Gene Expression Profiling to Detect New Treatment Targets in Leukemia and Lymphoma: A Future Perspective
Gertjan J. L. Kaspers, Bertrand Coiffier, Michael C. Heinrich, Elihu Estey in Innovative Leukemia and Lymphoma Therapy, 2019
The U133 two-array set provides comprehensive coverage of well-substantiated genes in the human genome. It can be used to analyze the expression level of 39,000 transcripts and variants, including greater than 33,000 human genes. The two arrays comprise more than 45,000 probe sets and 1,000,000 distinct oligonucleotide features. The sequences from which these probe sets were derived were selected from GenBank, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 133, April 20, 2001) and then refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the University of California, Santa Cruz, Golden-Path human genome database (April 2001 release). In addition, an advanced understanding of probe uniqueness and hybridization characteristics allowed an improved selection of probes based on predicted behavior. The U133 chip design uses a multiple linear regression model that was derived from a thermodynamic model of nucleic acid duplex formation. This model predicts probe binding affinity and linearity of signal changes in response to varying target concentrations. The two arrays are manufactured as standard format arrays with a feature size of 18 µm and use 11 probe pairs per sequence. The oligonucleotide length is 25 mer.
Protein Degradation Inducers SNIPERs and Protacs against Oncogenic Proteins
Peter Grunwald in Pharmaceutical Biocatalysis, 2019
In addition to SNIPERs and PROTACs, downregulation of oncogenic proteins can be achieved by genetic knockdown technologies such as antisense oligonucleotides, RNA interference, and genome editing (CRISPR-CAS). Currently, oligonucleotide therapeutics have been developed extensively and are emerging as a new platform for drug development (Yoshida et al., 2018). The U.S. Food and Drug Administration (FDA) have approved five oligonucleotide therapeutics (formivirsen, pegaptanib, mipomersen, eteplirsen, and nusinersen) for clinical treatment (Stein et al., 2017). Despite its great therapeutic potential, genetic knockdown remains clinically challenging because oligonucleotide therapeutics are not efficiently taken up by cells, and delivery to the desired target tissues is technically difficult. SNIPERs and PROTACs are small molecules, so their uptake by cells and delivery to desired target tissues are expected to be easier compared with genetic knockdown technologies. As mentioned above, several SNIPERs and PROTACs against oncogenic proteins have been successfully developed, and some of them suppress the growth of tumor cells in vivo (Winter et al., 2015; Raina et al., 2016; Ohoka et al., 2017b; Winter et al., 2017).
RNA Expression Profiling
Attila Lorincz in Nucleic Acid Testing for Human Disease, 2016
A synthetic oligonucleotide (60 to 70 mers) is bound to a glass surface. Most of the process can be automated (oligonucleotide concentrations are therefore more comparable), resulting in fewer sample mix-ups and smaller losses of samples. The main advantage is that this technique is not difficult to applys and is thus becoming increasingly available. The main disadvantages are the high cost and the fact that one can run out of a given batch of synthesized oligonucleotides.
A multi-storey DNA nanostructure containing doxorubicin and AS1411 aptamer for targeting breast cancer cells
Published in Journal of Drug Targeting, 2022
Elnaz Yaghoobi, TaranehSadat Zavvar, Mohammad Ramezani, Mona Alibolandi, Sara Rahimzadeh Oskuei, Mahsa Zahiri, Morteza Alinezhad Nameghi, Khalil Abnous, Seyed Mohammad Taghdisi
Seven different single-stranded DNA oligonucleotides were designed in a way that each sequence was complementary to some part of the following sequence. In the design of non-complementary parts of sequences 1 and 7, we put the AS1411 aptamer sequence to use this DNA nanostructure as a smart and targeted drug delivery carrier. At first, the 2nd and 3rd sequences were added to each other and in a different microtube the 5th and 6th sequences were incubated with each other. In the next stage, the first sequence was added to the combination of the 2nd and 3rd sequences. After that, the 4th sequence was added to the previous structure (conjugation of 1, 2 and 3). Next, the combination of the 5th and 6th sequence was added to the microtube containing 1 + 2 + 3 + 4 DNA nanostructure. In the final stage, the 7th sequence was added to the previous structure (conjugation of 1, 2, 3, 4, 5 and 6). Each sequence was mixed with the mentioned sequence at room temperature in phosphate-buffered saline (PBS, pH 7.4) buffer containing 50 mM MgCl2. The incubation time between each addition was considered 3 h and the amount of each oligonucleotide was 3 µM in the final reaction. To confirm the development of multi-storey DNA nanostructure, the 2.5% agarose gel electrophoresis test (stained with GelRed®) was conducted.
Meeting report: oligonucleotide ADME workshop
Published in Xenobiotica, 2022
Steve Hood, David Kenworthy, Jesper Kammersgaard Christensen
Oligonucleotides represent a powerful therapeutic modality capable of selectively impacting the production or splicing of RNA that might otherwise be difficult to target with classical small molecule drugs or biologics. This has been clearly demonstrated by the large number of oligonucleotides in clinical trials and successfully launched therapies on the market. However, specifically targeting mRNA in extra-hepatic tissues and cell types after systemic administration continues to be a challenge. The OligoNova scientific network aims to build national and international collaborations to tackle scientific challenges within the area of therapeutic oligonucleotides such as targeted delivery, enhanced cellular uptake and intracellular trafficking. All together OligoNova will help catalyse and translate novel ideas into oligonucleotide therapeutics that will benefit patients and strengthen research capabilities in the field in Sweden.
A perspective on RNA interference-based therapeutics for metabolic liver diseases
Published in Expert Opinion on Investigational Drugs, 2021
Several classes of therapeutic oligonucleotides have been developed over the past few decades. Antisense oligonucleotides (ASOs) consist of 15 to 20 nucleotides in length and act in the nucleus by selectively cleaving complementary pre-mRNAs by using a ribonuclease H (RNase H) dependent mechanism [8]. Double-stranded short interfering RNAs (siRNAs) are typically 20–27 base pairs in length that are separated into their single strand components by a helicase enzyme. The antisense strand (also called the guide strand) binds with perfect complementary to its target mRNA sequence leading to its degradation through the RNA-induced silencing complex (RISC) [9,10] (Figure 1). The endogenous microRNAs (miRs) are small non-coding RNAs that contain 20 to 24 nucleotides and function at the post-transcriptional level to regulate gene expression [11]. miRs typically bind to the 3′-untranslated regions (3ʹ-UTR) of the corresponding target mRNAs of protein-coding genes resulting in inhibition of mRNA translation or target mRNA degradation.
Related Knowledge Centers
- DNA
- DNA Profiling
- DNA Sequencing
- Genetic Testing
- Oligomer
- Polymerase Chain Reaction
- Recombinant DNA
- Rna
- DNA
- Rna
- Recombinant DNA
- DNA Profiling
- Oligonucleotide Synthesis
- Artificial Gene Synthesis
- DNA Sequencing