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2. Robust Asymmetric Loss for Multi-Label Long-Tailed Learning

Author

Park, Wongi, Park, Inhyuk, Kim, Sungeun, and Ryu, Jongbin

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

In real medical data, training samples typically show long-tailed distributions with multiple labels. Class distribution of the medical data has a long-tailed shape, in which the incidence of different diseases is quite varied, and at the same time, it is not unusual for images taken from symptomatic patients to be multi-label diseases. Therefore, in this paper, we concurrently address these two issues by putting forth a robust asymmetric loss on the polynomial function. Since our loss tackles both long-tailed and multi-label classification problems simultaneously, it leads to a complex design of the loss function with a large number of hyper-parameters. Although a model can be highly fine-tuned due to a large number of hyper-parameters, it is difficult to optimize all hyper-parameters at the same time, and there might be a risk of overfitting a model. Therefore, we regularize the loss function using the Hill loss approach, which is beneficial to be less sensitive against the numerous hyper-parameters so that it reduces the risk of overfitting the model. For this reason, the proposed loss is a generic method that can be applied to most medical image classification tasks and does not make the training process more time-consuming. We demonstrate that the proposed robust asymmetric loss performs favorably against the long-tailed with multi-label medical image classification in addition to the various long-tailed single-label datasets. Notably, our method achieves Top-5 results on the CXR-LT dataset of the ICCV CVAMD 2023 competition. We opensource our implementation of the robust asymmetric loss in the public repository: https://github.com/kalelpark/RAL.

Published
2023

3. A data‐driven examination of apathy and depressive symptoms in dementia with independent replication

Author

Da Silva, Miguel Vasconcelos, Melendez‐Torres, Gerardo Javier, Ismail, Zahinoor, Testad, Ingelin, Ballard, Clive, Creese, Byron, Weiner, Michael, Aisen, Paul, Petersen, Ronald, Jack, Clifford R, Jagust, William, Trojanowki, John Q, Toga, Arthur W, Beckett, Laurel, Green, Robert C, Saykin, Andrew J, Morris, John, Shaw, Leslie M, Liu, Enchi, Montine, Tom, Thomas, Ronald G, Donohue, Michael, Walter, Sarah, Gessert, Devon, Sather, Tamie, Jiminez, Gus, Harvey, Danielle, Bernstein, Matthew, Fox, Nick, Thompson, Paul, Schuff, Norbert, DeCArli, Charles, Borowski, Bret, Gunter, Jeff, Senjem, Matt, Vemuri, Prashanthi, Jones, David, Kantarci, Kejal, Ward, Chad, Koeppe, Robert A, Foster, Norm, Reiman, Eric M, Chen, Kewei, Mathis, Chet, Landau, Susan, Cairns, Nigel J, Householder, Erin, Reinwald, Lisa Taylor, Lee, Virginia, Korecka, Magdalena, Figurski, Michal, Crawford, Karen, Neu, Scott, Foroud, Tatiana M, Potkin, Steven, Shen, Li, Kelley, Faber, Kim, Sungeun, Nho, Kwangsik, Kachaturian, Zaven, Frank, Richard, Snyder, Peter J, Molchan, Susan, Kaye, Jeffrey, Quinn, Joseph, Lind, Betty, Carter, Raina, Dolen, Sara, Schneider, Lon S, Pawluczyk, Sonia, Beccera, Mauricio, Teodoro, Liberty, Spann, Bryan M, Brewer, James, Van der Swag, Helen, Fleisher, Adam, Heidebrink, Judith L, Lord, Joanne L, Mason, Sara S, Albers, Colleen S, Knopman, David, Johnson, Kris, Doody, Rachelle S, Meyer, Javier Villanueva, Chowdhury, Munir, Rountree, Susan, Dang, Mimi, Stern, Yaakov, Honig, Lawrence S, Bell, Karen L, Ances, Beau, Morris, John C, Carroll, Maria, Leon, Sue, Mintun, Mark A, Schneider, Stacy, and Oliver, Angela

Subjects
Clinical and Health Psychology, Biomedical and Clinical Sciences, Psychology, Brain Disorders, Mental Health, Depression, Mental Illness, Mental health, Alzheimer's Disease Neuroimaging Initiative, apathy, dementia, depression, latent class analysis, Genetics, Neurosciences, Biological psychology
Abstract

Apathy is one of the most common neuropsychiatric symptoms (NPS) and is associated with poor clinical outcomes. Research that helps define the apathy phenotype is urgently needed, particularly for clinical and biomarker studies. We used latent class analysis (LCA) with two independent cohorts to understand how apathy and depression symptoms co-occur statistically. We further explored the relationship between latent class membership, demographics, and the presence of other NPS. The LCA identified a four-class solution (no symptoms, apathy, depression, and combined apathy/depression), reproducible over both cohorts, providing robust support for an apathy syndrome distinct from depression and confirming that an apathy/depression syndrome exists, supported by the model fit test with the four-class solution scores evidencing better fitting (Bayesian information criterion adjusted and entropy R 2). Using a data-driven method, we show distinct and statistically meaningful co-occurrence of apathy and depressive symptoms. There was evidence that these classes have different clinical associations, which may help inform diagnostic categories for research studies and clinical practice.HighlightsWe found four classes: no symptoms, apathy, depression and apathy/depression.Apathy conferred a higher probability for agitation.Apathy diagnostic criteria should include accompanying neuropsychiatric symptoms.

Published
2023

7. Phenotypic overlap between atopic dermatitis and autism

Author

Shin, Kyong-Oh, Crumrine, Debra A, Kim, Sungeun, Lee, Yerin, Kim, Bogyeong, Abuabara, Katrina, Park, Chaehyeong, Uchida, Yoshikazu, Wakefield, Joan S, Meyer, Jason M, Jeong, Sekyoo, Park, Byeong Deog, Park, Kyungho, and Elias, Peter M

Subjects
Biological Psychology, Biomedical and Clinical Sciences, Psychology, Behavioral and Social Science, Brain Disorders, Neurosciences, Autism, Pediatric, Intellectual and Developmental Disabilities (IDD), Mental Health, Aetiology, 2.1 Biological and endogenous factors, Neurological, Skin, Animals, Anticonvulsants, Autistic Disorder, Dermatitis, Atopic, Female, Inflammation Mediators, Maze Learning, Mice, Mice, Inbred BALB C, Phenotype, Pregnancy, Prenatal Exposure Delayed Effects, Valproic Acid, Atopic dermatitis, Autism spectrum disorders, Blood-brain barrier, IFN gamma, IL-4, 5, 13 and 17A, TNF alpha, Valproic acid mouse model, Blood–brain barrier, IFNγ, TNFα, Biochemistry and Cell Biology, Cognitive Sciences, Neurology & Neurosurgery, Biological psychology
Abstract

BackgroundAutism, a childhood behavioral disorder, belongs to a large suite of diseases, collectively referred to as autism spectrum disorders (ASD). Though multifactorial in etiology, approximately 10% of ASD are associated with atopic dermatitis (AD). Moreover, ASD prevalence increases further as AD severity worsens, though these disorders share no common causative mutations. We assessed here the link between these two disorders in the standard, valproic acid mouse model of ASD. In prior studies, there was no evidence of skin involvement, but we hypothesized that cutaneous involvement could be detected in experiments conducted in BALB/c mice. BALB/c is an albino, laboratory-bred strain of the house mouse and is among the most widely used inbred strains used in animal experimentation.MethodsWe performed our studies in valproic acid (VPA)-treated BALB/c hairless mice, a standard mouse model of ASD. Mid-trimester pregnant mice received a single intraperitoneal injection of either valproic acid sodium salt dissolved in saline or saline alone on embryonic day 12.5 and were housed individually until postnatal day 21. Only the brain and epidermis appeared to be affected, while other tissues remain unchanged. At various postnatal time points, brain, skin and blood samples were obtained for histology and for quantitation of tissue sphingolipid content and cytokine levels.ResultsAD-like changes in ceramide content occurred by day one postpartum in both VPA-treated mouse skin and brain. The temporal co-emergence of AD and ASD, and the AD phenotype-dependent increase in ASD prevalence correlated with early appearance of cytokine markers (i.e., interleukin [IL]-4, 5, and 13), as well as mast cells in skin and brain. The high levels of interferon (IFN)γ not only in skin, but also in brain likely account for a significant decline in esterified very-long-chain N-acyl fatty acids in brain ceramides, again mimicking known IFNγ-induced changes in AD.ConclusionBaseline involvement of both AD and ASD could reflect concurrent neuro- and epidermal toxicity, possibly because both epidermis and neural tissues originate from the embryonic neuroectoderm. These studies illuminate the shared susceptibility of the brain and epidermis to a known neurotoxin, suggesting that the atopic diathesis could be extended to include ASD.

Published
2021

9. An odd $[1,b]$-factor in regular graphs from eigenvalues

Author

Kim, Sungeun, O, Suil, Park, Jihwan, and Ree, Hyo

Subjects
Mathematics - Combinatorics, 05C50, 05C70
Abstract

An odd $[1,b]$-factor of a graph $G$ is a spanning subgraph $H$ such that for each vertex $v \in V(G)$, $d_H(v)$ is odd and $1\le d_H(v) \le b$. Let $\lambda_3(G)$ be the third largest eigenvalue of the adjacency matrix of $G$. For positive integers $r \ge 3$ and even $n$, Lu, Wu, and Yang [10] proved a lower bound for $\lambda_3(G)$ in an $n$-vertex $r$-regular graph $G$ to gurantee the existence of an odd $[1,b]$-factor in $G$. In this paper, we improve the bound; it is sharp for every $r$., Comment: 6 pages

Published
2020
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11. Circular-SWAT for deep learning based diagnostic classification of Alzheimer's disease: application to metabolome data

Author

Kaddurah-Daouk, Rima, Kueider-Paisley, Alexandra, Doraiswamy, P. Murali, Blach, Colette, Moseley, Arthur, Thompson, Will, St John-Williams, Lisa, Mahmoudiandehkhordi, Siamak, Tenenbaum, Jessica, Welsh-Balmer, Kathleen, Plassman, Brenda, Saykin, Andrew J., Nho, Kwangsik, Risacher, Shannon L., Kastenmüller, Gabi, Arnold, Matthias, Han, Xianlin, Baillie, Rebecca, Knight, Rob, Dorrestein, Pieter, Brewer, James, Mayer, Emeran, Labus, Jennifer, Baldi, Pierre, Gupta, Arpana, Fiehn, Oliver, Barupal, Dinesh, Meikle, Peter, Mazmanian, Sarkis, Rader, Dan, Kling, Mitchel, Shaw, Leslie, Trojanowski, John, van Duijin, Cornelia, Nevado-Holgado, Alejo, Bennett, David, Krishnan, Ranga, Keshavarzian, Ali, Vogt, Robin, Ikram, Arfan, Hankemeier, Thomas, Thiele, Ines, Price, Nathan, Funk, Cory, Baloni, Priyanka, Jia, Wei, Wishart, David, Brinton, Roberta, Chang, Rui, Farrer, Lindsay, Au, Rhoda, Qiu, Wendy, Würtz, Peter, Koal, Therese, Mangravite, Lara, Krumsiek, Jan, Suhre, Karsten, Newman, John, Moreno, Herman, Foroud, Tatania, Sacks, Frank, Jansson, Janet, Weiner, Michael W., Aisen, Paul, Petersen, Ronald, Jack, Clifford R., Jr., Jagust, William, Trojanowki, John Q., Toga, Arthur W., Beckett, Laurel, Green, Robert C., Morris, John C., Perrin, Richard J., Shaw, Leslie M., Khachaturian, Zaven, Carrillo, Maria, Potter, William, Barnes, Lisa, Bernard, Marie, Gonzalez, Hector, Ho, Carole, Hsiao, John K., Jackson, Jonathan, Masliah, Eliezer, Masterman, Donna, Okonkwo, Ozioma, Perrin, Richard, Ryan, Laurie, Silverberg, Nina, Fleisher, Adam, Sacrey, Diana Truran, Fockler, Juliet, Conti, Cat, Veitch, Dallas, Neuhaus, John, Jin, Chengshi, Nosheny, Rachel, Ashford, Miriam, Flenniken, Derek, Kormos, Adrienne, Montine, Tom, Rafii, Michael, Raman, Rema, Jimenez, Gustavo, Donohue, Michael, Gessert, Devon, Salazar, Jennifer, Zimmerman, Caileigh, Cabrera, Yuliana, Walter, Sarah, Miller, Garrett, Coker, Godfrey, Clanton, Taylor, Hergesheimer, Lindsey, Smith, Stephanie, Adegoke, Olusegun, Mahboubi, Payam, Moore, Shelley, Pizzola, Jeremy, Shaffer, Elizabeth, Sloan, Brittany, Harvey, Danielle, Forghanian-Arani, Arvin, Borowski, Bret, Ward, Chad, Schwarz, Christopher, Jones, David, Gunter, Jeff, Kantarci, Kejal, Senjem, Matthew, Vemuri, Prashanthi, Reid, Robert, Fox, Nick C., Malone, Ian, Thompson, Paul, Thomopoulos, Sophia I., Nir, Talia M., Jahanshad, Neda, DeCarli, Charles, Knaack, Alexander, Fletcher, Evan, Tosun-Turgut, Duygu, Chen, Stephanie Rossi, Choe, Mark, Crawford, Karen, Yushkevich, Paul A., Das, Sandhitsu, Koeppe, Robert A., Reiman, Eric M., Chen, Kewei, Mathis, Chet, Landau, Susan, Cairns, Nigel J., Householder, Erin, Franklin, Erin, Bernhardt, Haley, Taylor-Reinwald, Lisa, Korecka, Magdalena, Figurski, Michal, Neu, Scott, Apostolova, Liana G., Shen, Li, Foroud, Tatiana M., Nudelman, Kelly, Faber, Kelley, Wilmes, Kristi, Thal, Leon, Silbert, Lisa C., Lind, Betty, Crissey, Rachel, Kaye, Jeffrey A., Carter, Raina, Dolen, Sara, Quinn, Joseph, Schneider, Lon S., Pawluczyk, Sonia, Becerra, Mauricio, Teodoro, Liberty, Dagerman, Karen, Spann, Bryan M., Vanderswag, Helen, Ziolkowski, Jaimie, Heidebrink, Judith L., Zbizek-Nulph, Lisa, Lord, Joanne L., Mason, Sara S., Albers, Colleen S., Knopman, David, Johnson, Kris, Villanueva-Meyer, Javier, Pavlik, Valory, Pacini, Nathaniel, Lamb, Ashley, Kass, Joseph S., Doody, Rachelle S., Shibley, Victoria, Chowdhury, Munir, Rountree, Susan, Dang, Mimi, Stern, Yaakov, Honig, Lawrence S., Mintz, Akiva, Ances, Beau, Winkfield, David, Carroll, Maria, Stobbs-Cucchi, Georgia, Oliver, Angela, Creech, Mary L., Mintun, Mark A., Schneider, Stacy, Geldmacher, David, Love, Marissa Natelson, Griffith, Randall, Clark, David, Brockington, John, Marson, Daniel, Grossman, Hillel, Goldstein, Martin A., Greenberg, Jonathan, Mitsis, Effie, Shah, Raj C., Lamar, Melissa, Samuels, Patricia, Duara, Ranjan, Greig-Custo, Maria T., Rodriguez, Rosemarie, Albert, Marilyn, Onyike, Chiadi, Farrington, Leonie, Rudow, Scott, Brichko, Rottislav, Kielb, Stephanie, Smith, Amanda, Raj, Balebail Ashok, Fargher, Kristin, Sadowski, Martin, Wisniewski, Thomas, Shulman, Melanie, Faustin, Arline, Rao, Julia, Castro, Karen M., Ulysse, Anaztasia, Chen, Shannon, Sheikh, Mohammed O., Singleton-Garvin, Jamika, Petrella, JeffreyR., James, Olga, Wong, Terence Z., Borges-Neto, Salvador, Karlawish, Jason H., Wolk, David A., Vaishnavi, Sanjeev, Clark, Christopher M., Arnold, Steven E., Smith, Charles D., Jicha, Gregory A., Raslau, Flavius D., Lopez, Oscar L., Oakley, MaryAnn, Simpson, Donna M., Porsteinsson, Anton P., Martin, Kim, Kowalski, Nancy, Keltz, Melanie, Goldstein, Bonnie S., Makino, Kelly M., Ismail, M. Saleem, Brand, Connie, Thai, Gaby, Pierce, Aimee, Yanez, Beatriz, Sosa, Elizabeth, Witbracht, Megan, Kelley, Brendan, Nguyen, Trung, Womack, Kyle, Mathews, Dana, Quiceno, Mary, Levey, Allan I., Lah, James J., Hajjar, Ihab, Cellar, Janet S., Burns, Jeffrey M., Swerdlow, Russell H., Brooks, William M., Silverman, Daniel H.S., Kremen, Sarah, Apostolova, Liana, Tingus, Kathleen, Lu, Po H., Bartzokis, George, Woo, Ellen, Teng, Edmond, Graff-Radford, Neill R., Parfitt, Francine, Poki-Walker, Kim, Farlow, Martin R., Hake, Ann Marie, Matthews, Brandy R., Brosch, Jared R., Herring, Scott, van, Christopher H., Mecca, Adam P., Good, Susan P., MacAvoy, Martha G., Carson, Richard E., Varma, Pradeep, Chertkow, Howard, Vaitekunis, Susan, Hosein, Chris, Black, Sandra, Stefanovic, Bojana, Heyn, Chris (Chinthaka), Robin Hsiung, Ging-Yuek, Kim, Ellen, Mudge, Benita, Sossi, Vesna, Feldman, Howard, Assaly, Michele, Finger, Elizabeth, Pasternak, Stephen, Rachinsky, Irina, Kertesz, Andrew, Drost, Dick, Rogers, John, Grant, Ian, Muse, Brittanie, Rogalski, Emily, Robson, Jordan, Mesulam, M.-Marsel, Kerwin, Diana, Wu, Chuang-Kuo, Johnson, Nancy, Lipowski, Kristine, Weintraub, Sandra, Bonakdarpour, Borna, Pomara, Nunzio, Hernando, Raymundo, Sarrael, Antero, Rosen, Howard J., Miller, Bruce L., Perry, David, Turner, Raymond Scott, Johnson, Kathleen, Reynolds, Brigid, MCCann, Kelly, Poe, Jessica, Sperling, Reisa A., Johnson, Keith A., Marshall, Gad A., Yesavage, Jerome, Taylor, Joy L., Chao, Steven, Coleman, Jaila, White, Jessica D., Lane, Barton, Rosen, Allyson, Tinklenberg, Jared, Belden, Christine M., Atri, Alireza, Clark, Kelly A., Zamrini, Edward, Sabbagh, Marwan, Killiany, Ronald, Stern, Robert, Mez, Jesse, Kowall, Neil, Budson, Andrew E., Obisesan, Thomas O., Ntekim, Oyonumo E., Wolday, Saba, Khan, Javed I., Nwulia, Evaristus, Nadarajah, Sheeba, Lerner, Alan, Ogrocki, Paula, Tatsuoka, Curtis, Fatica, Parianne, Maillard, Pauline, Olichney, John, Carmichael, Owen, Bates, Vernice, Capote, Horacio, Rainka, Michelle, Borrie, Michael, Lee, T.-Y., Bartha, Dr Rob, Johnson, Sterling, Asthana, Sanjay, Carlsson, Cynthia M., Perrin, Allison, Burke, Anna, Scharre, Douglas W., Kataki, Maria, Tarawneh, Rawan, Hart, David, Zimmerman, Earl A., Celmins, Dzintra, Miller, Delwyn D., BolesPonto, Laura L., Smith, Karen Ekstam, Koleva, Hristina, Shim, Hyungsub, Nam, Ki Won, Schultz, Susan K., Williamson, Jeff D., Craft, Suzanne, Cleveland, Jo, Yang, Mia, Sink, Kaycee M., Ott, Brian R., Drake, Jonathan, Tremont, Geoffrey, Daiello, Lori A., Drake, Jonathan D., Ritter, Aaron, Bernick, Charles, Munic, Donna, O'Connelll, Abigail, Mintzer, Jacobo, Wiliams, Arthur, Masdeu, Joseph, Shi, Jiong, Garcia, Angelica, Newhouse, Paul, Potkin, Steven, Salloway, Stephen, Malloy, Paul, Correia, Stephen, Kittur, Smita, Pearlson, Godfrey D., Blank, Karen, Anderson, Karen, Flashman, Laura A., Seltzer, Marc, Hynes, Mary L., Santulli, Robert B., Relkin, Norman, Chiang, Gloria, Lee, Athena, Lin, Michael, Ravdin, Lisa, Petersen, Ron, Neylan, Thomas, Grafman, Jordan, Danowski, Sarah, Nguyen-Barrera, Catherine, Hayes, Jacqueline, Finley, Shannon, Bernstein, Matthew, Senjem, Matt, Foster, Norm, Kim, Sungeun, Sood, Ajay, Blanchard, Kimberly S., Fleischman, Debra, Arfanakis, Konstantinos, Varon, Daniel, Greig, Maria T., Petrella, Jeffrey R., Goldstein, Bonnie, Martin, Kimberly S., Reist, Christopher, Sadowsky, Carl, Martinez, Walter, Villena, Teresa, Rosen, Howard, Marshall, Gad, Peskind, Elaine R., Petrie, Eric C., Li, Gail, Mackin, Scott, Jimenez-Maggiora, Gustavo, Drake, Erin, Donohue, Mike, Nelson, Craig, Bickford, David, Butters, Meryl, Zmuda, Michelle, Reyes, Denise, Faber, Kelley M., Nudelman, Kelly N., Au, Yiu Ho, Scherer, Kelly, Catalinotto, Daniel, Stark, Samuel, Ong, Elise, Fernandez, Dariella, Jo, Taeho, Kim, Junpyo, Bice, Paula, Huynh, Kevin, Wang, Tingting, Meikle, Peter J., and Giles, Corey

Published
2023
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15. Genome‐wide transcriptome analysis identifies novel dysregulated genes implicated in Alzheimer's pathology

Author

Nho, Kwangsik, Nudelman, Kelly, Allen, Mariet, Hodges, Angela, Kim, Sungeun, Risacher, Shannon L, Apostolova, Liana G, Lin, Kuang, Lunnon, Katie, Wang, Xue, Burgess, Jeremy D, Ertekin‐Taner, Nilüfer, Petersen, Ronald C, Wang, Lisu, Qi, Zhenhao, He, Aiqing, Neuhaus, Isaac, Patel, Vishal, Foroud, Tatiana, Faber, Kelley M, Lovestone, Simon, Simmons, Andrew, Weiner, Michael W, Saykin, Andrew J, and Initiative, for the Alzheimer's Disease Neuroimaging

Subjects
Biomedical and Clinical Sciences, Biological Psychology, Clinical Sciences, Neurosciences, Psychology, Neurodegenerative, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Genetics, Alzheimer's Disease, Acquired Cognitive Impairment, Human Genome, Aging, Brain Disorders, Dementia, Biotechnology, 2.1 Biological and endogenous factors, Aetiology, Neurological, Aged, Alzheimer Disease, Amyloid beta-Peptides, Aniline Compounds, Atrophy, Brain, Cyclic AMP Response Element-Binding Protein A, Entorhinal Cortex, Ethylene Glycols, Female, Gene Expression Profiling, Genotyping Techniques, Humans, Male, Positron-Emission Tomography, Alzheimer's disease, amyloid beta, ADNI, CREB5, imaging genetics, microarray gene expression, Alzheimer's Disease Neuroimaging Initiative, amyloid β, Geriatrics, Clinical sciences, Biological psychology
Abstract

IntroductionAbnormal gene expression patterns may contribute to the onset and progression of late-onset Alzheimer's disease (LOAD).MethodsWe performed transcriptome-wide meta-analysis (N = 1440) of blood-based microarray gene expression profiles as well as neuroimaging and cerebrospinal fluid (CSF) endophenotype analysis.ResultsWe identified and replicated five genes (CREB5, CD46, TMBIM6, IRAK3, and RPAIN) as significantly dysregulated in LOAD. The most significantly altered gene, CREB5, was also associated with brain atrophy and increased amyloid beta (Aβ) accumulation, especially in the entorhinal cortex region. cis-expression quantitative trait loci mapping analysis of CREB5 detected five significant associations (P < 5 × 10-8 ), where rs56388170 (most significant) was also significantly associated with global cortical Aβ deposition measured by [18 F]Florbetapir positron emission tomography and CSF Aβ1-42 .DiscussionRNA from peripheral blood indicated a differential gene expression pattern in LOAD. Genes identified have been implicated in biological processes relevant to Alzheimer's disease. CREB, in particular, plays a key role in nervous system development, cell survival, plasticity, and learning and memory.

Published
2020

16. Exosomes from Human Adipose Tissue-Derived Mesenchymal Stem Cells Promote Epidermal Barrier Repair by Inducing de Novo Synthesis of Ceramides in Atopic Dermatitis.

Author

Shin, Kyong-Oh, Ha, Dae Hyun, Kim, Jin Ock, Crumrine, Debra A, Meyer, Jason M, Wakefield, Joan S, Lee, Yerin, Kim, Bogyeong, Kim, Sungeun, Kim, Hyun-Keun, Lee, Joon, Kwon, Hyuck Hoon, Park, Gyeong-Hun, Lee, Jun Ho, Lim, Jihye, Park, Sejeong, Elias, Peter M, Park, Kyungho, Yi, Yong Weon, and Cho, Byong Seung

Subjects
ASC-exosomes, anti-inflammation, atopic dermatitis, ceramides, lamella body, restoration, skin barrier
Abstract

Atopic dermatitis (AD) is a multifactorial, heterogeneous disease associated with epidermal barrier disruption and intense systemic inflammation. Previously, we showed that exosomes derived from human adipose tissue-derived mesenchymal stem cells (ASC-exosomes) attenuate AD-like symptoms by reducing multiple inflammatory cytokine levels. Here, we investigated ASC-exosomes' effects on skin barrier restoration by analyzing protein and lipid contents. We found that subcutaneous injection of ASC-exosomes in an oxazolone-induced dermatitis model remarkably reduced trans-epidermal water loss, while enhancing stratum corneum (SC) hydration and markedly decreasing the levels of inflammatory cytokines such as IL-4, IL-5, IL-13, TNF-α, IFN-γ, IL-17, and TSLP, all in a dose-dependent manner. Interestingly, ASC-exosomes induced the production of ceramides and dihydroceramides. Electron microscopic analysis revealed enhanced epidermal lamellar bodies and formation of lamellar layer at the interface of the SC and stratum granulosum with ASC-exosomes treatment. Deep RNA sequencing analysis of skin lesions demonstrated that ASC-exosomes restores the expression of genes involved in skin barrier, lipid metabolism, cell cycle, and inflammatory response in the diseased area. Collectively, our results suggest that ASC-exosomes effectively restore epidermal barrier functions in AD by facilitating the de novo synthesis of ceramides, resulting in a promising cell-free therapeutic option for treating AD.

Published
2020

17. Women can bear a bigger burden: ante- and post-mortem evidence for reserve in the face of tau

Author

Digma, Leonardino A, Madsen, John R, Rissman, Robert A, Jacobs, Diane M, Brewer, James B, Banks, Sarah J, Weiner, Michael, Aisen, Paul, Petersen, Ronald, Jack, Clifford R, Jagust, William, Trojanowki, John Q, Toga, Arthur W, Beckett, Laurel, Green, Robert C, Saykin, Andrew J, Morris, John, Shaw, Leslie M, Liu, Enchi, Montine, Tom, Thomas, Ronald G, Donohue, Michael, Walter, Sarah, Gessert, Devon, Sather, Tamie, Jiminez, Gus, Harvey, Danielle, Bernstein, Matthew, Fox, Nick, Thompson, Paul, Schuff, Norbert, DeCArli, Charles, Borowski, Bret, Gunter, Jeff, Senjem, Matt, Vemuri, Prashanthi, Jones, David, Kantarci, Kejal, Ward, Chad, Koeppe, Robert A, Foster, Norm, Reiman, Eric M, Chen, Kewei, Mathis, Chet, Landau, Susan, Cairns, Nigel J, Householder, Erin, Reinwald, Lisa Taylor, Lee, Virginia, Korecka, Magdalena, Figurski, Michal, Crawford, Karen, Neu, Scott, Foroud, Tatiana M, Potkin, Steven, Shen, Li, Kelley, Faber, Kim, Sungeun, Nho, Kwangsik, Kachaturian, Zaven, Frank, Richard, Snyder, Peter J, Molchan, Susan, Kaye, Jeffrey, Quinn, Joseph, Lind, Betty, Carter, Raina, Dolen, Sara, Schneider, Lon S, Pawluczyk, Sonia, Beccera, Mauricio, Teodoro, Liberty, Spann, Bryan M, Brewer, James, Vanderswag, Helen, Fleisher, Adam, Heidebrink, Judith L, Lord, Joanne L, Mason, Sara S, Albers, Colleen S, Knopman, David, Johnson, Kris, Doody, Rachelle S, Meyer, Javier Villanueva, Chowdhury, Munir, Rountree, Susan, Dang, Mimi, Stern, Yaakov, Honig, Lawrence S, Bell, Karen L, Ances, Beau, Morris, John C, Carroll, Maria, Leon, Sue, Mintun, Mark A, Schneider, Stacy, and Oliver, Angela

Subjects
Biological Psychology, Psychology, Brain Disorders, Neurodegenerative, Alzheimer's Disease, Neurosciences, Acquired Cognitive Impairment, Women's Health, Aging, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Dementia, Clinical Research, tau, verbal memory, sex differences, Alzheimer's disease, Alzheimer’s Disease Neuroimaging Initiative, Alzheimer’s disease, Clinical sciences, Biological psychology
Abstract

In this study, we aimed to assess whether women are able to withstand more tau before exhibiting verbal memory impairment. Using data from 121 amyloid-β-positive Alzheimer's Disease Neuroimaging Initiative participants, we fit a linear model with Rey Auditory Verbal Learning Test score as the response variable and tau-PET standard uptake value ratio as the predictor and took the residuals as an estimate of verbal memory reserve for each subject. Women demonstrated higher reserve (i.e. residuals), whether the Learning (t = 2.78, P = 0.006) or Delay (t = 2.14, P = 0.03) score from the Rey Auditory Verbal Learning Test was used as a measure of verbal memory ability. To validate these findings, we examined 662 National Alzheimer's Coordinating Center participants with a C2/C3 score (Consortium to Establish a Registry for Alzheimer's Disease) at autopsy. We stratified our National Alzheimer's Coordinating Center sample into Braak 1/2, Braak 3/4 and Braak 5/6 subgroups. Within each subgroup, we compared Logical Memory scores between men and women. Men had worse verbal memory scores within the Braak 1/2 (Logical Memory Immediate: β = -5.960 ± 1.517, P

Published
2020

18. CO Outflow Survey of 68 Very Low Luminosity Objects: a Search for Proto-Brown Dwarf Candidates

Author

Kim, Gwanjeong, Lee, Chang Won, Maheswar, Gopinathan, Kim, Mi-Ryang, Soam, Archana, Saito, Masao, Kiyokane, Kazuhiro, and Kim, Sungeun

Subjects
Astrophysics - Astrophysics of Galaxies
Abstract

We present the results of a systematic search for molecular outflows in 68 Very Low Luminosity Objects (VeLLOs) from single-dish observations in CO isotopologues which find 16 VeLLOs showing clear outflow signatures in the CO maps. With additional three VeLLOs from the literature, we analyzed the outflow properties for 19 VeLLOs, identifying 15 VeLLOs as proto-Brown Dwarf (BD) candidates and four VeLLOs as likely faint protostar candidates. The proto-BD candidates are found to have a mass accretion rate ($\sim 10^{-8} - 10^{-7}$ $\rm M_{\odot}$ yr$^{-1}$) lower than that of the protostar candidates ($\gtrsim 10^{-6}$ $\rm M_{\odot}$ yr$^{-1}$). Their accretion luminosities are similar to or smaller than their internal luminosities, implying that many proto-BD candidates might have had either small accretion activity in a quiescent manner throughout their lifetime, or be currently exhibiting a relatively higher (or episodic) mass accretion than the past. There are strong trends that outflows of many proto-BDs are less active if they are fainter or have less massive envelopes. The outflow forces and internal luminosities for more than half of the proto-BD candidates seem to follow an evolutionary track of a protostar with its initial envelope mass of $\sim$0.08 $\rm M_{\odot}$, indicating that some BDs may form in less massive dense cores in a way similar to normal stars. But, because there also exists a significant fraction (about 40%) of proto-BDs with much weaker outflow force than expected by the relations for protostars, we should not rule out the possibility of other formation mechanism for the BDs., Comment: 32 pages, 9 Figures, 5 Tables, Accepted for publication in ApJS

Published
2018
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19. Genetic architecture of subcortical brain structures in 38,851 individuals

Author

Satizabal, Claudia L, Adams, Hieab HH, Hibar, Derrek P, White, Charles C, Knol, Maria J, Stein, Jason L, Scholz, Markus, Sargurupremraj, Muralidharan, Jahanshad, Neda, Roshchupkin, Gennady V, Smith, Albert V, Bis, Joshua C, Jian, Xueqiu, Luciano, Michelle, Hofer, Edith, Teumer, Alexander, van der Lee, Sven J, Yang, Jingyun, Yanek, Lisa R, Lee, Tom V, Li, Shuo, Hu, Yanhui, Koh, Jia Yu, Eicher, John D, Desrivières, Sylvane, Arias-Vasquez, Alejandro, Chauhan, Ganesh, Athanasiu, Lavinia, Rentería, Miguel E, Kim, Sungeun, Hoehn, David, Armstrong, Nicola J, Chen, Qiang, Holmes, Avram J, den Braber, Anouk, Kloszewska, Iwona, Andersson, Micael, Espeseth, Thomas, Grimm, Oliver, Abramovic, Lucija, Alhusaini, Saud, Milaneschi, Yuri, Papmeyer, Martina, Axelsson, Tomas, Ehrlich, Stefan, Roiz-Santiañez, Roberto, Kraemer, Bernd, Håberg, Asta K, Jones, Hannah J, Pike, G Bruce, Stein, Dan J, Stevens, Allison, Bralten, Janita, Vernooij, Meike W, Harris, Tamara B, Filippi, Irina, Witte, A Veronica, Guadalupe, Tulio, Wittfeld, Katharina, Mosley, Thomas H, Becker, James T, Doan, Nhat Trung, Hagenaars, Saskia P, Saba, Yasaman, Cuellar-Partida, Gabriel, Amin, Najaf, Hilal, Saima, Nho, Kwangsik, Mirza-Schreiber, Nazanin, Arfanakis, Konstantinos, Becker, Diane M, Ames, David, Goldman, Aaron L, Lee, Phil H, Boomsma, Dorret I, Lovestone, Simon, Giddaluru, Sudheer, Le Hellard, Stephanie, Mattheisen, Manuel, Bohlken, Marc M, Kasperaviciute, Dalia, Schmaal, Lianne, Lawrie, Stephen M, Agartz, Ingrid, Walton, Esther, Tordesillas-Gutierrez, Diana, Davies, Gareth E, Shin, Jean, Ipser, Jonathan C, Vinke, Louis N, Hoogman, Martine, Jia, Tianye, Burkhardt, Ralph, Klein, Marieke, Crivello, Fabrice, Janowitz, Deborah, Carmichael, Owen, Haukvik, Unn K, Aribisala, Benjamin S, and Schmidt, Helena

Subjects
Biological Sciences, Genetics, Neurosciences, Biotechnology, Mental Health, Human Genome, Brain Disorders, Aetiology, 2.1 Biological and endogenous factors, Neurological, Adult, Aged, Animals, Brain, Cohort Studies, Drosophila melanogaster, Genetic Variation, Genome-Wide Association Study, Humans, Magnetic Resonance Imaging, Middle Aged, Neurodevelopmental Disorders, Organ Size, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Subcortical brain structures are integral to motion, consciousness, emotions and learning. We identified common genetic variation related to the volumes of the nucleus accumbens, amygdala, brainstem, caudate nucleus, globus pallidus, putamen and thalamus, using genome-wide association analyses in almost 40,000 individuals from CHARGE, ENIGMA and UK Biobank. We show that variability in subcortical volumes is heritable, and identify 48 significantly associated loci (40 novel at the time of analysis). Annotation of these loci by utilizing gene expression, methylation and neuropathological data identified 199 genes putatively implicated in neurodevelopment, synaptic signaling, axonal transport, apoptosis, inflammation/infection and susceptibility to neurological disorders. This set of genes is significantly enriched for Drosophila orthologs associated with neurodevelopmental phenotypes, suggesting evolutionarily conserved mechanisms. Our findings uncover novel biology and potential drug targets underlying brain development and disease.

Published
2019

21. Cancer Prediction With Machine Learning of Thrombi From Thrombectomy in Stroke: Multicenter Development and Validation

Author

Heo, JoonNyung, Lee, Hyungwoo, Seog, Young, Kim, Sungeun, Baek, Jang-Hyun, Park, Hyungjong, Seo, Kwon-Duk, Kim, Gyu Sik, Cho, Han-Jin, Baik, Minyoul, Yoo, Joonsang, Kim, Jinkwon, Lee, Jun, Chang, Yoonkyung, Song, Tae-Jin, Seo, Jung Hwa, Ahn, Seong Hwan, Lee, Heow Won, Kwon, Il, Park, Eunjeong, Kim, Byung Moon, Kim, Dong Joon, Kim, Young Dae, and Nam, Hyo Suk

Published
2023
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23. Telomere Shortening in the Alzheimer’s Disease Neuroimaging Initiative Cohort

Author

Nudelman, Kelly NH, Lin, Jue, Lane, Kathleen A, Nho, Kwangsik, Kim, Sungeun, Faber, Kelley M, Risacher, Shannon L, Foroud, Tatiana M, Gao, Sujuan, Davis, Justin W, Weiner, Michael W, Saykin, Andrew J, and Initiative, for the Alzheimer’s Disease Neuroimaging

Subjects
Biomedical and Clinical Sciences, Biological Psychology, Clinical Sciences, Neurosciences, Psychology, Alzheimer's Disease, Dementia, Aging, Acquired Cognitive Impairment, Genetics, Brain Disorders, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Clinical Research, Neurodegenerative, Neurological, Age Factors, Aged, Alzheimer Disease, Databases, Factual, Disease Progression, Female, Humans, Male, Neuroimaging, Sex Factors, Telomere Homeostasis, Telomere Shortening, Alzheimer's disease, longitudinal, progression, shortening, telomere, Alzheimer’s Disease Neuroimaging Initiative, Alzheimer’s disease, Cognitive Sciences, Neurology & Neurosurgery, Clinical sciences, Biological psychology
Abstract

BackgroundAlthough shorter telomeres have been associated with Alzheimer's disease (AD), it is unclear whether longitudinal change in telomere length is associated with AD progression.ObjectiveTo investigate the association of telomere length change with AD diagnosis and progression.MethodsIn 653 individuals from the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort, T/S ratio (telomere versus single copy gene), a proxy of telomere length, was measured for up to five visits per participant (N = 1918 samples post-QC) using quantitative PCR (qPCR). T/S ratio was adjusted for batch effects and DNA storage time. A mixed effects model was used to evaluate association of telomere length with AD diagnostic group and interaction of age and diagnosis. Another mixed effects model was used to compare T/S ratio changes pre- to post-conversion to MCI or AD to telomere change in participants with stable diagnoses.ResultsShorter telomeres were associated with older age (Effect Size (ES) = -0.23) and male sex (ES = -0.26). Neither baseline T/S ratio (ES = -0.036) nor T/S ratio change (ES = 0.046) differed significantly between AD diagnostic groups. MCI/AD converters showed greater, but non-significant, telomere shortening compared to non-converters (ES = -0.186).ConclusionsAlthough AD compared to controls showed small, non-significant effects for baseline T/S ratio and T/S ratio shortening, we did observe a larger, though still non-significant effect for greater telomere shortening in converters compared to non-converters. Although our results do not support telomere shortening as a robust biomarker of AD progression, further investigation in larger samples and for subgroups of participants may be informative.

Published
2019

24. 18F-florbetapir Positron Emission Tomography–determined Cerebral &bgr;-Amyloid Deposition and Neurocognitive Performance after Cardiac Surgery

Author

Klinger, Rebecca Y, James, Olga G, Borges-Neto, Salvador, Bisanar, Tiffany, Li, Yi-Ju, Qi, Wenjing, Berger, Miles, Terrando, Niccolò, Newman, Mark F, Doraiswamy, P Murali, Mathew, Joseph P, Weiner, Michael W, Aisen, Paul, Weiner, Michael, Petersen, Ronald, Jack, Clifford R, Jagust, William, Trojanowki, John Q, Toga, Arthur W, Beckett, Laurel, Green, Robert C, Saykin, Andrew J, Morris, John, Shaw, Leslie M, Khachaturian, Zaven, Sorensen, Greg, Carrillo, Maria, Kuller, Lew, Raichle, Marc, Paul, Steven, Davies, Peter, Fillit, Howard, Hefti, Franz, Holtzman, David, Mesulam, M Marcel, Potter, William, Snyder, Peter, Schwartz, Adam, Montine, Tom, Thomas, Ronald G, Donohue, Michael, Walter, Sarah, Gessert, Devon, Sather, Tamie, Jiminez, Gus, Balasubramanian, Archana B, Mason, Jennifer, Sim, Iris, Harvey, Danielle, Bernstein, Matthew, Fox, Nick, Thompson, Paul, Schuff, Norbert, DeCArli, Charles, Borowski, Bret, Gunter, Jeff, Senjem, Matt, Vemuri, Prashanthi, Jones, David, Kantarci, Kejal, Ward, Chad, Koeppe, Robert A, Foster, Norm, Reiman, Eric M, Chen, Kewei, Mathis, Chet, Landau, Susan, Morris, John C, Cairns, Louis Nigel J, Franklin, Erin, Taylor-Reinwald, Lisa, Lee, Virginia, Korecka, Magdalena, Figurski, Michal, Crawford, Karen, Neu, Scott, Foroud, Tatiana M, Potkin, Steven, Shen, Li, Faber, Kelley, Kim, Sungeun, Nho, Kwangsik, Thal, Lean, Thal, Leon, and Buckholtz, Neil

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Mental Health, Aging, Brain Disorders, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Behavioral and Social Science, Biomedical Imaging, Clinical Research, Neurosciences, Alzheimer's Disease, Dementia, Neurodegenerative, Acquired Cognitive Impairment, 2.1 Biological and endogenous factors, Neurological, Aged, Amyloid beta-Peptides, Aniline Compounds, Brain, Cardiac Surgical Procedures, Cognitive Dysfunction, Ethylene Glycols, Female, Fluorine Radioisotopes, Humans, Male, Mental Status and Dementia Tests, Middle Aged, Positron-Emission Tomography, Postoperative Complications, Prospective Studies, Alzheimer’s Disease Neuroimaging Initiative (ADNI) Study Group, Neurologic Outcomes Research Group, Anesthesiology, Clinical sciences
Abstract

BackgroundAmyloid deposition is a potential contributor to postoperative cognitive dysfunction. The authors hypothesized that 6-week global cortical amyloid burden, determined by F-florbetapir positron emission tomography, would be greater in those patients manifesting cognitive dysfunction at 6 weeks postoperatively.MethodsAmyloid deposition was evaluated in cardiac surgical patients at 6 weeks (n = 40) and 1 yr (n = 12); neurocognitive function was assessed at baseline (n = 40), 6 weeks (n = 37), 1 yr (n = 13), and 3 yr (n = 9). The association of 6-week amyloid deposition with cognitive dysfunction was assessed by multivariable regression, accounting for age, years of education, and baseline cognition. Differences between the surgical cohort with cognitive deficit and the Alzheimer's Disease Neuroimaging Initiative cohorts (normal and early/late mild cognitive impairment) was assessed, adjusting for age, education, and apolipoprotein E4 genotype.ResultsThe authors found that 6-week abnormal global cortical amyloid deposition was not associated with cognitive dysfunction (13 of 37, 35%) at 6 weeks postoperatively (median standard uptake value ratio [interquartile range]: cognitive dysfunction 0.92 [0.89 to 1.07] vs. 0.98 [0.93 to 1.05]; P = 0.455). In post hoc analyses, global cortical amyloid was also not associated with cognitive dysfunction at 1 or 3 yr postoperatively. Amyloid deposition at 6 weeks in the surgical cohort was not different from that in normal Alzheimer's Disease Neuroimaging Initiative subjects, but increased over 1 yr in many areas at a rate greater than in controls.ConclusionsIn this study, postoperative cognitive dysfunction was not associated with 6-week cortical amyloid deposition. The relationship between cognitive dysfunction and regional amyloid burden and the rate of postoperative amyloid deposition merit further investigation.

Published
2018

25. Identification of genetic risk factors in the Chinese population implicates a role of immune system in Alzheimer’s disease pathogenesis

Author

Zhou, Xiaopu, Chen, Yu, Mok, Kin Y, Zhao, Qianhua, Chen, Keliang, Chen, Yuewen, Hardy, John, Li, Yun, Fu, Amy KY, Guo, Qihao, Ip, Nancy Y, Saykin, Andrew J, Toga, Arthur W, Borowski, Bret, Ward, Chad, DeCarli, Charles, Mathis, Chet, Jack, Clifford R, Harvey, Danielle, Holtzman, David, Jones, David, Gessert, Devon, Lilly, Eli, Reiman, Eric M, Franklin, Erin, Hefti, Franz, Sorensen, Greg, Jimenez, Gustavo, Fillit, Howard, Gunter, Jeff, Salazar, Jennifer, Hsiao, John, Morris, John, Trojanowki, John Q, Neu, Karen Crawford Scott, Kantarci, Kejal, Faber, Kelley, Harless, Kelly, Chen, Kewei, Nho, Kwangsik, Beckett, Laurel, Thal, Lean, Thal, Leon, Shaw, Leslie M, Kuller, Lew, Shen, Li, Hergesheimer, Lindsey, Taylor-Reinwald, Lisa, Mesulam, M Marcel, Korecka, Magdalena, Raichle, Marc, Carrillo, Maria, Albert, Marilyn, Senjem, Matt, Bernstein, Matthew, Donohue, Michael, Weiner, Michael, Figurski, Michal, Buckholtz, Neil, Fox, Nick, Cairns, Nigel J, Schuff, Norbert, Foster, Norm, Aisen, Paul, Thompson, Paul, Davies, Peter, Snyder, Peter J, Snyder, Peter, Vemuri, Prashanthi, Frank, Richard, Koeppe, Robert A, Green, Robert C, Petersen, Ronald, Walter, Sarah, Paul, Steven, Potkin, Steven, Kim, Sungeun, Foroud, Tatiana M, Montine, Tom, Lee, Virginia, Jagust, William, Potter, William, Cabrera, Yuliana, Khachaturian, Zaven, Fleisher, Adam, Pierce, Aimee, Mintz, Akiva, Lerner, Alan, Norbash, Alexander, Levey, Allan I, Rosen, Allyson, Smith, Amanda, Ulysse, Anaztasia, Budson, Andrew E, Kertesz, Andrew, Oliver, Angela, Hake, Ann Marie, Burke, Anna, Sarrael, Antero, and Porsteinsson, Anton P

Subjects
Biological Sciences, Genetics, Dementia, Acquired Cognitive Impairment, Prevention, Brain Disorders, Aging, Human Genome, Neurosciences, Alzheimer's Disease, Neurodegenerative, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), 2.1 Biological and endogenous factors, Aetiology, Detection, screening and diagnosis, 4.1 Discovery and preclinical testing of markers and technologies, Good Health and Well Being, Age of Onset, Aged, Aged, 80 and over, Alzheimer Disease, Apolipoproteins E, Asian People, China, Cohort Studies, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Genotype, Humans, Immune System, Male, Middle Aged, Potassium Channels, Inwardly Rectifying, Risk Factors, Alzheimer’s Disease Neuroimaging Initiative, Alzheimer’s disease, GWAS, immune, risk variant, whole-genome sequencing
Abstract

Alzheimer's disease (AD) is a leading cause of mortality among the elderly. We performed a whole-genome sequencing study of AD in the Chinese population. In addition to the variants identified in or around the APOE locus (sentinel variant rs73052335, P = 1.44 × 10-14), two common variants, GCH1 (rs72713460, P = 4.36 × 10-5) and KCNJ15 (rs928771, P = 3.60 × 10-6), were identified and further verified for their possible risk effects for AD in three small non-Asian AD cohorts. Genotype-phenotype analysis showed that KCNJ15 variant rs928771 affects the onset age of AD, with earlier disease onset in minor allele carriers. In addition, altered expression level of the KCNJ15 transcript can be observed in the blood of AD subjects. Moreover, the risk variants of GCH1 and KCNJ15 are associated with changes in their transcript levels in specific tissues, as well as changes of plasma biomarkers levels in AD subjects. Importantly, network analysis of hippocampus and blood transcriptome datasets suggests that the risk variants in the APOE, GCH1, and KCNJ15 loci might exert their functions through their regulatory effects on immune-related pathways. Taking these data together, we identified common variants of GCH1 and KCNJ15 in the Chinese population that contribute to AD risk. These variants may exert their functional effects through the immune system.

Published
2018

26. Targeted neurogenesis pathway-based gene analysis identifies ADORA2A associated with hippocampal volume in mild cognitive impairment and Alzheimer's disease

Author

Horgusluoglu-Moloch, Emrin, Nho, Kwangsik, Risacher, Shannon L, Kim, Sungeun, Foroud, Tatiana, Shaw, Leslie M, Trojanowski, John Q, Aisen, Paul S, Petersen, Ronald C, Jack, Clifford R, Lovestone, Simon, Simmons, Andrew, Weiner, Michael W, Saykin, Andrew J, and Initiative, Alzheimer's Disease Neuroimaging

Subjects
Biological Psychology, Psychology, Neurosciences, Neurodegenerative, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Aging, Acquired Cognitive Impairment, Stem Cell Research, Mental Health, Alzheimer's Disease, Behavioral and Social Science, Dementia, Brain Disorders, Genetics, 2.1 Biological and endogenous factors, Aetiology, Mental health, Neurological, Aged, Aged, 80 and over, Alleles, Alzheimer Disease, Cognition, Cognitive Dysfunction, Female, Genome-Wide Association Study, Hippocampus, Humans, Male, Middle Aged, Neurogenesis, Organ Size, Receptor, Adenosine A2A, ADORA2A, Hippocampal volume, Memory, Alzheimer's disease, Gene-based association analysis, NMDA-receptor antagonist, Alzheimer's Disease Neuroimaging Initiative, Clinical Sciences, Neurology & Neurosurgery, Biological psychology
Abstract

Alzheimer's disease (AD) patients display hippocampal atrophy, memory impairment, and cognitive decline. New neurons are generated throughout adulthood in 2 regions of the brain implicated in AD, the dentate gyrus of the hippocampus and the subventricular zone of the olfactory bulb. Disruption of this process contributes to neurodegenerative diseases including AD, and many of the molecular players in AD are also modulators of adult neurogenesis. However, the genetic mechanisms underlying adult neurogenesis in AD have been underexplored. To address this gap, we performed a gene-based association analysis in cognitively normal and impaired participants using neurogenesis pathway-related candidate genes curated from existing databases, literature mining, and large-scale genome-wide association study findings. A gene-based association analysis identified adenosine A2a receptor (ADORA2A) as significantly associated with hippocampal volume and the association between rs9608282 within ADORA2A and hippocampal volume was replicated in the meta-analysis after multiple comparison adjustments (p = 7.88 × 10-6). The minor allele of rs9608282 in ADORA2A is associated with larger hippocampal volumes and better memory.

Published
2017

31. Phenotypic Overlap between Atopic Dermatitis and Autism

Author

Shin, Kyong‑Oh, primary, Crumrine, Debra A, additional, Kim, Sungeun, additional, Lee, Yerin, additional, Kim, Bogyeong, additional, Abuabara, Katrina, additional, Park, Chaehyeong, additional, Uchida, Yoshikazu, additional, Wakefield, Joan S, additional, Meyer, Jason M, additional, Jeong, Sekyoo, additional, Park, Byeong Deog, additional, Park, Kyungho, additional, and Elias, Peter M, additional

Published
2022
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32. Metabolic network failures in Alzheimer's disease: A biochemical road map

Author

Toledo, Jon B, Arnold, Matthias, Kastenmüller, Gabi, Chang, Rui, Baillie, Rebecca A, Han, Xianlin, Thambisetty, Madhav, Tenenbaum, Jessica D, Suhre, Karsten, Thompson, J Will, St. John‐Williams, Lisa, MahmoudianDehkordi, Siamak, Rotroff, Daniel M, Jack, John R, Motsinger‐Reif, Alison, Risacher, Shannon L, Blach, Colette, Lucas, Joseph E, Massaro, Tyler, Louie, Gregory, Zhu, Hongjie, Dallmann, Guido, Klavins, Kristaps, Koal, Therese, Kim, Sungeun, Nho, Kwangsik, Shen, Li, Casanova, Ramon, Varma, Sudhir, Legido‐Quigley, Cristina, Moseley, M Arthur, Zhu, Kuixi, Henrion, Marc YR, van der Lee, Sven J, Harms, Amy C, Demirkan, Ayse, Hankemeier, Thomas, van Duijn, Cornelia M, Trojanowski, John Q, Shaw, Leslie M, Saykin, Andrew J, Weiner, Michael W, Doraiswamy, P Murali, and Kaddurah‐Daouk, Rima

Subjects
Medical Biochemistry and Metabolomics, Biomedical and Clinical Sciences, Clinical Research, Neurosciences, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Neurodegenerative, Alzheimer's Disease, Acquired Cognitive Impairment, Aging, Dementia, Brain Disorders, Aetiology, 2.1 Biological and endogenous factors, Neurological, Aged, Aged, 80 and over, Alzheimer Disease, Amino Acids, Amyloid beta-Peptides, Aniline Compounds, Cognitive Dysfunction, Cohort Studies, Cross-Sectional Studies, Fasting, Female, Humans, Male, Metabolic Diseases, Metabolic Networks and Pathways, Metabolomics, Peptide Fragments, Phosphatidylcholines, Sphingomyelins, Thiazoles, tau Proteins, Metabonomics, Pharmacometabolomics, Pharmacometabonomics, Biomarkers, Serum, Metabolism, Systems biology, Biochemical networks, Precision medicine, Alzheimer's disease, Branched-chain amino acids, Phospholipids, Acylcarnitines, Alzheimer's Disease Neuroimaging Initiative and the Alzheimer Disease Metabolomics Consortium, Clinical Sciences, Geriatrics, Clinical sciences, Biological psychology
Abstract

IntroductionThe Alzheimer's Disease Research Summits of 2012 and 2015 incorporated experts from academia, industry, and nonprofit organizations to develop new research directions to transform our understanding of Alzheimer's disease (AD) and propel the development of critically needed therapies. In response to their recommendations, big data at multiple levels are being generated and integrated to study network failures in disease. We used metabolomics as a global biochemical approach to identify peripheral metabolic changes in AD patients and correlate them to cerebrospinal fluid pathology markers, imaging features, and cognitive performance.MethodsFasting serum samples from the Alzheimer's Disease Neuroimaging Initiative (199 control, 356 mild cognitive impairment, and 175 AD participants) were analyzed using the AbsoluteIDQ-p180 kit. Performance was validated in blinded replicates, and values were medication adjusted.ResultsMultivariable-adjusted analyses showed that sphingomyelins and ether-containing phosphatidylcholines were altered in preclinical biomarker-defined AD stages, whereas acylcarnitines and several amines, including the branched-chain amino acid valine and α-aminoadipic acid, changed in symptomatic stages. Several of the analytes showed consistent associations in the Rotterdam, Erasmus Rucphen Family, and Indiana Memory and Aging Studies. Partial correlation networks constructed for Aβ1-42, tau, imaging, and cognitive changes provided initial biochemical insights for disease-related processes. Coexpression networks interconnected key metabolic effectors of disease.DiscussionMetabolomics identified key disease-related metabolic changes and disease-progression-related changes. Defining metabolic changes during AD disease trajectory and its relationship to clinical phenotypes provides a powerful roadmap for drug and biomarker discovery.

Published
2017

33. Association analysis of rare variants near the APOE region with CSF and neuroimaging biomarkers of Alzheimer’s disease

Author

Nho, Kwangsik, Kim, Sungeun, Horgusluoglu, Emrin, Risacher, Shannon L, Shen, Li, Kim, Dokyoon, Lee, Seunggeun, Foroud, Tatiana, Shaw, Leslie M, Trojanowski, John Q, Aisen, Paul S, Petersen, Ronald C, Jack, Clifford R, Weiner, Michael W, Green, Robert C, Toga, Arthur W, Saykin, Andrew J, and for the Alzheimer’s Disease Neuroimaging Initiative (ADNI)

Subjects
Biological Sciences, Genetics, Human Genome, Dementia, Alzheimer's Disease, Acquired Cognitive Impairment, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Biomedical Imaging, Prevention, Neurodegenerative, Clinical Research, Neurosciences, Aging, Brain Disorders, 4.1 Discovery and preclinical testing of markers and technologies, Aetiology, 2.1 Biological and endogenous factors, Detection, screening and diagnosis, Neurological, Alzheimer Disease, Amyloid beta-Peptides, Apolipoproteins E, Chromosomes, Human, Pair 19, Female, Humans, Male, Neuroimaging, Peptide Fragments, Polymorphism, Single Nucleotide, Whole Genome Sequencing, Whole genome sequencing, Rare variants, Near APOE, ADNI, CSF, Alzheimer’s Disease Neuroimaging Initiative, Medical Biochemistry and Metabolomics, Oncology and Carcinogenesis, Genetics & Heredity, Medical biochemistry and metabolomics
Abstract

BackgroundThe APOE ε4 allele is the most significant common genetic risk factor for late-onset Alzheimer's disease (LOAD). The region surrounding APOE on chromosome 19 has also shown consistent association with LOAD. However, no common variants in the region remain significant after adjusting for APOE genotype. We report a rare variant association analysis of genes in the vicinity of APOE with cerebrospinal fluid (CSF) and neuroimaging biomarkers of LOAD.MethodsWhole genome sequencing (WGS) was performed on 817 blood DNA samples from the Alzheimer's Disease Neuroimaging Initiative (ADNI). Sequence data from 757 non-Hispanic Caucasian participants was used in the present analysis. We extracted all rare variants (MAF (minor allele frequency)

Published
2017

34. Novel genetic loci associated with hippocampal volume.

Author

Hibar, Derrek P, Adams, Hieab HH, Jahanshad, Neda, Chauhan, Ganesh, Stein, Jason L, Hofer, Edith, Renteria, Miguel E, Bis, Joshua C, Arias-Vasquez, Alejandro, Ikram, M Kamran, Desrivières, Sylvane, Vernooij, Meike W, Abramovic, Lucija, Alhusaini, Saud, Amin, Najaf, Andersson, Micael, Arfanakis, Konstantinos, Aribisala, Benjamin S, Armstrong, Nicola J, Athanasiu, Lavinia, Axelsson, Tomas, Beecham, Ashley H, Beiser, Alexa, Bernard, Manon, Blanton, Susan H, Bohlken, Marc M, Boks, Marco P, Bralten, Janita, Brickman, Adam M, Carmichael, Owen, Chakravarty, M Mallar, Chen, Qiang, Ching, Christopher RK, Chouraki, Vincent, Cuellar-Partida, Gabriel, Crivello, Fabrice, Den Braber, Anouk, Doan, Nhat Trung, Ehrlich, Stefan, Giddaluru, Sudheer, Goldman, Aaron L, Gottesman, Rebecca F, Grimm, Oliver, Griswold, Michael E, Guadalupe, Tulio, Gutman, Boris A, Hass, Johanna, Haukvik, Unn K, Hoehn, David, Holmes, Avram J, Hoogman, Martine, Janowitz, Deborah, Jia, Tianye, Jørgensen, Kjetil N, Karbalai, Nazanin, Kasperaviciute, Dalia, Kim, Sungeun, Klein, Marieke, Kraemer, Bernd, Lee, Phil H, Liewald, David CM, Lopez, Lorna M, Luciano, Michelle, Macare, Christine, Marquand, Andre F, Matarin, Mar, Mather, Karen A, Mattheisen, Manuel, McKay, David R, Milaneschi, Yuri, Muñoz Maniega, Susana, Nho, Kwangsik, Nugent, Allison C, Nyquist, Paul, Loohuis, Loes M Olde, Oosterlaan, Jaap, Papmeyer, Martina, Pirpamer, Lukas, Pütz, Benno, Ramasamy, Adaikalavan, Richards, Jennifer S, Risacher, Shannon L, Roiz-Santiañez, Roberto, Rommelse, Nanda, Ropele, Stefan, Rose, Emma J, Royle, Natalie A, Rundek, Tatjana, Sämann, Philipp G, Saremi, Arvin, Satizabal, Claudia L, Schmaal, Lianne, Schork, Andrew J, Shen, Li, Shin, Jean, Shumskaya, Elena, Smith, Albert V, Sprooten, Emma, Strike, Lachlan T, and Teumer, Alexander

Subjects
Hippocampus, Humans, Alzheimer Disease, Genetic Predisposition to Disease, Protein-Serine-Threonine Kinases, Glycoproteins, Microtubule-Associated Proteins, Nerve Tissue Proteins, Organ Size, Cohort Studies, Adolescent, Adult, Aged, Aged, 80 and over, Middle Aged, Child, Female, Male, Genome-Wide Association Study, Young Adult, Methionine Sulfoxide Reductases, Genetic Loci, Dipeptidyl Peptidase 4, Human Genome, Aging, Brain Disorders, Clinical Research, Acquired Cognitive Impairment, Neurodegenerative, Dementia, Neurosciences, Prevention, Genetics, Alzheimer's Disease, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Mental Health, 2.1 Biological and endogenous factors, Mental health, Neurological
Abstract

The hippocampal formation is a brain structure integrally involved in episodic memory, spatial navigation, cognition and stress responsiveness. Structural abnormalities in hippocampal volume and shape are found in several common neuropsychiatric disorders. To identify the genetic underpinnings of hippocampal structure here we perform a genome-wide association study (GWAS) of 33,536 individuals and discover six independent loci significantly associated with hippocampal volume, four of them novel. Of the novel loci, three lie within genes (ASTN2, DPP4 and MAST4) and one is found 200 kb upstream of SHH. A hippocampal subfield analysis shows that a locus within the MSRB3 gene shows evidence of a localized effect along the dentate gyrus, subiculum, CA1 and fissure. Further, we show that genetic variants associated with decreased hippocampal volume are also associated with increased risk for Alzheimer's disease (rg=-0.155). Our findings suggest novel biological pathways through which human genetic variation influences hippocampal volume and risk for neuropsychiatric illness.

Published
2017

35. Plasma Tau Association with Brain Atrophy in Mild Cognitive Impairment and Alzheimer’s Disease

Author

Deters, Kacie D, Risacher, Shannon L, Kim, Sungeun, Nho, Kwangsik, West, John D, Blennow, Kaj, Zetterberg, Henrik, Shaw, Leslie M, Trojanowski, John Q, Weiner, Michael W, and Saykin, Andrew J

Subjects
Biological Psychology, Psychology, Clinical Research, Neurosciences, Brain Disorders, Neurodegenerative, Aging, Clinical Trials and Supportive Activities, Dementia, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Acquired Cognitive Impairment, Alzheimer's Disease, Aetiology, 2.1 Biological and endogenous factors, Neurological, Aged, Aged, 80 and over, Alzheimer Disease, Apolipoproteins E, Atrophy, Brain, Cognitive Dysfunction, Cross-Sectional Studies, Female, Humans, Magnetic Resonance Imaging, Male, Neuropsychological Tests, Psychiatric Status Rating Scales, tau Proteins, Alzheimer disease, magnetic resonance imaging, mild cognitive impairment, plasma, tau protein, Alzheimer Disease Neuroimaging Initiative, Clinical Sciences, Cognitive Sciences, Neurology & Neurosurgery, Clinical sciences, Biological psychology
Abstract

BackgroundPeripheral (plasma) and central (cerebrospinal fluid, CSF) measures of tau are higher in Alzheimer's disease (AD) relative to prodromal stages and controls. While elevated CSF tau concentrations have been shown to be associated with lower grey matter density (GMD) in AD-specific regions, this correlation has yet to be examined for plasma in a large study.ObjectiveDetermine the neuroanatomical correlates of plasma tau using voxel-based analysis.MethodsCross-sectional data for 508 ADNI participants were collected for clinical, plasma total-tau (t-tau), CSF amyloid (Aβ42) and tau, and MRI variables. The relationship between plasma tau and GMD and between CSF t-tau and GMD were assessed on a voxel-by-voxel basis using regression models. Age, sex, APOEɛ4 status, diagnosis, and total intracranial volume were used as covariates where appropriate. Participants were defined as amyloid positive (Aβ+) if CSF Aβ42 was

Published
2017

36. Novel genetic loci underlying human intracranial volume identified through genome-wide association

Author

Adams, Hieab HH, Hibar, Derrek P, Chouraki, Vincent, Stein, Jason L, Nyquist, Paul A, Rentería, Miguel E, Trompet, Stella, Arias-Vasquez, Alejandro, Seshadri, Sudha, Desrivières, Sylvane, Beecham, Ashley H, Jahanshad, Neda, Wittfeld, Katharina, Van der Lee, Sven J, Abramovic, Lucija, Alhusaini, Saud, Amin, Najaf, Andersson, Micael, Arfanakis, Konstantinos, Aribisala, Benjamin S, Armstrong, Nicola J, Athanasiu, Lavinia, Axelsson, Tomas, Beiser, Alexa, Bernard, Manon, Bis, Joshua C, Blanken, Laura ME, Blanton, Susan H, Bohlken, Marc M, Boks, Marco P, Bralten, Janita, Brickman, Adam M, Carmichael, Owen, Chakravarty, M Mallar, Chauhan, Ganesh, Chen, Qiang, Ching, Christopher RK, Cuellar-Partida, Gabriel, Braber, Anouk Den, Doan, Nhat Trung, Ehrlich, Stefan, Filippi, Irina, Ge, Tian, Giddaluru, Sudheer, Goldman, Aaron L, Gottesman, Rebecca F, Greven, Corina U, Grimm, Oliver, Griswold, Michael E, Guadalupe, Tulio, Hass, Johanna, Haukvik, Unn K, Hilal, Saima, Hofer, Edith, Hoehn, David, Holmes, Avram J, Hoogman, Martine, Janowitz, Deborah, Jia, Tianye, Kasperaviciute, Dalia, Kim, Sungeun, Klein, Marieke, Kraemer, Bernd, Lee, Phil H, Liao, Jiemin, Liewald, David CM, Lopez, Lorna M, Luciano, Michelle, Macare, Christine, Marquand, Andre, Matarin, Mar, Mather, Karen A, Mattheisen, Manuel, Mazoyer, Bernard, McKay, David R, McWhirter, Rebekah, Milaneschi, Yuri, Mirza-Schreiber, Nazanin, Muetzel, Ryan L, Maniega, Susana Muñoz, Nho, Kwangsik, Nugent, Allison C, Loohuis, Loes M Olde, Oosterlaan, Jaap, Papmeyer, Martina, Pappa, Irene, Pirpamer, Lukas, Pudas, Sara, Pütz, Benno, Rajan, Kumar B, Ramasamy, Adaikalavan, Richards, Jennifer S, Risacher, Shannon L, Roiz-Santiañez, Roberto, Rommelse, Nanda, Rose, Emma J, Royle, Natalie A, Rundek, Tatjana, Sämann, Philipp G, and Satizabal, Claudia L

Subjects
Biological Psychology, Biomedical and Clinical Sciences, Neurosciences, Psychology, Brain Disorders, Biotechnology, Neurodegenerative, Prevention, Genetics, Human Genome, Aging, Clinical Research, 2.1 Biological and endogenous factors, Brain, Cognition, Genetic Loci, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Oncogene Protein v-akt, Parkinson Disease, Phenotype, Phosphatidylinositol 3-Kinases, Polymorphism, Single Nucleotide, White People, Cognitive Sciences, Neurology & Neurosurgery, Biological psychology
Abstract

Intracranial volume reflects the maximally attained brain size during development, and remains stable with loss of tissue in late life. It is highly heritable, but the underlying genes remain largely undetermined. In a genome-wide association study of 32,438 adults, we discovered five previously unknown loci for intracranial volume and confirmed two known signals. Four of the loci were also associated with adult human stature, but these remained associated with intracranial volume after adjusting for height. We found a high genetic correlation with child head circumference (ρgenetic = 0.748), which indicates a similar genetic background and allowed us to identify four additional loci through meta-analysis (Ncombined = 37,345). Variants for intracranial volume were also related to childhood and adult cognitive function, and Parkinson's disease, and were enriched near genes involved in growth pathways, including PI3K-AKT signaling. These findings identify the biological underpinnings of intracranial volume and their link to physiological and pathological traits.

Published
2016

41. Bayesian model reveals latent atrophy factors with dissociable cognitive trajectories in Alzheimer’s disease

Author

Zhang, Xiuming, Mormino, Elizabeth C, Sun, Nanbo, Sperling, Reisa A, Sabuncu, Mert R, Yeo, BT Thomas, Weiner, Michael W, Aisen, Paul, Weiner, Michael, Petersen, Ronald, Jack, Clifford R, Jagust, William, Trojanowki, John Q, Toga, Arthur W, Beckett, Laurel, Green, Robert C, Saykin, Andrew J, Morris, John, Shaw, Leslie M, Khachaturian, Zaven, Sorensen, Greg, Carrillo, Maria, Kuller, Lew, Raichle, Marc, Paul, Steven, Davies, Peter, Fillit, Howard, Hefti, Franz, Holtzman, David, Mesulam, M Marcel, Potter, William, Snyder, Peter, Schwartz, Adam, Montine, Tom, Thomas, Ronald G, Donohue, Michael, Walter, Sarah, Gessert, Devon, Sather, Tamie, Jiminez, Gus, Balasubramanian, Archana B, Mason, Jennifer, Sim, Iris, Harvey, Danielle, Bernstein, Matthew, Fox, Nick, Thompson, Paul, Schuff, Norbert, DeCArli, Charles, Borowski, Davis Bret, Gunter, Jeff, Senjem, Matt, Vemuri, Prashanthi, Jones, David, Kantarci, Kejal, Ward, Chad, Koeppe, Robert A, Foster, Norm, Reiman, Eric M, Chen, Kewei, Mathis, Chet, Landau, Susan, Morris, John C, Cairns, Nigel J, Franklin, Erin, Taylor-Reinwald, Lisa, Lee, Virginia, Korecka, Magdalena, Figurski, Michal, Crawford, Karen, Neu, Scott, Foroud, Tatiana M, Potkin, Steven, Shen, Li, Faber, Kelley, Kim, Sungeun, Nho, Kwangsik, Thal, Lean, Thal, Leon, Buckholtz, Neil, Snyder, Peter J, Albert, Marilyn, and Frank, Richard

Subjects
Biological Psychology, Psychology, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Alzheimer's Disease, Clinical Research, Aging, Brain Disorders, Dementia, Neurosciences, Neurodegenerative, Acquired Cognitive Impairment, Aetiology, 2.1 Biological and endogenous factors, Neurological, Alzheimer Disease, Atrophy, Bayes Theorem, Brain, Cognitive Dysfunction, Female, Humans, Magnetic Resonance Imaging, Male, Risk Factors, mental disorder subtypes, Alzheimer's disease subtypes, Alzheimer's disease heterogeneity, voxel-based morphometry, unsupervised machine learning, Alzheimer’s Disease Neuroimaging Initiative, Alzheimer’s disease heterogeneity, Alzheimer’s disease subtypes
Abstract

We used a data-driven Bayesian model to automatically identify distinct latent factors of overlapping atrophy patterns from voxelwise structural MRIs of late-onset Alzheimer's disease (AD) dementia patients. Our approach estimated the extent to which multiple distinct atrophy patterns were expressed within each participant rather than assuming that each participant expressed a single atrophy factor. The model revealed a temporal atrophy factor (medial temporal cortex, hippocampus, and amygdala), a subcortical atrophy factor (striatum, thalamus, and cerebellum), and a cortical atrophy factor (frontal, parietal, lateral temporal, and lateral occipital cortices). To explore the influence of each factor in early AD, atrophy factor compositions were inferred in beta-amyloid-positive (Aβ+) mild cognitively impaired (MCI) and cognitively normal (CN) participants. All three factors were associated with memory decline across the entire clinical spectrum, whereas the cortical factor was associated with executive function decline in Aβ+ MCI participants and AD dementia patients. Direct comparison between factors revealed that the temporal factor showed the strongest association with memory, whereas the cortical factor showed the strongest association with executive function. The subcortical factor was associated with the slowest decline for both memory and executive function compared with temporal and cortical factors. These results suggest that distinct patterns of atrophy influence decline across different cognitive domains. Quantification of this heterogeneity may enable the computation of individual-level predictions relevant for disease monitoring and customized therapies. Factor compositions of participants and code used in this article are publicly available for future research.

Published
2016

42. Integration of bioinformatics and imaging informatics for identifying rare PSEN1 variants in Alzheimer’s disease

Author

Nho, Kwangsik, Horgusluoglu, Emrin, Kim, Sungeun, Risacher, Shannon L, Kim, Dokyoon, Foroud, Tatiana, Aisen, Paul S, Petersen, Ronald C, Jack, Clifford R, Shaw, Leslie M, Trojanowski, John Q, Weiner, Michael W, Green, Robert C, Toga, Arthur W, Saykin, Andrew J, and ADNI

Subjects
Biological Sciences, Genetics, Acquired Cognitive Impairment, Bioengineering, Biomedical Imaging, Biotechnology, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Networking and Information Technology R&D (NITRD), Neurosciences, Alzheimer's Disease, Aging, Human Genome, Neurodegenerative, Dementia, Clinical Research, Brain Disorders, 2.1 Biological and endogenous factors, Aetiology, Neurological, Aged, Alzheimer Disease, Brain, Female, Genomics, Humans, Magnetic Resonance Imaging, Male, Neuroimaging, Polymorphism, Single Nucleotide, Presenilin-1, Whole genome sequencing, Imaging genetics, Gene-based association of rare variants, PSEN1, ADNI, Medical Biochemistry and Metabolomics, Oncology and Carcinogenesis, Genetics & Heredity, Medical biochemistry and metabolomics
Abstract

BackgroundPathogenic mutations in PSEN1 are known to cause familial early-onset Alzheimer's disease (EOAD) but common variants in PSEN1 have not been found to strongly influence late-onset AD (LOAD). The association of rare variants in PSEN1 with LOAD-related endophenotypes has received little attention. In this study, we performed a rare variant association analysis of PSEN1 with quantitative biomarkers of LOAD using whole genome sequencing (WGS) by integrating bioinformatics and imaging informatics.MethodsA WGS data set (N = 815) from the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort was used in this analysis. 757 non-Hispanic Caucasian participants underwent WGS from a blood sample and high resolution T1-weighted structural MRI at baseline. An automated MRI analysis technique (FreeSurfer) was used to measure cortical thickness and volume of neuroanatomical structures. We assessed imaging and cerebrospinal fluid (CSF) biomarkers as LOAD-related quantitative endophenotypes. Single variant analyses were performed using PLINK and gene-based analyses of rare variants were performed using the optimal Sequence Kernel Association Test (SKAT-O).ResultsA total of 839 rare variants (MAF

Published
2016

45. Circular-SWAT for deep learning based diagnostic classification of Alzheimer's disease: application to metabolome data

Author

Jo, Taeho, primary, Kim, Junpyo, additional, Bice, Paula, additional, Huynh, Kevin, additional, Wang, Tingting, additional, Arnold, Matthias, additional, Meikle, Peter J., additional, Giles, Corey, additional, Kaddurah-Daouk, Rima, additional, Saykin, Andrew J., additional, Nho, Kwangsik, additional, Kueider-Paisley, Alexandra, additional, Doraiswamy, P. Murali, additional, Blach, Colette, additional, Moseley, Arthur, additional, Thompson, Will, additional, St John-Williams, Lisa, additional, Mahmoudiandehkhordi, Siamak, additional, Tenenbaum, Jessica, additional, Welsh-Balmer, Kathleen, additional, Plassman, Brenda, additional, Risacher, Shannon L., additional, Kastenmüller, Gabi, additional, Han, Xianlin, additional, Baillie, Rebecca, additional, Knight, Rob, additional, Dorrestein, Pieter, additional, Brewer, James, additional, Mayer, Emeran, additional, Labus, Jennifer, additional, Baldi, Pierre, additional, Gupta, Arpana, additional, Fiehn, Oliver, additional, Barupal, Dinesh, additional, Meikle, Peter, additional, Mazmanian, Sarkis, additional, Rader, Dan, additional, Kling, Mitchel, additional, Shaw, Leslie, additional, Trojanowski, John, additional, van Duijin, Cornelia, additional, Nevado-Holgado, Alejo, additional, Bennett, David, additional, Krishnan, Ranga, additional, Keshavarzian, Ali, additional, Vogt, Robin, additional, Ikram, Arfan, additional, Hankemeier, Thomas, additional, Thiele, Ines, additional, Price, Nathan, additional, Funk, Cory, additional, Baloni, Priyanka, additional, Jia, Wei, additional, Wishart, David, additional, Brinton, Roberta, additional, Chang, Rui, additional, Farrer, Lindsay, additional, Au, Rhoda, additional, Qiu, Wendy, additional, Würtz, Peter, additional, Koal, Therese, additional, Mangravite, Lara, additional, Krumsiek, Jan, additional, Suhre, Karsten, additional, Newman, John, additional, Moreno, Herman, additional, Foroud, Tatania, additional, Sacks, Frank, additional, Jansson, Janet, additional, Weiner, Michael W., additional, Aisen, Paul, additional, Petersen, Ronald, additional, Jack, Clifford R., additional, Jagust, William, additional, Trojanowki, John Q., additional, Toga, Arthur W., additional, Beckett, Laurel, additional, Green, Robert C., additional, Morris, John C., additional, Perrin, Richard J., additional, Shaw, Leslie M., additional, Khachaturian, Zaven, additional, Carrillo, Maria, additional, Potter, William, additional, Barnes, Lisa, additional, Bernard, Marie, additional, Gonzalez, Hector, additional, Ho, Carole, additional, Hsiao, John K., additional, Jackson, Jonathan, additional, Masliah, Eliezer, additional, Masterman, Donna, additional, Okonkwo, Ozioma, additional, Perrin, Richard, additional, Ryan, Laurie, additional, Silverberg, Nina, additional, Fleisher, Adam, additional, Sacrey, Diana Truran, additional, Fockler, Juliet, additional, Conti, Cat, additional, Veitch, Dallas, additional, Neuhaus, John, additional, Jin, Chengshi, additional, Nosheny, Rachel, additional, Ashford, Miriam, additional, Flenniken, Derek, additional, Kormos, Adrienne, additional, Montine, Tom, additional, Rafii, Michael, additional, Raman, Rema, additional, Jimenez, Gustavo, additional, Donohue, Michael, additional, Gessert, Devon, additional, Salazar, Jennifer, additional, Zimmerman, Caileigh, additional, Cabrera, Yuliana, additional, Walter, Sarah, additional, Miller, Garrett, additional, Coker, Godfrey, additional, Clanton, Taylor, additional, Hergesheimer, Lindsey, additional, Smith, Stephanie, additional, Adegoke, Olusegun, additional, Mahboubi, Payam, additional, Moore, Shelley, additional, Pizzola, Jeremy, additional, Shaffer, Elizabeth, additional, Sloan, Brittany, additional, Harvey, Danielle, additional, Forghanian-Arani, Arvin, additional, Borowski, Bret, additional, Ward, Chad, additional, Schwarz, Christopher, additional, Jones, David, additional, Gunter, Jeff, additional, Kantarci, Kejal, additional, Senjem, Matthew, additional, Vemuri, Prashanthi, additional, Reid, Robert, additional, Fox, Nick C., additional, Malone, Ian, additional, Thompson, Paul, additional, Thomopoulos, Sophia I., additional, Nir, Talia M., additional, Jahanshad, Neda, additional, DeCarli, Charles, additional, Knaack, Alexander, additional, Fletcher, Evan, additional, Tosun-Turgut, Duygu, additional, Chen, Stephanie Rossi, additional, Choe, Mark, additional, Crawford, Karen, additional, Yushkevich, Paul A., additional, Das, Sandhitsu, additional, Koeppe, Robert A., additional, Reiman, Eric M., additional, Chen, Kewei, additional, Mathis, Chet, additional, Landau, Susan, additional, Cairns, Nigel J., additional, Householder, Erin, additional, Franklin, Erin, additional, Bernhardt, Haley, additional, Taylor-Reinwald, Lisa, additional, Korecka, Magdalena, additional, Figurski, Michal, additional, Neu, Scott, additional, Apostolova, Liana G., additional, Shen, Li, additional, Foroud, Tatiana M., additional, Nudelman, Kelly, additional, Faber, Kelley, additional, Wilmes, Kristi, additional, Thal, Leon, additional, Silbert, Lisa C., additional, Lind, Betty, additional, Crissey, Rachel, additional, Kaye, Jeffrey A., additional, Carter, Raina, additional, Dolen, Sara, additional, Quinn, Joseph, additional, Schneider, Lon S., additional, Pawluczyk, Sonia, additional, Becerra, Mauricio, additional, Teodoro, Liberty, additional, Dagerman, Karen, additional, Spann, Bryan M., additional, Vanderswag, Helen, additional, Ziolkowski, Jaimie, additional, Heidebrink, Judith L., additional, Zbizek-Nulph, Lisa, additional, Lord, Joanne L., additional, Mason, Sara S., additional, Albers, Colleen S., additional, Knopman, David, additional, Johnson, Kris, additional, Villanueva-Meyer, Javier, additional, Pavlik, Valory, additional, Pacini, Nathaniel, additional, Lamb, Ashley, additional, Kass, Joseph S., additional, Doody, Rachelle S., additional, Shibley, Victoria, additional, Chowdhury, Munir, additional, Rountree, Susan, additional, Dang, Mimi, additional, Stern, Yaakov, additional, Honig, Lawrence S., additional, Mintz, Akiva, additional, Ances, Beau, additional, Winkfield, David, additional, Carroll, Maria, additional, Stobbs-Cucchi, Georgia, additional, Oliver, Angela, additional, Creech, Mary L., additional, Mintun, Mark A., additional, Schneider, Stacy, additional, Geldmacher, David, additional, Love, Marissa Natelson, additional, Griffith, Randall, additional, Clark, David, additional, Brockington, John, additional, Marson, Daniel, additional, Grossman, Hillel, additional, Goldstein, Martin A., additional, Greenberg, Jonathan, additional, Mitsis, Effie, additional, Shah, Raj C., additional, Lamar, Melissa, additional, Samuels, Patricia, additional, Duara, Ranjan, additional, Greig-Custo, Maria T., additional, Rodriguez, Rosemarie, additional, Albert, Marilyn, additional, Onyike, Chiadi, additional, Farrington, Leonie, additional, Rudow, Scott, additional, Brichko, Rottislav, additional, Kielb, Stephanie, additional, Smith, Amanda, additional, Raj, Balebail Ashok, additional, Fargher, Kristin, additional, Sadowski, Martin, additional, Wisniewski, Thomas, additional, Shulman, Melanie, additional, Faustin, Arline, additional, Rao, Julia, additional, Castro, Karen M., additional, Ulysse, Anaztasia, additional, Chen, Shannon, additional, Sheikh, Mohammed O., additional, Singleton-Garvin, Jamika, additional, Petrella, JeffreyR., additional, James, Olga, additional, Wong, Terence Z., additional, Borges-Neto, Salvador, additional, Karlawish, Jason H., additional, Wolk, David A., additional, Vaishnavi, Sanjeev, additional, Clark, Christopher M., additional, Arnold, Steven E., additional, Smith, Charles D., additional, Jicha, Gregory A., additional, Raslau, Flavius D., additional, Lopez, Oscar L., additional, Oakley, MaryAnn, additional, Simpson, Donna M., additional, Porsteinsson, Anton P., additional, Martin, Kim, additional, Kowalski, Nancy, additional, Keltz, Melanie, additional, Goldstein, Bonnie S., additional, Makino, Kelly M., additional, Ismail, M. Saleem, additional, Brand, Connie, additional, Thai, Gaby, additional, Pierce, Aimee, additional, Yanez, Beatriz, additional, Sosa, Elizabeth, additional, Witbracht, Megan, additional, Kelley, Brendan, additional, Nguyen, Trung, additional, Womack, Kyle, additional, Mathews, Dana, additional, Quiceno, Mary, additional, Levey, Allan I., additional, Lah, James J., additional, Hajjar, Ihab, additional, Cellar, Janet S., additional, Burns, Jeffrey M., additional, Swerdlow, Russell H., additional, Brooks, William M., additional, Silverman, Daniel H.S., additional, Kremen, Sarah, additional, Apostolova, Liana, additional, Tingus, Kathleen, additional, Lu, Po H., additional, Bartzokis, George, additional, Woo, Ellen, additional, Teng, Edmond, additional, Graff-Radford, Neill R., additional, Parfitt, Francine, additional, Poki-Walker, Kim, additional, Farlow, Martin R., additional, Hake, Ann Marie, additional, Matthews, Brandy R., additional, Brosch, Jared R., additional, Herring, Scott, additional, van, Christopher H., additional, Mecca, Adam P., additional, Good, Susan P., additional, MacAvoy, Martha G., additional, Carson, Richard E., additional, Varma, Pradeep, additional, Chertkow, Howard, additional, Vaitekunis, Susan, additional, Hosein, Chris, additional, Black, Sandra, additional, Stefanovic, Bojana, additional, Heyn, Chris (Chinthaka), additional, Robin Hsiung, Ging-Yuek, additional, Kim, Ellen, additional, Mudge, Benita, additional, Sossi, Vesna, additional, Feldman, Howard, additional, Assaly, Michele, additional, Finger, Elizabeth, additional, Pasternak, Stephen, additional, Rachinsky, Irina, additional, Kertesz, Andrew, additional, Drost, Dick, additional, Rogers, John, additional, Grant, Ian, additional, Muse, Brittanie, additional, Rogalski, Emily, additional, Robson, Jordan, additional, Mesulam, M.-Marsel, additional, Kerwin, Diana, additional, Wu, Chuang-Kuo, additional, Johnson, Nancy, additional, Lipowski, Kristine, additional, Weintraub, Sandra, additional, Bonakdarpour, Borna, additional, Pomara, Nunzio, additional, Hernando, Raymundo, additional, Sarrael, Antero, additional, Rosen, Howard J., additional, Miller, Bruce L., additional, Perry, David, additional, Turner, Raymond Scott, additional, Johnson, Kathleen, additional, Reynolds, Brigid, additional, MCCann, Kelly, additional, Poe, Jessica, additional, Sperling, Reisa A., additional, Johnson, Keith A., additional, Marshall, Gad A., additional, Yesavage, Jerome, additional, Taylor, Joy L., additional, Chao, Steven, additional, Coleman, Jaila, additional, White, Jessica D., additional, Lane, Barton, additional, Rosen, Allyson, additional, Tinklenberg, Jared, additional, Belden, Christine M., additional, Atri, Alireza, additional, Clark, Kelly A., additional, Zamrini, Edward, additional, Sabbagh, Marwan, additional, Killiany, Ronald, additional, Stern, Robert, additional, Mez, Jesse, additional, Kowall, Neil, additional, Budson, Andrew E., additional, Obisesan, Thomas O., additional, Ntekim, Oyonumo E., additional, Wolday, Saba, additional, Khan, Javed I., additional, Nwulia, Evaristus, additional, Nadarajah, Sheeba, additional, Lerner, Alan, additional, Ogrocki, Paula, additional, Tatsuoka, Curtis, additional, Fatica, Parianne, additional, Maillard, Pauline, additional, Olichney, John, additional, Carmichael, Owen, additional, Bates, Vernice, additional, Capote, Horacio, additional, Rainka, Michelle, additional, Borrie, Michael, additional, Lee, T.-Y., additional, Bartha, Dr Rob, additional, Johnson, Sterling, additional, Asthana, Sanjay, additional, Carlsson, Cynthia M., additional, Perrin, Allison, additional, Burke, Anna, additional, Scharre, Douglas W., additional, Kataki, Maria, additional, Tarawneh, Rawan, additional, Hart, David, additional, Zimmerman, Earl A., additional, Celmins, Dzintra, additional, Miller, Delwyn D., additional, BolesPonto, Laura L., additional, Smith, Karen Ekstam, additional, Koleva, Hristina, additional, Shim, Hyungsub, additional, Nam, Ki Won, additional, Schultz, Susan K., additional, Williamson, Jeff D., additional, Craft, Suzanne, additional, Cleveland, Jo, additional, Yang, Mia, additional, Sink, Kaycee M., additional, Ott, Brian R., additional, Drake, Jonathan, additional, Tremont, Geoffrey, additional, Daiello, Lori A., additional, Drake, Jonathan D., additional, Ritter, Aaron, additional, Bernick, Charles, additional, Munic, Donna, additional, O'Connelll, Abigail, additional, Mintzer, Jacobo, additional, Wiliams, Arthur, additional, Masdeu, Joseph, additional, Shi, Jiong, additional, Garcia, Angelica, additional, Newhouse, Paul, additional, Potkin, Steven, additional, Salloway, Stephen, additional, Malloy, Paul, additional, Correia, Stephen, additional, Kittur, Smita, additional, Pearlson, Godfrey D., additional, Blank, Karen, additional, Anderson, Karen, additional, Flashman, Laura A., additional, Seltzer, Marc, additional, Hynes, Mary L., additional, Santulli, Robert B., additional, Relkin, Norman, additional, Chiang, Gloria, additional, Lee, Athena, additional, Lin, Michael, additional, Ravdin, Lisa, additional, Petersen, Ron, additional, Neylan, Thomas, additional, Grafman, Jordan, additional, Danowski, Sarah, additional, Nguyen-Barrera, Catherine, additional, Hayes, Jacqueline, additional, Finley, Shannon, additional, Bernstein, Matthew, additional, Senjem, Matt, additional, Foster, Norm, additional, Kim, Sungeun, additional, Sood, Ajay, additional, Blanchard, Kimberly S., additional, Fleischman, Debra, additional, Arfanakis, Konstantinos, additional, Varon, Daniel, additional, Greig, Maria T., additional, Petrella, Jeffrey R., additional, Goldstein, Bonnie, additional, Martin, Kimberly S., additional, Reist, Christopher, additional, Sadowsky, Carl, additional, Martinez, Walter, additional, Villena, Teresa, additional, Rosen, Howard, additional, Marshall, Gad, additional, Peskind, Elaine R., additional, Petrie, Eric C., additional, Li, Gail, additional, Mackin, Scott, additional, Jimenez-Maggiora, Gustavo, additional, Drake, Erin, additional, Donohue, Mike, additional, Nelson, Craig, additional, Bickford, David, additional, Butters, Meryl, additional, Zmuda, Michelle, additional, Reyes, Denise, additional, Faber, Kelley M., additional, Nudelman, Kelly N., additional, Au, Yiu Ho, additional, Scherer, Kelly, additional, Catalinotto, Daniel, additional, Stark, Samuel, additional, Ong, Elise, additional, and Fernandez, Dariella, additional

Published
2023
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47. APOE effect on Alzheimer's disease biomarkers in older adults with significant memory concern.

Author

Risacher, Shannon L, Kim, Sungeun, Nho, Kwangsik, Foroud, Tatiana, Shen, Li, Petersen, Ronald C, Jack, Clifford R, Beckett, Laurel A, Aisen, Paul S, Koeppe, Robert A, Jagust, William J, Shaw, Leslie M, Trojanowski, John Q, Weiner, Michael W, Saykin, Andrew J, and Alzheimer's Disease Neuroimaging Initiative (ADNI)

Subjects
Alzheimer's Disease Neuroimaging Initiative, Brain, Humans, Alzheimer Disease, tau Proteins, Positron-Emission Tomography, Magnetic Resonance Imaging, Memory, Neuropsychological Tests, Genotype, Heterozygote, Adult, Aged, Aged, 80 and over, Female, Male, Apolipoprotein E4, Amyloid beta-Peptides, Healthy Volunteers, Biomarkers, Cognitive Dysfunction, ADNI, APOE, Apolipoprotein E, CSF, Cerebrospinal fluid, FDG, Neuroimaging, PET, SCD, SMC, Significant memory concern, Structural magnetic resonance imaging, Subjective cognitive decline, [(18)F]Florbetapir PET, [(18)F]Fluorodeoxyglucose, [F-18] Florbetapir PET, [F-18] Fluorodeoxyglucose, and over, Geriatrics, Neurosciences, Clinical Sciences
Abstract

IntroductionThis study assessed apolipoprotein E (APOE) ε4 carrier status effects on Alzheimer's disease imaging and cerebrospinal fluid (CSF) biomarkers in cognitively normal older adults with significant memory concerns (SMC).MethodsCognitively normal, SMC, and early mild cognitive impairment participants from Alzheimer's Disease Neuroimaging Initiative were divided by APOE ε4 carrier status. Diagnostic and APOE effects were evaluated with emphasis on SMC. Additional analyses in SMC evaluated the effect of the interaction between APOE and [(18)F]Florbetapir amyloid positivity on CSF biomarkers.ResultsSMC ε4+ showed greater amyloid deposition than SMC ε4-, but no hypometabolism or medial temporal lobe (MTL) atrophy. SMC ε4+ showed lower amyloid beta 1-42 and higher tau/p-tau than ε4-, which was most abnormal in APOE ε4+ and cerebral amyloid positive SMC.DiscussionSMC APOE ε4+ show abnormal changes in amyloid and tau biomarkers, but no hypometabolism or MTL neurodegeneration, reflecting the at-risk nature of the SMC group and the importance of APOE in mediating this risk.

Published
2015

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