{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T20:39:43Z","timestamp":1778099983598,"version":"3.51.4"},"reference-count":55,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2021,9,15]],"date-time":"2021-09-15T00:00:00Z","timestamp":1631664000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Nasu-Hakola Disease (NHD) is a recessively inherited systemic leukodystrophy disorder characterized by a combination of frontotemporal presenile dementia and lytic bone lesions. NHD is known to be genetically related to a structural defect of TREM2 and DAP12, two genes that encode for different subunits of the membrane receptor signaling complex expressed by microglia and osteoclast cells. Because of its rarity, molecular or proteomic studies on this disorder are absent or scarce, only case reports based on neuropsychological and genetic tests being reported. In light of this, the aim of this paper is to provide evidence on the potential of a label-free proteomic platform based on the Multidimensional Protein Identification Technology (MudPIT), combined with in-house software and on-line bioinformatics tools, to characterize the protein expression trends and the most involved pathways in NHD. The application of this approach on the Lymphoblastoid cells from a family composed of individuals affected by NHD, healthy carriers and control subjects allowed for the identification of about 3000 distinct proteins within the three analyzed groups, among which proteins anomalous to each category were identified. Of note, several differentially expressed proteins were associated with neurodegenerative processes. Moreover, the protein networks highlighted some molecular pathways that may be involved in the onset or progression of this rare frontotemporal disorder. Therefore, this fully automated MudPIT platform which allowed, for the first time, the generation of the whole protein profile of Lymphoblastoid cells from Nasu-Hakola subjects, could be a valid approach for the investigation of similar neurodegenerative diseases.<\/jats:p>","DOI":"10.3390\/ijms22189959","type":"journal-article","created":{"date-parts":[[2021,9,15]],"date-time":"2021-09-15T12:00:44Z","timestamp":1631707244000},"page":"9959","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["A Shotgun Proteomic Platform for a Global Mapping of Lymphoblastoid Cells to Gain Insight into Nasu-Hakola Disease"],"prefix":"10.3390","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5937-8604","authenticated-orcid":false,"given":"Antonella","family":"De Palma","sequence":"first","affiliation":[{"name":"Proteomics and Metabolomics Unit, Institute for Biomedical Technologies (ITB-CNR), 20054 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna Maria","family":"Agresta","sequence":"additional","affiliation":[{"name":"Proteomics and Metabolomics Unit, Institute for Biomedical Technologies (ITB-CNR), 20054 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5020-478X","authenticated-orcid":false,"given":"Simona","family":"Viglio","sequence":"additional","affiliation":[{"name":"Biochemistry Unit, Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0313-7083","authenticated-orcid":false,"given":"Rossana","family":"Rossi","sequence":"additional","affiliation":[{"name":"Proteomics and Metabolomics Unit, Institute for Biomedical Technologies (ITB-CNR), 20054 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1294-3121","authenticated-orcid":false,"given":"Maura","family":"D\u2019Amato","sequence":"additional","affiliation":[{"name":"Biochemistry Unit, Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7143-6229","authenticated-orcid":false,"given":"Dario","family":"Di Silvestre","sequence":"additional","affiliation":[{"name":"Proteomics and Metabolomics Unit, Institute for Biomedical Technologies (ITB-CNR), 20054 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4364-0393","authenticated-orcid":false,"given":"Pierluigi","family":"Mauri","sequence":"additional","affiliation":[{"name":"Proteomics and Metabolomics Unit, Institute for Biomedical Technologies (ITB-CNR), 20054 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paolo","family":"Iadarola","sequence":"additional","affiliation":[{"name":"Biochemistry Unit, Department of Biology and Biotechnologies \u201cL. Spallanzani\u201d, University of Pavia, 27100 Pavia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2021,9,15]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Alzheimer\u2019s Association (2017). Report 2017. Alzheimer\u2019s disease facts and figures. Alzheimer\u2019s Dementia, 13, 325\u2013373.","DOI":"10.1016\/j.jalz.2017.02.001"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"600","DOI":"10.1016\/j.arcmed.2012.11.003","article-title":"Epidemiology of dementias and Alzheimer\u2019s disease","volume":"43","author":"Castillo","year":"2012","journal-title":"Arch. Med. Res."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1111\/jnc.13654","article-title":"The clinical spectrum of sporadic and familial forms of frontotemporal dementia","volume":"138","author":"Woollacott","year":"2016","journal-title":"J. Neurochem."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1023\/B:CEMN.0000012721.08168.ee","article-title":"Nasu\u2013Hakola Disease (Polycystic Lipomembranous Osteodysplasia with Sclerosing Leukoencephalopathy\u2014PLOSL): A dementia associated with bone cystic lesions. From clinical to genetic and molecular aspects","volume":"24","author":"Bianchin","year":"2004","journal-title":"Cell. Mol. Neurobiol."},{"key":"ref_5","unstructured":"Adam, M.P., Ardinger, H.H., Pagon, R.A., Wallace, S.E., Bean, L.J.H., Mirzaa, G., and Amemiya, A. (2002). Polycystic Lipomembranous Osteodysplasia with Sclerosing Leukoencephalopathy. GeneReviews\u00ae [Internet], University of Washington, Seattle."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1016\/j.molmed.2017.03.008","article-title":"TREM2, microglia, and neurodegenerative diseases","volume":"23","author":"Yeh","year":"2017","journal-title":"Trends Mol. Med."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1086\/342259","article-title":"Mutations in two genes encoding different subunits of a receptor signaling complex result in an identical disease phenotype","volume":"71","author":"Paloneva","year":"2002","journal-title":"Am. J. Hum. Genet."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1502","DOI":"10.1212\/01.WNL.0000160304.00003.CA","article-title":"The genetic causes of basal ganglia calcification, dementia, and bone cysts: DAP12 and TREM2","volume":"64","author":"Klunemann","year":"2005","journal-title":"Neurology"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2617","DOI":"10.1111\/j.1460-9568.2004.03729.x","article-title":"Distribution and signaling of TREM2\/DAP12, the receptor system mutated in human polycystic lipomembraneous osteodysplasia with sclerosing leukoencephalopathy dementia","volume":"20","author":"Sessa","year":"2004","journal-title":"Eur. J. Neurosci."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1084\/jem.20030027","article-title":"DAP12\/TREM2 Deficiency results in impaired osteoclast differentiation and osteoporotic features","volume":"198","author":"Paloneva","year":"2003","journal-title":"J. Exp. Med."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Giuliano, S., Agresta, A.M., De Palma, A., Viglio, S., Mauri, P., Fumagalli, M., Iadarola, P., Montalbetti, L., Salvini, R., and Bardoni, A. (2014). Proteomic Analysis of lymphoblastoid cells from nasu-hakola patients: A step forward in our understanding of this neurodegenerative disorder. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0110073"},{"key":"ref_12","first-page":"38","article-title":"MudPIT: A powerful proteomics tool for discovery","volume":"3","author":"Schirmer","year":"2003","journal-title":"Discov. Med."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"2320","DOI":"10.1002\/pmic.201000479","article-title":"A comparative MudPIT analysis identifies different expression profiles in heart compartments","volume":"11","author":"Comunian","year":"2011","journal-title":"Proteomics"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/S0076-6879(08)02206-4","article-title":"A proteomic approach to the analysis of RNA degradosome composition in Escherichia coli","volume":"447","author":"Mauri","year":"2008","journal-title":"Methods Enzymol."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Roffia, V., De Palma, A., Lonati, C., Di Silvestre, D., Rossi, R., Mantero, M., Gatti, S., Dondossola, D., Valenza, F., and Mauri, P. (2018). Proteome investigation of rat lungs subjected to ex vivo perfusion (EVLP). Molecules, 23.","DOI":"10.3390\/molecules23123061"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1093\/bib\/bbn005","article-title":"Approaches to dimensionality reduction in proteomic biomarker studies","volume":"9","author":"Hilario","year":"2007","journal-title":"Brief. Bioinform."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1021\/acs.jproteome.8b00702","article-title":"Cytoscape StringApp: Network analysis and visualization of proteomics data","volume":"18","author":"Doncheva","year":"2019","journal-title":"J. Proteome Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1069","DOI":"10.1038\/nmeth.2212","article-title":"A travel guide to Cytoscape plugins","volume":"9","author":"Saito","year":"2012","journal-title":"Nat. Methods"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1007\/s00702-007-0800-y","article-title":"Glycolitic enzymes are targets of oxidation in aged human frontal cortex and oxidative damage of these proteins is increased in progressive supranuclear palsy","volume":"115","author":"Muntane","year":"2008","journal-title":"J. Neural Transm."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1016\/S0891-5849(02)00914-0","article-title":"Proteomic identification of oxidatively modified proteins in Alzheimer\u2019s disease brain. part I: Creatine kinase BB, glutamine synthase, and ubiquitin carboxy-terminal hydrolase L-1","volume":"33","author":"Castegna","year":"2002","journal-title":"Free Radic. Biol. Med."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1016\/j.neurobiolaging.2004.11.010","article-title":"Oxidative modification of proteins in the frontal cortex of Alzheimer\u2019s disease brain","volume":"27","author":"Korolainen","year":"2006","journal-title":"Neurobiol. Aging"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1007\/s00702-002-0772-x","article-title":"Cortical glucose metabolism is altered in aged transgenic Tg2576 mice that demonstrate Alzheimer plaque pathology","volume":"110","author":"Bigl","year":"2003","journal-title":"J. Neural Transm."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1239","DOI":"10.1016\/j.neurobiolaging.2005.07.001","article-title":"Proteomic identification of proteins specifically oxidized in caenorhabditis elegans expressing human A\u03b2(1\u201342): Implications for Alzheimer\u2019s disease","volume":"27","author":"Poon","year":"2006","journal-title":"Neurobiol. Aging"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1002\/jnr.20876","article-title":"Protective effect of D609 against amyloid-beta1\u201342-induced oxidative modification of neuronal proteins: Redox proteomics study","volume":"84","author":"Sultana","year":"2006","journal-title":"J. Neurosci. Res."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.exger.2017.07.004","article-title":"A cross-sectional comparison of brain glucose and ketone metabolism in cognitively healthy older adults, mild cognitive impairment and early Alzheimer\u2019s disease","volume":"107","author":"Croteau","year":"2018","journal-title":"Exp. Gerontol."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Jensen, N.J., Wodschow, H.Z., Nilsson, M., and Rungby, J. (2020). Effects of ketone bodies on brain metabolism and function in neurodegenerative diseases. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21228767"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"B\u0142aszczyk, J.W. (2020). Energy metabolism decline in the aging brain\u2014Pathogenesis of neurodegenerative disorders. Metabolites, 10.","DOI":"10.20944\/preprints202009.0539.v1"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1016\/j.biopsych.2010.06.031","article-title":"The neuroproteomics of schizophrenia","volume":"69","author":"English","year":"2011","journal-title":"Biol. Psychiatry"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1016\/j.ejphar.2004.07.039","article-title":"Proteomic approaches in brain research and neuropharmacology","volume":"500","author":"Vercauteren","year":"2004","journal-title":"Eur. J. Pharmacol."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Kazuno, A.-A., Ohtawa, K., Otsuki, K., Usui, M., Sugawara, H., Okazaki, Y., and Kato, T. (2013). Proteomic analysis of lymphoblastoid cells derived from monozygotic twins discordant for bipolar disorder: A preliminary study. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0053855"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1016\/j.nbd.2006.02.002","article-title":"Identification of protein biomarkers for schizophrenia and bipolar disorder in the postmortem prefrontal cortex using SELDI-TOF-MS ProteinChip profiling combined with MALDI-TOF-PSD-MS analysis","volume":"23","author":"Novikova","year":"2006","journal-title":"Neurobiol. Dis."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1038\/sj.mp.4000696","article-title":"Disease-specific alterations in frontal cortex brain proteins in schizophrenia, bipolar disorder, and major depressive disorder","volume":"5","author":"Sims","year":"2000","journal-title":"Mol. Psychiatry"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1189\/jlb.1206763","article-title":"Crosstalk among Jak-STAT, Toll-like receptor, and ITAM-dependent pathways in macrophage activation","volume":"82","author":"Hu","year":"2007","journal-title":"J. Leukoc. Biol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"2354","DOI":"10.18632\/oncotarget.6221","article-title":"Overexpression of TREM2 enhances glioma cell proliferation and invasion: A therapeutic target in human glioma","volume":"7","author":"Wang","year":"2016","journal-title":"Oncotarget"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"2612","DOI":"10.4049\/jimmunol.1102836","article-title":"TREM2 and \u03b2-Catenin regulate bone homeostasis by controlling the rate of osteoclastogenesis","volume":"188","author":"Otero","year":"2012","journal-title":"J. Immunol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1111\/j.1471-4159.2009.06130.x","article-title":"The surface-exposed chaperone, Hsp60, is an agonist of the microglial TREM2 receptor","volume":"110","author":"Stefano","year":"2009","journal-title":"J. Neurochem."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1016\/j.bone.2009.06.007","article-title":"Heat shock protein 60 causes osteoclastic bone resorption via toll-like receptor-2 in estrogen deficiency","volume":"45","author":"Koh","year":"2009","journal-title":"Bone"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/s13024-016-0085-4","article-title":"Frontotemporal dementia: Insights into the biological underpinnings of disease through gene co-expression network analysis","volume":"11","author":"Ferrari","year":"2016","journal-title":"Mol. Neurodegener."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Novellino, F., Sacc\u00e0, V., Donato, A., Zaffino, P., Spadea, M.F., Vismara, M., Arcidiacono, B., Malara, N., Presta, I., and Donato, G. (2020). Innate immunity: A common denominator between neurodegenerative and neuropsychiatric diseases. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21031115"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1186\/s40478-014-0143-5","article-title":"Traumatic brain injury causes selective, CD74-dependent peripheral lymphocyte activation that exacerbates neurodegeneration","volume":"2","author":"Tobin","year":"2014","journal-title":"Acta Neuropathol. Commun."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1007\/s00592-014-0616-9","article-title":"CD74 indicates microglial activation in experimental diabetic retinopathy and exogenous methylglyoxal mimics the response in normoglycemic retina","volume":"51","author":"Wang","year":"2014","journal-title":"Acta Diabetol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1002\/ana.24425","article-title":"Alzheimer\u2019s disease pathology is attenuated in a CD38-deficient mouse model","volume":"78","author":"Blacher","year":"2015","journal-title":"Ann. Neurol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"2869","DOI":"10.1172\/JCI28775","article-title":"PLC\u03b32 regulates osteoclastogenesis via its interaction with ITAM proteins and GAB2","volume":"116","author":"Mao","year":"2006","journal-title":"J. Clin. Investig."},{"key":"ref_44","first-page":"171","article-title":"Nasu-Hakola disease: A rare entity in Italy. Critical review of the literature","volume":"19","author":"Montalbetti","year":"2004","journal-title":"Funct. Neurol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"267","DOI":"10.31887\/DCNS.2016.18.3\/dgurwitz","article-title":"Human iPSC-derived neurons and lymphoblastoid cells for personalized medicine research in neuropsychiatric disorders","volume":"18","author":"Gurwitz","year":"2016","journal-title":"Dialogues Clin. Neurosci."},{"key":"ref_46","first-page":"71","article-title":"Neuropsychological tests and functional nuclear neuroimaging provide evidence of subclinical impairment in Nasu-Hakola disease heterozygotes","volume":"20","author":"Montalbetti","year":"2005","journal-title":"Funct. Neurol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1136\/jnnp.74.6.825-a","article-title":"An Italian family affected by Nasu-Hakola disease with a novel genetic mutation in the TREM2 gene","volume":"74","author":"Soragna","year":"2003","journal-title":"J. Neurol. Neurosurg. Psychiatry"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1002\/jms.578","article-title":"Acid-labile surfactant improves in-sodium dodecyl sulfate polyacrylamide gel protein digestion for matrix-assisted laser desorption\/ionization mass spectrometric peptide mapping","volume":"39","author":"Nomura","year":"2004","journal-title":"J. Mass Spectrom."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"D447","DOI":"10.1093\/nar\/gkv1145","article-title":"2016 update of the PRIDE database and its related tools","volume":"44","author":"Csordas","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"976","DOI":"10.1016\/1044-0305(94)80016-2","article-title":"An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database","volume":"5","author":"Eng","year":"1994","journal-title":"J. Am. Soc. Mass Spectrom."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1145\/331499.331504","article-title":"Data clustering","volume":"31","author":"Jain","year":"1999","journal-title":"ACM Comput. Surv."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1385\/MB:31:1:055","article-title":"Data clustering in life sciences","volume":"31","author":"Zhao","year":"2005","journal-title":"Mol. Biotechnol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: A software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Bader, G.D., and Hogue, C.W.V. (2003). An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinform., 4.","DOI":"10.1186\/1471-2105-4-2"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"3448","DOI":"10.1093\/bioinformatics\/bti551","article-title":"BiNGO: A Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks","volume":"21","author":"Maere","year":"2005","journal-title":"Bioinformatics"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/22\/18\/9959\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T06:59:59Z","timestamp":1760165999000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/22\/18\/9959"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,9,15]]},"references-count":55,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2021,9]]}},"alternative-id":["ijms22189959"],"URL":"https:\/\/doi.org\/10.3390\/ijms22189959","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,9,15]]}}}