2024/12/18 (三)
Quantitative methylation analysis for long-read seq. (wk5)
2024/12/10 (二)
Quantitative methylation analysis for long-read seq. (wk4)
2024/12/03 (二)
Quantitative methylation analysis for long-read seq. (wk3)
2024/11/26 (二)
Quantitative methylation analysis for long-read seq. (wk2)
2024/11/19 (二)
Quantitative methylation analysis for long-read seq. (wk 1)
2024/11/12 (二)
Finalize data representation of AP061 and AP062.
2024/11/05 (二)
練習 IGV with PromethION reads analysis.
2024/10/30 (三)
練習 IGV with PromethION reads analysis
2024/10/21 (一)
Dan visited (10/17 TPE airport), brought us long-read sequences. Each sample takes about 100 GB 😆
2024/10/15
Finalize AP060 & AP061 results.
TY: 大於15個fields時，去掉最大和最小、也就是離SD最遠之data!
SF: No, no, no 當一塊惡性程度高度異的腫瘤要妳做staging時， 有一部分 stage 4, 一部分 stage 2, 妳要說這塊tumor是stage多少?
2024/10/08
分享開會心得二
2024/10/01
分享開會心得一
20240917、0924 TY 日本九州福岡國際會議中心開會
The 83rd Annual Meeting of the Japanese Cancer Association (JCA) (Link).
Venue: Fukuoka international Congress Center, Marine Messe Fukuoka Hall B
2024/09/10
Poster for 83rd JCA (Link).
2024/09/03
Continue K2-Experiment 2 (R8) and Experiment 4 (R12).
K6- 3 AIG assays, all using p120+R4
Quisinostat = QST
2024/08/27
Experiment 2 (R8) started! (although cell density seems to be a little bit lower, but week seems OK; Experiment 3 (R10) started and failed in agarose solidification. So plan for a new Experiment 3 using R12.
2024/08/20
LabLog AP060: Photo-taking for Experiment 1 (R4) Week 4
Experiment 2 (R8) started! (although cell density seems to be a little bit lower, but week seems OK; Experiment 3 (R10) started and failed in agarose solidification. So plan for a new Experiment 3 using R12.
2024/08/13
LabLog AP060: Photo-taking for Experiment 1 (R4) Week 3
–80 冰箱兩個壓縮機都壞了，感恩Wayne 老師將幫付修理費(~9萬、10萬元?)
2024/08/06
LabLog AP060: Photo-taking for Experiment 1 (R4) Week 2
There are two ongoing Experiments (R8 and R10).
LabLog AP061: Quisinostat on AIG formation–K6-CTRL and K6-AC
2024/07/30
LabLog AP060: Photo-taking for Week 1
2024/07/23
Continue on LabLog AP060: 剛種下K2-CTRL and K2-AC細胞 (Experiment 1)，下週二之前可照第一週生長情形。
討論OEC-M1 TW2.6 + miR-000 後，細胞老化染色實驗及相關資訊。
2024/07/16
Continue on LabLog AP060
2024/07/09
LabLog AP060: Quisinostat on AIG formation–K2-CTRL and K2-AC.
2024/07/02
(06/24–07/15) Conduct pilot study using K2-AC cells.
先看藥有沒有效 (20 nM Quisinostat) 用K2-AC 細胞測試 (使用六孔盤)
— A: Vehicle control (add DMSO in 8-ml KDF for 3 weeks)
— B: Add Quisinostat in 8-ml KDF for 3 weeks
— C: Add Quisinostat in 8-ml KDF for 24h, then KDF for 3 weeks
— D: Add Quisinostat in 8-ml KDF for 72h, then KDF for 3 weeks
— E: mix Quisinostat with cells in Agar when plating, then KDF for 3 weeks
— F: pretreat Quisinostat 24 hours, , then KDF for 3 weeks
今日TY回報：A、E有長，B、D死得較嚴重。
2024/06/25
- TY took photos for her friend (老師，那個…不好意思，明天的meeting可以再延一次嗎？琬琦要參加明天國衛院自辦的畢業典禮，找我幫她拍照助陣，時間是10-14點)
2024/06/19
- 6/12-18 改成處理一天 成功！！
- 先拿K2-AC 測量抑制效果
- Medium最後1L，look for Dr., then KDF for helps from Dr. 夏 or 陳。
2024/06/11
- 夏老師Lab Meeting改成今日上午。
- OKF4 IC50測試完畢!
2024/06/04
- TYL: Ferropotosis pathway is not in GSEA/KEGG pathway! 因此分析時要小心!
- https://www.kegg.jp/pathway/map=map04216&keyword=ferroptosis
- SFL: induced pluripotent pathway 是在Molas分析時發現的，不是DAVID 🤔🤔🤔
2024/05/28
- IC50測試 K2 and K6 control ~40nM.
- K2_AC and K6_AC 15~38nM.
- How to perform AIG with inhibitors?
2024/05/21
- share freeform white board “TYL-Lab Meeting” with TY
- 細胞解凍順利，開始進行IC50測試!
2024/05/14
- 本週與夏老師家meeting衝期，故暫停一週 😃
2024/05/07
- 已拿到藥了！
- Prepare for IC50 test. (10 uM-> 2X dilution)
- All three paired lines will be evaluated.
AP059: Quisinostat on AIG formation–pilot study
2024/04/30
- H1F0 inhibitor 伯森代購: 5mg 6620元！
- 已將 V85 pFlag Cpo TO 交給怡芝學姊!
- IC50 ?
2024/04/23 (分享 Dr. Tsai, Hsin-Jen 蔡性真醫學博士Talk)
- Easwaran H., Hsing-Chen Tsai, and Stephen B. Baylin (JHU), Review paper (Cancer Epigenetics: Tumor Heterogeneity, Plasticity of Stem-like States, and Drug Resistance Mol Cell 2014 Vol 54, p716 pdf 4065)
- After returning to Taiwan, use of two drugs (decitabine and Azacitidine, Aza) to “demethylate” DNA methylation and found:
- Myc expression 下降
- Antigen-Presentation and Immune response genes 上升!
- Immunotherapy (anti-PD1) in cancer with DNA methylation inhibitor –> improve treatment efficacy
- DNA methylation inhibitor increases gamma delta T cell numbers
- T cell methylomes
2024/04/16
- H1F0 inhibitor Quisinostat (群研科技 0800-200-202)。
- 5mg 9500元，依論文中100nM使用濃度預估，總共可以泡100L！
2024/03/26
- 生醫年會參加會後感。
2024/03/12 and 03/19
- 準備2024生醫年會口頭報告。
2024/03/05
- 熟悉wordpress網誌及本頁面操作
- 準備2024生醫年會口頭報告，預計先在夏家預演一次 (著重檳榔鹼之致癌機轉)，上場前再與SF預演一次。
2024/02/27
- 整理紙本筆記本，盡快把title寫入ExpLog 2024。
- EPI2ME 軟體已下載，嘗試使用(stop)。
- Arecoline paper 準備 re-submit to oncogene
2024/02/20
- ExpLog 2024 補正
2024/02/06 (02/12 初二收細胞，02/16 交貨給怡宓老師)
- Prepare cells for Nanopore sequencing
- Navigate analysis procedures (EP2ME and DeepVariant)
- SF 02/03 與 Dan/Yi-Mi 討論合作事宜
2024/01/09, 01/16, 01/23, 01/30
- Thaw cells, purified cDNAs, qRT-PCR
- ZNF671, STAT5A retained downregulation in AC cells
- 做qPCR時，technical replication 至少做3-wells; 做二個 well一上一下時，不如不做。
- 完成冬令營海報製作及報告
- 此次拿掉downregulation部分，只留stemness gene activation部分，且多加入GSE227919 datset。
- 所以。。。大部分問題已在之前個會議中被問及➜只剩一題：或許比較(K2-AC+K6-AC) versus (K2+K6) 可萃取出更多transformation associated genes.
2023/12/12, 12/19, 12/26
Continue to dig in GSE227919
2023/12/05
Look for more clinical datasets for clinical evidence;
準備冬令營Abstract
<真的假的>How ChatGPT Can Aid in Tailoring Research Papers for Specific Scientific Journals (eScienceInfo)
2023/11/30 L0168
2023/11/28 NTHU–NHRI annual meeting
- Got it ! 🌷💐🌹🤣🤣🤣🍆🍺🥂
- 評審委員三位(明姿老師、慧嫻老師、清大黃ㄓˋㄓㄥˋ老師)
- 建議抽掉OKF4 保留已E6/E7 不朽化的細胞株
- 內容宜再精簡，去掉不相關的data
2023/11/21
- remove downregulation part to supplemental data
- K-M plots for 36 potential oncogenes in KEGG HSA04550
- SF 不死心，來試試DotPlot for scRNA-seq tumor cells (Not bad@!)
2023/11/14
- NHRI-NTHU thesis progress report (+莊老師、夏老師)
2023/11/07
- Revise all IHC results (本來scale bar 都模糊不清，現在都已清楚可見)
2023/10/24
- TY was concerned about Paloa’s GEO submission, in which Quisinostat inhibition had no effect in ID1 nor FZD expression
- 討論清大國衛院11/25研討會abstract及年度進度報告。
2023/10/17
- ID1/FZD6 是否為幹細胞標記?
- Puram dataset 證實 head and cancer is a heterogeneous disease
- EMT <-> p-EMT 被Hanahan “3rd Hallmark of Cancer” 舉例為 new enabling characteristics之一 “Nonmutational epigenetic reporgramming” SCC9 is the prototypic cell line
- 2007 PNAS (IL Weissman為共作) 界定CD44為 stem cell marker, co-stained with KRT5 and KRT14 (大心, 更換foreskin paper)
- 2020.12 Nat Genet Kinker et al. Pan-cancer single-cell RNA-seq identifies recurring programs of cellular heterogeneity (更多HNSCC cell line data.)
- Puram dataset 證實 head and cancer is a heterogeneous disease
- 十月底交NHRI-NTHU年會Abstract，11/25 會議
- 11月中舉辦進度報告(邀請莊老師、夏老師)
2023/09/26 討論Puram Object in Seurat (10/10放假)
- Cancer stem cell 約佔整個tumor cell population的多少百分比?
- heterogeneity
- CD133 1-3% (ref)
2023/09/19 討論Puram Object in Seurat
- Tumor 2491 連繫組蛋白排序向下
- 請TY查出 cancer stem cell 約佔整個群組的多少百分比?
- SFL 分享 Puram_GSE103322_1021.Rmd and Puram202103.rds
2023/09/12 討論manuscript 新圖
- H1F0 versus oncogenes and stemness markers
2023/09/05 討論manuscript 重點放在 activation of self-renewal and tumorigenesis
- Qiagene AllPrep® DNA/RNA Micro Handbook
2023/08/22 討論CPTAC新文章, hypermethylation of STAT5A
- Wen-Wei Liang et al. (wustl.edu) 這一篇，確定 HNSC tumor cell 致癌過程中有一個” immunosuppression switch”. 文章中說是STAT5A, 我們自己的dataset可以好好看一下。第二個重點，proteogenomic analysis把kinase又了連回來，好比FGFR2, EGFR 治療靶點有了更強的依據。第三點，Graphic abstract清楚劃出 hypomethylation 導致 FGFR2 濃度上升; hypermethylation 導致 STAT5A 濃度下降，這張圖給了我們Biomedicines review很棒的支持! (OKF4-AC ⬆️ ; K2-AC K6-AC ⬇️ 在KEGG-JAK/STAT pathway 中排名85 although non-significant)
2023/08/08 Paper submission
- Google Scholar Metrics (指標) is a good place to evaluate “visibility”.
- 08/23: The Way to Malignant Transformation 收到第一次citation)
2023/07/19 討論H1F0 and chromatin organization
2023/03/18 生醫年會、03/21 NHRI Research Day
- QA-1: 靜娟老師asked about patent、development of prognostic kits.
- QA-2: 張文祥老師asked about …
- QA-3: 莊懷佳老師對使用NOG鼠有疑慮，請參照下面幾篇典範論文
- 2009/07 Majieti et al. CD47 Is an Adverse Prognostic Factor and Therapeutic Antibody Target on Human Acute Myeloid Leukemia Stem Cells (PubMed)
- 2014/03 Kreso et al. Evolution of the cancer stem cell model (PubMed)
- 2020/04 Morales et al. Selective inhibition of cancer cell self-renewal through a Quisinostat-histone H1.0 axis (PubMed)
Poster 站內連結
2023/02/16 補記先前 meeting notes
- ROS induced cell death or arrest
- Apoptosis, Necroptosis, Ferroptosis
- Arrest, senescence
- ROS and transformation
- Antioxidant (NRF2, GCLC)
- MDM2 degrades p53 + CDKN2A (p16) stabilized p53
- E7 (KDM6A, KDM6B)
| OKF4-AC/OKF4-CTRL | K2-AC/K2-CTRL | K6-AC/K6-CTRL | |
| GSH synthesis | ⬇︎ | ⬆︎ | － |
| TXN Antioxidant | |||
| NRF2 Antioxidant |
| Chromosome | OKF4-AC | |
|---|---|---|
| CDKN1A (p21/CIP1) | 6p21.2 | 顯著下降 |
| CDKN1B (p27/KIP1) | 12p13.1 | 顯著上升 |
| CDKN1C (p57) | 11p15.4 | 下降 |
| CDKN2A (p16/INK4A–p19/ARF) | 9p21.3 | 顯著上升 |
| CDKN2B (p15/INK4B) | 9p21.3 | |
| CDKN2C (p18/INK4C) | 1p32.3 | |
| CDKN2D (p19/INK4D) | 19p13.2 | |
| G0/G1 | 顯著下降 | |
| TP53, CDKN1A, CDKN1C | ||
| S phase | 顯著上升 | |
| E2F1,2,5, MYC, ORC1,2,6, CCNA2 | 上升 | |
| G2/M | 上升 | |
| CDK1, CDT1,CDC25B, WEE1,PKMYT1, PLK1, ESPL1, ANAPC11, CDC26 | 上升 | |
| TP53, MDM2 (Apoptosis) | 下降 |
2023/02/14 (AP055)
| normal | malignant transformed | cancer | |
| 高醫(n=39) | n=22 | n=17 | n=0 |
| 中山(n=38) | n=15 | n=17 | n=6 |
| 蠟塊捲片做RNA-seq | |||
| Coxph有時間 | |||
| Logistic model (大約等同於limma) |
2022/11 NTHU-NHRI annual meeting
- 清大張壯榮老師 (1. should consider endogenous ROS (inhibitor TBO?), 2. stemness ext telomere
- 清大郭崇涵 (神經 xxx 研究所?
- 清大莊雅菁(LMP1 and RON in Tsai’s Lab at NTU, now working on endometria cancer)+陳韋靜老師 came to ask couple questions
2021/12/19 GSE26549 Heatmap and K-M plots (AP054)
- Cancer-free (n=51) + Cancer-development (n=35)
- Up: FZD6, DNMT3B, GCLM, SKIL, FGFR2, ID1 etc.
- Down: HRAS, HOXD1 etc.
- K-M plots FZD6 (8q22.3) + ZNRF1 (16q23.1)
2021/05/01- 搞定 AC-specific nitrosamine
- 1983/01 Wenke and Hoffmann pdf 5793-
- Hypothesis: 苯環結構式 CH3/COOCH3 + nitrate ==> carcinogenic nitrosamine (NG, MNPN, MNPA)
- 2004/ IARC Vol-85 Betel-quid and Areca-nut Chewing and Some Areca-nut-derived Nitrosamines 2003 Jun
- 2012/ IARC Vol-100E Personal habits and indoor combustions 2009 meeting
- 2022/ IARC Vol-128 (pdf 5943 Lancet Oncol) Group 2B C03-Arecoline-128-editable 2021 Nov