JoVE Journal

Biology

A subscription to JoVE is required to view this content.

Cost-Efficient Transcriptomic-Based Drug Screening

888 Views

•

06:40 min

•

February 23rd, 2024

DOI :

10.3791/65930-v

February 23rd, 2024

•

Jacqueline Leidner¹^,², Heidi Theis³, Michael Kraut³, Alice Ragogna¹, Marc Beyer¹^,³^,⁴, Joachim Schultze¹^,²^,³, Jonas Schulte-Schrepping¹^,², Caterina Carraro¹^,², Lorenzo Bonaguro¹^,²

¹Systems Medicine, German Center for Neurodegenerative Diseases (DZNE) eV., ²Genomics & Immunoregulation, LIMES Institute, University of Bonn, ³PRECISE Platform for Single Cell Genomics and Epigenomics, DZNE and University of Bonn, ⁴Immunogenomics & Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE) eV.

Transcript

Transcriptomics enable us to gain a deep understanding of cellular program and their reaction towards external changes. However, despite a considerable reduction in library production and sequencing costs over the last decades, the application of this technology, at the scale needed for drug screening, is still unaffordable, hindering the great potential of these methods. Our study present a cost-effective system for transcriptome-based drug screening, combining miniaturized perturbation cultures with mini-bulk transcriptomics.

The optimized mini-bulk protocol provides informative biological signal at cost-effective sequencing depth, enabling extensive screening of known drugs and new molecules. One of the key benefits of combining transcriptomics with unbiased drug screening is the potential to identify new drug targets that have not been previously considered. Conventional drug screening approaches often focus on established target molecules or pathways, hindering the identification of new targets, and potentially resulting in drugs with unforeseen side effects and restricted effectiveness.

Summary

This protocol describes a workflow from ex vivo or in vitro cell cultures to transcriptomic data pre-processing for cost-effective transcriptome-based drug screening.

Explore More Videos

Transcriptomics

Drug Screening

Cost effective System

Miniaturized Cultures

Mini bulk Transcriptomics

Perturbation Responses

Sequencing Libraries

Sample Processing

Data Quality

Chapters in this video

0:00

Introduction

1:08

Drug Screening Using Peripheral Blood Mononuclear Cells (PBMCs) and Cell Lysate Preparation for mRNA Sequencing

3:01

cDNA Library Preparation from the Drug Treated‐Peripheral Blood Mononuclear Cell (PBMC) Lysate for mRNA Sequencing