Epoxide electrophiles as activity-dependent cysteine protease profiling and discovery tools

The present invention provides 6-modified bicyclic nucleoside analogs and oligomeric compounds comprising these nucleoside analogs. In preferred embodiments the nucleoside analogs have either (R) or (S)-chirality at the 6-position. These bicyclicnucleoside analogs are useful for enhancing properties of oligomeric compounds including nuclease resistance.

6-modified bicyclic nucleic acid analogs

The present invention provides 5′-modified bicyclic nucleoside analogs and oligomeric compounds comprising at least one of these nucleoside analogs. In preferred embodiments the nucleoside analogs have either (R) or (S)-chirality at the 5′-carbon. These bicyclic nucleoside analogs are useful for enhancing properties of oligomeric compounds including for example enhanced nuclease resistance.

5′-modified bicyclic nucleic acid analogs

Provided herein are bicyeMc nucleosides comprising a substituted amino group in the bridge, oligomeric compounds having at least one of these bi cyclic nucleosides and methods of using the oligomeric compounds. The bicyclic nucleosides comprising a substituted amino group in the bridge are useful for enhancing properties of oligomeric compounds including nuclease resistance, in certain embodiments, the oligomeric compounds hybridize to a portion of a target RNA resulting in loss of normal function of the target RNA.

N-substituted-aminomethylene bridged bicyclic nucleic acid analogs

Early detection is critical in cancer control and prevention. Biomarkers help in this process by providing valuable information about a the status of a cell at any given point in time. As a cell transforms from nondiseased to neoplastic, distinct changes occur that could be potentially detected through the identification of the appropriate biomarkers. Biomarker research has benefited from advances in technology such as proteomics. We discuss here ongoing research in this field, focusing on proteomic technologies. The advances in two-dimensional electrophoresis and mass spectrometry are discussed in light of their contribution to biomarker research. Chip-based techniques, such as surface-enhanced laser desorption, and ionization and emerging methods, such as tissue and antibody arrays, are also discussed. The development of bioinformatic tools that have and are being developed in parallel to proteomics is also addressed. This report brings into focus the efforts of the Early Detection Research Network at the National Cancer Institute in harnessing scientific expertise from leading institutions to identify and validate biomarkers for early detection and risk assessment.

Proteomics in Early Detection of Cancer

In recent years, genomics has increased the understanding of many diseases Proteomics is a rapidly growing research area that encompasses both genetic and environmental factors The protein composition represents the functional status of a biological compartment The five approaches presented here resulted in the detection of disease-associated proteins Calgranulin B was upregulated in colorectal cancer, and hepatoma-derived aldose reductase-like protein was reexpressed in a rat model during hepatocarcinogenesis In these two investigations, attention was focused on one protein, obviously differing in amount, directly after two-dimensional electrophoresis (2-DE) Additional methods, such as enzyme activity measurements and immunohistochemistry, confirmed the disease association of the two candidates resulting from 2-DE subtractive analysis The following three investigations take advantage of the holistic potential of the 2-DE approach The comparison of 2-DE patterns from dilated cardiomyopathy patients with those of controls revealed 25 statistically significant intensity differences, from which 12 were identified by amino acid analysis, Edman degradation or matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) A human myocardial 2-DE database was constructed, containing 3300 protein spots and 150 identified protein species The number of identified proteins was limited by the capacity of our group, rather than by the principle of feasibility Another field where proteomics proves to be a valuable tool in identifying proteins of importance for diagnosis is proteome analysis of pathogenic microorganisms such as Borrelia burgdorferi (Lyme disease) and Toxoplasma gondii (toxoplasmosis) Sera from patients with early or late symptoms of Lyme borreliosis contained antibodies of various classes against about 80 antigens each, containing the already described antigens OspA, B and C, flagellin, p83/100, and p39 Similarly, antibody reactivity to seven different marker antigens of T gondii allowed differentiation between acute and latent toxoplasmosis, an important diagnostic tool in both pregnancy and immunosuppressed patients

Proteomics in human disease: Cancer, heart and infectious diseases

Toxoplasma gondii is known to cause a variety of diseases ranging from asymptomatic infections to serious conditions in immunocompromised hosts such as AIDS-patients or transplant recipients. In addition they may cause abortion or fetal abnormalities during pregnancy. Despite the clinical importance, diagnosis, treatment and prevention still remain unsatisfactory. Analysis of the parasitic cell determinants, recognized by specific humoral and cellular immune responses, may have important implications for diagnosis, therapy and vaccination strategies. Two-dimensional electrophoresis (2-DE) was used to resolve and compare protein patterns from Toxoplasma gondii strains RH and BK (mouse virulent strains). Comparison of silver-stained gels showed that 35.2% to 60.3% of the spots had the same position. In a second series of experiments, the reactivity of the spots with human sera was tested. Proteins were transferred to PVDF membranes and were detected with sera from different patient groups. Depending upon the immunoglobulin class (IgG, IgM, IgA or IgE) different epitope patterns were observed. Some of the spots seemed to be recognized in different stages of infection. Sera of two patients with similar serology and comparable stage of infection were compared in order to demonstrate an individual immune response.

Wanda Sokolowska-Köhler

Papers

Proteomics in human disease: Cancer, heart and infectious diseases

Toxoplasma gondii infection: analysis of serological response by 2-DE immunoblotting.

Genotypic and phenotypic determination of five virulence markers in clinical isolates of