Day 1 :
National Institutes of Health, USA
Keynote: Integration of genomics with metabolomics and epigenomics and its implication in cancer control
Time : 10:00-10:30
Mukesh Verma is a Program Director and Chief in the Methods and Technologies Branch (MTB), Epidemiology and Genetics Research Program (EGRP) of the Division of Cancer Control and Population Sciences (DCCPS) at the National Cancer Institute (NCI), National Institutes of Health (NIH). Before coming to the DCCPS, he was a Program Director in the Division of Cancer Prevention (DCP), NCI, providing direction in the areas of biomarkers, early detection, risk assessment and prevention of cancer and cancers associated with infectious agents. He holds MSc from Pantnagar University and a PhD from Banaras Hindu University. He completed Post-doctoral research at Howard University and George Washington University and was a faculty member at Georgetown University. He has published 151 research articles and reviews and edited three books in cancer epigenetics and epidemiology field.
Precision medicine is an emerging science with the potential to improve early cancer diagnosis and enable the development of treatment based on an individual’s genetic background, family history and other characteristics. Identifying patients who may benefit from personalized and precision therapy depends on identifying accurate assays for the biomarkers that are needed to determine optimal treatment. Compared to the rapid progress in technology development, the progress in treatment timing has been slow. Most clinicians rely on pathology reports that become available in due time, which often is too late to control or treat cancer. Molecular profiling (mostly omics profiling based on genomics, metabolomics, epigenomics, transcriptomics and glycomics data) and molecular classification of cancer can be achieved in real time and may help to identify those cancer-associated biomarkers that are expressed much earlier than pathological symptoms and characteristics appear in histopathological analyses. Once these biomarkers are included in personalized medicine, it will enable treatment to be implemented earlier, which will produce better outcomes. Although the traditional approach to personalized medicine has been “reactive” in the future, it will be “Proactive.” These approaches might be useful in controlling cancer which is a priority at the National Cancer Institute (NCI) and the National Institutes of Health (NIH). An update from the Common Fund Metabolomics, Epigenomics Roadmap, Molecular Transducers of Physical Activity and the Cancer Genome Atlas (TCGA) will be presented.
National Institute of Biology, Slovenia
Time : 10:30-11:00
Tamara Lah Turnsek has completed her PhD from University of Ljubljana, Postdoctoral studies from Wayne State University School of Medicine. She is the Director of National Institute of Biology. She is also the Head of National Genetic Toxicology and Cancer Biology Program and full Professor at the University of Ljubljana, teaching Tumor Biology to postgraduate level students. She has published about 150 papers in reputed journals and is a recipient of many national and international (EU, ERAnet) and inter-regional grants, including the recent Brazil CNPQ grant with the University of Sao Paolo.
Tumour heterogeneity may be an additional reason for ineffective therapy, due the cooperation between stromal cells in the microenvironment and various subtypes of tumor cells. Previously, we addressed the molecular cross-talk in the most lethal of brain cancers, glioblastoma (GBM) cells and infiltrated mesenchymal stem cells, resulting in phenotypic alteration of GBM using transcriptomics-proteomics analyses. Here, we examined GBM U87, U251 and U373 cell lines as in vitro model of Intra-tumoral heterogeneity. First, we revealed so far unknown fact that U87 and U373 are two different GBM subtypes with the neural and mesenchymal transcriptomic fingerprints, respectively. When in co-cultures, the impact of their paracrine cross talk resulted in alteration in their stability, proliferation, invasion and resistance to temozolomide. U87 cell conditioned medium lowered the genomic stability of U373 and U251 cells, without affecting cell proliferation. In contrast, exposure of U87 cells to U373 and U251 medium, increased genomic stability, decreased proliferation and increased invasion of U87. This was due to a defined set of secreted cytokines, associated with altered expression of 264 genes in U87 cells, playing a role in proliferation, inflammation, migration and adhesion. In U373 cells, 221 altered genes were linked also to apoptosis, cell cycle and differentiation. Noteworthy, direct and indirect co-culturing of U87 and U373 cells showed mutually opposite effects on temozolomide resistance. In conclusion, transcriptional analyses of distinct GBM cell interactions provides better understanding of GBM heterogeneity and the basis for a more informed glioma treatment.
- Epigenetics and Cancer Genomics | Cancer Genome Therapy | Cell Fate in Cancer | Cancer Nanotechnology | Emerging Themes in Cancer Genomics | Hormone Dependent Cancer | New Fronteries in Gene Editing
Location: Conference Hall 1
National Institutes of Health, USA
Seoul National University, South Korea
Time : 11:20-11:50
Jasmonic acid (JA) is an important hormone mediating stress response in plant. JA response has been widely studied for the purpose of developing stress-resistant transgenic crops. Increasing numbers of studies reported that enhanced JA response improves resistance against stresses, but also induces negative effects on plant growth and productivity. Understanding of JA inhibition mechanism against growth is essential to develop transgenic plants carrying both stress-resistance and enhanced growth. To understand the JA-mediated growth inhibition mechanism, function of OsJAZ9 responsible for JA signaling was studied through genome editing by CRYSPR/CAS9 system. We traced temporal and spatial expression pattern of OsJAZ9, and also analyzed its mutant Osjaz9 generated by CRISPR/Cas9 system that can modify response of target genes with high accuracy. Through Agrobacterium-mediated callus transformation and selection, we collected 30 individual transgenic plants. Among them 8 individual plants (around 30%) carried mutated OsJAZ9 gene in their genome. From this study we found that expression pattern of OsJAZ9 changes along developmental stages, predominant expression in leaf at early developmental stage but in roots at late developmental stage. Further characterization of Osjaz9 mutants will expand our understanding how JA allows plants to coordinate dynamics of stress response and growth.
American University of Beirut, Lebanon
Title: Uptake, delivery and anticancer activity of thymoquinone nanoparticles in breast cancer cells
Time : 11:50-12:20
Hala Gali-Muhtasib is currently a Professor of Cell Biology at the American University of Beirut. She has received her PhD from Kansas State University, USA. Her research interests are in studying the role of natural products in cancer prevention and therapy. Her research focuses on cancer chemoprevention and chemotherapy; in particular, study of plant derived compounds. She has explored novel drugs that inhibit the mechanisms involved in colon cancer such as naturally occurring plant tannins, vitamin E and essential oils of the Lebanese sage plant, thymoquinone extract from black seed and extracts from Lebanese indigenous plants, all of which are ingested regularly by humans and thus may hold promise as anticancer agents. Her efforts have been directed towards understanding the cellular and molecular mechanisms of action of various anticancer agents using cellular biology techniques as well as an emerging array of molecular technologies. She has numerous publications on mechanisms of action of anticancer drugs. She is the recipient of three research achievement awards, Suad Al-Sabbah, Abdul Hameed Shoman Prize for Young Arab Researchers and ISESCO Science Prize for contributions in Biology.
Thymoquinone (TQ) is a promising anticancer molecule but its development is hindered by its limited bioavailability. Drug nanoparticle formulation is commonly used to overcome low drug solubility, limited bioavailability and nonspecific targeting. This project aimed at synthesizing different TQ nanoparticles (TQ-NP), characterizing them and assessing their uptake and delivery mechanisms as well as their anticancer potential in a panel of breast cancer cells. TQ-NP was prepared by flash nanoprecipitation. Dynamic light scattering and scanning electron microscopy were used for the characterization of the size, morphology and stability of the NPs. The anticancer activity was assessed by MTT. The uptake and subcellular intake mechanism of fluorescent TQ-NP were evaluated by both fluorometry and confocal microscopy. Four different TQ-NPs were formulated. The average diameter size ranged between 45-130 nm. All TQ-NPs were stable and had high entrapment efficiency (75-80%) and loading content (36-50%). In vitro, TQ-NP had equal or enhanced anticancer activity effects compared to TQ, in MCF-7 and aggressive MDA-MB-231 breast cancer cell lines. No significant cytotoxicity of the blank NP was noted. The uptake of fluorescent TQ-NP occurred in a time and concentration dependent manner. Treatment with inhibitors of endocytosis revealed the involvement of caveolin mediated endocytic pathway in TQ-NP uptake. This was also confirmed by subcellular localization findings, showing the colocalization of TQ-NP with both caveolin and transferrin as well as with the early and late markers of endocytosis, EEA-1 and lamp-1 proteins. Altogether, the results describe an approach for the enhancement of TQ anticancer activity and uncover the mechanisms behind cell-TQ-NP interaction, uptake and biodistribution.
Chonnam National University, South Korea
Time : 12:20-12:50
Young Hee Joung has completed her PhD from Korea University in South Korea and Postdoctoral studies from ARS, USDA. She is a Professor of School of Biological Sciences and Technology, Chonnam National University. She has published several papers in journals about plant molecular farming field.
The GA733-2, colorectal carcinoma associated antigen and epithelial cell adhesion molecule (EpCAM), is highly expressed on the surfaces of human colorectal carcinoma cells. It was utilized to produce a vaccine for colorectal cancer in a plant system. To develop a vaccine using a plant system, recombinant protein rGA733-2 and rGA733-2-Fc genes were cloned into plant expression vector (pBINPLUS) with an ER targeted signal peptide and KDEL retention codon. The cloned vectors were introduced into tobacco plants using Agrobacterium mediated stable transformation or agro-infiltrated transient transformation. The recombinant proteins, rGA733-2, rGA733-Fc and Fc were purified from transgenic tobacco leaves and evaluate their anti-cancer effects using MC38 cancer cells. Only the rGA733-Fc showed anti-cancer effects. To develop an edible colorectal cancer vaccine, the rGA733-Fc gene was introduced into tomato plants (Solanum lycopersicum cv. Micro-Tom). The rGA733- Fc expressed transgenic tomato fruits were administered orally to C57BL/6J mic and then colorectal cancer was induced in the oral treatment mice using MC38 cells injection. The plant derived rGA733-Fc treated mice showed amelioration of colorectal cancer is caused by rGA733-Fc induced anti-cancer immune response stimulation.
Hong Kong Polytechnic University, Hong Kong
Time : 12:50-13:20
Benjamin Yat Ming Yung has obtained his PhD in Pharmacology from Baylor College of Medicine. He did his Postdoctoral training in the Lab of the Nobel Laureate Arthur Kornberg at Stanford University. He is currently Chair-Professor of Biomedical Sciences. For the past 30 years, he has systematically explored the biological role of NPM in cancer. He has published over 100 scientific papers that cover broad range of scientific disciplines and techniques. His achievements and recognitions are reflected in many prestigious awards including Outstanding Researcher Award, Outstanding Cancer Research Award and Ministry of Education Outstanding Teacher Award.
Wayne State University, USA
Time : 14:05-14:35
Zeng-Quan Yang has completed his PhD from Tokyo Medical and Dental University and Post-doctoral studies from University of Michigan School of Medicine. Currently, he is an Associate Professor at the department of oncology, Wayne State University. His research interest is focused on investigating the genetic and epigenetic bases of human breast cancers and identifying novel therapeutic targets for cancer treatment. He has published more than 30 papers in reputed journals.
Methylation of lysine and arginine residues on histones and non-histone proteins plays critical roles in chromatin function, transcriptional regulation, genomic stability, cell differentiation and survival. These epigenetic methylations are mediated by antagonistic sets of enzymatic complexes—the methyl transferases, which catalyze methylation in a site-specific manner and the demethylases, which remove the methylation marks. Such methylation marks are interpreted by “reader” proteins that specifically bind to the modified histone. The largest and most diverse set of reader proteins includes the Tudor domain and plant homeodomain (PHD)-containing proteins. Accumulating evidence suggests that histone methylation pathways play an integral role in the sequential progression of cancer. It is shown that many histone methyl transferases/demethylases and “readers” are targeted for mutation and deregulation in cancer patients. However, the genomic landscape and clinical significance of these histone methylation modifiers in breast cancer remain poorly characterized. Here, we performed an integrated genomic and transcriptomic analysis of histone methyl transferases/demethylases and Tudor-containing “reader” proteins in breast cancer. We identified associations among recurrent copy number alterations, gene expressions, clinicopathological features and survival of patients. Furthermore, we interrogated cancer genomics data and functional small-interfering RNA (siRNA) screens to pinpoint potential oncogenes and novel targets, focusing on histone methylation modifiers in breast cancer. Integrative analysis identified a subset of histone methylation modifiers that are dysregulated by genetic alterations, classifying them as candidate therapeutic targets. Together, our findings provide a strong foundation for further mechanistic research and therapeutic options that target these histone methylation modifiers to treat breast cancer.
Seoul National University, South Korea
Time : 14:35-15:05
Plant transcriptome profiling has provided a tool for understanding the mechanisms by which plants respond to stress conditions. Analysis of genome-wide transcriptome will provides a useful dataset of drought responsive non-coding RNAs and their candidate target genes that may be involved in drought stress responses. Here RNA-seq analyses of leaves from drought stressed rice plants were performed, producing differential expression profiles of non-coding RNAs. We found that the transcript levels of 66 miRNAs changed significantly in response to drought conditions and that they were negatively correlated with putative target genes during the treatments. The negative correlations were further validated by qRT-PCR using total RNAs from both drought-treated leaves and various tissues at different developmental stages. The drought responsive miRNA/target pairs were confirmed by the presence of decay intermediates generated by miRNA-guided cleavages in Parallel Analysis of RNA Ends (PARE) libraries. We observed that the precursor miR171f produced two different mature miRNAs, miR171f-5p and miR171f-3p with 4 candidate target genes, the former of which was responsive to drought conditions. We found that the expression levels of the miR171f precursor negatively correlated with those of one candidate target gene but not with the others, suggesting that miR171f-5p was drought-responsive with Os03g0828701-00 being a likely target. Pre-miRNA expression profiling indicated that miR171f is involved in the progression of rice root development and growth, as well as the response to drought stress. Ninety-eight lncRNAs were also identified, together with their corresponding antisense transcripts, some of which were responsive to drought conditions.
University of Texas MD Anderson Cancer Center, USA
Title: Size matters: Challenges in implementing large Next-generation sequencing panels for routine clinical screening of tumors
Time : 15:05-15:35
Rajesh R Singh has completed his PhD in Biochemistry from The University of Mysore, India and Postdoctoral research from University of Texas, MD Anderson Cancer Center. He has extensive experience in cancer biology focusing on the deregulated oncogenic and tumor suppressor pathways in the origin and maintenance of solid tumors and hematological malignancies. He is an Assistant Professor and Director of Clinical NGS Development in the Molecular Diagnostics Laboratory at MD Anderson, where he supervises the design, validation and implementation of NGS assays for routine mutational screening of tumors. He has published more than 50 papers and 8 review articles in reputed journals.
Massively parallel sequencing capability of Next-generation sequencing technologies have made them genome sequencing platforms of choice for routine screening of clinically significant markers in tumors. Most popular approach generally includes screening of limited areas (mutational hotspots) of limited number of relevant genes in order to restrict costs and practical turn-around-time (TAT) for the results. However, rapid discovery of markers warrants increasing the number genes for routine screening which is challenging due to increased costs, complexity of interpretation and decreasing sequencing throughput. In this talk, the experience of implementing progressively large gene panels in a high-volume molecular diagnostic laboratory will be highlighted. The logistic issues of implementing large NGS panels and the steps taken to meet these challenges in the laboratory will be discussed.
Massachusetts General Hospital Cancer Center, USA
Title: Clinical implementation of tumor genotyping to guide development of personalized regimens for patients with metastatic breast cancer: Challenges and opportunities
Time : 15:35-16:05
Aditya Bardia is a board certified Medical Oncologist at the Massachusetts General Hospital Cancer Center of Harvard Medical School, USA. He has been involved in clinical development of tumor genotyping and circulating tumor cells (CTCs) to facilitate therapy selection. He is the Principal Investigator of several clinical trials investigating the role of targeted therapy combinations for breast cancer. He is on the Editorial Board of the ASCO University. He has received various research awards and is interested in developing successful targeted and personalized therapies to improve the outcomes of patients and families afflicted with breast cancer.
It is now well recognized that cancer is not one disease. Molecular characterization of tumor is particularly important because identification of actionable targets could potentially lead to rational therapy selection and enhance access to matched personalized therapy for that individual. Our group along with others recently demonstrated the presence of acquired mutations in the ligand binding domain of estrogen receptor (ESR1) which can lead to constitutional activation of the estrogen receptor in the absence of ligand (estrogen) and thereby result in resistance to standard endocrine therapies particularly aromatase inhibitors. Furthermore, genotyping can also help identify the molecular traits associated with “exceptional responders” and help select “right drug for the right patient”. Circulating tumor cells (CTCs) can serve as potential “liquid biopsies” offering a potential relatively non-invasive tool for tumor genotyping as well generation of ex vivo cultures as demonstrated by our group. In this talk we will review how routine genotyping of tumor and circulating tumor cells could be utilized in the clinic for targeted therapy selection and development of personalized therapies for patients with cancer.
Beijing New Oriental Foreign Language School at Yangzhou, China
Title: Screening chemo-resistant related genes via digital gene expression profiling and small RNA sequencing in esophageal squamous cell carcinomar
Time : 16:25-16:55
Yikun Cheng, as an Intern, participated in the study of “Screening chemo-resistant related genes via digital gene expression profiling and small RNA sequencing in esophageal squamous cell carcinoma”, which was funded by the National Natural Science Foundation of China (81330063) and the Key Project of Chinese Ministry of Education (NO213005A).
Esophageal cancer (EC) represents the sixth leading cause of cancer deaths worldwide. Although many reports have indicated that patients who receive chemoradiation therapy had a significantly better 5 year survival rate, it is unclear why certain patients respond better than others to chemotherapy. Unambiguous molecular markers are needed to identify which patients are likely to respond best to particular treatments. To identify potential genes and miRNAs associated with chemoresistance in chemo-sensitive and chemo-resistant esophageal squamous cell carcinoma (ESCC) cell lines, a variety of ESCC cell lines were treated with different kind of chemotherapy drugs. By comparison of IC50, the chemo-sensitive and chemoresistant cell lines were obtained and subjected to digital gene expression profiling (DGE) and small RNA sequencing analyses. In total of 238 candidate genes including two well-known chemo-resistant related genes (MDR1 and ZEB2) and some novel chemo-resistant related genes (such as PHF15, MYO15B, FAM84B, DSEL) were up-regulated in chemo-resistant cell lines with more than 5 fold compared to that of chemo-sensitive cell lines. KEGG Pathway analyses showed these genes involved in tumor angiogenesis, tumor occurrence, tumor development and metabolism process control. Moreover, 224 of novel chemoresistant related miRNA were identified via small RNA-seq (>5 fold); of which, 27 of miRNA showed statistical significance between chemo-resistant and chemo-sensitive cells (P<0.0001), which involving in Notch and cell cycle pathways. The miR- 140-3p is one of the miRNAs with dramatically statistical significance among three resistant/sensitive cells (>20 fold, P<0.0001) and its potential target gene (NFYA) were also identified by the DGE profiling screening. Further study demonstrated that overexpression of miR-140-3p down-regulated the NFYA mRNA level. Collectively, our study identified a set of key genes and miRNAs associated with chemo-resistance in ESCC. Of note, miR-140-3p may play critical roles via regulating its target gene NFYA in chemo-resistance in ESCC.