bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2693: Inflammatory signalling in the colon tumour microenvironment enhances stromal cell mediated suppression of anti-tumour immune responses
Authors: O'Malley Grace , Lynch Kevin , Naicker Serika , Lohan Paul , Rigalou Athina , Ritter Thomas , Egan Laurence J. , Ryan Aideen E.
Published: July 2017

The colon tumour microenvironment (TME) comprises many cell types including endothelial cells, stromal cells and immune cells. Recent evidence suggests that high tumour stromal cell density correlates with a poor prognosis for colon cancer patients. The majority of these stromal cells are of mesenchymal origin (MSCs) and are known contributors to tumour angiogenesis and invasiveness. Little is known about the role of their immunosuppressive potential in the colon TME. We investigated the molecular regulation of the induced immunosuppressive, tumour-promoting phenotype of tumour-associated MSCs, and the effect of inflammation on this process. Balb/c bone marrow derived MSCs were treated with conditioned medium from untreated CT26 tumour cells (MSCTCM) or TNF-α treated CT26 cells (MSCTNF-TCM). Cell surface analysis of MSCs after 72h revealed an increased expression of TCR ligands MHC-I, MHC-II and PD-L1 compared to MSCControl. This was further potentiated by TNF-α induced tumour cell inflammation. MSCTCM co-cultured with syngeneic activated T cells displayed an enhanced ability to suppress CD8+ T cell proliferation, which was further potentiated by inflammatory activation of CT26 (MSCTNF-TCM). This effect was dependent on induced PD-L1 expression on MSCs as PD-1 blockade restored CD8+ T cell proliferation, activation and granzyme B secretion. In an immunocompetent Balb/c syngeneic model, we assessed tumour growth and anti-tumour immune responses following sub-cutaneous injection of CT26 cells alone or co-injection with MSCControl/MSCTNF-TCM. Co-injection of MSCControl significantly promoted tumour growth, and this was further potentiated by the co-injection of MSCTNF-TCM. This effect was associated with significantly reduced tumour infiltration of CD8 Granzyme B secreting T cells. We showed that this stromal cell mediated tumour promotion could be reversed by administration of a PD-1 blocking antibody, via restoration of granzyme B secreting CD8+ T cells. We show for the first time that stromal cells in the inflammatory TME directly modulate anti-tumour immune responses via PD-L1. This data could lead to better stratification of patients for immunotherapeutic regimens resulting in more targeted and durable responses to overcome stromal mediated tumour immunosuppression in colon cancer.

Citation Format: Grace O'Malley, Kevin Lynch, Serika Naicker, Paul Lohan, Athina Rigalou, Thomas Ritter, Laurence J. Egan, Aideen E. Ryan. Inflammatory signalling in the colon tumour microenvironment enhances stromal cell mediated suppression of anti-tumour immune responses [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2693. doi:10.1158/1538-7445.AM2017-2693
Abstract 270: Trends in colorectal cancer survival in Arab World, 1990-2009
Authors: Zaidi Zoubida , Cherif Mokhtar Hamdi
Published: July 2017

Introduction: Cancer survival is a key measure of the effectiveness of health-care systems. Globally, colon and rectum cancer ranked third for cancer incidence and fourth for cancer death in 2013. For developed countries it ranked second for incidence and mortality, and in developing countries it ranked fourth for both incidence and mortality. An increasing trend in incidence is reported from various registries of Arab world, Kuwait and Saudi Arabia present the highest incidences worldwide.

Objective: To describe the trends of the survival of colorectal cancer patients diagnosed in Arab countries.

Material and Methods: This report is a summary of the two survival figures of CONCORD study 1 (1990-1994) and CONCORD study 2 (1995-2009). Individual colon and rectum tumour records were submitted by 06 population-based cancer registries in Arab countries (Jordan, Saoudi Arabia, Qatar, Algeria, Lybia and Tunisia) for 9050 patients (15-99 years) diagnosed during 1990-2009 and followed up to 31 December 2009 . Estimated five-year net survival, adjusted for background mortality by single year of age, sex, calendar year in each country.

Results : For patients diagnosed during the period 2005-2009, the age-standardized five-years net survivals were respectively higher 68,2% for colon cancer and 77,8% for rectum cancer in Qatar and the lowest rate for rectal cancer 21% in Jordan, between 1995-1999 and 2005-2009, Survival increased in Algeria, but this trend is less reliable

Conclusions: Comparison of population-based cancer survival CONCORD study showed very wide variations in survival from colorectal cancer in Arab world. Cancer survival research is being used to formulate cancer control and the need to implement effective strategies of primary prevention.

Note: This abstract was not presented at the meeting.

Citation Format: Zoubida Zaidi, Mokhtar Hamdi Cherif. Trends in colorectal cancer survival in Arab World, 1990-2009 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 270. doi:10.1158/1538-7445.AM2017-270
Abstract 2700: Intestinal Vitamin D receptor deficiency increases susceptibility for the DSS-induced colon disease
Authors: Kim Jung-Hwan , Yamaori Satoshi , Gonzalez Frank J.
Published: July 2017

To investigate the function of the intestinal Vdr gene in inflammatory bowel disease (IBD), in conjunction with the discovery of possible metabolic markers for IBD using intestine-specific Vdr knockout mice. VdrΔIEpC mice were generated, phenotyped and treated with a time-course of 3% dextran sulfate sodium (DSS) to induce colitis. Colitis was diagnosed by evaluating clinical symptoms and intestinal histopathology. Gene expression analysis was carried out. In addition, metabolic markers of IBD were explored by metabolomics. VdrΔIEpC mice showed abnormal body size, colon structures and feces color. Calcium, collagen, and intestinal proliferation-related gene expression were all decreased, and serum alkaline phosphatase was highly increased. In the acute model which was treated with 3% DSS for six days, VdrΔIEpC mice showed a high score of IBD symptoms; enlarged mucosal layer and damaged muscularis layer. In the recovery experiment model, where mice were treated with 3% DSS for four days and water for three days, VdrΔIEpC mice showed a high score of IBD symptoms; severe damage of mucosal layer and increased expression of genes encoding proinflammatory cytokines. Feces metabolomics revealed decreased concentrations of taurine, taurocholic acid, taurodeoxycholic acid and cholic acid in Vdr ΔIEpC mice. In conclusion, disruption of the intestinal Vdr gene showed phenotypical changes. These factors combined may exacerbate IBD. Taken together, the results suggest that VDR may play an important role in IBD.

Citation Format: Jung-Hwan Kim, Satoshi Yamaori, Frank J. Gonzalez. Intestinal Vitamin D receptor deficiency increases susceptibility for the DSS-induced colon disease [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2700. doi:10.1158/1538-7445.AM2017-2700
Abstract 2707: Targeted RNA sequencing reveals thus far unknown diagnostically relevant fusion partners confirming its diagnostic potential
Authors: Nadarajah Niroshan , Meggendorfer Manja , Haferlach Torsten , Kern Wolfgang , Haferlach Claudia
Published: July 2017

Introduction: The genomic landscape of hematological malignancies has been resolved mainly based on whole exome and whole genome sequencing, primarily targeting gene mutations. In addition to mutations, gene fusions have also been identified as therapeutic targets, impressively shown e.g. for BCR-ABL1 and ETV6-PDGFRB. Even though fluorescence in situ hybridization (FISH) is the current gold standard in fusion detection, it is by concept limited to the selected genes it is applied to. In contrast, targeted RNA sequencing is a valuable hypothesis-free approach to discover all possible fusion junctions in a single reaction.

Aim: Explore the value of targeted RNA sequencing in a routine diagnostic work up.

Patients and Methods: We sequenced 134 cases in parallel to our routine diagnostics workflow using chromosome banding analysis (CBA), FISH and real-time quantitative (RQ-PCR). Targeted RNA sequencing was performed on the NextSeq 500 using the TruSight RNA Fusion panel (Illumina, San Diego, CA) consisting of 7690 probes covering 507 genes known to be involved in gene fusions. Analysis was performed with the RNA-Seq Alignment App v1.2.0 (BaseSpace Sequence Hub) using Star for Alignment and Manta for gene fusion calling with default parameters (Illumina, San Diego, CA).

Results: In 127 of 134 (95%) cases the results of FISH, subsequently confirmed with RT-PCR were also picked up by RNA Seq. This included diagnostically highly relevant fusions like BCR-ABL1 (n=8), KMT2A rearrangements (n=7), PML-RARA (n=4), and ETV6 and NPM1 rearrangements. In addition to the confirmation of orthogonal results, we were able to identify novel rare gene fusions, which we subsequently confirmed by RQ-PCR. This included immediately targetable fusions like TNIP1-PDGFRB and ETV6-EFL1, ETV6-FOXO1, IRF2PB1-RARA, RARA-SAE1).

Conclusion: 1) In the vast majority of instances targeted RNA sequencing confirmed results obtained by FISH/RT-PCR and in addition discovered new rare gene fusions 2) Targetable genetic aberrations were identified, which were not identifiable by chromosome banding analysis but would now lead to more individualized treatment. 3) Thus, targeted RNA sequencing may be a valuable tool in routine diagnostics and for patients with rearrangements unresolved by standard techniques, also paving the way to precision medicine in a considerable number of patients.

Citation Format: Niroshan Nadarajah, Manja Meggendorfer, Torsten Haferlach, Wolfgang Kern, Claudia Haferlach. Targeted RNA sequencing reveals thus far unknown diagnostically relevant fusion partners confirming its diagnostic potential [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2707. doi:10.1158/1538-7445.AM2017-2707
Abstract 2708: A custom gene expression panel for consensus molecular subtype classification of archival primary and metastatic colorectal cancers
Authors: Huw Ling-Yuh , Piskol Robert , Melo Felipe de Sosa e , Kim Doris , Qu Xueping , Koeppen Hartmut , Lackner Mark , Hampton Garret , Kabbarah Omar , Tam Rachel
Published: July 2017

Stratification of Colorectal Cancer (CRC) into actionable molecular subtypes has tremendous clinical value. Recently, a consolidated classifier identified four molecularly distinct CRC subtypes (CMS1-4) that were associated with unique biology and clinical outcomes based on global transcriptional analysis of frozen tissues. Here, we developed and applied a novel CRC panel that is ideally suited for transcriptional classification of archival clinical samples. Findings from in silico analysis demonstrated that the 800 genes on our panel could accurately classify CRC samples from external public datasets into the correct CMS subtypes. We applied our panel in the analysis of a novel cohort of 312 formalin-fixed paraffin-embedded (FFPE) tissues from 205 patients, and were able to detect all 4 CMS subtypes in primary CRCs and in metastases. When we examined the CMS subtypes of primary tumors and matched metastases from 50 patients we found 70% of cases to be concordant, as were key biologies, such as WNT/MYC pathway activation in CMS2 and EMT features in tumors of the CMS4 subtypes. This was confirmed by in situ hybridization (ISH) using the markers ASCL2 for CMS2 and SPARC for CMS4, respectively. Discordance in the CMS subtypes between primary tumors and matched metastases were observed in 30% of cases and may reflect tumor heterogeneity. Our findings suggest that our CRC-focused panel many have clinical utility for CMS classification of FFPE samples, and point to potential risks of using CMS subtypes of primary tumors to inform clinical decision-making at the metastatic stage in a subset of patients.

Citation Format: Ling-Yuh Huw, Robert Piskol, Felipe de Sosa e Melo, Doris Kim, Xueping Qu, Hartmut Koeppen, Mark Lackner, Garret Hampton, Omar Kabbarah, Rachel Tam. A custom gene expression panel for consensus molecular subtype classification of archival primary and metastatic colorectal cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2708. doi:10.1158/1538-7445.AM2017-2708
Abstract 272: Circadian disruption and cancer risk in the United States
Authors: Caporaso Neil E. , Gu Fangyi , Xu Shangda , Devesa Susan S. , Zhang Fanni , Klerman Elizabeth B. , Graubard Barry
Published: July 2017

Circadian disruption is a probable human carcinogen. Dawn and dusk times occur latter in western compared to eastern regions of each time zone, producing discrepancies between individuals’ biological clock and social time which may lead to circadian disruption and increased risk of cancer. We examined associations between longitude distance from the time zone meridian and age-standardized county-specific cancer incidence rates for total and 23 specific cancers by gender. Four million whites were diagnosed with cancer during 2000-2012 in the Surveillance, Epidemiology and End Results Program in residents of 607 counties in 11 continental US states. The models were adjusted for latitude, poverty, smoking, and state as well as rural/urban location, obesity, and Hispanic composition.

The total cancer incidence rates for counties located in the western regions of time zones were significantly elevated for both men and women after Bonferroni correction. The rate ratio (RR) per five degrees of longitude toward the west (corresponding to 20 minutes delay of sunrise) was 1.03 (95% confidence intervals, CI, 1.02-1.04, p=2.7×10-6) for men and 1.04 (95% CI, 1.03-1.05, p=3.8 ×10-10) for women. Chronic lymphocytic leukemia rates for counties in the western portions of time zones were significantly elevated for both men (RR=1.13, 95% CI=1.08-1.20, p=3.1 x10-6) and women (RR=1.12, 95%CI=1.05-1.19, p=3.7 x10-4). Among men, western location within a time zone was associated with elevated risk of prostate cancer (RR=1.04, 95% CI=1.02-1.07, p=4.8 x 10-4). Among women, western location within a time zone was associated with an increase in breast cancer (RR=1.04, 95% CI=1.02-1.06, p=6.5 x 10-5) and corpus uteri cancer (RR=1.10, 95% CI=1.07-1.14, p=2.4 x 10-9 among others.

The increased cancer risk with western residency within a time zone is in accord with the circadian disruption hypothesis. Our findings suggest that circadian disruption is not a rare phenomenon affecting only shift workers or international travelers but may be widespread in the general population which has broader implications for public health than generally appreciated.

Citation Format: Neil E. Caporaso, Fangyi Gu, Shangda Xu, Susan S. Devesa, Fanni Zhang, Elizabeth B. Klerman, Barry Graubard. Circadian disruption and cancer risk in the United States [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 272. doi:10.1158/1538-7445.AM2017-272
Abstract 2724: Brush biopsy miRNA based OSCC detection and diagnosis
Authors: Adami Guy R. , Schwartz Joel L. , Zhou Yalu , Tang Jessica L. , Markiewicz Michael , Jefferson Gina D. , Epstein Joel , Kolokythas Antonia
Published: July 2017

RNA based diagnosis and prognosis of squamous cell carcinoma has been slow to come to the clinic. Improvements in RNA measurement, statistical evaluation, and sample preservation still have not made these methods accurate enough to allow truly independent external validation. We propose that in the case of squamous cell carcinoma of the oral cavity that a chief source of variability is sample dissection which leads to variable amounts of stroma mixed in with tumor epithelium. We have used brush biopsy of suspicious lesions to characterize miRNA expression in OSCC epithelium. We used it to show an 11 miRNA signature for OSCC that can differentiate OSCC in both smokers and never smokers from normal tissue. We will report on efforts to optimize this classifier to distinguish OSCC from benign oral lesions such as lichen planus and leukoplakia that can be mistaken for OSCC. We also provide evidence that body fluid samples show similar changes in RNAs with OSCC that are seen in brush biopsy samples -suggesting much of the RNA is coming from the same source tumor epithelium. Finally, using a variation of mirPath designed to eliminate false positive, we have identified the neurotrophin signaling pathway as disregulated in most OSCC epithelium, and for the first time highlight the miRNAs that may control this pathway in OSCC, miR-486-5p, miR-7-5p, miR-146-5p, miR-101-3p, miR-18b-5p, miR-10b-5p, miR-21-5p, miR-20b-5p, miR-126-3p and miR-31-5p.

Citation Format: Guy R. Adami, Joel L. Schwartz, Yalu Zhou, Jessica L. Tang, Michael Markiewicz, Gina D. Jefferson, Joel Epstein, Antonia Kolokythas. Brush biopsy miRNA based OSCC detection and diagnosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2724. doi:10.1158/1538-7445.AM2017-2724
Abstract 2727: Clinical significance of PTEN in UTUC
Authors: Li Liang-Chen , Chuang Cheng-Keng , Chiang Hung-Ying , Chen Ying-Tzu , Lin Po-Hung , Yu Kai-Jie , Pang See-Tong , Weng* Wen Hui
Published: July 2017

Upper tract urothelial carcinoma (UTUC) is a rare malignancy accounts for about 5% of all urothelial tumours. The cancer cells start in the layer of tissue urothelium, and found in the renal pelvis, renal calyces or ureters. When compare the UTUC to the bladder urothelial carcinoma, the pathological and clinical findings are often look and act alike. Previous studies indicated that deletion of phosphatase and tensin homologue (PTEN) gene is common to be found in bladder cancer. As known tumor suppressor gene PTEN is located on chromosome ten and considered as an important negative regulator for the PIP3/Akt signaling pathway to promote cell proliferation and inhibit apoptosis. Thus, this study we aimed to determine clinical significance of PTEN in UTUC. We collected sixty-eight formalin-fixed paraffin-embedded (FFPE) UTUC samples, the tumor stage was according to American Joint Committee on Cancer (AJCC) with Ta (n=15), T1 (n=11), T2 (n=10), T3 (n=18), T4 (n=7) and seven patients with unknown; in which male no.32, female no.36; the median age is 68 y/o (range 40-85 y/o). Fluorescence in situ hybridization (FISH) was performed to exam the PTEN gene copy number or gene structure alterations of UTUC; besides, immunohistochemistry (IHC) analysis were used to observe the PTEN protein expression in the tumor. Our results showed PTEN mutations were observed in twenty-two tumors with heterozygous PTEN deletion; one tumor with homozygous PTEN deletion, and three tumors with PTEN monosomy. Further, heterozygous PTEN deletion was shown significantly associated with stage of pTa, pT1 and pT2 (P=0.048) and history of smoking (P=0.030). The IHC results showed lower expression level was common to be observed in the tumor area. Our findings suggest loss of PTEN is associated with the low-risk group of UTUC but not the high-risk group, the unknown mechanisms between these two subtypes might be existed. Besides, smoking could also as a factor highly emerge from genetic alterations in UTUC. In conclusion, PTEN genomic loss might act a predictive indicator of classification of UTUC, however, the clinical treatment could be different due to the underlying diversity of the molecular activities.

Citation Format: Liang-Chen Li, Cheng-Keng Chuang, Hung-Ying Chiang, Ying-Tzu Chen, Po-Hung Lin, Kai-Jie Yu, See-Tong Pang, Wen Hui Weng*. Clinical significance of PTEN in UTUC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2727. doi:10.1158/1538-7445.AM2017-2727
Abstract 2728: Frequency and prognostic value of PI3KCA mutations in early stage of colorectal cancer in Mexican patients
Authors: Ruiz-Garcia Erika , Ortega Alette , Bahena Antonio , Fernandez Edith , Calderillo German , Camarillo Cesar Lopez , Marchat Laurence , Guadarrama Jorge , Meneses-Garcia Abelardo , Vega Horacio Astudillo-de la
Published: July 2017

Background: There are molecular associations between mutated profiles and microsatelital instability, both related with tumor growth and oncogenic development by activating tyrosine receptors families in colorectal cancer (CRC). It is known that exon 9 and exon 20 (H1047R) mutations in PIK3CA increased PI3K activity. Moreover, PIK3CA mutations are significantly associated with tumor recurrence and poor overall survival. The frequency of PIK3CA mutations in CCR occurs in 15-20%, being the catalytic subunit more frequently affected. The aim of our study was to investigate the frequencies and clinical implications of these genetic alterations in advanced CRC.

Methods: Retrospectively, we analyzed the initial paraffin embedded tissue block of 71 Mexican patients with CCR stage II. We evaluated mutations frequency of PIK3CA exon 9 (E542K, E545K) and exon 20 (H1047R) using qBiomarker Somatic Mutation PCR for real-time PCR-based. These methodology increases specificity, multiplex PCR and allelic discrimination. The data analysis was done using Ct values and Analysis Webportal.

Results: We found in our population a frequency of PIK3CA mutations of 26%. Of those, double mutants were present in 7% with a higher frequency for E545K/H1047R. Clinical implication that we found is that any active mutation of PIK3CA is associated to an increase of recurrence risk (HR 1.86;CI 95% =0.46-7.5), but most important is for E545K mutation (HR 4.17; CI 95% 0.85-20.39), meanwhile comparing no mutated with H1074R mutated samples there were no differences in HR (0.53 vs. 0.60, respectively).

Conclusions: We found a higher number of PI3KCA mutations that literature reports and that E545K mutation have a worst prognostic implication but we need to increase our sample looking for statistical significance results. Data from H1047R mutation raise de hypothesis that it could exist a compensatory mechanism related to structural interactions between both helicoidal and catalitic domains.

Citation Format: Erika Ruiz-Garcia, Alette Ortega, Antonio Bahena, Edith Fernandez, German Calderillo, Cesar Lopez Camarillo, Laurence Marchat, Jorge Guadarrama, Abelardo Meneses-Garcia, Horacio Astudillo-de la Vega. Frequency and prognostic value of PI3KCA mutations in early stage of colorectal cancer in Mexican patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2728. doi:10.1158/1538-7445.AM2017-2728
Abstract 2739: Low-pass whole genome sequencing detects copy number variations in circulating tumor DNA
Authors: Chen Xiaoji , Spoerke Jill M. , Yoh Kathryn , Darbonne Walter C. , Huw Ling-Yuh , Gendreau Steven , Huang Shih-Min A. , Lackner Mark R.
Published: July 2017

Circulating tumor DNA (ctDNA) is released from necrotic/apoptotic tumor cells into the bloodstream. Recent studies have demonstrated the value of using ctDNA as biomarkers in cancer diagnosis, prognosis, and drug resistance. Unlike local tissue biopsy, ctDNA collection and analysis is non-invasive, allows continuous monitoring of clonal evolution, and provides an overview of tumor heterogeneity. Copy number variations (CNVs) play an important role in cancer biology. However, traditional CNV analyses of ctDNA using droplet digital PCR (ddPCR) and SNP arrays can only assess a small number of genes due to the low abundance of ctDNA in the majority of patient samples. Next generation sequencing (NGS) offers a more efficient and high-throughput way to study CNVs in ctDNA.

Here, we evaluated the use of low-pass whole genome sequencing (WGS) in determining CNVs in ctDNA. In this work, cell-free DNA was isolated from 1-5 ml of plasma from phase II clinical trial patients with metastatic breast cancer and non-small cell lung cancer (NSCLC) using the QIAamp Circulating Nucleic Acid Kit (QIAGEN). DNA yield was determined by ddPCR, with a range from 2-4000 ng. Sequencing libraries were prepared using 2-10 ng DNA by the ThruPLEX Plasma-Seq Kit (Rubicon Genomics). WGS at 0.1x, 0.25x, 0.5x, and 1x coverage was performed on Illumina NextSeq, and data was analyzed using Nexus Copy Number software (BioDiscovery). As a reference, we sequenced DNA from peripheral blood mononuclear cells (PBMCs) of 20 healthy donors at the same coverage. Low-pass WGS was also performed on a subset of matched tumor tissue samples as comparisons.

Our results showed that WGS of ctDNA at 0.5x coverage was efficient to identify CNVs. CNVs were detected in ctDNA from about half of the patients analyzed, and in general CNVs identified in ctDNA matched the ones found in tumor tissue from the same patient. We also found that CNV patterns from different time points of the same patients clustered together. With this promising system, we will present CNV analysis in ctDNA from breast cancer and NSCLC patients enrolled in phase II clinical trials of the PI3K inhibitor pictilisib. We will evaluate the ability of the method to classify patients into different subgroups, monitor tumor progression, and identify drug resistance mechanisms.

Citation Format: Xiaoji Chen, Jill M. Spoerke, Kathryn Yoh, Walter C. Darbonne, Ling-Yuh Huw, Steven Gendreau, Shih-Min A. Huang, Mark R. Lackner. Low-pass whole genome sequencing detects copy number variations in circulating tumor DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2739. doi:10.1158/1538-7445.AM2017-2739
Abstract 2744: Inter-site comparison of performance of an ultra-sensitive sequencing technology for circulating tumor DNA
Authors: Yaung Stephanie , Lovejoy Alex , Klass Dan , Casey Fergal , Arcot Aruna , Loyzer Melissa , Chiu William , Azhar Nabil , Beckert Sophie , Lange Maria , Siemann Sandra , Froehler Sebastian , Gunn Shelly , Palma John F.
Published: July 2017

The combination of liquid biopsies and ultra-sensitive next-generation sequencing (NGS) holds tremendous promise in oncology for the detection and surveillance of somatic mutations that correlate with diagnosis, prognosis, response prediction, resistance monitoring and tumor burden. We have developed a capture-based NGS workflow that provides ultra-sensitive detection of 4 mutation classes - single nucleotide variants (SNVs), insertions/deletions, copy number amplifications (CNAs) and fusions - from low input cell-free DNA isolated from plasma. Sensitivity and specificity of 2 different AVENIO ctDNA Analysis Kits (for Research Use Only) across 3 sites for 48 samples that included contrived DNA blends with known mutations validated by digital PCR and normal reference plasma samples were assessed. The AVENIO ctDNA Targeted Kit (Targeted) was designed to detect mutations in 17 genes, across 80kb, included in NCCN Guidelines for solid tumors plus additional variants relevant for therapy selection. The AVENIO ctDNA Expanded Kit (Expanded) was designed to detect mutations in 77 genes, across 200kb, associated with solid tumor including variants relevant for clinical trial research. Testing sites achieved 100% sensitivity for SNVs and fusions at 0.5% and 1% allelic frequency, respectively, from 30 ng of input DNA for both kits. Median coverage of 4,200-6,400X was greater with the Targeted kit relative to that of 2,700-3,800X with the Expanded kit. Specificity was 100% for the Targeted kit either by sample or variant. The Expanded kit had a specificity of 91.7-100% by sample and 99.7-100% by variant. At an expected 5X or 8X copy number amplification for multiple genes, both the Targeted and Expanded kits were 100% sensitive and 93.1-98.4% specific per gene. The specificity for fusion detection was 100% for both kits down to 1% mutant allele frequency. The AVENIO ctDNA Analysis Kits for plasma and NGS applications provide exquisite sensitivity and specificity for the simultaneous detection of 4 different mutation classes.

Citation Format: Stephanie Yaung, Alex Lovejoy, Dan Klass, Fergal Casey, Aruna Arcot, Melissa Loyzer, William Chiu, Nabil Azhar, Sophie Beckert, Maria Lange, Sandra Siemann, Sebastian Froehler, Shelly Gunn, John F. Palma. Inter-site comparison of performance of an ultra-sensitive sequencing technology for circulating tumor DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2744. doi:10.1158/1538-7445.AM2017-2744
Abstract 2749: Liquid biopsy testing allows highly-sensitive detection of plasma cfDNA mutations in 87 breast cancer-related genes
Authors: Lira Maruja E. , Xie Tao , Deng Shibing , Kinong Jennifer , Gao Jingjin , Zhu Zhou , Lee Nathan , Rejto Paul , Bienkowska Jadwiga , Hardwick James , Wang Kai , Huang Stephen
Published: July 2017

Liquid biopsies have the potential to revolutionize the way physicians select personalized anti-cancer therapies, monitor patient responses to treatment, and characterize acquired resistance to cancer drugs. New tests that use a simple peripheral blood draw offer snapshots of a patient‘s total tumor DNA mutation profile and are attractive because of their minimally-invasive modality and because they integrate information from both primary and metastatic disease. Currently, most plasma cell-free DNA (cfDNA) mutation detection tests used in clinical research detect known hotspot mutations in a limited number of genes. Technologies that interrogate multi-gene panels in cfDNA are advancing, but commercially-available options suitable for clinical use are limited, come at a high cost, and are not customizable. We designed and developed a customized, next generation sequencing-based, liquid biopsy assay capable of detecting somatic mutations in 87 breast cancer genes involved in cell cycle and estrogen receptor signaling. Targeted regions (147 Kb) were enriched using hybrid capture resulting in an average capture specificity and uniformity of 65.93% and 96.38%, respectively. When tested on cfDNA from healthy donors (n=14), we demonstrated a level of specificity >99.99%. Analytical sensitivity of 0.1% was established on HapMap and reference mutant cell line DNA. Using a pool of HapMap genomic DNA (n=10), 96% (48/50) of SNPs with expected allele frequency of 0.1% were detected. In reference mutant cell line DNA with 1% or 0.1% mutant allele frequencies, we were able to reliably detect all mutations present at 1% and mutations at 0.1% in 50% of the cases. Assay validation on plasma cfDNA with matching tumor from ER+, HER2- breast cancer patients will be presented. In conclusion, we developed a highly sensitive and specific liquid biopsy assay to interrogate 87 breast cancer-related genes. The high level of specificity and sensitivity makes the test ideal not only for detecting known cancer gene hotspot mutations but also for detection of novel gene mutations that may arise during treatment as a result of acquired drug resistance.

Citation Format: Maruja E. Lira, Tao Xie, Shibing Deng, Jennifer Kinong, Jingjin Gao, Zhou Zhu, Nathan Lee, Paul Rejto, Jadwiga Bienkowska, James Hardwick, Kai Wang, Stephen Huang. Liquid biopsy testing allows highly-sensitive detection of plasma cfDNA mutations in 87 breast cancer-related genes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2749. doi:10.1158/1538-7445.AM2017-2749
Abstract 2762: The comparison of allogeneic stem cell transplantation outcomes between haploidentical donor and international donor: A retrospective multi-institutional study in Korea
Authors: Park Hyunkyung , Lee Yoo Jin , Shin Sang-Jin , Lee Jayoun , Kim Inho , Yoon Sung-Soo , Park Silvia , Lee Hyewon , Moon Joonho , Jang Jun Ho , Koh Youngil
Published: July 2017

Introduction: The successful rate of hematopoietic stem cell transplantation (HSCT) from HLA-mismatched donor has been increased according to the development in management of complications including graft versus host disease (GVHD) and infections. Especially, haploidentical HSCT provides an opportunity for all patients who do not have HLA-matched sibling donor.

Methods: In this study, we compared HSCT outcomes between haploidentical familiar donor and international donor (donors from Japan, China, Germany, Unites States of America and Taiwan) in acute leukemia patients. We reviewed the overall survival (OS), relapse free survival (RFS) and complications.

Results: Total 142 acute leukemia patients performed HSCT from 2000 to 2016; 98 patients underwent haploidentical donor transplantation and 44 patients underwent international donor transplantation. Major variables such as age, sex, disease status and the number of CD34 stem cells were not statistically different between two groups. In survival analysis, there was no significant difference according to the donor-type. 1-year OS rate for haploidentical transplantation group was 44.1% and 52.3% for international transplantation group (p=0.345). 1-year RFS rate was 36.6% versus 40.9%, respectively (p=0.362). In addition, the incidence of complication events was similar between two groups. The acute GVHD in haploidentical group and international group were 42.9% and 43.2% (P=0.97), and the infection event within 30days after transplantation were 49.5% in haploidentical group and 34.1% in international group (p=0.09). The cumulative incidence of chronic GVHD was no significantly different (P=0.34), respectively.

Conclusion: These data suggest that HSCT from haploidentital donor shows similar outcomes including survival outcomes and complications with international donor transplantation. Therefore, haploidentitial donor transplantation can be good choice for acute leukemia patients who have no HLA_matched sibling donor.

Citation Format: Hyunkyung Park, Yoo Jin Lee, Sang-Jin Shin, Jayoun Lee, Inho Kim, Sung-Soo Yoon, Silvia Park, Hyewon Lee, Joonho Moon, Jun Ho Jang, Youngil Koh. The comparison of allogeneic stem cell transplantation outcomes between haploidentical donor and international donor: A retrospective multi-institutional study in Korea [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2762. doi:10.1158/1538-7445.AM2017-2762
Abstract 2766: Esophageal stenting in resource-limited settings
Authors: Mwachiro Michael M. , Parker Robert K. , Burgert Stephen , Lando Justus , Rankeeti Sinkeet , Chepkwony Robert , Kiniga Emmanuel , Dawsey Sanford , Topazian Mark , White Russell E.
Published: July 2017

Background: Esophageal cancer is the 6th leading cause of cancer death globally, with geographical high-risk areas in Asia, the Middle East, and eastern and southern Africa. Esophageal squamous cell carcinoma (ESCC) is the more common variant in Africa. In Kenya, its incidence is 2nd in men after prostate cancer and 3rd in women after breast and cervix-uteri cancers. Late presentation is a common occurrence in developing countries and is multifactorial due to challenges in access to health care, low socioeconomic status and delayed or missed diagnosis. A large percentage of these tumors are thus unresectable and are only eligible for palliative care via stenting. Our hospital is a 300-bed referral center in southwestern Kenya, which is a hotspot for ESCC, and we see over 400 cases of ESCC annually.

Methods: We have developed a technique for placement of esophageal self-expanding metallic stents (SEMS) without fluoroscopy that is safe and easily reproducible. This is an outpatient procedure, with the majority done under conscious sedation, and routine followup is not necessary. The tumor margins are noted at time of video endoscopy, a guidewire is placed, and dilation done with Savary dilators as required. The SEMS are then loaded on the stent delivery device and deployed into the proper position based on measurements, and placement is subsequently confirmed via endoscopic visualization.

Results: A total of 3000 SEMS have been placed to date at our hospital, without using fluoroscopy. The male: female ratio has been 1.5:1, and the average age has been 60.4 years. The distribution of tumor locations was 67% in the middle and distal third. The most common complications were tumor overgrowth with obstruction and stent migration. Procedure related mortality was 0.3%. Post-procedure improvement in dysphagia score was seen in over 80% , and patient satisfaction was high. Initial data puts our post stent survival time around 8 months/ 250 days

Conclusions: Placement of SEMS for ESCC, without fluoroscopy, is a safe and reproducible procedure which has a low rate of adverse events. This procedure results in effective palliation of a difficult disease and can easily be done in resource-limited settings which have endoscopy capabilities. Current efforts are ongoing to increase opportunities for training endoscopists in this procedure and for provision of affordable stents in Africa.

Citation Format: Michael M. Mwachiro, Robert K. Parker, Stephen Burgert, Justus Lando, Sinkeet Rankeeti, Robert Chepkwony, Emmanuel Kiniga, Sanford Dawsey, Mark Topazian, Russell E. White. Esophageal stenting in resource-limited settings [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2766. doi:10.1158/1538-7445.AM2017-2766
Abstract 2768: Treosulfan induces differential gonadal toxicity profile compared with Busulfan
Authors: Levi Mattan , Stemmer Salomon , Stein Jerry , Shalgi Ruth , Ben-Aharon Irit
Published: July 2017

Background: Treosulfan (L-treitol-1,4-bis-methanesulfonate), an alkylating agent with myeloablative and immunosuppressive traits, has been increasingly incorporated as a main conditioning protocol for hematopoietic stem cell transplantation (HSCT) in pediatric malignant and non-malignant diseases. Treosulfan has been shown to present lower toxicity profile compared with conventional myeloablative regimens such as busulfan. Yet, while busulfan is considered highly gonadotoxic, the gonadal toxicity profile of treosulfan remains to be elucidated. Our aim was to study the short and long term gonadal effect of treosulfan in comparison to busulfan.

Methods: Mature 2 months old male and 3 months old female mice (“pubertal cohort”) were injected with treosulfan 2000 mg/kg or busulfan 40 mg/kg and were sacrificed one week, one month or six months post drug administration. Immature male and female mice (“prepubertal cohort”) were injected with treosulfan 750 mg/kg or busulfan 15 mg/kg and were sacrificed one week or three months post drug administration. Testicular function was assessed by measurements of sperm count and motility, testes and epididymides weight, serum anti-Mullerian Hormone (AMH) and testicular ID4 or GFRA1 mRNA (markers for stem spermatogonia). Immunohistochemistry was performed to evaluate testicular proliferation (Ki-67), apoptosis (TUNEL) and meiotic-active spermatocytes (DAZL-PCNA). Ovarian function was assessed by measurements of ovary weight, serum AMH, follicles count and ovarian SOHLH2, NOBOX of FIGLA mRNA (markers for primordial follicles). Immunohistochemistry was performed to evaluate ovarian proliferation (Ki-67), apoptosis (TUNEL) and growing follicles (AMH-PCNA).

Results: Treosulfan testicular toxicity was milder compared to busulfan toxicity, in both mature and immature male mice, while stem spermatogonia were spared. However, ovarian toxicity of both treosulfan and busulfan was severe and permanent in both mature and immature female mice; possibly by a short term irreversible reduction of reserve primordial follicles in the ovaries.

Conclusion: Our results indicate that treosulfan exerts a differential gonadal toxicity profile compared with busulfan, manifested by mild testicular toxicity and severe ovarian toxicity.

Citation Format: Mattan Levi, Salomon Stemmer, Jerry Stein, Ruth Shalgi, Irit Ben-Aharon. Treosulfan induces differential gonadal toxicity profile compared with Busulfan [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2768. doi:10.1158/1538-7445.AM2017-2768
Abstract 2769: Project Survival: Prospective clinical study utilizing multiomics and artificial intelligence to discover novel molecular markers for detection, stratification, and outcome in pancreatic cancer
Authors: Sarangarajan Rangaprasad , Crowley John , Stoll-D'Astice Amy , Bussberg Valerie , Nguyen Cindy , Rodrigues Leonardo O. , Chen Emily , Grund Eric Michael , Vishnudas Vivek K. , Kiebish Michael , Akmaev Viatcheslav R. , Hidalgo Manuel , Narain Niven R. , Moser A. James
Published: July 2017

Pancreatic adenocarcinoma is the third leading cause of cancer death and has an extremely poor response to first line therapies. There is a critical unmet need to discover and implement effective diagnostic panels to stratify this disease and personalize treatment. Project Survival is a prospective study designed to discover biomarkers for patient diagnosis, stratification, and prognostics for pancreatic cancer. The multisite study is in year 2 of enrolling subjects within 6 categories: healthy volunteers with a relative with pancreatic cancer (N=50), pancreatitis (N=50), pancreatic cystic neoplasm (N=50), suspicious pancreatic masses with pathology other than pancreatic cancer (N=50), early stage (N=200) and metastatic pancreatic cancer (N=200). The study analyzes matched subject sera, plasma, buffy coat, saliva, urine, and tumor/adjacent normal tissues and integrates them with full clinical annotation. Multiple time points per subject per year are taken longitudinally over the course of the six year timeline enabling dynamic modeling. Samples are analyzed by Mass Spectrometry for the proteome, signaling lipidome, structural lipidome, and metabolome. The BERG Interrogative Biology® platform utilizes Artificial Intelligence to integrate multiomic profiles with medical annotation and clinical endpoints. Utilizing the power of the Bayesian Network learner, bAIcis™ (BERG Artificial Intelligence Clinical Information System), multiomic profiles were aligned to the longitudinal clinical information and subjected to the AI-algorithms that inferred probabilistic cause-and-effect relationships among molecular and clinical variables inferring markers of pancreatic cancer status and defining the interconnectivity of molecular features with clinical phenotype. Network features linking clinical endpoints and key network pressure points will be identified as molecular drivers. The drivers of clinical endpoints will be analyzed to rank potential biomarkers.

Citation Format: Rangaprasad Sarangarajan, John Crowley, Amy Stoll-D'Astice, Valerie Bussberg, Cindy Nguyen, Leonardo O. Rodrigues, Emily Chen, Eric Michael Grund, Vivek K. Vishnudas, Michael Kiebish, Viatcheslav R. Akmaev, Manuel Hidalgo, Niven R. Narain, A. James Moser. Project Survival: Prospective clinical study utilizing multiomics and artificial intelligence to discover novel molecular markers for detection, stratification, and outcome in pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2769. doi:10.1158/1538-7445.AM2017-2769
Abstract 2788: High ALDH1, S phase fraction, p16INK4A in esophageal squamous cell carcinoma could predict response to neoadjuvant chemotherapy
Authors: Kumar Rajeev , Kannan R. Ravi , Verma Akalesh Kumar , Talukdar Anuradha , Deka Monoj Kumar , Tapkire Ritesh , Vermani Litika , Ghosh Sankar Kumar
Published: July 2017

Background: The prevalence of locally advanced esophageal squamous cell carcinoma (ESCC) remains high despite technological advancements in its diagnosis. This leads to prolonged multimodality treatment often resulting in poor response eventually leading to poor prognosis. Currently, there are no biomarkers available to predict response to neoadjuvant chemotherpy. Aldehyde dehydrogenase 1 (ALDH1), human epidermal growth factor receptor-2 (HER2), p16INK4A, ploidy and S phase fraction are considered significant biomarkers in various solid malignancies. However, there is paucity of data on their clinical significance in ESCC. In the present study, we investigated their significance in predicting the response to neoadjuvant chemotherapy (NACT) in ESCC patients.

Methods: Immunohistochemisty of ALDH1, HER2, p16INK4A and propidium iodide based cell cycle analysis through flow cytometer was performed in pre treatment biopsy sample collected from 108 ESCC patients who were presented at a comprehensive cancer centre in northeast India and all of them subsequently received neo adjuvant chemotherapy. Results: ALDH 1, HER2 and p16INK4A were found positive in 65.7%, 7.4% and 22% of pre treatment ESCC specimens respectively. ALDH1 expression correlates with poor response to neo adjuvant chemotherapy (P<0.001). A significant proportion of poor responders were found to be smokers (P=0.004). Poor responders also tends to correlate with increased mortality (P=0.009). HER2 couldn’t predict response to NACT. However, all HER2 positive cases were associated with high ALDH1 expression (P=0.034). 50% of those with pathologically complete response were p16 positive on the contrary only 15% non responders were positive for p16 (P<0.001). 84% of the ESCC patients reported aneuploid tumor status and responder's were found having high S phase fraction (P=0.041). Conclusion: High ALDH1 expression can predict poor response whereas high p16 and S phase fraction can indicate good response to neoadjuvant chemotherapy in ESCC patients. HER2 seems having no clinical significance in the response assessment of neo adjuvant chemotherapy in ESCC.

Citation Format: Rajeev Kumar, R. Ravi Kannan, Akalesh Kumar Verma, Anuradha Talukdar, Monoj Kumar Deka, Ritesh Tapkire, Litika Vermani, Sankar Kumar Ghosh. High ALDH1, S phase fraction, p16INK4A in esophageal squamous cell carcinoma could predict response to neoadjuvant chemotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2788. doi:10.1158/1538-7445.AM2017-2788