Can inhibit transcription

References and Recommended Reading Pulverer, B. Journal of Biological Chemistry , — Remenyi, A. Cell 98 , 1—4 Sproul, D. Article History Close. Share Cancel. Revoke Cancel. Keywords Keywords for this Article. Save Cancel. Flag Inappropriate The Content is: Objectionable. Flag Content Cancel. Email your Friend. Submit Cancel. This content is currently under construction. Explore This Subject. Consequences of Gene Regulation. Gene Responses to Environment. Regulation of Transcription.

Transcription Factors. From DNA to Protein. Organization of Chromatin. Topic rooms within Gene Expression and Regulation Close.

No topic rooms are there. Or Browse Visually. Other Topic Rooms Genetics. Student Voices. Creature Cast. Simply Science. Green Screen. Green Science. Bio 2. The Success Code. Why Science Matters. The Beyond. Plant ChemCast. Postcards from the Universe. Brain Metrics. Mind Read. Eyes on Environment. Even though silvestrol is effectively cytotoxic against multiple cancer cell lines in vitro , only partial protein synthesis inhibition was observed in mice models of lymphoma Bordeleau et al.

The main issue with silvestrol and its analogs is that they upregulate multi-drug-resistant gene ABCB1 and that they are substrates of p-glycoprotein, a well-known resistance-causing efflux transporter Gupta et al. Despite the decade long research, silvestrol and its analogs remain at the preclinical drug research stage, and none of them has made it into clinical trials Peters et al.

Omacetaxine, formerly known as homoharringtone Figure 8 , is a plant alkaloid from Cephalotoxus fortune. It was identified in s as the inhibitor of the initial elongation step of translation Huang, ; Fresno et al. Because omacetaxine affects the elongation step, it is a more general translation inhibitor than other molecules that target translation initiation which inhibit only the translation of specific sequences Wetzler and Segal, Treatment with omacetaxine leads to a rapid decrease in the number of proteins with short half-lives, including the oncogenic cyclin D1 and c-Myc Robert et al.

Omacetaxine was intensely studied after its discovery both in vitro and in vivo against chronic myeloid leukemia but after the approval of imatinib and other tyrosine kinase inhibitors, the scientific interest toward it dwindled Wetzler and Segal, Recently, new clinical studies around omacetaxine have been started due to its synergistic effect with tyrosine kinase inhibitors, especially in the treatment of cancers with mutations in the tyrosine kinase genes Marin et al.

Omacetaxine is approved by the FDA for the treatment of chronic myeloid leukemia if the disease does not respond to two or more tyrosine kinase inhibitors Cortes et al. This way, omacetaxine can help patients who suffer from lack of effect of those drugs, intolerance or drug-drug interactions.

The most common adverse effects of omacetaxine are myelosuppression and thrombocytopenia which are observed in almost all patients but they can be managed with supportive care, dose delays and reduction in the number of days that omacetaxine is administered Rosshandler et al. In the cell, these oligonucleotides can hybridize to target RNA sequences, including mRNA and non-coding nc RNA to inhibit their expression and thereby regulate the availability of specific proteins.

Different chemical modifications of synthesized oligonucleotides have been made to increase their nuclease stability, decrease non-specific effects and to improve their cellular uptake Karaki et al. In addition to increased stability, some of these modifications have also enabled the oligomer binding to double-stranded DNA and have altered mechanisms of action.

ASOs have different mechanisms of actions including enzyme-mediated target RNA degradation, steric-hindrance of translation, as well as modulation of splicing and transcription MacLeod and Crooke, This is efficiently mediated by the ubiquitous RNase H and has the advantage that the oligonucleotide can be targeted to any part of the RNA molecule.

However, problems of specificity due to activation following partial hybridization have been observed and pose a concern. Modified oligomers deviate from RNase H-induced cleavage and can inhibit protein expression via other mRNA quality control decay pathways.

These include the non-sense-mediated decay NMD Ward et al. Interestingly, this can be used either to block mature protein expression or to correct aberrant splicing thereby restoring the protein function.

Furthermore, oligonucleotides can result in steric hindrance of translation by preventing ribosome binding when targeted near the translation initiation codon Chery, ; Goyal and Narayanaswami, In recent years with the growing identification and appreciation of the role of non-coding RNAs in transcription and gene regulation, ASO targeting non-coding RNAs have now also been implicated in modulation of transcription.

It is likely, that new effects on transcription will be identified with increasing use of ASOs in the non-coding RNA field and better understanding of their functions. The power of ASOs as therapeutic agents has long been realized with FDA approval of the first ASO already in and 5 approved to date for nervous muscular or familial metabolic diseases Stein and Castanotto, ; Yamakawa et al.

However, antisense therapy for cancer treatment has lagged behind and to date there are no approved ASO therapeutic for cancer. Nevertheless, there are many ongoing clinical trials using ASOs targeting primarily cell proliferation and signaling as well as cancer stroma and resistance to chemotherapy. With these encouraging results a multicenter phase III trial was initiated, however it was discontinued due to patient recruitment failure NCT AP has also been tested for the treatment of patients with advanced pancreatic carcinoma, metastasizing melanoma, or metastatic colorectal carcinoma and a phase II trial demonstrated encouraging survival results Stauder et al.

In addition, cellular trafficking and localization of AZD across different tumor cell lines have been characterized and was found to vary Linnane et al.

Following completion of a phase I trial the molecule was demonstrated to be safe and well-tolerated, but it was discontinued by AstraZeneca because of its insufficient efficacy possibly due to targeting both mutant and wild-type KRAS mRNA Yang et al. The partial base pairing compromises the AGO slicer catalytic activity and instead results in either translation repression or degradation of mRNA. Activation of RNAi and the use of siRNA for therapeutic means have the appeal of small molecules but have the added value of specificity and the flexibility of target selection.

For these reasons some siRNA molecules were already in clinical trials within 10 years of their discovery. However, early clinical trials with siRNAs failed, some of which due to non-specific activation of the innate immunity. For a comprehensive review see Khvorova and Watts, These modifications not only served to increase safety by avoiding dsRNA activation of the immune response, but they also increased the potency and stability of dsRNA by increasing their resistance to endonucleases, as well as in some instances facilitating antisense strand selectivity Zuckerman and Davis, In addition to chemical modifications of dsRNA, progress in targeting and packaging of these for improved delivery of RNAi drugs was also necessary Pecot et al.

Successful packaging of dsRNA was achieved in nanoparticles, polymers and dendrimers to name a few, and targeting has been accomplished with aptamers, antibodies, peptides and small molecules Zhou and Rossi, ; Springer and Dowdy, In cases where antagonism of the miRNA is desired a synthetic, single-stranded RNA is introduced to target the miRNA for degradation and thereby inhibit its activity and disease progression.

Both of these strategies can be useful for cancer treatment, either in inhibiting oncogenes or gene products facilitating cancer growth or to reactivate miRNAs that are downregulated in tumors Van Roosbroeck and Calin, ; Takahashi et al.

RNA therapeutic avenues are likely to extend in the future, as we are not limited to RNAi mechanisms in the cytoplasm but dsRNAs can also act in the nucleus to cause transcriptional gene silencing TGS via modification of epigenetic marks Castel and Martienssen, ; Martienssen and Moazed, In addition, siRNA targeting gene promoters can also cause transcriptional activation Laham-Karam et al.

Today, many RNAi drugs for cancer therapy are in clinical trials. LODER is a polymeric matrix of poly lactic-co-glycolic acid that facilitates prolonged delivery of siRNA and has been tested for the treatment of pancreatic cancer. Following preclinical safety and toxicity assessment Ramot et al. The RNAi drug was found to be safe and well-tolerated despite some adverse reactions and importantly demonstrated anticancer effects.

It has now proceeded to Phase II trials. EphA2 is a tyrosine kinase receptor that normally functions in neuronal development but its overexpression has been observed in human cancers and decreased expression can reduce tumorigenicity Ieguchi and Maru, Both prodrugs of it and mimics have been tested for cancer treatment Zhao et al. Although miRNA targeted therapy remains appealing the feasibility of such therapy is still to be proven.

Although different chemical modification of synthetic RNA molecules intended for RNAi therapeutics have increased stability and demonstrated favorable pharmacokinetics properties, these Chemo-engineered RNAs are different from naturally transcribed RNA molecules in living cells, which are largely unmodified.

This difference affects the structure, properties, and possibly the activity and immunogenicity of these molecules reviewed in Yu et al. Also, effort has been made to bioengineer RNA molecules in living cells, including in bacteria and yeast Huang et al. Importantly, the BERAs produced have demonstrated biological activity in cells and in animal models.

Examples of these tested for tumor treatment, are miRa prodrugs. Likewise, systemic delivery of an improved miRa-5p prodrug significantly decreased metastatic lung xenograft tumor growth in mice Ho et al. In addition, other formulation of miRa prodrugs have resulted in similar findings in orthotopic osteosarcoma xenograft tumor mouse model Zhao et al. In both these studies, it was also shown that the therapeutic doses of mira prodrug were well-tolerated as indicated in blood chemistry profiles monitoring for hepatic and renal toxicities.

Recently, another miRNA prodrug was investigated targeting pancreatic cancer Li et al. A bioengineered miR was tested alone or in combination with chemotherapy treatment in PANC-1 xenograft and pancreatic cancer patients derived xenograft PDX mouse models and was found to be effective in reducing tumor growth and was well-tolerated Tu et al.

This can be done by cationic lipids, polymers, and peptides Kim et al. Specifically, polyethylenimine PEI -based polyplexes complexes of nucleotides and polycations have facilitated efficient delivery in tumor models Zhao et al. However due to potential toxicity of polyplexes Lv et al. Increased serum stability of these BERAs as well as improved delivery, therapeutic effectiveness and survival of tumor bearing mice were observed.

These positive results encourage the further development of BERA for tumor therapy. Oncogenes are genes that can cause cancer once mutated or when expressed at high levels Croce, Many oncogenic pathways lead to altered transcription or translation of various proteins. In order to keep the topic of this review we will focus on two oncogenic targets that are involved with transcription and translation; transcription factors and KRAS.

Both of these oncogenes were previously thought to be undruggable but nevertheless, a few inhibitors for both of them have been published in the last few years. The readers interested in the drugs designed for oncogenic kinases or other oncogenic pathways are referred to other reviews Bhullar et al. The idea of targeting transcription factors in cancer has been around about 20 years Darnell, Transcription factors can drive oncogenesis as fusion proteins or by chromosomal translocation events Bushweller, The DNA binding site of transcription factors with its positively charged environment is a difficult target for developing small-molecule inhibitors, and thus most of the recent efforts have been aimed for the protein-protein interaction PPI inhibition, such as RG Arkin et al.

Transcription factors can be directly targeted by disrupting their transcription or translation, stabilizing their auto-inhibitory states, inducing covalent modifications with cysteine bridges or changing their post-translational modifications Bushweller, Here we will shortly present the most advanced molecules that target transcription factors and are in or close to starting clinical trials Figure 9. More detailed insights of targeting transcription factors in cancer can be found in the excellent review by Bushweller, Figure 9.

Molecules that target transcription factors and are in clinical trials or close to starting them. So far, four different PPI inhibitors that target transcription factors have made it into the clinical trials or are very close to starting them Bushweller, Two of these, RG idasanutlin and HDM siremadlin; Figure 9 , prevent MDM2 binding to p53 which prevents the degradation of p53 and increases its cellular levels leading to increased cell death Ding et al.

RG and HDM have multiple phase I clinical trials ongoing both against solid tumors such as melanoma as well as hematological malignancies such as leukemia. The clinical trials in leukemia are planned for KO and SNDX which target the mixed lineage leukemia MLL transcription factor and inhibit its binding to menin which prevents this fusion protein from activating genes driving leukemia.

Unfortunately, the structures of these inhibitors have not been made public yet. The inhibition with SY leads to decreased levels of multiple oncogenic transcription factors and it exhibits the inhibitory effects on multiple cancer cell lines at nanomolar level. In addition, mouse xenograft studies showed modest antitumor activity in both AML as well as ovarian cancer, and a synergistic effect with venetoclax Hu et al.

Both inhibitors lower the expression levels of the c-Myc oncogene and the proliferation rates of multiple cancer cell lines, and in animal models they display suitable properties for oral dosing in humans. The clinical trials are ongoing for advanced cancers, both solid tumors and leukemias. Drugs affecting transcription and translation are difficult to develop.

As RAS proteins are the most commonly mutated proteins in cancer and at the same time are part of the signaling cascade from the EGFR receptor, these have been a natural target for drug discovery. Those interested to know more about RAS protein structure and function are advised to look at recently published review Pantsar, and another review about early drug discovery work on RAS by Ostrem and Shokat As there are no other clear druggable pockets in RAS direct targeting seemed to be an impossible mission.

The problem was partially solved by the seminal work of Shokat lab which demonstrated that covalent interaction targeting mutated G12C residues is able to deliver in vivo relevant inhibition of RAS activation Ostrem et al.

The initial compounds presented were developed by disulphide-fragment based screening using tethering compounds. After early hit-optimization guided by X-ray crystallography an optimized G12C targeting covalent inhibitor was presented.

In the optimized compounds disulfides were replaced by different electrophilic warheads and especially acrylamides were used.

Upon covalent interaction G12C position compounds were binding previously unknown allosteric pocket. This is not surprising as such, but more surprising is a very recent report concerning the rapid non-uniform adaptation to KRAS G12C inhibition Xue et al. According to Xue et al. Partially this effect might be specific for the currently used G12C inhibitor ARS but due to similar binding mode as with AMG it seems that this conclusion will be a general one Janes et al.

History has shown us that it is indeed not straight-forward to develop transcription or translation inhibitors. Even more difficult is to target these inhibitors only toward malignant cells. There have been a few clinical successes in their development, such as the CDK inhibitors, especially in combination with other chemotherapeutics.

Targeting these central cellular processes has advantages to be more directed to cancer cells than non-specific chemotherapeutic agents such as cisplatin. On the side of disadvantages, targeting transcription and translation may affect multiple pathways hence circumventing the targeted pathway, and there are inevitable side effects arising from the fact that all cells require transcription and translation for their proper function.

Transcription and translation are fundamental processes that targeting them is bound to result in cell death, as such cancer treatment based on these processes needs to be done in a manner that is safe for healthy cells.

To achieve the specific and effective treatment, the myriad of proteins involved will continue to offer drug design possibilities far into the future. In addition, RNA was previously considered to be undruggable and not suitable as a drug itself, but now RNA-targeting and RNA-based drugs can be used as very precise methods to target some cancers.

The recently discovered RNA activation of transcription offers uncharted possibilities in the treatment of cancer. Furthermore, transcription factors and oncogenes were also thought to be undruggable, but within the last few years we have seen some molecules targeting them entering clinical trials.

By widening the scope of drug targets from traditional proteins with specified binding sites to transcription factors, oncogenes and RNA molecules, we are discovering new and specific ways to target cancer cells. So far, we have produced some highly specific, safe and efficacious cancer therapies which inhibit transcription and translation, and the newly discovered targets and our ever-increasing knowledge about the biological basics of these processes is bound to keep this field of inhibitor development ongoing far into the future.

All authors contributed to manuscript revision, read and approved the submitted version. The authors thank Maire Taponen Foundation NL-K personal grant and competitive funding to strengthen university research profiles, 5th call, funding to University of Eastern Finland, funded by the Academy of Finland, funding decision The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

The authors apologize for colleagues whose work could not be referenced due to word count limits. Abdelrahim, M. TAS preclinical, clinical and beyond. Oncology 85, — Alqahtani, A. Bromodomain and extra-terminal motif inhibitors: a review of preclinical and clinical advances in cancer therapy. Future Sci. Arkin, M. Small-molecule inhibitors of protein-protein interactions: progressing toward the reality. Arruebo, M.

Assessment of the evolution of cancer treatment therapies. Cancers 3, — Asghar, U. The history and future of targeting cyclin-dependent kinases in cancer therapy. Babokhov, M. Local chromatin motion and transcription. Balakrishnan, K. Blood , — Ballou, L.

Rapamycin and mTOR kinase inhibitors. Banerjee, S. Minnelide, a novel drug for pancreatic and liver cancer. Pancreatology 15, S39—S Bartsch, R.

Ribociclib: a valuable addition to treatment options in breast cancer? ESMO Open Beg, M. Phase I study of MRX34, a liposomal miRa mimic, administered twice weekly in patients with advanced solid tumors. Invest New Drugs 35, — Bhat, M. Targeting the translation machinery in cancer.

Drug Discov. Bhullar, K. Kinase-targeted cancer therapies: progress, challenges and future directions. Cancer Blachly, J.

Emerging drug profile: cyclin-dependent kinase inhibitors. Lymphoma 54, — Blum, K. Risk factors for tumor lysis syndrome in patients with chronic lymphocytic leukemia treated with the cyclin-dependent kinase inhibitor, flavopiridol. Leukemia 25, — Bogdahn, U. Neuro Oncol. Bolden, J. Inducible in vivo silencing of Brd4 identifies potential toxicities of sustained BET protein inhibition.

Cell Rep. Bordeleau, M. Therapeutic suppression of translation initiation modulates chemosensitivity in a mouse lymphoma model. Bouras, E. Gene promoter methylation and cancer: an umbrella review. Gene , — Brian, P. Wortmannin, an antibiotic produced by Penicillium wortmanni. Buettner, R. Bushweller, J. Targeting transcription factors in cancer — from undruggable to reality. Cancer 19, — Byrd, J. Flavopiridol administered using a pharmacologically derived schedule is associated with marked clinical efficacy in refractory, genetically high-risk chronic lymphocytic leukemia.

Bywater, M. Inhibition of RNA polymerase I as a therapeutic strategy to promote cancer-specific activation of p Cancer Cell 22, 51— Canon, J. Nature , — Castel, S. Cencic, R. Antitumor activity and mechanism of action of the cyclopenta[b]benzofuran, silvestrol. Chen, P. Spectrum and degree of CDK drug interactions predicts clinical performance.

Cancer Ther. Chen, Q. A general approach to high-yield biosynthesis of chimeric RNAs bearing various types of functional small RNAs for broad applications. Nucleic Acids Res 43, — Chen, W.

Silvestrol induces early autophagy and apoptosis in human melanoma cells. BMC Cancer Cheng, Y. Targeting epigenetic regulators for cancer therapy: mechanisms and advances in clinical trials. Signal Trans. Targeted Therap. Chery, J. Postdoc J. Choo, A. Chung, J. Rapamycin-FKBP specifically blocks growth-dependent activation of and signaling by the 70 kd S6 protein kinases.

Cell 69, — Cochet-Meilhac, M. Mechanism of the inhibition of RNA polymerases B by amatoxins. Acta , — Colis, L. Oncotarget 5, — Cortes, J. Phase 2 study of subcutaneous omacetaxine mepesuccinate for chronic-phase chronic myeloid leukemia patients resistant to or intolerant of tyrosine kinase inhibitors.

Cramer, P. Eukaryotic transcription turns Cell , — Croce, C. Oncogenes and cancer. Crooke, S. Molecular mechanisms of antisense oligonucleotides. New York: W. Freeman; Section Active repression mechanisms of eukaryotic transcription repressors. Trends in Genetics, 12 6 , — Transcriptional repression in eukaryotes. Trends in Genetics, 6, — Please enter your institutional email to check if you have access to this content. Please create an account to get access.

Forgot Password? Please enter your email address so we may send you a link to reset your password. To request a trial, please fill out the form below. A JoVE representative will be in touch with you shortly. You have already requested a trial and a JoVE representative will be in touch with you shortly. If you need immediate assistance, please email us at subscriptions jove.

Thank You. Please enjoy a free hour trial. In order to begin, please login. Please click here to activate your free hour trial. If you do not wish to begin your trial now, you can log back into JoVE at any time to begin. Save to playlist. Filter by:. Eggs therefore contain many maternally originated mRNA transcripts as a ready reserve for translation after fertilization Figure 1.

On the degradative side of the balance, cells can rapidly adjust their protein levels through the enzymatic breakdown of RNA transcripts and existing protein molecules. Both of these actions result in decreased amounts of certain proteins. Often, this breakdown is linked to specific events in the cell. The eukaryotic cell cycle provides a good example of how protein breakdown is linked to cellular events.

This cycle is divided into several phases, each of which is characterized by distinct cyclin proteins that act as key regulators for that phase. Before a cell can progress from one phase of the cell cycle to the next, it must degrade the cyclin that characterizes that particular phase of the cycle.

Failure to degrade a cyclin stops the cycle from continuing. Some regions are removed introns during initial mRNA processing.

The remaining exons are then spliced together, and the spliced mRNA molecule red is prepared for export out of the nucleus through addition of an endcap sphere and a polyA tail. Once in the cytoplasm, the mRNA can be used to construct a protein. At the top of the diagram, within the nucleus, is a grey DNA double helix.

A transparent, rectangular box is drawn on top of most of the double helix. The rectangular box is shaded with two alternating colors; the purple segments represent exons, and the light-green segments represent introns. The pre-mRNA molecule is shown as a grey, single-stranded RNA molecule made up of a linear backbone with vertical rectangles arranged along its length. The tops of the rectangles are either pointed, rounded, cupped, or V-shaped to represent different nucleotides. A transparent, rectangular box is drawn over most of the pre-mRNA molecule, with red regions that align with the purple DNA exons and light-green regions that align with the light-green introns in the DNA template.

The mature mRNA also has a light peach-colored sphere attached to its left end to represent the 5-prime cap, and four adenosine molecules attached to its right end to represent the poly-A tail. In the background of the cytoplasm, thin black lines show silhouettes of cytoplasmic organelles, including the Golgi apparatus and endoplasmic reticulum. Translation of mRNA into protein occurs in the cytoplasm. Only a fraction of the genes in a cell are expressed at any one time. The variety of gene expression profiles characteristic of different cell types arise because these cells have distinct sets of transcription regulators.

Some of these regulators work to increase transcription, whereas others prevent or suppress it. This sequence is almost always located just upstream from the starting point for transcription the 5' end of the DNA , though it can be located downstream of the mRNA 3' end.

In recent years, researchers have discovered that other DNA sequences, known as enhancer sequences , also play an important part in transcription by providing binding sites for regulatory proteins that affect RNA polymerase activity. Binding of regulatory proteins to an enhancer sequence causes a shift in chromatin structure that either promotes or inhibits RNA polymerase and transcription factor binding. A more open chromatin structure is associated with active gene transcription.

In contrast, a more compact chromatin structure is associated with transcriptional in activity Figure 2. Some regulatory proteins affect the transcription of multiple genes. This occurs because multiple copies of the regulatory protein binding sites exist within the genome of a cell. Consequently, regulatory proteins can have different roles for different genes, and this is one mechanism by which cells can coordinate the regulation of many genes at once.