Locked in a vicious cycle: the connection between genomic instability and a loss of protein homeostasis
Tóm tắt
Từ khóa
Tài liệu tham khảo
Abel, H. J., Larson, D. E., Regier, A. A., Chiang, C., Das, I., Kanchi, K. L., et al. (2020). Mapping and characterization of structural variation in 17,795 human genomes. Nature, 583(7814), 83–89. https://doi.org/10.1038/s41586-020-2371-0
Adegbuyiro, A., Sedighi, F., Pilkington, A. W., Groover, S., & Legleiter, J. (2017). Proteins containing expanded polyglutamine tracts and neurodegenerative disease. Biochemistry, 56(9), 1199–1217. https://doi.org/10.1021/acs.biochem.6b00936
Aguilera, A., & Gómez-González, B. (2008). Genome instability: A mechanistic view of its causes and consequences. Nature Reviews Genetics, 9(3), 204–217. https://doi.org/10.1038/nrg2268
Aivazidis, S., Coughlan, C. M., Rauniyar, A. K., Hua Jiang, L., Liggett, A., Maclean, K. N., & Roede, J. R. (2017). The burden of trisomy 21 disrupts the proteostasis network in down syndrome. PLoS ONE, 12(4), e0176307. https://doi.org/10.1371/journal.pone.0176307
Åkerfelt, M., Morimoto, R. I., & Sistonen, L. (2010). Heat shock factors: Integrators of cell stress, development and lifespan. Nature Reviews Molecular Cell Biology, 11(8), 545–555. https://doi.org/10.1038/nrm2938
Alupei, M. C., Maity, P., Esser, P. R., Krikki, I., Tuorto, F., Parlato, R., et al. (2018). Loss of proteostasis is a pathomechanism in cockayne syndrome. Cell Reports, 23(6), 1612–1619. https://doi.org/10.1016/j.celrep.2018.04.041
Amm, I., Sommer, T., & Wolf, D. H. (2014). Protein quality control and elimination of protein waste: The role of the ubiquitin–proteasome system. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, 1843(1), 182–196. https://doi.org/10.1016/j.bbamcr.2013.06.031
Anon. (2020). Pan-cancer analysis of whole genomes. Nature, 578(7793), 82–93. https://doi.org/10.1038/s41586-020-1969-6
Antonarakis, S. E., Skotko, B. G., Rafii, M. S., Strydom, A., Pape, S. E., Bianchi, D. W., et al. (2020). Down syndrome. Nature Reviews Disease Primers, 6(1), 9. https://doi.org/10.1038/s41572-019-0143-7
Arczewska, K. D., Tomazella, G. G., Lindvall, J. M., Kassahun, H., Maglioni, S., Torgovnick, A., et al. (2013). Active transcriptomic and proteomic reprogramming in the C. Elegans nucleotide excision repair mutant xpa-1. Nucleic Acids Research, 41(10), 5368–5381. https://doi.org/10.1093/nar/gkt225
Arlow, T., Scott, K., Wagenseller, A., & Gammie, A. (2013). Proteasome inhibition rescues clinically significant unstable variants of the mismatch repair protein Msh2. Proceedings of the National Academy of Sciences, 110(1), 246–251. https://doi.org/10.1073/pnas.1215510110
Baker, M. (2012). Structural variation: The genome’s hidden architecture. Nature Methods, 9(2), 133–137. https://doi.org/10.1038/nmeth.1858
Balch, W. E., Morimoto, R. I., Dillin, A., & Kelly, J. W. (2008). Adapting proteostasis for disease intervention. Science, 319(5865), 916–919. https://doi.org/10.1126/science.1141448
Balendra, R., & Isaacs, A. M. (2018). C9orf72-mediated ALS and FTD: Multiple pathways to disease. Nature Reviews Neurology, 14(9), 544–558. https://doi.org/10.1038/s41582-018-0047-2
Banez-Coronel, M., & Ranum, L. P. W. (2019). Repeat-associated non-AUG (RAN) translation: Insights from pathology. Laboratory Investigation, 99(7), 929–942. https://doi.org/10.1038/s41374-019-0241-x
Barzilai, A., Rotman, G., & Shilow, Y. (2002). ATM deficiency and oxidative stress: A new dimension of defective response to DNA damage. DNA Repair, 1(1), 3–25. https://doi.org/10.1016/S1568-7864(01)00007-6
Basu, S., Je, G., & Kim, Y.-S. (2015). Transcriptional mutagenesis by 8-OxodG in α-synuclein aggregation and the pathogenesis of Parkinson’s disease. Experimental & Molecular Medicine, 47(8), e179–e179. https://doi.org/10.1038/emm.2015.54
Ben Yehuda, A., Risheq, M., Novoplansky, O., Bersuker, K., Kopito, R. R., Goldberg, M., & Brandeis, M. (2017). Ubiquitin accumulation on disease associated protein aggregates is correlated with nuclear ubiquitin depletion, histone de-ubiquitination and impaired DNA damage response. PLoS ONE, 12(1), e0169054. https://doi.org/10.1371/journal.pone.0169054
Bence, N. F. (2001). Impairment of the ubiquitin-proteasome system by protein aggregation. Science, 292(5521), 1552–1555. https://doi.org/10.1126/science.292.5521.1552
Benson, M. D., Liepnieks, J. J., Yazaki, M., Yamashita, T., Asl, K. H., Guenther, B., & Kluve-Beckerman, B. (2001). A New human hereditary amyloidosis: The result of a stop-codon mutation in the apolipoprotein aii gene. Genomics, 72(3), 272–277. https://doi.org/10.1006/geno.2000.6499
Bento, C. F., Renna, M., Ghislat, G., Puri, C., Ashkenazi, A., Vicinanza, M., et al. (2016). Mammalian autophagy: How does it work? Annual Review of Biochemistry, 85(1), 685–713. https://doi.org/10.1146/annurev-biochem-060815-014556
Bergink, S., & Jentsch, S. (2009). Principles of ubiquitin and SUMO modifications in DNA repair. Nature, 458(7237), 461–467. https://doi.org/10.1038/nature07963
Bernardi, L., & Bruni, A. C. (2019). Mutations in prion protein gene: Pathogenic mechanisms in C-terminal vs. N-terminal domain, a review. International Journal of Molecular Sciences, 20(14), 3606. https://doi.org/10.3390/ijms20143606
Biebl, M. M., & Buchner, J. (2019). Structure, function, and regulation of the Hsp90 machinery. Cold Spring Harbor Perspectives in Biology, 11(9), a034017. https://doi.org/10.1101/cshperspect.a034017
Blokzijl, F., De Ligt, J., Jager, M., Sasselli, V., Roerink, S., Sasaki, N., et al. (2016). Tissue-specific mutation accumulation in human adult stem cells during life. Nature, 538(7624), 260–264. https://doi.org/10.1038/nature19768
Bondarev, S., Antonets, K., Kajava, A., Nizhnikov, A., & Zhouravleva, G. (2018). Protein co-aggregation related to amyloids: Methods of investigation, diversity, and classification. International Journal of Molecular Sciences, 19(8), 2292. https://doi.org/10.3390/ijms19082292
Boopathy, S., Silvas, T. V., Tischbein, M., Jansen, S., Shandilya, S. M., Zitzewitz, J. A., et al. (2015). Structural basis for mutation-induced destabilization of profilin 1 in ALS. Proceedings of the National Academy of Sciences, 112(26), 7984–7989. https://doi.org/10.1073/pnas.1424108112
Booth, D. R., Sunde, M., Bellotti, V., Robinson, C. V., Hutchinson, W. L., Fraser, P. E., et al. (1997). Instability, unfolding and aggregation of human lysozyme variants underlying amyloid fibrillogenesis. Nature, 385(6619), 787–793. https://doi.org/10.1038/385787a0
Bordoni, M., Pansarasa, O., Dell’Orco, M., Crippa, V., Gagliardi, S., Sproviero, D., et al. (2019). Nuclear phospho-SOD1 protects DNA from oxidative stress damage in amyotrophic lateral sclerosis. Journal of Clinical Medicine, 8(5), 729. https://doi.org/10.3390/jcm8050729
Borkovich, K. A., Farrelly, F. W., Finkelstein, D. B., Taulien, J., & Lindquist, S. (1989). Hsp82 is an essential protein that is required in higher concentrations for growth of cells at higher temperatures. Molecular and Cellular Biology, 9(9), 3919–3930. https://doi.org/10.1128/MCB.9.9.3919
Bossy-Wetzel, E., Petrilli, A., & Knott, A. B. (2008). Mutant huntingtin and mitochondrial dysfunction. Trends in Neurosciences, 31(12), 609–616. https://doi.org/10.1016/j.tins.2008.09.004
Boysen, M., Kityk, R., & Mayer, M. P. (2019). Hsp70- and Hsp90-mediated regulation of the conformation of P53 DNA binding domain and P53 cancer variants. Molecular Cell, 74(4), 831-843.e4. https://doi.org/10.1016/j.molcel.2019.03.032
Brazhnik, K., Sun, S., Alani, O., Kinkhabwala, M., Wolkoff, A. W., Maslov, A. Y., et al. (2020). Single-cell analysis reveals different age-related somatic mutation profiles between stem and differentiated cells in human liver. Science Advances, 6(5), 2659. https://doi.org/10.1126/sciadv.aax2659
Brégeon, D., Doddridge, Z. A., You, H. J., Weiss, B., & Doetsch, P. W. (2003). Transcriptional mutagenesis induced by uracil and 8-oxoguanine in Escherichia Coli. Molecular Cell, 12(4), 959–970. https://doi.org/10.1016/S1097-2765(03)00360-5
Brégeon, D., & Doetsch, P. W. (2011). Transcriptional mutagenesis: Causes and involvement in tumour development. Nature Reviews Cancer, 11(3), 218–227. https://doi.org/10.1038/nrc3006
Brennan, C. M., Vaites, L. P., Wells, J. N., Santaguida, S., Paulo, J. A., Zuzana Storchova, J., et al. (2019). Protein aggregation mediates stoichiometry of protein complexes in aneuploid cells. Genes & Development, 33(15–16), 1031–1047. https://doi.org/10.1101/gad.327494.119
Brinkmann, K., Schell, M., Hoppe, T., & Kashkar, H. (2015). Regulation of the DNA damage response by ubiquitin conjugation. Frontiers in Genetics. https://doi.org/10.3389/fgene.2015.00098
Brown, J. S., & Jackson, S. P. (2015). Ubiquitylation, neddylation and the DNA damage response. Open Biology, 5(4), 150018. https://doi.org/10.1098/rsob.150018
Bryant, E. E., Šunjevarić, I., Berchowitz, L., Rothstein, R., & Reid, R. J. D. (2019). Rad5 dysregulation drives hyperactive recombination at replication forks resulting in cisplatin sensitivity and genome instability. Nucleic Acids Research, 47(17), 9144–9159. https://doi.org/10.1093/nar/gkz631
Calderwood, S. K., & Gong, J. (2016). Heat shock proteins promote cancer: It’s a protection racket. Trends in Biochemical Sciences, 41(4), 311–323. https://doi.org/10.1016/j.tibs.2016.01.003
Cancel, G., Gourfinkel-An, I., Stevanin, G., Didierjean, O., Abbas, N., Hirsch, E., et al. (1998). Somatic mosaicism of the CAG repeat expansion in spinocerebellar ataxia type 3/machado-joseph disease. Human Mutation, 11(1), 23–27. https://doi.org/10.1002/(SICI)1098-1004(1998)11:1%3c23::AID-HUMU4%3e3.0.CO;2-M
Carvalho, C. M. B., & Lupski, J. R. (2016). Mechanisms underlying structural variant formation in genomic disorders. Nature Reviews Genetics, 17(4), 224–238. https://doi.org/10.1038/nrg.2015.25
Castel, A. L., Cleary, J. D., & Pearson, C. E. (2010). Repeat instability as the basis for human diseases and as a potential target for therapy. Nature Reviews Molecular Cell Biology, 11(3), 165–170. https://doi.org/10.1038/nrm2854
Chatzidoukaki, O., Goulielmaki, E., Schumacher, B., & Garinis, G. A. (2020). DNA damage response and metabolic reprogramming in health and disease. Trends in Genetics. https://doi.org/10.1016/j.tig.2020.06.018
Chen, G., Bradford, W. D., Seidel, C. W., & Li, R. (2012). Hsp90 stress potentiates rapid cellular adaptation through induction of aneuploidy. Nature, 482(7384), 246–250. https://doi.org/10.1038/nature10795
Chen, G.-F., Ting-hai, Xu., Yan, Y., Zhou, Y.-R., Jiang, Yi., Melcher, K., & Eric Xu, H. (2017). Amyloid beta: Structure, biology and structure-based therapeutic development. Acta Pharmacologica Sinica, 38(9), 1205–1235. https://doi.org/10.1038/aps.2017.28
Cheng, A. N., Fan, C.-C., Lo, Y.-K., Kuo, C.-L., Hui-Chun Wang, I., Lien, H., et al. (2017). Cdc7-Dbf4-mediated phosphorylation of HSP90-S164 stabilizes HSP90-HCLK2-MRN complex to enhance ATR/ATM signaling that overcomes replication stress in cancer. Scientific Reports, 7(1), 17024. https://doi.org/10.1038/s41598-017-17126-2
Chiti, F., & Dobson, C. M. (2017). Protein misfolding, amyloid formation, and human disease: A summary of progress over the last decade. Annual Review of Biochemistry, 86(1), 27–68. https://doi.org/10.1146/annurev-biochem-061516-045115
Ciosi, M., Maxwell, A., Cumming, S. A., Hensman, D. J., Moss, A. M., Alshammari, M. D., et al. (2019). A genetic association study of glutamine-encoding DNA sequence structures, somatic CAG expansion, and DNA repair gene variants, with huntington disease clinical outcomes. EBioMedicine, 48, 568–580. https://doi.org/10.1016/j.ebiom.2019.09.020
Ciryam, P., Kundra, R., Freer, R., Morimoto, R. I., Dobson, C. M., & Vendruscolo, M. (2016). A transcriptional signature of Alzheimer’s disease is associated with a metastable subproteome at risk for aggregation. Proceedings of the National Academy of Sciences, 113(17), 4753–4758. https://doi.org/10.1073/pnas.1516604113
Cleary, J. D., Pattamatta, A., & Ranum, L. P. W. (2018). Repeat-associated non-ATG (RAN) translation. Journal of Biological Chemistry, 293(42), 16127–16141. https://doi.org/10.1074/jbc.R118.003237
Clementi, E., Inglin, L., Beebe, E., Gsell, C., Garajova, Z., & Markkanen, E. (2020). Persistent DNA damage triggers activation of the integrated stress response to promote cell survival under nutrient restriction. BMC Biology, 18(1), 36. https://doi.org/10.1186/s12915-020-00771-x
Corcoles-Saez, I., Dong, K., Johnson, A. L., Waskiewicz, E., Costanzo, M., Boone, C., & Cha, R. S. (2018). Essential function of Mec1, the budding yeast ATM/ATR checkpoint-response kinase, in protein homeostasis. Developmental Cell, 46(4), 495-503.e2. https://doi.org/10.1016/j.devcel.2018.07.011
Cordaux, R., & Batzer, M. A. (2009). The impact of retrotransposons on human genome evolution. Nature Reviews Genetics, 10(10), 691–703. https://doi.org/10.1038/nrg2640
Cortese, A., Simone, R., Sullivan, R., Vandrovcova, J., Tariq, H., Yau, W. Y., et al. (2019). Biallelic expansion of an intronic repeat in RFC1 Is a common cause of late-onset Ataxia. Nature Genetics, 51(4), 649–658. https://doi.org/10.1038/s41588-019-0372-4
Croteau, D. L., Popuri, V., Opresko, P. L., & Bohr, V. A. (2014). Human RecQ helicases in DNA repair, recombination, and replication. Annual Review of Biochemistry , 83(1), 519–552. https://doi.org/10.1146/annurev-biochem-060713-035428
Curtin, N. J. (2012). DNA repair dysregulation from cancer driver to therapeutic target. Nature Reviews Cancer, 12(12), 801–817. https://doi.org/10.1038/nrc3399
Dai, C., Dai, S., & Cao, J. (2012). Proteotoxic stress of cancer: Implication of the heat-shock response in oncogenesis. Journal of Cellular Physiology, 227(8), 2982–2987. https://doi.org/10.1002/jcp.24017
Dantuma, N. P., Groothuis, T. A. M., Salomons, F. A., & Neefjes, J. (2006). A dynamic ubiquitin equilibrium couples proteasomal activity to chromatin remodeling. Journal of Cell Biology, 173(1), 19–26. https://doi.org/10.1083/jcb.200510071
de Baets, G., van Doorn, L., Rousseau, F., & Schymkowitz, J. (2015). Increased aggregation is more frequently associated to human disease-associated mutations than to neutral polymorphisms. PLOS Computational Biology, 11(9), e1004374. https://doi.org/10.1371/journal.pcbi.1004374
de Sousa Leal, A. M., de Azevedo Medeiros, L. B., Muñoz-Cadavid, C. O., de Paula, O. R., de Souza Timóteo, A. R., de Oliveira, A. H., et al. (2020). XPA deficiency affects the ubiquitin-proteasome system function. DNA Repair, 94, 102937. https://doi.org/10.1016/j.dnarep.2020.102937
Deller, M. C., Kong, L., & Rupp, B. (2016). Protein stability: A crystallographer’s perspective. Acta Crystallographica Section F Structural Biology Communications, 72(2), 72–95. https://doi.org/10.1107/S2053230X15024619
DePristo, M. A., Weinreich, D. M., & Hartl, D. L. (2005). Missense meanderings in sequence space: A biophysical view of protein evolution. Nature Reviews Genetics, 6(9), 678–687. https://doi.org/10.1038/nrg1672
Deshaies, R. J. (2014). Proteotoxic crisis, the ubiquitin-proteasome system, and cancer therapy. BMC Biology, 12(1), 94. https://doi.org/10.1186/s12915-014-0094-0
Dettmer, U., Newman, A. J., Soldner, F., Luth, E. S., Kim, N. C., von Saucken, V. E., et al. (2015). Parkinson-causing α-synuclein missense mutations shift native tetramers to monomers as a mechanism for disease initiation. Nature Communications, 6(1), 7314. https://doi.org/10.1038/ncomms8314
Dikic, I., & Elazar, Z. (2018). Mechanism and medical implications of mammalian autophagy. Nature Reviews Molecular Cell Biology, 19(6), 349–364.
Dobson, C. M. (2017). The amyloid phenomenon and its links with human disease. Cold Spring Harbor Perspectives in Biology, 9(6), a023648. https://doi.org/10.1101/cshperspect.a023648
Donnelly, N., Passerini, V., Dürrbaum, M., Stingele, S., & Storchová, Z. (2014). HSF1 deficiency and impaired HSP90-dependent protein folding are hallmarks of aneuploid human cells. The EMBO Journal, 33(20), 2374–2387. https://doi.org/10.15252/embj.201488648
Dote, H., Burgan, W. E., Camphausen, K., & Tofilon, P. J. (2006). Inhibition of Hsp90 compromises the DNA damage response to radiation. Cancer Research, 66(18), 9211–9220. https://doi.org/10.1158/0008-5472.CAN-06-2181
Dubrez, L., Causse, S., Bonan, N. B., Dumétier, B., & Garrido, C. (2020). Heat-shock proteins: Chaperoning DNA repair. Oncogene, 39(3), 516–529. https://doi.org/10.1038/s41388-019-1016-y
Echtenkamp, F. J., Zelin, E., Oxelmark, E., Woo, J. I., Andrews, B. J., Garabedian, M., & Freeman, B. C. (2011). Global functional map of the P23 molecular chaperone reveals an extensive cellular network. Molecular Cell, 43(2), 229–241. https://doi.org/10.1016/j.molcel.2011.05.029
Ellerby, L. M. (2019). Repeat expansion disorders: Mechanisms and therapeutics. Neurotherapeutics, 16(4), 924–927. https://doi.org/10.1007/s13311-019-00823-3
Enchev, R. I., Schulman, B. A., & Peter, M. (2015). Protein neddylation: Beyond Cullin–RING ligases. Nature Reviews Molecular Cell Biology, 16(1), 30–44. https://doi.org/10.1038/nrm3919
Enokido, Y., Tamura, T., Ito, H., Arumughan, A., Komuro, A., Shiwaku, H., et al. (2010). Mutant huntingtin impairs Ku70-mediated DNA repair. Journal of Cell Biology, 189(3), 425–443. https://doi.org/10.1083/jcb.200905138
Evans, S. A., Horrell, J., & Neretti, N. (2019). The three-dimensional organization of the genome in cellular senescence and age-associated diseases. Seminars in Cell & Developmental Biology, 90, 154–160. https://doi.org/10.1016/j.semcdb.2018.07.022
Fang, Q., Inanc, B., Schamus, S., Wang, X.-H., Wei, L., Brown, A. R., et al. (2014). HSP90 regulates DNA repair via the interaction between XRCC1 and DNA polymerase β. Nature Communications, 5(1), 5513. https://doi.org/10.1038/ncomms6513
Fares, M. A., Ruiz-González, M. X., Moya, A., Elena, S. F., & Barrio, E. (2002). GroEL buffers against deleterious mutations. Nature, 417(6887), 398–398. https://doi.org/10.1038/417398a
Farmer, K. M., Ghag, G., Puangmalai, N., Montalbano, M., Bhatt, N., & Kayed, R. (2020). P53 aggregation, interactions with tau, and impaired DNA damage response in Alzheimer’s disease. Acta Neuropathologica Communications, 8(1), 132. https://doi.org/10.1186/s40478-020-01012-6
Farrawell, N. E., Lambert-Smith, I., Mitchell, K., McKenna, J., McAlary, L., Ciryam, P., et al. (2018). SOD1-A4V aggregation alters ubiquitin homeostasis in a cell model of ALS. Journal of Cell Science, 131(11), 209122. https://doi.org/10.1242/jcs.209122
Forsberg, L. A., Rasi, C., Razzaghian, H. R., Pakalapati, G., Waite, L., Thilbeault, K. S., et al. (2012). Age-related somatic structural changes in the nuclear genome of human blood cells. The American Journal of Human Genetics, 90(2), 217–228. https://doi.org/10.1016/j.ajhg.2011.12.009
Fusakio, M. E., Willy, J. A., Wang, Y., Mirek, E. T., Al Baghdadi, R. J., Adams, C. M., et al. (2016). Transcription factor ATF4 directs basal and stress-induced gene expression in the unfolded protein response and cholesterol metabolism in the liver. Molecular Biology of the Cell, 27(9), 1536–1551. https://doi.org/10.1091/mbc.E16-01-0039
Gao, R., Chakraborty, A., Geater, C., Pradhan, S., Gordon, K. L., Snowden, J., et al. (2019). Mutant huntingtin impairs PNKP and ATXN3, disrupting DNA repair and transcription. ELife. https://doi.org/10.7554/eLife.42988
Georgiadis, M. M., Chen, Q., Meng, J., Guo, C., Wireman, R., Reed, A., et al. (2016). Small molecule activation of apurinic/apyrimidinic endonuclease 1 reduces DNA damage induced by cisplatin in cultured sensory neurons. DNA Repair, 41, 32–41. https://doi.org/10.1016/j.dnarep.2016.03.009
Ghosh, K., & Dill, K. (2010). Cellular proteomes have broad distributions of protein stability. Biophysical Journal, 99(12), 3996–4002. https://doi.org/10.1016/j.bpj.2010.10.036
Gidalevitz, T. (2006). Progressive disruption of cellular protein folding in models of polyglutamine diseases. Science, 311(5766), 1471–1474. https://doi.org/10.1126/science.1124514
Gidalevitz, T., Kikis, E. A., & Morimoto, R. I. (2010). A cellular perspective on conformational disease: The role of genetic background and proteostasis networks. Current Opinion in Structural Biology, 20(1), 23–32. https://doi.org/10.1016/j.sbi.2009.11.001
Gidalevitz, T., Krupinski, T., Garcia, S., & Morimoto, R. I. (2009). Destabilizing protein polymorphisms in the genetic background direct phenotypic expression of mutant SOD1 toxicity. PLoS Genetics, 5(3), e1000399. https://doi.org/10.1371/journal.pgen.1000399
Gidalevitz, T., Prahlad, V., & Morimoto, R. I. (2011). The stress of protein misfolding: From single cells to multicellular organisms. Cold Spring Harbor Perspectives in Biology, 3(6), a009704–a009704. https://doi.org/10.1101/cshperspect.a009704
Gidalevitz, T., Wang, N., Deravaj, T., Alexander-Floyd, J., & Morimoto, R. I. (2013). Natural genetic variation determines susceptibility to aggregation or toxicity in a C. elegansmodel for polyglutamine disease. BMC Biology, 11(1), 100. https://doi.org/10.1186/1741-7007-11-100
Giglia-Mari, G., Zotter, A., & Vermeulen, W. (2011). DNA damage response. Cold Spring Harbor Perspectives in Biology, 3(1), a000745–a000745. https://doi.org/10.1101/cshperspect.a000745
Gioia, U., Francia, S., Cabrini, M., Brambillasca, S., Michelini, F., Jones-Weinert, C. W., & di Fagagna, F. D. (2019). Pharmacological boost of DNA damage response and repair by enhanced biogenesis of DNA damage response RNAs. Scientific Reports, 9(1), 6460. https://doi.org/10.1038/s41598-019-42892-6
Goldschmidt, L., Teng, P. K., Riek, R., & Eisenberg, D. (2010). Identifying the amylome, proteins capable of forming amyloid-like fibrils. Proceedings of the National Academy of Sciences, 107(8), 3487–3492. https://doi.org/10.1073/pnas.0915166107
Gonzalo, S., & Kreienkamp, R. (2015). DNA repair defects and genome instability in Hutchinson-Gilford progeria syndrome. Current Opinion in Cell Biology, 34, 75–83. https://doi.org/10.1016/j.ceb.2015.05.007
Gragerov, A., Nudler, E., Komissarova, N., Gaitanaris, G. A., Gottesman, M. E., & Nikiforov, V. (1992). Cooperation of GroEL/GroES and DnaK/DnaJ heat shock proteins in preventing protein misfolding in Escherichia Coli. Proceedings of the National Academy of Sciences, 89(21), 10341–10344. https://doi.org/10.1073/pnas.89.21.10341
Green, K. M., Rebecca Glineburg, M., Kearse, M. G., Flores, B. N., Linsalata, A. E., Fedak, S. J., et al. (2017). RAN translation at C9orf72-associated repeat expansions is selectively enhanced by the integrated stress response. Nature Communications, 8(1), 2005. https://doi.org/10.1038/s41467-017-02200-0
Gsponer, J., Futschik, M. E., Teichmann, S. A., & Babu, M. M. (2008). Tight regulation of unstructured proteins: From transcript synthesis to protein degradation. Science, 322(5906), 1365–1368. https://doi.org/10.1126/science.1163581
Guo, C., & Zhao, Y. (2020). Autophagy and DNA damage repair. Genome Instability & Disease. https://doi.org/10.1007/s42764-020-00016-9
Guo, Z., Kozlov, S., Lavin, M. F., Person, M. D., & Paull, T. T. (2010). ATM activation by oxidative stress. Science, 330(6003), 517–521. https://doi.org/10.1126/science.1192912
Hamczyk, M. R., Villa‐Bellosta. R., Quesada, V., Gonzalo, P., Vidak, S., Nevado, R. M., Andrés‐Manzano, M. J., Misteli, T., López‐Otín, C., Andrés, V. (2019) Progerin accelerates atherosclerosis by inducing endoplasmic reticulum stress in vascular smooth muscle cells. EMBO Molecular Medicine 11 (4)
Hansen, M., Rubinsztein, D. C., & Walker, D. W. (2018). Autophagy as a promoter of longevity: Insights from model organisms. Nature Reviews Molecular Cell Biology, 19(9), 579–593. https://doi.org/10.1038/s41580-018-0033-y
Hartl, F. U., Bracher, A., & Hayer-Hartl, M. (2011). Molecular chaperones in protein folding and proteostasis. Nature, 475(7356), 324–332. https://doi.org/10.1038/nature10317
Haslbeck, M., & Vierling, E. (2015). A first line of stress defense: Small heat shock proteins and their function in protein homeostasis. Journal of Molecular Biology, 427(7), 1537–1548. https://doi.org/10.1016/j.jmb.2015.02.002
Herrero, A. B., Miguel, J. S., & Gutierrez, N. C. (2015). Deregulation of DNA double-strand break repair in multiple myeloma: Implications for genome stability. PLoS ONE, 10(3), e0121581. https://doi.org/10.1371/journal.pone.0121581
Hewitt, G., Carroll, B., Sarallah, R., Correia-Melo, C., Ogrodnik, M., Nelson, G., et al. (2016). SQSTM1/P62 mediates crosstalk between autophagy and the UPS in DNA repair. Autophagy, 12(10), 1917–1930. https://doi.org/10.1080/15548627.2016.1210368
Hewitt, G., & Korolchuk, V. I. (2017). Repair, reuse, recycle: The expanding role of autophagy in genome maintenance. Trends in Cell Biology, 27(5), 340–351. https://doi.org/10.1016/j.tcb.2016.11.011
Hipp, M. S., Kasturi, P., & Ulrich Hartl, F. (2019). The proteostasis network and its decline in ageing. Nature Reviews Molecular Cell Biology, 20(7), 421–435. https://doi.org/10.1038/s41580-019-0101-y
Hirata, K., Nambara, T., Kawatani, K., Nawa, N., Yoshimatsu, H., Kusakabe, H., et al. (2020). 4-Phenylbutyrate ameliorates apoptotic neural cell death in down syndrome by reducing protein aggregates. Scientific Reports, 10(1), 14047. https://doi.org/10.1038/s41598-020-70362-x
Hou, Y., Song, H., Croteau, D. L., Akbari, M., & Bohr, V. A. (2017). Genome instability in Alzheimer disease. Mechanisms of Ageing and Development, 161, 83–94. https://doi.org/10.1016/j.mad.2016.04.005
Illuzzi, J., Yerkes, S., Parekh-Olmedo, H., & Kmiec, E. B. (2009). DNA breakage and induction of DNA damage response proteins precede the appearance of visible mutant huntingtin aggregates. Journal of Neuroscience Research, 87(3), 733–747. https://doi.org/10.1002/jnr.21881
Ishiura, H., Shibata, S., Yoshimura, J., Suzuki, Y., Wei, Qu., Koichiro Doi, M., et al. (2019). Noncoding CGG repeat expansions in neuronal intranuclear inclusion disease, oculopharyngodistal myopathy and an overlapping disease. Nature Genetics, 51(8), 1222–1232. https://doi.org/10.1038/s41588-019-0458-z
Janin, J., Bahadur, R. P., & Chakrabarti, P. (2008). Protein–protein interaction and quaternary structure. Quarterly Reviews of Biophysics, 41(2), 133–180. https://doi.org/10.1017/S0033583508004708
Jarosz, D. F., Taipale, M., & Lindquist, S. (2010). Protein homeostasis and the phenotypic manifestation of genetic diversity: Principles and mechanisms. Annual Review of Genetics, 44(1), 189–216. https://doi.org/10.1146/annurev.genet.40.110405.090412
Jeggo, P. A., Pearl, L. H., & Carr, A. M. (2016). DNA repair, genome stability and cancer: A historical perspective. Nature Reviews Cancer, 16(1), 35–42. https://doi.org/10.1038/nrc.2015.4
Jeppesen, D. K., Bohr, V. A., & Stevnsner, T. (2011). DNA repair deficiency in neurodegeneration. Progress in Neurobiology, 94(2), 166–200. https://doi.org/10.1016/j.pneurobio.2011.04.013
Jönsson, M. E., Garza, R., Johansson, P. A., & Jakobsson, J. (2020). Transposable elements: A common feature of neurodevelopmental and neurodegenerative disorders. Trends in Genetics, 36(8), 610–623. https://doi.org/10.1016/j.tig.2020.05.004
Kampinga, H. H., & Bergink, S. (2016). Heat shock proteins as potential targets for protective strategies in neurodegeneration. The Lancet Neurology, 15(7), 748–759. https://doi.org/10.1016/S1474-4422(16)00099-5
Kampinga, H. H., & Craig, E. A. (2010). The HSP70 chaperone machinery: J proteins as drivers of functional specificity. Nature Reviews Molecular Cell Biology, 11(8), 579–592. https://doi.org/10.1038/nrm2941
Karpov, D. S., Spasskaya, D. S., Tutyaeva, V. V., Mironov, A. S., & Karpov, V. L. (2013). Proteasome inhibition enhances resistance to DNA damage via upregulation of Rpn4-dependent DNA repair genes. FEBS Letter, 587(18), 3108–3114. https://doi.org/10.1016/j.febslet.2013.08.007
Karras, G. I., Yi, S., Sahni, N., Fischer, M., Xie, J., Vidal, M., et al. (2017). HSP90 shapes the consequences of human genetic variation. Cell, 168(5), 856-866.e12. https://doi.org/10.1016/j.cell.2017.01.023
Kaya, A., Mariotti, M., Tyshkovskiy, A., Zhou, X., Hulke, M. L., Ma, S., et al. (2020). Molecular signatures of aneuploidy-driven adaptive evolution. Nature Communications, 11(1), 588. https://doi.org/10.1038/s41467-019-13669-2
Kennedy, L. (2003). Dramatic tissue-specific mutation length increases are an early molecular event in huntington disease pathogenesis. Human Molecular Genetics, 12(24), 3359–3367. https://doi.org/10.1093/hmg/ddg352
Klaips, C. L., Jayaraj, G. G., & Ulrich Hartl, F. (2018). Pathways of cellular proteostasis in aging and disease. Journal of Cell Biology, 217(1), 51–63. https://doi.org/10.1083/jcb.201709072
Knighton, L. E., & Truman, A. W. (2019). Role of the molecular chaperones Hsp70 and Hsp90 in the DNA damage response (pp. 345–358). Cham: Springer.
Ko, J.-C., Chen, H.-J., Huang, Y.-C., Tseng, S.-C., Weng, S.-H., Wo, T.-Y., et al. (2012). HSP90 inhibition induces cytotoxicity via down-regulation of Rad51 expression and DNA repair capacity in non-small cell lung cancer cells. Regulatory Toxicology and Pharmacology, 64(3), 415–424. https://doi.org/10.1016/j.yrtph.2012.10.003
Kraemer, K. H. (1987). Xeroderma pigmentosum. Cutaneous, ocular, and neurologic abnormalities in 830 published cases. Archives of Dermatology, 123(2), 241–250. https://doi.org/10.1001/archderm.123.2.241
Kuiper, E. F. E., de Mattos, E. P., Jardim, L. B., Kampinga, H. H., & Bergink, S. (2017). Chaperones in polyglutamine aggregation: Beyond the Q-stretch. Frontiers in Neuroscience. https://doi.org/10.3389/fnins.2017.00145
Labbadia, J., & Morimoto, R. I. (2015). The biology of proteostasis in aging and disease. Annual Review of Biochemistry, 84(1), 435–464. https://doi.org/10.1146/annurev-biochem-060614-033955
Lans, H., Hoeijmakers, J. H. J., Vermeulen, W., & Marteijn, J. A. (2019). The DNA damage response to transcription stress. Nature Reviews Molecular Cell Biology, 20(12), 766–784. https://doi.org/10.1038/s41580-019-0169-4
Lanzillotta, C., Tramutola, A., Meier, S., Schmitt, F., Barone, E., Perluigi, M., et al. (2018). Early and selective activation and subsequent alterations to the unfolded protein response in down syndrome mouse models. Journal of Alzheimer’s Disease, 62(1), 347–359. https://doi.org/10.3233/JAD-170617
Laurie, C. C., Laurie, C. A., Rice, K., Doheny, K. F., Zelnick, L. R., McHugh, C. P., et al. (2012). Detectable clonal mosaicism from birth to old age and its relationship to cancer. Nature Genetics, 44(6), 642–650. https://doi.org/10.1038/ng.2271
Lévy, E., el Banna, N., Baïlle, D., Heneman-Masurel, A., Truchet, S., Rezaei, H., et al. (2019). Causative links between protein aggregation and oxidative stress: A review. International Journal of Molecular Sciences, 20(16), 3896. https://doi.org/10.3390/ijms20163896
Li, W., Lee, M. H., Henderson, L., Tyagi, R., Bachani, M., Steiner, J., et al. (2015). Human endogenous retrovirus-K contributes to motor neuron disease. Science Translational Medicine, 7(307), 307153. https://doi.org/10.1126/scitranslmed.aac8201
Liebelt, F., & Vertegaal, A. C. O. (2016). Ubiquitin-dependent and independent roles of SUMO in proteostasis. American Journal of Physiology-Cell Physiology, 311(2), C284–C296. https://doi.org/10.1152/ajpcell.00091.2016
Lim, K. H., Dasari, A. K. R., Ma, R., Hung, I., Gan, Z., Kelly, J. W., & Fitzgerald, M. C. (2017). Pathogenic mutations induce partial structural changes in the native β-sheet structure of transthyretin and accelerate aggregation. Biochemistry, 56(36), 4808–4818. https://doi.org/10.1021/acs.biochem.7b00658
Liu, Na., Stoica, G., Yan, M., Scofield, V. L., Qiang, W., Lynn, W. S., & Wong, P. K. Y. (2005). ATM deficiency induces oxidative stress and endoplasmic reticulum stress in astrocytes. Laboratory Investigation, 85(12), 1471–1480. https://doi.org/10.1038/labinvest.3700354
Lodato, M. A., Rodin, R. E., Bohrson, C. L., Coulter, M. E., Barton, A. R., Kwon, M., et al. (2018). Aging and neurodegeneration are associated with increased mutations in single human neurons. Science, 359(6375), 555–559. https://doi.org/10.1126/science.aao4426
Lott, I. T., & Head, E. (2019). Dementia in down syndrome: Unique insights for Alzheimer disease research. Nature Reviews Neurology, 15(3), 135–147. https://doi.org/10.1038/s41582-018-0132-6
Ludtmann, M. H., Angelova, P. R., Horrocks, M. H., Choi, M. L., Rodrigues, M., Baev, A. Y., et al. (2018). α-synuclein oligomers interact with ATP synthase and open the permeability transition pore in parkinson’s disease. Nature Communications, 9(1), 2293. https://doi.org/10.1038/s41467-018-04422-2
Maina, B., Mahmoud, Y.-H., & Serpell, L. (2016). Nuclear tau and its potential role in Alzheimer’s disease. Biomolecules, 6(1), 9. https://doi.org/10.3390/biom6010009
Maisnier-Patin, S., Roth, J. R., Fredriksson, Å., Nyström, T., Berg, O. G., & Andersson, D. I. (2005). Genomic buffering mitigates the effects of deleterious mutations in bacteria. Nature Genetics, 37(12), 1376–1379. https://doi.org/10.1038/ng1676
Martincorena, I., & Campbell, P. J. (2015). Somatic mutation in cancer and normal cells. Science, 349(6255), 1483–1489. https://doi.org/10.1126/science.aab4082
Martincorena, I., Roshan, A., Gerstung, M., Ellis, P., van Loo, P., McLaren, S., et al. (2015). High burden and pervasive positive selection of somatic mutations in normal human skin. Science, 348(6237), 880–886. https://doi.org/10.1126/science.aaa6806
Mason, J. M., Logan, H. L., Budke, B., Wu, M., Pawlowski, M., Weichselbaum, R. R., et al. (2014). The RAD51-stimulatory compound RS-1 can exploit the RAD51 overexpression that exists in cancer cells and tumors. Cancer Research, 74(13), 3546–3555. https://doi.org/10.1158/0008-5472.CAN-13-3220
Matsui, D., Nakano, S., Dadashipour, M., & Asano, Y. (2017). Rational identification of aggregation hotspots based on secondary structure and amino acid hydrophobicity. Scientific Reports, 7(1), 9558. https://doi.org/10.1038/s41598-017-09749-2
Mayer, M. P. (2018). Intra-molecular pathways of allosteric control in Hsp70s. Philosophical Transactions of the Royal Society B: Biological Sciences, 373(1749), 20170183. https://doi.org/10.1098/rstb.2017.0183
McKinnon, P. J. (2012). ATM and the molecular pathogenesis of ataxia telangiectasia. Annual Review of Pathology: Mechanisms of Disease, 7(1), 303–321. https://doi.org/10.1146/annurev-pathol-011811-132509
Mimnaugh, E. G., Chen, H. Y., Davie, J. R., Celis, J. E., & Neckers, L. (1997). Rapid deubiquitination of nucleosomal histones in human tumor cells caused by proteasome inhibitors and stress response inducers: Effects on replication, transcription, translation, and the cellular stress response †. Biochemistry, 36(47), 14418–14429. https://doi.org/10.1021/bi970998j
Monaco, A., & Fraldi, A. (2020). Protein aggregation and dysfunction of autophagy-lysosomal pathway: A vicious cycle in lysosomal storage diseases. Frontiers in Molecular Neuroscience. https://doi.org/10.3389/fnmol.2020.00037
Morales, F., Couto, J. M., Higham, C. F., Hogg, G., Cuenca, P., Braida, C., et al. (2012). Somatic instability of the expanded CTG triplet repeat in myotonic dystrophy type 1 is a heritable quantitative trait and modifier of disease severity. Human Molecular Genetics, 21(16), 3558–3567. https://doi.org/10.1093/hmg/dds185
Morán Luengo, T., Matthias, P. M., & Stefan, G. D. R. (2019). The Hsp70–Hsp90 chaperone cascade in protein folding. Trends in Cell Biology, 29(2), 164–177. https://doi.org/10.1016/j.tcb.2018.10.004
Moreira, P. I., Carvalho, C., Zhu, X., Smith, M. A., & Perry, G. (2010). Mitochondrial dysfunction is a trigger of Alzheimer’s disease pathophysiology. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, 1802(1), 2–10. https://doi.org/10.1016/j.bbadis.2009.10.006
Muotri, A. R., Chu, V. T., Marchetto, M. C., Deng, W., Moran, J. V., & Gage, F. H. (2005). Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. Nature, 435(7044), 903–910. https://doi.org/10.1038/nature03663
Musich, P. R., & Zou, Y. (2009). Genomic instability and DNA damage responses in progeria arising from defective maturation of prelamin A. Aging, 1(1), 28–37. https://doi.org/10.18632/aging.100012
Nagata, Y., Anan, T., Yoshida, T., Mizukami, T., Taya, Y., Fujiwara, T., et al. (1999). The stabilization mechanism of mutant-type P53 by impaired ubiquitination: The loss of wild-type P53 function and the Hsp90 association. Oncogene, 18(44), 6037–6049. https://doi.org/10.1038/sj.onc.1202978
Nakamura, M., Kaneko, S., Dickson, D. W., & Kusaka, H. (2019). Aberrant accumulation of BRCA1 in Alzheimer disease and other tauopathies. Journal of Neuropathology & Experimental Neurology. https://doi.org/10.1093/jnen/nlz107
Nawa, N., Hirata, K., Kawatani, K., Nambara, T., Omori, S., Banno, K., et al. (2019). Elimination of protein aggregates prevents premature senescence in human trisomy 21 fibroblasts. PLoS ONE, 14(7), e0219592. https://doi.org/10.1371/journal.pone.0219592
Negrini, S., Gorgoulis, V. G., & Halazonetis, T. D. (2010). Genomic instability—an evolving Hallmark of cancer. Nature Reviews Molecular Cell Biology, 11(3), 220–228. https://doi.org/10.1038/nrm2858
Niblock, M., & Gallo, J.-M. (2012). Tau alternative splicing in familial and sporadic tauopathies. Biochemical Society Transactions, 40(4), 677–680. https://doi.org/10.1042/BST20120091
Niedernhofer, L. J., Gurkar, A. U., Wang, Y., Vijg, J., Hoeijmakers, J. H. J., & Robbins, P. D. (2018). Nuclear genomic instability and aging. Annual Review of Biochemistry, 87(1), 295–322. https://doi.org/10.1146/annurev-biochem-062917-012239
Njomen, E., & Tepe, J. J. (2019). Proteasome activation as a new therapeutic approach to target proteotoxic disorders. Journal of Medicinal Chemistry, 62(14), 6469–6481. https://doi.org/10.1021/acs.jmedchem.9b00101
Nordin, A., Akimoto, C., Wuolikainen, A., Alstermark, H., Jonsson, P., Birve, A., et al. (2015). Extensive size variability of the GGGGCC expansion in C9orf72 in both neuronal and non-neuronal tissues in 18 patients with ALS or FTD. Human Molecular Genetics, 24(11), 3133–3142. https://doi.org/10.1093/hmg/ddv064
Oda, T., Hayano, T., Miyaso, H., Takahashi, N., & Yamashita, T. (2007). Hsp90 regulates the fanconi anemia DNA damage response pathway. Blood, 109(11), 5016–5026. https://doi.org/10.1182/blood-2006-08-038638
Oromendia, A. B., & Amon, A. (2014). Aneuploidy: Implications for protein homeostasis and disease. Disease Models & Mechanisms, 7(1), 15–20. https://doi.org/10.1242/dmm.013391
Oromendia, A. B., Dodgson, S. E., & Amon, A. (2012). Aneuploidy causes proteotoxic stress in yeast. Genes & Development, 26(24), 2696–2708. https://doi.org/10.1101/gad.207407.112
Otto, F. B., & Thumm, M. (2020). Nucleophagy—implications for microautophagy and health. International Journal of Molecular Sciences, 21(12), 4506. https://doi.org/10.3390/ijms21124506
Ou, H.-L., & Schumacher, B. (2018). DNA damage responses and P53 in the aging process. Blood, 131(5), 488–495. https://doi.org/10.1182/blood-2017-07-746396
Palumbo, E., Zhao, Bi., Xue, B., Uversky, V. N., & Davé, V. (2020). Analyzing aggregation propensities of clinically relevant PTEN mutants: A new culprit in pathogenesis of cancer and other PTENopathies. Journal of Biomolecular Structure and Dynamics, 38(8), 2253–2266. https://doi.org/10.1080/07391102.2019.1630005
Papandreou, M.-E., & Tavernarakis, N. (2019). Nucleophagy: From homeostasis to disease. Cell Death & Differentiation, 26(4), 630–639. https://doi.org/10.1038/s41418-018-0266-5
Paradisi, M., McClintock, D., Boguslavsky, R. L., Pedicelli, C., Worman, H. J., & Djabali, K. (2005). Dermal fibroblasts in Hutchinson-Gilford progeria syndrome with the lamin A G608G mutation have dysmorphic nuclei and are hypersensitive to heat stress. BMC Cell Biology, 6(1), 27. https://doi.org/10.1186/1471-2121-6-27
Park, C.-W., & Ryu, K.-Y. (2014). Cellular ubiquitin pool dynamics and homeostasis. BMB Reports, 47(9), 475–482. https://doi.org/10.5483/BMBRep.2014.47.9.128
Park, J. S., Lee, J., Jung, E. S., Kim, M. H., Kim, I. B., Son, H., et al. (2019). Brain somatic mutations observed in Alzheimer’s disease associated with aging and dysregulation of tau phosphorylation. Nature Communications, 10(1), 3090. https://doi.org/10.1038/s41467-019-11000-7
Park, Y.-E., Hayashi, Y. K., Bonne, G., Arimura, T., Noguchi, S., Nonaka, I., & Nishino, I. (2009). Autophagic degradation of nuclear components in mammalian cells. Autophagy, 5(6), 795–804. https://doi.org/10.4161/auto.8901
Paulson, H. (2018). Repeat expansion diseases. Handb Clin Neurol., 2018(147), 105–123. https://doi.org/10.1016/B978-0-444-63233-3.00009-9.
Perez-Rodriguez, D., Kalyva, M., Leija-Salazar, M., Lashley, T., Tarabichi, M., Chelban, V., et al. (2019). Investigation of somatic CNVs in brains of synucleinopathy cases using targeted SNCA analysis and single cell sequencing. Acta Neuropathologica Communications, 7(1), 219. https://doi.org/10.1186/s40478-019-0873-5
Petr, M. A., Tulika, T., Carmona-Marin, L. M., & Scheibye-Knudsen, M. (2020). Protecting the aging genome. Trends in Cell Biology, 30(2), 117–132. https://doi.org/10.1016/j.tcb.2019.12.001
Pickles, S., Vigié, P., & Youle, R. J. (2018). Mitophagy and quality control mechanisms in mitochondrial maintenance. Current Biology, 28(4), R170–R185. https://doi.org/10.1016/j.cub.2018.01.004
Pirone, L., Caldinelli, L., di Lascio, S., di Girolamo, R., di Gaetano, S., Fornasari, D., et al. (2019). Molecular insights into the role of the polyalanine region in mediating <scp>PHOX</Scp> 2B aggregation. The FEBS Journal, 286(13), 2505–2521. https://doi.org/10.1111/febs.14841
Pohl, C., & Dikic, I. (2019). Cellular quality control by the ubiquitin-proteasome system and autophagy. Science, 366(6467), 818–822. https://doi.org/10.1126/science.aax3769
Poletto, M., Yang, Di., Fletcher, S. C., Vendrell, I., Fischer, R., Legrand, A. J., & Dianov, G. L. (2017). Modulation of proteostasis counteracts oxidative stress and affects DNA base excision repair capacity in ATM-deficient cells. Nucleic Acids Research, 45(17), 10042–10055. https://doi.org/10.1093/nar/gkx635
Polling, S., Ormsby, A. R., Wood, R. J., Lee, K., Shoubridge, C., Hughes, J. N., et al. (2015). Polyalanine expansions drive a shift into α-helical clusters without amyloid-fibril formation. Nature Structural & Molecular Biology, 22(12), 1008–1015. https://doi.org/10.1038/nsmb.3127
Potter, H., Chial, H. J., Caneus, J., Elos, M., Elder, N., Borysov, S., & Granic, A. (2019). Chromosome instability and mosaic aneuploidy in neurodegenerative and neurodevelopmental disorders. Frontiers in Genetics. https://doi.org/10.3389/fgene.2019.01092
Priestley, P., Baber, J., Lolkema, M. P., Steeghs, N., de Bruijn, E., Shale, C., et al. (2019). Pan-cancer whole-genome analyses of metastatic solid tumours. Nature, 575(7781), 210–216. https://doi.org/10.1038/s41586-019-1689-y
Prohaska, A., Racimo, F., Schork, A. J., Sikora, M., Stern, A. J., Ilardo, M., et al. (2019). Human disease variation in the light of population genomics. Cell, 177(1), 115–131. https://doi.org/10.1016/j.cell.2019.01.052
Quanz, M., Herbette, A., Sayarath, M., de Koning, L., Dubois, T., Sun, J.-S., & Dutreix, M. (2012). Heat shock protein 90α (Hsp90α) is phosphorylated in response to DNA damage and accumulates in repair foci. Journal of Biological Chemistry, 287(12), 8803–8815. https://doi.org/10.1074/jbc.M111.320887
Raimondi, S., Guglielmi, F., Giorgetti, S., di Gaetano, S., Arciello, A., Monti, D. M., et al. (2011). Effects of the known pathogenic mutations on the aggregation pathway of the amyloidogenic peptide of apolipoprotein A-I. Journal of Molecular Biology, 407(3), 465–476. https://doi.org/10.1016/j.jmb.2011.01.044
Rancati, G., Pavelka, N., Fleharty, B., Noll, A., Trimble, R., Walton, K., et al. (2008). Aneuploidy underlies rapid adaptive evolution of yeast cells deprived of a conserved cytokinesis motor. Cell, 135(5), 879–893. https://doi.org/10.1016/j.cell.2008.09.039
Ravanelli, S., den Brave, F., & Hoppe, T. (2020). Mitochondrial quality control governed by ubiquitin. Frontiers in Cell and Developmental Biology. https://doi.org/10.3389/fcell.2020.00270
Redler, R. L., Das, J., Diaz, J. R., & Dokholyan, N. V. (2016). Protein destabilization as a common factor in diverse inherited disorders. Journal of Molecular Evolution, 82(1), 11–16. https://doi.org/10.1007/s00239-015-9717-5
Revay, T., Oluwole, O., Kroetsch, T., & Allan King, W. (2017). In vivo and in vitro ageing results in accumulation of de Novo copy number variations in bulls. Scientific Reports, 7(1), 1631. https://doi.org/10.1038/s41598-017-01793-2
Roseaulin, L. C., Noguchi, C., & Noguchi, E. (2013). Proteasome-dependent degradation of replisome components regulates faithful DNA replication. Cell Cycle, 12(16), 2564–2569. https://doi.org/10.4161/cc.25692
Rovelet-Lecrux, A., Hannequin, D., Raux, G., le Meur, N., Laquerrière, A., Vital, A., et al. (2006). APP locus duplication causes autosomal dominant early-onset Alzheimer disease with cerebral amyloid angiopathy. Nature Genetics, 38(1), 24–26. https://doi.org/10.1038/ng1718
Rubinsztein, D. C., Codogno, P., & Levine, B. (2012). Autophagy modulation as a potential therapeutic target for diverse diseases. Nature Reviews Drug Discovery, 11(9), 709–730. https://doi.org/10.1038/nrd3802
Rudiger, S., Germeroth, L., Schneider-Mergener, J., & Bukau, B. (1997). Substrate specificity of the dnak chaperone determined by screening cellulose-bound peptide libraries. The EMBO Journal, 16(7), 1501–1507.
Russo, C., Osterburg, C., Sirico, A., Antonini, D., Ambrosio, R., Würz, J. M., et al. (2018). Protein aggregation of the P63 transcription factor underlies severe skin fragility in AEC syndrome. Proceedings of the National Academy of Sciences, 115(5), E906–E915. https://doi.org/10.1073/pnas.1713773115
Sanchez-Contreras, M., & Cardozo-Pelaez, F. (2017). Age-related length variability of polymorphic CAG repeats. DNA Repair, 49, 26–32. https://doi.org/10.1016/j.dnarep.2016.10.003
Sauna, Z. E., & Kimchi-Sarfaty, C. (2011). Understanding the contribution of synonymous mutations to human disease. Nature Reviews Genetics, 12(10), 683–691. https://doi.org/10.1038/nrg3051
Schaser, A. J., Osterberg, V. R., Dent, S. E., Stackhouse, T. L., Wakeham, C. M., Boutros, S. W., et al. (2019). Alpha-synuclein Is a DNA binding protein that modulates DNA repair with implications for lewy body disorders. Scientific Reports, 9(1), 10919. https://doi.org/10.1038/s41598-019-47227-z
Sciascia, N., Wei, Wu., Zong, D., Sun, Y., Wong, N., John, S., et al. (2020). Suppressing proteasome mediated processing of topoisomerase II DNA-protein complexes preserves genome integrity. ELife. https://doi.org/10.7554/eLife.53447
Sekimoto, T., Oda, T., Pozo, F. M., Murakumo, Y., Masutani, C., Hanaoka, F., & Yamashita, T. (2010). The molecular chaperone Hsp90 regulates accumulation of DNA polymerase η at replication stalling sites in UV-irradiated cells. Molecular Cell, 37(1), 79–89. https://doi.org/10.1016/j.molcel.2009.12.015
Sepe, S., Milanese, C., Gabriels, S., Derks, K. W., Payan-Gomez, C., van Ijcken, W. F., et al. (2016). Inefficient DNA repair is an aging-related modifier of Parkinson’s disease. Cell Reports, 15(9), 1866–1875. https://doi.org/10.1016/j.celrep.2016.04.071
Shendure, J., & Akey, J. M. (2015). The origins, determinants, and consequences of human mutations. Science, 349(6255), 1478–1483. https://doi.org/10.1126/science.aaa9119
Shepherd, C. E., Yang, Y., & Halliday, G. M. (2018). Region- and cell-specific aneuploidy in brain aging and neurodegeneration. Neuroscience, 374, 326–334. https://doi.org/10.1016/j.neuroscience.2018.01.050
Shigemizu, D., Fujimoto, A., Akiyama, S., Abe, T., Nakano, K., Boroevich, K. A., et al. (2013). A practical method to detect SNVs and indels from whole genome and exome sequencing data. Scientific Reports, 3(1), 2161. https://doi.org/10.1038/srep02161
Shiloh, Y. (2020). The cerebellar degeneration in ataxia-telangiectasia: A case for genome instability. DNA Repair, 95, 102950. https://doi.org/10.1016/j.dnarep.2020.102950
Solier, S., Kohn, K. W., Scroggins, B., Xu, W., Trepel, J., Neckers, L., & Pommier, Y. (2012). Heat shock protein 90 (HSP90), a substrate and chaperone of DNA-PK necessary for the apoptotic response. Proceedings of the National Academy of Sciences, 109(32), 12866–12872. https://doi.org/10.1073/pnas.1203617109
Solomon, J. P., Page, L. J., Balch, W. E., & Kelly, J. W. (2012). Gelsolin amyloidosis: Genetics, biochemistry, pathology and possible strategies for therapeutic intervention. Critical Reviews in Biochemistry and Molecular Biology, 47(3), 282–296. https://doi.org/10.3109/10409238.2012.661401
Sottile, M. L., & Nadin, S. B. (2018). Heat shock proteins and DNA repair mechanisms: An updated overview. Cell Stress and Chaperones, 23(3), 303–315. https://doi.org/10.1007/s12192-017-0843-4
Spielmann, M., Lupiáñez, D. G., & Mundlos, S. (2018). Structural variation in the 3D genome. Nature Reviews Genetics, 19(7), 453–467. https://doi.org/10.1038/s41576-018-0007-0
Spillantini, M. G., & Goedert, M. (2013). Tau pathology and neurodegeneration. The Lancet Neurology, 12(6), 609–622. https://doi.org/10.1016/S1474-4422(13)70090-5
Stingele, S., Stoehr, G., Peplowska, K., Cox, J., Mann, M., & Storchova, Z. (2012). Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells. Molecular Systems Biology, 8(1), 608. https://doi.org/10.1038/msb.2012.40
Suberbielle, E., Djukic, B., Evans, M., Kim, D. H., Taneja, P., Wang, X., et al. (2015). DNA repair factor BRCA1 depletion occurs in Alzheimer brains and impairs cognitive function in mice. Nature Communications, 6(1), 8897. https://doi.org/10.1038/ncomms9897
Sunshine, A. B., Ong, G. T., Nickerson, D. P., Carr, D., Murakami, C. J., Wasko, B. M., et al. (2016). Aneuploidy shortens replicative lifespan in Saccharomyces Cerevisiae. Aging Cell, 15(2), 317–324. https://doi.org/10.1111/acel.12443
Swami, M., Hendricks, A. E., Gillis, T., Massood, T., Mysore, J., Myers, R. H., & Wheeler, V. C. (2009). Somatic expansion of the Huntington’s disease CAG repeat in the brain is associated with an earlier age of disease onset. Human Molecular Genetics, 18(16), 3039–3047. https://doi.org/10.1093/hmg/ddp242
Sy, S.-H., Guo, Y., Lan, Y., Ng, H., & Huen, M.-Y. (2020). Preemptive homology-directed DNA repair fosters complex genomic rearrangements in hepatocellular carcinoma. Translational Oncology, 13(9), 100796. https://doi.org/10.1016/j.tranon.2020.100796
Talaei, F., van Praag, V. M., & Henning, R. H. (2013). Hydrogen sulfide restores a normal morphological phenotype in werner syndrome fibroblasts, attenuates oxidative damage and modulates MTOR pathway. Pharmacological Research, 74, 34–44. https://doi.org/10.1016/j.phrs.2013.04.011
Tamás, M., Sharma, S., Ibstedt, S., Jacobson, T., & Christen, P. (2014). Heavy metals and metalloids as a cause for protein misfolding and aggregation. Biomolecules, 4(1), 252–267. https://doi.org/10.3390/biom4010252
Tartaglia, G. G., Pechmann, S., Dobson, C. M., & Vendruscolo, M. (2007). Life on the edge: A link between gene expression levels and aggregation rates of human proteins. Trends in Biochemical Sciences, 32(5), 204–206. https://doi.org/10.1016/j.tibs.2007.03.005
Thibaudeau, T. A., Anderson, R. T., & Smith, D. M. (2018). A common mechanism of proteasome impairment by neurodegenerative disease-associated oligomers. Nature Communications, 9(1), 1097. https://doi.org/10.1038/s41467-018-03509-0
Tokuriki, N., & Tawfik, D. S. (2009). Stability effects of mutations and protein evolvability. Current Opinion in Structural Biology, 19(5), 596–604. https://doi.org/10.1016/j.sbi.2009.08.003
Tubbs, A., & Nussenzweig, A. (2017). Endogenous DNA damage as a source of genomic instability in cancer. Cell, 168(4), 644–656. https://doi.org/10.1016/j.cell.2017.01.002
Upton, K. R., Gerhardt, D. J., Samuel Jesuadian, J., Richardson, S. R., Sánchez-Luque, F. J., Bodea, G. O., et al. (2015). Ubiquitous L1 mosaicism in hippocampal neurons. Cell, 161(2), 228–239. https://doi.org/10.1016/j.cell.2015.03.026
Uversky, V. N. (2019). Intrinsically disordered proteins and their ‘mysterious’ (meta)physics. Frontiers in Physics. https://doi.org/10.3389/fphy.2019.00010
van den Bos, H., Spierings, D. C. J., Foijer, F., & Lansdorp, P. M. (2017). Does aneuploidy in the brain play a role in neurodegenerative disease? Chromosomal abnormalities—a hallmark manifestation of genomic instability. London: InTech.
van Ham TJ, Breitling R, Swertz MA, Nollen EA. (2009) Neurodegenerative diseases: Lessons from genome-wide screens in small model organisms. EMBO Molecular Medicine 1(8, 9):360–370. https://doi.org/10.1002/emmm.200900051
Vasquez, V., Mitra, J., Hegde, P. M., Pandey, A., Sengupta, S., Mitra, S., et al. (2017). Chromatin-bound oxidized α-synuclein causes strand breaks in neuronal genomes in in vitro models of Parkinson’s disease. Journal of Alzheimer’s Disease, 60(s1), S133–S150. https://doi.org/10.3233/JAD-170342
Vehvilainen, P., Koistinaho, J., & Gundars, G. (2014). Mechanisms of mutant SOD1 induced mitochondrial toxicity in amyotrophic lateral sclerosis. Frontiers in Cellular Neuroscience. https://doi.org/10.3389/fncel.2014.00126
Vendruscolo, M., Knowles, T. P. J., & Dobson, C. M. (2011). Protein solubility and protein homeostasis: A generic view of protein misfolding disorders. Cold Spring Harbor Perspectives in Biology, 3(12), a010454–a010454. https://doi.org/10.1101/cshperspect.a010454
Vessoni, A. T., Guerra, C. C., Kajitani, G. S., Nascimento, L. L., & Garcia, C. C. (2020). Cockayne syndrome: The many challenges and approaches to understand a multifaceted disease. Genetics and Molecular Biology. https://doi.org/10.1590/1678-4685-gmb-2019-0085
Vijg, J., & Dong, X. (2020). Pathogenic mechanisms of somatic mutation and genome mosaicism in aging. Cell, 182(1), 12–23. https://doi.org/10.1016/j.cell.2020.06.024
Vijg, J., & Suh, Y. (2013). Genome instability and aging. Annual Review of Physiology, 75(1), 645–668. https://doi.org/10.1146/annurev-physiol-030212-183715
Villela, D., Suemoto, C. K., Leite, R., Pasqualucci, C. A., Grinberg, L. T., Pearson, P., & Rosenberg, C. (2018). Increased DNA copy number variation mosaicism in elderly human brain. Neural Plasticity, 2018, 1–9. https://doi.org/10.1155/2018/2406170
Vogelstein, B., Papadopoulos, N., Velculescu, V. E., Zhou, S., Diaz, L. A., & Kinzler, K. W. (2013). Cancer genome landscapes. Science, 339(6127), 1546–1558. https://doi.org/10.1126/science.1235122
Walsh, I. M., Bowman, M. A., Soto, I. F., Santarriaga, A. R., & Clark, P. L. (2020). Synonymous codon substitutions perturb cotranslational protein folding in vivo and impair cell fitness. Proceedings of the National Academy of Sciences, 117(7), 3528–3534. https://doi.org/10.1073/pnas.1907126117
Walter, D., Hoffmann, S., Komseli, E.-S., Rappsilber, J., Gorgoulis, V., & Sørensen, C. S. (2016). SCFCyclin F-dependent degradation of CDC6 suppresses DNA re-replication. Nature Communications, 7(1), 10530. https://doi.org/10.1038/ncomms10530
Wang, H., Guo, W., Mitra, J., Hegde, P. M., Vandoorne, T., Eckelmann, B. J., et al. (2018). Mutant FUS causes DNA ligation defects to inhibit oxidative damage repair in amyotrophic lateral sclerosis. Nature Communications, 9(1), 3683. https://doi.org/10.1038/s41467-018-06111-6
Wang, P., Deng, J., Dong, J., Liu, J., Bigio, E. H., Mesulam, M., et al. (2019). TDP-43 induces mitochondrial damage and activates the mitochondrial unfolded protein response. PLOS Genetics, 15(5), e1007947. https://doi.org/10.1371/journal.pgen.1007947
Wang, Z., Zhu, W.-G., & Xingzhi, Xu. (2017). Ubiquitin-like Modifications in the DNA damage response. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 803–805, 56–75. https://doi.org/10.1016/j.mrfmmm.2017.07.001
Weischenfeldt, J., Symmons, O., Spitz, F., & Korbel, J. O. (2013). Phenotypic impact of genomic structural variation: Insights from and for human disease. Nature Reviews Genetics, 14(2), 125–138. https://doi.org/10.1038/nrg3373
Whitesell, L., & Lindquist, S. L. (2005). HSP90 and the chaperoning of cancer. Nature Reviews Cancer, 5(10), 761–772. https://doi.org/10.1038/nrc1716
Wilcken, R., Wang, G., Boeckler, F. M., & Fersht, A. R. (2012). Kinetic mechanism of P53 oncogenic mutant aggregation and its inhibition. Proceedings of the National Academy of Sciences, 109(34), 13584–13589. https://doi.org/10.1073/pnas.1211550109
Xie, J. L., & Jarosz, D. F. (2018). Mutations, protein homeostasis, and epigenetic control of genome integrity. DNA Repair, 71, 23–32. https://doi.org/10.1016/j.dnarep.2018.08.004
Yan, M., Shen, J., Person, M. D., Kuang, X., Lynn, W. S., Atlas, D., & Wong, P. K. Y. (2008). Endoplasmic reticulum stress and unfolded protein response in atm-deficient thymocytes and thymic lymphoma cells are attributable to oxidative stress. Neoplasia, 10(2), 160–167. https://doi.org/10.1593/neo.07935
Yi, K., & Young Seok, Ju. (2018). Patterns and mechanisms of structural variations in human cancer. Experimental & Molecular Medicine, 50(8), 98. https://doi.org/10.1038/s12276-018-0112-3
Yu, M., & Ren, B. (2017). The three-dimensional organization of mammalian genomes. Annual Review of Cell and Developmental Biology, 33(1), 265–289. https://doi.org/10.1146/annurev-cellbio-100616-060531
Zhang, L., Dong, X., Lee, M., Maslov, A. Y., Wang, T., & Vijg, J. (2019). Single-cell whole-genome sequencing reveals the functional landscape of somatic mutations in B lymphocytes across the human lifespan. Proceedings of the National Academy of Sciences, 116(18), 9014–9019. https://doi.org/10.1073/pnas.1902510116
Zhao, L., Vecchi, G., Vendruscolo, M., Körner, R., Hayer-Hartl, M., & Ulrich Hartl, F. (2019). The Hsp70 chaperone system stabilizes a thermo-sensitive subproteome in E. Coli. Cell Reports, 28(5), 1335-1345.e6. https://doi.org/10.1016/j.celrep.2019.06.081
Zhu, P. J., Khatiwada, S., Cui, Ya., Reineke, L. C., Dooling, S. W., Kim, J. J., et al. (2019). Activation of the ISR mediates the behavioral and neurophysiological abnormalities in down syndrome. Science, 366(6467), 843–849. https://doi.org/10.1126/science.aaw5185