Alternative poly-adenylation modulates α1-antitrypsin expression in chronic obstructive pulmonary disease

α1-anti-trypsin (A1AT), encoded by SERPINA1, is a neutrophil elastase inhibitor that controls the inflammatory response in the lung. Severe A1AT deficiency increases risk for Chronic Obstructive Pulmonary Disease (COPD), however, the role of A1AT in COPD in non-deficient individuals is not well known. We identify a 2.1-fold increase (p = 2.5x10-6) in the use of a distal poly-adenylation site in primary lung tissue RNA-seq in 82 COPD cases when compared to 64 controls and replicate this in an independent study of 376 COPD and 267 controls. This alternative polyadenylation event involves two sites, a proximal and distal site, 61 and 1683 nucleotides downstream of the A1AT stop codon. To characterize this event, we measured the distal ratio in human primary tissue short read RNA-seq data and corroborated our results with long read RNA-seq data. Integrating these results with 3' end RNA-seq and nanoluciferase reporter assay experiments we show that use of the distal site yields mRNA transcripts with over 50-fold decreased translation efficiency and A1AT expression. We identified seven RNA binding proteins using enhanced CrossLinking and ImmunoPrecipitation precipitation (eCLIP) with one or more binding sites in the SERPINA1 3' UTR. We combined these data with measurements of the distal ratio in shRNA knockdown experiments, nuclear and cytoplasmic fractionation, and chemical RNA structure probing. We identify Quaking Homolog (QKI) as a modulator of SERPINA1 mRNA translation and confirm the role of QKI in SERPINA1 translation with luciferase reporter assays. Analysis of single-cell RNA-seq showed differences in the distribution of the SERPINA1 distal ratio among hepatocytes, macrophages, αβ-Tcells and plasma cells in the liver. Alveolar Type 1,2, dendritic cells and macrophages also vary in their distal ratio in the lung. Our work reveals a complex post-transcriptional mechanism that regulates alternative polyadenylation and A1AT expression in COPD.

0162 Mental Stress Compromises Human Sleep Through a Biological, Not Psychological, Pathway

Introduction

The extent to which mental stress causes sleep disturbance is unknown as experimental studies of stress and sleep have yielded mixed results. Potential mechanisms linking stress to poor sleep are also poorly characterized. The current study aimed to 1) assess the impact of experimentally-induced mental stress on daytime sleep and 2) test candidate mechanisms including physiological and emotional stress reactivity, stress rumination, attentional threat bias, and insensitivity to future consequences.

Methods

Participants (N=30) were randomized to a control (n=14) or stress group (n=16). Both groups were given a 60-minute nap opportunity at midday (≈13:30). Prior to sleep, participants in the stress group completed a socially evaluative mental arithmetic stress task and were instructed that they would be required to give a brief speech upon awakening. Sleep was monitored with polysomnography and scored according to standard AASM criteria. Measures of heart rate (HR), blood pressure (BP) and self-reported stress were recorded during the stress task. Self-reported stress rumination was measured upon awakening. Attentional threat bias was measured using an emotional dot probe and performance on the Iowa Gambling Task quantified insensitivity to future consequences.

Results

Acute mental stress significantly increased HR and BP (all p<.001, all Cohen’s d>1.24) and participants reported significant increases in self-reported stress (p<.001). The stress group exhibited longer sleep latency (p=.038, d=.82), shorter sleep duration (p=.044, d=.78), and worse sleep continuity (p=.045, d=.79). Subjective sleep quality was not different across groups (p=.39, d=.32). Of all candidate mechanisms, physiological reactivity was the only one significantly related to sleep measures. Greater HR reactivity predicted longer sleep latency (r=.37), shorter sleep duration (r=-.59), and worse sleep continuity (r=-.59).

Conclusion

Acute mental stress caused significant disturbances in a single episode of daytime sleep. The degree of disturbance was, to an extent, predicted by the amount of physiological reactivity to stress.

Support

This work was supported a Washington and Lee University Summer Lenfest Grant and the Summer Research Scholars Program.

P3-04-01: Molecular Characterization of African Breast Cancer; Results from a Large Tissue Microarray Study

Introduction: Breast cancer in African women has been understudied for decades. Evidence derived mainly from studies on African-American women, supports that tumours of black women are biologically different and more aggressive than those occurring in the white population. Of the 4 main taxonomic groups of breast cancer, basal tumours are more represented in those women. In the present state of knowledge, very little is known about the biology and molecular profile of breast cancer in Africa. The aim of this study was to test the hypothesis that the molecular profile of African breast cancer is distinct from its Western counterpart. This was achieved by collecting a large cohort of breast carcinomas from an indigenous African population for phenotypical characterization and testing for expression of potential predictive and prognostic markers.

Methods: Breast tumours were collected via collaboration with five centres in Nigeria (the most populous country in Africa) and assembled into tissue microarrays (TMAs). All tumours were reviewed by a specialist breast pathologist following the Royal College of Pathologists (RCPath) guidelines to confirm diagnosis, type, grade and nodal status. Patients age, tumour size and clinical data, where available, were collected from the original pathology reports and case notes. Representative tumour areas were selected and marked for TMA construction. TMA sections were stained for a range of markers including hormone receptors (ERα, ERβ, PR, AR), cyclin D, HER2, Ki67, bcl2, basal (CK5/6, CK14) and luminal cytokeratins (CK18, 19).

Results: A total of 830 tumours were assembled into TMAs. The mean age at diagnosis was 47.69yrs with 58% of patients presenting under the age of 50. Only 8.5% of tumours were of grade 1. Most tumours (87%) were of ductal no special type, followed by lobular and metaplastic carcinomas. The majority of the tumours were ERα, PR and HER2 negative (77%, 80% and 81% respectively). The triple negative tumours were the predominant phenotype (55.6%). Luminal A type tumours comprised 24.3% followed by the HER2 positive (13.9%) and luminal B tumours (6.2%). The differences of all those parameters were statistically highly significant (p<0.001). Most tumours expressed ERß including 75% of those that were ERα/PR negative. A large proportion of the tumours (22%) were of the basal phenotype of which two thirds were also triple negative. Over half of the triple negative tumours were also node positive.

Hierarchal cluster analysis showed the basal tumours dendrogram to comprise two groups; one showing clustering of ***ERα/PR/HER2 and the second showing clustering of ERß with CK5 and CK14.

Conclusion: To our knowledge, this is largest and most comprehensive study of African breast cancer to date. Our data confirms the hypothesis that African breast cancer is biologically distinct and shows remarkable differences in histological type, grade, hormone receptors & HER2 status when compared with breast cancer in white women. The early age at presentation, predominance of high grade and triple negative, but not necessarily basal phenotype, may explain the poor prognosis and requires tailoring treatment strategies to target this unique profile.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P3-04-01.

Report of an international expanded access program of imatinib in adults with Philadelphia chromosome positive leukemias

BACKGROUND

Imatinib is a selective inhibitor of the BCR/ABL tyrosine kinase. The remarkable initial results of the first phase I clinical trial published in 1999 prompted the rapid initiation of large phase II trials. They also generated intense media coverage and significant interest from patients and clinicians and demand for access to imatinib before marketing approval. In response, a worldwide expanded access program (EAP) for imatinib was implemented in May 2000.

PATIENTS

In total, 7380 patients with chronic myeloid leukemia (CML) and acute lymphoblastic leukemia failing prior therapies were enrolled in 106 centers in 34 countries.

RESULTS

Time to progression and overall survival, as well as the safety profile, were similar to those observed in published phase II studies. At the end of the program, patients benefiting from treatment were continued on imatinib therapy by transferring to national health care systems or patient assistance programs.

CONCLUSION

The imatinib EAP successfully provided therapy to patients with CML before marketing approval. The program provides an efficient framework for the development of global EAPs for innovative investigational anticancer agents in patients without a satisfactory therapeutic alternative.

The impact of non-compliance with imatinib (IM) therapy on health care costs

6083

Background: While compliance to drug therapy is vital to receive optimal patient benefits, the costs of delivering adequate medical care for cancer patients remain an important consideration for society and payers. This study examined the relationship between compliance with IM therapy and health care costs for patients with CML and GIST. Methods: Claims data from 6/1/01–3/31/04 from a US health plan were used to identify non-Medicare IM-treated patients with a CML or GIST diagnosis who had continuous pharmacy and medical benefits in the 3 months prior and 12 months following initiation of IM therapy. Compliance was defined by medication possession ratio (MPR=total days IM supply in the first year ÷365) and patients were stratified into three segments by MPR (<50%, 50–90%, 90–100%). Total health care costs include hospital, laboratory testing, office, ER, and pharmacy charges. Disease-related health care costs were also analyzed. Multivariate analyses were used to examine the relationship between MPR and first-year health care costs, controlling for age, sex, number of medications, initial starting dose, diagnosis (CML or GIST), year of initial IM fill, and complications due to underlying disease. Results: Total 878 IM-treated patients were identified of whom 413 had at least 15 months of continuous eligibility. Of these, 307 were non-Medicare CML or GIST patients. Total health care costs per patient in the first year of therapy in MPR < 50%, 50–90%, and 90–100% groups were $163,828, $53,924, and $40,924 respectively (p < 0.001). The corresponding numbers for disease-related health care costs were $103,118, $36,436, and $34,086 (p<0.001). Controlling for the variables listed above, a 10% increase in MPR is associated with a 5% decrease in total health care costs (p=0.021). Similar association was found between MPR and disease-related health care costs. Conclusions: Improved compliance with imatinib therapy is associated with decreased total health care costs and disease-related health care costs. Improving compliance to imatinib therapy may not only optimize clinical outcomes but may also reduce the overall societal burden of health care costs associated with cancer.

[Table: see text]

Compliance and persistency with imatinib

6038

Background: Imatinib is an oral therapy with efficacy in chronic myelogenous leukemia (CML) and gastrointestinal stromal tumors (GIST). Optimal dosing and adherence to treatment is critical to achieve the best clinical outcomes. This study examined compliance and persistency with imatinib and identified the clinical and patient characteristics related to compliance. Methods: Claims data from a US health plan were used to identify imatinib-treated patients from 6/1/01–3/31/04 who had continuous pharmacy and medical benefits in the 3 months prior and 12 months following initiation of imatinib therapy, and a diagnosis of CML or GIST (ICD-9-CM 205.1, 205.10, or 205.11 for CML; 159.0, 159.8, or 159.9 for GIST). Compliance was defined by medication possession ratio (MPR = total days supply of imatinib in the first year divided by 365). Persistency was defined as failure to refill imatinib within 30 days from the run-out date of the prior prescription. Multivariate analyses were used to identify key factors associated with compliance. Results: Total 878 imatinib-treated patients were identified of whom 413 had at least 15 months’ continuous eligibility. Sixty-nine percent (n = 286) were diagnosed with CML, 8% (n = 34) with GIST, and 23% (n = 93) with neither. Results are presented for CML and GIST patients. The average age was 51 and 58% were males. The average starting daily dose was 424 mg, with 80% (n = 255) initiating on 400 mg daily. The mean MPR was 76%. Overall, 28% patients discontinued imatinib for at least 30 consecutive days during the 1-year follow up period. Multivariate analyses indicated MPR improved with age until age 51 and then deteriorated (p < 0.001) but at a diminishing rate, decreased as the number of medications increased (p < 0.001), and was lower in women (p = 0.005) and patients with more cancer complications (p < 0.001). In addition, women were more likely to discontinue than men (OR = 2.08; p = 0.003). Conclusions: Compliance to imatinib was about 75% with 30% of patients interrupting therapy for at least 30 consecutive days in the first year. It has been found that interruption of imatinib therapy may lead to rapid tumor progression in GIST (PASCO05 Le Cesne #9031). Not having patients take the correct doses on a regular basis may lead to sub therapeutical clinical outcomes.

[Table: see text]

Portable ultrasonic scanning of the anterior neck before percutaneous dilatational tracheostomy

We used portable ultrasound scans to identify relevant anatomical structures in the necks of 30 patients before percutaneous tracheostomy. We identified the tracheal midline, thyroid isthmus and blood vessels and located a safe level for needle insertion. Anterior jugular veins were seen in 15 patients; eight were near the midline and were considered vulnerable. Three veins were more than 4 mm in diameter and these larger vessels were electively ligated. Four patients had arteries which were considered vulnerable to damage. All patients underwent successful percutaneous tracheostomy. Portable ultrasound provides a simple method of screening for vulnerable blood vessels in the neck and for locating the midline before percutaneous tracheostomy. This method is particularly suitable for patients with landmarks that are difficult to visualise or palpate. Based on the ultrasonic findings we can make an informed decision about referral for surgical tracheostomy.

Portable ultrasound for difficult central venous access

Central venous catheterization can be difficult and can cause serious complications. Ultrasound-guided venous access is increasingly used but reports concern only routine cases. We performed a prospective observational study in 'difficult' or 'failed' procedures to assess the usefulness of ultrasound guidance. We used the technique in 33 patients; 23 had previous failed attempts or had suffered complications from such attempts. Ultrasound provided an anatomical reason for failure in 16 patients. Ten other patients were expected to be difficult before catheterization. Ultrasound identified a suitable site for catheterization in all 33 patients. Real-time ultrasound was used to successfully catheterize 22 patients. In nine patients, a surface landmark technique was used, which failed in three patients. In these three patients, ultrasound guidance allowed successful cannulation. Ultrasound guidance is a useful technique to aid central venous access when difficulties or complications have been encountered or anticipated.

Osteoporotic fracture complicating Guillain-Barré syndrome

Guillain–Barré syndrome is an acute inflammatory demyelinating polyradiculoneuropathy often associated with a prolonged period of immobilization. Between 71 and 80% of patients make a full or near full recovery, but there is a 5–11% mortality and the remainder have an incomplete recovery (Rees, 1995; The Italian Guillain–Barré Study Group, 1996). The paralysed patient with Guillain–Barré is susceptible to the complications of immobility: venous thromboembolism, hypostatic pneumonia and contractures. Osteoporosis is a silent, poorly recognized risk and contributes to significant morbidity and increased hospital stay.

Hepatic artery aneurysms: evaluation using three-dimensional spiral CT angiography

Hepatic artery aneurysms are rare and frequently difficult to diagnose. Computed tomography (CT) and ultrasound rarely make the definitive diagnosis and angiography is usually required. We present three cases of hepatic artery aneurysms in which the definitive diagnosis was made on three-dimensional (3-D) spiral CT angiography-to our knowledge, this has not previously been described. Our experience shows that in many cases of hepatic artery aneurysm, conventional angiography need only be performed as a prelude to embolization.

[Mini-probe ultrasound of the upper gastrointestinal tract--1995 state of the art and perspectives. Workshop on Mini-Probe Ultrasound in Gastroenterology, Münster, 28 October 1995]

Endoscopic ultrasound (EUS) allows for intraluminal sonographic imaging of the oesophagus, stomach, pancreatobiliary duct system, the papilla of Vater, as well as the colon and rectum. EUS has proved valuable for diagnosis and staging of tumours of the upper intestinal tract. EUS can also provide valuable additional information concerning lesions that cannot be immediately classified. As doing this involves, first, removal of the conventional endoscope and, second, insertion of the echo endoscope, EUS is not suitable for routine examinations. Therefore EUS has remained an independent endoscopic diagnostic modality. Moreover, due to their diameter conventional echoendoscopes cannot be inserted into the pancreatobiliary duct system. Fine calibre high frequency ultrasound probes promise a resolution of less than 2 mm in diameter. The following report is a summary of a one-day workshop which took place in Muenster, Germany on Oct. 28, 1995. Its goal was to define the current state of the art of miniaturised endoscopic ultrasound probes in the field of gastroenterology. During this workshop, possible clinical applications for diagnosis, therapy, as well as follow-up were described and discussed. The potential of miniaturised endoscopic ultrasound probes was explored in terms of possible future technical developments.

Upper intestinal surveillance in familial adenomatous polyposis

Our understanding of the natural history of upper gastrointestinal (GI) involvement in familial adenomatous polyposis (FAP) is still evolving, although we know that the main cause of death after colectomy in FAP is upper GI malignancy, affecting 5% of patients. The aim of duodenal surveillance is to target high risk individuals and identify cancers early. We have screened 200 patients prospectively and have observed that duodenal polyposis progresses slowly, but there are some young people who have severe disease who merit close observation. We pay particular attention to endoscopic technique and histological detail, and use a duodenal staging system. Patients are offered randomisation to studies of chemopreventive agents, and those with advanced disease are considered for surgery. Successful management is inhibited by our deficient knowledge of the natural history of upper gastrointestinal polyposis, and by our inability to identify high risk individuals with histological markers rather than because of any technological deficiencies in endoscopic equipment.

Aziridinylbenzoquinone in recurrent, progressive glioma of the central nervous system. A Phase II study by the Illinois Cancer Council

Aziridinylbenzoquinone (AZQ) was studied in a Phase II protocol for persons with glioma of the central nervous system (CNS) recurrent or progressive after surgery and radiotherapy. Patients received AZQ, 30 mg/m2 intravenously every 3 weeks if previously untreated or 27.5 mg/m2 if previously exposed to cytotoxic drugs. Partial response was defined as a reduction of at least 50% reduction in the product of the two longest perpendicular diameters of the indicator lesion persisting for a minimum of 28 days. Twenty-eight patients are evaluable for response at this time. Objective response (OR) occurred in four (14.3%): two complete and two partial. Stabilization of disease (SD) was seen in 7 (25.0%). Median survival, in weeks, was greater than 46.0 for responders, 41.7 for SD, and 19.3 for those with progressive disease. The survival experiences are significantly different (P = 0.030 [Breslow]). The OR rate was 21.1% in 19 without prior chemotherapy and 0% in 9 previously treated patients. There were two AZQ-related deaths in patients with prior exposure to nitrosoureas (1 CNS hemorrhage; 1 aspiration pneumonia). One patient had an anaphylactic reaction. Three patients whose tumor initially increased in size subsequently had marked tumor shrinkage. AZQ is an active agent that must be used with added caution in patients who have received nitrosoureas. Initial tumor enlargement may precede response. Although response appears to prolong survival, the correlation between stabilization of disease and survival is not well-defined.

Cooperative groups and community hospitals. Measurement of impact in the community hospitals

The Eastern Cooperative Oncology Group, composed of major cancer treatment centers, has an outreach program which involves community hospitals in ongoing cancer clinical trials. A prevalence survey was carried out in February 1981 among 104 community hospitals and 21 member institutions to determine the characteristics of patients being treated, their staffing, and reasons why patients were not on protocol studies. The survey sampled 25 (50) consecutive patients from community hospitals (member institutions). The purpose of the study was to assess the impact of a community cancer control program. The results of the study demonstrated that 16% of patients surveyed in the affiliated community hospitals were being treated on a research protocol. In addition, a further 35% had their treatment plan influenced by a protocol. Consequently protocols have impacted directly or indirectly on 51% of the patients. The corresponding figures in member institutions were 23% and 38% for a total of 61%. In studying protocol availability, it was found that 66% of all patients were ineligible for any protocol. Of patients eligible for a protocol but not registered on one, 52% were not registered because of physician preference for a specific treatment. The affiliates surveyed were shown to be on average half as large as member institutions in terms of number of beds and staff size. Also, staff/patient ratios are generally smaller in the community hospitals. The median age of patients was considerably lower than SEER incidence data. Also, elderly patients were slightly more prevalent in community hospitals than in member institutions. A clear relationship between disease stage and age in breast cancer patients was noted with the representation of early-stage disease much higher in young women.

Primary sclerosing cholangitis associated with inflammatory bowel disease in Cape Town, 1975 - 1981

Patients with inflammatory bowel disease and serum alkaline phosphatase persistently raised to more than twice the normal level were investigated to assess the frequency of primary sclerosing cholangitis (PSC) in the Gastro-intestinal Clinic from 1975 to 1981. Twelve patients had a persistently raised alkaline phosphatase level of hepatic origin, 9 out of 250 with ulcerative colitis and 3 out of 164 with Crohn's disease. PSC was demonstrated in 8(3%) of the patients with ulcerative colitis, and carcinoma of the pancreas in the remaining 1. Three of the patients with PSC also had gallstones. The colitis antedated the biliary symptoms and signs in all but 1 patient. There was no correlation between the duration, extent and activity of the colitis and the development and outcome of the liver involvement. Investigations in the 3 patients with Crohn's disease revealed the presence of PSC in 2 (1,2%) and chronic active hepatitis in the 3rd. Of the 2 with PSC, one had cholelithiasis and has had recurrent episodes of cholangitis. The other has had only mild symptoms.

Ranitidine heals duodenal ulcers

A double-blind placebo-controlled study of ranitidine 150 mg given twice daily for 4 weeks was carried out in 80 ambulant patients with endoscopically proven duodenal ulceration. Fifteen patients were withdrawn because of poor compliance or default. Of the remaining 65 patients, endoscopic healing (with or without residual erosion) was noted in 28 of the 34 ranitidine-treated patients (82%) and in 14 of the 31 placebo-treated patients (45%) (P less than 0.005). Twenty-three patients whose ulcers were unhealed after 4 weeks of ranitidine therapy or placebo were then given ranitidine for a further 4-week period. Four of these patients were withdrawn, but ulcer healing was achieved in 16 of the remaining 19 patients (4 out of 5 (80%) initially treated with ranitidine and 12 of 14 (86%) initially treated with placebo). No significant clinical, biochemical or haematological adverse reactions were noted in either treatment group. It is concluded that ranitidine is a safe and effective therapy in patients with duodenal ulceration and that initial unsuccessful treatment with placebo does not appear to influence the subsequent response to ranitidine.

Cholangiopancreatography and pancreatic cytology in carcinoma of the pancreas

Twenty-three histologically proved cases of carcinoma of the pancreas were investigated preoperatively with endoscopic retrograde cholangiopancreatography and cytologic examination of pure pancreatic juice collected after secretin stimulation. In 12 cases in which radiology was highly suggestive of carcinoma, cytology confirmed the result in seven. When radiologic findings were equivocal, cytology was helpful in two of six cases. Cytology was most helpful in the patients in whom no diagnosis could be reached radiologically due to tumor invasion of the structures adjacent to the papilla. Malignant cells were found in all cases.

Whole-gut perfusion for therapeutic purgation

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