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2. Neurotransmission-related gene expression in the frontal pole is altered in subjects with bipolar disorder and schizophrenia

Author

Medina, Adriana M, Hagenauer, Megan Hastings, Krolewski, David M, Hughes, Evan, Forrester, Liam Cannon Thew, Walsh, David M, Waselus, Maria, Richardson, Evelyn, Turner, Cortney A, Sequeira, P Adolfo, Cartagena, Preston M, Thompson, Robert C, Vawter, Marquis P, Bunney, Blynn G, Myers, Richard M, Barchas, Jack D, Lee, Francis S, Schatzberg, Alan F, Bunney, William E, Akil, Huda, and Watson, Stanley J

Subjects
Pharmacology and Pharmaceutical Sciences, Biomedical and Clinical Sciences, Psychology, Mental Health, Genetics, Serious Mental Illness, Brain Disorders, Neurosciences, Aetiology, 2.1 Biological and endogenous factors, Mental health, Good Health and Well Being, Humans, Adolescent, Bipolar Disorder, Schizophrenia, Frontal Lobe, Gene Expression, Synaptic Transmission, Clinical Sciences, Public Health and Health Services, Clinical sciences, Biological psychology
Abstract

The frontal pole (Brodmann area 10, BA10) is the largest cytoarchitectonic region of the human cortex, performing complex integrative functions. BA10 undergoes intensive adolescent grey matter pruning prior to the age of onset for bipolar disorder (BP) and schizophrenia (SCHIZ), and its dysfunction is likely to underly aspects of their shared symptomology. In this study, we investigated the role of BA10 neurotransmission-related gene expression in BP and SCHIZ. We performed qPCR to measure the expression of 115 neurotransmission-related targets in control, BP, and SCHIZ postmortem samples (n = 72). We chose this method for its high sensitivity to detect low-level expression. We then strengthened our findings by performing a meta-analysis of publicly released BA10 microarray data (n = 101) and identified sources of convergence with our qPCR results. To improve interpretation, we leveraged the unusually large database of clinical metadata accompanying our samples to explore the relationship between BA10 gene expression, therapeutics, substances of abuse, and symptom profiles, and validated these findings with publicly available datasets. Using these convergent sources of evidence, we identified 20 neurotransmission-related genes that were differentially expressed in BP and SCHIZ in BA10. These results included a large diagnosis-related decrease in two important therapeutic targets with low levels of expression, HTR2B and DRD4, as well as other findings related to dopaminergic, GABAergic and astrocytic function. We also observed that therapeutics may produce a differential expression that opposes diagnosis effects. In contrast, substances of abuse showed similar effects on BA10 gene expression as BP and SCHIZ, potentially amplifying diagnosis-related dysregulation.

Published
2023

4. Rare coding variants in ten genes confer substantial risk for schizophrenia.

Author

Singh, Tarjinder, Poterba, Timothy, Curtis, David, Akil, Huda, Al Eissa, Mariam, Barchas, Jack D, Bass, Nicholas, Bigdeli, Tim B, Breen, Gerome, Bromet, Evelyn J, Buckley, Peter F, Bunney, William E, Bybjerg-Grauholm, Jonas, Byerley, William F, Chapman, Sinéad B, Chen, Wei J, Churchhouse, Claire, Craddock, Nicholas, Cusick, Caroline M, DeLisi, Lynn, Dodge, Sheila, Escamilla, Michael A, Eskelinen, Saana, Fanous, Ayman H, Faraone, Stephen V, Fiorentino, Alessia, Francioli, Laurent, Gabriel, Stacey B, Gage, Diane, Gagliano Taliun, Sarah A, Ganna, Andrea, Genovese, Giulio, Glahn, David C, Grove, Jakob, Hall, Mei-Hua, Hämäläinen, Eija, Heyne, Henrike O, Holi, Matti, Hougaard, David M, Howrigan, Daniel P, Huang, Hailiang, Hwu, Hai-Gwo, Kahn, René S, Kang, Hyun Min, Karczewski, Konrad J, Kirov, George, Knowles, James A, Lee, Francis S, Lehrer, Douglas S, Lescai, Francesco, Malaspina, Dolores, Marder, Stephen R, McCarroll, Steven A, McIntosh, Andrew M, Medeiros, Helena, Milani, Lili, Morley, Christopher P, Morris, Derek W, Mortensen, Preben Bo, Myers, Richard M, Nordentoft, Merete, O'Brien, Niamh L, Olivares, Ana Maria, Ongur, Dost, Ouwehand, Willem H, Palmer, Duncan S, Paunio, Tiina, Quested, Digby, Rapaport, Mark H, Rees, Elliott, Rollins, Brandi, Satterstrom, F Kyle, Schatzberg, Alan, Scolnick, Edward, Scott, Laura J, Sharp, Sally I, Sklar, Pamela, Smoller, Jordan W, Sobell, Janet L, Solomonson, Matthew, Stahl, Eli A, Stevens, Christine R, Suvisaari, Jaana, Tiao, Grace, Watson, Stanley J, Watts, Nicholas A, Blackwood, Douglas H, Børglum, Anders D, Cohen, Bruce M, Corvin, Aiden P, Esko, Tõnu, Freimer, Nelson B, Glatt, Stephen J, Hultman, Christina M, McQuillin, Andrew, Palotie, Aarno, Pato, Carlos N, Pato, Michele T, Pulver, Ann E, and St Clair, David

Subjects
Humans, Genetic Predisposition to Disease, Receptors, N-Methyl-D-Aspartate, Case-Control Studies, Schizophrenia, Mutation, Exome, Neurodevelopmental Disorders, Human Genome, Biotechnology, Mental Health, Neurosciences, Brain Disorders, Genetics, Serious Mental Illness, Aetiology, 2.1 Biological and endogenous factors, Mental health, Neurological, General Science & Technology
Abstract

Rare coding variation has historically provided the most direct connections between gene function and disease pathogenesis. By meta-analysing the whole exomes of 24,248 schizophrenia cases and 97,322 controls, we implicate ultra-rare coding variants (URVs) in 10 genes as conferring substantial risk for schizophrenia (odds ratios of 3-50, P

Published
2022

5. Mitochondria DNA copy number, mitochondria DNA total somatic deletions, Complex I activity, synapse number, and synaptic mitochondria number are altered in schizophrenia and bipolar disorder

Author

Das, Sujan C, Hjelm, Brooke E, Rollins, Brandi L, Sequeira, Adolfo, Morgan, Ling, Omidsalar, Audrey A, Schatzberg, Alan F, Barchas, Jack D, Lee, Francis S, Myers, Richard M, Watson, Stanley J, Akil, Huda, Bunney, William E, and Vawter, Marquis P

Subjects
Biological Psychology, Pharmacology and Pharmaceutical Sciences, Biomedical and Clinical Sciences, Psychology, Brain Disorders, Serious Mental Illness, Mental Health, Neurosciences, Eye Disease and Disorders of Vision, Schizophrenia, Mental health, Bipolar Disorder, DNA Copy Number Variations, DNA, Mitochondrial, Female, Humans, Mitochondria, Synapses, Clinical Sciences, Public Health and Health Services, Clinical sciences, Biological psychology
Abstract

Mitochondrial dysfunction is a neurobiological phenomenon implicated in the pathophysiology of schizophrenia and bipolar disorder that can synergistically affect synaptic neurotransmission. We hypothesized that schizophrenia and bipolar disorder share molecular alterations at the mitochondrial and synaptic levels. Mitochondria DNA (mtDNA) copy number (CN), mtDNA common deletion (CD), mtDNA total deletion, complex I activity, synapse number, and synaptic mitochondria number were studied in the postmortem human dorsolateral prefrontal cortex (DLPFC), superior temporal gyrus (STG), primary visual cortex (V1), and nucleus accumbens (NAc) of controls (CON), and subjects with schizophrenia (SZ), and bipolar disorder (BD). The results showed (i) the mtDNA CN is significantly higher in DLPFC of both SZ and BD, decreased in the STG of BD, and unaltered in V1 and NAc of both SZ and BD; (ii) the mtDNA CD is significantly higher in DLPFC of BD while unaltered in STG, V1, and NAc of both SZ and BD; (iii) The total deletion burden is significantly higher in DLPFC in both SZ and BD while unaltered in STG, V1, and NAc of SZ and BD; (iv) Complex I activity is significantly lower in DLPFC of both SZ and BD, which is driven by the presence of medications, with no alteration in STG, V1, and NAc. In addition, complex I protein concentration, by ELISA, was decreased across three cortical regions of SZ and BD subjects; (v) The number of synapses is decreased in DLPFC of both SZ and BD, while the synaptic mitochondria number was significantly lower in female SZ and female BD compared to female controls. Overall, these findings will pave the way to understand better the pathophysiology of schizophrenia and bipolar disorder for therapeutic interventions.

Published
2022

7. Splice-Break: exploiting an RNA-seq splice junction algorithm to discover mitochondrial DNA deletion breakpoints and analyses of psychiatric disorders

Author

Hjelm, Brooke E, Rollins, Brandi, Morgan, Ling, Sequeira, Adolfo, Mamdani, Firoza, Pereira, Filipe, Damas, Joana, Webb, Michelle G, Weber, Matthieu D, Schatzberg, Alan F, Barchas, Jack D, Lee, Francis S, Akil, Huda, Watson, Stanley J, Myers, Richard M, Chao, Elizabeth C, Kimonis, Virginia, Thompson, Peter M, Bunney, William E, and Vawter, Marquis P

Subjects
Neurosciences, Genetics, Brain Disorders, Human Genome, 1.1 Normal biological development and functioning, Underpinning research, Mental health, Algorithms, Base Sequence, Brain, Computational Biology, DNA Breaks, DNA, Mitochondrial, Depressive Disorder, Major, Female, Humans, Male, Polymerase Chain Reaction, RNA Splice Sites, Sequence Analysis, RNA, Sequence Deletion, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Developmental Biology
Abstract

Deletions in the 16.6 kb mitochondrial genome have been implicated in numerous disorders that often display muscular and/or neurological symptoms due to the high-energy demands of these tissues. We describe a catalogue of 4489 putative mitochondrial DNA (mtDNA) deletions, including their frequency and relative read rate, using a combinatorial approach of mitochondria-targeted PCR, next-generation sequencing, bioinformatics, post-hoc filtering, annotation, and validation steps. Our bioinformatics pipeline uses MapSplice, an RNA-seq splice junction detection algorithm, to detect and quantify mtDNA deletion breakpoints rather than mRNA splices. Analyses of 93 samples from postmortem brain and blood found (i) the 4977 bp 'common deletion' was neither the most frequent deletion nor the most abundant; (ii) brain contained significantly more deletions than blood; (iii) many high frequency deletions were previously reported in MitoBreak, suggesting they are present at low levels in metabolically active tissues and are not exclusive to individuals with diagnosed mitochondrial pathologies; (iv) many individual deletions (and cumulative metrics) had significant and positive correlations with age and (v) the highest deletion burdens were observed in major depressive disorder brain, at levels greater than Kearns-Sayre Syndrome muscle. Collectively, these data suggest the Splice-Break pipeline can detect and quantify mtDNA deletions at a high level of resolution.

Published
2019

9. Sex-Dependent Shared and Nonshared Genetic Architecture Across Mood and Psychotic Disorders

Author

Ripke, Stephan, Neale, Benjamin M., Corvin, Aiden, Walters, James T.R., Farh, Kai-How, Holmans, Peter A., Lee, Phil, Bulik-Sullivan, Brendan, Collier, David A., Huang, Hailiang, Pers, Tune H., Agartz, Ingrid, Agerbo, Esben, Albus, Margot, Alexander, Madeline, Amin, Farooq, Bacanu, Silviu A., Begemann, Martin, Belliveau, Richard A., Jr., Bene, Judit, Bergen, Sarah E., Bevilacqua, Elizabeth, Bigdeli, Tim B., Black, Donald W., Bruggeman, Richard, Buccola, Nancy G., Buckner, Randy L., Byerley, William, Cahn, Wiepke, Cai, Guiqing, Campion, Dominique, Cantor, Rita M., Carr, Vaughan J., Carrera, Noa, Catts, Stanley V., Chambert, Kimberly D., Chan, Raymond C.K., Chen, Ronald Y.L., Chen, Eric Y.H., Cheng, Wei, Cheung, Eric F.C., Chong, Siow Ann, Cloninger, C. Robert, Cohen, David, Cohen, Nadine, Cormican, Paul, Craddock, Nick, Crowley, James J., Curtis, David, Davidson, Michael, Davis, Kenneth L., Degenhardt, Franziska, Del Favero, Jurgen, Demontis, Ditte, Dikeos, Dimitris, Dinan, Timothy, Djurovic, Srdjan, Donohoe, Gary, Drapeau, Elodie, Duan, Jubao, Dudbridge, Frank, Durmishi, Naser, Eichhammer, Peter, Eriksson, Johan, Escott-Price, Valentina, Essioux, Laurent, Fanous, Ayman H., Farrell, Martilias S., Frank, Josef, Franke, Lude, Freedman, Robert, Freimer, Nelson B., Friedl, Marion, Friedman, Joseph I., Fromer, Menachem, Genovese, Giulio, Georgieva, Lyudmila, Giegling, Ina, Giusti-Rodríguez, Paola, Godard, Stephanie, Goldstein, Jacqueline I., Golimbet, Vera, Gopal, Srihari, Gratten, Jacob, de Haan, Lieuwe, Hammer, Christian, Hamshere, Marian L., Hansen, Mark, Hansen, Thomas, Haroutunian, Vahram, Hartmann, Annette M., Henskens, Frans A., Herms, Stefan, Hirschhorn, Joel N., Hoffmann, Per, Hofman, Andrea, Hollegaard, Mads V., Hougaard, David M., Ikeda, Masashi, Joa, Inge, Julià, Antonio, Kahn, René S., Kalaydjieva, Luba, Karachanak-Yankova, Sena, Karjalainen, Juha, Kavanagh, David, Keller, Matthew C., Kennedy, James L., Khrunin, Andrey, Kim, Yunjung, Klovins, Janis, Knowles, James A., Konte, Bettina, Kucinskas, Vaidutis, Kucinskiene, Zita Ausrele, Kuzelova-Ptackova, Hana, Kähler, Anna K., Laurent, Claudine, Lee Chee Keong, Jimmy, Lee, S. Hong, Legge, Sophie E., Lerer, Bernard, Li, Miaoxin, Li, Tao, Liang, Kung-Yee, Lieberman, Jeffrey, Limborska, Svetlana, Loughland, Carmel M., Lubinski, Jan, Lönnqvist, Jouko, Macek, Milan, Jr., Magnusson, Patrik K.E., Maher, Brion S., Maier, Wolfgang, Mallet, Jacques, Marsal, Sara, Mattheisen, Manuel, Mattingsdal, Morten, McCarley, Robert W., McDonald, Colm, McIntosh, Andrew M., Meier, Sandra, Meijer, Carin J., Melegh, Bela, Melle, Ingrid, Mesholam-Gately, Raquelle I., Metspalu, Andres, Michie, Patricia T., Milani, Lili, Milanova, Vihra, Mokrab, Younes, Morris, Derek W., Mors, Ole, Murphy, Kieran C., Murray, Robin M., Myin-Germeys, Inez, Müller-Myhsok, Bertram, Nelis, Mari, Nenadic, Igor, Nertney, Deborah A., Nestadt, Gerald, Nicodemus, Kristin K., Nikitina-Zake, Liene, Nisenbaum, Laura, Nordin, Annelie, O’Callaghan, Eadbhard, O’Dushlaine, Colm, O’Neill, F. Anthony, Oh, Sang-Yun, Olincy, Ann, Olsen, Line, Van Os, Jim, Pantelis, Christos, Papadimitriou, George N., Papiol, Sergi, Parkhomenko, Elena, Pato, Michele T., Paunio, Tiina, Pejovic-Milovancevic, Milica, Perkins, Diana O., Pietiläinen, Olli, Pimm, Jonathan, Pocklington, Andrew J., Powell, John, Price, Alkes, Pulver, Ann E., Purcell, Shaun M., Quested, Digby, Rasmussen, Henrik B., Reichenberg, Abraham, Reimers, Mark A., Richards, Alexander L., Roffman, Joshua L., Roussos, Panos, Ruderfer, Douglas M., Salomaa, Veikko, Sanders, Alan R., Schall, Ulrich, Schubert, Christian R., Schulze, Thomas G., Schwab, Sibylle G., Scolnick, Edward M., Scott, Rodney J., Seidman, Larry J., Shi, Jianxin, Sigurdsson, Engilbert, Silagadze, Teimuraz, Silverman, Jeremy M., Sim, Kang, Slominsky, Petr, Smoller, Jordan W., So, Hon-Cheong, Spencer, Chris C.A., Stahl, Eli A., Stefansson, Hreinn, Steinberg, Stacy, Stogmann, Elisabeth, Straub, Richard E., Strengman, Eric, Strohmaier, Jana, Stroup, T. Scott, Subramaniam, Mythily, Suvisaari, Jaana, Svrakic, Dragan M., Szatkiewicz, Jin P., Söderman, Erik, Thirumalai, Srinivas, Toncheva, Draga, Tosato, Sarah, Veijola, Juha, Waddington, John, Walsh, Dermot, Wang, Dai, Wang, Qiang, Webb, Bradley T., Weiser, Mark, Wildenauer, Dieter B., Williams, Nigel M., Williams, Stephanie, Witt, Stephanie H., Wolen, Aaron R., Wong, Emily H.M., Wormley, Brandon K., Xi, Hualin Simon, Zai, Clement C., Zheng, Xuebin, Zimprich, Fritz, Wray, Naomi R., Stefansson, Kari, Visscher, Peter M., Adolfsson, Rolf, Andreassen, Ole A., Blackwood, Douglas H.R., Bramon, Elvira, Buxbaum, Joseph D., Børglum, Anders D., Cichon, Sven, Darvasi, Ariel, Domenici, Enrico, Ehrenreich, Hannelore, Esko, Tõnu, Gejman, Pablo V., Gill, Michael, Gurling, Hugh, Hultman, Christina M., Iwata, Nakao, Jablensky, Assen V., Jönsson, Erik G., Kendler, Kenneth S., Kirov, George, Knight, Jo, Lencz, Todd, Levinson, Douglas F., Li, Qingqin S., Liu, Jianjun, Malhotra, Anil K., McCarroll, Steven A., McQuillin, Andrew, Moran, Jennifer L., Mortensen, Preben B., Periyasamy, Sathish, Cairns, Murray J., Tooney, Paul A., Wu, Jing Qin, Kelly, Brian, Mowry, Bryan J., Nöthen, Markus M., Ophoff, Roel A., Owen, Michael J., Palotie, Aarno, Pato, Carlos N., Petryshen, Tracey L., Posthuma, Danielle, Rietschel, Marcella, Riley, Brien P., Rujescu, Dan, Sham, Pak C., Sklar, Pamela, St Clair, David, Weinberger, Daniel R., Wendland, Jens R., Werge, Thomas, Daly, Mark J., Sullivan, Patrick F., O’Donovan, Michael C., Donnelly, Peter, Barroso, Ines, Blackwell, Jenefer M., Brown, Matthew A., Casas, Juan P., Deloukas, Panos, Duncanson, Audrey, Jankowski, Janusz, Markus, Hugh S., Mathew, Christopher G., Palmer, Colin N.A., Plomin, Robert, Rautanen, Anna, Sawcer, Stephen J., Trembath, Richard C., Viswanathan, Ananth C., Wood, Nicholas W., Band, Gavin, Bellenguez, Céline, Freeman, Colin, Giannoulatou, Eleni, Hellenthal, Garrett, Pearson, Richard, Pirinen, Matti, Strange, Amy, Su, Zhan, Vukcevic, Damjan, Langford, Cordelia, Blackburn, Hannah, Bumpstead, Suzannah J., Dronov, Serge, Edkins, Sarah, Gillman, Matthew, Gray, Emma, Gwilliam, Rhian, Hammond, Naomi, Hunt, Sarah E., Jayakumar, Alagurevathi, Liddle, Jennifer, McCann, Owen T., Potter, Simon C., Ravindrarajah, Radhi, Ricketts, Michelle, Tashakkori-Ghanbaria, Avazeh, Waller, Matthew, Weston, Paul, Whittaker, Pamela, Widaa, Sara, McCarthy, Mark I., Arranz, Maria J., Bakker, Steven, Bender, Stephan, Crespo-Facorro, Benedicto, Hall, Jeremy, Iyegbe, Conrad, Lawrie, Stephen, Lewis, Cathryn M., Lin, Kuang, Linszen, Don H., Mata, Ignacio, Walshe, Muriel, Weisbrod, Matthias, Wiersma, Durk, Breen, Gerome, Forstner, Andreas J., Trubetskoy, Vassily, Wang, Yunpeng, Coleman, Jonathan R.I., Gaspar, Héléna A., de Leeuw, Christiaan A., Whitehead Pavlides, Jennifer M., Trzaskowski, Maciej, Byrne, Enda M., Abbott, Liam, Akil, Huda, Albani, Diego, Alliey-Rodriguez, Ney, Als, Thomas D., Anjorin, Adebayo, Antilla, Verneri, Awasthi, Swapnil, Badner, Judith A., Bækvad-Hansen, Marie, Barchas, Jack D., Bass, Nicholas, Bauer, Michael, Belliveau, Richard, Pedersen, Carsten Bøcker, Bøen, Erlend, Boks, Marco P., Boocock, James, Budde, Monika, Bunney, William, Burmeister, Margit, Bybjerg-Grauholm, Jonas, Casas, Miquel, Cerrato, Felecia, Cervantes, Pablo, Chambert, Kimberly, Charney, Alexander W., Chen, Danfeng, Churchhouse, Claire, Clarke, Toni-Kim, Coryell, William, Craig, David W., Cruceanu, Cristiana, Czerski, Piotr M., Dale, Anders M., de Jong, Simone, Del-Favero, Jurgen, DePaulo, J. Raymond, Dobbyn, Amanda L., Dumont, Ashley, Elvsåshagen, Torbjørn, Fan, Chun Chieh, Fischer, Sascha B., Flickinger, Matthew, Foroud, Tatiana M., Forty, Liz, Fraser, Christine, Gade, Katrin, Gage, Diane, Garnham, Julie, Giambartolomei, Claudia, Pedersen, Marianne Giørtz, Goldstein, Jaqueline, Gordon, Scott D., Gordon-Smith, Katherine, Green, Elaine K., Green, Melissa J., Greenwood, Tiffany A., Grove, Jakob, Guan, Weihua, Guzman-Parra, José, Hautzinger, Martin, Heilbronner, Urs, Hipolito, Maria, Holland, Dominic, Huckins, Laura, Jamain, Stéphane, Johnson, Jessica S., Kandaswamy, Radhika, Karlsson, Robert, Kittel-Schneider, Sarah, Kogevinas, Manolis, Koller, Anna C., Kupka, Ralph, Lavebratt, Catharina, Lawrence, Jacob, Lawson, William B., Leber, Markus, Lee, Phil H., Levy, Shawn E., Li, Jun Z., Liu, Chunyu, Lucae, Susanne, Maaser, Anna, MacIntyre, Donald J., Mahon, Pamela B., Martinsson, Lina, McCarroll, Steve, McGuffin, Peter, McInnis, Melvin G., McKay, James D., Medeiros, Helena, Medland, Sarah E., Meng, Fan, Montgomery, Grant W., Mühleisen, Thomas W., Mullins, Niamh, Nguyen, Hoang, Nievergelt, Caroline M., Adolfsson, Annelie Nordin, Nwulia, Evaristus A., O'Donovan, Claire, Olde Loohuis, Loes M., Ori, Anil P.S., Oruc, Lilijana, Ösby, Urban, Perlis, Roy H., Perry, Amy, Pfennig, Andrea, Potash, James B., Regeer, Eline J., Reif, Andreas, Reinbold, Céline S., Rice, John P., Rivas, Fabio, Rivera, Margarita, Ryu, Euijung, Sánchez-Mora, Cristina, Schatzberg, Alan F., Scheftner, William A., Schork, Nicholas J., Weickert, Cynthia Shannon, Shehktman, Tatyana, Shilling, Paul D., Slaney, Claire, Smeland, Olav B., Sobell, Janet L., Hansen, Christine Søholm, Spijker, Anne T., Steffens, Michael, Strauss, John S., Streit, Fabian, Szelinger, Szabolcs, Thompson, Robert C., Thorgeirsson, Thorgeir E., Treutlein, Jens, Vedder, Helmut, Wang, Weiqing, Watson, Stanley J., Weickert, Thomas W., Xi, Simon, Xu, Wei, Young, Allan H., Zandi, Peter, Zhang, Peng, Zöllner, Sebastian, Abdellaoui, Abdel, Adams, Mark J., Air, Tracy M., Andlauer, Till F.M., Bacanu, Silviu-Alin, Beekman, Aartjan T.F., Binder, Elisabeth B., Bryois, Julien, Buttenschøn, Henriette N., Cai, Na, Castelao, Enrique, Christensen, Jane Hvarregaard, Colodro-Conde, Lucía, Couvy-Duchesne, Baptiste, Crawford, Gregory E., Davies, Gail, Deary, Ian J., Derks, Eske M., Direk, Nese, Dolan, Conor V., Dunn, Erin C., Eley, Thalia C., Hassan Kiadeh, Farnush Farhadi, Finucane, Hilary K., Foo, Jerome C., Goes, Fernando S., Hall, Lynsey S., Hansen, Thomas F., Hickie, Ian B., Homuth, Georg, Horn, Carsten, Hottenga, Jouke-Jan, Howard, David M., Ising, Marcus, Jansen, Rick, Jones, Ian, Jones, Lisa A., Jorgenson, Eric, Kohane, Isaac S., Kraft, Julia, Kretzschmar, Warren W., Kutalik, Zoltán, Li, Yihan, Lind, Penelope A., MacKinnon, Dean F., Maier, Robert M., Marchini, Jonathan, Mbarek, Hamdi, McGrath, Patrick, Mehta, Divya, Middeldorp, Christel M., Mihailov, Evelin, Milaneschi, Yuri, Mondimore, Francis M., Mostafavi, Sara, Nauck, Matthias, Ng, Bernard, Nivard, Michel G., Nyholt, Dale R., O'Reilly, Paul F., Oskarsson, Hogni, Painter, Jodie N., Peterson, Roseann E., Peyrot, Wouter J., Pistis, Giorgio, Quiroz, Jorge A., Qvist, Per, Mirza, Saira Saeed, Schoevers, Robert, Schulte, Eva C., Shen, Ling, Shyn, Stanley I., Sinnamon, Grant C.B., Smit, Johannes H., Smith, Daniel J., Tansey, Katherine E., Teismann, Henning, Teumer, Alexander, Thompson, Wesley, Thomson, Pippa A., Traylor, Matthew, Uitterlinden, André G., Umbricht, Daniel, Van der Auwera, Sandra, van Hemert, Albert M., Viktorin, Alexander, Weinsheimer, Shantel Marie, Wellmann, Jürgen, Willemsen, Gonneke, Wu, Yang, Xi, Hualin S., Yang, Jian, Zhang, Futao, Arolt, Volker, Baune, Bernhard T., Berger, Klaus, Boomsma, Dorret I., Dannlowski, Udo, de Geus, Eco J.C., Domschke, Katharina, Grabe, Hans J., Hamilton, Steven P., Hayward, Caroline, Heath, Andrew C., Kloiber, Stefan, Lewis, Glyn, Madden, Pamela AF., Magnusson, Patrik K., Martin, Nicholas G., Mortensen, Preben Bo, Nordentoft, Merete, O'Donovan, Michael C., Paciga, Sara A., Pedersen, Nancy L., Penninx, Brenda W.J.H., Porteous, David J., Preisig, Martin, Schaefer, Catherine, Tiemeier, Henning, Uher, Rudolf, Völzke, Henry, Weissman, Myrna M., Alda, Martin, Blokland, Gabriëlla A.M., Bortolato, Marco, Bralten, Janita, Bulik, Cynthia M., Burton, Christie L., Carey, Caitlin E., Davis, Lea K., Duncan, Laramie E., Edenberg, Howard J., Erdman, Lauren, Faraone, Stephen V., Goldstein, Jill M., Goleva, Slavina B., Guo, Wei, Hübel, Christopher, Huckins, Laura M., Khramtsova, Ekaterina A., Martin, Joanna, Mathews, Carol A., Robinson, Elise, Stahl, Eli, Stranger, Barbara E., Traglia, Michela, Walters, Raymond K., Weiss, Lauren A., Winham, Stacey J., Yao, Yin, Skajaa, Kristjar, Nöthen, Markus, Owen, Michael, Yolken, Robert H., Plath, Niels, Mill, Jonathan, Geschwind, Daniel, Chen, Chia-Yen, Cotsapas, Chris, Tobet, Stuart, Handa, Robert, Steixner-Kumar, Agnes, Lee, Jimmy, Molden, Espen, Bass, Nicholas J., Fullerton, Janice M., Mitchell, Philip B., Schofield, Peter R., Schaupp, Sabrina, Comes, Ashley L., Sirignano, Lea, Grigoroiu-Serbanescu, Maria, Hauser, Joanna, Lissowska, Jolanta, Mayoral, Fermin, Świątkowska, Beata, Kelsoe, John, Leboyer, Marion, Etain, Bruno, Bellivier, Frank, Vincent, John B., O’Donovan, Claire, Biernacka, Joanna M., Frye, Mark, McElroy, Susan L., Scott, Laura J., Landén, Mikael, Vaaler, Arne E., Air, Tracy, and Völker, Uwe

Published
2022
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11. Genetic Liability for Internalizing Versus Externalizing Behavior Manifests in the Developing and Adult Hippocampus: Insight From a Meta-analysis of Transcriptional Profiling Studies in a Selectively Bred Rat Model

Author

Birt, Isabelle A., Hagenauer, Megan H., Clinton, Sarah M., Aydin, Cigdem, Blandino, Peter, Jr., Stead, John D.H., Hilde, Kathryn L., Meng, Fan, Thompson, Robert C., Khalil, Huzefa, Stefanov, Alex, Maras, Pamela, Zhou, Zhifeng, Hebda-Bauer, Elaine K., Goldman, David, Watson, Stanley J., Jr., and Akil, Huda

Published
2021
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12. The Genetics of the Mood Disorder Spectrum: Genome-wide Association Analyses of More Than 185,000 Cases and 439,000 Controls

Author

Byrne, Enda M., Forstner, Andreas J., Holmans, Peter A., de Leeuw, Christiaan A., Mattheisen, Manuel, McQuillin, Andrew, Whitehead Pavlides, Jennifer M., Pers, Tune H., Ripke, Stephan, Stahl, Eli A., Steinberg, Stacy, Trubetskoy, Vassily, Trzaskowski, Maciej, Wang, Yunpeng, Abbott, Liam, Abdellaoui, Abdel, Adams, Mark J., Adolfsson, Annelie Nordin, Agerbo, Esben, Akil, Huda, Albani, Diego, Alliey-Rodriguez, Ney, Als, Thomas D., Andlauer, Till F.M., Anjorin, Adebayo, Antilla, Verneri, Van der Auwera, Sandra, Awasthi, Swapnil, Bacanu, Silviu-Alin, Badner, Judith A., Bækvad-Hansen, Marie, Barchas, Jack D., Bass, Nicholas, Bauer, Michael, Beekman, Aartjan T.F., Belliveau, Richard, Bergen, Sarah E., Bigdeli, Tim B., Binder, Elisabeth B., Bøen, Erlend, Boks, Marco, Boocock, James, Budde, Monika, Bunney, William, Burmeister, Margit, Buttenschøn, Henriette N., Bybjerg-Grauholm, Jonas, Byerley, William, Cai, Na, Casas, Miquel, Castelao, Enrique, Cerrato, Felecia, Cervantes, Pablo, Chambert, Kimberly, Charney, Alexander W., Chen, Danfeng, Christensen, Jane Hvarregaard, Churchhouse, Claire, St Clair, David, Clarke, Toni-Kim, Colodro-Conde, Lucía, Coryell, William, Couvy-Duchesne, Baptiste, Craig, David W., Crawford, Gregory E., Cruceanu, Cristiana, Czerski, Piotr M., Dale, Anders M., Davies, Gail, Deary, Ian J., Degenhardt, Franziska, Del-Favero, Jurgen, DePaulo, J Raymond, Derks, Eske M., Direk, Nese, Djurovic, Srdjan, Dobbyn, Amanda L., Dolan, Conor V., Dumont, Ashley, Dunn, Erin C., Eley, Thalia C., Elvsåshagen, Torbjørn, Escott-Price, Valentina, Fan, Chun Chieh, Finucane, Hilary K., Fischer, Sascha B., Flickinger, Matthew, Foo, Jerome C., Foroud, Tatiana M., Forty, Liz, Frank, Josef, Fraser, Christine, Freimer, Nelson B., Frisén, Louise, Gade, Katrin, Gage, Diane, Garnham, Julie, Giambartolomei, Claudia, Goes, Fernando S., Goldstein, Jaqueline, Gordon, Scott D., Gordon-Smith, Katherine, Green, Elaine K., Green, Melissa J., Greenwood, Tiffany A., Grove, Jakob, Guan, Weihua, Hall, Lynsey S., Hamshere, Marian L., Hansen, Christine Søholm, Hansen, Thomas F., Hautzinger, Martin, Heilbronner, Urs, van Hemert, Albert M., Herms, Stefan, Hickie, Ian B., Hipolito, Maria, Hoffmann, Per, Holland, Dominic, Homuth, Georg, Horn, Carsten, Hottenga, Jouke-Jan, Huckins, Laura, Ising, Marcus, Jamain, Stéphane, Jansen, Rick, Johnson, Jessica S., de Jong, Simone, Jorgenson, Eric, Juréus, Anders, Kandaswamy, Radhika, Karlsson, Robert, Kennedy, James L., Hassan Kiadeh, Farnush Farhadi, Kittel-Schneider, Sarah, Knowles, James A., Kogevinas, Manolis, Kohane, Isaac S., Koller, Anna C., Kraft, Julia, Kretzschmar, Warren W., Krogh, Jesper, Kupka, Ralph, Kutalik, Zoltán, Lavebratt, Catharina, Lawrence, Jacob, Lawson, William B., Leber, Markus, Lee, Phil H., Levy, Shawn E., Li, Jun Z., Li, Yihan, Lind, Penelope A., Liu, Chunyu, Olde Loohuis, Loes M., Maaser, Anna, MacIntyre, Donald J., MacKinnon, Dean F., Mahon, Pamela B., Maier, Wolfgang, Maier, Robert M., Marchini, Jonathan, Martinsson, Lina, Mbarek, Hamdi, McCarroll, Steve, McGrath, Patrick, McGuffin, Peter, McInnis, Melvin G., McKay, James D., Medeiros, Helena, Medland, Sarah E., Mehta, Divya, Meng, Fan, Middeldorp, Christel M., Mihailov, Evelin, Milaneschi, Yuri, Milani, Lili, Mirza, Saira Saeed, Mondimore, Francis M., Montgomery, Grant W., Morris, Derek W., Mostafavi, Sara, Mühleisen, Thomas W., Mullins, Niamh, Nauck, Matthias, Ng, Bernard, Nguyen, Hoang, Nievergelt, Caroline M., Nivard, Michel G., Nwulia, Evaristus A., Nyholt, Dale R., O'Donovan, Claire, O'Reilly, Paul F., Ori, Anil P.S., Oruc, Lilijana, Ösby, Urban, Oskarsson, Hogni, Painter, Jodie N., Parra, José Guzman, Pedersen, Carsten Bøcker, Pedersen, Marianne Giørtz, Perry, Amy, Peterson, Roseann E., Pettersson, Erik, Peyrot, Wouter J., Pfennig, Andrea, Pistis, Giorgio, Purcell, Shaun M., Quiroz, Jorge A., Qvist, Per, Regeer, Eline J., Reif, Andreas, Reinbold, Céline S., Rice, John P., Riley, Brien P., Rivas, Fabio, Rivera, Margarita, Roussos, Panos, Ruderfer, Douglas M., Ryu, Euijung, Sánchez-Mora, Cristina, Schatzberg, Alan F., Scheftner, William A., Schoevers, Robert, Schork, Nicholas J., Schulte, Eva C., Shehktman, Tatyana, Shen, Ling, Shi, Jianxin, Shilling, Paul D., Shyn, Stanley I., Sigurdsson, Engilbert, Slaney, Claire, Smeland, Olav B., Smit, Johannes H., Smith, Daniel J., Sobell, Janet L., Spijker, Anne T., Steffens, Michael, Strauss, John S., Streit, Fabian, Strohmaier, Jana, Szelinger, Szabolcs, Tansey, Katherine E., Teismann, Henning, Teumer, Alexander, Thompson, Robert C., Thompson, Wesley, Thomson, Pippa A., Thorgeirsson, Thorgeir E., Traylor, Matthew, Treutlein, Jens, Uitterlinden, André G., Umbricht, Daniel, Vedder, Helmut, Viktorin, Alexander, Visscher, Peter M., Wang, Weiqing, Watson, Stanley J., Webb, Bradley T., Weickert, Cynthia Shannon, Weickert, Thomas W., Weinsheimer, Shantel Marie, Wellmann, Jürgen, Willemsen, Gonneke, Witt, Stephanie H., Wu, Yang, Xi, Hualin S., Xu, Wei, Yang, Jian, Young, Allan H., Zandi, Peter, Zhang, Peng, Zhang, Futao, Zollner, Sebastian, Adolfsson, Rolf, Agartz, Ingrid, Alda, Martin, Arolt, Volker, Backlund, Lena, Baune, Bernhard T., Bellivier, Frank, Berger, Klaus, Berrettini, Wade H., Biernacka, Joanna M., Blackwood, Douglas H.R., Boehnke, Michael, Boomsma, Dorret I., Corvin, Aiden, Craddock, Nicholas, Daly, Mark J., Dannlowski, Udo, Domenici, Enrico, Domschke, Katharina, Esko, Tõnu, Etain, Bruno, Frye, Mark, Fullerton, Janice M., Gershon, Elliot S., de Geus, E.J.C., Gill, Michael, Goes, Fernando, Grabe, Hans J., Grigoroiu-Serbanescu, Maria, Hamilton, Steven P., Hauser, Joanna, Hayward, Caroline, Heath, Andrew C., Hougaard, David M., Hultman, Christina M., Jones, Ian, Jones, Lisa A., Kahn, René S., Kendler, Kenneth S., Kirov, George, Kloiber, Stefan, Landén, Mikael, Leboyer, Marion, Lewis, Glyn, Li, Qingqin S., Lissowska, Jolanta, Lucae, Susanne, Madden, Pamela A.F., Magnusson, Patrik K., Martin, Nicholas G., Mayoral, Fermin, McElroy, Susan L., McIntosh, Andrew M., McMahon, Francis J., Melle, Ingrid, Metspalu, Andres, Mitchell, Philip B., Morken, Gunnar, Mors, Ole, Mortensen, Preben Bo, Müller-Myhsok, Bertram, Myers, Richard M., Neale, Benjamin M., Nimgaonkar, Vishwajit, Nordentoft, Merete, Nöthen, Markus M., O'Donovan, Michael C., Oedegaard, Ketil J., Owen, Michael J., Paciga, Sara A., Pato, Carlos, Pato, Michele T., Pedersen, Nancy L., Penninx, Brenda W.J. H., Perlis, Roy H., Porteous, David J., Posthuma, Danielle, Potash, James B., Preisig, Martin, Ramos-Quiroga, Josep Antoni, Ribasés, Marta, Rietschel, Marcella, Rouleau, Guy A., Schaefer, Catherine, Schalling, Martin, Schofield, Peter R., Schulze, Thomas G., Serretti, Alessandro, Smoller, Jordan W., Stefansson, Hreinn, Stefansson, Kari, Stordal, Eystein, Tiemeier, Henning, Turecki, Gustavo, Uher, Rudolf, Vaaler, Arne E., Vieta, Eduard, Vincent, John B., Völzke, Henry, Weissman, Myrna M., Werge, Thomas, Andreassen, Ole A., Børglum, Anders D., Cichon, Sven, Edenberg, Howard J., Di Florio, Arianna, Kelsoe, John, Levinson, Douglas F., Lewis, Cathryn M., Nurnberger, John I., Ophoff, Roel A., Scott, Laura J., Sklar, Pamela, Sullivan, Patrick F., Wray, Naomi R., Coleman, Jonathan R.I., Gaspar, Héléna A., Bryois, Julien, and Breen, Gerome

Published
2020
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15. Cell-Type Specific Reductions in Interneuron Gene Expression within Subregions of the Anterior and Posterior Cingulate Gyrus of Schizophrenia and Bipolar Disorder Subjects

Author

Krolewski, David M, primary, Waselus, Maria, additional, Bunney, Blynn G, additional, Myers, Richard M., additional, Barchas, Jack D, additional, Lee, Francis S., additional, Schatzberg, Alan F, additional, Bunney, William E, additional, Akil, Huda, additional, and Watson, Stanley J, additional

Published
2024
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17. Quantitative Trait Locus and Brain Expression of HLA-DPA1 Offers Evidence of Shared Immune Alterations in Psychiatric Disorders.

Author

Morgan, Ling Z, Rollins, Brandi, Sequeira, Adolfo, Byerley, William, DeLisi, Lynn E, Schatzberg, Alan F, Barchas, Jack D, Myers, Richard M, Watson, Stanley J, Akil, Huda, Bunney, William E, and Vawter, Marquis P

Subjects
alternative splicing, exon array, expression quantitative trait locus, major histocompatibility locus II, Medical Biotechnology
Abstract

Genome-wide association studies of schizophrenia encompassing the major histocompatibility locus (MHC) were highly significant following genome-wide correction. This broad region implicates many genes including the MHC complex class II. Within this interval we examined the expression of two MHC II genes (HLA-DPA1 and HLA-DRB1) in brain from individual subjects with schizophrenia (SZ), bipolar disorder (BD), major depressive disorder (MDD), and controls by differential gene expression methods. A third MHC II mRNA, CD74, was studied outside of the MHC II locus, as it interacts within the same immune complex. Exon microarrays were performed in anterior cingulate cortex (ACC) in BD compared to controls, and both HLA-DPA1 and CD74 were decreased in expression in BD. The expression of HLA-DPA1 and CD74 were both reduced in hippocampus, amygdala, and dorsolateral prefrontal cortex regions in SZ and BD compared to controls by specific qPCR assay. We found several novel HLA-DPA1 mRNA variants spanning HLA-DPA1 exons 2-3-4 as suggested by exon microarrays. The intronic rs9277341 SNP was a significant cis expression quantitative trait locus (eQTL) that was associated with the total expression of HLA-DPA1 in five brain regions. A biomarker study of MHC II mRNAs was conducted in SZ, BD, MDD, and control lymphoblastic cell lines (LCL) by qPCR assay of 87 subjects. There was significantly decreased expression of HLA-DPA1 and CD74 in BD, and trends for reductions in SZ in LCLs. The discovery of multiple splicing variants in brain for HLA-DPA1 is important as the HLA-DPA1 gene is highly conserved, there are no reported splicing variants, and the functions in brain are unknown. Future work on the function and localization of MHC Class II proteins in brain will help to understand the role of alterations in neuropsychiatric disorders. The HLA-DPA1 eQTL is located within a large linkage disequilibrium block that has an irrefutable association with schizophrenia. Future tests in a larger cohort are needed to determine the significance of this eQTL association with schizophrenia. Our findings support the long-held hypothesis that alterations in immune function are associated with the pathophysiology of psychiatric disorders.

Published
2016

22. Mitochondrial Mutations in Subjects with Psychiatric Disorders

Author

Sequeira, Adolfo, Rollins, Brandi, Magnan, Christophe, van Oven, Mannis, Baldi, Pierre, Myers, Richard M, Barchas, Jack D, Schatzberg, Alan F, Watson, Stanley J, Akil, Huda, Bunney, William E, and Vawter, Marquis P

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Biological Psychology, Psychology, Pharmacology and Pharmaceutical Sciences, Mental Health, Biotechnology, Brain Disorders, Schizophrenia, Human Genome, Neurosciences, Aetiology, 2.1 Biological and endogenous factors, Mental health, Adult, Case-Control Studies, DNA Mutational Analysis, DNA, Mitochondrial, Electrophoresis, Agar Gel, Female, Genetic Loci, Humans, Male, Mental Disorders, Middle Aged, Molecular Sequence Data, Mutation, Prefrontal Cortex, General Science & Technology
Abstract

A considerable body of evidence supports the role of mitochondrial dysfunction in psychiatric disorders and mitochondrial DNA (mtDNA) mutations are known to alter brain energy metabolism, neurotransmission, and cause neurodegenerative disorders. Genetic studies focusing on common nuclear genome variants associated with these disorders have produced genome wide significant results but those studies have not directly studied mtDNA variants. The purpose of this study is to investigate, using next generation sequencing, the involvement of mtDNA variation in bipolar disorder, schizophrenia, major depressive disorder, and methamphetamine use. MtDNA extracted from multiple brain regions and blood were sequenced (121 mtDNA samples with an average of 8,800x coverage) and compared to an electronic database containing 26,850 mtDNA genomes. We confirmed novel and rare variants, and confirmed next generation sequencing error hotspots by traditional sequencing and genotyping methods. We observed a significant increase of non-synonymous mutations found in individuals with schizophrenia. Novel and rare non-synonymous mutations were found in psychiatric cases in mtDNA genes: ND6, ATP6, CYTB, and ND2. We also observed mtDNA heteroplasmy in brain at a locus previously associated with schizophrenia (T16519C). Large differences in heteroplasmy levels across brain regions within subjects suggest that somatic mutations accumulate differentially in brain regions. Finally, multiplasmy, a heteroplasmic measure of repeat length, was observed in brain from selective cases at a higher frequency than controls. These results offer support for increased rates of mtDNA substitutions in schizophrenia shown in our prior results. The variable levels of heteroplasmic/multiplasmic somatic mutations that occur in brain may be indicators of genetic instability in mtDNA.

Published
2015

23. Altered choroid plexus gene expression in major depressive disorder

Author

Turner, Cortney A, Thompson, Robert C, Bunney, William E, Schatzberg, Alan F, Barchas, Jack D, Myers, Richard M, Akil, Huda, and Watson, Stanley J

Subjects
cytoskeleton, mRNA, hippocampus, depression, brainfibroblast-growth-factor, messenger-rna, dentate gyrus, fluid barrier, brain, adult, astrocytes, suicide, protein, neurogenesis
Published
2014

25. Connective Tissue Growth Factor Is a Novel Prodepressant

Author

Turner, Cortney A., Sharma, Vikram, Hagenauer, Megan H., Chaudhury, Sraboni, O’Connor, Angela M., Hebda-Bauer, Elaine K., Thompson, Robert C., Myers, Richard M., Bunney, William E., Barchas, Jack D., Lee, Francis S., Schatzberg, Alan F., Watson, Stanley J., Jr., and Akil, Huda

Published
2018
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26. Genomic Dissection of Bipolar Disorder and Schizophrenia, Including 28 Subphenotypes

Author

Ruderfer, Douglas M., Ripke, Stephan, McQuillin, Andrew, Boocock, James, Stahl, Eli A., Pavlides, Jennifer M. Whitehead, Mullins, Niamh, Charney, Alexander W., Ori, Anil P.S., Loohuis, Loes M. Olde, Domenici, Enrico, Di Florio, Arianna, Papiol, Sergi, Kalman, Janos L., Trubetskoy, Vassily, Adolfsson, Rolf, Agartz, Ingrid, Agerbo, Esben, Akil, Huda, Albani, Diego, Albus, Margot, Alda, Martin, Alexander, Madeline, Alliey-Rodriguez, Ney, Als, Thomas D., Amin, Farooq, Anjorin, Adebayo, Arranz, Maria J., Awasthi, Swapnil, Bacanu, Silviu A., Badner, Judith A., Baekvad-Hansen, Marie, Bakker, Steven, Band, Gavin, Barchas, Jack D., Barroso, Ines, Bass, Nicholas, Bauer, Michael, Baune, Bernhard T., Begemann, Martin, Bellenguez, Celine, Belliveau, Richard A., Jr., Bellivier, Frank, Bender, Stephan, Bene, Judit, Bergen, Sarah E., Berrettini, Wade H., Bevilacqua, Elizabeth, Biernacka, Joanna M., Bigdeli, Tim B., Black, Donald W., Blackburn, Hannah, Blackwell, Jenefer M., Blackwood, Douglas H.R., Pedersen, Carsten Bocker, Boehnke, Michael, Boks, Marco, Borglum, Anders D., Bramon, Elvira, Breen, Gerome, Brown, Matthew A., Bruggeman, Richard, Buccola, Nancy G., Buckner, Randy L., Budde, Monika, Bulik-Sullivan, Brendan, Bumpstead, Suzannah J., Bunney, William, Burmeister, Margit, Buxbaum, Joseph D., Bybjerg-Grauholm, Jonas, Byerley, William, Cahn, Wiepke, Cai, Guiqing, Cairns, Murray J., Campion, Dominique, Cantor, Rita M., Carr, Vaughan J., Carrera, Noa, Casas, Juan P., Casas, Miquel, Catts, Stanley V., Cervantes, Pablo, Chambert, Kimberley D., Chan, Raymond C.K., Chen, Eric Y.H., Chen, Ronald Y.L., Cheng, Wei, Cheung, Eric F.C., Chong, Siow Ann, Clarke, Toni-Kim, Cloninger, C. Robert, Cohen, David, Cohen, Nadine, Coleman, Jonathan R.I., Collier, David A., Cormican, Paul, Coryell, William, Craddock, Nicholas, Craig, David W., Crespo-Facorro, Benedicto, Crowley, James J., Cruceanu, Cristiana, Curtis, David, Czerski, Piotr M., Dale, Anders M., Daly, Mark J., Dannlowski, Udo, Darvasi, Ariel, Davidson, Michael, Davis, Kenneth L., de Leeuw, Christiaan A., Degenhardt, Franziska, Del Favero, Jurgen, DeLisi, Lynn E., Deloukas, Panos, Demontis, Ditte, DePaulo, J. Raymond, di Forti, Marta, Dikeos, Dimitris, Dinan, Timothy, Djurovic, Srdjan, Dobbyn, Amanda L., Donnelly, Peter, Donohoe, Gary, Drapeau, Elodie, Dronov, Serge, Duan, Jubao, Dudbridge, Frank, Duncanson, Audrey, Edenberg, Howard, Edkins, Sarah, Ehrenreich, Hannelore, Eichhammer, Peter, Elvsashagen, Torbjorn, Eriksson, Johan, Escott-Price, Valentina, Esko, Tonu, Essioux, Laurent, Etain, Bruno, Fan, Chun Chieh, Farh, Kai-How, Farrell, Martilias S., Flickinger, Matthew, Foroud, Tatiana M., Forty, Liz, Frank, Josef, Franke, Lude, Fraser, Christine, Freedman, Robert, Freeman, Colin, Freimer, Nelson B., Friedman, Joseph I., Fromer, Menachem, Frye, Mark A., Fullerton, Janice M., Gade, Katrin, Garnham, Julie, Gaspar, Helena A., Gejman, Pablo V., Genovese, Giulio, Georgieva, Lyudmila, Giambartolomei, Claudia, Giannoulatou, Eleni, Giegling, Ina, Gill, Michael, Gillman, Matthew, Pedersen, Marianne Giortz, Giusti-Rodriguez, Paola, Godard, Stephanie, Goes, Fernando, Goldstein, Jacqueline I., Gopal, Srihari, Gordon, Scott D., Gordon-Smith, Katherine, Gratten, Jacob, Gray, Emma, Green, Elaine K., Green, Melissa J., Greenwood, Tiffany A., Grigoroiu-Serbanescu, Maria, Grove, Jakob, Guan, Weihua, Gurling, Hugh, Parra, Jose Guzman, Gwilliam, Rhian, de Haan, Lieuwe, Hall, Jeremy, Hall, Mei-Hua, Hammer, Christian, Hammond, Naomi, Hamshere, Marian L., Hansen, Mark, Hansen, Thomas, Haroutunian, Vahram, Hartmann, Annette M., Hauser, Joanna, Hautzinger, Martin, Heilbronner, Urs, Hellenthal, Garrett, Henskens, Frans A., Herms, Stefan, Hipolito, Maria, Hirschhorn, Joel N., Hoffmann, Per, Hollegaard, Mads V., Hougaard, David M., Huang, Hailiang, Huckins, Laura, Hultman, Christina M., Hunt, Sarah E., Ikeda, Masashi, Iwata, Nakao, Iyegbe, Conrad, Jablensky, Assen V., Jamain, Stephane, Jankowski, Janusz, Jayakumar, Alagurevathi, Joa, Inge, Jones, Ian, Jones, Lisa A., Jonsson, Erik G., Julia, Antonio, Jureus, Anders, Kahler, Anna K., Kahn, Rene S., Kalaydjieva, Luba, Kandaswamy, Radhika, Karachanak-Yankova, Sena, Karjalainen, Juha, Karlsson, Robert, Kavanagh, David, Keller, Matthew C., Kelly, Brian J., Kelsoe, John, Kennedy, James L., Khrunin, Andrey, Kim, Yunjung, Kirov, George, Kittel-Schneider, Sarah, Klovins, Janis, Knight, Jo, Knott, Sarah V., Knowles, James A., Kogevinas, Manolis, Konte, Bettina, Kravariti, Eugenia, Kucinskas, Vaidutis, Kucinskiene, Zita Ausrele, Kupka, Ralph, Kuzelova-Ptackova, Hana, Landen, Mikael, Langford, Cordelia, Laurent, Claudine, Lawrence, Jacob, Lawrie, Stephen, Lawson, William B., Leber, Markus, Leboyer, Marion, Lee, Phil H., Keong, Jimmy Lee Chee, Legge, Sophie E., Lencz, Todd, Lerer, Bernard, Levinson, Douglas F., Levy, Shawn E., Lewis, Cathryn M., Li, Jun Z., Li, Miaoxin, Li, Qingqin S., Li, Tao, Liang, Kung-Yee, Liddle, Jennifer, Lieberman, Jeffrey, Limborska, Svetlana, Lin, Kuang, Linszen, Don H., Lissowska, Jolanta, Liu, Chunyu, Liu, Jianjun, Lonnqvist, Jouko, Loughland, Carmel M., Lubinski, Jan, Lucae, Susanne, Macek, Milan, Jr., MacIntyre, Donald J., Magnusson, Patrik K.E., Maher, Brion S., Mahon, Pamela B., Maier, Wolfgang, Malhotra, Anil K., Mallet, Jacques, Malt, Ulrik F., Markus, Hugh S., Marsal, Sara, Martin, Nicholas G., Mata, Ignacio, Mathew, Christopher G., Mattheisen, Manuel, Mattingsdal, Morten, Mayoral, Fermin, McCann, Owen T., McCarley, Robert W., McCarroll, Steven A., McCarthy, Mark I., McDonald, Colm, McElroy, Susan L., McGuffin, Peter, McInnis, Melvin G., McIntosh, Andrew M., McKay, James D., McMahon, Francis J., Medeiros, Helena, Medland, Sarah E., Meier, Sandra, Meijer, Carin J., Melegh, Bela, Melle, Ingrid, Meng, Fan, Mesholam-Gately, Raquelle I., Metspalu, Andres, Michie, Patricia T., Milani, Lili, Milanova, Vihra, Mitchell, Philip B., Mokrab, Younes, Montgomery, Grant W., Moran, Jennifer L., Morken, Gunnar, Morris, Derek W., Mors, Ole, Mortensen, Preben B., Mowry, Bryan J., Mühleisen, Thomas W., Müller-Myhsok, Bertram, Murphy, Kieran C., Murray, Robin M., Myers, Richard M., Myin-Germeys, Inez, Neale, Benjamin M., Nelis, Mari, Nenadic, Igor, Nertney, Deborah A., Nestadt, Gerald, Nicodemus, Kristin K., Nievergelt, Caroline M., Nikitina-Zake, Liene, Nimgaonkar, Vishwajit, Nisenbaum, Laura, Nordentoft, Merete, Nordin, Annelie, Nöthen, Markus M., Nwulia, Evaristus A., O’Callaghan, Eadbhard, O’Donovan, Claire, O’Dushlaine, Colm, O’Neill, F. Anthony, Oedegaard, Ketil J., Oh, Sang-Yun, Olincy, Ann, Olsen, Line, Oruc, Lilijana, Van Os, Jim, Owen, Michael J., Paciga, Sara A., Palmer, Colin N.A., Palotie, Aarno, Pantelis, Christos, Papadimitriou, George N., Parkhomenko, Elena, Pato, Carlos, Pato, Michele T., Paunio, Tiina, Pearson, Richard, Perkins, Diana O., Perlis, Roy H., Perry, Amy, Pers, Tune H., Petryshen, Tracey L., Pfennig, Andrea, Picchioni, Marco, Pietilainen, Olli, Pimm, Jonathan, Pirinen, Matti, Plomin, Robert, Pocklington, Andrew J., Posthuma, Danielle, Potash, James B., Potter, Simon C., Powell, John, Price, Alkes, Pulver, Ann E., Purcell, Shaun M., Quested, Digby, Ramos-Quiroga, Josep Antoni, Rasmussen, Henrik B., Rautanen, Anna, Ravindrarajah, Radhi, Regeer, Eline J., Reichenberg, Abraham, Reif, Andreas, Reimers, Mark A., Ribases, Marta, Rice, John P., Richards, Alexander L., Ricketts, Michelle, Riley, Brien P., Rivas, Fabio, Rivera, Margarita, Roffman, Joshua L., Rouleau, Guy A., Roussos, Panos, Rujescu, Dan, Salomaa, Veikko, Sanchez-Mora, Cristina, Sanders, Alan R., Sawcer, Stephen J., Schall, Ulrich, Schatzberg, Alan F., Scheftner, William A., Schofield, Peter R., Schork, Nicholas J., Schwab, Sibylle G., Scolnick, Edward M., Scott, Laura J., Scott, Rodney J., Seidman, Larry J., Serretti, Alessandro, Sham, Pak C., Weickert, Cynthia Shannon, Shehktman, Tatyana, Shi, Jianxin, Shilling, Paul D., Sigurdsson, Engilbert, Silverman, Jeremy M., Sim, Kang, Slaney, Claire, Slominsky, Petr, Smeland, Olav B., Smoller, Jordan W., So, Hon-Cheong, Sobell, Janet L., Soderman, Erik, Hansen, Christine Soholm, Spencer, Chris C.A., Spijker, Anne T., St Clair, David, Stefansson, Hreinn, Stefansson, Kari, Steinberg, Stacy, Stogmann, Elisabeth, Stordal, Eystein, Strange, Amy, Straub, Richard E., Strauss, John S., Streit, Fabian, Strengman, Eric, Strohmaier, Jana, Stroup, T. Scott, Su, Zhan, Subramaniam, Mythily, Suvisaari, Jaana, Svrakic, Dragan M., Szatkiewicz, Jin P., Szelinger, Szabolcs, Tashakkori-Ghanbaria, Avazeh, Thirumalai, Srinivas, Thompson, Robert C., Thorgeirsson, Thorgeir E., Toncheva, Draga, Tooney, Paul A., Tosato, Sarah, Toulopoulou, Timothea, Trembath, Richard C., Treutlein, Jens, Turecki, Gustavo, Vaaler, Arne E., Vedder, Helmut, Vieta, Eduard, Vincent, John, Visscher, Peter M., Viswanathan, Ananth C., Vukcevic, Damjan, Waddington, John, Waller, Matthew, Walsh, Dermot, Walshe, Muriel, Walters, James T.R., Wang, Dai, Wang, Qiang, Wang, Weiqing, Wang, Yunpeng, Watson, Stanley J., Webb, Bradley T., Weickert, Thomas W., Weinberger, Daniel R., Weisbrod, Matthias, Weiser, Mark, Werge, Thomas, Weston, Paul, Whittaker, Pamela, Widaa, Sara, Wiersma, Durk, Wildenauer, Dieter B., Williams, Nigel M., Williams, Stephanie, Witt, Stephanie H., Wolen, Aaron R., Wong, Emily H.M., Wood, Nicholas W., Wormley, Brandon K., Wu, Jing Qin, Xi, Simon, Xu, Wei, Young, Allan H., Zai, Clement C., Zandi, Peter, Zhang, Peng, Zheng, Xuebin, Zimprich, Fritz, Zollner, Sebastian, Corvin, Aiden, Fanous, Ayman H., Cichon, Sven, Rietschel, Marcella, Gershon, Elliot S., Schulze, Thomas G., Cuellar-Barboza, Alfredo B., Forstner, Andreas J., Holmans, Peter A., Nurnberger, John I., Andreassen, Ole A., Lee, S. Hong, O’Donovan, Michael C., Sullivan, Patrick F., Ophoff, Roel A., Wray, Naomi R., Sklar, Pamela, and Kendler, Kenneth S.

Published
2018
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27. Evidence of allelic imbalance in the schizophrenia susceptibility gene ZNF804A in human dorsolateral prefrontal cortex

Author

Guella, Ilaria, Sequeira, Adolfo, Rollins, Brandi, Morgan, Ling, Myers, Richard M, Watson, Stanley J, Akil, Huda, Bunney, William E, Delisi, Lynn E, Byerley, William, and Vawter, Marquis P

Subjects
Pharmacology and Pharmaceutical Sciences, Biomedical and Clinical Sciences, Brain Disorders, Biotechnology, Neurosciences, Genetics, Mental Health, Schizophrenia, Serious Mental Illness, Aetiology, 2.1 Biological and endogenous factors, Mental health, Allelic Imbalance, Bipolar Disorder, Cohort Studies, Costa Rica, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Genotype, Humans, Kruppel-Like Transcription Factors, Male, Polymorphism, Single Nucleotide, Postmortem Changes, Prefrontal Cortex, Bipolar disorder, ZNF804A, Association study, rs1344706, Allelic-specific expression, Medical and Health Sciences, Psychology and Cognitive Sciences, Psychiatry, Clinical sciences
Abstract

The rs1344706, an intronic SNP within the zinc-finger protein 804A gene (ZNF804A), was identified as one of the most compelling risk SNPs for schizophrenia (SZ) and bipolar disorder (BD). It is however not clear by which molecular mechanisms ZNF804A increases disease risk. We evaluated the role of ZNF804A in SZ and BD by genotyping the originally associated rs1344706 SNP and an exonic SNP (rs12476147) located in exon four of ZNF804A in a sample of 422 SZ, 382 BD, and 507 controls from the isolated population of the Costa Rica Central Valley. We also investigated the rs1344706 SNP for allelic specific expression (ASE) imbalance in the dorsolateral prefrontal cortex (DLPFC) of 46 heterozygous postmortem brains. While no significant association between rs1344706 and SZ or BD was observed in the Costa Rica sample, we observed an increased risk of SZ for the minor allele (A) of the exonic rs12476147 SNP (p=0.026). Our ASE assay detected a significant over-expression of the rs12476147 A allele in DLPFC of rs1344706 heterozygous subjects. Interestingly, cDNA allele ratios were significantly different according to the intronic rs1344706 genotypes (p-value=0.03), with the rs1344706 A allele associated with increased ZNF804A rs12476147 A allele expression (average 1.06, p-value=0.02, for heterozygous subjects vs. genomic DNA). In conclusion, we have demonstrated a significant association of rs12476147 with SZ, and using a powerful within-subject design, an allelic expression imbalance of ZNF804A exonic SNP rs12476147 in the DLPFC. Although this data does not preclude the possibility of other functional variants in ZNF804A, it provides evidence that the rs1344706 SZ risk allele is the cis-regulatory variant directly responsible for this allelic expression imbalance in adult cortex.

Published
2014

28. Gene Expression Changes in the Prefrontal Cortex, Anterior Cingulate Cortex and Nucleus Accumbens of Mood Disorders Subjects That Committed Suicide

Author

Sequeira, Adolfo, Morgan, Ling, Walsh, David M., Cartagena, Preston M., Choudary, Prabhakara, Li, Jun, Schatzberg, Alan F., Watson, Stanley J., Akil, Huda, Myers, Richard M., Jones, Edward G., Bunney, William E., and Vawter, Marquis P.

Subjects
metallothionein messenger-rna, bipolar affective-disorder, adenylyl-cyclase activity, pituitary-adrenal axis, postmortem human-brain, serotonin 2a receptor, major depression, frontal-cortex, urinary 17-hydroxycorticosteroids, wolfram-syndrome
Abstract

Suicidal behaviors are frequent in mood disorders patients but only a subset of them ever complete suicide. Understanding predisposing factors for suicidal behaviors in high risk populations is of major importance for the prevention and treatment of suicidal behaviors. The objective of this project was to investigate gene expression changes associated with suicide in brains of mood disorder patients by microarrays (Affymetrix HG-U133 Plus2.0) in the dorsolateral prefrontal cortex (DLPFC: 6 Non-suicides, 15 suicides), the anterior cingulate cortex (ACC: 6NS, 9S) and the nucleus accumbens (NAcc: 8NS, 13S). ANCOVA was used to control for age, gender, pH and RNA degradation, with P≤0.01 and fold change±1.25 as criteria for significance. Pathway analysis revealed serotonergic signaling alterations in the DLPFC and glucocorticoid signaling alterations in the ACC and NAcc. The gene with the lowest p-value in the DLPFC was the 5-HT2A gene, previously associated both with suicide and mood disorders. In the ACC 6 metallothionein genes were down-regulated in suicide (MT1E, MT1F, MT1G, MT1H, MT1X, MT2A) and three were down-regulated in the NAcc (MT1F, MT1G, MT1H). Differential expression of selected genes was confirmed by qPCR, we confirmed the 5-HT2A alterations and the global down-regulation of members of the metallothionein subfamilies MT 1 and 2 in suicide completers. MTs 1 and 2 are neuro-protective following stress and glucocorticoid stimulations, suggesting that in suicide victims neuroprotective response to stress and cortisol may be diminished. Our results thus suggest that suicide-specific expression changes in mood disorders involve both glucocorticoids regulated metallothioneins and serotonergic signaling in different regions of the brain.

Published
2012

30. The impact of COVID-19 on a college freshman sample reveals genetic and nongenetic forms of susceptibility and resilience to stress

Author

Turner, Cortney A., primary, Khalil, Huzefa, additional, Murphy-Weinberg, Virginia, additional, Hagenauer, Megan H., additional, Gates, Linda, additional, Tang, Yu, additional, Weinberg, Lauren, additional, Grysko, Robert, additional, Floran-Garduno, Leonor, additional, Dokas, Thomas, additional, Samaniego, Catherine, additional, Zhao, Zhuo, additional, Fang, Yu, additional, Sen, Srijan, additional, Lopez, Juan F., additional, Watson, Stanley J., additional, and Akil, Huda, additional

Published
2023
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31. Allele biased transcription factor binding across human brain regions gives mechanistic insight into eQTLs

Author

Moyers, Belle A., primary, Loupe, Jacob M., additional, Felker, Stephanie A., additional, Lawlor, James M.J., additional, Anderson, Ashlyn G., additional, Rodriguez-Nunez, Ivan, additional, Bunney, William E., additional, Bunney, Blynn G., additional, Cartagena, Preston M., additional, Sequeira, Adolfo, additional, Watson, Stanley J., additional, Akil, Huda, additional, Mendenhall, Eric M., additional, Cooper, Gregory M., additional, and Myers, Richard M., additional

Published
2023
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32. Adolescent environmental enrichment induces social resilience and alters neural gene expression in a selectively bred rodent model with anxious phenotype

Author

O’Connor, Angela M., primary, Hagenauer, Megan H., additional, Thew Forrester, Liam Cannon, additional, Maras, Pamela M., additional, Arakawa, Keiko, additional, Hebda-Bauer, Elaine K., additional, Khalil, Huzefa, additional, Richardson, Evelyn R., additional, Rob, Farizah I., additional, Sannah, Yusra, additional, Watson, Stanley J., additional, and Akil, Huda, additional

Published
2023
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33. Mitochondrial Variants in Schizophrenia, Bipolar Disorder, and Major Depressive Disorder

Author

Rollins, Brandi, Martin, Maureen V., Sequeira, P. Adolfo, Moon, Emily A., Morgan, Ling Z., Watson, Stanley J., Schatzberg, Alan, Akil, Huda, Myers, Richard M., Jones, Edward G., Wallace, Douglas C., Bunney, William E., and Vawter, Marquis P.

Subjects
magnetic-resonance-spectroscopy, postmortem human-brain, mtdna point mutations, subunit gene ndufv2, dna deletion levels, complex-i, oxidative stress, parental transmission, maternal inheritance, rapid identification
Abstract

BackgroundMitochondria provide most of the energy for brain cells by the process of oxidative phosphorylation. Mitochondrial abnormalities and deficiencies in oxidative phosphorylation have been reported in individuals with schizophrenia (SZ), bipolar disorder (BD), and major depressive disorder (MDD) in transcriptomic, proteomic, and metabolomic studies. Several mutations in mitochondrial DNA (mtDNA) sequence have been reported in SZ and BD patients.Methodology/Principal FindingsDorsolateral prefrontal cortex (DLPFC) from a cohort of 77 SZ, BD, and MDD subjects and age-matched controls (C) was studied for mtDNA sequence variations and heteroplasmy levels using Affymetrix mtDNA resequencing arrays. Heteroplasmy levels by microarray were compared to levels obtained with SNaPshot and allele specific real-time PCR. This study examined the association between brain pH and mtDNA alleles. The microarray resequencing of mtDNA was 100% concordant with conventional sequencing results for 103 mtDNA variants. The rate of synonymous base pair substitutions in the coding regions of the mtDNA genome was 22% higher (p = 0.0017) in DLPFC of individuals with SZ compared to controls. The association of brain pH and super haplogroup (U, K, UK) was significant (p = 0.004) and independent of postmortem interval time.ConclusionsFocusing on haplogroup and individual susceptibility factors in psychiatric disorders by considering mtDNA variants may lead to innovative treatments to improve mitochondrial health and brain function.

Published
2009

34. Exon expression in lymphoblastoid cell lines from subjects with schizophrenia before and after glucose deprivation

Author

Martin, Maureen V, Rollins, Brandi, Sequeira, P Adolfo, Mesen, Andrea, Byerley, William, Stein, Richard, Moon, Emily A, Akil, Huda, Jones, Edward G, Watson, Stanley J, Barchas, Jack, DeLisi, Lynn E, Myers, Richard M, Schatzberg, Alan, Bunney, William E, and Vawter, Marquis P

Subjects
global gene-expression, bipolar disorder, prefrontal-cortex, psychiatric-disorders, brain disorders, messenger-rna, blood, disease, microarrays, stress
Abstract

Background: The purpose of this study was to examine the effects of glucose reduction stress on lymphoblastic cell line (LCL) gene expression in subjects with schizophrenia compared to non-psychotic relatives. Methods: LCLs were grown under two glucose conditions to measure the effects of glucose reduction stress on exon expression in subjects with schizophrenia compared to unaffected family member controls. A second aim of this project was to identify cis-regulated transcripts associated with diagnosis. Results: There were a total of 122 transcripts with significant diagnosis by probeset interaction effects and 328 transcripts with glucose deprivation by probeset interaction probeset effects after corrections for multiple comparisons. There were 8 transcripts with expression significantly affected by the interaction between diagnosis and glucose deprivation and probeset after correction for multiple comparisons. The overall validation rate by qPCR of 13 diagnosis effect genes identified through microarray was 62%, and all genes tested by qPCR showed concordant up- or down-regulation by qPCR and microarray. We assessed brain gene expression of five genes found to be altered by diagnosis and glucose deprivation in LCLs and found a significant decrease in expression of one gene, glutaminase, in the dorsolateral prefrontal cortex (DLPFC). One SNP with previously identified regulation by a 3' UTR SNP was found to influence IRF5 expression in both brain and lymphocytes. The relationship between the 3' UTR rs10954213 genotype and IRF5 expression was significant in LCLs (p = 0.0001), DLPFC (p = 0.007), and anterior cingulate cortex (p = 0.002). Conclusion: Experimental manipulation of cells lines from subjects with schizophrenia may be a useful approach to explore stress related gene expression alterations in schizophrenia and to identify SNP variants associated with gene expression.

Published
2009

36. Sample matching by inferred agonal stress in gene expression analyses of the brain

Author

Li, Jun Z, Meng, Fan, Tsavaler, Larisa, Evans, Simon J, Choudary, Prabhakara V, Tomita, Hiroaki, Vawter, Marquis P, Walsh, David, Shokoohi, Vida, Chung, Tisha, Bunney, William E, Jones, Edward G, Akil, Huda, Watson, Stanley J, and Myers, Richard M

Subjects
population-structure, microarray data, structured populations, american population, bipolar disorder, cell-populations, genomic control, association, stratification, schizophrenia
Abstract

BackgroundGene expression patterns in the brain are strongly influenced by the severity and duration of physiological stress at the time of death. This agonal effect, if not well controlled, can lead to spurious findings and diminished statistical power in case-control comparisons. While some recent studies match samples by tissue pH and clinically recorded agonal conditions, we found that these indicators were sometimes at odds with observed stress-related gene expression patterns, and that matching by these criteria still sometimes results in identifying case-control differences that are primarily driven by residual agonal effects. This problem is analogous to the one encountered in genetic association studies, where self-reported race and ethnicity are often imprecise proxies for an individual's actual genetic ancestry.ResultsWe developed an Agonal Stress Rating (ASR) system that evaluates each sample's degree of stress based on gene expression data, and used ASRs in post hoc sample matching or covariate analysis. While gene expression patterns are generally correlated across different brain regions, we found strong region-region differences in empirical ASRs in many subjects that likely reflect inter-individual variabilities in local structure or function, resulting in region-specific vulnerability to agonal stress.ConclusionVariation of agonal stress across different brain regions differs between individuals, revealing a new level of complexity for gene expression studies of brain tissues. The Agonal Stress Ratings quantitatively assess each sample's extent of regulatory response to agonal stress, and allow a strong control of this important confounder.

Published
2007

37. Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data

Author

Dai, Manhong, Wang, Pinglang, Boyd, Andrew D., Kostov, Georgi, Athey, Brian, Jones, Edward G., Bunney, William E., Myers, Richard M., Speed, Terry P., Akil, Huda, Watson, Stanley J., and Meng, Fan

Subjects
density oligonucleotide arrays, national center, biotechnology, normalization, resources, sequence, genes
Abstract

Genome-wide expression profiling is a powerful tool for implicating novel gene ensembles in cellular mechanisms of health and disease. The most popular platform for genome-wide expression profiling is the Affymetrix GeneChip. However, its selection of probes relied on earlier genome and transcriptome annotation which is significantly different from current knowledge. The resultant informatics problems have a profound impact on analysis and interpretation the data. Here, we address these critical issues and offer a solution. We identified several classes of problems at the individual probe level in the existing annotation, under the assumption that current genome and transcriptome databases are more accurate than those used for GeneChip design. We then reorganized probes on more than a dozen popular GeneChips into gene-, transcript- and exon-specific probe sets in light of up-to-date genome, cDNA/EST clustering and single nucleotide polymorphism information. Comparing analysis results between the original and the redefined probe sets reveals ∼30–50% discrepancy in the genes previously identified as differentially expressed, regardless of analysis method. Our results demonstrate that the original Affymetrix probe set definitions are inaccurate, and many conclusions derived from past GeneChip analyses may be significantly flawed. It will be beneficial to re-analyze existing GeneChip data with updated probe set definitions.

Published
2005

46. Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer’s disease-specific cis-regulatory elements

Author

Anderson, Ashlyn G., primary, Rogers, Brianne B., additional, Loupe, Jacob M., additional, Rodriguez-Nunez, Ivan, additional, Roberts, Sydney C., additional, White, Lauren M., additional, Brazell, J. Nicholas, additional, Bunney, William E., additional, Bunney, Blynn G., additional, Watson, Stanley J., additional, Cochran, J. Nicholas, additional, Myers, Richard M., additional, and Rizzardi, Lindsay F., additional

Published
2023
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48. Fibroblast growth factor 9 is a novel modulator of negative affect

Author

Aurbach, Elyse L., Inui, Edny Gula, Turner, Cortney A., Hagenauer, Megan H., Prater, Katherine E., Li, Jun Z., Absher, Devin, Shah, Najmul, Blandino, Peter, Bunney, William E., Myers, Richard M., Barchas, Jack D., Schatzberg, Alan F., Watson, Stanley J., and Akil, Huda

Published
2015

49. Effect of selective lesions of nucleus accumbens µ-opioid receptor-expressing cells on heroin self-administration in male and female rats: a study with novelOprm1-Creknock-in rats

Author

Bossert, Jennifer M., primary, Mejias-Aponte, Carlos A., additional, Saunders, Thomas, additional, Altidor, Lindsay, additional, Emery, Michael, additional, Fredriksson, Ida, additional, Batista, Ashley, additional, Claypool, Sarah M., additional, Caldwell, Kiera E., additional, Reiner, David J., additional, Chow, Jonathan J., additional, Foltz, Matthew, additional, Kumar, Vivek, additional, Seasholtz, Audrey, additional, Hughes, Elizabeth, additional, Filipiak, Wanda, additional, Harvey, Brandon K., additional, Richie, Christopher T., additional, Vautier, Francois, additional, Gomez, Juan L., additional, Michaelides, Michael, additional, Kieffer, Brigitte L., additional, Watson, Stanley J., additional, Akil, Huda, additional, and Shaham, Yavin, additional

Published
2023
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50. Genome-wide association study in a rat model of temperament identifies multiple loci for exploratory locomotion and anxiety-like traits

Author

Chitre, Apurva S., primary, Hebda-Bauer, Elaine K., additional, Blandino, Peter, additional, Bimschleger, Hannah, additional, Nguyen, Khai-Minh, additional, Maras, Pamela, additional, Li, Fei, additional, Ozel, A. Bilge, additional, Pan, Yanchao, additional, Polesskaya, Oksana, additional, Cheng, Riyan, additional, Flagel, Shelly B., additional, Watson, Stanley J., additional, Li, Jun, additional, Akil, Huda, additional, and Palmer, Abraham A., additional

Published
2023
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