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Clear cell renal cell carcinomas (ccRCCs) represent ∼75% of RCC cases and account for most RCC-associated deaths. Inter- and intratumoral heterogeneity (ITH) results in varying prognosis and treatment outcomes. To obtain the most comprehensive profile of ccRCC, we perform integrative histopathologic, proteogenomic, and metabolomic analyses on 305 ccRCC tumor segments and 166 paired adjacent normal tissues from 213 cases. Combining histologic and molecular profiles reveals ITH in 90% of ccRCCs, with 50% demonstrating immune signature heterogeneity. High tumor grade, along with BAP1 mutation, genome instability, increased hypermethylation, and a specific protein glycosylation signature define a high-risk disease subset, where UCHL1 expression displays prognostic value. Single-nuclei RNA sequencing of the adverse sarcomatoid and rhabdoid phenotypes uncover gene signatures and potential insights into tumor evolution. In vitro cell line studies confirm the potential of inhibiting identified phosphoproteome targets. This study molecularly stratifies aggressive histopathologic subtypes that may inform more effective treatment strategies.

Background Medulloblastoma is the most common malignant brain tumor of childhood and is considered a tumor with low mutational burden (~1 Mut/Mb). Therefore, though the medulloblastoma genomes have been extensively characterized in literature, reports on potential hypermutations and underlying mutagenic processes in medulloblastomas are limited. Aim In this report, we studied the landscape of mutational burden in primary and recurrent medulloblastoma. Furthermore, we wanted to understand the differences in underlying mutagenic mechanisms in medulloblastoma with low and high mutational burdens. Methods Fifty-three primary and recurrent medulloblastoma genomic sequence were downloaded from the European Genome Archive as BAM files. Thirty-three cases were obtained from formalin-fixed paraffin-embedded tissues from pathology diagnostic archives of Spectrum Health and Cooperative Human Tissue Network. Somatic mutations were called using Mutect2, following best practices guidelines for Genome Analysis Toolkit V4. Mutational signatures were analyzed using deconstructSigs. Results We identified nine medulloblastoma cases with high mutational burden (>5 Mut/Mb). Of them, five cases met the criteria of hypermutation (>10Mut/Mb), two of the five tumors had canonical mutations in the POLE proof-reading domain, where a large proportion of mutations in these tumor genomes contributed to signature 10. The hypermutated cases also demonstrated mutational signatures 14, 15, and 21, indicating the role of mis match repair deficiency in their mutagenesis. Of the four known molecular subgroups in medulloblastoma-SHH, WNT, Group 3, and Group 4-both the POLE-mutated cases belonged to the SHH subgroup. This report identifies rare cases of hypermutation in medulloblastoma driven by defects in DNA repair mechanisms. Conclusion Hypermutation in medulloblastoma can impact therapeutic decisions, especially at recurrence in otherwise fatal high risk SHH-medulloblastomas. A defect in DNA repair leading to SHH -medulloblastoma is yet another important mechanism that should be further investigated in the genesis of these tumors. Therefore, this report provides important scientific and clinical rationale for future research looking for incidence of hypermutation in large cohorts of medulloblastoma patients.

Multiple myeloma is a treatable, but currently incurable, hematological malignancy of plasma cells characterized by diverse and complex tumor genetics for which precision medicine approaches to treatment are lacking. The MMRF CoMMpass study is a longitudinal, observational clinical study of newly diagnosed multiple myeloma patients where tumor samples are characterized using whole genome, exome, and RNA sequencing at diagnosis and progression, and clinical data is collected every three months. Analyses of the baseline cohort identified genes that are the target of recurrent gain- and loss-of-function events. Consensus clustering identified 8 and 12 unique copy number and expression subtypes of myeloma, respectively, identifying high- risk genetic subtypes and elucidating many of the molecular underpinnings of these unique biological groups. Analysis of serial samples showed 25.5% of patients transition to a high-risk expression subtype at progression. We observed robust expression of immunotherapy targets in this subtype, suggesting a potential therapeutic option.

Glioblastoma (GBM) is the most aggressive nervous system cancer. Understanding its molecular pathogenesis is crucial to improving diagnosis and treatment. Integrated analysis of genomic, proteomic, post-translational modification and metabolomic data on 99 treatment-naive GBMs provides insights to GBM biology. We identify key phosphorylation events (e.g., phosphorylated PTPN11 and PLCG1) as potential switches mediating oncogenic pathway activation, as well as potential targets for EGFR-, TP53-, and RB1-altered tumors. Immune subtypes with distinct immune cell types are discovered using bulk omics methodologies, validated by snRNA-seq, and correlated with specific expression and histone acetylation patterns. Histone H2B acetylation in classical-like and immune-low GBM is driven largely by BRDs, CREBBP, and EP300. Integrated metabolomic and proteomic data identify specific lipid distributions across subtypes and distinct global metabolic changes in IDH-mutated tumors. This work highlights biological relationships that could contribute to stratification of GBM patients for more effective treatment. Wang et al. perform integrated proteogenomic analysis of adult glioblastoma (GBM), including metabolomics, lipidomics, and single nuclei RNA-Seq, revealing insights into the immune landscape of GBM, cell-specific nature of EMT signatures, histone acetylation in classical GBM, and the existence of signaling hubs which could provide therapeutic vulnerabilities.

We present a proteogenomic study of 108 human papilloma virus (HPV)-negative head and neck squamous cell carcinomas (HNSCCs). Proteomic analysis systematically catalogs HNSCC-associated proteins and phosphosites, prioritizes copy number drivers, and highlights an oncogenic role for RNA processing genes. Proteomic investigation of mutual exclusivity between FAT1 truncating mutations and 11q13.3 amplifications reveals dysregulated actin dynamics as a common functional consequence. Phosphoproteomics characterizes two modes of EGFR activation, suggesting a new strategy to stratify HNSCCs based on EGFR ligand abundance for effective treatment with inhibitory EGFR monoclonal antibodies. Widespread deletion of immune modulatory genes accounts for low immune infiltration in immune-cold tumors, whereas concordant upregulation of multiple immune checkpoint proteins may underlie resistance to anti-programmed cell death protein 1 monotherapy in immune-hot tumors. Multi-omic analysis identifies three molecular subtypes with high potential for treatment with CDK inhibitors, anti-EGFR antibody therapy, and immunotherapy, respectively. Altogether, proteogenomics provides a systematic framework to inform HNSCC biology and treatment.

Patients with head and neck squamous cell carcinomas (HNSCCs) are treated with surgery, radiation, chemotherapy, and limited targeted therapies. Compared to human papillomavirus (HPV)-positive HNSCCs, HPV-negative cases have worse treatment response and prognosis and represent an unmet clinical need. We performed comprehensive proteogenomic characterization of tumor specimens, matched normal adjacent tissues (NATs), and blood samples from 109 HPV-negative HNSCC patients. This cohort is dominated by tumors from oral cavity (45, 41%) and larynx (49, 45%). Somatic mutation and somatic copy number analyses validated previously reported genomic aberrations in HPV-negative HNSCC. Proteomics analysis linked p53 loss of heterozygosity to increased expression of EPCAM, a stemness marker. Additionally, FAT1 truncation mutations were associated with increased expression of proteins involved in keratinization, a key feature of SCC differentiation. Deletions of 3p and 9p led to the loss of genes encoding p16, chemokine receptors, and interferon/JAK/STAT signaling pathway proteins, whereas amplifications of 3q and 11q led to overexpression of proteins involved in cell proliferation and anti-apoptosis pathways. Comparative analysis of tumor and NAT proteomes and phosphoproteomes identified putative diagnostic biomarkers and druggable targets, and proteogenomic integration further identified putative neoantigens. Tumor site-specific characterization associated epigenetic silencing of neurofilaments with laryngeal but not oral cavity SCC. Protein targets of FDA approved or investigational drugs for HNSCC treatment showed high inter-tumor heterogeneity in their protein abundances. DNA copy number and RNA expression level were good surrogates of protein abundance for some targets, such as EGFR and PD-L1, but they failed to reflect protein levels or kinase activities for other targets, such as MMP9 and MTOR. Thus, there is a critical need for protein biomarker-driven treatment stratification. Deconvolution of bulk tumor gene expression data revealed an immune-hot subgroup and an immune-cold subgroup. Immune-hot tumors broadly overexpressed multiple immune checkpoints including PD-L1, IDO1, and CTLA4, underscoring the necessity of combination immune checkpoint inhibition to improve treatment efficacy. Immune-cold tumors were characterized by smoking, chromosomal instability, and activation of the CDK4/6-pRb axis, suggesting they could be targeted by CDK4/6 inhibitors. We also noted that EGFR-amplified tumors frequently harbor copy number aberrations of downstream signaling components of the EGFR pathway. This may explain the low response rate of EGFR-amplified tumors to EGFR inhibitors, and targeting multiple pathway components, including EGFR, PIK3CA and STAT3, may be required for these tumors. In summary, our integrative proteogenomic characterization revealed multiple novel insights into the pathogenesis and treatment of HPV-negative HNSCCs. Citation Format: Chen Huang, Lijun Chen, Yize Li, Sara Savage, Michael Schnaubelt, Felipe V. Leprevost, Marcin Cieslik, Yongchao Dou, Bo Wen, Jonathan T. Lei, Kai Li, Eric Jaehnig, Zhiao Shi, Meenakshi Anurag, Jianbo Pan, Yingwei Hu, Rodrigo V. Eguez, David J. Clark, Matthew Wyczalkowski, Saravana M. Dhanasekaran, Chandan Kumar, Antonio Colaprico, Karsten Krug, Michael Gillette, D. R. Mani, Seungyeul Yoo, Jiayi Ji, Xiaoyu Song, Weiping Ma, Xi Steven Chen, Alex Pico, Nathan J. Edwards, Scott D. Jewell, Mathangi Thiagarajan, Emily S. Boja, Henry Rodriguez, Andrew Sikora, Pei Wang, Matthew Ellis, Gilbert S. Omenn, Li Ding, Alexey I. Nesvizhskii, Adel K. EI-Naggar, Daniel W. Chan, Hui Zhang, Bing Zhang, Clinical Proteomic Tumor Analysis Consortium. Proteogenomics characterization of HPV-negative head and neck squamous cell carcinomas [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5118.

Multiple Myeloma (MM) is a plasma cell malignancy with significantly greater incidence and mortality rates among African Americans (AA) compared to Caucasians (CA). The overall goal of this study is to elucidate differences in molecular alterations in MM as a function of self-reported race and genetic ancestry. Our study utilized somatic whole exome, RNA-sequencing, and correlated clinical data from 718 MM patients from the Multiple Myeloma Research Foundation CoMMpass study Interim Analysis 9. Somatic mutational analyses based upon self-reported race corrected for ancestry revealed significant differences in mutation frequency between groups. Of interest, BCL7A, BRWD3, and AUTS2 demonstrate significantly higher mutation frequencies among AA cases. These genes are all involved in translocations in B-cell malignancies. Moreover, we detected a significant difference in mutation frequency of TP53 and IRF4 with frequencies higher among CA cases. Our study provides rationale for interrogating diverse tumor cohorts to best understand tumor genomics across populations., Author summary This study represents the largest comprehensive molecular analysis of ethnically defined newly diagnosed treatment naïve Multiple Myeloma (MM). We revealed significant differences in mutation frequencies for important cancer genes between AA and CA MM. This study provides support for interrogating diverse tumor cohorts to best understand tumor genomics across populations.

Background: In retrospective studies, loss of p27Kip1 (p27), a cyclin-dependent kinase inhibitor, has been associated with poor prognosis following colorectal cancer treatment. In a prospective study, we validated this relationship in patients enrolled on a trial of adjuvant chemotherapy for stage III colon cancer. Methods: Cancer and Leukemia Group B protocol 89803 randomized 1,264 stage III colon cancer patients to receive weekly bolus 5-fluorouracil/leucovorin or weekly bolus irinotecan, 5-fluorouracil, and leucovorin (IFL). The primary endpoint was overall survival (OS); disease-free survival was a secondary endpoint. Expression of p27 and DNA mismatch repair proteins were determined by immunohistochemistry in primary tumor and normal tissue from paraffin blocks. Data were analyzed using log-rank test. Results: Of 601 tumors analyzed, 207 (34.4%) showed p27 loss, 377 (62.8%) retained p27, and 17 (2.8%) were indeterminate. Patients with p27-negative tumors showed reduced OS [5-year OS 66%: 95% confidence interval (95% CI), 0.59-0.72 versus 75%: 95% CI, 0.70-0.79; log-rank P = 0.021]. This relationship was not influenced by treatment arm. Combination of p27 status with mismatch repair status, however, identified a small subset of patients that may benefit from IFL (n = 36; 5-year disease-free survival 81%: 95% CI, 0.64-0.98 versus 47%: 95% CI, 0.21-0.72; log-rank P = 0.042; 5-year OS 81%: 95% CI, 0.64-0.98 versus 60%: 95% CI, 0.35-0.85; log-rank P = 0.128). Conclusions: Loss of p27 is associated with reduced survival in stage III colon cancer but by itself does not indicate a significant difference in outcome between patients treated IFL or 5-fluorouracil/leucovorin.

Recommendations for specimen collection and handling have been developed for adoption across breast cancer clinical trials conducted by the Breast International Group (BIG)-sponsored Groups and the National Cancer Institute (NCI)-sponsored North American Cooperative Groups. These recommendations are meant to promote identifiable standards for specimen collection and handling within and across breast cancer trials, such that the variability in collection/handling practices that currently exists is minimized and specimen condition and quality are enhanced, thereby maximizing results from specimen-based diagnostic testing and research. Three working groups were formed from the Cooperative Group Banking Committee, BIG groups, and North American breast cancer cooperative groups to identify standards for collection and handling of (1) formalin-fixed, paraffin-embedded (FFPE) tissue; (2) blood and its components; and (3) fresh/frozen tissue from breast cancer trials. The working groups collected standard operating procedures from multiple group specimen banks, administered a survey on banking practices to those banks, and engaged in a series of discussions from 2005 to 2007. Their contributions were synthesized into this document, which focuses primarily on collection and handling of specimens to the point of shipment to the central bank, although also offers some guidance to central banks. Major recommendations include submission of an FFPE block, whole blood, and serial serum or plasma from breast cancer clinical trials, and use of one fixative and buffer type (10% neutral phosphate-buffered formalin, pH 7) for FFPE tissue across trials. Recommendations for proper handling and shipping were developed for blood, serum, plasma, FFPE, and fresh/frozen tissue.

Recent studies using ovarian cancer cells have shown that the catecholamine hormones norepinephrine (norepi) and epinephrine (epi) may influence cancer progression by modulating the expression of matrix metalloproteinases (MMP) and vascular endothelial growth factor (VEGF). The purpose of this study is to determine if the stress hormone norepi can influence the expression of MMP-2, MMP-9, and VEGF in nasopharyngeal carcinoma (NPC) tumors by using three NPC tumor cell lines. The NPC cell lines HONE-1, HNE-1, and CNE-1 were treated with norepi. The effects of norepi on MMP-2, MMP-9, and VEGF synthesis were measured by ELISA; functional MMP activity was measured by the invasive potential of the cells using a membrane invasion culture system whereas functional activity of VEGF was analyzed using a human umbilical vein endothelial cell tube formation assay. Norepi treatment increased MMP-2, MMP-9, and VEGF levels in culture supernatants of HONE-1 cells, which could be inhibited by the β-blocker propranolol. Norepi induced the invasiveness of all NPC cell lines in a dose-dependent manner, which was blocked by CMT-3, an MMP inhibitor, and propranolol. Norepi stimulated the release of functional angiogenic VEGF by HONE-1 cells as well. Finally, HONE-1 cells were shown to express β-adrenergic receptors as did seven of seven NPC biopsies examined. The data suggest that catecholamine hormones produced by the sympathetic-adrenal medullary axis may affect NPC tumor progression, in part, through modulation of key angiogenic cytokines. (Cancer Res 2006; 66(21): 10357-64)

Purpose To determine whether sentinel lymph node (LN) sampling (SLNS) could reduce the number of nodes required to characterize micrometastatic disease (MMD) in patients with potentially curable colon cancer. Patients and Methods Cancer and Leukemia Group B 80001 was a study to determine whether SLNS could identify a subset of LNs that predicted the status of the nodal basin for resectable colon cancer and, therefore, could be extensively evaluated for the presence of micrometastases. Patients enrolled onto this study underwent SLNS after injection of 1% isosulfan blue, and both sentinel nodes (SNs) and non-SNs obtained during primary tumor resection were sectioned at multiple levels and stained using anti–carcinoembryonic antigen and anticytokeratin antibodies. Results Using standard histopathology, SNs failed to predict the presence of nodal disease in 13 (54%) of 24 node-positive patients. Immunostains were performed for patients whose LNs were negative by standard histopathology. Depending on the immunohistochemical criteria used to assign LN positivity, SN examination resulted in either an unacceptably high false-positive rate (20%) or a low sensitivity for detection of MMD (40%). Conclusion By examining both SNs and non-SNs, this multi-institutional study showed that SNs did not accurately predict the presence of either conventionally defined nodal metastases or MMD. As a result, SLNS is not a useful technique for the study of MMD in patients with colon cancer.

Biospecimen procurement, processing, banking, and distribution is an essential component of the cancer research infrastructure and provides an invaluable resource when specimens are associated with clinical information from patients treated on randomized clinical trials. The Cancer and Leukemia Group B (CALGB) is one of several NCI-sponsored cooperative oncology clinical trials research groups in the United States conducting biospecimen research to correlate with clinical endpoints. In addition to the contribution of specimens from research subjects and the support of pathologists across the nation, the effective coordination of biospecimens for use in clinical cancer research is a formidable and evolving process. In this paper, we describe some of the salient features of the CALGB Pathology Coordinating Office (CALGB-PCO), addressing policies, procedures, and new technologies to support high-quality biospecimen research.

The role of innate and adaptive immunity in a wide range of human tumors has shown critical roles, though sometimes competing, in numerous immune components in both the tumor and the tumor microenvironment (TME). The PD-1/PD-L1 interaction in both tumor and the TME has become high priority in correlative biomarkers of human disease with increasing number of targeted agents showing high levels of durable response. The in situ analysis of viral defense pathway, interferon response, and PD-L1 status has provided strong preliminary data of correlative staining by immunohistochemistry in colon and lung carcinomas. Generally, such human tumors arise in organs with frequent and high exposure to external/foreign antigens. Here we expand our IHC staining to include human tumors arising from sites with varied immune activity to include uterine wall (leiomyosarcoma), subcutaneous connective tissue to include dermatofibrosarcoma protuberans (DFSP), soft tissue sarcoma, fibrosarcoma, and osteosarcoma. IHC panel includes immune markers of CD4, CD8, CD68 (M1 macrophages), CD163 (M2 macrophages); dsRNA antibodies (J2 and K1); MDA 5, RIG 1, STAT 1, and pSTAT1; PD-L1 and PD-1; and interferon response markers IRF 3, IRF 7, and IFIT 1. Immunostaining is ongoing and supports preliminary sarcoma phenotype of quite varied PD-L1 immunoreactivity with lower prevalence than lung and colon carcinomas. Immune markers of T-cell subset and macrophage M1 and M2 are significantly lower in sarcoma samples and detailed analysis of M1 and M2 macrophages in DFSP, STS, fibrosarcomas, and osteosarcoma. Each tumor type is represented on single TMA with 8-12 samples each from the Van Andel Institute Biorepository Core. In our experience, tissue site density and macrophage subtypes and difference in polarized macrophages (M2) in relation to CD4 and CD8 markers were significant in relation to PD-L1 and require further exploration. Improved characterization of PD-L1 pathway and potential surrogate markers to compile immune competency profiles will include early results from our IHC staining for dsRNA fragments to lend support to endogenous retroviral activation in a wide range of both carcinomas and sarcomas. Citation Format: Galen Hostetter, Lorenzo Sempere, Scott Jewell, Steve Baylin. Assessing macrophage polarization in sarcomas with PD-L1 correlates [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr B33.

Immunohistochemical staining intensity for ganglioside GD1b was determined for 108 human neuroectodermal tumors. Most of the tissue elements that immunostained were tumor cells; only a few axons and occasional neurons reacted in some specimens. All pilocytic astrocytomas stained very positively, whereas none of the ependymomas and only 11% of primitive neuroectodermal tumors, 20% of glioblastomas, and 28% of anaplastic astrocytomas showed more than faint staining. A similar association between grade and immunostaining was seen in tumors containing an oligodendrogliomatous component, but reactivity was not as strong as in astrocytic tumors or primitive neuroectodermal tumors. Results of Cox regression showed significant associations between immunostaining intensity and survival for all cases taken together (P = 0.007); for the group consisting of astrocytomas, oligoastrocytomas, and oligodendrogliomas (P = 0.002); and for astrocytomas alone (P = 0.04). Results were also significant using a proportional hazards model controlling for patient age (all cases P = 0.005; astrocytomas only P = 0.02), but not when controlling for tumor grade. Our results indicate that immunohistochemical staining for GD1b is correlated with tumor grade and that it may be of prognostic utility in some primary human brain tumors, especially astrocytomas.

Author(s): Glaser, Ronald; Andridge, Rebecca; Yang, Eric V; Shana'ah, Arwa Y; Di Gregorio, Michael; Chen, Min; Johnson, Sheri L; De Renne, Lawrence A; Lambert, David R; Jewell, Scott D; Bechtel, Mark A; Hearne, Dean W; Herron, Joel Bain; Kiecolt-Glaser, Janice K | Abstract: BackgroundBasal cell carcinoma (BCC) tumors are the most common skin cancer and are highly immunogenic.ObjectiveThe goal of this study was to assess how immune-cell related gene expression in an initial BCC tumor biopsy was related to the appearance of subsequent BCC tumors.Materials and methodsLevels of mRNA for CD3e (a T-cell receptor marker), CD25 (the alpha chain of the interleukin (IL)-2 receptor expressed on activated T-cells and B-cells), CD68 (a marker for monocytes/macrophages), the cell surface glycoprotein intercellular adhesion molecule-1 (ICAM-1), the cytokine interferon-γ (IFN-γ) and the anti-inflammatory cytokine IL-10 were measured in BCC tumor biopsies from 138 patients using real-time PCR.ResultsThe median follow-up was 26.6 months, and 61% of subjects were free of new BCCs two years post-initial biopsy. Patients with low CD3e CD25, CD68, and ICAM-1 mRNA levels had significantly shorter times before new tumors were detected (p = 0.03, p = 0.02, p = 0.003, and p = 0.08, respectively). Furthermore, older age diminished the association of mRNA levels with the appearance of subsequent tumors.ConclusionsOur results show that levels of CD3e, CD25, CD68, and ICAM-1 mRNA in BCC biopsies may predict risk for new BCC tumors.

Practice-changing evidence requires confirmation, preferably in multi-institutional clinical trials. The collection of tissue within such trials has enabled biomarker studies and evaluation of companion diagnostic tests. Tissue microarrays (TMAs) have become a standard approach in many cooperative oncology groups. A principal goal is to maximize the number of assays with this precious tissue. However, production strategies for these arrays have not been standardized, possibly decreasing the value of the study. In this article, members of the Cancer and Leukemia Group B Pathology Committee relay our experiences as array facility directors and propose guidelines regarding the production of high-quality TMAs for cooperative group studies. We also discuss statistical issues arising from having a proportion of patients available for TMAs and the possibility that patients with TMAs fail to represent the greater study population.

Human biospecimens are subjected to collection, processing, and storage that can significantly alter their molecular composition and consistency. These biospecimen preanalytical factors, in turn, influence experimental outcomes and the ability to reproduce scientific results. Currently, the extent and type of information specific to the biospecimen preanalytical conditions reported in scientific publications and regulatory submissions varies widely. To improve the quality of research that uses human tissues, it is crucial that information on the handling of biospecimens be reported in a thorough, accurate, and standardized manner. The Biospecimen Reporting for Improved Study Quality (BRISQ) recommendations outlined herein are intended to apply to any study in which human biospecimens are used. The purpose of reporting these details is to supply others, from researchers to regulators, with more consistent and standardized information to better evaluate, interpret, compare, and reproduce the experimental results. The BRISQ guidelines are proposed as an important and timely resource tool to strengthen communication and publications on biospecimen-related research and to help reassure patient contributors and the advocacy community that their contributions are valued and respected. Cancer (Cancer Cytopathol) 2011;119:92-101. Published 2011 by the American Cancer Society.*

Purpose Colon cancers exhibiting DNA mismatch repair (MMR) defects demonstrate distinct clinical and pathologic features, including better prognosis and reduced response to fluorouracil (FU) –based chemotherapy. This prospective study investigated adjuvant chemotherapy containing FU and irinotecan in patients with MMR deficient (MMR-D) colon cancers. Patients and Methods Cancer and Leukemia Group B 89803 randomly assigned 1,264 patients with stage III colon cancer to postoperative weekly bolus FU/leucovorin (LV) or weekly bolus irinotecan, FU, and LV (IFL). The primary end point was overall survival; disease-free survival (DFS) was a secondary end point. Tumor expression of the MMR proteins, MLH1 and MSH2, was determined by immunohistochemistry (IHC). DNA microsatellite instability was also assessed using a panel of mono- and dinucleotide markers. Tumors with MMR defects were those demonstrating loss of MMR protein expression (MMR-D) and/or microsatellite instability high (MSI-H) genotype. Results Of 723 tumor cases examined by genotyping and IHC, 96 (13.3%) were MMR-D/MSI-H. Genotyping results were consistent with IHC in 702 cases (97.1%). IFL-treated patients with MMR-D/MSI-H tumors showed improved 5-year DFS as compared with those with mismatch repair intact tumors (0.76; 95% CI, 0.64 to 0.88 v 0.59; 95% CI, 0.53 to 0.64; P = .03). This relationship was not observed among patients treated with FU/LV. A trend toward longer DFS was observed in IFL-treated patients with MMR-D/MSI-H tumors as compared with those receiving FU/LV (0.57; 95% CI, 0.42 to 0.71 v 0.76; 95% CI, 0.64 to 0.88; P = .07; hazard ratio interaction between tumor status and treatment, 0.51; likelihood ratio P = .117). Conclusion Loss of tumor MMR function may predict improved outcome in patients treated with the IFL regimen as compared with those receiving FU/LV.

Purpose Increased expression of eicosanoids in cancer has been associated with adverse prognosis. We performed a randomized phase II trial to test the hypothesis that inhibitors of two eicosanoid pathways (cyclooxygenase-2 [COX-2], celecoxib and 5-lipoxygenase [5-LOX], zileuton) added to chemotherapy would improve outcome in advanced non–small-cell lung cancer (NSCLC). Patients and Methods Patients with advanced NSCLC, a performance status of 0 to 2, and no prior therapy were eligible. All patients received carboplatin area under the curve (AUC) 5.5 mg/mL · min day 1 + gemcitabine (1,000 mg/m2) days 1 and 8. Patients were randomly assigned to: (a) zileuton 600 mg PO qid, (b) celecoxib 400 mg PO bid, or (c) celecoxib and zileuton at the same doses. Immunohistochemical staining for COX-2 and 5-LOX was performed without knowledge of outcomes. Results One hundred forty patients were entered and 134 were eligible and treated. There was no survival difference between the arms. COX-2 expression was a negative prognostic marker for overall survival (OS; hazard ratio [HR] = 2.51, P = .019 for index ≥ 4; HR = 4.16, P = .005 for index = 9) for patients not receiving celecoxib. Patients with increased COX-2 expression (index ≥ 4), receiving celecoxib had better survival than did COX-2–expressing patients not receiving drug (HR = .342, P = .005 for OS; HR = .294, P = .002 for failure-free survival). Multivariate analysis confirmed the interaction of COX-2 and celecoxib on survival. 5-LOX expression was neither prognostic nor predictive. Conclusion This study failed to demonstrate the value of dual eicosanoid inhibition or benefit from either agent alone in addition to chemotherapy. However, a prospectively defined subset analysis suggests an advantage for celecoxib and chemotherapy for patients with moderate to high COX-2 expression.

The Multiple Myeloma Research Foundation (MMRF) CoMMpass trial (NCT145429) is a longitudinal study of 1000 patients with newly-diagnosed multiple myeloma from clinical sites in the United States, Canada, Spain, and Italy. Each patient receives a treatment regimen containing a proteasome inhibitor, immunumodulatory agent, or both. Clinical parameters are collected at study enrollment and every three months through the five-year observation period. To identify molecular determinants of clinical outcome each baseline and progression tumor specimen is characterized using Whole Genome Sequencing, Exome Sequencing, and RNA sequencing. This will be the first public presentation of the interim analysis seven cohort with 760 enrolled patients of whom 565 are molecularly characterized. This cohort of patients includes 14 patients with baseline and secondary samples along with 7 patients with characterized tumor samples from the bone marrow and peripheral blood. Although the median follow-up time for the cohort is only 260 days the patients on proteasome and IMiD based combinations are currently showing a PFS and OS benefit compared to those receiving combinations with each agent alone. From the raw mutational analysis we identified 24 significant genes that are recurrently mutated and the mutated allele is detectably expressed in all but one, DNAH5. Suggesting these mutations are likely contributing to myelomagenesis through an unconventional mechanism. Interestingly, DIS3 mutations are independent of KRAS, NRAS, and BRAF indicating a potential mechanistic link while PRKD2 mutations are associated with t(4;14). To identify events driving the initiation of myeloma we performed a detailed clonality analysis using a bayesian clustering method that corrects for copy number abnormalities and tumor purity to assign mutations into distinct clonal branches versus the initiating trunk mutations. On average 63.8% of mutations are trunk mutations and in 86.7% of patients at least one trunk mutation is associated with somatic hypermutation of an immunoglobulin gene as expected in a late stage B-cell malignancy. This identified many expressed trunk mutations that did not come out in the classic significance analysis like ATM, EGR1, and CCND1. To identify molecular subtypes we performed unsupervised clustering using a consensus clustering approach on independent discovery and validation cohorts, which identified 12 distinct subtypes, using a combination of silhouette score and cumulative distribution of consensus scores. This analysis identified two distinct groups associated with t(4;14) with mutations in FGFR3 and DIS3 being exclusive to one subgroup. In addition, this analysis separates patients with cyclin D translocations into three different groups, with one group having the second lowest PFS proportion. Three patients without CCND1 or CCND3 translocations were found to have IgH translocations targeting CCND2. The MAF subgroup was associated with the lowest OS and PFS proportion, and the three MAF/MAFB translocation negative patients in the subgroup all had MAFA translocations. The remaining 6 subgroups are associated with hyperdiploid copy number profiles and harbor the majority of the IgH-MYC translocation events. Two of the hyperdiploid groups are associated with a low level of NFKB activation compared to the remaining four, one of these is defined by the highest proliferation index but paradoxically the other has the second worst OS proportion. Another group is enriched with FAM46C and NRAS mutations. The genomic profiles of the paired tumors isolated from the peripheral blood and bone marrow are highly similar indicating these are not genetically distinct tumor compartments, at least in this subset of seven patients. Applying our bayesian clustering method to the serial samples resolved additional clonal clusters as mutations with similar cancer cell fractions at diagnosis clearly diverged at later timepoints. These analyses have identified tumor initiating mutations and new subtypes of myeloma, which are associated with distinct molecular events and clinical outcomes. Disclosures Jagannath: Novartis: Honoraria; Bristol Myers Squibb: Honoraria; Celgene: Honoraria; Merck: Honoraria; Janssen: Honoraria. Siegel:Celgene Corporation: Consultancy, Speakers Bureau; Amgen: Speakers Bureau; Takeda: Speakers Bureau; Novartis: Speakers Bureau; Merck: Speakers Bureau. Vij:Takeda, Onyx: Research Funding; Celgene, Onyx, Takeda, Novartis, BMS, Sanofi, Janssen, Merck: Consultancy. Zimmerman:Amgen: Honoraria, Speakers Bureau; Celgene: Honoraria, Speakers Bureau; Millennium: Honoraria, Speakers Bureau; Onyx: Honoraria. Niesvizky:Celgene: Consultancy, Speakers Bureau. Rifkin:Onyx Pharmaceuticals: Consultancy, Membership on an entity's Board of Directors or advisory committees; Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees; Millennium Pharmaceuticals, Inc., Cambridge, MA, USA, a wholly owned subsidiary of Takeda Pharmaceutical Company Limited: Consultancy, Membership on an entity's Board of Directors or advisory committees. Lonial:Millennium: Consultancy, Research Funding; Onyx: Consultancy, Research Funding; Novartis: Consultancy, Research Funding; Bristol-Myers Squibb: Consultancy, Research Funding; Janssen: Consultancy, Research Funding; Celgene: Consultancy, Research Funding.

Stress and sunlight and are two factors that affect many people’s daily lives. Both can be beneficial in moderation, but long-term exposure to either can be detrimental in that both may contribute to the development and/or exacerbation of disease. It is estimated that over 2–3 million new cases of non-melanoma skin cancer occur each year (1). Due to a host of psycho-socio-political factors, stress has become an increasing and inevitable part of people’s lives. Chronic stress has been shown to dysregulate immune function (2) and is thought to play a role in the etiology of many diseases. Given the increasing prevalence of exposure to chronic stress and UV and their ability to independently induce pathologic effects, it becomes important to understand whether and how these factors may act together to increase susceptibility to disease. Stress is defined as a constellation of events—a stimulus (stressor) that precipitates a reaction in the brain (stress perception) and activates physiologic fight/flight systems in the body (stress response) (3,4). Chronic stress, defined as stress that persists for several hours a day for weeks, months, or years (3,4), has been shown to have immunosuppressive effects (2) that include suppression of skin cell mediated immunity (3). The ultraviolet B (UVB) component of sunlight is a complete carcinogen and is responsible for most non-melanoma skin cancers (5). Immediate effects of UVB radiation include DNA damage, epidermal hyperplasia and inflammation (6). UVB also suppresses lymphocyte trafficking, T cell, natural killer (NK) cell function (7), and immune responses that are directed against squamous cell carcinoma (8,9). Here we test the hypothesis that chronic stress accelerates the emergence and progression of UVB induced squamous cell carcinoma and inhibits its regression. We examined the effects of moderate chronic stress on the emergence, progression, and regression of squamous cell carcinoma induced by low level (minimal erythemal dose [MED], i.e., without blistering) exposure to UVB radiation in a mouse model. Our goal was to identify potential molecular and cellular immunologic mediators of the exacerbating effects of chronic stress on the emergence and progression of squamous cell carcinoma. Because both squamous cell carcinoma and basal cell carcinoma are immunogenic non-melanoma skin cancers, our findings may also be applicable to basal cell carcinoma, which is the most common form of skin cancer in the United States (10).

The collection and preservation of tissues from surgery to the lab affects the quality and value of research and/or healthcare applications for cancer patients. To this end we are further defining best practices in the management of surgically resected tissues through the analysis of a systems biology model. In the first steps of this process we defined an experimental animal model to assess gene expression signatures of biological pathways related to preservation intervals. Athymic nude murine tissues (kidney, liver, brain, and PDX-models) were excised at baseline and immediately aliquots of tissue were incubated at varying intervals (t=0, 0.5, 1, 3, 6, 9 hours, temperature during intervals was maintained at 37°C). All tissues were preserved at -80C and total RNA was extracted from these tissues using a uniform RNA isolation kit (RNeasy Mini Kit from Qiagen, Inc.) by the same technician. The RNA Integrity Number (RIN) was obtained using the Agilent's BioAnalyzer 2100 and RNA concentration using the Nanodrop 8000. Subsequently, cDNA was synthesized using Thermo Scientific's RevertAid First Strand cDNA Synthesis Kit, and qPCR analysis of each tissue was performed using the Qiagen RT2 Profiler PCR Arrays including the Cell Death PathwayFinder (murine origin liver, kidney, brain) and Hypoxia Signaling Pathway (human origin PDX-model) arrays. Results show a variation of transcripts s that were upregulated (Bax, Bcl2, Fos, Egr1, Tnfrsf10b) or downregulated (Ctss, Hmox1, Epo, Snca) with increased length of tissue incubation and tissue-specific patterns of regulation were observed. Furthermore, these changes in gene expression did not correlate with a decrease in RIN scores, which raises questions about the suitability of RIN as a comprehensive assessment of RNA quality at the transcript level. These findings have important implications for cancer research, namely that tissues that have not been stabilized within several minutes of excision from the host might have undergone degradation of RNA templates that reflect tissue management-related biological activity versus disease-related transcriptome. In future work, we plan to compare macroanalytes such as microRNAs, non-coding RNAs and proteins across different tissue types with an assumption that gene signatures and biological effects will differ per tissue type. We will use results from our experimental biopreservation model to continue the emphasis on transcriptome changes within the context of biological relevance. Citation Format: Scott D. Jewell, Eric Collins, John Beck, David Monsma, Dawna Dylewski, Andrew Borgman, Mary Winn, Galen Hostetter. Illuminating the effects of tissue degradation to improve the management of tissues used in cancer research or clinical applications. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 361. doi:10.1158/1538-7445.AM2014-361

The objectives of the present study were to evaluate the expression of three proliferation markers, viz., epidermal growth factor receptor (EGFR), transforming growth factor-alpha (TGF-alpha) and proliferating cell nuclear antigen (PCNA) and one genomic marker, c-myc in OSMF. Oral tissues were stained with monoclonal antibodies to PCNA, c-myc, TGF-alpha and EGFR. The results were analyzed with Photoquant image analysis software. The expression of PCNA, c-myc, TGF-alpha and EGFR was higher in oral submucous fibrosis (OSMF) than in normal control oral mucosa. The oral epithelium was divided into a proliferative compartment (stratum germinativum) and a differentiated compartment (stratum spinosum). A differential pattern of expression of PCNA and c-myc was observed in OSMF. While the intensity of staining decreased, the percent area of expression of PCNA and c-myc increased in stratum germinativum in OSMF (P

The Multiple Myeloma Research Foundation (MMRF) CoMMpass trial is the cornerstone of the MMRF Personalized Medicine Initiative. The accrual goal is 1000 patients with newly-diagnosed active multiple with sufficient tumor material for the comprehensive analysis of each tumor genome. Each eligible patient will be followed from initial diagnosis longitudinally for a minimum of 8 years. Additional tumor samples will be collected and comprehensively analyzed when possible for each patient at time of suspect CR, recurrence or progression of disease. The clinical study (NCT0145429) opened in July 2011 and now includes 56 sites in the US and Canada that have enrolled over 300 patients as of Aug. 1, 2013. The frontline treatments permitted in this study include current standard of care therapies containing a proteasome inhibitor, an IMiD or both. The comprehensive analysis of each tumor and matched normal genome involves; Long-Insert Whole Genome Sequencing (WGS) to identify somatic copy number alterations and structural changes, Whole Exome Sequencing (WES) to identify somatic single nucleotide variants and indels, and RNA sequencing (RNAseq) to define transcript expression levels and fusion transcripts. In addition, BRAF pyrosequencing and immunophenotyping analysis are being done in CAP-CLIA certified labs. An extensive, open-access, public clinical and molecular database, the CoMMpass Researcher Gateway (RG) (https://research.themmrf.org), is being developed to facilitate the rapid dissemination of the results and provides the myeloma community with a mechanism to analyze the results. The clinical endpoints and outcomes also include Quality of Life measures and health care resource utilization. An initial interim analysis on the first 178 cases has just been completed and made publicly available through the CoMMpass RG. At the molecular level, BRAF analysis on this serial sample set of newly diagnosed patients identified V600E mutations at rate of 5.7%, confirming our previous observations from a mixture of non-consecutive treated and untreated patient samples in our previous genomic efforts. The flow cytometry panel was designed to provide a comprehensive immunofingerprint of each patient that could be used for minimal residual disease monitoring and to monitor potentially therapeutic options; MS4A1/CD20, CD52, KIT/CD117, and FGFR3. These studies have identified tumors which are 100% positive for these actionable antigens at frequencies of; 16.0% for CD20, 5.7% for CD52, 49.7% for CD117, and 8.5% for FGFR3. Of the 178 cases, 34 were profiled through WGS, WES and RNAseq before this interim analysis. We identified 553 variants (median 19 per patient, range 11-55) were the variant allele detected by WES was also detected by RNAseq, suggesting the variant is potentially biologically relevant. Of these genes, 36 were seen more than once and 7 were identified in three or more patients. This includes NRAS (23.5%), KRAS (14.7%), BRAF (8.8%), DIS3 (8.8%), FAM46C (8.8%), TRAF3 (8.8%), and ZNF100 (8.8%). Interestingly, all three ZNF100 variants show preferential expression of the mutant allele. Within this cohort the only recurrent fusion gene identified is the classic IgH-MMSET fusion transcripts associate with t(4;14). The MMRF CoMMpass is providing unprecedented molecular characterization and correlating clinical datasets that will help define the determinants of response to anti-myeloma agents, reveal new, actionable targets and/or those shared with other cancers and facilitate future clinical trial designs, thus serving as a stepping stone toward personalized medicine for myeloma patients. Disclosures: Auclair: MMRC: Employment. Harrison:MMRC: Employment. Jagannath:Celgene: Honoraria; Millennium: Honoraria. Siegel:Celgene: Honoraria, Speakers Bureau; Millennium: Honoraria, Speakers Bureau; Onyx: Honoraria, Speakers Bureau. Vij:Celgene: Honoraria, Research Funding, Speakers Bureau; Millennium: Honoraria, Speakers Bureau; Onyx: Honoraria, Research Funding, Speakers Bureau. Zimmerman:Celgene: Honoraria; Millenium: Honoraria; Onyx: Honoraria. Capone:MMRC: Employment. Lonial:Millennium: Consultancy; Celgene: Consultancy; Novartis: Consultancy; BMS: Consultancy; Sanofi: Consultancy; Onyx: Consultancy.

Abstract 3980 The Multiple Myeloma Research Foundation (MMRF) CoMMpassSM trial plans to analyze the tumor genome from 1000 patients with newly-diagnosed active multiple myeloma (ND-MM) from initial diagnosis over a period of 8 yrs [http://clinicaltrials.gov/ct2/show/NCT01454297]. Eligible patients include those with symptomatic MM who have not received prior therapy and provide consent for submission of paired specimens of bone marrow aspirate containing tumor cells and peripheral blood specimens for molecular analysis and biobanking. Individual tumor genomes will be sequenced to reveal the molecular and genetic changes underpinning tumor response and clinical benefit of therapies for MM and to facilitate future clinical trial designs. An extensive clinical and molecular database is being developed to facilitate association studies. The clinical endpoints and outcomes also include Quality of Life measures and health care resource utilization. The molecular database includes data from Whole Genome Sequencing, Whole Exome Sequencing and RNA sequencing comparing tumor to normal health mononuclear cells as part of the longitudinal profile of MM disease progression and clinical response in individual patients. The clinical study opened in July 2011 and includes 55 sites in the US contributing over 180 patients as of Aug 8, 2012. The frontline treatments permitted in this study include current standard of care therapies containing a proteasome inhibitor, an IMiD or both. Screening of 1500 individuals presenting with suspected myeloma in primary care community and academic centers is expected to identify individuals with asymptomatic MGUS, SMM and active MM patients. Patients with a confirmed diagnosis of asymptomatic myeloma or MGUS will be invited to re-enroll in CoMMpassSM Study upon conversion to active disease. Centralized bone marrow aspirate and peripheral blood specimen processing is being conducted to support profiling of the patient samples. The workflow for biospecimens includes real time analysis of bone marrow aspirates by multiplex flow cytometry to identify patient-specific immunophenotypic markers to follow evidence of Minimal Residual Disease (MDR), recurrence of disease and emergence or expansion of new tumor cell clonal populations3. B-raf pyrosequencing and immunophenotyping are performed in CAP-CLIA certified labs and results are provided to physicians. Included in these assays are potentially actionable drug targets include the following proteins: CD52 [CAMPATH-1], CD117 [c-kit], FGFR3, B-raf V600E and CD20. CD138-positive tumor cells purified from BM aspirates and paired healthy cells undergo sequencing analysis comprising Shallow Whole Genome and Whole Exome sequencing and transcriptome analysis. Chromosomal alterations and ploidy will be assessed by cytogenetic and FISH analysis. Altogether, these efforts will provide an unprecedented myeloma dataset on structural and copy number variation, mutation and gene expression. Samples collected at suspected Complete Response will also be evaluated by flow cytometry using multiple markers to follow immunophenotypic changes and to monitor minimal residual disease (MRD) and clonal evolution of the tumor population over time. The MMRF CoMMpassSM study will comprehensively catalog genomic alterations in patients treated with standard-of-care 1st line agents at significant clinical events, such as suspected CR, recurrence or progression of disease. The knowledge base developed from CoMMpassSM will fuel key insights into mechanisms of disease and drug response in myeloma, new drug targets and pathways, prognostic and predictive biomarkers for clinical validation and development and refine molecular classification of MM subtypes. The MMRF CoMMpassSM Research database and Myeloma Community portal will serve as a foundation to build personalized medical care strategies for MM patients. Disclosures: Keats: Tgen: Employment. Carpten:Life Technologies: Research Funding. Anderson:celgene: Membership on an entity's Board of Directors or advisory committees; millennium: Membership on an entity's Board of Directors or advisory committees; onyx: Membership on an entity's Board of Directors or advisory committees; bristol myers squibb: Membership on an entity's Board of Directors or advisory committees; acetylon: Membership on an entity's Board of Directors or advisory committees; oncopep: Membership on an entity's Board of Directors or advisory committees. Lonial:Millennium: Consultancy; Celgene: Consultancy; Novartis: Consultancy; Bristol-Myers Squibb: Consultancy; Onyx: Consultancy; Merck: Consultancy.

The Multiple Myeloma Research Foundation (MMRF) CoMMpass®; trial opened in July 2011 and will follow 1000 patients with newly diagnosed multiple myeloma (ND-MM) [http://clinicaltrials.gov/ct2/show/NCT01454297]. The goal of this study is to understand the molecular and genetic changes underpinning the evolution of myeloma in individuals and to facilitate future clinical trials based on those results. Comprehensive clinical annotation will accompany individual molecular profiles at baseline, treatment response and disease recurrence over the course of 5-8 years. The study will yield an extensive molecular and clinical database providing information on the longitudinal aspect of multiple myeloma disease progression in individual patients. Eligible patients include those with symptomatic ND-MM who have not received prior therapy. Initial treatments permitted in the study include those containing either a proteasome inhibitor, an IMiD or both. Centralized bone marrow aspirate and peripheral blood specimen processing building upon the experience of the Multiple Myeloma Research Consortium (MMRC) Tissue Bank is being conducted to support profiling of the patient samples. Here we describe the workflow for biospecimens and characterization including the analysis of bone marrow aspirates by multiplex flow cytometry to identify patient-specific immunophenotypic markers and sequencing of BRAF V600 mutations. CD138-enriched tumor cells derived from the aspirates will enable a breadth of sequencing analysis comprising whole genome and whole exome sequencing, as well as, transcriptome analysis via RNA Seq. Chromosomal alterations and ploidy will be assessed by cytogenetic and FISH analysis. Altogether, these efforts will provide an unprecedented myeloma dataset on copy number variation, mutation and levels of gene expression. Samples collected at suspected complete response will be evaluated by quantitative flow cytometry using multiple markers to follow immunophenotypic changes and to monitor minimal residual disease. The MMRF CoMMpass® study aims to comprehensively catalog genetic alterations in patients treated with standard-of-care 1st line agents and at milestones of relapse. The knowledge obtained in CoMMpass® will provide key insights into mechanisms of disease and drug response in myeloma, reveal targets and biomarkers for drug development, provide insights into refined classification of subtypes of myeloma and be used as a foundation to build personalized medical care initiatives for myeloma patients. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4561. doi:1538-7445.AM2012-4561

4012 Background: LOH at 18q is associated with poorer overall survival in patients with colon cancer; however available studies are retrospective and vary in analysis methods. We recently completed an 18qLOH assay method validation study, and after standardizing technique, this prospective study investigated the role of 18qLOH among patients with low-risk stage II colon cancer. Methods: In Cancer and Leukemia Group B (CALGB) protocol 9581, we randomized 1738 stage II patients to post-operative treatment with a 500 mg loading dose of monoclonal antibody 17–1A followed by four infusions of 100 mg every 28 days or observation. The primary endpoint was overall survival (OS); disease free survival (DFS) was a secondary endpoint. Status of 18qLOH was assessed in patients with available tissue and interpretable PCR results. Patients were excluded if their tumors were uninformative for 18qLOH or if their tumors displayed microsatellite instability. Results: We report 18qLOH data on 156 patients. Patient characteristics including treatment, age, gender, performance status, site and grade of tumor, were similar between all patients enrolled and the subset of patients with tumor samples analyzed. The DFS and OS for treated and observed patients were no different (5-yr DFS: 0.81 and 0.80, p= 0.96; 5-yr OS: 0.88 and 0.86, p=0.44 at a median of 6.8 yrs of follow-up) and the data were pooled across the study's arms. Of the tumors examined, 101 (65%) were positive for 18qLOH. A significantly lower proportion of patients with 18qLOH-positive tumors had proximal tumors (46.5% vs 65.5%; p=0.02). Significantly decreased DFS and OS were observed in patients with 18qLOH-positive tumors. Five-year DFS among patients with 18qLOH-positive tumors was 0.78 vs 0.93 among patients with 18qLOH-negative tumors [HR 0.39; 95% CI (0.16, 0.94); logrank p=0.03 based on 33 events]. Five-year OS among patients with 18qLOH-positive tumors was 0.85 vs 0.98 among patients with 18qLOH-negative tumors [HR 0.25; 95% CI (0.07, 0.83); logrank p=0.01 based on 24 events]. Conclusions LOH at 18q was prognostic for DFS and OS among patients with available tissue for analysis after resection of low-risk stage II colon cancer who were not treated with chemotherapy in the adjuvant setting. [Table: see text]

10003 Background: Colon cancers exhibiting a high level of microsatellite instability (MSI-H) show distinct clinicopathological features, including both better prognosis and reduced response to 5-fluorouracil (5-FU)-based chemotherapy. We investigated the impact of adjuvant chemotherapy containing irinotecan in patients with MSI-H colon cancers. Methods: CALGB protocol 89803 randomized 1264 patients with resected stage III colon cancer to receive post-operative 5-FU and leucovorin (LV) with or without irinotecan. Paraffin blocks containing primary tumor and normal tissue were collected. Microsatellite instablility was assessed using a panel of mono- and di-nucleotide markers. Disease free survival (DFS) was measured from trial entry until documented disease progression or death from any cause. A statistical significance level of 0.2 was used in screening to generate hypotheses regarding MSI status and outcome. Median follow-up at analysis was 3.8 years. Overall C89803 showed no advantage for addition of irinotecan to 5-FU/LV. Results: Patients with and without tumor samples analyzed did not differ by treatment, age, gender, primary site, T-stage, differentiation, # positive nodes, or mucinous type. Of 482 tumors analyzed, 75 (16%) demonstrated MSI-H. MSI-H cancers were more likely to be located in the proximal colon (p [Table: see text]

A new intraoperative approach to tumor localization using radiolabelled monoclonal antibody (MAb) B72.3 involves the use of a hand-held gamma-detecting probe (GDP) by the surgeon and, subsequently, the pathologist. We report here the use of 125j-labelled MAb B72.3 IgG and a GDP to localize primary and metastatic colorectal cancer in 31 patients. The patients were administered radiolabelled MAb i. v., and all underwent surgical exploration 5 to 35 days post-injection. In vivo localization of the MAb was evaluated using a GDP, with tumor and normal tissue counts being obtained. In each case, the subsequent tumor and normal tissue that were resected were analyzed in vitro for MAb localization; this was evaluated by calculating the radiolocalization index, i. e., the ratio of the injected dose per gram localized to tumor versus that of normal tissue. When the GDP was used intraoperatively, MAb B72.3 localized tumors in 68% (21/31) of the patients; the arbitrary criterion of tumor-to-normal tissue ratios higher than or equal to 2.0: I in vivo being taken as positive. Resected tumor radiolocalization indices ranged from 0.5 to 543, and 71% (22/31) of the patients studied had tumors with radiolocalization indices higher than or equal to 3. Of 50 carcinoma biopsies, 34 that were probe-positive were antigen-positive when B72.3 was used in immunoperoxidase assays, while 4 carcinoma biopsies that were probe-negative were also antigen-negative. Twelve of 50 biopsies were probe-negative and antigen-positive, but many of these lesions only contained a few antigen-positive cells; none of the 50 was probe-positive and antigen-negative. Tumors of all histologic grades localized injected MAb and, in general, higher in vivo probe ratios and radiolocalization indices were obtained from patients who underwent surgery 20 to 35 days following injection of the MAb. MAb B72.3 localized tumor in all sites to which colon carcinoma commonly metastasizes, including mesenteric and peri-aortic lymph nodes, liver, lung, and peri-rectal soft tissue. There was a strong statistical correlation (p = 0.001) between detecting MAb B72.3 localization to tumors using the GDP intraoperatively and subsequent in vitro analysis of cpm/g for tumor versus normal tissues. These studies thus further validate the use of 125I-labelled MAb B72.3 IgG and of a hand-held gamma probe for the intraoperative detection of carcinomatous lesions.

Introduction Eicosanoids, including PGE-2 and 5-HETE, can increase levels of plasma vascular endothelial growth factor (VEGF). Overexpression of COX-2 or 5-LOX increases levels of PGE-2 and 5-HETE, respectively. Elevated levels of VEGF are common in patients with non-small cell lung cancer (NSCLC). We prospectively measured VEGF in serum collected from patients enrolled in Cancer and Leukemia Group B 30203, a randomized phase II study of eicosanoid modulation in addition to chemotherapy in patients with advanced NSCLC, to determine whether these levels had prognostic significance and whether they correlated with COX-2 expression and/or responded to inhibition of COX-2 or 5-LOX. Methods Pre- and post-treatment serum was collected from patients enrolled in CALGB 30203. Serum VEGF levels were determined using enzyme-linked immunosorbent assay methodology. Statistical analyses were performed to determine the correlation between pretreatment serum VEGF levels and time of overall survival. Pretreatment formalin fixed tissue was stained for 5-LOX and COX-2 by immunohistochemistry. Results The median baseline VEGF level was 502 pg/ml (range, 55–3453 pg/ml). Dichotomized serum VEGF levels at median inversely correlated with survival time ( p = 0.008), as did VEGF levels as a continuous variable in multivariate analysis ( p = 0.035). VEGF levels were significantly correlated neither with baseline COX-2 expression (Pearson r = 0.1524, p = 0.271) nor with 5-LOX expression. Treatment with COX-2 or 5-LOX inhibitors did not alter the levels. Conclusion These data indicate that elevated serum VEGF is a negative prognostic variable in NSCLC. VEGF levels are neither correlated with baseline tumor COX-2 expression nor do they respond to COX-2 and/or 5-LOX inhibition plus chemotherapy.