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microRNA as Biomarkers and Diagnostics

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Recent research has shown small, non-coding microRNAs to be master regulators of cellular processes, and expression patterns have revealed their potential as diagnostic, prognostic, and treatment response biomarkers. Cambridge Healthtech Institute’s Twelfth Annual microRNA as Biomarkers and Diagnostics will cover the latest research in the use of microRNAs for early detection of disease, monitoring cancer progression and therapeutic response, and understanding immunity. Implications for the future of personalized medicine and issues in translating microRNA biomarkers to the clinic will also be discussed.

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Recommended Dinner Short Course*

Sunday, April 3, 5:00-8:00 pm
(SC1) Data Normalization Challenges and Solutions

*Separate registration required


Monday, April 4

7:00 am Conference Registration and Morning Coffee

8:00 Welcome Remarks from Conference Director


microRNAs as Non-Invasive Diagnostic and Predictive Biomarkers

8:10 Chairperson’s Opening Remarks

Ajay Goel, Ph.D., Professor and Director, Center for Gastrointestinal Research, and Director, Center for Epigenetics, Cancer Prevention and Cancer Genomics, Baylor Research Institute, Baylor University Medical Center

8:15 Non-Coding RNA Biomarkers in Colorectal Cancer

Ajay Goel, Ph.D., Professor and Director, Center for Gastrointestinal Research, and Director, Center for Epigenetics, Cancer Prevention and Cancer Genomics, Baylor Research Institute, Baylor University Medical Center

Non-coding RNAs (ncRNAs) are emerging as important regulators of gene expression in cancer. Overexpression of specific non-coding RNAs (including microRNAs, snoRNAs, piRNAs and circular RNAs) has been linked to the stepwise disease progression in colorectal cancer (CRC). Given their cancer-specific pattern of expression, remarkable stability and presence in blood and other body fluids, ncRNAs are considered to be highly promising cancer biomarkers. Accumulating evidence firmly supports the existence of unique ‘ncRNA 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.

8:45 Non-Invasive miRNA Biomarkers for Kidney Disease

Vishal S. Vaidya, Ph.D., Associate Professor, Medicine & Environmental Health, Harvard Medical School, Harvard T.H. Chan School of Public Health, Brigham and Women’s Hospital

MiRNAs play a critical regulatory role in health and disease. Abundant expression, lower complexity, stability in various detection matrices and amplifiable signals are qualities that make extracellular miRNAs attractive as biomarkers reflecting a variety of pathophysiological conditions. We highlight the transformative potential of miRNAs as mechanistic biomarkers in translational medicine.

9:15 Circulating microRNAs in Cardiac Disease and Dysfunction

Yuri D’Alessandra, Ph.D., Senior Researcher, Immunology and Functional Genomics Unit, Centro Cardiologico Monzino

Circulating microRNAs are emerging as biomarkers of several heart-related diseases. We have conducted studies encompassing many different cardiac maladies and identified specific circulating miRNAs as potential diagnostic markers.

9:45 Cell-Free Circulating microRNAs as a Reflection of Liver Disease

Steven Lockton, Ph.D., Senior Scientist, microMarkers, Regulus Therapeutics

MicroRNAs are stable in circulation and can be dysregulated with disease. Because microRNA expression is often organ-specific, cell-free circulating microRNA expression often reflects the diseased organ’s pathophysiology. To map microRNAs to organs we profiled microRNA expression in mouse tissues. In a transgenic mouse model of hepatocellular carcinoma this serum reflection of liver distress was clearly demonstrated upon inducing HRAS. Similarly, in HCV-infected patients, aberrant serum microRNA expression was restored to a healthy-like state after treatment.

10:15 Coffee Break in the Exhibit Hall with Poster Viewing


Identifying microRNA Biomarkers in Tissue and Biofluids

10:45 Gender-Specific, Population-Specific, and Race-Specific Regulatory Non-Coding RNAs

Isidore Rigoutsos, Ph.D., Professor and Director, Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University

By analyzing human transcriptomes from different people and different tissues, we found two types of short regulatory RNAs that are produced constitutively, and demonstrated that their composition and abundances depend on a person’s gender, population and race as well as on tissue, tissue state, and disease subtype. The first type of short RNAs comprises numerous isoforms of mature microRNAs (miRNAs) that arise from virtually every known miRNA precursor. The second type of short RNAs comprises numerous fragments of mature transfer RNAs (tRNAs). We also discovered a novel category of tRNA fragments, the i-tRFs, which are wholly internal to the span of the mature tRNA and contribute much of the observed difference across individuals and tissues. The findings have direct implications for Precision Medicine and our understanding of the mechanisms underlying the onset and progression of disease.

11:15 Identification of microRNA Signatures Predicting Survival and Treatment Response in Glioblastoma

Josie Hayes, Ph.D., Postdoctoral Fellow, Neurosurgery, Helen Diller Family Cancer Center, University of California, San Francisco

11:45 microRNA Signatures in Renal Disease: A Meta-Analysis of Tissue and Urine Datasets

Christos Argyropoulos, M.D., Ph.D., MS, Assistant Professor, Nephrology, Department of Internal Medicine, University of New Mexico School of Medicine

MicroRNA (miRNA) are negative regulators of gene translation and an emerging biomarker in a wide variety of diseases. Little is known about the ability of miRNA to correctly classify patients with clinically significant renal pathology. We undertook a meta-analysis of miRNA profiles from clinical samples (biopsy or biofluid) in Gene Expression Omnibus. MiRNA profiles from 31 urine samples and 117 biopsy samples were available for analyses. A short signature of 19 miRNAs achieved a superior classification performance for renal pathology (cross-validated AUC 0.96).

12:15 pm Enjoy Lunch on Your Own


microRNAs in Drug Development

1:25 Chairperson’s Remarks

Bing-Hua Jiang, Ph.D., Professor, Pathology, Anatomy and Cell Biology, Thomas Jefferson University

1:30 MicroRNA Profiling Identifies Potential Biomarkers of Hepatobiliary Injury Following Exposure to Several Toxicants in the Rat

Rachel J. Church, Ph.D., Director, Organ Injury Biomarker Core; Research Investigator, Institute for Drug Safety Sciences; Research Assistant Professor, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill

2:00 Evaluation of Noninvasive microRNAs as Biomarkers of Injury for Drug Safety

Xi Yang, Ph.D., Research Biologist, Systems Biology, National Center for Toxicological Research, FDA

Drug-induced liver injury is an important regulatory concern and a common reason for drug withdrawal. Acetaminophen (APAP) overdose is a major cause of acute liver failure in the Western world. Sensitive and specific biomarkers are required as diagnosis tools in the clinic and in screening assays during drug development stages. In our recent study, urinary miRNAs’ potential as diagnostic biomarkers has been explored.

2:30 Use of microRNAs to Understand Differential Signaling between Lung Tumor Subtypes and Predict Therapeutic Response

Molly A. Taylor, Ph.D., Senior Scientist, AstraZeneca

We have classified three novel subtypes of lung squamous cell carcinoma that each have unique microRNA expression and therapeutic response profiles. Combined analysis of activated pathways and microRNA promoters has identified transcription factors driven by activated pathways that drive differences in microRNA expression. Overall, these microRNAs and transcription factors may function as biomarkers of pathway activation and aid in distinguishing patient subtypes to predict response to therapy.

3:00 Refreshment Break in the Exhibit Hall with Poster Viewing

3:30 MicroRNA Therapy in Advanced Malignancies

David S. Hong, M.D., Associate Professor and Chair, Investigational Cancer Therapeutics, University of Texas MD Anderson Cancer Center

4:00 MicroRNAs in Cancer and Therapeutic Resistance

Bing-Hua Jiang, Ph.D., Professor, Pathology, Anatomy and Cell Biology, Thomas Jefferson University

We initially demonstrated that PI3K and AKT play an important role in tumor angiogenesis. We found recently that reactive oxygen species (ROS) levels are increased in ovarian, prostate and breast cancer cells; and are involved in activating PI3K/AKT and HER2/HER3 signaling and suppressing several key microRNAs for regulating cancer development, drug resistance, tumor growth and angiogenesis. We found that microRNA dysregulations regulate tumor growth, angiogenesis and drug resistance in several kinds of human cancers. To understand the potential link of ROS and microRNA dysregulations, we showed that ROS can suppress a number of microRNA expression through DNA methylation for inducing some pro-oncogene expression such as HER2/HER3. In addition, we find that miRNA depression is regulated by DNA methylation and transcriptional activation. MiRNA dysregulation is involved in cancer development, autophagy and therapeutic resistance.

4:30 Novel Anti-Hepatitis C Virus (HCV) Therapeutics Targeting the Host Factor microRNA-122 (miR-122)

Amy K. Patick, Ph.D., Patick Pharmaceutical and Scientific Consulting

MiR-122 is a liver-specific miRNA that is abundantly expressed in hepatocytes and known to be involved with fatty acid and cholesterol metabolism. Studies demonstrating that miR-122 is essential for HCV proliferation by binding to specific sites in the 5' HCV untranslated region have provided the rationale for the development of the anti-miR-122 oligonucleotides miravirsen and RG-101. Preclinical and clinical studies of this class of therapeutics will be presented.

5:00 Welcome Reception in the Exhibit Hall with Poster Viewing



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Tuesday, April 5

7:30 am Breakfast Roundtable Discussions

Roundtable discussion are interactive, topic-specific discussions hosted by expert moderators and open to all attendees. These session provide a forum for discussing key issues.

  • Topic 1: Targeting of microRNAs for Therapeutics

    Moderator: Amy K. Patick, Ph.D., Principal, Patick Pharmaceutical and Scientific Consulting

  • Topic 2: Next-Generation Sequencing

    Moderator: Andreas Keller, Ph.D., Chair and Professor, Clinical Bioinformatics, University Hospital, Saarland University

  • Topic 3: miRNA as Cancer Biomarkers and Related Issues

    Moderator: Jingfang Ju, Ph.D., Associate Professor and Co-Director, Translational Research, Pathology, Stony Brook University

  • Topic 4: miRNAs and Exosomes

    Moderator: John Chevillet, Ph.D., Principal Scientist, N-of-One



Challenges of NGS

8:25 Chairperson’s Remarks

Andreas Keller, Ph.D., Chair and Professor, Clinical Bioinformatics, University Hospital, Saarland University

8:30 Discovery of New Blood-Borne miRNAs in Human Pathologies by NGS

Andreas Keller, Ph.D., Chair and Professor, Clinical Bioinformatics, University Hospital, Saarland University

Although over 2,500 mature human miRNAs are known there is still a race for novel markers. Screening of blood cell fractions using NGS is a reasonable approach for discovering such minimally-invasive disease markers. With NGS as a high-throughput technique, however, a significant number of false positive biomarker candidates is reported. We present a complete pipeline: efficient discovery of novel miRNAs, filtering of false positives, and validation. The performance of the novel pipeline is demonstrated using neurological diseases as well as lung cancer.

9:00 microRNA Expression in Bronchial Epithelium for Lung Cancer Detection

Ana Brandusa Pavel, Ph.D., Researcher, Computational Biomedicine, Boston University School of Medicine

Using bronchial brushings from current and former smokers undergoing bronchoscopy for suspect lung cancer, we profiled microRNA expression via small RNAseq on the Illumina HiSeq 2000 platform. We found microRNA expression profiles significantly associated with lung cancer and that these microRNAs target mRNA whose expression was previously reported to be associated with lung cancer. Importantly, we show that integrating microRNA expression together with a gene-expression lung cancer biomarker increases performance.

Bioo Scientific9:30 Reducing Bias and Improving Small RNA-Sequencing

Adam Morris, Ph.D., Senior Scientist, Bioo Scientific

Small RNA sequencing has typically suffered from three major drawbacks: 1) severe bias, such that sequencing data does not reflect original miRNA abundances, 2) the need to gel-purify final libraries, and 3) lack of low-input protocols. Here we present a method combining reduced bias with gel-free or low-input protocols.

9:45 Coffee Break in the Exhibit Hall with Poster Viewing


Role of microRNAs in Cancer Pathways

10:25 Chairperson’s Remarks

Richard I. Gregory, Ph.D., Associate Professor, Department of Biological Chemistry and Molecular Pharmacology, Department of Pediatrics, Harvard Medical School, Harvard Stem Cell Institute, The Stem Cell Program at Boston Children’s Hospital

10:30 Predictive and Functional Roles of miRNA in Metastatic Melanoma

Eva Hernando, Ph.D., Associate Professor and Vice Chair for Science, Department of Pathology; Co-Leader, Melanoma Program, NYU Langone Medical Center

Our laboratory has identified a miRNA signature in primary melanomas predictive of recurrence and metastasis. We have also demonstrated that some components of that signature which are lost in aggressive primary tumors act as metastasis suppressors. Our data supports that a miRNA-based prognostic assay could identify patients at higher risk of developing metastatic disease who could be subjected to increased surveillance or adjuvant therapies. Moreover our results support that miRNA changes can capture the molecular heterogeneity that dictates metastatic behavior since early tumor stages.

11:00 microRNA Biogenesis Pathways in Cancer

Richard I. Gregory, Ph.D., Associate Professor, Department of Biological Chemistry and Molecular Pharmacology, Department of Pediatrics, Harvard Medical School, Harvard Stem Cell Institute, The Stem Cell Program at Boston Children’s Hospital

Amplification and overexpression of individual ‘oncomiRs’ or genetic loss of tumor suppressor miRNAs promotes tumorigenesis. Furthermore, global miRNA depletion caused by genetic and epigenetic alterations in components of the miRNA biogenesis machinery is oncogenic. This, together with the recent identification of novel miRNA regulatory factors and pathways, highlights the importance of miRNA dysregulation in cancer.

11:30 Elimination of Colon Cancer Stem Cells by miR-140 through SMAD2 and Autophagy

Jingfang Ju, Ph.D., Associate Professor and Co-Director, Translational Research, Pathology, Stony Brook University

Colorectal cancer (CRC) is the third highest mortality cancer in the US and frequently metastasizes to liver and lung. Smad2 is a key element downstream of the TGF-β signaling pathway to regulate cancer metastasis by promoting epithelial to mesenchymal transition and maintaining the cancer stem cell (CSC) phenotype. In this study, we show that hsa-miR-140-5p directly targets Smad2 and overexpression of hsa-miR-140-5p in CRC cell lines decreases Smad2 expression levels, leading to decreased cell invasion and proliferation, and increasing cell cycle arrest. The functional and clinical significance of hsa-miR-140-5p suggests that it is a key regulator in CRC progression and metastasis, and may have potential as a novel therapeutic molecule to treat CRC.

12:00 pm Close of Conference



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