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.     

Yarrow (<Emphasis Type="Italic">Achillea millefolium</Emphasis> L.): A Neglected Panacea? A Review of Ethnobotany,Bioactivity, and Biomedical Research<Superscript>1</Superscript>

Yarrow ( Achillea millefolium L.): A Neglected Panacea? A Review of Ethnobotany, Bioactivity, and Biomedical Research. Yarrow (Achillea millefolium L.) is one of the most widely used medicinal plants in the world, primarily for wounds, digestive problems, respiratory infections, and skin conditions, and secondarily, among other uses, for liver disease and as a mild sedative. Preclinical studies indicate that it may have anti-inflammatory, anti-ulcer, hepatoprotective, anxiolytic, and perhaps antipathogenic activities. Animal studies have also shown that yarrow is generally safe and well tolerated. The claim that yarrow has been shown to be specifically contraindicated during pregnancy is based on a single low-quality rat study the results of which were incorrectly interpreted. The combination of human use data from multiple cultures, independently reporting similar activities for yarrow, and the discovery of potentially relevant bioactivities by in vitro and animal studies represent meaningful evidence of the plant’s efficacy. We therefore argue that human clinical trials should be funded and conducted.     

UNC-97/PINCH is involved in the assembly of integrin cell adhesion complexes in Caenorhabditis elegans body wall muscle

UNC-97/PINCH is an evolutionarily conserved protein that contains five LIM domains and is located at cell-extracellular matrix attachment sites known as cell adhesion complexes. To understand the role of UNC-97/PINCH in cell adhesion, we undertook a combined genetic and cell biological approach to identify the steps required to assemble cell adhesion complexes in Caenorhabditis elegans. First, we have generated a complete loss of function mutation in the unc-97 coding region. unc-97 null mutants arrest development during embryogenesis and reveal that the myofilament lattice and its attachment structures, which include PAT-4/ILK (integrin-linked kinase) and integrin fail to assemble into properly organized arrays. Although in the absence of UNC-97/PINCH, PAT-4/ILK and integrin fail to organize normally, they are capable of colocalizing together at the muscle cell membrane. Alternatively, in integrin and pat-4 mutants, UNC-97/PINCH fails to localize to the muscle cell membrane and instead is found diffusely throughout the muscle cell cytoplasm. In agreement with mammalian studies, we show that LIM domain 1 of UNC-97/PINCH is required for its interaction with PAT-4/ILK in yeast two-hybrid assays. Additionally, we find, by LIM domain deletion analysis, that LIM1 is required for the localization of UNC-97/PINCH to cell adhesion complexes. Our results provide evidence that UNC-97/PINCH is required for the development of C. elegans and is required for the formation of integrin based adhesion structures.     

Digital image correlation and finite element modelling as a method to determine mechanical properties of human soft tissue in vivo

The mechanical properties of human soft tissue are crucial for impact biomechanics, rehabilitation engineering, and surgical simulation. Validation of these constitutive models using human data remains challenging and often requires the use of non-invasive imaging and inverse finite element (FE) analysis. Post-processing data from imaging methods such as tagged magnetic resonance imaging (MRI) can be challenging. Digital image correlation (DIC), however, is a relatively straightforward imaging method. DIC has been used in the past to study the planar and superficial properties of soft tissue and excised soft tissue layers. However, DIC has not been used to non-invasive study of the bulk properties of human soft tissue in vivo. Thus, the goal of this study was to assess the use of DIC in combination with FE modelling to determine the bulk material properties of human soft tissue. Indentation experiments were performed on a silicone gel soft tissue phantom. A two camera DIC setup was then used to record the 3D surface deformation. The experiment was then simulated using a FE model. The gel was modelled as Neo-Hookean hyperelastic, and the material parameters were determined by minimising the error between the experimental and FE data. The iterative FE analysis determined material parameters (μ=1.80 kPa, K=2999 kPa) that were in close agreement with parameters derived independently from regression to uniaxial compression tests (μ=1.71 kPa, K=2857 kPa). Furthermore the FE model was capable of reproducing the experimental indentor force as well as the surface deformation found (R²=0.81). It was therefore concluded that a two camera DIC configuration combined with FE modelling can be used to determine the bulk mechanical properties of materials that can be represented using hyperelastic Neo-Hookean constitutive laws.     

An Integrated Strategy to Study Muscle Development and Myofilament Structure in Caenorhabditis elegans

A crucial step in the development of muscle cells in all metazoan animals is the assembly and anchorage of the sarcomere, the essential repeat unit responsible for muscle contraction. In Caenorhabditis elegans, many of the critical proteins involved in this process have been uncovered through mutational screens focusing on uncoordinated movement and embryonic arrest phenotypes. We propose that additional sarcomeric proteins exist for which there is a less severe, or entirely different, mutant phenotype produced in their absence. We have used Serial Analysis of Gene Expression (SAGE) to generate a comprehensive profile of late embryonic muscle gene expression. We generated two replicate long SAGE libraries for sorted embryonic muscle cells, identifying 7,974 protein-coding genes. A refined list of 3,577 genes expressed in muscle cells was compiled from the overlap between our SAGE data and available microarray data. Using the genes in our refined list, we have performed two separate RNA interference (RNAi) screens to identify novel genes that play a role in sarcomere assembly and/or maintenance in either embryonic or adult muscle. To identify muscle defects in embryos, we screened specifically for the Pat embryonic arrest phenotype. To visualize muscle defects in adult animals, we fed dsRNA to worms producing a GFP-tagged myosin protein, thus allowing us to analyze their myofilament organization under gene knockdown conditions using fluorescence microscopy. By eliminating or severely reducing the expression of 3,300 genes using RNAi, we identified 122 genes necessary for proper myofilament organization, 108 of which are genes without a previously characterized role in muscle. Many of the genes affecting sarcomere integrity have human homologs for which little or nothing is known.