Biomarkers For Disease Prognosis Research Articles

Polyclonal Serum Free Light Chains: A Biomarker of Disease Prognosis or of Immune Senescence?

growing body of literature on the prognostic role of elevated poly- clonal serum free light chains (sFLCs) in clinical settings. Of note, increased polyclonal sFLCs have been detected in conditions that are characterized by chronic B-cell activation: rheumatoid arthritis, Sjogren's syndrome, systemic lupus erythematosus, severe atopic and nonatopic asthma and dermatitis, idiopathic pulmonaryfibrosis, and chronic hypersensitivity pneumonitis. Furthermore, infections, dia- betesmellitus,renalimpairment,andinflammatoryboweldiseaseare significant known causes of polyclonal increase in sFLCs. 2,3 Because the incidence of these diseases increases with age, and aging is another cause of elevated polyclonal sFLCs, I would have expected that the authors 1 would include the presence of comorbidi- ties in their analysis. The sFLC half-life of only 2 to 6 hours would potentially indicate the immediate occurrence of B-cell dysfunction/ activity; thus, intrapatient variations are strictly correlated with the activity of the underlying disease and may be influenced by therapy. 3

Toward Prediction of Immune Mechanisms and Design of Immunotherapies in Melanoma

Malignant melanoma, the most lethal skin cancer, is considered as a representative model for cross talk between immune responses and malignancy. Efforts to elucidate the nature of these interactions have translated into immunotherapeutic strategies. Adjuvant therapeutics such as IL-2 and IFNα2b have reached clinical application, and emerging therapies targeting key immunomodulatory molecules such as CTLA-4 have renewed excitement in the field, highlighting the potential of manipulating immune responses in the clinical setting, but also the merits for further elucidating complex underlying immunological pathways. Screening technologies have yielded new insights leading to identification of biomarkers for disease prognosis and applied clinical immunotherapies. The promise of systems biology is to integrate diverse biomedical characterizations into detailed models of underlying mechanisms and therapies through suitable computational and mathematical formalisms. In this review, we discuss recent developments in dissecting the complex and diverse immune responses associated with melanoma through both computational and experimental means. We show the significance of devising new, improved approaches that can better serve as models of immune interactions and therapies. We propose that efforts in this direction may realize the potential of personalized medicine and facilitate development of the next generation of efficacious tools to treat patients.

The role of mTOR and hypoxia pathway activation in promoting tumorigenesis of intrahepatic cholangiocarcinoma.

218 Background: Cholangiocarcinoma (CC) is an aggressive malignancy that often presents in advanced stages with poor response rates to conventional chemotherapy. Recent studies of CC have uncovered several oncogenes and tumor suppressors implicated in the transition from biliary hyperplasia to malignancy. We have developed a mouse model of intrahepatic CC that results from deletion of the phosphatase and tensin homolog (PTEN) gene and the von Hippel Lindau (VHL) gene, a tumor suppressor that regulates hypoxia inducible factor (HIF) expression. Immunohistochemical (IHC) analysis of the liver tumors revealed strong staining of p-AKT and HIF-1α. This study aims to determine the expression of the same downstream targets p-AKT and HIF1α in a dataset of human CC tumors. Methods: Archived samples from 33 CC patients were sectioned and stained via IHC for p-AKT and HIF1α expression. Samples were evaluated using a proportion score (PS) for neoplastic cells on a scale of 0 to 5, and an intensity score (IS) expressed on a scale of 0 to 3. Normal liver samples were used as controls. Results: Using a combined score of at least 5 to determine positive expression, 18% of the 33 evaluated samples displayed positive p-AKT expression and 61% displayed positive HIF1α expression. 15% of cases displayed concomitant expression of both p-AKT and HIF1α, while 39% of evaluated samples had expression of neither protein. Conclusions: Delineating the molecular pathways that lead to CC formation is crucial in developing novel therapeutics for a disease in drastic need of more effective therapies. Our group has developed a mouse model of intrahepatic CC that suggests a synergistic role of PTEN and VHL in the tumorigenesis of CC with upregulation of p-AKT and HIF1α. A modest percentage of a cohort of human samples demonstrates a similar expression pattern, potentially defining a distinct molecular subtype of this cancer with implications for tumor behavior and response to treatment. Future studies will correlate these molecularly-defined subtypes to the clinicopathologic characteristics of the tumors with the ultimate aim of establishing biomarkers of disease prognosis as well as potential predictive indicators of treatment activity. No significant financial relationships to disclose.

Exon Array Analysis of Head and Neck Cancers Identifies a Hypoxia Related Splice Variant of LAMA3 Associated with a Poor Prognosis

The identification of alternatively spliced transcript variants specific to particular biological processes in tumours should increase our understanding of cancer. Hypoxia is an important factor in cancer biology, and associated splice variants may present new markers to help with planning treatment. A method was developed to analyse alternative splicing in exon array data, using probeset multiplicity to identify genes with changes in expression across their loci, and a combination of the splicing index and a new metric based on the variation of reliability weighted fold changes to detect changes in the splicing patterns. The approach was validated on a cancer/normal sample dataset in which alternative splicing events had been confirmed using RT-PCR. We then analysed ten head and neck squamous cell carcinomas using exon arrays and identified differentially expressed splice variants in five samples with high versus five with low levels of hypoxia-associated genes. The analysis identified a splice variant of LAMA3 (Laminin α 3), LAMA3-A, known to be involved in tumour cell invasion and progression. The full-length transcript of the gene (LAMA3-B) did not appear to be hypoxia-associated. The results were confirmed using qualitative RT-PCR. In a series of 59 prospectively collected head and neck tumours, expression of LAMA3-A had prognostic significance whereas LAMA3-B did not. This work illustrates the potential for alternatively spliced transcripts to act as biomarkers of disease prognosis with improved specificity for particular tissues or conditions over assays which do not discriminate between splice variants.

Epithelial Brush Border Proteomics and Associated Cell Dysfunction

Functions and structures of epithelial cells vary, depending upon their locations in organs/tissues. Pathophysi- ological responses of epithelia are associated with challenges, severities, durations and diseases. Epithelial proteomics has been used to understand the role of these cells in the pathogenesis of several diseases, and has the potential to identify novel biomarkers for disease prognosis, diagnosis and therapies. Epithelial brush border membranes (BBMs) are involved in digestion, absorption, metabolism, and transport of nutrients and drugs, clearance of and defense against toxins, and ini- tiation of intracellular signaling and maintenance of cellular structural integrity. The present article review proteomic re- search on epithelial brush borders to understand the potential links among the function and disease associations of epithe- lial BBM proteomics. We found that the amount and functional ratio of epithelial cell BBM proteomic profiles obviously vary among species, cell locations, organ functions, research groups, and methodologies utilized. Many of these proteins may be identified and their functions elucidated, probably providing potential new markers for epithelial-associated dis- eases and potential therapeutic targets. There is still a great need for proteomic studies for analysis and comparisons of BBM protein profiles associated with normal physiological and pathophysiological states, organ function and dysfunction, and clinical health and disease.

Alternative splicing and the progesterone receptor in breast cancer

Progesterone receptor status is a marker for hormone responsiveness and disease prognosis in breast cancer. Progesterone receptor negative tumours have generally been shown to have a poorer prognosis than progesterone receptor positive tumours. The observed loss of progesterone receptor could be through a range of mechanisms, including the generation of alternatively spliced progesterone receptor variants that are not detectable by current screening methods. Many progesterone receptor mRNA variants have been described with deletions of various whole, multiple or partial exons that encode differing protein functional domains. These variants may alter the progestin responsiveness of a tissue and contribute to the abnormal growth associated with breast cancer. Absence of specific functional domains from these spliced variants may also make them undetectable or indistinguishable from full length progesterone receptor by conventional antibodies. A comprehensive investigation into the expression profile and activity of progesterone receptor spliced variants in breast cancer is required to advance our understanding of tumour hormone receptor status. This, in turn, may aid the development of new biomarkers of disease prognosis and improve adjuvant treatment decisions.

Receiver operating characteristic (ROC) to determine cut-off points of biomarkers in lung cancer patients.

The role of biomarkers in disease prognosis continues to be an important investigation in many cancer studies. In order for these biomarkers to have practical application in clinical decision making regarding patient treatment and follow-up, it is common to dichotomize patients into those with low vs. high expression levels. In this study, receiver operating characteristic (ROC) curves, area under the curve (AUC) of the ROC, sensitivity, specificity, as well as likelihood ratios were calculated to determine levels of growth factor biomarkers that best differentiate lung cancer cases versus control subjects. Selected cut-off points for p185erbB-2 and EGFR membrane appear to have good discriminating power to differentiate control tissues versus uninvolved tissues from patients with lung cancer (AUC = 89% and 90%, respectively); while AUC increased to at least 90% for selected cut-off points for p185erbB-2 membrane, EGFR membrane, and FASE when comparing between control versus carcinoma tissues from lung cancer cases. Using data from control subjects compared to patients with lung cancer, we presented a simple and intuitive approach to determine dichotomized levels of biomarkers and validated the value of these biomarkers as surrogate endpoints for cancer outcome.