A genomic case study of mixed fibrolamellar hepatocellular carcinoma

We report the first comprehensive genomic analysis of a case of mixed conventional and fibrolamellar HCC (mFL-HCC). This study confirms the expression of DNAJB1:PRKACA, a fusion previously associated with pure FL-HCC but not conventional HCC, in mFL-HCC. These results indicate the DNAJB1:PRKACA fusion has diagnostic utility for both pure and mixed FL-HCC.

Background

Mixed fibrolamellar hepatocellular carcinoma (mFL-HCC) is a rare liver tumor defined by the presence of both pure FL-HCC and conventional HCC components, represents up to 25% of cases of FL-HCC, and has been associated with worse prognosis. Recent genomic characterization of pure FL-HCC identified a highly recurrent transcript fusion (DNAJB1:PRKACA) not found in conventional HCC.

Patients and Methods

We performed exome and transcriptome sequencing of a case of mFL-HCC. A novel BAC-capture approach was developed to identify a 400 kb deletion as the underlying genomic mechanism for a DNAJB1:PRKACA fusion in this case. A sensitive Nanostring Elements assay was used to screen for this transcript fusion in a second case of mFL-HCC, 112 additional HCC samples and 44 adjacent non-tumor liver samples.

Results

We report the first comprehensive genomic analysis of a case of mFL-HCC. No common HCC-associated mutations were identified. The very low mutation rate of this case, large number of mostly single-copy, long-range copy number variants, and high expression of ERBB2 were more consistent with previous reports of pure FL-HCC than conventional HCC. In particular, the DNAJB1:PRKACA fusion transcript specifically associated with pure FL-HCC was detected at very high expression levels. Subsequent analysis revealed the presence of this fusion in all primary and metastatic samples, including those with mixed or conventional HCC pathology. A second case of mFL-HCC confirmed our finding that the fusion was detectable in conventional components. An expanded screen identified a third case of fusion-positive HCC, which upon review, also had both conventional and fibrolamellar features. This screen confirmed the absence of the fusion in all conventional HCC and adjacent non-tumor liver samples.

Conclusion

These results indicate that mFL-HCC is similar to pure FL-HCC at the genomic level and the DNAJB1:PRKACA fusion can be used as a diagnostic tool for both pure and mFL-HCC.

Effectiveness of a group opt-in session on uptake and graduation rates for pulmonary rehabilitation

Pulmonary rehabilitation (PR) is an effective intervention in the treatment of patients with chronic obstructive pulmonary disease (COPD). Unfortunately some patients offered this treatment either fail to take up the offer or fail to complete the course. Studies have indicated a number of factors influencing uptake and completion rates. We describe the introduction of an intervention, the group opt-in session (GOIS), prior to individualised baseline assessment and entry to the PR course, with the intention being to improve uptake and completion rates. A 1.5-hour-long GOIS was offered as the first face-to-face contact to all patients referred for PR. Drop-out rates at all stages of the pathway from referral to graduation were collected on 200 patients prior to the introduction of the GOIS (non-GOIS group) and compared to the first 400 patients following introduction (the GOIS group). Possible independent predictors of course uptake and completion were examined in the GOIS group. The proportion of referred patients taking up the offer of individualised baseline assessment or a GOIS was similar (75% vs. 72.2%, p value not significant [ns]). However, since in the GOIS group the opt-in session preceded the individualised baseline assessment and some patients opted-out, a smaller proportion of referred patients underwent this assessment than in the non-GOIS group (58.7% vs. 75%, p < 0.001). In addition, dropouts following individualised baseline assessments were also reduced (7% vs. 22%, p < 0.001). Both of these factors reduced ‘wasted’ assessments. Similar proportions of patients referred began the PR course in both groups (53% vs. 51.7%, ns), but a higher proportion of patients graduated in the GOIS group (87.9% vs. 76.4%, p < 0.05). Drop-out rates due to illness were similar in both groups (8.5% pre vs. 6.8% post, ns). However, drop-out rates not due to illness were much higher in the non-GOIS group (15.1% vs. 5.3%, p < 0.001). In the GOIS group, patients who did not attend the GOIS were, on average, younger (64.6 years vs. 69.7 years, p < 0.001) and had a higher mean percent predicted Forced Expiratory Volume (50.6% vs. 43.8%, p < 0.05) than those that did attend. A greater proportion of patients who opted in to the GOIS and attended the PR course lived less than 25 minutes from the PR centre than either those who did not attend the GOIS or who attended and then opted out (77.4% vs. 63%, p<0.005). The GOIS improved the graduation rates at The North Bristol Lung Centre PR Course and reduced wasted assessments. There was no effect on initial uptake. Analysis of the behaviour of patients invited to a GOIS suggested that age, lung function and travel distance were important factors influencing patient choice.

Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis

Comparative sequence analysis has facilitated the discovery of protein coding genes and important functional sequences within proteins, but has been less useful for identifying functional sequence elements in nonprotein-coding DNA because the relatively rapid rate of change of nonprotein-coding sequences and the relative simplicity of non-coding regulatory sequence elements necessitates the comparison of sequences of relatively closely related species. We tested the use of comparative DNA sequence analysis to aid identification of promoter regulatory elements, nonprotein-coding RNA genes, and small protein-coding genes by surveying random DNA sequences of several Saccharomyces yeast species, with the goal of learning which species are best suited for comparisons with S. cerevisiae. We also determined the DNA sequence of a few specific promoters and RNA genes of several Saccharomyces species to determine the degree of conservation of known functional elements within the genome. Our results lead us to conclude that comparative DNA sequence analysis will enable identification of functionally conserved elements within the yeast genome, and suggest a path for obtaining this information.

Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana

The higher plant Arabidopsis thaliana (Arabidopsis) is an important model for identifying plant genes and determining their function. To assist biological investigations and to define chromosome structure, a coordinated effort to sequence the Arabidopsis genome was initiated in late 1996. Here we report one of the first milestones of this project, the sequence of chromosome 4. Analysis of 17.38 megabases of unique sequence, representing about 17% of the genome, reveals 3,744 protein coding genes, 81 transfer RNAs and numerous repeat elements. Heterochromatic regions surrounding the putative centromere, which has not yet been completely sequenced, are characterized by an increased frequency of a variety of repeats, new repeats, reduced recombination, lowered gene density and lowered gene expression. Roughly 60% of the predicted protein-coding genes have been functionally characterized on the basis of their homology to known genes. Many genes encode predicted proteins that are homologous to human and Caenorhabditis elegans proteins.

Office-based surgery and cost avoidance in an obstetrics and gynecology residency program

AUDIENCE

This article is designed both for graduate medical educators and financial officers of teaching hospitals.

GOAL

To present the financial and clinical implications of a resident-run, attending-supervised office-based surgery center.

OBJECTIVES

1. Describe the recent changes in volume of patients available for resident education in obstetrics and gynecology. 2. Describe the accounting method of calculating the cost of office versus hospital outpatient procedures. 3. Describe the financial and educational benefits of an office-based surgery program run by residents with the supervision of attending physicians.

Effect of aspirin and ifetroban on skeletal muscle blood flow in patients with congestive heart failure treated with Enalapril. Ifetroban Study Group

OBJECTIVES

The purpose of this study was to determine the acute and chronic effects of cyclooxygenase inhibition with aspirin and thromboxane A2 receptor blockade with ifetroban on the chronic vasodilating effects of enalapril in the skeletal muscle circulation of patients with heart failure.

BACKGROUND

Angiotensin-converting enzyme inhibition and antiplatelet therapy with aspirin independently reduce the risk for subsequent nonfatal coronary events in survivors of myocardial infarction. The safety of the combined administration of angiotensin-converting enzyme inhibitors and aspirin has been questioned due to their divergent effects on the vascular synthesis of vasodilating prostaglandins.

METHODS

Forearm blood flow (ml/min/100 ml) at rest and during rhythmic handgrip exercise and after transient arterial occlusion was determined by strain gauge plethysmography before and 4 h and six weeks after combined administration of enalapril with either aspirin, ifetroban or placebo in a multicenter, double-blind, randomized trial of 62 patients with mild to moderate heart failure.

RESULTS

Before randomization, forearm hemodynamics were similar in the three treatment groups except for increased resting forearm blood flow and decreased resting forearm vascular resistance in the aspirin group when compared with the placebo group. After combined administration of enalapril and study drug for 4 h and six weeks, changes from prerandomization values of mean arterial pressure, forearm blood flow and forearm vascular resistance at rest, during handgrip exercise and after transient arterial occlusion did not differ among the three treatment groups.

CONCLUSIONS

These findings demonstrate that the vasodilating effects of enalapril in the skeletal muscle circulation of patients with heart failure are not critically dependent on prostaglandin pathways.

First reported case of hantavirus pulmonary syndrome in Oklahoma

Hantavirus Pulmonary Syndrome (HPS) is a condition of rapidly progressive pulmonary failure with a case-fatality rate of almost 50 percent. Rodents serve as the reservoir for hantaviruses and human infection occurs primarily via aerosolized virus in rodent excreta. The rodent reservoir for the disease is widespread across Oklahoma and the first case of HPS has recently been confirmed in an Oklahoma resident. Physicians should suspect HPS in a previously healthy person who develops a febrile illness and respiratory insufficiency and has potentially been exposed to the virus. Common laboratory findings include a left-shifted neutrophilic leukocytosis, elevated hematocrit and thrombocytopenia. Therapy is supportive. If HPS is suspected, the patient should be immediately transferred to a facility that can provide aggressive supportive care.

Precise mapping and characterization of the RNA primers of DNA replication for a yeast hypersuppressive petite by in vitro capping with guanylyltransferase

The active origins of DNA replication for yeast (Saccharomyces cerevisiae) mitochondrial DNA share 280 conserved base pairs and have a promoter. Since intact replication intermediates retain their initiating ribonucleotide triphosphate, we used guanylyltransferase to in vitro cap the replication intermediates present in restriction enzyme-cut DNA from an ori-5 hypersuppressive petite. Restriction mapping and RNA sequencing of these labeled intermediates showed that each DNA strand is primed at a single discrete nucleotide, that one primer starts at the promoter and that the other primer starts 34 nt away, outside the conserved region. Deoxyribonuclease digestion of the capped fragments left resistant RNA primers, which enabled identification of zones of transition from RNA to DNA synthesis. Some of the results contradict the prevailing model for priming at the yeast mitochondrial origins.

Adverse events after discontinuing medications in elderly outpatients

BACKGROUND

Discontinuation of drug therapy is an important intervention in elderly outpatients receiving multiple medications, but it may be associated with adverse drug withdrawal events (ADWEs).

OBJECTIVE

To determine the frequency, types, timing, severity, and factors associated with ADWEs after discontinuing medications in elderly outpatients.

PATIENTS

One hundred twenty-four ambulatory elderly participants in 1-year health service intervention trial at the Durham Veterans Affairs General Medicine Clinic in Durham, NC, who stopped taking medications.

METHODS

A geriatrician retrospectively reviewed computerized medication records and clinical charts to determine medications no longer being taken and adverse events in the subsequent 4-month period. Possible ADWEs, determined by using the Naranjo causality algorithm, were categorized by therapeutic class, organ system, and severity.

RESULTS

Of 238 drugs stopped, 62 (26%) resulted in 72 ADWEs among 38 patients. Cardiovascular (42%) and central nervous system (18%) drug classes were most frequently associated with ADWEs. The ADWEs most commonly involved the circulatory (51%) and central nervous (13%) systems, and 88% were attributed to exacerbations of underlying disease. Twenty-six ADWEs (36%) resulted in hospitalization or an emergency department or urgent care clinic visit. Only the number of medications stopped was associated with ADWE occurrence (adjusted odds ratio, 1.89; 95% confidence interval, 1.33-2.67).

CONCLUSIONS

Most medications can be stopped in elderly outpatients without an ADWE occurrence. However, when ADWEs occur they resulted in substantial health care utilization. Practitioners should strive to discontinue drug therapy in the elderly but be vigilant for disease recurrence.

Case report: locally acquired trichinosis in an immigrant from Southeast Asia

The authors report a case of trichinosis acquired in Oklahoma City by an immigrant from Southeast Asia. The 49-year-old female reported having abdominal discomfort, nausea, and vomiting, and had purchased and eaten lightly cooked pork. She also complained of fatigue, anorexia, and muscle aches for several months. An immigrant from Laos, she stated that she regularly eats pork and prefers it rare or mildly cooked. The authors caution local physicians to be aware of the increased risk of trichinosis among Southeast Asian immigrants in the area, particularly those from Laos and Cambodia. Continued emphasis on the need to thoroughly cook all pork products is necessary if the incidence of trichinosis in the U.S. is to be controlled.

HIV seroprevalence in Oklahoma childbearing women

From October 1989 through September 1990, we conducted an unlinked seroprevalence survey in Oklahoma to determine the prevalence of human immunodeficiency virus, type 1 (HIV) in women at the time of childbirth. Blood specimens obtained from 41,809 newborns in conjunction with the state's newborn metabolic screening program were tested for HIV after personal identifiers were removed. The overall HIV seroprevalence rate was 0.02% (10/41,809). Rates were highest for mothers aged 30 to 39 years (0.06%, 3/5,158). No difference was found between the HIV seroprevalence rates for women residing in standard metropolitan areas (MSAs) of the state (0.03%, 6/21,105) and women residing in non-metropolitan areas (0.03%, 3/11,904). When compared to other states where surveys have been done, Oklahoma's rate of HIV infection in childbearing women was low.

Advances in antineoplastic therapy

Despite advances in early diagnosis and treatment of cancer, more than a million new cases of cancer will have been diagnosed in 1990, with an estimated 10% mortality within a year of diagnosis. Thus, the search continues for new or improved antineoplastic agents with a wide spectrum of activity and decreased toxicity. The major advances in single-agent antineoplastic drug therapy include the introduction of cisplatin almost 20 years ago and of etoposide (VP-16) in the mid-1980s. However, within the past two years, analogues of existing antineoplastic agents have been purified and marketed. These drugs offer an enhanced therapeutic index when used alone or in combination with other therapies as well as decreased toxicity and, thus, may enhance patient tolerance.

Ondansetron: a new entity in emesis control

Nausea and vomiting are serious problems for patients receiving cancer chemotherapy. Dopamine receptor and cholinergic receptor antagonism have been the target mechanism for agents used to combat drug-induced nausea and vomiting; more recently, blockade of serotonin receptors has been used for this indication. Current therapies are limited by extrapyramidal adverse effects, as well as drowsiness, sedation, respiratory depression, and cardiac effects. Ondansetron is an investigational serotonin antagonist that has documented effectiveness for cancer chemotherapy-induced emesis. Ondansetron appears to be well tolerated, with the possible exception of headaches and transient increases in liver enzymes. No extrapyramidal toxicities have been reported with this agent. While ondansetron looks promising, further studies are needed to fully define its role as an antiemetic.

Early postoperative intraperitoneal chemotherapy as an adjuvant therapy to surgery for peritoneal carcinomatosis from gastrointestinal cancer: pharmacological studies

Gastrointestinal malignancy may spread to peritoneal surfaces in the absence of lymphatic or hematogenous metastases. To treat peritoneal carcinomatosis, a uniformly lethal disease process, extensive cytoreductive surgery and i.p. chemotherapy were combined. Early postoperative i.p. chemotherapy was instilled in the first few days after the surgical procedure in an attempt to treat anatomic sites that would be sealed off by postoperative adhesions. Mitomycin C was given on the first postoperative day at two doses, 10 and 12 mg/m2. 5-Fluorouracil was given on postoperative days 2-5 at 15 and 20 mg/kg, respectively. Median area under the curve ratio i.p./i.v. was 117 for 5-fluorouracil and 21.6 for mitomycin C. Elevated intraportal levels of drug were observed for i.p. 5-fluorouracil but not for mitomycin C. The marked pharmacokinetic advantage of postoperative i.p. suggests that this treatment strategy should be considered in a clinical trial in patients at risk for progression of peritoneal carcinomatosis.

Rationale for integrating early postoperative intraperitoneal chemotherapy into the surgical treatment of gastrointestinal cancer

A new concept in the natural history of gastrointestinal (GI) cancer suggests that recurrence of this malignancy can be separated into two types. Hematogenous and lymphatic metastases occur before surgical removal of the primary cancer. The spread of cancer to the resection site and to peritoneal surfaces occurs at the time of surgical removal of the primary tumor. Surgical trauma leads to a dispersal of malignant tumor emboli, which then implant within the raw tissue surfaces of the resection site and abraded peritoneal surfaces. Instillation of chemotherapy directly into the peritoneal cavity, as part of GI surgery, provides cytotoxic levels of drug that may change the natural history of GI cancer. The most common sites of disease recurrence have been, in the past, at the resection site and on peritoneal surfaces. With the optimal use of intraperitoneal chemotherapy, these sites of surgical treatment failure should no longer occur. Early phase I and II and pharmacologic studies suggest that an effective dose and schedule have been achieved, that toxicity is at reasonable levels, and that responses with small volumes of intra-abdominal cancer are exceptionally high. Chemotherapy that has an impact on the surgical event by decreasing cancer spread to the resection site and to peritoneal surfaces may significantly improve survival and quality of life in patients with GI cancer.

Acral erythema secondary to high-dose cytosine arabinoside with pain worsened by cyclosporine infusions

Acral erythema after high-dose cytosine arabinoside (Ara-C) has been described as a painful, sharply demarcated, and intense erythema of the palms and soles. This phenomenon occurred and is described in three out of three allogeneic bone marrow transplant (BMT) recipients who received high-dose Ara-C and total-body irradiation for conditioning therapy via the same protocol. These patients also received cyclosporine and methotrexate as prophylaxis for acute graft-versus-host disease. Two of the three patients experienced an increase in the pain associated with acral erythema during cyclosporine infusions and required large doses of narcotic analgesics. Since alcohol intensifies the pain of stomatitis and cyclosporine is manufactured in an alcohol base, the high alcohol content is suspect as the causative factor for this adverse reaction/drug interaction.

Drug-induced toxicities associated with high-dose cytosine arabinoside infusions

The frequency and significance of central nervous system (CNS), ocular, and dermatologic toxicities associated with high-dose cytosine arabinoside (HDARA-C) infusions was evaluated. Patients were selected from one of three Southeastern Cancer Study Group protocols using HDARA-C 2-3 g/m2 body surface area (BSA) and their medical records were reviewed to identify and document the frequency of the toxicities. Those exhibiting CNS toxicity were compared across age, sex, race, previous standard-dose ARA-C or HDARA-C therapy, and infusion rate for toxicity occurrence. Statistical analysis was performed using Fisher's exact test with p less than 0.05. Of the 53 patients evaluated, 37.7% exhibited CNS, 37.7% ocular, and 45.3% dermatologic toxicities. Of the risk factors evaluated, only increasing age and previous ARA-C therapy approached statistical significance. The CNS toxicities associated with HDARA-C are clinically significant since permanent damage may result. Ocular and dermatologic toxicities usually resolve without medical intervention when HDARA-C therapy is discontinued. Further study is necessary to determine appropriate prophylaxis for these toxicities.

On the interaction of cobra venom protein cardiotoxins with erythrocytes

The principally active hemolytic toxin (cardiotoxin) previously purified from the venom of the Thailand cobra, Naja naja siamensis, was shown to produce spontaneous twitching, contractures and membrane depolarization in sartorius muscles from the frog, Rana pipiens. Spontaneous twitching, observed at concentrations greater than 0.1 uM was completely abolished by addition of tetrodotoxin and not affected by d-tubocurarine. Dose and time dependent membrane depolarization of muscle fibers was observed to occur within 10-30 min at 0.2 to 1.0 uM concentrations of the toxin. These observations, taken together with an amino acid analysis characteristic of previously described cobra venom cardiotoxins, characterized this hemolytic toxin as a cardiotoxin. In the absence of EDTA the initial velocities of erythrocyte hemolysis for this toxin showed a sigmoidal concentration dependence which became hyperbolic in the presence of EDTA. The largest increases in hemolysis rates on addition of 1 mM EDTA were observed at low toxin concentrations. In the presence of EDTA extracellular and membrane associated divalent cations are complexed, thus alleviating their competition with toxin for binding to the membrane, a key and apparently rate-determining initial step which leads to hemolysis. In the presence of EDTA hemolysis rates increased linearly at low toxin concentration and reached an extrapolated maximum value at toxin concentrations at which, given its molecular dimensions, there are just sufficient toxin molecules to cover the entire membrane surface area provided by the erythrocytes.

Treatment of L-asparaginase allergic reaction

The treatment of an allergic reaction to L-asparaginase is discussed in the presentation of a case of a 26-year-old man with chronic myelogenous leukemia who was undergoing methotrexate-L-asparaginase rescue therapy. The possible mechanism of action of L-asparaginase is reviewed, and precautions for use of L-asparaginase in combination therapy with methotrexate are presented.

Late sequelae of allergic bronchopulmonary aspergillosis

Seven patients with late sequelae of allergic bronchopulmonary aspergillosis (ABPA) are described. All seven had significant chronic symptoms from asthma. At the time of diagnosis of ABPA all patients had marked irreversible pulmonary function abnormalities; symptoms of chronic bronchitis were present in all. Pulmonary fibrosis was present in six of seven patients. Three patients have died from irreversible lung disease with terminal cardiac failure. Despite the difficulty in establishing an early diagnosis of ABPA, its importance must be emphasized in order to attempt to prevent progression of the disease to severe irreversible and potentially fatal end-stage lung disease.