OPT Congress
OPT Congress

Oligonucleotide Discovery and Delivery

Recent advances in nucleic acid medicinal chemistry and delivery have led to the creation of a new generation of oligonucleotide therapies harnessing chemical modifications and conjugations to improve their stability, bioavailability, specificity and potency. These advances, along with a robust development landscape, and several late-stage clinical products poised for approval, have led to a sharp resurgence of interest in the discovery of oligonucleotide-based therapeutics.

Due to the remarkable success of the Inaugural event, Cambridge Healthtech Institute is delighted to host the Second Annual Oligonucleotide Discovery and Delivery conference, March 27-28, in Cambridge, MA. Join leading oligonucleotide developers and discovery scientists to discuss technological and scientific advances in nucleic acid synthesis, medicinal chemistry and delivery, as well as preclinical and clinical findings.

Final Agenda

Sunday, March 26

Recommended Pre-Conference Dinner Short Course*

5:00-8:00 pm SC1: Oligonucleotide Therapeutics: From Discovery to Manufacturing
* Separate registration required.  

Monday, March 27

7:00 am Registration and Morning Coffee


8:00 Welcome Remarks from Conference Director

Kip Harry, Senior Conference Director, Cambridge Healthtech Institute

8:10 Chairperson’s Opening Remarks

Muthiah (Mano) Manoharan, Ph.D., Senior Vice President, Drug Discovery, Alnylam Pharmaceuticals, Inc.

8:15 Novel Phosphorodiamidate Oligomers (PMOs) for the Treatment of Genetic and Infectious Diseases 

Bruce_WentworthBruce Wentworth, Ph.D., Principal Owner, BMW Research Consulting



8:45 Messenger RNA as a Novel Therapeutic Approach

Melissa_MooreMelissa J. Moore, Ph.D., CSO, mRNA Research Platform, Moderna

The contemplation of mRNA as a therapeutic platform has historically been shunned owing to challenges in oligonucleotide delivery and, maybe more importantly, the perceived shortcomings of mRNA with regard to stability and immunogenicity. Significant advances in oligonucleotide delivery have been realized over the past decade thereby enabling mRNA therapeutics. Recent discoveries in mRNA chemistry further enhance the attractiveness of this platform by eliminating innate immune activation and maximizing protein expression.

9:15 siRNA Therapeutics for Extrahepatic Indications: Quark’s Case Study

Elena_FeinsteinElena Feinstein, M.D., Ph.D., CSO, Quark Pharmaceuticals

Quark is active in the field of discovery and development of siRNA therapeutics focusing on acute or subacute indications involving organs other than liver. An overview of advanced clinical (Phase III) and some of nonclinical programs will be provided.

9:45 Selected Presentation: Defined Multimeric Oligonucleotides for Enhanced Therapeutic Effect

Jonathan Miles Brown, Ph.D., Consultant, MPEG LA, LLC.

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

10:45 Challenges in the Synthesis of Conjugated LNA Oligonucleotides

Dennis_Jul_HansenDennis Jul Hansen, MSc, Ph.D., Scientist, Oligo Synthesis, Discovery Operations, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S

Recently there has been considerable focus in the conjugation of oligonucleotides with non-nucleotide moieties which, for example, enable targeting of therapeutic oligonucleotides to specific organs and tissues in vivo. The conjugation of different chemical moieties to oligonucleotides is often achieved by post-synthetic amide bond formation. This approach requires the synthesis of LNA-oligonucleotides with a primary amine the 5' end. During this work we noticed a (to us) new impurity with M+28. The post-synthetic conjugation reactions are traditionally performed in aqueous solvents and require several equivalents of conjugate group, thus increasing the cost of manufacture. We will here present the work to identify the M+28 impurity, how to remove it and ultimately how avoid its formation, together with the work on performing the conjugation reaction under nonaqueous conditions, which allows for drastic reduction of the amount of conjugate needed.

11:15 Breakthrough Innovation in Phosphorodiamidate Morpholino Oligomer (PMO) Delivery Chemistry

Gunnar_HansonGunnar J. Hanson, Ph.D., Senior Director, Research Chemistry, Sarepta Therapeutics, Inc.

Antisense oligonucleotides show great promise as gene therapeutics for the treatment of debilitating genetic diseases such as Duchenne Muscular Dystrophy. In particular, phosphorodiamidate morpholino oligomers (PMOs) enable Watson-Crick binding to pre-mRNA in the nucleus and thereby enable the control of new definitions of intron-exon junctions within the spliceosome. Such splice alteration is limited by the efficiency of PMO delivery into the cytosol and nucleus. To solve this 40-year old delivery problem, new cell-penetrating peptides (CPPs) were designed, which by covalent attachment to PMOs, dramatically enhance the delivery of these macromolecules into the cytosol and nucleus. An outgrowth of this research is a novel CPP-PMO conjugate that will enter clinical trials in 2017 as a new exon skipping Duchenne Muscular Dystrophy (DMD) therapeutic.

11:45 GalNAc-Conjugated siRNAs as a New Paradigm in Oligonucleotide Therapeutics

Muthiah_ManoharanMuthiah (Mano) Manoharan, Ph.D., Senior Vice President, Drug Discovery, Alnylam Pharmaceuticals, Inc.

During this presentation, I will discuss the progress in the advancement of RNAi therapeutics and review delivery of RNAi and where the field is going. I will also discuss conjugated delivery of oligonucleotides to the liver and combining novel chemical modifications with conjugation strategies.

12:15 pm Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own


1:55 Chairperson’s Remarks

Thazha P. Prakash, Director, Medicinal Chemistry, Ionis Pharmaceuticals

2:00 Approaches to Improve Potency of Antisense Oligonucleotides in Extrahepatic Tissues

Thazha P. Prakash, Director, Medicinal Chemistry, Ionis Pharmaceuticals

Antisense oligonucleotide (ASO)-based drug development is evolving as an effective therapeutic modality. In order to fully realize the potential of this technology, it is necessary to improve the potency of ASOs in extrahepatic tissues. We investigated the effect of conjugating hydrophobic ligand capable of interacting with plasma proteins on productive uptake of ASO into extrahepatic tissues. Our results suggest that conjugation of hydrophobic ligands improved potency of ASOs in extrahepatic tissues.

2:30 Development of SB 9200 that Activates RIG-I as Antiviral Agent

Kris_IyerR.P. (Kris) Iyer, Ph.D., Co-Founder & CSO, Spring Bank Pharmaceuticals

Compounds that activate cellular pattern recognition receptors (PRRs) such as RIG-I, NOD2, and STING are of immense interest in the development of new generation antiviral and anticancer agents. We have discovered SB 9200 as an oral broad-spectrum antiviral dinucleotide, that activates RIG-I and NOD2, thereby causing the induction of expression of intracellular Interferons, ISGs and cytokines. SB 9200 has entered global Phase II clinical trials against HBV following extensive preclinical studies. SB 9200 was shown to be an anti-HCV agent in the recently concluded Phase I clinical trials in HCV-infected patients. This talk will focus on the key aspects of development of this next-generation antiviral agent.

3:00 Third-Generation Antisense (3GA) Technology: Insights into Mechanism of Action

Reina_ImprogoReina Improgo, Ph.D., Research Scientist, Idera Pharmaceuticals, Inc.

Development of the antisense oligonucleotide approach has been hampered by off-target effects and inflammatory responses. Based on the insights gained from our previous work, we have designed third-generation antisense (3GA) oligonucleotides with the goal of improving therapeutic index. The 3GA design consists of two antisense oligonucleotides linked together via their 5’ end. We have conducted preclinical proof-of-concept studies in cell-based assays and in vivo mouse models using 3GAs against multiple gene targets.

3:30 Refreshment Break in the Exhibit Hall with Poster Viewing


4:00 High-Throughput Quantitative Bioanalysis and Metabolite Profiling Using LC-HRAM to Support Discovery and Development of Oligonucleotide Therapeutics

Laixin Wang, Ph.D., Vice President, Bioanalytical, NovaBioAssays LLC

This presentation will discuss the challenges and solutions of sample preparations and LC-MS analysis of oligonucleotides in a variety of biological matrices, including cell culture, urine, plasma, and tissues. The pros and cons of these extraction methods and instrument platforms will be discussed with case studies for different structured oligonucleotides.

4:30 Solid-Phase Purification of Synthetic DNA Sequences and/or Development of 2’-Hydroxy Protecting Groups for Ribonucleosides and Oligoribonucleotides

Serge Beaucage, Ph.D., Chief, Laboratory of Biological Chemistry, CDER, FDA

Little has been done to develop high-throughput procedures for the purification of synthetic nucleic acid sequences. An efficient process for solid-phase purification of phosphorothioate and native DNA sequences will be presented. Furthermore, an innovative cleavage of 2’-hydroxy protecting groups from ribonucleosides and oligoribonucleotides through an intramolecular decarboxylative elimination process will also be discussed.

5:00 Selected Presentation: Therapeutic Suppression of the KRAS-MYC Oncogenic Axis in Human Pancreatic Cancer Xenografts with U1 Adaptor Oligonucleotide–RGD Peptide Conjugates

Samuel Gunderson, Ph.D., President and Co-Founder, SilaGene, Inc.

OligoFactory5:30 Welcome Reception in the Exhibit Hall with Poster Viewing

 6:15 Short Course Registration

Recommended Dinner Short Course*

6:30-9:30 SC3: CRISPR-Based Gene Editing for Targeted Therapies
* Separate registration required.

Tuesday, March 28

7:30 am Breakfast Roundtable Discussions

Grab a cup of coffee and join a roundtable discussion. These are moderated discussions with brainstorming and interactive problem solving, allowing participants from diverse backgrounds to exchange ideas and experiences and develop future collaborations around a focused topic.

View Roundtable Discussions


8:25 Chairperson’s Remarks

Balkrishen (Bal) Bhat, Ph.D., Vice President, Chemistry, RaNA Therapeutics, Inc.

8:30 Novel Strategies for Endogenous mRNA Upregulation

Balkrishen_BhatBalkrishen (Bal) Bhat, Ph.D., Vice President, Chemistry, RaNA Therapeutics, Inc.

We are developing two gene upregulation platforms. The first approach targets lncRNAs (long non-coding RNA) with chemically modified oligonucleotides to block recruitment of PRC2 to the target gene of interest which results in significant upregulation of mRNA and protein. In the second approach, we selectively upregulate target mRNA and the corresponding protein by stabilizing identified regions of mRNA with chemically modified oligonucleotides.

9:00 microRNA Targeted Therapies for Hematological Malignancies and Pathological Fibrosis: Translation from Basic Sciences to the Clinic

William_MarshallWilliam S. Marshall, Ph.D., President and CEO, miRagen Therapeutics

9:30 Development of Novel Breakthrough Cancer Therapies Based on the Unique Functions of miRNAs

Roel_SchaapveldRoel Q.J. Schaapveld, Ph.D., MBA, CEO, InteRNA Technologies BV

To explore miRNAs as therapeutic agents for the treatment of cancer, InteRNA Technologies has performed functional screens in cell lines covering different types of cancer. Lead candidates are now advancing in preclinical development programs with a focus on hepatocellular cancer. This presentation will provide insights into the latest progress in the preclinical development of InteRNA’s lead miRNA compounds.

10:00 Coffee Break in the Exhibit Hall with Poster Viewing


10:40 Chairperson’s Remarks

Anastasia Khvorova, Ph.D., Professor, Molecular Medicine, RNA Therapeutics Institute, University of Massachusetts Medical School

10:45 Expanding the Chemical Diversity of Therapeutic Oligonucleotides

Anastasia_KhvorovaAnastasia Khvorova, Ph.D., Professor, Molecular Medicine, RNA Therapeutics Institute, University of Massachusetts Medical School

Using fully chemically modified siRNA scaffolds, we systematically screened a wide range of bioactive conjugates and demonstrated that the chemical nature of the conjugation modality has a major impact on brain tissue retention, distribution and cellular internalization. We have identified several novel chemical classes of conjugates that demonstrate markedly improved brain distribution and robust in vivo efficacy. Direct conjugation of a fully chemically modified siRNA to docosahexaenoic acid (DHA), the most abundant poly-unsaturated fatty acid in the brain, results in improved tissue retention with wide distribution and robust efficacy in the striatum and cortex after single injection. Most importantly, DHA-hsiRNA conjugates do not induce neural cell death or measurable innate immune activation following administration of concentrations 20-fold over the efficacious dose, establishing a new approach toward development of RNAi-based therapeutics for a wide range of neurodegenerative disorders.

11:15 Extracellular Vesicles Mediate Delivery of siRNAs for the Treatment of Neurodegenerative Disease

Reka_HarasztiRéka Haraszti, M.D., Research Scientist, Knvorova Lab, RNA Therapeutics Institute, University of Massachusetts Medical School

Extracellular vesicles (EVs) are implicated in the transfer of endogenous small RNAs between cells. We developed a robust method to load modified siRNAs to exosomes via conjugation of a hydrophobic moiety to the sense strand (hsiRNA). Cellular uptake and hsiRNA potency were enhanced when formulated into EVs in a source cell-dependent manner. When source cells were serum-starved before EV purification, up to 15 fold enhancement in potency was observed. Functional as well as proteomic and lipidomic studies confirmed that source cells affect EV trafficking and composition. Serum-starved mesenchymal stem cell EVs were the most potent delivery vesicles for therapeutic hsiRNA.

11:45 Enjoy Lunch on Your Own


1:25 Chairperson’s Remarks

Cy A. Stein, M.D., Ph.D., Professor, Medicine and Experimental Therapeutics & Molecular and Cellular Biology, City of Hope National Medical Center

1:30 Development of Lipid-Based Oligonucleotide Delivery Systems

Steffen_SchubertSteffen Schubert, Ph.D., Head, In Vitro Pharmacology – Drug Discovery, Silence Therapeutics

In vivo delivery is still one of the most challenging parts when it comes to the therapeutic application of nucleotides like siRNA and mRNA. Here we discuss how Silence Therapeutics has broadened its portfolio of lipid-based formulations, how lipid chemistry influences specificity and activity, and certain process parameters that led to new formulations characteristics.

2:00 A Novel Nano-Medicine Platform for Oligonucleotide Discovery and Delivery

Andy_GeallAndy Geall, Ph.D., Vice President, Formulations and Chemistry, Avidity NanoMedicines

Despite the considerable promise, delivery has proven to be one of the central challenges of oligonucleotide-based therapeutics. Oligonucleotides are large, hydrophilic and highly negatively charged, so they don’t cross cell membranes. We have pioneered the development of Precision NanoMedicines, which are targeted, polymeric nanoparticles encapsulating siRNA drug payloads for delivery to specific tumor types. These self-assembling nanoparticles can be decorated with antibodies, proteins, peptides and small molecules to bind to extracellular receptors and facilitate cellular uptake.

2:30 Intracellular Trafficking of Splice Switching LNA Oligonucleotides

Cy_SteinCy A. Stein, M.D., Ph.D., Professor, Medicine and Experimental Therapeutics & Molecular and Cellular Biology, City of Hope National Medical Center

While antisense silencing of gene function may occur in either the cell cytoplasm or nucleus, splice-switching occurs solely in the nucleus. Further, the local concentration of LNA-oligo required for nuclear splice switching (LNA-SSO) is far lower than what is required for cytoplasmic antisense activity. We have discovered that after egress from the late endsosome, LNA-SSOs become associated with a protein complex that includes nucleolin and Ago2, in addition to other shuttling proteins. This complex appears to be able to translocate to the nucleus, where it can be observed as “nuclear speckles.” Factors that contribute to this translocation, and which synergize with each other as determined by the Chou-Talalay Combination Index method, will be discussed.

3:00 Selected Presentation: Fluorocarbons Enhance Intracellular Delivery of Short STAT3 Oligonucleotide Duplexes

Surong Zhang, Ph.D., Instructor, Laboratory of Molecular Imaging Probes, Department of Radiology, University of Massachusetts Medical School

3:15 Refreshment Break in the Exhibit Hall with Poster Viewing

3:45 Development of Anti-Fibrosis siRNA Therapeutics Using HKP Polypeptide Nanoparticle Technology

Patrick_LuPatrick Y. Lu, Ph.D., President & CSO, Sirnaomics, Inc.

Using a proprietary and optimized polypeptide-based delivery technology, we have developed the novel anti-fibrotic therapeutics with siRNAs targeting both TGFß1 and Cox-2 simultaneously, for initial indication of skin hypertrophic scar followed with liver fibrosis and other fibrotic conditions. I will discuss the unique advantage of HKP polypeptide nanoparticle technology for efficient siRNA delivery, its pharmaceutical properties for manufacturing and its preclinical safety profile.

4:15 Self-Delivering RNAi Compounds (sd-rxRNA™) for the Treatment of Ocular Disorders

Pamela_PavcoPamela Pavco, Ph.D., Chief Development Officer, RXi Pharmaceuticals Corp.

RXi’s proprietary sd-rxRNA® technology is perfectly suited for direct, local delivery to cells and tissues. This aspect has been exploited in our initial two program areas, dermatology and ophthalmology, to evaluate clinically the reduction of connective tissue growth factor as a potential way to decrease the progression of fibrosis in the skin and the eye. An exciting new program uses the sd-rxRNA technology to target checkpoints, singly or in combination, to augment cell therapy in the immuno-oncology space, as a possibility to treat both hematological and solid tumors. An overview of ongoing programs will be provided.

4:45 Therapeutic Protein Expression in vivo Using Messenger RNA-Lipid Nanoparticles

Thomas_MaddenThomas D. Madden, Ph.D., President and CEO, Acuitas Therapeutics

Therapeutic applications of messenger RNA (mRNA) are currently being advanced into clinical development. However, mRNA is relatively labile and requires a delivery system to efficiently access the cytoplasmic compartment where the mRNA is translated. Acuitas is developing lipid nanoparticle systems (LNP) that allow the efficient delivery and expression of mRNA via different routes of administration. Biophysical characteristics that facilitate efficient mRNA delivery and provide a favorable safety profile will be discussed. In addition we will present preclinical results illustrating the potential application of mRNA-LNP therapeutics in a several clinical areas.

5:15 Close of Conference