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O’Reilly M, Krstic A, Iglesias-Martinez LF, Ryan ÉJ, Moran B, Winter D, Sheahan K, McDermott R, Kolch W. Genomic and Transcriptomic Analysis of a Patient with Early-Onset Colorectal Cancer and Therapy-Induced Focal Nodular Hyperplasia: A Case Report. J Pers Med 2024; 14:639. [PMID: 38929861 PMCID: PMC11204579 DOI: 10.3390/jpm14060639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/04/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Early-onset colorectal cancer (EOCRC), defined as colorectal cancer in individuals under 50 years of age, has shown an alarming increase in incidence worldwide. We report a case of a twenty-four-year-old female with a strong family history of colorectal cancer (CRC) but without an identified underlying genetic predisposition syndrome. Two years after primary surgery and adjuvant chemotherapy, the patient developed new liver lesions. Extensive diagnostic imaging was conducted to investigate suspected liver metastases, ultimately leading to a diagnosis of focal nodular hyperplasia. The young age of the patient has prompted comprehensive genomic and transcriptomic profiling in order to identify potential oncogenic drivers and inform further clinical management of the patient. Besides a number of oncogenic mutations identified in the patient's tumour sample, including KRAS G12D, TP53 R248W and TTN L28470V, we have also identified a homozygous deletion of 24.5 MB on chromosome 8. A multivariate Cox regression analysis of this patient's mutation profile conferred a favourable prognosis when compared with the TCGA COADREAD database. Notably, the identified deletion on chromosome 8 includes the WRN gene, which could contribute to the patient's overall positive response to chemotherapy. The complex clinical presentation, including the need for emergency surgery, early age at diagnosis, strong family history, and unexpected findings on surveillance imaging, necessitated a multidisciplinary approach involving medical, radiation, and surgical oncologists, along with psychological support and reproductive medicine specialists. Molecular profiling of the tumour strongly indicates that patients with complex mutational profile and rare genomic rearrangements require a prolonged surveillance and personalised informed interventions.
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Affiliation(s)
- Mary O’Reilly
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland; (A.K.); (L.F.I.-M.); (W.K.)
- St. Vincent’s University Hospital, University College Dublin, D04 V1W8 Dublin, Ireland; (É.J.R.); (B.M.); (D.W.); (K.S.); (R.M.)
| | - Aleksandar Krstic
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland; (A.K.); (L.F.I.-M.); (W.K.)
| | - Luis F. Iglesias-Martinez
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland; (A.K.); (L.F.I.-M.); (W.K.)
| | - Éanna J. Ryan
- St. Vincent’s University Hospital, University College Dublin, D04 V1W8 Dublin, Ireland; (É.J.R.); (B.M.); (D.W.); (K.S.); (R.M.)
| | - Bruce Moran
- St. Vincent’s University Hospital, University College Dublin, D04 V1W8 Dublin, Ireland; (É.J.R.); (B.M.); (D.W.); (K.S.); (R.M.)
| | - Des Winter
- St. Vincent’s University Hospital, University College Dublin, D04 V1W8 Dublin, Ireland; (É.J.R.); (B.M.); (D.W.); (K.S.); (R.M.)
| | - Kieran Sheahan
- St. Vincent’s University Hospital, University College Dublin, D04 V1W8 Dublin, Ireland; (É.J.R.); (B.M.); (D.W.); (K.S.); (R.M.)
| | - Ray McDermott
- St. Vincent’s University Hospital, University College Dublin, D04 V1W8 Dublin, Ireland; (É.J.R.); (B.M.); (D.W.); (K.S.); (R.M.)
| | - Walter Kolch
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland; (A.K.); (L.F.I.-M.); (W.K.)
- Conway Institute, University College Dublin, D04 V1W8 Dublin, Ireland
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2
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Gopalakrishnan V, Roy U, Srivastava S, Kariya KM, Sharma S, Javedakar SM, Choudhary B, Raghavan SC. Delineating the mechanism of fragility at BCL6 breakpoint region associated with translocations in diffuse large B cell lymphoma. Cell Mol Life Sci 2024; 81:21. [PMID: 38196006 PMCID: PMC11072719 DOI: 10.1007/s00018-023-05042-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/05/2023] [Accepted: 11/07/2023] [Indexed: 01/11/2024]
Abstract
BCL6 translocation is one of the most common chromosomal translocations in cancer and results in its enhanced expression in germinal center B cells. It involves the fusion of BCL6 with any of its twenty-six Ig and non-Ig translocation partners associated with diffuse large B cell lymphoma (DLBCL). Despite being discovered long back, the mechanism of BCL6 fragility is largely unknown. Analysis of the translocation breakpoints in 5' UTR of BCL6 reveals the clustering of most of the breakpoints around a region termed Cluster II. In silico analysis of the breakpoint cluster sequence identified sequence motifs that could potentially fold into non-B DNA. Results revealed that the Cluster II sequence folded into overlapping hairpin structures and identified sequences that undergo base pairing at the stem region. Further, the formation of cruciform DNA blocked DNA replication. The sodium bisulfite modification assay revealed the single-strandedness of the region corresponding to hairpin DNA in both strands of the genome. Further, we report the formation of intramolecular parallel G4 and triplex DNA, at Cluster II. Taken together, our studies reveal that multiple non-canonical DNA structures exist at the BCL6 cluster II breakpoint region and contribute to the fragility leading to BCL6 translocation in DLBCL patients.
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Affiliation(s)
- Vidya Gopalakrishnan
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560 012, India
- Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, 560 100, India
- Department of Zoology, St. Joseph's College (Autonomous), Irinjalakuda, Kerala, 680121, India
| | - Urbi Roy
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560 012, India
| | - Shikha Srivastava
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560 012, India
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Tonk, Rajasthan, 304022, India
| | - Khyati M Kariya
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560 012, India
| | - Shivangi Sharma
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560 012, India
| | - Saniya M Javedakar
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560 012, India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, 560 100, India.
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560 012, India.
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Zhang S, Shao H, Li KB, Shi W, Han DM. Nanofluidic sensing platform for PNK assay using nonlinear hybridization chain reaction and its application in DNA logic circuit. Biosens Bioelectron 2023; 240:115632. [PMID: 37647684 DOI: 10.1016/j.bios.2023.115632] [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: 05/07/2023] [Revised: 08/14/2023] [Accepted: 08/22/2023] [Indexed: 09/01/2023]
Abstract
In this study, a polyethyleneimine (PEI)/Zr4+-functionalized nanofluidic sensing platform based on nonlinear hybridization chain reaction (NHCR) was developed for PNK activity assay. With the existence of PNK, the hairpin HPNK was cleaved by λ exonuclease, liberating the initiator T-DNA. Then T-DNA triggered the nonlinear HCR in solution and the reaction products were absorbed onto the nanopore, which changed the surface charge of nanofluidic device and could be detected by current-voltage characteristic curves. Compared to traditional linear HCR, the nonlinear HCR exhibits a higher sensitivity and order of growth kinetics, making it a powerful signal amplifier in bioanalysis. Due to the powerful amplification efficiency of nonlinear HCR, high sensitivity of the nanopore and specific recognition site of PNK/λ-Exo, an ultrasensitive and selective PNK sensing approach had been developed and applied to precisely quantitate the PNK activity with a LOD of 0.0001 U/mL. Moreover, utilizing this nanofluidic system as a foundation, we constructed a logic circuit that utilized PNK, adenosine diphosphate (ADP), and (NH4)2SO4 as input elements. ADP and (NH4)2SO4 had a crucial function in facilitating the PNK to regulate the DNA logic gate. By modifying the target and inhibitors, the nanofluidic device could detect a variety of stimuli and execute more advanced logical operations.
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Affiliation(s)
- Siqi Zhang
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang, Zhejiang, 318000, China
| | - Huahao Shao
- Zhijiang College of Zhejiang University of Technology, Shaoxing, Zhejiang, 312000, China
| | - Kai-Bin Li
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang, Zhejiang, 318000, China.
| | - Wei Shi
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang, Zhejiang, 318000, China
| | - De-Man Han
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang, Zhejiang, 318000, China.
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Sun N, Shen J, Shi Y, Liu B, Gao S, Chen Y, Sun J. TRIM58 functions as a tumor suppressor in colorectal cancer by promoting RECQL4 ubiquitination to inhibit the AKT signaling pathway. World J Surg Oncol 2023; 21:231. [PMID: 37516854 PMCID: PMC10385910 DOI: 10.1186/s12957-023-03124-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/23/2023] [Indexed: 07/31/2023] Open
Abstract
BACKGROUND This study aimed to investigate the underlying molecular mechanisms of TRIM58 in the development of colorectal cancer (CRC). CRC is one of the most common cancers of the digestive tract worldwide. The ubiquitin-proteasome system regulates many oncogenic or tumor-suppressive proteins. TRIM58, an E3 ubiquitin ligase and a member of the tripartite motif protein family, is a potential prognostic marker that indicates poor prognosis in cancer. Currently, the precise molecular mechanisms for the TRIM58-mediated CRC progression remain unclear. METHODS To examine the effects of TRIM58 on cell viability, cell cycle progression, and apoptosis in CRC, Cell Counting Kit-8 and flow cytometry assays were employed. The AKT inhibitor LY294002 was used to examine the effects of AKT signaling on TRIM58-mediated cell viability, cell cycle progression, and apoptosis in CRC. Additionally, Co-IP and ubiquitination assays were used to examine the correlation between TRIM58 and RECQL4. RESULTS TRIM58 overexpression inhibited CRC cell viability and promoted cell cycle arrest and apoptosis, in which the TRIM58 knockdown demonstrated inversed effects via the AKT signaling pathway. TRIM58 inhibited RECQL4 protein levels through its ubiquitin ligase activity, and RECQL4 overexpression inhibited TRIM58 overexpression-mediated CRC cell viability, cell cycle progression, and apoptosis. The downregulation of TRIM58 and upregulation of RECOL4 were observed in human CRC tissue, and TRIM58 demonstrated antitumor effects in CRC-induced tumor growth in a mouse model. CONCLUSIONS TRIM58 acts as a tumor suppressor in CRC through the promotion of RECQL4 ubiquitination and inhibition of the AKT signaling pathway and may be investigated for the successful treatment of CRC.
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Affiliation(s)
- Naizhi Sun
- Department of General Surgery, North Hospital of Yancheng Third People's Hospital, The Yancheng School of Clinical Medicine of Nanjing Medical, Theater Road No. 75, Tinghu District, Yancheng, 224000, Jiangsu Province, China
| | - Jiacheng Shen
- Department of General Surgery, North Hospital of Yancheng Third People's Hospital, The Yancheng School of Clinical Medicine of Nanjing Medical, Theater Road No. 75, Tinghu District, Yancheng, 224000, Jiangsu Province, China
| | - Yuhua Shi
- Department of General Surgery, North Hospital of Yancheng Third People's Hospital, The Yancheng School of Clinical Medicine of Nanjing Medical, Theater Road No. 75, Tinghu District, Yancheng, 224000, Jiangsu Province, China
| | - Biao Liu
- Department of General Surgery, North Hospital of Yancheng Third People's Hospital, The Yancheng School of Clinical Medicine of Nanjing Medical, Theater Road No. 75, Tinghu District, Yancheng, 224000, Jiangsu Province, China
| | - Shengguo Gao
- Department of General Surgery, North Hospital of Yancheng Third People's Hospital, The Yancheng School of Clinical Medicine of Nanjing Medical, Theater Road No. 75, Tinghu District, Yancheng, 224000, Jiangsu Province, China
| | - Yichuan Chen
- Department of General Surgery, North Hospital of Yancheng Third People's Hospital, The Yancheng School of Clinical Medicine of Nanjing Medical, Theater Road No. 75, Tinghu District, Yancheng, 224000, Jiangsu Province, China
| | - Jinwei Sun
- Department of General Surgery, North Hospital of Yancheng Third People's Hospital, The Yancheng School of Clinical Medicine of Nanjing Medical, Theater Road No. 75, Tinghu District, Yancheng, 224000, Jiangsu Province, China.
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5
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Wang JE, Zhou YC, Wu BH, Chen XC, Zhai J, Tan JH, Huang ZS, Chen SB. A rapid and highly sensitive immunosorbent assay to monitor helicases unwinding diverse nucleic acid structures. Analyst 2023; 148:2343-2351. [PMID: 37185609 DOI: 10.1039/d2an01989b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Helicases are crucial enzymes in DNA and RNA metabolism and function by unwinding particular nucleic acid structures. However, most convenient and high-throughput helicase assays are limited to the typical duplex DNA. Herein, we developed an immunosorbent assay to monitor the Werner syndrome (WRN) helicase unwinding a wide range of DNA structures, such as a replication fork, a bubble, Holliday junction, G-quadruplex and hairpin. This assay could sensitively detect the unwinding of DNA structures with detection limits around 0.1 nM, and accurately monitor the substrate-specificity of WRN with a comparatively less time-consuming and high throughput process. Remarkably, we have established that this new assay was compatible in evaluating helicase inhibitors and revealed that the inhibitory effect was substrate-dependent, suggesting that diverse substrate structures other than duplex structures should be considered in discovering new inhibitors. Our study provided a foundational example for using this new assay as a powerful tool to study helicase functions and discover potent inhibitors.
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Affiliation(s)
- Jia-En Wang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
| | - Ying-Chen Zhou
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
| | - Bi-Han Wu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
| | - Xiu-Cai Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
| | - Junqiu Zhai
- Guangzhou University of Chinese Medicine, Guangzhou, Guangzhou 510330, China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
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6
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Ma W, Guan X, Miao Y, Zhang L. Whole Genome Resequencing Revealed the Effect of Helicase yqhH Gene on Regulating Bacillus thuringiensis LLP29 against Ultraviolet Radiation Stress. Int J Mol Sci 2023; 24:ijms24065810. [PMID: 36982883 PMCID: PMC10054049 DOI: 10.3390/ijms24065810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/23/2023] [Accepted: 03/01/2023] [Indexed: 03/30/2023] Open
Abstract
Bacillus thuringiensis (Bt) is a widely used microbial pesticide. However, its duration of effectiveness is greatly shortened due to the irradiation of ultraviolet rays, which seriously hinders the application of Bt preparations. Therefore, it is of great importance to study the resistance mechanism of Bt to UV at the molecular level to improve the UV-resistance of Bt strains. In order to know the functional genes in the UV resistance, the genome of UV-induced mutant Bt LLP29-M19 was re-sequenced and compared with the original strain Bt LLP29. It was shown that there were 1318 SNPs, 31 InDels, and 206 SV between the mutant strain and the original strain Bt LLP29 after UV irradiation, which were then analyzed for gene annotation. Additionally, a mutated gene named yqhH, a member of helicase superfamily II, was detected as an important candidate. Then, yqhH was expressed and purified successfully. Through the result of the enzymatic activity in vitro, yqhH was found to have ATP hydrolase and helicase activities. In order to further verify its function, the yqhH gene was knocked out and complemented by homologous recombinant gene knockout technology. The survival rate of the knockout mutant strain Bt LLP29-ΔyqhH was significantly lower than that of the original strain Bt LLP29 and the back-complemented strain Bt LLP29-ΔyqhH-R after treated with UV. Meanwhile, the total helicase activity was not significantly different on whether Bt carried yqhH or not. All of these greatly enrich important molecular mechanisms of Bt when it is in UV stress.
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Affiliation(s)
- Weibo Ma
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education & Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiong Guan
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ying Miao
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lingling Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education & Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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7
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Liu XW, Liu WJ, Meng Y, Hu J, Zhang CY. Development of a tandem signal amplification strategy for label-free sensing polynucleotide kinase activity in cancer cells. Talanta 2023. [DOI: 10.1016/j.talanta.2022.124001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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8
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Construction of a simple, localized and homogeneous fluorescence detection platform for T4 PNK activity based on tetrahedral DNA nanostructure-mediated primer exchange reaction. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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9
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Zhang Q, Zhang X, Ma F, Zhang CY. Advances in quantum dot-based biosensors for DNA-modifying enzymes assay. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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10
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Wei L, Kong X, Wang M, Zhang Y, Pan R, Cheng Y, Lv Z, Zhou J, Ming J. A label-free T4 polynucleotide kinase fluorescence sensor based on split dimeric G-quadruplex and ligation-induced dimeric G-quadruplex/thioflavin T conformation. Anal Bioanal Chem 2022; 414:7923-7933. [PMID: 36136111 DOI: 10.1007/s00216-022-04327-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 11/01/2022]
Abstract
The phosphorylation process of DNA by T4 polynucleotide kinase (T4 PNK) plays a crucial role in DNA recombination, DNA replication, and DNA repair. Traditional monomeric G-quadruplex (G4) systems are always activated by single cation such as K+ or Na+. The conformation transformation caused by the coexistence of multiple cations may interfere with the signal readout and limit their applications in physiological system. In view of the stability of dimeric G4 in multiple cation solution, we reported a label-free T4 PNK fluorescence sensor based on split dimeric G4 and ligation-induced dimeric G4/thioflavin T (ThT) conformation. The dimeric G4 was divided into two independent pieces of one normal monomeric G4 and the other monomeric G4 fragment phosphorylated by T4 PNK in order to decrease the background signal. With the introduction of template DNA, DNA ligase, and invasive DNA, the dimeric G4 could be generated and liberated to combine with ThT to show obvious fluorescence signal. Using our strategy, the linear range from 0.005 to 0.5 U mL-1, and the detection limit of 0.0021 U mL-1 could be achieved without the consideration of interference caused by the coexistence of multiple cations. Additionally, research in real sample determination and inhibition effect investigations indicated its further potential application value in biochemical process research and clinic diagnostics.
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Affiliation(s)
- Liuya Wei
- School of Pharmacy, Weifang Medical University, Weifang, 261053, People's Republic of China
| | - Xianglong Kong
- School of Pharmacy, Weifang Medical University, Weifang, 261053, People's Republic of China
| | - Mengran Wang
- School of Pharmacy, Weifang Medical University, Weifang, 261053, People's Republic of China
| | - Yixin Zhang
- School of Clinical Medicine, Weifang Medical University, Weifang, 261053, People's Republic of China
| | - Ruiyan Pan
- School of Pharmacy, Weifang Medical University, Weifang, 261053, People's Republic of China
| | - Yuanzheng Cheng
- School of Pharmacy, Weifang Medical University, Weifang, 261053, People's Republic of China
| | - Zhihua Lv
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, People's Republic of China.
| | - Jin Zhou
- School of Pharmacy, Weifang Medical University, Weifang, 261053, People's Republic of China.
| | - Jingjing Ming
- School of Pharmacy, Weifang Medical University, Weifang, 261053, People's Republic of China.
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11
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Liu J, Liu Y, Zhang L, Fu S, Su X. Ultra-specific fluorescence detection of DNA modifying enzymes by dissipation system. Biosens Bioelectron 2022; 215:114561. [PMID: 35841766 DOI: 10.1016/j.bios.2022.114561] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 12/24/2022]
Abstract
Abnormal expression of DNA modifying enzymes (DMEs) is linked to a variety of diseases including cancers. It is desirable to develop accurate methods for DME detection. However, the substrate-based probe for target DMEs is disturbed by various non-target DMEs that have similar activity resulting in a loss of specificity. Here we utilized dissipative DNA networks to develop an ultra-specific fluorescence assay for DME, absolutely distinguishing between target and non-target enzymes. Unlike the conventional sensors in which the discrimination of target and non-target relies on signal intensity, in our system, target DMEs exhibit featured fluorescence oscillatory signals, while non-target DMEs show irreversible 'one-way' fluorescence increase. These dissipation-enabled probes (DEPs) exhibit excellent generality for various types of DMEs including DNA repair enzyme apurinic/apyrimidinic endonuclease 1 (APE1), polynucleotide kinase (T4 PNK), and methyltransferase (Dam). DEPs provide a novel quantification mode based on area under curve which is more robust than those intensity-based quantifications. The detection limits of APE1, T4 PNK, and Dam reach 0.025 U/mL, 0.44 U/mL, and 0.113 U/mL, respectively. DEPs can accurately identify their corresponding DMEs with excellent specificity in cell extracts. Fluorescence sensors based on DEPs herein represent a conceptually new class of methods for enzyme detection, which can be easily adapted to other sensing platforms such as electrochemical sensors.
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Affiliation(s)
- Jiajia Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yu Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Linghao Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shengnan Fu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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12
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Jia D, Fan W, Ren W, Liu C. One-step detection of T4 polynucleotide kinase activity based on single particle-confined enzyme reaction and digital particle counting. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Yang J, He G, Wu W, Deng W, Tan Y, Xie Q. Sensitive photoelectrochemical determination of T4 polynucleotide kinase using AuNPs/SnS 2/ZnIn 2S 4 photoactive material and enzymatic reaction-induced DNA structure switch strategy. Talanta 2022; 249:123660. [PMID: 35689947 DOI: 10.1016/j.talanta.2022.123660] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 12/30/2022]
Abstract
We report here Au nanoparticles (AuNPs)/SnS2/ZnIn2S4 as a high-performance active material for sensitive photoelectrochemical (PEC) determination of T4 polynucleotide kinase (T4 PNK) using an enzymatic reaction-induced DNA structure switch strategy. To construct the PEC biosensor, a double-stranded DNA probe consisting of a CdS quantum dots (QDs)-labeled single-stranded DNA (sDNA) and its complementary DNA (cDNA) is immobilized on the AuNPs/SnS2/ZnIn2S4 photoactive material. T4 PNK can catalyze the phosphorylation of 5'-OH-terminated sDNA in the double-stranded DNA probe when ATP is present, and λ-exonuclease can catalyze the degradation of the phosphorylated sDNA into small fragments. Then the cDNA forms a hairpin structure so that CdS QDs and AuNPs are in close contact, which can induce exciton-plasma interactions between CdS QDs and AuNPs. The exciton-plasma interactions significantly boost the photocurrent, enabling the "signal on" PEC determination of T4 PNK in the range of 10-4 - 1 U mL-1 with a detection limit of 6 × 10-5 U mL-1. The PEC biosensor can also be used to screen enzyme inhibitors.
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Affiliation(s)
- Jinhua Yang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China
| | - Guihua He
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China
| | - Wenying Wu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China
| | - Wenfang Deng
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China.
| | - Yueming Tan
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China.
| | - Qingji Xie
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China
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Lan C, Yamashita YI, Hayashi H, Nakagawa S, Imai K, Mima K, Kaida T, Matsumoto T, Maruno M, Liu Z, Wu X, Wei F, Baba H. High Expression of Bloom Syndrome Helicase is a Key Factor for Poor Prognosis and Advanced Malignancy in Patients with Pancreatic Cancer: A Retrospective Study. Ann Surg Oncol 2022; 29:3551-3564. [PMID: 35419757 DOI: 10.1245/s10434-022-11500-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/18/2022] [Indexed: 12/20/2022]
Abstract
BACKGROUND Bloom syndrome helicase (BLM) is overexpressed in multiple types of cancers and its overexpression may induce genomic instability. This study aimed to determine the function of BLM expression in pancreatic cancer. METHODS BLM messenger RNA (mRNA) expression was analyzed using public datasets to determine its relationship with pancreatic cancer prognosis. Overall, 182 patients with pancreatic cancer who underwent radical resection at our institution were enrolled. BLM expression was evaluated by immunohistochemistry (IHC). We explored the effect of BLM on the proliferation, invasion, migration, and chemoresistance of pancreatic cancer cells via small-interfering RNAs and performed pathway analysis using gene set enrichment analysis. RESULTS BLM mRNA expression was higher in tumor tissue than in normal tissue and had a prognostic effect on overall survival (OS) and recurrence-free survival. The same results were validated by IHC. Multivariate analysis showed that high BLM expression was an independent poor prognostic factor for OS (hazard ratio [HR] 1.678, p = 0.029). In subgroup analysis, the effect of high BLM expression was more significant on OS in patients with younger age (HR 2.27, p = 0.006), male sex (HR 2.39, p = 0.002), high cancer antigen 19-9 level (HR 2.44, p = 0.001), advanced tumor stage (HR 2.25, p = 0.001), lymph node metastasis (HR 2.51, p = 0.001), nerve invasion (HR 2.07, p = 0.002), and adjuvant chemotherapy (HR 2.66, p < 0.001). In vitro, BLM suppression resulted in reduced tumor proliferation, invasion, migration, and chemoresistance. Mechanistically, BLM expression may be associated with E2F1 and E2F2. CONCLUSION BLM expression is a prognostic factor for patients with pancreatic cancer, especially in those with advanced malignancies and receiving chemotherapy.
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Affiliation(s)
- Chuan Lan
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
- Department of Hepatobiliary Surgery and Center of Severe Acute Pancreatitis, The Affiliated Hospital of North Sichuan Medical College, Nanchong, People's Republic of China
| | - Yo-Ichi Yamashita
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hiromitsu Hayashi
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Shigeki Nakagawa
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Katsunori Imai
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Kosuke Mima
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Takayoshi Kaida
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Takashi Matsumoto
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Masataka Maruno
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Zhao Liu
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Xiyu Wu
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Feng Wei
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan.
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Tao J, Liu Z, Zhu Z, Zhang Y, Wang H, Pang P, Yang C, Yang W. Electrochemical detection of T4 polynucleotide kinase activity based on magnetic Fe 3O 4@TiO 2 nanoparticles triggered by a rolling circle amplification strategy. Talanta 2022; 241:123272. [PMID: 35121542 DOI: 10.1016/j.talanta.2022.123272] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 12/29/2022]
Abstract
An ultrasensitive electrochemical detection of the activity and inhibition of T4 polynucleotide kinase (T4 PNK) was developed by using magnetic Fe3O4@TiO2 core-shell nanoparticles, which was triggered by a rolling circle amplification strategy (Fe3O4@TiO2-RCA). We used Fe3O4@TiO2 as a substrate to anchor a DNA primer. DNA S1 with 5'-OH termini was phosphorylated in the presence of T4 PNK and ATP, which was adsorbed on the surface of Fe3O4@TiO2 NPs and served as the primer for subsequent RCA reactions. After adding circular template DNA S2, RCA was initiated in the presence of phi29 DNA polymerase and dNTPs. Then, Fc-labeled DNA S3 (Fc-S3) was hybridized with RCA. The obtained Fe3O4@TiO2-RCA was adsorbed on the surface of a magnetic gold electrode (MGE) by magnetic enrichment, resulting in an enhanced electrochemical signal. The T4 PNK activity can be monitored by measuring the electrochemical signal generated. This electrochemical assay is sensitive to the activity of T4 PNK with a dynamic linear range of 0.00001-20 U/mL and a low detection limit of 3.0 × 10-6 U/mL. The proposed strategy can be used to screen the T4 PNK inhibitors, so it has great potential in the discovery of nucleotide kinase-target drug and early clinical diagnosis of cancer.
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Affiliation(s)
- Jinpeng Tao
- National and Local Joint Engineering Research Center for Green Preparation Technology of Biobased Materials, Yunnan Minzu University, Kunming, 650500, PR China
| | - Zaiqiong Liu
- National and Local Joint Engineering Research Center for Green Preparation Technology of Biobased Materials, Yunnan Minzu University, Kunming, 650500, PR China
| | - Zhenyu Zhu
- National and Local Joint Engineering Research Center for Green Preparation Technology of Biobased Materials, Yunnan Minzu University, Kunming, 650500, PR China
| | - Yanli Zhang
- National and Local Joint Engineering Research Center for Green Preparation Technology of Biobased Materials, Yunnan Minzu University, Kunming, 650500, PR China.
| | - Hongbin Wang
- National and Local Joint Engineering Research Center for Green Preparation Technology of Biobased Materials, Yunnan Minzu University, Kunming, 650500, PR China
| | - Pengfei Pang
- National and Local Joint Engineering Research Center for Green Preparation Technology of Biobased Materials, Yunnan Minzu University, Kunming, 650500, PR China.
| | - Chun Yang
- Shaanxi Geological Survey Center, Xi'an, 710068, PR China
| | - Wenrong Yang
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, 3217, Australia
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16
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Bi L, Qin Z, Hou XM, Modesti M, Sun B. Simultaneous Mechanical and Fluorescence Detection of Helicase-Catalyzed DNA Unwinding. Methods Mol Biol 2022; 2478:329-347. [PMID: 36063326 DOI: 10.1007/978-1-0716-2229-2_12] [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] [Indexed: 06/15/2023]
Abstract
Helicases are ubiquitous molecular motor proteins that utilize the energy derived from the hydrolysis of nucleoside triphosphates (NTPs) to transiently convert the duplex form of nucleic acids to single-stranded intermediates for many biological processes. These enzymes play vital roles in nearly all aspects of nucleic acid metabolism, such as DNA repair and RNA splicing. Understanding helicase's functional roles requires methods to dissect the mechanisms of motor proteins at the molecular level. In the past three decades, there has been a large increase in the application of single-molecule approaches to investigate helicases. These techniques, such as optical tweezers and single-molecule fluorescence, offer capabilities to monitor helicase motions with unprecedented spatiotemporal resolution, to apply quantitative forces to probe the chemo-mechanical activities of these motors and to resolve helicase heterogeneity at the single-molecule level. In this chapter, we describe a single-molecule method that combines optical tweezers with confocal fluorescence microscopy to study helicase-catalyzed DNA unwinding. Using Bloom syndrome protein (BLM), a multifunctional helicase that maintains genome stability, as an example, we show that this method allows for the simultaneous detection of displacement, force and fluorescence signals of a single DNA molecule during unwinding in real time, leading to the discovery of a distinct bidirectional unwinding mode of BLM that is activated by a single-stranded DNA binding protein called replication protein A (RPA). We provide detailed instructions on how to prepare two DNA templates to be used in the assays, purify the BLM and RPA proteins, perform single-molecule experiments, and acquire and analyse the data.
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Affiliation(s)
- Lulu Bi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhenheng Qin
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xi-Miao Hou
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Mauro Modesti
- Cancer Research Center of Marseille, Marseille, France
| | - Bo Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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17
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Transcriptional regulation by a RecQ helicase. Methods Enzymol 2022; 673:227-249. [PMID: 35965009 PMCID: PMC9379128 DOI: 10.1016/bs.mie.2022.03.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
RecQ helicases participate in a variety of DNA metabolic processes through their multiple biochemical activities. In vitro characterization and cellular studies have suggested that RECQ1 (also known as RECQL or RECQL1) performs its diverse functions through specific interactions with DNA and protein partners. We have taken an unbiased approach to determine the contribution of RECQ1 in genome maintenance and as a putative susceptibility factor in breast cancer. Here, we provide methodology to map the genome-wide binding sites of RECQ1 together with the profiling of RECQ1-dependent transcriptome to investigate its role in gene regulation. The described approach will be helpful to develop a mechanistic framework for elucidating critical functions of RECQ1 and other RecQ homologs in distinct chromatin and biological contexts.
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18
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Exome Sequencing Reveals Novel Variants and Expands the Genetic Landscape for Congenital Microcephaly. Genes (Basel) 2021; 12:genes12122014. [PMID: 34946966 PMCID: PMC8700965 DOI: 10.3390/genes12122014] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/12/2021] [Accepted: 12/15/2021] [Indexed: 11/23/2022] Open
Abstract
Congenital microcephaly causes smaller than average head circumference relative to age, sex and ethnicity and is most usually associated with a variety of neurodevelopmental disorders. The underlying etiology is highly heterogeneous and can be either environmental or genetic. Disruption of any one of multiple biological processes, such as those underlying neurogenesis, cell cycle and division, DNA repair or transcription regulation, can result in microcephaly. This etiological heterogeneity manifests in a clinical variability and presents a major diagnostic and therapeutic challenge, leaving an unacceptably large proportion of over half of microcephaly patients without molecular diagnosis. To elucidate the clinical and genetic landscapes of congenital microcephaly, we sequenced the exomes of 191 clinically diagnosed patients with microcephaly as one of the features. We established a molecular basis for microcephaly in 71 patients (37%), and detected novel variants in five high confidence candidate genes previously unassociated with this condition. We report a large number of patients with mutations in tubulin-related genes in our cohort as well as higher incidence of pathogenic mutations in MCPH genes. Our study expands the phenotypic and genetic landscape of microcephaly, facilitating differential clinical diagnoses for disorders associated with most commonly disrupted genes in our cohort.
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Shang J, Yu S, Chen Y, Gao Y, Hong C, Li F, Wang F. Real-Time Investigation of Intracellular Polynucleotide Kinase Using a Cascaded Amplification Circuit. Anal Chem 2021; 93:15559-15566. [PMID: 34748706 DOI: 10.1021/acs.analchem.1c04033] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polynucleotide kinase (PNK) shows an in-depth correlationship with DNA repair and metabolism processes. The in situ visualization of intracellular PNK revealed an extremely biological significance in supplementing reliable and quantitative information on its spatiotemporal distribution in live cells. Herein, we developed a versatile cascaded DNA amplification circuit through the integration of catalytic DNA assembly and hybridization chain reaction circuits and realized the accurate evaluation of intracellular PNK activity via the Förster resonance energy transfer (FRET) principle. Initially, without PNK, trigger T was firmly caged in the PNK-recognizing hairpin HT, resulting in no disturbance of the concatenated circuit. However, with the introduction of PNK, the 5'-OH terminal of PNK-addressing HT was phosphorylated, then the phosphorylated HT could be subsequently digested by λ exonuclease (λ Exo) to produce trigger T of the cascaded DNA circuit. As a result, the integrated circuit was stimulated to produce an amplified FRET signal for quantitatively monitoring the activity of PNK. Due to the λ Exo-specific digestion of 5'-phosphate DNA and the high signal gain of the cascade circuit, our proposed strategy enables the sensitive analysis of PNK activity in vitro and in complex biological samples. Furthermore, our PNK-sensing platform was extensively explored in HeLa cells for realizing reliable intracellular PNK imaging and thus showed high potential in the future diagnosis and treatment of kinase-related diseases.
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Affiliation(s)
- Jinhua Shang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Shanshan Yu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yingying Chen
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yuhui Gao
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Chen Hong
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Fengzhe Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
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20
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Single-molecule studies of helicases and translocases in prokaryotic genome-maintenance pathways. DNA Repair (Amst) 2021; 108:103229. [PMID: 34601381 DOI: 10.1016/j.dnarep.2021.103229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/22/2022]
Abstract
Helicases involved in genomic maintenance are a class of nucleic-acid dependent ATPases that convert the energy of ATP hydrolysis into physical work to execute irreversible steps in DNA replication, repair, and recombination. Prokaryotic helicases provide simple models to understand broadly conserved molecular mechanisms involved in manipulating nucleic acids during genome maintenance. Our understanding of the catalytic properties, mechanisms of regulation, and roles of prokaryotic helicases in DNA metabolism has been assembled through a combination of genetic, biochemical, and structural methods, further refined by single-molecule approaches. Together, these investigations have constructed a framework for understanding the mechanisms that maintain genomic integrity in cells. This review discusses recent single-molecule insights into molecular mechanisms of prokaryotic helicases and translocases.
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21
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Balajee AS. Human RecQL4 as a Novel Molecular Target for Cancer Therapy. Cytogenet Genome Res 2021; 161:305-327. [PMID: 34474412 DOI: 10.1159/000516568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/24/2021] [Indexed: 11/19/2022] Open
Abstract
Human RecQ helicases play diverse roles in the maintenance of genomic stability. Inactivating mutations in 3 of the 5 human RecQ helicases are responsible for the pathogenesis of Werner syndrome (WS), Bloom syndrome (BS), Rothmund-Thomson syndrome (RTS), RAPADILINO, and Baller-Gerold syndrome (BGS). WS, BS, and RTS patients are at increased risk for developing many age-associated diseases including cancer. Mutations in RecQL1 and RecQL5 have not yet been associated with any human diseases so far. In terms of disease outcome, RecQL4 deserves special attention because mutations in RecQL4 result in 3 autosomal recessive syndromes (RTS type II, RAPADILINO, and BGS). RecQL4, like other human RecQ helicases, has been demonstrated to play a crucial role in the maintenance of genomic stability through participation in diverse DNA metabolic activities. Increased incidence of osteosarcoma in RecQL4-mutated RTS patients and elevated expression of RecQL4 in sporadic cancers including osteosarcoma suggest that loss or gain of RecQL4 expression is linked with cancer susceptibility. In this review, current and future perspectives are discussed on the potential use of RecQL4 as a novel cancer therapeutic target.
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Affiliation(s)
- Adayabalam S Balajee
- Cytogenetic Biodosimetry Laboratory, Radiation Emergency Assistance Center/Training Site, Oak Ridge Institute for Science and Education, Oak Ridge Associated Universities, Oak Ridge, Tennessee, USA
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22
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Li Y, Liu Q, Cui L, Liu W, Qiu JG, Zhang CY. Zirconium ion-mediated assembly of a single quantum dot-based nanosensor for kinase assay. Chem Commun (Camb) 2021; 57:6376-6379. [PMID: 34081069 DOI: 10.1039/d1cc02035h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate the zirconium ion-mediated assembly of a single quantum dot (QD)-based nanosensor for accurate detection of protein kinases (PKA) and polynucleotide kinases (PNK). This nanosensor is very sensitive with a detection limit of 8.82 × 10-4 U mL-1 for PKA and 1.40 × 10-5 U mL-1 for PNK. Moreover, it can be used to analyze the enzyme kinetic parameters and screen the inhibitors of PKA and PNK, with potential applications in drug discovery and clinical diagnosis.
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Affiliation(s)
- Yueying Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China.
| | - Qian Liu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China.
| | - Lin Cui
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China.
| | - Wenjing Liu
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450000, China.
| | - Jian-Ge Qiu
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450000, China.
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China.
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23
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Zhang J, Lian H, Chen K, Pang Y, Chen M, Huang B, Zhu L, Xu S, Liu M, Zhong C. RECQ1 Promotes Stress Resistance and DNA Replication Progression Through PARP1 Signaling Pathway in Glioblastoma. Front Cell Dev Biol 2021; 9:714868. [PMID: 34381789 PMCID: PMC8350743 DOI: 10.3389/fcell.2021.714868] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/29/2021] [Indexed: 11/22/2022] Open
Abstract
Glioblastoma (GBM) is the most common aggressive primary malignant brain tumor, and patients with GBM have a median survival of 20 months. Clinical therapy resistance is a challenging barrier to overcome. Tumor genome stability maintenance during DNA replication, especially the ability to respond to replication stress, is highly correlated with drug resistance. Recently, we identified a protective role for RECQ1 under replication stress conditions. RECQ1 acts at replication forks, binds PCNA, inhibits single-strand DNA formation and nascent strand degradation in GBM cells. It is associated with the function of the PARP1 protein, promoting PARP1 recruitment to replication sites. RECQ1 is essential for DNA replication fork protection and tumor cell proliferation under replication stress conditions, and as a target of RECQ1, PARP1 effectively protects and restarts stalled replication forks, providing new insights into genomic stability maintenance and replication stress resistance. These findings indicate that tumor genome stability targeting RECQ1-PARP1 signaling may be a promising therapeutic intervention to overcome therapy resistance in GBM.
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Affiliation(s)
- Jing Zhang
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China.,Institute for Advanced Study, Tongji University, Shanghai, China
| | - Hao Lian
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Kui Chen
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Ying Pang
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Mu Chen
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Bingsong Huang
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Lei Zhu
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Siyi Xu
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Min Liu
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Chunlong Zhong
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
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Rahman MM, Mohiuddin M, Shamima Keka I, Yamada K, Tsuda M, Sasanuma H, Andreani J, Guerois R, Borde V, Charbonnier JB, Takeda S. Genetic evidence for the involvement of mismatch repair proteins, PMS2 and MLH3, in a late step of homologous recombination. J Biol Chem 2021; 295:17460-17475. [PMID: 33453991 DOI: 10.1074/jbc.ra120.013521] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 09/28/2020] [Indexed: 12/15/2022] Open
Abstract
Homologous recombination (HR) repairs DNA double-strand breaks using intact homologous sequences as template DNA. Broken DNA and intact homologous sequences form joint molecules (JMs), including Holliday junctions (HJs), as HR intermediates. HJs are resolved to form crossover and noncrossover products. A mismatch repair factor, MLH3 endonuclease, produces the majority of crossovers during meiotic HR, but it remains elusive whether mismatch repair factors promote HR in nonmeiotic cells. We disrupted genes encoding the MLH3 and PMS2 endonucleases in the human B cell line, TK6, generating null MLH3-/- and PMS2-/- mutant cells. We also inserted point mutations into the endonuclease motif of MLH3 and PMS2 genes, generating endonuclease death MLH3DN/DN and PMS2EK/EK cells. MLH3-/- and MLH3DN/DN cells showed a very similar phenotype, a 2.5-fold decrease in the frequency of heteroallelic HR-dependent repair of restriction enzyme-induced double-strand breaks. PMS2-/- and PMS2EK/EK cells showed a phenotype very similar to that of the MLH3 mutants. These data indicate that MLH3 and PMS2 promote HR as an endonuclease. The MLH3DN/DN and PMS2EK/EK mutations had an additive effect on the heteroallelic HR. MLH3DN/DN/PMS2EK/EK cells showed normal kinetics of γ-irradiation-induced Rad51 foci but a significant delay in the resolution of Rad51 foci and a 3-fold decrease in the number of cisplatin-induced sister chromatid exchanges. The ectopic expression of the Gen1 HJ re-solvase partially reversed the defective heteroallelic HR of MLH3DN/DN/PMS2EK/EK cells. Taken together, we propose that MLH3 and PMS2 promote HR as endonucleases, most likely by processing JMs in mammalian somatic cells.
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Affiliation(s)
- Md Maminur Rahman
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mohiuddin Mohiuddin
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Islam Shamima Keka
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kousei Yamada
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masataka Tsuda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroyuki Sasanuma
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Jessica Andreani
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Raphael Guerois
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Valerie Borde
- Institut Curie, CNRS, UMR3244, PSL Research University, Paris, France
| | - Jean-Baptiste Charbonnier
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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25
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Liu M, Qiu JG, Ma F, Zhang CY. Advances in single-molecule fluorescent nanosensors. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2021; 13:e1716. [PMID: 33779063 DOI: 10.1002/wnan.1716] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 12/21/2022]
Abstract
Single-molecule detection represents the ultimate sensitivity in measurement science with the characteristics of simplicity, rapidity, low sample consumption, and high signal-to-noise ratio and has attracted considerable attentions in biosensor development. In recent years, a variety of functional nanomaterials with unique chemical, optical, mechanical, and electronic features have been synthesized. The integration of single-molecule detection with functional nanomaterials enables the construction of novel single-molecule fluorescent nanosensors with excellent performance. Herein, we review the advance in single-molecule fluorescent nanosensors constructed by novel nanomaterials including quantum dots, gold nanoparticles, upconversion nanoparticles, fluorescent conjugated polymer nanoparticles, nanosheets, and magnetic nanoparticles in the past decade (2011-2020), and discuss the strategies, features, and applications of single-molecule fluorescent nanosensors in the detection of microRNAs, DNAs, enzymes, proteins, viruses, and live cells. Moreover, we highlight the future direction and challenges in this area. This article is categorized under: Diagnostic Tools > Biosensing Diagnostic Tools > In Vitro Nanoparticle-Based Sensing Diagnostic Tools > Diagnostic Nanodevices.
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Affiliation(s)
- Meng Liu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, China
| | - Jian-Ge Qiu
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Fei Ma
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, China
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Genome-Wide Analysis Unveils DNA Helicase RECQ1 as a Regulator of Estrogen Response Pathway in Breast Cancer Cells. Mol Cell Biol 2021; 41:MCB.00515-20. [PMID: 33468559 DOI: 10.1128/mcb.00515-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/07/2021] [Indexed: 02/07/2023] Open
Abstract
Susceptibility to breast cancer is significantly increased in individuals with germ line mutations in RECQ1 (also known as RECQL or RECQL1), a gene encoding a DNA helicase essential for genome maintenance. We previously reported that RECQ1 expression predicts clinical outcomes for sporadic breast cancer patients stratified by estrogen receptor (ER) status. Here, we utilized an unbiased integrative genomics approach to delineate a cross talk between RECQ1 and ERα, a known master regulatory transcription factor in breast cancer. We found that expression of ESR1, the gene encoding ERα, is directly activated by RECQ1. More than 35% of RECQ1 binding sites were cobound by ERα genome-wide. Mechanistically, RECQ1 cooperates with FOXA1, the pioneer transcription factor for ERα, to enhance chromatin accessibility at the ESR1 regulatory regions in a helicase activity-dependent manner. In clinical ERα-positive breast cancers treated with endocrine therapy, high RECQ1 and high FOXA1 coexpressing tumors were associated with better survival. Collectively, these results identify RECQ1 as a novel cofactor for ERα and uncover a previously unknown mechanism by which RECQ1 regulates disease-driving gene expression in ER-positive breast cancer cells.
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Queuine Is a Nutritional Regulator of Entamoeba histolytica Response to Oxidative Stress and a Virulence Attenuator. mBio 2021; 12:mBio.03549-20. [PMID: 33688012 PMCID: PMC8092309 DOI: 10.1128/mbio.03549-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Entamoeba histolytica is a unicellular parasite that causes amebiasis. The parasite resides in the colon and feeds on the colonic microbiota. Queuosine is a naturally occurring modified ribonucleoside found in the first position of the anticodon of the transfer RNAs for Asp, Asn, His, and Tyr. Eukaryotes lack pathways to synthesize queuine, the nucleobase precursor to queuosine, and must obtain it from diet or gut microbiota. Here, we describe the effects of queuine on the physiology of the eukaryotic parasite Entamoeba histolytica, the causative agent of amebic dysentery. Queuine is efficiently incorporated into E. histolytica tRNAs by a tRNA-guanine transglycosylase (EhTGT) and this incorporation stimulates the methylation of C38 in
tRNAGUCAsp. Queuine protects the parasite against oxidative stress (OS) and antagonizes the negative effect that oxidation has on translation by inducing the expression of genes involved in the OS response, such as heat shock protein 70 (Hsp70), antioxidant enzymes, and enzymes involved in DNA repair. On the other hand, queuine impairs E. histolytica virulence by downregulating the expression of genes previously associated with virulence, including cysteine proteases, cytoskeletal proteins, and small GTPases. Silencing of EhTGT prevents incorporation of queuine into tRNAs and strongly impairs methylation of C38 in
tRNAGUCAsp, parasite growth, resistance to OS, and cytopathic activity. Overall, our data reveal that queuine plays a dual role in promoting OS resistance and reducing parasite virulence.
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Dhar S, Datta A, Brosh RM. DNA helicases and their roles in cancer. DNA Repair (Amst) 2020; 96:102994. [PMID: 33137625 DOI: 10.1016/j.dnarep.2020.102994] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 12/15/2022]
Abstract
DNA helicases, known for their fundamentally important roles in genomic stability, are high profile players in cancer. Not only are there monogenic helicase disorders with a strong disposition to cancer, it is well appreciated that helicase variants are associated with specific cancers (e.g., breast cancer). Flipping the coin, DNA helicases are frequently overexpressed in cancerous tissues and reduction in helicase gene expression results in reduced proliferation and growth capacity, as well as DNA damage induction and apoptosis of cancer cells. The seminal roles of helicases in the DNA damage and replication stress responses, as well as DNA repair pathways, validate their vital importance in cancer biology and suggest their potential values as targets in anti-cancer therapy. In recent years, many laboratories have characterized the specialized roles of helicase to resolve transcription-replication conflicts, maintain telomeres, mediate cell cycle checkpoints, remodel stalled replication forks, and regulate transcription. In vivo models, particularly mice, have been used to interrogate helicase function and serve as a bridge for preclinical studies that may lead to novel therapeutic approaches. In this review, we will summarize our current knowledge of DNA helicases and their roles in cancer, emphasizing the latest developments.
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Affiliation(s)
- Srijita Dhar
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Arindam Datta
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
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Lin M, Wan H, Zhang J, Wang Q, Hu X, Xia F. Electrochemical DNA Sensors Based on MoS 2-AuNPs for Polynucleotide Kinase Activity and Inhibition Assay. ACS APPLIED MATERIALS & INTERFACES 2020; 12:45814-45821. [PMID: 32877162 DOI: 10.1021/acsami.0c13385] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The determination of T4 polynucleotide kinase (PNK) activity and the screening of PNK inhibitors are critical to disease diagnosis and drug discovery. Numerous electrochemical strategies have been developed for the sensitive measurement of PNK activity and inhibition. However, they often suffer from additional labels and multiple steps of the detection process for the electrochemical readout. Herein, we have demonstrated an electrochemical DNA (E-DNA) sensor for the one-step detection of PNK with "signal-on" readout with no need for additional labels. In our design, the highly switchable double-stranded DNA (dsDNA) probes are immobilized on the gold nanoparticle-decorated molybdenum disulfide nanomaterial (MoS2-AuNPs), which possesses large surface area and high conductivity for elevating the signal gain in the PNK detection. This signal-on E-DNA sensor integrated with MoS2-AuNPs exhibits a much higher sensitivity than that without MoS2-AuNPs, showing a detection limit of 2.18 × 10-4 U/mL. Furthermore, this assay shows high selectivity, with the ability to discriminate PNK from other enzymes and proteins, and can be utilized to screen inhibitors. The proposed sensor is easy to operate with one-step readout and robust for PNK detection in the biological matrix and shows great potential for point-of-care in clinical diagnostics and drug screening.
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Affiliation(s)
- Meihua Lin
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Hao Wan
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Jian Zhang
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Quan Wang
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Xinyu Hu
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
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Datta A, Dhar S, Awate S, Brosh RM. Synthetic Lethal Interactions of RECQ Helicases. Trends Cancer 2020; 7:146-161. [PMID: 33041245 DOI: 10.1016/j.trecan.2020.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/20/2020] [Accepted: 09/04/2020] [Indexed: 02/06/2023]
Abstract
DNA helicases have risen to the forefront as genome caretakers. Their prominent roles in chromosomal stability are demonstrated by the linkage of mutations in helicase genes to hereditary disorders with defects in DNA repair, the replication stress response, and/or transcriptional activation. Conversely, accumulating evidence suggests that DNA helicases in cancer cells have a network of pathway interactions such that codeficiency of some helicases and their genetically interacting proteins results in synthetic lethality (SL). Such genetic interactions may potentially be exploited for cancer therapies. We discuss the roles of RECQ DNA helicases in cancer, emphasizing some of the more recent developments in SL.
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Affiliation(s)
- Arindam Datta
- Section on DNA Helicases, Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Srijita Dhar
- Section on DNA Helicases, Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Sanket Awate
- Section on DNA Helicases, Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Robert M Brosh
- Section on DNA Helicases, Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
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31
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Mao J, Chen X, Xu H, Xu X. DNAzyme-driven DNA walker biosensor for amplified electrochemical detection of T4 polynucleotide kinase activity and inhibition. J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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32
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Schnabel F, Kornak U, Wollnik B. Premature aging disorders: A clinical and genetic compendium. Clin Genet 2020; 99:3-28. [PMID: 32860237 DOI: 10.1111/cge.13837] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 12/22/2022]
Abstract
Progeroid disorders make up a heterogeneous group of very rare hereditary diseases characterized by clinical signs that often mimic physiological aging in a premature manner. Apart from Hutchinson-Gilford progeria syndrome, one of the best-investigated progeroid disorders, a wide spectrum of other premature aging phenotypes exist, which differ significantly in their clinical presentation and molecular pathogenesis. Next-generation sequencing (NGS)-based approaches have made it feasible to determine the molecular diagnosis in the early stages of a disease. Nevertheless, a broad clinical knowledge on these disorders and their associated symptoms is still fundamental for a comprehensive patient management and for the interpretation of variants of unknown significance from NGS data sets. This review provides a detailed overview on characteristic clinical features and underlying molecular genetics of well-known as well as only recently identified premature aging disorders and also highlights novel findings towards future therapeutic options.
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Affiliation(s)
- Franziska Schnabel
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Uwe Kornak
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable cells" (MBExC), University of Göttingen, Göttingen, Germany
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Selmoni O, Rochat E, Lecellier G, Berteaux‐Lecellier V, Joost S. Seascape genomics as a new tool to empower coral reef conservation strategies: An example on north-western Pacific Acropora digitifera. Evol Appl 2020; 13:1923-1938. [PMID: 32908595 PMCID: PMC7463334 DOI: 10.1111/eva.12944] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/10/2020] [Accepted: 02/17/2020] [Indexed: 12/25/2022] Open
Abstract
Coral reefs are suffering a major decline due to the environmental constraints imposed by climate change. Over the last 20 years, three major coral bleaching events occurred in concomitance with anomalous heatwaves, provoking a severe loss of coral cover worldwide. The conservation strategies for preserving reefs, as they are implemented now, cannot cope with global climatic shifts. Consequently, researchers are advocating for preservation networks to be set-up to reinforce coral adaptive potential. However, the main obstacle to this implementation is that studies on coral adaption are usually hard to generalize at the scale of a reef system. Here, we study the relationships between genotype frequencies and environmental characteristics of the sea (seascape genomics), in combination with connectivity analysis, to investigate the adaptive potential of a flagship coral species of the Ryukyu Archipelago (Japan). By associating genotype frequencies with descriptors of historical environmental conditions, we discovered six genomic regions hosting polymorphisms that might promote resistance against heat stress. Remarkably, annotations of genes in these regions were consistent with molecular roles associated with heat responses. Furthermore, we combined information on genetic and spatial distances between reefs to predict connectivity at a regional scale. The combination of these results portrayed the adaptive potential of this population: we were able to identify reefs carrying potential heat stress adapted genotypes and to understand how they disperse to neighbouring reefs. This information was summarized by objective, quantifiable and mappable indices covering the whole region, which can be extremely useful for future prioritization of reefs in conservation planning. This framework is transferable to any coral species on any reef system and therefore represents a valuable tool for empowering preservation efforts dedicated to the protection of coral reefs in warming oceans.
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Affiliation(s)
- Oliver Selmoni
- Laboratory of Geographic Information Systems (LASIG)School of Architecture, Civil and Environmental EngineeringEcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Estelle Rochat
- Laboratory of Geographic Information Systems (LASIG)School of Architecture, Civil and Environmental EngineeringEcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Gael Lecellier
- UMR250/9220 ENTROPIE IRD‐CNRS‐URLabex CORAILNoumeaNew Caledonia
- UVSQUniversité de Paris‐SaclayVersaillesFrance
| | | | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG)School of Architecture, Civil and Environmental EngineeringEcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
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Werner Syndrome Protein Expression in Breast Cancer. Clin Breast Cancer 2020; 21:57-73.e7. [PMID: 32919863 DOI: 10.1016/j.clbc.2020.07.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 07/09/2020] [Accepted: 07/16/2020] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Werner protein (WRN) plays an important role in DNA repair, replication, transcription, and consequently genomic stability via its DNA-helicase and exonuclease activity. Loss of function of WRN is associated with Werner syndrome (WS), which is characterized by premature aging and cancer predisposition. Malignancies that are commonly linked to WS are thyroid carcinoma, melanoma, breast cancer, meningioma, and soft tissue and bone sarcomas. Currently, the clinicopathologic significance of WRN in breast cancer is largely unknown. PATIENTS AND METHODS We investigated the clinicopathologic and prognostic significance of WRN protein expression in a cohort of clinically annotated series of sporadic (n = 1650) and BRCA-mutated (n = 75) invasive breast cancers. We correlated WRN protein expression to clinicopathologic characteristics, DNA repair protein expression, and survival outcomes. RESULTS There is strong evidence of association between low nuclear and cytoplasmic WRN co-expression and low levels of KU70/KU80, DNA-PK, DNA Pol-B, CKD18, cytoplasmic RECQL4, and nuclear BLM protein expression (adjusted P-values < .05). Tumors with low nuclear or cytoplasmic WRN expression have worse overall breast cancer-specific survival (BCSS) (adjusted P-values < .05). In topoisomerase I overexpressed tumors, low WRN nuclear expression was associated with poor BCSS (P-value < .05). In BRCA-mutated tumors, low WRN cytoplasmic expression conferred shortest BCSS (P < .05). CONCLUSIONS Low WRN protein expression is associated with poor BCSS in patients with breast cancer. This can be used to optimize the risk stratification for personalized treatment.
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Debnath S, Sharma S. RECQ1 Helicase in Genomic Stability and Cancer. Genes (Basel) 2020; 11:E622. [PMID: 32517021 PMCID: PMC7348745 DOI: 10.3390/genes11060622] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/01/2020] [Accepted: 06/03/2020] [Indexed: 12/13/2022] Open
Abstract
RECQ1 (also known as RECQL or RECQL1) belongs to the RecQ family of DNA helicases, members of which are linked with rare genetic diseases of cancer predisposition in humans. RECQ1 is implicated in several cellular processes, including DNA repair, cell cycle and growth, telomere maintenance, and transcription. Earlier studies have demonstrated a unique requirement of RECQ1 in ensuring chromosomal stability and suggested its potential involvement in tumorigenesis. Recent reports have suggested that RECQ1 is a potential breast cancer susceptibility gene, and missense mutations in this gene contribute to familial breast cancer development. Here, we provide a framework for understanding how the genetic or functional loss of RECQ1 might contribute to genomic instability and cancer.
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Affiliation(s)
- Subrata Debnath
- Department of Biochemistry and Molecular Biology, College of Medicine, Howard University, 520 W Street, NW, Washington, DC 20059, USA;
| | - Sudha Sharma
- Department of Biochemistry and Molecular Biology, College of Medicine, Howard University, 520 W Street, NW, Washington, DC 20059, USA;
- National Human Genome Center, College of Medicine, Howard University, 520 W Street, NW, Washington, DC 20059, USA
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36
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Jain CK, Mukhopadhyay S, Ganguly A. RecQ Family Helicases in Replication Fork Remodeling and Repair: Opening New Avenues towards the Identification of Potential Targets for Cancer Chemotherapy. Anticancer Agents Med Chem 2020; 20:1311-1326. [PMID: 32418530 DOI: 10.2174/1871520620666200518082433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 08/08/2019] [Accepted: 12/30/2019] [Indexed: 11/22/2022]
Abstract
Replication fork reversal and restart has gained immense interest as a central response mechanism to replication stress following DNA damage. Although the exact mechanism of fork reversal has not been elucidated precisely, the involvement of diverse pathways and different factors has been demonstrated, which are central to this phenomenon. RecQ helicases known for their vital role in DNA repair and maintaining genome stability has recently been implicated in the restart of regressed replication forks. Through interaction with vital proteins like Poly (ADP) ribose polymerase 1 (PARP1), these helicases participate in the replication fork reversal and restart phenomenon. Most therapeutic agents used for cancer chemotherapy act by causing DNA damage in replicating cells and subsequent cell death. These DNA damages can be repaired by mechanisms involving fork reversal as the key phenomenon eventually reducing the efficacy of the therapeutic agent. Hence the factors contributing to this repair process can be good selective targets for developing more efficient chemotherapeutic agents. In this review, we have discussed in detail the role of various proteins in replication fork reversal and restart with special emphasis on RecQ helicases. Involvement of other proteins like PARP1, recombinase rad51, SWI/SNF complex has also been discussed. Since RecQ helicases play a central role in the DNA damage response following chemotherapeutic treatment, we propose that targeting these helicases can emerge as an alternative to available intervention strategies. We have also summarized the current research status of available RecQ inhibitors and siRNA based therapeutic approaches that targets RecQ helicases. In summary, our review gives an overview of the DNA damage responses involving replication fork reversal and provides new directions for the development of more efficient and sustainable chemotherapeutic approaches.
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Affiliation(s)
- Chetan K Jain
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Swagata Mukhopadhyay
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Agneyo Ganguly
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
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37
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Zhang G, Chai H, Tian M, Zhu S, Qu L, Zhang X. Zirconium–Metalloporphyrin Frameworks–Luminol Competitive Electrochemiluminescence for Ratiometric Detection of Polynucleotide Kinase Activity. Anal Chem 2020; 92:7354-7362. [DOI: 10.1021/acs.analchem.0c01262] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Guangyao Zhang
- Research Center for Intelligent and Wearable Technology, College of Textiles and Clothing, Qingdao University, Qingdao 266071, China
- State Key Laboratory of Bio-Fibers and Eco-Textiles, Qingdao University, Qingdao 266071, China
| | - Huining Chai
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao 266033, China
| | - Mingwei Tian
- Research Center for Intelligent and Wearable Technology, College of Textiles and Clothing, Qingdao University, Qingdao 266071, China
- State Key Laboratory of Bio-Fibers and Eco-Textiles, Qingdao University, Qingdao 266071, China
| | - Shifeng Zhu
- Research Center for Intelligent and Wearable Technology, College of Textiles and Clothing, Qingdao University, Qingdao 266071, China
- State Key Laboratory of Bio-Fibers and Eco-Textiles, Qingdao University, Qingdao 266071, China
| | - Lijun Qu
- Research Center for Intelligent and Wearable Technology, College of Textiles and Clothing, Qingdao University, Qingdao 266071, China
- State Key Laboratory of Bio-Fibers and Eco-Textiles, Qingdao University, Qingdao 266071, China
| | - Xueji Zhang
- Research Center for Intelligent and Wearable Technology, College of Textiles and Clothing, Qingdao University, Qingdao 266071, China
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
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Zhao H, Yan Y, Chen M, Hu T, Wu K, Liu H, Ma C. Exonuclease III-assisted signal amplification strategy for sensitive fluorescence detection of polynucleotide kinase based on poly(thymine)-templated copper nanoparticles. Analyst 2020; 144:6689-6697. [PMID: 31598619 DOI: 10.1039/c9an01659g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A sensitive and label-free fluorometric method has been developed for the determination of polynucleotide kinase (PNK) activity, by employing exonuclease III (Exo III)-assisted cyclic signal amplification and poly(thymine)-templated copper nanoparticles (polyT-CuNPs). In the presence of PNK, cDNA with 5'-hydroxyl termini was phosphorylated and then hybridized with tDNA to form the cDNA/tDNA duplex, which subsequently triggered the λ exonuclease cleavage reaction, eventually resulting in the release of tDNA. The released tDNA could unfold the hairpin structure of HP DNA to generate partially complementary duplex (tDNA/HP DNA), wherein the HP DNA possessed T-rich sequences (T30) and tDNA recognition sequence. With the help of Exo III digestion, the tDNA was able to initiate the cycle for the generation of T-rich sequences, the template for the formation of fluorescent CuNPs. Conversely, the cDNA could not be cleaved by λ exonuclease without PNK and individual HP DNA could not be hydrolyzed by Exo III. The T-rich sequence was caged in HP DNA, resulting in a weak fluorescence signal. Under optimized conditions, the fluorescence intensity was linearly correlated to a concentration range of 0.001 to 1 U mL-1 with a low detection limit of 2 × 10-4 U mL-1. Considering the intriguing analytical performance, this approach could be explored to screen T4 PNK inhibitors and hold promising applications in drug discovery and disease therapy.
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Affiliation(s)
- Han Zhao
- School of Life Sciences, Central South University, Changsha 410013, China.
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Shang J, Wei J, Wang Q, Wang J, Zhou Y, Yu S, Liu X, Wang F. Adaption of an autonomously cascade DNA circuit for amplified detection and intracellular imaging of polynucleotide kinase with ultralow background. Biosens Bioelectron 2020; 152:111994. [DOI: 10.1016/j.bios.2019.111994] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/15/2019] [Accepted: 12/23/2019] [Indexed: 12/20/2022]
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40
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Brosh RM, Matson SW. History of DNA Helicases. Genes (Basel) 2020; 11:genes11030255. [PMID: 32120966 PMCID: PMC7140857 DOI: 10.3390/genes11030255] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 12/13/2022] Open
Abstract
Since the discovery of the DNA double helix, there has been a fascination in understanding the molecular mechanisms and cellular processes that account for: (i) the transmission of genetic information from one generation to the next and (ii) the remarkable stability of the genome. Nucleic acid biologists have endeavored to unravel the mysteries of DNA not only to understand the processes of DNA replication, repair, recombination, and transcription but to also characterize the underlying basis of genetic diseases characterized by chromosomal instability. Perhaps unexpectedly at first, DNA helicases have arisen as a key class of enzymes to study in this latter capacity. From the first discovery of ATP-dependent DNA unwinding enzymes in the mid 1970's to the burgeoning of helicase-dependent pathways found to be prevalent in all kingdoms of life, the story of scientific discovery in helicase research is rich and informative. Over four decades after their discovery, we take this opportunity to provide a history of DNA helicases. No doubt, many chapters are left to be written. Nonetheless, at this juncture we are privileged to share our perspective on the DNA helicase field - where it has been, its current state, and where it is headed.
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Affiliation(s)
- Robert M. Brosh
- Section on DNA Helicases, Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
- Correspondence: (R.M.B.J.); (S.W.M.); Tel.: +1-410-558-8578 (R.M.B.J.); +1-919-962-0005 (S.W.M.)
| | - Steven W. Matson
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Correspondence: (R.M.B.J.); (S.W.M.); Tel.: +1-410-558-8578 (R.M.B.J.); +1-919-962-0005 (S.W.M.)
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41
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Gupta SV, Schmidt KH. Maintenance of Yeast Genome Integrity by RecQ Family DNA Helicases. Genes (Basel) 2020; 11:E205. [PMID: 32085395 PMCID: PMC7074392 DOI: 10.3390/genes11020205] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/11/2020] [Accepted: 02/14/2020] [Indexed: 12/28/2022] Open
Abstract
With roles in DNA repair, recombination, replication and transcription, members of the RecQ DNA helicase family maintain genome integrity from bacteria to mammals. Mutations in human RecQ helicases BLM, WRN and RecQL4 cause incurable disorders characterized by genome instability, increased cancer predisposition and premature adult-onset aging. Yeast cells lacking the RecQ helicase Sgs1 share many of the cellular defects of human cells lacking BLM, including hypersensitivity to DNA damaging agents and replication stress, shortened lifespan, genome instability and mitotic hyper-recombination, making them invaluable model systems for elucidating eukaryotic RecQ helicase function. Yeast and human RecQ helicases have common DNA substrates and domain structures and share similar physical interaction partners. Here, we review the major cellular functions of the yeast RecQ helicases Sgs1 of Saccharomyces cerevisiae and Rqh1 of Schizosaccharomyces pombe and provide an outlook on some of the outstanding questions in the field.
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Affiliation(s)
- Sonia Vidushi Gupta
- Department of Cell Biology, Microbiology and Molecular Biology, University of South, Florida, Tampa, FL 33620, USA;
| | - Kristina Hildegard Schmidt
- Department of Cell Biology, Microbiology and Molecular Biology, University of South, Florida, Tampa, FL 33620, USA;
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research, Institute, Tampa, FL 33612, USA
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42
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Jin T, Zhang J, Zhao Y, Huang X, Tan C, Sun S, Tan Y. Magnetic bead-gold nanoparticle hybrids probe based on optically countable gold nanoparticles with dark-field microscope for T4 polynucleotide kinase activity assay. Biosens Bioelectron 2020; 150:111936. [DOI: 10.1016/j.bios.2019.111936] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 11/12/2019] [Accepted: 11/27/2019] [Indexed: 12/12/2022]
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43
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Li XY, Cui YX, Du YC, Tang AN, Kong DM. Isothermal cross-boosting extension–nicking reaction mediated exponential signal amplification for ultrasensitive detection of polynucleotide kinase. Analyst 2020; 145:3742-3748. [DOI: 10.1039/c9an02569c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A novel nucleic acid-based isothermal signal amplification strategy, named cross-boosting extension–nicking reaction (CBENR) is developed and successfully used for rapid and ultrasensitive detection of polynucleotide kinase (PNK) activity.
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Affiliation(s)
- Xiao-Yu Li
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
| | - Yun-Xi Cui
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
| | - Yi-Chen Du
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
| | - An-Na Tang
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
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44
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Du YC, Wang SY, Li XY, Wang YX, Tang AN, Kong DM. Terminal deoxynucleotidyl transferase-activated nicking enzyme amplification reaction for specific and sensitive detection of DNA methyltransferase and polynucleotide kinase. Biosens Bioelectron 2019; 145:111700. [DOI: 10.1016/j.bios.2019.111700] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/28/2019] [Accepted: 09/11/2019] [Indexed: 12/19/2022]
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45
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Wang M, Kong D, Su D, Liu Y, Su X. Ratio fluorescence analysis of T4 polynucleotide kinase activity based on the formation of a graphene quantum dot-copper nanocluster nanohybrid. NANOSCALE 2019; 11:13903-13908. [PMID: 31304938 DOI: 10.1039/c9nr02901j] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In this work, a ratio fluorescence method was developed for T4 polynucleotide kinase (PNK) activity analysis based on the formation of a dual-emitting graphene quantum dot-copper nanocluster (GQD-CuNC) nanohybrid. An amino capped single-strand DNA (ssDNA) was firstly used to modify GQDs (GQD-ssDNA) and then hybridize with its complementary DNA strand to form double-stranded DNA functionalized GQDs (GQD-dsDNA). The dsDNA of GQD-dsDNA can act as an effective template for the preparation of CuNCs with fluorescence emission at 594 nm. When the dsDNA of GQD-dsDNA was phosphorylated through T4 PNK and subsequently degraded via λ exonuclease (λ exo) to produce mononucleotides and GQD-ssDNA, the formation of fluorescence CuNCs in GQD-CuNCs was blocked due to the lack of an effective dsDNA substrate, during which the fluorescence of GQDs at 446 nm in the nanohybrid was mostly not influenced. Thus, with the CuNCs serving as the reporter and GQDs as the reference signal, T4 PNK activity can be monitored through the change in the fluorescence intensity ratio (F594/F446) in the range of 0.01-10 U mL-1 with a detection limit (LOD) of 0.0037 U mL-1. Furthermore, the practicality of this T4 PNK activity analysis strategy in a complex sample was tested in cell lysates.
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Affiliation(s)
- Mengke Wang
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, PR China.
| | - Deshuai Kong
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun 130012, PR China
| | - Dandan Su
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, PR China.
| | - Yang Liu
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, PR China.
| | - Xingguang Su
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, PR China.
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Chen Y, Zhao J, Duan Z, Gong T, Chen W, Wang S, Xu H. miR‑27b‑3p and miR‑607 cooperatively regulate BLM gene expression by directly targeting the 3'‑UTR in PC3 cells. Mol Med Rep 2019; 19:4819-4831. [PMID: 30957187 PMCID: PMC6522798 DOI: 10.3892/mmr.2019.10135] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 03/26/2019] [Indexed: 02/07/2023] Open
Abstract
BLM RecQ like helicase (BLM) has a pivotal role in genetic recombination, transcription, DNA replication and DNA repair, which presents the possibility of using BLM as an anti-cancer target for treatment. However, the post-transcriptional control regulation of BLM gene expression is not fully understood and limits the application of drugs targeting BLM for carcinoma therapy in the future. MicroRNAs (miRNAs) inhibit gene expression through interaction with the 3′ untranslated region (3′-UTR) of mRNA at the post-transcriptional stage. Therefore, the current study screened for miRNAs that regulate BLM gene expression, with software predicting that miRNA (miR)-27b-3p, miR-607, miR-361-3p, miR-628-5p and miR-338-3p. BLM gene expression levels in the PC3 prostate cancer cell line and RWPE-2 normal prostate epithelium cell line were detected by reverse transcription-quantitative PCR. Additionally, BLM mRNA levels were following miRNA overexpression for 24 and 48 h. For further miRNA filtration and validation, a dual-luciferase reporter system and western blot analysis were performed, which demonstrated that miR-27b-3p and miR-607 reduce BLM gene expression by directly targeting the BLM mRNA 3′-UTR. A Box-Behnken design experiment suggested that miR-27b-3p and miR-607 have synergetic mutual effects on BLM gene expression. Finally, the suppressive effect of miR-27b-3p and miR-607 on PC3 cell proliferation, colony formation, migration and invasion indicated the benefit of studying BLM as a drug target in cancer. In conclusion, the findings of the current provide evidence that miR-27b-3p and miR-607 have an oncosuppressive function in PC3 cells and cooperatively downregulate BLM expression at the post-transcriptional level.
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Affiliation(s)
- Yinglian Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, P.R. China
| | - Jiafu Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, P.R. China
| | - Zhiqiang Duan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, P.R. China
| | - Ting Gong
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, P.R. China
| | - Wei Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, P.R. China
| | - Sainan Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, P.R. China
| | - Houqiang Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, P.R. China
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Díaz-Gay M, Franch-Expósito S, Arnau-Collell C, Park S, Supek F, Muñoz J, Bonjoch L, Gratacós-Mulleras A, Sánchez-Rojas PA, Esteban-Jurado C, Ocaña T, Cuatrecasas M, Vila-Casadesús M, Lozano JJ, Parra G, Laurie S, Beltran S, Castells A, Bujanda L, Cubiella J, Balaguer F, Castellví-Bel S. Integrated Analysis of Germline and Tumor DNA Identifies New Candidate Genes Involved in Familial Colorectal Cancer. Cancers (Basel) 2019; 11:cancers11030362. [PMID: 30871259 PMCID: PMC6468873 DOI: 10.3390/cancers11030362] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/08/2019] [Accepted: 03/09/2019] [Indexed: 12/29/2022] Open
Abstract
Colorectal cancer (CRC) shows aggregation in some families but no alterations in the known hereditary CRC genes. We aimed to identify new candidate genes which are potentially involved in germline predisposition to familial CRC. An integrated analysis of germline and tumor whole-exome sequencing data was performed in 18 unrelated CRC families. Deleterious single nucleotide variants (SNV), short insertions and deletions (indels), copy number variants (CNVs) and loss of heterozygosity (LOH) were assessed as candidates for first germline or second somatic hits. Candidate tumor suppressor genes were selected when alterations were detected in both germline and somatic DNA, fulfilling Knudson’s two-hit hypothesis. Somatic mutational profiling and signature analysis were also performed. A series of germline-somatic variant pairs were detected. In all cases, the first hit was presented as a rare SNV/indel, whereas the second hit was either a different SNV (3 genes) or LOH affecting the same gene (141 genes). BRCA2, BLM, ERCC2, RECQL, REV3L and RIF1 were among the most promising candidate genes for germline CRC predisposition. The identification of new candidate genes involved in familial CRC could be achieved by our integrated analysis. Further functional studies and replication in additional cohorts are required to confirm the selected candidates.
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Affiliation(s)
- Marcos Díaz-Gay
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, 08036 Barcelona, Spain; (M.D.-G.); (S.F.-E.); (C.A.-C.); (J.M.); (L.B.); (A.G.-M.); (P.A.S.-R.); (C.E.-J.); (T.O.); (A.C.); (F.B.)
| | - Sebastià Franch-Expósito
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, 08036 Barcelona, Spain; (M.D.-G.); (S.F.-E.); (C.A.-C.); (J.M.); (L.B.); (A.G.-M.); (P.A.S.-R.); (C.E.-J.); (T.O.); (A.C.); (F.B.)
| | - Coral Arnau-Collell
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, 08036 Barcelona, Spain; (M.D.-G.); (S.F.-E.); (C.A.-C.); (J.M.); (L.B.); (A.G.-M.); (P.A.S.-R.); (C.E.-J.); (T.O.); (A.C.); (F.B.)
| | - Solip Park
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain;
| | - Fran Supek
- Institut de Recerca Biomedica (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain;
| | - Jenifer Muñoz
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, 08036 Barcelona, Spain; (M.D.-G.); (S.F.-E.); (C.A.-C.); (J.M.); (L.B.); (A.G.-M.); (P.A.S.-R.); (C.E.-J.); (T.O.); (A.C.); (F.B.)
| | - Laia Bonjoch
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, 08036 Barcelona, Spain; (M.D.-G.); (S.F.-E.); (C.A.-C.); (J.M.); (L.B.); (A.G.-M.); (P.A.S.-R.); (C.E.-J.); (T.O.); (A.C.); (F.B.)
| | - Anna Gratacós-Mulleras
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, 08036 Barcelona, Spain; (M.D.-G.); (S.F.-E.); (C.A.-C.); (J.M.); (L.B.); (A.G.-M.); (P.A.S.-R.); (C.E.-J.); (T.O.); (A.C.); (F.B.)
| | - Paula A. Sánchez-Rojas
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, 08036 Barcelona, Spain; (M.D.-G.); (S.F.-E.); (C.A.-C.); (J.M.); (L.B.); (A.G.-M.); (P.A.S.-R.); (C.E.-J.); (T.O.); (A.C.); (F.B.)
| | - Clara Esteban-Jurado
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, 08036 Barcelona, Spain; (M.D.-G.); (S.F.-E.); (C.A.-C.); (J.M.); (L.B.); (A.G.-M.); (P.A.S.-R.); (C.E.-J.); (T.O.); (A.C.); (F.B.)
| | - Teresa Ocaña
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, 08036 Barcelona, Spain; (M.D.-G.); (S.F.-E.); (C.A.-C.); (J.M.); (L.B.); (A.G.-M.); (P.A.S.-R.); (C.E.-J.); (T.O.); (A.C.); (F.B.)
| | | | - Maria Vila-Casadesús
- Bioinformatics Platform, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08036 Barcelona, Spain; (M.V.-C.); (J.J.L.)
| | - Juan José Lozano
- Bioinformatics Platform, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08036 Barcelona, Spain; (M.V.-C.); (J.J.L.)
| | - Genis Parra
- Centre Nacional d’Anàlisi Genòmica-Centre de Regulació Genòmica (CNAG-CRG), Parc Científic de Barcelona, 08028 Barcelona, Spain; (G.P.); (S.L.); (S.B.)
| | - Steve Laurie
- Centre Nacional d’Anàlisi Genòmica-Centre de Regulació Genòmica (CNAG-CRG), Parc Científic de Barcelona, 08028 Barcelona, Spain; (G.P.); (S.L.); (S.B.)
| | - Sergi Beltran
- Centre Nacional d’Anàlisi Genòmica-Centre de Regulació Genòmica (CNAG-CRG), Parc Científic de Barcelona, 08028 Barcelona, Spain; (G.P.); (S.L.); (S.B.)
| | - EPICOLON Consortium
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, 08036 Barcelona, Spain; (M.D.-G.); (S.F.-E.); (C.A.-C.); (J.M.); (L.B.); (A.G.-M.); (P.A.S.-R.); (C.E.-J.); (T.O.); (A.C.); (F.B.)
- Gastroenterology Department, Hospital Donostia-Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Basque Country University (UPV/EHU), 20014 San Sebastián, Spain;
- Gastroenterology Department, Complexo Hospitalario Universitario de Ourense, Instituto de Investigación Sanitaria Galicia Sur, 32005 Ourense, Spain;
| | - Antoni Castells
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, 08036 Barcelona, Spain; (M.D.-G.); (S.F.-E.); (C.A.-C.); (J.M.); (L.B.); (A.G.-M.); (P.A.S.-R.); (C.E.-J.); (T.O.); (A.C.); (F.B.)
| | - Luis Bujanda
- Gastroenterology Department, Hospital Donostia-Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Basque Country University (UPV/EHU), 20014 San Sebastián, Spain;
| | - Joaquín Cubiella
- Gastroenterology Department, Complexo Hospitalario Universitario de Ourense, Instituto de Investigación Sanitaria Galicia Sur, 32005 Ourense, Spain;
| | - Francesc Balaguer
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, 08036 Barcelona, Spain; (M.D.-G.); (S.F.-E.); (C.A.-C.); (J.M.); (L.B.); (A.G.-M.); (P.A.S.-R.); (C.E.-J.); (T.O.); (A.C.); (F.B.)
| | - Sergi Castellví-Bel
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, 08036 Barcelona, Spain; (M.D.-G.); (S.F.-E.); (C.A.-C.); (J.M.); (L.B.); (A.G.-M.); (P.A.S.-R.); (C.E.-J.); (T.O.); (A.C.); (F.B.)
- Correspondence: ; Tel.: +34-93227-5400 (ext. 4183)
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48
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Li J, Ma J, Zhang Y, Zhang Z, He G. A fluorometric method for determination of the activity of T4 polynucleotide kinase by using a DNA-templated silver nanocluster probe. Mikrochim Acta 2019; 186:48. [DOI: 10.1007/s00604-018-3157-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 12/07/2018] [Indexed: 12/31/2022]
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49
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Shen XP, Ge J, Chen J, Shen YM, Meng HM, Li ZH, Qu LB. A novel fluorescence method for the highly sensitive detection of T4 polynucleotide kinase based on polydopamine nanotubes. NEW J CHEM 2019. [DOI: 10.1039/c9nj04381k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A novel fluorescence method has been developed for the detection of T4 PNK using FRET between dye-labeled ssDNA and PDANTs.
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Affiliation(s)
- Xue-Ping Shen
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Jia Ge
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Juan Chen
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Yan-Mei Shen
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Hong-Min Meng
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Zhao-Hui Li
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Ling-Bo Qu
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
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50
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Zhou H, Tong C, Zou W, Yang Y, Liu Y, Li B, Qin Y, Dang W, Liu B, Wang W. A novel fluorescence method for activity assay and drug screening of T4 PNK by coupling rGO with ligase reaction. Analyst 2019; 144:1187-1196. [DOI: 10.1039/c8an02147c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
T4 polynucleotide kinase (PNK) is the primary member of the 5′-kinase family that can transfer the γ-phosphate residue of ATP to the 5′-hydroxyl group of oligonucleotides.
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Affiliation(s)
| | - Chunyi Tong
- College of Biology
- Hunan University
- Changsha
- China
| | - Wei Zou
- NHC key laboratory of birth defects research
- prevention and treatment
- Hunan Provincial Maternal and Child Health Care Hospital
- Changsha 410008
- PR China
| | - Yupei Yang
- TCM and Ethnomedicine Innovation & Development International Laboratory
- Innovative Material Medical Research Institute
- School of Pharmacy
- Hunan University of Chinese Medicine
- Changsha
| | - Yongbei Liu
- TCM and Ethnomedicine Innovation & Development International Laboratory
- Innovative Material Medical Research Institute
- School of Pharmacy
- Hunan University of Chinese Medicine
- Changsha
| | - Bin Li
- TCM and Ethnomedicine Innovation & Development International Laboratory
- Innovative Material Medical Research Institute
- School of Pharmacy
- Hunan University of Chinese Medicine
- Changsha
| | - Yan Qin
- TCM and Ethnomedicine Innovation & Development International Laboratory
- Innovative Material Medical Research Institute
- School of Pharmacy
- Hunan University of Chinese Medicine
- Changsha
| | - Wenya Dang
- College of Biology
- Hunan University
- Changsha
- China
| | - Bin Liu
- College of Biology
- Hunan University
- Changsha
- China
- TCM and Ethnomedicine Innovation & Development International Laboratory
| | - Wei Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory
- Innovative Material Medical Research Institute
- School of Pharmacy
- Hunan University of Chinese Medicine
- Changsha
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