (ORR) and progression-free survival (PFS) at 24 weeks. Patients were stratified by mismatch repair (MMR) status and carcinosarcoma histology. Using a Simon two-stage minimax design, we determined 40 patients per arm would provide 90% power and Type 1 error of 10%.

RESULTS

Eighty-two patients were enrolled; 77 were evaluable for toxicity (Arm 1: 38, Arm 2: 39) and 75 evaluable for efficacy (Arm 1: 37, Arm 2: 38). Patient were stratified by MMR status (Arm 1: 5, Arm 2: 4 were MMR-deficient). The ORR in Arm 1 was 10.8% (one-sided 90% CI: 4.8-100%); the ORR in Arm 2 was 5.3% (one-sided 90% CI: 1.4-100%). Since the primary endpoint of ORR was not met, 24-week PFS was not compared to historical controls per protocol specification. No new safety signals were identified.

CONCLUSIONS

In these patients with predominantly MMR-proficient endometrial cancer, there was limited response with single-agent and combined immune checkpoint blockade. The pre-specified efficacy thresholds were not met for further evaluation. A deeper understanding of potential mechanisms of resistance to immunotherapy in MMR-proficient endometrial cancer is needed for the development of novel therapeutic approaches.

Small cell neuroendocrine carcinoma of the cervix: Analysis of prognostic factors and patterns of metastasis

•

A two-tier system (limited- or extensive-stage) has been used for small cell neuroendocrine carcinomas of the cervix.

•

Concordance probability estimates found that the 2018 FIGO staging system predicted outcome better than the two-tier system.

•

38% of patients had metastases at initial diagnosis, and an additional 38% at subsequent recurrence.

•

38 patients (60%) had brain imaging: 1 (3%) had brain metastasis at diagnosis and 8 (21%) at subsequent recurrence.

•

Providers should have a low threshold for brain imaging in patients with advanced disease or neurologic symptoms.

Objectives

To describe characteristics and outcomes of patients with small cell neuroendocrine carcinoma of the cervix (SCNCC) and determine the staging system most predictive of outcome—the two-tier (limited-stage [LS] vs. extensive-stage [ES]) or International Federation of Gynecology and Obstetrics (FIGO) staging system.

Methods

Patients with SCNCC evaluated at our institution from 1/1/1990–6/30/2021 were included. Medical records were reviewed for variables of interest. Appropriate statistical tests were performed to determine associations. Survival curves were created using the Kaplan-Meier method. Concordance probability estimates (CPEs) were calculated to evaluate the prediction probability of the staging systems.

Results

Of 63 patients, 41 had LS and 22 ES SCNCC. Patients with ES disease were significantly older than those with LS disease (median, 54 and 37 years, respectively; p < 0.001). Smoking status, race, and history of HPV were not associated with stage or outcomes. Forty-eight patients had metastatic disease (24 [50%] at initial diagnosis). The most common first sites of metastasis were lung (n = 20/48, 42%), lymph nodes (n = 19/48, 40%), and liver (n = 13/48, 27%). Nine patients had brain metastasis (8 symptomatic at recurrence; 1 asymptomatic at initial diagnosis). Both staging systems were associated with progression-free and overall survival. Adjusted CPE found the FIGO staging system was more predictive of outcomes than the two-tier staging system.

Conclusions

Providers should have a low threshold to obtain brain imaging for patients with SCNCC, especially in the presence of visceral metastases. FIGO staging should be used to classify SCNCC. Further research is necessary to understand prognostic factors of this rare disease.

310 T cell intrinsic DNA damage and repair response as a novel marker associated with clinical response to PD-1 blockade

Background

Despite the success of immune checkpoint blockade (ICB), many patients still fail to achieve durable clinical benefit. Previous studies have shown that CD8 T cells are reinvigorated by ICB. However, not all patients with this immunological response experience an effective clinical response, suggesting additional parameters may be relevant.DNA damage and repair (DDR) has been extensively studied in the context of inducing cell death of highly-proliferating tumor cells. However, whether T cell-intrinsic DDR impacts T cell differentiation and function, and how the coordination of DDR affects immunological and clinical response to proliferation-inducing ICBs have been largely unexplored. We hypothesized that the T celI-intrinsic DDR responses to proliferative and genotoxic stress might contribute to the disparity between immunological and clinical response.

Methods

To understand the impact of cell-intrinsic DDR on T cell differentiation and responses to cancer therapies, we developed a novel high-dimensional cytometry platform. This DDR-Immune platform enables simultaneous analysis of T cell differentiation state and multiple DDR pathways at single cell resolution. We then investigated immune reinvigoration and its association with DDR, in a cohort of chemotherapy-resistant hypermutated or microsatellite instability-high (MSI-H) uterine cancer patients treated with nivolumab. Peripheral blood samples were examined every 2–4 weeks after initiating anti-PD-1 treatment (N = 21).

Results

The DDR-Immune platform revealed consistent T cell subset specific patterns of DDR, as well as specific DDR pathways induced by different types of DNA damage, such as γ-irradiation (IR), UV irradiation (UV) or proliferative stress (i.e. anti-CD3/CD28 stimulation). For example, terminally differentiated effector cells had higher DNA damage accumulation and cell death. In contrast, stem cell memory (TSCM) and regulatory T cells (Treg) displayed high DDR with less cell death, suggesting better cell-intrinsic DDR against genotoxic stress for survival advantage. In hypermutated MSI-H uterine cancer patients, CD8 T cells underwent rapid pharmacodynamic proliferation 2–4 weeks after starting PD-1 blockade, which did not correlate with clinical response. Application of the DDR-Immune platform to this cohort revealed, however, that in clinical responders but not clinical non-responders, Ki67+ CD8 T cells responding to PD-1 blockade had rapid induction of DDR represented as a spike increase of phosphorylated-ATM, presumably adapting T cell ‘fitness’ in response to proliferative stress induced by PD-1 blockade.

Conclusions

Collectively, the new platform reveals previously unrecognized roles for T cell-intrinsic DDR as a novel determinant of immune responsiveness and clinical outcome to ICB and have potential application to other cancer therapies including chemotherapy and radiotherapy.

Ethics Approval

The study was approved by MSKCC Ethics Board, approval number 17–180 (NCT03241745).

BRCA Mutations, Homologous DNA Repair Deficiency, Tumor Mutational Burden, and Response to Immune Checkpoint Inhibition in Recurrent Ovarian Cancer

PURPOSE

Homologous DNA repair-deficient (HRD) ovarian cancers (OCs), including those with BRCA1/2 mutations, have higher levels of genetic instability, potentially resulting in higher immunogenicity, and have been suggested to respond better to immune checkpoint inhibitors (ICIs) than homologous DNA repair-proficient OCs. However, clinical evidence is lacking. The study aimed to evaluate the associations between BRCA1/2 mutations, HRD, and other genomic parameters and response to ICIs and survival in OC.

METHODS

This is a single-institution retrospective analysis of women with recurrent OC treated with ICIs. BRCA1/2 mutation status and clinicopathologic variables were abstracted from the medical records. Targeted and whole-exome sequencing data available for a subset of patients were used to assess tumor mutational burden (TMB), HRD, and fraction of genome altered (FGA). ICI response was defined as lack of disease progression for ≥ 24 weeks. Associations of BRCA1/2 status and genomic alterations with progression-free survival (PFS) and overall survival (OS) were determined using Cox proportional hazards models.

RESULTS

Of the 143 women treated with ICIs, 134 had known BRCA1/2 mutation status. Deleterious germline or somatic BRCA1/2 mutations were present in 31 women (24%). There was no association between presence of BRCA1/2 mutations and response (P = .796) or survival. Genomic analysis in 73 women found no association between TMB (P = .344) or HRD (P = .222) and response, PFS, or OS. There were also no significant differences in somatic genetic alterations between responders and nonresponders. High FGA was associated with an improvement in PFS (P = .014) and OS (P = .01).

CONCLUSION

TMB, BRCA1/2 mutations, and HRD are not associated with response or survival, cautioning against their use as selection criteria for ICI in recurrent OC. FGA should be investigated further as a biomarker of response to immunotherapy in OC.

Utility of serum CA-125 monitoring in patients with ovarian cancer undergoing immune checkpoint inhibitor therapy

OBJECTIVE

This study aimed to evaluate the utility of serum cancer antigen-125 (CA-125) levels to monitor patients with epithelial ovarian cancer (EOC) undergoing immune checkpoint inhibitor (ICI) therapy.

METHOD

This was a single-center retrospective review of all patients with EOC who were treated with ICI therapy from January 2013 to May 2017. This study compared the percentage change in baseline CA-125 in patients who had clinical benefit, defined as complete response, partial response, or stable disease by RECIST 1.1, with duration ≥24 weeks, versus those who did not. The groups were compared by Wilcoxon rank-sum test.

RESULTS

Fifty-nine (66%) of 89 patients who underwent ICI therapy had CA-125 data at baseline and during treatment. Of those who derived clinical benefit, 11/15 (73%) experienced an increase in CA-125 from baseline to end of treatment. Of those who did not derive clinical benefit, 36/44 (82%) experienced a CA-125 increase (p = 0.48). The average % increase from baseline to within 12 weeks of treatment initiation for patients with and without clinical benefit was 34% and 195%, respectively (p = 0.008).

CONCLUSION

Our analysis demonstrates a statistically significant difference in the magnitude of increase in CA-125 levels within the first 12 weeks of treatment between patients who achieved clinical benefit and those who did not. However, both groups of patients were equally likely to experience an increase in CA-125 within 12 weeks. These findings suggest that physicians should apply caution when using early CA-125 data to guide treatment decisions for patients with EOC undergoing ICI therapy.

Subsequent therapies and survival after immunotherapy in recurrent ovarian cancer

OBJECTIVES

Immune checkpoint inhibitors (ICIs) have modest activity in ovarian cancer (OC), yet little is known about their effects on subsequent treatment. Preclinical studies suggest immunotherapy may enhance response to chemotherapy. We sought to evaluate the impact of ICIs on subsequent therapies and survival in recurrent OC.

METHODS

A retrospective review was conducted to identify women with recurrent OC who received ICI from 01/2013 to 5/2017 and ≥1 subsequent treatment. Treatment duration after ICI was calculated using time-to-event analysis. Kaplan-Meier survival analysis and Cox proportional hazards models were used to calculate overall survival (OS) from first treatment after ICI and to assess survival differences by clinical benefit from ICI, defined by long (≥24 weeks) versus short (<24 weeks) ICI treatment duration.

RESULTS

Of 79 evaluable women identified, 66 (84%) had platinum-resistant OC. Median age at diagnosis was 57 years. Median time from diagnosis to ICI was 39.7 months, with median of 4 prior treatments (range, 1-12). Median number of treatments after ICI was 2 (range, 1-8). Median duration of first-line treatment after ICI was 3.7 months (95% CI, 2.9-6.0) and declined with each subsequent line. The most common therapies after ICI were taxanes, platinum-based regimens, and pegylated liposomal doxorubicin. Bevacizumab was used in 47 women (59%). Median OS after ICI was 18.3 months (95% CI, 11.8-22.7) and did not differ between long versus short ICI.

CONCLUSIONS

In this heavily pretreated population of patients with recurrent OC, therapies after ICI resulted in promising survival, suggesting that ICI may improve efficacy of subsequent chemotherapy.

Clinical Utility of Prospective Molecular Characterization in Advanced Endometrial Cancer

PURPOSE

Advanced-stage endometrial cancers have limited treatment options and poor prognosis, highlighting the need to understand genetic drivers of therapeutic vulnerabilities and/or prognostic predictors. We examined whether prospective molecular characterization of recurrent and metastatic disease can reveal grade and histology-specific differences, facilitating enrollment onto clinical trials.

EXPERIMENTAL DESIGN

We integrated prospective clinical sequencing and IHC data with detailed clinical and treatment histories for 197 tumors, profiled by MSK-IMPACT from 189 patients treated at Memorial Sloan Kettering Cancer Center.

RESULTS

Patients had advanced disease and high-grade histologies, with poor progression-free survival on first-line therapy (PFS₁). When matched for histology and grade, the genomic landscape was similar to that of primary untreated disease profiled by TCGA. Using multiple complementary genomic and mutational signature-based methods, we identified patients with microsatellite instability (MSI), even when standard MMR protein IHC staining failed. Tumor and matched normal DNA sequencing identified rare pathogenic germline mutations in BRCA2 and MLH1. Clustering the pattern of DNA copy-number alterations revealed a novel subset characterized by heterozygous losses across the genome and significantly worse outcomes compared with other clusters (median PFS₁ 9.6 months vs. 17.0 and 17.4 months; P = 0.006). Of the 68% of patients harboring potentially actionable mutations, 27% were enrolled to matched clinical trials, of which 47% of these achieved clinical benefit.

CONCLUSIONS

Prospective clinical sequencing of advanced endometrial cancer can help refine prognosis and aid treatment decision making by simultaneously detecting microsatellite status, germline predisposition syndromes, and potentially actionable mutations. A small overall proportion of all patients tested received investigational, genomically matched therapy as part of clinical trials.

Abstract CT035: A phase Ib study of miransertib (ARQ 092) in combination with anastrozole in patients with PIK3CA or AKT1-mutant ER+ endometrial or ovarian cancer

Background: Activating PI3K pathway mutations are common in endometrial and a subset of non-serous ovarian cancers and are frequently found in tumors that co-express the estrogen receptor (ER). We evaluated the safety and preliminary efficacy of miransertib, a potent pan-AKT inhibitor, in combination with the aromatase inhibitor (AI) anastrozole in pts with PIK3CA and AKT1-mutant ER+ endometrial and ovarian cancer.

Methods: Eligible patients included endometrial and ovarian cancer patients (pts) with ER+ by immunohistochemistry and a PIK3CA or AKT1 mutation documented by local sequencing assays. There was no limit to prior lines of therapy including prior AIs. Miransertib dose was escalated according to a 3+3 design. TEAEs were assessed per CTCAE v. 4.03. Tumor responses were evaluated per RECIST 1.1.

Results: A total of 11 pts (8 endometrial, 3 ovarian) were enrolled (median age 60 years). Pts were treated at one of 2 miransertib doses: 200 mg QD, 5 days on/9 days off (n=6) or 150 mg QD, 5 days on/9 days off (n=5). All pts received anastrozole 1 mg QD administered continuously. 2 DLTs observed (both at the miransertib 200mg): grade 3 ALT increase and grade 3 rash. Across all cycles, a total of 4 pts experienced a Grade 3 miransertib-related AE including rash (n=2), ALT increase (n=1), and hyperglycemia (n=1). There were no grade 4/5 miransertib-related AEs. Miransertib 150mg was selected as the recommended dose. 4 pts achieved a response (1 confirmed CR, 3 unconfirmed PRs - 1 pending confirmation, see Table). All responses (confirmed and unconfirmed) were in endometrial cancer (4/8 pts). In responding pts, mutations involved PIK3CA (n=3) and AKT1 (n=1). 50% (2/4) responding pts had received ≥1 prior line of endocrine therapy. Responses were ongoing in 2 of 4 patients, with the longest continuing at 60 weeks.

Conclusions: The combination of miransertib and anastrozole demonstrated a manageable safety profile and preliminary efficacy. Responses were observed in endometrial pts with PIK3CA or AKT1 mutation and those who had received prior endocrine therapy. Enrollment at the recommended combination dose is ongoing and updated response data will be presented.

*pt had PD at 24 weeks but continues for ongoing benefit at 56 weeks.Pt IDPrimary SiteHistologyGradeMutationLines of prior therapyBest RECIST response (confirmed)Duration on treatment (weeks)1EndometrialMixed endometriod/serous1PIK3CA H1047R3CR60+2EndometrialEndometriod2PIK3CA H1047R4uPR24*3EndometrialEndometriod1PIK3CA H1047R4SD124EndometrialSerous3PIK3CA R115L1PD85EndometrialEndometriod1PIK3CA E545K and H1047L2NE46OvarySerous3PIK3CA H1047R5PD77OvaryEndometriod1PIK3CA T1025S2PD88EndometrialSerous3PIK3CA N345K2uPR169OvarySerous3PIK3CA E542K5PD510EndometrialSerous3AKT1 E17K1uPR**12+11EndometrialSerous3PIK3CA C901F3PD9*pt had PD at 24 weeks but continues for ongoing benefit at 56 weeks**pending confirmation

Citation Format: David Hyman, Michael Bonafede, Roisin O'Cearbhaill, Rachel Grisham, Dmitriy Zamarin, William Tew, Carol Aghajanian, Karen Cadoo, Claire Friedman, Ron E. Savage, Feng Chai, Brian Schwartz, Vicky Makker. A phase Ib study of miransertib (ARQ 092) in combination with anastrozole in patients with PIK3CA or AKT1-mutant ER+ endometrial or ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr CT035.

Development of a battery of tests to measure attitudes and intended behaviours of dental students towards people with disability or those in marginalised groups

INTRODUCTION

Recommended curricula in Special Care Dentistry (SCD) outline learning objectives that include the domain of attitudes and behaviours, but these are notoriously difficult to measure. The aims of this study were (i) to develop a test battery comprising adapted and new scales to evaluate values, attitudes and intentions of dental students towards people with disability and people in marginalised groups and (ii) to determine reliability (interitem consistency) and validity of the scales within the test battery.

MATERIALS AND METHODS

A literature search identified pre-existing measures and models for the assessment of attitudes in healthcare students. Adaptation of three pre-existing scales was undertaken, and a new scale was developed based upon the Theory of Planned Behaviour (TPB) using an elicitation survey. These scales underwent a process of content validation. The three adapted scales and the TPB scale were piloted by 130 students at 5 different professional stages, from 4 different countries.

RESULTS

The scales were adjusted to ensure good internal reliability, variance, distribution, and face and content validity. In addition, the different scales showed good divergent validity.

DISCUSSION

These results are positive, and the scales now need to be validated in the field.

CONCLUSIONS

It is hoped that these tools will be useful to educators in SCD to evaluate the impact of teaching and clinical exposure on their students.

Hemodialysis-Associated Febrile Episodes: Surveillance before and after Major Alteration in the Water Treatment System

Surveillance for bacteremic or pyrogenic episodes associated with hemodialysis was undertaken before and after the reconstruction of the water treatment system at our University medical center. The new water system included a holding tank with iodination treatment. The water delivered to individual dialysis stations had only occasional positive bacterial cultures (3 of 21 samples before completion of construction, 2 of 16 samples afterwards) and intermittent detection of endotoxin (6 of 21 samples before completion of construction, 9 of 16 samples afterwards) at monthly sampling. Among 51 individual dialysis treatments (25 patients) before reconstruction and 56 treatments (29 patients), after, only 2 and 3 febrile events were identified, respectively. All of these were associated with underlying infectious illness and not with the hemodialysis procedure itself. Overall, we conclude that pyrogenic episodes associated directly with hemodialysis treatment are infrequent, and that the addition of a water storage tank with iodination treatment does not appear to increase the risk of bacteremia or pyrogenic episodes.

Evaluating Natural Language Processors in the Clinical Domain

Evaluating natural language processing (NLP) systems in the clinical domain is a difficult task which is important for advancement of the field. A number of NLP systems have been reported that extract information from free-text clinical reports, but not many of the systems have been evaluated. Those that were evaluated noted good performance measures but the results were often weakened by ineffective evaluation methods. In this paper we describe a set of criteria aimed at improving the quality of NLP evaluation studies. We present an overview of NLP evaluations in the clinical domain and also discuss the Message Understanding Conferences (MUC) [1-41. Although these conferences constitute a series of NLP evaluation studies performed outside of the clinical domain, some of the results are relevant within medicine. In addition, we discuss a number of factors which contribute to the complexity that is inherent in the task of evaluating natural language systems.

Extracting Findings from Narrative Reports: Software Transferability and Sources of Physician Disagreement

While natural language processing systems are beginning to see clinical use, it remains unclear whether they can be disseminated effectively through the health care community. MedLEE, a general-purpose natural language processor developed for Columbia-Presbyterian Medical Center, was compared to physicians' ability to detect seven clinical conditions in 200 Brigham and Women's Hospital chest radiograph reports. Using the system on the new institution's reports resulted in a small but measurable drop in performance (it was distinguishable from physicians at p = 0.011). By making adjustments to the interpretation of the processor's coded output (without changing the processor itself), local behavior was better accommodated, and performance improved so that it was indistinguishable from the physicians. Pairs of physicians disagreed on at least one condition for 22% of reports; the source of disagreement appeared to be interpretation of findings, gauging likelihood and degree of disease, and coding errors.

The kinematics of the California sea lion foreflipper during forward swimming

To determine the two-dimensional kinematics of the California sea lion foreflipper during thrust generation, a digital, high-definition video is obtained using a non-research female sea lion at the Smithsonian National Zoological Park in Washington, DC. The observational videos are used to extract maneuvers of interest--forward acceleration from rest using the foreflippers and banked turns. Single camera videos are analyzed to digitize the flipper during the motions using 10 points spanning root to tip in each frame. Digitized shapes were then fitted with an empirical function that quantitatively allows for both comparison between different claps, and for extracting kinematic data. The resulting function shows a high degree of curvature (with a camber of up to 32%). Analysis of sea lion acceleration from rest shows thrust production in the range of 150-680 N and maximum flipper angular velocity (for rotation about the shoulder joint) as high as 20 rad s⁻¹. Analysis of turning maneuvers indicate extreme agility and precision of movement driven by the foreflipper surfaces.

Similarity-based modeling applied to signal detection in pharmacovigilance

One of the main objectives in pharmacovigilance is the detection of adverse drug events (ADEs) through mining of healthcare databases, such as electronic health records or administrative claims data. Although different approaches have been shown to be of great value, research is still focusing on the enhancement of signal detection to gain efficiency in further assessment and follow-up. We applied similarity-based modeling techniques, using 2D and 3D molecular structure, ADE, target, and ATC (anatomical therapeutic chemical) similarity measures, to the candidate associations selected previously in a medication-wide association study for four ADE outcomes. Our results showed an improvement in the precision when we ranked the subset of ADE candidates using similarity scorings. This method is simple, useful to strengthen or prioritize signals generated from healthcare databases, and facilitates ADE detection through the identification of the most similar drugs for which ADE information is available.

Pretreatment vitamin D level and response to neoadjuvant chemotherapy in women with breast cancer on the I-SPY trial (CALGB 150007/150015/ACRIN6657)

Laboratory studies suggest that vitamin D (vitD) enhances chemotherapy-induced cell death. The objective of this study was to determine whether pretreatment vitD levels were associated with response to neoadjuvant chemotherapy (NACT) in women with breast cancer. Study patients (n = 82) were enrolled on the I-SPY TRIAL, had HER2-negative tumors, and available pretreatment serum. VitD levels were measured via DiaSorin radioimmunoassay. The primary outcome was pathologic residual cancer burden (RCB; dichotomized 0/1 vs. 2/3). Secondary outcomes included biomarkers of proliferation, differentiation, and apoptosis (Ki67, grade, Bcl2, respectively) and 3-year relapse-free survival (RFS). Mean and median vitD values were 22.7 ng/mL (SD 11.9) and 23.1 ng/mL, respectively; 72% of patients had levels deemed “insufficient” (<30 ng/mL) by the Institute of Medicine (IOM). VitD level was not associated with attaining RCB 0/1 after NACT (univariate odds ratio [OR], 1.01; 95% CI, 0.96–1.05) even after adjustment for hormone receptor status (HR), grade, Ki67, or body mass index (BMI). Lower vitD levels were associated with higher tumor Ki67 adjusting for race (OR, 0.95; 95% CI, 0.90–0.99). VitD level was not associated with 3-year RFS, either alone (hazard ratio [HzR], 0.98; 95% CI, 0.95–1.02) or after adjustment for HR, grade, Ki-67, BMI, or response. VitD insufficiency was common at the time of breast cancer diagnosis among women who were candidates for NACT and was associated with a more proliferative phenotype. However, vitD levels had no impact on tumor response to NACT or short-term prognosis.

Methods for identifying suicide or suicidal ideation in EHRs

Electronic health records contain important data elements for detection of novel adverse drug reactions, genotype/phenotype identification and psychosocial factor analysis, and the role of each of these as risk factors for suicidality warrants further investigation. Suicide and suicidal ideation are documented in clinical narratives. The specific purpose of this study was to define an algorithm for automated detection of this serious event. We found that ICD-9 E-Codes had the lowest positive predictive value: 0.55 (90% CI: 0.42-0.67), while combining ICD-9 and NLP had the best PPV: 0.97 (90% CI: 0.92-0.99). A qualitative analysis and classification of the types of errors by ICD-9 and NLP automated coding compared to manual review are also discussed.

Detection of pharmacovigilance-related adverse events using electronic health records and automated methods

Electronic health records (EHRs) are an important source of data for detection of adverse drug reactions (ADRs). However, adverse events are frequently due not to medications but to the patients' underlying conditions. Mining to detect ADRs from EHR data must account for confounders. We developed an automated method using natural-language processing (NLP) and a knowledge source to differentiate cases in which the patient's disease is responsible for the event rather than a drug. Our method was applied to 199,920 hospitalization records, concentrating on two serious ADRs: rhabdomyolysis (n = 687) and agranulocytosis (n = 772). Our method automatically identified 75% of the cases, those with disease etiology. The sensitivity and specificity were 93.8% (confidence interval: 88.9-96.7%) and 91.8% (confidence interval: 84.0-96.2%), respectively. The method resulted in considerable saving of time: for every 1 h spent in development, there was a saving of at least 20 h in manual review. The review of the remaining 25% of the cases therefore became more feasible, allowing us to identify the medications that had caused the ADRs.

Novel data-mining methodologies for adverse drug event discovery and analysis

An important goal of the health system is to identify new adverse drug events (ADEs) in the postapproval period. Datamining methods that can transform data into meaningful knowledge to inform patient safety have proven essential for this purpose. New opportunities have emerged to harness data sources that have not been used within the traditional framework. This article provides an overview of recent methodological innovations and data sources used to support ADE discovery and analysis.

Biclustering of adverse drug events in the FDA's spontaneous reporting system

In this article, we present a new pharmacovigilance data mining technique based on the biclustering paradigm, which is designed to identify drug groups that share a common set of adverse events (AEs) in the spontaneous reporting system (SRS) of the US Food and Drug Administration (FDA). A taxonomy of biclusters is developed, revealing that a significant number of bona fide adverse drug event (ADE) biclusters have been identified. Statistical tests indicate that it is extremely unlikely that the bicluster structures thus discovered, as well as their content, could have arisen by mere chance. Some of the biclusters classified as indeterminate provide support for previously unrecognized and potentially novel ADEs. In addition, we demonstrate the potential importance of the proposed methodology in several important aspects of pharmacovigilance such as providing insight into the etiology of ADEs, facilitating the identification of novel ADEs, suggesting methods and a rationale for aggregating terminologies, highlighting areas of focus, and providing an exploratory tool for data mining.

Prevalence of psychotropic medication use among cosmetic and medical dermatology patients: a comparative study

BACKGROUND

Little is known about the psychologic status of cosmetically oriented dermatology patients.

OBJECTIVE

We sought to determine the prevalence of psychotropic medication use among such patients to offer insight into the rates of psychopathology in this group.

METHODS

We conducted a retrospective chart review of patients seeking consultation at a cosmetic dermatology practice, recorded patients' use of psychotropic medicines, and compared this with data from a control group of medical dermatology patients.

RESULTS

Both groups reported rates of psychotropic medication use above those expected in the general population. There was no statistically significant difference in the prevalence of psychotropic drug use between cosmetic (18%) and medical (17%) dermatology patients.

LIMITATIONS

There is not a one-to-one correspondence between psychotropic medication use and the presence of psychopathology. Data are based on patient health histories and, thus, may be subject to underreporting.

CONCLUSIONS

There is a relatively high rate of psychotropic drug use among all patients seeking care from dermatologists, but this does not appear to be more common among patients interested in undergoing cosmetic procedures.

Biological nomenclatures: a source of lexical knowledge and ambiguity

There has been increased work in developing automated systems that involve natural language processing (NLP) to recognize and extract genomic information from the literature. Recognition and identification of biological entities is a critical step in this process. NLP systems generally rely on nomenclatures and ontological specifications as resources for determining the names of the entities, assigning semantic categories that are consistent with the corresponding ontology, and assignment of identifiers that map to well-defined entities within a particular nomenclature. Although nomenclatures and ontologies are valuable for text processing systems, they were developed to aid researchers and are heterogeneous in structure and semantics. A uniform resource that is automatically generated from diverse resources, and that is designed for NLP purposes would be a useful tool for the field, and would further database interoperability. This paper presents work towards this goal. We have automatically created lexical resources from four model organism nomenclature systems (mouse, fly, worm, and yeast), and have studied performance of the resources within an existing NLP system, GENIES. Using nomenclatures is not straightforward because issues concerning ambiguity, synonymy, and name variations are quite challenging. In this paper we focus mainly on ambiguity. We determined that the number of ambiguous gene names within the individual nomenclatures, across the four nomenclatures, and with general English ranged from 0%-10.18%, 1.187%-20.30%, and 0%-2.49% respectively. When actually processing text, we found the rate of ambiguous occurrences (not counting ambiguities stemming from English words) to range from 2.4%-32.9% depending on the organisms considered.

Hormonal regulation of interleukin-6 production in human adipocytes

OBJECTIVE

To elucidate the hormonal regulation of interleukin-6 (IL-6) production by human adipose tissue and its relation to leptin.

DESIGN

In vitro study. Human adipocytes were incubated with dexamethasone (with or without RU486), norepinephrine and epinephrine (with or without propranolol), or insulin.

MEASUREMENTS

IL-6 and leptin secretion by human adipocytes.

RESULTS

A gradual increase in IL-6 secretion by adipocytes during differentiation was observed. A positive correlation was found between basal IL-6 release and both glycerol 3-phosphate dehydrogenase activity--a marker of adipocyte differentiation-and leptin release. Dexamethasone decreased IL-6 secretion and increased leptin secretion in a dose-dependent manner. Both catecholamines increased IL-6 and leptin secretion. The effects of dexamethasone and catecholamines on IL-6 and leptin were abrogated by RU486 and propranolol, respectively. Incubation with insulin resulted in a dose-dependent stimulation of IL-6 and leptin secretion.

CONCLUSIONS

IL-6 is produced by human adipocytes and is a potential marker of adipocyte differentiation. Furthermore it is a hormonally regulated cytokine, suppressed by glucocorticoids, and stimulated by catecholamines and insulin in physiological concentrations.

GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles

Systems that extract structured information from natural language passages have been highly successful in specialized domains. The time is opportune for developing analogous applications for molecular biology and genomics. We present a system, GENIES, that extracts and structures information about cellular pathways from the biological literature in accordance with a knowledge model that we developed earlier. We implemented GENIES by modifying an existing medical natural language processing system, MedLEE, and performed a preliminary evaluation study. Our results demonstrate the value of the underlying techniques for the purpose of acquiring valuable knowledge from biological journals.

The efficacy and safety of once-daily Kytril (granisetron hydrochloride) tablets in the prophylaxis of nausea and emesis following fractionated upper abdominal radiotherapy

This multicenter, randomized, double-blind study compared the efficacy and safety of once-daily oral granisetron 2 mg (n = 134) and placebo (n = 126) as prophylaxis for nausea and emesis in patients receiving upper abdominal fractionated radiotherapy. Patients were scheduled to receive 10-30 fractions of radiotherapy; granisetron (two 1-mg tablets) or placebo was administered 1 hr before radiotherapy on each scheduled treatment day. Treatment comparisons were made at 24 hr and at 10 and 20 fractions. Patients treated with granisetron experienced greater emetic control than those treated with placebo as evidenced by median times to first emesis (35 vs. 9 days, p < 0.001) and first nausea (11 vs. 1 day, p < 0.001). Overall endpoint analysis showed that proportionally more granisetron than placebo patients were emesis free (57.5% vs. 42.1%, p = 0.0047) and nausea free (30.6% vs. 16.7%, p = 0.0042). Furthermore, 25% more granisetron-treated than placebo-treated patients were emesis free and 20% more were nausea free on at least 80% of study treatment days. The most commonly reported adverse experiences in granisetron-treated patients were diarrhea, asthenia, and constipation. These findings demonstrate that a once-daily, 2-mg dose of oral granisetron is well tolerated and significantly more effective than placebo in preventing nausea and emesis induced by fractionated radiotherapy to the upper abdomen.

Identification of non-functional human VNO receptor genes provides evidence for vestigiality of the human VNO

In mammals, the vomeronasal organ (VNO) contains chemosensory receptor cells that bind to pheromones and induce a variety of social and reproductive behaviors. It has been traditionally assumed that the human VNO (Jacobson's organ) is a vestigial structure, although recent studies have shown minor evidence for a structurally intact and possibly functional VNO. The presence and function of the human VNO remains controversial, however, as pheromones and VNO receptors have not been well characterized. In this study we screened a human Bacterial Artificial Chromosome (BAC) library with multiple primer sets designed from human cDNA sequences homologous to mouse VNO receptor genes. Utilizing these BAC sequences in addition to mouse VNO receptor sequences, we screened the High Throughput Genome Sequence (HTGS) database to find additional human putative VNO receptor genes. We report the identification of 56 BACs carrying 34 distinct putative VNO receptor gene sequences, all of which appear to be pseudogenes. Sequence analysis indicates substantial homology to mouse V1R and V2R VNO receptor families. Furthermore, chromosomal localization via FISH analysis and RH mapping reveal that the majority of the BACs are localized to telomeric and centromeric chromosomal localizations and may have arisen through duplication events. These data yield insight into the present state of pheromonal olfaction in humans and into the evolutionary history of human VNO receptors.

Transcriptional activity of multiple copies of a subtelomerically located olfactory receptor gene that is polymorphic in number and location

We report here on the transcriptional activity of multiple copies of a subtelomerically located olfactory receptor (OR) gene, OR-A. Due to recent duplication events, both the copy number and chromosomal location of OR-A vary among humans. Sequence analyses of 180 copies of this gene, derived from 12 chromosome ends in 22 individuals, show that the main coding exon of all but one copy is an intact open reading frame with 0-5 predicted amino acid differences. We detected transcription of OR-A in both olfactory epithelium and testis tissue using RT-PCR amplification with primers designed on the basis of a computationally predicted gene structure. Two alternatively spliced forms of transcripts, one encoding an isoform with an extended N-terminus, were found in both tissues. A third transcript, derived from a second promoter, was also observed in testes. The start methionine is predicted in all transcripts to lie in an upstream exon rather than the main coding exon, as is typical for most other OR genes. By examining sequence variants among transcripts, we show that transcription of this gene occurs at multiple chromosomal locations. Our results lend credence to the idea that OR diversity could be generated in rearrangement-prone subtelomeric regions and show that polymorphism in subtelomeric regions could lead to individual-to-individual variation in the expressed repertoire of OR genes.

Electronic chart review as an aid to postdischarge surgical site surveillance: increased case finding

BACKGROUND

At the University of Michigan Hospitals and Health Centers, there is increasing use of an electronic medical record. Because orthopedic surgeons dictate all outpatient visits to the patient's electronic record, total knee arthroplasties were chosen to determine whether the use of electronic medical records increased case finding.

METHODS

All patients who underwent a total knee arthroplasty during the study period (1996-1999) were followed prospectively with the use of the National Nosocomial Infection Surveillance System definitions. Traditional surveillance methods were used to ascertain infections. In addition, each patient's postdischarge outpatient clinic chart was reviewed electronically for 1 year after operation.

RESULTS

From 1996 to 1999, 555 procedures were performed. Overall, 25 infections were identified after operation. Seven infections were identified through traditional surveillance methods, which resulted in an average surgical site infection rate of 1.3%. The use of electronic chart review surveillance after discharge revealed a rate of 4.5%, which was significantly higher than traditional surveillance (P <.01). Eighteen of 25 infections (72%) would not have been identified with the use of traditional surveillance methods.

CONCLUSION

Postdischarge electronic chart review enhanced case finding significantly, which resulted in a more accurate infection rate. Awareness should be given to the institutions' surveillance methods and intensity when comparing to published rates.

Disambiguating ambiguous biomedical terms in biomedical narrative text: an unsupervised method

With the growing use of Natural Language Processing (NLP) techniques for information extraction and concept indexing in the biomedical domain, a method that quickly and efficiently assigns the correct sense of an ambiguous biomedical term in a given context is needed concurrently. The current status of word sense disambiguation (WSD) in the biomedical domain is that handcrafted rules are used based on contextual material. The disadvantages of this approach are (i) generating WSD rules manually is a time-consuming and tedious task, (ii) maintenance of rule sets becomes increasingly difficult over time, and (iii) handcrafted rules are often incomplete and perform poorly in new domains comprised of specialized vocabularies and different genres of text. This paper presents a two-phase unsupervised method to build a WSD classifier for an ambiguous biomedical term W. The first phase automatically creates a sense-tagged corpus for W, and the second phase derives a classifier for W using the derived sense-tagged corpus as a training set. A formative experiment was performed, which demonstrated that classifiers trained on the derived sense-tagged corpora achieved an overall accuracy of about 97%, with greater than 90% accuracy for each individual ambiguous term.

Genomic analysis of orthologous mouse and human olfactory receptor loci

Olfactory receptor (OR) genes represent approximately 1% of genomic coding sequence in mammals, and these genes are clustered on multiple chromosomes in both the mouse and human genomes. We have taken a comparative genomics approach to identify features that may be involved in the dynamic evolution of this gene family and in the transcriptional control that results in a single OR gene expressed per olfactory neuron. We sequenced approximately 350 kb of the murine P2 OR cluster and used synteny, gene linkage, and phylogenetic analysis to identify and sequence approximately 111 kb of an orthologous cluster in the human genome. In total, 18 mouse and 8 human OR genes were identified, including 7 orthologs that appear to be functional in both species. Noncoding homology is evident between orthologs and generally is confined within the transcriptional unit. We find no evidence for common regulatory features shared among paralogs, and promoter regions generally do not contain strong promoter motifs. We discuss these observations, as well as OR clustering, in the context of evolutionary expansion and transcriptional regulation of OR repertoires.

A homogeneous fluorometric assay for measuring cell adhesion to immobilized ligand using V-well microtiter plates

We have developed a homogeneous high-capacity assay format for measuring integrin- and selectin-dependent cell binding to immobilized ligand using V-well microtiter plates. 2',7'-Bis(2-carboxyethyl)-5-(and-6)-carboxylfluorescence, acetoxymethylester-labeled cells are added to ligand-coated V-shaped microtiter wells. Bound cells are separated from free cells using centrifugal force to produce shear stress. Nonadherent cells accumulate in the nadir of the well and are measured using a fluorescence plate reader. Antibody or low-molecular-weight inhibitors of either the ligand or the cell surface receptor result in less cell binding, more cells in the pellet, and increased signal. The optimization and validation of the very late antigen-4/vascular cell adhesion molecule-1 assay is described in detail. We demonstrate that this assay can be rapidly adapted to measure other integrin- and selectin-mediated interactions. This assay format has several advantages over conventional assays. The centrifugal process is biologically relevant and eliminates the washing steps to remove nonadherent cells that can cause well-to-well and plate-to-plate variation. Because the assay is robust with a high signal-to-noise ratio and low variability, it is ideally suited for studying multiple parameters of cell adhesion and for high capacity screening.

Efficacy of intravenous granisetron to control nausea and vomiting during multiple cycles of cisplatin-based chemotherapy

The safety and efficacy of granisetron (10 micrograms/kg and 40 micrograms/kg) were evaluated during a second (n = 393) and third (n = 200) cycle of chemotherapy in this multicenter, double-blind, randomized, parallel-group study. Granisetron was administered as a single intravenous dose before the start of cisplatin chemotherapy (> or = 60 mg/m2). Total control (no vomiting, no retching, no nausea, and no use of antiemetic rescue medication) after the first 24 hr following chemotherapy was achieved in 40% and 49% of patients in Cycles 2 and 3, respectively, for the 10 micrograms/kg group, and in 42% and 38% of patients in Cycles 2 and 3, respectively, for the 40 micrograms/kg group. Both dose levels of granisetron were well tolerated. The results demonstrate comparable efficacy between the 10 micrograms/kg and 40 micrograms/kg doses of granisetron in preventing nausea and vomiting during repeat cycles of high-dose cisplatin-based chemotherapy. The results of this study show that granisetron 10 micrograms/kg is safe and well tolerated, and remains effective with repeat cycle use.

Randomized trial of supplemental beta-carotene to prevent second head and neck cancer

Beta-carotene has established efficacy in animal models of oral carcinogenesis and has been shown to regress oral precancerous lesions in humans. The purpose of this study was to see whether these effects extended to the prevention of oral/pharyngeal/laryngeal (head and neck) cancer in humans. The subject population for this randomized, placebo-controlled, double-blinded clinical trial included 264 patients who had been curatively treated for a recent early-stage squamous cell carcinoma of the oral cavity, pharynx, or larynx. Patients were assigned randomly to receive 50 mg of beta-carotene per day or placebo and were followed for up to 90 months for the development of second primary tumors and local recurrences. After a median follow-up of 51 months, there was no difference between the two groups in the time to failure [second primary tumors plus local recurrences: relative risk (RR), 0.90; 95% confidence interval (CI), 0.56-1.45]. In site-specific analyses, supplemental beta-carotene had no significant effect on second head and neck cancer (RR, 0.69; 95% CI, 0.39-1.25) or lung cancer (RR, 1.44; 95% CI, 0.62-3.39). Total mortality was not significantly affected by this intervention (RR, 0.86; 95% CI, 0.52-1.42). Whereas none of the effects were statistically significant, the point estimates suggested a possible decrease in second head and neck cancer risk but a possible increase in lung cancer risk. These effects are consistent with the effects observed in trials using intermediate end point biological markers in humans, in which beta-carotene has established efficacy in oral precancerous lesions but has no effect or slightly worsens sputum cytology, and in animal carcinogenicity studies, in which beta-carotene has established efficacy in buccal pouch carcinogenesis in hamsters but not in animal models of respiratory tract/lung carcinogenesis, with some suggestions of tumor-promoting effects in respiratory tract/lung. If our results are replicated by other ongoing/completed trials, this suggests a critical need for mechanistic studies addressing differential responses in one epithelial site (head and neck) versus another (lung).

A physical map of the human genome

The human genome is by far the largest genome to be sequenced, and its size and complexity present many challenges for sequence assembly. The International Human Genome Sequencing Consortium constructed a map of the whole genome to enable the selection of clones for sequencing and for the accurate assembly of the genome sequence. Here we report the construction of the whole-genome bacterial artificial chromosome (BAC) map and its integration with previous landmark maps and information from mapping efforts focused on specific chromosomal regions. We also describe the integration of sequence data with the map.