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Diagnostics of Colorectal Cancer

#3737


Transcriptopmic and Proteomic Biomarkers Patterning for Early Differential Diagnosis, Prognosis and Monitoring of Colorectal Cancer

Tech Area / Field

  • BIO-CGM/Cytology, Genetics and Molecular Biology/Biotechnology
  • BIO-CHM/Biochemistry/Biotechnology
  • BIO-INF/Bioinformatics/Biotechnology

Status
8 Project completed

Registration date
09.04.2007

Completion date
08.10.2010

Senior Project Manager
Melnikov V G

Leading Institute
Engelhardt Institute of Molecular Biology, Russia, Moscow

Supporting institutes

  • Institute of Highly Pure Biopreparations, Russia, St Petersburg

Collaborators

  • Karolinska Institute / Microbiology and Tumor Biology Center, Sweden, Stockholm

Project summary

The colorectal cancer (CRC) represents the second-third cause of deaths from oncological diseases in Russia and in developed countries of Europe and North America. The success of treatment of cancer patients is predominantly defined by early diagnostics. Specificity and sensitivity of existing colorectal biomarkers is insufficient to apply them properly at early stages of a disease. The aim of the proposed project is to develop easy-to-use and cost-effective technologies able to use patient samples in the clinical settings to identify, evaluate and validate molecular biomarkers set (patterning) for the early detection of CRC, precancerous lesions and benign tumors, prognosis, monitoring and aid to physicians in selection of the CRC treatment.

Staff participants of the current project exhibit high level experience in the modern bioinformatics, genomics, transcriptomics and proteomics for cancer research; they have tens of publications in the field of cancer research. Several participants worked for substantial periods of time abroad in universities medical schools, hospitals and cancer centers including Memorial Sloan-Kettering Cancer Center, New York, USA, Karolinska Institute, Stockholm, Sweden, Institute Jacques Monod, University Paris 7, France, etc.

In the course of this project, application of transcriptomic and proteomic methods will help to develop sensitive and highly selective molecular biomarkers for early differential diagnostics of precancerous adenomas and adenocarcinomas, identification of high-risk patients as well as monitoring and aid to physicians in selection of the proper treatment.

In terms of the project objective and expected results for two years research, it is intended to solve a number of tasks differing in complexity and labor-consumption. The experimental objectives of the project are subpided into five Tasks. Task 1 (specimen collection) will continue for a two years. Task 2 (bioinformatics search and assessment of candidate genes for early CRC diagnostics and design and synthesis of set of primers) will be carried out in the first year and half of the second year. Task 3 (evaluation and validation of transcriptomic biomarkers patterning for early CRC diagnostics) will start in the quarter 3 and will continue for 5 quarters. Task 4 (evaluation and validation of proteomic biomarkers patterning for early CRC diagnostics) will be started in the quarter 4 and will be finished at the end of the second year. Diagnostic kit proposal and testing (Task 5) will cover the second half of the second year.

During this project, collection of surgery and serum specimens will be performed. Samples of normal and tumor tissues will be collected from not less than hundred patients. In addition, normal serum samples for controls will be collected from patients and healthy donors. Using bioinformatic approaches, a set of candidate genes will be identified and selected whose expression is significantly changed in CRC versus benign tumors and normal tissues at the level of mRNA and protein synthesis. A set of specific oligodeoxyribonucleotide primers will be selected for experimental evaluation of mRNA expression levels from patient tissue samples using real-time PCR analysis.

After collecting statistically significant data for set of gene transcription levels alterations, they will be analyzed aiming of selecting a minimum genes that is most informative in transcription in distinguishing normal, benign and CRC tissues. It is anticipated that at least three genes will be evaluated and validated as transcriptomic biomarker patterning for early CRC.

The whole gene set used for establishing of transcriptomic biomarker patterning will subjected for analysis of expression levels of corresponding proteins. These proteins (or their fragments) will be expressed in bacteria after cloning of certain genes in plasmids, purified to homogeneity, and used to generate high-affinity, sequence-specific polyclonal monoreactive antibodies.

These monoreactive antibodies after testing for their specificity towards their antigens will be used for measuring experimentally level of their antigenes in normal/benign/CRC tissues. The set of most informative antibodies in distinguishing three types of tissues will be selected and corresponding proteins will be validated as proteomic biomarker patterning for detection of CRC using immunofluorescence assays. Finally the reliable diagnostic kit based on both transcriptomic and proteomic biomarker patterning will be proposed. The implementation of the project will, provide peaceful research opportunity to the scientists from State Research Institute of Highly Pure Biopreparations, prior involved in medico-biological testing of chemical and biological weapons defence, to reorient their efforts, knowledge and rich experience to Cancer Research in the Public Interest.


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