B6 SOW_SAM.gov.pdf

Version 11-30-2016-1 FAR Part 11—Describing Agency Needs

STATEMENT OF WORK (SERVICES)

(SOW)

GENERAL INFORMATION

Title of Project:

Transcriptomics study – RNA-seq in Liver Spheroids Phase One

Statement of Need and Purpose:

This requisition establishes a contract to evaluate the RNA expression in liver toxicity associated with the systemic administration of antisense oligonucleotides (ASOs) in the previously tested human, rat and mouse animal models. The project's phase one goal is to develop a predictive model of candidate ASO therapies' safety and acute toxicity.

The National Center for Advancing Translational Sciences (NCATS) focuses on treating rare diseases. A significant emphasis of NCATS is the rapid development of effective therapies for patients diagnosed with these conditions. Although each condition is individually rare, cumulative rare diseases lead to considerable morbidity and mortality among the American population. NCATS is directly addressing this problem by discovering new technologies and other approaches, such as ASO therapies, that could significantly accelerate developing and deploying solutions that all translational researchers can use.

The most significant bottleneck in terms of time and cost of ASO drug development is the animal toxicology experiments requested by the FDA. Having faster and cheaper screening methods for toxicology would address this critical issue. To facilitate the development of therapeutic ASOs, NCATS aims to develop streamlined and low-cost predictive toxicology assays for N=1 ASOs. These screening platforms rely on iPS cell cultures, organoids, and tissue bio-printing to predict the toxic side effects of ASOs and improve the safety pharmacology of this drug class. A parallel focus of our effort is to develop algorithms that predict toxicity, allowing toxic ASOs to be eliminated in the design phase. In this way, we aim to make developing disease-modifying therapies for rare diseases cheaper and faster by decreasing the burden of regulatory approval.

In our previous efforts we used the 20-mer gapmer ASOs with phosphorothioate backbones and 2'-O-methoxyethyl-RNA (2'-MOE) modifications. We now want to validate the RNA expression of 7 of the ASOs in these cell-based screening organoids in animal models. This contract aims to provide sufficient and confirmatory in vivo data to the point that the FDA accepts cell-based in vitro data in place of conventional animal toxicology studies.

NCATS is seeking technical support to evaluate the safety and acute liver toxicity of candidate ASOs by checking the gene expression. The results from these studies, in conjunction with existing cell-based assays, will help better predict the safety of future candidate ASOs intended for clinical use.

Background Information and Objective:

There are over 7,000 different rare diseases that affect 350 million globally and about 35 million people in the U.S. Sadly, about half of these rare diseases have onset in childhood, and the vast majority (~95%) have no FDA-approved treatment. Most rare diseases have a known single gene cause, making them potentially amenable to oligonucleotide therapeutics like ASOs.

ASOs are short strands of modified RNA and DNA that bind to target RNA and can act by modulating splicing, inhibiting translation, or inducing mRNA degradation. ASOs are increasingly being deployed as individualized medicines as they are rapidly customizable, relatively easy to deliver, and inexpensive to manufacture. Although there is a growing number of clinical examples and safety data for ASOs, there is a need to reduce the cost and development timelines to test these therapies in more patients with rapidly progressing life-threatening diseases faster without compromising safety.

Antisense oligonucleotides comprise 16 to 20 nucleotide bases, often with chemical modifications of the phosphate backbone. It is thought that the sequence and backbone chemistry of the ASOs determine whether administering a particular ASO molecule will lead to liver toxicity. However, the broader development of high-affinity gapmer ASOs for rare diseases has been hampered by hepatotoxicity. An unanswered question is whether the 3D liver microtissues can accurately predict the hepatotoxicity of ASOs. The project is designed to answer this question.

The objective of this contract is to generate proof-of-concept data for evaluating the ability of the 3D liver microtissue platform to predict the hepatoxicity of individual ASOs. If successful, this will represent a new means to screen ASOs for this type of toxicity that is cheaper, faster, and has high throughput. NCATS is seeking technical support to evaluate the safety and acute liver toxicity of candidate ASOs by checking the gene expression. The results from these studies, in conjunction with existing cell-based assays, will help better predict the safety of future candidate ASOs intended for clinical use.

Period of Performance:

The study will commence 8 to 9 weeks after receipt of the order or sooner and will run 9 weeks.

The report will be due after the completion of the study.

The period of performance is two months.

SCOPE OF WORK

General Requirements:

Independently and not as an agent of the Government, the Contractor shall furnish all the necessary services, qualified personnel, material, equipment, and facilities, not otherwise provided by the Government as needed to perform the Statement of Work below:

Specific Requirements:

This contract (Quote Number: Q3240126) aims to determine if the 3D Insight liver spheroids developed by InSphero can predict the hepatic cytotoxicity of ASOs. The studies are designed to characterize the efficiency of the assays. These studies will use a set of 8 ASOs known to be hepatotoxic in humans or rodents (hepatotoxic ASOs) and a group of ASOs that show no hepatotoxicity in humans or rodents (safe ASOs). This project will generate proof-of-concept data.

The contractor will test each ASOs on multi-donor human, rat (Sprague Dawley) and mouse (C57/BL6) 3D Insight liver spheroids.

WP1: Transcriptomics study - Transcriptomics 1 Piece study, sample prep for low input bulk RNA seq for 8 ASOs, 2 concentrations, 2 time points (2 & 7), n=7 Plus: Initial Transcriptomics – Sequencing and analysis

Work package 1 – Low-input bulk RNA Transcriptomic sequencing

Goal • Investigative toxicology study of the therapeutic compound.

3D InSightTM Liver model • Human 3D InSight™ liver microtissues Test groups • Test compound: 8

• Test concentrations:

o IC10ATP o 0.1-fold of IC10ATP

• Timepoints:

o 2 days o 7 days

• Biological replicates: 7

• Vehicle control: PBS

Compound procurement By client

• All compounds

General Protocol • Medium: BSA-free 3D Insight™ LiMM Tox

• 7 days compound treatment with compound application on day 0, 2 & 4.

• Sample preparation for RNA sequencing at selected timepoints Measurements • Low input bulk RNA sequencing

LEVEL OF EFFORT:

PhD level scientists with knowledge and training in ASOs shall run the tests.

GOVERNMENT RESPONSIBILITIES

The Government will provide the 50 candidate ASOs to the Contractor for evaluation.

DELIVERY OR DELIVERABLES

The contractor will provide a report of the extracted RNAs in the assay results for each animal and each measured time point.

REPORTING REQUIREMENTS

The vendor shall send a full report with raw data and explanations at the end of the project.

OTHER CONSIDERATIONS

Travel:

N/A

Key Personnel:

N/A

Information System Security Plan:

N/A

Data Rights:

All the information and data will be kept confidential.

Section 508—Electronic and Information Technology Standards:

N/A

Publications and Publicity:

N/A

Confidentiality of Information:

All the information and data will be kept confidential.