Showing posts with label NICR. Show all posts
Showing posts with label NICR. Show all posts

Aug 3, 2014

Cancer Epigenomics_Folate

由 sufang 在 日, 08/03/2014 - 09:28 發表 Pre-published Cancer epigenomics Folate MATHFR Methionine Methylation SAM

重要文獻 (Research Notes: Cacner epigenomics (folate))
1.    Kane, M. A. (2005) The role of folates in squamous cell carcinoma of the head and neck. Cancer detection and prevention 29, 46-53. (pdf 4099.)    The primary objective of this review is to explore the hypothesis that folate insufficiency may be important in the pathogenesis of squamous cell carcinomas of the head and neck (SCCHN) and that folate repletion may be an effective component of chemoprevention. The main results are that folate insufficiency disrupts DNA global and specific gene methylation patterns such that the activity of certain tumor suppressor genes such as p16 and possibly p53 may be lost. Folate pool imbalance and impaired repair mechanisms may contribute to DNA instability and strand breaks. Sensitive methods exist for identification of individuals with folate insufficiency in contrast to the relatively insensitive conventional serum or red cell folate assays with broad "normal" ranges. The impact of folate supplementation can thus be quantified. Folate imbalance may result from alterations in folate cellular uptake by the reduced folate carrier (RFC) and/or the folate receptor (FR) and polymorphisms in enzymes important in folate retention such as folylpolyglutamate synthetase and in folate modification such as methylene tetrahydrofolate reductase (MTHFR). Known predisposing factors for SCCHN such as alcohol and tobacco carcinogens may influence folate balance. Folate supplementation may reduce primary or secondary risk of cancer. Formal studies of folate sufficiency in persons at risk for or diagnosed and treated for SCCHN are needed to define the role of folate supplementation in the prevention of these cancers.

Jul 5, 2014

缺口計畫相關資訊

由 sufang 在 六, 07/05/2014 - 17:12 發表 Pre-published Arecoline COE (Cancer of Excellence) OPMD Potentially malignant disorder

10/05/2014 (SUN) PK大賽
第二期癌症研究缺口補強計畫評選會議議程
開會時間:103年10月5日(星期日)上午10時
開會地點:本部204會議室
壹、主席致詞


貳、報告

Jun 28, 2014

劉柯的4NQO老鼠與40T/N交叉比對部分

由 sufang 在 六, 06/28/2014 - 15:59 發表 Oral Cancer 4NQO Oral Cancer

說在前頭: 目前我拿的還是Illumina normalized的"group" data. 這和江博前次所提,做過SVA1的M0, M1, M2, M3稍稍不同。等江博轉好他的data給我,我會儘快送入Molas,到時就可reconfirm大家心目中有興趣的基因/pathway在兩組資料中有 沒有差很大。
所以,我再囉唆一次,因為看了下面兩個圖後,我把stage 2的資料先不加入分析,因此僅看 stage 0, stage1, stage 3, stage 4的基因變化趨勢,共篩出543個基因,也就是Pathway Book v1中的"mouse model"部份。

Janelle的部份

由 sufang 在 六, 06/28/2014 - 16:03 發表 Oral Cancer DOK NIC nicotine Oral Cancer

Nicotine (NIC) - treated DOK: 針對NIC4, NIC5, NIC6 vs DOK1的array data, 配合日前所提, NIC-treated DOK clones 有明顯增加cell proliferation及migration的現象, 可能參與的pathway/genes有:
  1. DNA replication: MCM10 (3.37x), RECQL4 (2.32x), GINS2 (2.32x), CDC25A (3.01x), CDC7 (2.227x), NASP (2.19x), DTL (2.38x)。
  2. Cell cycle: E2F2 (2.22x), CDC6 (2.75x), CDC7(2.27x), CDC25A (3.01x), PKMYT1 (2.31x), CDKN1A (=p21, 0.44x), SOX9 (0.31x), HBP1 (0.38x), STEAP3 (0.4x), RPS6KA2 (0.22x), RPS6KA3 (0.39x)
  3. Transcriptional misregulation in cancers: SIN3A (0.52x), NUPR1 (0.39x)
  4. Fibroblast growth factor binding: TGFBR3 (3.63x), FGFBP1 (2.51x), FGFR3 (2.83x, NIC獨有的)
  5. TGF-beta signaling pathway: BMP4 (4.56x), BMP7 (8,98x)
  6. Focal adhesion: COL5A1 (0.49x), LAMA3 (0.38x), THBS3 (0.53x), ITGA3 (0.5x) , ITGA5 (0.37x), MET (0.49x), ITGB5 (0.49x), VEGFA (0.37x), VEGFC (0.5x), SHC1 (0.52x), MAP2K1 (0.52x), CTNNB1 (0.42x) 細胞focal adhesion能力下降?
  7. Cell adhesion: CLDN1 (0.46x), LPXN (0.34x), AMTN (0.21x) 細胞貼附能力下降?
  8. Stress fiber: GAS2L1 (2.65x), ENAH (2.26x), NEBL (2.67x)
  9. Epidermis development: KRT13 (75.39x, 可是不知為何去到40TN及4NQO mouse呈下降或不變趨勢)
小記一下:
–許多基因的上或下,AC和NNK較一致,但如果nicotine是由NNK來的,會期望看到nicotine與NNK較一致。先按下不表。
–KRT13被記載在下列這些GO中: tongue morphogenesis, keratin filament, intermediate filament, extracellular vesicular exosome, cellular response to retinoic acid, epidermis development, response to radiation

Jun 25, 2014

新書發表-Pathway Book v1

由 sufang 在 三, 06/25/2014 - 10:37 發表 Pre-published 40TN 4NQO DOK Molas Oral Cancer

親愛的大家:我心目中的pathway mapping結果終於做好了! (按我下載Pathway book v1)。這是由三項microarray 分析結果而得到的結果, including (1) 40對T/N病人檢體; (2) (娟與夏的)AC, NNK, NIC-treated DOK cells; (3) 劉柯的 4NQO/AC-mouse. (按我下載 40TN_DOK_4NQO_Combo v1)。

May 7, 2014

DOK_MOLAS analysis related

由 sufang 在 三, 05/07/2014 - 16:40 發表 Oral Cancer DOK Molas Oral Cancer
提醒:
MOLAS入口:
  • 40T/N: 請用「Library comparison」, compare "average" and "N".
  • 4NQO mouse: 可按「Cludtering」--> view clustering result 玩玩看。
  • DOK project.
login:
pwd:
05/07 SFL小notes:
  • ASS1 in NNK and AC treatment 都有下降。
  • Shiah's AC vs DOK3: "GO: microtubule binding" ranks the best p-score. 共有17個genes invovled (ex kinesin families), 多是表現上升趨勢。
  • 娟' AC vs DOK2: "GO:mitotic cell cycle" ranks the best. 而且involve的基因 member高達138個, AURKA, AURKB都在裡面耶!! (讀值都大於500, 倍數均增加兩倍以上)


Mar 27, 2014

OrCa小組會議_DOK related

由 sufang 在 四, 03/27/2014 - 00:00 發表 Oral Cancer Arecoline DOK nicotine NNK

OrCa小組會議 (03/27/2014)
素芳的筆記本:
  • nicotine: 500 uM
  • NNK: 10 uM
  • arecoline (AC): 50 uM or 100 uM
  • treated for ~ 1 year, looking for carcinoge-tolerant cell clones, eg. NNK4, NNK5, NNK6, NIC4, NIC5, NIC6
  • doubling time
  • migration assay
  • In vivo tumorigenesis
  • Expression array  analysis ("Merged_Kuo_Shiah" from Jonhson on 4/18/2014)
    • from 靜娟 (第一次DOK1等七片arrray, 第二次DOK2等三片arrray)
      • DOK pool 1 (DOK1)
      • NIC4 (NIC4)
      • NIC5 (NIC5)
      • NIC6 (NIC6)
      • NNK4 (NNK4)
      • NNK5 (NNK5)
      • NNK6 (NNK6)
      • ------------------------------------------
      • DOK pool 2 (DOK2)
      • AC50 pool (AC50)
      • AC100 pool (AC100)
    • from 夏博 (5片arrray, S=Shiah, QN=quantile normalization):
      • Dok (DOK3)
      • Arecoline 50 uM 5-day (AC50_short)
      • Arecoline 50 uM 12-mo (來自靜娟;命名為 AC50_1)
      • NNK 10 uM 5-day (NNK_short)
      • NNK6 12-mo (來自靜娟;命名為 NNK6_1)
  • ARE: anti-oxidant responsive element; Nrf2/ARE
  • NRF2=NFE2L2
  • KEAP1 (E3 ligase adaptor)
  • AKR1C2, C3, C4
  • SOD1, 2, 3
  • nAchRa9

Jul 29, 2013

KegArray Results

由 sufang 在 一, 07/29/2013 - 20:10 發表 Pre-published 40 T/N ECM KEGG Microarray


Stiffer: Up in COL, LAM, FN, SPP1 (OPN), TNC, AGRN, IBSP (BSP), LOX, LOXL1, LOXL.
ITGA3/A5/A6/B3/B4/B6