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Fang J, Wang Y, Li C, Liu W, Wang W, Wu X, Wang Y, Zhang S, Zhang J. A hypoxia-derived gene signature to suggest cisplatin-based therapeutic responses in patients with cervical cancer. Comput Struct Biotechnol J 2024; 23:2565-2579. [PMID: 38983650 PMCID: PMC11231957 DOI: 10.1016/j.csbj.2024.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 07/11/2024] Open
Abstract
Cervical cancer remains a significant global public health concern, often exhibits cisplatin resistance in clinical settings. Hypoxia, a characteristic of cervical cancer, substantially contributes to cisplatin resistance. To evaluate the therapeutic efficacy of cisplatin in patients with cervical cancer and to identify potential effective drugs against cisplatin resistance, we established a hypoxia-inducible factor-1 (HIF-1)-related risk score (HRRS) model using clinical data from patients treated with cisplatin. Cox and LASSO regression analyses were used to stratify patient risks and prognosis. Through qRT-PCR, we validated nine potential prognostic HIF-1 genes that successfully predict cisplatin responsiveness in patients and cell lines. Subsequently, we identified fostamatinib, an FDA-approved spleen tyrosine kinase inhibitor, as a promising drug for targeting the HRRS-high group. We observed a positive correlation between the IC50 values of fostamatinib and HRRS in cervical cancer cell lines. Moreover, fostamatinib exhibited potent anticancer effects on high HRRS groups in vitro and in vivo. In summary, we developed a hypoxia-related gene signature that suggests cisplatin response prediction in cervical cancer and identified fostamatinib as a potential novel treatment approach for resistant cases.
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Affiliation(s)
- Jin Fang
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
| | - Ying Wang
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
| | - Chen Li
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
- MOE Key Laboratory of Tumor Molecular Biology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
| | - Weixiao Liu
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
| | - Wannan Wang
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
- MOE Key Laboratory of Tumor Molecular Biology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
| | - Xuewei Wu
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
| | - Yang Wang
- MOE Key Laboratory of Tumor Molecular Biology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
| | - Shuixing Zhang
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
- MOE Key Laboratory of Tumor Molecular Biology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
| | - Jing Zhang
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
- MOE Key Laboratory of Tumor Molecular Biology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
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Barta N, Ördög N, Pantazi V, Berzsenyi I, Borsos BN, Majoros H, Páhi ZG, Ujfaludi Z, Pankotai T. Identifying Suitable Reference Gene Candidates for Quantification of DNA Damage-Induced Cellular Responses in Human U2OS Cell Culture System. Biomolecules 2023; 13:1523. [PMID: 37892205 PMCID: PMC10605043 DOI: 10.3390/biom13101523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
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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Affiliation(s)
- Nikolett Barta
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Állomás utca 1, H-6725 Szeged, Hungary; (N.B.); (N.Ö.); (V.P.); (I.B.); (B.N.B.); (H.M.); (Z.G.P.)
- Competence Centre of the Life Sciences Cluster of the Centre of Excellence for Interdisciplinary Research, Development and Innovation, University of Szeged, Dugonics tér 13, H-6720 Szeged, Hungary
| | - Nóra Ördög
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Állomás utca 1, H-6725 Szeged, Hungary; (N.B.); (N.Ö.); (V.P.); (I.B.); (B.N.B.); (H.M.); (Z.G.P.)
| | - Vasiliki Pantazi
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Állomás utca 1, H-6725 Szeged, Hungary; (N.B.); (N.Ö.); (V.P.); (I.B.); (B.N.B.); (H.M.); (Z.G.P.)
- Competence Centre of the Life Sciences Cluster of the Centre of Excellence for Interdisciplinary Research, Development and Innovation, University of Szeged, Dugonics tér 13, H-6720 Szeged, Hungary
| | - Ivett Berzsenyi
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Állomás utca 1, H-6725 Szeged, Hungary; (N.B.); (N.Ö.); (V.P.); (I.B.); (B.N.B.); (H.M.); (Z.G.P.)
- Competence Centre of the Life Sciences Cluster of the Centre of Excellence for Interdisciplinary Research, Development and Innovation, University of Szeged, Dugonics tér 13, H-6720 Szeged, Hungary
| | - Barbara N. Borsos
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Állomás utca 1, H-6725 Szeged, Hungary; (N.B.); (N.Ö.); (V.P.); (I.B.); (B.N.B.); (H.M.); (Z.G.P.)
| | - Hajnalka Majoros
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Állomás utca 1, H-6725 Szeged, Hungary; (N.B.); (N.Ö.); (V.P.); (I.B.); (B.N.B.); (H.M.); (Z.G.P.)
- Competence Centre of the Life Sciences Cluster of the Centre of Excellence for Interdisciplinary Research, Development and Innovation, University of Szeged, Dugonics tér 13, H-6720 Szeged, Hungary
| | - Zoltán G. Páhi
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Állomás utca 1, H-6725 Szeged, Hungary; (N.B.); (N.Ö.); (V.P.); (I.B.); (B.N.B.); (H.M.); (Z.G.P.)
- Competence Centre of the Life Sciences Cluster of the Centre of Excellence for Interdisciplinary Research, Development and Innovation, University of Szeged, Dugonics tér 13, H-6720 Szeged, Hungary
- Genome Integrity and DNA Repair Core Group, Hungarian Centre of Excellence for Molecular Medicine (HCEMM), University of Szeged, Budapesti út 9, H-6728 Szeged, Hungary
| | - Zsuzsanna Ujfaludi
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Állomás utca 1, H-6725 Szeged, Hungary; (N.B.); (N.Ö.); (V.P.); (I.B.); (B.N.B.); (H.M.); (Z.G.P.)
- Competence Centre of the Life Sciences Cluster of the Centre of Excellence for Interdisciplinary Research, Development and Innovation, University of Szeged, Dugonics tér 13, H-6720 Szeged, Hungary
| | - Tibor Pankotai
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Állomás utca 1, H-6725 Szeged, Hungary; (N.B.); (N.Ö.); (V.P.); (I.B.); (B.N.B.); (H.M.); (Z.G.P.)
- Competence Centre of the Life Sciences Cluster of the Centre of Excellence for Interdisciplinary Research, Development and Innovation, University of Szeged, Dugonics tér 13, H-6720 Szeged, Hungary
- Genome Integrity and DNA Repair Core Group, Hungarian Centre of Excellence for Molecular Medicine (HCEMM), University of Szeged, Budapesti út 9, H-6728 Szeged, Hungary
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Wang X, Ran X, Niu X, Huang S, Li S, Wang J. Whole-genome sequence analysis reveals selection signatures for important economic traits in Xiang pigs. Sci Rep 2022; 12:11823. [PMID: 35821031 PMCID: PMC9276726 DOI: 10.1038/s41598-022-14686-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 06/10/2022] [Indexed: 11/30/2022] Open
Abstract
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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Affiliation(s)
- Xiying Wang
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China.,Tongren University, Tongren, 554300, China
| | - Xueqin Ran
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China.
| | - Xi Niu
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Shihui Huang
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Sheng Li
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Jiafu Wang
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China.
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