Search

The review describes the changes observed in long noncoding RNA (lncRNA) content and function at various stages of carcinogenesis, as well as the prospects of lncRNA application in cancer prognosis. [ABSTRACT FROM AUTHOR]

This review describes the current methods of protein immunoanalysis, including radioimmunoanalysis, ELISA, immuno-PCR, electrochemical analysis, and chromatin immunoprecipitation, as well as their principal areas of application [ABSTRACT FROM AUTHOR]

A new immuno-PCR format based on the detection of CDH17 membrane protein in serum exosomes is proposed. Using the technique described, it was possible to distinguish between serum specimens obtained from healthy donors and colon cancer patients. The results suggest that the new technique may enable the serological diagnosis of colon cancer in high-risk groups. [ABSTRACT FROM AUTHOR]

The review summarizes our current knowledge on the role of tumor-derived exosomes and microvesicles in the progression, metastasis, and angiogenesis of tumors, as well as in the suppression of adaptive and innate immunity. [ABSTRACT FROM AUTHOR]

All- trans-retinoic acid (ATRA) is the main biologically active metabolite of retinol (vitamin A) that is required for the regulation of processes such as embryogenesis, tissue differentiation, proliferation, and others. Multiple alcohol, retinol, and retinaldehyde dehydrogenases (ADHs, RDHs, and RALDHs), as well as aldo-keto reductases (AKRs) catalyze the biosynthesis of retinoic acid in humans. For many normal and neoplastic tissues, the key ATRA-synthesizing enzymes remain unknown. We identified ATRA-generating genes that are expressed in normal and malignant gastric tissues using the transcriptomic database analysis. Quantitative changes in the expression levels of these genes in gastric cancer were determined by semi-quantitative RT-PCR and real-time PCR. Significant decreases in the mRNA levels of genes that encode the enzymes that catalyze the reversible oxidation/reduction of retinol and retinaldehyde ( ADH4, ADH1B, ADH1C, RDHL, AKR1B10, AKR1B1, and RDH12), as well as the oxidation of retinaldehyde ( RALDH1) were revealed in most tumor samples. A sharp reduction in the expression levels of genes encoding the key enzymes that convert retinol and retinaldehyde to retinoic acid could lead to a significant decrease in the content of ATRA, the transcriptional regulator of many genes, which can in turn lead to the dysregulation of cell proliferation/differentiation and initiate the development of cancer. [ABSTRACT FROM AUTHOR]

This review describes the most popular methods of searching for serological markers of tumors that are used in a clinical setting, as well as a comparison of their efficiency. [ABSTRACT FROM AUTHOR]

A new DNA reporter construct has been designed for protein quantification by immuno-PCR. It has been shown that the amplification efficiency of a reporter that contains a fragment of human adenovirus 2 flanked by homoprimer sequences is much higher than standard PCR format based on two different primers. The further application of the new construct and its homoprimer-based detection could represent new ways to increase the sensitivity of the immuno-PCR and the efficiency of single-molecule PCR. [ABSTRACT FROM AUTHOR]

The review summarizes the current data on the structure of enteric α-defensins, their functions in innate and adaptive immunity systems, and their role in intestinal illnesses. [ABSTRACT FROM AUTHOR]

A comparison of protein expression profiles in intestinal and diffuse gastric tumors and normal tissues by 2D gel electrophoresis identified three proteins (SOD2, S100A6, and TXN) overexpressed in tumors. SOD2 and TXN were more frequently overexpressed in diffuse tumors than in intestinal ones. Based on the published data on comparative 2DE protein expression analysis, a control panel of eleven proteins overexpressed in gastric tumors was compiled. A bioinformatic search for the respective mRNAs in the Oncomine database (representing mRNA transcription levels in tumor vs. normal tissues) showed the agreement of proteomic and transcriptomic data for seven of 11 proteins. [ABSTRACT FROM AUTHOR]

New algorithm of bioinformatic search for potential serum tumor markers has been worked out, including: (1) identification of microRNAs with the level of synthesis most evidently and often decreasing in tumors; (2) search for target mRNAs regulated by microRNAs; (3) selection of targets encoding secretory proteins; (4) comparative analysis of transcription level of the targets in normal and tumor tissues. Practical use of the algorithm has allowed us to detect seven potential serum markers of colon tumors: ADAMTS14, ANGPT2, CCL7, DEFA5, MMP11, MMP14, and PLAU. It has been experimentally indicated that the level of synthesis of two of seven proteins (MMP14 and DEFA5) is significantly increased in colon tumors compared to normal tissue. [ABSTRACT FROM AUTHOR]

modified method of proteome comparative analysis based on preliminary removal of cell structural proteins by extraction using salt buffer and subsequent separation of extracts by two-dimensional gel electrophoresis was developed. Identification of differentially expressed proteins by mass spectrometry has revealed three proteins with noticeably increased level of synthesis in most samples of papillary thyroid tumors compared to normal tissues. An increase in ubiquitin content was found for the first time. Oncomarker search efficiencies by two-dimensional gel electrophoresis and bioinformatic search were compared. [ABSTRACT FROM AUTHOR]

A modification of proteome differential analysis was developed; it comprises initial removal of the cell structural proteins by extraction with buffered saline and protein fractionation by gel filtration with subsequent separation by two-dimensional gel electrophoresis and identification by mass-spectrometry. This approach provided for detection of 12 proteins with significantly elevated expression levels in the majority of the analyzed malignant colorectal tumor specimens as compared with normal tissues. Increased contents of eight proteins were discovered for the first time. The efficiencies of the search for tumor markers by 2D analysis and serial analysis of gene expression (SAGE) were compared using the control panel of 19 potential colorectal tumor markers, identified earlier or independently found by other researchers. The 2D data for the control panel matched the earlier published data, whereas the search of SAGE database succeeded in detection only one-third of the markers. [ABSTRACT FROM AUTHOR]

Colorectal cancer is one of the most common cancers in the world. Changes in AKR1B1 and AKR1B10 expression levels, whose diagnostic value was previously shown for several other cancer types, were studied in colorectal tumors. These genes encode aldose reductases, members of the aldo-keto reductase superfamily, which comprises enzymes capable to reduce a range of aromatic and aliphatic aldehydes and ketones. They are also involved in retinoid metabolism and carcinogenesis. AKR1B1 and AKR1B10 mRNA levels were compared in paired specimens of normal and colorectal tumor tissues using RT-PCR and quantitative real-time PCR. For the first time, the downregulation of these genes was demonstrated in colorectal carcinoma. AKR1B10 expression was decreased in most tumor specimens (88%, 65/74) even at the early stages, and in more than 60% of cases mRNA levels were decreased more than 10-fold. AKR1B1 mRNA levels were decreased in 10% of specimens. Therefore, these two structurally similar genes show quite different mRNA expression patterns in colorectal cancer, suggestive of their different functional roles in the intestine. Significant downregulation of AKR1B10 expression can be considered a potential diagnostic marker of colorectal cancer. [ABSTRACT FROM AUTHOR]

Colorectal cancer is one of the most common malignancies in developed countries. Scarce clinical signs at the early stages of the disease and the lack of fast and sensitive diagnostic techniques based on the detection of tumor specific protein markers contribute greatly to the high mortality rate. The search for such markers is significantly complicated by the high levels of major structural and cytoskeletal proteins in normal and tumor tissues. Extraction with 0.2 M NaCl in the presence of the nonionic detergent NP-40 was performed to enrich the soluble protein fraction. This modification resulted in a considerably increased sensitivity of detection of minor proteins that may enter the circulation during carcinogenesis. The soluble protein profiles of the paired colon adenocarcinoma and normal tissue specimens were compared using 2D gel electrophoresis, which enabled the detection of 10 proteins whose levels in tumors were elevated at least 10-fold as compared to normal tissue. The proteins were identified by MALDI-TOF mass spectrometry, and two new protein markers of colon cancer, TAF9 and CISH, were discovered. Low levels of CISH synthesis in most normal human tissues and tumors other than colorectal cancer make it a prospective candidate diagnostic marker for this type of cancer. [ABSTRACT FROM AUTHOR]

Modern proteomic techniques make it possible to identify numerous changes in protein expression in tumors as compared to normal tissues. Although proteomics is currently widely used, identification of proteins differentially expressed in particular types of cancer remains a challenging task. The goal of our study was to detect novel protein markers of colorectal cancer using comparative proteomics of protein extracts obtained from primary tumors and adjacent normal tissues. Coloreetal cancer is nearly asymptomatic at the early stages, which calls for development of fast and sensitive methods for molecular diagnostics. Proteomes of 11 paired specimens of primary colorectal tumors and adjacent histologically normal tissues were studied using comparative 2D PAGE. Altogether, 16 proteins with altered expression levels were detected, including 13 proteins with increased levels and three proteins with decreased levels in tumor tissues. These proteins were identified using MALDI-TOF mass spectrometry. The proteins GPD1, RRBP1 (increased levels), HNRNPH1, and SERPINB6 (decreased levels) have been associated with colorectal cancer for the first time. [ABSTRACT FROM AUTHOR]

Rpn4p is an extremely short-lived proteasome-associated protein that acts both as a positive and negative transcriptional regulator of the ubiquitin-proteasome system and as its substrate. The mechanisms of proteasomal degradation of Rpn4p have been studied in great detail; however, the mechanisms of its own action remain unclear and, first of all, its functional domains are unknown. To map the functionally important regions, a set of Rpn4p deletion derivates was constructed. The mutant proteins were expressed in Saccharomyces cerevisiae strain rpn4-Δ, their contents were determined by Western blotting, and their activity was assessed by measuring the mRNA levels of proteasome genes. Deletions of the C-terminal region, containing DNA-binding zinc finger domains, and the N-terminal region, having no homology to the transactivation domains of any known transcription factor, completely inactivated Rpn4p. Only one of the two acidic regions, putative transactivation domains, proved to participate in transcriptional activation. Deletions of the N-terminal region, NAD, or zinc finger domains rendered Rpn4p metabolically stable. These data provide new insights into the mechanisms of the Rpn4p functioning and degradation. [ABSTRACT FROM AUTHOR]

A rapid method for mapping exposed cytosine residues in 5′-[P]-labeled RNA molecules is suggested. The exposed cytosines (C's) are converted into uracyls (U's) by bisulphite treatment at pH 5.8 in the presence of Mg, followed by complete modification of the residual (non-exposed) C's by a methoxyamine and bisulphite mixture at pH 5.0. The control RNA is modified only by methoxyamine and bisulphite without the preliminary C→U conversion. The location of the exposed C's is determined by comparing the products of partial T, T, A and U ribonuclease digestions of the C → U converted and control RNAs after slab gel polyacrylamide electrophoresis and autoradiography. The method has been applied for mapping exposed cytosine bases in tRNA (yeast) which have been found in the anticodon loop and at the 3′-end of the molecule. In tRNA (beef liver), in addition to the same exposed bases, C in the diHU-loop is exposed. The data obtained are in full agreement with that is known about exposed C's for other tRNAs. [ABSTRACT FROM AUTHOR]

The screening for enteric α-defensin was performed in the blood serum of oncology patients and healthy donors. Enteric α-defensin was not detected in all serum samples from five healthy donors, while serum samples from two of the five oncology patients had the processed form of this protein. The acquired results allow us to suggest the possibility of the serological diagnostics of large intestinal tumors in high-risk groups. [ABSTRACT FROM AUTHOR]