// Hyo Song Kim 1, * , Hanna Lee 2, * , Su-Jin Shin 3, * , Seung-Hoon Beom 1 , Minkyu Jung 1 , Sujin Bae 2 , Eun Young Lee 2 , Kyu Hyun Park 4 , Yoon Young Choi 5 , Taeil Son 5 , Hyoung-Il Kim 5 , Jae-Ho Cheong 5 , Woo Jin Hyung 5 , Jun Chul Park 6 , Sung Kwan Shin 6 , Sang Kil Lee 6 , Yong Chan Lee 6 , Woong Sub Koom 7 , Joon Seok Lim 8 , Hyun Cheol Chung 1, 4 , Sung Hoon Noh 5 , Sun Young Rha 1, 4 , Hyunki Kim 3 , Soonmyung Paik 2 1 Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea 2 Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea 3 Hanyang University, College of Medicine, Seoul, Republic of Korea 4 Cancer Metastasis Research Center, Song Dang Institute for Cancer Research, Yonsei University College of Medicine, Seoul, Republic of Korea 5 Department of Surgery, Yonsei University College of Medicine, Seoul, Republic of Korea 6 Division of Gastroenterology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea 7 Department of Radiation Oncology, Yonsei University College of Medicine, Seoul, Republic of Korea 8 Department of Radiology, Yonsei University College of Medicine, Seoul, Republic of Korea * These authors contributed equally to this work as co-first authors Correspondence to: Soonmyung Paik, email: SOONMYUNGPAIK@yuhs.ac Hyunki Kim, email: kimhyunki@yuhs.ac Sun Young Rha, email: rha7655@ yuhs.ac Keywords: gastric cancer, molecular subtypes, next-generation sequencing, immunohistochemistry, matched therapy Received: November 23, 2016 Accepted: February 20, 2017 Published: March 21, 2017 ABSTRACT We tested the clinical utility of combined profiling of Ion Torrent PGM based next-generation sequencing (NGS) and immunohistochemistry (IHC) for assignment to molecularly targeted therapies. A consecutive cohort of 93 patients with advanced/metastatic GC who underwent palliative chemotherapy between March and December 2015 were prospectively enrolled. Formalin fixed paraffin embedded tumor biopsy specimens were subjected to a 10 GC panels [Epstein Barr virus encoding RNA in-situ hybridization, IHC for mismatch repair proteins (MMR; MLH1, PMS2, MSH2, and MSH6), receptor tyrosine kinases (HER2, EGFR, and MET), PTEN, and p53 protein], and a commercial targeted NGS panel of 52 genes (Oncomine Focus Assay). Treatment was based on availability of targeted agents at the time of molecular diagnosis. Among the 81 cases with available tumor samples, complete NGS and IHC profiles were successfully achieved in 66 cases (81.5%); only IHC results were available for 15 cases. Eight cases received matched therapy based on sequencing results; ERBB2 amplification, trastuzumab ( n = 4); PIK3CA mutation, Akt inhibitor ( n = 2); and FGFR2 amplification, FGFR2b inhibitor ( n = 2). Eleven cases received matched therapy based on IHC; ERBB2 positivity, trastuzumab ( n = 5); PTEN loss ( n = 2), PI3Kβ inhibitor; MMR deficiency ( n = 2), PD-1 inhibitor; and EGFR positivity ( n = 2), pan-ERBB inhibitor. A total of 19 (23.5%) and 62 (76.5%) cases were treated with matched and non-matched therapy, respectively. Matched therapy had significantly higher overall response rate than non-matched therapy (55.6% vs 13.1%, P = 0.001). NGS and IHC markers provide complementary utility in identifying patients who may benefit from targeted therapies.
Introduction We aimed to determine whether KRAS and BRAF mutant colorectal cancer (CRC) cells exhibit distinct sensitivities to the multi-target angiokinase inhibitor, TKI258 (dovitinib). Materials and methods We screened 10 CRC cell lines by using receptor tyrosine kinase (RTK) array to identify activated RTKs. MTT assays, anchorage-independent colony-formation assays, and immunoblotting assays were performed to evaluate the in vitro anti-tumor effects of TKI258. In vivo efficacy study followed by pharmacodynamic evaluation was done. Results Fibroblast Growth Factor Receptor 1 (FGFR1) and FGFR3 were among the most highly activated RTKs in CRC cell lines. In in vitro assays, the BRAF mutant HT-29 cells were more resistant to the TKI258 than the KRAS mutant LoVo cells. However, in xenograft assays, TKI258 equally delayed the growth of tumors induced by both cell lines. TUNEL assays showed that the apoptotic index was unchanged following TKI258 treatment, but staining for Ki-67 and CD31 was substantially reduced in both xenografts, implying an anti-angiogenic effect of the drug. TKI258 treatment was effective in delaying CRC tumor growth in vivo regardless of the KRAS and BRAF mutation status. Conclusions Our results identify FGFRs as potential targets in CRC treatment and suggest that combined targeting of multiple RTKs with TKI258 might serve as a novel approach to improve outcome of patients with CRC.
Purpose: The metastatic animal model of human cancer is important from a practical point of view in the research of cancer metastasis, because it resembles the original tumors morphologically, biologically and biochemically. We developed the animal model to investigate the clinically relevant metastasis of gastric cancer which is the leading cause of death in Korea. Methods: Seven to eight-week-old specific-pathogen-free(SPF) BALB/c-nu mice were used. We developed an orthotopic transplantation model using the tissue obtained from an inoculation of the gastric cancer cell suspension (YCC-3) into a subcutaneous layer of mice. The mice were kept in laminar-flow cabinets under SPF condition and inspected everyday. Results: Mice were sacrificed 8~12 weeks after the operation when they showed either a measurable mass or signs of distress. The metastatic pattern of this animal model was very similar to that of human gastric cancer. At autopsy, the local growth of the gastric cancer, lymph node metastasis and any distant metastasis were noted. Conclusion: We developed an animal model for human gastric cancer metastasis that will enhance our understanding of the biology of cancer metastasis and it will contribute to the development of the research and treatment of cancer metastasis.
Abstract Osteosarcoma is the most common malignant bone tumor in children and adolescents with frequent lung metastasis. As the survival has not been improved with chemotherapy for the last two decades, novel therapeutic approaches are required to efficiently treat osteosarcoma. Genomic analyses have revealed biologically useful information and genetically altered therapeutic targets. The subject of this study was a 25 year old patient with conventional high-grade osteosarcoma with multiple metastasis of lung, lymph nodes and chest wall, who had failed from several palliative systemic chemotherapies and radiotherapy. We performed whole exome sequencing of the gDNA from peripheral blood mononucleated cells (PBMC) and formalin fixed paraffin embedded (FFPE) tissues of primary tumor, secondary (recurrence 1) and tertiary (recurrence 2) metastatic tumors. Samples were sequenced using one lane of paired-end, 100 bp reads on Illumina Hiseq for each sample. Here, we present an analysis result using VarScan and custom-made programs for the detection of somatic mutations and loss of heterozygosity (LOHs) in exome data from changes of genetic variations throughout the disease progression compared to blood germ-line sequencing data. As a result, we observed the 36 common somatic mutated genes, including p73 and TSHR, in three tumor types. And we indentified the somatic mutations affecting the functions of known cancer genes, RBM15, SYNE1, GNAQ and XPA, which were only present in the secondary and/or tertiary metastatic tumors but not in the primary tumor. Especially, GNAQ mutations which is found in the metastatic tumors, is known to be mutated in 50% of melanoma and driven constitutive activity of the MAPK pathway. Therefore, GNAQ mutation in recurrent osteosarcoma patient might be a potential marker for new therapeutic strategies of inhibiting MAPK pathway. In conclusion, the ability to track clonal evolution in cancers may provide new strategies and opportunities for drug development, especially in refractory and rare diseases. Citation Format: Su Jin Heo, Ji Woong Kim, Woo Sun Kwon, Hyo Ki Kim, Min Hee Hong, Woo Ick Yang, Se-Kyu Kim, Hyo Song Kim, Hyun Cheol Chung, Tae Hyun Hwang, Sun Young Rha. Serial whole exome sequencing showed the genetic aggravation of refractory osteosarcoma. [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 3421. doi:10.1158/1538-7445.AM2014-3421
<p>Supplementary Table 1: Clinicopathological Parameters of samples used Supplementary Table 2: Read Mapping Statistics of NanoChIP-seq Libraries Supplementary Table 3: Non coding RNAs associated with Somatic Promoters Supplementary Table 4: Alternative Promoters Supplementary Table 5: Spectral Counts from CRC samples of N terminal peptides predicted to be gained in GC Supplementary Table 6: HLA prediction of GC samples Supplementary Table 7: Recurrent N terminal sequences with high affinity to MHC Class I Supplementary Table 8: P values of Wilcoxon test between ACRG samples with high and low somatic promoter usage Supplementary Table 9: HLA types of healthy PBMC donors Supplementary Table 10: Peptide pools for alternative promoters Supplementary Table 11: Cytokine Responses of N terminal Peptides Supplementary Table 12: Somatic Promoters Overlapping EZH2/SUZ12 Binding Sites Supplementary Table 13: RACE Primers</p>
Temsirolimus is effective in the treatment for metastatic non-clear cell renal cell carcinoma (nccRCC) with poor prognosis. We aim to investigate the efficacy and tolerability of temsirolimus in treatment of naïve Asian patients with metastatic/recurrent nccRCC.From January 2008 to July 2017, data of treatment-naïve, metastatic/recurrent nccRCC patients, who were treated with temsirolimus according to the standard protocol, were collected. The primary end-point was progression-free survival (PFS). Secondary end points were overall survival (OS), objective response rate (ORR), and tolerability of temsirolimus.Forty-four metastatic/recurrent nccRCC patients, 10 from prospective and 34 from retrospective groups, were enrolled; 24 patients (54%) were papillary type, and other histology subtypes included 11 chromophobes (25%), two collecting ducts (5%), one Xp11.2 translocation (2%), and six others (14%). The median PFS and OS were 7.6 months and 17.6 months, res-pectively. ORR was 11% and disease control rate was 83%. Patients with prior nephrectomy had longer PFS (hazard ratio [HR], 0.16; 95% confidence interval [CI], 0.06 to 0.42; p < 0.001) and OS (HR, 0.15; 95% CI, 0.05 to 0.45; p < 0.001). Compared to favorable/intermediate prognosis group, poor prognosis group had shorter median PFS (4.7 months vs. 7.6 months [HR, 2.91; 95% CI, 1.39 to 6.12; p=0.005]) and median OS (9.2 months vs. 17.6 months [HR, 2.84; 95% CI, 1.23 to 6.56; p=0.015]).Temsirolimus not only benefits poor-risk nccRCC patients, but it is also effective in favorable or intermediate-risk group in Asians. Temsirolimus was well-tolerated with manageable adverse events.
The growing volume and the diversity of clinical research has led to related laws and regulations as well as the Institutional Review Board (IRB) approval process becoming more stringent. To conduct clinical research efficiently and while following regulations, information about the IRB approval process and feedback is important for investigators. This has yet to be studied.We included 381 gastrointestinal disease research proposals (79 with inflammatory bowel disease [IBD], and 302 with non-IBD) reviewed by the IRB of Severance Hospital between January 2009 and December 2013. We retrospectively analyzed research characteristics including research risk levels, results of initial reviews, frequencies of continuing review, numbers of IRB comments, frequencies of IRB comments, and durations from submission to approval.Investigators' decisions on risk level were higher in the IBD group than in the non-IBD group (P<0.05). Results of initial reviews, frequencies of continuing reviews, the numbers of IRB review comments, and durations from submission to approval were not different between the two groups, but IRB decisions on risk level were higher in the IBD group (P<0.05). In subgroup analysis, the number of IRB comments from initial review on informed consent forms and procedures as well were quest of more information were significantly higher in the IBD group than in the non-IBD group (P<0.001 and 0.01, respectively).In Korea, rare diseases such as IBD require more information for the IRB process due to their distinct characteristics. IBD researchers should develop research protocols more carefully and make their research as subject-friendly as possible.
Abstract A large number of studies have been performed to iden-tify biomarkers that will allow efficient detection and de-termination of the precise status of a patient’s disease. The use of microarrays to assess biomarker status is expected to improve prediction accuracies, because a whole-genome approach is used. Despite their potential, however, patient samples can differ with respect to bio-marker status when analyzed on different platforms, making it more difficult to make accurate predictions, because bias may exist between any two different ex-perimental conditions. Because of this difficulty in ex-perimental standardization of microarray data, it is cur-rently difficult to utilize microarray-based gene sets in the clinic. To address this problem, we propose a meth-od that predicts disease status using gene expression data that are transformed by their ranks, a concept that is easily applied to two datasets that are obtained using different experimental platforms. NCI and colon cancer datasets, which were assessed using both Affymetrix and cDNA microarray platforms, were used for method validation. Our results demonstrate that the proposed method is able to achieve good predictive performance for datasets that are obtained under different ex-perimental conditions.Keywords: biomarker, different platform, microarray, gene expression, rank, prediction
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