Extracellular Biomarkers Summit

March 16-18, 2015
Hyatt Regency Cambridge | Cambridge, MA
DINNER COURSES
MARCH 16
⊲ Systems Biology, Evidence Synthesis
and in silico Discovery Approaches to
microRNA Biomarkers
⊲ Executive ThinkTank: Development
of Exosome-Based Diagnostics
MARCH 17
⊲ RNA-Seq: A Fundamental Guide to the Field
⊲ Circulating Nucleic Acid Biomarkers for
Development of Non-Invasive Prenatal Tests
ExtracellularBiomarkers.com
FEATURED SPEAKERS
Carlo M. Croce
Director, Genetics Institute
The Ohio State University
Susan Freier
Vice President
Isis Pharmaceuticals
Ajay Goel
Director, Cancer Prevention
Baylor Research Institute
Raghu Kalluri
Chair, Cancer Biology
MD Anderson Cancer Center
Frank Slack
Director, Institute for RNA Medicine
Beth Israel Deaconess Medical Center
Nicole Meisner-Kober
Senior Investigator, RNA Biology
Novartis
EXTRACELLULAR
BIOMARKERS
SUMMIT
Register Early for Maximum Savings
microRNA as Biomarkers
and Diagnostics
Long Non-Coding RNA
in Cancer
Exosomes and Microvesicles
as Biomarkers and Diagnostics
Extracellular RNA in Drug
and Diagnostic Development
Organized by
Cambridge Healthtech Institute

2 | ExtracellularBiomarkers.com
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Hyatt Regency Cambridge
575 Memorial Drive
Cambridge, MA 02139
Phone: 1-888-421-1442
Discounted Room Rate: $209 s/d
Discounted Room Cut-off Date: February 16, 2015
Please call the hotel directly to reserve your sleeping accommodations. You
will need to identify yourself as a Cambridge Healthtech Institute conference
attendee to receive the discounted room rate with the host hotel. Reservations
made after the cut-off date or after the group room block has been filled
(whichever comes first) will be accepted on a space- and rate-availability basis.
Rooms are limited, so please book early.
Top Reasons to Stay at the Hyatt Regency Cambridge:
• Complimentary internet in guestrooms
• Hotel will provide shuttle to/from Kendall and Harvard Square each
evening from 6-10pm
• Approximately 15 minutes from Boston Logan International Airport
• Sundeck overlooks the beautiful Boston skyline along the
Charles River
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Car rental discounts are available.
Visit ExtracellularBiomarkers.com for details.
Hotel & Travel
For additional information, please contact:
Carolyn Benton, Business Development Manager
781-972-5412 | cbenton@healthtech.com
About the Event
Extracellular Biomarkers Summit, the newest addition to Cambridge Healthtech Institute’s notable biomarker and diagnostics portfolio,
merges the well-established microRNA as Biomarkers and Diagnostics conference with focused discussions on other leading areas of
research: the role of circulating microRNA, exosomes and microvesicles, long non-coding RNA and extracellular RNA in cancer and other
diseases, as well as their potential to serve as biomarkers in drug and diagnostic development. Discussions will include the isolation and
characterization of exosomes and exRNA, including expression profiling and sequencing of exRNA; understanding the role of miRNA, lncRNA,
and exosomes in disease mechanism, tumor metastasis, and intracellular communication; their potential as biomarkers in drug development,
drug toxicity assessment, and patient stratification; and finally, their role as circulating biomarkers for disease diagnosis and prognosis.
Please join us to gain comprehensive coverage of extracellular biomarkers and hear from industry leaders on cutting-edge research,
technologies and applications.

Dinner Short Courses*
MONDAY, MARCH 16, 6:30-9:30 PM
⊲ SC1:
Systems Biology, Evidence Synthesis and in silico Discovery
Approaches to microRNA Biomarkers
Instructors:
Christos Argyropoulos, M.D., Ph.D., Assistant Professor, Nephrology,
Department of Internal Medicine, University of New Mexico School of
Medicine
John Chevillet, Ph.D., Postdoctoral Research Fellow, Laboratory of Leroy
Hood, Institute for Systems Biology
There currently exists no standard systematic way to identify candidate
microRNAs for experimental evaluation and verification of their utility as
disease biomarkers. In this course we will present a putative framework for
the identification of candidate circulating microRNA biomarkers, based on in
silico, systems biology and quantitative evidence synthesis techniques. We
will discuss the implementation of circulating miRNA studies and examine
relevant workflows, specimen collection and handling, quantification and
data analysis techniques.
⊲ SC2:
Executive ThinkTank: Development of Exosome-Based
Diagnostics
As the demand for more cost-effective treatments increases and the benefit
of personalized medicine is clear, the goal of developing accurate, non-
invasive diagnostics becomes ever more urgent. Exosomes are especially
useful for clinical diagnostics because of their tissue specificity and stability
in biofluids, yet issues still remain in their development as diagnostics.
What are the optimal methods for isolation and purification? What assays
should be used to quantitate exosomal biomarkers? How should exosomal
biomarkers be normalized? What theoretical and logistical challenges are
bottlenecks for exosomal biomarker development and qualification? These
topics and others will be explored in this moderated panel discussion.
Moderator:
Peter Yuen, Ph.D., Staff Scientist, Renal Diagnostics & Therapeutics Unit,
National Institute of Diabetes and Digestive and Kidney Diseases, National
Institutes of Health
Panelists:
• Clark C. Chen, M.D., Ph.D., Associate Professor and Chief, Stereotactic
and Radiosurgery; Vice-Chairman, Academic Affairs, Neurosurgery,
University of California, San Diego
• Hakho Lee, Ph.D., Assistant Professor, Center for Systems Biology,
Massachusetts General Hospital, Harvard Medical School
• Radha Munagala, Ph.D., Assistant Professor, Department of Medicine,
James Graham Brown Cancer Center, University of Louisville
• Qiang Shi, Ph.D., Visiting Scientist, Division of Systems Biology,
National Center for Toxicological Research, U.S. Food and Drug
Administration
• David T.W. Wong, D.M.D., DMSc, Professor and Associate Dean of
Research, UCLA School of Dentistry; Director, Dental Research Institute
TUESDAY, MARCH 17, 6:00-9:00 PM
⊲ SC3:
RNA-Seq: A Fundamental Guide to the Field
Instructor:
Seth Crosby, M.D., Director, Partnerships & Alliances, Washington
University School of Medicine
A practical introduction for those considering the RNA-seq journey, and
what’s new for those who have already set off.
Whether or not you are new to the field, this all-encompassing workshop
will give detailed insight, in an interactive format, across the entire RNA-Seq
landscape. RNA sources and preparation, the myriad library construction
options, sequencing: to pair or not to pair, and the world of analysis, from the
Tuxedo suite to STAR and beyond – all will be covered and discussed in this
complete learning experience.
Leave this workshop with:
• A comprehensive understanding of the RNA-Seq landscape
• Further development of the questions to ask when considering
RNA-Seq
• A review of the bench and informatic technologies that are right for
your specific research needs
⊲ SC4:
Circulating Nucleic Acid Biomarkers for Development of
Non-Invasive Prenatal Tests
Instructor:
Louise C. Laurent, M.D., Ph.D., Assistant Professor, Department of
Reproductive Medicine, University of California San Diego Health Science
This course will review both currently available technologies and potential
future approaches based on non-invasive analysis of circulating fetal nucleic
acids (CNAs) in the maternal blood for detection of pregnancies affected by
fetal genetic abnormalities and prediction of adverse pregnancy outcomes,
such as preterm birth and pre-eclampsia. The majority of these tests use
next-gen sequencing for quantitative evaluation of specific sequences in
circulating fetal DNA or RNA (notably, RNA-based strategies are all still in
the research and development stage). Technical considerations in assay
development for C-based prenatal testing applications will also be covered.
*Separate registration required

microRNA as Biomarkers and Diagnostics
E L E V E N T H A N N U A L
MONDAY, MARCH 16
7:00 am Conference Registration and Morning Coffee
8:00 Welcome Remarks from Conference Director
Exosomal RNA/DNA in Cancer
8:10 Chairperson’s Opening Remarks
Janusz Rak, M.D., Ph.D., McGill University, Montreal Children’s Hospital
8:15The Biology and Functional Contribution of Exosomes in Cancer
Progression and Metastasis
Raghu Kalluri, M.D., Ph.D., Professor and Chair, Cancer Biology, University of
Texas MD Anderson Cancer Center
8:40 Exosomic microRNAs Affect the Biology of theTumor
Microenvironment
Muller Fabbri, M.D., Ph.D., Assistant Professor, Pediatrics and Molecular
Microbiology & Immunology, University of Southern California Keck School of
Medicine, Children’s Hospital Los Angeles
microRNAs (miRNAs) are small non-coding RNAs which regulate the expression
of about 30% of genes. miRNAs are secreted by cancer cells within exosomes,
nanovesicles able to transfer intercellularly their content of DNA, RNA and
proteins. We and others showed that specific exosomic miRNAs released by
cancer cells can bind to receptors in surrounding cells and affect the biology of
the tumor microenvironment. This lecture will highlight how interfering with this
exosomic-miRNA-mediated cross-talk might lead to new anti-cancer treatments.
9:05 Exosomal microRNAs in Urine - Promising
Biomarkers for Prostate Cancer
Sponsored by
Peter Mouritzen, Vice President Research and Development,
Exiqon A/S
We have developed a highly sensitive LNA™-based qPCR platform for microRNA
detection, which enables profiling in biofluids where microRNA levels are
extremely low. The qPCR system has been applied to identify promising
diagnostic prostate cancer biomarkers in exosomes from urine purified with
our recently developed exosome enrichment kit. In general, sample and
data qualification is critical in biofluids to secure high quality data, which we
will demonstrate.
9:20 Networking Coffee Break
microRNA Biomarkers in Drug Development
9:50 Chairperson’s Remarks
Pavan Kumar, Ph.D., Senior Scientist, Biomarkers and Personalized Medicine, Eisai
9:55 Identification of Urinary microRNA Biomarkers of Glomerular Injury
Rounak Nassirpour, Ph.D., Principal Scientist, Investigative Pathology Laboratory,
Drug Safety R&D, Pfizer
Recent studies have reported significant levels of microRNAs in a variety of body
fluids, raising the possibility that microRNAs could serve as useful biomarkers.
Here we describe urinary microRNA expression alterations in preclinical models
of kidney injury. We describe microRNA changes in both the isolated glomeruli as
well as the urine specimen from these established models of glomerular injury.
The microRNAs identified may be promising preclinical urinary biomarkers for
drug-induced glomerular injury.
10:20 MiRNAs as Circulating Biomarkers for Neurodegenerative
Disorders
Pavan Kumar, Ph.D., Senior Scientist, Biomarkers and Personalized Medicine, Eisai
A non-invasive and quantitative assay for early detection of Alzheimer’s disease
(AD) is required to aid patient selection in clinical trials, monitor disease
progression and early response to treatment, and to better plan patient clinical
care. microRNAs have immense potential as biomarkers for clinical use because
of their stability and ease of detection in most tissues, especially blood. Data
will be presented on follow-up studies to our original 7-miRNA signature for AD
diagnostics, including current activity in circulating miRNAs in the AD space.
10:45 MicroRNAs as Biomarkers in Clinical Fluids
Martin Beaulieu, Ph.D., Director, MicroMarkers™, Regulus Therapeutics
microRNAs (miRs) are regulatory factors that function to repress the transcription
of mRNA. Because each miR contains a seed sequence that is complementary
to the UTR region of up to ~50 mRNA, the biological impact from the modulation
of just a single miR can be significant. Expression profiles are deregulated in
cells undergoing pathophysiologic stress suggesting potential as markers of
disease states. miRs are ubiquitous and highly stable in the circulation due to
the fact that they are short (~22 nt), protein bound and often travel encapsulated
in microvesicles. Based on these favorable characteristics as biomarkers, we
developed a miR profiling platform to discover new therapy response (predictive)
and prognostic markers. Under the Regulus MicroMarkers™ division, Regulus
has conducted large-scale profiling studies and has profiled over 3,000 clinical
samples to date and has identified potential miR biomarkers for a variety of
disease conditions. Recent results and new biological insights are planned to
be presented.
11:10 MiRNAs as Biomarkers for Cancer Development and Drug
Resistance
Bing-Hua Jiang, Ph.D., Professor, Pathology, Anatomy and Cell Biology, Thomas
Jefferson University
Our recent study demonstrates that a number of microRNAs (miRNAs) are
downregulated in several kinds of human cancers including ovarian, breast, lung,
colon and glioma; and that levels of miRNA suppression are associated with
cancer development and drug resistance, and are involved in regulating tumor
growth and angiogenesis. To understand the mechanism, we found that some
miRNAs are inhibited by DNA methylation, while some miRNAs are inhibited by
higher levels of reactive oxygen species (ROS) production in cancer cells.
11:35 Universal ScreeningTest Based on Analysis of Circulating Organ-
Enriched microRNAs
Kira Sheinerman, Ph.D., CEO, DiamiR Biosciences Corp.
Early detection is critical for effective treatment of neurodegenerative diseases,
cancer and other pathologies, where disease progression frequently leads to
irreversible changes in underlying pathophysiological processes. DiamiR has
developed a novel framework for early detection of pathology in a particular
organ system, organ or tissue based on analysis of circulating organ-enriched
microRNAs, the Universal Screening Test (UST). Data on detection of pathologies
in three organ systems - gastrointestinal, pulmonary, and neurological - will be
presented. UST applications and ongoing and future studies will be discussed.
12:05 pm Luncheon Presentation: Identification
and Validation of microRNA Biomarkers on the
nCounter® Platform
Sponsored by
Lucas Dennis, Ph.D., Senior Scientist, NanoString Technologies
MicroRNAs are implicated in the regulation of many biological processes and
recent work has focused on investigating the promise of miRNA expression
signatures as prognostic indicators of disease states. nCounter miRNA
Expression assays enable users to rapidly, efficiently, and simultaneously profile
>800 highly curated human miRNAs on the nCounter platform. These assays
are compatible with total RNA isolated from any source. This unique targeted
discovery and validation tool enables collection of expression data quickly
with minimal handling, making it an ideal solution for both targeted biomarker
discovery and validation.
microRNAs in Personalized Medicine
Ajay Goel, Ph.D., Baylor Research Institute
1:35 Presentation to be Announced
2:00 Circulating miRNAs in Autoimmune Disorders – Opportunities as
Biomarkers for Patient Stratification and Challenges
Hungyun Lin, Ph.D., Principal Scientist, Drug Safety R&D, Pfizer
Unique miRNA expressions have been described in the intestinal epithelial cells
and in the peripheral blood of Crohn’s disease (CD) patients. Selective miRNAs
with important roles in regulating key pathogenesis in CD inflammation were
assembled as an assay panel for screening of plasma from CD patients and
healthy volunteers. The profile of a number of circulating miRNAs is capable of
distinguishing CD patients from healthy volunteers. The results demonstrated the
potential utility of circulating miRNAs as biomarkers for CD detection.

MARCH 16-17
2:25 MiRNA Biomarkers for Colorectal Cancers
Ajay Goel, Ph.D., Director, Epigenetics and Cancer Prevention, Baylor Research
Institute
microRNAs (or miRNAs) are emerging as important regulators of gene expression
in cancer. Overexpression of specific miRNAs has been linked to the stepwise
disease progression during the normal-adenoma-cancer sequence in colorectal
cancer (CRC). Given their cancer-specific pattern of expression, remarkable
stability and presence in blood and other body fluids, miRNAs are considered to
be highly promising cancer biomarkers. Accumulating evidence firmly supports
the existence of unique ‘miRNA signatures’ that can not only facilitate earlier
detection of the tumor, but can also assist in predicting disease recurrence and
therapeutic outcome to current treatment regimens.
2:50 Sponsored Presentation (Opportunity Available)
3:05 Refreshment Break in the Exhibit Hall with Poster Viewing
microRNA in Disease Diagnostics
David Henshall, Ph.D., Royal College of Surgeons in Ireland
3:45 Circulating miRNA Markers for Disease Diagnosis
Xuemei Zhao, Ph.D., Principal Scientist, Molecular Biomarkers and Diagnostics
Laboratory, Merck
This presentation will cover: 1) circulating miRNAs hold great promise as disease
diagnosis markers, and 2) a multiplexed RT-qPCR platform is utilized to identify a
miRNA classifier for disease diagnosis.
4:10 MicroRNA Biofluid Profiles as Diagnostic Biomarkers in Epilepsy
David Henshall, Ph.D., Professor, Physiology & Medical Physics, Royal College of
Surgeons in Ireland, Dublin, Ireland
Epilepsy is a common, serious neurological disorder characterized by recurring
seizures that may result from often subtle brain injuries. There is a major unmet
need for a molecular biomarker of epilepsy to assist prognosis, diagnosis and
treatment decisions. Emerging data show brain-specific microRNAs exert potent
effects on seizures but whether these molecules are suitable biomarkers is
uncertain. Data will be presented from microRNA profiling of biofluids from
epilepsy patients and experimental models which support the potential of
microRNAs as diagnostic biomarkers in epilepsy.
4:35 Circulating microRNAs Show Promising Clinical Implications for
Type 2 Diabetes
Elena Flowers, Ph.D., Assistant Professor, Physiological Nursing, University of
California, San Francisco
Type 2 diabetes is a pervasive public health problem that affects nearly 10% of
the US population and is associated with increased mortality and healthcare
costs. There is strong evidence that circulating microRNAs are prodromal
biomarkers for risk for type 2 diabetes. Further, circulating microRNAs may be
useful for predicting individual response to risk reduction interventions. Given
these observations, microRNAs have the potential to meaningfully improve
prevention, detection, and treatment of the type 2 diabetes epidemic.
5:15 Welcome Reception in the Exhibit Hall with Poster Viewing
6:15 Short Course Registration
Recommended Dinner Short Course*
6:30-9:30 (SC1) Systems Biology, Evidence Synthesis and in silico
Discovery Approaches to microRNA Biomarkers
*Separate registration required. See page 3 for details.
TUESDAY, MARCH 17
7:30 am Breakfast Roundtable Discussions
Roundtable discussions are interactive, topic-specific discussions hosted by
expert moderators and open to all attendees. These sessions provide a forum for
discussing key issues:
• Topic 1: microRNA Normalization Strategy
Moderator: Christos Argyropoulos, M.D., Ph.D., University of New
Mexico School of Medicine
• Topic 2: Quantitation Issues
Moderator: John Chevillet, Ph.D., Institute for Systems Biology
• Topic 3: Biomarker Biology: Delineating between Biomarkers that
are the Drivers vs. Passengers in Disease Initiation, Progression
and Maintenance
Moderator: Andrea Kasinski, Ph.D., Purdue University
microRNA as Predictive Cancer Biomarkers
Subrata Sen, Ph.D., University of Texas MD Anderson Cancer Center
8:20TalkTitle to be Announced
Frank J. Slack, Ph.D., Director, Institute for RNA Medicine, Beth Israel Deaconess
Medical Center, Harvard Medical School
8:45Tumor-Associated Circulating microRNAs as Biomarkers of
Pancreatic Cancer
Subrata Sen, Ph.D., Professor and Deputy Chair, Translational Molecular Pathology,
University of Texas MD Anderson Cancer Center
Pancreatic cancer remains the fourth leading cause of cancer related death in
the United States. Aberrantly expressing microRNAs (miRs) associated with
deregulated genetic pathways contributing to the development of transformed
cellular phenotypes have been reported in various human malignancies including
pancreatic cancer. Varying levels of these aberrantly expressing tumor associated
miRs have been detected in blood and body fluids of cancer patients. Our results
indicate that tumor specific miRNA profiles in blood and body fluids can be
developed as biomarkers of disease detection, prognosis and response to therapy
for patients with pancreatic cancer.
9:10 MiRNAs as Predictors of Recurrence and Death in Melanoma
Iman Osman, M.D., Associate Director, NYU Cancer Institute & Professor,
Oncology, and Director, NYU Interdisciplinary Melanoma Coop Group, New York
University Langone Medical Center
Identification of melanoma patients at the highest risk of recurrence remains a
critical challenge. We recently reported our array-based discovery of prognostic
serum miRNAs in melanoma. In this study, we show that 4 miRNAs (miR-
150,30d, 15b, and 425) in combination with stage separated patients by
recurrence-free survival and overall survival and improved prediction of recurrence
over stage alone in both the training and validation cohorts (training RFS and OS,
P < .001; validation RFS, P < .001; OS, P = .005). Our data demonstrate that serum
miRNAs can improve melanoma patient stratification.
9:35 MicroRNAs that Control the PI3K Survival Pathway
Andrei Thomas-Tikhonenko, Ph.D., Professor, Pathology and Laboratory Medicine,
University of Pennsylvania
The PI3K pathway plays a major role in both intrinsic cancer cell survival and its
responses to chemotherapy. Members of this pathway are frequently affected
by oncogenic mutations, PIK3CA and PTEN being prime examples. However,
what controls this pathway in PIK3CA/PTEN non-mutated tumors is incompletely
understood. Evidence will be presented that several microRNAs are major
regulators of the PI3K pathway and that this regulation could be affected by
single-nucleotide polymorphisms in the 3’ untranslated regions, making them
potential biomarkers.
10:00 Coffee Break in the Exhibit Hall with Poster Viewing
microRNAs in Cancer Pathways
David S. Hong, M.D., University of Texas MD Anderson Cancer Center

MARCH 16-17
10:45 Epigenetic Regulation of miRNAs in a HumanT Cell Leukemia
Sundararajan Jayaraman, Ph.D., Clinical Associate Professor, Surgery, University
of Illinois at Chicago
The epigenetic regulation of non-protein coding miRNAs was determined in a T
cell leukemia cell line, Jurkat following treatment with the histone deacetylase
inhibitor, Trichostatin A (TSA). Global expression profiling of miRNAs revealed
that in contrast to other tumors, TSA-mediated apoptosis in Jurkat cells was
accompanied by an enhanced level of miR-494. Consistently, siRNA mediated
silencing of miR-494 failed to block TSA-induced apoptosis. However, miR-494
knockout relieved TSA-mediated suppression of histone H2BE and poliovirus
receptor related immunoglobulin domain containing gene (PVRIG), without
affecting the level of non-protein coding nuclear paraspeckle assembly transcript
(NEAT-1). These data provide significant insights into the role of miRNAs in T cell
leukemias and identify novel targets for leukemia treatment.
11:25 A Combinatorial microRNATherapeutics Approach to Eradicating
Non-Small Cell Lung Cancer
Andrea Kasinski, Ph.D., Assistant Professor, Biological Sciences, Purdue
University
Studies which have been instrumental in transitioning miRNA therapeutics into a
clinical setting will be described including the successful attempts at treating the
aggressive Kras;p53 NSCLC mouse tumor model. In this model we demonstrate
the combined efficacy of two tumor-suppressive miRNAs, miR-34 and let-7.
Half the dose of both miRNAs suppresses tumor growth leading to a survival
advantage, without obvious toxicity. Clinical utility is reinforced through the use of
a delivery vehicle already in clinical practice. This combinatorial miRNA therapeutic
approach strikes numerous components of tumor-cell addictive pathways and
highlights the ability to deliver multiple miRNAs in a safe and effective manner to
the target lung tissue.
11:50 MicroRNA asTherapy – MRX34, a First-in-Human, First-in-Class
microRNATherapy in Advanced Cancer and Heme Malignancies
David S. Hong, M.D., Associate Professor and Chair, Investigational Cancer
Therapeutics, University of Texas MD Anderson Cancer Center
MRX34 is a liposome-formulated double-stranded mimic of the tumor suppressor
microRNA-34 (miR-34). miR-34 functions in the p53 tumor suppressor pathway
and regulates the expression of more than 20 cancer-related genes including
BCL2, E2F3, HDAC1, MET, MEK1, CDK4/6, PDGFR-α, SIRT1, WNT1/3, NOTCH-1,
β-catenin, CD44, Nanog and AXL. miR-34 also suppresses stem-like properties
in cancer cells. Safety and preliminary efficacy data from 50 patients with
hematologic malignancy or solid tumor enrolled in a Phase I clinical trial of MRX34
will be presented.
12:15 pm Close of Conference
Current Peer Research Posters
Present a Poster & Save!
Cambridge Healthtech Institute encourages
attendees to gain further exposure by showcasing
their current research in our dedicated
poster sessions.
• Present your work to the leading pharmaceutical
and academic researchers and scientists
• Gain exposure through the inclusion of your
research abstract in conference materials
• Receive $50 off your registration fee
To secure a poster board and inclusion in the
conference materials, your abstract must be
submitted, approved and your registration paid in full
by February 13, 2015.

Exosomes and Microvesicles as Biomarkers and Diagnostics
S E C O N D A N N U A L
MONDAY, MARCH 16
7:00 am Conference Registration and Morning Coffee
8:00 Welcome Remarks from Conference Director
Exosomal RNA/DNA in Cancer
Janusz Rak, M.D., Ph.D., Jack Cole Chair in Pediatric Hematology/Oncology
Professor of Pediatrics, McGill University, Montreal Children’s Hospital, RI MUHC
8:15The Biology and Functional Contribution of Exosomes in Cancer
Progression and Metastasis
Raghu Kalluri, M.D., Ph.D., Professor and Chair, Cancer Biology, University of
Texas MD Anderson Cancer Center
8:40 Exosomic microRNAs Affect the Biology of theTumor
Microenvironment
Muller Fabbri, M.D., Ph.D., Assistant Professor, Pediatrics and Molecular
Microbiology & Immunology, University of Southern California Keck School of
Medicine, Children’s Hospital Los Angeles
microRNAs (miRNAs) are small non-coding RNAs which regulate the expression
of about 30% of genes. miRNAs are secreted by cancer cells within exosomes,
nanovesicles able to transfer intercellularly their content of DNA, RNA and
proteins. We and others showed that specific exosomic miRNAs released by
cancer cells can bind to receptors in surrounding cells and affect the biology of
the tumor microenvironment. This lecture will highlight how interfering with this
exosomic-miRNA-mediated cross-talk might lead to new anti-cancer treatments.
9:20 Networking Coffee Break
Exosome Profiling for Nucleic Acid and
Protein Biomarkers
9:55 Oncogenic Cargo of Extracellular Vesicles – From DNA to Active
Protein
Janusz Rak, M.D., Ph.D., Jack Cole Chair in Pediatric Hematology/Oncology
Professor of Pediatrics, McGill University, Montreal Children’s Hospital, RI MUHC
Cancer cells shed extracellular vesicles (EVs) containing qualitatively altered,
mutant molecular cargo. In this regard driver mutations are of special interest,
as they possess a causative role in disease, exert transformation-like biological
effects and reflect the genetic evolution of the underlying malignancy in real
time. Oncogenic EV emission includes double-stranded DNA, transcripts and
oncoproteins, while changes in the genome, transcriptome, proteome and
phosphoproteome of EVs circulating in biofluids may reflect cancer progression
and the effects of targeted anticancer agents.
10:20 Large-Scale Glycan and Lipid Profiling of Blood Exosomes from
Human Cancers
Richard R. Drake, Ph.D., Professor and Director, Pharmacology, Medical University
of South Carolina Proteomics Center
Several thousand serum and plasma samples from donors with colon and
other cancers were used for rapid, bulk exosome/microvesicle precipitation by
a commercial kit. The pellets were extracted in organic solvents to obtain lipid/
glycolipid fractions or digested with peptide N-glycosidase to release N-linked
glycans. Lipids and glycans were profiled on a high resolution 7T FTICR-MALDI
mass spectrometer, generating hundreds of analyte signals per sample. Panels
and individual species were assessed for their ability to stratify cancer from
non-cancer samples.
10:45 Waste and/or Communication? Dissection of Subpopulations
of Extracellular Microvesicles Deriving from Different Intracellular
Pathways
Nicole Meisner-Kober, Ph.D., Senior Investigator, RNA Biology, Developmental and
Molecular Pathways, Novartis Institutes for Biomedical Research
After their initial discovery in the early 1980s, exosomes had been primarily
assigned a role in cellular waste disposal. Today it is well established that
exosomes play an important role in cell-to-cell communication, both by direct
contact as well as functional transfer of protein and RNA cargo. Here we report
the dissection of different subpopulations of extracellular vesicles using single
molecule spectroscopy and imaging, and reveal that exosome samples comprise
vesicle subpopulations originating from different intracellular biogenesis pathways,
with differential surface markers, cargo and function specialized to either waste
disposal or cellular communication, thereby reconciling these apparently opposing
functions assigned to exosomes.
11:10 Redefining the Exosomal Proteome
Austin Yang, Ph.D., Associate Professor, Anatomy and Neurobiology, University of
Maryland
We will present an integrated mass spectrometry and bioinformatics pipeline
to unbiasedly define the “exosomal” proteome. By using various stable isotope
quantitative proteomic approaches, we have carefully analyzed exosomal
proteomes isolated from various sources and established a robust computational
model to increase the sub-cellular resolution of exosomal proteomes. In particular,
we will discuss our open source software package, IsoQuant, which provides a
user friendly user interface to analyze exosomal proteomic datasets generated by
various shotgun proteomic analyses.
11:35 D- and L-MARCKS-ED as Novel Exosome Probes
Hang Hubert Yin, Ph.D., Associate Professor, Chemistry & Biochemistry and the
BioFrontiers Institute, University of Colorado Boulder
Curved membranes are a common and important attribute in exosomes and
microvesicles. Our interest focuses on identifying and designing peptides that can
sense membrane curvature based on established elements observed in natural
curvature-sensing proteins. We have successfully identified a 25-mer peptide,
MARCKS-ED, as well as its D-isomer that can both recognize PS with preferences
for highly curved vesicles in a specific manner. These studies provide coveted
specific probes for exosomes and microvesicles that may be of diagnostic and
prognostic potential.
12:00 pm Luncheon Presentation (Sponsorship Opportunity Available) or
Lunch onYour Own
Potential of Exosomes as Biomarkers and Diagnostics
David T.W. Wong, D.M.D., DMSc, Professor and Associate Dean of Research,
UCLA School of Dentistry; Director, Dental Research Institute
1:35 Salivary Exosome and Extracellular RNA: Biology andTranslational
Utilities
David T.W. Wong, D.M.D., DMSc, Professor and Associate Dean of Research,
UCLA School of Dentistry; Director, Dental Research Institute
Using RNA-Seq, we have generated a comprehensive landscape of non-coding
RNA (ncRNA) in human saliva. In a comparative analysis of >90 RNA-Seq data of
different origins, we observed that piRNAs were surprisingly abundant in saliva
compared to other bodily fluid or intracellular samples, which, nonetheless,
resembled the level of piRNAs in embryonic stem cells and skin cells. In addition,
to the best of our knowledge, we present the first global characterization and
experimental validation of circRNAs in any type of extracellular bodily fluid.
2:00 Validation and Characterization of Endothelial Microvesicles in
Sprague Dawley Rats
Sharon Sokolowski, Ph.D. Principal Scientist, Pfizer Global Research &
Development
Microvesicles (0.5 – 1μM) in the peripheral blood of Sprague Dawley rats have
been evaluated as potential biomarkers of vascular toxicity. Validation steps were
completed to more fully characterize and understand the changes observed in
peripheral blood microvesicle absolute counts in normal, dosed, and diseased
animals. Taking into consideration the advantages and caveats of microvesicle
evaluation, application of microvesicles as safety and efficacy biomarkers during
drug development was explored.
2:25 Circulating Extracellular Vesicles as Possible New Biomarkers for
Drug-Induced Liver Injury
Qiang Shi, Ph.D., Visiting Scientist, Division of Systems Biology, National Center
for Toxicological Research, U.S. Food and Drug Administration
Drug induced liver injury (DILI) is the leading cause for acute liver injury, and a
major reason for approved drugs being withdrawn from the market. Currently
used DILI biomarkers lack organ specificity. Circulating extracellular vesicles (EVs)
are being vigorously explored as a potential source of novel DILI biomarkers. EVs
from both the blood and urine have been found to contain mRNAs, microRNAs
or proteins that not only reflected liver injury per se, but also were indicative of
DILI etiology.

MARCH 16-17
3:45 Non-Invasive Intracellular Kidney Biopsies:The Promise of Urine
Exosomal Biomarkers
Peter Yuen, Ph.D., Staff Scientist, Renal Diagnostics & Therapeutics Unit, National
Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of
Health
Proximal fluid biomarkers can add organ specificity to circulating biomarkers.
Exosomes, although a minor subfraction of urine, provide unique insights into
kidney function because their biogenesis preserves cytoplasmic and plasma
membrane information content from all epithelial cells along the nephron. Two
types of exosomal biomarkers have emerged: a) functional markers (channels,
transporters, and mRNA) that reflect the current functional state of the kidney,
and b) decision-making molecules (transcription factors and miRNA) that predict
the future status of kidney epithelial cells.
4:10 Extracellular Vesicles (EVs) as a Molecular Diagnostic Platform
Clark C. Chen, M.D., Ph.D., Associate Professor and Chief, Stereotactic and
Radiosurgery; Vice-Chairman, Academic Affairs, Neurosurgery, University of
California, San Diego
Extracellular vesicles (EVs) are cell-secreted vesicles that range 30-2,000
nm in size. These vesicles are secreted by both normal and neoplastic
cells. Physiologically, EVs serve multiple critical biologic functions, including
cellular remodeling, intracellular communication, modulation of the tumor
microenvironment, and regulation of immune function. Because EVs contain
genetic and proteomic contents that reflect the cell of origin, it is possible to
detect tumor-specific material in EVs secreted by cancer cells. Importantly,
EVs secreted by cancer cells transgress anatomic compartments and can be
detected in the blood, cerebrospinal fluid, and other bio-fluids of cancer patients.
In this context, there is a growing interest in analyzing EVs from the bio-fluid of
cancer patients as a means of disease diagnosis and therapeutic monitoring.
This talk will focus on the development of EVs as a diagnostic platform for the
most common form of brain cancer, glioblastoma, and discuss potential clinical
translational opportunities.
4:35 Point-of-Care DiagnosticTechnologies for Exosomal Analysis
Hakho Lee, Ph.D., Assistant Professor, Center for Systems Biology,
Massachusetts General Hospital, Harvard Medical School
This presentation will review the portable platforms that we have developed
for exosome analysis. These include 1) in-flow filtration devices to enrich
exosomes directly from biological fluids; 2) a nano-plasmonic chip to profile
exosomal protein; and 3) microfluidic systems for on-chip RNA detection. Clinical
applications of the developed platforms will also be discussed.
5:15 Welcome Reception in the Exhibit Hall with Poster Viewing
6:30-9:30 (SC2) ExecutiveThinkTank: Development of Exosome-
Based Diagnostics
TUESDAY, MARCH 17
7:30 am Breakfast Presentation (Sponsorship Opportunity Available) or
Morning Coffee
Role of Exosomes in Cancer Mechanism and
Cancer Biomarkers
Theresa Whiteside, Ph.D., M.D.H.C., Professor, Pathology, Immunology &
Otolaryngology, University of Pittsburgh Cancer Institute
8:20Tumor-Derived Exosomes (TEX) as Biomarkers of Human Immune
Cell Dysfunction andTumor Progression
Theresa Whiteside, Ph.D., M.D.H.C., Professor, Pathology, Immunology &
Otolaryngology, University of Pittsburgh Cancer Institute
Dysfunction of immune effector cells is common in human cancers and is linked
to poor outcome. The magnitude and mechanisms responsible for dysfunction
are tumor-growth dependent. TEX carry a molecular cargo that down-regulates
anti-tumor activities of immune cells. Elevated plasma levels of TEX and their
molecular/genetic profile serve as surrogate indicators of immune cell dysfunction
and thus as prognostic non-invasive biomarkers in cancer.
8:45Tumor Extracellular Vesicle-Induced Signaling in Recipient Cells: It’s
All About theTumor
Michael Graner, Ph.D., Associate Professor, Neurosurgery, University of Colorado
School of Medicine
Extracellular vesicles (EVs) are virus-sized membrane-enclosed particles released
from cells into the extracellular milieu. EVs are compact information packets
containing proteins, lipids, nucleic acid species, and other metabolites reflecting
their cell of origin, but can also have dramatic impacts on cells that interact with
EVs. We determined altered signaling pathways in recipient cells (tumor and
“normal” cells) upon encounter with glioma EVs. Generally, tumor signaling
pathways trend towards aggression, while pathways in other cells result in
entities that also benefit the tumor.
9:10 Circulatory Exosomal Cargo as Biomarkers of Recurrent Lung
Tumors
Radha Munagala, Ph.D., Assistant Professor, Department of Medicine, James
Graham Brown Cancer Center, University of Louisville
Poor outcomes and relapse in non-small cell lung cancer patients indicate the
need for new screening and biomarkers for early detection. We examined
circulatory serum exosomes from primary and recurrent lung tumor-bearing mice
and noted distinct exosomal protein markers and miRNA profile. In addition,
unique recurrence associated miRNAs were observed in exosomes from
recurrent compared to primary tumor mice. The data suggest that the circulatory
exosomes can be a true representation of tumor-profile and have significant
biomarker potential.
9:35 Exosomes as Mediators of JAK/Stat Activation-Regulation of
Metastasis
Jacqueline Bromberg, M.D., Ph.D., Physician-Scientist, Breast Cancer, Memorial
Sloan-Kettering Cancer Center
Tumors constitutively release membrane-derived nano-vesicles or exosomes
(TDExo) that are readily detected in body fluids and have been found to play
important roles in signaling, immunomodulation and metastasis. In examining the
molecular mediators of the cross-talk between tumor exosomes and the host,
our preliminary and published work identifies the pro-inflammatory cytokine IL6/
JAK/Stat3 axis not only in local tumor:stoma cross-talk but also as a critical and
targetable contributor to the metastatic inductive properties of TDExos.
Exosomes as Disease Biomarkers
10:45 LRRK2 and Other Novel Exosome Proteins in Parkinson’s Disease
Andrew West, Ph.D., John A. and Ruth R. Jurenko Professor of Neurology;
Associate Professor, Neurology and Neurobiology; Co-Director, Center for
Neurodegeneration and Experimental Therapeutics, The University of Alabama at
Birmingham
11:10 Novel Role of Microvesicles in Cardiovascular and Autoimmune
Diseases
Ming-Lin Liu, M.D., Ph.D., Research Assistant Professor, Dermatology, Perelman
School of Medicine, University of Pennsylvania
Microvesicles are small membrane vesicles released from different cell types
in various human diseases. Microvesicles have been detected in the circulation
and in human tissues. These microvesicles may carry bioactive molecules
including lipids, proteins or nucleic acids, and contribute to the development of
cardiovascular disease and autoimmune inflammation. The changes in number
and composition of microvesicles may reflect the pathophysiological conditions
of human diseases. Therefore, detection of microvesicles may serve as potential
biomarkers for diagnostic and prognostic use.
11:35 Extracellular Vesicles in Pulmonary Vascular Disease – Friend or
Foe?
Jason Aliotta, M.D., Assistant Professor, Medicine, Warren Alpert Medical School,
Brown University
Pulmonary arterial hypertension is a disease that is characterized by pulmonary
vascular remodeling resulting in right ventricular failure and death. We have found
that extracellular vesicles (EVs) isolated from mice with monocrotaline-induced
pulmonary hypertension induce features of this disease when injected into
normal mice. In addition, EVs isolated from mesenchymal stem cells can reverse
this disease phenotype. Our hope is that these studies may someday aid in the
development of new strategies to treat this lethal disease.
12:00 pm Close of Conference

Long Non-Coding RNA in Cancer
I N A U G U R A L
TUESDAY, MARCH 17
12:00 pm Conference Registration
Long ncRNA as Cancer Biomarkers
Jingfang Ju, Ph.D., Associate Professor and Co-Director, Translational Research,
Pathology, Stony Brook University
1:35 Non-Coding RNAs in Cancer
Carlo M. Croce, M.D., Distinguished University Professor, The John W. Wolfe Chair
in Human Cancer Genetics, Director, Genetics Institute, The Ohio State University
2:00 Clinical Significance of Long Intergenic Non-Coding RNA-p21 in
Colorectal Cancer
Jingfang Ju, Ph.D., Associate Professor and Co-Director, Translational Research,
Pathology, Stony Brook University
Tumor suppressor p53 regulates a number of non-coding RNAs. We quantified the
expression of lincRNA-p21 in colorectal cancer patients. The expression level of
lincRNA-p21 was significantly lower in CRC tumor tissue. Rectum tumors showed
a higher level of lincRNA-p21 than tumors in the colon. In addition, lincRNA-p21
was significantly higher in stage III than stage I tumors. Elevated levels of
lincRNA-p21 were significantly associated with vascular invasion. These results
suggest that lincRNA-p21 may contribute to CRC disease progression.
2:25 PCAT18 as a Novel Biomarker andTherapeuticTarget in Prostate
Cancer
Cheryl Helgason, Ph.D., Senior Scientist, Experimental Therapeutics, BC Cancer
Research Center
We utilized RNA sequencing to identify lncRNAs differentially expressed in
metastatic prostate cancer (PCa), an incurable disease. PCAT18, the most
highly up-regulated transcript, is prostate and PCa specific. It is detectable in
plasma and able to discriminate localized versus metastatic PCa. Functional
studies demonstrate a specific role in blocking PCa cell proliferation, invasion
and migration. These results position PCAT18 as a potential therapeutic target
and biomarker for metastatic PCa. Additional studies have identified a potential
oncosuppressive lncRNA with prognostic significance.
Role of lncRNA in Cancer Progression
Richard I. Gregory, Ph.D., Associate Professor, Biological Chemistry and Molecular
Pharmacology, Children’s Hospital Boston, Harvard Stem Cell Institute (HSCI),
Harvard Medical School
4:15Targeting lncRNA in Ovarian Cancer
Anil K. Sood, M.D., Professor and Vice Chairman, Gynecologic Oncology and
Reproductive Medicine, University of Texas MD Anderson Cancer Center
4:40 Role of Long Non-Coding RNAs in microRNA Regulation and
Cancer
Richard I. Gregory, Ph.D., Associate Professor, Biological Chemistry and Molecular
Pharmacology, Children’s Hospital Boston, Harvard Stem Cell Institute (HSCI),
Harvard Medical School
It is emerging that long non-coding RNAs (lncRNAs) can have important roles
in gene regulation. Dysregulation of these pathways is associated with cancer.
We are investigating the role of lncRNAs in stem cell biology and cancer with a
particular focus on how lncRNAs impact microRNA expression and function. Our
most recent progress in this area will be presented.
5:05 A lincRNA Locus Associated with Metastatic Melanoma
Laurent Lessard, Ph.D., Assistant Professor, Molecular Oncology, John Wayne
Cancer Institute
In a search for novel melanoma-associated lincRNA genes, we identified the
CASC15 locus as a frequently gained and actively transcribed lincRNA domain
in melanoma tumors. This talk will describe the molecular characterization,
biomarker utility, and functional significance of CASC15 in metastatic
melanoma progression.
5:30 Close of Day
6:00-9:00 (SC3) RNA-Seq: A Fundamental Guide to the Field
WEDNESDAY, MARCH 18
Morning Coffee
Linking lncRNAs to Cancer
Myriam Gorospe, Ph.D., Senior Investigator, Laboratory of Genetics, National
Institute on Aging-Intramural Research Program, National Institutes of Health
8:05 Senescence LncRNPs
Myriam Gorospe, Ph.D., Senior Investigator, Laboratory of Genetics, National
Institute on Aging-Intramural Research Program, National Institutes of Health
Senescent cells accumulate in aging tissues, and their metabolic and gene
expression profiles are linked to many age-related pathologies including
cancer. I discuss our recent studies on the expression patterns and functions
of senescence-associated long noncoding RNAs (lncRNAs), focusing on three
lncRNAs differentially expressed with senescence: LincRNA-p21 (Mol Cell, 2012)
which suppresses translation of select mRNAs, HOTAIR (Nat Commun, 2013),
which promotes ubiquitin-mediated proteolysis of select proteins, and 7SL (Nuc
Acids Res, 2014) which suppresses p53 translation.
8:30 LncRNA PVT1 Augments MYC in Human Cancers
Anindya Bagchi, Ph.D., Assistant Professor, Masonic Cancer Center, University of
Minnesota
In cancers with 8q24 gain, a common mutation found in almost all human
cancers, MYC is co-gained with adjacent lncRNA PVT1. We recently showed
that PVT1 augments MYC in these cancers. In this lecture I will discuss the
possibility of exploiting lncRNA PVT1 as a surrogate target for MYC, an otherwise
undruggable cancer gene in human cancers.
8:55 Long Non-Coding RNA as Regulator of Aggressive Prostate Cancer
Dimple Chakravarty, Ph.D., Assistant Professor, Pathology, Weill Cornell Medical
College
LncRNAs comprise a heterogeneous group of non-coding transcripts (>200 nt)
that have emerged as key mediators of cellular homeostasis. Some lncRNAs like
NEAT1 have evolved to achieve functional specialization. Our ongoing studies
indicate that NEAT1 nucleates with cellular proteins to regulate fundamental like
transcription and DDR. NEAT1 functions as a driver of prostate cancer progression
and therapy resistance. Using a combination of next-generation sequencing and
biochemical methods our studies will explain the intricate molecular mechanisms
that link DDR to oncogenic modulation.
Functional Characterization of lncRNAs
Alexander Pertsemlidis, Ph.D., Associate Professor, Pediatrics and Cellular &
Structural Biology, University of Texas Health Science Center at San Antonio
10:35The Pivotal Role of the Oncofetal H19 lncRNA in Human Cancer
Abraham Hochberg, Ph.D., Professor, Biological Chemistry, Hebrew University of
Jerusalem; Co-Founder and CSO, BioCancell
Imad Matouk, Ph.D., Senior Researcher, Laboratory of Abraham Hochberg,
Hebrew University of Jerusalem
The imprinted H19 gene transcribes an onco-fetal lncRNA that is essential for
human tumor growth. H19 is highly expressed in embryogenesis and cancer and
serves as a precursor for miR-675. H19 is induced by hypoxic stress in a p53-
dependent manner. Furthermore, numerous EMT inducers also induced H19/miR-

MARCH 17-18
675 expression to enhance metastasis. H19 is involved in multi-drug resistance
and possesses both diagnostic and prognostic values. All of these highlight the
importance of developing DNA-based therapy centered on a lncRNA system. We
have successfully used regulatory elements of H19 for the treatment of bladder,
ovarian, and pancreatic cancers and liver metastases in clinical trials.
11:00 Antisense Oligonucleotides for Regulation of Long Non-Coding
RNA
Susan Freier, Ph.D., Vice President and Distinguished Research Fellow, Isis
Pharmaceuticals
Large scale evaluation of RNA expression continues to identify an increasing
number of long non-coding RNAs (lncRNA) expressed in mammalian systems.
Antisense oligonucleotides (ASO) provide a straightforward method for
determining function for these RNAs by specific ASO-mediated targeted
degradation of the lncRNA in vitro or in vivo. MALAT1 is a ubiquitous, highly
expressed, nuclear retained lncRNA with a demonstrated role in lung cancer
metastasis. ASO-mediated depletion of tumor MALAT1 levels has been shown to
prevent primary tumor metastasis after tumor implantation. The use of ASOs to
evaluate the roles of MALAT1 and other lncRNAs in vivo will be presented.
11:25 Using ncRNAs to Identify Cancer Cell Vulnerabilities
Alexander Pertsemlidis, Ph.D., Associate Professor, Pediatrics and Cellular &
Structural Biology, University of Texas Health Science Center at San Antonio
In an unbiased and comprehensive approach, we have combined a high-
throughput screening platform with libraries of inhibitors of short and long non-
coding RNAs. We use this platform to identify ncRNAs that reduce cell viability
in general, and those that specifically sensitize cells to microtubule-targeting
agents. Regulatory targets of candidate ncRNAs are identified and the response
of cancer cells to perturbations in candidate ncRNA levels are assessed through a
combination of in vitro, in silico and in vivo approaches.
11:50 Functional Characterization of Long Non-Coding RNAs in the p53
Tumor Suppressor Pathway
Nadya Dimitrova, Ph.D., Postdoctoral Fellow, Laboratory of Tyler Jacks, David
H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of
Technology
We are studying long non-coding RNAs (lncRNAs) that are directly regulated by
the transcription factor p53. Using the mouse as a model organism, we have
developed genetic tools to address the contribution of p53-regulated lncRNAs
to this important tumor suppressor pathway. Our findings indicate a key role for
lncRNAs in the transcriptional control of proteins downstream of p53 and reveal
an unanticipated layer of regulation in the p53 tumor suppressor network.
12:15 pm Luncheon Co-Presentation:The Use of LncRNA
Regulatory Elements for Innovative AnticancerTherapy;
Oncofetal H19: Mechanism, Clinical Applications and
Future Development
Sponsored by
Mark L. Tykocinski, M.D., Scientific Advisory Board, BioCancell
Michal Gilon, Ph.D., Vice President, R&D, BioCancell
The H19 long-non-coding-RNA gene, highly and specifically expressed in a wide
spectrum of tumors, is the ideal basis for highly selective anti-cancer therapy.
Using the H19 regulatory elements to drive the expression of Diphtheria toxin,
we have created a cancer-targeted DNA-based killing drug that leaves the healthy
surrounding tissues unharmed. Our talk will review H19 mechanism of action,
the creation of a “ killing chromosome “ that combines H19 and IGF2 regulatory
elements, and our promising clinical findings, which have lead us towards phase
III clinical trial in bladder cancer.
Epigenetic Mechanisms
1:30 pm Chairperson’s Remarks
Subhrangsu S. Mandal, Ph.D., Associate Professor, Chemistry & Biochemistry,
University of Texas Arlington
1:35 Endocrine Regulation and Disruption of Non-Coding RNAs
Subhrangsu S. Mandal, Ph.D., Associate Professor, Chemistry & Biochemistry,
University of Texas Arlington
Non-coding RNAs are emerging players in regulation of gene expression and
chromatin dynamics and their misregulations are associated with a variety of
human diseases including cancer. Studies from our laboratory demonstrate
that long non-coding RNAs (lncRNAs) are transcriptionally regulated by steroid
hormones such as estrogen and potentially disrupted upon exposure to
estrogenic endocrine disrupting chemicals. Here we will present our recent
findings on the epigenetic mechanism of endocrine regulation and disruption of
selected lncRNA in vitro and in vivo and their roles in tumorigenesis.
2:00 LncRNAs in Epigenetic Regulation
Mamta Gupta, Ph.D., Assistant Professor, Medicine, Mayo Clinic
2:25 Epigenetic Regulation of the Human Genome by lincRNAs
Ahmad M. Khalil, Ph.D., Assistant Professor, Genetics and Genome Sciences,
Case Western Reserve University School of Medicine
It is now estimated that the human genome encodes over 8,000 long intergenic
non-coding RNAs (lincRNAs), but the biological functions of only a few lincRNAs
have been elucidated to date. We have utilized state-of-the-art transcriptomic
approaches both in vitro and in vivo to identify lincRNAs that are deregulated
in several cancer types, with the hope of identifying tumor-suppressor and
oncogenic lincRNAs. Subsequent functional studies are providing insights into the
role of these lincRNAs in cancer initiation, progression and metastasis.
2:50 Selectively Activating Gene Expression byTargeting Long Non-
Coding RNA
Caroline J. Woo, Ph.D., Scientist, RaNA Therapeutics
Long non-coding RNAs (lncRNA) can regulate transcription by recruiting epigenetic
modifying complexes to target genes. PRC2, an epigenetic transcriptional
repressor complex, is recruited to its target gene, via a specific lncRNA, to inhibit
gene expression. We use synthetic oligonucleotides to selectively block PRC2
binding to a specific lncRNA, thereby de-repressing the expression of an mRNA,
and resulting in increased amounts of the therapeutic protein.
3:15 Close of Conference

Extracellular RNA in Drug and Diagnostic Development
I N A U G U R A L
TUESDAY, MARCH 17
12:00 pm Conference Registration
Sequencing and Profiling Strategies for
Extracellular RNA Analysis
Aleksandar Milosavljevic, Ph.D., Professor, Molecular and Human Genetics, Baylor
College of Medicine
1:35The Rat microRNA Body Atlas:Towards Understanding Serum
microRNA Changes andTheir Utilization as Biomarkers of Specific
OrganToxicity
Aaron Smith, Senior Toxicologist, Investigative Toxicology, Lilly Research
Laboratories
microRNAs (miRs) have many attributes which have elicited considerable interest
in their use as serum-based biomarkers of organ injury. In order to identify
tissue specific/enriched miRs and to understand serum miR changes, we have
constructed a rat miR body atlas using Illumina miR sequencing of 22 rat tissues
of toxicologic interest. These data provide a valuable miR platform to identify
serum miR changes reflecting their organ-specific origin during injury to the liver
and pancreas in vivo.
2:00 MicroRNA Biomarkers Circulate in Multiple Biophysical States:
Implications for Diagnostics Development
John Chevillet, Ph.D., Postdoctoral Research Fellow, Laboratory of Leroy Hood,
Institute for Systems Biology
Circulating microRNAs have been reported to exist in multiple biophysical states,
including most famously as cargo of 50-100 nm extracellular vesicles known as
exosomes. Our understanding of circulating miRNA biomarkers is rapidly evolving
and the development of sensitive, accurate and precise analytic approaches can
be substantially assisted by a quantitative understanding of their distribution in
physical and biochemical fractions of patient specimens.
2:25 Picoliter Droplet-Based Digital PCR and microRNA Quantification
Valerie Taly, Ph.D., Group leader, CNRS researcher, University Paris-Descartes
Droplet-based microfluidics has led to the development of highly powerful
systems that represent a new paradigm in high-throughput screening where
individual assays are compartmentalized within microdroplet microreactors.
In particular, picoliter droplet-based digital PCR has recently demonstrated its
pertinence to perform millions of single molecule reactions in parallel for the
detection and quantification of cancer genetic markers. We will present the
development and validation of this new technology for the multiplex detection of
clinically relevant microRNA.
Extracellular RNA Analysis and Toxicity Biomarkers
Matthew Roth, Ph.D., Assistant Professor & Co-Director, Bioinformatics Research
Lab, Baylor College of Medicine; Data Management & Resource Repository of the
Extracellular RNA Consortium (NIH)
4:15 Evaluation of Circulating microRNAs as Biomarkers ofToxicity in
Drug Discovery
Tatiana Sharapova, Ph.D., Scientist I, Cellular and Molecular Biology, AbbVie
At AbbVie we conducted investigations designed to evaluate the potential utility
of circulating miRNAs as biomarkers of drug induced toxicity in various tissues
including testicular, pancreatic, renal and liver injuries. Altogether, the data
indicate that serum and/or urinary miRNAs could have utility as biomarkers of
toxicity and support the future development of multiplexed panels of miRNAs to
monitor multiple toxic changes from a single sample.
4:40 Potential of Extracellular microRNAs as Biomarkers of
AcetaminophenToxicity in Children
Xi Yang, Ph.D., Research Biologist, Systems Biology, FDA/National Center for
Toxicological Research
Recent studies of adults with acetaminophen (APAP) -induced liver injury have
reported human serum microRNA-122 (miR-122) as a novel biomarker. The goal
of this study was to examine blood and urine extracellular miRNAs as potential
biomarkers for APAP liver injury in children. Our results demonstrate that urinary
extracellular miRNAs (miR-375) have the potential to be used as biomarkers in
children to detect APAP-induced hepatotoxicity in clinical practice.
5:05 Quantitative PCR Profiling for Selection of Candidate microRNA
Kidney Damage Markers
Mira Pavkovic, Ph.D., Bayer Pharma AG, GDD-GED-Toxicology; currently
Postdoctoral Fellow, Systems Pharmacology, Harvard
Extracellular microRNAs (miRNAs) have emerged as novel biomarkers (BMs)
for various pathological states. Issues like low miRNA content in biofluids and
questions concerning normalization strategies represent clear challenges in terms
of detection methods and analysis workflows. To evaluate these issues for urinary
miRNAs we performed rat studies with two differently acting nephrotoxicants
and developed a possible analysis approach for selection of BM candidates from
profiling data of urinary miRNAs using PCR.
5:30 Close of Day
6:00-9:00 (SC4): Circulating Nucleic Acid Biomarkers for Development
of Non-Invasive PrenatalTests
WEDNESDAY, MARCH 18
Morning Coffee
Challenges in Biomarker Applications of
Circulating RNA
Saumya Das, M.D., Ph.D., Assistant Professor, Medicine, Harvard Medical School
8:05 Bioinformatics Challenges
Aleksandar Milosavljevic, Ph.D., Professor, Molecular and Human Genetics, Baylor
College of Medicine
8:30 Important Considerations for exRNA Biomarker Discovery
Louise C. Laurent, M.D., Ph.D., Assistant Professor, Reproductive Medicine,
University of California San Diego Health Science
This presentation will cover work and lessons learned from the NIH External RNA
Communication Consortium (ERCC) Sample and Assays Working Group.
8:55 Panel Discussion: Standardization Issues for Extracellular RNA
Research
Moderator: Matthew Roth, Ph.D., Assistant Professor & Co-Director,
Bioinformatics Research Lab, Baylor College of Medicine; Data Management &
Resource Repository of the Extracellular RNA Consortium (NIH)
Panelists:
Louise C. Laurent, M.D., Ph.D., Assistant Professor, Reproductive Medicine,
University of California San Diego Health Science
Tatiana Sharapova, Ph.D., Scientist I, Cellular and Molecular Biology, AbbVie
Aaron Smith, Senior Toxicologist, Department of Investigative Toxicology, Lilly
Research Laboratories
Scott J. Tebbutt, Ph.D., Associate Professor, University of British Columbia, &
CSO, PROOF Centre of Excellence, Vancouver, Canada
• RNA isolation and quantification challenges
• Bioinformatics challenges unique to exRNA data
• Microarrays v. qPCR v. RNA-Seq
• Unique advantages of exRNA biomarkers
• Rate limiting steps for progress in biomarker applications

Long Non-Coding Extracellular RNA Biomarkers
Richard P. Kraig, M.D., Ph.D., Professor, Neurology, The University of Chicago
Medical Center
10:35 Extracellular, Long Non-Coding RNA Markers for Lung Cancer
Lynn Hlatky, Ph.D., Professor, Medicine, and Director of Cancer Systems Biology,
Tufts University
11:00 Circulating Ang2mRNA as a Prognostic Marker for Lung Cancer
Ana Coelho, Ph.D., Professor, Oncology, Portuguese Oncology Institute
Lung cancer remains a disease with a dismal prognosis. The development of
prognostic markers would allow patients the choice of more aggressive and
prolonged therapies. Circulating prognostic markers, such as mRNA levels, are
practical tools, since peripheral blood samples are easy to obtain, not relying on
the availability of adequate biopsy specimen. Moreover, circulating Ang-2 mRNA
levels could help in the stratification of NSCLC patients and can easily be included
in the design of preclinical studies.
11:25 PCA3: A Non-Invasive, Long Non-Coding RNA Marker of Prostate
Cancer
Gerald W. Verhaegh, Ph.D., Senior Scientist, Laboratory of Jack Schalken,
Department of Experimental Urology, Radboud University Medical Center
The PCA3 gene, encoding a long non-coding RNA, is over-expressed by prostate
cancer cells in comparison with all other cells studied. The differential expression
is great, permitting detection of the RNA in cancer cells shed into the urine after
attentive digital rectal exam. Urinary PCA3 appears useful as a highly specific
marker for prostate cancer.
11:50 Luncheon Presentation (Sponsored Opportunity Available) or Lunch
onYour Own
Functional and Diagnostic Roles for Extracellular RNA
1:30 pm Chairperson’s Remarks
1:35 Exosomes and miR-219 in MS Myelination and Migraine
Richard P. Kraig, M.D., Ph.D., Professor, Neurology, The University of Chicago
Medical Center
Multiple sclerosis (MS) and migraine are clinically correlated. Work from our
laboratory establishes a pathophysiological link involving myelin disruption
between these disorders. Importantly, we discovered that environment
enrichment (increased social, physical and creative activity) prompts release of
microRNA-containing exosomes from blood that promote myelination. These
nutritive exosomes can be harvested from dendritic cells grown in vitro. We
are developing microRNA-containing exosomes that emulate environmental
enrichment as a scalable therapeutic against brain demyelination including that
seen from MS and migraine.
2:00 A Functional Role for Extracellular RNAs in Cardiac Remodeling
Saumya Das, M.D., Ph.D., Assistant Professor, Medicine, Harvard Medical School
As mortality from acute myocardial infarctions has decreased, its sequelae,
heart failure and sudden cardiac death, have contributed significantly to disease
burden. Novel insights into cardiac remodeling that follows the initial stress would
provide novel biomarkers and therapeutic targets for cardiac remodeling. Here
we describe our efforts to identify extracellular RNA biomarkers associated with
cardiac remodeling using a microarray and an RNA-seq platform, and examine the
possible functional role of selected ex-RNAs in disease pathogenesis.
2:25Towards Establishing Blood-Based, RNA Diagnostics for Acute
Heart Failure Recovery
Scott J. Tebbutt, Ph.D., Associate Professor, University of British Columbia, &
CSO, PROOF Centre of Excellence, Vancouver, Canada
Severe inotrope-dependent acute heart failure (AHF) is associated with poor
clinical outcomes. There are currently no well-defined biomarkers of response to
treatment that can be used to guide treatment or evaluate recovery in this patient
population. In the present study, we are characterizing microRNAs as novel and
emerging tissue and circulating biomarkers of HF in patients with severe inotrope-
dependent AHF over the first 30 days of medical management or mechanical
circulatory support (MCS).
2:50 Extracellular RNAs as Diagnostic Biomarkers of Cardiovascular
Disease
Yigal Pinto, Ph.D., Professor, Cardiology and The Heart Failure Research Center,
Academic Medical Center, Netherlands
Biomarkers have profoundly changed cardiology. By measuring circulating heart-
specific proteins, diagnosis and management of the most important cardiac
syndromes have dramatically changed. The next frontier is to combine different
biomarkers into so-called multi-marker panels. Small RNAs like microRNAs are
measurable in the circulation. This holds great promise as technologies emerge
that allow us to measure with great accuracy multiple microRNAs together with
standard protein biomarkers. This is expected to again redefine some major
diagnostic and therapeutic areas in cardiology.
3:15 Close of Conference
MARCH 17-18
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Pricing and Registration Information
SHORT COURSE PRICING
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Commercial Hospital-affiliated
One short course $699 $399
Two short courses $999 $699
March 16 March 17
SC1: Systems Biology, Evidence Synthesis and in silico Discovery
Approaches to microRNA Biomarkers
SC3: RNA-Seq: A Fundamental Guide to the Field
SC2: Executive ThinkTank: Development of Exosome-Based Diagnostics
SC4: Circulating Nucleic Acid Biomarkers for Development of
Non-Invasive Prenatal Tests
CONFERENCE PRICING
SUMMIT PRICING - BEST VALUE! (Includes access to 2 conferences, excludes short courses)
Early Registration Deadline until December 12, 2014 $2549 $1149
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Advance Registration Deadline until February 6, 2015 $1649 $759
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March 16-17 March 17-18
microRNA as Biomarkers and Diagnostics Long Non-Coding RNA in Cancer
Exosomes and Microvesicles as Biomarkers and Diagnostics Extracellular RNA in Drug and Diagnostic Development
CONFERENCE DISCOUNTS
Poster Submission - Discount ($50 Off): Poster abstracts are due by February 13, 2015. Once your registration has been fully processed, we will send
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EXTRACELLULAR
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