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Kar A, Degtyareva NP, Doetsch PW. Human NTHL1 expression and subcellular distribution determines cisplatin sensitivity in human lung epithelial and non-small cell lung cancer cells. NAR Cancer 2024; 6:zcae006. [PMID: 38384388 PMCID: PMC10880605 DOI: 10.1093/narcan/zcae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/11/2024] [Accepted: 02/09/2024] [Indexed: 02/23/2024] Open
Abstract
Base excision repair is critical for maintaining genomic stability and for preventing malignant transformation. NTHL1 is a bifunctional DNA glycosylase/AP lyase that initiates repair of oxidatively damaged pyrimidines. Our recent work established that transient over-expression of NTHL1 leads to acquisition of several hallmarks of cancer in non-tumorigenic immortalized cells likely through interaction with nucleotide excision repair protein XPG. Here, we investigate how NTHL1 expression levels impact cellular sensitivity to cisplatin in non-tumorigenic immortalized cells and five non-small cell lung carcinomas cell lines. The cell line with lowest expression of NTHL1 (H522) shows the highest resistance to cisplatin indicating that decrease in NTHL1 levels may modulate resistance to crosslinking agents in NSCLC tumors. In a complementation study, overexpression of NTHL1 in H522 cell line sensitized it to cisplatin. Using NTHL1 N-terminal deletion mutants defective in nuclear localization we show that cisplatin treatment can alter NTHL1 subcellular localization possibly leading to altered protein-protein interactions and affecting cisplatin sensitivity. Experiments presented in this study reveal a previously unknown link between NTHL1 expression levels and cisplatin sensitivity of NSCLC tumor cells. These findings provide an opportunity to understand how altered NTHL1 expression levels and subcellular distribution can impact cisplatin sensitivity in NSCLC tumor cells.
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Affiliation(s)
- Anirban Kar
- Mutagenesis & DNA Repair Regulation Group, National Institute of Environmental Health Sciences, 111 TW Alexander Dr, Durham, NC 27709, USA
| | - Natalya P Degtyareva
- Mutagenesis & DNA Repair Regulation Group, National Institute of Environmental Health Sciences, 111 TW Alexander Dr, Durham, NC 27709, USA
| | - Paul W Doetsch
- Mutagenesis & DNA Repair Regulation Group, National Institute of Environmental Health Sciences, 111 TW Alexander Dr, Durham, NC 27709, USA
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Al-Sadek T, Yusuf N. Ultraviolet Radiation Biological and Medical Implications. Curr Issues Mol Biol 2024; 46:1924-1942. [PMID: 38534742 DOI: 10.3390/cimb46030126] [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: 02/05/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/28/2024] Open
Abstract
Ultraviolet (UV) radiation plays a crucial role in the development of melanoma and non-melanoma skin cancers. The types of UV radiation are differentiated by wavelength: UVA (315 to 400 nm), UVB (280 to 320 nm), and UVC (100 to 280 nm). UV radiation can cause direct DNA damage in the forms of cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4PPs). In addition, UV radiation can also cause DNA damage indirectly through photosensitization reactions caused by reactive oxygen species (ROS), which manifest as 8-hydroxy-2'-deoxyguanine (8-OHdG). Both direct and indirect DNA damage can lead to mutations in genes that promote the development of skin cancers. The development of melanoma is largely influenced by the signaling of the melanocortin one receptor (MC1R), which plays an essential role in the synthesis of melanin in the skin. UV-induced mutations in the BRAF and NRAS genes are also significant risk factors in melanoma development. UV radiation plays a significant role in basal cell carcinoma (BCC) development by causing mutations in the Hedgehog (Hh) pathway, which dysregulates cell proliferation and survival. UV radiation can also induce the development of squamous cell carcinoma via mutations in the TP53 gene and upregulation of MMPs in the stroma layer of the skin.
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Affiliation(s)
- Tarek Al-Sadek
- Department of Dermatology, UAB Heersink School of Medicine, Birmingham, AL 35294, USA
| | - Nabiha Yusuf
- Department of Dermatology, UAB Heersink School of Medicine, Birmingham, AL 35294, USA
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3
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de Andrade FAG, Cavalcanti CEDO, Isoldi FC, Ferreira LM. Therapeutics of xeroderma pigmentosum: A PRISMA-compliant systematic review. Indian J Dermatol Venereol Leprol 2021; 87:176-189. [PMID: 33769755 DOI: 10.25259/ijdvl_431_19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 02/01/2020] [Indexed: 01/13/2023]
Abstract
Xeroderma pigmentosum is a rare hereditary autosomal recessive genodermatosis. At present, there are many treatment options for xeroderma pigmentosum, covering medical/procedural, surgical and combined modalities. However, the quality of these interventions has not been assessed. Our study aimed to perform a systematic review of the literature regarding the treatment of xeroderma pigmentosum. Multiple medical databases were accessed with the Medical Subject Headings terms; "xeroderma pigmentosum," "therapeutics" and "surgical procedures, operative" from January 2000 to April 2019, including articles published in Portuguese, Spanish and English (PROSPERO-CRD42018114858). Two hundred and ninety-eight studies were found in the databases researched, of which, after applying the inclusion criteria, only 33 studies remained. The 33 complete articles were read by three of the authors, having been found: 16 reported medical/procedural and 17 reported surgical treatments. Only one clinical study presented a good level of evidence (EL: 2): a randomized clinical trial using a T4 endonuclease V (T4N5) liposome lotion which reduced the development of skin lesions in patients with xeroderma pigmentosum. Amongst surgical modalities, all studies presented low evidence level (EL: 4). Three illustrative cases are also presented, to emphasize the multiple number of times that surgical modalities may be required in these patients. The therapeutic modalities, both clinical and surgical, for xeroderma pigmentosum presented a low level of scientific evidence which did not allow meta-analysis. More therapeutic studies, both clinical and surgical, with better scientific evidence are needed.
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Oliveira RKDM, Hurtado FA, Gomes PH, Puglia LL, Ferreira FF, Ranjan K, Albuquerque P, Poças-Fonseca MJ, Silva-Pereira I, Fernandes L. Base Excision Repair AP-Endonucleases-Like Genes Modulate DNA Damage Response and Virulence of the Human Pathogen Cryptococcus neoformans. J Fungi (Basel) 2021; 7:jof7020133. [PMID: 33673204 PMCID: PMC7917787 DOI: 10.3390/jof7020133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/29/2021] [Accepted: 02/05/2021] [Indexed: 11/16/2022] Open
Abstract
Pathogenic microbes are exposed to a number of potential DNA-damaging stimuli during interaction with the host immune system. Microbial survival in this situation depends on a fine balance between the maintenance of DNA integrity and the adaptability provided by mutations. In this study, we investigated the association of the DNA repair response with the virulence of Cryptococcus neoformans, a basidiomycete that causes life-threatening meningoencephalitis in immunocompromised individuals. We focused on the characterization of C. neoformansAPN1 and APN2 putative genes, aiming to evaluate a possible role of the predicted Apurinic/apyrimidinic (AP) endonucleases 1 and 2 of the base excision repair (BER) pathway on C. neoformans response to stress conditions and virulence. Our results demonstrated the involvement of the putative AP-endonucleases Apn1 and Apn2 in the cellular response to DNA damage induced by alkylation and by UV radiation, in melanin production, in tolerance to drugs and in virulence of C. neoformans in vivo. We also pointed out the potential use of DNA repair inhibitor methoxy-amine in combination with conventional antifungal drugs, for the development of new therapeutic approaches against this human fungal pathogen. This work provides new information about the DNA damage response of the highly important pathogenic fungus C. neoformans.
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Affiliation(s)
- Rayssa Karla de Medeiros Oliveira
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília 70.910-900, Brazil; (R.K.d.M.O.); (F.A.H.); (P.H.G.); (L.L.P.)
| | - Fabián Andrés Hurtado
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília 70.910-900, Brazil; (R.K.d.M.O.); (F.A.H.); (P.H.G.); (L.L.P.)
| | - Pedro Henrique Gomes
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília 70.910-900, Brazil; (R.K.d.M.O.); (F.A.H.); (P.H.G.); (L.L.P.)
| | - Luiza Lassi Puglia
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília 70.910-900, Brazil; (R.K.d.M.O.); (F.A.H.); (P.H.G.); (L.L.P.)
| | - Fernanda Fonsêca Ferreira
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília, Brasília 70.910-900, Brazil; (F.F.F.); (K.R.)
| | - Kunal Ranjan
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília, Brasília 70.910-900, Brazil; (F.F.F.); (K.R.)
| | | | - Márcio José Poças-Fonseca
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília, Brasília 70.910-900, Brazil; (F.F.F.); (K.R.)
- Correspondence: (M.J.P.-F.); (I.S.-P.); (L.F.)
| | - Ildinete Silva-Pereira
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília 70.910-900, Brazil; (R.K.d.M.O.); (F.A.H.); (P.H.G.); (L.L.P.)
- Correspondence: (M.J.P.-F.); (I.S.-P.); (L.F.)
| | - Larissa Fernandes
- Faculty of Ceilândia, University of Brasília, Brasília 72.220-275, Brazil;
- Correspondence: (M.J.P.-F.); (I.S.-P.); (L.F.)
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Panchal NK, Bhale A, Verma VK, Beevi SS. Computational and molecular dynamics simulation approach to analyze the impactof XPD gene mutation on protein stability and function. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1810852] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Nagesh Kishan Panchal
- Cancer Biology Division, KIMS Foundation and Research Centre, KIMS Hospitals, Secunderabad, India
| | - Aishwarya Bhale
- Cancer Biology Division, KIMS Foundation and Research Centre, KIMS Hospitals, Secunderabad, India
| | - Vinod Kumar Verma
- Cancer Biology Division, KIMS Foundation and Research Centre, KIMS Hospitals, Secunderabad, India
| | - Syed Sultan Beevi
- Cancer Biology Division, KIMS Foundation and Research Centre, KIMS Hospitals, Secunderabad, India
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DNA repair and cell synthesis proteins: immunohistochemical expression and correlation with recurrence-regrowth in meningiomas. J Mol Histol 2020; 51:411-420. [PMID: 32617895 DOI: 10.1007/s10735-020-09892-7] [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: 01/20/2020] [Accepted: 06/25/2020] [Indexed: 10/23/2022]
Abstract
Meningiomas are considered the second most common neoplasm of the central nervous system in adults. Most of them are benign with slow growth, frequent in women and with a high recurrence rate. In tumors, DNA error repair processes lose efficacy, providing mutagenesis and genomic instability. This work evaluated the expression of proteins involved in cell synthesis (cyclin D1) and DNA errors repair (MUTYH, XPF, XPG) in meningiomas, relating them to clinical, tumor and survival variables. The study included 85 patients, with a mean age of 52 ± 13.3 years and most of them women (2:1 ratio). Sixty-seven cases were grade I (79%). Grade II tumors were independent predictors of recurrence-regrowth (HR: 2.8; p = 0.038). The high expression of cyclin D1 was associated with grade II (p = 0.001) and low MUTYH expression with grade I (p = 0.04). Strong expression of XPF and XPG was associated with grade II (p = 0.002; p < 0.001) and with recurrence-regrowth (p = 0.04; p = 0.003). Strong XPF expression was significantly related to large tumors (p = 0.03). An association of cyclin D1, MUTYH and XPF were found. Survival was not associated with the expression of any of the proteins studied. To know the role of DNA repair proteins and cell synthesis is important for understanding the processes of origin and tumor development. Grade II meningiomas and strong expression of XPF and XPG were predictors of recurrence or regrowth and may assist in clinical management, considering the high recurrence of meningiomas and the absence of consensus regarding treatment.
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Russo LC, Farias JO, Forti FL. DUSP3 maintains genomic stability and cell proliferation by modulating NER pathway and cell cycle regulatory proteins. Cell Cycle 2020; 19:1545-1561. [PMID: 32380926 DOI: 10.1080/15384101.2020.1762043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The DUSP3 phosphatase regulates cell cycle, proliferation, apoptosis and senescence of different cell types, lately shown as a mediator of DNA repair processes. This work evaluated the impact of DUSP3 loss of function (lof) on DNA repair-proficient fibroblasts (MRC-5), NER-deficient cell lines (XPA and XPC) and translesion DNA synthesis (TLS)-deficient cells (XPV), after UV-radiation stress. The levels of DNA strand breaks, CPDs and 6-4-PPs have accumulated over time in all cells under DUSP3 lof, with a significant increase in NER-deficient lines. The inefficient repair of these lesions increased sub-G1 population of XPA and XPC cells 24 hours after UV treatment, notably marked by DUSP3 lof, which is associated with a reduced cell population in G1, S and G2/M phases. It was also detected an increase in S and G2/M populations of XPV and MRC-5 cells after UV-radiation exposure, which was slightly attenuated by DUSP3 lof due to a discrete increase in sub-G1 cells. The cell cycle progression was accompanied by changes in the levels of the main Cyclins (A1, B1, D1 or E1), CDKs (1, 2, 4 or 6), and the p21 Cip1 inhibitor, in a DUSP3-dependent manner. DUSP3 lof affected the proliferation of MRC-5 and XPA cells, with marked worsening of the XP phenotype after UV radiation. This work highlights the roles of DUSP3 in DNA repair fitness and in the fine control of regulatory proteins of cell cycle, essential mechanisms to maintenance of genomic stability.
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Affiliation(s)
- Lilian Cristina Russo
- Laboratory of Signaling in Biomolecular Systems, Department of Biochemistry, Institute of Chemistry, University of Sao Paulo , São Paulo-SP, Brazil
| | - Jessica Oliveira Farias
- Laboratory of Signaling in Biomolecular Systems, Department of Biochemistry, Institute of Chemistry, University of Sao Paulo , São Paulo-SP, Brazil
| | - Fabio Luis Forti
- Laboratory of Signaling in Biomolecular Systems, Department of Biochemistry, Institute of Chemistry, University of Sao Paulo , São Paulo-SP, Brazil
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8
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XPA: DNA Repair Protein of Significant Clinical Importance. Int J Mol Sci 2020; 21:ijms21062182. [PMID: 32235701 PMCID: PMC7139726 DOI: 10.3390/ijms21062182] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/18/2020] [Accepted: 03/18/2020] [Indexed: 02/08/2023] Open
Abstract
The nucleotide excision repair (NER) pathway is activated in response to a broad spectrum of DNA lesions, including bulky lesions induced by platinum-based chemotherapeutic agents. Expression levels of NER factors and resistance to chemotherapy has been examined with some suggestion that NER plays a role in tumour resistance; however, there is a great degree of variability in these studies. Nevertheless, recent clinical studies have suggested Xeroderma Pigmentosum group A (XPA) protein, a key regulator of the NER pathway that is essential for the repair of DNA damage induced by platinum-based chemotherapeutics, as a potential prognostic and predictive biomarker for response to treatment. XPA functions in damage verification step in NER, as well as a molecular scaffold to assemble other NER core factors around the DNA damage site, mediated by protein–protein interactions. In this review, we focus on the interacting partners and mechanisms of regulation of the XPA protein. We summarize clinical oncology data related to this DNA repair factor, particularly its relationship with treatment outcome, and examine the potential of XPA as a target for small molecule inhibitors.
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Zheng H, Jarvis IWH, Bottai M, Dreij K, Stenius U. TGF beta promotes repair of bulky DNA damage through increased ERCC1/XPF and ERCC1/XPA interaction. Carcinogenesis 2020; 40:580-591. [PMID: 30418489 DOI: 10.1093/carcin/bgy156] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 10/30/2018] [Accepted: 11/07/2018] [Indexed: 12/15/2022] Open
Abstract
Transforming growth factor beta (TGFβ) is multifunctional cytokine that is involved in the coordination and regulation of many cellular homeostatic processes. Compromised TGFβ activity has been attributed to promotion of human cancers. Recent studies have identified a role for TGFβ in response to radiation-induced DNA damage, suggesting a link between TGFβ and the DNA damage response with implications for cancer development. In this study, the effects of TGFβ on promoting the repair of bulky DNA damage, through modulation of nucleotide excision repair (NER), were investigated. We show that treatment of cells with exogenous TGFβ leads to enhanced repair of DNA damage formed by polycyclic aromatic hydrocarbons and ultraviolet-C radiation; similarly, cells with constitutively activated endogenous TGFβ signaling show comparable responses. This effect of TGFβ is independent of the cell cycle. The response to TGFβ is decreased in cells that have compromised TGFβ signaling through RNA interference of Smad4 and is decreased in NER-deficient cells and cells with compromised NER through RNA interference of excision repair cross-complementing group 1 (ERCC1). Increased interaction and nuclear localization of ERCC1/xeroderma pigmentosum (XP) F and ERCC1/XPA proteins is observed after TGFβ treatment. Our study represents the first experimental evidence of a role for TGFβ in the repair of bulky DNA damage resulting from promotion of the interaction and localization of repair protein complexes involved in the incision step of NER.
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Affiliation(s)
- Huiyuan Zheng
- Unit of Biochemical Toxicology, Karolinska Institutet, Stockholm, Sweden
| | - Ian W H Jarvis
- Unit of Biochemical Toxicology, Karolinska Institutet, Stockholm, Sweden
| | - Matteo Bottai
- Unit of Biostatistics, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kristian Dreij
- Unit of Biochemical Toxicology, Karolinska Institutet, Stockholm, Sweden
| | - Ulla Stenius
- Unit of Biochemical Toxicology, Karolinska Institutet, Stockholm, Sweden
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10
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Synofzik M, Puccio H, Mochel F, Schöls L. Autosomal Recessive Cerebellar Ataxias: Paving the Way toward Targeted Molecular Therapies. Neuron 2019; 101:560-583. [PMID: 30790538 DOI: 10.1016/j.neuron.2019.01.049] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/20/2018] [Accepted: 01/23/2019] [Indexed: 12/22/2022]
Abstract
Autosomal-recessive cerebellar ataxias (ARCAs) comprise a heterogeneous group of rare degenerative and metabolic genetic diseases that share the hallmark of progressive damage of the cerebellum and its associated tracts. This Review focuses on recent translational research in ARCAs and illustrates the steps from genetic characterization to preclinical and clinical trials. The emerging common pathways underlying ARCAs include three main clusters: mitochondrial dysfunction, impaired DNA repair, and complex lipid homeostasis. Novel ARCA treatments might target common hubs in pathogenesis by modulation of gene expression, stem cell transplantation, viral gene transfer, or interventions in faulty pathways. All these translational steps are addressed in current ARCA research, leading to the expectation that novel treatments for ARCAs will be reached in the next decade.
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Affiliation(s)
- Matthis Synofzik
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Hoppe-Seyler-Str. 3, 72076 Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Hélène Puccio
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France; INSERM, U1258, 67404 Illkirch, France; CNRS, UMR7104, 67404 Illkirch, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Fanny Mochel
- Sorbonne Université, UPMC-Paris 6, UMR S 1127 and Inserm U 1127, and CNRS UMR 7225, and Institut du Cerveau et de la Moelle épinière, 75013 Paris, France; Department of Genetics and Reference Centre for Adult Neurometabolic Diseases, AP-HP, La Pitié-Salpêtriere University Hospital, Paris, France
| | - Ludger Schöls
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Hoppe-Seyler-Str. 3, 72076 Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany.
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11
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Structural characterization of the redefined DNA-binding domain of human XPA. Biochem Biophys Res Commun 2019; 514:985-990. [DOI: 10.1016/j.bbrc.2019.05.050] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 05/06/2019] [Indexed: 12/11/2022]
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12
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Baxter LL, Watkins-Chow DE, Pavan WJ, Loftus SK. A curated gene list for expanding the horizons of pigmentation biology. Pigment Cell Melanoma Res 2019; 32:348-358. [PMID: 30339321 PMCID: PMC10413850 DOI: 10.1111/pcmr.12743] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 09/01/2018] [Accepted: 09/29/2018] [Indexed: 12/27/2022]
Abstract
Over the past century, studies of human pigmentary disorders along with mouse and zebrafish models have shed light on the many cellular functions associated with visible pigment phenotypes. This has led to numerous genes annotated with the ontology term "pigmentation" in independent human, mouse, and zebrafish databases. Comparisons among these datasets revealed that each is individually incomplete in documenting all genes involved in integument-based pigmentation phenotypes. Additionally, each database contained inherent species-specific biases in data annotation, and the term "pigmentation" did not solely reflect integument pigmentation phenotypes. This review presents a comprehensive, cross-species list of 650 genes involved in pigmentation phenotypes that was compiled with extensive manual curation of genes annotated in OMIM, MGI, ZFIN, and GO. The resulting cross-species list of genes both intrinsic and extrinsic to integument pigment cells provides a valuable tool that can be used to expand our knowledge of complex, pigmentation-associated pathways.
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Affiliation(s)
- Laura L Baxter
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Dawn E Watkins-Chow
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Stacie K Loftus
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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Greber BJ, Nogales E. The Structures of Eukaryotic Transcription Pre-initiation Complexes and Their Functional Implications. Subcell Biochem 2019; 93:143-192. [PMID: 31939151 DOI: 10.1007/978-3-030-28151-9_5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transcription is a highly regulated process that supplies living cells with coding and non-coding RNA molecules. Failure to properly regulate transcription is associated with human pathologies, including cancers. RNA polymerase II is the enzyme complex that synthesizes messenger RNAs that are then translated into proteins. In spite of its complexity, RNA polymerase requires a plethora of general transcription factors to be recruited to the transcription start site as part of a large transcription pre-initiation complex, and to help it gain access to the transcribed strand of the DNA. This chapter reviews the structure and function of these eukaryotic transcription pre-initiation complexes, with a particular emphasis on two of its constituents, the multisubunit complexes TFIID and TFIIH. We also compare the overall architecture of the RNA polymerase II pre-initiation complex with those of RNA polymerases I and III, involved in transcription of ribosomal RNA and non-coding RNAs such as tRNAs and snRNAs, and discuss the general, conserved features that are applicable to all eukaryotic RNA polymerase systems.
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Affiliation(s)
- Basil J Greber
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA.
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Eva Nogales
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
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14
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Analysis of the conserved NER helicases (XPB and XPD) and UV-induced DNA damage in Hydra. Biochim Biophys Acta Gen Subj 2018; 1862:2031-2042. [PMID: 29959982 DOI: 10.1016/j.bbagen.2018.06.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/04/2018] [Accepted: 06/26/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Nucleotide excision repair (NER) pathway is an evolutionarily conserved mechanism of genome maintenance. It detects and repairs distortions in DNA double helix. Xeroderma Pigmentosum group B (XPB) and group D (XPD) are important helicases in NER and are also critical subunits of TFIIH complex. We have studied XPB and XPD for the first time from the basal metazoan Hydra which exhibits lack of organismal senescence. METHODS In silico analysis of proteins was performed using MEGA 6.0, Clustal Omega, Swiss Model, etc. Gene expression was studied by in situ hybridization and qRT-PCR. Repair of CPDs was studied by DNA blot assay. Interactions between proteins were determined by co- immunoprecipitation. HyXPB and HyXPD were cloned in pET28b, overexpressed and helicase activity of purified proteins was checked. RESULTS In silico analysis revealed presence of seven classical helicase motifs in HyXPB and HyXPD. Both proteins revealed polarity-dependent helicase activity. Hydra repairs most of the thymine dimers induced by UVC (500 J/m2) by 72 h post-UV exposure. HyXPB and HyXPD transcripts, localized all over the body column, remained unaltered post-UV exposure indicating their constitutive expression. In spite of high levels of sequence conservation, XPB and XPD failed to rescue defects in human XPB- and XPD-deficient cell lines. This was due to their inability to get incorporated into the TFIIH multiprotein complex. CONCLUSIONS Present results along with our earlier work on DNA repair proteins in Hydra bring out the utility of Hydra as model system to study evolution of DNA repair mechanisms in metazoans.
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Bukowska B, Karwowski BT. Actual state of knowledge in the field of diseases related with defective nucleotide excision repair. Life Sci 2018; 195:6-18. [DOI: 10.1016/j.lfs.2017.12.035] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 12/19/2017] [Accepted: 12/24/2017] [Indexed: 12/11/2022]
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Hu J, Selby CP, Adar S, Adebali O, Sancar A. Molecular mechanisms and genomic maps of DNA excision repair in Escherichia coli and humans. J Biol Chem 2017; 292:15588-15597. [PMID: 28798238 DOI: 10.1074/jbc.r117.807453] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Nucleotide excision repair is a major DNA repair mechanism in all cellular organisms. In this repair system, the DNA damage is removed by concerted dual incisions bracketing the damage and at a precise distance from the damage. Here, we review the basic mechanisms of excision repair in Escherichia coli and humans and the recent genome-wide mapping of DNA damage and repair in these organisms at single-nucleotide resolution.
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Affiliation(s)
- Jinchuan Hu
- From the Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7260 and
| | - Christopher P Selby
- From the Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7260 and
| | - Sheera Adar
- From the Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7260 and.,the Department of Microbiology and Molecular Genetics, Hebrew University-Hadassah Medical School, Ein Kerem 71120, Jerusalem, Israel
| | - Ogun Adebali
- From the Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7260 and
| | - Aziz Sancar
- From the Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7260 and
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17
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Ebert C, Simon N, Schneider S, Carell T. Structural Insights into the Recognition of N
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-Aryl- and C8-Aryl DNA Lesions by the Repair Protein XPA/Rad14. Chembiochem 2017; 18:1379-1382. [DOI: 10.1002/cbic.201700169] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Charlotte Ebert
- Center for Integrated Protein Science at the Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 München Germany
| | - Nina Simon
- Center for Integrated Protein Science at the Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 München Germany
| | - Sabine Schneider
- Center for Integrated Protein Science at the Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85748 Garching Germany
| | - Thomas Carell
- Center for Integrated Protein Science at the Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 München Germany
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Modulation of Colorectal Cancer Risk by Polymorphisms in 51Gln/His, 64Ile/Val, and 148Asp/Glu of APEX Gene; 23Gly/Ala of XPA Gene; and 689Ser/Arg of ERCC4 Gene. Gastroenterol Res Pract 2017; 2017:3840243. [PMID: 28386271 PMCID: PMC5366231 DOI: 10.1155/2017/3840243] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 12/01/2016] [Accepted: 12/07/2016] [Indexed: 12/14/2022] Open
Abstract
Polymorphisms in DNA repair genes may affect the activity of the BER (base excision repair) and NER (nucleotide excision repair) systems. Using DNA isolated from blood taken from patients (n = 312) and a control group (n = 320) with CRC, we have analyzed the polymorphisms of selected DNA repair genes and we have demonstrated that genotypes 51Gln/His and 148Asp/Glu of APEX gene and 23Gly/Ala of XPA gene may increase the risk of colorectal cancer. At the same time analyzing the gene-gene interactions, we suggest the thesis that the main factor to be considered when analyzing the impact of polymorphisms on the risk of malignant transformation should be intergenic interactions. Moreover, we are suggesting that some polymorphisms may have impact not only on the malignant transformation but also on the stage of the tumor.
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