Citations

PurposeThe optimal management of stage I follicular lymphoma, according to consensus guidelines, is based on uncontrolled experiences of select institutions. Diverse treatment approaches are used despite guidelines that recommend radiation therapy (XRT).Patients and MethodsWe analyzed outcomes of patients with stage I follicular lymphoma enrolled onto the National LymphoCare database.ResultsOf 471 patients with stage I follicular lymphoma, 206 patients underwent rigorous staging as defined by both a bone marrow aspirate and biopsy and an imaging study (a computed tomography [CT] scan of the whole body, a positron emission tomography [PET]/CT scan, or both). Rigorously staged patients had superior progression-free survival (PFS) compared with nonrigorously staged patients (hazard ratio [HR], 0.63). Treatments given to rigorously staged patients were rituximab/chemotherapy (R-chemo; 28%), XRT (27%), observation (17%), systemic therapy + XRT (13%), rituximab monotherapy (12%), and other (3%). With a median follow-up of 57 months for PFS, there were 44 progression events (in 21% of patients) for rigorously staged patients. For these patients, PFS was significantly improved with either R-chemo or systemic therapy + XRT compared with patients receiving XRT alone after adjustment for histology, LDH, and the presence of B symptoms. There were no differences in overall survival.ConclusionIn this largest, prospectively enrolled group of patients with stage I follicular lymphoma, variable treatment approaches resulted in similar excellent outcomes, which challenges the paradigm that XRT should be standard for this presentation.

Objective Eosinophil predominant inflammation characterises histological features of eosinophilic oesophagitis (EoE). Endoscopy with biopsy is currently the only method to assess oesophageal mucosal inflammation in EoE. We hypothesised that measurements of luminal eosinophil-derived proteins would correlate with oesophageal mucosal inflammation in children with EoE. Design The Enterotest diagnostic device was used to develop an oesophageal string test (EST) as a minimally invasive clinical device. EST samples and oesophageal mucosal biopsies were obtained from children undergoing upper endoscopy for clinically defined indications. Eosinophil-derived proteins including eosinophil secondary granule proteins (major basic protein-1, eosinophil-derived neurotoxin, eosinophil cationic protein, eosinophil peroxidase) and Charcot–Leyden crystal protein/galectin-10 were measured by ELISA in luminal effluents eluted from ESTs and extracts of mucosal biopsies. Results ESTs were performed in 41 children with active EoE (n=14), EoE in remission (n=8), gastro-oesophageal reflux disease (n=4) and controls with normal oesophagus (n=15). EST measurement of eosinophil-derived protein biomarkers significantly distinguished between children with active EoE, treated EoE in remission, gastro-oesophageal reflux disease and normal oesophagus. Levels of luminal eosinophil-derived proteins in EST samples significantly correlated with peak and mean oesophageal eosinophils/high power field (HPF), eosinophil peroxidase indices and levels of the same eosinophil-derived proteins in extracts of oesophageal biopsies. Conclusions The presence of eosinophil-derived proteins in luminal secretions is reflective of mucosal inflammation in children with EoE. The EST is a novel, minimally invasive device for measuring oesophageal eosinophilic inflammation in children with EoE.

Abstract A hypoxic microenvironment is believed to be a characteristic of solid tumors including pancreatic adenocarcinoma (PAC) and is associated with resistance to chemotherapy. The hypoxia-activated prodrug, TH-302, is designed to specifically target the hypoxic microenvironment. Combining G with TH-302 may enable the targeting of both the normoxic and hypoxic regions of PAC. TH-302 was investigated with full-dose G as part of a Phase 1/2 study with a 21% response, median PFS and OS of 5.9 and 8.5 months, respectively, and one-year survival of >40%. Based upon these data, a randomized Phase 2B study (NCT01144455) was conducted to assess the benefit of G+T to standard dose G for first-line therapy of PAC. An open-label multi-center study of two dose levels of TH-302 (240 mg/m2 or 340 mg/m2) in combination with G versus G alone (randomized 1:1:1) was initiated in June 2010. G (1000 mg/m2) and T were administered IV over 30-60 minutes on Days 1, 8 and 15 of a 28-day cycle. Patients on the G arm could crossover after progression and be randomized to a G+T arm. The primary efficacy endpoint is a comparison of progression-free survival (PFS) between the combination arms and G alone (80% power to detect 50% improvement in PFS with one-sided alpha of 10%). 214 pts (69 G: 71 G+T240: 74 G+T340) with advanced PAC including 77% distant metastases, 62% involving liver and 11% with prior adjuvant tx; median age: 65 (range 29-86); 126 M/88 F; 79/128 ECOG 0/1. Median cycles received: G - 4, G+T240 - 5, G+T340 - 6. Median PFS was 3.6 mo in G vs 5.6 mo in G+T arms with HR of 0.61 (95% CI: 0.43 - 0.87) and logrank p-value of 0.005. Median PFS in G + T340 was 6.0 mo. RECIST best response was 12% in G, 17% in G+T 240 and 27% in G+T340. 153 (71%) patients had elevated CA19-9 and follow-up. CA19-9 decreases were significantly greater in the G+T groups and greatest in the G+T340 arm which had 37 of 53 (70%) pts with a greater than 50% CA19-9 decrease. One death (suicide) was considered possibly related to study drug. Adverse events leading to discontinuation were: 16% G, 15% G+T240 and 11% G+T340. Serious adverse events were balanced across the treatment arms. The most common non-laboratory events, fatigue (49%), nausea (43%), constipation (34%) and peripheral edema (38%), were similar across groups. Rash (14% G, 39% G+T240 and 45% G+T340) and stomatitis (6% G, 17% G+T240 and 36% G+T340) were significantly greater with G+T combination but no Grd 4 (4 pts with Grade 3). Grd 3/4 thrombocytopenia (11% G, 39% G+T240 and 59% G+T340) and Grd 3/4 neutropenia (28% G, 56% G+T240 and 59% G+T340) were higher with G+T. G+T combination with full dose G improved the efficacy of G with significantly longer PFS, higher response rate and greater CA19-9 declines. The G+T combination was well tolerated. Skin and mucosal toxicity and myelosuppression were the most common related adverse events with no increase in treatment discontinuation. 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 LB-121. doi:1538-7445.AM2012-LB-121

Abstract Background: Colon cancer is categorized by the acquisition of a number of molecular alterations in both oncogenes and in tumor suppressor genes. Although cMYC alterations have been reported in colon cancer cell lines, little other information exists in primary colon tumors. We sought to determine the frequency of cMYC amplification in primary colon cancer and its relationship to other well defined colon tumor alterations. Methods: An initial set of 392 tumors were evaluated. All samples were tested for the BRAF V600E mutation and all were classified as proficient mismatch repair (pMMR) based on both IHC and microsatellite analysis of tumor tissue. A second set of 522 tumors was selected to replicate associations identified in the first set of samples. Similar to the initial cohort, both the BRAF V600E and the mismatch repair status of the tumors were assessed. The second cohort, however, included tumors that were both pMMR and dMMR. In both sets of samples, fluorescent in situ hybridization was used to evaluate cMYC gene amplification. Results: In cohort 1, cMYC amplification was observed in 15 of the 362 (4%) pMMR tumors successfully analyzed (Table 1). cMYC amplification was detected in 10 of 323 (3%) tumors with normal BRAF status vs. 5 of 39 (13%) tumors with altered BRAF status (p=0.015). In the second cohort, cMYC amplification was found in 20 of the 522 (4%) tumors. Only 1 of the 152 (<1%) dMMR tumors had cMYC amplification vs. 19 of the 370 (5%) pMMR tumors (p=0.012). Of the pMMR tumors, cMYC amplification was detected in 13 of 333 (4%) tumors with normal BRAF status vs. 6 of 37 (16%) tumors with altered BRAF status (p=0.007), nearly identical to the first group. Conclusion: cMYC amplification in colon cancer is an infrequent event. However, when present, cMYC amplification occurs almost exclusively in tumors that are pMMR. Additionally, among pMMR tumors, cMYC amplification is associated with the presence of the BRAF V600E mutation. 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 1151. doi:1538-7445.AM2012-1151

Abstract Background: Estrogen receptors are over-expressed in around 70% of breast cancer cases. The genetic changes that occur during aromatase inhibitor (AI) treatment are not well understood and may differ depending upon the patient's response phenotype. Methods: We performed whole genome sequencing (WGS) of matched blood, pre-treatment, and post-treatment biopsy samples from 22 estrogen receptor positive breast cancer patients treated with neoadjuvant aromatase inhibitors. For 5 cases, we performed the whole genome sequencing (WGS) on patients’ matched normal, two pre AI-treatment, and two post AI-treatment DNA isolates from biopsy samples. We validated all putative coding and non-coding somatic mutations using deep sequencing. By comparing the validated somatic mutations from pre- and post- AI treatment biopsy samples, we were able to determine the alterations in the tumor genomes. In every case we defined the clonal architecture of each pair of pre-treatment and post-treatment biopsy samples by comparing the variant allele frequencies from thousands of validated somatic mutations. Results: Comparisons of the two pre AI-treatment biopsy samples from the same patient indicates that the variant allele frequencies of mutations showed high concordances in all 5 cases, 0.74 to 0.95 range of correlation coefficient. Only a small percentage of somatic mutations were detected in one pre-treatment sample and not the other (4.65% overall). In comparing the somatic variations between pre-treatment and matched post-treatment biopsy samples in 22 cases, we found that patients with good clinical response to AI treatment retained known driver mutations only in their pre-treatment tumors. Conversely, those patients with poor clinical response presented new driver mutations in their post-treatment samples. Furthermore, the variant allele frequency for most mutated genes decreased in post AI treatment samples for patients with good AI treatment response; on the contrary, the variant allele frequency increased for patients with poor clinical response. Conclusions: From WGS of matched normal, pre-treatment, and post-treatment biopsy samples, we identified new driver genes mutated in patients with poor clinical response, while patients with good clinical response had lost mutated driver genes in their post-treatment biopsy samples. The genetic landscape revealed by WGS of pre-treatment and post-treatment biopsy samples reveals mutational repertoires are remodeled by AI therapy. This finding suggests deep sequencing of AI treated samples will be necessary to reveal the complete complement of mutations present in a patient's tumor. 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 LB-423. doi:1538-7445.AM2012-LB-423

Abstract Introduction: Only few genetic studies have been performed in PCNSL, partly due to the rarity of the tumors and the limited amount of available tissue. Unlike nodal DLBCL, PCNSL is poorly understood in terms of its precise histogenetic origin and molecular pathogenesis. It is still a matter of debate whether PCNSL differs from nodal DLBCL with respect to their molecular features and pathogenesis and also if there is a genomic signature PCNSL-specific. Materials and Methods: To determine the pattern of genetic alterations, 17 immunocompetent (EBV-, HIV-) PCNSL were analyzed by aCGH. Seven cases were analyzed using fresh tumor samples and 10 using formalin-fixed paraffin embedded (FFPE) tissues. B-cell differentiation status was characterized by immunostains for CD10, MUM-1, and BCL-6. The aCGH profile from PCNSL cases was compared with aCGH data obtained from 59 nodal DLBCL. Results: We found a complex karyotype with a median of 21 copy-number abnormalities (CNA) per case (range 10-49). Overall, 18 regions (10 losses and 8 gains) were affected in >20% of cases. Loss of 9p21 (CDKN2A) was the commonest CNA (82% of cases). Other common CNAs were loss of 6q23.3 (TNFAIP3; 59%), 6p21 (HLA genes; 53%), 6q21 (PRDM1; 47%) and gain of 12q21-q24 (53%), 7q21-q31 (35%) and 19q13 (35%). Five novel recurrent focal CNAs were found in PCNSL; loss of 3p21.31, 3q26.32, 10p15.3-p14, 12q24.31 and 16q12.1-q21 (29% of cases each). All of them, excluding –16q12.1-q21, were found either in less than 5% or absent in nodal DLBCL, thus suggesting to be unique to PCNSL. Recurrent homozygous deletions were found in CDKN2A, TMEM30A, TOX and CD58, the latter two involved in T-cell development and activation. CD58 was also recurrently affected by small focal deletions in the Ig-like C2-type domain. Furthermore, DNA sequencing analysis showed missense mutations in the Toll/IL-1 receptor domain of MYD88 in 35% of PCNSLs. Another 34 genes, including B2M, ETV6, MHC class II genes, PRDM1, and TNFRSF10A were homozygously deleted. Bioinformatics analysis including the most commonly affected genes showed an enrichment of networks associated with immune response, NF-kB pathway, proliferation, regulation of the apoptosis and lymphocyte differentiation and activation. Conclusions: We showed evidence of a highly complex genome and identified a subset of genes with potential relevance in PCNSL pathogenesis. The genomic profile described here reinforces the existence of a specific molecular signature in PCNSL, thus helping to genetically differentiate this entity from the nodal DLBCL and related lymphomas. Additionally, the results obtained from FFPE samples are encouraging and larger archival tissue collections can now be analyzed in order to complement the still fragmented knowledge we have of the genetic basis of the disease. 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 5081. doi:1538-7445.AM2012-5081

Abstract Motivation: Overexpression of HER2 (the product of the ERBB2 gene) occurs in about 15% of all breast tumors. We have undertaken to use next generation transcriptome sequencing technology to identify genomic features that are unique to HER2+ tumors. Interactome mapping was then used to integrate the genes associated with these features into a transcriptome landscape model, with a view towards identifying nodes of interaction that might be targeted in HER2+ tumors. Methods: We performed 50nt paired-end RNA-sequencing for 24 breast tumors: 8 each HER2+, ER+, triple negatives (TN). In addition to breast adenocarcinomas, we also sequenced 8 early passage non-transformed HMEC cell lines as normal controls. Reads from RNA sequencing were aligned to the genome and exon junctions using TopHat software. Gene counts were summarized and annotations were performed using our in-house programs. Tukey's test was used to obtain genes or transcripts that are specific to HER2 tumor group compared to other tumors/normal. A combination of bioinformatics softwares and algorithms were used to identify SNVs. Results: Only 13527 genes with median gene count greater than 16 reads in at least one of the 4 groups were considered for differential gene expression and splicing analysis. Some 696 genes were differentially expressed in HER2+ tumors compared to ER+, TN tumors and HMECs. We identified 272 alternately spliced transcripts for which the HER2+ tumors exhibited a mean transcript expression ratio significantly different from the means of other tumor groups. We also identified 4735 expressed single nucleotide variants that are uniquely associated with HER2+ tumors compared to other tumors/normal groups. Among these 3579/4735 sequence polymorphisms were not present in the 1000 genome germline sequence database or in the dbSNP132 database of naturally occurring germline polymorphisms. Integration of all the genes obtained from genomic feature analyses (differential expression, alternative splicing, single nucleotide variance) has been carried out to indentify biological processes that are specific to the HER2+ tumor subtype. Key nodes and pathways that are specific to HER2+ tumors will be evaluated for association with clinical outcome in a large series of patients who have received HER2-targeted therapy. 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 4926. doi:1538-7445.AM2012-4926

Abstract Objective. Molecularly distinct PCNSL signatures with divergent clinical behavior are now recognized. Implied within this heterogeneity are mechanisms for treatment response and pattern of failure. Recent cytogenetic and genomic studies demonstrated influences of select chromosomal regions on outcome to treatment and survival. These included genetic and epigenetic alterations affecting CDKN2A (9p21.3) that distinguished PCNSL from its systemic counterpart. We now report that deletion of 9p21.3/p16 is associated with a negative effect on survival. Methods and Patients. Well-annotated and population-based formalin fixed paraffin embedded (FFPE) patient samples were sourced from the SEER TRP. Specimens were retrieved from the Hawaii, Iowa and Los Angeles County (LA Co) tissue repositories. “Home Brew” fluorescent in situ hybridization (FISH) probes for BCL6, and ptpr-α were prepared according to a standard protocol (Cady et al. J Clin Oncol 2008;26:4814-9). FISH probes for 9p.21 were prepared similarly and then compared to a commercially available probe. Survival was based on the SEER TRP clinical annotations. Results. Thirty five patients were sourced - twelve from Iowa, 13 from Hawaii, and 10 from LA County. The test cohort was 23 from Iowa and Hawaii; the FISH probe failed in 9 and three had insufficient remaining tumor for analysis. For the Iowa and Hawaii registries and for the registries combined the lack of FISH probe detection of 9p.21/p16 correlated with survival (p=0.0159) and was independent of BCL6 (p=0.8788) and ptpr-α (p=0.3724). Conclusion. Deletion of p16 confers a negative effect on survival of PCNSL patients and appears to be independent of treatment, age, BCL6 and ptpr-α status. These results need to be confirmed in a larger sample size. 9p21.3 detection by FISH in feasible in surgical specimens and may aid in the stratification of such patients into different and/or more intensive treatment regimens. 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 4507. doi:1538-7445.AM2012-4507