Tissue specific LRRK2 interactomes reveal a distinct striatal functional unit
Mutations in LRRK2 are the most common genetic cause of Parkinson's disease. Despite substantial research efforts, the physiological and pathological role of this multidomain protein remains poorly defined. In this study, we used a systematic approach to construct the general protein-protein in...
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| Veröffentlicht in: | PLoS computational biology 2023-01, Vol.19 (1), p.e1010847-e1010847 |
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| creator | Zhao, Yibo Vavouraki, Nikoleta Lovering, Ruth C Escott-Price, Valentina Harvey, Kirsten Lewis, Patrick A Manzoni, Claudia |
| description | Mutations in LRRK2 are the most common genetic cause of Parkinson's disease. Despite substantial research efforts, the physiological and pathological role of this multidomain protein remains poorly defined. In this study, we used a systematic approach to construct the general protein-protein interactome around LRRK2, which was then evaluated taking into consideration the differential expression patterns and the co-expression behaviours of the LRRK2 interactors in 15 different healthy tissue types. The LRRK2 interactors exhibited distinct expression features in the brain as compared to the peripheral tissues analysed. Moreover, a high degree of similarity was found for the LRRK2 interactors in putamen, caudate and nucleus accumbens, thus defining a potential LRRK2 functional cluster within the striatum. The general LRRK2 interactome paired with the expression profiles of its members constitutes a powerful tool to generate tissue-specific LRRK2 interactomes. We exemplified the generation of the tissue-specific LRRK2 interactomes and explored the functions highlighted by the "core LRRK2 interactors" in the striatum in comparison with the cerebellum. Finally, we illustrated how the LRRK2 general interactome reported in this manuscript paired with the expression profiles can be used to trace the relationship between LRRK2 and specific interactors of interest, here focusing on the LRRK2 interactors belonging to the Rab protein family. |
| doi_str_mv | 10.1371/journal.pcbi.1010847 |
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Despite substantial research efforts, the physiological and pathological role of this multidomain protein remains poorly defined. In this study, we used a systematic approach to construct the general protein-protein interactome around LRRK2, which was then evaluated taking into consideration the differential expression patterns and the co-expression behaviours of the LRRK2 interactors in 15 different healthy tissue types. The LRRK2 interactors exhibited distinct expression features in the brain as compared to the peripheral tissues analysed. Moreover, a high degree of similarity was found for the LRRK2 interactors in putamen, caudate and nucleus accumbens, thus defining a potential LRRK2 functional cluster within the striatum. The general LRRK2 interactome paired with the expression profiles of its members constitutes a powerful tool to generate tissue-specific LRRK2 interactomes. We exemplified the generation of the tissue-specific LRRK2 interactomes and explored the functions highlighted by the "core LRRK2 interactors" in the striatum in comparison with the cerebellum. Finally, we illustrated how the LRRK2 general interactome reported in this manuscript paired with the expression profiles can be used to trace the relationship between LRRK2 and specific interactors of interest, here focusing on the LRRK2 interactors belonging to the Rab protein family.</description><identifier>ISSN: 1553-7358</identifier><identifier>ISSN: 1553-734X</identifier><identifier>EISSN: 1553-7358</identifier><identifier>DOI: 10.1371/journal.pcbi.1010847</identifier><identifier>PMID: 36716346</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Biology and Life Sciences ; Brain - metabolism ; Cancer ; Causes of ; Cerebellum ; Comparative analysis ; Corpus Striatum ; Dictionaries ; Genetic aspects ; Health aspects ; Humans ; Kinases ; Leucine-Rich Repeat Serine-Threonine Protein Kinase-2 - genetics ; LRRK2 protein ; Medical research ; Medicine and Health Sciences ; Medicine, Experimental ; Methods ; Movement disorders ; Mutation ; Mutation (Biology) ; Neostriatum ; Neurodegenerative diseases ; Nucleus Accumbens ; Parkinson Disease ; Parkinson's disease ; Phosphotransferases ; Physiological aspects ; Proteins ; Putamen ; Quality control ; Rab protein ; Research and Analysis Methods ; Tissue analysis ; Tissues</subject><ispartof>PLoS computational biology, 2023-01, Vol.19 (1), p.e1010847-e1010847</ispartof><rights>Copyright: © 2023 Zhao et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</rights><rights>COPYRIGHT 2023 Public Library of Science</rights><rights>2023 Zhao et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2023 Zhao et al 2023 Zhao et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c610t-f624b1794000f79af69e4ff1800909e24363772d3c196bdb3e4170a9dd2df3303</cites><orcidid>0000-0002-4520-8476</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9910798/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9910798/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79343,79344</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/36716346$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Andrade-Navarro, Miguel A.</contributor><creatorcontrib>Zhao, Yibo</creatorcontrib><creatorcontrib>Vavouraki, Nikoleta</creatorcontrib><creatorcontrib>Lovering, Ruth C</creatorcontrib><creatorcontrib>Escott-Price, Valentina</creatorcontrib><creatorcontrib>Harvey, Kirsten</creatorcontrib><creatorcontrib>Lewis, Patrick A</creatorcontrib><creatorcontrib>Manzoni, Claudia</creatorcontrib><title>Tissue specific LRRK2 interactomes reveal a distinct striatal functional unit</title><title>PLoS computational biology</title><addtitle>PLoS Comput Biol</addtitle><description>Mutations in LRRK2 are the most common genetic cause of Parkinson's disease. Despite substantial research efforts, the physiological and pathological role of this multidomain protein remains poorly defined. In this study, we used a systematic approach to construct the general protein-protein interactome around LRRK2, which was then evaluated taking into consideration the differential expression patterns and the co-expression behaviours of the LRRK2 interactors in 15 different healthy tissue types. The LRRK2 interactors exhibited distinct expression features in the brain as compared to the peripheral tissues analysed. Moreover, a high degree of similarity was found for the LRRK2 interactors in putamen, caudate and nucleus accumbens, thus defining a potential LRRK2 functional cluster within the striatum. The general LRRK2 interactome paired with the expression profiles of its members constitutes a powerful tool to generate tissue-specific LRRK2 interactomes. We exemplified the generation of the tissue-specific LRRK2 interactomes and explored the functions highlighted by the "core LRRK2 interactors" in the striatum in comparison with the cerebellum. Finally, we illustrated how the LRRK2 general interactome reported in this manuscript paired with the expression profiles can be used to trace the relationship between LRRK2 and specific interactors of interest, here focusing on the LRRK2 interactors belonging to the Rab protein family.</description><subject>Biology and Life Sciences</subject><subject>Brain - metabolism</subject><subject>Cancer</subject><subject>Causes of</subject><subject>Cerebellum</subject><subject>Comparative analysis</subject><subject>Corpus Striatum</subject><subject>Dictionaries</subject><subject>Genetic aspects</subject><subject>Health aspects</subject><subject>Humans</subject><subject>Kinases</subject><subject>Leucine-Rich Repeat Serine-Threonine Protein Kinase-2 - genetics</subject><subject>LRRK2 protein</subject><subject>Medical research</subject><subject>Medicine and Health Sciences</subject><subject>Medicine, Experimental</subject><subject>Methods</subject><subject>Movement disorders</subject><subject>Mutation</subject><subject>Mutation (Biology)</subject><subject>Neostriatum</subject><subject>Neurodegenerative diseases</subject><subject>Nucleus Accumbens</subject><subject>Parkinson Disease</subject><subject>Parkinson's disease</subject><subject>Phosphotransferases</subject><subject>Physiological aspects</subject><subject>Proteins</subject><subject>Putamen</subject><subject>Quality control</subject><subject>Rab protein</subject><subject>Research and Analysis Methods</subject><subject>Tissue analysis</subject><subject>Tissues</subject><issn>1553-7358</issn><issn>1553-734X</issn><issn>1553-7358</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNqVkk1vEzEQhlcIREvhHyBYiQscEuwdr72-IFUVHxEBpFDOltc7Do4262B7K_j3OM22alAvyAePx8-886EpiueUzCkI-nbjxzDofr4zrZtTQknDxIPilNY1zATUzcM79knxJMYNIdmU_HFxAlxQDoyfFl8uXYwjlnGHxllnyuVq9bkq3ZAwaJP8FmMZ8Ap1X-qyczG5waQypuB0yj475qfzuY5yHFx6Wjyyuo_4bLrPih8f3l9efJotv31cXJwvZ4ZTkmaWV6ylQjJCiBVSWy6RWUsbQiSRWDHgIETVgaGSt10LyKggWnZd1VkAAmfFy4PurvdRTZOIqhJCMEZ4wzOxOBCd1xu1C26rwx_ltVPXDh_WSofkTI-KWjDC1KxtAZhh2HRaMltZynjT1tpkrXdTtrHdYmdwSEH3R6LHP4P7qdb-SklJiZBNFng9CQT_a8SY1NZFg32vB_Tjdd0UADjZ1_3qH_T-7iZqrXMDbrA-5zV7UXUuQACtWL2n5vdQ-XS4dcYPaF32HwW8OQrITMLfaa3HGNXi--o_2K_HLDuwJvgYA9rb2VGi9st806TaL7OaljmHvbg799ugm-2Fv8_m7qk</recordid><startdate>20230101</startdate><enddate>20230101</enddate><creator>Zhao, Yibo</creator><creator>Vavouraki, Nikoleta</creator><creator>Lovering, Ruth C</creator><creator>Escott-Price, Valentina</creator><creator>Harvey, Kirsten</creator><creator>Lewis, Patrick A</creator><creator>Manzoni, Claudia</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>ISN</scope><scope>ISR</scope><scope>3V.</scope><scope>7QO</scope><scope>7QP</scope><scope>7TK</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AL</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>JQ2</scope><scope>K7-</scope><scope>K9.</scope><scope>LK8</scope><scope>M0N</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-4520-8476</orcidid></search><sort><creationdate>20230101</creationdate><title>Tissue specific LRRK2 interactomes reveal a distinct striatal functional unit</title><author>Zhao, Yibo ; Vavouraki, Nikoleta ; Lovering, Ruth C ; Escott-Price, Valentina ; Harvey, Kirsten ; Lewis, Patrick A ; Manzoni, Claudia</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c610t-f624b1794000f79af69e4ff1800909e24363772d3c196bdb3e4170a9dd2df3303</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Biology and Life Sciences</topic><topic>Brain - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PLoS computational biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhao, Yibo</au><au>Vavouraki, Nikoleta</au><au>Lovering, Ruth C</au><au>Escott-Price, Valentina</au><au>Harvey, Kirsten</au><au>Lewis, Patrick A</au><au>Manzoni, Claudia</au><au>Andrade-Navarro, Miguel A.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Tissue specific LRRK2 interactomes reveal a distinct striatal functional unit</atitle><jtitle>PLoS computational biology</jtitle><addtitle>PLoS Comput Biol</addtitle><date>2023-01-01</date><risdate>2023</risdate><volume>19</volume><issue>1</issue><spage>e1010847</spage><epage>e1010847</epage><pages>e1010847-e1010847</pages><issn>1553-7358</issn><issn>1553-734X</issn><eissn>1553-7358</eissn><abstract>Mutations in LRRK2 are the most common genetic cause of Parkinson's disease. Despite substantial research efforts, the physiological and pathological role of this multidomain protein remains poorly defined. In this study, we used a systematic approach to construct the general protein-protein interactome around LRRK2, which was then evaluated taking into consideration the differential expression patterns and the co-expression behaviours of the LRRK2 interactors in 15 different healthy tissue types. The LRRK2 interactors exhibited distinct expression features in the brain as compared to the peripheral tissues analysed. Moreover, a high degree of similarity was found for the LRRK2 interactors in putamen, caudate and nucleus accumbens, thus defining a potential LRRK2 functional cluster within the striatum. The general LRRK2 interactome paired with the expression profiles of its members constitutes a powerful tool to generate tissue-specific LRRK2 interactomes. We exemplified the generation of the tissue-specific LRRK2 interactomes and explored the functions highlighted by the "core LRRK2 interactors" in the striatum in comparison with the cerebellum. Finally, we illustrated how the LRRK2 general interactome reported in this manuscript paired with the expression profiles can be used to trace the relationship between LRRK2 and specific interactors of interest, here focusing on the LRRK2 interactors belonging to the Rab protein family.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>36716346</pmid><doi>10.1371/journal.pcbi.1010847</doi><tpages>e1010847</tpages><orcidid>https://orcid.org/0000-0002-4520-8476</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Biology and Life Sciences Brain - metabolism Cancer Causes of Cerebellum Comparative analysis Corpus Striatum Dictionaries Genetic aspects Health aspects Humans Kinases Leucine-Rich Repeat Serine-Threonine Protein Kinase-2 - genetics LRRK2 protein Medical research Medicine and Health Sciences Medicine, Experimental Methods Movement disorders Mutation Mutation (Biology) Neostriatum Neurodegenerative diseases Nucleus Accumbens Parkinson Disease Parkinson's disease Phosphotransferases Physiological aspects Proteins Putamen Quality control Rab protein Research and Analysis Methods Tissue analysis Tissues |
| title | Tissue specific LRRK2 interactomes reveal a distinct striatal functional unit |
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