Day 1
院長致詞: 十一月份還會有一個retreat
Emerging Trends and Opportunities for Microbiota Research
高承源副研究員 (免疫醫學中心)

– Microbiota is not just about bacteria, viruses, fungi are also included.
– Analytic tools of microbiota (e.g.assembling the human gut Microbiota in metabolic diseases.
– Metaproteomics workflow
– Models for human microbiota research
– Organ-on-a-chip RootChip (different levels of oxygen at different layers of matrix)
– Ex vivo models for microbiota research
– Experimental approaches for defining functional roles of mirobes in the human gut (PMID: 24024637)
* lost of function
* gain-of function approaches
– Determining causality in animal models
– From human fecal to mice
* germ-free mouse facility in NLAC: isolator
* Isolator at cage level
– Natural product…
– The progression of microbiota research
Observation –> Correlative –> Causative (germ-free mice) –> Mechanistic (still very rare studies)
* US NIH HMP type1, type2 diabetes
* The earth microbiome project is. A systematic attempt to
* France
* China
* Crowdfunding microbiome project
* (UCSD) American gut
* Taiwan gut citizen science project
– Microabiota is the new key to finger many diseases
– Gordon lab.: the father of microbiome
$ Yin-yang of obesity ion the gut microbiota
$ an obesity-associated gut microbiome with increased capacity for energy harvest (Nature)
$ Causality: gut bug transmitted obsity 2013/Science
– A microbial protein that alleviates metabolic syndrome (Scientists at Belgium) A.muciniohilia (Akk bacteria)
– Dusp6 knockout mice
– CTLA4 blockade relies on gut microbiota
– How the Microbiota modulate chemotherapy and
– Gut Microbes can shape response to cancer immunotherapy
– Three papers in Science (end of 2017)
– FMT ——>
### Non-antibiotic drugs have effects on gut Microbiota
Nature article: extensive impact of non-antibiotic drugs on human gut bacteria
ClinicalTrials.gov
## Bugs as drugs ## Drug the bugs
## bacterial metabolites ## new biomarkers
– Personalized therapies & precision medicine
# guys bacteria can stop cancer drugs from working
– The microbiome understood by AI
– Microbiota research is multidisplinarity
– Key players in the microbiome (Gordon Lab, Belgium, China, Germany, Sweden)
– Synthetic and metablome
– Computational
– Metabolism and inflammation
2016/May US White House —> The microbiome Project
The most needed Taiwanese microbiome projects
— baseline studies
— healthy subjects
A potentially unique yet important baseline study project tin Taiwan
Fecal Microbiota Transplantation (FMT) for Clostridium Difficile Infection and Other Diseases 邱政洵教授 (林口長庚醫院兒童感染科)
Taiwan FMT Expert Consensus
吳俊穎主任 (臺北榮民總醫院 轉譯研究科) 微菌叢植入治療

1st Characteristics
Gut-brain Axis: a Fundamental Mechanism Modulating Alzheimer’s Progression
莊志立研究員 (分子與基因醫學研究所)
Bioinformatics in Microbiome Analysis
廖玉潔副研究員 (群體健康科學研究所)

Day 2
Opportunities and Challenges of Current Immuno-oncology Landscape
林文傑助研究員 (免疫醫學中心)
Oncolytic Virotherapy for Making Cold Tumors “HOT”
徐祖安研究員 (生技與藥物研究所)
Development and Opportunities of Antibody-based Immunotherapeutics in Mainstream Oncology 官建村副所長 (生技中心生物製藥研究所) (Duke University)
Dynamic Interplay Between Tumor Cells and Macrophages
楊慕華副校長 (陽明大學)

Opportunities for Small Molecules in Immuno-oncology
顏婉菁研究員 (生技與藥物研究所)
Mitochondrial DNA Leakage and Inflammatory Cytokines Activate Innate Immune Signaling and M2-macrophage in Tumor Microenvironment
李岳倫副研究員 (癌症研究所)
*The stress phenotypes in tumor microenvironment
• hypoxia • ROS • Genome instability • Acidosis
* Tumor microenvironment targeted therapies
Mitochondrion
• mitochondria can perform multiple cellular functions including bienergy production metabolism, Ca2+ signaling, apoptosis, and autophjagy
• Mitochondria are a major source or ROS in cells
• mitochondrial respiratory complex proteins are a major source of cellular ROS
• Miochondrial resporatory
* Mitochondrial Lon-induced oxidative stress in tumorigenesis
* High ROS level as a stress phenotype in tumor
* ROS are crucial signaling molecules of signal transduction pathways that promote proliferation , inflammatory,
* Lon overexpression induces. NF-KB and IFN pathways
* Lon overexpression induces the expression of IL6 IL1B IL4 and IL13 (NF-KB directed)
* Tumor associated inflammatory cytokines regulate macrophage function
* Increased Lon expression is involved in the differentiation and activation
* The effect of Lon-overexpressing cancer cells on macrophage
* OECM1
With Lon-overexpression or shRNA of Lon
* Lon overexpression —> mitochondrial DNA —> STING, IFN, NF-KB
* Innate immunity is involved STING-TBK1-IRF3 in HSC3
* Cancer Research (2016) STING promotes the growth of tumors characterized
* KO STING (in HSC3??? )decreases TBK1, IRF3/7, IDO1/PDL1
Taiwan Cancer Moonshot: Pathway to Next Generation Cancer Precision Medicine
陳玉如所長 (中央研院化學研究所)
–Protein network critical regulation in cellular function and diseases
• Abnormal protein network is often the cause of disease initiation and progression
• Substrat, site-specific PTM regulation?
• Pathways crosstalk?
• Heterogeneity at individual patient level
–Mass spectrometry-based strategies: membrane proteome and modification
–New proteomics strategies or membrane proteome and post-translational modification
Membrane proteomics, phosphorylation, nitrosylation + others, glycosylation
–Application of proteomics strategies for delineation of disease/biology mechanism
–Nanoprobe-based affinity mass
Revised chemistry for phosphoproteomics by immobialized metal affinity chromatogranphy (IMAC)
–Ph / acid controlled IMAC 90% purification specificity and recovery
–Sequencing fractionation by IMAC-stage tip (Ti 4+, Fe 3+ Ga3+)
–Mass sepctrometry revealed dynamic interplay of phosphorylation and O-Glunacylation to switch B cell activation apoptosis. (Kudos-I Lin, Na Comm 2016)
– Lsp1 dynastic phosphorylation and O-GlcNacylation of Lsp1 switches B-cell activation and apoptosis
– Quantitative depiction of precise in biology Stoichoimetry
Phosphorylation stoichiometry is it significant
Two-fold regulation of suite stoichiometry could result from either fractional occupancy changes of 10 to 20% c=or 50 to 100% which likely represent
Are we able to differentiate changes in eithe rprotien or phosphorylation stoichiometry??
Example for phosphorylation stoichiometry measurement
The measurement of phosphorylation of
Identifying drug-resultant target through phosphoproteomic network of EGFRVIII and CK2 substrates
On the comparison between the TKI-sensitive and resistant lung cancer cell
More dramatic chang at phosphorylation level : in the resultant lung cance cell, the phosphorylation HMGA1 KD could reverse drug resistance in NSCLC PTM is important for drug resistance
Dynamic stoichiometry of EGFRVIII signaling pathway
———————-
Precious biology
An informatics-assisted mass spectrometry approach for personalized timmues membrane protein is
STOML2 as a noninvasive serological biomarker candidate fo prognosis and early CRC diagnosis
1452 origin were identified
3-protein candidates for early detection f gastric cancer. (197 protein membrane proteins)
Cancer Moonshot
US NCI 2006. Tissue Proteogenomics
CRC Nature 2014.
Proteomics identified new subtypes in colorectal cancer stage III,.. new molecular subtype
MOU signed in 2015 July
Cancer Moonshot announced by Obama 2016 Jan
VP Biden announced international al cancer Moonshot 2016, Sept)
Cancer Moonshot was included in national policy program (2016, nov) (生醫產業推動方案
2016 Taipei HUPO
International cancer proteogenome consortium
Genetic background and environmental factors contribute to unique feature of cancers in Taiwan/Asia
NSCLS
Early stage patients (n=200)
Late stage patients (n=200)
First high multi-om is atlas of personalized Taiwanese cancer cohort
Lung cancer n=400 breast cancer n=400
CRC n=400
Acre
Which platform can provide biological content to address. The unment clinical needs]]proteomics > 10,000
Phosphpoproteimics > 26000 phosphorylation sites
Most proteins in NSCLC pathways (94%) were identified
569 kinases were quantified in NSCLC tissues
Identify low abundant protein tyrosine phosphatases
Does gene subtype accurately describe a patient at the (phosphatases)
Allied specific expression profiling in lung cancer
Personalized profile in NSCLC pathway
39 SNV of somatic mutation identified in 44 patients
Night mutation rate in Asioam female (58%)
Sensitive to TKI with Del 19 and L858R mutation develop resistance within 12 moths
Personalized proteogenomic atlas revealed differential activation of signaling pathway
Gene X
Germinline mutation
Up-regulated protein level in 90% patient
X signaling and EGFRVIII-pathway (243 proteins0
Differential activation in NSCLC subtype
Degradation of extra cellular matrix
B cell receptor signaling by interleulinw
M
Taiwan protein project (2016-2019)
Applying state of the art proteogenomics to rapidly identify unique targets and pathways of cancer for detection and intervention
Targeting MCT-1/IL-6/IL-6R Signaling Inhibits EMT Progression, Cancer Stemness and M2 Macrophage Polarization in Aggressive Breast Cancer 徐欣伶副研究員 (分子與基因醫學研究所)
MCT1DENR-MCT1 heterodimer promotes …
PUA domain a highly conserved motif in …
Translational control of cancer (cancer translatome)
MCT1 abundance in intra-ducal and invasive breast carcinoma (IHC staining)
MCT1 overexpression associates with worse clinical outcomes indifferent type of breast cancer
MCT1 induces normal breast cell proliferation and causes malignant Alina morph Jolene’s is
CD163 as M2 macrophage marker
In vitro THP1 polarization M2 marker Arginase 1 , IL10?
qRT-PCR confirmed by using CD163, CD206 primers
MCT1 stimulates MCP1 GMCSF and IL6 secretion cytokine array. <— highly likely to involve M2 differentiation
Tocilizuman (Actemra) a humanized recombinant IL6R mAb

Discussion Session
Time
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Topics
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Speakers
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13:30~13:40
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Opening Remarks 梁賡義院長
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Microbiome
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Moderator
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蔡世峯處長
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13:40~14:25
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Emerging Trends and Opportunities for Microbiota Research
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高承源副研究員 (免疫醫學中心)
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14:25~15:10
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Fecal Microbiota Transplantation (FMT) for Clostridium Difficile Infection and Other Diseases
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邱政洵教授 (林口長庚醫院兒童感染科)
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15:10~15:55
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Taiwan FMT Expert Consensus
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吳俊穎主任
(臺北榮民總醫院 轉譯研究科) |
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15:55~16:20
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Break
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16:20~16:50
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Gut-brain Axis: a Fundamental Mechanism Modulating Alzheimer’s Progression
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莊志立研究員 (分子與基因醫學研究所)
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16:50~17:20
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Bioinformatics in Microbiome Analysis
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廖玉潔副研究員 (群體健康科學研究所)
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17:20~18:00
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Discussion Session
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18:00~
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Dinner
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Time
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Topics
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Speakers
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Cancer Immunology I
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Moderator
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司徒惠康副院長
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09:00~09:45
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Opportunities and Challenges of Current Immuno-oncology Landscape
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林文傑助研究員 (免疫醫學中心)
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09:45~10:20
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Oncolytic Virotherapy for Making Cold Tumors “HOT”
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徐祖安研究員 (生技與藥物研究所)
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10:20~10:30
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Break
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10:30~11:15
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Development and
Opportunities of Antibody-based Immunotherap eutics in Mainstream Oncology |
官建村副所長 (生技中心生物製藥研究所)
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11:15~12:00
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Dynamic Interplay Between Tumor Cells and Macrophages
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楊慕華副校長 (陽明大學)
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12:00~13:30
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Discussion Session & Lunch
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Cancer Immunology II
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Moderator
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施修明所長
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13:30~14:00
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Opportunities for Small Molecules in Immuno-oncology
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顏婉菁研究員 (生技與藥物研究所)
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14:00~14:30
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Mitochondrial DNA Leakage and Inflammatory Cytokines Activate Innate Immune Signaling and M2-macrophage in Tumor Microenvironment
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李岳倫副研究員 (癌症研究所)
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14:30~15:15
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Taiwan Cancer Moonshot: Pathway to Next Generation Cancer Precision Medicine
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陳玉如所長 (中央研院化學研究所)
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15:15~15:45
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Targeting MCT-1/IL-6/IL-6R Signaling Inhibits EMT Progression, Cancer Stemness and M2 Macrophage Polarization in Aggressive Breast Cancer
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徐欣伶副研究員 (分子與基因醫學研究所)
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15:45~
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Discussion Session
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