Thread by @_HeartofGrace_

1/ 🧵🚨
Plasmid DNA is a contaminant in 💉🦠🧬and is double stranded (ds) DNA: it contains CpG oligonucleotide (ODN).
A STUDY: Researchers found differences in cellular responses+ different gene responses to ds DNA and its effect on GENE MODIFICATION--transient transfection.

2/ The STUDY (HEAVY SCIENCE THREAD):
"Differential cellular responses to exogenous DNA in mammalian cells and its effect on oligonucleotide directed gene modification"
Igoucheva, O et al.
Gene therapy vol. 13,3 (2006): 266-75. doi:10.1038/sj.gt.3302643
sci-hub.se/10.1038/sj.gt.…

3/ Researchers wanted to know how cells respond to the presence of double-stranded DNA (dsDNA), and the influence that different dsDNA (different sizes/types) have on different cellular processes, and the impact on different genes. They found a variety of results.

4/ They used two types of cell lines, NIH3T3 and CHO-K1, and introduced plasmid dsDNA into the cells. The introduction of dsDNA was achieved by transient transfection, where external genetic material (in this case, dsDNA) is introduced into cells (DNA/lipid complex).

5/ After adding the dsDNA to the cells, the researchers observed how the cells' gene expression changed, especially the transcriptional response, which means they studied how genes were "turned on" or "turned off" in response to the presence of dsDNA inside the cells.

6/ The researchers analyzed the activity of various genes in response to dsDNA. The genes they examined are associated with processes like DNA repair, cell cycle regulation, apoptosis (cell death), and other cellular responses, such as uncontrolled cell growth, and cancer.

7/ They found "cell-type dependency". Different cell types exhibit remarkably different rates of gene modification in response to the dsDNA.
Introduction of dsDNA activated transcription of many genes involved in DNA damage signaling and repair.

8/ Long dsDNA induced genes responsible for sensing DNA damage, like ATR-dependent signaling, nucleotide excision repair (NER), and mismatch repair (MMR).
ATR (ataxia telangiectasia and Rad3-related) was identified as the primary sensor of DNA replication

9/ blockage resulting from lesions by DNA adducts, UV, and DNA synthesis inhibitors.
The study observed a strong induction of ATR and several genes participating in ATR-dependent signaling.
ATR is paramount in maintaining stability of the genome.
Mutations or dysregulation of

10/ ATR can lead to disease and cancer.
ATR is also part of the activation of cell cycle checkpoints. Dysregulation is another hallmark in cancer. ATR is also a tumor suppressor. Loss of function or mutations in ATR may contribute to the development of cancer.

11/ This table shows transcription in response to the presence of dsDNA in the two cell types. The data is for various genes associated w/ different cellular pathways. The fold induction values represent ratio of intensity of each gene in cells transfected.

12/

13/ The ones that are related to cancer:

ATR (Ataxia Telangiectasia and Rad3 Related):
Implication in Cancer: Dysregulation of ATR has been associated with genomic instability and cancer. ATR mutations or altered expression can contribute to uncontrolled cell proliferation.

14/ ATM (Ataxia Telangiectasia Mutated):

ATM is involved in DNA repair and cell cycle control.
Mutations in ATM are linked to an increased risk of cancer. ATM is a tumor suppressor, and its dysfunction can lead to genomic instability and cancer development.

15/ Cyclin-Dependent Kinase Inhibitor 1A (p21):
p21 is a cyclin-dependent kinase inhibitor, regulating the cell cycle.

p21 acts as a tumor suppressor by inhibiting cell cycle progression.

Dysregulation can lead to uncontrolled cell division and contribute to cancer.

16/ Bcl-2 Homologous Antagonist/Killer (Bak):
apoptosis and regulation of cell death.

Dysregulation of apoptosis is a common feature in cancer.

Altered Bak function may affect the balance between cell survival and death, contributing to cancer development.

17/ B-cell Leukemia/Lymphoma 6 (Bcl6):

cell cycle regulation and apoptosis.

Aberrant expression of Bcl6 is associated with lymphomas and other cancers. It can promote cell survival and inhibit apoptosis, contributing to tumor development.

18/ Growth Arrest and DNA-Damage-Inducible 45 (GADD45):
cell cycle arrest and DNA damage response.

GADD45 genes play a role in preventing genomic instability. Dysregulation can contribute to cancer by affecting cell cycle control and DNA repair.

19/ p53 (Tumor Protein 53):

tumor suppressor, regulating the cell cycle, DNA repair, and apoptosis.

Mutations in p53 are common in various cancers. Loss of p53 function allows for uncontrolled cell division and survival of damaged cells, contributing to cancer progression.

20/ BRCA1 and BRCA2:
DNA repair. Mutations in BRCA1 and BRCA2 are associated with an increased risk of breast and ovarian cancers. genomic integrity.
***
Tumor Necrosis Factor (TNF):
apoptosis and inflammation.
Dysregulation of TNF signaling : chronic inflammation and cancer.

21/ 🚨🚨Telomerase Reverse Transcriptase (TERT):
maintains telomere length.
Activation of telomerase, including TERT, is common in cancer cells, allowing for unlimited cell division.

unlimited cell division

22/ Xeroderma Pigmentosum Genes (XPA, XPC):
DNA repair.
I Mutations in XPA and XPC are associated with an increased susceptibility to skin cancer.

These genes play a crucial role in repairing DNA damage caused by UV radiation.

23/ Nuclear Protein and Cellular Processes:

nuclear protein (PA26) associated with the gene suggests involvement in nuclear activities (nucleus).

(BF537978) may be under the regulation of the P53 protein.

Both were impacted in this study by the dsDNA, including other genes.

24/ Other studies exist on the impact of dsDNA on signaling pathways, and specific genes.

More threads to follow.

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