Computational identification of specific splicing regulatory elements from RNA-seq in lung cancer.

BACKGROUND: Lung cancer is the most common cause of cancer-related death worldwide. Recently, deep transcriptional sequencing has been used as an effective genomic assay to get an insight into this disease. AIM: This study is carried out to identify specific regulatory elements (SREs) in lung cancer. MATERIALS AND METHODS: The RNA-sequencing data on lung cancer sample and normal sample were downloaded from NCBI. TopHat and Cufflinks were used to analyze differential alternative splicing in lung cancer by using RNA-sequencing data. Further, we searched specific SREs in lung cancer through finding over-represented hexamers around high expression exons. RESULTS: According to the Jensen-Shannon divergence between two samples and the p-value of t-test, we found 53 genes with differential alternative splicing in lung cancer. In the analysis of SREs, we found 763 specific SREs between lung cancer sample and normal sample. CONCLUSIONS: These results may give an insight into how alternative splicing causes differential expression in lung cancer.

MiR-31 aggravates inflammation and apoptosis in COPD rats via activating the NF-κB signaling pathway.

OBJECTIVE: To study the effect of micro ribonucleic acid (miR)-31 on rats with chronic obstructive pulmonary disease (COPD) by activating the nuclear factor-κB (NF-κB) signaling pathway. MATERIALS AND METHODS: A total of 36 Sprague-Dawley rats were randomly divided into normal group (n=12), model group (n=12) and miR-31 mimics group (n=12). The rats were fed normally in normal group. In model group, the COPD model was first established, followed by intervention using normal saline. In miR-31 mimics group, the COPD model was also first established, followed by intervention using miR-31 mimics. The expression of NF-κB was detected via immunohistochemistry. Protein expressions of B-cell lymphoma-2 (Bcl-2) and Bcl-2 associated X protein (Bax) were determined through Western blotting. Serum levels of interleukin-6 (IL-6), IL-18 and tumor necrosis factor-α (TNF-α) were measured via enzyme-linked immunosorbent assay (ELISA). Moreover, the apoptosis was examined via terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) assay, and the relative expression of miR-31 was detected by means of quantitative polymerase chain reaction (qPCR). RESULTS: The immunohistochemistry results showed that the positive expression of NF-κB was significantly higher in the other two groups than that in normal group (p<0.05), while it was also remarkably higher in miR-31 mimics group than that in model group (p<0.05). The results of Western blotting revealed that the relative protein expression of Bax significantly increased, while that of Bcl-2 notably declined in the other two groups compared with those in normal group (p<0.05). Similarly, the relative protein expression of Bax was upregulated, while that of Bcl-2 was distinctly reduced in miR-31 mimics group compared with those in model group (p<0.05). It was found via ELISA that the model group and miR-31 mimics group had evidently higher levels of IL-6, IL-18 and TNF-α than those in normal group (p<0.05), while miR-31 mimics group also had prominently higher levels than those in model group (p<0.05). In addition, according to the TUNEL assay, the apoptosis rate remarkably increased in the other two groups in comparison with that in normal group (p<0.05), while it remarkably rose in miR-31 mimics group compared with that in model group (p<0.05). Finally, a significantly higher expression of miR-31 was observed in the other two groups than that in normal group via qPCR (p<0.05), and such a higher expression was also found in miR-31 mimics group than that in model group (p<0.05). CONCLUSIONS: MiR-31 aggravates inflammation and apoptosis in COPD rats by activating the NF-κB signaling pathway.

Bevacizumab plus chemotherapy for patients with advanced pulmonary adenocarcinoma harboring EGFR mutations.

PURPOSE: Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) and bevacizumab plus chemotherapy were effective for EGFR-mutant patients. However, the appropriated treatment orders remained controvertible. We investigated the efficacy of treatment orders between bevacizumab plus chemotherapy and EGFR-TKIs for EGFR-mutant patients with advanced pulmonary adenocarcinoma. PATIENTS AND METHODS: This study involved 40 EGFR-mutant patients with advanced pulmonary adenocarcinoma who were treated with bevacizumab plus carboplatin and paclitaxel (Bev + CP) and EGFR-TKIs in different treatment orders or gemcitabine plus cisplatin (GP) in first-line setting. Seventeen patients were treated with Bev + CP and 10 cases with GP in first-line treatment. Thirteen patients received EGFR-TKIs after first-line Bev + CP regimen, while 13 patients were treated with first-line EGFR-TKIs. Progression-free survival (PFS), the response rate (ORR) and overall survival (OS) were evaluated. RESULTS: Median PFS of Bev + CP treatment was significantly longer in first-line than non-first-line settings (11.7 vs. 5.6 months, P = 0.003). Median OS was 37.8 months for EGFR-mutant patients with first-line Bev + CP followed by second-line EGFR-TKIs and 31.0 months for those with first-line EGFR-TKIs and non-first-line Bev + CP, respectively (P = 0.509). Median PFS was 11.7 (95% CI 10.6-12.8) months for Bev + CP group and 4.7 (95% CI 4.4-5.0) months for GP group with the hazard ratio of 0.17 (P = 0.001). ORR was 70.6 and 50.0% in the two groups, respectively (P = 0.415). However, there was no significant difference in median OS (33.7 vs 27.8 months, P = 0.293). CONCLUSIONS: First-line Bev + CP followed by EGFR-TKIs might possibly provide favorable prognosis for EGFR-mutant patients. Bev + CP regimen significantly prolonged PFS in first-line than non-first-line settings. These findings warrant further investigations.

Improved treatment results for childhood acute myeloid leukemia in Taiwan.

To improve treatment results for children with de novo acute myeloid leukemia (AML), we introduced a novel protocol, Taiwan Pediatric Oncology Group-AML-97A, for AML other than acute promyelocytic leukemia (APL), for which modified conventional protocols were used. From January 1, 1997, to December 31, 2002, 141 children younger than 17 years old with de novo AML were enrolled. In total, 117 patients with non-APL AML were treated with induction therapy of idarubicin and cytarabine (Ara-C), postremission therapy with high-dose Ara-C - containing regimens for four monthly courses, and moderate-dose therapy with idarubicin and Ara-C for four monthly courses. The first 19 patients with APL were treated with all-trans retinoic acid, idarubicin and Ara-C, with the remaining five patients receiving all-trans retinoic acid and idarubicin, followed by maintenance therapy for 2 years. Stem cell transplantation was performed in 29 patients in first remission with a similar outcome as chemotherapy alone. The remission rate in the AML-97A study was 90%, the 5-year survival 51 +/- 5.3% (s.e.) and the 5-year event-free survival 50 +/- 4.8%; for APL, these were 100%, 86 +/- 7.0, and 75 +/- 9.8%. For the whole group, the 5-year survival was 57 +/- 4.7% and the 5-year event-free survival 54 +/- 4.4%. The AML-97A regimen was well tolerated.

Dose-dependent transthyretin inhibition of T4 uptake from cerebrospinal fluid in sheep.

Transthyretin (TTR), synthesized by the choroid plexuses (CP) has an important role in transporting thyroxine from blood to cerebrospinal fluid (CSF). However, the role of TTR on thyroxine transport from CSF to either blood or brain is not clear. By using the incubated isolated ovine brain tissues technique, we found the CP accumulated most 125I-T4 compared to ventricular ependymal, frontal cortex or cerebellum. The accumulation was higher in the young CP than the old. There was dose-dependent inhibition by TTR on 125I-T4 accumulation in the brain tissues, and kinetics of T4 accumulation in presence of TTR was obtained by plotting a double reciprocal of B (bound) versus TTR concentration curve. The KD of 125I-T4 binding to TTR was higher in the CP compared to other tissues, suggesting that CP competes with TTR for T4 binding to a greater extent than the other tissues. Using the isolated perfused CP preparation, TTR significantly inhibited 125I-T4 efflux across CP from the CSF to blood side. Bovine serum albumin (BSA) was also able to inhibit 125I-T4 accumulation in the incubated tissues, but required higher concentrations to reach the level of inhibition seen with TTR. In conclusion, this study found a significant role for CSF TTR in preventing T4 loss to blood across the CP, and TTR inhibited both CP and selected brain tissue uptake in a dose-dependent manner. The physiological relevance of TTR may relate to preventing T4 loss from CSF and encouraging redistribution of hormone around the brain in CSF.

Monoclonal antibodies against human recombinant tumor necrosis factor: prevention of endotoxic shock.

Six murine monoclonal antibodies, AT-1, 2, 3, 4, 5, and 6 were produced against human recombinant tumor necrosis factor (gamma TNF). AT-1, -2, -3, -4, and -6 were IgG1, and AT-5 was IgG2a. AT-1, -2, and -3 neutralized the activity of gamma TNF (2 X 10(3) U/ml) over a range of dilutions between 5 and 500 micrograms/ml of IgG, while AT-4, -5 and -6 failed to neutralize the activity in these concentrations. All the antibodies showed immunoprecipitating activity for gamma TNF (2 X 10(3) U/ml) over a range of dilutions between 0.5 and 500 micrograms/ml. The AT-6 was weaker than the rest. AT-1, which neutralized gamma TNF activity efficiently, and AT-4, which did not neutralize the activity, were used to protect mice against endotoxic shock. AT-1 protected mice from the lethal effects of endotoxin, while AT-4 failed to do so. AT-1, -2, and -3 also neutralized the activity of human and mouse natural TNF. AT-1, -2, and -3 neutralized the activity of gamma TNF, but not that of lymphotoxin (LT) and interferon (IFN).

Niemann-Pick disease type C (a cellular cholesterol lipidosis) treated by bone marrow transplantation.

Bone marrow transplantation (BMT) has been used for a wide variety of lysosomal storage diseases with encouraging results. We report a 3-year 5-month-old girl with Niemann-Pick type C disease (NPC) who received an allogeneic BMT. The patient presented with repeated lower respiratory tract infections, hepatosplenomegaly, failure to thrive, and developmental delay. Chest computed tomography (CT) revealed diffuse interstitial lung infiltration. Bone marrow and liver biopsies revealed abundant lipid-filled foamy macrophages. Skin fibroblast sphingomyelinase assay revealed partial deficiency. The ability of her skin fibroblasts to esterify cholesterol was very low, and the cells stained brightly for free cholesterol. She received BMT from a healthy HLA-identical male sibling donor at the age of 2 year 6 months. Full engraftment was evidenced by repeated bone marrow sex chromosome studies. Regression of the hepatosplenomegaly, markedly reduced foamy macrophage infiltration in bone marrow, and decreased interstitial lung infiltration was noted 6 months after BMT. Her neurological status, however, deteriorated. Follow-up magnetic resonance image (MRI) revealed progressive, diffuse brain atrophy. We conclude that resolution occurred in the liver, spleen, bone marrow and lung following successful engraftment. Such a response is remarkable since the underlying problem involves a membrane receptor for cholesterol. This positive response might be due to replacement of the monocyte-phagocytic system or it may imply the existence of cross-correction in the NPC membrane receptor defect by BMT approach. Since BMT did not halt the neurological deterioration, it is unlikely to be an adequate treatment for NPC.

Fulminant childhood hemophagocytic syndrome mimicking histiocytic medullary reticulosis. An atypical form of Epstein-Barr virus infection.

Ten cases of pediatric fulminant hemophagocytic syndrome, encountered between 1986 and 1989, are described. They occurred in the summer, and the patients presented with fever, jaundice, hepatosplenomegaly, pancytopenia, coagulopathy, and abnormal liver function. Bone marrow studies revealed infiltration by atypical T-lymphoid cells, rare B immunoblasts, and mature histiocytes with hemophagocytosis. Initially, histiocytic medullary reticulosis was suspected in six cases. The clinical course was characterized by rapid deterioration, with a mean period of 16 days from onset of fever to death. The main causes of death were coagulopathy with multiple organ failure and opportunistic infection. In seven of eight cases studied by serologic assay and Southern blot hybridization, acute or active Epstein-Barr virus (EBV) infection was documented. It is suggested that an atypical or fulminant form of primary EBV infection distinct from classic infectious mononucleosis was prevalent in previously healthy children in Taiwan. Younger age involvement and seasonal clustering were characteristic of the disorder described.

Characterization of an important enzymatic component in collagenase that is essential for the effective digestion of the human and porcine pancreas.

Recent clinical results from Edmonton have demonstrated the feasibility of achieving normoglycemia in type I diabetic patients by islet transplantation. One of the key issues in obtaining this success was transplanting sufficient numbers of islets by sequential transplants. Although the development of semipurified endotoxin-free Clostridium histolyticum-derived collagenase (Liberase) has improved islet yields from the human pancreas, batch-to-batch variation and loss of activity with time still hampers progress in obtaining consistent islet preparations. In order to define key components of crude collagenase, a panel of monoclonal antibodies (McAbs) was raised against crude collagenase. Monoclonal antibodies were generated by fusions between splenocytes of BALB/c mice immunized with Boheringer P collagenase and the myeloma cell line NS-0. These monoclonal antibodies were used as probes to study molecular differences between effective and ineffective collagenase batches using Western blotting. Two monoclonal antibodies (LDS71 and LDS81) were raised and characterized as recognizing separate epitopes on a 125-kDa component. Western blotting indicated that the 125-kDa band was rapidly broken down by storage or by dialysis in the presence of dithiothreitol. However, this breakdown could be prevented by the addition of leupeptin (a protease inhibitor) to the dialysis buffer. On testing fractions at 5-min intervals from the "Ricordi" digestion circuit during porcine and human pancreas digestion, the 125-kDa component was rapidly broken down in relatively ineffective collagenase batches but in effective batches was present throughout the digestion process. The correlation between the presence of the 125-kDa band and effectiveness of pancreas digestion suggests that this may be a key component in the formulation of C. histolyticum collagenase.

Cytogenetic characterization of Epstein-Barr virus-associated T-cell malignancies.

Recently, Epstein-Barr virus (EBV) infection has been found not only to be associated with Burkitt lymphoma and nasopharyngeal carcinoma but also with some T-cell malignancies. Cytogenetic studies were performed on four Chinese patients with EBV-associated T-cell neoplasms: three peripheral T-cell lymphomas and one large granular lymphocyte leukemia with coexpression of T-cell antigen. Clonal chromosomal abnormalities were detected in all four patients. Rearrangements of chromosome 7 were observed in three patients: one at 7p22, one at 7q35 or 36, and the remaining one at both sites. The last patient also had a chromosomal abnormality involving 14q11. Trisomy of part of the 1q segment was detected in two patients. The results revealed that the chromosomal abnormalities in these patients were similar to those observed in other T-cell lymphomas. Further studies on more patients are necessary to find out whether there are specific chromosomal aberrations in EBV-associated T-cell neoplasms.

Hemophagocytic syndrome in Epstein-Barr virus-associated T-lymphoproliferative disorders: disease spectrum, pathogenesis, and management.

The Epstein-Barr virus (EBV) has been shown to infect T lymphocytes and is associated with two recently recognized human T-lymphoproliferative disorders: childhood EBV-associated hemophagocytic syndrome (VAHS) representing a primary or active EBV infection of T cells in young children, and the EBV-containing T cell lymphoma in adults predominantly affecting the nose, skin and gastrointestinal tract. In both diseases, hemophagocytic syndrome (HS) accounts for the major cause of mortality. The patients developing HS share common clinicopathologic features such as fever, skin lesions, lung infiltrates, hepatosplenomegaly with jaundice, cytopenias, and coagulopathy. The liver, spleen, lymph nodes, and bone marrow usually show florid histiocytic proliferation with hemophagocytosis in addition to the proliferation of atypical T lymphocytes or immunoblasts. The HS in T cell lymphoma may develop simultaneously with initial lymphoma presentation, at tumor relapse, or even during remission. The cytokines, in particular tumor necrosis factor-alpha, released from the EBV-infected T lymphocytes are presumed to cause the histiocytic activation and the subsequent hemophagocytic process. Chemotherapy or antiviral agents fail to arrest the hemophagocytic process in both diseases. Immunomodulatory treatment incorporating etoposide and intravenous immunoglobulin, however, has been effective in the control of the progression of the hemophagocytic process in a substantial number of VAHS patients. Preliminary data suggest that bone marrow transplantation may be a promising way for eliminating both the virus and the proliferating T cells. Further investigations are mandatory for combating this aggressive hemophagocytic process in EBV-associated T lymphoproliferative disorders.

Probing for the threshold energy for visual transduction: red-shifted visual pigment analogs from 3-methoxy-3-dehydroretinal and related compounds.

While azulenic retinal analogs failed to yield a red-shifted visual pigment analog, the 9-cis isomers of the push-pull polyenals 3-methoxy-3-dehydroretinal and 14F-3-methoxy-3-dehydroretinal yielded iodopsin pigment analogs with absorption maxima at, respectively, 663 and 720 nm. The former gave a relatively stable batho product (700 nm) and was able to activate transducin. A lower activity was observed for the latter. One possible explanation for the combined results is that the excitation energies of these red-shifted pigments are approaching the threshold energy for visual transduction (although at this time we cannot rigorously exclude a role of the added F-atom in reducing the transducin activity).

Paroxysmal nocturnal hemoglobinuria presenting as moyamoya syndrome.

We report an 11-year-old girl who has paroxysmal nocturnal hemoglobinuria (PNH) and was admitted because of recurrent cerebrovascular accidents (CVA) and intermittent hemoglobinuria. Internal carotid angiography revealed bilateral typical moyamoya patterns. Although CVA due to arterial thrombosis may occur in PNH, the basal moyamoya vessels were never mentioned in case reports yet. The moyamoya syndrome has been reported in a variety of diseases and represents the nonspecific response to an impairment of arterial flow at specific sites in the brain. Our case discloses that PNH may present as moyamoya syndrome.

Hypotonia, congenital nystagmus, and abnormal auditory brainstem response.

A Taiwanese boy, 1 year, 8 months of age, is reported with poor weight gain, hypotonia, trunk ataxia, motor developmental retardation, and horizontal pendular nystagmus with only wave I on auditory brainstem responses. Our patient clinically resembled 9 patients reported in the Japanese literature. Because of its male predominance, occurrence in siblings, early onset, nonprogressive course, and characteristic auditory brainstem response findings, the syndrome may be of genetic origin and attributable to a dysgenetic brainstem lesion.

Lung cancer mortality update and prevalence of smoking among copper miners and smelters.

OBJECTIVES: The aim of this investigation was to study the cancer mortality of Chinese copper miners and smelters further, with particular reference to that from lung cancer, and smoking prevalence. METHODS: From an earlier follow-up (1970-1985) of the mortality of the two cohorts, all new death cases registered since 1985 were recorded, and the mortality analysis was extended through 1992. A questionnaire survey of smoking habits was carried out in three samples, randomly chosen from the copper miners (N = 1125), smelters (N = 603), and local residents (N = 1517) of Tongling city. RESULTS: Lung cancer was significantly increased among the copper miners [standardized mortality ratio (SMR) 152, 95% confidence interval (95% CI) 123-187], but not among the copper smelters (SMR 102, 95% CI 53-178). Smoking was more prevalent among copper miners than among local male residents (71.7 versus 64.3%, P < 0.001), whereas among the smelters it was significantly less prevalent (57.4 versus 64.3%, P < 0.005). Similar patterns were found for the average number of cigarettes smoked daily among the miners (21.6 +/- 7.2), smelters (15 +/- 7.1), and local male residents (19.2 +/- 7.3). CONCLUSIONS: In addition to occupational exposures, cigarette smoking may partly play a role in influencing mortality from lung cancer among Chinese copper miners and smelters.

Congenital intractable diarrhea with possible defective crypt regeneration: report of a case.

A male infant, born uneventfully from a consanguinous marriage, presented with intractable watery diarrhea from his third day of life, with subsequent malnutrition and failure to thrive. He received central parenteral nutrition beginning at three months of age after a poor response to a semielemental diet and peripheral parenteral nutrition. He was totally dependent on central parenteral nutrition thereafter. Although diarrhea disappeared with strict bowel rest, intolerance to minimal enteral feedings persisted throughout his 2 years 4 months of life. Investigations including stool examinations and repeated cultures, immune function studies, radiologic studies of the small bowel and screening for galactosemia and cystic fibrosis could not demonstrate a specific cause for the diarrhea. Repeated small intestinal biopsies at 1 month, 4 months and 1 year 5 months of age showed persistent villous atrophy with crypt hypoplasia and a low crypt mitotic index. Electron microscopic examination revealed normal-appearing microvilli. This child may have had a congenital enteropathy due to an inborn crypt regeneration defect causing lifelong intolerance to enteral feedings.

Congenital factor VII deficiency complicated with hemoperitoneum and intracranial hemorrhage: report of a case.

Hypoproconvertinemia, or factor VII deficiency, is a rare congenital coagulopathy. We report on a female infant with congenital factor VII deficiency complicated by hemoperitoneum and intracranial hemorrhage. Most reports indicate that the bleeding of victims tends to be mild and confined to the superficial mucosa area. However, other reports and our experience with this patient suggest that it can result in fatal cerebral hemorrhage and necessitate early diagnosis, effective treatment and careful genetic counseling.

Hemorrhagic pericardial effusion in beta-thalassemia major: report of a case.

Although sterile pericardial effusion occurs in about half of the patients with massive iron overload, hemorrhagic pericardial effusion is rarely seen in beta-thalassemia major patients. A 10-year-old girl with beta-thalassemia major who was diagnosed in her early infancy developed a massive hemorrhagic pericardial effusion. She was receiving blood transfusions every 4-6 weeks without chelating therapy with an average hemoglobin (Hb) level of 6-9 g/dL. Progressive hepatospenomegaly was noted during the course. She had complained of orthopnea with palpitation and bilateral leg edema before admission. After evaluation, a massive pericardial effusion was found and pericardiocentesis was performed twice, which revealed a bloody and uncoagulable effusion. Finally a pericardial window was performed to eliminate the bloody effusion. Negative etiological evaluations of blood and pericardial effusion were reported. Pathological examination of the pericardial biopsy revealed hemosiderosis with a few lymphocytic infiltrates. We report this case for its rarity and its necessity for urgent treatment.