Calorimetry-based profiling of blood plasma from colorectal cancer patients.

BACKGROUND: Differential scanning calorimetry (DSC), a highly sensitive technique for resolving thermally-induced protein folding/unfolding transitions, recently was recognized as a novel tool for disease diagnosis and monitoring. To further elaborate this approach we have applied DSC in a study of blood plasma from patients with colorectal cancer (CRC) at different stages of tumor development and localization. METHODS: Blood plasma from patients diagnosed with CRC was analyzed by DSC. The CRC thermograms were compared to those of healthy individuals and patients with gastric cancer and non-cancerous soft tissue inflammation. The thermodynamic parameters: excess heat capacity and enthalpy of the transitions corresponding to the most abundant plasma proteins, as well as transition and first moment temperatures were determined from the calorimetric profiles. RESULTS: The calorimetric profiles of blood plasma from CRC patients are found to be distinct from those of healthy individuals and those of patients with soft tissue, non-cancerous inflammation. Generally the CRC thermograms exhibit reduced heat capacity of the major albumin/globulin-assigned thermal transitions, lower enthalpy and a featureless high temperature region compared to healthy individuals. CONCLUSIONS: A classification of blood plasma proteome from patients with colorectal cancer (CRC1, CRC2 and CRC3 groups, and subgroups within each group CRC1(1-2), CRC2(1-2) and CRC3(1-2)) is proposed based on the derived thermodynamic parameters. GENERAL SIGNIFICANCE: The presented data demonstrate a proof of principle and confirm that the DSC technique has a potential to monitor changes in the CRC blood plasma proteome. This study is a further step toward the validation of calorimetry as a diagnostic tool.

Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix.

It is now possible to slow and trap a single molecule of double-stranded DNA (dsDNA), by stretching it using a nanopore, smaller in diameter than the double helix, in a solid-state membrane. By applying an electric force larger than the threshold for stretching, dsDNA can be impelled through the pore. Once a current blockade associated with a translocating molecule is detected, the electric field in the pore is switched in an interval less than the translocation time to a value below the threshold for stretching. According to molecular dynamics (MD) simulations, this leaves the dsDNA stretched in the pore constriction with the base-pairs tilted, while the B-form canonical structure is preserved outside the pore. In this configuration, the translocation velocity is substantially reduced from 1 bp/10 ns to approximately 1 bp/2 ms in the extreme, potentially facilitating high fidelity reads for sequencing, precise sorting, and high resolution (force) spectroscopy.

Microscopic mechanics of hairpin DNA translocation through synthetic nanopores.

Nanoscale pores have proved useful as a means to assay DNA and are actively being developed as the basis of genome sequencing methods. Hairpin DNA (hpDNA), having both double-helical and overhanging coil portions, can be trapped in a nanopore, giving ample time to execute a sequence measurement. In this article, we provide a detailed account of hpDNA interaction with a synthetic nanopore obtained through extensive all-atom molecular dynamics simulations. For synthetic pores with minimum diameters from 1.3 to 2.2 nm, we find that hpDNA can translocate by three modes: unzipping of the double helix and--in two distinct orientations--stretching/distortion of the double helix. Furthermore, each of these modes can be selected by an appropriate choice of the pore size and voltage applied transverse to the membrane. We demonstrate that the presence of hpDNA can dramatically alter the distribution of ions within the pore, substantially affecting the ionic current through it. In experiments and simulations, the ionic current relative to that in the absence of DNA can drop below 10% and rise beyond 200%. Simulations associate the former with the double helix occupying the constriction and the latter with accumulation of DNA that has passed through the constriction.

Analysis of the K-ras/B-raf/Erk signal cascade, p53 and CMAP as markers for tumor progression in colorectal cancer patients.

Colorectal cancer patients may succumb to their disease because of local recurrence or formation of metastasis. To develop a prognostic tool for these fatal types of progression, 23 patients with colorectal carcinoma were included in this study for the detection at the time of surgery of the incidence of K-ras, B-raf and p53 mutations, the phosphorylation status of Erk and the expression of cystatin-like metastasis-associated protein (CMAP) in tumor, mucosa and liver samples. Polymerase chain reaction-restriction fragment length polymorphism and PCR-SSCP were used to detect the respective mutations. The results of these assays were complemented by sequencing the K-ras, B-raf and p53 mutations. A multiplex RT-PCR assay was used to detect the CMAP mRNA levels and the phosphorylation status of Erk in tumor samples was assessed by Western blot using a phosphospecific Erk antibody. The carcinomas were classified as stages T4 (70%), T3 (17%), T2 (9%) and T1 (4%) and thus represent a group of advanced colorectal carcinomas. The carcinomas (8 out of 23, 39.1%) were mutated in K-ras codons 12 or 13 and two patients had a B-raf (V599) mutation in their tumor. Of 22 tumors, 11 (50%) were positive for pErk, indicating the activation of the RAS/RAF/ERK signaling pathway. Of the 23 tumors, 13 (65.5%) showed an increased CMAP RNA level. Notably, 10 of these 13 patients have already died and two developed liver metastasis. Mutations in p53 were found in only 6 patients (26%), with 6 being detected in carcinoma, 1 in mucosa and 1 in liver tissue. These alterations were classified as non-sense (n=1), mis-sense (n=2) and frame-shift mutations (n=1) as well as intron polymorphisms (n=5). There was a significant correlation between Erk activation and K-ras codon 12 mutation (p=0.016), but not between K-ras codon 13 or B-raf mutations and Erk activation. Furthermore, there was a significant correlation of each positive marker with tumor stage (p=0.001).