Copy number alterations and allelic ratio in relation to recurrence of rectal cancer

Background

In rectal cancer, total mesorectal excision surgery combined with preoperative (chemo)radiotherapy reduces local recurrence rates but does not improve overall patient survival, a result that may be due to the harmful side effects and/or co-morbidity of preoperative treatment. New biomarkers are needed to facilitate identification of rectal cancer patients at high risk for local recurrent disease. This would allow for preoperative (chemo)radiotherapy to be restricted to high-risk patients, thereby reducing overtreatment and allowing personalized treatment protocols. We analyzed genome-wide DNA copy number (CN) and allelic alterations in 112 tumors from preoperatively untreated rectal cancer patients. Sixty-six patients with local and/or distant recurrent disease were compared to matched controls without recurrence. Results were validated in a second cohort of tumors from 95 matched rectal cancer patients. Additionally, we performed a meta-analysis that included 42 studies reporting on CN alterations in colorectal cancer and compared results to our own data.

Results

The genomic profiles in our study were comparable to other rectal cancer studies. Results of the meta-analysis supported the hypothesis that colon cancer and rectal cancer may be distinct disease entities. In our discovery patient study cohort, allelic retention of chromosome 7 was significantly associated with local recurrent disease. Data from the validation cohort were supportive, albeit not statistically significant, of this finding.

Conclusions

We showed that retention of heterozygosity on chromosome 7 may be associated with local recurrence in rectal cancer. Further research is warranted to elucidate the mechanisms and effect of retention of chromosome 7 on the development of local recurrent disease in rectal cancer.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1550-0) contains supplementary material, which is available to authorized users.     

Dynamic exchange between stabilized conformations predicted for hyaluronan tetrasaccharides: comparison of molecular dynamics simulations with available NMR data

Studies of the hyaluronan (HA) tetrasaccharides are important for understanding hydrogen-bonding in the HA polymer, as they are probably the smallest oligomers in which characteristics of the constituent monosaccharides and the polymer are simultaneously exhibited. Here we present extensive molecular dynamics simulations of the two tetrasaccharides of HA in dilute aqueous solution. These simulations have confirmed the existence of intramolecular hydrogen-bonds between the neighboring sugar residues of HA in solution, as proposed by Scott (1989). However, our simulations predict that these intramolecular hydrogen-bonds are not static as previously proposed, but are in constant dynamic exchange on the sub-nanosecond time-scale. This process results in discrete internal motion of the HA tetrasaccharides where they rapidly move between low energy conformations. Specific interactions between water and intramolecular hydrogen-bonds involving the hydroxymethyl group were found to result in differing conformations and dynamics for the two alternative tetrasaccharides of HA. This new observation suggests that this residue may play a key role in the entropy and stability of HA in solution, allowing it to stay soluble up to high concentration. The vicinal coupling constants3 J NHCH of the acetamido groups have been calculated from our aqueous simulations of HA. We found that high values of 3J NHCH approximately 8 Hz, as experimentally measured for HA, are consistent with mixtures of both trans and cis conformations, and thus3 J NHCH cannot be used to imply a purely trans conformation of the acetamido. The rapid exchange of intramolecular hydrogen-bonds indicates that although the structure is at any moment stabilized by these hydrogen-bonds, no one hydrogen-bond exists for an extended period of time. This could explain why NMR often fails to provide evidence for intramolecular hydrogen-bonds in HA and other aqueous carbohydrate structures.      

Seasonal inhibition of puberty in domestic gilts is overcome by melatonin administered orally, but not by implant.

The ability of exogenous melatonin, applied either orally or by implant, to overcome the seasonal inhibition of puberty in domestic gilts was tested in two experiments. In Expt 1, 24 gilts received two melatonin implants at 126 days of age and again at 161 days and 196 days, while 24 gilts acted as controls. All gilts were slaughtered at a mean age of 223 days. Blood samples were collected by venepuncture from eight gilts in each treatment at 126, 144 and 178 days of age and the plasma was assayed for melatonin concentration by direct radioimmunoassay. In Expt 2A, four gilts (125 days of age) were fed either 0, 1, 2 or 4 mg of melatonin at 14:00 h on each of four consecutive days. Blood samples for melatonin assay were collected via indwelling jugular catheters every 30 or 60 min from 12:00 to 22:00 h. In Expt 2B, 27 gilts were fed 1 mg of melatonin at 15:00 h each day from 129 days of age until slaughter at 221 days, while 25 gilts acted as controls. In both experiments, the presence of morphologically normal corpora lutea at slaughter was the criterion for puberty. In Expt 1, constant-release melatonin implants had no effect on the percentage of gilts which reached puberty. Among the 24 control gilts, two (8.3%) reached puberty compared with one of the 24 (4.2%) gilts with implants. In all the samples from control gilts, and in the samples taken from treated gilts prior to implantation at 126 days of age, mean plasma melatonin concentration was below the sensitivity of the assay (3.6 pg/ml).(ABSTRACT TRUNCATED AT 250 WORDS)     

Erythrocyte hexose monophosphate shunt is intact in healthy aged humans

The integrity of the erythrocyte (RBC) hexose monophosphate shunt was investigated in a group of 33 healthy elderly individuals by determining their RBC glutathione content, glucose-6-phosphate dehydrogenase activity and glutathione regeneration. When these parameters were compared with those of the controls, 44 young healthy adults, no significant differences were found. This study indicates that the RBC hexose monophosphate shunt in healthy elderly individuals is intact. Factors other than senescence per se should be sought in elderly individuals who exhibit dysfunction of this shunt.     

Stem cell death and survival in heart regeneration and repair

Cardiovascular diseases are major causes of mortality and morbidity. Cardiomyocyte apoptosis disrupts cardiac function and leads to cardiac decompensation and terminal heart failure. Delineating the regulatory signaling pathways that orchestrate cell survival in the heart has significant therapeutic implications. Cardiac tissue has limited capacity to regenerate and repair. Stem cell therapy is a successful approach for repairing and regenerating ischemic cardiac tissue; however, transplanted cells display very high death percentage, a problem that affects success of tissue regeneration. Stem cells display multipotency or pluripotency and undergo self-renewal, however these events are negatively influenced by upregulation of cell death machinery that induces the significant decrease in survival and differentiation signals upon cardiovascular injury. While efforts to identify cell types and molecular pathways that promote cardiac tissue regeneration have been productive, studies that focus on blocking the extensive cell death after transplantation are limited. The control of cell death includes multiple networks rather than one crucial pathway, which underlies the challenge of identifying the interaction between various cellular and biochemical components. This review is aimed at exploiting the molecular mechanisms by which stem cells resist death signals to develop into mature and healthy cardiac cells. Specifically, we focus on a number of factors that control death and survival of stem cells upon transplantation and ultimately affect cardiac regeneration. We also discuss potential survival enhancing strategies and how they could be meaningful in the design of targeted therapies that improve cardiac function.