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1. Survey on the Impact of the COVID-19 Pandemic on Patients with Parkinson’s Disease and Their Caregivers in Japan

Author

Hattori N, Okada Y, Kawata Y, Furusawa Y, Imai T, Yoshida H, Ota M, Arai M, Shintani A, and Fernandez J

Subjects
parkinson’s disease, covid-19, questionnaire design, caregiver burden, Medicine (General), R5-920
Abstract

Nobutaka Hattori,1 Yoshiko Okada,2 Yayoi Kawata,3 Yoshihiko Furusawa,3 Takumi Imai,4 Hisako Yoshida,4 Mihoko Ota,3 Masaki Arai,3 Ayumi Shintani,4 Jovelle Fernandez3 1Department of Neurology, Juntendo University, Tokyo, Japan; 2Japan Parkinson Congress, Tokyo, Japan; 3Japan Medical Office, Takeda Pharmaceutical Company Limited, Tokyo, Japan; 4Department of Medical Statistics, Graduate School of Medicine, Osaka Metropolitan University, Osaka, JapanCorrespondence: Yoshihiko Furusawa, Japan Medical Office, Takeda Pharmaceutical Company Limited, 2 Chome-1-1 Nihonbashihoncho, Chuo City, Tokyo, 103-0023, Japan, Tel +81-3-3278-2111, Fax +81-3-3278-2000, Email yoshihiko.furusawa@takeda.comObjective: The coronavirus disease 2019 (COVID-19) pandemic changed the lives of patients with Parkinson’s disease (PD) and their caregivers. This study aimed to investigate changes in patient behavior and PD symptoms and their effect on caregiver burden resulting from the COVID-19 pandemic in Japan.Methods: This nationwide, observational, cross-sectional survey included patients with self-reported PD and caregivers (members of the Japan Parkinson’s Disease Association). The primary objective was to evaluate changes in behaviors, self-assessed PD symptoms, and caregiver burden from pre–COVID-19 (February 2020) to post–national state of emergency (August 2020 and February 2021).Results: Responses from 1883 patients and 1382 caregivers from 7610 distributed surveys were analyzed. Mean (standard deviation) age of patients and caregivers was 71.6 (8.2) and 68.5 (11.4) years, respectively; 41.6% of patients had a Hoehn and Yahr (HY) scale of 3. Patients (> 40.0%) reported decreased frequency of going out. Most patients (> 70.0%) reported no change in treatment visit frequency, voluntary training, or rehabilitation and nursing care insurance services. Symptoms worsened for approximately 7– 30% of patients; the proportion with HY scale 4– 5 increased from pre–COVID-19 (25.2%) to February 2021 (40.1%). Aggravated symptoms included bradykinesia, walking, gait speed, depressed mood, fatigue, and apathy. Caregivers’ burden increased because of patients’ worsened symptoms and reduced time going out.Conclusion: Control measures during infectious disease epidemics should consider that patients’ symptoms may worsen; therefore, patient and caregiver support is needed to reduce burden of care.Keywords: Parkinson’s disease, COVID-19, questionnaire design, caregiver burden

Published
2023

2. Association Between Patient Preference for Inhaler Medications and Asthma Outcomes

Author

Nakanishi Y, Iwamoto H, Miyamoto S, Nakao S, Higaki N, Yamaguchi K, Sakamoto S, Horimasu Y, Masuda T, Matsumoto N, Nakashima T, Onari Y, Fujitaka K, Haruta Y, Hamada H, Hozawa S, and Hattori N

Subjects
asthma control, exacerbation, inhaled corticosteroids, inhaler adherence, patient preference, Immunologic diseases. Allergy, RC581-607
Abstract

Yu Nakanishi,1 Hiroshi Iwamoto,1 Shintaro Miyamoto,1 Satoshi Nakao,1 Naoko Higaki,1 Kakuhiro Yamaguchi,1 Shinjiro Sakamoto,1 Yasushi Horimasu,1 Takeshi Masuda,1 Naoko Matsumoto,2 Taku Nakashima,1 Yojiro Onari,3 Kazunori Fujitaka,1 Yoshinori Haruta,4 Hironobu Hamada,5 Soichiro Hozawa,6 Noboru Hattori1 1Department of Molecular and Internal Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan; 2Department of Respiratory Medicine, Hiroshima Red Cross Hospital & Atomic-Bomb Survivors Hospital, Hiroshima, Japan; 3Department of Respiratory Medicine, Hiroshima Mazda Hospital, Hiroshima, Japan; 4Haruta Respiratory Clinic, Hiroshima, Japan; 5Department of Physical Analysis and Therapeutic Sciences, Graduate School of Biomedical and Health Sciences Hiroshima University, Hiroshima, Japan; 6Hiroshima Allergy and Respiratory Clinic, Hiroshima, JapanCorrespondence: Hiroshi Iwamoto, Department of Molecular and Internal Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan, Tel +81-82-257-5196, Email iwamotohiroshig@gmail.comPurpose: Asthma guidelines recommend considering the patient preference to optimize medication choices. Patient preference for inhaler medication may affect asthma outcomes, but evidence regarding this is lacking. This study investigated the associations between patient preference for inhaler medications and asthma outcomes.Patients and Methods: A multicenter questionnaire survey was conducted among 351 adult patients with asthma treated with regular inhaled corticosteroids. Agreement between patients’ preferences and current medication was evaluated using two questions: matched preference was defined as patients answering that the current inhaler medication was the most preferred treatment and they were satisfied with it. Mismatched preference was defined as when patients reported that the current inhaler medication was not the most preferred treatment and/or they were not satisfied with it. We investigated the factors associated with patient preference for asthma inhaler medications.Results: In total, 269 (76.6%) patients were classified into the matched preference group and 82 (23.4%) patients into the mismatched preference group. Multivariate analyses showed that matched preference was independently associated with higher asthma control test scores (P< 0.001), fewer exacerbations (P=0.009), less regular oral corticosteroid use (P=0.009), and better inhaler adherence (P=0.006) than the mismatched preference group. In subgroup analysis, younger age was associated with matched preference in patients using dry powder inhalers but not in those using pressurized metered dose inhalers.Conclusion: The use of preference-matched inhaler medication was associated with better asthma outcomes. Evaluation of patients’ preference for inhaler medication might provide useful information for individualized treatment with asthma inhaler medications.Keywords: patient preference, asthma control, inhaled corticosteroids, inhaler adherence, shared decision-making

Published
2022

3. Observational study of Safinamide as an add-on to levodopa monotherapy for Parkinson's disease patients with wearing-off in Japan

Author

Nishikawa, N., primary, Hatano, T., additional, Nishioka, K., additional, Ueno, S.-I., additional, Saiki, S., additional, Nakamura, R., additional, Yoritaka, A., additional, Ogawa, T., additional, Shimo, Y., additional, Sako, W., additional, Shimura, H., additional, Furukawa, Y., additional, Kamei, T., additional, Ozawa, T., additional, Ishida, T., additional, and Hattori, N., additional

Published
2024
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5. Ordering of mutations in acute myeloid leukemia with partial tandem duplication of MLL (MLL-PTD)

Author

Sun, Q-Y, Ding, L-W, Tan, K-T, Chien, W, Mayakonda, A, Lin, D-C, Loh, X-Y, Xiao, J-F, Meggendorfer, M, Alpermann, T, Garg, M, Lim, S-L, Madan, V, Hattori, N, Nagata, Y, Miyano, S, Yeoh, AEJ, Hou, H-A, Jiang, Y-Y, Takao, S, Liu, L-Z, Tan, S-Z, Lill, M, Hayashi, M, Kinoshita, A, Kantarjian, HM, Kornblau, SM, Ogawa, S, Haferlach, T, Yang, H, and Koeffler, HP

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Hematology, Cancer, Childhood Leukemia, Pediatric, Genetics, Pediatric Cancer, Rare Diseases, 2.1 Biological and endogenous factors, Aetiology, Cell Proliferation, Clone Cells, Exome, Histone-Lysine N-Methyltransferase, Humans, Leukemia, Myeloid, Acute, Mutation, Mutation Rate, Myeloid-Lymphoid Leukemia Protein, Nucleophosmin, Tandem Repeat Sequences, Time Factors, Clinical Sciences, Immunology, Cardiovascular medicine and haematology, Clinical sciences, Oncology and carcinogenesis
Abstract

Partial tandem duplication of MLL (MLL-PTD) characterizes acute myeloid leukemia (AML) patients often with a poor prognosis. To understand the order of occurrence of MLL-PTD in relation to other major AML mutations and to identify novel mutations that may be present in this unique AML molecular subtype, exome and targeted sequencing was performed on 85 MLL-PTD AML samples using HiSeq-2000. Genes involved in the cohesin complex (STAG2), a splicing factor (U2AF1) and a poorly studied gene, MGA were recurrently mutated, whereas NPM1, one of the most frequently mutated AML gene, was not mutated in MLL-PTD patients. Interestingly, clonality analysis suggests that IDH2/1, DNMT3A, U2AF1 and TET2 mutations are clonal and occur early, and MLL-PTD likely arises after these initial mutations. Conversely, proliferative mutations (FLT3, RAS), typically appear later, are largely subclonal and tend to be unstable. This study provides important insights for understanding the relative importance of different mutations for defining a targeted therapeutic strategy for MLL-PTD AML patients.

Published
2017

6. Comprehensive mutational analysis of primary and relapse acute promyelocytic leukemia

Author

Madan, V, Shyamsunder, P, Han, L, Mayakonda, A, Nagata, Y, Sundaresan, J, Kanojia, D, Yoshida, K, Ganesan, S, Hattori, N, Fulton, N, Tan, K-T, Alpermann, T, Kuo, M-C, Rostami, S, Matthews, J, Sanada, M, Liu, L-Z, Shiraishi, Y, Miyano, S, Chendamarai, E, Hou, H-A, Malnassy, G, Ma, T, Garg, M, Ding, L-W, Sun, Q-Y, Chien, W, Ikezoe, T, Lill, M, Biondi, A, Larson, RA, Powell, BL, Lübbert, M, Chng, WJ, Tien, H-F, Heuser, M, Ganser, A, Koren-Michowitz, M, Kornblau, SM, Kantarjian, HM, Nowak, D, Hofmann, W-K, Yang, H, Stock, W, Ghavamzadeh, A, Alimoghaddam, K, Haferlach, T, Ogawa, S, Shih, L-Y, Mathews, V, and Koeffler, HP

Subjects
Biomedical and Clinical Sciences, Cardiovascular Medicine and Haematology, Clinical Sciences, Oncology and Carcinogenesis, Cancer, Human Genome, Childhood Leukemia, Pediatric Cancer, Genetics, Rare Diseases, Hematology, Clinical Research, Pediatric, Cell Differentiation, DNA Mutational Analysis, DNA-Binding Proteins, Exome, Gene Expression Profiling, Humans, Leukemia, Promyelocytic, Acute, Nuclear Proteins, Recurrence, Transcription Factors, Immunology, Cardiovascular medicine and haematology, Clinical sciences, Oncology and carcinogenesis
Abstract

Acute promyelocytic leukemia (APL) is a subtype of myeloid leukemia characterized by differentiation block at the promyelocyte stage. Besides the presence of chromosomal rearrangement t(15;17), leading to the formation of PML-RARA (promyelocytic leukemia-retinoic acid receptor alpha) fusion, other genetic alterations have also been implicated in APL. Here, we performed comprehensive mutational analysis of primary and relapse APL to identify somatic alterations, which cooperate with PML-RARA in the pathogenesis of APL. We explored the mutational landscape using whole-exome (n=12) and subsequent targeted sequencing of 398 genes in 153 primary and 69 relapse APL. Both primary and relapse APL harbored an average of eight non-silent somatic mutations per exome. We observed recurrent alterations of FLT3, WT1, NRAS and KRAS in the newly diagnosed APL, whereas mutations in other genes commonly mutated in myeloid leukemia were rarely detected. The molecular signature of APL relapse was characterized by emergence of frequent mutations in PML and RARA genes. Our sequencing data also demonstrates incidence of loss-of-function mutations in previously unidentified genes, ARID1B and ARID1A, both of which encode for key components of the SWI/SNF complex. We show that knockdown of ARID1B in APL cell line, NB4, results in large-scale activation of gene expression and reduced in vitro differentiation potential.

Published
2016

7. Safety and Efficacy of Lenvatinib Treatment in Child–Pugh A and B Patients with Unresectable Hepatocellular Carcinoma in Clinical Practice: A Multicenter Analysis

Author

Ogushi K, Chuma M, Uojima H, Hidaka H, Numata K, Kobayashi S, Hirose S, Hattori N, Fujikawa T, Nakazawa T, Wada N, Iwasaki S, Fukushima T, Sano Y, Ueno M, Kawano K, Tsuruya K, Shomura M, Watanabe T, Matsunaga K, Kunishi Y, Saigusa Y, Irie K, Iwabuchi S, Kako M, Morimoto M, Kagawa T, Tanaka K, and Maeda S

Subjects
lenvatinib, tyrosine kinase inhibitor, hepatocellular carcinoma, child-pugh, adverse events, overall survival, Diseases of the digestive system. Gastroenterology, RC799-869
Abstract

Katsuaki Ogushi,1,* Makoto Chuma,1,* Haruki Uojima,2 Hisashi Hidaka,2 Kazushi Numata,1 Satoshi Kobayashi,3 Shunji Hirose,4 Nobuhiro Hattori,5 Tomoaki Fujikawa,6 Takahide Nakazawa,2 Naohisa Wada,2 Shuitirou Iwasaki,2 Taito Fukushima,3 Yusuke Sano,3 Makoto Ueno,3 Kuniyuki Kawano,3 Kota Tsuruya,4 Masako Shomura,4 Tsunamasa Watanabe,5 Kotaro Matsunaga,5 Yosuke Kunishi,7 Yusuke Saigusa,8 Kuniyasu Irie,9 Shogo Iwabuchi,6 Makoto Kako,10 Manabu Morimoto,3 Tatehiro Kagawa,4 Katsuaki Tanaka,11 Shin Maeda9 1Gastroenterological Center, Yokohama City University Medical Center, Yokohama, Japan; 2Department of Gastroenterology, Internal Medicine, Kitasato University School of Medicine, Sagamihara, Japan; 3Hepatobiliary and Pancreatic Medical Oncology, Kanagawa Cancer Center Hospital, Yokohama, Japan; 4Division of Gastroenterology and Hepatology, Department of Internal Medicine, Tokai University School of Medicine, Isehara, Japan; 5Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan; 6Department of Gastroenterology, Shonan Fujisawa General Hospital, Fujisawa, Japan; 7Department of Gastroenterology, Kanagawa Prefectural Ashigarakami Hospital, Kanagawa, Japan; 8Department of Biostatistics, Yokohama City University Graduate School of Medicine, Yokohama, Japan; 9Department of Gastroenterology, Yokohama City University Hospital, Yokohama, Japan; 10Department of Gastroenterology, Shonan Kamakura General Hospital, Kamakura, Japan; 11Gastroenterology Division, Hadano Red Cross Hospital, Hadano, Japan*These authors contributed equally to this workCorrespondence: Makoto Chuma Gastroenterological CenterYokohama City University Medical Center, 4-57 Urafune-Cho, Minami-Ku, Yokohama, Kanagawa 2320024, JapanTel +81 45 261 5656Fax +81 45 253 9955Email chuma@yokohama-cu.ac.jpPurpose: To assess the safety, efficacy and prognostic impact of clinical factors related to lenvatinib treatment in Child-Pugh class A (CP-A) and class B (CP-B) patients with unresectable hepatocellular carcinoma (u-HCC).Methods: Patients with u-HCC who were treated with lenvatinib at multiple centers in Japan were retrospectively analyzed for treatment outcomes according to their respective CP status. Radiological objective response (OR) was assessed using modified response evaluation criteria in solid tumors (mRECIST) guidelines.Results: Baseline demographic parameters were comparable between 126 (69.6%) patients with CP-A disease and 55 patients (30.4%) with CP-B disease. Frequency of lenvatinib-related adverse events, including decreased appetite (P=0.034), diarrhea (P=0.040), elevated serum bilirubin (P=0.016) and vomiting (P=0.009), were higher in CP-B than in CP-A patients. Relative dose intensity (RDI) was significantly higher in CP-A (0.69) than CP-B patients (0.50, P < 0.001). Furthermore, OR rate (44.0%) was markedly higher in CP-A5 patients as compared to CP-A6 (25.5%), CP-B7 (22.2%), and CP-B8 patients (5.3%), respectively (P=0.002). In multivariable analysis, performance status (0 vs 1, 2, P=0.026), CP class (A vs B, P=0.045) and RDI (≥ 0.7 vs < 0.7, P=0.034) were identified as factors associated with response to lenvatinib treatment. Overall survival (OS) at 12 months was significantly different between CP-A (66.3%) and CP-B patients (30.0%, P=0.002), and between CP 5– 7 (59.2%) and CP 8 patients (34.8%, P=0.003). In multivariable analysis, CP class (A vs B, P=0.007) and Barcelona clinic liver cancer (BCLC) stage (B vs C, P=0.002) were associated with OS following lenvatinib treatment.Conclusion: Lenvatinib treatment offers significant benefits in patients with good liver function in real-world practice. The various characteristics identified in this study might be helpful as clinical predictors of response to lenvatinib and survival in clinical practice. Further studies are required to address eligibility for lenvatinib treatment in CP 7 patients.Keywords: lenvatinib, tyrosine kinase inhibitor, hepatocellular carcinoma, Child-Pugh, adverse events, overall survival

Published
2020

8. Sputum Vitamin D Binding Protein (VDBP) GC1S/1S Genotype Predicts Airway Obstruction: A Prospective Study in Smokers with COPD

Author

Gao J, Törölä T, Li CX, Ohlmeier S, Toljamo T, Nieminen P, Hattori N, Pulkkinen V, Iwamoto H, and Mazur W

Subjects
vitamin d binding protein (vdbp), genotype, copd, prospective study, sputum, Diseases of the respiratory system, RC705-779
Abstract

Jing Gao,1,* Tanja Törölä,1,* Chuan-Xing Li,2 Steffen Ohlmeier,3 Tuula Toljamo,4 Pentti Nieminen,5 Noboru Hattori,6 Ville Pulkkinen,1 Hiroshi Iwamoto,6 Witold Mazur1 1Heart and Lung Centre, Department of Pulmonary Medicine, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; 2Pulmonomics Group, Respiratory Medicine Unit, Department of Medicine & Centre for Molecular Medicine, Karolinska Institute, Stockholm, Sweden; 3Proteomics Core Facility, Biocentre Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland; 4Department of Pulmonary Medicine, Lapland Central Hospital, Rovaniemi, Finland; 5Medical Informatics and Statistics Group, University of Oulu, Oulu, Finland; 6Department of Molecular and Internal Medicine, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan*These authors contributed equally to this workCorrespondence: Jing GaoHeart and Lung Centre, Department of Pulmonary Medicine, University of Helsinki and Helsinki University Hospital, FinlandTel +358417071559Email jing.gao@helsinki.fi, HelsinkiIntroduction: The vitamin D binding protein (VDBP, also known as GC-globulin) and vitamin D deficiency have been associated with chronic obstructive pulmonary disease (COPD). rs7041 and rs4588 are two single nucleotide polymorphisms of the VDBP gene, including three common allelic variants (GC1S, GC1F and GC2). Previous studies primarily assessed the serum levels of vitamin D and VDBP in COPD. However, less is known regarding the impact of the local release of VDBP on COPD lung function. Thus, we examined the association of sputum and plasma VDBP with lung function at baseline and at four years, and examined potential genetic polymorphism interactions.Methods: The baseline levels of sputum VDBP, plasma VDBP and plasma 25-OH vitamin D, as well as the GC rs4588 and rs7041 genotypes, were assessed in a 4-year Finnish follow-up cohort (n = 233) of non-smokers, and smokers with and without COPD. The associations between the VDBP levels and the longitudinal decline of lung function were further analysed.Results: High frequencies of the haplotypes in rs7041/rs4588 were homozygous GC1S/1S (42.5%). Higher sputum VDBP levels in stage I and stage II COPD were observed only in carriers with GC1S/1S genotype when compared with non-smokers (p = 0.034 and p = 0.002, respectively). Genotype multivariate regression analysis indicated that the baseline sputum VDBP and FEV1/FVC ratio at baseline independently predicted FEV1% at follow-up.Discussion and Conclusion: The baseline sputum VDBP expression was elevated in smokers with COPD among individuals with the GC1S/1S genotype, and predicted follow-up airway obstruction. Our results suggest that the GC polymorphism should be considered when exploring the potential of VDBP as a biomarker for COPD.Keywords: vitamin D binding protein, VDBP, genotype, COPD, prospective study, sputum

Published
2020

9. Investigation of Shared Genetic Risk Factors Between Parkinson's Disease and Cancers

Author

Sugier, P, Lucotte, E, Domenighetti, C, Law, M, Iles, M, Brown, K, Amos, C, Mckay, J, Hung, R, Karimi, M, Bacq-Daian, D, Boland-Auge, A, Olaso, R, Deleuze, J, Lesueur, F, Ostroumova, E, Kesminiene, A, de Vathaire, F, Guenel, P, Sreelatha, A, Schulte, C, Grover, S, May, P, Bobbili, D, Radivojkov-Blagojevic, M, Lichtner, P, Singleton, A, Hernandez, D, Edsall, C, Mellick, G, Zimprich, A, Pirker, W, Rogaeva, E, Lang, A, Koks, S, Taba, P, Lesage, S, Brice, A, Corvol, J, Chartier-Harlin, M, Mutez, E, Brockmann, K, Deutschlander, A, Hadjigeorgiou, G, Dardiotis, E, Stefanis, L, Simitsi, A, Valente, E, Petrucci, S, Straniero, L, Zecchinelli, A, Pezzoli, G, Brighina, L, Ferrarese, C, Annesi, G, Quattrone, A, Gagliardi, M, Matsuo, H, Nakayama, A, Hattori, N, Nishioka, K, Chung, S, Kim, Y, Kolber, P, van de Warrenburg, B, Bloem, B, Aasly, J, Toft, M, Pihlstrom, L, Guedes, L, Ferreira, J, Bardien, S, Carr, J, Tolosa, E, Ezquerra, M, Pastor, P, Diez-Fairen, M, Wirdefeldt, K, Pedersen, N, Ran, C, Belin, A, Puschmann, A, Rodstrom, E, Clarke, C, Morrison, K, Tan, M, Krainc, D, Burbulla, L, Farrer, M, Kruger, R, Gasser, T, Sharma, M, Truong, T, Elbaz, A, Sugier P. -E., Lucotte E. A., Domenighetti C., Law M. H., Iles M. M., Brown K., Amos C., McKay J. D., Hung R. J., Karimi M., Bacq-Daian D., Boland-Auge A., Olaso R., Deleuze J. -F., Lesueur F., Ostroumova E., Kesminiene A., de Vathaire F., Guenel P., Sreelatha A. A. K., Schulte C., Grover S., May P., Bobbili D. R., Radivojkov-Blagojevic M., Lichtner P., Singleton A. B., Hernandez D. G., Edsall C., Mellick G. D., Zimprich A., Pirker W., Rogaeva E., Lang A. E., Koks S., Taba P., Lesage S., Brice A., Corvol J. -C., Chartier-Harlin M. -C., Mutez E., Brockmann K., Deutschlander A. B., Hadjigeorgiou G. M., Dardiotis E., Stefanis L., Simitsi A. M., Valente E. M., Petrucci S., Straniero L., Zecchinelli A., Pezzoli G., Brighina L., Ferrarese C., Annesi G., Quattrone A., Gagliardi M., Matsuo H., Nakayama A., Hattori N., Nishioka K., Chung S. J., Kim Y. J., Kolber P., van de Warrenburg B. P. C., Bloem B. R., Aasly J., Toft M., Pihlstrom L., Guedes L. C., Ferreira J. J., Bardien S., Carr J., Tolosa E., Ezquerra M., Pastor P., Diez-Fairen M., Wirdefeldt K., Pedersen N., Ran C., Belin A. C., Puschmann A., Rodstrom E. Y., Clarke C. E., Morrison K. E., Tan M., Krainc D., Burbulla L. F., Farrer M. J., Kruger R., Gasser T., Sharma M., Truong T., Elbaz A., Sugier, P, Lucotte, E, Domenighetti, C, Law, M, Iles, M, Brown, K, Amos, C, Mckay, J, Hung, R, Karimi, M, Bacq-Daian, D, Boland-Auge, A, Olaso, R, Deleuze, J, Lesueur, F, Ostroumova, E, Kesminiene, A, de Vathaire, F, Guenel, P, Sreelatha, A, Schulte, C, Grover, S, May, P, Bobbili, D, Radivojkov-Blagojevic, M, Lichtner, P, Singleton, A, Hernandez, D, Edsall, C, Mellick, G, Zimprich, A, Pirker, W, Rogaeva, E, Lang, A, Koks, S, Taba, P, Lesage, S, Brice, A, Corvol, J, Chartier-Harlin, M, Mutez, E, Brockmann, K, Deutschlander, A, Hadjigeorgiou, G, Dardiotis, E, Stefanis, L, Simitsi, A, Valente, E, Petrucci, S, Straniero, L, Zecchinelli, A, Pezzoli, G, Brighina, L, Ferrarese, C, Annesi, G, Quattrone, A, Gagliardi, M, Matsuo, H, Nakayama, A, Hattori, N, Nishioka, K, Chung, S, Kim, Y, Kolber, P, van de Warrenburg, B, Bloem, B, Aasly, J, Toft, M, Pihlstrom, L, Guedes, L, Ferreira, J, Bardien, S, Carr, J, Tolosa, E, Ezquerra, M, Pastor, P, Diez-Fairen, M, Wirdefeldt, K, Pedersen, N, Ran, C, Belin, A, Puschmann, A, Rodstrom, E, Clarke, C, Morrison, K, Tan, M, Krainc, D, Burbulla, L, Farrer, M, Kruger, R, Gasser, T, Sharma, M, Truong, T, Elbaz, A, Sugier P. -E., Lucotte E. A., Domenighetti C., Law M. H., Iles M. M., Brown K., Amos C., McKay J. D., Hung R. J., Karimi M., Bacq-Daian D., Boland-Auge A., Olaso R., Deleuze J. -F., Lesueur F., Ostroumova E., Kesminiene A., de Vathaire F., Guenel P., Sreelatha A. A. K., Schulte C., Grover S., May P., Bobbili D. R., Radivojkov-Blagojevic M., Lichtner P., Singleton A. B., Hernandez D. G., Edsall C., Mellick G. D., Zimprich A., Pirker W., Rogaeva E., Lang A. E., Koks S., Taba P., Lesage S., Brice A., Corvol J. -C., Chartier-Harlin M. -C., Mutez E., Brockmann K., Deutschlander A. B., Hadjigeorgiou G. M., Dardiotis E., Stefanis L., Simitsi A. M., Valente E. M., Petrucci S., Straniero L., Zecchinelli A., Pezzoli G., Brighina L., Ferrarese C., Annesi G., Quattrone A., Gagliardi M., Matsuo H., Nakayama A., Hattori N., Nishioka K., Chung S. J., Kim Y. J., Kolber P., van de Warrenburg B. P. C., Bloem B. R., Aasly J., Toft M., Pihlstrom L., Guedes L. C., Ferreira J. J., Bardien S., Carr J., Tolosa E., Ezquerra M., Pastor P., Diez-Fairen M., Wirdefeldt K., Pedersen N., Ran C., Belin A. C., Puschmann A., Rodstrom E. Y., Clarke C. E., Morrison K. E., Tan M., Krainc D., Burbulla L. F., Farrer M. J., Kruger R., Gasser T., Sharma M., Truong T., and Elbaz A.

Abstract

Background: Epidemiological studies that examined the association between Parkinson's disease (PD) and cancers led to inconsistent results, but they face a number of methodological difficulties. Objective: We used results from genome-wide association studies (GWASs) to study the genetic correlation between PD and different cancers to identify common genetic risk factors. Methods: We used individual data for participants of European ancestry from the Courage-PD (Comprehensive Unbiased Risk Factor Assessment for Genetics and Environment in Parkinson's Disease; PD, N = 16,519) and EPITHYR (differentiated thyroid cancer, N = 3527) consortia and summary statistics of GWASs from iPDGC (International Parkinson Disease Genomics Consortium; PD, N = 482,730), Melanoma Meta-Analysis Consortium (MMAC), Breast Cancer Association Consortium (breast cancer), the Prostate Cancer Association Group to Investigate Cancer Associated Alterations in the Genome (prostate cancer), International Lung Cancer Consortium (lung cancer), and Ovarian Cancer Association Consortium (ovarian cancer) (N comprised between 36,017 and 228,951 for cancer GWASs). We estimated the genetic correlation between PD and cancers using linkage disequilibrium score regression. We studied the association between PD and polymorphisms associated with cancers, and vice versa, using cross-phenotypes polygenic risk score (PRS) analyses. Results: We confirmed a previously reported positive genetic correlation of PD with melanoma (Gcorr = 0.16 [0.04; 0.28]) and reported an additional significant positive correlation of PD with prostate cancer (Gcorr = 0.11 [0.03; 0.19]). There was a significant inverse association between the PRS for ovarian cancer and PD (odds ratio [OR] = 0.89 [0.84; 0.94]). Conversely, the PRS of PD was positively associated with breast cancer (OR = 1.08 [1.06; 1.10]) and inversely associated with ovarian cancer (OR = 0.95 [0.91; 0.99]). The association between PD and ovarian cancer was mostly driven b

Published
2023

10. LNK (SH2B3): paradoxical effects in ovarian cancer

Author

Ding, L-W, Sun, Q-Y, Lin, D-C, Chien, W, Hattori, N, Dong, X-M, Gery, S, Garg, M, Doan, NB, Said, JW, Xiao, J-F, Yang, H, Liu, L-Z, Meng, X, Huang, RY-J, Tang, K, and Koeffler, HP

Subjects
Biochemistry and Cell Biology, Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Biological Sciences, Rare Diseases, Cancer, Ovarian Cancer, 2.1 Biological and endogenous factors, Aetiology, 14-3-3 Proteins, Adaptor Proteins, Signal Transducing, Animals, Cell Adhesion, Cell Line, Tumor, Cell Movement, Cell Proliferation, Cell Size, Female, Humans, Intracellular Signaling Peptides and Proteins, Mice, Mice, Inbred NOD, Mice, SCID, Mitogen-Activated Protein Kinases, Neoplasm Transplantation, Ovarian Neoplasms, Protein Binding, Proteins, Proto-Oncogene Proteins c-akt, Signal Transduction, Transplantation, Heterologous, Clinical Sciences, Oncology & Carcinogenesis, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

LNK (SH2B3) is an adaptor protein studied extensively in normal and malignant hematopoietic cells. In these cells, it downregulates activated tyrosine kinases at the cell surface resulting in an antiproliferative effect. To date, no studies have examined activities of LNK in solid tumors. In this study, we found by in silico analysis and staining tissue arrays that the levels of LNK expression were elevated in high-grade ovarian cancer. To test the functional importance of this observation, LNK was either overexpressed or silenced in several ovarian cancer cell lines. Remarkably, overexpression of LNK rendered the cells resistant to death induced by either serum starvation or nutrient deprivation, and generated larger tumors using a murine xenograft model. In contrast, silencing of LNK decreased ovarian cancer cell growth in vitro and in vivo. Western blot studies indicated that overexpression of LNK upregulated and extended the transduction of the mitogenic signal, whereas silencing of LNK produced the opposite effects. Furthermore, forced expression of LNK reduced cell size, inhibited cell migration and markedly enhanced cell adhesion. Liquid chromatography-mass spectroscopy identified 14-3-3 as one of the LNK-binding partners. Our results suggest that in contrast to the findings in hematologic malignancies, the adaptor protein LNK acts as a positive signal transduction modulator in ovarian cancers.

Published
2015

11. SETDB1 accelerates tumourigenesis by regulating the WNT signalling pathway

Author

Sun, QY, Ding, LW, Xiao, JF, Chien, W, Lim, SL, Hattori, N, Goodglick, L, Chia, D, Mah, V, Alavi, M, Kim, SR, Doan, NB, Said, JW, Loh, XY, Xu, L, Liu, LZ, Yang, H, Hayano, T, Shi, S, Xie, D, Lin, DC, and Phillip Koeffler, H

Subjects
Pathology, Clinical Sciences
Abstract

We investigated the oncogenic role of SETDB1, focusing on non-small cell lung cancer (NSCLC), which has high expression of this protein. A total of 387 lung cancer cases were examined by immunohistochemistry; 72% of NSCLC samples were positive for SETDB1 staining, compared to 46% samples of normal bronchial epithelium (106 cases) (p

Published
2015

12. A Prospective Cohort Study to Define the Clinical Features and Outcome of Lung Cancers Harboring HER2 Aberration in Japan (HER2-CS STUDY)

Author

Gemba, K., Ikeda, G., Yasugi, M., Kurimoto, E., Nakano, K., Moritaka, T., Inoue, K., Miyoshi, S., Hamaguchi, N., Ito, R., Sano, Y., Takata, I., Mitani, A., Nishisaka, T., Shoda, H., Nishida, A., Tamamoto, S., Fujitaka, K., Masuda, T., Miyamoto, S., Hattori, N., Sugimoto, K., Fujii, S., Ueda, Y., Sakugawa, M., Fukamatsu, N., Ogata, Y., Bandoh, S., Kanaji, N., Takigawa, N., Yamane, H., Ochi, N., Honda, Y., Oka, M., Kittaka, M., Kubota, T., Yokoyama, A., Yokoyama, T., Sato, E., Shiota, Y., Horita, N., Kanematsu, T., Awaya, Y., Nakamasu, A., Murakami, I., Kuyama, S., Kudo, K., Tamura, T., Umeno, T., Morichika, D., Fujiwara, K., Sato, K., Harada, D., Nogami, N., Nishii, K., Fuchimoto, Y., Kishimoto, T., Kawai, H., Watanabe, K., Tokumo, K., Isobe, T., Tsubata, Y., Inoue, M., Ichikawa, H., Nishioka, Y., Hanibuchi, M., Goto, H., Sumikawa, T., Kodani, M., Suyama, H., Makino, H., Kinosita, N., Shimizu, E., Obata, H., Ikegami, H., Chikamori, K., Maeda, T., Kishino, T., Kamei, H., Ueoka, H., Kunihiro, Y., Kobayashi, T., Ueda, K., Hayashi, M., Kamiya, M., Murakami, J., Sato, A., Ichihara, E., Kubo, T., Ninomiya, T., Hirata, T., Minami, D., Kato, Y., Higo, H., Makimoto, G., Toyota, Y., Oda, N., Nakanishi, M., Kayatani, H., Senoo, S., Kano, H., Watanabe, H., Ando, T., Nakasuka, T., Hara, N., Itano, J., Nakashima, H., Tabata, M., Ninomiya, Kiichiro, Hata, Tae, Yoshioka, Hiroshige, Ohashi, Kadoaki, Bessho, Akihiro, Hosokawa, Shinobu, Ishikawa, Nobuhisa, Yamasaki, Masahiro, Shibayama, Takuo, Aoe, Keisuke, Kozuki, Toshiyuki, Harita, Shingo, Ueda, Yutaka, Murakami, Toshi, Fujimoto, Nobukazu, Yanai, Hiroyuki, Toyooka, Shinichi, Takata, Minoru, Hotta, Katsuyuki, and Kiura, Katsuyuki

Published
2019
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13. KPT-330 has antitumour activity against non-small cell lung cancer

Author

Sun, H, Hattori, N, Chien, W, Sun, Q, Sudo, M, E-Ling, GL, Ding, L, Lim, SL, Shacham, S, Kauffman, M, Nakamaki, T, and Koeffler, HP

Subjects
Lung Cancer, Genetics, Cancer, Lung, 5.1 Pharmaceuticals, Development of treatments and therapeutic interventions, Animals, Antineoplastic Agents, Antineoplastic Combined Chemotherapy Protocols, Apoptosis, Carcinoma, Non-Small-Cell Lung, Cell Growth Processes, Cell Line, Tumor, Cisplatin, G1 Phase, Genes, p53, Humans, Hydrazines, Karyopherins, Lung Neoplasms, Male, Mice, Mice, Inbred NOD, Mice, SCID, Mutation, Receptors, Cytoplasmic and Nuclear, Triazoles, Xenograft Model Antitumor Assays, CRM1, SINE, NSCLC, p53, p73, Oncology and Carcinogenesis, Public Health and Health Services, Oncology & Carcinogenesis
Abstract

BackgroundWe investigated the biologic and pharmacologic activities of a chromosome region maintenance 1 (CRM1) inhibitor against human non-small cell lung cancer (NSCLC) cells both in vitro and in vivo.MethodsThe in vitro and in vivo effects of a novel CRM1 inhibitor (KPT-330) for a large number of anticancer parameters were evaluated using a large panel of 11 NSCLC cell lines containing different key driver mutations. Mice bearing human NSCLC xenografts were treated with KPT-330, and tumour growth was assessed.ResultsKPT-330 inhibited proliferation and induced cell cycle arrest and apoptosis-related proteins in 11 NSCLC cells lines. Moreover, the combination of KPT-330 with cisplatin synergistically enhanced the cell kill of the NSCLC cells in vitro. Human NSCLC tumours growing in immunodeficient mice were markedly inhibited by KPT-330. Also, KPT-330 was effective even against NSCLC cells with a transforming mutation of either exon 20 of EGFR, TP53, phosphatase and tensin homologue, RAS or PIK3CA, suggesting the drug might be effective against a variety of lung cancers irrespective of their driver mutation.ConclusionsOur results support clinical testing of KPT-330 as a novel therapeutic strategy for NSCLC.

Published
2014

14. OC 06.3 Final Analysis Results from a Phase Iii Study of Emicizumab Prophylaxis for Acquired Hemophilia A (AGEHA)

Author

Shima, M., primary, Suzuki, N., additional, Nishikii, H., additional, Amano, K., additional, Ogawa, Y., additional, Kobayashi, R., additional, Ozaki, R., additional, Yoneyama, K., additional, Mizuno, N., additional, Sakaida, E., additional, Saito, M., additional, Okamura, T., additional, Ito, T., additional, Hattori, N., additional, Higasa, S., additional, Seki, Y., additional, and Nogami, K., additional

Published
2023
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18. Mendelian Randomisation Study of Smoking, Alcohol, and Coffee Drinking in Relation to Parkinson's Disease

Author

Domenighetti, C, Sugier, P, Sreelatha, A, Schulte, C, Grover, S, Mohamed, O, Portugal, B, May, P, Bobbili, D, Radivojkov-Blagojevic, M, Lichtner, P, Singleton, A, Hernandez, D, Edsall, C, Mellick, G, Zimprich, A, Pirker, W, Rogaeva, E, Lang, A, Koks, S, Taba, P, Lesage, S, Brice, A, Corvol, J, Chartier-Harlin, M, Mutez, E, Brockmann, K, Deutschlander, A, Hadjigeorgiou, G, Dardiotis, E, Stefanis, L, Simitsi, A, Valente, E, Petrucci, S, Duga, S, Straniero, L, Zecchinelli, A, Pezzoli, G, Brighina, L, Ferrarese, C, Annesi, G, Quattrone, A, Gagliardi, M, Matsuo, H, Kawamura, Y, Hattori, N, Nishioka, K, Chung, S, Kim, Y, Kolber, P, Van De Warrenburg, B, Bloem, B, Aasly, J, Toft, M, Pihlstrom, L, Guedes, L, Ferreira, J, Bardien, S, Carr, J, Tolosa, E, Ezquerra, M, Pastor, P, Diez-Fairen, M, Wirdefeldt, K, Pedersen, N, Ran, C, Belin, A, Puschmann, A, Hellberg, C, Clarke, C, Morrison, K, Tan, M, Krainc, D, Burbulla, L, Farrer, M, Kruger, R, Gasser, T, Sharma, M, Elbaz, A, Domenighetti C., Sugier P. -E., Sreelatha A. A. K., Schulte C., Grover S., Mohamed O., Portugal B., May P., Bobbili D. R., Radivojkov-Blagojevic M., Lichtner P., Singleton A. B., Hernandez D. G., Edsall C., Mellick G. D., Zimprich A., Pirker W., Rogaeva E., Lang A. E., Koks S., Taba P., Lesage S., Brice A., Corvol J. -C., Chartier-Harlin M. -C., Mutez E., Brockmann K., Deutschlander A. B., Hadjigeorgiou G. M., Dardiotis E., Stefanis L., Simitsi A. M., Valente E. M., Petrucci S., Duga S., Straniero L., Zecchinelli A., Pezzoli G., Brighina L., Ferrarese C., Annesi G., Quattrone A., Gagliardi M., Matsuo H., Kawamura Y., Hattori N., Nishioka K., Chung S. J., Kim Y. J., Kolber P., Van De Warrenburg B. P. C., Bloem B. R., Aasly J., Toft M., Pihlstrom L., Guedes L. C., Ferreira J. J., Bardien S., Carr J., Tolosa E., Ezquerra M., Pastor P., Diez-Fairen M., Wirdefeldt K., Pedersen N. L., Ran C., Belin A. C., Puschmann A., Hellberg C., Clarke C. E., Morrison K. E., Tan M., Krainc D., Burbulla L. F., Farrer M. J., Kruger R., Gasser T., Sharma M., Elbaz A., Domenighetti, C, Sugier, P, Sreelatha, A, Schulte, C, Grover, S, Mohamed, O, Portugal, B, May, P, Bobbili, D, Radivojkov-Blagojevic, M, Lichtner, P, Singleton, A, Hernandez, D, Edsall, C, Mellick, G, Zimprich, A, Pirker, W, Rogaeva, E, Lang, A, Koks, S, Taba, P, Lesage, S, Brice, A, Corvol, J, Chartier-Harlin, M, Mutez, E, Brockmann, K, Deutschlander, A, Hadjigeorgiou, G, Dardiotis, E, Stefanis, L, Simitsi, A, Valente, E, Petrucci, S, Duga, S, Straniero, L, Zecchinelli, A, Pezzoli, G, Brighina, L, Ferrarese, C, Annesi, G, Quattrone, A, Gagliardi, M, Matsuo, H, Kawamura, Y, Hattori, N, Nishioka, K, Chung, S, Kim, Y, Kolber, P, Van De Warrenburg, B, Bloem, B, Aasly, J, Toft, M, Pihlstrom, L, Guedes, L, Ferreira, J, Bardien, S, Carr, J, Tolosa, E, Ezquerra, M, Pastor, P, Diez-Fairen, M, Wirdefeldt, K, Pedersen, N, Ran, C, Belin, A, Puschmann, A, Hellberg, C, Clarke, C, Morrison, K, Tan, M, Krainc, D, Burbulla, L, Farrer, M, Kruger, R, Gasser, T, Sharma, M, Elbaz, A, Domenighetti C., Sugier P. -E., Sreelatha A. A. K., Schulte C., Grover S., Mohamed O., Portugal B., May P., Bobbili D. R., Radivojkov-Blagojevic M., Lichtner P., Singleton A. B., Hernandez D. G., Edsall C., Mellick G. D., Zimprich A., Pirker W., Rogaeva E., Lang A. E., Koks S., Taba P., Lesage S., Brice A., Corvol J. -C., Chartier-Harlin M. -C., Mutez E., Brockmann K., Deutschlander A. B., Hadjigeorgiou G. M., Dardiotis E., Stefanis L., Simitsi A. M., Valente E. M., Petrucci S., Duga S., Straniero L., Zecchinelli A., Pezzoli G., Brighina L., Ferrarese C., Annesi G., Quattrone A., Gagliardi M., Matsuo H., Kawamura Y., Hattori N., Nishioka K., Chung S. J., Kim Y. J., Kolber P., Van De Warrenburg B. P. C., Bloem B. R., Aasly J., Toft M., Pihlstrom L., Guedes L. C., Ferreira J. J., Bardien S., Carr J., Tolosa E., Ezquerra M., Pastor P., Diez-Fairen M., Wirdefeldt K., Pedersen N. L., Ran C., Belin A. C., Puschmann A., Hellberg C., Clarke C. E., Morrison K. E., Tan M., Krainc D., Burbulla L. F., Farrer M. J., Kruger R., Gasser T., Sharma M., and Elbaz A.

Abstract

Background: Previous studies showed that lifestyle behaviors (cigarette smoking, alcohol, coffee) are inversely associated with Parkinson's disease (PD). The prodromal phase of PD raises the possibility that these associations may be explained by reverse causation. Objective: To examine associations of lifestyle behaviors with PD using two-sample Mendelian randomisation (MR) and the potential for survival and incidence-prevalence biases. Methods: We used summary statistics from publicly available studies to estimate the association of genetic polymorphisms with lifestyle behaviors, and from Courage-PD (7,369 cases, 7,018 controls; European ancestry) to estimate the association of these variants with PD. We used the inverse-variance weighted method to compute odds ratios (ORIVW) of PD and 95%confidence intervals (CI). Significance was determined using a Bonferroni-corrected significance threshold (p = 0.017). Results: We found a significant inverse association between smoking initiation and PD (ORIVW per 1-SD increase in the prevalence of ever smoking = 0.74, 95%CI = 0.60-0.93, p = 0.009) without significant directional pleiotropy. Associations in participants =67 years old and cases with disease duration =7 years were of a similar size. No significant associations were observed for alcohol and coffee drinking. In reverse MR, genetic liability toward PD was not associated with smoking or coffee drinking but was positively associated with alcohol drinking. Conclusion: Our findings are in favor of an inverse association between smoking and PD that is not explained by reverse causation, confounding, and survival or incidence-prevalence biases. Genetic liability toward PD was positively associated with alcohol drinking. Conclusions on the association of alcohol and coffee drinking with PD are hampered by insufficient statistical power.

Published
2022

19. Dairy Intake and Parkinson's Disease: A Mendelian Randomization Study

Author

Domenighetti, C, Sugier, P, Ashok Kumar Sreelatha, A, Schulte, C, Grover, S, Mohamed, O, Portugal, B, May, P, Bobbili, D, Radivojkov-Blagojevic, M, Lichtner, P, Singleton, A, Hernandez, D, Edsall, C, Mellick, G, Zimprich, A, Pirker, W, Rogaeva, E, Lang, A, Koks, S, Taba, P, Lesage, S, Brice, A, Corvol, J, Chartier-Harlin, M, Mutez, E, Brockmann, K, Deutschlander, A, Hadjigeorgiou, G, Dardiotis, E, Stefanis, L, Simitsi, A, Valente, E, Petrucci, S, Duga, S, Straniero, L, Zecchinelli, A, Pezzoli, G, Brighina, L, Ferrarese, C, Annesi, G, Quattrone, A, Gagliardi, M, Matsuo, H, Kawamura, Y, Hattori, N, Nishioka, K, Chung, S, Kim, Y, Kolber, P, van de Warrenburg, B, Bloem, B, Aasly, J, Toft, M, Pihlstrom, L, Correia Guedes, L, Ferreira, J, Bardien, S, Carr, J, Tolosa, E, Ezquerra, M, Pastor, P, Diez-Fairen, M, Wirdefeldt, K, Pedersen, N, Ran, C, Belin, A, Puschmann, A, Hellberg, C, Clarke, C, Morrison, K, Tan, M, Krainc, D, Burbulla, L, Farrer, M, Kruger, R, Gasser, T, Sharma, M, Elbaz, A, Domenighetti C., Sugier P. -E., Ashok Kumar Sreelatha A., Schulte C., Grover S., Mohamed O., Portugal B., May P., Bobbili D. R., Radivojkov-Blagojevic M., Lichtner P., Singleton A. B., Hernandez D. G., Edsall C., Mellick G. D., Zimprich A., Pirker W., Rogaeva E., Lang A. E., Koks S., Taba P., Lesage S., Brice A., Corvol J. -C., Chartier-Harlin M. -C., Mutez E., Brockmann K., Deutschlander A. B., Hadjigeorgiou G. M., Dardiotis E., Stefanis L., Simitsi A. M., Valente E. M., Petrucci S., Duga S., Straniero L., Zecchinelli A., Pezzoli G., Brighina L., Ferrarese C., Annesi G., Quattrone A., Gagliardi M., Matsuo H., Kawamura Y., Hattori N., Nishioka K., Chung S. J., Kim Y. J., Kolber P., van de Warrenburg B. P. C., Bloem B. R., Aasly J., Toft M., Pihlstrom L., Correia Guedes L., Ferreira J. J., Bardien S., Carr J., Tolosa E., Ezquerra M., Pastor P., Diez-Fairen M., Wirdefeldt K., Pedersen N. L., Ran C., Belin A. C., Puschmann A., Hellberg C., Clarke C. E., Morrison K. E., Tan M., Krainc D., Burbulla L. F., Farrer M. J., Kruger R., Gasser T., Sharma M., Elbaz A., Domenighetti, C, Sugier, P, Ashok Kumar Sreelatha, A, Schulte, C, Grover, S, Mohamed, O, Portugal, B, May, P, Bobbili, D, Radivojkov-Blagojevic, M, Lichtner, P, Singleton, A, Hernandez, D, Edsall, C, Mellick, G, Zimprich, A, Pirker, W, Rogaeva, E, Lang, A, Koks, S, Taba, P, Lesage, S, Brice, A, Corvol, J, Chartier-Harlin, M, Mutez, E, Brockmann, K, Deutschlander, A, Hadjigeorgiou, G, Dardiotis, E, Stefanis, L, Simitsi, A, Valente, E, Petrucci, S, Duga, S, Straniero, L, Zecchinelli, A, Pezzoli, G, Brighina, L, Ferrarese, C, Annesi, G, Quattrone, A, Gagliardi, M, Matsuo, H, Kawamura, Y, Hattori, N, Nishioka, K, Chung, S, Kim, Y, Kolber, P, van de Warrenburg, B, Bloem, B, Aasly, J, Toft, M, Pihlstrom, L, Correia Guedes, L, Ferreira, J, Bardien, S, Carr, J, Tolosa, E, Ezquerra, M, Pastor, P, Diez-Fairen, M, Wirdefeldt, K, Pedersen, N, Ran, C, Belin, A, Puschmann, A, Hellberg, C, Clarke, C, Morrison, K, Tan, M, Krainc, D, Burbulla, L, Farrer, M, Kruger, R, Gasser, T, Sharma, M, Elbaz, A, Domenighetti C., Sugier P. -E., Ashok Kumar Sreelatha A., Schulte C., Grover S., Mohamed O., Portugal B., May P., Bobbili D. R., Radivojkov-Blagojevic M., Lichtner P., Singleton A. B., Hernandez D. G., Edsall C., Mellick G. D., Zimprich A., Pirker W., Rogaeva E., Lang A. E., Koks S., Taba P., Lesage S., Brice A., Corvol J. -C., Chartier-Harlin M. -C., Mutez E., Brockmann K., Deutschlander A. B., Hadjigeorgiou G. M., Dardiotis E., Stefanis L., Simitsi A. M., Valente E. M., Petrucci S., Duga S., Straniero L., Zecchinelli A., Pezzoli G., Brighina L., Ferrarese C., Annesi G., Quattrone A., Gagliardi M., Matsuo H., Kawamura Y., Hattori N., Nishioka K., Chung S. J., Kim Y. J., Kolber P., van de Warrenburg B. P. C., Bloem B. R., Aasly J., Toft M., Pihlstrom L., Correia Guedes L., Ferreira J. J., Bardien S., Carr J., Tolosa E., Ezquerra M., Pastor P., Diez-Fairen M., Wirdefeldt K., Pedersen N. L., Ran C., Belin A. C., Puschmann A., Hellberg C., Clarke C. E., Morrison K. E., Tan M., Krainc D., Burbulla L. F., Farrer M. J., Kruger R., Gasser T., Sharma M., and Elbaz A.

Abstract

Background: Previous prospective studies highlighted dairy intake as a risk factor for Parkinson's disease (PD), particularly in men. It is unclear whether this association is causal or explained by reverse causation or confounding. Objective: The aim is to examine the association between genetically predicted dairy intake and PD using two-sample Mendelian randomization (MR). Methods: We genotyped a well-established instrumental variable for dairy intake located in the lactase gene (rs4988235) within the Courage-PD consortium (23 studies; 9823 patients and 8376 controls of European ancestry). Results: Based on a dominant model, there was an association between genetic predisposition toward higher dairy intake and PD (odds ratio [OR] per one serving per day = 1.70, 95% confidence interval = 1.12–2.60, P = 0.013) that was restricted to men (OR = 2.50 [1.37–4.56], P = 0.003; P-difference with women = 0.029). Conclusions: Using MR, our findings provide further support for a causal relationship between dairy intake and higher PD risk, not biased by confounding or reverse causation. Further studies are needed to elucidate the underlying mechanisms. © 2022 International Parkinson and Movement Disorder Society.

Published
2022

21. Investigation of Shared Genetic Risk Factors Between Parkinson's Disease and Cancers

Author

Sugier, P.E., Lucotte, E.A., Domenighetti, C., Law, M.H., Iles, M.M., Brown, K., Amos, C., McKay, J.D., Hung, R.J., Karimi, M., Bacq-Daian, D., Boland-Augé, A., Olaso, R., Deleuze, J.F., Lesueur, F., Ostroumova, E., Kesminiene, A., Vathaire, F. de, Guénel, P., Sreelatha, A.A.K., Schulte, C., Grover, S., May, P., Bobbili, D.R., Radivojkov-Blagojevic, M., Lichtner, P., Singleton, A.B., Hernandez, D.G., Edsall, C., Mellick, G.D., Zimprich, A., Pirker, W., Rogaeva, E., Lang, A.E., Koks, S., Taba, P., Lesage, S., Brice, A., Corvol, J.C., Chartier-Harlin, M.C., Mutez, E., Brockmann, K., Deutschländer, A.B., Hadjigeorgiou, G.M., Dardiotis, E., Stefanis, L., Simitsi, A.M., Valente, E.M., Petrucci, S., Straniero, L., Zecchinelli, A., Pezzoli, G., Brighina, L., Ferrarese, C., Annesi, G., Quattrone, A., Gagliardi, M., Matsuo, H., Nakayama, A., Hattori, N., Nishioka, K., Chung, S.J., Kim, Y. J., Kolber, P., Warrenburg, B.P.C. van de, Bloem, B.R., Aasly, J., Toft, M., Pihlstrøm, L., Guedes, L.C., Ferreira, J.J., Bardien, S., Carr, J., Tolosa, E., Ezquerra, M., Pastor, P., Diez-Fairen, M., Wirdefeldt, K., Pedersen, N., Ran, C., Belin, A.C., Puschmann, A., Rödström, E.Y., Clarke, C.E., Morrison, K.E., Tan, M., Krainc, D., Burbulla, L.F., Farrer, M.J., Kruger, R., Gasser, T., Sharma, M., Truong, T., Elbaz, A., Sugier, P.E., Lucotte, E.A., Domenighetti, C., Law, M.H., Iles, M.M., Brown, K., Amos, C., McKay, J.D., Hung, R.J., Karimi, M., Bacq-Daian, D., Boland-Augé, A., Olaso, R., Deleuze, J.F., Lesueur, F., Ostroumova, E., Kesminiene, A., Vathaire, F. de, Guénel, P., Sreelatha, A.A.K., Schulte, C., Grover, S., May, P., Bobbili, D.R., Radivojkov-Blagojevic, M., Lichtner, P., Singleton, A.B., Hernandez, D.G., Edsall, C., Mellick, G.D., Zimprich, A., Pirker, W., Rogaeva, E., Lang, A.E., Koks, S., Taba, P., Lesage, S., Brice, A., Corvol, J.C., Chartier-Harlin, M.C., Mutez, E., Brockmann, K., Deutschländer, A.B., Hadjigeorgiou, G.M., Dardiotis, E., Stefanis, L., Simitsi, A.M., Valente, E.M., Petrucci, S., Straniero, L., Zecchinelli, A., Pezzoli, G., Brighina, L., Ferrarese, C., Annesi, G., Quattrone, A., Gagliardi, M., Matsuo, H., Nakayama, A., Hattori, N., Nishioka, K., Chung, S.J., Kim, Y. J., Kolber, P., Warrenburg, B.P.C. van de, Bloem, B.R., Aasly, J., Toft, M., Pihlstrøm, L., Guedes, L.C., Ferreira, J.J., Bardien, S., Carr, J., Tolosa, E., Ezquerra, M., Pastor, P., Diez-Fairen, M., Wirdefeldt, K., Pedersen, N., Ran, C., Belin, A.C., Puschmann, A., Rödström, E.Y., Clarke, C.E., Morrison, K.E., Tan, M., Krainc, D., Burbulla, L.F., Farrer, M.J., Kruger, R., Gasser, T., Sharma, M., Truong, T., and Elbaz, A.

Abstract

Item does not contain fulltext, BACKGROUND: Epidemiological studies that examined the association between Parkinson's disease (PD) and cancers led to inconsistent results, but they face a number of methodological difficulties. OBJECTIVE: We used results from genome-wide association studies (GWASs) to study the genetic correlation between PD and different cancers to identify common genetic risk factors. METHODS: We used individual data for participants of European ancestry from the Courage-PD (Comprehensive Unbiased Risk Factor Assessment for Genetics and Environment in Parkinson's Disease; PD, N = 16,519) and EPITHYR (differentiated thyroid cancer, N = 3527) consortia and summary statistics of GWASs from iPDGC (International Parkinson Disease Genomics Consortium; PD, N = 482,730), Melanoma Meta-Analysis Consortium (MMAC), Breast Cancer Association Consortium (breast cancer), the Prostate Cancer Association Group to Investigate Cancer Associated Alterations in the Genome (prostate cancer), International Lung Cancer Consortium (lung cancer), and Ovarian Cancer Association Consortium (ovarian cancer) (N comprised between 36,017 and 228,951 for cancer GWASs). We estimated the genetic correlation between PD and cancers using linkage disequilibrium score regression. We studied the association between PD and polymorphisms associated with cancers, and vice versa, using cross-phenotypes polygenic risk score (PRS) analyses. RESULTS: We confirmed a previously reported positive genetic correlation of PD with melanoma (G(corr) = 0.16 [0.04; 0.28]) and reported an additional significant positive correlation of PD with prostate cancer (G(corr) = 0.11 [0.03; 0.19]). There was a significant inverse association between the PRS for ovarian cancer and PD (odds ratio [OR] = 0.89 [0.84; 0.94]). Conversely, the PRS of PD was positively associated with breast cancer (OR = 1.08 [1.06; 1.10]) and inversely associated with ovarian cancer (OR = 0.95 [0.91; 0.99]). The association between PD and ovarian cancer was mostly driv

Published
2023

22. Establishing an online resource to facilitate global collaboration and inclusion of underrepresented populations: Experience from the MJFF Global Genetic Parkinson's Disease Project.

Author

Vollstedt, E.J., Madoev, H., Aasly, A., Ahmad-Annuar, A., Al-Mubarak, B., Alcalay, R.N., Alvarez, V., Amorin, I., Annesi, G., Arkadir, D., Bardien, S., Barker, R.A., Barkhuizen, M., Basak, A.N., Bonifati, V., Boon, A., Brighina, L., Brockmann, K., Carmine Belin, A., Carr, J., Clarimon, J., Cornejo-Olivas, M., Correia Guedes, L., Corvol, J.C., Crosiers, D., Damásio, J., Das, P., Carvalho Aguiar, P. de, Rosa, A. De, Dorszewska, J., Ertan, S., Ferese, R., Ferreira, J., Gatto, E., Genç, G., Giladi, N., Gómez-Garre, P., Hanagasi, H., Hattori, N., Hentati, F., Hoffman-Zacharska, D., Illarioshkin, S.N., Jankovic, J., Jesús, S., Kaasinen, V., Kievit, A., Klivenyi, P., Kostic, V., Koziorowski, D., Kühn, A.A., Lang, A.E., Lim, S.Y., Lin, Chih-Yu, Lohmann, K., Markovic, V., Martikainen, M.H., Mellick, G., Merello, M., Milanowski, L., Mir, P., Öztop-Çakmak, Ö., Pimentel, M.M.G., Pulkes, T., Puschmann, A., Rogaeva, E., Sammler, E.M., Skaalum Petersen, M., Skorvanek, M., Spitz, M., Suchowersky, O., Tan, A.H., Termsarasab, P., Thaler, Avner, Tumas, V., Valente, E.M., Warrenburg, B.P.C. van de, Williams-Gray, C.H., Wu, R.M., Zhang, B., Zimprich, A., Solle, J., Padmanabhan, S., Klein, Christine, Vollstedt, E.J., Madoev, H., Aasly, A., Ahmad-Annuar, A., Al-Mubarak, B., Alcalay, R.N., Alvarez, V., Amorin, I., Annesi, G., Arkadir, D., Bardien, S., Barker, R.A., Barkhuizen, M., Basak, A.N., Bonifati, V., Boon, A., Brighina, L., Brockmann, K., Carmine Belin, A., Carr, J., Clarimon, J., Cornejo-Olivas, M., Correia Guedes, L., Corvol, J.C., Crosiers, D., Damásio, J., Das, P., Carvalho Aguiar, P. de, Rosa, A. De, Dorszewska, J., Ertan, S., Ferese, R., Ferreira, J., Gatto, E., Genç, G., Giladi, N., Gómez-Garre, P., Hanagasi, H., Hattori, N., Hentati, F., Hoffman-Zacharska, D., Illarioshkin, S.N., Jankovic, J., Jesús, S., Kaasinen, V., Kievit, A., Klivenyi, P., Kostic, V., Koziorowski, D., Kühn, A.A., Lang, A.E., Lim, S.Y., Lin, Chih-Yu, Lohmann, K., Markovic, V., Martikainen, M.H., Mellick, G., Merello, M., Milanowski, L., Mir, P., Öztop-Çakmak, Ö., Pimentel, M.M.G., Pulkes, T., Puschmann, A., Rogaeva, E., Sammler, E.M., Skaalum Petersen, M., Skorvanek, M., Spitz, M., Suchowersky, O., Tan, A.H., Termsarasab, P., Thaler, Avner, Tumas, V., Valente, E.M., Warrenburg, B.P.C. van de, Williams-Gray, C.H., Wu, R.M., Zhang, B., Zimprich, A., Solle, J., Padmanabhan, S., and Klein, Christine

Abstract

Item does not contain fulltext, Parkinson's disease (PD) is the fastest-growing neurodegenerative disorder, currently affecting ~7 million people worldwide. PD is clinically and genetically heterogeneous, with at least 10% of all cases explained by a monogenic cause or strong genetic risk factor. However, the vast majority of our present data on monogenic PD is based on the investigation of patients of European White ancestry, leaving a large knowledge gap on monogenic PD in underrepresented populations. Gene-targeted therapies are being developed at a fast pace and have started entering clinical trials. In light of these developments, building a global network of centers working on monogenic PD, fostering collaborative research, and establishing a clinical trial-ready cohort is imperative. Based on a systematic review of the English literature on monogenic PD and a successful team science approach, we have built up a network of 59 sites worldwide and have collected information on the availability of data, biomaterials, and facilities. To enable access to this resource and to foster collaboration across centers, as well as between academia and industry, we have developed an interactive map and online tool allowing for a quick overview of available resources, along with an option to filter for specific items of interest. This initiative is currently being merged with the Global Parkinson's Genetics Program (GP2), which will attract additional centers with a focus on underrepresented sites. This growing resource and tool will facilitate collaborative research and impact the development and testing of new therapies for monogenic and potentially for idiopathic PD patients.

Published
2023

23. Embracing monogenic Parkinson's disease: the MJFF Global Genetic PD cohort

Author

Ertan, Fatoş Sibel (ORCID 0000-0003-1339-243X & YÖK ID 112829), Vollstedt, E.J.; Schaake, S.; Lohmann, K.; Padmanabhan, S.; Brice, A.; Lesage, S.; Tesson, C.; Vidailhet, M.; Wurster, I.; Hentati, F.; Mirelman, A.; Giladi, N.; Marder, K.; Waters, C.; Fahn, S.; Kasten, M.; Brüggemann, N.; Borsche, M.; Foroud, T.; Tolosa, E.; Garrido, A.; Annesi, G.; Gagliardi, M.; Bozi, M.; Stefanis, L.; Ferreira, J.J.; Guedes, L.C.; Avenali, M.; Petrucci, S.; Clark, L.; Fedotova, E.Y.; Abramycheva, N.Y.; Alvarez, V.; Menéndez-González, M.; Maestre, SJ.; Gómez-Garre, P.; Mir, P.; Belin, A.C.; Ran, C.; Lin, C.H.; Kuo, M.C.; Crosiers, D.; Wszolek, Z.K.; Ross, O.A.; Jankovic, J.; Nishioka, K.; Funayama, M.; Clarimon, J.; Williams-Gray, C.H.; Camacho, M.; Cornejo-Olivas, M.; Torres-Ramirez, L.; Wu, YR.; Lee-Chen, G.J.; Morgadinho, A.; Pulkes, T.; Termsarasab, P.; Berg, D.; Kuhlenbäumer, G.; Kühn, A.A.; Borngräber, F.; de Michele, G.; De Rosa, A.; Zimprich, A.; Puschmann, A.; Mellick, GD.; Dorszewska, J.; Carr, J.; Ferese, R.; Gambardella, S.; Chase, B.; Markopoulou, K.; Satake, W.; Toda, T.; Rossi, M.; Merello, M.; Lynch, T.; Olszewska, D.A.; Lim, S.Y.; Ahmad-Annuar, A.; Tan, A.H.; Al-Mubarak, B.; Hanagasi, H.; Koziorowski, D.; Genç, G.; Aguiar, P.D.; Barkhuizen, M.; Pimentel, M.M.G.; Saunders-Pullman, R.; van de Warrenburg, B.; Bressman, S.; Toft, M.; Appel-Cresswell, S.; Lang, A.E.; Skorvanek, M.; Boon, A.J.W.; Krüger, R.; Sammler, E.M.; Tumas, V.; Zhang, B.R.; Garraux, G.; Chung, SJ.; Kim, Y.J.; Winkelmann, J.; Sue, C.M.; Tan, E.K.; Damásio, J.; Klivényi, P.; Kostic, V.S.; Arkadir, D.; Martikainen, M.; Borges, V.; Hertz, J.M.; Brighina, L.; Spitz, M.; Suchowersky, O.; Riess, O.; Das, P.; Mollenhauer, B.; Gatto, E.M.; Petersen, M.S.; Hattori, N.; Wu, R.M.; Illarioshkin, S.N.; Valente, E.M.; Aasly, J.O.; Aasly, A.; Alcalay, R.N.; Thaler, A.; Farrer, M.J.; Brockmann, K.; Corvol, J.C.; Klein, C., School of Medicine, Ertan, Fatoş Sibel (ORCID 0000-0003-1339-243X & YÖK ID 112829), Vollstedt, E.J.; Schaake, S.; Lohmann, K.; Padmanabhan, S.; Brice, A.; Lesage, S.; Tesson, C.; Vidailhet, M.; Wurster, I.; Hentati, F.; Mirelman, A.; Giladi, N.; Marder, K.; Waters, C.; Fahn, S.; Kasten, M.; Brüggemann, N.; Borsche, M.; Foroud, T.; Tolosa, E.; Garrido, A.; Annesi, G.; Gagliardi, M.; Bozi, M.; Stefanis, L.; Ferreira, J.J.; Guedes, L.C.; Avenali, M.; Petrucci, S.; Clark, L.; Fedotova, E.Y.; Abramycheva, N.Y.; Alvarez, V.; Menéndez-González, M.; Maestre, SJ.; Gómez-Garre, P.; Mir, P.; Belin, A.C.; Ran, C.; Lin, C.H.; Kuo, M.C.; Crosiers, D.; Wszolek, Z.K.; Ross, O.A.; Jankovic, J.; Nishioka, K.; Funayama, M.; Clarimon, J.; Williams-Gray, C.H.; Camacho, M.; Cornejo-Olivas, M.; Torres-Ramirez, L.; Wu, YR.; Lee-Chen, G.J.; Morgadinho, A.; Pulkes, T.; Termsarasab, P.; Berg, D.; Kuhlenbäumer, G.; Kühn, A.A.; Borngräber, F.; de Michele, G.; De Rosa, A.; Zimprich, A.; Puschmann, A.; Mellick, GD.; Dorszewska, J.; Carr, J.; Ferese, R.; Gambardella, S.; Chase, B.; Markopoulou, K.; Satake, W.; Toda, T.; Rossi, M.; Merello, M.; Lynch, T.; Olszewska, D.A.; Lim, S.Y.; Ahmad-Annuar, A.; Tan, A.H.; Al-Mubarak, B.; Hanagasi, H.; Koziorowski, D.; Genç, G.; Aguiar, P.D.; Barkhuizen, M.; Pimentel, M.M.G.; Saunders-Pullman, R.; van de Warrenburg, B.; Bressman, S.; Toft, M.; Appel-Cresswell, S.; Lang, A.E.; Skorvanek, M.; Boon, A.J.W.; Krüger, R.; Sammler, E.M.; Tumas, V.; Zhang, B.R.; Garraux, G.; Chung, SJ.; Kim, Y.J.; Winkelmann, J.; Sue, C.M.; Tan, E.K.; Damásio, J.; Klivényi, P.; Kostic, V.S.; Arkadir, D.; Martikainen, M.; Borges, V.; Hertz, J.M.; Brighina, L.; Spitz, M.; Suchowersky, O.; Riess, O.; Das, P.; Mollenhauer, B.; Gatto, E.M.; Petersen, M.S.; Hattori, N.; Wu, R.M.; Illarioshkin, S.N.; Valente, E.M.; Aasly, J.O.; Aasly, A.; Alcalay, R.N.; Thaler, A.; Farrer, M.J.; Brockmann, K.; Corvol, J.C.; Klein, C., and School of Medicine

Abstract

Background: as gene-targeted therapies are increasingly being developed for Parkinson's disease (PD), identifying and characterizing carriers of specific genetic pathogenic variants is imperative. Only a small fraction of the estimated number of subjects with monogenic PD worldwide are currently represented in the literature and availability of clinical data and clinical trial-ready cohorts is limited. Objective: the objectives are to (1) establish an international cohort of affected and unaffected individuals with PD-linked variants; (2) provide harmonized and quality-controlled clinical characterization data for each included individual; and (3) further promote collaboration of researchers in the field of monogenic PD. Methods: we conducted a worldwide, systematic online survey to collect individual-level data on individuals with PD-linked variants in SNCA, LRRK2, VPS35, PRKN, PINK1, DJ-1, as well as selected pathogenic and risk variants in GBA and corresponding demographic, clinical, and genetic data. All registered cases underwent thorough quality checks, and pathogenicity scoring of the variants and genotype–phenotype relationships were analyzed. Results: we collected 3888 variant carriers for our analyses, reported by 92 centers (42 countries) worldwide. Of the included individuals, 3185 had a diagnosis of PD (ie, 1306 LRRK2, 115 SNCA, 23 VPS35, 429 PRKN, 75 PINK1, 13 DJ-1, and 1224 GBA) and 703 were unaffected (ie, 328 LRRK2, 32 SNCA, 3 VPS35, 1 PRKN, 1 PINK1, and 338 GBA). In total, we identified 269 different pathogenic variants; 1322 individuals in our cohort (34%) were indicated as not previously published. Conclusions: within the MJFF Global Genetic PD Study Group, we (1) established the largest international cohort of affected and unaffected individuals carrying PD-linked variants; (2) provide harmonized and quality-controlled clinical and genetic data for each included individual; (3) promote collaboration in the field of genetic PD with a view toward, Open Access funding enabled and organized by Projekt DEAL. Funding text 1: Carolyn M. Sue: Intellectual Property Rights: WO 2015/157794 A1. Advisory Boards: AbbVie. Employment: Northern Sydney Local Health District, Sydney, Australia. Honoraria: The International Movement Disorder Society for course directorships and invited lectures. Patents: WO 2015/157794 A1. Grants: 2018–22 NHMRC Partnership grant (APP1151906); 2018–22 MRFF NHMRC Practitioner Fellowship (App1136800); 2020–2025 NHMRC Partnership grant (APP11179029); 2020–2023 NHMRC Ideas Grant (APP1184403); 2021–5 MRFF 2020 Genomics Health Futures Mission Grant (APP2007959); 2021–23 ASAP Project grant ; Funding text 2: Natalya Y. Abramycheva: Employment: Research Center of Neurology, Ministry of Science and Higher Education of the Russian Federation, Moscow, Russia. Grants: Russian Science Foundation ; Funding text 3: Rachel Saunders?Pullman: Employment: Icahn School of Medicine at Mount Sinai, New York City, New York, USA. Grants: NIH 1U01NS107016?01A1; Bigglesworth Family Foundation. Others: Bachmann?Strauss Chair ; Funding text 4: Zbigniew K. Wszolek: Advisory Boards: Vigil Neuroscience, Inc. Employment: Mayo Clinic, Jacksonville, Florida, USA. Grants: NIH/NIA and NIH/NINDS (1U19AG063911, FAIN: U19AG063911), Mayo Clinic Center for Regenerative Medicine, PI or co?PI on Biohaven Pharmaceuticals, Inc. (BHV4157?206 and BHV3241?301), Neuraly, Inc. (NLY01?PD?1), and Vigil Neuroscience, Inc. (VGL101?01.001 and VGL101?01.002). He also serves as the co?PI of the Mayo Clinic APDA Center for Advanced Research. Others: Donations from the Donald G. and Jodi P. Heeringa Family, the Haworth Family Professorship in Neurodegenerative Diseases fund, and The Albertson Parkinson's Research Foundation ; Funding text 5: Vladimir S. Kostic: Employment: School of Medicine, University of Belgrade, Serbia. Grants: Project No 175090 Ministry of Education, Science and Technological Development of Serbia. Project ??28 Serbian Academy of S

Published
2023

24. 45O Clonal evolution of dedifferentiated liposarcoma

Author

Sekita, T., primary, Asano, N., additional, Kubo, T., additional, Mitani, S., additional, Hattori, N., additional, Yoshida, A., additional, Kobayashi, E., additional, Komiyama, M., additional, Toshikazu, U., additional, Nakayama, R., additional, Kawai, A., additional, Nakamura, M., additional, and Ichikawa, H., additional

Published
2023
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25. Characterization of sputum biomarkers for asthma–COPD overlap syndrome

Author

Gao J, Iwamoto H, Koskela J, Alenius H, Hattori N, Kohno N, Laitinen T, Mazur W, and Pulkkinen V

Subjects
COPD pathology, asthma, ACOS., Diseases of the respiratory system, RC705-779
Abstract

Jing Gao,1 Hiroshi Iwamoto,2 Jukka Koskela,3 Harri Alenius,4 Noboru Hattori,2 Nobuoki Kohno,5 Tarja Laitinen,6 Witold Mazur,1 Ville Pulkkinen1 1Heart and Lung Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; 2Department of Molecular and Internal Medicine, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan; 3Clinical Research Unit of Pulmonary Diseases and Division of Pulmonology, Heart and Lung Center, University of Helsinki and Helsinki University Hospital, 4Unit of Systems Toxicology, Finnish Institute of Occupational Health, Helsinki, Finland; 5Hiroshima Cosmopolitan University, Hiroshima, Japan; 6Department of Pulmonary Diseases and Clinical Allergology, Turku University Hospital, University of Turku, Turku, Finland Abstract: Asthma–COPD overlap syndrome (ACOS) is a commonly encountered chronic airway disease. However, ACOS is still a consensus-based clinical phenotype and the underlying inflammatory mechanisms are inadequately characterized. To clarify the inflammatory mediatypical for ACOS, five biomarkers, namely interleukin (IL)-13, myeloperoxidase (MPO), neutrophil gelatinase-associated lipocalin (NGAL), chitinase-like protein (YKL-40), and IL-6, were selected. This study hypothesized that sputum biomarkers relevant for airway inflammation in asthma (IL-13), COPD (MPO, NGAL), or in both asthma and COPD (YKL-40, IL-6) could be used to differentiate ACOS from COPD and asthma. The aim of this study was to characterize the inflammatory profile and improve the recognition of ACOS. Induced sputum levels of IL-13, MPO, NGAL, YKL-40, and IL-6 were measured by enzyme-linked immunosorbent assay/Luminex assay in a Finnish discovery cohort (n=90) of nonsmokers, smokers, and patients with asthma, COPD, and ACOS and validated in a Japanese cohort (n=135). The classification accuracy of potential biomarkers was compared with area under the receiver operating characteristic curves. Only sputum NGAL levels could differentiate ACOS from asthma (P

Published
2016

28. Airway inflammation in Japanese COPD patients compared with smoking and nonsmoking controls

Author

Ishikawa N, Hattori N, Kohno N, Kobayashi A, Hayamizu T, and Johnson M

Subjects
Diseases of the respiratory system, RC705-779
Abstract

Nobuhisa Ishikawa,1 Noboru Hattori,2 Nobuoki Kohno,2 Akihiro Kobayashi,3 Tomoyuki Hayamizu,4 Malcolm Johnson5 1Department of Respiratory Medicine, Hiroshima Prefectural Hospital, Hiroshima, Japan; 2Department of Molecular and Internal Medicine, Hiroshima University, Hiroshima, Japan; 3Biomedical Data Science Department, 4Medical Affairs Respiratory Department, GlaxoSmithKline Shibuya-ku, Tokyo, Japan; 5Respiratory Global Franchise, GlaxoSmithKline, Uxbridge, UK Purpose: To assess the importance of inflammation in chronic obstructive pulmonary disease (COPD) by measuring airway and systemic inflammatory biomarkers in Japanese patients with the disease and relevant control groups.Patients and methods: This was the first study of its type in Japanese COPD patients. It was a non-treatment study in which 100 participants were enrolled into one of three groups: nonsmoking controls, current or ex-smoking controls, and COPD patients. All participants underwent standard lung function assessments and provided sputum and blood samples from which the numbers of inflammatory cells and concentrations of biomarkers were measured, using standard procedures.Results: The overall trends observed in levels of inflammatory cells and biomarkers in sputum and blood in COPD were consistent with previous reports in Western studies. Increasing levels of neutrophils, interleukin 8 (IL-8), surfactant protein D (SP-D), and Krebs von den Lungen 6 (KL-6) in sputum and clara cell 16 (CC-16), high-sensitivity C-reactive protein (hs-CRP), and KL-6 in serum and plasma fibrinogen were seen in the Japanese COPD patients compared with the non-COPD control participants. In sputum, significant correlations were seen between total cell count and matrix metalloproteinase 9 (MMP-9; P

Published
2015

29. EP08.01-064 Serum NY-ESO-1 and XAGE1 Antibodies Predict and Monitor Clinical Responses to Immune Checkpoint Therapy for NSCLC

Author

Oka, M., primary, Kurose, K., additional, Sakaeda, K., additional, Fukuda, M., additional, Sakai, Y., additional, Atarashi, Y., additional, Shimizu, K., additional, Masuda, T., additional, Nakatomi, K., additional, Kawase, S., additional, Suetsugu, T., additional, Mizuno, K., additional, Takemoto, S., additional, Yamaguchi, H., additional, Inoue, H., additional, Hattori, N., additional, Nakata, M., additional, Mukae, H., additional, and Oga, T., additional

Published
2022
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36. Mendelian Randomisation Study of Smoking, Alcohol, and Coffee Drinking in Relation to Parkinson's Disease

Author

Domenighetti, C., Sugier, P.E., Sreelatha, A.A.K., Schulte, C., Grover, S., Mohamed, O., Portugal, B., May, P., Bobbili, D.R., Radivojkov-Blagojevic, M., Lichtner, P., Singleton, A.B., Hernandez, D.G., Edsall, C., Mellick, G.D., Zimprich, A., Pirker, W., Rogaeva, E., Lang, A.E., Koks, S., Taba, P., Lesage, S., Brice, A., Corvol, J.C., Chartier-Harlin, M.C., Mutez, E., Brockmann, K., Deutschländer, A.B., Hadjigeorgiou, G.M., Dardiotis, E., Stefanis, L., Simitsi, A.M., Valente, E.M., Petrucci, S., Duga, S., Straniero, L., Zecchinelli, A., Pezzoli, G., Brighina, L., Ferrarese, C., Annesi, G., Quattrone, A., Gagliardi, M., Matsuo, H., Kawamura, Y., Hattori, N., Nishioka, K., Chung, S.J., Kim, Y. J., Kolber, P., Warrenburg, B.P.C. van de, Bloem, B.R., Aasly, J., Toft, M., Pihlstrøm, L., Guedes, L.C., Ferreira, J.J., Bardien, S., Carr, J., Tolosa, E., Ezquerra, M., Pastor, P., Diez-Fairen, M., Wirdefeldt, K., Pedersen, N.L., Ran, C., Belin, A.C., Puschmann, A., Hellberg, C., Clarke, C.E., Morrison, K.E., Tan, M., Krainc, D., Burbulla, L.F., Farrer, M.J., Krüger, R., Gasser, T., Sharma, M., Elbaz, A., Domenighetti, C., Sugier, P.E., Sreelatha, A.A.K., Schulte, C., Grover, S., Mohamed, O., Portugal, B., May, P., Bobbili, D.R., Radivojkov-Blagojevic, M., Lichtner, P., Singleton, A.B., Hernandez, D.G., Edsall, C., Mellick, G.D., Zimprich, A., Pirker, W., Rogaeva, E., Lang, A.E., Koks, S., Taba, P., Lesage, S., Brice, A., Corvol, J.C., Chartier-Harlin, M.C., Mutez, E., Brockmann, K., Deutschländer, A.B., Hadjigeorgiou, G.M., Dardiotis, E., Stefanis, L., Simitsi, A.M., Valente, E.M., Petrucci, S., Duga, S., Straniero, L., Zecchinelli, A., Pezzoli, G., Brighina, L., Ferrarese, C., Annesi, G., Quattrone, A., Gagliardi, M., Matsuo, H., Kawamura, Y., Hattori, N., Nishioka, K., Chung, S.J., Kim, Y. J., Kolber, P., Warrenburg, B.P.C. van de, Bloem, B.R., Aasly, J., Toft, M., Pihlstrøm, L., Guedes, L.C., Ferreira, J.J., Bardien, S., Carr, J., Tolosa, E., Ezquerra, M., Pastor, P., Diez-Fairen, M., Wirdefeldt, K., Pedersen, N.L., Ran, C., Belin, A.C., Puschmann, A., Hellberg, C., Clarke, C.E., Morrison, K.E., Tan, M., Krainc, D., Burbulla, L.F., Farrer, M.J., Krüger, R., Gasser, T., Sharma, M., and Elbaz, A.

Abstract

Item does not contain fulltext, BACKGROUND: Previous studies showed that lifestyle behaviors (cigarette smoking, alcohol, coffee) are inversely associated with Parkinson's disease (PD). The prodromal phase of PD raises the possibility that these associations may be explained by reverse causation. OBJECTIVE: To examine associations of lifestyle behaviors with PD using two-sample Mendelian randomisation (MR) and the potential for survival and incidence-prevalence biases. METHODS: We used summary statistics from publicly available studies to estimate the association of genetic polymorphisms with lifestyle behaviors, and from Courage-PD (7,369 cases, 7,018 controls; European ancestry) to estimate the association of these variants with PD. We used the inverse-variance weighted method to compute odds ratios (ORIVW) of PD and 95%confidence intervals (CI). Significance was determined using a Bonferroni-corrected significance threshold (p = 0.017). RESULTS: We found a significant inverse association between smoking initiation and PD (ORIVW per 1-SD increase in the prevalence of ever smoking = 0.74, 95%CI = 0.60-0.93, p = 0.009) without significant directional pleiotropy. Associations in participants ≤67 years old and cases with disease duration ≤7 years were of a similar size. No significant associations were observed for alcohol and coffee drinking. In reverse MR, genetic liability toward PD was not associated with smoking or coffee drinking but was positively associated with alcohol drinking. CONCLUSION: Our findings are in favor of an inverse association between smoking and PD that is not explained by reverse causation, confounding, and survival or incidence-prevalence biases. Genetic liability toward PD was positively associated with alcohol drinking. Conclusions on the association of alcohol and coffee drinking with PD are hampered by insufficient statistical power.

Published
2022

37. Dairy Intake and Parkinson's Disease: A Mendelian Randomization Study

Author

Domenighetti, C., Sugier, P‐E, Ashok Kumar Sreelatha, A., Schulte, C., Grover, S., Mohamed, O., Portugal, B., May, P., Bobbili, D.R., Radivojkov‐Blagojevic, M., Lichtner, P., Singleton, A.B., Hernandez, D.G., Edsall, C., Mellick, G.D., Zimprich, A., Pirker, W., Rogaeva, E., Lang, A.E., Kõks, S., Taba, P., Lesage, S., Brice, A., Corvol, J‐C, Chartier‐Harlin, M‐C, Mutez, E., Brockmann, K., Deutschländer, A.B., Hadjigeorgiou, G.M., Dardiotis, E., Stefanis, L., Simitsi, A.M., Valente, E.M., Petrucci, S., Duga, S., Straniero, L., Zecchinelli, A., Pezzoli, G., Brighina, L., Ferrarese, C., Annesi, G., Quattrone, A., Gagliardi, M., Matsuo, H., Kawamura, Y., Hattori, N., Nishioka, K., Chung, S.J., Kim, Y.J., Kolber, P., Warrenburg, B.P.C., Bloem, B.R., Aasly, J., Toft, M., Pihlstrøm, L., Correia Guedes, L., Ferreira, J.J., Bardien, S., Carr, J., Tolosa, E., Ezquerra, M., Pastor, P., Diez‐Fairen, M., Wirdefeldt, K., Pedersen, N.L., Ran, C., Belin, A.C., Puschmann, A., Hellberg, C., Clarke, C.E., Morrison, K.E., Tan, M., Krainc, D., Burbulla, L.F., Farrer, M.J., Krüger, R., Gasser, T., Sharma, M., Elbaz, A., Domenighetti, C., Sugier, P‐E, Ashok Kumar Sreelatha, A., Schulte, C., Grover, S., Mohamed, O., Portugal, B., May, P., Bobbili, D.R., Radivojkov‐Blagojevic, M., Lichtner, P., Singleton, A.B., Hernandez, D.G., Edsall, C., Mellick, G.D., Zimprich, A., Pirker, W., Rogaeva, E., Lang, A.E., Kõks, S., Taba, P., Lesage, S., Brice, A., Corvol, J‐C, Chartier‐Harlin, M‐C, Mutez, E., Brockmann, K., Deutschländer, A.B., Hadjigeorgiou, G.M., Dardiotis, E., Stefanis, L., Simitsi, A.M., Valente, E.M., Petrucci, S., Duga, S., Straniero, L., Zecchinelli, A., Pezzoli, G., Brighina, L., Ferrarese, C., Annesi, G., Quattrone, A., Gagliardi, M., Matsuo, H., Kawamura, Y., Hattori, N., Nishioka, K., Chung, S.J., Kim, Y.J., Kolber, P., Warrenburg, B.P.C., Bloem, B.R., Aasly, J., Toft, M., Pihlstrøm, L., Correia Guedes, L., Ferreira, J.J., Bardien, S., Carr, J., Tolosa, E., Ezquerra, M., Pastor, P., Diez‐Fairen, M., Wirdefeldt, K., Pedersen, N.L., Ran, C., Belin, A.C., Puschmann, A., Hellberg, C., Clarke, C.E., Morrison, K.E., Tan, M., Krainc, D., Burbulla, L.F., Farrer, M.J., Krüger, R., Gasser, T., Sharma, M., and Elbaz, A.

Abstract

Background Previous prospective studies highlighted dairy intake as a risk factor for Parkinson's disease (PD), particularly in men. It is unclear whether this association is causal or explained by reverse causation or confounding. Objective The aim is to examine the association between genetically predicted dairy intake and PD using two-sample Mendelian randomization (MR). Methods We genotyped a well-established instrumental variable for dairy intake located in the lactase gene (rs4988235) within the Courage-PD consortium (23 studies; 9823 patients and 8376 controls of European ancestry). Results Based on a dominant model, there was an association between genetic predisposition toward higher dairy intake and PD (odds ratio [OR] per one serving per day = 1.70, 95% confidence interval = 1.12–2.60, P = 0.013) that was restricted to men (OR = 2.50 [1.37–4.56], P = 0.003; P-difference with women = 0.029). Conclusions Using MR, our findings provide further support for a causal relationship between dairy intake and higher PD risk, not biased by confounding or reverse causation. Further studies are needed to elucidate the underlying mechanisms. © 2022 International Parkinson and Movement Disorder Society

Published
2022

40. Mendelian Randomisation Study of Smoking, Alcohol, and Coffee Drinking in Relation to Parkinson's Disease

Author

Domenighetti, C. Sugier, P.-E. Sreelatha, A.A.K. Schulte, C. Grover, S. Mohamed, O. Portugal, B. May, P. Bobbili, D.R. Radivojkov-Blagojevic, M. Lichtner, P. Singleton, A.B. Hernandez, D.G. Edsall, C. Mellick, G.D. Zimprich, A. Pirker, W. Rogaeva, E. Lang, A.E. Koks, S. Taba, P. Lesage, S. Brice, A. Corvol, J.-C. Chartier-Harlin, M.-C. Mutez, E. Brockmann, K. Deutschländer, A.B. Hadjigeorgiou, G.M. Dardiotis, E. Stefanis, L. Simitsi, A.M. Valente, E.M. Petrucci, S. Duga, S. Straniero, L. Zecchinelli, A. Pezzoli, G. Brighina, L. Ferrarese, C. Annesi, G. Quattrone, A. Gagliardi, M. Matsuo, H. Kawamura, Y. Hattori, N. Nishioka, K. Chung, S.J. Kim, Y.J. Kolber, P. Van De Warrenburg, B.P.C. Bloem, B.R. Aasly, J. Toft, M. Pihlstrøm, L. Guedes, L.C. Ferreira, J.J. Bardien, S. Carr, J. Tolosa, E. Ezquerra, M. Pastor, P. Diez-Fairen, M. Wirdefeldt, K. Pedersen, N.L. Ran, C. Belin, A.C. Puschmann, A. Hellberg, C. Clarke, C.E. Morrison, K.E. Tan, M. Krainc, D. Burbulla, L.F. Farrer, M.J. Krüger, R. Gasser, T. Sharma, M. Elbaz, A.

Abstract

Background: Previous studies showed that lifestyle behaviors (cigarette smoking, alcohol, coffee) are inversely associated with Parkinson's disease (PD). The prodromal phase of PD raises the possibility that these associations may be explained by reverse causation. Objective: To examine associations of lifestyle behaviors with PD using two-sample Mendelian randomisation (MR) and the potential for survival and incidence-prevalence biases. Methods: We used summary statistics from publicly available studies to estimate the association of genetic polymorphisms with lifestyle behaviors, and from Courage-PD (7,369 cases, 7,018 controls; European ancestry) to estimate the association of these variants with PD. We used the inverse-variance weighted method to compute odds ratios (ORIVW) of PD and 95%confidence intervals (CI). Significance was determined using a Bonferroni-corrected significance threshold (p = 0.017). Results: We found a significant inverse association between smoking initiation and PD (ORIVW per 1-SD increase in the prevalence of ever smoking = 0.74, 95%CI = 0.60-0.93, p = 0.009) without significant directional pleiotropy. Associations in participants =67 years old and cases with disease duration =7 years were of a similar size. No significant associations were observed for alcohol and coffee drinking. In reverse MR, genetic liability toward PD was not associated with smoking or coffee drinking but was positively associated with alcohol drinking. Conclusion: Our findings are in favor of an inverse association between smoking and PD that is not explained by reverse causation, confounding, and survival or incidence-prevalence biases. Genetic liability toward PD was positively associated with alcohol drinking. Conclusions on the association of alcohol and coffee drinking with PD are hampered by insufficient statistical power. © 2022 - IOS Press. All rights reserved.

Published
2022

41. Patient perspectives on Parkinson’s disease therapy in Japan and the United States: results of two patient surveys

Author

Hattori N, Fujimoto K, Kondo T, Murata M, and Stacy M

Subjects
Medicine (General), R5-920
Abstract

Nobutaka Hattori,1 Kenichi Fujimoto,2 Tomoyoshi Kondo,3 Miho Murata,4 Mark Stacy51Department of Neurology, Juntendo University School of Medicine, Tokyo; 2Department of Neurology, Jichi Medical University, Tochigi; 3Department of Neurology, Wakayama Medical University, Wakayama; 4Department of Neurology, National Center Hospital of Neurology and Psychiatry, Tokyo, Japan; 5Division of Neurology, Duke University, Durham, NC, USABackground: Despite evidence suggesting that patient attitudes towards therapy may influence treatment outcomes, the impact of these factors on treatment for Parkinson’s disease is poorly understood. These two surveys, based in Japan and the US, investigated the attitudes of patients towards antiparkinsonian medications, the complications of these therapies, and how these differ across geographies.Methods: The US PRELUDE survey collected data from May 13 to May 20, 2003, from 300 interviews with patients with Parkinson’s disease from the National Parkinson Foundation. The Japanese survey was carried out from June to December 2008 in a stepwise manner using questionnaires (n = 3548) followed by interviews with those who had consented to participate in the questionnaire (n = 407). Both surveys assessed the attitudes of patients towards therapies for Parkinson’s disease and associated complications.Results: Dyskinesia was not a major challenge of therapy for Parkinson’s disease, and wearing-off caused greater concern in the US, while hallucinations had a greater emphasis in Japan. Patients who had previously experienced dyskinesia were less concerned about this side effect than those who had not. Although pill burden was thought to be a concern in the US, Japanese patients did not indicate that pill burden would limit their drug intake. There were also discrepancies between the perspectives and concerns of patients and those of their treating physicians.Conclusion: Recognizing patient perspectives regarding therapies for Parkinson’s disease and associated complications, as well as certain cultural influences, is important in the management of parkinsonian symptoms. Acknowledging these concerns may improve the standard of care in patients with Parkinson’s disease. In addition, improved patient education and effective patient–physician communication in both countries may improve compliance and treatment outcomes in patients with the disease.Keywords: Parkinson’s disease, patient concerns, dyskinesia, wearing-off, hallucinations

Published
2012

42. Characterization of sputum biomarkers for asthma–COPD overlap syndrome [Erratum]

Author

Gao J, Iwamoto H, Koskela J, Alenius H, Hattori N, Kohno N, Laitinen T, Mazur W, and Pulkkinen V

Subjects
Diseases of the respiratory system, RC705-779
Abstract

Gao J, Iwamoto H, Koskela J, et al. International Journal of Chronic Obstructive Pulmonary Disease. 2016;11: 2457–2465. On page 2457, Abstract, line 3, the text “To clarify the inflammatory mediatypical for ACOS, five biomarkers, namely interleukin (IL)-13, myeloperoxidase (MPO), neutrophil gelatinase-associated lipocalin (NGAL), chitinase-like protein (YKL-40), and IL-6, were selected” should be “To clarify the inflammatory mediators typical for ACOS, five biomarkers, namely interleukin (IL)-13, myeloperoxidase (MPO), neutrophil gelatinase-associated lipocalin (NGAL), chitinase-like protein (YKL-40), and IL-6, were selected.” Read the original article

Published
2017

48. Using global team science to identify genetic parkinson's disease worldwide

Author

Vollstedt, E, Kasten, M, Klein, C, Aasly, J, Adler, C, Ahmad-Annuar, A, Albanese, A, Alcalay, R, Al-Mubarak, B, Alvarez, V, Andree-Munoz, B, Annesi, G, Appel-Cresswell, S, Arkadir, D, Armasu, S, Barber, T, Bardien, S, Barkhuizen, M, Barrett, M, Basak, A, Beach, T, Benitez, B, Berg, D, Bhatia, K, Binkofski, F, Blauwendraat, C, Bonifati, V, Borges, V, Bozi, M, Brice, A, Brighina, L, Brockmann, K, Brucke, T, Bruggemann, N, Camacho, M, Cardoso, F, Belin, A, Carr, J, Chan, P, Chang-Castello, J, Chase, B, Chen-Plotkin, A, Ju Chung, S, Cilia, R, Clarimon, J, Clark, L, Cornejo-Olivas, M, Corvol, J, Cosentino, C, Cras, P, Crosiers, D, Damasio, J, Das, P, de Carvalho Aguiar, P, De Michele, G, De Rosa, A, Dieguez, E, Dorszewska, J, Erer, S, Ertan, S, Farrer, M, Fedotova, E, Ferese, R, Ferrarese, C, Ferraz, H, Fiala, O, Foroud, T, Friedman, A, Frigerio, R, Funayama, M, Gambardella, S, Garraux, G, Gatto, E, Genc, G, Giladi, N, Goldwurm, S, Gomez-Esteban, J, Gomez-Garre, P, Gorostidi, A, Grosset, D, Hanagasi, H, Hardy, J, Hassan, A, Hattori, N, Hauser, R, Hedera, P, Hentati, F, Hertz, J, Holton, J, Houlden, H, Hutz, M, Ikeuchi, T, Illarioshkin, S, Inca-Martinez, M, Infante, J, Jankovic, J, Jeon, B, Jesus, S, Jimenez-Del-Rio, M, Kaasinen, V, Kataoka, H, Kawakami, H, Kim, Y, Klivenyi, P, Koks, S, Konig, I, Kostic, V, Koziorowski, D, Kruger, R, Krygowska-Wajs, A, Kulisevsky, J, Lai, D, Lang, A, Ledoux, M, Lesage, S, Lim, S, Lin, C, Lohmann, K, Lopera, F, Lopez, G, Lu, C, Lynch, T, Machaczka, M, Madoev, H, Magalhaes, M, Majamaa, K, Maraganore, D, Marder, K, Markopoulou, K, Martikainen, M, Mata, I, Mazzetti, P, Mellick, G, Menendez-Gonzalez, M, Micheli, F, Mirelman, A, Mir, P, Morino, H, Morris, H, Munhoz, R, Naito, A, Olszewska, D, Ozelius, L, Padmanabhan, S, Paisan-Ruiz, C, Payami, H, Peluso, S, Petkovic, S, Petrucci, S, Pezzoli, G, Pimentel, M, Pirker, W, Pramstaller, P, Pulkes, T, Puschmann, A, Quattrone, A, Raggio, V, Ransmayr, G, Rieder, C, Riess, O, Rodriguez-Porcel, F, Rogaeva, E, Ross, O, Ruiz-Martinez, J, Sammler, E, San Luciano, M, Satake, W, Saunders-Pullman, R, Sazci, A, Scherzer, C, Schrag, A, Schumacher-Schuh, A, Sharma, M, Sidransky, E, Singleton, A, Petersen, M, Smolders, S, Spitz, M, Stefanis, L, Struhal, W, Sue, C, Swan, M, Swanberg, M, Taba, P, Taipa, R, Tan, M, Tan, A, Tan, E, Tang, B, Tayebi, N, Thaler, A, Thomas, A, Toda, T, Toft, M, Torres, L, Tumas, V, Valente, E, Van Broeckhoven, C, Vecsei, L, Velez-Pardo, C, Vidailhet, M, Warner, T, Williams-Gray, C, Winkelmann, J, Woitalla, D, Wood, N, Wszolek, Z, Wu, R, Wu, Y, Xie, T, Yoshino, H, Zhang, B, Zimprich, A, Vollstedt E. -J., Kasten M., Klein C., Aasly J., Adler C., Ahmad-Annuar A., Albanese A., Alcalay R. N., Al-Mubarak B., Alvarez V., Andree-Munoz B., Annesi G., Appel-Cresswell S., Arkadir D., Armasu S., Barber T. R., Bardien S., Barkhuizen M., Barrett M. J., Basak A. N., Beach T., Benitez B. A., Berg D., Bhatia K., Binkofski F., Blauwendraat C., Bonifati V., Borges V., Bozi M., Brice A., Brighina L., Brockmann K., Brucke T., Bruggemann N., Camacho M., Cardoso F., Belin A. C., Carr J., Chan P., Chang-Castello J., Chase B., Chen-Plotkin A., Ju Chung S., Cilia R., Clarimon J., Clark L., Cornejo-Olivas M., Corvol J. -C., Cosentino C., Cras P., Crosiers D., Damasio J., Das P., de Carvalho Aguiar P., De Michele G., De Rosa A., Dieguez E., Dorszewska J., Erer S., Ertan S., Farrer M., Fedotova E., Ferese R., Ferrarese C., Ferraz H., Fiala O., Foroud T., Friedman A., Frigerio R., Funayama M., Gambardella S., Garraux G., Gatto E. M., Genc G., Giladi N., Goldwurm S., Gomez-Esteban J. C., Gomez-Garre P., Gorostidi A., Grosset D., Hanagasi H., Hardy J., Hassan A., Hattori N., Hauser R. A., Hedera P., Hentati F., Hertz J. M., Holton J. L., Houlden H., Hutz M. H., Ikeuchi T., Illarioshkin S., Inca-Martinez M., Infante J., Jankovic J., Jeon B. S., Jesus S., Jimenez-Del-Rio M., Kaasinen V., Kataoka H., Kawakami H., Kim Y. J., Klivenyi P., Koks S., Konig I. R., Kostic V., Koziorowski D., Kruger R., Krygowska-Wajs A., Kulisevsky J., Lai D., Lang A., LeDoux M., Lesage S., Lim S. -Y., Lin C. -H., Lohmann K., Lopera F., Lopez G., Lu C. -S., Lynch T., Machaczka M., Madoev H., Magalhaes M., Majamaa K., Maraganore D., Marder K., Markopoulou K., Martikainen M. H., Mata I., Mazzetti P., Mellick G., Menendez-Gonzalez M., Micheli F., Mirelman A., Mir P., Morino H., Morris H., Munhoz R. P., Naito A., Olszewska D. A., Ozelius L. J., Padmanabhan S., Paisan-Ruiz C., Payami H., Peluso S., Petkovic S., Petrucci S., Pezzoli G., Pimentel M., Pirker W., Pramstaller P. P., Pulkes T., Puschmann A., Quattrone A., Raggio V., Ransmayr G., Rieder C., Riess O., Rodriguez-Porcel F., Rogaeva E., Ross O. A., Ruiz-Martinez J., Sammler E., San Luciano M., Satake W., Saunders-Pullman R., Sazci A., Scherzer C., Schrag A., Schumacher-Schuh A., Sharma M., Sidransky E., Singleton A. B., Petersen M. S., Smolders S., Spitz M., Stefanis L., Struhal W., Sue C. M., Swan M., Swanberg M., Taba P., Taipa R., Tan M., Tan A. H., Tan E. -K., Tang B., Tayebi N., Thaler A., Thomas A., Toda T., Toft M., Torres L., Tumas V., Valente E. M., Van Broeckhoven C., Vecsei L., Velez-Pardo C., Vidailhet M., Warner T. T., Williams-Gray C. H., Winkelmann J., Woitalla D., Wood N. W., Wszolek Z. K., Wu R. -M., Wu Y. -R., Xie T., Yoshino H., Zhang B., Zimprich A., Vollstedt, E, Kasten, M, Klein, C, Aasly, J, Adler, C, Ahmad-Annuar, A, Albanese, A, Alcalay, R, Al-Mubarak, B, Alvarez, V, Andree-Munoz, B, Annesi, G, Appel-Cresswell, S, Arkadir, D, Armasu, S, Barber, T, Bardien, S, Barkhuizen, M, Barrett, M, Basak, A, Beach, T, Benitez, B, Berg, D, Bhatia, K, Binkofski, F, Blauwendraat, C, Bonifati, V, Borges, V, Bozi, M, Brice, A, Brighina, L, Brockmann, K, Brucke, T, Bruggemann, N, Camacho, M, Cardoso, F, Belin, A, Carr, J, Chan, P, Chang-Castello, J, Chase, B, Chen-Plotkin, A, Ju Chung, S, Cilia, R, Clarimon, J, Clark, L, Cornejo-Olivas, M, Corvol, J, Cosentino, C, Cras, P, Crosiers, D, Damasio, J, Das, P, de Carvalho Aguiar, P, De Michele, G, De Rosa, A, Dieguez, E, Dorszewska, J, Erer, S, Ertan, S, Farrer, M, Fedotova, E, Ferese, R, Ferrarese, C, Ferraz, H, Fiala, O, Foroud, T, Friedman, A, Frigerio, R, Funayama, M, Gambardella, S, Garraux, G, Gatto, E, Genc, G, Giladi, N, Goldwurm, S, Gomez-Esteban, J, Gomez-Garre, P, Gorostidi, A, Grosset, D, Hanagasi, H, Hardy, J, Hassan, A, Hattori, N, Hauser, R, Hedera, P, Hentati, F, Hertz, J, Holton, J, Houlden, H, Hutz, M, Ikeuchi, T, Illarioshkin, S, Inca-Martinez, M, Infante, J, Jankovic, J, Jeon, B, Jesus, S, Jimenez-Del-Rio, M, Kaasinen, V, Kataoka, H, Kawakami, H, Kim, Y, Klivenyi, P, Koks, S, Konig, I, Kostic, V, Koziorowski, D, Kruger, R, Krygowska-Wajs, A, Kulisevsky, J, Lai, D, Lang, A, Ledoux, M, Lesage, S, Lim, S, Lin, C, Lohmann, K, Lopera, F, Lopez, G, Lu, C, Lynch, T, Machaczka, M, Madoev, H, Magalhaes, M, Majamaa, K, Maraganore, D, Marder, K, Markopoulou, K, Martikainen, M, Mata, I, Mazzetti, P, Mellick, G, Menendez-Gonzalez, M, Micheli, F, Mirelman, A, Mir, P, Morino, H, Morris, H, Munhoz, R, Naito, A, Olszewska, D, Ozelius, L, Padmanabhan, S, Paisan-Ruiz, C, Payami, H, Peluso, S, Petkovic, S, Petrucci, S, Pezzoli, G, Pimentel, M, Pirker, W, Pramstaller, P, Pulkes, T, Puschmann, A, Quattrone, A, Raggio, V, Ransmayr, G, Rieder, C, Riess, O, Rodriguez-Porcel, F, Rogaeva, E, Ross, O, Ruiz-Martinez, J, Sammler, E, San Luciano, M, Satake, W, Saunders-Pullman, R, Sazci, A, Scherzer, C, Schrag, A, Schumacher-Schuh, A, Sharma, M, Sidransky, E, Singleton, A, Petersen, M, Smolders, S, Spitz, M, Stefanis, L, Struhal, W, Sue, C, Swan, M, Swanberg, M, Taba, P, Taipa, R, Tan, M, Tan, A, Tan, E, Tang, B, Tayebi, N, Thaler, A, Thomas, A, Toda, T, Toft, M, Torres, L, Tumas, V, Valente, E, Van Broeckhoven, C, Vecsei, L, Velez-Pardo, C, Vidailhet, M, Warner, T, Williams-Gray, C, Winkelmann, J, Woitalla, D, Wood, N, Wszolek, Z, Wu, R, Wu, Y, Xie, T, Yoshino, H, Zhang, B, Zimprich, A, Vollstedt E. -J., Kasten M., Klein C., Aasly J., Adler C., Ahmad-Annuar A., Albanese A., Alcalay R. N., Al-Mubarak B., Alvarez V., Andree-Munoz B., Annesi G., Appel-Cresswell S., Arkadir D., Armasu S., Barber T. R., Bardien S., Barkhuizen M., Barrett M. J., Basak A. N., Beach T., Benitez B. A., Berg D., Bhatia K., Binkofski F., Blauwendraat C., Bonifati V., Borges V., Bozi M., Brice A., Brighina L., Brockmann K., Brucke T., Bruggemann N., Camacho M., Cardoso F., Belin A. C., Carr J., Chan P., Chang-Castello J., Chase B., Chen-Plotkin A., Ju Chung S., Cilia R., Clarimon J., Clark L., Cornejo-Olivas M., Corvol J. -C., Cosentino C., Cras P., Crosiers D., Damasio J., Das P., de Carvalho Aguiar P., De Michele G., De Rosa A., Dieguez E., Dorszewska J., Erer S., Ertan S., Farrer M., Fedotova E., Ferese R., Ferrarese C., Ferraz H., Fiala O., Foroud T., Friedman A., Frigerio R., Funayama M., Gambardella S., Garraux G., Gatto E. M., Genc G., Giladi N., Goldwurm S., Gomez-Esteban J. C., Gomez-Garre P., Gorostidi A., Grosset D., Hanagasi H., Hardy J., Hassan A., Hattori N., Hauser R. A., Hedera P., Hentati F., Hertz J. M., Holton J. L., Houlden H., Hutz M. H., Ikeuchi T., Illarioshkin S., Inca-Martinez M., Infante J., Jankovic J., Jeon B. S., Jesus S., Jimenez-Del-Rio M., Kaasinen V., Kataoka H., Kawakami H., Kim Y. J., Klivenyi P., Koks S., Konig I. R., Kostic V., Koziorowski D., Kruger R., Krygowska-Wajs A., Kulisevsky J., Lai D., Lang A., LeDoux M., Lesage S., Lim S. -Y., Lin C. -H., Lohmann K., Lopera F., Lopez G., Lu C. -S., Lynch T., Machaczka M., Madoev H., Magalhaes M., Majamaa K., Maraganore D., Marder K., Markopoulou K., Martikainen M. H., Mata I., Mazzetti P., Mellick G., Menendez-Gonzalez M., Micheli F., Mirelman A., Mir P., Morino H., Morris H., Munhoz R. P., Naito A., Olszewska D. A., Ozelius L. J., Padmanabhan S., Paisan-Ruiz C., Payami H., Peluso S., Petkovic S., Petrucci S., Pezzoli G., Pimentel M., Pirker W., Pramstaller P. P., Pulkes T., Puschmann A., Quattrone A., Raggio V., Ransmayr G., Rieder C., Riess O., Rodriguez-Porcel F., Rogaeva E., Ross O. A., Ruiz-Martinez J., Sammler E., San Luciano M., Satake W., Saunders-Pullman R., Sazci A., Scherzer C., Schrag A., Schumacher-Schuh A., Sharma M., Sidransky E., Singleton A. B., Petersen M. S., Smolders S., Spitz M., Stefanis L., Struhal W., Sue C. M., Swan M., Swanberg M., Taba P., Taipa R., Tan M., Tan A. H., Tan E. -K., Tang B., Tayebi N., Thaler A., Thomas A., Toda T., Toft M., Torres L., Tumas V., Valente E. M., Van Broeckhoven C., Vecsei L., Velez-Pardo C., Vidailhet M., Warner T. T., Williams-Gray C. H., Winkelmann J., Woitalla D., Wood N. W., Wszolek Z. K., Wu R. -M., Wu Y. -R., Xie T., Yoshino H., Zhang B., and Zimprich A.

Published
2019

49. Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Author

Grapotte M., Saraswat M., Bessiere C., Menichelli C., Ramilowski J. A., Severin J., Hayashizaki Y., Itoh M., Tagami M., Murata M., Kojima-Ishiyama M., Noma S., Noguchi S., Kasukawa T., Hasegawa A., Suzuki H., Nishiyori-Sueki H., Frith M. C., Abugessaisa I., Aitken S., Aken B. L., Alam I., Alam T., Alasiri R., Alhendi A. M. N., Alinejad-Rokny H., Alvarez M. J., Andersson R., Arakawa T., Araki M., Arbel T., Archer J., Archibald A. L., Arner E., Arner P., Asai K., Ashoor H., Astrom G., Babina M., Baillie J. K., Bajic V. B., Bajpai A., Baker S., Baldarelli R. M., Balic A., Bansal M., Batagov A. O., Batzoglou S., Beckhouse A. G., Beltrami A. P., Beltrami C. A., Bertin N., Bhattacharya S., Bickel P. J., Blake J. A., Blanchette M., Bodega B., Bonetti A., Bono H., Bornholdt J., Bttcher M., Bougouffa S., Boyd M., Breda J., Brombacher F., Brown J. B., Bult C. J., Burroughs A. M., Burt D. W., Busch A., Caglio G., Califano A., Cameron C. J., Cannistraci C. V., Carbone A., Carlisle A. J., Carninci P., Carter K. W., Cesselli D., Chang J. -C., Chen J. C., Chen Y., Chierici M., Christodoulou J., Ciani Y., Clark E. L., Coskun M., Dalby M., Dalla E., Daub C. O., Davis C. A., de Hoon M. J. L., de Rie D., Denisenko E., Deplancke B., Detmar M., Deviatiiarov R., Di Bernardo D., Diehl A. D., Dieterich L. C., Dimont E., Djebali S., Dohi T., Dostie J., Drablos F., Edge A. S. B., Edinger M., Ehrlund A., Ekwall K., Elofsson A., Endoh M., Enomoto H., Enomoto S., Faghihi M., Fagiolini M., Farach-Carson M. C., Faulkner G. J., Favorov A., Fernandes A. M., Ferrai C., Forrest A. R. R., Forrester L. M., Forsberg M., Fort A., Francescatto M., Freeman T. C., Frith M., Fukuda S., Funayama M., Furlanello C., Furuno M., Furusawa C., Gao H., Gazova I., Gebhard C., Geier F., Geijtenbeek T. B. H., Ghosh S., Ghosheh Y., Gingeras T. R., Gojobori T., Goldberg T., Goldowitz D., Gough J., Greco D., Gruber A. J., Guhl S., Guigo R., Guler R., Gusev O., Gustincich S., Ha T. J., Haberle V., Hale P., Hallstrom B. M., Hamada M., Handoko L., Hara M., Harbers M., Harrow J., Harshbarger J., Hase T., Hashimoto K., Hatano T., Hattori N., Hayashi R., Herlyn M., Hettne K., Heutink P., Hide W., Hitchens K. J., Sui S. H., 't Hoen P. A. C., Hon C. C., Hori F., Horie M., Horimoto K., Horton P., Hou R., Huang E., Huang Y., Hugues R., Hume D., Ienasescu H., Iida K., Ikawa T., Ikemura T., Ikeo K., Inoue N., Ishizu Y., Ito Y., Ivshina A. V., Jankovic B. R., Jenjaroenpun P., Johnson R., Jorgensen M., Jorjani H., Joshi A., Jurman G., Kaczkowski B., Kai C., Kaida K., Kajiyama K., Kaliyaperumal R., Kaminuma E., Kanaya T., Kaneda H., Kapranov P., Kasianov A. S., Katayama T., Kato S., Kawaguchi S., Kawai J., Kawaji H., Kawamoto H., Kawamura Y. I., Kawasaki S., Kawashima T., Kempfle J. S., Kenna T. J., Kere J., Khachigian L., Kiryu H., Kishima M., Kitajima H., Kitamura T., Kitano H., Klaric E., Klepper K., Klinken S. P., Kloppmann E., Knox A. J., Kodama Y., Kogo Y., Kojima M., Kojima S., Komatsu N., Komiyama H., Kono T., Koseki H., Koyasu S., Kratz A., Kukalev A., Kulakovskiy I., Kundaje A., Kunikata H., Kuo R., Kuo T., Kuraku S., Kuznetsov V. A., Kwon T. J., Larouche M., Lassmann T., Law A., Le-Cao K. -A., Lecellier C. -H., Lee W., Lenhard B., Lennartsson A., Li K., Li R., Lilje B., Lipovich L., Lizio M., Lopez G., Magi S., Mak G. K., Makeev V., Manabe R., Mandai M., Mar J., Maruyama K., Maruyama T., Mason E., Mathelier A., Matsuda H., Medvedeva Y. A., Meehan T. F., Mejhert N., Meynert A., Mikami N., Minoda A., Miura H., Miyagi Y., Miyawaki A., Mizuno Y., Morikawa H., Morimoto M., Morioka M., Morishita S., Moro K., Motakis E., Motohashi H., Mukarram A. K., Mummery C. L., Mungall C. J., Murakawa Y., Muramatsu M., Nagasaka K., Nagase T., Nakachi Y., Nakahara F., Nakai K., Nakamura K., Nakamura Y., Nakazawa T., Nason G. P., Nepal C., Nguyen Q. H., Nielsen L. K., Nishida K., Nishiguchi K. M., Nishiyori H., Nitta K., Notredame C., Ogishima S., Ohkura N., Ohno H., Ohshima M., Ohtsu T., Okada Y., Okada-Hatakeyama M., Okazaki Y., Oksvold P., Orlando V., Ow G. S., Ozturk M., Pachkov M., Paparountas T., Parihar S. P., Park S. -J., Pascarella G., Passier R., Persson H., Philippens I. H., Piazza S., Plessy C., Pombo A., Ponten F., Poulain S., Poulsen T. M., Pradhan S., Prezioso C., Pridans C., Qin X. -Y., Quackenbush J., Rackham O., Ramilowski J., Ravasi T., Rehli M., Rennie S., Rito T., Rizzu P., Robert C., Roos M., Rost B., Roudnicky F., Roy R., Rye M. B., Sachenkova O., Saetrom P., Sai H., Saiki S., Saito M., Saito A., Sakaguchi S., Sakai M., Sakaue S., Sakaue-Sawano A., Sandelin A., Sano H., Sasamoto Y., Sato H., Saxena A., Saya H., Schafferhans A., Schmeier S., Schmidl C., Schmocker D., Schneider C., Schueler M., Schultes E. A., Schulze-Tanzil G., Semple C. A., Seno S., Seo W., Sese J., Sheng G., Shi J., Shimoni Y., Shin J. W., SimonSanchez J., Sivertsson A., Sjostedt E., Soderhall C., Laurent G. S., Stoiber M. H., Sugiyama D., Summers K. M., Suzuki A. M., Suzuki K., Suzuki M., Suzuki N., Suzuki T., Swanson D. J., Swoboda R. K., Taguchi A., Takahashi H., Takahashi M., Takamochi K., Takeda S., Takenaka Y., Tam K. T., Tanaka H., Tanaka R., Tanaka Y., Tang D., Taniuchi I., Tanzer A., Tarui H., Taylor M. S., Terada A., Terao Y., Testa A. C., Thomas M., Thongjuea S., Tomii K., Triglia E. T., Toyoda H., Tsang H. G., Tsujikawa M., Uhlen M., Valen E., van de Wetering M., van Nimwegen E., Velmeshev D., Verardo R., Vitezic M., Vitting-Seerup K., von Feilitzen K., Voolstra C. R., Vorontsov I. E., Wahlestedt C., Wasserman W. W., Watanabe K., Watanabe S., Wells C. A., Winteringham L. N., Wolvetang E., Yabukami H., Yagi K., Yamada T., Yamaguchi Y., Yamamoto M., Yamamoto Y., Yamanaka Y., Yano K., Yasuzawa K., Yatsuka Y., Yo M., Yokokura S., Yoneda M., Yoshida E., Yoshida Y., Yoshihara M., Young R., Young R. S., Yu N. Y., Yumoto N., Zabierowski S. E., Zhang P. G., Zucchelli S., Zwahlen M., Chatelain C., Brehelin L., Grapotte, M., Saraswat, M., Bessiere, C., Menichelli, C., Ramilowski, J. A., Severin, J., Hayashizaki, Y., Itoh, M., Tagami, M., Murata, M., Kojima-Ishiyama, M., Noma, S., Noguchi, S., Kasukawa, T., Hasegawa, A., Suzuki, H., Nishiyori-Sueki, H., Frith, M. C., Abugessaisa, I., Aitken, S., Aken, B. L., Alam, I., Alam, T., Alasiri, R., Alhendi, A. M. N., Alinejad-Rokny, H., Alvarez, M. J., Andersson, R., Arakawa, T., Araki, M., Arbel, T., Archer, J., Archibald, A. L., Arner, E., Arner, P., Asai, K., Ashoor, H., Astrom, G., Babina, M., Baillie, J. K., Bajic, V. B., Bajpai, A., Baker, S., Baldarelli, R. M., Balic, A., Bansal, M., Batagov, A. O., Batzoglou, S., Beckhouse, A. G., Beltrami, A. P., Beltrami, C. A., Bertin, N., Bhattacharya, S., Bickel, P. J., Blake, J. A., Blanchette, M., Bodega, B., Bonetti, A., Bono, H., Bornholdt, J., Bttcher, M., Bougouffa, S., Boyd, M., Breda, J., Brombacher, F., Brown, J. B., Bult, C. J., Burroughs, A. M., Burt, D. W., Busch, A., Caglio, G., Califano, A., Cameron, C. J., Cannistraci, C. V., Carbone, A., Carlisle, A. J., Carninci, P., Carter, K. W., Cesselli, D., Chang, J. -C., Chen, J. C., Chen, Y., Chierici, M., Christodoulou, J., Ciani, Y., Clark, E. L., Coskun, M., Dalby, M., Dalla, E., Daub, C. O., Davis, C. A., de Hoon, M. J. L., de Rie, D., Denisenko, E., Deplancke, B., Detmar, M., Deviatiiarov, R., Di Bernardo, D., Diehl, A. D., Dieterich, L. C., Dimont, E., Djebali, S., Dohi, T., Dostie, J., Drablos, F., Edge, A. S. B., Edinger, M., Ehrlund, A., Ekwall, K., Elofsson, A., Endoh, M., Enomoto, H., Enomoto, S., Faghihi, M., Fagiolini, M., Farach-Carson, M. C., Faulkner, G. J., Favorov, A., Fernandes, A. M., Ferrai, C., Forrest, A. R. R., Forrester, L. M., Forsberg, M., Fort, A., Francescatto, M., Freeman, T. C., Frith, M., Fukuda, S., Funayama, M., Furlanello, C., Furuno, M., Furusawa, C., Gao, H., Gazova, I., Gebhard, C., Geier, F., Geijtenbeek, T. B. H., Ghosh, S., Ghosheh, Y., Gingeras, T. R., Gojobori, T., Goldberg, T., Goldowitz, D., Gough, J., Greco, D., Gruber, A. J., Guhl, S., Guigo, R., Guler, R., Gusev, O., Gustincich, S., Ha, T. J., Haberle, V., Hale, P., Hallstrom, B. M., Hamada, M., Handoko, L., Hara, M., Harbers, M., Harrow, J., Harshbarger, J., Hase, T., Hashimoto, K., Hatano, T., Hattori, N., Hayashi, R., Herlyn, M., Hettne, K., Heutink, P., Hide, W., Hitchens, K. J., Sui, S. H., 't Hoen, P. A. C., Hon, C. C., Hori, F., Horie, M., Horimoto, K., Horton, P., Hou, R., Huang, E., Huang, Y., Hugues, R., Hume, D., Ienasescu, H., Iida, K., Ikawa, T., Ikemura, T., Ikeo, K., Inoue, N., Ishizu, Y., Ito, Y., Ivshina, A. V., Jankovic, B. R., Jenjaroenpun, P., Johnson, R., Jorgensen, M., Jorjani, H., Joshi, A., Jurman, G., Kaczkowski, B., Kai, C., Kaida, K., Kajiyama, K., Kaliyaperumal, R., Kaminuma, E., Kanaya, T., Kaneda, H., Kapranov, P., Kasianov, A. S., Katayama, T., Kato, S., Kawaguchi, S., Kawai, J., Kawaji, H., Kawamoto, H., Kawamura, Y. I., Kawasaki, S., Kawashima, T., Kempfle, J. S., Kenna, T. J., Kere, J., Khachigian, L., Kiryu, H., Kishima, M., Kitajima, H., Kitamura, T., Kitano, H., Klaric, E., Klepper, K., Klinken, S. P., Kloppmann, E., Knox, A. J., Kodama, Y., Kogo, Y., Kojima, M., Kojima, S., Komatsu, N., Komiyama, H., Kono, T., Koseki, H., Koyasu, S., Kratz, A., Kukalev, A., Kulakovskiy, I., Kundaje, A., Kunikata, H., Kuo, R., Kuo, T., Kuraku, S., Kuznetsov, V. A., Kwon, T. J., Larouche, M., Lassmann, T., Law, A., Le-Cao, K. -A., Lecellier, C. -H., Lee, W., Lenhard, B., Lennartsson, A., Li, K., Li, R., Lilje, B., Lipovich, L., Lizio, M., Lopez, G., Magi, S., Mak, G. K., Makeev, V., Manabe, R., Mandai, M., Mar, J., Maruyama, K., Maruyama, T., Mason, E., Mathelier, A., Matsuda, H., Medvedeva, Y. A., Meehan, T. F., Mejhert, N., Meynert, A., Mikami, N., Minoda, A., Miura, H., Miyagi, Y., Miyawaki, A., Mizuno, Y., Morikawa, H., Morimoto, M., Morioka, M., Morishita, S., Moro, K., Motakis, E., Motohashi, H., Mukarram, A. K., Mummery, C. L., Mungall, C. J., Murakawa, Y., Muramatsu, M., Nagasaka, K., Nagase, T., Nakachi, Y., Nakahara, F., Nakai, K., Nakamura, K., Nakamura, Y., Nakazawa, T., Nason, G. P., Nepal, C., Nguyen, Q. H., Nielsen, L. K., Nishida, K., Nishiguchi, K. M., Nishiyori, H., Nitta, K., Notredame, C., Ogishima, S., Ohkura, N., Ohno, H., Ohshima, M., Ohtsu, T., Okada, Y., Okada-Hatakeyama, M., Okazaki, Y., Oksvold, P., Orlando, V., Ow, G. S., Ozturk, M., Pachkov, M., Paparountas, T., Parihar, S. P., Park, S. -J., Pascarella, G., Passier, R., Persson, H., Philippens, I. H., Piazza, S., Plessy, C., Pombo, A., Ponten, F., Poulain, S., Poulsen, T. M., Pradhan, S., Prezioso, C., Pridans, C., Qin, X. -Y., Quackenbush, J., Rackham, O., Ramilowski, J., Ravasi, T., Rehli, M., Rennie, S., Rito, T., Rizzu, P., Robert, C., Roos, M., Rost, B., Roudnicky, F., Roy, R., Rye, M. B., Sachenkova, O., Saetrom, P., Sai, H., Saiki, S., Saito, M., Saito, A., Sakaguchi, S., Sakai, M., Sakaue, S., Sakaue-Sawano, A., Sandelin, A., Sano, H., Sasamoto, Y., Sato, H., Saxena, A., Saya, H., Schafferhans, A., Schmeier, S., Schmidl, C., Schmocker, D., Schneider, C., Schueler, M., Schultes, E. A., Schulze-Tanzil, G., Semple, C. A., Seno, S., Seo, W., Sese, J., Sheng, G., Shi, J., Shimoni, Y., Shin, J. W., Simonsanchez, J., Sivertsson, A., Sjostedt, E., Soderhall, C., Laurent, G. S., Stoiber, M. H., Sugiyama, D., Summers, K. M., Suzuki, A. M., Suzuki, K., Suzuki, M., Suzuki, N., Suzuki, T., Swanson, D. J., Swoboda, R. K., Taguchi, A., Takahashi, H., Takahashi, M., Takamochi, K., Takeda, S., Takenaka, Y., Tam, K. T., Tanaka, H., Tanaka, R., Tanaka, Y., Tang, D., Taniuchi, I., Tanzer, A., Tarui, H., Taylor, M. S., Terada, A., Terao, Y., Testa, A. C., Thomas, M., Thongjuea, S., Tomii, K., Triglia, E. T., Toyoda, H., Tsang, H. G., Tsujikawa, M., Uhlen, M., Valen, E., van de Wetering, M., van Nimwegen, E., Velmeshev, D., Verardo, R., Vitezic, M., Vitting-Seerup, K., von Feilitzen, K., Voolstra, C. R., Vorontsov, I. E., Wahlestedt, C., Wasserman, W. W., Watanabe, K., Watanabe, S., Wells, C. A., Winteringham, L. N., Wolvetang, E., Yabukami, H., Yagi, K., Yamada, T., Yamaguchi, Y., Yamamoto, M., Yamamoto, Y., Yamanaka, Y., Yano, K., Yasuzawa, K., Yatsuka, Y., Yo, M., Yokokura, S., Yoneda, M., Yoshida, E., Yoshida, Y., Yoshihara, M., Young, R., Young, R. S., Yu, N. Y., Yumoto, N., Zabierowski, S. E., Zhang, P. G., Zucchelli, S., Zwahlen, M., Chatelain, C., Brehelin, L., Institute of Biotechnology, Biosciences, Institut de Génétique Moléculaire de Montpellier (IGMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Computationnelle (IBC), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), RIKEN Center for Integrative Medical Sciences [Yokohama] (RIKEN IMS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), National Institute of Advanced Industrial Science and Technology (AIST), SANOFI Recherche, University of British Columbia (UBC), Experimental Immunology, Infectious diseases, AII - Infectious diseases, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)

Subjects
0301 basic medicine, General Physics and Astronomy, Genome, Mice, 0302 clinical medicine, Transcription (biology), Promoter Regions, Genetic, Transcription Initiation, Genetic, 0303 health sciences, Multidisciplinary, 1184 Genetics, developmental biology, physiology, High-Throughput Nucleotide Sequencing, Neurodegenerative Diseases, 222 Other engineering and technologies, Genomics, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], humanities, Enhancer Elements, Genetic, Microsatellite Repeat, Transcription Initiation Site, Sequence motif, Transcription Initiation, Human, Enhancer Elements, Neural Networks, Science, 610 Medicine & health, Computational biology, Biology, Article, General Biochemistry, Genetics and Molecular Biology, Promoter Regions, 03 medical and health sciences, Computer, Deep Learning, Tandem repeat, Genetic, Clinical Research, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Machine learning, Genetics, Animals, Humans, Polymorphism, Enhancer, Transcriptomics, Gene, A549 Cell, 030304 developmental biology, Polymorphism, Genetic, Neurodegenerative Disease, Base Sequence, Animal, Genome, Human, Human Genome, Computational Biology, Promoter, General Chemistry, 113 Computer and information sciences, Cap analysis gene expression, 030104 developmental biology, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Cardiovascular and Metabolic Diseases, A549 Cells, Minion, Generic health relevance, 3111 Biomedicine, Neural Networks, Computer, 610 Medizin und Gesundheit, 030217 neurology & neurosurgery, FANTOM consortium, Microsatellite Repeats
Abstract

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism., Nature Communications, 12 (1), ISSN:2041-1723

Published
2020
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