Aug 29, 2014

Citrix, 告別了…… 單國璽樞機, human protein atlas

由 sufang 在 五, 08/29/2014 - 08:56 發表 Pre-published Important message
Citrix is at http://faq.nhri.org.tw ,  進入 ”用戶端軟體存取平台系統 “


告別了…… 單國璽樞機 感念他
以及舅舅 2012/08/23

The Human Protein Atlas: http://www.proteinatlas.org/

Aug 27, 2014

2014/09/02 Journal Club

The role of insulin-like growth factor binding protein-3 in the breast cancer cell response to DNA-damaging agents (PubMed Link) (pdf 按我下載)

Aug 21, 2014

NICR LIN LAB

由 sufang 在 四, 08/21/2014 - 09:57 發表 Pre-published Temp

Head and neck cancers, including oral cancer and nasopharyngeal carcinoma (NPC), are caused by known extrinsic factors and develop within pre-neoplastic fields of genetically or epigenetically altered cells. In Taiwan, betel quid chewing in oral cancer and Epstein-Barr virus (EBV) infection in NPC are thought to be unique etiologies that promote tumor progression. My lab have been directed our efforts on two main projects:
  1. To identify overexpressed protein tyrosine kinases (PTKs) in oral caner cells.
  2. To elucidate the role of EBV lytic cycle replication in NPC pathogenesis.
For the first project we hypothesized that by knowing what protein tyrosine kinases (PTKs) that drive oral cancer cell survive, would provide rational molecularly targeted therapies for oral cancer. For the second project we specifically asked what are the host factors that restrict EBV lytic cycle replication in nasopharyngeal cells.
Research Activities & Accomplishment
  1. Role of collagen receptor DDR1 in oral cancer pathogenesis:
    • DDR1-mediated cell survival
    • DDR1-mediated collective cancer cell migration
  2. FGFR3 gene fusions in head and neck cancer:
    • Prevalence of FGFR3-TACC3 gene fusion in oral cancer
    • Oncogenic role of FGFR3-TACC3 gene fusion in oral cancer cells
  3. EBV Rta interferes with CTCF binding in both host and viral genomes:
    • Rta expression enhances DNA methylation in cellular CpG islands
    • Rta expression disrupts the bindings of CTCF in EBV genome


舊貨不刪:
  1. Dr. Lin's laboratory is directed at understanding the reactivation mechanism of two human herpesviruses: Epstein-Barr virus (EBV) and Kaposi's sarcoma associated herpesvirus (KSHV). During their infections, the conversion of an EBV or KSHV latent genome into a lytic replicating one is defined as reactivation. In single-gene systems, several EBV and KSHV encoded latent proteins are oncogenic, indicating that these latent proteins are crucial to EBV and KSHV pathogenesis. Recently, emerging evidence indicates that repeated lytic reactivation may also play a role in EBV and KSHV tumorigenesis. To delineate the molecular processes of EBV and KSHV lytic reactivations, we established a doxycycline inducible system in HEK293 cells that produces a nearly permissive replication phenotype for both EBV and KSHV. Because this system is homogeneous and robust, it is now feasible to elucidate host and viral factors that contribute to regulate the EBV and KSHV reactivations. For more details, please visit Here.
  2. Dr. Lin’s second research interest is focused on identifying oncogenic protein tyrosine kinases (PTK) that are involved in oral cancers. Precise molecular classification of cancer subtypes coupled with target inhibition of altered PTK activity has been clinically proven in chronic myelogenous leukemia (ABL), gastrointestinal stromal tumors (c-KIT), ERBB2 positive breast cancer (ERBB2), and a portion of advanced non-small-cell lung cancer (mutated EGFR). A prerequisite to the success of these role models is to precisely uncover the dys-regulated or activated PTK in the cancer cells. To this end, Dr. Lin’s lab has recently identified four PTKs over-expressed in Taiwanese oral squamous cell carcinoma cells. There pathologic relevance in oral cancer progression are under investigations. For more details, please explore Here.
Research Activities & Accomplishment
  1. Overexpression of DDR1 in oral cancer cells
  2. Protein phosphorylation of KSHV RTA/ORF50 is involved in KSHV lytic reactivation
  3. Suppressive regulation of KSHV RTA/ORF50 with O-GlcNAcylation
  4. Roles of OSCC-specific PTKs in oral cancer pathogenesis
08/21/2014
Asia/Taipei

Aug 19, 2014

EBV and KSHV EBV infection HOK

20140812 lab meeting_YCK
由 ingrid 在 二, 08/19/2014 - 10:48 發表 EBV and KSHV EBV infection HOK Ingrid LabMeeting YCK




















Aug 5, 2014

2014/08/05 關於FGFR3 IHC

 

整理FGFR3已發表文章中使用Santa Cruz的anti-FGFR3(B9) 的條件及染色情形(圖片1-4)(圖片5為DDR1染在細胞核及染在細胞質)

1.後來發現  原參考論文2013 J Pathol中的CC1 buffer為偏鹼的條件(PH=8) (之前疏忽了 抱歉!!)

  所以 使用PH=6的buffer應該是較不恰當(non-specific較高) 因此會請小夏詢價 買CC1 buffer再做做看 應該就可知道答案了

2. 雖然大多FGFR3都染在細胞質或膜上 但不能排除FGFR3 fusion可能出在核中

tou_ying_pian_1_0.jpgtou_ying_pian_2_0.jpgtou_ying_pian_3_0.jpgtou_ying_pian_4_0.jpgtou_ying_pian_5_0.jpg

 

08/05/2014
Asia/Taipei


IHC of FGFR3 in oral and bladder tissue microar

http://eln.nhri.org.tw/lims/?q=node/1798

By Natsumi, published on 2014/10/9

有關2013 J Pathol中的使用CC1 buffer

2013 J Pathol使用的unmasking buffer: CC1 (Tris/Borate/EDTA, pH8)
 
詢問結果如下:
Cell Conditioning 1 (CC1)
Catalog Number: 950-124
Quantity: 2 L bottle
Format: Ready to Use (非10倍!!)
售價:NTD 28,000/ bottle  (沒錯,沒有多一個0!!!)
 
網站連結有package insert及MSDS
 
是撘配VENTANA做IHC機器所使用的buffer,CC1是他們偏鹼的buffer (pH8),另外一個CC2是偏酸的buffer (pH6)。
因為價格也滿昂貴的,我想不適合我們使用。
 
這樣我們兩個選擇就是

0.1M citrate buffer, pH6 與 TEG, pH9 (10mM Tris+ 0.5mM EGTA)這兩個unmasking buffer。
 
 
我也粗淺判斷了一下後面的圖,回應於下方(要到下一頁看,並且要上下頁來回對應一下了,Sorry...)。

加入H&E stain 的AE715

Antigen retrieval在ph9的條件下,染在的位置大部分在細胞質(如黑色箭頭所示),

而pH6的條件下,FGFR3染到的位置主要在細胞核(如紅色箭頭所示)。

那TW2.6呢?

在pH9也有許多positive啊! 恐怕這才是non-specific staining吧! 還有,在已發表的paper中,即便是低視野,藍染部份都看得到,為什麼我們的染色大部分都是咖啡色?

 

TW2.6沒有染到咖啡色喔

1. 我覺得 TW2.6並沒有染到咖啡色 (LiLi也是這樣說的) 

2. paper中藍色的核 可以看到是因為 FGFR3的咖啡色染在細胞質

3. PH6的染色  看不到核的藍色  是因為咖啡色都疊在它上面(所以 判定他在核內) 

回應

1. 妳的意思是說 pH9, TW2.6那些都不算是染到,但是它上面的C9就算? 可以請妳們把這個panel, C9中是的都圈起來(紅色outline), TW2.6中不是的也都圈起來(白色outline).
2. 同意。
3. 可以把你們覺得沒有染到的細胞、應該看得到藍色的細胞圈起來嗎? C9/TW2.6都好。我catch不到妳們所謂的藍色核在哪裡, 長得怎麼樣。唯有把核的顏色與形狀弄清楚 再來判斷C9細胞中FGFR3-TACC3咖啡色染色情形。

我圈出細胞核的部份

還有因為染的FGFR3的顏色不深  所以LiLi建議hematoxylin不要染太久 否則會蓋過FGFR3的染色 因此藍色很淡(這部分應該可以再調整) 細胞核我用綠色圈出來(我沒有每顆圈)(相對藍色的地方  就是核) TW2.6幾乎染不到 咖啡色

tou_ying_pian_7.jpgtou_ying_pian_5_1.jpg

 

說明核與質的H&E染色

先利用H&E stain解釋一下細胞核跟細胞質的位置

H(hematoxylin)& E(eosin) staining,其中hematoxylin為鹼性的dye,所以會染上核(藍色),eosin為酸性的dye 所以會染上細胞質顏色為桃紅色 如下所示(綠圈圈為核)

tou_ying_pian_2_1.jpgtou_ying_pian_3_1.jpg

我把C9 positive圈起來(紅色框)

我把C9 positive 用紅色框框圈起來 如下

tou_ying_pian_8.jpg

























































































請問Paper上的圖 (Figure

請問Paper上的圖 (Figure 5),如果不看Figure legend的話,是核還是質? 需要請病理醫師協助嗎?

 
Figure S3 in another paper.
 

我也初淺判斷一下

Fig 5

FGFR2 病人1:細胞質 病人2:細胞質 病人3:細胞質與細胞核 病人4:細胞質 病人5:細胞質與細胞核 病人6:細胞質與細胞核。

FGFR3 看起來6位病人細胞質與細胞核都有。

 

FigS3

以Tumor FGFR2 fusion(-)比較Tumor FGFR2 fusion(+) positive staining在細胞質與細胞核皆有。

 

==> 這些PAPER看起,FGFR2 or FGFR3的細胞質在這些病人當中皆有positive staining,

當中有些病人是除了細胞質以外,細胞核也有positive staining。

細胞質與細胞核都有的染色幾乎是整片深褐色。

我貼的DDR1 IHC就是由朱醫生判定的喔

若我來看覺得

1.Fig5 (同樣都是patient4)

FGFR2: 在細胞質  FGFR3: 在核跟質

2.FigS3

FGFR2: 在細胞核跟質

3.我貼的DDR1染色 是朱醫師判定的

summary

1. 原則上anti-FGFR3 (Santa Cruz, clone:B9) 不論在PH=6或PH=9 retrival條件下對於C9及TW2.6都是有區分性的

  (C9: +, TW2.6: -)

2. 但由於PH=6下主要染到細胞核(雖然有一些些染到細胞質) 覺得有點奇怪 (因為分核質的實驗應該有點參考性),而且只要呈30 sec顏色就出來了,所以覺得這條件下應該非特異性結合高,誤判比例可能會增高

3. 在PH=9下主要染到細胞質也有細胞核,而且用肉眼看比例也不少

4. 再根據以往利用anti-FGFR3 (Santa Cruz, clone:B9) 所發表的paper大多都是在微鹼(PH=8-9)下進行,所以我們認為微鹼下進行retrial的條件應該是比較適合的

tou_ying_pian_6_0.jpgtou_ying_pian_4_1.jpg