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2024/11/19 (二)

Quantitative methylation analysis for long-read seq

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

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

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

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.)
  • 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

2023/07/19 討論H1F0 and chromatin organization

  • 2016/09 The linker histone H1.0 generates epigenetic and functional intratumor heterogeneity (Morales Torres et al. Science)
  • 2020/04 Selective inhibition of cancer cell self-renewal through a Quisinostat-histone H1.0 axis (Morales Torres et al. Nat Comm)

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
    1. 2009/07 Majieti et al. CD47 Is an Adverse Prognostic Factor and Therapeutic Antibody Target on Human Acute Myeloid Leukemia Stem Cells (PubMed)
    2. 2014/03 Kreso et al. Evolution of the cancer stem cell model (PubMed)
    3. 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-CTRLK2-AC/K2-CTRLK6-AC/K6-CTRL
GSH synthesis⬇︎⬆︎－
TXN Antioxidant
NRF2 Antioxidant
ChromosomeOKF4-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)

normalmalignant transformedcancer
高醫(n=39)n=22n=17n=0
中山(n=38)n=15n=17n=6
蠟塊捲片做RNA-seq
Coxph有時間
Logistic model (大約等同於limma)
02/20 江老師 provided excel: 高醫31個檢體，中山醫大17個檢體。其餘資料仍無法取得。

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
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