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Guerra G, Wendt G, McCoy L, Hansen HM, Kachuri L, Molinaro AM, Rice T, Guan V, Capistrano L, Hsieh A, Kalsi V, Sallee J, Taylor JW, Clarke JL, Rodriguez Almaraz E, Wiencke JK, Eckel-Passow JE, Jenkins RB, Wrensch M, Francis SS. Functional germline variants in DNA damage repair pathways are associated with altered survival in adults with glioma treated with temozolomide. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.10.13.23296963. [PMID: 39417102 PMCID: PMC11482862 DOI: 10.1101/2023.10.13.23296963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
Background Temozolomide (TMZ) treatment has demonstrated, but variable, impact on glioma prognosis. This study examines associations of survival with DNA repair gene germline polymorphisms among glioma patients who did and did not have TMZ treatment. Identifying genetic markers which sensitize tumor cells to TMZ could personalize therapy and improve outcomes. Methods We evaluated TMZ-related survival associations of pathogenic germline SNPs and genetically predicted transcript levels within 34 DNA repair genes among 1504 glioma patients from the UCSF Adult Glioma Study and Mayo Clinic whose diagnoses spanned pre- and post-TMZ eras within the major known glioma prognostic molecular subtypes. Results Among those who received TMZ, 5 SNPs were associated with overall survival, but not in those who did not receive TMZ. Only rs2308321-G, in MGMT, was associated with decreased survival (HR=1.21, p=0.019) for all glioma subtypes. Rs73191162-T (near UNG), rs13076508-C (near PARP3), rs7840433-A (near NEIL2), and rs3130618-A (near MSH5) were only associated with survival and TMZ treatment for certain subtypes, suggesting subtype-specific germline chemo-sensitization.Genetically predicted elevated compared to normal brain expression of PNKP was associated with dramatically worse survival for TMZ-treated patients with IDH-mutant and 1p/19q non-codeleted gliomas (p=0.015). Similarly, NEIL2 and TDG expressions were associated with altered TMZ-related survival only among certain subtypes. Conclusions Functional germline alterations within DNA repair genes were associated with TMZ sensitivity, measured by overall survival, among adults with glioma, these variants should be evaluated in prospective analyses and functional studies.
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Affiliation(s)
- Geno Guerra
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - George Wendt
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Lucie McCoy
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Helen M. Hansen
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Linda Kachuri
- Department of Epidemiology & Population Health, Stanford University School of Medicine, Stanford, CA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Annette M. Molinaro
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Terri Rice
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Victoria Guan
- School of Pharmacy, University of California San Francisco, San Francisco, CA, USA
| | - Lianne Capistrano
- School of Pharmacy, University of California San Francisco, San Francisco, CA, USA
| | - Allison Hsieh
- School of Pharmacy, University of California San Francisco, San Francisco, CA, USA
| | - Veruna Kalsi
- School of Pharmacy, University of California San Francisco, San Francisco, CA, USA
| | - Jaimie Sallee
- School of Pharmacy, University of California San Francisco, San Francisco, CA, USA
| | - Jennie W. Taylor
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Jennifer L. Clarke
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Eduardo Rodriguez Almaraz
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - John K. Wiencke
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | | | - Robert B. Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Margaret Wrensch
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Stephen S. Francis
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
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Hua AB, Sweasy JB. Functional roles and cancer variants of the bifunctional glycosylase NEIL2. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024; 65 Suppl 1:40-56. [PMID: 37310399 DOI: 10.1002/em.22555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/23/2023] [Accepted: 06/08/2023] [Indexed: 06/14/2023]
Abstract
Over 70,000 DNA lesions occur in the cell every day, and the inability to properly repair them can lead to mutations and destabilize the genome, resulting in carcinogenesis. The base excision repair (BER) pathway is critical for maintaining genomic integrity by repairing small base lesions, abasic sites and single-stranded breaks. Monofunctional and bifunctional glycosylases initiate the first step of BER by recognizing and excising specific base lesions, followed by DNA end processing, gap filling, and finally nick sealing. The Nei-like 2 (NEIL2) enzyme is a critical bifunctional DNA glycosylase in BER that preferentially excises cytosine oxidation products and abasic sites from single-stranded, double-stranded, and bubble-structured DNA. NEIL2 has been implicated to have important roles in several cellular functions, including genome maintenance, participation in active demethylation, and modulation of the immune response. Several germline and somatic variants of NEIL2 with altered expression and enzymatic activity have been reported in the literature linking them to cancers. In this review, we provide an overview of NEIL2 cellular functions and summarize current findings on NEIL2 variants and their relationship to cancer.
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Affiliation(s)
- Anh B Hua
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, Tucson, Arizona, USA
| | - Joann B Sweasy
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, Tucson, Arizona, USA
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Siddaiah R, Emery L, Stephens H, Donnelly A, Erkinger J, Wisecup K, Hicks SD, Kawasawa YI, Oji-Mmuo C, Amatya S, Silveyra P. Early Salivary miRNA Expression in Extreme Low Gestational Age Newborns. Life (Basel) 2022; 12:506. [PMID: 35454997 PMCID: PMC9029747 DOI: 10.3390/life12040506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/07/2022] [Accepted: 03/23/2022] [Indexed: 11/17/2022] Open
Abstract
Background: MicroRNAs (miRNA) are small non-coding RNAs that regulate gene expression playing a key role in organogenesis. MiRNAs are studied in tracheal aspirates (TA) of preterm infants. However; this is difficult to obtain in infants who are not intubated. This study examines early salivary miRNA expression as non-invasive early biomarkers in extremely low gestational age newborns (ELGANs). Methods: Saliva was collected using DNA-genotek swabs, miRNAs were analyzed using RNA seq and RT PCR arrays. Salivary miRNA expression was compared to TA using RNA seq at 3 days of age, and longitudinal changes at 28 days of age were analyzed using RT PCR arrays in ELGANs. Results: Approximately 822 ng of RNA was extracted from saliva of 7 ELGANs; Of the 757 miRNAs isolated, 161 miRNAs had significant correlation in saliva and TA at 3 days of age (r = 0.97). Longitudinal miRNA analysis showed 29 miRNAs downregulated and 394 miRNAs upregulated at 28 days compared to 3 days of age (adjusted p < 0.1). Bioinformatic analysis (Ingenuity Pathway Analysis) of differentially expressed miRNAs identified organismal injury and abnormalities and cellular development as the top physiological system development and cellular function. Conclusion: Salivary miRNA expression are source for early biomarkers of underlying pathophysiology in ELGANs.
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Affiliation(s)
- Roopa Siddaiah
- Department of Pediatrics, Penn State Health Children’s Hospital, Hershey, PA 17036, USA; (H.S.); (K.W.); (S.D.H.); (C.O.-M.); (S.A.)
| | - Lucy Emery
- Penn State Health College of Medicine, Hershey, PA 17036, USA;
| | - Heather Stephens
- Department of Pediatrics, Penn State Health Children’s Hospital, Hershey, PA 17036, USA; (H.S.); (K.W.); (S.D.H.); (C.O.-M.); (S.A.)
| | - Ann Donnelly
- Department of Respiratory Therapy Penn State Health Children’s Hospital, Hershey, PA 17036, USA; (A.D.); (J.E.)
| | - Jennifer Erkinger
- Department of Respiratory Therapy Penn State Health Children’s Hospital, Hershey, PA 17036, USA; (A.D.); (J.E.)
| | - Kimberly Wisecup
- Department of Pediatrics, Penn State Health Children’s Hospital, Hershey, PA 17036, USA; (H.S.); (K.W.); (S.D.H.); (C.O.-M.); (S.A.)
| | - Steven D. Hicks
- Department of Pediatrics, Penn State Health Children’s Hospital, Hershey, PA 17036, USA; (H.S.); (K.W.); (S.D.H.); (C.O.-M.); (S.A.)
| | - Yuka Imamura Kawasawa
- Departments of Pharmacology, Biochemistry and Molecular Biology, Penn State Health College of Medicine, Hershey, PA 17036, USA;
| | - Christiana Oji-Mmuo
- Department of Pediatrics, Penn State Health Children’s Hospital, Hershey, PA 17036, USA; (H.S.); (K.W.); (S.D.H.); (C.O.-M.); (S.A.)
| | - Shaili Amatya
- Department of Pediatrics, Penn State Health Children’s Hospital, Hershey, PA 17036, USA; (H.S.); (K.W.); (S.D.H.); (C.O.-M.); (S.A.)
| | - Patricia Silveyra
- Department of Environmental and Occupational Health, School of Public Health, Indiana University, Bloomington, IN 47405, USA;
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Kakhkharova ZI, Zharkov DO, Grin IR. A Low-Activity Polymorphic Variant of Human NEIL2 DNA Glycosylase. Int J Mol Sci 2022; 23:ijms23042212. [PMID: 35216329 PMCID: PMC8879280 DOI: 10.3390/ijms23042212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/14/2022] [Accepted: 02/14/2022] [Indexed: 01/05/2023] Open
Abstract
Human NEIL2 DNA glycosylase (hNEIL2) is a base excision repair protein that removes oxidative lesions from DNA. A distinctive feature of hNEIL2 is its preference for the lesions in bubbles and other non-canonical DNA structures. Although a number of associations of polymorphisms in the hNEIL2 gene were reported, there is little data on the functionality of the encoded protein variants, as follows: only hNEIL2 R103Q was described as unaffected, and R257L, as less proficient in supporting the repair in a reconstituted system. Here, we report the biochemical characterization of two hNEIL2 variants found as polymorphisms in the general population, R103W and P304T. Arg103 is located in a long disordered segment within the N-terminal domain of hNEIL2, while Pro304 occupies a position in the β-turn of the DNA-binding zinc finger motif. Similar to the wild-type protein, both of the variants could catalyze base excision and nick DNA by β-elimination but demonstrated a lower affinity for DNA. Steady-state kinetics indicates that the P304T variant has its catalytic efficiency (in terms of kcat/KM) reduced ~5-fold compared with the wild-type hNEIL2, whereas the R103W enzyme is much less affected. The P304T variant was also less proficient than the wild-type, or R103W hNEIL2, in the removal of damaged bases from single-stranded and bubble-containing DNA. Overall, hNEIL2 P304T could be worthy of a detailed epidemiological analysis as a possible cancer risk modifier.
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Affiliation(s)
- Zarina I. Kakhkharova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia;
| | - Dmitry O. Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia;
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence: (D.O.Z.); (I.R.G.)
| | - Inga R. Grin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia;
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence: (D.O.Z.); (I.R.G.)
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