Rare Angiogenin and Ribonuclease 4 variants associated with amyotrophic lateral sclerosis exhibit loss-of-function: a comprehensive in silico study
Amyotrophic Lateral Sclerosis (ALS), a debilitating neurodegenerative disorder is related to mutations in a number of genes, and certain genes of the Ribonuclease (RNASE) superfamily trigger ALS more frequently. Even though missense mutations in Angiogenin (ANG) and Ribonuclease 4 (RNASE4) have been previously shown to cause ALS through loss-of-function mechanisms, understanding the role of rare variants with a plausible explanation of their functional loss mechanisms is an important mission. The study aims to understand if any of the rare ANG and RNASE4 variants catalogued in Project MinE consortium caused ALS due to loss of ribonucleolytic or nuclear translocation or both these activities. Several in silico analyses in combination with extensive molecular dynamics (MD) simulations were performed on wild-type ANG and RNASE4, along with six rare variants (T11S-ANG, R122H-ANG, D2E-RNASE4, N26K-RNASE4, T79A-RNASE4 and G119S-RNASE4) to study the structural and dynamic changes in the catalytic triad and nuclear localization signal residues responsible for ribonucleolytic and nuclear translocation activities respectively. Our comprehensive analyses comprising 1.2 μs simulations with a focus on physicochemical, structural and dynamic properties reveal that T11S-ANG, N26K-RNASE4 and T79A-RNASE4 variants would result in loss of ribonucleolytic activity due to conformational switching of catalytic His114 and His116 respectively but none of the variants would lose their nuclear translocation activity. Our study not only highlights the importance of rare variants but also demonstrates that elucidating the structure-function relationship of mutant effectors is crucial to gain insights into ALS pathophysiology and in developing effective therapeutics.
KeywordsAmyotrophic lateral sclerosis Angiogenin Loss-of-functions Molecular dynamics Physicochemical properties Rare variants Ribonuclease 4
Aditya K. Padhi acknowledges Council of Scientific and Industrial Research (CSIR), Government of India for research fellowship. Priyam Narain is thankful to IIT Delhi for Senior Research Fellowship. Helpful suggestions from Prof B. Jayaram (IIT Delhi) are gratefully acknowledged.
AKP; Collection of variants: PN; Analyzed the data: AKP, PN and JG; Contributed to the writing of the manuscript: AKP, PN and JG.
Compliance with ethical standards
Conflict of interest
The authors declare no conflicts of interest.
Research involving in human and animal rights
This article does not contain any study with human or animal subjects performed by any of the authors.
- Andersen PM, Al-Chalabi A (2011) Clinical genetics of amyotrophic lateral sclerosis: what do we really know? Nat Rev NeurolGoogle Scholar
- Cady J, Allred P, Bali T, Pestronk A, Goate A, Miller TM, Mitra RD, Ravits J, Harms MB, Baloh RH (2015) Amyotrophic lateral sclerosis onset is influenced by the burden of rare variants in known amyotrophic lateral sclerosis genes. Ann Neurol 77:100–113. https://doi.org/10.1002/ana.24306 CrossRefPubMedGoogle Scholar
- Case DA, Babin V, Berryman JT et al (2014) Amber 14. University of California, San Francisco, CAGoogle Scholar
- Chow CY, Landers JE, Bergren SK, Sapp PC, Grant AE, Jones JM, Everett L, Lenk GM, McKenna-Yasek DM, Weisman LS, Figlewicz D, Brown RH, Meisler MH (2009) Deleterious variants of FIG4, a phosphoinositide phosphatase, in patients with ALS. Am J Hum Genet 84:85–88. https://doi.org/10.1016/j.ajhg.2008.12.010 CrossRefPubMedPubMedCentralGoogle Scholar
- Crabtree B, Thiyagarajan N, Prior SH, Wilson P, Iyer S, Ferns T, Shapiro R, Brew K, Subramanian V, Acharya KR (2007) Characterization of human angiogenin variants implicated in amyotrophic lateral sclerosis. Biochemistry. 46:11810–11818. https://doi.org/10.1021/bi701333h CrossRefPubMedGoogle Scholar
- DeJesus-Hernandez M, Mackenzie IR, Boeve BF, Boxer AL, Baker M, Rutherford NJ, Nicholson AM, Finch NCA, Flynn H, Adamson J, Kouri N, Wojtas A, Sengdy P, Hsiung GYR, Karydas A, Seeley WW, Josephs KA, Coppola G, Geschwind DH, Wszolek ZK, Feldman H, Knopman DS, Petersen RC, Miller BL, Dickson DW, Boylan KB, Graff-Radford NR, Rademakers R (2011) Expanded GGGGCC Hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p-linked FTD and ALS. Neuron. 72:245–256. https://doi.org/10.1016/j.neuron.2011.09.011 CrossRefPubMedPubMedCentralGoogle Scholar
- Ferraiuolo L, Kirby J, Grierson AJ, et al (2011) Molecular pathways of motor neuron injury in amyotrophic lateral sclerosis. Nat Rev NeurolGoogle Scholar
- Greenway MJ, Alexander MD, Ennis S et al (2004) A novel candidate region for ALS on chromosome 14q11.2. Neurology. https://doi.org/10.1212/01.WNL.0000144344.39103.F6 CrossRefGoogle Scholar
- Krüger S, Battke F, Sprecher A, Munz M, Synofzik M, Schöls L, Gasser T, Grehl T, Prudlo J, Biskup S (2016) Rare variants in neurodegeneration associated genes revealed by targeted panel sequencing in a German ALS cohort. Front Mol Neurosci 9. https://doi.org/10.3389/fnmol.2016.00092
- Leonidas DD, Shapiro R, Allen SC, Subbarao GV, Veluraja K, Acharya KR (1999) Refined crystal structures of native human angiogenin and two active site variants: implications for the unique functional properties of an enzyme involved in neovascularisation during tumour growth. J Mol Biol 285:1209–1233. https://doi.org/10.1006/jmbi.1998.2378 CrossRefPubMedGoogle Scholar
- Li S, Sheng J, Hu JK, Yu W, Kishikawa H, Hu MG, Shima K, Wu D, Xu Z, Xin W, Sims KB, Landers JE, Brown RH, Hu GF (2013) Ribonuclease 4 protects neuron degeneration by promoting angiogenesis, neurogenesis, and neuronal survival under stress. Angiogenesis. 16:387–404. https://doi.org/10.1007/s10456-012-9322-9 CrossRefPubMedGoogle Scholar
- Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19:1639–1662. https://doi.org/10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B CrossRefGoogle Scholar
- Narain P, Gomes J, Bhatia R, Singh I, Vivekanandan P (2017) C9orf72 hexanucleotide repeat expansions and Ataxin 2 intermediate length repeat expansions in Indian patients with amyotrophic lateral sclerosis. Neurobiol Aging 56:211.e9–211.e14. https://doi.org/10.1016/j.neurobiolaging.2017.04.011 CrossRefGoogle Scholar
- Narain P, Pandey A, Gupta S, Gomes J, Bhatia R, Vivekanandan P (2018) Targeted next-generation sequencing reveals novel and rare variants in Indian patients with amyotrophic lateral sclerosis. Neurobiol Aging 71:265.e9–265.e14. https://doi.org/10.1016/j.neurobiolaging.2018.05.012 CrossRefGoogle Scholar
- Padhi AK, Jayaram B, Gomes J (2013a) Prediction of functional loss of human angiogenin mutants associated with ALS by molecular dynamics simulations. Sci Rep 3. https://doi.org/10.1038/srep01225
- Pang SYY, Hsu JS, Teo KC, Li Y, Kung MHW, Cheah KSE, Chan D, Cheung KMC, Li M, Sham PC, Ho SL (2017) Burden of rare variants in ALS genes influences survival in familial and sporadic ALS. Neurobiol Aging 58:238.e9–238.e15. https://doi.org/10.1016/j.neurobiolaging.2017.06.007 CrossRefGoogle Scholar
- Renton AE, Majounie E, Waite A, Simón-Sánchez J, Rollinson S, Gibbs JR, Schymick JC, Laaksovirta H, van Swieten JC, Myllykangas L, Kalimo H, Paetau A, Abramzon Y, Remes AM, Kaganovich A, Scholz SW, Duckworth J, Ding J, Harmer DW, Hernandez DG, Johnson JO, Mok K, Ryten M, Trabzuni D, Guerreiro RJ, Orrell RW, Neal J, Murray A, Pearson J, Jansen IE, Sondervan D, Seelaar H, Blake D, Young K, Halliwell N, Callister JB, Toulson G, Richardson A, Gerhard A, Snowden J, Mann D, Neary D, Nalls MA, Peuralinna T, Jansson L, Isoviita VM, Kaivorinne AL, Hölttä-Vuori M, Ikonen E, Sulkava R, Benatar M, Wuu J, Chiò A, Restagno G, Borghero G, Sabatelli M, Heckerman D, Rogaeva E, Zinman L, Rothstein JD, Sendtner M, Drepper C, Eichler EE, Alkan C, Abdullaev Z, Pack SD, Dutra A, Pak E, Hardy J, Singleton A, Williams NM, Heutink P, Pickering-Brown S, Morris HR, Tienari PJ, Traynor BJ (2011) A hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD. Neuron. 72:257–268. https://doi.org/10.1016/j.neuron.2011.09.010 CrossRefPubMedPubMedCentralGoogle Scholar
- Rosen DR, Siddique T, Patterson D, Figlewicz DA, Sapp P, Hentati A, Donaldson D, Goto J, O'Regan JP, Deng HX, Rahmani Z, Krizus A, McKenna-Yasek D, Cayabyab A, Gaston SM, Berger R, Tanzi RE, Halperin JJ, Herzfeldt B, van den Bergh R, Hung WY, Bird T, Deng G, Mulder DW, Smyth C, Laing NG, Soriano E, Pericak–Vance MA, Haines J, Rouleau GA, Gusella JS, Horvitz HR, Brown RH (1993) Mutations in cu/Zn superoxide dismutase gene are associated with familial amyotrophic lateral sclerosis. Nature. 362:59–62. https://doi.org/10.1038/362059a0 CrossRefPubMedGoogle Scholar
- Sanner MF (1999) Python: a programming language for software integration and development. J Mol Graph ModelGoogle Scholar
- Tripolszki K, Danis J, Padhi AK, Gomes J, Bozó R, Nagy ZF, Nagy D, Klivényi P, Engelhardt JI, Széll M (2019) Angiogenin mutations in Hungarian patients with amyotrophic lateral sclerosis: clinical, genetic, computational, and functional analyses. Brain Behav. https://doi.org/10.1002/brb3.1293
- Van Blitterswijk M, Landers JE (2010) RNA processing pathways in amyotrophic lateral sclerosis. NeurogeneticsGoogle Scholar
- Venselaar H, te Beek TAH, Kuipers RKP, Hekkelman ML, Vriend G (2010) Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. BMC Bioinformatics https://doi.org/10.1186/1471-2105-11-548