FPKMs for C8, C9, K2, K6, OC3, OEC-M1 and TW2.6

先致謝一下: UMich的好朋友們、中研院資訊科學研究所林仲彥老師、蘇聖堯同學。

Molas Portal Site (http://molas.iis.sinica.edu.tw/OralCancer/login.php)。

username: OralCancer  password: sufang

對有興趣的基因請先在NCBI_Gene找到gene symbol, 如DDR1, CBX8, COL4A5 etc.

然後按 "Full text search on annotation table" ，輸入gene symbol. 若成功跳出來該筆資料則直接click該gene symbol. 進去後一直拉到最下面即可看到這個基因在7株細胞中的FPKM值! 下圖是DDR1的搜尋結果。

另外、若使用 "Enrichment analysis"，則可以輸入多個gene symbol，一次可同時找多個基因。下圖是輸入FGFR四個gene symbol，做GO analysis所得結果。

大力感謝中研院林仲彥老師、蘇聖堯同學幫忙建立這個Portal Site!

所長來函 RE: 4/16(三)口腔癌合作討畫討論會議

由 sufang 在 二, 04/15/2014 - 11:10 發表 Pre-published CHASE SUN para-toluenesulfonamide PTS（对-甲苯磺酰胺注射液） 吳宜莊 林懋元 紅日藥業 美商PTS國際公司 鍾南山

Dear all,

口腔癌合作討畫討論會議訊息，提供本所竹南口腔癌研究團隊卓參
時間：4/16(三)上午11時
地點：研究大樓 R2-1042
與會人員：林懋元先生、吳宜莊博士、Dr.王陸海、Dr.洪文俊、Dr.劉柯俊、Dr.莊志立、Dr.陳雅雯、Dr.李家惠
林懋元先生、吳宜莊博士現在任職於生技公司(林懋元先生現為該公司負責人)
他們二位會進行公司簡報, 我們則出席聽取簡報即可
再視狀況看是否有合作的可能及機會

會議敬備有餐盒，若有老師茹素，敬請提前告知，謝謝。

佩瑩

________________________________________
從: 洪文俊
寄件日期: 2014年4月15日 上午 09:01
至: 林佩瑩; 陳立宗; 劉柯俊
副本: 郭靜娟; 蔣秀月
主旨: RE: 4/16(三)口腔癌合作討畫討論會議

Dear All,
The message sent by Pon is correct. But his name is NanShan Zhong. Please see attached website for your reference.

http://english.cast.org.cn/n1181872/n1182069/13431984.html

The compound he developed seems to be para-toluenesulfonamide (PTS, also their company name). I attached a paper published by his group in 2013 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3755678/).

Acturally, Dr. Zhong is the Editor-in-Chief of the jounral (Journal of Thoracic Disease). The PTS company is now listed in the biocompanues in Nasdaq. However, its budeget seems to be small. http://www.nasdaq.com/symbol/ptsh

Dear KJ,
Please represent our oral cancer team to express your ideas.
I will have a meeting at KMU in the afternoon and will leave at 11:50 am. Thanks.

Wen-Chun
________________________________________
從: 林佩瑩
寄件日期: 2014年4月14日 下午 09:18
至: 陳立宗; 洪文俊; 劉柯俊
副本: 郭靜娟; 蔣秀月; 林佩瑩
主旨: FW: 4/16(三)口腔癌合作討畫討論會議

Dear all,
4月16日王副院長安排的會議
原本中國工程院的鍾南山(Chong Nan San)院士將不會出席 (我想應該是此人吧!) http://zh.wikipedia.org/zh-tw/%E9%92%9F%E5%8D%97%E5%B1%B1
出席的是現在任職於生技公司的林懋元先生、吳宜莊博士(先前的資料) http://www.pitdc.org.tw/news/news.asp?id=1547
他們二位會進行公司簡報, 我們則出席聽取簡報即可
再視狀況看是否有合作的可能及機會
Dr.郭靜娟亦不克出席(上海開會)
竹南的PI 我明天會徵詢出席的意願

以上訊息, 提供各位卓參
佩瑩

________________________________________
從: LTCHEN [k153chen@gmail.com]
寄件日期: 2014年4月14日 下午 09:10
至: 洪文俊; 王陸海
副本: 謝淑珍; 林佩瑩
主旨: Re: 4/16(三)口腔癌合作討畫討論會議

Dear WC:

Thanks, Dr. J Liu Ko will join the meeting and we shall also invite our oral cancer team members in 竹南 to participate it as well!

Best

LT Chen

在 2014/4/14 下午6:25 時， 洪文俊 寫到：

>
> 王副院長您好
>
> 今天因感冒請假一天所以剛收郵件
> 週三陳所長到台大評鑑   我代表出席主管會議
> 我很高興參加此合作討畫討論會議  將重要訊息帶回給陳所長及同仁
> 不過我下午必須到高醫大開會  所以十二點必須離開  無法參加用餐
> 目前我沒有進行口腔癌研究  後續可請劉柯俊副研究員(口腔癌團隊負責人)代表
> 謝謝您
>
> 淑珍妳好
> 請不需訂我的餐盒  謝謝
>
> 文俊
> ________________________________________
> 從: 謝淑珍
> 寄件日期: 2014年4月14日 下午 02:29
> 至: 林佩瑩; 劉柯俊; 洪文俊; 莊志立
> 副本: 王陸海
> 主旨: 4/16(三)口腔癌合作討畫討論會議
>
> 各位老師您好：
>
> 有關口腔癌合作討畫討論會議，預計會議時間及地點如下：
> 時間：4/16(三)上午11時
> 地點：研究大樓R2-1042
> 與會人員：林懋元先生、吳宜莊博士、Dr.王陸海、Dr.洪文俊、Dr.劉柯俊、Dr.莊志立
>
> 敬請各位老師預留該時段，會議備有餐盒，若有老師茹素，敬請提前告知，謝謝。
>
> 謝淑珍敬上
> 財團法人國家衛生研究院
> 副院長室
> Tel：(037)246-166 ext.31011
> Fax：(037)582-946
> E-mail：shu_chen@nhri.org.tw<mailto:shu_chen@nhri.org.tw>
>

 

 

Hi Pon: I have other plans, so I am not going. Thanks and best,  Su-Fang 2014/04/15

NRPB 計畫

雖然DDR1的構想書未獲通過，但台大盧醫師的RNA-Seq的有過。好好寫 full proposal，至少有了一點希望。

學程指導教師說明座談會 (04/09, Wed)

會議中、最讓大家驚喜的是下面這個: 編制內助理滿三年可以在職進修工讀學位!!

按我連結 intranet. 

所長來函 FW: MicroRNA expression profiling in laryngeal carcinoma

林佩瑩 Apr 8 (1 day ago)
      
to Shine-Gwo, 張憶壽, Shih, 李家惠, 林素芳, 李岳倫, 陳雅雯, 劉滄梧, 洪文俊, 張書銘, 劉柯俊, 張光裕, 陳立宗

Dear all,

所長提供之" MicroRNA expression profiling in laryngeal carcinoma"

轉知本所口腔癌研究團隊 PI 存參

MICRO ribonucleic acid expression profiling and bioinformatic target gene analyses in laryngeal carcinoma

敬祝  研安!

佩瑩

從: LTCHEN [k153chen@gmail.com]
寄件日期: 2014年4月8日 上午 06:16
至: 林佩瑩
副本: 劉柯俊
主旨: Fwd: MicroRNA expression profiling in laryngeal carcinoma

Dear Pon:

Please forward it to the oral cancer team members! thanks!

LTC

---

Note by sufang: miR-21-3p, miR-106b-3p, let-7f-5p, miR-10a-5p, miR-125a-5p, miR-144-3p, miR-195-5p, and miR-203

所長來函: Increased ENO1 positive cells in pancreatic cancer CSCs

LTCHEN Apr 7 (2 days ago)
      
Reply to Kelvin, hung1228, 施能耀 Shih), 劉柯俊 Liu), 顏伶汝, 林素芳, Pon
Dear ALL:
We need such close collaboration for the exchange of idea, resource and material in order to speed up data and paper/patent generations! Thanks!
LT Chen
PS: SF, Have your FGFR2 mRNA ready?

在 2014/4/7 下午10:22 時， Kelvin K. Tsai 寫到：
> Thanks Joe. Will ask my RA to get the cells from your lab.
>
> Can you by the way send me your previous papers about ENO1? I want to know if its role in pancreatic cancer stemness can generate a quick paper if you don't object. Many thanks.
>
> Kelvin
>
>
> On Mon, Apr 7, 2014 at 10:06 PM, 施能耀 <jshih@nhri.org.tw> wrote:
>
>     Dear Dr. Tsai:
>
>     Yes, I am glad to see the positive result, showing that ENO1 may be one of CSC biomarkers for PDAC. I can provide the PANC-1 cells with ENO1 gene downregulated. Please come over to pick up and discuss more in detail for future collaboration.
>
>     Best,
>
>     Joe from NHRI (04/07/14)
>
>
>     ________________________________________
>     從: Kelvin K. Tsai [kkctsai@gmail.com]
>     寄件日期: 2014年4月3日 下午 01:16
>     至: 陳立宗; 施能耀
>     主旨: Increased ENO1 positive cells in pancreatic cancer CSCs
>
>     Dear Leo and,
>
>     Attached please find the result of the percent ENO1 positive cells in CD133+CD44+ Panc-1 cells. I think that what we guess might be true that ENO1 is a genuine CSC marker in PDAC.
>
>     Shall we try to knockdown ENO1 in PANC1 cells?
>
>     Kelvin

劉 柯俊 via mail2.nhri.org.tw  Apr 8 (1 day ago)
      
Reply
to LTCHEN, 劉柯俊, Kelvin, 洪文俊, 施能耀, 顏伶汝, 林素芳, 林佩瑩
Dear All:
FYI.  These are the results of ENO1 expression in various human and mouse pancreatic cancer cell lines, lung sphere-forming cells and iPS.

KJL

Kelvin K. Tsai  Apr 8 (1 day ago)
Reply to 劉 柯俊, LTCHEN, 劉柯俊, 洪文俊副所長, 施能耀, 顏伶汝, 林素芳, 林佩瑩 Pon
Have you checked the ENO1 expression in pancreatic CSCs, Kojiun?
Shall we have a group meeting to share these exciting findings, Leo?

劉柯俊  Apr 8 (1 day ago)
      
Reply to Kelvin, LTCHEN, 洪文俊副所長, 施能耀, 顏伶汝, 林素芳, 林佩瑩 Pon
We will also use the sphere-foming method to study the pancreatic cancer cells in our hands.

LTCHEN  Apr 8 (1 day ago)
      
Reply to Kelvin, 劉 柯俊, 施能耀 Shih), 劉柯俊 Liu), 洪文俊副所長, 顏伶汝, 林素芳, 林佩瑩 Pon
You guys never sleep?
I totally agree with you that we should organize a special task force to work on the ENO-1 for all the tumor type we have in hand and to seek collaboration for what we do not have!
Leo
Su-Fang Lin sflin1@gmail.com  Apr 8 (1 day ago)
      
Reply to LTCHEN
Dear 所長:
You mean (1) RNAs/cDNA to Daw-Yang? or (2) 60 RNAs from TLCN?
For (1), yes, I sent three RNA samples to Daw-Yang last week. Two of them are with FGFR3 fusion, the other one serves as a negative control. Didn't tell him who is who, but he said he will get them all right!! :)
For (2), well, I thought you might want to do some ​modificatons on the application form and letter of intent, do you get any chance to look at them? Let me resend the files to you in the next mail!
Best,
Su-Fang​

顏伶汝  Apr 8 (1 day ago)
      
Reply
to LTCHEN, Kelvin, 劉 柯俊, 施能耀, 劉柯俊, 洪文俊, 林素芳, 林佩瑩
I wonder if there is a correlation of ENO1 levels with hours of sleep?
Betty
Su-Fang Lin sflin1@gmail.com
  
2:26 PM (21 hours ago)
      
Reply to 顏伶汝, LTCHEN, Kelvin, 劉 柯俊, 施能耀, 劉柯俊, 洪文俊, 林佩瑩
Dear All,
I don't have any clue about ENO1 and cancer cell stemness in OSCC​, but h​​​ere is what I've done​
​:​ 1. Pour out expressions of ENO1, ENO2, ENO3, CD133/PROM1, CD44, CTGF, NANOG, SOX2, POU5F1​
​(Yang, MH paper: Connective tissue growth factor activates pluripotency genes and mesenchymal-epithelial transition in head and neck cancer cells)​ from the expression spreadsheet of the 40 T/N ​OrCA patients
2. Perform ​Pearson correlation coefficient analysis.
3. The results indicate that only ENO2 is statistically correlated with NANOG.  (pls see the attached figure)
Therefore, I think probably the chance of ENO1 in OSCC stemness is low.. Is there any expression correlations of ENO1 and CD133/CD44 in PanCA samples?  Am I using a wrong way to correlate ENO1 and cancer stemenss?
Best,
Su-Fang
PS: CTGF的expression在這一片array的hybridization似乎不佳 (p-value > 0.05)，所以我以灰色字表示。它和NANOG, SOX2未如楊慕華醫師的paper所述、具相關性，以及和ENO3表現有負相關, 都只能當考用。

---

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顏伶汝  Apr 9 (2 days ago)
      
Reply to me, LTCHEN, Kelvin, 劉 柯俊, 施能耀, 劉柯俊, 洪文俊, 林佩瑩
Hi SF,
Thanks for the info. Nanog is the least upregulated of all pluripotency genes in ESCs/iPS, and the 1st to get downregulated when these pluripotent stem cells (PSCs) differentiate. Don't forget, Yamanaka did not need Nanog in his 2006 paper. However, it has been subsequently demonstrated that the KLF family factors act together to turn on Nanog expression (at enhancer elements, I think) in PSCs. That said, most PSC scientists are pretty convinced that Nanog is still necessary to confer pluripotency by working together with Oct4 & Sox2.
Don't know if this is useful to anyone.
Best,
Betty

---

Dear Betty,

Really appreciate your comments!
----------------------------------------

I then checked R&D WebSite, it lists ABCG2, ALDH1A1, BMI-1, CD44, c-MET, LGR5 as CSC markers for head and neck cancer. So I update the results in a new attached table! Again, gene symbol in grey are low hybridization signals (Illumina BeadChip/Human Ref8-V1實在不可以這樣、重要的基因偵測值都不太可信..上次的p16/CDKN2A也是), use ENO1 as query, its expression correlations with other interested genes in the 40 OSCC T/N pairs are shown (in alphabetically order).

就這樣子囉，個人覺得以現有40對臨床檢體而言，ENO1似乎未在oral cancer的CSC中增加表現量(RNA level). 或者、OSCC根本沒有CSC??  (快閃, 免得被追殺....)   br, Su-Fang