Nucleic Acid therapeutics Flashcards

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1
Q

What are some examples of nucleic acid-based therapeutics that have gained regulatory approval?

A

Gendicine (approved only in China) - a gene therapy product
Glybera (approved in Europe in 2012, withdrawn in 2017) - a gene therapy product
Vitravene - the first antisense-based product approved by the FDA
Macugen - an aptamer
Kynamro - an oligonucleotide
Eteplirsen - an oligonucleotide
Defitelio - an oligonucleotide
Spinraza - an oligonucleotide

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2
Q

How does the number of nucleic acid-based products approved compare to protein-based biopharmaceuticals?

A

By the early 2020s, only a handful of nucleic acid-based products had gained regulatory approval, while hundreds of protein-based biopharmaceuticals had been approved.

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3
Q

What is THPdb?

A

THPdb is a manually curated repository of FDA approved therapeutic proteins. It provides comprehensive information on FDA approved therapeutic peptides, proteins, and their drug variants.

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4
Q

What are some current developments in nucleic acid-based therapeutics?

A

Current developments include gene therapy, antisense technology, RNA interference (RNAi), ribozymes, aptamers, and CRISPR genome editing technology.

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5
Q

Can you provide an example of a gene therapy product?

A

Gendicine is an example of a gene therapy product that has gained regulatory approval, although it is approved only in China.

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6
Q

What was the first antisense-based product approved by the FDA?

A

Vitravene was the first antisense-based product approved by the FDA.

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7
Q

What is the fundamental principle of gene therapy?

A

The fundamental principle of gene therapy is the stable introduction of a gene into the genetic complement of a cell to achieve a therapeutic goal.

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8
Q

Which disease category has been the focus of the majority of gene therapy trials?

A

Two-thirds of all gene therapy trials conducted to date aim to treat cancer.

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9
Q

Where are the majority of gene therapy trials conducted?

A

Approximately 67% of gene therapy trials are being conducted in the United States, with the remaining trials being conducted in Europe, mainly in the UK and Germany.

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10
Q

What percentage of gene therapy trials reach Phase III?

A

Only about 2.2% of all gene therapy trials reach Phase III.

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11
Q

What are the two basic approaches to gene therapy?

A

The two basic approaches to gene therapy are cell-based delivery (in vitro approach) and direct delivery (in vivo approach).

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12
Q

What is the in vitro approach in gene therapy?

A

The in vitro approach involves removing target cells from the body, culturing them in vitro, and incubating them with the vector containing the desired gene(s) before reintroduction into the body.

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13
Q

What is the in situ approach in gene therapy?

A

The in situ approach involves the direct injection or administration of the gene-containing vector to the target cells in the immediate vicinity within the body.

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14
Q

What is the in vivo approach in gene therapy?

A

The in vivo approach focuses on developing vectors capable of recognizing specific cell types and delivering genes directly to those cells in the body.

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15
Q

What are the advantages of using retroviral vectors in gene therapy?

A

Retroviral vectors can integrate into the host cell genome, allowing for long-term expression of the transferred genetic material.

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16
Q

What are the disadvantages of retroviral vectors?

A

Retroviral vectors are labile and can be damaged during purification and concentration steps. They can only infect dividing cells, limiting their target range. There is also a risk of disrupting essential genes or activating proto-oncogenes, potentially leading to cancer.

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17
Q

How do adenovirus vectors differ from retroviral vectors?

A

Adenovirus vectors have a larger dsDNA genome and do not integrate into the host cell DNA. However, they prompt a strong immune response, limiting their efficacy in repeat administrations.

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18
Q

What are the characteristics of adeno-associated virus (AAV) vectors?

A

AAV vectors are small ssDNA viruses that require co-infection with adenovirus for replication. They can introduce relatively small genes into non-dividing cells and facilitate long-term expression of the transferred genetic material. AAV vectors can integrate into the recipient cell genome.

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19
Q

What are the advantages of using non-viral vectors in gene therapy?

A

Non-viral vectors have low or non-immunogenicity and do not integrate into the host genome, minimizing the potential for disrupting essential genes or activating host oncogenes.

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20
Q

What was the initial approach for non-viral gene delivery?

A

The initial approach involved administering naked plasmid DNA, which was shown to be expressed in mouse muscle cells after injection. However, the transfection rate was low, and the DNA was not integrated into the host cell’s chromosome.

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21
Q

How can DNA be delivered using a gene gun?

A

DNA can be coated on microscopic gold beads and propelled into the epidermis of test animals using a gene gun. This method has been shown to result in gene expression in the animal’s skin.

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22
Q

What are the commonly used carrier molecules in non-viral gene delivery?

A

Cationic lipids and polylysine chains are commonly used carrier molecules. Cationic lipids can form vesicles or liposomes that interact with DNA, providing physical protection to the therapeutic gene.

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23
Q

What is the challenge in the formation of lipoplexes for gene delivery?

A

The process of lipoplex formation is not easily controlled, and different batches made under seemingly identical conditions may not be structurally identical.

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24
Q

Why has the application of gene therapy to treat genetic diseases made little impact in practice?

A

The slow progress in gene therapy for genetic diseases can be attributed to factors such as a modest number of identified and studied disease-causing genes, unsatisfactory gene-delivery vectors, complexity of some genetic diseases affecting multiple organs/cell types, problematic regulation of transgene expression levels, and limited patient populations for cost recovery.

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25
Q

Which two genetic diseases were among the earliest targets for gene therapy?

A

The two earliest genetic diseases targeted for gene therapy were SCID (bubble baby syndrome) and Cystic Fibrosis.

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26
Q

How does a lack of adenosine deaminase (ADA) activity contribute to SCID?

A

One form of SCID is caused by a lack of ADA activity, which plays a central role in the degradation of purine nucleosides. The deficiency leads to B- and T-cell dysfunction, resulting in a compromised immune system.

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27
Q

What setback occurred in gene therapy in 1999?

A

In 1999, gene therapy suffered a major setback with the death of Jesse Gelsinger during a clinical trial for ornithine transcarboxylase deficiency. His death was believed to be triggered by a severe immune response to the adenovirus vector used in the therapy.

28
Q

What happened in gene therapy trials using retroviral vectors in blood stem cells in 2003?

A

In January 2003, the FDA placed a temporary halt on all gene therapy trials using retroviral vectors in blood stem cells. This action was taken after a second child treated in a French gene therapy trial developed a leukemia-like condition, despite successful treatment for SCID using gene therapy.

29
Q

What has been the focus of the majority of gene therapy trials to date?

A

The majority of gene therapy trials have aimed to cure cancer rather than inherited diseases.

30
Q

What are some factors contributing to the lack of definitive cancer cures through gene therapy?

A

The lack of definitive cancer cures through gene therapy can be attributed to the need for improved vector systems, a better understanding of how cancer cells evade the immune response, and the ethical limitation of treating advanced and widespread terminal cancer patients.

31
Q

What was one of the earliest cancer gene therapy trials, and what was the rationale behind it?

A

One of the earliest cancer gene therapy trials involved introducing the TNF gene into Tumor-infiltrating lymphocytes (TILs). The rationale was that TIL cells reintroduced into the body would infiltrate the tumor and produce TNF at the tumor site.

32
Q

What is Gendicine, and for what cancer was it approved?

A

Gendicine is a gene therapy medicine based on a replication-incompetent human serotype 5 adenovirus engineered to contain the p53 tumor suppressor gene. It gained approval in China in 2003 for the treatment of head and neck squamous cell carcinoma.

33
Q

What were the results and usage of Gendicine in China?

A

According to company data, Gendicine showed complete tumor regression in 64% of patients when used in combination with radiotherapy. By 2006, it was believed to have been administered to around 50,000 patients in China and was being tested for other cancers in late-stage clinical trials.

34
Q

What are some examples of Western companies pursuing similar approaches to gene therapy for cancer?

A

Introgen Therapeutics developed Advexin, a p53 adenoviral-based drug for squamous cell carcinoma, which entered phase III clinical trials in 2006. UniQure released Glybera in Europe in 2012 for lipoprotein lipase deficiency (LPL) but withdrew it in 2017 due to high treatment costs.

35
Q

What is antisense technology?

A

Antisense technology is a nucleic acid-based approach that down-regulates the inappropriate production/over-production of gene products associated with various diseases.

36
Q

What are antisense oligonucleotides?

A

Antisense oligonucleotides are short, single-stranded nucleic acids that can bind to specific DNA or mRNA sequences, preventing gene expression.

37
Q

What are the desirable characteristics of antisense oligos as potential drugs?

A

The desirable characteristics of antisense oligos include specificity, low toxicity, ease of manufacture, and low effective doses.

38
Q

When was Vitravene (fomivirsen) approved for general medical use?

A

Vitravene (fomivirsen) was approved for general medical use by the FDA in August 1998.

39
Q

What is the base sequence of Vitravene?

A

The base sequence of Vitravene is 5’-G-C-G-T-T-T-G-C-T-C-T-T-C-T-T-C-T-T-G-C-G-3’.

40
Q

What is the mechanism of action of Vitravene?

A

Vitravene inhibits replication of human cytomegalovirus (CMV) by binding to complementary sequences in the mRNA transcripts of the major immediate early region (IE2 region) of CMV, blocking viral replication.

41
Q

What disease does Vitravene treat?

A

Vitravene is used to treat CMV retinitis in AIDS patients.

42
Q

What is RNA interference (RNAi)?

A

RNA interference (RNAi) is an innate cellular process that silences selected genes through an antisense mechanism.

43
Q

When was RNAi first discovered?

A

RNAi was first discovered in 1998 in C. elegans.

44
Q

What is the function of the RNAi pathway?

A

The RNAi pathway functions in most eukaryotes and protects genomes from viruses, transposons, and insertable genetic elements.

45
Q

How is short interfering RNA (siRNA) generated?

A

dsRNA is cleaved by the enzyme Dicer into short interfering RNAs (siRNAs), which are 21-23 nucleotides long.

46
Q

What is the role of the RNA-induced silencing complex (RISC)?

A

siRNA is incorporated into the RNA-induced silencing complex (RISC), where the antisense strand targets and degrades specific mRNA.

47
Q

What was the first demonstration of RNAi’s therapeutic potential?

A

The first demonstration of RNAi’s therapeutic potential was in 2002 when siRNA disrupted the hepatitis C virus in mice.

48
Q

When was the first clinical trial based on siRNA reported?

A

The first clinical trial based on siRNA was reported in 2010, showing efficacy in treating skin cancer melanoma.

49
Q

What is Patisiran and what is it used for?

A

Patisiran, marketed as Onpattro, is the first siRNA drug approved by the FDA. It is used for treating polyneuropathy in individuals with TTR-mediated amyloidosis.

50
Q

How does Patisiran work?

A

Patisiran targets the 3’ untranslated region of TTR mRNA, reducing the synthesis of the TTR protein and alleviating symptoms of the disease.

51
Q

What are ribozymes?

A

Ribozymes are RNA sequences that function as catalysts.

52
Q

How do ribozymes function?

A

Ribozymes catalyze cleavage at specific sequences in a specific mRNA structure.

53
Q

What triplet nucleotide sequence do many ribozymes cleave at?

A

Many ribozymes cleave their target mRNA at the triplet nucleotide sequence G-U-C.

54
Q

How can ribozymes be directed to a specific mRNA?

A

Ribozymes can be directed to a specific mRNA by introducing short flanking oligos that are complementary to the target mRNA.

55
Q

What diseases have ribozymes been targeted against in preclinical trials?

A

Ribozymes have been targeted against hepatitis C, SARS-CoV-2, and Influenza in preclinical trials.

56
Q

What are aptamers?

A

What is the unique characteristic of aptamers that allows them to bind specific target molecules?

57
Q

How does the binding affinity of aptamers compare to antibodies?

A

Aptamers have high specificity and can distinguish between closely related molecules or different conformational states of the same protein.

58
Q

What are some potential applications of aptamers?

A

The binding affinity of aptamers is high, in the nanomolar to picomolar range, comparable to antibodies.

59
Q

What are some potential applications of aptamers?

A

Aptamers can be used for affinity-based purification, diagnostics, and therapeutics.

60
Q

Can you provide an example of an FDA-approved aptamer and its indication?

A

Macugen is an FDA-approved aptamer marketed by Eyetech Pharmaceuticals and Pfizer. It is used for the treatment of neovascular age-related macular degeneration (AMD) by binding to vascular endothelial growth factor (VEGF) and inhibiting its activity.

61
Q

What is the function of CRISPR-Cas9 in bacteria?

A

CRISPR-Cas9 provides bacteria with adaptive immunity.

62
Q

What are the three steps involved in conferring immunity through CRISPR-Cas9?

A

Acquisition: Cas proteins incorporate foreign DNA as new spacers within the CRISPR array.
Expression: The CRISPR array is transcribed and processed to form CRISPR RNA (crRNA).
Interference: The effector complex, including crRNA, tracrRNA, and Cas9 protein, targets and degrades invading DNA.

63
Q

How does Cas9 identify its target DNA sequence?

A

Cas9 scans the genomic DNA for a sequence called the protospacer adjacent motif (PAM), which distinguishes bacterial-self from non-self DNA.

64
Q

What is the role of sgRNA in CRISPR-Cas9?

A

The engineered single-guide RNA (sgRNA) combines CRISPR RNA (crRNA) and trans-activating crRNA (tracrRNA) into a single RNA molecule, enabling Cas9 to recognize and cleave the target DNA.

65
Q

What is the most promising CRISPR/Cas9-based genome-editing therapy currently undergoing clinical trials?

A

CTX001, developed by Vertex Pharmaceuticals and CRISPR Therapeutics, targets two monogenic diseases: Transfusion-dependent β-thalassemia (TDT) and Sickle Cell Disease (SCD).

66
Q

How does CTX001 alleviate symptoms in TDT and SCD patients?

A

CTX001 elevates the levels of fetal hemoglobin (HbF), thereby reducing transfusion requirements for TDT patients and alleviating painful crises in SCD patients.