Antisense Oligonucleotide Screening

Antisense Oligonucleotides (ASOs) are single-stranded deoxynucleotide analogs, usually 15–20 bp in length. Their sequence is complementary to the sense sequence of target mRNA. ASOs can be used in traditional drug discovery workflows for target identification and validation and are now being explored as therapeutics themselves.  ASO-based therapy is an active area of drug development designed to treat a variety of gene specific diseases, especially in the setting of personalized medicine and orphan diseases.  iXCells Biotechnologies has extensive experience with ASO in vitro screening using various disease relevant cellular models, including human iPSC-derived neurons and primary cells.

Overview of Capabilities

We have a team of scientists dedicated to primary cell culture, custom iPSC generation, genome editing and directed differentiation to help our customers to generate their own “Disease-in-a-Dish” models. Combining our in depth understanding of cell biology with gene based knockdown technologies like siRNA and ASO positions iXCells Biotechnologies as a leader in providing Target Identification/Validation (TIV) for gene-based diseases.  In order to provide our customers with a front to back solution for their drug discovery we have built out our screening capabilities to include automated liquid handling (Video 1) and 384-well based qPCR solutions.

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Video 1.  High throughput ASO screening using ASSIST PLUS pipetting robot

Figure 1.  High throughput gene-expression analysis using SNP-variant specific TaqMan probes

These services provide our customers with disease-relevant, patient-derived models which continue to accelerate the pace of drug discovery and disease understanding. Our workflows align closely with direction provided by regulatory agencies such as the FDA.

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"Following decades of research and study, a new class of drug, known as antisense oli-gonucleotides (ASO), are maturing as drug development efforts advance. In tandem with a growing ASO pipeline, FDA has recently issued a draft guidance for dealing with ASO investiga-tional new drug (IND) filings (1)."

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"This N-of-1+ initiative is focused on the development of antisense oligonucleotide (ASO) therapeutics for patients with a serious, life-threatening rare disease where there are fewer than ~100 known patients worldwide. These individuals would be candidates for treatment with the specific ASO and would be expected to benefit from this treatment. However, due to low patient numbers there is little or no commercial incentive to develop these ASOs (Khvorova & Watts, 2017; Kim, 2019)."

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Case Study

Let iXCells Biotechnologies help you develop your “Disease-in-a-Dish” model and get you into the clinic faster with this exciting new class of drugs.

In the following example, patient specific iPSC-derived neurons were prepared in large scale by our stem cell experts. ~500 ASOs were tested at two concentrations to reduce the target gene expression in the patient-derived iPSC neurons.

Highlights: 

  • Screening format in 96-well cell culture and ASO treatment
  • Automated sample handling using integra ASSIST PLUS pipetting robot
  • TaqMan-probe-based readout of normal and disease-specific SNPs in 384-well format

 

Figure 2a. Robust Performance and Large Screening Window using Positive and Negative Control ASO Reagents
Figure 2b. High Reproducibility Across Biologic Replicates

Figure 2a. Robust Performance and Large Screening Window using Positive and Negative Control ASO Reagents

Figure 2b. High Reproducibility Across Biologic Replicates

  • Large screening window and dose dependence of positive control ASO reagents across screening plates (Figure 2a)
  • Minimal effect of Negative control ASO reagents on Target Gene across screening plates (Figure 2a)
  • Tight correlation of biologic replicates both within and across screening plates (Figure 2b)