Long-Term Transcriptional Gene Silencing by RNA Viruses

Supplemental Information

Long-term transcriptional gene silencing by RNA viruses

Juozas Baltusnikasa*, Saulius Satkauskasa, Kenneth Lundstromb

aBiophysical Research Group, Vytautas Magnus University, Vileikos str. 8, LT44404, Kaunas, Lithuania.

bPanTherapeutics, Route de Lvaux 49, CH1095, Lutry, Switzerland.

*Correspondence: (J. Baltusnikas).

Inventory

Supplemental items (Text Box S1 and Table S1) relationship to the main figures and tables:

1.Text Box S1 (In main text goes first, before all main elements);

2.Figure 1, Key Figure;

3.Figure 2;

4.Figure 3;

5.Table S1 (In main text goes last, after all main elements).

Box S1. Clinical success of viral andsmall RNA therapy

Currently, many clinical trials seek to exploit small interfering RNA (siRNA) and microRNA for the treatment of various diseases [S1]. For instance, post-transcriptional gene silencing (pTGS) was successfully applied in treating hereditary ATTR amyloidosis in a phase II clinical trial [S2] and now it is evaluated in a phase III clinical trial. Also, in a phase Iclinical trial, pTGS was successfully used to inhibit proprotein convertase subtilisin–kexin type 9 expression and to decrease low-density lipoprotein cholesterol [S3]. pTGS was also used in a phase I clinical trial, where siRNAs targeting VEGFA and KIF11 mRNAs induced regression of metastases in liver [S4]. Adeno-associated virus-mediated delivery has been approved for the treatment of lipoprotein lipase deficiency [S5]. Also,ex vivo retrovirus gene therapy was approved to treat severe combined immunodeficiency, which is caused by the lack of adenosine deaminase enzyme [S6]. These and many other studies have proven that the success of viral gene therapy and pTGS has highly increased. Nevertheless, in many clinical cases substantial step forward could be expected from self-replicating RNA virus induced long-term transcriptional gene silencing, where a single administration could lead to long-term therapeutic effect.

Table S1. Advantages and disadvantages of self-replicating RNA viruses for induction of long-term transcriptional gene silencing (TGS).

Genus / Polarity / Groupa / Segmented / Site of Action / Cell entry mechanismb / Advantages / Disadvantages
Sindbis virus / -Alphavirus / -Positive / -IV / -No / -Cytoplasm / -Endocytosis / -Very high expression levels
-Transduction of neurons.
-Low-toxicity vectors / -Cytotoxicity
-Induction of apoptosis
-Broad host cell range
Semliki forest virus / -Alphavirus / -Positive / -IV / -No / -Cytoplasm / -Endocytosis / -Very high expression levels
-Transduction of neurons
-Low-toxicity vectors / -Cytotoxicity
-Induction of apoptosis
-Broad host cell range
Kunjin virus / -Flavivirus / -Positive / -IV / -No / -Cytoplasm / -Endocytosis / -Very high expression levels
-Low-toxicity strains
-Potential inhibition of interferon action / -Induction of long-term TGS might require regulation of long-term sRNA expression
-Broad host cell range
Vesicular stomatitis virus / -Vesiculovirus / -Negative / -V / -No / -Cytoplasm / -Endocytosis / -High expression levels / -Cytotoxicity
-Induction of apoptosis
-Broad host cell range
Sendai virus / -Respirovirus / -Negative / -V / -No / -Cytoplasm / -Membrane fusion / -High expression levels
-Non-toxic strains (Cl.151)
-Interferon resistance / -Induction of long-term TGS might require regulation of long-term sRNA expression
-Broad host cell range
Influenza virus / -Influenzavirus A / -Negative / -V / -Yes / -Nucleus / -Endocytosis / -Transcription in nucleusc. -No pre-existing immunity due to envelope protein antigen evolvement / -Cytotoxicity
-Induction of apoptosis
-Broad host cell range

aThe Baltimore Classification has 7 groups, which are based on the mechanism of viral mRNA synthesis.

bPseudotyping might change the mechanism of cell entry.

cAdvantages of small RNA transcription in nucleus in order to induce long-term TGS needs to be clarified.

References

S1. Chakraborty, C. et al. (2017) Therapeutic miRNA and siRNA: Moving from Bench to Clinic as Next Generation Medicine. Mol Ther Nucleic Acids 8, 132-143.

S2. Suhr, O.B. et al. (2015) Efficacy and safety of patisiran for familial amyloidotic polyneuropathy: a phase II multi-dose study. Orphanet J Rare Dis 10, 109.

S3. Fitzgerald, K. et al. (2017) A Highly Durable RNAi Therapeutic Inhibitor of PCSK9. N Engl J Med 376 (1), 41-51.

S4. Tabernero, J. et al. (2013) First-in-humans trial of an RNA interference therapeutic targeting VEGF and KSP in cancer patients with liver involvement. Cancer Discov 3 (4), 406-17.

S5. Haddley, K. (2013) Alipogene tiparvovec for the treatment of lipoprotein lipase deficiency. Drugs Today (Barc) 49 (3), 161-70.

S6. Schimmer, J. and Breazzano, S. (2016) Investor Outlook: Rising from the Ashes; GSK's European Approval of Strimvelis for ADA-SCID. Hum Gene Ther Clin Dev 27 (2), 57-61.