Bruno A. Benitez Laboratory

One of the research interests in our lab is focused on the deep-molecular characterization of a clinically well-defined cohort of patients anchored in genomic data. Alzheimer’s (AD) and Parkinson’s disease (PD) are heterogeneous disorders with identifiable clinical-pathological subtypes based on symptom severity and predominance. An accurate molecular profile could reduce clinical heterogeneity among AD and PD patients. Our laboratory uses high-throughput and hypothesis-free “omics” technologies to address this important translational aspect, including next-generation DNA sequencing, epigenomics, transcriptomics, proteomics, metabolomics, and lipidomics, to generate a highly detailed molecular atlas for AD and PD. We aim to create a framework for uncovering proteins, genes, pathways, and potential biomarkers that will improve our understanding of underlying disease mechanisms, predict disease course, and improve the design of clinical trials.

Detailed molecular characterization of cell-specific transcriptomic states throughout multiple brain regions beyond nigrostriatal dopaminergic degeneration will provide mechanistic insights into both motor and non-motor PD symptoms. We will integrate neuropathology and snRNA-Seq data to identify a divergent molecular signature and/or shared aberrant pathways in various affected brain regions in PD. We will integrate snRNA-Seq data and GWAS hits from PD and Dementia with Lewy Bodies (DLB) to identify cell-type-specific expression and quantitative trait loci and to determine the genes involved in genetically enriched causal pathways. We will also use the expression signatures from snRNA-seq to prioritize causal genes under multi-gene genome-wide loci. We expect to uncover cell-type-specific differentially expressed genes (DEGs) in unexplored but affected brain regions in PD that will provide the foundation for understanding novel cellular and molecular mechanisms in PD.

The integration of multi-omics data sets can help to unravel the underlying mechanisms across multiple omic layers. We will leverage multi-omics data to profile the heterogeneity of pathways contributing to PD. Our unique study design combining clinical and neuropathological data with genomics, epigenomics, transcriptomics, proteomics, and metabolomics data from PD patients will identify analytes linked to PD and subtypes of PD with differentiating features. We will generate a detailed molecular landscape of PD and decipher the genetic architecture that underlies neurobiological pathways, linking these factors to PD and related dementias. In addition, multi-omic data can identify novel and potentially high-value therapeutic targets for the treatment and prevention of PD and related dementias.

We have successfully identified multiple novel genetic associations between AD and common and rare variants in endolysosomal genes (PLD3, RAB10, GRN12, TMEM106B, CPAMD8, MS4A4A). Recently, we performed a systematic, comprehensive evaluation of the contribution of coding variants in each endolysosomal gene to the risk of developing late-onset AD. We found that heterozygous loss-of-function (LoF) variants in several lysosomal enzyme genes are significantly enriched in AD patients. The largest and latest meta-analysis of PD GWAS found that common variants in several lysosomal genes are associated with PD risk. However, there is currently no in vitro or in vivo validation of most of those genetic associations. We performed intrastriatal inoculation of α-Syn PFFs in hemizygous and knockout (KO) GALC, ASAH1, and NAGLU mice, as well as in wild-type littermates. These studies aim to determine the role of these lysosomal enzymes on α-Synuclein (α-Syn) uptake, trafficking, aggregation, and clearance.

In 2011, we discovered that mutations in the DNAJC5 gene cause a neurodegenerative disease, the autosomal dominant form of neuronal ceroid lipofuscinosis (AD-ANCL). DNAJC5 encodes cysteine-string protein alpha (CSPα). In subsequent studies, we demonstrated in vitro and in vivo that CSPα plays a physiological role in the endo-lysosomes. In recent years, increasing in vitro evidence suggests that the misfolding-associated protein secretion (MAPS) pathway plays a role in the cell-to-cell transmission of prone-to-aggregate proteins such as α‐syn, tau, and amyloid. α-Syn and tau secretion seem to be primarily mediated by MAPS. CSPα is a crucial regulator of MAPS by mediating the cargo entry to the late endosomes. However, whether α-Syn or amyloid secretion and spreading in vivo are DNAJC5-dependent has yet to be determined. We study the role of variants in DNAJC5 on the risk of developing AD and PD using CRISPR/Cas9-corrected patient-derived induced pluripotent stem cells and primary cells to determine the role of DNAJC5 on the secretion and spreading of α-Syn and amyloid.

1. Benitez BA, Belálcazar HM, Anastasía A, Mamah DT, Zorumski CF, Mascó DH, Herrera DG, de Erausquin GA. Functional reduction of SK3-mediated currents precedes AMPA-receptor-mediated excitotoxicity in dopaminergic neurons. Neuropharmacology. 2011 Jun;60(7-8):1176-86. PubMed PMID: 21044638; PubMed Central PMCID: PMC4301957.
2. Benitez BA, Alvarado D, Cai Y, Mayo K, Chakraverty S, Norton J, Morris JC, Sands MS, Goate A, Cruchaga C. Exome-sequencing confirms DNAJC5 mutations as cause of adult neuronal ceroid-lipofuscinosis. PLoS One. 2011;6(11):e26741. PubMed PMID: 22073189; PubMed Central PMCID: PMC3208569.
3. Benitez BA, Cooper B, Pastor P, Jin SC, Lorenzo E, Cervantes S, Cruchaga C. TREM2 is associated with the risk of Alzheimer's disease in Spanish population. Neurobiol Aging. 2013 Jun;34(6):1711.e15-7. PubMed PMID: 23391427; PubMed Central PMCID: PMC3596468.
4. Benitez BA, Cruchaga C. TREM2 and neurodegenerative disease. N Engl J Med. 2013 Oct 17;369(16):1567-8. PubMed PMI: 24131187; PubMed Central PMCID: PMC4380008.
5. Benitez BA, Karch CM, Cai Y, Jin SC, Cooper B, Carrell D, Bertelsen S, Chibnik L, Schneider JA, Bennett DA, Fagan AM, Holtzman D, Morris JC, Goate AM, Cruchaga C. The PSEN1, p.E318G variant increases the risk of Alzheimer's disease in APOE-ε4 carriers. PLoS Genet. 2013;9(8):e1003685. PubMed PMID: 23990795; PubMed Central PMCID: PMC3750021.
6. Benitez BA, Jin SC, Guerreiro R, Graham R, Lord J, Harold D, Sims R, Lambert JC, Gibbs JR, Bras J, Sassi C, Harari O, Bertelsen S, Lupton MK, Powell J, Bellenguez C, Brown K, Medway C, Haddick PC, van der Brug MP, Bhangale T, Ortmann W, Behrens T, Mayeux R, Pericak-Vance MA, Farrer LA, Schellenberg GD, Haines JL, Turton J, Braae A, Barber I, Fagan AM, Holtzman DM, Morris JC, Williams J, Kauwe JS, Amouyel P, Morgan K, Singleton A, Hardy J, Goate AM, Cruchaga C. Missense variant in TREML2 protects against Alzheimer's disease. Neurobiol Aging. 2014 Jun;35(6):1510.e19-26. PubMed PMID: 24439484; PubMed Central PMCID: PMC3961557.
7. Benitez BA, Davis AA, Jin SC, Ibanez L, Ortega-Cubero S, Pastor P, Choi J, Cooper B, Perlmutter JS, Cruchaga C. Resequencing analysis of five Mendelian genes and the top genes from genome-wide association studies in Parkinson's Disease. Mol Neurodegener. 2016 Apr 19;11:29. PubMed PMID: 27094865; PubMed Central PMCID: PMC4837564. *Corresponding author
8. Benitez BA, Sands MS. Primary fibroblasts from CSPα mutation carriers recapitulate hallmarks of the adult onset neuronal ceroid lipofuscinosis. Sci Rep. 2017 Jul 24;7(1):6332. PubMed PMID: 28740222; PubMed Central PMCID: PMC5524943. *Corresponding author
9. Ibanez L, Dube U, Davis AA, Fernandez MV, Budde J, Cooper B, Diez-Fairen M, Ortega-Cubero S, Pastor P, Perlmutter JS, Cruchaga C, Benitez BA*. Pleiotropic Effects of Variants in Dementia Genes in Parkinson Disease. Front Neurosci. 2018 Apr 10;12:230. eCollection 2018. PMID: 29692703 PubMed Central PMCID: PMC5902712. *Corresponding author
10. Deming Y, Filipello F, Cignarella F, Cantoni C, Hsu S, Mikesell R, Li Z, Del-Aguila JL, Dube U, Farias FG, Bradley J, Budde J, Ibanez L, Fernandez MV, Blennow K, Zetterberg H, Heslegrave A, Johansson PM, Svensson J, Nellgård B, Lleo A, Alcolea D, Clarimon J, Rami L, Molinuevo JL, Suárez-Calvet M, Morenas-Rodríguez E, Kleinberger G, Ewers M, Harari O, Haass C, Brett TJ, Benitez BA^, Karch CM^, Piccio L^, Cruchaga C^. The MS4A gene cluster is a key modulator of soluble TREM2 and Alzheimer's disease risk. Sci Transl Med. 2019 Aug 14;11(505)PubMed PMID: 31413141; PubMed Central PMCID: PMC6697053. ^Equal contribution
11. Li Y, Xu Y, Benitez BA, Nagree MS, Dearborn JT, Jiang X, Guzman MA, Woloszynek JC, Giaramita A, Yip BK, Elsbernd J, Babcock MC, Lo M, Fowler SC, Wozniak DF, Vogler CA, Medin JA, Crawford BE, Sands MS. Genetic ablation of acid ceramidase in Krabbe disease confirms the psychosine hypothesis and identifies a new therapeutic target. Proc Natl Acad Sci U S A. 2019 Oct 1;116(40):20097-20103. PubMed PMID: 31527255; PubMed Central PMCID: PMC6778236.
12. Mikulka CR, Dearborn JT, Benitez BA, Strickland A, Liu L, Milbrandt J, Sands MS. Cell-autonomous expression of the acid hydrolase galactocerebrosidase. Proc Natl Acad Sci U S A. 2020 Apr 21;117(16):9032-9041. PubMed PMID: 32253319; PubMed Central PMCID: PMC7183170
13. Ibanez L, Bahena JA, Yang C, Dube U, Farias FHG, Budde JP, Bergmann K, Brenner-Webster C, Morris JC, Perrin RJ, Cairns NJ, O'Donnell J, Álvarez I, Diez-Fairen M, Aguilar M, Miller R, Davis AA, Pastor P, Kotzbauer P, Campbell MC, Perlmutter JS, Rhinn H, Harari O, Cruchaga C, Benitez BA*. Functional genomic analyses uncover APOE-mediated regulation of brain and cerebrospinal fluid beta-amyloid levels in Parkinson disease. Acta Neuropathol Commun. 2020 Nov 19;8(1):196. PubMed PMID: 33213513; PubMed Central PMCID: PMC7678051. *Corresponding author
14. Davis AA, Inman CE, Wargel ZM, Dube U, Freeberg BM, Galluppi A, Haines JN, Dhavale DD, Miller R, Choudhury FA, Sullivan PM, Cruchaga C, Perlmutter JS, Ulrich JD, Benitez BA, Kotzbauer PT, Holtzman DM. APOE genotype regulates pathology and disease progression in synucleinopathy. Sci Transl Med. 2020 Feb 5;12(529)PubMed PMID: 32024799; PubMed Central PMCID: PMC7289511
15. 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, Benitez BA, Rhinn H, Harari O, Cruchaga C. Genomic atlas of the proteome from brain, CSF and plasma prioritizes proteins implicated in neurological disorders. Nat Neurosci. 2021 Sep;24(9):1302-1312. PMID: 34239129.
16. Brase L, You SF, del Aguila J, Dai Y, Novotny BC, Soriano-Tarraga C, Dykstra T, Fernandez MV, Budde JP, Bergmann K, Morris JC, Bateman RJ, Perrin RJ, McDade E, Xiong C, Goate A, Farlow M, Chhatwal JP, Schofield P, Chui H, D. I. A. N. (DIAN), Sutherland GT, Kipnis J, Karch CM^, Benitez BA^, Cruchaga C^, Harari O, A landscape of the genetic and cellular heterogeneity in Alzheimer disease, medRxiv , 2021.11.30.21267072 (2021). ^Senior author equal contribution
17. Novotny, BC, Fernandez, MV, Bahena, J, Budde, JP, Bergmann, K, Eteleeb, A, Bradley, J, Webster, C, Ebl, C, Norton, J, Gentsch, J, Dube, U, Wang, F, Morris, JC, Bateman, RJ, Perrin, RJ, McDade, E, Xiong, C, Chhatwal, J, Goate A, Farlow M, Schofield P, Chui H, Karch CM, Benitez BA^, Cruchaga C^, Harari O, the DIAN(DIAN) Group. Metabolomic and lipidomic signatures in autosomal dominant and late-onset Alzheimer disease brains. MedRxiv, 2021.11.04.21265941. ^Senior author equal contribution

Funding for projects in our lab has been through the National Institutes of Health (NINDS, NIA). We are also sincerely grateful to the patients, family members, and caregivers who donated their time, brains, and biospecimens for biomedical research.

Our lab is located in the Longwood Medical Area in the Center for Life Sciences 6th Floor, room #630, surrounded by collaborators from the Departments of Neurology and Medicine at BIDMC.