COLONOMICS - integrative omics data of one hundred paired normal-tumoral samples from colon cancer patients

Colonomics is a multi-omics dataset that includes 250 samples: 50 samples from healthy colon mucosa donors and 100 paired samples from colon cancer patients (tumor/adjacent). From these samples, Colonomics project includes data from genotyping, DNA methylation, gene expression, whole exome sequencing and micro-RNAs (miRNAs) expression. It also includes data from copy number variation (CNV) from tumoral samples. In addition, clinical data from all these samples is available. The aims of the project were to explore and integrate these datasets to describe colon cancer at molecular level and to compare normal and tumoral tissues. Also, to improve screening by finding biomarkers for the diagnosis and prognosis of colon cancer. This project has its own website including four browsers allowing users to explore Colonomics datasets. Since generated data could be reuse for the scientific community for exploratory or validation purposes, here we describe omics datasets included in the Colonomics project as well as results from multi-omics layers integration.

Polygenic risk score across distinct colorectal cancer screening outcomes: from premalignant polyps to colorectal cancer

BACKGROUND

Different risk-based colorectal cancer (CRC) screening strategies, such as the use of polygenic risk scores (PRS), have been evaluated to improve effectiveness of these programs. However, few studies have previously assessed its usefulness in a fecal immunochemical test (FIT)-based screening study.

METHODS

A PRS of 133 single nucleotide polymorphisms was assessed for 3619 participants: population controls, screening controls, low-risk lesions (LRL), intermediate-risk (IRL), high-risk (HRL), CRC screening program cases, and clinically diagnosed CRC cases. The PRS was compared between the subset of cases (n = 648; IRL+HRL+CRC) and controls (n = 956; controls+LRL) recruited within a FIT-based screening program. Positive predictive values (PPV), negative predictive values (NPV), and the area under the receiver operating characteristic curve (aROC) were estimated using cross-validation.

RESULTS

The overall PRS range was 110-156. PRS values increased along the CRC tumorigenesis pathway (Mann-Kendall P value 0.007). Within the screening subset, the PRS ranged 110-151 and was associated with higher risk-lesions and CRC risk (OR_D10vsD1 1.92, 95% CI 1.22-3.03). The cross-validated aROC of the PRS for cases and controls was 0.56 (95% CI 0.53-0.59). Discrimination was equal when restricted to positive FIT (aROC 0.56), but lower among negative FIT (aROC 0.55). The overall PPV among positive FIT was 0.48. PPV were dependent on the number of risk alleles for positive FIT (PPVp10-p90 0.48-0.57).

CONCLUSIONS

PRS plays an important role along the CRC tumorigenesis pathway; however, in practice, its utility to stratify the general population or as a second test after a FIT positive result is still doubtful. Currently, PRS is not able to safely stratify the general population since the improvement on PPV values is scarce.

Non-Lynch Familial and Early-Onset Colorectal Cancer Explained by Accumulation of Low-Risk Genetic Variants

A large proportion of familial and/or early-onset cancer patients do not carry pathogenic variants in known cancer predisposing genes. We aimed to assess the contribution of previously validated low-risk colorectal cancer (CRC) alleles to familial/early-onset CRC (fCRC) and to serrated polyposis. We estimated the association of CRC with a 92-variant-based weighted polygenic risk score (wPRS) using 417 fCRC patients, 80 serrated polyposis patients, 1077 hospital-based incident CRC patients, and 1642 controls. The mean wPRS was significantly higher in fCRC than in controls or sporadic CRC patients. fCRC patients in the highest (20th) wPRS quantile were at four-fold greater CRC risk than those in the middle quantile (10th). Compared to low-wPRS fCRC, a higher number of high-wPRS fCRC patients had developed multiple primary CRCs, had CRC family history, and were diagnosed at age ≥50. No association with wPRS was observed for serrated polyposis. In conclusion, a relevant proportion of mismatch repair (MMR)-proficient fCRC cases might be explained by the accumulation of low-risk CRC alleles. Validation in independent cohorts and development of predictive models that include polygenic risk score (PRS) data and other CRC predisposing factors will determine the implementation of PRS into genetic testing and counselling in familial and early-onset CRC.

Tumor Expression of Cyclin-Dependent Kinase 5 (Cdk5) Is a Prognostic Biomarker and Predicts Outcome of Oxaliplatin-Treated Metastatic Colorectal Cancer Patients

In recent years, an increasing number of studies have shown that elevated expression of cyclin dependent kinase (Cdk5) contributes to the oncogenic initiation and progression of many types of cancers. In this study, we investigated the expression pattern of Cdk5 in colorectal cancer (CRC) cell lines and in a large number of tumor samples in order to evaluate its relevance in this pathogenesis and possible use as a prognostic marker. We found that Cdk5 is highly expressed and activated in CRC cell lines and that silencing of the kinase decreases their migration ability. In tumor tissues, Cdk5 is overexpressed compared to normal tissues due to a copy number gain. In patients with localized disease, we found that high Cdk5 levels correlate with poor prognosis, while in the metastatic setting, this was only the case for patients receiving an oxaliplatin-based treatment. When exploring the Cdk5 levels in the consensus molecular subtypes (CMS), we found the lowest levels in subtype 1, where high Cdk5 again was associated with a poorer prognosis. In conclusion, we confirm that Cdk5 is involved in CRC and disease progression and that it could serve as a prognostic and predictive biomarker in this disease.

Low adherence to the western and high adherence to the mediterranean dietary patterns could prevent colorectal cancer

PURPOSE

To assess if the associations found between three previously identified dietary patterns with breast, prostate and gastric cancer are also observed for colorectal cancer (CRC).

METHODS

MCC-Spain is a multicase-control study that collected information of 1629 incident cases of CRC and 3509 population-based controls from 11 Spanish provinces. Western, Prudent and Mediterranean data-driven dietary patterns-derived in another Spanish case-control study-were reconstructed in MCC-Spain. Their association with CRC was assessed using mixed multivariable logistic regression models considering a possible interaction with sex. Risk by tumor site (proximal colon, distal colon, and rectum) was evaluated using multinomial regression models.

RESULTS

While no effect of the Prudent pattern on CRC risk was observed, a high adherence to the Western dietary pattern was associated with increased CRC risk for both males [OR_{fourth(Q4) vs. first(Q1)quartile} (95% CI): 1.45 (1.11;1.91)] and females [OR_{Q4 vs. Q1} (95% CI): 1.50 (1.07;2.09)] but seem to be confined to distal colon [OR_{fourth(Q4) vs. first(Q1)quartile} (95% CI): 2.02 (1.44;2.84)] and rectal [OR_{Q4 vs. Q1} (95% CI): 1.46 (1.05;2.01)] tumors. The protective effect of the Mediterranean dietary pattern against CRC was observed for both sexes [males: OR_{Q4 vs. Q1} (95% CI): 0.71 (0.55;0.92); females: OR_{Q4 vs. Q1} (95% CI): 0.56 (0.40;0.77)] and for all cancer sites: proximal colon [OR_{Q4 vs. Q1} (95% CI): 0.70 (0.51;0.97)], distal colon [OR_{Q4 vs. Q1} (95% CI): 0.65 (0.48;0.89)], and rectum (OR_{Q4 vs. Q1} (95% CI): 0.60 (0.45;0.81)].

CONCLUSION

Our results are consistent with most of the associations previously found between these patterns and breast, prostate and gastric cancer risk and indicate that consuming whole fruits, vegetables, legumes, olive oil, nuts, and fish and avoiding red and processed meat, refined grains, sweets, caloric drinks, juices, convenience food, and sauces might reduce CRC risk.

Effect of treatment with prostaglandin E1 and N-acetylcysteine on pediatric liver transplant recipients: a single-center study

Prostaglandin E1 (PGE1) and N-acetylcysteine (NAC) have been used as single agents to decrease reperfusion injury and improve outcome after solid-organ transplantation (Tx). We hypothesized that combined treatment with NAC and PGE1 would be safe and reduce reperfusion injury. We therefore carried out a pilot study to assess the safety of this drug combination and gain information regarding the efficacy of treating pediatric liver transplant recipients with NAC and PGE1. The pilot study took the form of an open-label study incorporating 25 pediatric liver transplant recipients (12 children in the treatment group and 13 children as controls). NAC (70 mg/kg) was given intravenously over 1 h following reperfusion and then every 12 h for 6 days. PGE1 (0.4 mg/kg/h) was given as a continuous intravenous infusion for 6 days, starting after the first NAC dose. The primary outcome was the safety of combined treatment with NAC and PGE1. Patient survival, graft survival, allograft rejection within the first 90 days after Tx, peak post-transplant serum alanine aminotransferase (ALT) concentration, post-transplant length of hospitalization, and post-operative complications were secondary outcomes. Post-operative complications occurred at similar rates in both control and treated groups. No complications or adverse events occurred in the treated group as a result of study drugs. The 3-month patient survival rate was 100% for both groups. For the group treated with NAC and PGE1, peak serum ALT was lower and median length of stay was shorter but the differences did not reach statistical significance. The proportion of patients with allograft rejection was not significantly different between the two groups. However, rejection was more severe in the control group than in the treated group. In summary, infusions of NAC and PGE1 were safely administered to pediatric liver transplant recipients. However, a randomized controlled study is needed to determine the efficacy of treatment with NAC and PGE1.

Causes and management of portal hypertension in the pediatric population

Therapeutic options for children with portal hypertension now include a broad range of pharmacologic, endoscopic, and surgical procedures. Thoughtful application of all of these options can improve quality of life by decreasing the complications of portal hypertension and can decrease mortality by preventing the consequences of variceal hemorrhage. The development of portal hypertensive gastropathy following palliative procedures such as endoscopic sclerotherapy and band ligation may limit their long-term success in children. The excellent results now obtained with selective portosystemic shunts and liver transplantation assure that definitive surgical treatments will continue to be important components in the treatment of children with portal hypertensive complications or progressive liver disease. Evolving procedures, such as TIPS, represent excellent short-term life-preserving techniques to stabilize critically ill patients while awaiting liver transplantation. Their role in the future, long-term management of children is yet to be defined.

Long-term survival after liver transplantation

BACKGROUND

Liver transplantation (LT) remains a high-risk operation, especially during the first months after LT when technical complications and preexisting illness exert their influence on survival. However, there are late deaths. The authors have reviewed their experience to identify factors impacting on long-term survival.

METHODS

A total of 150 patients who had undergone liver transplantation over an 11-year period were reviewed. Thirty-three patients died after LT (22%). Of these, 18 of 33 (55%) died in the first 3 postoperative months. One hundred thirty-two patients survived beyond 3 months, and 15 patients (11%) suffered late deaths. This review concentrates on the latter group.

RESULTS

The primary cause of death was sepsis in 11 of 15 (73%). In two, sepsis complicated retransplantation in chronically debilitated patients. Two additional patients had late-presenting postoperative complications (bile leak or abscess, intestinal obstruction with perforation). In two cases, pneumocystis carinii pneumonia occurred; noncompliance or unplanned discontinuation of prophylaxis was directly responsible. Multiple organ system failure from presumed immunoincompetence developed in four patients; one had undergone bone marrow transplantation for aplastic anemia (AA) after fulminant hepatic failure (FHF). Lymphoproliferative disease (LPD) was the cause of death in 3 of 15 cases (20%). In only three cases was the cause of death related to the patient's primary disease (chronic hepatitis, Alper's syndrome or seizures, and AA with FHF). Pretransplant diagnosis, and UNOS status at the time of LT did not influence the long-term survival.

CONCLUSIONS

Long-term survival in patients who have undergone LT was compromised by immunosuppressive complications and sepsis. Early mortality factors, such as UNOS status, age at LT, primary diagnosis, and technical complications do not predict late deaths. In children who adhere to their medical regimen and have good initial allograft function, late postoperative infection, especially with Ebstein-Barr virus, accounts for most of the late mortality. Improved and decreased immunosuppression may further improve these long-term results.

Current concepts in pediatric liver transplant

Orthotopic liver transplantation has significantly improved the survival rate of children with end-stage liver disease. Efforts to correct abnormalities existing prior to transplantation coupled with improved surgical techniques and immunosuppression have led to better quality of life and 1-year survival rates approaching 90% in many centers. Despite this success the expanding waiting list population of all ages has driven development of operative techniques to expand the donor pool. Building on the success of reduced-size transplantation, split-liver and living-donor transplantation are now suitable alternatives, especially when used in candidates with satisfactory clinical stability. In the post-operative period, infectious complications represent an important cause of morbidity and mortality. Although antimicrobial regimens are effective in the immediate post-operative phase, acquisition of viral infections represents a major concern particularly in the young liver recipient. Early detection and development of new anti-viral agents are likely to decrease occurrence of post-transplant proliferative disorders and optimize longterm transplantation outcome.

Biliary atresia: pathogenesis and treatment

Biliary atresia is a disorder of infants in which there is obliteration or discontinuity of the extrahepatic biliary system, resulting in obstruction of bile flow. Untreated, the resulting cholestasis leads to progressive conjugated hyperbilirubinemia, cirrhosis, and hepatic failure. Biliary atresia has an incidence of approximately one in 10,000 live births worldwide. Evidence to date supports a number of pathogenic mechanisms for the development of biliary atresia. An infectious cause, such as by a virus, would seem most pausible in many cases. The clinical observation that biliary atresia is rarely encountered in premature infants would support an agent acting late in gestation. However, no infectious or toxic agent has been conclusively implicated in biliary atresia. Genetic mechanisms likely play important roles, even regarding susceptibility to other specific causes, but no gene whose altered function would result in obstruction or atresia of the biliary tree has been identified. The variety of clinical presentations support the notion that the proposed mechanisms are not mutually exclusive but may play roles individually or in combination in certain patients. Biliary atresia, when untreated, is fatal within 2 years, with a median survival of 8 months. The natural history of biliary atresia has been favorably altered by the Kasai portoenterostomy. Approximately 25 to 35% of patients who undergo a Kasai portoenterostomy will survive more than 10 years without liver transplantation. One third of the patients drain bile but develop complications of cirrhosis and require liver transplantation before age 10. For the remaining one third of patients, bile flow is inadequate following portoenterostomy and the children develop progressive fibrosis and cirrhosis. The portoenterostomy should be done before there is irreversible sclerosis of the intrahepatic bile ducts. Consequently, a prompt evaluation is indicated for any infant older than 14 days with jaundice to determine if conjugated hyperbilirubinemia is present. If infectious, metabolic, endocrine disorders are unlikely and if the child has findings consistent with biliary atresia, then exploratory laparotomy and intraoperative cholangiogram should be done expeditiously by a surgeon who has experience doing the Kasai portoenteostomy. Biliary atresia represents the most common indication for pediatric liver transplantation, representing more than 50% of cases in most series. Transplantation is indicated when symptoms of end stage liver disease occur, including recurrent cholangitis, progressive jaundice, portal hypertension complications, ascites, decreased synthetic function, and growth/nutritional failure.

Biliary atresia--surgical management and treatment options as they relate to outcome

Results show that the use of sequential surgical treatment, employing Kasai portoenterostomy in infancy, followed by selective liver transplantation for children with progressive hepatic deterioration yields improved overall survival. All children with successful Kasai portoenterostomy procedures who do not require OLT are survivors. Using newer transplant techniques, the 5-year survival rate for children who receive transplants with a primary diagnosis of biliary atresia was 82%. This yields an overall survival rate of 86% in this entire study population. Limited donor availability and increased complications after liver transplantation in infants less than 1 year of age mitigate against the use of primary liver transplantation without prior portoenterostomy for infants with biliary atresia. At present, these two operative procedures should be used as sequential and complementary modes of treatment rather than as competitive procedures. When biliary atresia is not recognized in infancy and established cirrhosis has resulted, primary transplantation should be offered as the initial surgical treatment.

A percutaneous technique for venovenous bypass in orthotopic cadaver liver transplantation and comparison with the open technique

Venovenous bypass minimizes the hemodynamic alterations during the anhepatic phase of liver transplantation. A new technique for the percutaneous placement of the bypass cannulae is described and compared to the cut-down ("open") technique. The records of 81 patients who underwent 94 liver transplants between August 1991 and April 1994 were reviewed for indications for transplant, United Network for Organ Sharing status, mean age, body surface area, bypass technique and time, flow rates, cardiac output, mean arterial pressure and central venous pressure during bypass, the development of deep venous thrombophlebitis, and lymphoceles. Femoral flow rates were higher in the open group (2054 +/- 74 mL/min), compared with the percutaneous group (1726 +/- 74 mL/min) (p = 0.003). Total flow rates in the open (2238 +/- 58 mL/min) and percutaneous (2197 +/- 67 mL/min) groups were not different. Maximum cardiac outputs (L/ min) were higher in the open (10.1 +/- 0.6) versus percutaneous group (7.0 +/- 0.5) (p < 0.0002). Similarly, minimum cardiac outputs (L/min) were higher in the open (8.9 +/- 0.7) versus percutaneous group (5.8 +/- 0.5) (p = 0.003). Other hemodynamic parameters (mean arterial pressure, central venous pressure) were not different between groups. Venous thrombosis occurred in 1/50 (2.0%) and 4/34 (11.8%) patients in the open and percutaneous groups, respectively (p = 0.153). Nineteen lymphoceles occurred in 102 (18.6%) at-risk sites in the open group, whereas no lymphoceles occurred in 66 at-risk sites in the percutaneous group (p < 0.001). Groin lymphoceles occurred in 7/50 (14%) and 0/34 at-risk sites in the open and percutaneous groups, respectively (p = 0.039). Axillary lymphoceles occurred in 12/52 (23.1%) and 0/32 at-risk sites in the open and percutaneous groups, respectively (p = 0.0031). Operative repair of a lymphocele was required in 11/16 (69%) patients. The percutaneous placement of catheters for venovenous bypass has the advantage of comparable flow rates with satisfactory hemodynamics without the lymphatic complications of the cut-down technique.

Late hepatic artery thrombosis in liver allograft recipients is associated with intrahepatic biliary necrosis

Hepatic artery thrombosis (HAT) after liver transplantation is a potentially life-threatening complication that occurs in 2-25% of patients, depending on several risk factors and the patient population studied. Arterial thrombosis occurring early after liver transplantation is associated with acute fulminant hepatic failure, biliary tract necrosis and leaks, or relapsing bacteremia and is associated with a high rate of graft loss and patient mortality. The onset of late posttransplant HAT (after 6 months) has been thought to have a more benign and often asymptomatic course. The reasons for the differences between the manifestations of early and late HAT are not well understood. We reviewed the adult liver transplant experience at the University of Cincinnati and found four patients with late HAT, three of whom developed severe intrahepatic biliary necrosis. Two patients were successfully retransplanted and 1 patient who refused retransplantation died. One patient had mild, transient graft damage due to gradual arterial stenosis and the development of arterial collaterals prior to thrombosis. Late HAT has a significant potential for irreversible graft damage requiring retransplantation. Screening for the development of hepatic artery stenosis prior to late thrombosis may be worthwhile.