snRNA-seq stratifies multiple sclerosis patients into distinct white matter glial responses

Authors: Macnair, Will ^{1, 12, ∗}, Calini, Daniela ^{1, 12}, Agirre, Eneritz ^{2, 13}, Bryois, Julien ^{1, 13}, Jäkel, Sarah ^{3, 4, 13}, Smith, Rebecca Sherrard ¹⁰, Kukanja, Petra ², Stokar-Regenscheit, Nadine ⁵, Ott, Virginie ⁵, Foo, Lynette C. ¹, Collin, Ludovic ¹, Schippling, Sven ¹, Urich, Eduard ¹, Nutma, Erik ⁶, Marzin, Manuel ⁶, Ansaloni, Federico ², Amor, Sandra ⁶, Magliozzi, Roberta ⁷, Heidari, Elyas ⁸, Robinson, Mark D. ⁸, ffrench-Constant, Charles ^{9, 14, 15, ∗∗}, Castelo-Branco, Gonçalo ^{2, 14, 15, ∗∗∗}, Williams, Anna ^{10, 14, 15, 16, ∗∗∗∗}, Malhotra, Dheeraj ^{1, 11, 14, 15, ∗∗∗∗∗}

Source: In Neuron 5 February 2025 113(3):396-410

Cross-disorder and disease-specific pathways in dementia revealed by single-cell genomics

Authors: Rexach, Jessica E., Cheng, Yuyan, Chen, Lawrence, Polioudakis, Damon, Lin, Li-Chun, Mitri, Vivianne, Elkins, Andrew, Han, Xia, Yamakawa, Mai, Yin, Anna, Calini, Daniela, Kawaguchi, Riki, Ou, Jing, Huang, Jerry, Williams, Christopher, Robinson, John, Gaus, Stephanie E., Spina, Salvatore, Lee, Edward B., Grinberg, Lea T., Vinters, Harry, Trojanowski, John Q., Seeley, William W., Malhotra, Dheeraj, Geschwind, Daniel H.

Source: In Cell 3 October 2024 187(20):5753-5774

Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility

Authors: Meijer, Mandy, Agirre, Eneritz, Kabbe, Mukund, van Tuijn, Cassandra A., Heskol, Abeer, Zheng, Chao, Mendanha Falcão, Ana, Bartosovic, Marek, Kirby, Leslie, Calini, Daniela, Johnson, Michael R., Corces, M. Ryan, Montine, Thomas J., Chen, Xingqi, Chang, Howard Y., Malhotra, Dheeraj, Castelo-Branco, Gonçalo

Source: In Neuron 6 April 2022 110(7):1193-1210

Pathogenic Huntingtin Repeat Expansions in Patients with Frontotemporal Dementia and Amyotrophic Lateral Sclerosis

Authors: Adeleye, Adelani, Alba, Camille, Bacikova, Dagmar, Hupalo, Daniel N., Martinez, Elisa McGrath, Pollard, Harvey B., Sukumar, Gauthaman, Soltis, Anthony R., Tuck, Meila, Zhang, Xijun, Wilkerson, Matthew D., Smith, Bradley N., Ticozzi, Nicola, Fallini, Claudia, Gkazi, Athina Soragia, Topp, Simon D., Kost, Jason, Scotter, Emma L., Kenna, Kevin P., Miller, Jack W., Tiloca, Cinzia, Vance, Caroline, Danielson, Eric W., Troakes, Claire, Colombrita, Claudia, Al-Sarraj, Safa, Lewis, Elizabeth A., King, Andrew, Calini, Daniela, Pensato, Viviana, Castellotti, Barbara, de Belleroche, Jacqueline, Baas, Frank, ten Asbroek, Anneloor L.M.A., Sapp, Peter C., McKenna-Yasek, Diane, McLaughlin, Russell L., Polak, Meraida, Asress, Seneshaw, Esteban-Pérez, Jesús, Muñoz-Blanco, José Luis, Stevic, Zorica, D’Alfonso, Sandra, Mazzini, Letizia, Comi, Giacomo P., Del Bo, Roberto, Ceroni, Mauro, Gagliardi, Stella, Querin, Giorgia, Bertolin, Cinzia, van Rheenen, Wouter, Diekstra, Frank P., Rademakers, Rosa, van Blitterswijk, Marka, Boylan, Kevin B., Lauria, Giuseppe, Duga, Stefano, Corti, Stefania, Cereda, Cristina, Corrado, Lucia, Sorarù, Gianni, Williams, Kelly L., Nicholson, Garth A., Blair, Ian P., Leblond-Manry, Claire, Rouleau, Guy A., Hardiman, Orla, Morrison, Karen E., Veldink, Jan H., van den Berg, Leonard H., Al-Chalabi, Ammar, Pall, Hardev, Shaw, Pamela J., Turner, Martin R., Talbot, Kevin, Taroni, Franco, García-Redondo, Alberto, Wu, Zheyang, Gellera, Cinzia, Ratti, Antonia, Brown, Robert H., Jr., Shaw, Christopher E., Ambrose, John C., Arumugam, Prabhu, Baple, Emma L., Bleda, Marta, Boardman-Pretty, Freya, Boissiere, Jeanne M., Boustred, Christopher R., Brittain, H., Caulfield, Mark J., Chan, Georgia C., Craig, Clare E.H., Daugherty, Louise C., de Burca, Anna, Devereau, Andrew, Elgar, Greg, Foulger, Rebecca E., Fowler, Tom, Furió-Tarí, Pedro, Hackett, Joanne M., Halai, Dina, Hamblin, Angela, Henderson, Shirley, Holman, James E., Hubbard, Tim J.P., Jackson, Rob, Jones, Louise J., Kasperaviciute, Dalia, Kayikci, Melis, Lahnstein, Lea, Lawson, Kay, Leigh, Sarah E.A., Leong, Ivonne U.S., Lopez, Javier F., Maleady-Crowe, Fiona, Mason, Joanne, McDonagh, Ellen M., Moutsianas, Loukas, Mueller, Michael, Murugaesu, Nirupa, Need, Anna C., Odhams, Chris A., Patch, Christine, Perez-Gil, Daniel, Polychronopoulos, Dimitris, Pullinger, John, Rahim, Tahrima, Rendon, Augusto, Riesgo-Ferreiro, Pablo, Rogers, Tim, Savage, Kevin, Sawant, Kushmita, Scott, Richard H., Siddiq, Afshan, Sieghart, Alexander, Smedley, Damian, Smith, Katherine R., Sosinsky, Alona, Spooner, William, Stevens, Helen E., Stuckey, Alexander, Sultana, Razvan, Thomas, Ellen R.A., Thompson, Simon R., Tregidgo, Carolyn, Walsh, Emma, Watters, Sarah A., Welland, Matthew J., Williams, Eleanor, Witkowska, Katarzyna, Wood, Suzanne M., Zarowiecki, Magdalena, Arepalli, Sampath, Auluck, Pavan, Baloh, Robert H., Bowser, Robert, Brice, Alexis, Broach, James, Camu, William, Chiò, Adriano, Cooper-Knock, John, Corcia, Philippe, Drepper, Carsten, Drory, Vivian E., Dunckley, Travis L., Faghri, Faraz, Farren, Jennifer, Feldman, Eva, Floeter, Mary Kay, Fratta, Pietro, Gerhard, Glenn, Gibson, Summer B., Goutman, Stephen A., Heiman-Patterson, Terry D., Hernandez, Dena G., Hoover, Ben, Jansson, Lilja, Kamel, Freya, Kirby, Janine, Kowall, Neil W., Laaksovirta, Hannu, Landi, Francesco, Le Ber, Isabelle, Lumbroso, Serge, MacGowan, Daniel JL., Maragakis, Nicholas J., Mora, Gabriele, Mouzat, Kevin, Myllykangas, Liisa, Nalls, Mike A., Orrell, Richard W., Ostrow, Lyle W., Pamphlett, Roger, Pioro, Erik, Pulst, Stefan M., Ravits, John M., Renton, Alan E., Robberecht, Wim, Robey, Ian, Rogaeva, Ekaterina, Rothstein, Jeffrey D., Sendtner, Michael, Sidle, Katie C., Simmons, Zachary, Stone, David J., Tienari, Pentti J., Trojanowski, John Q., Troncoso, Juan C., Valori, Miko, Van Damme, Philip, Van Den Bosch, Ludo, Zinman, Lorne, Albani, Diego, Borroni, Barbara, Padovani, Alessandro, Bruni, Amalia, Clarimon, Jordi, Dols-Icardo, Oriol, Illán-Gala, Ignacio, Lleó, Alberto, Danek, Adrian, Galimberti, Daniela, Scarpini, Elio, Serpente, Maria, Graff, Caroline, Chiang, Huei-Hsin, Khoshnood, Behzad, Öijerstedt, Linn, Morris, Christopher M., Nacmias, Benedetta, Sorbi, Sandro, Nielsen, Jorgen E., Hjermind, Lynne E., Novelli, Valeria, Puca, Annibale A., Pastor, Pau, Alvarez, Ignacio, Diez-Fairen, Monica, Aguilar, Miquel, Perneczky, Robert, Diehl-Schimd, Janine, Rossi, Mina, Ruiz, Agustin, Boada, Mercè, Hernández, Isabel, Moreno-Grau, Sonia, Schlachetzki, Johannes C., Aarsland, Dag, Albert, Marilyn S., Attems, Johannes, Barrett, Matthew J., Beach, Thomas G., Bekris, Lynn M., Bennett, David A., Besser, Lilah M., Bigio, Eileen H., Black, Sandra E., Boeve, Bradley F., Bohannan, Ryan C., Brett, Francesca, Brunetti, Maura, Caraway, Chad A., Palma, Jose-Alberto, Calvo, Andrea, Canosa, Antonio, Dickson, Dennis, Duyckaerts, Charles, Faber, Kelley, Ferman, Tanis, Flanagan, Margaret E., Floris, Gianluca, Foroud, Tatiana M., Fortea, Juan, Gan-Or, Ziv, Gentleman, Steve, Ghetti, Bernardino, Gibbs, Jesse Raphael, Goate, Alison, Goldstein, David, González-Aramburu, Isabel, Graff-Radford, Neill R., Hodges, Angela K., Hu, Heng-Chen, Hupalo, Daniel, Infante, Jon, Iranzo, Alex, Kaiser, Scott M., Kaufmann, Horacio, Keith, Julia, Kim, Ronald C., Klein, Gregory, Krüger, Rejko, Kukull, Walter, Kuzma, Amanda, Lage, Carmen, Lesage, Suzanne, Leverenz, James B., Logroscino, Giancarlo, Lopez, Grisel, Love, Seth, Mao, Qinwen, Marti, Maria Jose, Martinez-McGrath, Elisa, Masellis, Mario, Masliah, Eliezer, May, Patrick, McKeith, Ian, Mesulam, Marek-Marsel, Monuki, Edwin S., Newell, Kathy L., Norcliffe-Kaufmann, Lucy, Palmer, Laura, Perkins, Matthew, Pletnikova, Olga, Molina-Porcel, Laura, Reynolds, Regina H., Rodríguez-Rodríguez, Eloy, Rohrer, Jonathan D., Sanchez-Juan, Pascual, Scherzer, Clemens R., Serrano, Geidy E., Shakkottai, Vikram, Sidransky, Ellen, Tayebi, Nahid, Thomas, Alan J., Tilley, Bension S., Walton, Ronald L., Woltjer, Randy, Wszolek, Zbigniew K., Xiromerisiou, Georgia, Zecca, Chiara, Phatnani, Hemali, Kwan, Justin, Sareen, Dhruv, Broach, James R., Arcila-Londono, Ximena, Lee, Edward B., Shneider, Neil A., Fraenkel, Ernest, Zaitlen, Noah, Berry, James D., Malaspina, Andrea, Cox, Gregory A., Thompson, Leslie M., Finkbeiner, Steve, Dardiotis, Efthimios, Miller, Timothy M., Chandran, Siddharthan, Pal, Suvankar, Hornstein, Eran, MacGowan, Daniel J., Heiman-Patterson, Terry, Hammell, Molly G., Patsopoulos, Nikolaos.A., Butovsky, Oleg, Dubnau, Joshua, Nath, Avindra, Harms, Matt, Aronica, Eleonora, Poss, Mary, Phillips-Cremins, Jennifer, Crary, John, Atassi, Nazem, Lange, Dale J., Adams, Darius J., Stefanis, Leonidas, Gotkine, Marc, Babu, Suma, Raj, Towfique, Paganoni, Sabrina, Shalem, Ophir, Smith, Colin, Zhang, Bin, Harris, Brent, Broce, Iris, Drory, Vivian, Ravits, John, McMillan, Corey, Menon, Vilas, Wu, Lani, Altschuler, Steven, Amar, Khaled, Archibald, Neil, Bandmann, Oliver, Capps, Erica, Church, Alistair, Coebergh, Jan, Costantini, Alyssa, Critchley, Peter, Ghosh, Boyd CP., Hu, Michele T.M., Kobylecki, Christopher, Leigh, P. Nigel, Mann, Carl, Massey, Luke A., Morris, Huw R., Nath, Uma, Pavese, Nicola, Paviour, Dominic, Sharma, Jagdish, Vaughan, Jenny, Dewan, Ramita, Chia, Ruth, Ding, Jinhui, Hickman, Richard A., Stein, Thor D., Abramzon, Yevgeniya, Ahmed, Sarah, Sabir, Marya S., Portley, Makayla K., Tucci, Arianna, Ibáñez, Kristina, Shankaracharya, F.N.U., Keagle, Pamela, Rossi, Giacomina, Caroppo, Paola, Tagliavini, Fabrizio, Waldo, Maria L., Johansson, Per M., Nilsson, Christer F., Rowe, James B., Benussi, Luisa, Binetti, Giuliano, Ghidoni, Roberta, Jabbari, Edwin, Viollet, Coralie, Glass, Jonathan D., Singleton, Andrew B., Silani, Vincenzo, Ross, Owen A., Ryten, Mina, Torkamani, Ali, Tanaka, Toshiko, Ferrucci, Luigi, Resnick, Susan M., Pickering-Brown, Stuart, Brady, Christopher B., Kowal, Neil, Hardy, John A., Van Deerlin, Vivianna, Vonsattel, Jean Paul, Harms, Matthew B., Ferrari, Raffaele, Landers, John E., Gibbs, J. Raphael, Dalgard, Clifton L., Scholz, Sonja W., Traynor, Bryan J.

Source: In Neuron 3 February 2021 109(3):448-460

A structured evaluation of cryopreservation in generating single-cell transcriptomes from cerebrospinal fluid

Authors: Touil, Hanane, Roostaei, Tina, Calini, Daniela, Diaconu, Claudiu, Epstein, Samantha, Raposo, Catarina, Onomichi, Kaho, Thakur, Kiran T., Craveiro, Licinio, Callegari, Ilaria, Bryois, Julien, Riley, Claire S., Menon, Vilas, Derfuss, Tobias, De Jager, Philip L., Malhotra, Dheeraj

Source: In Cell Reports Methods 24 July 2023 3(7)

TARDBP mutations in a cohort of Italian patients with Parkinson’s disease and atypical parkinsonisms.

Authors: Tiloca, Cinzia, Goldwurm, Stefano, Calcagno, Narghes, Verde, Federico, Peverelli, Silvia, Calini, Daniela, Zecchinelli, Anna Lena, Sangalli, Davide, Ratti, Antonia, Pezzoli, Gianni, Silani, Vincenzo, Ticozzi, Nicola

Source: Frontiers in Aging Neuroscience; 9/29/2022, Vol. 14, p1-8, 8p

Subject Terms: GENETIC mutation, SEQUENCE analysis, PARKINSON'S disease, DNA-binding proteins, GENETIC markers, PARKINSONIAN disorders, TDP-43 proteinopathies, LONGITUDINAL method, NEURODEGENERATION

Geographic Terms: ITALY

C9orf72 repeat expansions are restricted to the ALS-FTD spectrum

Authors: Ticozzi, Nicola, Tiloca, Cinzia, Calini, Daniela, Gagliardi, Stella, Altieri, Alessandra, Colombrita, Claudia, Cereda, Cristina, Ratti, Antonia, Pezzoli, Gianni, Borroni, Barbara, Goldwurm, Stefano, Padovani, Alessandro, Silani, Vincenzo

Source: In Neurobiology of Aging April 2014 35(4):936-936

Analysis of hnRNPA1, A2/B1, and A3 genes in patients with amyotrophic lateral sclerosis

Authors: Calini, Daniela, Corrado, Lucia, Del Bo, Roberto, Gagliardi, Stella, Pensato, Viviana, Verde, Federico, Corti, Stefania, Mazzini, Letizia, Milani, Pamela, Castellotti, Barbara, Bertolin, Cinzia, Sorarù, Gianni, Cereda, Cristina, Comi, Giacomo P., D'Alfonso, Sandra, Gellera, Cinzia, Ticozzi, Nicola, Landers, John E., Ratti, Antonia, Silani, Vincenzo

Source: In Neurobiology of Aging November 2013 34(11):2695-2695

C9ORF72 repeat expansion in a large Italian ALS cohort: evidence of a founder effect

Authors: Ratti, Antonia, Corrado, Lucia, Castellotti, Barbara, Del Bo, Roberto, Fogh, Isabella, Cereda, Cristina, Tiloca, Cinzia, D'Ascenzo, Carla, Bagarotti, Alessandra, Pensato, Viviana, Ranieri, Michela, Gagliardi, Stella, Calini, Daniela, Mazzini, Letizia, Taroni, Franco, Corti, Stefania, Ceroni, Mauro, Oggioni, Gaia D., Lin, Kuang, Powell, John F., Sorarù, Gianni, Ticozzi, Nicola, Comi, Giacomo P., D'Alfonso, Sandra, Gellera, Cinzia, Silani, Vincenzo

Source: In Neurobiology of Aging October 2012 33(10):2528-2528

Enrichment of Glial Cells From Human Post-mortem Tissue for Transcriptome and Proteome Analysis Using Immunopanning.

Authors: Nolle, Anna, van Dijken, Irene, Waelti, Ciril M., Calini, Daniela, Bryois, Julien, Lezan, Emmanuelle, Golling, Sabrina, Augustin, Angelique, Foo, Lynette, Hoozemans, Jeroen J. M.

Source: Frontiers in Cellular Neuroscience; 12/13/2021, Vol. 15, p1-9, 9p

Subject Terms: NEUROGLIA, PROTEOMICS, TRANSCRIPTOMES, CHEMICAL purification, MICROGLIA, CENTRAL nervous system, FETAL brain

CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data.

Authors: Lütge, Almut, Zyprych-Walczak, Joanna, Kunzmann, Urszula Brykczynska, Crowell, Helena L., Calini, Daniela, Malhotra, Dheeraj, Soneson, Charlotte, Robinson, Mark D.

Source: Life Science Alliance; Jun2021, Vol. 4 Issue 6, p1-17, 17p

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Exome-wide Rare Variant Analysis Identifies TUBA4A Mutations Associated with Familial ALS

Authors: D’Alfonso, Sandra, Mazzini, Letizia, Comi, Giacomo P., Del Bo, Roberto, Ceroni, Mauro, Gagliardi, Stella, Querin, Giorgia, Bertolin, Cinzia, Smith, Bradley N., Ticozzi, Nicola, Fallini, Claudia, Gkazi, Athina Soragia, Topp, Simon, Kenna, Kevin P., Scotter, Emma L., Kost, Jason, Keagle, Pamela, Miller, Jack W., Calini, Daniela, Vance, Caroline, Danielson, Eric W., Troakes, Claire, Tiloca, Cinzia, Al-Sarraj, Safa, Lewis, Elizabeth A., King, Andrew, Colombrita, Claudia, Pensato, Viviana, Castellotti, Barbara, de Belleroche, Jacqueline, Baas, Frank, ten Asbroek, Anneloor LMA, Sapp, Peter C., McKenna-Yasek, Diane, McLaughlin, Russell L., Polak, Meraida, Asress, Seneshaw, Esteban-Pérez, Jesús, Muñoz-Blanco, José Luis, Simpson, Michael, van Rheenen, Wouter, Diekstra, Frank P., Lauria, Giuseppe, Duga, Stefano, Corti, Stefania, Cereda, Cristina, Corrado, Lucia, Sorarù, Gianni, Morrison, Karen E., Williams, Kelly L., Nicholson, Garth A., Blair, Ian P., Dion, Patrick A., Leblond, Claire S., Rouleau, Guy A., Hardiman, Orla, Veldink, Jan H., van den Berg, Leonard H., Al-Chalabi, Ammar, Pall, Hardev, Shaw, Pamela J., Turner, Martin R., Talbot, Kevin, Taroni, Franco, García-Redondo, Alberto, Wu, Zheyang, Glass, Jonathan D., Gellera, Cinzia, Ratti, Antonia, Brown, Robert H., Jr., Silani, Vincenzo, Shaw, Christopher E., Landers, John E.

Source: In Neuron 22 October 2014 84(2):324-331

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The role of de novo mutations in the development of amyotrophic lateral sclerosis.

Authors: Doormaal, Perry T.C., Ticozzi, Nicola, Weishaupt, Jochen H., Kenna, Kevin, Diekstra, Frank P., Verde, Federico, Andersen, Peter M., Dekker, Annelot M., Tiloca, Cinzia, Marroquin, Nicolai, Overste, Daniel J., Pensato, Viviana, Nürnberg, Peter, Pulit, Sara L., Schellevis, Raymond D., Calini, Daniela, Altmüller, Janine, Francioli, Laurent C., Muller, Bernard, Castellotti, Barbara

Source: Human Mutation; Nov2017, Vol. 38 Issue 11, p1534-1541, 8p

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