{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T12:58:37Z","timestamp":1790945917936,"version":"4.1.0"},"reference-count":28,"publisher":"American Chemical Society (ACS)","issue":"10","license":[{"start":{"date-parts":[[2027,9,16]],"date-time":"2027-09-16T00:00:00Z","timestamp":1821052800000},"content-version":"vor","delay-in-days":365,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"name":"AviadoBio Ltd"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Unequivocal identification and reproducible quantitation of proteins are key components of research and development activity in drug discovery. In some cases, the target protein might be a protein highly conserved across species; antibody-based assays are not specific enough to discriminate between orthologues, thus forcing drug developers to use multiple analytical platforms across preclinical models. Here, we present a modular mass spectrometry-based assay for the analysis of orthologous proteins across species in the context of translational science using ataxin-2 (ATXN2) as an example. Instead of relying on recombinant proteins, we applied rational peptide design to target human, mouse, human\/pig\/non-human primates (NHP), or pan-species regions of the full-length protein. Specificity and sensitivity of the method were proven in wild-type and transgenic models. Dose\u2013response upon treatment with different doses of an adeno-associated virus (AAV)-delivering microRNA (miRNA) targeting ATXN2 showed that knock-down at the transcript level was consistent with downregulation at the protein level, confirming the assay suitability for target engagement evaluation. Furthermore, the data presented here indicate that this method is readily transferable to minipigs, ensuring analytical continuity across preclinical studies. More broadly, this work provides a translational blueprint that can be adapted to other orthologues, reducing cost and timeline in drug development.<\/jats:p>","DOI":"10.1021\/acs.jproteome.5c01164","type":"journal-article","created":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T01:02:15Z","timestamp":1789606935000},"page":"5091-5102","source":"Crossref","is-referenced-by-count":0,"title":["Development\nof a Translational Assay for Identification\nand Quantitation of Orthologous Proteins to Aid Drug Development in\nPreclinical Models"],"prefix":"10.1021","volume":"25","author":[{"given":"Blandine","family":"Rougemont","sequence":"first","affiliation":[{"name":"Inoviv , Fox Court, 14 Gray\u2019s Inn Road , ,","place":["London, U.K., WC1X 8HN"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julie","family":"Borgel","sequence":"additional","affiliation":[{"name":"Inoviv , Fox Court, 14 Gray\u2019s Inn Road , ,","place":["London, U.K., WC1X 8HN"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zoe","family":"Walker","sequence":"additional","affiliation":[{"name":"AviadoBio Ltd , 20 Water Street , ,","place":["London, U.K., E14 5GX"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Irene","family":"Zubiri","sequence":"additional","affiliation":[{"name":"Inoviv , Fox Court, 14 Gray\u2019s Inn Road , ,","place":["London, U.K., WC1X 8HN"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4767-6142","authenticated-orcid":true,"given":"Ronan","family":"O\u2019Cualain","sequence":"additional","affiliation":[{"name":"Inoviv , Fox Court, 14 Gray\u2019s Inn Road , ,","place":["London, U.K., WC1X 8HN"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Neda","family":"Ali Mohammadi Nafchi","sequence":"additional","affiliation":[{"name":"Maurice Wohl Clinical Neuroscience Institute , 5 Cutcombe Road , ,","place":["London, U.K., SE5 9RT"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher E.","family":"Shaw","sequence":"additional","affiliation":[{"name":"AviadoBio Ltd , 20 Water Street , ,","place":["London, U.K., E14 5GX"]},{"name":"Maurice Wohl Clinical Neuroscience Institute , 5 Cutcombe Road , ,","place":["London, U.K., SE5 9RT"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ernestas","family":"Sirka","sequence":"additional","affiliation":[{"name":"Inoviv , Fox Court, 14 Gray\u2019s Inn Road , ,","place":["London, U.K., WC1X 8HN"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Isaac","sequence":"additional","affiliation":[{"name":"AviadoBio Ltd , 20 Water Street , ,","place":["London, U.K., E14 5GX"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlos J.","family":"Miranda","sequence":"additional","affiliation":[{"name":"AviadoBio Ltd , 20 Water Street , ,","place":["London, U.K., E14 5GX"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3296-2514","authenticated-orcid":true,"given":"Anna","family":"Ettorre","sequence":"additional","affiliation":[{"name":"AviadoBio Ltd , 20 Water Street , ,","place":["London, U.K., E14 5GX"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,16]]},"reference":[{"key":"2026100208413865400_cit1","doi-asserted-by":"crossref","DOI":"10.1201\/9780429202872-1","article-title":"Definitions\nand conceptual framework of biomarkers in precision medicine","volume-title":"Handbook of Biomarkers and Precision Medicine","author":"Carini","year":"2019"},{"issue":"1","key":"2026100208413865400_cit2","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1038\/nri1999","article-title":"Identifying and hurdling\nobstacles to translational research","volume":"7","author":"Sabroe","year":"2007","journal-title":"Nat. Rev.\nImmunol."},{"issue":"6","key":"2026100208413865400_cit3","doi-asserted-by":"publisher","first-page":"393","DOI":"10.4103\/ijp.ijp_860_22","article-title":"Translational research:\nBridging the gap between preclinical and clinical research","volume":"54","author":"Mahalmani","year":"2022","journal-title":"Indian J. Pharmacol."},{"key":"2026100208413865400_cit4","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1002\/humu.10151","article-title":"Dynamics of\nCAG repeat loci revealed by the analysis of their variability","volume":"21","author":"Andre\u0301s","year":"2003","journal-title":"Hum. Mutat."},{"key":"2026100208413865400_cit5","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1038\/s41419-024-06812-5","article-title":"The polyglutamine\nprotein ATXN2: from its molecular functions to its involvement in\ndisease","volume":"15","author":"Costa","year":"2024","journal-title":"Cell Death Dis."},{"key":"2026100208413865400_cit6","doi-asserted-by":"publisher","first-page":"1069","DOI":"10.1038\/nature09320","article-title":"Ataxin-2 intermediate-length\npolyglutamine expansions are associated with increased risk for ALS","volume":"466","author":"Elden","year":"2010","journal-title":"Nature"},{"issue":"4","key":"2026100208413865400_cit7","doi-asserted-by":"publisher","first-page":"958","DOI":"10.1016\/j.cell.2018.03.025","article-title":"Stress Granule Assembly\nDisrupts Nucleocytoplasmic Transport","volume":"173","author":"Zhang","year":"2018","journal-title":"Cell"},{"key":"2026100208413865400_cit8","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1038\/ng.2853","article-title":"Therapeutic modulation\nof eIF2alpha phosphorylation rescues TDP-43 toxicity in amyotrophic\nlateral sclerosis disease models","volume":"46","author":"Kim","year":"2014","journal-title":"Nat. Genet."},{"key":"2026100208413865400_cit9","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1038\/s41593-017-0022-z","article-title":"Reducing the RNA binding\nprotein TIA1 protects against tau-mediated neurodegeneration in vivo","volume":"21","author":"Apicco","year":"2018","journal-title":"Nat. Neurosci."},{"key":"2026100208413865400_cit10","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1038\/nature22038","article-title":"Therapeutic reduction\nof ataxin-2 extends lifespan and reduces pathology in TDP-43 mice","volume":"544","author":"Becker","year":"2017","journal-title":"Nature"},{"issue":"4","key":"2026100208413865400_cit11","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1005182","article-title":"Ataxin-2 regulates RGS8\ntranslation in a new BAC-SCA2 transgenic mouse model","volume":"11","author":"Dansithong","year":"2015","journal-title":"PLoS Genet."},{"issue":"1","key":"2026100208413865400_cit12","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1016\/j.bbrc.2005.10.186","article-title":"Generation\nand characterization\nof Sca2 (ataxin-2) knockout mice","volume":"339","author":"Kiehl","year":"2006","journal-title":"Biochem. Biophys.\nRes. Commun."},{"issue":"3","key":"2026100208413865400_cit13","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1002\/mas.21540","article-title":"The Skyline ecosystem:\nInformatics for quantitative mass spectrometry proteomics","volume":"39","author":"Pino","year":"2020","journal-title":"Mass Spectrom. Rev."},{"issue":"8","key":"2026100208413865400_cit14","doi-asserted-by":"publisher","first-page":"711","DOI":"10.1038\/nrd1470","article-title":"Can the pharmaceutical industry reduce attrition rates?","volume":"3","author":"Kola","year":"2004","journal-title":"Nat. Rev. Drug Discovery"},{"key":"2026100208413865400_cit15","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1038\/nrd3078","article-title":"How to improve R&D\nproductivity: the pharmaceutical industry\u2019s grand challenge","volume":"9","author":"Paul","year":"2010","journal-title":"Nat. Rev. Drug Discovery"},{"key":"2026100208413865400_cit16","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1016\/j.jhealeco.2016.01.012","article-title":"Innovation in the pharmaceutical\nindustry: New estimates of R&D costs","volume":"47","author":"DiMasi","year":"2016","journal-title":"J.\nHealth Econ."},{"issue":"2","key":"2026100208413865400_cit17","doi-asserted-by":"publisher","first-page":"11","DOI":"10.3390\/jpbi3020011","article-title":"Identification\nand Development of New Medicines","volume":"3","author":"Vita","year":"2026","journal-title":"J. Pharm.\nBioTech Ind."},{"issue":"9\u201310","key":"2026100208413865400_cit18","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1016\/j.drudis.2011.12.020","article-title":"Can the flow of medicines\nbe improved? Fundamental pharmacokinetic and pharmacological principles\ntoward improving Phase II survival","volume":"17","author":"Morgan","year":"2012","journal-title":"Drug Discovery\nToday"},{"issue":"5","key":"2026100208413865400_cit19","doi-asserted-by":"publisher","first-page":"998","DOI":"10.1016\/j.bmcl.2014.12.076","article-title":"Target engagement\nin lead generation","volume":"25","author":"Durham","year":"2015","journal-title":"Bioorg. Med. Chem. Lett."},{"issue":"5","key":"2026100208413865400_cit20","doi-asserted-by":"publisher","first-page":"1728","DOI":"10.1074\/mcp.M115.056770","article-title":"Ataxin-2 (Atxn2)-Knock-Out\nMice Show Branched Chain Amino Acids and Fatty Acids Pathway Alterations","volume":"15","author":"Meierhofer","year":"2016","journal-title":"Mol. Cell. Proteomics"},{"key":"2026100208413865400_cit21","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1186\/s42466-019-0025-1","article-title":"New alternative splicing\nvariants of the ATXN2 transcript","volume":"1","author":"Lastres-Becker","year":"2019","journal-title":"Neurol Res.\nPract."},{"issue":"3","key":"2026100208413865400_cit22","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1006\/geno.1997.5131","article-title":"Genomic\nstructure of\nthe human gene for spinocerebellar ataxia type 2 (SCA2) on chromosome\n12q24.1","volume":"47","author":"Sahba","year":"1998","journal-title":"Genomics"},{"issue":"1","key":"2026100208413865400_cit23","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1016\/S0378-1119(01)00402-4","article-title":"Identification of alternative\nsplicing of spinocerebellar ataxia type 2 gene","volume":"267","author":"Affaitati","year":"2001","journal-title":"Gene"},{"issue":"8","key":"2026100208413865400_cit24","doi-asserted-by":"publisher","first-page":"1301","DOI":"10.1093\/hmg\/7.8.1301","article-title":"The mouse SCA2 gene:\ncDNA sequence, alternative splicing and protein expression","volume":"7","author":"Nechiporuk","year":"1998","journal-title":"Hum. Mol. Genet."},{"issue":"4","key":"2026100208413865400_cit25","doi-asserted-by":"publisher","first-page":"200","DOI":"10.1038\/nchembio.1211","article-title":"Determining target engagement in\nliving systems","volume":"9","author":"Simon","year":"2013","journal-title":"Nat. Chem. Biol."},{"issue":"4","key":"2026100208413865400_cit26","doi-asserted-by":"publisher","first-page":"1615","DOI":"10.3390\/ijms22041615","article-title":"Targeting for Success: Demonstrating\nProof-of-Concept with Mechanistic Early Phase Clinical Pharmacology\nStudies for Disease-Modification in Neurodegenerative Disorders","volume":"22","author":"Vissers","year":"2021","journal-title":"Int. J. Mol. Sci."},{"issue":"10","key":"2026100208413865400_cit27","doi-asserted-by":"publisher","first-page":"630","DOI":"10.1038\/s41576-020-0258-4","article-title":"mRNAs, proteins and\nthe emerging principles of gene\nexpression control","volume":"21","author":"Buccitelli","year":"2020","journal-title":"Nat. Rev. Genet."},{"key":"2026100208413865400_cit28","doi-asserted-by":"publisher","first-page":"108720","DOI":"10.1016\/j.biotechadv.2025.108720","article-title":"Gene expression and protein abundance:\nJust how associated are these molecular traits?","volume":"86","author":"Samih","year":"2026","journal-title":"Biotechnol. Adv."}],"container-title":["Journal of Proteome Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jproteome.5c01164","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jprobs\/article-pdf\/25\/10\/5091\/68538883\/acs.jproteome.5c01164.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jprobs\/article-pdf\/25\/10\/5091\/68538883\/acs.jproteome.5c01164.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T12:51:40Z","timestamp":1790945500000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jprobs\/article\/25\/10\/5091\/5431722\/Development-of-a-Translational-Assay-for"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,16]]},"references-count":28,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2026,9,16]]},"published-print":{"date-parts":[[2026,10,2]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jproteome.5c01164","relation":{},"ISSN":["1535-3893","1535-3907"],"issn-type":[{"value":"1535-3893","type":"print"},{"value":"1535-3907","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,16]]}}}