HepatoScore-14: Measures of Biological Heterogeneity Significantly Improve Prediction of Hepatocellular Carcinoma Risk

BACKGROUND AND AIMS

Therapeutic, clinical trial entry and stratification decisions for hepatocellular carcinoma (HCC) are made based on prognostic assessments, using clinical staging systems based on small numbers of empirically selected variables that insufficiently account for differences in biological characteristics of individual patients' disease.

APPROACH AND RESULTS

We propose an approach for constructing risk scores from circulating biomarkers that produce a global biological characterization of individual patient's disease. Plasma samples were collected prospectively from 767 patients with HCC and 200 controls, and 317 proteins were quantified in a Clinical Laboratory Improvement Amendments-certified biomarker testing laboratory. We constructed a circulating biomarker aberration score for each patient, a score between 0 and 1 that measures the degree of aberration of his or her biomarker panel relative to normal, which we call HepatoScore. We used log-rank tests to assess its ability to substratify patients within existing staging systems/prognostic factors. To enhance clinical application, we constructed a single-sample score, HepatoScore-14, which requires only a subset of 14 representative proteins encompassing the global biological effects. Patients with HCC were split into three distinct groups (low, medium, and high HepatoScore) with vastly different prognoses (medial overall survival 38.2/18.3/7.1 months; P < 0.0001). Furthermore, HepatoScore accurately substratified patients within levels of existing prognostic factors and staging systems (P < 0.0001 for nearly all), providing substantial and sometimes dramatic refinement of expected patient outcomes with strong therapeutic implications. These results were recapitulated by HepatoScore-14, rigorously validated in repeated training/test splits, concordant across Myriad RBM (Austin, TX) and enzyme-linked immunosorbent assay kits, and established as an independent prognostic factor.

CONCLUSIONS

HepatoScore-14 augments existing HCC staging systems, dramatically refining patient prognostic assessments and therapeutic decision making and enrollment in clinical trials. The underlying strategy provides a global biological characterization of disease, and can be applied broadly to other disease settings and biological media.

Abstract 2500: Analysis of protein biomakers in prostate and colorectal tumor lysates

Traditional tumor biomarkers are proteins that have been shed in the bloodstream and have been critical in identifying and treating cancer. We sought to survey proteins relevant to oncology in colon and prostate tumors; in order to identify potential proteins of interest for cancer research. Four colon and three prostate tumors were homogenized and 115 proteins were analyzed from the Oncology MAP 2.0. Each tumor had 2 fractions homogenized to look at heterogeneity of the protein with the tumor. In all of the samples measured 102 of the 115 protein showed levels above the LLOQ. Five proteins (PSP94, Tenascin-X, lipocalin-1, Tie-1 and BAFF) were 100 fold higher in prostate tumors compared to colon tumors (P&lt;0.001). PSP94 has been shown to be a prostate cancer marker in serum; however, none of the other markers have been shown to be markers of prostate tumors. Eight proteins (PECAM-1, CA 72-4, Eotaxin-2, HGF-R, CA 15-3, TATI, CEACAM6 and CEA) were greater than 10 fold higher in colon tumors compared to prostate tumors (P&lt;0.001). Although oncology MAP 2.0 was developed for serum biomarkers, it may provide a valuable tool for examining proteins biomarkers in tumors.

Citation Format: Laurie L. Stephen, Marc Damour, Josh Kemp, Karri L. Ballard, Ralph L. McDade, James P. Mapes. Analysis of protein biomakers in prostate and colorectal tumor lysates. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2500. doi:10.1158/1538-7445.AM2013-2500

SMA-MAP: a plasma protein panel for spinal muscular atrophy

Objectives

Spinal Muscular Atrophy (SMA) presents challenges in (i) monitoring disease activity and predicting progression, (ii) designing trials that allow rapid assessment of candidate therapies, and (iii) understanding molecular causes and consequences of the disease. Validated biomarkers of SMA motor and non-motor function would offer utility in addressing these challenges. Our objectives were (i) to discover additional markers from the Biomarkers for SMA (BforSMA) study using an immunoassay platform, and (ii) to validate the putative biomarkers in an independent cohort of SMA patients collected from a multi-site natural history study (NHS).

Methods

BforSMA study plasma samples (N = 129) were analyzed by immunoassay to identify new analytes correlating to SMA motor function. These immunoassays included the strongest candidate biomarkers identified previously by chromatography. We selected 35 biomarkers to validate in an independent cohort SMA type 1, 2, and 3 samples (N = 158) from an SMA NHS. The putative biomarkers were tested for association to multiple motor scales and to pulmonary function, neurophysiology, strength, and quality of life measures. We implemented a Tobit model to predict SMA motor function scores.

Results

12 of the 35 putative SMA biomarkers were significantly associated (p<0.05) with motor function, with a 13^th analyte being nearly significant. Several other analytes associated with non-motor SMA outcome measures. From these 35 biomarkers, 27 analytes were selected for inclusion in a commercial panel (SMA-MAP) for association with motor and other functional measures.

Conclusions

Discovery and validation using independent cohorts yielded a set of SMA biomarkers significantly associated with motor function and other measures of SMA disease activity. A commercial SMA-MAP biomarker panel was generated for further testing in other SMA collections and interventional trials. Future work includes evaluating the panel in other neuromuscular diseases, for pharmacodynamic responsiveness to experimental SMA therapies, and for predicting functional changes over time in SMA patients.

Abstract 4954: Development and validation of 50 serum cancer multiplexed biomarkers

Biomarkers are indicators of normal biological processes and can be monitored to look at physiological changes. In cancer, a pattern of biomarkers may be useful for the detection, reoccurrence and response to treatment. We have identified 50 biomarkers implicated in cancer and have developed bead-based multiplexed immunoassays for the Luminex system, defined as the OncologyMAP™. Multiplexing is a cost effective method which allows for the measurement of multiple proteins with little sample volume. The OncologyMAP™ consists of markers of cell damage (Annexin A1, HMGB1), soluble receptors (uPAR, TIE-2), enzymes (PSAT-1, aldose reductase), signaling molecules (calcvasculin, EpCAM)) and growth factors (endostatin, BAFF). All markers showed positive signals in either normal serum and plasma samples or cancer serum. Multiplexed assays were run on a TECAN EVO and showed good precision, linearity and spike recovery. The OncologyMAP™ is a valuable tool for cancer biomarker discovery

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4954.