2015/05 Methylation Marker Paper from JAMA Oncology

Correlation of Smoking-Associated DNA Methylation Changes in Buccal Cells With DNA Methylation Changes in Epithelial Cancer JAMA Oncol. Published online May 14, 2015. doi:10.1001/jamaoncol.2015.1053

Andrew E. Teschendorff, PhD^1,2; Zhen Yang, PhD²; Andrew Wong, PhD^3; Christodoulos P. Pipinikas, PhD⁴; Yinming Jiao, MSc²; Allison Jones, BSc⁵; Shahzia Anjum, PhD⁵; Rebecca Hardy, PhD³; Helga B. Salvesen, MD⁶; Christina Thirlwell, PhD⁴; Samuel M. Janes, PhD⁷; Diana Kuh, PhD³; Martin Widschwendter, MD⁵

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At a Glance

¶ The purpose of the research was to assess the suitability of buccal cells as an epithelial source of tissue to examine the effects of smoking on the epigenome, and to test whether these effects are also seen in smoke-related epithelial cancers.

¶ Smoking is associated with widespread changes in the DNA methylation landscape of buccal cells.

¶ Some smoking-associated DNA methylation changes are common to buccal and blood tissue, but buccal cells exhibit significantly more changes than blood cells.

¶ Smoking-associated DNA methylation changes in buccal cells correlate with DNA methylation changes in epithelial cancers and do so most strongly in smoke-related epithelial cancer.

2016/105年待辦事項

2016/105年待辦事項

由 sufang 在 三, 05/27/2015 - 08:45 發表 Pre-published Gene Fusion HOK Lin Lab Oral Cancer

Paper Submission

宛樺: DDR1 overexpression in OSCC 

嬿如: EBV Rta mediated DNA methylation in the host genome

 

FGFR Gene Fusion related (玉蓮、奕宏)

1. FGFR2 gene fusion in cholangiocarcinoma (Post 連結)

2. FGFR3 gene fusion in oral cancer (Post 連結)

 

Carcinogen induced epigenetic transformation in human oral keratinocytes (嬿如、英潔)

1. Molas analysis of RNA-Seq data (Post 連結)

2. MTHFR SNPs and epigenetic transformation

3. Develop methylation markers for head and neck patients

 

Mutational landscape of cholangiocarcinoma (Post 連結)

 

Mutational landscape of OSPCC and Oral Cancer (Post 連結)

 

Grant Proposal and Report

1. 104-CAPP05

    月報 x 12 (in progress)

    期中報告 (done by 佩瑩)

    期末報告

2. 105-CAPP  執行與考核點設定

3. 106-CAPP  計畫書撰寫

4. MOHW 衛福部OPMD計畫

    實驗進行 (記得送OSCC DNA給Jeffrey Lab. 一併測試MTHFR)

5. 105-MOST 科技部計畫 (11月中 call for proposal)

6. 105-MOST PPG (LOI submitted)

Reading Notes

Wiki  Biological action (2015/05/17)

In many Asian cultures, the areca nut is chewed along with betel leaf to obtain a stimulating effect. Arecoline is the primary active ingredient responsible for the central nervous system effects of the areca nut. Arecoline has been compared to nicotine; however, nicotine acts primarily on the nicotinic acetylcholine receptor. Arecoline is known to be a partial agonist of muscarinic acetylcholine M1, M2, M3 receptors and M4 which is believed to be the primary cause of its parasympathetic effects (such as pupillary constriction, bronchial constriction, etc.).

LD50: 100 mg/kg, administered subcutaneously in mouse.

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2015/05/25

pdf 4377 2014-Feb New nucleophilic mechanisms of ROS-dependent epigenetic modifications: comparison of aging and cancer

Igor Afanas'ev Vitamine Research Institute, Moscow, Russia, Poetom Portugal

ROS-induced DNA Methylation in Cancer 共舉12例

2015-05-05 Journal Club

各位老師學長學姊大家好:

我是下周二要在journal club報告的學生-Yi-Hong

題目:

Massive parallel sequencing uncovers actionable ​FGFR2–​PPHLN1 fusion and ​ARAF mutations in intrahepatic cholangiocarcinoma

本文文章

supplementary information

RBBS

RBBS
由 sufang 在 三, 04/01/2015 - 09:00 發表 Pre-published RBBS

須細讀, 台大擬用此法screen HNSCC patients.

Start: 04/01/2015

2015-04-21 Journal Club Paper

大家好: 這篇是我下周要報的paper

感謝!

OSCC Cell Line STR information 20150312 更新版

OSCC Cell Line STR information 20150312 更新版
由 sufang 在 一, 03/30/2015 - 08:45 發表 Oral Cancer OSCC Cell Line STR analysis

Dear all,

更新oral cancer相關細胞株之STR資訊
共有16個細胞株, 其中DOK, FaDu, HOK, HSC-3, KB, OEC-M1, SCC-15, SCC-9, Tu-183(共9株)有送件STR的資訊(詳如附件)
須請大家注意的資訊如下:
1. HSC-3, 於Dr.郭靜娟's lab的新HSC-3為真, 請非此來源者把舊的細胞扔了吧! (p.s Dr. 李岳倫於2014年7月及9月分別定的STR結果同新HSC-3, 推測亦為可用細胞株)
2. KB, 於Dr.郭靜娟's lab定STR結果為HeLa細胞, ATCC/JCRB資料庫也證明KB為HeLa. 請勿使用此細胞株!
3. SCC-15, Dr.李岳倫's lab 於2014年9月及10月分別定的STR結果皆與SAS細胞株相符(90.9% match), 使用此細胞株請小心!
4. Tu-183, 於Dr.江士昇's lab於2014年12月所定STR結果未比對到現今資料庫中任何細胞株, 推測可能為可用細胞株. 但Dr. 江提供資訊:expression pattern與預期不同, 大家使用此細胞株請小心!

以上,
如有問題或錯誤的地方, 敬請不吝指正! 謝謝!

敬祝 研究順利

嬿如 敬上

原檔按我下載 (2015_0320_cell_lines_str_information20150312ding_gao.xlsx)

大家講過的Paper大全

2015/03/24 陳貞佩

Monensin inhibits epidermal growth factor receptor trafficking and activation: synergistic cytotoxicity in combination with EGFR inhibitors

2015/03/10 楊韻涵 

NRF2-driven miR-125B1 and miR-29B1 transcriptional regulation controls a novel anti-apoptotic miRNA regulatory network for AML survival

2015/02/10 王思涵

Exosomes mediate stromal mobilization of autocrine Wnt-PCP signaling in breast cancer cell migration 

2015/01/06 小嬿

RFTS-deleted DNMT1 enhances tumorigenicity with focal hypermethylation and global hypomethylation

2015-03-24 Journal Club Paper

Dear all:

附件為我下週要報告的paper
請查收,謝謝!

貞佩

Monensin inhibits epidermal growth factor receptor trafficking and activation: synergistic cytotoxicity in combination with EGFR inhibitors

2015-03-10 Journal Club Paper

各位老師、學長學姊大家好:
附檔是我這周要報告的paper
請查收 謝謝大家

祝 研安
韻涵 敬上

NRF2-driven miR-125B1 and miR-29B1 transcriptional regulation controls a novel anti-apoptotic miRNA regulatory network for AML survival

2015/01/30 國長會議

由 sufang 在 五, 03/13/2015 - 08:29 發表 Pre-published 國長會議 長庚

國衛院長庚雙邊會議 2015/01/30 (五) at 林口長庚

王陸海: miR491-3p is responsible for oral cancer metastasis
葉大森: bile duct cancer (miRNA 200下降), liver cancer (miRNA 200 上升，which is correlated with EMT)
陳鈴津教授介紹 閻紫宸教授另外一個專長是 radio pharmatheutical research (新藥開發 GMP等等)
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趙盈凱 副教授【胸腔外科】可吸收性生物醫材在食道癌之應用
東方人食道癌 是由ABC引起的、西方的食道癌則多由胃食道逆流
證實CCRT+Surgert is better therapy than just surgery
-Big Database (2400 病人 由該醫師和助理慢慢build up)
-健保加值資料庫
-cisplatin membrane
biodegradable polymers in thoracic disease
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陳立宗 特聘研究員兼所長 【國衛院癌症研究所】 Pancreatobiliary Cancer Clinical Trial in Taiwan
–TCOG很多東西需要長庚醫院幫忙 e.g. 陳敏夫教授 adjuvant interferon alpha 2b TCPG T1297 (this is a negative study, indicating that Taiwanese surgery was very successful)
–原來文獻建議 肝癌患者 開完刀後若能 加上抗病毒藥物治療 可有效降低recurrence rate.
但是由TCOG的結果看來, not necessary.
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ds-cDNA prep for gene fusion detection

3/6/2015 DR 提醒

1: Daw-Yang seems to use Clontech ds-cDNA prep for single cell Seq + Tagmentation

2: There is no way to add specific primer in this way...

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According to Daw-Yang:  I will use Nexera XT for DNA prep.

Figure 1 AMP for targeted RNA and DNA sequencing (pdf 4231). 

Double-stranded cDNA (dscDNA) synthesis starts with total nucleic acid or RNA from fresh or FFPE material without ribosomal RNA or genomic DNA(gDNA) depletion. Solid-phase reversible immobilization (SPRI)-cleaned double-stranded cDNA or fragmented genomic DNA is processed with end repair and dA tailing, directly followed by ligation with a half-functional adapter. SPRI-cleaned, ligated fragments are amplified with 10–14 cycles of multiplex PCR1 using gene-specific primers (GSP1 pool) containing a PCR multiplexing tag (brown) and a primer complementary to a portion of the universal ligated adapter (short green). An unknown fusion partner or target sequence is indicated by a question mark. SPRI-cleaned PCR1 amplicons are amplified with a second round of 10-cycle multiplex PCR2 using a combination of GSP2 pool nested gene-specific primers (3' downstream of GSP1), which are tagged with the second adapter sequence specific for Ion Torrent (black-blue) or Illumina (black-red, subsequently tagged with an indexing primer (red-orange-purple)), and a second nested primer against the ligated universal adapter (long green). After a final SPRI cleanup, the target amplicon library is ready for quantitation, downstream clonal amplification and sequencing. 

 

 

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Fluidigm 4-Primer Amplicon Tagging

The Access Array 4-primer amplicon tagging scheme is based on a step-out four primer PCR strategy where tagged target-specific (TS) primer pairs are combined with sample-specific primer pairs that contain a barcoding sequence and the adaptor sequences used by Illumina sequencing systems. By incorporating sample-specific barcodes, all 2,304 PCR products generated from a 48.48 Access Array Integrated Fluidic Circuit (IFC) are unique and can be pooled together to run in a single sequencing experiment.

 

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Nextera_xt_sample_prep