Publications

Selected Publications

Sung YJ, Yang C, Norton J, Johnson M, Fagan A, Bateman RJ, Perrin RJ, Morris JC, Farlow MR, Chhatwal JP, Schofield PR, Chui H, Wang F, Karch C, Schindler SE, Rhinn H, Johnson ECB, Oh HS, Rutledge JE, Dammer EB, Seyfried NT, Wyss-Coray T, Cruchaga C. Proteomics of brain, CSF, and plasma identifies molecular signatures for distinguishing sporadic and genetic Alzheimer’s disease. Sci Transl Med. 2023 Jul 5;15(703):eabq5923. doi: 10.1126/scitranslmed.abq5923. Epub 2023 Jul 5.PMID: 37406134 Read the news for this paper on Medical XPress, Genome Web, or AlzForum.
Yang C, Farias FHG, Ibanez L, Suhy A, Sadler B, Fernandez MV, Wang F, Bradley JL, Eiffert B, Bahena JA, Budde JP, Li Z, Dube U, Sung YJ, Mihindukulasuriya KA, Morris JC, Fagan AM, Perrin RJ,, Rhinn H, Cruchaga C. Genomic atlas of the proteome from brain, CSF and plasma prioritizes proteins implicated in neurological disorders. Nat Neurosci. 2021 Jul 8. doi: 10.1038/s41593-021-00886-6. Epub ahead of print. PMID: 34239129. Read the news for this paper here
Yuetiva Deming, Fabia Filipello, Francesca Cignarella, Claudia Cantoni, Simon Hsu, Robert Mikesell, Zeran Li, Jorge L Del-Aguila, Umber Dube, Fabiana Geraldo Farias, Joseph Bradley, John Budde, Laura Ibanez, Maria Victoria Fernandez,…, Christian Haass, Thomas J Brett, Celeste M. Karch, Laura Piccio, Carlos Cruchaga. The MS4A gene cluster is a key regulator of soluble TREM2 and Alzheimer disease risk. Sci Transl Med. 2019 Aug 14;11(505). pii: eaau2291. doi: 10.1126/scitranslmed.aau2291. PMID: 31413141 Read the news for this paper here
Cruchaga C, Karch CM, Jin SC, Cai Y, Guerreiro R, Norton J, Budde J, Bertelsen S, Jeng AT, Cooper B, Skorupa T, Carrell D, Levitch D, Hsu S, Choi J, Ryten M; UK Brain Expression Consortium, … Cairns N, Morris JC, Kauwe JS, Goate AM. Rare coding variants in the phospholipase D3 gene confer risk for Alzheimer’s disease. Nature 2014; 505(7484):550-4. PMCID: PMC4050701

2025

1. Euesden J, Ali M, Robins C, Surendran P, Gormley P, Alzheimer’s Disease Neuroimaging Initiative (ADMI), Pulford D, Cruchaga C. Patient stratification by genetic risk in Alzheimer’s disease is only effective in the presence of phenotypic heterogeneity. PLoS ONE 20(1): e0310977 https:doi.org/10.1371/journal.pone.0310977

2024

1. Wang C, Yang C, Western D, Ali M, Wang Y, Phuah CL, Budde J, Wang L, Gorijala P, Timsina J, Ruiz A, Pastor P, Fernandez MV; Dominatly Inherited Alzheimer Network (DIAN); Alzheimer’s Disease Neuroimaging Initiative (ADNI) Panyard DJ, Engelman CD, Deming Y, Boada M, Cano A, Garcia-Gonzalez P, Graff-Radford NR, Mori H, Lee JH, Perrin RJ, Ibanez L, Sung YJ, Cruchaga C. Genetic architecture of cerebrospinal fluid and brain metabolite levels and the genetic colocalization of metabolites with human traits. Nat Genet. 2024 Dec: 56(12):2685-2695. doi: 10.1038/s41588-024-01973-7. Epub 2024 Nov 11. PMID: 39528826

2. Western D, Timsina J, Wang L, Wang C, Yang C, Phillips B, Wang Y, Liu M, Ali M, Beric A, Gorijala P, Kohlfeld P, Budde J, Levey Al, Morris JC, Perrin RJ, Ruiz A, Marquie M, Boada M, de Rojas I, Rutledge J, Oh H, Wilson, EN, Le Guen Y, Reus LM, Tijms B, Visser PJ, van der Lee SJ Pijnenburg YAL, Teunissen CE, Del Campo Milan M, Alvarez I, Aguilar M; Dominatly Inherited Alzheimer Network (DIAN); Alzheier’s Disease Neuroimaging Initiative (ADNI) Greicius MD, Pastor P, Pulford DJ, Ibanez L, Wyss-Coray T, Sung-YJ, Cruchaga C. Proteogenomic analysis of human cerebrospinal fluid identifies neurologically relevant regulation and implicates causal proteins for Alzheimer’s disease. Nat Genet. 2024 Dec. 56(12):2672-2684. doi: 10.1038/s41588-024-01972-8. Epub 2024 Nov 11. PMID: 39528825

3. Ibanez L, Liu M, Beric A, Timsina J, Kohlfeld P, Bergmann K, Lowery J, Sykora N, Sanchez-Montejo B, Brock W, Budde JP, Bateman RJ, Barthelemy N, Schindler SE, Holtzman DM, Benzinger TLS, Xiong C, Tarawneh R, Moulder K, Morris JC, Sung YJ, Cruchaga C. Benchmarking of a multi-biomarker low-volume panel for Alzheimer’s disease and related dementia research. Alzheimers Dement 2024 Nov 22. doi: 10.1002/alz.14413. PMID: 39575871

4. Shen Y, Timsina J, Heo G, Beric A, Ali M, Wang C, Yang C, Wang Y, Western D, Liu M, Gorijala P, Budde J, Do A, Liu H, Gordon B, Llibre-Guerra J, Joseph-Mathurin N, Perrin RJ, Maschi D, Wyss-Coray T, Pastor P, Renton A, Surace E, Johnson ECB, Levey A, Alvarez I, Levin J, Ringman J, Allegri RF, Seyfried N, Day G, Wu Q, Fernandez MV, Tarawneh R, McDade E, Morris J, Bateman RJ, Goate A, Dominantly Inherited Alzheimer Network, Ibanez L, Sung YS, Cruchaga C. CSF Proteomics identifies early changes in autosomal dominant Alzheimer’s disease. Cell 2024 Oct 31. 187(22):6309-6326.e15. doi: 10.1016/j.cell2024.08.049. PMID: 39332414

5. Marsh TW, Western D, Timsina J, Gorijala P, Yang C, Pastor P, Liu M, Morris JC, Bateman RJ, Schindler SE, Sung YJ; Dominantly Inherited Alzheimer Network; Cruchaga C. A genetic and proteomic comparison of key AD biomarkers across tissues. Alzheimers Dement. 2024 Jul 30. doi: 10.1002/alz.14139. PMID: 39077866

6. Fernandez MV, Liu M, Beric A, Johnson M, Cetin A, Patel M, Budde J, Kohlfeld P, Bergmann K, Lowery J, Flynn A, Brock W, Sanchez Montejo B, Gentsch J, Sykora N, Norton J, Gentsch J, Valdez O, Gorijala P, Sanford J, Sun Y, Wang C, Western D, Timsina J, Mangetti Goncalves T, Do AN, Sung YJ, Zhao G, Morris JC, Moulder K, Holtzman DM, Bateman RJ, Karch C, Hassenstab J, Xiong C, Schindler SE, Balls-Berry JJ, Benzinger TLS, Perrin RJ, Denny A, Snider BJ, Stark SL, Ibanez L, Cruchaga C. Genetic and multi-omic resources for Alzheimer disease and related dementia from the Knight Alzheimer Disease Research Center. Sci Data. 2024 Jul 12;11(1):768. doi: 10.1038/s41597-024-03485-9.PMID: 38997326.

7. Timsina J, Dinasarapu A, Kilic-Berkmen G, Budde J, Sung YJ, Klein AM, Cruchaga C, Jinnah HA. Blood-Based Proteomics for Adult-Onset Focal Dystonias. Ann Neurol. 2024 Jul;96(1):110-120. doi: 10.1002/ana.26929. Epub 2024 Apr 5.PMID: 38578115.

8. Timsina J, Ali M, Do A, Wang L, Western D, Sung YJ, Cruchaga C.Harmonization of CSF and imaging biomarkers in Alzheimer’s disease: Need and practical applications for genetics studies and preclinical classification. Neurobiol Dis. 2024 Jan;190:106373. doi: 10.1016/j.nbd.2023.106373. Epub 2023 Dec 9. PMID: 38072165

9. Wang L, Nykänen NP, Western D, Gorijala P, Timsina J… Graff-Radford N, Mori H, Goate A, Levin J, Sung YJ, Cruchaga C.Proteo-genomics of soluble TREM2 in cerebrospinal fluid provides novel insights and identifies novel modulators for Alzheimer’s disease. Mol Neurodegener. 2024 Jan 3;19(1):1. doi: 10.1186/s13024-023-00687-4.PMID: 38172904

10. Daniel Western, Jigyasha Timsina, Lihua Wang, Ciyang Wang, Chengran Yang, Bridget Phillips, Yueyao Wang, Menghan Liu, Muhammad Ali, Aleksandra Beric, Priyanka Gorijala, Pat Kohlfeld, John Budde, Allan I. Levey, John C. Morris, Richard J. Perrin, Agustin Ruiz, Marta Marquié, Mercè Boada, Itziar de Rojas, Jarod Rutledge, Hamilton Oh, Edward N. Wilson, Yann Le Guen, Lianne M. Reus, Betty Tijms, Pieter Jelle Visser, Sven J. van der Lee, Yolande A.L. Pijnenburg, Charlotte E. Teunissen, Marta del Campo Milan, Ignacio Alvarez, Miquel Aguilar, Dominantly Inherited Alzheimer Network (DIAN), the Alzheimer’s Disease Neuroimaging Initiative (ADNI), Michael D. Greicius, Pau Pastor, David J. Pulford, Laura Ibanez, Tony Wyss-Coray, Yun Ju Sung, Carlos Cruchaga. Proteogenomic analysis of human cerebrospinal fluid identifies neurologically relevant regulation and informs causal proteins for Alzheimer’s disease. Nat Genet. 2024 Nov 11: doi: 10.1038/s41588-024-01972-8. PMID: 39528825

11. Carlos Cruchaga, Chengran Yang, Priyanka Gorijala, Jigyasha Timsina, Lihua Wang, Menghan Liu, Ciyang Wang, William Brock, Yueyao Wang, Yun Ju Sung, Carlos Cruchaga. European and African stratified plasma protein-QTL and metabolite-QTL analyses identify ancestry-specific T2D effector proteins and metabolites. 2024 Jul 22:rs.3.rs-3617016. doi: 10.21203/rs.3.rs-3617016/v1.PMID: 39108494.

12. Ciyang Wang, Dan Western, Chengran Yang, Muhammad Ali, Lihua Wang, Priyanka Gorijala, Jigyasha Timsina, Agustín Ruiz, Pau Pastor, Maria Fernandez, Daniel Panyard, Corinne Engelman, Yuetiva Deming, Merce Boada, Amanda Cano, Pablo García-González, Neill Graff-Radford, Hiroshi Mori, Jae-Hong Lee, Richard Perrin, Yun Ju Sung, Dominantly Inherited Alzheimer Network (DIAN), Alzheimer’s Disease Neuroimaging Initiative (ADNI). Unique genetic architecture of CSF and brain metabolites pinpoints the novel targets for the traits of human wellness. Nat Genet. 2024 Nov 11. doi: 10.1038/s41588-024-01973-7.PMID: 39528826

2023

1. Gorijala P, Aslam MM, Dang LT, Xicota L, Fernandez MV, Sung YJ, Fan KH, Feingold E, Surace EI, Chhatwal JP, Hom CL; Dominantly Inherited Alzheimer Network (DIAN), the Alzheimer’s Disease Neuroimaging Initiative (ADNI); NIA-LOAD family study, for the Alzheimer’s Biomarkers Consortium-Down Syndrome (ABC-DS) Investigators; Hartley SL, Hassenstab J, Perrin RJ, Mapstone M, Zaman SH, Ances BM, Kamboh MI, Lee JH, Cruchaga C. Alzheimer’s polygenic risk scores are associated with cognitive phenotypes in Down syndrome. Alzheimers Dement. 2023 Oct 19. doi: 10.1002/alz.13506. PMID: 37855447

2. Phillips B, Western D, Wang L, Timsina J, Sun Y, Gorijala P, Yang C, Do A, Nykänen NP, Alvarez I, Aguilar M, Pastor P, Morris JC, Schindler SE, Fagan AM, Puerta R, García-González P, de Rojas I, Marquié M, Boada M, Ruiz A, Perlmutter JS; Dominantly Inherited Alzheimer Network (DIAN) Consortia; Ibanez L, Perrin RJ, Sung YJ, Cruchaga C. Proteome wide association studies of LRRK2 variants identify novel causal and druggable proteins for Parkinson’s disease. NPJ Parkinsons Dis. 2023 Jul 8;9(1):107. doi: 10.1038/s41531-023-00555-4.PMID: 37422510

3. Bradley J, Gorijala P, Schindler SE, Sung YJ, Ances B; Alzheimer’s Disease Neuroimaging Initiative, the Human Connectome Project; Fernandez MV, Cruchaga C. Genetic architecture of plasma Alzheimer disease biomarkers. Hum Mol Genet. 2023 Jul 20;32(15):2532-2543. doi: 10.1093/hmg/ddad087.PMID: 37208024.

4. Ali M, Archer DB, Gorijala P, Western D, Timsina J, Fernández MV, Wang TC, Satizabal CL, Yang Q, Beiser AS, Wang R, Chen G, Gordon B, Benzinger TLS, Xiong C, Morris JC, Bateman RJ, Karch CM, McDade E, Goate A, Seshadri S, Mayeux RP, Sperling RA, Buckley RF, Johnson KA, Won HH, Jung SH, Kim HR, Seo SW, Kim HJ, Mormino E, Laws SM, Fan KH, Kamboh MI, Vemuri P, Ramanan VK, Yang HS, Wenzel A, Rajula HSR, Mishra A, Dufouil C, Debette S, Lopez OL, DeKosky ST, Tao F, Nagle MW; Knight Alzheimer Disease Research Center (Knight ADRC); Dominantly Inherited Alzheimer Network (DIAN); Alzheimer’s Disease Neuroimaging Initiative (ADNI); ADNI-DOD, A4 Study Team; Australian Imaging Biomarkers, Lifestyle (AIBL) Study; Hohman TJ, Sung YJ, Dumitrescu L, Cruchaga C. Large multi-ethnic genetic analyses of amyloid imaging identify new genes for Alzheimer disease. Acta Neuropathol Commun. 2023 Apr 26;11(1):68. doi: 10.1186/s40478-023-01563-4.PMID: 37101235

5. Wang L, Western D, Timsina J, Repaci C, Song WM, Norton J, Kohlfeld P, Budde J, Climer S, Butt OH, Jacobson D, Garvin M, Templeton AR, Campagna S, O’Halloran J, Presti R, Goss CW, Mudd PA, Ances BM, Zhang B, Sung YJ, Cruchaga C. Plasma proteomics of SARS-CoV-2 infection and severity reveals impact on Alzheimer’s and coronary disease pathways. iScience. 2023 Apr 21;26(4):106408. doi: 10.1016/j.isci.2023.106408. Epub 2023 Mar 14.PMID: 36974157