Literature DB >> 29120328

Neuropathological and transcriptomic characteristics of the aged brain.

Jeremy A Miller1, Angela Guillozet-Bongaarts1, Laura E Gibbons2, Nadia Postupna3, Anne Renz4, Allison E Beller3, Susan M Sunkin1, Lydia Ng1, Shannon E Rose3, Kimberly A Smith1, Aaron Szafer1, Chris Barber1, Darren Bertagnolli1, Kristopher Bickley1, Krissy Brouner1, Shiella Caldejon1, Mike Chapin1, Mindy L Chua3, Natalie M Coleman3, Eiron Cudaback3, Christine Cuhaciyan1, Rachel A Dalley1, Nick Dee1, Tsega Desta1, Tim A Dolbeare1, Nadezhda I Dotson1, Michael Fisher1, Nathalie Gaudreault1, Garrett Gee1, Terri L Gilbert1, Jeff Goldy1, Fiona Griffin1, Caroline Habel1, Zeb Haradon1, Nika Hejazinia1, Leanne L Hellstern3, Steve Horvath5, Kim Howard3, Robert Howard1, Justin Johal1, Nikolas L Jorstad3, Samuel R Josephsen3, Chihchau L Kuan1, Florence Lai1, Eric Lee1, Felix Lee1, Tracy Lemon1, Xianwu Li3, Desiree A Marshall3, Jose Melchor1, Shubhabrata Mukherjee2, Julie Nyhus1, Julie Pendergraft1, Lydia Potekhina1, Elizabeth Y Rha3, Samantha Rice3, David Rosen1, Abharika Sapru3, Aimee Schantz3, Elaine Shen1, Emily Sherfield3, Shu Shi1, Andy J Sodt1, Nivretta Thatra1, Michael Tieu1, Angela M Wilson3, Thomas J Montine3, Eric B Larson4, Amy Bernard1, Paul K Crane2, Richard G Ellenbogen6, C Dirk Keene3, Ed Lein1.   

Abstract

As more people live longer, age-related neurodegenerative diseases are an increasingly important societal health issue. Treatments targeting specific pathologies such as amyloid beta in Alzheimer's disease (AD) have not led to effective treatments, and there is increasing evidence of a disconnect between traditional pathology and cognitive abilities with advancing age, indicative of individual variation in resilience to pathology. Here, we generated a comprehensive neuropathological, molecular, and transcriptomic characterization of hippocampus and two regions cortex in 107 aged donors (median = 90) from the Adult Changes in Thought (ACT) study as a freely-available resource (http://aging.brain-map.org/). We confirm established associations between AD pathology and dementia, albeit with increased, presumably aging-related variability, and identify sets of co-expressed genes correlated with pathological tau and inflammation markers. Finally, we demonstrate a relationship between dementia and RNA quality, and find common gene signatures, highlighting the importance of properly controlling for RNA quality when studying dementia.

Entities:  

Keywords:  Alzheimer's disease; aging; dementia; gene expression; human; neuroscience

Mesh:

Year:  2017        PMID: 29120328      PMCID: PMC5679757          DOI: 10.7554/eLife.31126

Source DB:  PubMed          Journal:  Elife        ISSN: 2050-084X            Impact factor:   8.140


  82 in total

1.  Genome-wide atlas of gene expression in the adult mouse brain.

Authors:  Ed S Lein; Michael J Hawrylycz; Nancy Ao; Mikael Ayres; Amy Bensinger; Amy Bernard; Andrew F Boe; Mark S Boguski; Kevin S Brockway; Emi J Byrnes; Lin Chen; Li Chen; Tsuey-Ming Chen; Mei Chi Chin; Jimmy Chong; Brian E Crook; Aneta Czaplinska; Chinh N Dang; Suvro Datta; Nick R Dee; Aimee L Desaki; Tsega Desta; Ellen Diep; Tim A Dolbeare; Matthew J Donelan; Hong-Wei Dong; Jennifer G Dougherty; Ben J Duncan; Amanda J Ebbert; Gregor Eichele; Lili K Estin; Casey Faber; Benjamin A Facer; Rick Fields; Shanna R Fischer; Tim P Fliss; Cliff Frensley; Sabrina N Gates; Katie J Glattfelder; Kevin R Halverson; Matthew R Hart; John G Hohmann; Maureen P Howell; Darren P Jeung; Rebecca A Johnson; Patrick T Karr; Reena Kawal; Jolene M Kidney; Rachel H Knapik; Chihchau L Kuan; James H Lake; Annabel R Laramee; Kirk D Larsen; Christopher Lau; Tracy A Lemon; Agnes J Liang; Ying Liu; Lon T Luong; Jesse Michaels; Judith J Morgan; Rebecca J Morgan; Marty T Mortrud; Nerick F Mosqueda; Lydia L Ng; Randy Ng; Geralyn J Orta; Caroline C Overly; Tu H Pak; Sheana E Parry; Sayan D Pathak; Owen C Pearson; Ralph B Puchalski; Zackery L Riley; Hannah R Rockett; Stephen A Rowland; Joshua J Royall; Marcos J Ruiz; Nadia R Sarno; Katherine Schaffnit; Nadiya V Shapovalova; Taz Sivisay; Clifford R Slaughterbeck; Simon C Smith; Kimberly A Smith; Bryan I Smith; Andy J Sodt; Nick N Stewart; Kenda-Ruth Stumpf; Susan M Sunkin; Madhavi Sutram; Angelene Tam; Carey D Teemer; Christina Thaller; Carol L Thompson; Lee R Varnam; Axel Visel; Ray M Whitlock; Paul E Wohnoutka; Crissa K Wolkey; Victoria Y Wong; Matthew Wood; Murat B Yaylaoglu; Rob C Young; Brian L Youngstrom; Xu Feng Yuan; Bin Zhang; Theresa A Zwingman; Allan R Jones
Journal:  Nature       Date:  2006-12-06       Impact factor: 49.962

2.  A novel sorting nexin modulates endocytic trafficking and alpha-secretase cleavage of the amyloid precursor protein.

Authors:  Susanne Schöbel; Stephanie Neumann; Maren Hertweck; Bastian Dislich; Peer-Hendrik Kuhn; Elisabeth Kremmer; Brian Seed; Ralf Baumeister; Christian Haass; Stefan F Lichtenthaler
Journal:  J Biol Chem       Date:  2008-03-19       Impact factor: 5.157

3.  Ecology of the aging human brain.

Authors:  Joshua A Sonnen; Karen Santa Cruz; Laura S Hemmy; Randall Woltjer; James B Leverenz; Kathleen S Montine; Clifford R Jack; Jeffrey Kaye; Kelvin Lim; Eric B Larson; Lon White; Thomas J Montine
Journal:  Arch Neurol       Date:  2011-08

4.  Inositol trisphosphate 3-kinase B is increased in human Alzheimer brain and exacerbates mouse Alzheimer pathology.

Authors:  Virginie Stygelbout; Karelle Leroy; Valérie Pouillon; Kunie Ando; Eva D'Amico; Yonghui Jia; H Robert Luo; Charles Duyckaerts; Christophe Erneux; Stéphane Schurmans; Jean-Pierre Brion
Journal:  Brain       Date:  2014-01-08       Impact factor: 13.501

5.  Differential expression of inflammatory mediators in rat microglia cultured from different brain regions.

Authors:  L Ren; B Lubrich; K Biber; P J Gebicke-Haerter
Journal:  Brain Res Mol Brain Res       Date:  1999-03-05

6.  Differential neutrophil infiltration contributes to regional differences in brain inflammation in the substantia nigra pars compacta and cortex.

Authors:  Kyung-Ae Ji; Mi Young Eu; Seung-Hee Kang; Byoung Joo Gwag; Ilo Jou; Eun-Hye Joe
Journal:  Glia       Date:  2008-08-01       Impact factor: 7.452

7.  Glucose levels and risk of dementia.

Authors:  Paul K Crane; Rod Walker; Rebecca A Hubbard; Ge Li; David M Nathan; Hui Zheng; Sebastien Haneuse; Suzanne Craft; Thomas J Montine; Steven E Kahn; Wayne McCormick; Susan M McCurry; James D Bowen; Eric B Larson
Journal:  N Engl J Med       Date:  2013-08-08       Impact factor: 91.245

Review 8.  Chronic inflammation (inflammaging) and its potential contribution to age-associated diseases.

Authors:  Claudio Franceschi; Judith Campisi
Journal:  J Gerontol A Biol Sci Med Sci       Date:  2014-06       Impact factor: 6.053

9.  A systems level analysis of transcriptional changes in Alzheimer's disease and normal aging.

Authors:  Jeremy A Miller; Michael C Oldham; Daniel H Geschwind
Journal:  J Neurosci       Date:  2008-02-06       Impact factor: 6.167

10.  RNA-seq: impact of RNA degradation on transcript quantification.

Authors:  Irene Gallego Romero; Athma A Pai; Jenny Tung; Yoav Gilad
Journal:  BMC Biol       Date:  2014-05-30       Impact factor: 7.431

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  37 in total

1.  Selective Neuronal Vulnerability in Alzheimer's Disease: A Network-Based Analysis.

Authors:  Jean-Pierre Roussarie; Vicky Yao; Patricia Rodriguez-Rodriguez; Rose Oughtred; Jennifer Rust; Zakary Plautz; Shirin Kasturia; Christian Albornoz; Wei Wang; Eric F Schmidt; Ruth Dannenfelser; Alicja Tadych; Lars Brichta; Alona Barnea-Cramer; Nathaniel Heintz; Patrick R Hof; Myriam Heiman; Kara Dolinski; Marc Flajolet; Olga G Troyanskaya; Paul Greengard
Journal:  Neuron       Date:  2020-06-29       Impact factor: 17.173

2.  Specificity for latent C termini links the E3 ubiquitin ligase CHIP to caspases.

Authors:  Matthew Ravalin; Panagiotis Theofilas; Koli Basu; Kwadwo A Opoku-Nsiah; Victoria A Assimon; Daniel Medina-Cleghorn; Yi-Fan Chen; Markus F Bohn; Michelle Arkin; Lea T Grinberg; Charles S Craik; Jason E Gestwicki
Journal:  Nat Chem Biol       Date:  2019-07-18       Impact factor: 15.040

3.  The Allen Brain Atlas as a Resource for Teaching Undergraduate Neuroscience.

Authors:  Terri L Gilbert
Journal:  J Undergrad Neurosci Educ       Date:  2018-09-15

4.  Hippocampal gene expression patterns linked to late-life physical activity oppose age and AD-related transcriptional decline.

Authors:  Nicole C Berchtold; G Aleph Prieto; Michael Phelan; Daniel L Gillen; Pierre Baldi; David A Bennett; Aron S Buchman; Carl W Cotman
Journal:  Neurobiol Aging       Date:  2019-02-20       Impact factor: 4.673

5.  Transcriptomic Profiles of Sepsis in the Human Brain.

Authors:  Angela C Bustamante; Kristopher Opron; William J Ehlenbach; Eric B Larson; Paul K Crane; C Dirk Keene; Theodore J Standiford; Benjamin H Singer
Journal:  Am J Respir Crit Care Med       Date:  2020-04-01       Impact factor: 21.405

Review 6.  Revolution of Alzheimer Precision Neurology. Passageway of Systems Biology and Neurophysiology.

Authors:  Harald Hampel; Nicola Toschi; Claudio Babiloni; Filippo Baldacci; Keith L Black; Arun L W Bokde; René S Bun; Francesco Cacciola; Enrica Cavedo; Patrizia A Chiesa; Olivier Colliot; Cristina-Maria Coman; Bruno Dubois; Andrea Duggento; Stanley Durrleman; Maria-Teresa Ferretti; Nathalie George; Remy Genthon; Marie-Odile Habert; Karl Herholz; Yosef Koronyo; Maya Koronyo-Hamaoui; Foudil Lamari; Todd Langevin; Stéphane Lehéricy; Jean Lorenceau; Christian Neri; Robert Nisticò; Francis Nyasse-Messene; Craig Ritchie; Simone Rossi; Emiliano Santarnecchi; Olaf Sporns; Steven R Verdooner; Andrea Vergallo; Nicolas Villain; Erfan Younesi; Francesco Garaci; Simone Lista
Journal:  J Alzheimers Dis       Date:  2018       Impact factor: 4.472

Review 7.  The puzzle of preserved cognition in the oldest old.

Authors:  Orso Bugiani
Journal:  Neurol Sci       Date:  2019-11-12       Impact factor: 3.307

Review 8.  Harnessing endophenotypes and network medicine for Alzheimer's drug repurposing.

Authors:  Jiansong Fang; Andrew A Pieper; Ruth Nussinov; Garam Lee; Lynn Bekris; James B Leverenz; Jeffrey Cummings; Feixiong Cheng
Journal:  Med Res Rev       Date:  2020-07-13       Impact factor: 12.944

9.  MIR-NATs repress MAPT translation and aid proteostasis in neurodegeneration.

Authors:  Roberto Simone; Faiza Javad; Warren Emmett; Oscar G Wilkins; Filipa Lourenço Almeida; Natalia Barahona-Torres; Justyna Zareba-Paslawska; Mazdak Ehteramyan; Paola Zuccotti; Angelika Modelska; Kavitha Siva; Gurvir S Virdi; Jamie S Mitchell; Jasmine Harley; Victoria A Kay; Geshanthi Hondhamuni; Daniah Trabzuni; Mina Ryten; Selina Wray; Elisavet Preza; Demis A Kia; Alan Pittman; Raffaele Ferrari; Claudia Manzoni; Andrew Lees; John A Hardy; Michela A Denti; Alessandro Quattrone; Rickie Patani; Per Svenningsson; Thomas T Warner; Vincent Plagnol; Jernej Ule; Rohan de Silva
Journal:  Nature       Date:  2021-05-19       Impact factor: 49.962

10.  Increased excitatory to inhibitory synaptic ratio in parietal cortex samples from individuals with Alzheimer's disease.

Authors:  Julie C Lauterborn; Pietro Scaduto; Conor D Cox; Anton Schulmann; Gary Lynch; Christine M Gall; C Dirk Keene; Agenor Limon
Journal:  Nat Commun       Date:  2021-05-10       Impact factor: 14.919

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