Analysis of differentially expressed proteins in colorectal cancer using hydroxyapatite column and SDS-PAGE. Appl Biochem Biotechnol. 2011;165:1211-1224. [PMID: 21863284 DOI: 10.1007/s12010-011-9339-3]

Positive Correlation Between Somatic Mutations in RAS Gene and Colorectal Cancer in Telangana Population: Hospital-Based Study in a Cosmopolitan City

Colorectal cancer (CRC) ranks among the most prevalent cancer types in both men and women. Screening of RAS (Kirsten rat sarcoma viral oncogene homolog (KRAS), neuro-blastoma RAS viral oncogene homolog (NRAS), and v-raf murine sarcoma viral oncogene homolog B1 (BRAF)) somatic mutations is necessary prior to considering anti-epidermal growth factor receptor (EGFR) therapies in CRC patients. Next-generation sequencing studies have confirmed that RAS gene panels could be used while developing treatment strategies for patients with CRC. The present study explored genetic mutations in KRAS, NRAS, and BRAF in CRC patients in the Telangana state of India. Patients with confirmed CRC (n = 100) who visited the Apollo hospitals were evaluated. Genomic DNA was extracted from formalin-fixed, paraffin-embedded tissues, and pyrosequencing analysis was performed. Patient DNA samples were screened for 54 different KRAS, NRAS, and BRAF mutations, which revealed 34 somatic mutations. Exon 11 of BRAF possessed 4 mutations with highest individuals documented with G469A mutation. Pyrosequencing, a reliable method for analyzing somatic mutations present in RAS, could aid in taking treatment decisions for patients with CRC.

Synthesis and Characterization of Natural Nano-hydroxyapatite Derived from Turkey Femur-Bone Waste

Hydroxyapatite (HAp) is a bioactive and vital material which has found many applications in the biomedical and clinical fields. This bio-ceramic powder can be synthesized via different bio-waste materials. In this study, the production of natural nanohydroxyapatite was produced through calcination of untreated turkey femur-bone waste powder at 850 °C followed by ball milling the powder. The obtained powder was characterized using X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR) analysis. The morphology, size, and elemental composition of obtained turkey hydroxyapatite (THA) particles were investigated by scanning electron microcopy (SEM), transmission electron microcopy (TEM), and energy dispersive spectroscopy (EDS) analysis, in which the average particle size of ball milled THA was found to be about 85 nm with a Ca/P ratio of 1.63. The powder was then cold pressed and later sintered at 850, 950, 1050, and 1150 °C to evaluate its mechanical properties in terms of compressive strength and hardness. The results revealed that the strength and hardness of the samples increased by increasing the sintering temperature up to 1150 °C. Finally, the maximum values of hardness and compressive strength of the sintered THA were obtained at 1150 °C (37.44 MPa and 3.2 GPa, respectively).

Structure, function and regulation of jade family PHD finger 1 (JADE1)

The family of JADE proteins includes three paralogues encoded by individual genes and designated PHF17 (JADE1), PHF16 (JADE2), and PHF15 (JADE3). All three JADE proteins bear in tandem two Plant Homeo-domains (PHD) which are zinc finger domains. This review focuses on one member of the JADE family, JADE1. Studies addressing the biochemical, cellular and biological role of JADE1 are discussed. Recent discoveries of JADE1 function in the regulation of the epithelial cell cycle with potential relevance to disease are presented. Unresolved questions and future directions are formulated.

Genome-wide association study of colorectal cancer in Hispanics

This manuscript describes the first large-scale genome-wide association study of colorectal cancer in Hispanics and Latinos. Our results demonstrate the broad replication of known susceptibility regions and the importance of fine-mapping in ethnic minority populations.

Genome-wide association studies (GWAS) have identified 58 susceptibility alleles across 37 regions associated with the risk of colorectal cancer (CRC) with P < 5×10⁻⁸. Most studies have been conducted in non-Hispanic whites and East Asians; however, the generalizability of these findings and the potential for ethnic-specific risk variation in Hispanic and Latino (HL) individuals have been largely understudied. We describe the first GWAS of common genetic variation contributing to CRC risk in HL (1611 CRC cases and 4330 controls). We also examine known susceptibility alleles and implement imputation-based fine-mapping to identify potential ethnicity-specific association signals in known risk regions. We discovered 17 variants across 4 independent regions that merit further investigation due to suggestive CRC associations (P < 1×10⁻⁶) at 1p34.3 (rs7528276; Odds Ratio (OR) = 1.86 [95% confidence interval (CI): 1.47–2.36); P = 2.5×10⁻⁷], 2q23.3 (rs1367374; OR = 1.37 (95% CI: 1.21–1.55); P = 4.0×10⁻⁷), 14q24.2 (rs143046984; OR = 1.65 (95% CI: 1.36–2.01); P = 4.1×10⁻⁷) and 16q12.2 [rs142319636; OR = 1.69 (95% CI: 1.37–2.08); P=7.8×10⁻⁷]. Among the 57 previously published CRC susceptibility alleles with minor allele frequency ≥1%, 76.5% of SNPs had a consistent direction of effect and 19 (33.3%) were nominally statistically significant (P < 0.05). Further, rs185423955 and rs60892987 were identified as novel secondary susceptibility variants at 3q26.2 (P = 5.3×10^–5) and 11q12.2 (P = 6.8×10⁻⁵), respectively. Our findings demonstrate the importance of fine mapping in HL. These results are informative for variant prioritization in functional studies and future risk prediction modeling in minority populations.

Proteomics for discovery of candidate colorectal cancer biomarkers

Colorectal cancer (CRC) is the second most common cause of cancer-related deaths in Europe and other Western countries, mainly due to the lack of well-validated clinically useful biomarkers with enough sensitivity and specificity to detect this disease at early stages. Although it is well known that the pathogenesis of CRC is a progressive accumulation of mutations in multiple genes, much less is known at the proteome level. Therefore, in the last years many proteomic studies have been conducted to find new candidate protein biomarkers for diagnosis, prognosis and as therapeutic targets for this malignancy, as well as to elucidate the molecular mechanisms of colorectal carcinogenesis. An important advantage of the proteomic approaches is the capacity to look for multiple differentially expressed proteins in a single study. This review provides an overview of the recent reports describing the different proteomic tools used for the discovery of new protein markers for CRC such as two-dimensional electrophoresis methods, quantitative mass spectrometry-based techniques or protein microarrays. Additionally, we will also focus on the diverse biological samples used for CRC biomarker discovery such as tissue, serum and faeces, besides cell lines and murine models, discussing their advantages and disadvantages, and summarize the most frequently identified candidate CRC markers.

Serum proteomics in biomedical research: a systematic review

Proteins that are important indicators of physiological or pathological states may contribute to the early diagnosis of disease, which may provide a basis for identifying the underlying mechanism of disease development. Serum, contains an abundance of proteins, offers an easy and inexpensive approach for disease detection and possesses a high potential to revolutionize the diagnostics. These differentially expressed proteins in serum have become an important role to monitoring the state for disease. Availability of emerging proteomic techniques gives optimism that serum can eventually be placed as a biomedium for clinical diagnostics. Advancements have benefited biomarker research to the point where serum is now recognized as an excellent diagnostic medium for the detection of disease. Comprehensive proteome of human serum fluid with high accuracy and availability has the potential to open new doors for disease biomarker discovery and for disease diagnostics, providing insights useful for future study. Thus, this review presents an overview of the value of serum as a credible diagnostic tool, and we aim to summarize the proteomic technologies currently used for global analysis of serum proteins and to elaborate on the application of serum proteomics to the discovery of disease biomarkers, and discuss some of the critical challenges and perspectives for this emerging field.

Proteomic identification network analysis of haptoglobin as a key regulator associated with liver fibrosis

Liver fibrosis (LF) is the final stage of liver dysfunction, characterized by diffuse fibrosis which is the main response to the liver injury. Haptoglobin (HP) protein, produced as an acute phase reactant during LF, preventing liver damage, may be potential molecular targets for early LF diagnostics and therapeutic applications. However, protein networks associated with the HP are largely unknown. To address this issue, we used a pathological mouse model of LF that was induced by treatment with carbon tetrachloride for 8 days. HP protein was separated and identified by two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry. HP protein was subjected to functional pathway analysis using STRING and Cytoscape software for better understanding of the protein-protein interaction (PPI) networks in biological context. Bioinformatics analyses revealed that HP expression associated with fibrosis was upregulated, and suggested that HP responsible for fibrosis may precede the onset and progression of LF. Using the web-based database, functional pathway analysis suggested the modulation of multiple vital physiological pathways, including antioxidation immunity, signal transduction, metabolic process, energy production, cell apoptosis, oxidation reduction, DNA repair process, cell communication, and regulation of cellular process. The generation of protein interaction networks clearly enhances the interpretation and understanding of the molecular mechanisms of HP. HP protein represents targets for further experimental investigation that will provide biological insight and potentially could be exploited for novel therapeutic approaches to combat LF.