2017/02/02 Journal Club paper

Indomethacin Treatment of Mice with Premalignant Oral Lesions Sustains Cytokine Production and Slows Progression to Cancer.

< PubMed 連結> PMID: 27713748

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奕宏報告的PPT檔 按我預覽或下載

奕宏補充報告PPT檔 按我預覽或下載

2017/1/12 Journal Club Paper

Cancer cells induce metastasis-supporting neutrophil extracellular DNA traps.

PubMed 連結

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秀鈴 transformed the PPT file to two PDF because it's too huge to be attached.  Best, SL

PDF1 (按我預覽或下載)  PDF2 (按我預覽或下載)

The Schedule

Place: R2-3042; Time: 12:00-14:00; 30 min presentation + 30-40 min discussion

Please send the title and the PDF file of the paper being presented to all the members one week before the talk.
輪到你的時候，請在一周前把題目及pdf檔寄給大家謝謝。

For 奕宏 talk at "I Love Immunology" on 2/2

Dear 奕宏: 我覺得#4在講premalignant lesion和PGE2 (https://goo.gl/RjzJaX) 那篇不錯。

另外，這裡有作者簡介的新聞 PUBLIC RELEASE: 30-NOV-2016

I get by with help from my friends: Maintaining immune cells in head and neck cancer (https://goo.gl/FCs7Gg）

參加人員名單暫存區

黃麗蓉 Lab

鄭雲心 <cloudheard@gmail.com>, 

陳宥婕 <Emilyycchen@nhri.org.tw>,
黃麗蓉 < lrhuang@nhri.org.tw>,

蘇郁文 Lab

徐偉展 <weichanhsu@nhri.org.tw>,

陳明玉 <cmy6075@nhri.org.tw>, 

蘇郁文 <yuwensu@nhri.org.tw>,

許素菁 Lab

簡秀鈴 <sljian@nhri.org.tw>,

李宜珍 <ycli@nhri.org.tw>,
王復輝 <fhwang0919@gmail.com>,
莊雯婷 <chuangwenting@gmail.com>,

許素菁 <mschsu@nhri.org.tw>,

林素芳 Lab 

劉奕宏 <haloedition8@gmail.com>,

柯英潔 <ingridko0128@gmail.com>,

陳玉蓮 <lanie0407@gmail.com>,

林素芳 <sflin@nhri.org.tw>

17th Biennial EBV Meeting @ Switzerland (Aug/8-Aug/12)

有些abstract已被剪到GRC NPC個人檔案中

Monday, 2016/08/08 
Session 1: EBV epidemiology and sequence variation 2:30pm-
Chairpersons:
Henri-Jacques Delecluse, German Cancer Research Institute, Heidelberg, Germany

Alan Chiang, University of Hong Kong, China

1. Heterogeneity of the major internal repeat (IR1) of Epstein-Barr virus implicates interstrain recombination in pathogenesis, and includes a nonsense mutation of EBNA-LP in the prototype strain B95-8.
Mohammed Ba Abdullah, Imperial College London, UK
2. High levels of antibody that neutralize B-cell infection of Epstein-Barr virus and that bind EBV gp350 are associated with a lower risk of nasopharyngeal carcinoma
 Anna Coghill, National Cancer Institute, Bethesda, USA
3. Development of highly efficient and widely applicable CRISPR/Cas9-mediated cloning method of EBV genomes and its application to EBV-positive gastric cancer cell lines
 Teru Kanda, Aichi Cancer Center Research Institute, Nagoya, Japan
4. Association between cigarette smoking and oral EBV viral loads in China: a multicenter cross sectional study in 2013-2016
 Weihua Jia, Sun Yat-Sen University Cancer Center, Guangzhou, China
5. Determination and Genome-wide Analysis of EBV Sequences in EBV- associated Gastric Carcinoma from Guangdong, an endemic area of nasopharyngeal carcinoma 
Chun-kui Shao, Sun Yat-Sen University, Guangzhou, China
6. The dominating promoter variation of BRLF1 in nasopharyngeal carcinoma endemic area contributes to high efficacy of Epstein-Barr virus reactivation Jiangbo Zhang, Sun Yat-Sen University Cancer Center, Guangzhou, China

獵頭職場真相觀察

老闆要2個業務聯絡200個客戶...為什麼打完100通電話、「聽話」的人反而被解僱？
<撰文者江湖人稱S姐> 出處商業週刊按我

這是兩位業務在剛開始要做客戶開發時遇到的故事，可以拿來當借鏡。兩位員工暫且稱為小劉和小王好了，而這位主管的管理方式喜歡訓練員工思考。

主管：手邊這200個客戶跟聯繫窗口，你們分別聯繫100個，一周後我們來討論狀態。

小劉：好，我現在立馬來做。

小王 : 這100個名單裡面，哪些是比較重要但被忽略的客戶？哪些是久沒連繫的客戶？

討論一番以後，隔了一周，主管開會時分別和兩位業務詢問客戶狀態。

GRC NPC Index Page | EBV Meeting

• Clevers, Hans
• Delecluse, Henri-Jacques
• Fuchs, Elaine
• Futreal, Andrew
• Hildesheim, Allan
• Lieberman, Paul M.
• Liu, Fei-Fei
• Lo, Kwok-Wei
• Lo, Yuk-Ming Dennis
• Longnecker, Richard
• Lu, Xin
• Ma, Jun | Ngan, Roger | Bei, Jin-Xin
• Rooney, Cliona
• Tsai, Ming-Han
• Tsao, George SH
• Zeng, Mu-Sheng
• zur Hausen, Harald
• Unclassified (Hong Zheng, Honglin Chen, Brigette Ma, Wei Dai | TESSA, TGFBRI inhibitor, BPLF1 DUB)
• Group Photo

GRC NPC - Lieberman, Paul M.

2018 Madison Meeting
HENLE LECTURE
Paul M. Lieberman, Ph.D. The Wistar Institute Philadelphia, PA
Paul Lieberman obtained a Ph.D. at Johns Hopkins University, School of Medicine studying Epstein-Barr Virus reactivation in the laboratory of Dr. Gary and Diane Hayward. He completed a post-doctoral fellowship with Dr. Arnie Berk at UCLA investigating basic mechanisms of transcriptional activation by viral factors. He joined the Roche Institute of Molecular Biology as an Assistant Member and then moved to the Wistar Institute in Philadelphia in 1995. His research focuses on the molecular biology of Epstein-Barr Virus (EBV) and Kaposi’s Sarcoma-Associated Herpesvirus (KSHV) latency and persistence, with particular interests in epigenetic mechanisms and chromosome biology. His work combines biochemical, proteomic, and functional genomic methods to investigate regulation of viral latency, and how this contributes to viral carcinogenesis. The Lieberman group has leveraged this basic research to develop novel small molecule inhibitors and modulators of EBV and KSHV latency to treat viral-associated disease. Lieberman is presently the Hilary Koprowski Endowed Chair and Program Leader in Gene Expression and Regulation and the Director of the Center for Chemical Biology and Translational Medicine at the Wistar Institute.

Arch Pharm Res. 2017 Aug;40(8):894-905. doi: 10.1007/s12272-017-0939-5. Epub 2017 Aug 4.

DNA hypermethylation induced by Epstein-Barr virus in the development of Epstein-Barr virus-associated gastric carcinoma.

Choi SJ1, Shin YS2, Kang BW3, Kim JG3, Won KJ4, Lieberman PM5, Cho H6, Kang H7.

Author information

Abstract

Epstein-Barr virus (EBV)-associated gastric carcinoma (EBVaGC) is a recently recognized disease entity defined by the presence of EBV in gastric carcinoma cells. EBV infection causes major epigenetic alterations in the EBV genome and its cellular host genome, suggesting that EBV acts as a direct epigenetic driver for EBVaGC. One of the major epigenetic events in the viral and cellular genomes to control transcription is DNA hypo- or hyper-methylation. Particularly, local and global hypermethylation have been reported in EBVaGC. It is therefore important to understand the molecular mechanisms of DNA hypermethylation during EBVaGC carcinogenesis. To understand the functional roles of DNA methylation and suggest therapeutic target candidates for EBVaGC, we reviewed recent literature reporting DNA hypermethylation in EBVaGC. We summarized the identified candidate genes that are markedly hypermethylated in EBVaGC, which can potentially be targets for chemotherapies with demethylating agents. (pmid:28779374)

J Virol. 2017 Aug 9. pii: JVI.00804-17. doi: 10.1128/JVI.00804-17. [Epub ahead of print]

Coordinate Regulation of TET2 and EBNA2 Control DNA Methylation State of Latent Epstein-Barr Virus.

Lu F1, Wiedmer A1, Martin KA1, Wickramasinghe PJMS1, Kossenkov AV1, Lieberman PM2.

Author information

Abstract

Epstein-Barr Virus (EBV) latency and its associated carcinogenesis are regulated by dynamic changes in DNA methylation of both virus and host genomes. We show here that the Ten-Eleven Translocation 2 (TET2) gene, implicated in hydroxymethylation and active DNA demethylation, is a key regulator of EBV latency type DNA methylation patterning. EBV latency types are defined by DNA methylation patterns that restrict expression of viral latency genes. We show that TET2 mRNA and protein expression correlate with the highly demethylated EBV type III latency program permissive for expression of EBNA2, EBNA3s, and LMP transcripts. We show that shRNA depletion of TET2 results in a decrease in latency gene expression, but can also trigger a switch to lytic gene expression. TET2 depletion results in the loss of hydroxymethylated cytosine, and corresponding increase in cytosine methylation at key regulatory regions on the viral and host genomes. This also corresponded to a loss of RBP-jκ binding, and decreased histone H3K4 trimethylation at these sites. Furthermore, we show that the TET2 gene, itself, is regulated similar to the EBV genome. ChIP-Seq revealed that TET2 gene contains EBNA2-dependent RBP-jκ and EBF1 binding sites, and is subject to DNA methylation associated transcriptional silencing similar to EBV latency type III genomes. Finally, we provide evidence that TET2 colocalizes with EBNA2-EBF1-RBP-jκ binding sites, and can interact with EBNA2 by co-immunoprecipitation. Taken together, these findings indicate that TET2 gene transcripts are regulated similarly to EBV type III latency genes, and that TET2 protein is a cofactor of EBNA2 and co-regulator of the EBV type III latency program and DNA methylation state.

IMPORTANCE Epstein-Barr Virus(EBV) latency and carcinogenesis involves the selective epigenetic modification of viral and cellular genes. Here, we show that TET2, a cellular tumor suppressor involved in active DNA demethylation, plays a central role in regulating DNA methylation state during EBV latency. TET2 is coordinately regulated and functionally interacts with the viral oncogene EBNA2. TET2 and EBNA2 function cooperatively to demethylate genes important for EBV-driven B cells growth transformation. (PMID: 28794029)

PLoS Pathog. 2017 Aug 30;13(8):e1006596. doi: 10.1371/journal.ppat.1006596. eCollection 2017 Aug.

Deregulation of KSHV latency conformation by ER-stress and caspase-dependent RAD21-cleavage.

De Leo A1, Chen HS1, Hu CC1, Lieberman PM1.

Author information

Erratum in

• Correction: Deregulation of KSHV latency conformation by ER-stress and caspase-dependent RAD21-cleavage. [PLoS Pathog. 2018]

Abstract

Kaposi's sarcoma (KS)-associated herpesvirus (KSHV) is a human gammaherpesvirus recognized as the principal causative agent of KS and primary effusion lymphoma (PEL). KSHV establishes persistent latent infection in B lymphocytes where viral gene expression is restricted, in part, by a cohesin-dependent chromosome conformation. Here, we show that endoplasmic reticulum (ER) stress induces a rapid, caspase-dependent cleavage of cohesin subunit RAD21. ER stress-induced cleavage of RAD21 correlated with a rapid and strong viral lytic transcriptional activation. This effect was observed in several KSHV positive PEL cells, but not in other B-cells or non-B-cell models of KSHV latency. The cleaved-RAD21 does not dissociate from viral genomes, nor disassemble from other components of the cohesin complex. However, RAD21 cleavage correlated with the disruption of the latency genome conformation as revealed by chromosome conformation capture (3C). Ectopic expression of C-terminal RAD21 cleaved form could partially induce KSHV lytic genes transcription in BCBLI cells, suggesting that ER-stress induced RAD21 cleavage was sufficient to induce KSHV reactivation from latency in PEL cells. Taken together our results reveal a novel aspect for control and maintenance of KSHV genome latency conformation mediated by stress-induced RAD21 cleavage. Our studies also suggest that RAD21 cleavage may be a general regulatory mechanism for rapid alteration of cellular chromosome conformation and cohesin-dependent transcription regulation. (PubMed: 28854249)

PLoS Pathog. 2018 Jan 19;14(1):e1006844. doi: 10.1371/journal.ppat.1006844. eCollection 2018 Jan.

RNA-Seq of Kaposi's sarcoma reveals alterations in glucose and lipid metabolism.

Tso FY1, Kossenkov AV2, Lidenge SJ1,3,4, Ngalamika O5, Ngowi JR3, Mwaiselage J3,4, Wickramasinghe J2, Kwon EH1, West JT1, Lieberman PM2, Wood C1.

Author information

Abstract

Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiologic agent of Kaposi's sarcoma (KS). It is endemic in a number of sub-Saharan African countries with infection rate of >50%. The high prevalence of HIV-1 coupled with late presentation of advanced cancer staging make KS the leading cancer in the region with poor prognosis and high mortality. Disease markers and cellular functions associated with KS tumorigenesis remain ill-defined. Several studies have attempted to investigate changes of the gene profile with in vitro infection of monoculture models, which are not likely to reflect the cellular complexity of the in vivo lesion environment. Our approach is to characterize and compare the gene expression profile in KS lesions versus non-cancer tissues from the same individual. Such comparisons could identify pathways critical for KS formation and maintenance. This is the first study that utilized high throughput RNA-seq to characterize the viral and cellular transcriptome in tumor and non-cancer biopsies of African epidemic KS patients. These patients were treated anti-retroviral therapy with undetectable HIV-1 plasma viral load. We found remarkable variability in the viral transcriptome among these patients, with viral latency and immune modulation genes most abundantly expressed. The presence of KSHV also significantly affected the cellular transcriptome profile. Specifically, genes involved in lipid and glucose metabolism disorder pathways were substantially affected. Moreover, infiltration of immune cells into the tumor did not prevent KS formation, suggesting some functional deficits of these cells. Lastly, we found only minimal overlaps between our in vivo cellular transcriptome dataset with those from in vitro studies, reflecting the limitation of in vitro models in representing tumor lesions. These findings could lead to the identification of diagnostic and therapeutic markers for KS, and will provide bases for further mechanistic studies on the functions of both viral and cellular genes that are involved. (PubMed: 29352292)

2016 GRC NPC

GRC NPC Group Photo_2016

GRC NPC - Tsai, Ming-Han

2018 GRC NPC

• 1 ng/ml IL8 for 7 days —> Zta expression
• Transcriptome data
• Small RNA-associated TLRs 
• TLR3, TLR7 
• TLR7  is involved..

2016 GRC NPC

GRC NPC - Rooney, Cliona

Cliona Rooney (Baylor College of Medicine, USA)
"Cancer Immunotherapy and Challenges for NPC"

1. T cell for each patient, pre existing , 22% chance response
2. Vaccine an Ad-based LMP2, MVA-EBNA1-LMP2
3. LCL activated vEBVST
4. Singpore TESSA therapeutics (http://goo.gl/zdbYpA) 330 patients (與Wed Poster #5相關)
5. Ad LMP1/2/LCL activated T cell for NPC, not better for EBVST, but is better in lymphoma patients (type 2 malignancy lymphoma)
6. SFC, IFNG coated plate, 6 month 1.5 year
7. survivors epitome spread: MAGEA4 + SURVIVIN + PRAME
8. Dendritic cells are difficult to make in NPC patients
9. 1st stimulation: EBV EBNA1 ,LMP1, LMP2, BARF1
10. 2nd stimulation: Pepmix all possible MHC2
11. GRACE trial (patients of lymphoma)
12. Switch to IL15/7
13. High dose IL15 increase specificity
14. Fewer CD4 cells in high dose IL15 (SF: IL21 and IL15 are part of the gamma-chain cytokine family and are crucial for survival and proliferation of Tfh (follicular Th), cytotoxic and memory T cells, both IL21 and IL15 are being used in clinical trial)
15. IL15H increases central key EBVSTs
16. Post infusion expansion of EBVSTs in patients with lymphoma
17. heterogeneity in NPC TME
18. Importance for epitope spreading, maybe viral lytic genes are important (Mei-Ru asked what kind of lytic genes in her mind, she replied: IE genes)
19. TGFBR
20. Infiltrating barrier
21. Gottschalk PI is responsible
22. Lympho depletion/Reactivate EBV
23. Immuno checkpoint
24. Genetic TGFBR DN to increase T cells
25. Steve Rosenberg was mentioned again and again and again (https://goo.gl/LKXqYG)
26. T cells express NPC expressing cytokine 2 receptor to "homing"
27. GuangZhou published some promising results (ref: Oncoimmunology 2015)

From Ming-Han 

1. 1 Small molecules? (one drug for all patients)
2. 2 EBV-specific T cells;
3. 3 Chimeric antigen receptor (CAR) T cells?
4. 4 Gene-modified T cells? (EBVSTs)
5. One patient one drugs?

Ongoing trials

1. Chiun Hsu (許駿); NTU PD1 inhibitor (KEYTZUDA KEYNOTE 028 Overall Response rate 10.8 %)
2. LMP2 peptide pulsed DCs (HK): increase LMP2A specific T cells
3. Ad-dLMP1-LMP2 transduced DCs (Singapore by Prof. Toh): DTH but no elevated LMP specific T cells.
4. MVA-EBNA1-LMP2: functional in 50% patients with the elevated T cell responses.
5. LCL-activated EBVSTs for NPC (adjuvant (62%) remain diseases free / 2nd or relapse in 48.7%)
6. LCL activated EBVSTs after Chemotherapy? (Singapore (Toh, Ho): 35 patients; 97% type III diseases; Gemicitabin and carboplatin 4 cycles. (combine treatment?); 71.4% responses; overall survival 2yr 65%; 5yr 35%.)
7. Gemicibin alone vs Gemicibin + EBVSTs on going in 350 patients. (Ongoing)

Ad5f35-∆LMP1-LMP2 (Adenovim)

• infect PBMC --> boosted by EBV-LCLs (in between plus IL2) ---> wish to have LMP2A/1 T cell CTLs. (Bollard et al, J, Clin Onco 2014 32 (8) 798-808.)

EBVST treat for EBV lymphoma (CTC project)

to NKT lymphoma (remission 25/26)
- Epitope spreading after treatment of EBVSTs seems very important.

This strategy seems good BUT problems

• too long
• No LCL available from these EBV+lymphoma patients; either low B cell or the B cells can't be immortalised by EBV for?? reason.
• Require live virus.
• Many cases all T cells only in the end recognise EBNA3C.

Original plan:

• (PBMC infected by B95-8) --> LCL --> stimulated with DCs with LMP1/2A ---> T cells (peptide of LMP2A by using many many peptides; each 15mer but with 11aa overlapping each)

Now: 

• PBMC+peptide --> (+IL4/7) can have expansion 100X times T cells only within 10 days; enough time to treat PTLD.

Issue:

• This strategy works super well in healthy donor BUT IL4/7 doesn't work well for expansion of patient's T cell for ?? reason.

Phase I clinical trial design (GRACE)

• HL, BL… EBV+ lymphoma.
• Patients T cells with very low avidity;
• Patient with lymphoma have very few T cells.
• Growth of T cells from patients always badly.

New strategy:

IL4/7 vs IL7/15? which is better: 
found IL7/15 is better (high dose IL15: 100ng/ml; medium dose IL15: ? ng/ml)
But still IL7/15 still difficult to expand T cells from patients.

             IL4+IL7       IL7+IL15     IL7+IL15hi
CD4          50%          30%                ~0
CD8          50%          70%             ~100 %

Problem2: LMP1/2 actually not expressed in all tumor cells. For example; if stimulate T cells with BARF1, LMP2, EBNA1 or LMP1, in the end T cells only recognise one peptides…

Epitope spreading: 

• SSX2, NYESP, Survivin, Prame, Mage4 ---> these antigens only exists in lymphoma.
• after treatment patients have T cells against these peptides then the treatments outcome will be better.
• So far: 2/10 cases total cure; 4/10 with better response.

For NPC cases: 

• EBVSTs have less responses for NPC patients
• Possible reasons:  solid tumor; difficult for T cells to enter; Immune suppressive environment.

Requirements if want to treat NPC:

• migration to tumor site
• Infiltrate tumor parenchtmas?
• have to proliferate at tumor sites that express also MHCI

@Gottschalk (NPC clinical trials)
@Effective CAR and TIL stimulation
Requirement for human trials: GMP director; CMP CTL; everything GMP

-------------------------------- Q1: CD4/8 mix during T cell expansion; which one is better?

A1: hard to say. Some successfully with 90% CD4 the others with 90% CD8 but she thinks 50% 50% is the best.

Q2: Epitope spreading: spreading to cancer-associating T cells with viral antigens?
A2: not viral antigens.

Q3: LCL or peptide to stimulate T cells? why difference?
A3: use bacteria or baculovirus to stimulate? Different method might lose the chance to have correct epitopes; for example, phosphorylation. Now we don't use LCL to stimulate T cells; we use adenovirus-infected DCs it's better.

Q5: someone firstly transgene the T cells with specific chemokine receptor corresponding to chemokines secreted by tumor cells; is that good? Yes.

Q6: Combine EBVSTs with chemotherapy? which first?
A6: Suggest to firstly to irradiation or chemotherapy then inject T cells since tumor necrosis can attract T cells to the tumor sites.

In EBV Meeting Invited lecture on immunology, Plenary lecture hall KOH-B-10
Chairperson: Cliona Rooney, Baylor College of Medicine, Houston, USA
Lecturer: Jeffrey Cohen, National Institutes of Allergy and Infectious Diseases