Identification of a 14-gene signature that predicts survival in colorectal cancer with liver metastasis

e14037

Background: Colorectal cancer (CRC) is the third leading cause of cancer death in men and women combined in the USA. Colorectal liver metastasis (CLM), the most common metastasis of CRC, accounts for at least two thirds of CRC deaths. The purpose of this study is to identify a gene signature that predicts patient survival in patients with CLM. Methods: We analyzed the gene expression profiles of specimens from 24 CLM patients (M:F = 14:10) who underwent metastatic liver resection and unmatched primary CRC specimens from an independent cohort of 30 patients (M:F = 14:16). The association between gene expression levels and survival outcome was evaluated using Cox proportional hazards regression. Random Forests and risk scores were used to construct a gene expression-based survival classifier. Results: Based on survival classifier of CLM patients, a 14-gene signature was developed. According to leave-one-out cross validation, all 24 CLM patients (median follow-up time of 25 months) were correctly assigned into high-risk or low-risk groups (p=0.001). This 14-gene signature was then validated in an independent cohort of 30 primary CRC patients (median follow-up time of 42.2 months; p= 0.03) and a subset of 11 patients who were diagnosed at presentation or follow-up with liver metastasis (M:F = 5:6; median follow-up time of 27.6 months; p=0.04). Conclusions: We have identified a 14-gene signature that predicts the survival of CLM patients after liver resection, with validation in an independent cohort. Although sample size is small, the significance level achieved with our survival analysis warrants further investigation of this 14-gene signature in a larger sample size.

Molecular determinants of T cell epitope recognition to the common Timothy grass allergen

We investigated the molecular determinants of allergen-derived T cell epitopes in humans utilizing the Phleum pratense (Timothy grass) allergens (Phl p). PBMCs from allergic individuals were tested in ELISPOT assays with overlapping peptides spanning known Phl p allergens. A total of 43 distinct antigenic regions were recognized, illustrating the large breadth of grass-specific T cell epitopes. Th2 cytokines (as represented by IL-5) were predominant, whereas IFN-gamma, IL-10, and IL-17 were detected less frequently. Responses from specific immunotherapy treatment individuals were weaker and less consistent, yet similar in epitope specificity and cytokine pattern to allergic donors, whereas nonallergic individuals were essentially nonreactive. Despite the large breadth of recognition, nine dominant antigenic regions were defined, each recognized by multiple donors, accounting for 51% of the total response. Multiple HLA molecules and loci restricted the dominant regions, and the immunodominant epitopes could be predicted using bioinformatic algorithms specific for 23 common HLA-DR, DP, and DQ molecules. Immunodominance was also apparent at the Phl p Ag level. It was found that 52, 19, and 14% of the total response was directed to Phl p 5, 1, and 3, respectively. Interestingly, little or no correlation between Phl p-specific IgE levels and T cell responses was found. Thus, certain intrinsic features of the allergen protein might influence immunogenicity at the level of T cell reactivity. Consistent with this notion, different Phl p Ags were associated with distinct patterns of IL-5, IFN-gamma, IL-10, and IL-17 production.

TiArA: a virtual appliance for the analysis of Tiling Array data

Background

Genomic tiling arrays have been described in the scientific literature since 2003, yet there is a shortage of user-friendly applications available for their analysis.

Methodology/Principal Findings

Tiling Array Analyzer (TiArA) is a software program that provides a user-friendly graphical interface for the background subtraction, normalization, and summarization of data acquired through the Affymetrix tiling array platform. The background signal is empirically measured using a group of nonspecific probes with varying levels of GC content and normalization is performed to enforce a common dynamic range.

Conclusions/Significance

TiArA is implemented as a standalone program for Linux systems and is available as a cross-platform virtual machine that will run under most modern operating systems using virtualization software such as Sun VirtualBox or VMware. The software is available as a Debian package or a virtual appliance at http://purl.org/NET/tiara.

Mechanisms underlying the cardioinhibitory and pressor responses elicited from the medullary neurons in the gigantocellular tegmental field of cats

A stimulation of the gigantocellular tegmental field (FTG) in the medulla oblongata often increases systemic arterial blood pressure (SAP) and decreases heart rate (HR). We investigated if the cardioinhibitory/depressor areas, including the nucleus ambiguus (NA), the dorsal motor nucleus of vagus (DMV) and the caudal ventrolateral medulla (CVLM), underlied the functional expression of FTG neurons in regulating cardiovascular responses. In 73 chloralose-urethane anesthetized cats, the HR, SAP and vertebral nerve activity (VNA) were recorded. Neurons in the FTG, NA, DMV and CVLM were stimulated by microinjection of sodium glutamate (25 mM Glu, 70 nl). To study if the NA, DMV, and CVLM relayed the cardioinhibitory messages from the FTG, 24 mM kainic acid (KA, 100 nl) was used as an excitotoxic agent to lesion neurons in the NA, DMV or CVLM. We found that the cardioinhibition induced by FTG stimulation was significantly reduced by KA lesioning of the ipsilateral NA or DMV. Subsequently, a bilateral KA lesion of NA or DMV abolished the cardioinhibitory responses of FTG. Compared to the consequence of KA lesion of the DMV, only a smaller bradycardia was induced by FTG stimulation after KA lesion of the NA. The pressor response induced by Glu stimulation of the FTG was reduced by the KA lesion of the CVLM. Such an effect was dominant ipsilaterally. Our findings suggested that both NA and DMV mediated the cardioinhibitory responses of FTG. The pressor message from the FTG neurons might be partly working via a disinhibitory mechanism through the depressor neurons located in the CVLM.

The relationship between FTL and NA, DMV or CVLM in central cardiovascular control

The aim of the present study was to examine the relationship between the lateral tegmental field (FTL), a cardioinhibitory area, with other cardioinhibitory areas, i.e., the ambiguus nucleus (NA) and the dorsal motor nucleus of vagus (DMV) and the caudal ventrolateral medulla (CVLM), a vasopressor inhibitory area. In 55 cats anesthetized with chloralose (40 mg/kg) and urethane (400 mg/kg), the cardiovascular responses of heart rate (HR), systemic arterial blood pressure (SAP) and vertebral nerve activity (VNA) were recorded. The FTL, NA, DMV and CVLM were identified first by stimulation (rectangular pulses in 80 Hz, 0.5 ms, 50-100 microA) and then confirmed by microinjection of sodium glutamate (Glu, 0.25M, 70 nl). In studying the influence of NA, DMV, or CVLM lesion on the Gluinduced responses in FTL, kainic acid (KA, 24 mM, 100 nl) was microinjected into the NA, DMV or CVLM. FTL stimulation produced an average decrease of HR by 55%. After KA lesioning of the ipsilateral NA or the DMV, the decreased HR induced by FTL was significantly diminished. After subsequent lesion of the contralateral DMV or NA, the bradycardia of FTL was abolished. The reduction of resting HR was more intense after lesioning the NA than DMV and with the left side more than that of the right side. These studies suggest that the cardioinhibitory responses of FTL are mediated through both NA and DMV with predominance of the former, while the hypotensive effect of FTL is mediated through CVLM. The precise pathway responsible for the FTL-induced bradycardia and hypotension is to be determined.

A case of del(13)(q22) with multiple major congenital anomalies, imperforate anus and penoscrotal transposition

"13q-"syndrome is known to have widely variable manifestations, including retinoblastoma, mental & growth retardation, malformation of brain & heart, anal atresia, and anomalies of the face and limbs. Here we report a case of del(13)(q22) with multiple major congenital anomalies for the first time in Korea. The patient was born at 36(+4) weeks of pregnancy by caesarian section. Birth weight was 1490g. On examination the following features were noted: - imperforate anus, ambiguous genitalia (bifid scrotum, penoscrotal transposition, hypospadia), syndactyly of toes, absence of thumbs, abnormal facies (dolichocephaly, telecanthus, large low set ears, saddle nose, high arched palate, micrognathia). Neurocranial ultrasonography showed atrophy of the corpus callosum and multiple calcifications. He died at 14 days. Post-mortem autopsy findings showed cholestasis and fatty metamorphosis of liver, abnormal lobulation (Rt:2, Lt:1) and lymphangiectasis of the lung, VSD, ASD, PDA of heart, and acute tubular necrosis of kidney. Cytogenetic studies was confirmed to 46,XY,del(13) (q22) by Giemsa banded chromosomes from peripheral blood lymphocytes.

Post-partum acute exacerbation of chronic hepatitis in a hepatitis C-carrier mother

Hepatitis C virus infection is a global health problem; however, the interaction between pregnancy and chronic hepatitis C remains controversial. A Taiwanese woman with chronic hepatitis C had an uncomplicated pregnancy and gave birth to a female baby through spontaneous vaginal delivery. The serum levels of alanine aminotransferase and hepatitis C virus (HCV) RNA were measured before pregnancy, in the first and third trimesters, 1 and 3 months after delivery, respectively. During her pregnancy, the serum aminotransferase levels became normalized, while the serum HCV-RNA levels declined significantly and consecutively with the lowest viral load in the third trimester. One month after delivery, she had an abrupt elevation of serum HCV-RNA level, paralleling a hepatitis flare with serum aminotransferase level more than 20-fold the upper normal limit. The serum HCV-RNA levels declined thereafter, and serum aminotransferase levels became normalized 3 months postdelivery. She was infected with HCV genotype 1a throughout the entire follow-up period, and other causes of hepatitis flare were excluded. In conclusion, post-partum acute exacerbation of chronic hepatitis may occur in HCV-carrier mothers, and an abrupt elevation of serum HCV-RNA level may be associated with the acute exacerbation.

Hepatitis C and G virus infections in polytransfused children

The prevalence of hepatitis C virus (HCV) and a newly identified hepatitis G virus (HGV) and their clinical significance were studied in 42 polytransfused Taiwanese children. Serological assays for antibodies against HCV (anti-HCV) and polymerase chain reaction for serum HCV ribonucleic acid (RNA) and HGV RNA were performed. The prevalence of anti-HCV and HGV RNA was 17% and 14%, respectively in 42 polytransfused children. Anti-HCV seropositives had a significantly higher mean age, peak serum transaminase level, and longer transfusion duration than seronegatives, while children with HGV infection usually had no or only mild hepatitis activities. The prevalence of anti-HCV dropped sharply after implementation of anti-HCV screening, however the prevalence of HGV viraemia remained unchanged.

CONCLUSIONS

HGV infection is not uncommon in polytransfused Taiwanese children and the virus does not cause significant hepatitis compared to HCV infection. Current blood donor screening for anti-HCV can effectively protect polytransfused children from HCV infection but the impact of additional screening for HGV markers awaits further studies.

Factors related to detection of blood flow by color Doppler ultrasonography in intussusception

Color Doppler ultrasonography was performed in 125 patients with 134 intussusceptions. Color flow was present in 121 cases of intussusception (group A) and was absent in 13 cases (group B). Young age and duration of symptoms greater than 48 hr were significantly related to the nonvisualization of blood flow detected by color Doppler sonography (P < 0.05). The successful rate of air reduction was significantly higher in group A than in group B (109 of 121 versus 4 of 13). Color Doppler ultrasonography is useful to predict the reducibility of an intussuscepted intestine. The nonvisualization of blood flow by this method is not a contraindication for air reduction.

Diagnostic value of C-reactive protein in children with perforated appendicitis

The diagnostic value of serum C-reactive protein (CRP) levels in children with perforated appendicitis was prospectively studied in 78 consecutive patients with histologically confirmed appendicitis. The patients were divided into two groups: group A included 56 patients with perforated appendicitis and group B consisted of 22 patients with simple appendicitis. Serum CRP level and leucocyte count were assayed in all and abdominal ultrasonography was performed in 75. The mean age group A patient was significantly lower than that of group B patients (7.5 vs. 10.4 years, P < 0.001). Group A patients had a significantly higher mean serum CRP levels than group B patients (92 vs. 31 mg/l, P < 0.001), while the mean leucocyte count was comparable in the two groups. Of 75 examined patients, 73 (97%) had a pre-operative sonographic diagnosis of appendicitis.

CONCLUSION

Perforation is a common complication in children with appendicitis, especially in those of young age and with prolonged pain duration. Greatly increased serum CRP levels (> or = 50 mg/l) and abdominal ultrasonography are important diagnostic aids in such patients.

Pneumatic reduction of intussusception in children

Over the past decade, pneumatic reduction has been increasingly accepted as the treatment of choice for pediatric intussusception. However the effectiveness of air compared with the more traditional barium reduction of intussusception continues to be a source of concern and debate. From August 1993 to November 1994, pneumatic reduction was used to treat 75 episodes in 73 patients with proven intussusception at Chang Gung Memorial Hospital, Taoyuan. Two patients underwent air reduction twice because of recurrence following an initial successful reduction. The recurrence rate was 3%. Successful reduction was achieved in 65/75 (87%) episodes. None of the patients experienced any complications following the procedure. In two of the 10 patients in whom reduction failed, one was subsequently found to have a Meckel's diverticulum and the other a duplication cyst as a leading point. This prospective study indicates that air enema is a safe and effective form of treatment for intussusception in infants and children. Pneumatic reduction should be the treatment of choice in the initial management of intussusception.

Intussusception in infants and children: risk factors leading to surgical reduction

Intussusception is commonly the etiology of intestinal obstruction in infants and children. To investigate demographic data, clinicopathologic features and therapeutic prognosis of patients with intussusception, we reviewed 361 intussusceptions in 333 patients over an 11-year period. Most patients were below two years of age and there was a male preponderance of 1.6:1. There was no seasonal difference between the number of cases. The clinical triad of vomiting, abdominal colicky pain and bloody stools was manifested in only one-third of our patients. Secondary intussusception contributed to 6.6% of cases and Meckel's diverticulum was the most common pathologic cause. Positive findings were recorded in 82% of 67 patients undergoing sonographic examination. Intussusception of the ileo-colic type was most frequently encountered. Most patients (79%) were diagnosed within 48 hours and almost all cases underwent primary barium enema reduction. The success rate was 45%. Laparotomy was performed in 207 patients (57%) refractory to enema reduction or with critical illness, and intestinal resection was required in 28 (14%). Long-standing duration of illness (> 24 hours), positive clinical triad, positive pathologic lead point, and radiologic finding of bowel obstruction were identified as risk factors leading patients to surgical reduction (p < 0.001). Postoperative complications and recurrent intussusception developed in some patients, and the overall mortality was 0.6%. The clinical characteristics of intussusception in children generally remained unchanged as compared to previous reports. Early identification of patients with risk factors for surgical treatment is important to decrease the need for intestinal resection.

Extrapulmonary tuberculosis in children

Extrapulmonary tuberculosis is not a rare infection of children in Taiwan. From 1985 to 1989, we studied 39 children with the diagnosis of extrapulmonary tuberculosis from a total of 43 sites. They were diagnosed by routine diagnostic tests including bacteriologic cultures in 11, pathological features in 25, and clinical presentations in 2 patients. Positive mycobacterial DNA probe method was obtained from a patient with tuberculous meningitis. The most common sites of involvement were lymph nodes in 9 (20.9%), meninges in 7 (16.3%), bone in 7 (16.3%), joint in 6 (14.0%) and miliary infection in 6 (14.0%). The median age of the 2 patients with renal tuberculosis was 14.5 years, which was older compared to the patients with other organ systems involvement. Tuberculin skin tests were significantly positive (> 10 mm) in 54% of the tested children. Among the treated patients, 76% were cured after 9 to 12 months of antituberculous chemotherapy without sequelae, while 24% had sequelae associated with tuberculous infection despite treatment. There was no death reported during the study period. We conclude that extrapulmonary tuberculosis remains an important health problem to the pediatric population of this island despite the overall decline in the incidence of tuberculosis. Early detection and thorough treatment for a suitable period are mandatory to improve the prognosis of this potentially curable infectious disease.

Triflavin, an Arg-Gly-Asp-containing antiplatelet peptide inhibits cell-substratum adhesion and melanoma cell-induced lung colonization

Triflavin, an Arg-Gly-Asp (RGD) containing peptide purified from Trimeresurus flavoviridis snake venom, inhibits human platelet aggregation by blocking fibrinogen binding to fibrinogen receptors associated with glycoprotein IIb/IIIa complex. In this study, we show that triflavin (1-30 micrograms/mouse) inhibits B16-F10 melanoma cell-induced lung colonization in C57BL/6 mice in a dose-dependent manner. In vitro, triflavin dose-dependently inhibits adhesion of B16-F10 melanoma cells to extracellular matrices (ECMs; i.e., fibronectin, fibrinogen, vitronectin, and collagen type I). Triflavin is approximately 600-800 times more potent than GRGDS at inhibiting cell adhesion. In addition, triflavin dose-dependently inhibits B16-F10 cell-induced platelet aggregation. These results imply that the inhibitory effect of triflavin on the adhesion of tumor cells to ECMs (e.g., fibronectin, vitronectin and collagen type I) and/or tumor cell-induced platelet aggregation may be partially responsible for its antimetastatic activity in C57BL/6 mice.

Triflavin, an Arg-Gly-Asp containing snake venom peptide, inhibits aggregation of human platelets induced by human hepatoma cell line

Triflavin, an Arg-Gly-Asp (RGD)-containing peptide, purified from snake venom of Trimeresurus flavoviridis, inhibits human platelet aggregation through the blockade of fibrinogen binding to fibrinogen receptors associated with glycoprotein IIb/IIIa complex. In this report, we examined the effect of triflavin on tumor cells (human hepatoma J-5)-induced platelet aggregation (TCIPA) of heparinized platelet-rich plasma (PRP). ADP-scavenger agents, apyrase (10 U/ml) and creatine phosphate (5 mM)/creatine phosphokinase (5 U/ml) did not inhibit TCIPA while hirudin (5 U/ml) completely inhibited it. J-5 cells initially induced platelet aggregation, then blood coagulation occurred. J-5 cells concentration-dependently shortened the recalcification time of normal as well as Factor VIII, IX-deficient human plasmas, while it was inactive at shortening the recalcification time of Factor VII-deficient plasma, suggesting J-5 cells induced platelet aggregation through activation of extrinsic pathway, leading to thrombin formation as evidenced by the amidolytic activity on s-2238 by expressing tissue factor-like activity. Triflavin inhibited TCIPA in a dose-dependent manner (IC50, 0.02 microM). When compared on molar ratio, triflavin was approximately 30,000 times more potent than GRGDS (IC50, 0.58 mM). On the other hand, GRGES showed no significant effect on TCIPA, even its concentration was raised to 4 mM. Additionally, the monoclonal antibodies, raised against glycoprotein IIb/IIIa complex (i.e., 7E3 and 10 E5) inhibited J-5 TCIPA. In conclusion, we suggest the inhibitory effect of triflavin on J-5 TCIPA may be chiefly mediated by the binding of triflavin to the fibrinogen receptor associated with glycoprotein IIb/IIIa complex on platelet surface membrane.

Sex-linked agammaglobulinemia (Bruton's disease). A case report

X-linked agammaglobulinemia (Bruton's disease) is a rare disease characterized by marked decrease in all classes of immunoglobulins and absence of circulating B cells and plasma cells. The affected boys frequently present with recurrent respiratory tract infections after 6 months to 2 years of age. A combination regimen of intravenous human immunoglobulins and strong parenteral antibiotics remains the stone of treatment. Herein we report a one year and ten months old boy with Bruton's disease. He has had repeated infections of upper and lower respiratory tract since 6 months of age. Immunological studies revealed panhypogammaglobulinemia, nearly total absence of circulating B cells, negative isohemagglutinins and reversed CD4/CD8 ratio. Pedigree analysis suggests a sex-linked recessive inheritance. Intravenous immunoglobulins as well as parenteral antibiotics were administered to overcome pneumonia and purulent otitis media. He is currently undergoing co-trimethoxazole prophylaxis and periodic intravenous immunoglobulins infusion.