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1. Co-transcriptional splicing facilitates transcription of gigantic genes.

Author

Jaclyn M Fingerhut, Romain Lannes, Troy W Whitfield, Prathapan Thiru, and Yukiko M Yamashita

Subjects
Genetics, QH426-470
Abstract

Although introns are typically tens to thousands of nucleotides, there are notable exceptions. In flies as well as humans, a small number of genes contain introns that are more than 1000 times larger than typical introns, exceeding hundreds of kilobases (kb) to megabases (Mb). It remains unknown why gigantic introns exist and how cells overcome the challenges associated with their transcription and RNA processing. The Drosophila Y chromosome contains some of the largest genes identified to date: multiple genes exceed 4Mb, with introns accounting for over 99% of the gene span. Here we demonstrate that co-transcriptional splicing of these gigantic Y-linked genes is important to ensure successful transcription: perturbation of splicing led to the attenuation of transcription, leading to a failure to produce mature mRNA. Cytologically, defective splicing of the Y-linked gigantic genes resulted in disorganization of transcripts within the nucleus suggestive of entanglement of transcripts, likely resulting from unspliced long RNAs. We propose that co-transcriptional splicing maintains the length of nascent transcripts of gigantic genes under a critical threshold, preventing their entanglement and ensuring proper gene expression. Our study reveals a novel biological significance of co-transcriptional splicing.

Published
2024
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2. P831: NOVEL IMMUNOSUPPRESSIVE MYELOID POPULATIONS IN THE BONE MARROW (BM) AND OSTEOLYTIC LESIONS (OL) OF MULTIPLE MYELOMA (MM) PATIENTS

Author

Jens Hillengass, Romain Lannes, Saeed Daneshmandi, Cameron Macdonald, Qi Yan, Jeeeun Choi, Prashant Singh, Ahmed Belal, Ronald Alberico, Ian Lund, Megan Schaefer, Sarah Parker, Nikhil Munshi, Kenneth Anderson, Mehmet Samur, Philip Mccarthy, and Hemn Mohammadpour

Subjects
Diseases of the blood and blood-forming organs, RC633-647.5
Published
2023
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3. Rich Repertoire of Quorum Sensing Protein Coding Sequences in CPR and DPANN Associated with Interspecies and Interkingdom Communication

Author

Charles Bernard, Romain Lannes, Yanyan Li, Éric Bapteste, and Philippe Lopez

Subjects
CPR, DPANN, interkingdom signaling, microbial communication, microbiology, quorum sensing, Microbiology, QR1-502
Abstract

ABSTRACT The bacterial candidate phyla radiation (CPR) and the archaeal DPANN superphylum are two novel lineages that have substantially expanded the tree of life due to their large phylogenetic diversity. Because of their ultrasmall size, reduced genome, and lack of core biosynthetic capabilities, most CPR and DPANN members are predicted to be sustained through their interactions with other species. How the few characterized CPR and DPANN symbionts achieve these critical interactions is, however, poorly understood. Here, we conducted an in silico analysis on 2,597 CPR/DPANN genomes to test whether these ultrasmall microorganisms might encode homologs of reference proteins involved in the synthesis and/or the detection of 26 different types of communication molecules (quorum sensing [QS] signals), since QS signals are well-known mediators of intra- and interorganismic relationships. We report the discovery of 5,693 variants of QS proteins distributed across 63 CPR and 6 DPANN phyla and associated with 14 distinct types of communication molecules, most of which were characterized as interspecies QS signals. IMPORTANCE The selection of predicted genes for interspecies communication within the CPR and DPANN genomes sheds some light onto the underlying mechanisms supporting their inferred symbiotic lifestyle. Also, considering the lack of core pathways such as the de novo synthesis of nucleotides or amino acids in the CPR and DPANN lineages, the persistence of these genes highlights how determinant social traits can be for the survival of some microorganisms. Finally, the considerable number of variants of QS proteins identified among the 69 CPR and DPANN phyla substantially expands our knowledge of prokaryotic communication across the tree of life and suggests that the multiplicity of “dialects” in the microbial world is probably larger than previously appreciated.

Published
2020
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4. In Multiple Myeloma, High-Risk Secondary Genetic Events Observed at Relapse Are Present From Diagnosis in Tiny, Undetectable Subclonal Populations

Author

Romain Lannes, Mehmet Samur, Aurore Perrot, Celine Mazzotti, Marion Divoux, Titouan Cazaubiel, Xavier Leleu, Anaïs Schavgoulidze, Marie-Lorraine Chretien, Salomon Manier, Didier Adiko, Frederique Orsini-Piocelle, François Lifermann, Sabine Brechignac, Lauris Gastaud, Didier Bouscary, Margaret Macro, Alice Cleynen, Mohamad Mohty, Nikhil Munshi, Jill Corre, and Hervé Avet-Loiseau

Subjects
Cancer Research, Oncology
Abstract

PURPOSE Multiple myeloma (MM) is characterized by copy number abnormalities (CNAs), some of which influence patient outcomes and are sometimes observed only at relapse(s), suggesting their acquisition during tumor evolution. However, the presence of micro-subclones may be missed in bulk analyses. Here, we use single-cell genomics to determine how often these high-risk events are missed at diagnosis and selected at relapse. MATERIALS AND METHODS We analyzed 81 patients with plasma cell dyscrasias using single-cell CNA sequencing. Sixty-six patients were selected at diagnosis, nine at first relapse, and six in presymptomatic stages. A total of 956 newly diagnosed patients with MM and patients with first relapse MM have been identified retrospectively with required cytogenetic data to evaluate enrichment of CNA risk events and survival impact. RESULTS A total of 52,176 MM cells were analyzed. Seventy-four patients (91%) had 2-16 subclones. Among these patients, 28.7% had a subclone with high-risk features (del(17p), del(1p32), and 1q gain) at diagnosis. In a patient with a subclonal 1q gain at diagnosis, we analyzed the diagnosis, postinduction, and first relapse samples, which showed a rise of the high-risk 1q gain subclone (16%, 70%, and 92%, respectively). In our clinical database, we found that the 1q gain frequency increased from 30.2% at diagnosis to 43.6% at relapse (odds ratio, 1.78; 95% CI, 1.58 to 2.00). We subsequently performed survival analyses, which showed that the progression-free and overall survival curves were superimposable between patients who had the 1q gain from diagnosis and those who seemingly acquired it at relapse. This strongly suggests that many patients had 1q gains at diagnosis in microclones that were missed by bulk analyses. CONCLUSION These data suggest that identifying these scarce aggressive cells may necessitate more aggressive treatment as early as diagnosis to prevent them from becoming the dominant clone.

Published
2023

7. Primary plasma cell leukemias displaying t(11;14) have specific genomic, transcriptional, and clinical features

Author

Titouan Cazaubiel, Xavier Leleu, Aurore Perrot, Salomon Manier, Laure Buisson, Sabrina Maheo, Laura Do Souto Ferreira, Romain Lannes, Luka Pavageau, Cyrille Hulin, Jean-Pierre Marolleau, Laurent Voillat, Karim Belhadj, Marion Divoux, Borhane Slama, Sabine Brechignac, Margaret Macro, Anne-Marie Stoppa, Laurence Sanhes, Frédérique Orsini-Piocelle, Jean Fontan, Marie-Lorraine Chretien, Hélène Demarquette, Mohamad Mohty, Anais Schavgoulidze, Herve Avet-Loiseau, Jill Corre, Service d'Hématologie [CHU Poitiers], Centre hospitalier universitaire de Poitiers (CHU Poitiers), Service d'Hématologie [IUCT Toulouse], Université Fédérale Toulouse Midi-Pyrénées-Institut Universitaire du Cancer de Toulouse - Oncopole (IUCT Oncopole - UMR 1037), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU de Lille, Service des maladies du sang, Centre de Recherches en Cancérologie de Toulouse (CRCT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Universitaire du Cancer de Toulouse - Oncopole (IUCT Oncopole - UMR 1037), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Hôpital Haut-Lévêque [CHU Bordeaux], CHU Bordeaux [Bordeaux], CHU Amiens-Picardie, HEMATIM - Hématopoïèse et immunologie - UR UPJV 4666 (HEMATIM), Université de Picardie Jules Verne (UPJV)-CHU Amiens-Picardie-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Chalon-sur-Saône William Morey, Hôpital Henri Mondor, Université de Lorraine (UL), Avignon Université (AU), Hôpital Avicenne [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN), Service d’Hématologie [Institut Paoli Calmettes, Marseille], Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC), Centre Hospitalier Saint Jean de Perpignan, Centre Hospitalier Annecy-Genevois [Saint-Julien-en-Genevois], Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Service d'Hématologie Clinique (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Hôpital Claude Huriez [Lille], CHU Lille, CHU Saint-Antoine [AP-HP], Centre de Recherche Saint-Antoine (CRSA), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Centre Hospitalier Universitaire de Purpan (CHU Purpan), and CHU Toulouse [Toulouse]

Subjects
Chromosome Aberrations, [SDV]Life Sciences [q-bio], Immunology, Humans, Cell Biology, Hematology, Genomics, Multiple Myeloma, Prognosis, Transcriptome, Biochemistry, Leukemia, Plasma Cell
Abstract

Primary plasma cell leukemia (pPCL) is an aggressive form of multiple myeloma (MM) that has not benefited from recent therapeutic advances in the field. Because it is very rare and heterogeneous, it remains poorly understood at the molecular level. To address this issue, we performed DNA and RNA sequencing of sorted plasma cells from a large cohort of 90 newly diagnosed pPCL and compared with MM. We observed that pPCL presents a specific genomic landscape with a high prevalence of t(11;14) (about half) and high-risk genomic features such as del(17p), gain 1q, and del(1p32). In addition, pPCL displays a specific transcriptome when compared with MM. We then wanted to characterize specifically pPCL with t(11;14). We observed that this subentity displayed significantly fewer adverse cytogenetic abnormalities. This translated into better overall survival when compared with pPCL without t(11;14) (39.2 months vs 17.9 months, P = .002). Finally, pPCL with t(11;14) displayed a specific transcriptome, including differential expression of BCL2 family members. This study is the largest series of patients with pPCL reported so far.

Published
2022

8. OAB-016: High risk subclones detected at relapse are present from diagnosis in small subclones and impact the prognosis

Author

Romain Lannes, Mehmet Samur, Aurore Perrot, Celine Mazzotti, Marion Divoux, Titouan Cazaubiel, Anaïs Schavgoulidze, Marie-Lorraine Chretien, Salomon Manier, Didier Adiko, Frederique Orsini-Piocelle, François Lifermann, Sabine Brechignac, Lauris Gastaud, Didier Bouscary, Margaret Macro, Alice Cleynen, Mohamad Mohty, Nikhil Munshi, Jill Corre, and Hervé Avet-Loiseau

Subjects
Cancer Research, Oncology, Hematology
Published
2022

9. A global metagenomic map of urban microbiomes and antimicrobial resistance

Author

Nadine Farhat, Tomoki Takeda, Astred Castro, Ken McGrath, Khaliun Sanchir, Iman Hajirasouliha, Eunice So, Laraib Zafar, Diana N. Nunes, Harun Mustafa, Amy Zhang, Priscilla Lisboa, Christian Schori, Marisano James, Jasna Chalangal, Sebastien Halary, Shahryar Rana, Yunmi Lee, Oli Schacher, Liliana Godoy, David A. Coil, Phanthira Pugdeethosal, Michelle D. Williams, German Marchandon, Angela Cantillo, Naoya Takahashi, Christopher Mozsary, Juana Gonzalez, Patrick K. H. Lee, Gerardo de Lamotte, Alessandro Robertiello, Steven Du, Fabienne Velter, Stefan G. Stark, Miguel Carbajo, Vincent Matthys, David A. Westfall, Julia Boeri, Irène Mauricette Mendy, Jonathan Cedillo, Francesco Oteri, Robert W. Crawford, Takayuki Ito, Tina Wunderlin, Maureen Muscat, David Paez-Espino, Carmen Urgiles, Aida Nesimi, Steffen Schaaf, Adan Ramirez-Rojas, Kunihiko Miyake, Christopher E. Mason, Anais Cardenas, Sharah Islam, Diego Benítez, Melissa Pool Pizzi, Kianna Ciaramella, Ciro Borrelli, Riham Islam, Dorottya Nagy-Szakal, Abd-Manaaf Bakere, Ait-hamlat Adel, Olha Lakhneko, Badamnyambuu Iderzorig, Ana Valeria Castro, Adam Phillips, Robert A. Petit, Flavia Corsi, Romain Conte, Krista Ryon, Soojin Jang, Joseph Benson, Fernanda de Souza Gomes Kehdy, Cindy Wang, Nicole Mathews, Jenn-Wei Chen, Rachel Paras, Paulina Pastuszek, Abigail Lyons, Paul Roldán, Muntaha Munia, Pierre Nicolas, Cassie L. Ettinger, Kyrylo Pyrshev, Katterinne N. Mendez, Eduardo Castro-Nallar, Valeriia Dotsenko, Michelle Tuz, Krizzy Mallari, Eileen Png, Yuya Sonohara, Tanja Miketic, Stéphane Delmas, Shu Zhang, Masaki Sato, Yuanting Zheng, Jifeng Zhu, Roland Häusler, Lucie Bittner, Savlatjon Rahmatulloev, Jonathan Foox, Bruno D'Alessandro, Alketa Plaku, Faisal Alquaddoomi, Yang Zhang, Kern Rei Chng, Juliana Lago, Allaeddine Chettouh, Tamera Henry, Houtan Noushmehr, Tranette Gregory, Sara Abdul Majid, Frank J. Kelly, Benjamin Pulatov, Laurie Casalot, Takema Kajita, Lennard Epping, Thais Fernanda Bartelli, Eftar Moniruzzaman, Renee Vivancos-Koopman, Thirumalaisamy P. Velavan, Tracy W. Liu, Yelyzaveta Tymoshenko, Alma Plaku, Nika Gurianova, Ambar Mendez, Anna Tomaselli, Sonia Dorado, Donato Giovannelli, Hira Choudhry, Synti Ng, Sheelta S. Kumar, Jennifer Q. Lu, Weijun Liang, Ellen Koag, Dennis Gankin, Maria João Amorim, Gwenola Simon, Kiyoshi Suganuma, Mikhail Karasikov, Christos A. Ouzounis, Madelyn May, Eran Elhaik, Stephan Ossowski, Kevin Bolzli, Matthew Arthur, Yuya Oto, Jananan Pathmanathan, Salah Mahmoud, Kou Takahashi, Brunna Marques, Kelly French, Felipe Sepúlveda, Shusei Yoshikawa, Paulo Thiago de Souza Santos, Andrew N. Gray, Juliana S Bernardes, Felipe Segato, Björn Brindefalk, George C. Yeh, Jhovana L. Velasco Flores, Jill Sullivan, Silva Baburyan, Denisse Flores, Russell Y. Neches, Sabrina Persaud, Rasheena Wright, Takumi Togashi, Verónica Antelo, Nao Kato, Skye Felice, Tatjana Mustac, Daisy Donnellan, Katerine Carrillo, Anna Litskevitch, Catalina García, Sota Ito, Naya Eady, Andrew Wan, Irene Meng, Sophie Guasco, Danilo Ercolini, Francesca De Filippis, Vincent Lemaire, Luice Fan, Lothar H. Wieler, Mariia Rybak, Jorge Sanchez, Jonathan S. Gootenberg, Itsuki Tomita, Maritza S Mosella, Laura Garcia, Natalka Makogon, Daisy Cheung, Hitler Francois Vasquez Arevalo, Freddy Asenjo, Gabriela P. Branco, Erika Cifuentes, Chloé Dequeker, Aspassia D. Chatziefthimiou, Alexis Terrero, Roy Meoded, Isabelle de Oliveira Moraes, Shaleni K. Singh, Orgil-Erdene Molomjamts, Karishma Miah, Laurent David, Wolfgang Haehr, Dao Phuong Giang, Romain Lannes, Prashanthi Ratnanandan, Ryota Yamanaka, Riccardo Vicedomini, Sadaf Ayaz, Oluwatosin M. Osuolale, Laura E. Vann, Gregory Chem, Andrea Gonzalez, Aszia Burrell, Ariel Chernomoretz, Sakura Ishizuka, Michelle Rivera, Avigdor Nosrati, Michelle B. Chen, Juliette Auvinet, Nils Ordioni, Tomoro Warashina, Guillaume Blanc, Tomislav Ivankovic, Christina Black, Lauren E. Hittle, David Hess-Homeier, Michael Kozhar, Hamood Suliman, Karobi Moitra, Saher Rahiel, Spyridon Gkotzis, Jenny Arevalo, Shaikh B. Iqbal, Beth Mutai, Mohammed Mohsin, Scott Tighe, Sylvie Collin, Yoshitaka Saito, Wayne Menary, Youping Deng, Lucy Lee, Esmeralda Jiminez, Ayuki Watanabe, Nikos C. Kyrpides, Natasha Mohan, Angelika Pupiec, Dedan Githae, Simone Cawthorne, Jonathan A. Eisen, Tomoki Iwashiro, Chiaki Homma, Thomas Saw Aung, Laura Molina, Marcus H. Y. Leung, Ophélie Da Silva, Yan Ling Wong, Hosna Noorzi, Mario Moreno, Alina Butova, Leming Shi, Brian W. Wong, Sarah S. Jackson, Moses Lin, Annabelle Meagher, Pujita Das, Catherine Burke, Mitsuki Ota, Maria Domenica Moccia, Nicolas Sprinsky, Catherine E. Pugh, David C. Green, Fazlina Fauzi, Erdenetsetseg Batdelger, Annie Geiger, Valeria Ventorino, Tolulope Oluwadare, Delisia Cuebas, Catalina Truong, Leonardo Posada, Michael Angelov, Tathiane M. Malta, Amanda Ng, Francesca Nadalin, Arya Hawkins-Zafarnia, Yuh Shiwa, Athena Mitsios, Milton Ozório Moraes, Manolo Laiola, Kalyn Ali, Jaden J.A. Hastings, Ikuto Saito, Maheen Shakil, Chisato Suzuki, Elena M. Vayndorf, Hubert Rehrauer, Ajay Menon, Kaitlan Russell, Aliyah Shari, Rebecca Smith, Gregorio Iraola, Max Priestman, Alan Briones, Silver A. Wolf, Camila Gonzalez-Poblete, Eleonora De Lazzari, Shirley Chiu, Michelle Ki, Irene Hoxie, Marianne Jaubert, Ayantu Jinfessa, Ryan J. King, Nghiem Xuan Hoan, Jalia Bynoe, Jacob Friedman, Aneisa Ramcharan, Pablo Fresia, Cristina Muñoz, Muhammad Afaq, Anyi Tang, Médine Benchouaia, Isabella Kuniko T. Takenaka, Anastasia Chasapi, Areeg Naeem, Hannah Benisty, Cecilia N. Cossio, Nathalie Hüsser, Mahfuza Sabina, Thais S. Sabedot, JoAnn Jacobs, Camila P. E. de Souza, Manuela Oliveira, Jean-Pierre Bouly, Mariko Usui, Wilson Miranda, Natalia Marciniak, Hiram Caballero, Samuel Weekes, Alexandra B. Graf, Emily Leong, Tatyana Nikolayeva, Dominique Thomas, Charlotte Greselle, Cecilia Salazar, Sreya Ray Chaudhuri, Kevin Becher, Sandra Roth, Ryusei Miura, Kari Oline Bøifot, Dimitri Manoir, Oliver Toth, Chandrima Bhattacharya, Manuel Perez, Isha Lamba, Takafumi Tsurumaki, Timothy D. Read, Anna-Lena M. Schinke, Ryan Sankar, Le Huu Song, Narasimha Rao Nedunuri, Emmanuel Dias-Neto, Ana Flávia Costa, Adiell Melamed, Christelle Desnues, Natalie R. Davidson, Aaron E. Darling, Hyung Jun Kim, Josephine Galipon, Jacqueline Orrego, Dimitar Vassilev, Michael Huber, Nur Hazlin Hazrin-Chong, Gaston H. Gonnet, Kaymisha Knights, Osman U. Sezerman, Dmitry Meleshko, Eunice Thambiraja, Jingcheng Yang, Aubin Fleiss, Gloria Nguyen, Katelyn Jackson, Nuria Aventin, Stephanie L. Hyland, Andrea Hässig, Catharine Aquino, Simona Lysakova, Israel O. Osuolale, Kasia Sluzek, Rania Siam, Alina Frolova, Samuel Hernandez, Yui Him Lo, Bazartseren Boldgiv, Ben Young, Maryna Korshevniuk, Majelia Ampadu, Yuk Man Tang, Amanda L. Muehlbauer, Sade Thomas, Gabriel Figueroa, Alexis Rivera, Lisbeth Pineda, Alexandra Dutan, Jennifer M. Tran, Chris K. Deng, Vedbar S. Khadka, Paola Florez de Sessions, Elizabeth Humphries, Hugues Richard, Hiba Naveed, Nora C. Toussaint, Mahshid Khavari, Maria del Mar Vivanco Ruiz, Antonin Thiébaut, Nicolás Rascovan, Marius Dybwad, Orhan Özcan, Lawrence Kwong, David Danko, Shaira Khan, Andrea Tassinari, Silvia Beurmann, Tsoi Ying Lai, Nanami Kubota, Tieliu Shi, Diana Chicas, Evan E. Afshin, Hirokazu Yano, Jonas Krebs, Mayuko Nakagawa, Hyun Jung Lee, Irene González Navarrete, Rachid Ounit, Lucia E. Alvarado-Arnez, Masaki Nasu, Allison Chan, Harilanto Andrianjakarivony, Jennifer Amachee, Mahdi Taye, Wan Chiew Ng, Kathryn O’Brien, Shino Ishikawa, Tristan Bitard-Feildel, Sora Takagi, Felix Hartkopf, Niamh B. O’Hara, Marcos A. S. Fonseca, Subhamitra Pakrashi, Amrit Kaur, Eva Hell, Patricia Vera-Wolf, Naimah Munim, Luiza Ferreira de Araújo, Mizuki Igarashi, Brianna Pompa-Hogan, Alessandra Carbone, Anne-Sophie Benoiston, Eric Helfrich, Michael A. Suarez-Villamil, Omar O. Abudayyeh, Natasha Abdullah, Jaime J. Fuentes, Juan Carlos Forero, Tetiana Yeskova, Denis Bertrand, Sambhawa Priya, Denisse Maldonado, Agier Nicolas, Ana Valeria B Castro, Starr Chatziefthimiou, André Kahles, Aaishah Francis, Fernanda Arredondo, Emilio Tarcitano, Irvind Buttar, Alex Alexiev, Jennifer Molinet, Sarah Shalaby, Itunu A. Oluwadare, Jason Sperry, Katrin Bakhl, Ana M. Cañas, Sofia Ahsanuddin, Miar Elaskandrany, Elodie Laine, Sven Bönigk, Johannes Werner, Stephen Eduard Boja Ruiz, Gargi Dayama, Paulina Buczansla, Brandon Valentine, Bharath Prithiviraj, Toni Bode, Stas Zubenko, Jake Cohen, Guilllaume Jospin, Zulena Saravi, Per O. Ljungdahl, Inderjit Kaur, Mauricio Moldes, Giuseppe KoLoMonaco, Denise Syndercombe Court, Sonia Bouchard, Sonia Losim, Sookwon Moon, Heba Shaaban, Suraj Patel, Sibo Zhu, Sarh Aly, Arif Asyraf Md Supie, LaShonda Dorsey, Juan Guerra, François Baudon, Rantimi A. Olawoyin, Alexia Bordigoni, Iqra Faiz, Mathilde Garcia, Gabriella Mason-Buck, María Gabriela Portilla, Niranjan Nagarajan, Fumie Takahara, Nancy Merino, Watson Andrew, Gina Kim, Yuma Sato, Hyenah Shim, Marie-Laure Jerier, Affifah Saadah Ahmad Kassim, Katerina Kuchin, Daniel Butler, Paweł P. Łabaj, Nadezhda Kobko-Litskevitch, Emmanuel F. Mongodin, Yuto Togashi, Paula Rodríguez, Pilar Lopez Hernandez, Xiaoqing Chen, Maria A. Sierra, Olga Nikolayeva, Manon Loubens, Colleen Conger, Hikaru Shirahata, Chenhao Li, Timothy Donahoe, Youngja Park, Lucia Elena Alvarado Arnez, Salama Chaker, Francisco Chavez, Alessandra Breschi, Jorge L. Sanchez, Kaung Myat San, Nayra Aguilar Rojas, Marcos Abraao, Kai Sasaki, Bryan Nazario, Olena Yemets, Klas I. Udekwu, Lynn M. Schriml, Anisia Peters, Aliaksei Holik, Mark Hernandez, Emile Faure, Malay Bhattacharyya, Josef W. Moser, Núria Andreu Somavilla, María Mercedes Zambrano, Kannan Rajendran, Gabriela E. Albuquerque, Tao Qing, Kazutoshi Tsuda, Ymke De Jong, Princess Osma, Mayra Arauco Livia, Javier Quilez Oliete, Carl Chrispin, Hyun Woo Joo, Ingrid Lafontaine, Nala An, Seisuke Sato, Felipe Segato Dezem, Andrew Maltez Thomas, Alexandre Desert, Xiao Wen Cai, O. Osuolale, Jun Wu, Coral Pardo-Esté, Courtney Robinson, Yuri Matsuzaki, Marina Nieto-Caballero, Cem Meydan, Ralph Schlapbach, Mark Menor, Sofia Castro, Rachel Kwong, Brittany Blyther, Olexandr Lykhenko, Jason R. Schriml, Christian Brion, Jenessa Orpilla, Juan A. Ugalde, Elsy Mankah Ngwa, Álvaro Aranguren, Lauren Mak, Matías Giménez, Ashanti Narce, Torsten Semmler, Stefan I. Tsonev, Abdollahi Nika, Katherine E. Dahlhausen, Monika Devi, Gunnar Rätsch, Oasima Muner, Carla Bello, Muhammad Al-Fath Amran, Anyelic Rosario, Melissa Ortega, Andrea Patrignani, Ante Peros, Elias McComb, Ryo Sato, Ireen Alam, Clara N. Dias, Soma Tanaka, Dayana Calderon, Ran Blekhman, Mathilde Mignotte, Alicia Boyd, Jochen Hecht, Thomas Neff, Xinzhao Tong, Josue Alicea, Kiara Olmeda, Sonia Marinovic, Carme Arnan, Kohei Ito, Samantha L. Goldman, Marianna S. Serpa, Renee Richer, Kaisei Sato, Jordana M. Silva, Akash Keluth Chavan, Sangwan Kim, Laís Pereira Ferreira, Sophie Vacant, Nowshin Sayara, Haruo Suzuki, Madeline Leahy, Juan C. Severyn, Sierra Vincent, Masaru Tomita, Maliha Mamun, Lucinda B. Davenport, Gabriella Oken, Dagmara Lewandowska, Gustavo Adolfo Malca Salas, Andrii Kuklin, Tyler Wong, Charlie Feigin, Eric Minwei Liu, Sonia L. Ghose, Daniela Bezdan, Antonietta La Storia, Juan P. Escalera-Antezana, Nuno Rufino de Sousa, Samuel M. Gerner, Weill Cornell Medicine [New York], Icahn School of Medicine at Mount Sinai [New York] (MSSM), Genome Institute of Singapore (GIS), Centre for Genomic Regulation [Barcelona] (CRG), Universitat Pompeu Fabra [Barcelona] (UPF)-Centro Nacional de Analisis Genomico [Barcelona] (CNAG), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), AUTRES, Massachusetts Institute of Technology (MIT), Indian Statistical Institute [Kolkata], University of Minnesota System, Universidad Andrés Bello [Santiago] (UNAB), California State University [Sacramento], University of Naples Federico II, University of Hawaii, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Medical Genomics Group, University College of London [London] (UCL)-UCL Cancer Institute, Norwegian Defence Research Establishment (FFI), Lund University [Lund], Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, University of Vienna [Vienna], King‘s College London, University of Colorado [Boulder], Institut Pasteur de Montevideo, Réseau International des Instituts Pasteur (RIIP), Institut Pasteur Korea - Institut Pasteur de Corée, Fudan University [Shanghai], City University of Hong Kong [Hong Kong] (CUHK), Stockholm University, University of Maryland School of Medicine, University of Maryland System, Fundação Oswaldo Cruz (FIOCRUZ), University of São Paulo (USP), Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Barcelona Institute of Science and Technology (BIST), Elizade University, Acibadem Mehmet Ali Aydınlar University, Paléogénomique microbienne - Microbial paleogenomics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU), Robert Koch Institute [Berlin] (RKI), East China Normal University [Shangaï] (ECNU), Cairo University, Vietnamese-German Center for Medical Research, Keio University, Université du Vermont, Universidad del Desarrollo, University of Sofia, University of Alaska [Fairbanks] (UAF), Universitätsklinikum Tübingen - University Hospital of Tübingen, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Corporación Corpogen-Research Center, Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Weill Cornell Medicine [Cornell University], Cornell University [New York], University of Naples Federico II = Università degli studi di Napoli Federico II, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Universidade de São Paulo = University of São Paulo (USP), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Софийски университет = Sofia University, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Universidad Andrés Bello - UNAB (CHILE), Acibadem University Dspace, Danko, D., Bezdan, D., Afshin, E. E., Ahsanuddin, S., Bhattacharya, C., Butler, D. J., Chng, K. R., Donnellan, D., Hecht, J., Jackson, K., Kuchin, K., Karasikov, M., Lyons, A., Mak, L., Meleshko, D., Mustafa, H., Mutai, B., Neches, R. Y., Ng, A., Nikolayeva, O., Nikolayeva, T., Png, E., Ryon, K. A., Sanchez, J. L., Shaaban, H., Sierra, M. A., Thomas, D., Young, B., Abudayyeh, O. O., Alicea, J., Bhattacharyya, M., Blekhman, R., Castro-Nallar, E., Canas, A. M., Chatziefthimiou, A. D., Crawford, R. W., De Filippis, F., Deng, Y., Desnues, C., Dias-Neto, E., Dybwad, M., Elhaik, E., Ercolini, D., Frolova, A., Gankin, D., Gootenberg, J. S., Graf, A. B., Green, D. C., Hajirasouliha, I., Hastings, J. J. A., Hernandez, M., Iraola, G., Jang, S., Kahles, A., Kelly, F. J., Knights, K., Kyrpides, N. C., Labaj, P. P., Lee, P. K. H., Leung, M. H. Y., Ljungdahl, P. O., Mason-Buck, G., Mcgrath, K., Meydan, C., Mongodin, E. F., Moraes, M. O., Nagarajan, N., Nieto-Caballero, M., Noushmehr, H., Oliveira, M., Ossowski, S., Osuolale, O. O., Ozcan, O., Paez-Espino, D., Rascovan, N., Richard, H., Ratsch, G., Schriml, L. M., Semmler, T., Sezerman, O. U., Shi, L., Shi, T., Siam, R., Song, L. H., Suzuki, H., Court, D. S., Tighe, S. W., Tong, X., Udekwu, K. I., Ugalde, J. A., Valentine, B., Vassilev, D. I., Vayndorf, E. M., Velavan, T. P., Wu, J., Zambrano, M. M., Zhu, J., Zhu, S., Mason, C. E., Abdullah, N., Abraao, M., Adel, A. -H., Afaq, M., Al-Quaddoomi, F. S., Alam, I., Albuquerque, G. E., Alexiev, A., Ali, K., Alvarado-Arnez, L. E., Aly, S., Amachee, J., Amorim, M. G., Ampadu, M., Amran, M. A. -F., An, N., Andrew, W., Andrianjakarivony, H., Angelov, M., Antelo, V., Aquino, C., Aranguren, A., Araujo, L. F., Vasquez Arevalo, H. F., Arevalo, J., Arnan, C., Alvarado Arnez, L. E., Arredondo, F., Arthur, M., Asenjo, F., Aung, T. S., Auvinet, J., Aventin, N., Ayaz, S., Baburyan, S., Bakere, A. -M., Bakhl, K., Bartelli, T. F., Batdelger, E., Baudon, F., Becher, K., Bello, C., Benchouaia, M., Benisty, H., Benoiston, A. -S., Benson, J., Benitez, D., Bernardes, J., Bertrand, D., Beurmann, S., Bitard-Feildel, T., Bittner, L., Black, C., Blanc, G., Blyther, B., Bode, T., Boeri, J., Boldgiv, B., Bolzli, K., Bordigoni, A., Borrelli, C., Bouchard, S., Bouly, J. -P., Boyd, A., Branco, G. P., Breschi, A., Brindefalk, B., Brion, C., Briones, A., Buczansla, P., Burke, C. M., Burrell, A., Butova, A., Buttar, I., Bynoe, J., Bonigk, S., Boifot, K. O., Caballero, H., Cai, X. W., Calderon, D., Cantillo, A., Carbajo, M., Carbone, A., Cardenas, A., Carrillo, K., Casalot, L., Castro, S., Castro, A. V., Castro, A., Castro, A. V. B., Cawthorne, S., Cedillo, J., Chaker, S., Chalangal, J., Chan, A., Chasapi, A. I., Chatziefthimiou, S., Chaudhuri, S. R., Chavan, A. K., Chavez, F., Chem, G., Chen, X., Chen, M., Chen, J. -W., Chernomoretz, A., Chettouh, A., Cheung, D., Chicas, D., Chiu, S., Choudhry, H., Chrispin, C., Ciaramella, K., Cifuentes, E., Cohen, J., Coil, D. A., Collin, S., Conger, C., Conte, R., Corsi, F., Cossio, C. N., Costa, A. F., Cuebas, D., D'Alessandro, B., Dahlhausen, K. E., Darling, A. E., Das, P., Davenport, L. B., David, L., Davidson, N. R., Dayama, G., Delmas, S., Deng, C. K., Dequeker, C., Desert, A., Devi, M., Dezem, F. S., Dias, C. N., Donahoe, T. R., Dorado, S., Dorsey, L., Dotsenko, V., Du, S., Dutan, A., Eady, N., Eisen, J. A., Elaskandrany, M., Epping, L., Escalera-Antezana, J. P., Ettinger, C. L., Faiz, I., Fan, L., Farhat, N., Faure, E., Fauzi, F., Feigin, C., Felice, S., Ferreira, L. P., Figueroa, G., Fleiss, A., Flores, D., Velasco Flores, J. L., Fonseca, M. A. S., Foox, J., Forero, J. C., Francis, A., French, K., Fresia, P., Friedman, J., Fuentes, J. J., Galipon, J., Garcia, M., Garcia, L., Garcia, C., Geiger, A., Gerner, S. M., Ghose, S. L., Giang, D. P., Gimenez, M., Giovannelli, D., Githae, D., Gkotzis, S., Godoy, L., Goldman, S., Gonnet, G. H., Gonzalez, J., Gonzalez, A., Gonzalez-Poblete, C., Gray, A., Gregory, T., Greselle, C., Guasco, S., Guerra, J., Gurianova, N., Haehr, W., Halary, S., Hartkopf, F., Hawkins-Zafarnia, A., Hazrin-Chong, N. H., Helfrich, E., Hell, E., Henry, T., Hernandez, S., Hernandez, P. L., Hess-Homeier, D., Hittle, L. E., Hoan, N. X., Holik, A., Homma, C., Hoxie, I., Huber, M., Humphries, E., Hyland, S., Hassig, A., Hausler, R., Husser, N., Petit, R. A., Iderzorig, B., Igarashi, M., Iqbal, S. B., Ishikawa, S., Ishizuka, S., Islam, S., Islam, R., Ito, K., Ito, S., Ito, T., Ivankovic, T., Iwashiro, T., Jackson, S., Jacobs, J., James, M., Jaubert, M., Jerier, M. -L., Jiminez, E., Jinfessa, A., De Jong, Y., Joo, H. W., Jospin, G., Kajita, T., Ahmad Kassim, A. S., Kato, N., Kaur, A., Kaur, I., de Souza Gomes Kehdy, F., Khadka, V. S., Khan, S., Khavari, M., Ki, M., Kim, G., Kim, H. J., Kim, S., King, R. J., Kolomonaco, G., Koag, E., Kobko-Litskevitch, N., Korshevniuk, M., Kozhar, M., Krebs, J., Kubota, N., Kuklin, A., Kumar, S. S., Kwong, R., Kwong, L., Lafontaine, I., Lago, J., Lai, T. Y., Laine, E., Laiola, M., Lakhneko, O., Lamba, I., de Lamotte, G., Lannes, R., De Lazzari, E., Leahy, M., Lee, H., Lee, Y., Lee, L., Lemaire, V., Leong, E., Lewandowska, D., Li, C., Liang, W., Lin, M., Lisboa, P., Litskevitch, A., Liu, E. M., Liu, T., Livia, M. A., Lo, Y. H., Losim, S., Loubens, M., Lu, J., Lykhenko, O., Lysakova, S., Mahmoud, S., Majid, S. A., Makogon, N., Maldonado, D., Mallari, K., Malta, T. M., Mamun, M., Manoir, D., Marchandon, G., Marciniak, N., Marinovic, S., Marques, B., Mathews, N., Matsuzaki, Y., Matthys, V., May, M., Mccomb, E., Meagher, A., Melamed, A., Menary, W., Mendez, K. N., Mendez, A., Mendy, I. M., Meng, I., Menon, A., Menor, M., Meoded, R., Merino, N., Miah, K., Mignotte, M., Miketic, T., Miranda, W., Mitsios, A., Miura, R., Miyake, K., Moccia, M. D., Mohan, N., Mohsin, M., Moitra, K., Moldes, M., Molina, L., Molinet, J., Molomjamts, O. -E., Moniruzzaman, E., Moon, S., de Oliveira Moraes, I., Moreno, M., Mosella, M. S., Moser, J. W., Mozsary, C., Muehlbauer, A. L., Muner, O., Munia, M., Munim, N., Muscat, M., Mustac, T., Munoz, C., Nadalin, F., Naeem, A., Nagy-Szakal, D., Nakagawa, M., Narce, A., Nasu, M., Navarrete, I. G., Naveed, H., Nazario, B., Nedunuri, N. R., Neff, T., Nesimi, A., Ng, W. C., Ng, S., Nguyen, G., Ngwa, E., Nicolas, A., Nicolas, P., Nika, A., Noorzi, H., Nosrati, A., Nunes, D. N., O'Brien, K., O'Hara, N. B., Oken, G., Olawoyin, R. A., Oliete, J. Q., Olmeda, K., Oluwadare, T., Oluwadare, I. A., Ordioni, N., Orpilla, J., Orrego, J., Ortega, M., Osma, P., Osuolale, I. O., Osuolale, O. M., Ota, M., Oteri, F., Oto, Y., Ounit, R., Ouzounis, C. A., Pakrashi, S., Paras, R., Pardo-Este, C., Park, Y. -J., Pastuszek, P., Patel, S., Pathmanathan, J., Patrignani, A., Perez, M., Peros, A., Persaud, S., Peters, A., Phillips, A., Pineda, L., Pizzi, M. P., Plaku, A., Pompa-Hogan, B., Portilla, M. G., Posada, L., Priestman, M., Prithiviraj, B., Priya, S., Pugdeethosal, P., Pugh, C. E., Pulatov, B., Pupiec, A., Pyrshev, K., Qing, T., Rahiel, S., Rahmatulloev, S., Rajendran, K., Ramcharan, A., Ramirez-Rojas, A., Rana, S., Ratnanandan, P., Read, T. D., Rehrauer, H., Richer, R., Rivera, A., Rivera, M., Robertiello, A., Robinson, C., Rodriguez, P., Rojas, N. A., Roldan, P., Rosario, A., Roth, S., Ruiz, M., Boja Ruiz, S. E., Russell, K., Rybak, M., Sabedot, T. S., Sabina, M., Saito, I., Saito, Y., Malca Salas, G. A., Salazar, C., San, K. M., Sanchez, J., Sanchir, K., Sankar, R., de Souza Santos, P. T., Saravi, Z., Sasaki, K., Sato, Y., Sato, M., Sato, S., Sato, R., Sato, K., Sayara, N., Schaaf, S., Schacher, O., Schinke, A. -L. M., Schlapbach, R., Schori, C., Schriml, J. R., Segato, F., Sepulveda, F., Serpa, M. S., De Sessions, P. F., Severyn, J. C., Shakil, M., Shalaby, S., Shari, A., Shim, H., Shirahata, H., Shiwa, Y., Da Silva, O., Silva, J. M., Simon, G., Singh, S. K., Sluzek, K., Smith, R., So, E., Andreu Somavilla, N., Sonohara, Y., Rufino de Sousa, N., Souza, C., Sperry, J., Sprinsky, N., Stark, S. G., La Storia, A., Suganuma, K., Suliman, H., Sullivan, J., Supie, A. A. M., Suzuki, C., Takagi, S., Takahara, F., Takahashi, N., Takahashi, K., Takeda, T., Takenaka, I. K., Tanaka, S., Tang, A., Man Tang, Y., Tarcitano, E., Tassinari, A., Taye, M., Terrero, A., Thambiraja, E., Thiebaut, A., Thomas, S., Thomas, A. M., Togashi, Y., Togashi, T., Tomaselli, A., Tomita, M., Tomita, I., Toth, O., Toussaint, N. C., Tran, J. M., Truong, C., Tsonev, S. I., Tsuda, K., Tsurumaki, T., Tuz, M., Tymoshenko, Y., Urgiles, C., Usui, M., Vacant, S., Vann, L. E., Velter, F., Ventorino, V., Vera-Wolf, P., Vicedomini, R., Suarez-Villamil, M. A., Vincent, S., Vivancos-Koopman, R., Wan, A., Wang, C., Warashina, T., Watanabe, A., Weekes, S., Werner, J., Westfall, D., Wieler, L. H., Williams, M., Wolf, S. A., Wong, B., Wong, Y. L., Wong, T., Wright, R., Wunderlin, T., Yamanaka, R., Yang, J., Yano, H., Yeh, G. C., Yemets, O., Yeskova, T., Yoshikawa, S., Zafar, L., Zhang, Y., Zhang, S., Zhang, A., Zheng, Y., and Zubenko, S.

Subjects
Urban Population, Drug Resistance, Sequence assembly, Microbiologia, microbiome, global health, computer.software_genre, Medical and Health Sciences, shotgun sequencing, BGC, 0302 clinical medicine, Databases, Genetic, 11. Sustainability, Global health, AMR, 11 Medical and Health Sciences, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, built environment, metagenome, antimicrobial resistance, NGS, de novo assembly, biology, Shotgun sequencing, Microbiota, built Environment, Bacterial, Biodiversity, Biological Sciences, 3. Good health, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Infection, Biotechnology, Geospatial analysis, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Article, General Biochemistry, Genetics and Molecular Biology, Databases, 03 medical and health sciences, Antibiotic resistance, Genetic, Drug Resistance, Bacterial, International MetaSUB Consortium, Genetics, Humans, Microbiome, 030304 developmental biology, Human Genome, 06 Biological Sciences, 15. Life on land, biology.organism_classification, Resistènica als medicaments antiinfecciosos, SAÚDE PÚBLICA, Genòmica, 13. Climate action, Evolutionary biology, Metagenomics, Antimicrobial Resistance, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, computer, 030217 neurology & neurosurgery, Archaea, Developmental Biology
Abstract

Summary We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities., Graphical abstract, Highlights • Cities possess a consistent “core” set of non-human microbes • Urban microbiomes echo important features of cities and city-life • Antimicrobial resistance genes are widespread in cities • Cities contain many novel bacterial and viral species, This systematic, worldwide catalog of urban microbiomes represents a metagenomic atlas important for understanding the ecology, virulence, and antibiotic resistance of city-specific microbial communities.

Published
2021

10. Marine Ultrasmall Prokaryotes Likely Affect the Cycling of Carbon, Methane, Nitrogen, and Sulfur

Author

Eric Bapteste, Philippe Lopez, Romain Lannes, Louise Cavaud, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)

Subjects
0106 biological sciences, AcademicSubjects/SCI01140, Biogeochemical cycle, microbial dark matter, Letter, Nitrogen, [SDV]Life Sciences [q-bio], Oceans and Seas, chemistry.chemical_element, Biology, 010603 evolutionary biology, 01 natural sciences, Carbon cycle, Carbon Cycle, 03 medical and health sciences, Acetyl Coenzyme A, Genetics, Seawater, 14. Life underwater, Autotroph, marine ultrasmall organisms, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, metagenomics, Autotrophic Processes, Ecology, Microbiota, Carbon fixation, AcademicSubjects/SCI01130, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Sulfur, Carbon, Metabolic pathway, chemistry, Prokaryotic Cells, Metagenomics, metabolism, Methane, Metabolic Networks and Pathways
Abstract

Recently, we uncovered the genetic components from six carbon fixation autotrophic pathways in cleaned ultrasmall size fractions from marine samples (

Published
2020

11. Rich Repertoire of Quorum Sensing Protein Coding Sequences in CPR and DPANN Associated with Interspecies and Interkingdom Communication

Author

Eric Bapteste, Philippe Lopez, Romain Lannes, Charles Bernard, Yanyan Li, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), and Bapteste, Eric

Subjects
Physiology, In silico, [SDV]Life Sciences [q-bio], education, Computational biology, Ecological and Evolutionary Science, Biology, ENCODE, Biochemistry, Genome, interkingdom signaling, 03 medical and health sciences, Genetics, microbial communication, Molecular Biology, Gene, DPANN, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, 030306 microbiology, Phylum, microbiology, quorum sensing, QR1-502, Computer Science Applications, [SDV] Life Sciences [q-bio], Phylogenetic diversity, Quorum sensing, Modeling and Simulation, CPR, Interspecies communication, Research Article
Abstract

The selection of predicted genes for interspecies communication within the CPR and DPANN genomes sheds some light onto the underlying mechanisms supporting their inferred symbiotic lifestyle. Also, considering the lack of core pathways such as the de novo synthesis of nucleotides or amino acids in the CPR and DPANN lineages, the persistence of these genes highlights how determinant social traits can be for the survival of some microorganisms. Finally, the considerable number of variants of QS proteins identified among the 69 CPR and DPANN phyla substantially expands our knowledge of prokaryotic communication across the tree of life and suggests that the multiplicity of “dialects” in the microbial world is probably larger than previously appreciated., The bacterial candidate phyla radiation (CPR) and the archaeal DPANN superphylum are two novel lineages that have substantially expanded the tree of life due to their large phylogenetic diversity. Because of their ultrasmall size, reduced genome, and lack of core biosynthetic capabilities, most CPR and DPANN members are predicted to be sustained through their interactions with other species. How the few characterized CPR and DPANN symbionts achieve these critical interactions is, however, poorly understood. Here, we conducted an in silico analysis on 2,597 CPR/DPANN genomes to test whether these ultrasmall microorganisms might encode homologs of reference proteins involved in the synthesis and/or the detection of 26 different types of communication molecules (quorum sensing [QS] signals), since QS signals are well-known mediators of intra- and interorganismic relationships. We report the discovery of 5,693 variants of QS proteins distributed across 63 CPR and 6 DPANN phyla and associated with 14 distinct types of communication molecules, most of which were characterized as interspecies QS signals. IMPORTANCE The selection of predicted genes for interspecies communication within the CPR and DPANN genomes sheds some light onto the underlying mechanisms supporting their inferred symbiotic lifestyle. Also, considering the lack of core pathways such as the de novo synthesis of nucleotides or amino acids in the CPR and DPANN lineages, the persistence of these genes highlights how determinant social traits can be for the survival of some microorganisms. Finally, the considerable number of variants of QS proteins identified among the 69 CPR and DPANN phyla substantially expands our knowledge of prokaryotic communication across the tree of life and suggests that the multiplicity of “dialects” in the microbial world is probably larger than previously appreciated.

Published
2020

12. del(17p) without TP53 mutation confers a poor prognosis in intensively treated newly diagnosed patients with multiple myeloma

Author

Jill Corre, Denis Caillot, Jean-Pierre Marolleau, Naïs Prade, Philippe Moreau, Mamoun Dib, Karim Belhadj, Jean Fontan, Arnaud Jaccard, Sabine Brechignac, Stephane Minvielle, Laurence Sanhes, Margaret Macro, Laure Buisson, Lionel Karlin, Xavier Leleu, Hervé Avet-Loiseau, Thierry Facon, Laurent Voillat, Romain Lannes, Aurore Perrot, Mohamad Mohty, Frédérique Orsini-Piocelle, Stephanie Dufrechou, Lauriane Clement-Filliatre, Cyrille Hulin, and Laura Do Souto

Subjects
Oncology, Adult, Male, medicine.medical_specialty, Immunology, Population, Newly diagnosed, Tp53 mutation, Biochemistry, 03 medical and health sciences, Young Adult, 0302 clinical medicine, Internal medicine, medicine, Humans, Young adult, education, Multiple myeloma, Aged, Extremely Poor, education.field_of_study, business.industry, Cell Biology, Hematology, Middle Aged, medicine.disease, Prognosis, 3. Good health, Chromosome 17 (human), 030220 oncology & carcinogenesis, Cohort, Mutation, Female, Chromosome Deletion, Tumor Suppressor Protein p53, business, Multiple Myeloma, 030215 immunology, Chromosomes, Human, Pair 17
Abstract

Despite tremendous improvements in the outcome of patients with multiple myeloma in the past decade, high-risk patients have not benefited from the approval of novel drugs. The most important prognostic factor is the loss of parts of the short arm of chromosome 17, known as deletion 17p (del(17p)). A recent publication (on a small number of patients) suggested that these patients are at very high-risk only if del(17p) is associated with TP53 mutations, the so-called “double-hit” population. To validate this finding, we designed a much larger study on 121 patients presenting del(17p) in > 55% of their plasma cells, and homogeneously treated by an intensive approach. For these 121 patients, we performed deep next generation sequencing targeted on TP53. The outcome was then compared with a large control population (2505 patients lacking del(17p)). Our results confirmed that the “double hit” situation is the worst (median survival = 36 months), but that del(17p) alone also confers a poor outcome compared with the control cohort (median survival = 52.8 months vs 152.2 months, respectively). In conclusion, our study clearly confirms the extremely poor outcome of patients displaying “double hit," but also that del(17p) alone is still a very high-risk feature, confirming its value as a prognostic indicator for poor outcome.

Published
2020

13. In Multiple Myeloma, High-Risk Secondary Genetic Events Observed at Relapse Are Present from the Diagnosis in Tiny Undetectable Subclones

Author

Nikhil C. Munshi, Mohamad Mohty, Sabine Brechignac, Aurore Perrot, Didier Adiko, Marie-Lorraine Chretien, Hervé Avet-Loiseau, François Lifermann, Lauris Gastaud, Céline Mazzotti, Salomon Manier, Magaret Macro, Romain Lannes, Jill Corre, Titouan Cazaubiel, Anaïs Schavgoulidze, Frédérique Orsini-Piocelle, Xavier Leleu, Marion Divoux, and Didier Bouscary

Subjects
Oncology, medicine.medical_specialty, business.industry, Internal medicine, Immunology, medicine, Cell Biology, Hematology, business, medicine.disease, Biochemistry, health care economics and organizations, Multiple myeloma
Abstract

In multiple myeloma (MM), among the anomalies associated with shorter survival, it should be noted recurrent copy number variations (CNV), such as del(17p13), del(1p32), or 1q gains. These abnormalities are considered secondary, thus acquired during the course of the disease. Although they can be observed from diagnosis, they are only detected at the time of relapses in some patients. It is now clearly demonstrated that MM is a molecular subclonal disease, with the coexistence of different subclones of varying size. As in other cancers, it has also been shown that these different subclones can vary in size according to the different relapses, suggesting that an unnoticed minor subclone at diagnosis could become the major one at the time of relapse. Although subclonality has been largely reported at the mutational level, little is known about this phenomenon at the CNV level. Since a few CNV are associated with a poor outcome, and assuming they will impact the disease course, it would be clinically highly valuable to track these abnormalities at the time of diagnosis in minor subclones. Here, we report the first analysis at the single cell level of CNV of tumor cells from 81 patients with MM analyzed at the time of diagnosis, relapse or pre-symptomatic stages. A total of 52,176 single MM cells were analyzed. The number of analyzable tumor cells was variable from patients to patients, due to heterogeneity in the sample cellularity, but also variability in cell capture rate for the single cell analysis. The mean number of analyzable cells was 656 MM cells per patient (range=83-5192). To avoid possible false positive cases, we arbitrarily defined a subclone by at least 10 cells presenting the same CNV. In these 81 patients, at least one subclone was detected in 74 of them (91%). In this cohort, a subclonal high-risk CNV (not detected on the routine assessment) was observed in 19 patients (23.5%). We had the opportunity to also analyze at single cell level residual MM cells from one patient at the end of induction therapy, and early relapse. This patient displayed a 1q gain subclone at diagnosis (16 % of the analyzed cells), not detected in the bulk analysis. At the post-induction time (thus before high-dose melphalan and autologous stem cell transplantation), 70 % of the 202 analyzable tumor cells presented this high-risk feature. This patient did relapse only 18 months after diagnosis and at this time, 92% of the cells harbored the 1q gain (Figure 1). To address the question whether these high-risk subclonal features may impact outcome as soon as diagnosis, we explored our database. We found that 1q gains are observed in 34.1% of patients (1891/5539) at the time of diagnosis. When analyzing patients at relapse, 46.3% of them displayed a 1q gain (622/1341), thus a 12% increase. This increasing frequency reflects clonal selection of minor subclones already present at diagnosis but not detectable by conventional technique (found in comparable proportions), rather than actual acquisition after diagnosis during evolution of the disease. We then looked at the prognostic impact of 1q gain in patients displaying this CNV at diagnosis versus those presenting it only at the time of first relapse. Interestingly, the PFS and OS) curves were totally superimposable, suggesting that this subclonal 1q gain present from diagnosis in these latter patients impacts survival, possibly through early expansion. In order to go further in the molecular consequences of these high-risk subclones, we did perform single cell RNA-sequencing in 63 of the 81 patients. 1q gains defined specific subclones in the MM cells expression analyses from affected patients. Based on the expression of CDC28 protein kinase regulatory subunit 1B (CKS1B), located at 1q21, we found that high expression was restricted to specific subclones. In conclusion, our study highly suggests that high-risk CNVs are not acquired after, but are present from the diagnosis, and selected by the treatment. These findings may have implications in high-risk definition and patient's management, by reinforcing the therapeutic strategy in these patients as soon as the first line therapy to prevent the clonal selection of these aggressive subclones. Whether this finding could be extended to cancer in general but also in some pre-malignant stages is possible, but needs to be explored. Figure 1 Figure 1. Disclosures Perrot: GSK: Honoraria, Membership on an entity's Board of Directors or advisory committees; Janssen: Honoraria, Membership on an entity's Board of Directors or advisory committees; BMS Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees; Amgen: Honoraria, Membership on an entity's Board of Directors or advisory committees; Abbvie: Honoraria; Sanofi: Honoraria, Research Funding; Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding. Leleu: Carsgen Therapeutics Ltd: Honoraria; Celgene: Honoraria; Gilead Sciences: Honoraria; Janssen-Cilag: Honoraria; Karyopharm Therapeutics: Honoraria; Merck: Honoraria; Mundipharma: Honoraria; Novartis: Honoraria; Oncopeptides: Honoraria; Pierre Fabre: Honoraria; Roche: Honoraria; Sanofi: Honoraria; Bristol-Myers Squibb: Honoraria; Amgen: Honoraria; Takeda: Honoraria, Other: Non-financial support; AbbVie: Honoraria. Manier: Oncopeptides: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Roche: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; GSK: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Celgene - Bristol Myers Squibb: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Adaptive Biotechnologies: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Abbvie: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Amgen: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Janssen: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Takeda: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Regeneron: Consultancy, Research Funding; Novartis: Consultancy, Research Funding. Macro: Sanofi: Honoraria; GSK: Honoraria; Takeda: Honoraria, Other: Travel accomodation, Research Funding; Janssen: Honoraria, Other: Travel accomodation, Research Funding; Celgen/BMS: Honoraria. Mohty: Novartis: Honoraria; Celgene: Honoraria, Research Funding; Janssen: Honoraria, Research Funding; Amgen: Honoraria; Adaptive Biotechnologies: Honoraria; Bristol Myers Squibb: Honoraria; Astellas: Honoraria; Sanofi: Honoraria, Research Funding; Takeda: Honoraria; Gilead: Honoraria; Pfizer: Honoraria; Jazz: Honoraria, Research Funding. Munshi: Novartis: Consultancy; Takeda: Consultancy; Bristol-Myers Squibb: Consultancy; Janssen: Consultancy; Oncopep: Consultancy, Current equity holder in publicly-traded company, Other: scientific founder, Patents & Royalties; Abbvie: Consultancy; Amgen: Consultancy; Karyopharm: Consultancy; Celgene: Consultancy; Adaptive Biotechnology: Consultancy; Legend: Consultancy; Pfizer: Consultancy.

Published
2021

14. 16p Deletion Involving BCMA Locus Is Frequent and Predominantly Observed with del17p

Author

Romain Lannes, Hervé Avet-Loiseau, Anjan Thakurta, Mehmet Kemal Samur, Jill Corre, Kenneth C. Anderson, Anil Aktas-Samur, and Nikhil C. Munshi

Subjects
Genetics, Immunology, Locus (genetics), Cell Biology, Hematology, Biology, Biochemistry
Abstract

New generation immunotherapies in Multiple Myeloma (MM) targeting BCMA, have shown remarkable clinical benefits. However relapse still occurs due to tumor intrinsic and extrisic resistance mechanisms including antigen loss related to mutation, deletion and splicing pattern changes. Two recent case reports including ours highlighted biallelic loss of BCMA as a cause for resistance to anti-BCMA targeting therapy. In both studies BCMA locus at 16p was deleted bringing in focus importance of del16p. Here, we have evaluated 2883 MM patients at diagnosis and relapse to understand frequency characteristics of somatic events targeting BCMA. We first evaluated the frequency of deletion involving the BCMA locus (16p13.13) in MM patients from multiple studies using WGS sequencing data as well as using Affymetrix Cytoscan HD and SNP 6.0 arrays. We observed del16p in 8.58 % (7.6% to 14.6% in individual studies) of newly-diagnosed patients (n=2458). Similar frequency was observed in relapsed MM patients not previously exposed to BCMA targeting therapy. Next, we evaluated genome wide copy number alterations (CNAs) in all patients with loss of BCMA locus and observed similar frequency of loss in both hyperdiploid MM (HMM) and non-HMM suggesting its independence from cytogentic subtypes of MM. Overall copy number loss was significantly higher in patients with BCMA loss compared to rest of the MM patients. Patients with loss of BCMA locus have increased mutational load (8202 with 95% HDI 6921 and 9535) compared to those without BCMA locus loss (6975 with 95% HDI 6626 - 7343); probability of difference greater than 0 was 96.8% and difference of the means were 1222 [95% CI -112 - 2589] We next evaluated co-occurrence of BCMA loss with other high risk events and observed del1p and del17p as being significantly associated with loss of BCMA locus [Odds ratio 19.37 (13.13-25.80), FDR = 1.57e-65; and 8.8 (6.39-12.15), FDR = 5.57E-39, respectively)]. Furthermore, we observed that when both BCMA and TP53 loss are present, they have same log ratio (sequencing) or smoothed copy numbers (SNP array). Similarly, we used CDKN2C as a proxy to chromosome 1p loss and observed that when both BCMA and CKDN2C loss are present in the same patient they tend to show similar copy number values. These data suggested a possibility of co-occurrence of these events in the same cell. To further investigate this observation, we used single cell DNA sequencing data from patients with sub clonal and clonal BCMA locus loss. scDNA sequencing showed that almost all cells with BCMA deletion also had TP53 deletion (95%). Interestingly, almost all cells with BCMA loss also had p53 loss, while not all cells with p53 loss had BCMA loss suggesting that the chronology of this copy number alternation may suggest first p53 loss followed by BCMA loss. We further investigated whether a bi-allelic BCMA loss was observed after anti-BCMA targeted CAR-T cell therapy by imputing the copy number alterations using single cell RNA sequencing data. Our data from this case also indicated that BCMA loss tend to co-occur with TP53 deletions (OR=5.67 [95% CI 4.12-7.84], p value < 0.0001). Moreover, TP53 mutations were also more frequent in patients with del16p and del17p, compared to patients who only had del16p or del17p. In summary, our data from large scale copy number profiles at the diagnosis and relapse showed that monoallelic BCMA deletions are frequent events, patients with these events show increased aneuploidy, mostly deletions, potentially making these cells vulnerable for biallelic loss of genes, especially under the pressure of targeted therapy. Our results also highlight that BCMA expressions in bulk sample may not detect the presence or absence of cells with target loss and therefore combining strategies at bulk and single cell level are necessary to understand the disease status. These results suggest the need to study del16p in patients being targeted for BCMA-directed therapy and its association with other risk factors in MM. Disclosures Thakurta: Bristol Myers Squibb: Current Employment, Current equity holder in publicly-traded company. Anderson: Celgene: Membership on an entity's Board of Directors or advisory committees; Janssen: Membership on an entity's Board of Directors or advisory committees; Gilead: Membership on an entity's Board of Directors or advisory committees; Sanofi-Aventis: Membership on an entity's Board of Directors or advisory committees; Millenium-Takeda: Membership on an entity's Board of Directors or advisory committees; Bristol Myers Squibb: Membership on an entity's Board of Directors or advisory committees; Pfizer: Membership on an entity's Board of Directors or advisory committees; Scientific Founder of Oncopep and C4 Therapeutics: Current equity holder in publicly-traded company, Current holder of individual stocks in a privately-held company; AstraZeneca: Membership on an entity's Board of Directors or advisory committees; Mana Therapeutics: Membership on an entity's Board of Directors or advisory committees. Munshi: Takeda: Consultancy; Adaptive Biotechnology: Consultancy; Amgen: Consultancy; Karyopharm: Consultancy; Celgene: Consultancy; Abbvie: Consultancy; Oncopep: Consultancy, Current equity holder in publicly-traded company, Other: scientific founder, Patents & Royalties; Novartis: Consultancy; Legend: Consultancy; Pfizer: Consultancy; Janssen: Consultancy; Bristol-Myers Squibb: Consultancy.

Published
2021

15. OAB-022: Monoallelic deletion of BCMA locus is a frequent feature in MM and is associated with increased genomic loss

Author

Kenneth C. Anderson, Jill Corre, Hervé Avet-Loiseau, Anil Aktas-Samur, Romain Lannes, Nikhil C. Munshi, and Mehmet Kemal Samur

Subjects
Oncology, Cancer Research, medicine.medical_specialty, business.industry, Targeting therapy, medicine.medical_treatment, Locus (genetics), Hematology, Cellular level, Risk profile, Targeted therapy, Internal medicine, medicine, In patient, business, Gene
Abstract

Background Immunotherapies in MM targeting BCMA, have shown remarkable clinical benefits. However, two recent reports highlighted that biallelic loss of BCMA cause resistance to anti-BCMA therapy. In both studies BCMA locus was deleted bringing in focus importance of del16p. We have evaluated 2883 MM patients at diagnosis and relapse to understand frequency of BCMA targeting events and characteristics of MM patients with BCMA deletion. Methods We observed del16p in 8.58% (7.6% to14.6% in individual studies) of newly-diagnosed patients (n=2458).Frequency of 16p loss in both HMM and NHMM were similar, suggesting its independence from MM subtypes. Overall CN loss was significantly higher in patients with BCMA loss compared to rest of the MM patients. High risk deletion events such as del1p and del17p were more likely to be observed in patients with loss of BCMA locus (OR [95% CI] 19.3(13.1-25.8), FDR = 1.5e-65; and 8.8(6.3-12.1), FDR = 5.5E-39, respectively)]. MM patients with loss of BCMA locus have increased mutational load (8202 with 95% HDI 6921 and 9535) compared to those without BCMA locus loss (6975 with 95% HDI 6626 – 7343); probability of difference greater than 0 was 96.8% and difference of the means were 1222 [95% CI 112-2589]. To understand the risk profile of patients with loss of BCMA locus, we next focused on the observation that BCMA loss frequently co-occurs with other deletions. Results We observed that when BCMA and TP53 or BCMA and del1p loss are present in the same patient, they are likely to have same clonality. These data suggested a possibility of co-occurrence of these events in same cell. To further investigate this observation, we used single cell DNA sequencing data from patients with sub clonal and clonal BCMA locus loss. Interestingly, almost all cells with BCMA loss also had p53 loss, while not all p53 loss cells had BCMA loss suggesting that the chronology of this copy number alternation may suggest first p53 loss followed by BCMA loss. Our data from a patient with BCMA targeting therapy also indicated that BCMA loss tend to co-occur with TP53 deletions (OR=5.67 [95% CI 4.12-7.84], p value Conclusions Our data from large scale copy number profiles showed that even without treatment pressure, monoallelic BCMA deletions are frequent events. Moreover, patients with these events show increased genomic loss. Such behavior potentially make these cells vulnerable for biallelic loss of other genes. Our results highlight that by looking at mRNA or protein expressions at bulk sample would not directly indicate the presence or absence of cells with target loss and therefore evaluating single cell level data are necessary. These results suggest the need to study del16p in patients being targeted for BCMA-directed therapy and its association with del17p raises question about the role of BCMA targeted therapy in high-risk myeloma.

Published
2021

16. The Genomic and Transcriptomic Landscape of Plasma Cell Leukemia

Author

Cyrille Hulin, Aurore Perrot, Jill Corre, Laura Do Souto Ferreira, Hervé Avet-Loiseau, Laure Buisson, Titouan Cazaubiel, Sabrina Maheo, and Romain Lannes

Subjects
Transcriptome, Plasma cell leukemia, Immunology, Cancer research, medicine, Cell Biology, Hematology, Biology, medicine.disease, Biochemistry
Abstract

Background: Primary plasma cell leukemia (pPCL) is a rare and aggressive form of multiple myeloma (MM) with an extremely poor prognosis and distinct biological and clinical features. Because of its low incidence and its heterogeneity, biological knowledge about pPCL is lacking especially molecular process responsible for its aggressiveness. Here, we took advantage of a large series of pPCL to describe the genomic and transcriptomic landscape of pPCL, to identify potential driver mutations and pathways, and to determine their clinical impacts. Methods: To address these issues, we performed a targeted DNA sequencing and a RNA sequencing of sorted bone marrow plasma cells collected at the time of diagnosis from 96 patients with pPCL between 2014 and 2020. We compared their genomic profiles with those of 907 MM at diagnosis previously obtained in our laboratory and their transcriptomic profiles with those of 300 MM at diagnosis obtained from the IFM2009/DFCI trial (NCT01191060). Copy number aberrations (CNA), single nucleotide variants (SNV), translocations, mutations, gene expression (GE) and gene set enrichment were analyzed and correlated with clinical information (overall survival and progression-free survival). Results: Genome analysis highlighted a specific genomic profile of pPCL. Indeed, hyperdiploid karyotypes were less frequent in pPCL compared with MM (20% vs 57%, p RNA-seq analysis showed also a specific transcriptional landscape of pPCL. Indeed, unsupervised hierarchical clustering of gene expression profiles demonstrated two distinct clusters between pPCL and MM. Gene set enrichment analysis identified a significantly higher expression of genes involved in MYC Targets and G2M checkpoint, and a significantly lower expression of genes involved in P53 pathway, hypoxia and TNF alpha signaling via NF-κB. Furthermore, pPCL with and without t(11;14) presented two distinct transcriptomic patterns, in particular for genes implicated in the apoptotic machinery. Three members of the BCL2 family were differentially expressed with BCL2 and PMAIP1 [NOXA] significantly overexpressed and BCL2L1 significantly underexpressed in pPCL with t(11;14). Median PFS and OS of patients with pPCL were respectively at 11 and 15 months. Presence of TP53 mutations was associated with a significantly lower PFS (4 months, p Conclusion: To our knowledge, we present the study on the largest series of patients with pPCL. Our results provide new information on both genomic and transcriptomic landscape of pPCL. Despite their heterogeneity, pPCL present a specific mutational landscape with high prevalence of t(11;14) and high-risk genomic features. These results help to better understand oncogenicity and the aggressive behavior of pPCL and support the use of new treatment strategies such as BCL2 inhibitor (Venetoclax) for pPCL with t(11;14). Disclosures Perrot: Amgen, BMS/Celgene, Janssen, Sanofi, Takeda: Consultancy, Honoraria, Research Funding. Hulin:Celgene/Bristol-Myers Squibb, Janssen, GlaxoSmithKline, and Takeda: Honoraria.

Published
2020

17. The Methodology Behind Network Thinking: Graphs to Analyze Microbial Complexity and Evolution

Author

Andrew K, Watson, Romain, Lannes, Jananan S, Pathmanathan, Raphaël, Méheust, Slim, Karkar, Philippe, Colson, Eduardo, Corel, Philippe, Lopez, and Eric, Bapteste

Subjects
Evolution, Molecular, Gene Ontology, Microbiota, Multigene Family, Computational Biology, High-Throughput Nucleotide Sequencing, Metagenome, Gene Regulatory Networks, Molecular Sequence Annotation, Biodiversity, Metagenomics, Biological Evolution, Ecosystem
Abstract

In the post genomic era, large and complex molecular datasets from genome and metagenome sequencing projects expand the limits of what is possible for bioinformatic analyses. Network-based methods are increasingly used to complement phylogenetic analysis in studies in molecular evolution, including comparative genomics, classification, and ecological studies. Using network methods, the vertical and horizontal relationships between all genes or genomes, whether they are from cellular chromosomes or mobile genetic elements, can be explored in a single expandable graph. In recent years, development of new methods for the construction and analysis of networks has helped to broaden the availability of these approaches from programmers to a diversity of users. This chapter introduces the different kinds of networks based on sequence similarity that are already available to tackle a wide range of biological questions, including sequence similarity networks, gene-sharing networks and bipartite graphs, and a guide for their construction and analyses.

Published
2019

18. The Methodology Behind Network Thinking: Graphs to Analyze Microbial Complexity and Evolution

Author

Eric Bapteste, Slim Karkar, Andrew K Watson, Jananan S. Pathmanathan, Philippe Lopez, Raphaël Méheust, Philippe Colson, Eduardo Corel, Romain Lannes, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Adaptation, Intégration, Réticulation et Evolution (AIRE), Evolution Paris Seine, Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Unité Analyse et Traitement de l'Information (UNATI), Service NEUROSPIN (NEUROSPIN), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Université Pierre et Marie Curie - Paris 6 (UPMC), Université Pierre et Marie Curie - Paris 6 - UFR de Médecine Pierre et Marie Curie (UPMC), and Aix Marseille Université (AMU)

Subjects
0106 biological sciences, Computer science, Evolution, [SDV]Life Sciences [q-bio], 010603 evolutionary biology, 01 natural sciences, Genome, 03 medical and health sciences, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Molecular evolution, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Comparative genomics, 0303 health sciences, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Phylogenetic tree, Lateral gene transfer (LGT), Ecology, Data science, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Graph, ComputingMethodologies_PATTERNRECOGNITION, Metagenomics, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Bipartite graph, Mobile genetic elements, Gene remodeling, Sequence similarity network
Abstract

International audience; In the post genomic era, large and complex molecular datasets from genome and metagenome sequencing projects expand the limits of what is possible for bioinformatic analyses. Network-based methods are increasingly used to complement phylogenetic analysis in studies in molecular evolution, including comparative genomics, classification, and ecological studies. Using network methods, the vertical and horizontal relationships between all genes or genomes, whether they are from cellular chromosomes or mobile genetic elements, can be explored in a single expandable graph. In recent years, development of new methods for the construction and analysis of networks has helped to broaden the availability of these approaches from programmers to a diversity of users. This chapter introduces the different kinds of networks based on sequence similarity that are already available to tackle a wide range of biological questions, including sequence similarity networks, gene-sharing networks and bipartite graphs, and a guide for their construction and analyses.

Published
2019

19. Does the Presence of Transposable Elements Impact the Epigenetic Environment of Human Duplicated Genes?

Author

Romain Lannes, Emmanuelle Lerat, Carène Rizzon, Eléments transposables, évolution, populations, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Paris Seine (IBPS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-ENSIIE-Centre National de la Recherche Scientifique (CNRS), CNRS, University Lyon 1, Laboratory 'Biometrie et Biologie Evolutive', and Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Transposable element, Genome evolution, lcsh:QH426-470, Biology, Article, Epigenesis, Genetic, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Genes, Duplicate, Gene duplication, Gene expression, transposable elements, gene duplication, gene evolution, epigenetics, Genetics, Humans, Epigenetics, Gene, Genetics (clinical), food and beverages, Epigenome, Duplicated genes, lcsh:Genetics, 030104 developmental biology, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Evolutionary biology, Multigene Family, DNA Transposable Elements, 030217 neurology & neurosurgery
Abstract

International audience; Epigenetic modifications have an important role to explain part of the intra-and inter-species variation in gene expression. They also have a role in the control of transposable elements (TEs) whose activity may have a significant impact on genome evolution by promoting various mutations, which are expected to be mostly deleterious. A change in the local epigenetic landscape associated with the presence of TEs is expected to affect the expression of neighboring genes since these modifications occurring at TE sequences can spread to neighboring sequences. In this work, we have studied how the epigenetic modifications of genes are conserved and what the role of TEs is in this conservation. For that, we have compared the conservation of the epigenome associated with human duplicated genes and the differential presence of TEs near these genes. Our results show higher epigenome conservation of duplicated genes from the same family when they share similar TE environment, suggesting a role for the differential presence of TEs in the evolutionary divergence of duplicates through variation in the epigenetic landscape.

Published
2019

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