SerpinB10, a Serine Protease Inhibitor, Is Implicated in UV-Induced Cellular Response

Majoros, Hajnalka; Borsos, Barbara N.; Újfaludi, Zsuzsanna; Páhi, Zoltán Gábor; Mórocz, Mónika; Haracska, Lajos; Boros, Imre; Pankotai, Tibor

doi:10.3390/ijms22168500

Cited by 4 publications

(5 citation statements)

References 42 publications

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“…5 A). Notably, these gene sets have been reported to be associated with chemoresistance and malignant tumor progression [10] , [31] , [32] , [33] , [34] , [35] , [36] , [37] . Moreover, genes highly expressed in the low-risk group were significantly enriched in allograft rejection, interferon-γ response, and interferon-α response ( Fig.…”

Section: Resultsmentioning

confidence: 99%

A hypoxia-derived gene signature to suggest cisplatin-based therapeutic responses in patients with cervical cancer

Fang,

Wang,

et al. 2024

Computational and Structural Biotechnology Journal

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Section: Resultsmentioning

confidence: 99%

A hypoxia-derived gene signature to suggest cisplatin-based therapeutic responses in patients with cervical cancer

Fang,

Wang,

et al. 2024

Computational and Structural Biotechnology Journal

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“…We studied the potential impacts of UVB irradiation, which plays a main role in the activation of TC-NER, on the desired housekeeping genes [29,[37][38][39]. Only the B2M expression level was significantly altered by the UVB irradiation (Figure 1, upper row, second panel, NT versus 0.5 h, p = 0.0039); hence, this candidate was rejected as a reference gene.…”

Section: Resultsmentioning

confidence: 99%

Identifying Suitable Reference Gene Candidates for Quantification of DNA Damage-Induced Cellular Responses in Human U2OS Cell Culture System

Barta,

Ördög,

Pantazi

et al. 2023

Biomolecules

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DNA repair pathways trigger robust downstream responses, making it challenging to select suitable reference genes for comparative studies. In this study, our goal was to identify the most suitable housekeeping genes to perform comparable molecular analyses for DNA damage-related studies. Choosing the most applicable reference genes is important in any kind of target gene expression-related quantitative study, since using the housekeeping genes improperly may result in false data interpretation and inaccurate conclusions. We evaluated the expressional changes of eight well-known housekeeping genes (i.e., 18S rRNA, B2M, eEF1α1, GAPDH, GUSB, HPRT1, PPIA, and TBP) following treatment with the DNA-damaging agents that are most frequently used: ultraviolet B (UVB) non-ionizing irradiation, neocarzinostatin (NCS), and actinomycin D (ActD). To reveal the significant changes in the expression of each gene and to determine which appear to be the most acceptable ones for normalization of real-time quantitative polymerase chain reaction (RT-qPCR) data, comparative and statistical algorithms (such as absolute quantification, Wilcoxon Rank Sum Test, and independent samples T-test) were conducted. Our findings clearly demonstrate that the genes commonly employed as reference candidates exhibit substantial expression variability, and therefore, careful consideration must be taken when designing the experimental setup for an accurate and reproducible normalization of RT-qPCR data. We used the U2OS cell line since it is generally accepted and used in the field of DNA repair to study DNA damage-induced cellular responses. Based on our current data in U2OS cells, we suggest using 18S rRNA, eEF1α1, GAPDH, GUSB, and HPRT1 genes for UVB-induced DNA damage-related studies. B2M, HPRT1, and TBP genes are recommended for NCS treatment, while 18S rRNA, B2M, and PPIA genes can be used as suitable internal controls in RT-qPCR experiments for ActD treatment. In summary, this is the first systematic study using a U2OS cell culture system that offers convincing evidence for housekeeping gene selection following treatment with various DNA-damaging agents. Here, we unravel an indispensable issue for performing and assessing trustworthy DNA damage-related differential gene expressional analyses, and we create a “zero set” of potential reference gene candidates.

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“…Additionally, we also uncovered genes, which may play different roles in adaptation processes of Xiang pigs. These genes include NR2E1 for behavioral defense response 12 , SERPINB8 for maintaining the mechanical stability of skin 15 , SERPINB10 involved in the UV-induced cellular response 16 , UVSSA for response to ultra-violet (UV) radiation 30 , VEGFC responsible for regulating oxygen homeostasis 6 . The positive selection signatures identified here provided new insights into the potential adaptive mechanisms in XP.…”

Section: Discussionmentioning

confidence: 99%

“…To avoid low-quality reads, the raw paired-end reads were filtered and trimmed using the NGSQC Toolkit with default parameters 16 . High-quality reads were then aligned to the Sscrofa11.1 reference sequence using the Burrows-Wheeler Aligner (BWA) with the “bwa-mem” algorithms 72 .…”

Section: Methodsmentioning

confidence: 99%

Whole-genome sequence analysis reveals selection signatures for important economic traits in Xiang pigs

Wang

Ran

Niu

et al. 2022

Sci Rep

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Xiang pig (XP) is one of the best-known indigenous pig breeds in China, which is characterized by its small body size, strong disease resistance, high adaptability, favorite meat quality, small litter sizes, and early sexual maturity. However, the genomic evidence that links these unique traits of XP is still poorly understood. To identify the genomic signatures of selection in XP, we performed whole-genome resequencing on 25 unrelated individual XPs. We obtained 876.70 Gb of raw data from the genomic libraries. The LD analysis showed that the lowest level of linkage disequilibrium was observed in Xiang pig. Comparative genomic analysis between XPs and other breeds including Tibetan, Meishan, Duroc and Landrace revealed 3062, 1228, 907 and 1519 selected regions, respectively. The genes identified in selected regions of XPs were associated with growth and development processes (IGF1R, PROP1, TBX19, STAC3, RLF, SELENOM, MSTN), immunity and disease resistance (ZCCHC2, SERPINB2, ADGRE5, CYP7B1, STAT6, IL2, CD80, RHBDD3, PIK3IP1), environmental adaptation (NR2E1, SERPINB8, SERPINB10, SLC26A7, MYO1A, SDR9C7, UVSSA, EXPH5, VEGFC, PDE1A), reproduction (CCNB2, TRPM6, EYA3, CYP7B1, LIMK2, RSPO1, ADAM32, SPAG16), meat quality traits (DECR1, EWSR1), and early sexual maturity (TAC3). Through the absolute allele frequency difference (ΔAF) analysis, we explored two population-specific missense mutations occurred in NR6A1 and LTBP2 genes, which well explained that the vertebrae numbers of Xiang pigs were less than that of the European pig breeds. Our results indicated that Xiang pigs were less affected by artificial selection than the European and Meishan pig breeds. The selected candidate genes were mainly involved in growth and development, disease resistance, reproduction, meat quality, and early sexual maturity. This study provided a list of functional candidate genes, as well as a number of genetic variants, which would provide insight into the molecular basis for the unique traits of Xiang pig.

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SerpinB10, a Serine Protease Inhibitor, Is Implicated in UV-Induced Cellular Response

Cited by 4 publications

References 42 publications

A hypoxia-derived gene signature to suggest cisplatin-based therapeutic responses in patients with cervical cancer

A hypoxia-derived gene signature to suggest cisplatin-based therapeutic responses in patients with cervical cancer

Identifying Suitable Reference Gene Candidates for Quantification of DNA Damage-Induced Cellular Responses in Human U2OS Cell Culture System

Whole-genome sequence analysis reveals selection signatures for important economic traits in Xiang pigs

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