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Cell Metabolism and DNA Repair Pathways

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Dear Colleagues,

For this Special Issue of the International Journal of Molecular Sciences, we invite you to contribute either an original research article or a review article on any aspect of the subject of “Cell Metabolism and DNA Repair Pathways”. Metabolic reprogramming and DNA repair are hallmarks of cancer cells, allowing for their increased proliferation and survival. Targeting DNA repair and metabolism reprogramming is emerging as a potential therapeutic alternative to support conventional cancer therapies and to circumvent certain resistance pathways. In addition, alterations of DNA repair and of metabolism are also found in neurodegenerative disease. Therefore, increasing our comprehension of cell metabolism and DNA repair pathways (isolated or in combination) is of great importance to many biomedical fields. This includes but is not limited to the regulatory mechanisms involving transcriptional and post-transcriptional regulation of gene expression, epigenetics, and post-translational modifications of proteins. Review articles and original papers addressing specific mechanisms or wide-ranging omics studies are welcome in this Special Issue to support our knowledge of cellular metabolism and DNA repair pathways and their interconnections.

Prof. Dr. Benoît Chénais
Guest Editor

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Keywords

cell metabolism
cancer
DNA repair
neurodegenerative disease
cell signaling
metabolism reprogramming
transcription factors
epigenetics
cellular energy
post-translational modification

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12 pages, 3968 KiB

Open AccessArticle

Homozygous CRISPR/Cas9 Knockout Generated a Novel Functionally Active Exon 1 Skipping XPA Variant in Melanoma Cells

by Veronika Banicka, Marie Christine Martens, Rüdiger Panzer, David Schrama, Steffen Emmert, Lars Boeckmann and Alexander Thiem

Int. J. Mol. Sci. 2022, 23(19), 11649; https://doi.org/10.3390/ijms231911649 - 01 Oct 2022

Cited by 1 | Viewed by 1831

Abstract

Defects in DNA repair pathways have been associated with an improved response to immune checkpoint inhibition (ICI). In particular, patients with the nucleotide excision repair (NER) defect disease Xeroderma pigmentosum (XP) responded impressively well to ICI treatment. Recently, in melanoma patients, pretherapeutic XP gene expression was predictive for anti-programmed cell death-1 (PD-1) ICI response. The underlying mechanisms of this finding are still to be revealed. Therefore, we used CRISPR/Cas9 to disrupt XPA in A375 melanoma cells. The resulting subclonal cell lines were investigated by Sanger sequencing. Based on their genetic sequence, candidates from XPA exon 1 and 2 were selected and further analyzed by immunoblotting, immunofluorescence, HCR and MTT assays. In XPA exon 1, we established a homozygous (c.19delG; p.A7Lfs*8) and a compound heterozygous (c.19delG/c.19_20insG; p.A7Lfs*8/p.A7Gfs*55) cell line. In XPA exon 2, we generated a compound heterozygous mutated cell line (c.206_208delTTG/c.208_209delGA; p.I69_D70delinsN/p.D70Hfs*31). The better performance of the homozygous than the heterozygous mutated exon 1 cells in DNA damage repair (HCR) and post-UV-C cell survival (MTT), was associated with the expression of a novel XPA protein variant. The results of our study serve as the fundamental basis for the investigation of the immunological consequences of XPA disruption in melanoma. Full article

(This article belongs to the Special Issue Cell Metabolism and DNA Repair Pathways)

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14 pages, 2526 KiB

Open AccessArticle

Identification of HGD and GSTZ1 as Biomarkers Involved Metabolic Reprogramming in Kidney Renal Clear Cell Carcinoma

by Jiyan Wang, Hongkai Chang, Meng Su, Yaya Qiao, Huanran Sun, Yongshan Zhao, Shuai Zhang and Changliang Shan

Int. J. Mol. Sci. 2022, 23(9), 4583; https://doi.org/10.3390/ijms23094583 - 21 Apr 2022

Cited by 6 | Viewed by 2047

Abstract

Kidney renal clear cell carcinoma (KIRC) with poor prognosis is the main histological subtype of renal cell carcinoma, accounting for more than 80% of patients. Most patients are diagnosed at an advanced stage due to being asymptomatic early on. Advanced KIRC has an extremely poor prognosis due to its inherent resistance to radiotherapy and chemotherapy. Therefore, a comprehensive understanding of the molecular mechanisms of KIRC and the development of effective early diagnostic and therapeutic strategies is urgently needed. In this study, we aimed to identify the prognosis-related biomarker and analyzed its relationship with tumor progression. Metabolic changes are an important feature of kidney cancer, where the reduction of fumarate allows us to target the tyrosine metabolic pathway. The homogentisate 1,2-dioxygenase (HGD) and glutathione S-transferase zeta 1 (GSTZ1) related with prognosis of KIRC was identified through bioinformatics analysis based on The Cancer Genome Atlas (TCGA) databases. Mechanistically, we found that decreased HGD and GSTZ1 promote aerobic glycolysis in KIRC, coordinate the balance of amino acid metabolism and energy metabolism in tumor cells, and ultimately activate the tumor cell cycle and tumor progression. In summary, we identified the tyrosine metabolizing enzymes HGD and GSTZ1 as biomarkers of KIRC, which will further the understanding of the tumor metabolism profile, provide novel strategies and theoretical support for diagnosing and treating KIRC and as referential for future clinical research. Full article

(This article belongs to the Special Issue Cell Metabolism and DNA Repair Pathways)

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