Related Experiment Video

Updated: May 15, 2026

Use of Interferon-γ Enzyme-linked Immunospot Assay to Characterize Novel T-cell Epitopes of Human Papillomavirus
13:41

Use of Interferon-γ Enzyme-linked Immunospot Assay to Characterize Novel T-cell Epitopes of Human Papillomavirus

Published on: March 8, 2012

Lack of correlation between predicted and actual off-target effects of short-interfering RNAs targeting the human

J E Hanning1, H K Saini, M J Murray

  • 1Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK.

British Journal of Cancer
|January 10, 2013
PubMed
Abstract

Insights

Computational prediction of off-target effects (OTEs) in short-interfering RNA (siRNA) therapeutics does not accurately reflect actual transcriptional OTEs. This study found no correlation between predicted and observed OTEs, highlighting limitations in current prediction methods.

Area of Science:

  • RNA interference (RNAi) therapeutics
  • Computational biology
  • Molecular diagnostics

Background:

  • Therapeutic short-interfering RNAs (siRNAs) are designed to minimize off-target effects (OTEs).
  • Current prediction methods focus on matches between siRNA seed sequences and messenger RNA (mRNA) 3' UTRs.
  • It is assumed that more predicted OTEs lead to greater actual OTEs and detrimental phenotypic consequences.

Purpose of the Study:

  • To investigate the accuracy of computational prediction of OTEs for therapeutic siRNAs.
  • To evaluate the correlation between predicted and actual OTEs in HPV-negative cells.

Main Methods:

  • Investigated OTEs of siRNAs targeting the human papillomavirus (HPV) type-16 E7 oncogene.
  • Utilized HPV-negative squamous epithelial cells (normal cervix and HaCaT skin cells).
  • Analyzed transcriptional OTEs, including seed-dependent and unpredicted effects.

Main Results:

  • No correlation was observed between computationally predicted OTEs and actual seed-dependent OTEs (P=0.76).
  • Only 20.5% of actual transcriptional OTEs were predicted; unpredicted OTEs involved immune pathways and cancer-associated pathways.
  • Differential gene expression overlap between cell types was minimal (0-5.9%).

Conclusions:

  • Current computational methods for predicting siRNA OTEs are not well-supported by experimental data.
  • Actual OTEs encompass unpredicted effects, including immune responses and downstream pathway alterations.
  • The assumption that predicted OTEs correlate with actual OTEs is not supported by these findings.

More Related Videos

A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions13:56

A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions

Published on: July 18, 2013

Genome-wide RNAi Screening to Identify Host Factors That Modulate Oncolytic Virus Therapy08:51

Genome-wide RNAi Screening to Identify Host Factors That Modulate Oncolytic Virus Therapy

Published on: April 3, 2018

Related Concept Videos

Initiation of Translation02:33

Initiation of Translation

Initiating translation is complex because it involves multiple molecules. Initiator tRNA, ribosomal subunits, and eukaryotic initiation factors (eIFs) are all required to assemble on the initiation codon of mRNA. This process consists of several steps that are mediated by different eIFs.
First, the initiator tRNA must be selected from the pool of elongator tRNAs by eukaryotic initiation factor 2 (eIF2). The initiator tRNA (Met-tRNAi) has conserved sequence elements including modified bases at...
Rous Sarcoma Virus (RSV) and Cancer01:03

Rous Sarcoma Virus (RSV) and Cancer

Rous Sarcoma virus or RSV was discovered by F. Peyton Rous in the year 1911 as a filterable transmissible agent that could cause tumors in chickens. He won a Nobel Prize for this discovery in 1966. His experiments clearly demonstrated that some cancers could be caused by infectious agents and led to the discovery of many more cancer-causing viruses in animals as well as humans.
RSV is a retrovirus that contains two copies of a plus-strand  RNA genome. Its genome consists of four main open...
Rous Sarcoma Virus (RSV) and Cancer01:03

Rous Sarcoma Virus (RSV) and Cancer

Rous Sarcoma virus or RSV was discovered by F. Peyton Rous in the year 1911 as a filterable transmissible agent that could cause tumors in chickens. He won a Nobel Prize for this discovery in 1966. His experiments clearly demonstrated that some cancers could be caused by infectious agents and led to the discovery of many more cancer-causing viruses in animals as well as humans.
RSV is a retrovirus that contains two copies of a plus-strand  RNA genome. Its genome consists of four main open...
Mechanisms of Retrovirus-induced Cancers01:51

Mechanisms of Retrovirus-induced Cancers

Retroviruses are RNA viruses that have been shown to cause cancers in diverse species, including chickens, mice, cats, and monkeys. The RNA genomes of these viruses are first reverse-transcribed into single and then double-stranded DNA (dsDNA) copies. This dsDNA called proviral DNA then integrates into the host genome. Subsequently, the host cell transcribes the proviral DNA in concert with the chromosomal DNA. This leads to the production of viral RNA and proteins that assemble at the host...