Genomic and oncoproteomic advances in detection and treatment of colorectal cancer

<p>Abstract</p> <p>Aims</p> <p>We will examine the latest advances in genomic and proteomic laboratory technology. Through an extensive literature review we aim to critically appraise those studies which have utilized these latest technologies and ascertain their potential to identify clinically useful biomarkers.</p> <p>Methods</p> <p>An extensive review of the literature was carried out in both online medical journals and through the Royal College of Surgeons in Ireland library.</p> <p>Results</p> <p>Laboratory technology has advanced in the fields of genomics and oncoproteomics. Gene expression profiling with DNA microarray technology has allowed us to begin genetic profiling of colorectal cancer tissue. The response to chemotherapy can differ amongst individual tumors. For the first time researchers have begun to isolate and identify the genes responsible. New laboratory techniques allow us to isolate proteins preferentially expressed in colorectal cancer tissue. This could potentially lead to identification of a clinically useful protein biomarker in colorectal cancer screening and treatment.</p> <p>Conclusion</p> <p>If a set of discriminating genes could be used for characterization and prediction of chemotherapeutic response, an individualized tailored therapeutic regime could become the standard of care for those undergoing systemic treatment for colorectal cancer. New laboratory techniques of protein identification may eventually allow identification of a clinically useful biomarker that could be used for screening and treatment. At present however, both expression of different gene signatures and isolation of various protein peaks has been limited by study size. Independent multi-centre correlation of results with larger sample sizes is needed to allow translation into clinical practice.</p

Brownian dynamics simulations of dendrimers under shear flow

Brownian dynamics simulations of perfect dendrimers up to the sixth generation have been performed under the influence of simple shear flow. Hydrodynamic and excluded volume interactions have been taken into account explicitly. The onset of shear-thinning is observed to occur at lower shear rates for larger dendrimers (i.e. more generations). As the generation increases, the zero shear rate intrinsic viscosity reaches a maximum and begins to fall. The radius of gyration, the hydrodynamic radius, the translational mobility, and radial density profiles including the location of the terminal groups are also reported

Computer Simulations of Hyperbranched Polymers in Shear Flows

Brownian dynamics simulations of hyperbranched polymers with different degrees of branching have been performed under the influence of simple shear flow. Hydrodynamic and excluded-volume interactions have been taken into account explicitly. Shear-thinning effects have been observed for all simulated degrees of branching. As the molecular weight of highly branched structures increases, the zero shear rate intrinsic viscosity reaches a maximum and begins to fall similar to the intrinsic viscosity behavior of perfectly branched dendrimers. In the absence of shear, static structure factors, S(k), for hyperbranched polymers with the smallest number of monomers studied resemble those of a three-arm star. As the number of monomers increases and as the degree of branching increases, the S(k) curves for the hyperbranched polymers begin to illustrate features associated with S(k) curves for hard spheres. Further insight into the shape and interior density of these structures is obtained through the ratio of the radius of gyration, Rg, to the hydrodynamic radius, Rh. The ratio Rg/Rh is observed to approach unity as the number of monomers and the degree of branching increase

Brownian dynamics simulation of linear polymers under elongational flow: Bead–rod model with hydrodynamic interactions

Brownian dynamics (BD) simulations of a linear freely jointed bead–rod polymer chain with excluded volume (EV) interaction have been performed under elongational flow with and without the use of fluctuating hydrodynamic interactions (HI). The dependence of the chain size, shape and intrinsic elongational viscosity on the elongational rate are reported. A sharp coil–stretch transition is observed when exceeds a critical value, c. The inclusion of the HI leads to a shift in the coil–stretch transition to higher flow values. Chain deformation due to elongational flow is observed to first consist of the alignment of the chain with the direction of flow without significant chain extension followed by additional alignment of the bond vectors with the flow direction and chain extension as flow rate is increased further. The distribution function for the chain's radius of gyration becomes significantly broader within the transition region which implies an increase in fluctuations in the chain size in this region. The structure factors parallel and perpendicular to the flow direction illustrate different elongational rate dependencies. At high rates, the structure factor in the direction of the flow exhibits an oscillating dependence which corresponds to the theoretically predicted shape for a rigid-rod model. The mean squared orientation of each bond within the chain with respect to the flow direction as function of bond number is nearly parabolic in shape with the highest degree of orientation found within the chain's interior. The dependence of the critical elongational rate, c, on the chain length, N, is observed to be c~N–1.96 when hydrodynamic interactions are not employed and c~N–1.55 when they are invoked. These scaling exponents agree well with those obtained in previous BD simulations of bead-FENE (i.e., finitely extensible nonlinear elastic) spring chains as well as with the theoretical predictions of c~N–2 and c~N–1.5 without and with hydrodynamic interactions based on the Rouse and Zimm models, respectivel

Regulation of the expression of annexin VIII in acute promyelocytic leukemia

Annexin VIII is a calcium-dependent phospholipid-binding protein previously identified as a blood anticoagulant based on in vitro studies. However, the physiologic function of annexin VIII remains unknown. In acute promyelocytic leukemia (APL) the annexin VIII gene is highly expressed, but its expression is undetectable in the blasts of other acute leukemias. In the present investigation, we showed using the APL-derived NB4 cell line that expression of the annexin VIII gene is regulated at the transcription level during induced differentiation by all-trans retinoic acid (ATRA). The half-life of the annexin VIII mRNA is about 5 to 6 hours, as determined by using actinomycin D as a transcription inhibitor. Analysis of the expression of annexin VIII protein in NB4 cells and in APL samples showed a consistent expression of a predominant 36-kD protein and a weak 72-kD protein. After ATRA- induced differentiation of NB4 cells, the annexin VIII protein level reduced gradually, but a detectable level persisted even after 4 days of induction. Because annexin VIII mRNA becomes undetectable after 48 hours of ATRA induction, this result indicates that annexin VIII is a relatively stable protein. A multiple tissue Northern blot analysis was performed, and we found that annexin VIII is normally expressed in the placenta and the lung. Cellular localization of the annexin VIII protein was determined by immunofluorescence staining and subcellular fractionation. These results indicated that annexin VIII is predominantly localized to the plasma membrane. The annexin VIII is neither an extracellular protein nor associated with the cell surface suggesting that it does not play a role in blood coagulation in vivo. The plasma membrane localization and its property as a phospholipase inhibitor suggests that annexin VIII may have a role in the signal transduction pathway in the APL cells.</jats:p

Regulation of the expression of annexin VIII in acute promyelocytic leukemia

Abstract Annexin VIII is a calcium-dependent phospholipid-binding protein previously identified as a blood anticoagulant based on in vitro studies. However, the physiologic function of annexin VIII remains unknown. In acute promyelocytic leukemia (APL) the annexin VIII gene is highly expressed, but its expression is undetectable in the blasts of other acute leukemias. In the present investigation, we showed using the APL-derived NB4 cell line that expression of the annexin VIII gene is regulated at the transcription level during induced differentiation by all-trans retinoic acid (ATRA). The half-life of the annexin VIII mRNA is about 5 to 6 hours, as determined by using actinomycin D as a transcription inhibitor. Analysis of the expression of annexin VIII protein in NB4 cells and in APL samples showed a consistent expression of a predominant 36-kD protein and a weak 72-kD protein. After ATRA- induced differentiation of NB4 cells, the annexin VIII protein level reduced gradually, but a detectable level persisted even after 4 days of induction. Because annexin VIII mRNA becomes undetectable after 48 hours of ATRA induction, this result indicates that annexin VIII is a relatively stable protein. A multiple tissue Northern blot analysis was performed, and we found that annexin VIII is normally expressed in the placenta and the lung. Cellular localization of the annexin VIII protein was determined by immunofluorescence staining and subcellular fractionation. These results indicated that annexin VIII is predominantly localized to the plasma membrane. The annexin VIII is neither an extracellular protein nor associated with the cell surface suggesting that it does not play a role in blood coagulation in vivo. The plasma membrane localization and its property as a phospholipase inhibitor suggests that annexin VIII may have a role in the signal transduction pathway in the APL cells.</jats:p

HLA class II induction in human islet cells by interferon-gamma plus tumour necrosis factor or lymphotoxin.

HLA class II molecules are surface glycoproteins which are essential in the initiation of immune responses. It has been postulated that induction of class II in epithelial cells such as endocrine cells, which are normally class II negative, may result in autoimmunity. In type I diabetes, islet beta cells, the target of the autoimmune process, selectively express class II antigens. But in contrast to most other cell types, islet beta cells are not stimulated to express class II by interferon-gamma (IFN-gamma) and thus the conditions under which this induction occurs have been particularly elusive. The cytotoxins tumour necrosis factor (TNF) and lymphotoxin (LT) synergize with IFN-gamma in a number of activities. We report here that IFN-gamma in combination with either TNF or LT induces islet cell class II expression. This finding has important implications for the pathogenesis of type I diabetes and the understanding of the differential control of class II expression