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Song W, Shi Y, Lin GN. Haplotype function score improves biological interpretation and cross-ancestry polygenic prediction of human complex traits. eLife 2024; 12:RP92574. [PMID: 38639992 PMCID: PMC11031082 DOI: 10.7554/elife.92574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
We propose a new framework for human genetic association studies: at each locus, a deep learning model (in this study, Sei) is used to calculate the functional genomic activity score for two haplotypes per individual. This score, defined as the Haplotype Function Score (HFS), replaces the original genotype in association studies. Applying the HFS framework to 14 complex traits in the UK Biobank, we identified 3619 independent HFS-trait associations with a significance of p < 5 × 10-8. Fine-mapping revealed 2699 causal associations, corresponding to a median increase of 63 causal findings per trait compared with single-nucleotide polymorphism (SNP)-based analysis. HFS-based enrichment analysis uncovered 727 pathway-trait associations and 153 tissue-trait associations with strong biological interpretability, including 'circadian pathway-chronotype' and 'arachidonic acid-intelligence'. Lastly, we applied least absolute shrinkage and selection operator (LASSO) regression to integrate HFS prediction score with SNP-based polygenic risk scores, which showed an improvement of 16.1-39.8% in cross-ancestry polygenic prediction. We concluded that HFS is a promising strategy for understanding the genetic basis of human complex traits.
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Affiliation(s)
- Weichen Song
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Bioengineering, Shanghai Jiao Tong UniversityShanghaiChina
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong UniversityShanghaiChina
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong UniversityShanghaiChina
- Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X12 Institutes), Qingdao UniversityQingdaoChina
| | - Guan Ning Lin
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Bioengineering, Shanghai Jiao Tong UniversityShanghaiChina
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Crespiatico I, Zaghi M, Mastini C, D'Aliberti D, Mauri M, Mercado CM, Fontana D, Spinelli S, Crippa V, Inzoli E, Manghisi B, Civettini I, Ramazzotti D, Sangiorgio V, Gengotti M, Brambilla V, Aroldi A, Banfi F, Barone C, Orsenigo R, Riera L, Riminucci M, Corsi A, Breccia M, Morotti A, Cilloni D, Roccaro A, Sacco A, Stagno F, Serafini M, Mottadelli F, Cazzaniga G, Pagni F, Chiarle R, Azzoni E, Sessa A, Gambacorti-Passerini C, Elli EM, Mologni L, Piazza R. First-hit SETBP1 mutations cause a myeloproliferative disorder with bone marrow fibrosis. Blood 2024; 143:1399-1413. [PMID: 38194688 DOI: 10.1182/blood.2023021349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/11/2024] Open
Abstract
ABSTRACT SETBP1 mutations are found in various clonal myeloid disorders. However, it is unclear whether they can initiate leukemia, because SETBP1 mutations typically appear as later events during oncogenesis. To answer this question, we generated a mouse model expressing mutated SETBP1 in hematopoietic tissue: this model showed profound alterations in the differentiation program of hematopoietic progenitors and developed a myeloid neoplasm with megakaryocytic dysplasia, splenomegaly, and bone marrow fibrosis, prompting us to investigate SETBP1 mutations in a cohort of 36 triple-negative primary myelofibrosis (TN-PMF) cases. We identified 2 distinct subgroups, one carrying SETBP1 mutations and the other completely devoid of somatic variants. Clinically, a striking difference in disease aggressiveness was noted, with patients with SETBP1 mutation showing a much worse clinical course. In contrast to myelodysplastic/myeloproliferative neoplasms, in which SETBP1 mutations are mostly found as a late clonal event, single-cell clonal hierarchy reconstruction in 3 patients with TN-PMF from our cohort revealed SETBP1 to be a very early event, suggesting that the phenotype of the different SETBP1+ disorders may be shaped by the opposite hierarchy of the same clonal SETBP1 variants.
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Affiliation(s)
- Ilaria Crespiatico
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Mattia Zaghi
- Neuroepigenetics Unit, Division of Neuroscience, Istituto di Ricovero e Cura a Carattere Scientifico San Raffaele Scientific Institute, Milan, Italy
| | - Cristina Mastini
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Deborah D'Aliberti
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Mario Mauri
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Carl Mirko Mercado
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Diletta Fontana
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Silvia Spinelli
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Valentina Crippa
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Elena Inzoli
- Hematology Division and Bone Marrow Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico San Gerardo dei Tintori, Monza, Italy
| | - Beatrice Manghisi
- Hematology Division and Bone Marrow Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico San Gerardo dei Tintori, Monza, Italy
| | - Ivan Civettini
- Hematology Division and Bone Marrow Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico San Gerardo dei Tintori, Monza, Italy
| | - Daniele Ramazzotti
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Valentina Sangiorgio
- Hematology Division and Bone Marrow Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico San Gerardo dei Tintori, Monza, Italy
| | - Michele Gengotti
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | | | - Andrea Aroldi
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
- Hematology Division and Bone Marrow Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico San Gerardo dei Tintori, Monza, Italy
| | - Federica Banfi
- Neuroepigenetics Unit, Division of Neuroscience, Istituto di Ricovero e Cura a Carattere Scientifico San Raffaele Scientific Institute, Milan, Italy
| | - Cristiana Barone
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Roberto Orsenigo
- Biomedical Research in Melanoma-Animal Models and Cancer Laboratory, Vall d'Hebron Research Institute, Vall d'Hebron Hospital Barcelona UAB, Barcelona, Spain
| | - Ludovica Riera
- Department of Pathology, Azienda Ospedaliero Universitaria Città della Salute e della Scienza, Turin, Italy
| | - Mara Riminucci
- Department of Molecular Medicine, Azienda Policlinico Umberto I, Sapienza University of Rome, Rome, Italy
| | - Alessandro Corsi
- Department of Molecular Medicine, Azienda Policlinico Umberto I, Sapienza University of Rome, Rome, Italy
| | - Massimo Breccia
- Department of Translational and Precision Medicine, Azienda Policlinico Umberto I, Sapienza University of Rome, Rome, Italy
| | - Alessandro Morotti
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, Turin, Italy
| | - Daniela Cilloni
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, Turin, Italy
| | - Aldo Roccaro
- Clinical Trial Center, Translational Research and Phase I Unit, Azienda Socio Sanitaria Territoriale Spedali Civili di Brescia, Brescia, Italy
| | - Antonio Sacco
- Clinical Trial Center, Translational Research and Phase I Unit, Azienda Socio Sanitaria Territoriale Spedali Civili di Brescia, Brescia, Italy
| | - Fabio Stagno
- Division of Hematology, Azienda Ospedaliero Universitaria Policlinico G. Rodolico-S. Marco, Catania, Italy
| | - Marta Serafini
- Centro Tettamanti, Istituto di Ricovero e Cura a Carattere Scientifico San Gerardo dei Tintori, Monza, Italy
| | - Federica Mottadelli
- Centro Tettamanti, Istituto di Ricovero e Cura a Carattere Scientifico San Gerardo dei Tintori, Monza, Italy
| | - Giovanni Cazzaniga
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
- Centro Tettamanti, Istituto di Ricovero e Cura a Carattere Scientifico San Gerardo dei Tintori, Monza, Italy
| | - Fabio Pagni
- Department of Pathology, University of Milan-Bicocca, Monza, Italy
| | - Roberto Chiarle
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Italy
- Department of Pathology, Children's Hospital and Harvard Medical School, Boston, MA
- European Institute of Oncology Istituto di Ricovero e Cura a Carattere Scientifico, Division of Haematopathology, Milan, Italy
| | - Emanuele Azzoni
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Alessandro Sessa
- Neuroepigenetics Unit, Division of Neuroscience, Istituto di Ricovero e Cura a Carattere Scientifico San Raffaele Scientific Institute, Milan, Italy
| | - Carlo Gambacorti-Passerini
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
- Hematology Division and Bone Marrow Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico San Gerardo dei Tintori, Monza, Italy
| | - Elena Maria Elli
- Hematology Division and Bone Marrow Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico San Gerardo dei Tintori, Monza, Italy
| | - Luca Mologni
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Rocco Piazza
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
- Hematology Division and Bone Marrow Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico San Gerardo dei Tintori, Monza, Italy
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Yang S, Tang X, Wang L, Ni C, Wu Y, Zhou L, Zeng Y, Zhao C, Wu A, Wang Q, Xu X, Wang Y, Chen R, Zhang X, Zou L, Huang X, Wu J. Targeting TLR2/Rac1/cdc42/JNK Pathway to Reveal That Ruxolitinib Promotes Thrombocytopoiesis. Int J Mol Sci 2022; 23:ijms232416137. [PMID: 36555781 PMCID: PMC9787584 DOI: 10.3390/ijms232416137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Thrombocytopenia has long been considered an important complication of chemotherapy and radiotherapy, which severely limits the effectiveness of cancer treatment and the overall survival of patients. However, clinical treatment options are extremely limited so far. Ruxolitinib is a potential candidate. METHODS The impact of ruxolitinib on the differentiation and maturation of K562 and Meg-01 cells megakaryocytes (MKs) was examined by flow cytometry, Giemsa and Phalloidin staining. A mouse model of radiation-injured thrombocytopenia (RIT) was employed to evaluate the action of ruxolitinib on thrombocytopoiesis. Network pharmacology, molecular docking, drug affinity responsive target stability assay (DARTS), RNA sequencing, protein blotting and immunofluorescence analysis were applied to explore the targets and mechanisms of action of ruxolitinib. RESULTS Ruxolitinib can stimulate MK differentiation and maturation in a dose-dependent manner and accelerates recovery of MKs and thrombocytopoiesis in RIT mice. Biological targeting analysis showed that ruxolitinib binds directly to Toll Like Receptor 2 (TLR2) to activate Rac1/cdc42/JNK, and this action was shown to be blocked by C29, a specific inhibitor of TLR2. CONCLUSIONS Ruxolitinib was first identified to facilitate MK differentiation and thrombocytopoiesis, which may alleviate RIT. The potential mechanism of ruxolitinib was to promote MK differentiation via activating the Rac1/cdc42/JNK pathway through binding to TLR2.
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Affiliation(s)
- Shuo Yang
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Xiaoqin Tang
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Long Wang
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Chengyang Ni
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Yuesong Wu
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Ling Zhou
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Yueying Zeng
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Chunling Zhao
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Anguo Wu
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Qiaozhi Wang
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Xiyan Xu
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Yiwei Wang
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Rong Chen
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Xiao Zhang
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Lile Zou
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Xinwu Huang
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
- Correspondence: (X.H.); (J.W.); Tel.: +86-13808285526 (X.H.); +86-13982416641 (J.W.)
| | - Jianming Wu
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
- Education Ministry Key Laboratory of Medical Electrophysiology, Southwest Medical University, Luzhou 646000, China
- Correspondence: (X.H.); (J.W.); Tel.: +86-13808285526 (X.H.); +86-13982416641 (J.W.)
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5
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Yang J, Zhao S, Ma D. Biological Characteristics and Regulation of Early Megakaryocytopoiesis. Stem Cell Rev Rep 2020; 15:652-663. [PMID: 31230184 DOI: 10.1007/s12015-019-09905-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
For decades, megakaryocytopoiesis is believed to occur following a classical binary hierarchical developmental model. This model is based on an analysis of predefined flow-sorted cell populations by using cell surface markers. However, this classical model has been challenged by increasing evidences obtained with new techniques which integrating flow cytometric, transcriptomic and functional data at single-cell level and with lineage tracing technique. These recent advances in megakaryocytopoiesis proposed that commitment of haematopoietic stem cells (HSCs) towards megakaryocytic lineage occurs in much earlier stage than that postulated in the classical model. There may exist multipotent but megakaryocyte (MK)/platelet-biased HSCs within HSC compartment and even HSCs can directly differentiate into MKs in steady state or in response to stress. In this review, we focus on recent findings about differentiation from commitment of HSCs to MK and its regulation, and discuss future directions in this research field.
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Affiliation(s)
- Jingang Yang
- Department of Experimental Medicine, General Hospital of Northern Theatre Command, 83 Wenhua Road, Shenhe District, Shenyang, Liaoning, People's Republic of China
| | - Song Zhao
- Department of Experimental Medicine, General Hospital of Northern Theatre Command, 83 Wenhua Road, Shenhe District, Shenyang, Liaoning, People's Republic of China
| | - Dongchu Ma
- Department of Experimental Medicine, General Hospital of Northern Theatre Command, 83 Wenhua Road, Shenhe District, Shenyang, Liaoning, People's Republic of China.
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Ding J, Li F, Cong Y, Miao J, Wu D, Liu B, Wang L. Trichostatin A inhibits skeletal muscle atrophy induced by cigarette smoke exposure in mice. Life Sci 2019; 235:116800. [PMID: 31472151 DOI: 10.1016/j.lfs.2019.116800] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/21/2019] [Accepted: 08/27/2019] [Indexed: 12/20/2022]
Abstract
AIMS It is well known that cigarette smoke (CS) is the main risk factor for chronic obstructive pulmonary disease (COPD) accompanied by skeletal muscle atrophy. Histone deacetylases (HDACs) that remove acetyl groups from target proteins are necessary for the muscle atrophy associated with skeletal muscle disuse. However, the role of HDACs and trichostatin A (TSA), a HDAC inhibitor, in skeletal muscle atrophy caused by CS exposure remains poorly understood. MAIN METHODS Female mice were exposed to CS twice daily for 40 days and TSA injected intraperitoneally into CS-exposed mice on alternate days. Skeletal muscles were weighed and gastrocnemius (Gas) muscle histomorphology examined by hematoxylin and eosin staining. Histone deacetylases 1 and 2 (HDAC1/2), and markers of ubiquitin degradation, muscle differentiation, apoptosis, pyroptosis, and the cytoskeletal proteins were assessed by western blot and immunohistochemistry in Gas. KEYFINDINGS CS exposure decreased body and skeletal muscle weights and triggered an increase in the percentage of fiber with centralized nuclei in Gas. HDAC1/2 proteins were upregulated in the Gas of mice exposed to CS, while TSA effectively inhibited HDAC1/2 protein levels and attenuated the loss of body weight and skeletal muscle wet weight induced by CS exposure. Markers for ubiquitin degradation, muscle differentiation, cytoskeletal proteins, apoptosis and pyroptosis were all upregulated following CS exposure and effectively restored by TSA. SIGNIFICANCE TSA may inhibit skeletal muscle atrophy and histomorphological alterations induced by CS exposure by downregulating markers of ubiquitin degradation, muscle fiber differentiation, cytoskeletal proteins, apoptosis and pyroptosis via HDAC1/2 inhibition.
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Affiliation(s)
- Jingjing Ding
- Medical Research Center of Shengjing Hospital, China Medical University, Shenyang 110004, China; Key Laboratory of Research and Application of Animal Model for Environmental and Metabolic Diseases, Liaoning Province, China
| | - Fang Li
- Medical Research Center of Shengjing Hospital, China Medical University, Shenyang 110004, China; Key Laboratory of Research and Application of Animal Model for Environmental and Metabolic Diseases, Liaoning Province, China
| | - Yanfei Cong
- Medical Research Center of Shengjing Hospital, China Medical University, Shenyang 110004, China; Key Laboratory of Research and Application of Animal Model for Environmental and Metabolic Diseases, Liaoning Province, China
| | - Jianing Miao
- Medical Research Center of Shengjing Hospital, China Medical University, Shenyang 110004, China; Key Laboratory of Research and Application of Animal Model for Environmental and Metabolic Diseases, Liaoning Province, China
| | - Di Wu
- Medical Research Center of Shengjing Hospital, China Medical University, Shenyang 110004, China; Key Laboratory of Research and Application of Animal Model for Environmental and Metabolic Diseases, Liaoning Province, China
| | - Bo Liu
- Medical Research Center of Shengjing Hospital, China Medical University, Shenyang 110004, China; Key Laboratory of Research and Application of Animal Model for Environmental and Metabolic Diseases, Liaoning Province, China
| | - Lili Wang
- Medical Research Center of Shengjing Hospital, China Medical University, Shenyang 110004, China; Key Laboratory of Research and Application of Animal Model for Environmental and Metabolic Diseases, Liaoning Province, China.
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