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Hateley C, Olona A, Halliday L, Edin ML, Ko JH, Forlano R, Terra X, Lih FB, Beltrán-Debón R, Manousou P, Purkayastha S, Moorthy K, Thursz MR, Zhang G, Goldin RD, Zeldin DC, Petretto E, Behmoaras J. Multi-tissue profiling of oxylipins reveal a conserved up-regulation of epoxide:diol ratio that associates with white adipose tissue inflammation and liver steatosis in obesity. EBioMedicine 2024; 103:105127. [PMID: 38677183 PMCID: PMC11061246 DOI: 10.1016/j.ebiom.2024.105127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Obesity drives maladaptive changes in the white adipose tissue (WAT) which can progressively cause insulin resistance, type 2 diabetes mellitus (T2DM) and metabolic dysfunction-associated liver disease (MASLD). Obesity-mediated loss of WAT homeostasis can trigger liver steatosis through dysregulated lipid pathways such as those related to polyunsaturated fatty acid (PUFA)-derived oxylipins. However, the exact relationship between oxylipins and metabolic syndrome remains elusive and cross-tissue dynamics of oxylipins are ill-defined. METHODS We quantified PUFA-related oxylipin species in the omental WAT, liver biopsies and plasma of 88 patients undergoing bariatric surgery (female N = 79) and 9 patients (female N = 4) undergoing upper gastrointestinal surgery, using UPLC-MS/MS. We integrated oxylipin abundance with WAT phenotypes (adipogenesis, adipocyte hypertrophy, macrophage infiltration, type I and VI collagen remodelling) and the severity of MASLD (steatosis, inflammation, fibrosis) quantified in each biopsy. The integrative analysis was subjected to (i) adjustment for known risk factors and, (ii) control for potential drug-effects through UPLC-MS/MS analysis of metformin-treated fat explants ex vivo. FINDINGS We reveal a generalized down-regulation of cytochrome P450 (CYP)-derived diols during obesity conserved between the WAT and plasma. Notably, epoxide:diol ratio, indicative of soluble epoxide hydrolyse (sEH) activity, increases with WAT inflammation/fibrosis, hepatic steatosis and T2DM. Increased 12,13-EpOME:DiHOME in WAT and liver is a marker of worsening metabolic syndrome in patients with obesity. INTERPRETATION These findings suggest a dampened sEH activity and a possible role of fatty acid diols during metabolic syndrome in major metabolic organs such as WAT and liver. They also have implications in view of the clinical trials based on sEH inhibition for metabolic syndrome. FUNDING Wellcome Trust (PS3431_WMIH); Duke-NUS (Intramural Goh Cardiovascular Research Award (Duke-NUS-GCR/2022/0020); National Medical Research Council (OFLCG22may-0011); National Institute of Environmental Health Sciences (Z01 ES025034); NIHR Imperial Biomedical Research Centre.
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Affiliation(s)
- Charlotte Hateley
- Centre for Inflammatory Disease, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK; Imperial College Healthcare NHS Trust, St. Mary's Hospital, Praed Street, London, W2 1NY, UK
| | - Antoni Olona
- Centre for Computational Biology and Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Laura Halliday
- Department of Surgery and Cancer, Imperial College London, UK
| | - Matthew L Edin
- Division of Intramural Research, NIEHS/NIH, Research Triangle Park, NC, USA
| | - Jeong-Hun Ko
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | - Roberta Forlano
- Department of Metabolism, Digestion and Reproduction, Imperial College London, UK; Imperial College Healthcare NHS Trust, St. Mary's Hospital, Praed Street, London, W2 1NY, UK
| | - Ximena Terra
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, MoBioFood Research Group, Tarragona, Spain
| | - Fred B Lih
- Division of Intramural Research, NIEHS/NIH, Research Triangle Park, NC, USA
| | - Raúl Beltrán-Debón
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, MoBioFood Research Group, Tarragona, Spain
| | - Penelopi Manousou
- Department of Metabolism, Digestion and Reproduction, Imperial College London, UK; Imperial College Healthcare NHS Trust, St. Mary's Hospital, Praed Street, London, W2 1NY, UK
| | - Sanjay Purkayastha
- Imperial College Healthcare NHS Trust, St. Mary's Hospital, Praed Street, London, W2 1NY, UK; University of Brunel, Kingston Lane, Uxbridge, London, UB8 3PH, UK
| | - Krishna Moorthy
- Department of Surgery and Cancer, Imperial College London, UK; Imperial College Healthcare NHS Trust, St. Mary's Hospital, Praed Street, London, W2 1NY, UK
| | - Mark R Thursz
- Department of Metabolism, Digestion and Reproduction, Imperial College London, UK; Imperial College Healthcare NHS Trust, St. Mary's Hospital, Praed Street, London, W2 1NY, UK
| | - Guodong Zhang
- Department of Nutrition, College of Agriculture and Environmental Sciences, 3135 Meyer Hall, One Shields Avenue, UC Davis, Davis, CA, 95616, USA
| | - Robert D Goldin
- Department of Metabolism, Digestion and Reproduction, Imperial College London, UK; Imperial College Healthcare NHS Trust, St. Mary's Hospital, Praed Street, London, W2 1NY, UK
| | - Darryl C Zeldin
- Division of Intramural Research, NIEHS/NIH, Research Triangle Park, NC, USA
| | - Enrico Petretto
- Centre for Computational Biology and Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore; Institute for Big Data and Artificial Intelligence in Medicine, School of Science, China Pharmaceutical University (CPU), Nanjing, China
| | - Jacques Behmoaras
- Centre for Inflammatory Disease, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK; Centre for Computational Biology and Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore.
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Wallach I, Bernard D, Nguyen K, Ho G, Morrison A, Stecula A, Rosnik A, O’Sullivan AM, Davtyan A, Samudio B, Thomas B, Worley B, Butler B, Laggner C, Thayer D, Moharreri E, Friedland G, Truong H, van den Bedem H, Ng HL, Stafford K, Sarangapani K, Giesler K, Ngo L, Mysinger M, Ahmed M, Anthis NJ, Henriksen N, Gniewek P, Eckert S, de Oliveira S, Suterwala S, PrasadPrasad SVK, Shek S, Contreras S, Hare S, Palazzo T, O’Brien TE, Van Grack T, Williams T, Chern TR, Kenyon V, Lee AH, Cann AB, Bergman B, Anderson BM, Cox BD, Warrington JM, Sorenson JM, Goldenberg JM, Young MA, DeHaan N, Pemberton RP, Schroedl S, Abramyan TM, Gupta T, Mysore V, Presser AG, Ferrando AA, Andricopulo AD, Ghosh A, Ayachi AG, Mushtaq A, Shaqra AM, Toh AKL, Smrcka AV, Ciccia A, de Oliveira AS, Sverzhinsky A, de Sousa AM, Agoulnik AI, Kushnir A, Freiberg AN, Statsyuk AV, Gingras AR, Degterev A, Tomilov A, Vrielink A, Garaeva AA, Bryant-Friedrich A, Caflisch A, Patel AK, Rangarajan AV, Matheeussen A, Battistoni A, Caporali A, Chini A, Ilari A, Mattevi A, Foote AT, Trabocchi A, Stahl A, Herr AB, Berti A, Freywald A, Reidenbach AG, Lam A, Cuddihy AR, White A, Taglialatela A, Ojha AK, Cathcart AM, Motyl AAL, Borowska A, D’Antuono A, Hirsch AKH, Porcelli AM, Minakova A, Montanaro A, Müller A, Fiorillo A, Virtanen A, O’Donoghue AJ, Del Rio Flores A, Garmendia AE, Pineda-Lucena A, Panganiban AT, Samantha A, Chatterjee AK, Haas AL, Paparella AS, John ALS, Prince A, ElSheikh A, Apfel AM, Colomba A, O’Dea A, Diallo BN, Ribeiro BMRM, Bailey-Elkin BA, Edelman BL, Liou B, Perry B, Chua BSK, Kováts B, Englinger B, Balakrishnan B, Gong B, Agianian B, Pressly B, Salas BPM, Duggan BM, Geisbrecht BV, Dymock BW, Morten BC, Hammock BD, Mota BEF, Dickinson BC, Fraser C, Lempicki C, Novina CD, Torner C, Ballatore C, Bon C, Chapman CJ, Partch CL, Chaton CT, Huang C, Yang CY, Kahler CM, Karan C, Keller C, Dieck CL, Huimei C, Liu C, Peltier C, Mantri CK, Kemet CM, Müller CE, Weber C, Zeina CM, Muli CS, Morisseau C, Alkan C, Reglero C, Loy CA, Wilson CM, Myhr C, Arrigoni C, Paulino C, Santiago C, Luo D, Tumes DJ, Keedy DA, Lawrence DA, Chen D, Manor D, Trader DJ, Hildeman DA, Drewry DH, Dowling DJ, Hosfield DJ, Smith DM, Moreira D, Siderovski DP, Shum D, Krist DT, Riches DWH, Ferraris DM, Anderson DH, Coombe DR, Welsbie DS, Hu D, Ortiz D, Alramadhani D, Zhang D, Chaudhuri D, Slotboom DJ, Ronning DR, Lee D, Dirksen D, Shoue DA, Zochodne DW, Krishnamurthy D, Duncan D, Glubb DM, Gelardi ELM, Hsiao EC, Lynn EG, Silva EB, Aguilera E, Lenci E, Abraham ET, Lama E, Mameli E, Leung E, Christensen EM, Mason ER, Petretto E, Trakhtenberg EF, Rubin EJ, Strauss E, Thompson EW, Cione E, Lisabeth EM, Fan E, Kroon EG, Jo E, García-Cuesta EM, Glukhov E, Gavathiotis E, Yu F, Xiang F, Leng F, Wang F, Ingoglia F, van den Akker F, Borriello F, Vizeacoumar FJ, Luh F, Buckner FS, Vizeacoumar FS, Bdira FB, Svensson F, Rodriguez GM, Bognár G, Lembo G, Zhang G, Dempsey G, Eitzen G, Mayer G, Greene GL, Garcia GA, Lukacs GL, Prikler G, Parico GCG, Colotti G, De Keulenaer G, Cortopassi G, Roti G, Girolimetti G, Fiermonte G, Gasparre G, Leuzzi G, Dahal G, Michlewski G, Conn GL, Stuchbury GD, Bowman GR, Popowicz GM, Veit G, de Souza GE, Akk G, Caljon G, Alvarez G, Rucinski G, Lee G, Cildir G, Li H, Breton HE, Jafar-Nejad H, Zhou H, Moore HP, Tilford H, Yuan H, Shim H, Wulff H, Hoppe H, Chaytow H, Tam HK, Van Remmen H, Xu H, Debonsi HM, Lieberman HB, Jung H, Fan HY, Feng H, Zhou H, Kim HJ, Greig IR, Caliandro I, Corvo I, Arozarena I, Mungrue IN, Verhamme IM, Qureshi IA, Lotsaris I, Cakir I, Perry JJP, Kwiatkowski J, Boorman J, Ferreira J, Fries J, Kratz JM, Miner J, Siqueira-Neto JL, Granneman JG, Ng J, Shorter J, Voss JH, Gebauer JM, Chuah J, Mousa JJ, Maynes JT, Evans JD, Dickhout J, MacKeigan JP, Jossart JN, Zhou J, Lin J, Xu J, Wang J, Zhu J, Liao J, Xu J, Zhao J, Lin J, Lee J, Reis J, Stetefeld J, Bruning JB, Bruning JB, Coles JG, Tanner JJ, Pascal JM, So J, Pederick JL, Costoya JA, Rayman JB, Maciag JJ, Nasburg JA, Gruber JJ, Finkelstein JM, Watkins J, Rodríguez-Frade JM, Arias JAS, Lasarte JJ, Oyarzabal J, Milosavljevic J, Cools J, Lescar J, Bogomolovas J, Wang J, Kee JM, Kee JM, Liao J, Sistla JC, Abrahão JS, Sishtla K, Francisco KR, Hansen KB, Molyneaux KA, Cunningham KA, Martin KR, Gadar K, Ojo KK, Wong KS, Wentworth KL, Lai K, Lobb KA, Hopkins KM, Parang K, Machaca K, Pham K, Ghilarducci K, Sugamori KS, McManus KJ, Musta K, Faller KME, Nagamori K, Mostert KJ, Korotkov KV, Liu K, Smith KS, Sarosiek K, Rohde KH, Kim KK, Lee KH, Pusztai L, Lehtiö L, Haupt LM, Cowen LE, Byrne LJ, Su L, Wert-Lamas L, Puchades-Carrasco L, Chen L, Malkas LH, Zhuo L, Hedstrom L, Hedstrom L, Walensky LD, Antonelli L, Iommarini L, Whitesell L, Randall LM, Fathallah MD, Nagai MH, Kilkenny ML, Ben-Johny M, Lussier MP, Windisch MP, Lolicato M, Lolli ML, Vleminckx M, Caroleo MC, Macias MJ, Valli M, Barghash MM, Mellado M, Tye MA, Wilson MA, Hannink M, Ashton MR, Cerna MVC, Giorgis M, Safo MK, Maurice MS, McDowell MA, Pasquali M, Mehedi M, Serafim MSM, Soellner MB, Alteen MG, Champion MM, Skorodinsky M, O’Mara ML, Bedi M, Rizzi M, Levin M, Mowat M, Jackson MR, Paige M, Al-Yozbaki M, Giardini MA, Maksimainen MM, De Luise M, Hussain MS, Christodoulides M, Stec N, Zelinskaya N, Van Pelt N, Merrill NM, Singh N, Kootstra NA, Singh N, Gandhi NS, Chan NL, Trinh NM, Schneider NO, Matovic N, Horstmann N, Longo N, Bharambe N, Rouzbeh N, Mahmoodi N, Gumede NJ, Anastasio NC, Khalaf NB, Rabal O, Kandror O, Escaffre O, Silvennoinen O, Bishop OT, Iglesias P, Sobrado P, Chuong P, O’Connell P, Martin-Malpartida P, Mellor P, Fish PV, Moreira POL, Zhou P, Liu P, Liu P, Wu P, Agogo-Mawuli P, Jones PL, Ngoi P, Toogood P, Ip P, von Hundelshausen P, Lee PH, Rowswell-Turner RB, Balaña-Fouce R, Rocha REO, Guido RVC, Ferreira RS, Agrawal RK, Harijan RK, Ramachandran R, Verma R, Singh RK, Tiwari RK, Mazitschek R, Koppisetti RK, Dame RT, Douville RN, Austin RC, Taylor RE, Moore RG, Ebright RH, Angell RM, Yan R, Kejriwal R, Batey RA, Blelloch R, Vandenberg RJ, Hickey RJ, Kelm RJ, Lake RJ, Bradley RK, Blumenthal RM, Solano R, Gierse RM, Viola RE, McCarthy RR, Reguera RM, Uribe RV, do Monte-Neto RL, Gorgoglione R, Cullinane RT, Katyal S, Hossain S, Phadke S, Shelburne SA, Geden SE, Johannsen S, Wazir S, Legare S, Landfear SM, Radhakrishnan SK, Ammendola S, Dzhumaev S, Seo SY, Li S, Zhou S, Chu S, Chauhan S, Maruta S, Ashkar SR, Shyng SL, Conticello SG, Buroni S, Garavaglia S, White SJ, Zhu S, Tsimbalyuk S, Chadni SH, Byun SY, Park S, Xu SQ, Banerjee S, Zahler S, Espinoza S, Gustincich S, Sainas S, Celano SL, Capuzzi SJ, Waggoner SN, Poirier S, Olson SH, Marx SO, Van Doren SR, Sarilla S, Brady-Kalnay SM, Dallman S, Azeem SM, Teramoto T, Mehlman T, Swart T, Abaffy T, Akopian T, Haikarainen T, Moreda TL, Ikegami T, Teixeira TR, Jayasinghe TD, Gillingwater TH, Kampourakis T, Richardson TI, Herdendorf TJ, Kotzé TJ, O’Meara TR, Corson TW, Hermle T, Ogunwa TH, Lan T, Su T, Banjo T, O’Mara TA, Chou T, Chou TF, Baumann U, Desai UR, Pai VP, Thai VC, Tandon V, Banerji V, Robinson VL, Gunasekharan V, Namasivayam V, Segers VFM, Maranda V, Dolce V, Maltarollo VG, Scoffone VC, Woods VA, Ronchi VP, Van Hung Le V, Clayton WB, Lowther WT, Houry WA, Li W, Tang W, Zhang W, Van Voorhis WC, Donaldson WA, Hahn WC, Kerr WG, Gerwick WH, Bradshaw WJ, Foong WE, Blanchet X, Wu X, Lu X, Qi X, Xu X, Yu X, Qin X, Wang X, Yuan X, Zhang X, Zhang YJ, Hu Y, Aldhamen YA, Chen Y, Li Y, Sun Y, Zhu Y, Gupta YK, Pérez-Pertejo Y, Li Y, Tang Y, He Y, Tse-Dinh YC, Sidorova YA, Yen Y, Li Y, Frangos ZJ, Chung Z, Su Z, Wang Z, Zhang Z, Liu Z, Inde Z, Artía Z, Heifets A. AI is a viable alternative to high throughput screening: a 318-target study. Sci Rep 2024; 14:7526. [PMID: 38565852 PMCID: PMC10987645 DOI: 10.1038/s41598-024-54655-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 02/15/2024] [Indexed: 04/04/2024] Open
Abstract
High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery.
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Xie Y, Chen H, Chellamuthu VR, Lajam ABM, Albani S, Low AHL, Petretto E, Behmoaras J. Comparative Analysis of Single-Cell RNA Sequencing Methods with and without Sample Multiplexing. Int J Mol Sci 2024; 25:3828. [PMID: 38612639 PMCID: PMC11011421 DOI: 10.3390/ijms25073828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful technique for investigating biological heterogeneity at the single-cell level in human systems and model organisms. Recent advances in scRNA-seq have enabled the pooling of cells from multiple samples into single libraries, thereby increasing sample throughput while reducing technical batch effects, library preparation time, and the overall cost. However, a comparative analysis of scRNA-seq methods with and without sample multiplexing is lacking. In this study, we benchmarked methods from two representative platforms: Parse Biosciences (Parse; with sample multiplexing) and 10x Genomics (10x; without sample multiplexing). By using peripheral blood mononuclear cells (PBMCs) obtained from two healthy individuals, we demonstrate that demultiplexed scRNA-seq data obtained from Parse showed similar cell type frequencies compared to 10x data where samples were not multiplexed. Despite relatively lower cell capture affecting library preparation, Parse can detect rare cell types (e.g., plasmablasts and dendritic cells) which is likely due to its relatively higher sensitivity in gene detection. Moreover, a comparative analysis of transcript quantification between the two platforms revealed platform-specific distributions of gene length and GC content. These results offer guidance for researchers in designing high-throughput scRNA-seq studies.
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Affiliation(s)
- Yi Xie
- Programme in Cardiovascular and Metabolic Disorders and Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; (Y.X.)
| | - Huimei Chen
- Programme in Cardiovascular and Metabolic Disorders and Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; (Y.X.)
| | - Vasuki Ranjani Chellamuthu
- Translational Immunology Institute, SingHealth/Duke-NUS Academic Medical Centre, Academia, Singapore 169856, Singapore; (V.R.C.)
| | - Ahmad bin Mohamed Lajam
- Translational Immunology Institute, SingHealth/Duke-NUS Academic Medical Centre, Academia, Singapore 169856, Singapore; (V.R.C.)
| | - Salvatore Albani
- Translational Immunology Institute, SingHealth/Duke-NUS Academic Medical Centre, Academia, Singapore 169856, Singapore; (V.R.C.)
| | - Andrea Hsiu Ling Low
- Department of Rheumatology and Immunology, Singapore General Hospital, Academia, Singapore 169856, Singapore;
- SingHealth Duke-NUS Medicine Academic Clinical Programme, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Enrico Petretto
- Programme in Cardiovascular and Metabolic Disorders and Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; (Y.X.)
- Institute for Big Data and Artificial Intelligence in Medicine, School of Science, China Pharmaceutical University, Nanjing 210009, China
| | - Jacques Behmoaras
- Programme in Cardiovascular and Metabolic Disorders and Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; (Y.X.)
- Department of Immunology and Inflammation, Centre for Inflammatory Disease, Imperial College London, Hammersmith Hospital, London W12 0NN, UK
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Chen H, You R, Guo J, Zhou W, Chew G, Devapragash N, Loh JZ, Gesualdo L, Li Y, Jiang Y, Tan ELS, Chen S, Pontrelli P, Pesce F, Behmoaras J, Zhang A, Petretto E. WWP2 Regulates Renal Fibrosis and the Metabolic Reprogramming of Profibrotic Myofibroblasts. J Am Soc Nephrol 2024:00001751-990000000-00269. [PMID: 38502123 DOI: 10.1681/asn.0000000000000328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Key Points
WWP2 expression is elevated in the tubulointerstitium of fibrotic kidneys and contributes to CKD pathogenesis and progression.WWP2 uncouples the profibrotic activation and cell proliferation in renal myofibroblasts.WWP2 controls mitochondrial respiration in renal myofibroblasts through the metabolic regulator peroxisome proliferator-activated receptor gamma coactivator 1-alpha.
Background
Renal fibrosis is a common pathologic end point in CKD that is challenging to reverse, and myofibroblasts are responsible for the accumulation of a fibrillar collagen–rich extracellular matrix. Recent studies have unveiled myofibroblasts' diversity in proliferative and fibrotic characteristics, which are linked to different metabolic states. We previously demonstrated the regulation of extracellular matrix genes and tissue fibrosis by WWP2, a multifunctional E3 ubiquitin–protein ligase. Here, we investigate WWP2 in renal fibrosis and in the metabolic reprograming of myofibroblasts in CKD.
Methods
We used kidney samples from patients with CKD and WWP2-null kidney disease mice models and leveraged single-cell RNA sequencing analysis to detail the cell-specific regulation of WWP2 in fibrotic kidneys. Experiments in primary cultured myofibroblasts by bulk-RNA sequencing, chromatin immunoprecipitation sequencing, metabolomics, and cellular metabolism assays were used to study the metabolic regulation of WWP2 and its downstream signaling.
Results
The tubulointerstitial expression of WWP2 was associated with fibrotic progression in patients with CKD and in murine kidney disease models. WWP2 deficiency promoted myofibroblast proliferation and halted profibrotic activation, reducing the severity of renal fibrosis in vivo. In renal myofibroblasts, WWP2 deficiency increased fatty acid oxidation and activated the pentose phosphate pathway, boosting mitochondrial respiration at the expense of glycolysis. WWP2 suppressed the transcription of peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α), a metabolic mediator of fibrotic response, and pharmacologic inhibition of PGC-1α partially abrogated the protective effects of WWP2 deficiency on myofibroblasts.
Conclusions
WWP2 regulates the metabolic reprogramming of profibrotic myofibroblasts by a WWP2-PGC-1α axis, and WWP2 deficiency protects against renal fibrosis in CKD.
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Affiliation(s)
- Huimei Chen
- Programme in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Duke-NUS Medical School, Singapore
| | - Ran You
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Jing Guo
- Programme in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Duke-NUS Medical School, Singapore
| | - Wei Zhou
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Gabriel Chew
- Programme in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Duke-NUS Medical School, Singapore
| | - Nithya Devapragash
- Programme in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Duke-NUS Medical School, Singapore
| | - Jui Zhi Loh
- Programme in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Duke-NUS Medical School, Singapore
| | - Loreto Gesualdo
- Nephrology, Dialysis and Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari Aldo Moro, Bari, Italy
| | - Yanwei Li
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Yuteng Jiang
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Elisabeth Li Sa Tan
- Programme in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Duke-NUS Medical School, Singapore
| | - Shuang Chen
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
- School of Science, Institute for Big Data and Artificial Intelligence in Medicine, China Pharmaceutical University, Nanjing, China
| | - Paola Pontrelli
- Nephrology, Dialysis and Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari Aldo Moro, Bari, Italy
| | - Francesco Pesce
- Division of Renal Medicine, Fatebenefratelli Isola Tiberina-Gemelli Isola, Rome, Italy
| | - Jacques Behmoaras
- Programme in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Duke-NUS Medical School, Singapore
- Centre for Inflammatory Disease, Imperial College London, Hammersmith Hospital, London, United Kingdom
| | - Aihua Zhang
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Enrico Petretto
- Programme in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Duke-NUS Medical School, Singapore
- School of Science, Institute for Big Data and Artificial Intelligence in Medicine, China Pharmaceutical University, Nanjing, China
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Madan B, Wadia SR, Patnaik S, Harmston N, Tan E, Tan IBH, Nes WD, Petretto E, Virshup DM. The cholesterol biosynthesis enzyme FAXDC2 couples Wnt/β-catenin to RTK/MAPK signaling. J Clin Invest 2024; 134:e171222. [PMID: 38488003 PMCID: PMC10940096 DOI: 10.1172/jci171222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 01/17/2024] [Indexed: 03/18/2024] Open
Abstract
Wnts, cholesterol, and MAPK signaling are essential for development and adult homeostasis. Here, we report that fatty acid hydroxylase domain containing 2 (FAXDC2), a previously uncharacterized enzyme, functions as a methyl sterol oxidase catalyzing C4 demethylation in the Kandutsch-Russell branch of the cholesterol biosynthesis pathway. FAXDC2, a paralog of MSMO1, regulated the abundance of the specific C4-methyl sterols lophenol and dihydro-T-MAS. Highlighting its clinical relevance, FAXDC2 was repressed in Wnt/β-catenin-high cancer xenografts, in a mouse genetic model of Wnt activation, and in human colorectal cancers. Moreover, in primary human colorectal cancers, the sterol lophenol, regulated by FAXDC2, accumulated in the cancerous tissues and not in adjacent normal tissues. FAXDC2 linked Wnts to RTK/MAPK signaling. Wnt inhibition drove increased recycling of RTKs and activation of the MAPK pathway, and this required FAXDC2. Blocking Wnt signaling in Wnt-high cancers caused both differentiation and senescence; and this was prevented by knockout of FAXDC2. Our data show the integration of 3 ancient pathways, Wnts, cholesterol synthesis, and RTK/MAPK signaling, in cellular proliferation and differentiation.
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Affiliation(s)
- Babita Madan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Shawn R. Wadia
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Siddhi Patnaik
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Nathan Harmston
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
- Science Division, Yale-NUS College, Singapore
| | - Emile Tan
- Department of Colorectal Surgery, Singapore General Hospital, Singapore
| | - Iain Bee Huat Tan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
- Department of Medical Oncology, National Cancer Centre, Singapore
| | - W. David Nes
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Enrico Petretto
- Center for Computational Biology and Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
- Institute for Big Data and Artificial Intelligence in Medicine, School of Science, China Pharmaceutical University, Nanjing, China
| | - David M. Virshup
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
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6
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Ouyang JF, Mishra K, Xie Y, Park H, Huang KY, Petretto E, Behmoaras J. Systems level identification of a matrisome-associated macrophage polarisation state in multi-organ fibrosis. eLife 2023; 12:e85530. [PMID: 37706477 PMCID: PMC10547479 DOI: 10.7554/elife.85530] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 09/13/2023] [Indexed: 09/15/2023] Open
Abstract
Tissue fibrosis affects multiple organs and involves a master-regulatory role of macrophages which respond to an initial inflammatory insult common in all forms of fibrosis. The recently unravelled multi-organ heterogeneity of macrophages in healthy and fibrotic human disease suggests that macrophages expressing osteopontin (SPP1) associate with lung and liver fibrosis. However, the conservation of this SPP1+ macrophage population across different tissues and its specificity to fibrotic diseases with different etiologies remain unclear. Integrating 15 single-cell RNA-sequencing datasets to profile 235,930 tissue macrophages from healthy and fibrotic heart, lung, liver, kidney, skin, and endometrium, we extended the association of SPP1+ macrophages with fibrosis to all these tissues. We also identified a subpopulation expressing matrisome-associated genes (e.g., matrix metalloproteinases and their tissue inhibitors), functionally enriched for ECM remodelling and cell metabolism, representative of a matrisome-associated macrophage (MAM) polarisation state within SPP1+ macrophages. Importantly, the MAM polarisation state follows a differentiation trajectory from SPP1+ macrophages and is associated with a core set of regulon activity. SPP1+ macrophages without the MAM polarisation state (SPP1+MAM-) show a positive association with ageing lung in mice and humans. These results suggest an advanced and conserved polarisation state of SPP1+ macrophages in fibrotic tissues resulting from prolonged inflammatory cues within each tissue microenvironment.
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Affiliation(s)
- John F Ouyang
- Centre for Computational Biology, Duke-NUS Medical SchoolSingaporeSingapore
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical SchoolSingaporeSingapore
| | - Kunal Mishra
- Centre for Computational Biology, Duke-NUS Medical SchoolSingaporeSingapore
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical SchoolSingaporeSingapore
| | - Yi Xie
- Centre for Computational Biology, Duke-NUS Medical SchoolSingaporeSingapore
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical SchoolSingaporeSingapore
| | - Harry Park
- Centre for Computational Biology, Duke-NUS Medical SchoolSingaporeSingapore
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical SchoolSingaporeSingapore
| | - Kevin Y Huang
- Centre for Computational Biology, Duke-NUS Medical SchoolSingaporeSingapore
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical SchoolSingaporeSingapore
| | - Enrico Petretto
- Centre for Computational Biology, Duke-NUS Medical SchoolSingaporeSingapore
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical SchoolSingaporeSingapore
- Institute for Big Data and Artificial Intelligence in Medicine, School of Science, China Pharmaceutical University (CPU)NanjingChina
| | - Jacques Behmoaras
- Centre for Computational Biology, Duke-NUS Medical SchoolSingaporeSingapore
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical SchoolSingaporeSingapore
- Department of Immunology and Inflammation, Centre for Inflammatory Disease, Imperial College LondonLondonUnited Kingdom
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7
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Yap L, Chong LY, Tan C, Adusumalli S, Seow M, Guo J, Cai Z, Loo SJ, Lim E, Tan RS, Grishina E, Soong PL, Lath N, Ye L, Petretto E, Tryggvason K. Pluripotent stem cell-derived committed cardiac progenitors remuscularize damaged ischemic hearts and improve their function in pigs. NPJ Regen Med 2023; 8:26. [PMID: 37236990 DOI: 10.1038/s41536-023-00302-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Ischemic heart disease, which is often associated with irreversibly damaged heart muscle, is a major global health burden. Here, we report the potential of stem cell-derived committed cardiac progenitors (CCPs) have in regenerative cardiology. Human pluripotent embryonic stem cells were differentiated to CCPs on a laminin 521 + 221 matrix, characterized with bulk and single-cell RNA sequencing, and transplanted into infarcted pig hearts. CCPs differentiated for eleven days expressed a set of genes showing higher expression than cells differentiated for seven days. Functional heart studies revealed significant improvement in left ventricular ejection fraction at four and twelve weeks following transplantation. We also observed significant improvements in ventricular wall thickness and a reduction in infarction size after CCP transplantation (p-value < 0.05). Immunohistology analyses revealed in vivo maturation of the CCPs into cardiomyocytes (CM). We observed temporary episodes of ventricular tachyarrhythmia (VT) in four pigs and persistent VT in one pig, but the remaining five pigs exhibited normal sinus rhythm. Importantly, all pigs survived without the formation of any tumors or VT-related abnormalities. We conclude that pluripotent stem cell-derived CCPs constitute a promising possibility for myocardial infarction treatment and that they may positively impact regenerative cardiology.
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Affiliation(s)
- Lynn Yap
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore, 169857, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore.
| | - Li Yen Chong
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore, 169857, Singapore
| | - Clarissa Tan
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore, 169857, Singapore
| | - Swarnaseetha Adusumalli
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore, 169857, Singapore
| | - Millie Seow
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore, 169857, Singapore
| | - Jing Guo
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore, 169857, Singapore
| | - Zuhua Cai
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore, 169857, Singapore
| | - Sze Jie Loo
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, 169609, Singapore
| | - Eric Lim
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, 169609, Singapore
| | - Ru San Tan
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, 169609, Singapore
| | | | - Poh Loong Soong
- Ternion Biosciences, Singapore, 574329, Singapore
- Cardiovascular Disease Translational Research Program, Yong Loo Lin School of Medicine, NUS, Singapore, 169609, Singapore
| | - Narayan Lath
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, 169609, Singapore
| | - Lei Ye
- Department of Biomedical Engineering, University of Alabama, Birmingham, 35233, England
| | - Enrico Petretto
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore, 169857, Singapore
| | - Karl Tryggvason
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore, 169857, Singapore.
- Department of Medicine Duke University, Durham, NC, 27710, USA.
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77, Stockholm, Sweden.
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8
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Tay HG, Andre H, Chrysostomou V, Adusumalli S, Guo J, Ren X, Tan WS, Tor JE, Moreno-Moral A, Plastino F, Bartuma H, Cai Z, Tun SBB, Barathi VA, Siew Wei GT, Grenci G, Chong LY, Holmgren A, Kvanta A, Crowston JG, Petretto E, Tryggvason K. Photoreceptor laminin drives differentiation of human pluripotent stem cells to photoreceptor progenitors that partially restore retina function. Mol Ther 2023; 31:825-846. [PMID: 36638800 PMCID: PMC10014235 DOI: 10.1016/j.ymthe.2022.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 07/12/2022] [Accepted: 12/21/2022] [Indexed: 01/14/2023] Open
Abstract
Blindness caused by advanced stages of inherited retinal diseases and age-related macular degeneration are characterized by photoreceptor loss. Cell therapy involving replacement with functional photoreceptor-like cells generated from human pluripotent stem cells holds great promise. Here, we generated a human recombinant retina-specific laminin isoform, LN523, and demonstrated the role in promoting the differentiation of human embryonic stem cells into photoreceptor progenitors. This chemically defined and xenogen-free method enables reproducible production of photoreceptor progenitors within 32 days. We observed that the transplantation into rd10 mice were able to protect the host photoreceptor outer nuclear layer (ONL) up to 2 weeks post transplantation as measured by full-field electroretinogram. At 4 weeks post transplantation, the engrafted cells were found to survive, mature, and associate with the host's rod bipolar cells. Visual behavioral assessment using the water maze swimming test demonstrated visual improvement in the cell-transplanted rodents. At 20 weeks post transplantation, the maturing engrafted cells were able to replace the loss of host ONL by extensive association with host bipolar cells and synapses. Post-transplanted rabbit model also provided congruent evidence for synaptic connectivity with the degenerated host retina. The results may pave the way for the development of stem cell-based therapeutics for retina degeneration.
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Affiliation(s)
- Hwee Goon Tay
- Centre for Vision Research, Duke-NUS Medical School, Singapore; Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore.
| | - Helder Andre
- Department of Clinical Neuroscience, St. Erik Eye Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Vicki Chrysostomou
- Centre for Vision Research, Duke-NUS Medical School, Singapore; Academic Clinical Program, Duke-NUS Medical School, Singapore
| | | | - Jing Guo
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore
| | - Xiaoyuan Ren
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Wei Sheng Tan
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore
| | - Jia En Tor
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore
| | - Aida Moreno-Moral
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore
| | - Flavia Plastino
- Department of Clinical Neuroscience, St. Erik Eye Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Hammurabi Bartuma
- Department of Clinical Neuroscience, St. Erik Eye Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Zuhua Cai
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore
| | - Sai Bo Bo Tun
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Veluchamy Amutha Barathi
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore; Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Gavin Tan Siew Wei
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Gianluca Grenci
- Mechanobiology Institute (MBI) and Department of Biomedical Engineering, NUS, Singapore
| | - Li Yen Chong
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore
| | - Arne Holmgren
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Anders Kvanta
- Department of Clinical Neuroscience, St. Erik Eye Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Jonathan Guy Crowston
- Centre for Vision Research, Duke-NUS Medical School, Singapore; Academic Clinical Program, Duke-NUS Medical School, Singapore; Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Enrico Petretto
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore
| | - Karl Tryggvason
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden; Division of Nephrology, Department of Medicine, Duke University, Durham, NC, USA.
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9
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Widjaja AA, Viswanathan S, Shekeran SG, Adami E, Lim WW, Chothani S, Tan J, Goh JWT, Chen HM, Lim SY, Boustany-Kari CM, Hawkins J, Petretto E, Hübner N, Schafer S, Coffman TM, Cook SA. Targeting endogenous kidney regeneration using anti-IL11 therapy in acute and chronic models of kidney disease. Nat Commun 2022; 13:7497. [PMID: 36470928 PMCID: PMC9723120 DOI: 10.1038/s41467-022-35306-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/27/2022] [Indexed: 12/12/2022] Open
Abstract
The kidney has large regenerative capacity, but this is compromised when kidney damage is excessive and renal tubular epithelial cells (TECs) undergo SNAI1-driven growth arrest. Here we investigate the role of IL11 in TECs, kidney injury and renal repair. IL11 stimulation of TECs induces ERK- and p90RSK-mediated GSK3β inactivation, SNAI1 upregulation and pro-inflammatory gene expression. Mice with acute kidney injury upregulate IL11 in TECs leading to SNAI1 expression and kidney dysfunction, which is not seen in Il11 deleted mice or in mice administered a neutralizing IL11 antibody in either preemptive or treatment modes. In acute kidney injury, anti-TGFβ reduces renal fibrosis but exacerbates inflammation and tubule damage whereas anti-IL11 reduces all pathologies. Mice with TEC-specific deletion of Il11ra1 have reduced pathogenic signaling and are protected from renal injury-induced inflammation, fibrosis, and failure. In a model of chronic kidney disease, anti-IL11 therapy promotes TEC proliferation and parenchymal regeneration, reverses fibroinflammation and restores renal mass and function. These data highlight IL11-induced mesenchymal transition of injured TECs as an important renal pathology and suggest IL11 as a therapeutic target for restoring stalled endogenous regeneration in the diseased kidney.
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Affiliation(s)
- Anissa A Widjaja
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore.
| | - Sivakumar Viswanathan
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Shamini G Shekeran
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Eleonora Adami
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore.,Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Wei-Wen Lim
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore.,National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore
| | - Sonia Chothani
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Jessie Tan
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore
| | - Joyce Wei Ting Goh
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Hui Mei Chen
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Sze Yun Lim
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
| | | | - Julie Hawkins
- Boehringer Ingelheim, CardioMetabolic Disease Research, Berlin, Germany
| | - Enrico Petretto
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Norbert Hübner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347, Berlin, Germany.,Charité-Universitätsmedizin, 10117, Berlin, Germany
| | - Sebastian Schafer
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Thomas M Coffman
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Stuart A Cook
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore. .,National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore. .,MRC-London Institute of Medical Sciences, Hammersmith Hospital Campus, London, UK.
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10
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Chen H, Chew G, Devapragash N, Loh JZ, Huang KY, Guo J, Liu S, Tan ELS, Chen S, Tee NGZ, Mia MM, Singh MK, Zhang A, Behmoaras J, Petretto E. The E3 ubiquitin ligase WWP2 regulates pro-fibrogenic monocyte infiltration and activity in heart fibrosis. Nat Commun 2022; 13:7375. [PMID: 36450710 PMCID: PMC9712659 DOI: 10.1038/s41467-022-34971-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022] Open
Abstract
Non-ischemic cardiomyopathy (NICM) can cause left ventricular dysfunction through interstitial fibrosis, which corresponds to the failure of cardiac tissue remodeling. Recent evidence implicates monocytes/macrophages in the etiopathology of cardiac fibrosis, but giving their heterogeneity and the antagonizing roles of macrophage subtypes in fibrosis, targeting these cells has been challenging. Here we focus on WWP2, an E3 ubiquitin ligase that acts as a positive genetic regulator of human and murine cardiac fibrosis, and show that myeloid specific deletion of WWP2 reduces cardiac fibrosis in hypertension-induced NICM. By using single cell RNA sequencing analysis of immune cells in the same model, we establish the functional heterogeneity of macrophages and define an early pro-fibrogenic phase of NICM that is driven by Ccl5-expressing Ly6chigh monocytes. Among cardiac macrophage subtypes, WWP2 dysfunction primarily affects Ly6chigh monocytes via modulating Ccl5, and consequentially macrophage infiltration and activation, which contributes to reduced myofibroblast trans-differentiation. WWP2 interacts with transcription factor IRF7, promoting its non-degradative mono-ubiquitination, nuclear translocation and transcriptional activity, leading to upregulation of Ccl5 at transcriptional level. We identify a pro-fibrogenic macrophage subtype in non-ischemic cardiomyopathy, and demonstrate that WWP2 is a key regulator of IRF7-mediated Ccl5/Ly6chigh monocyte axis in heart fibrosis.
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Affiliation(s)
- Huimei Chen
- grid.428397.30000 0004 0385 0924Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, 169857 Singapore, Singapore ,grid.254147.10000 0000 9776 7793Institute for Big Data and Artificial Intelligence in Medicine, School of Science, China Pharmaceutical University, Nanjing, 210009 China
| | - Gabriel Chew
- grid.428397.30000 0004 0385 0924Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, 169857 Singapore, Singapore
| | - Nithya Devapragash
- grid.428397.30000 0004 0385 0924Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, 169857 Singapore, Singapore
| | - Jui Zhi Loh
- grid.428397.30000 0004 0385 0924Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, 169857 Singapore, Singapore
| | - Kevin Y. Huang
- grid.428397.30000 0004 0385 0924Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, 169857 Singapore, Singapore
| | - Jing Guo
- grid.428397.30000 0004 0385 0924Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, 169857 Singapore, Singapore
| | - Shiyang Liu
- grid.428397.30000 0004 0385 0924Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, 169857 Singapore, Singapore
| | - Elisabeth Li Sa Tan
- grid.428397.30000 0004 0385 0924Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, 169857 Singapore, Singapore
| | - Shuang Chen
- grid.254147.10000 0000 9776 7793Institute for Big Data and Artificial Intelligence in Medicine, School of Science, China Pharmaceutical University, Nanjing, 210009 China ,grid.452511.6Department of Nephrology, Children’s Hospital of Nanjing Medical University, Nanjing, 210008 China
| | - Nicole Gui Zhen Tee
- grid.419385.20000 0004 0620 9905National Heart Centre Singapore, Singapore, 169609 Singapore
| | - Masum M. Mia
- grid.428397.30000 0004 0385 0924Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, 169857 Singapore, Singapore
| | - Manvendra K. Singh
- grid.428397.30000 0004 0385 0924Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, 169857 Singapore, Singapore
| | - Aihua Zhang
- grid.452511.6Department of Nephrology, Children’s Hospital of Nanjing Medical University, Nanjing, 210008 China
| | - Jacques Behmoaras
- grid.428397.30000 0004 0385 0924Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, 169857 Singapore, Singapore ,grid.413629.b0000 0001 0705 4923Centre for Inflammatory Disease, Imperial College London, Hammersmith Hospital, London, W12 0NN UK
| | - Enrico Petretto
- grid.428397.30000 0004 0385 0924Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, 169857 Singapore, Singapore ,grid.254147.10000 0000 9776 7793Institute for Big Data and Artificial Intelligence in Medicine, School of Science, China Pharmaceutical University, Nanjing, 210009 China
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11
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Ji J, Anwar M, Petretto E, Emanueli C, Srivastava PK. PPMS: A framework to Profile Primary MicroRNAs from Single-cell RNA-sequencing datasets. Brief Bioinform 2022; 23:bbac419. [PMID: 36209413 PMCID: PMC9677482 DOI: 10.1093/bib/bbac419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/28/2022] [Accepted: 08/30/2022] [Indexed: 12/14/2022] Open
Abstract
MOTIVATION Single-cell/nuclei RNA-sequencing (scRNA-seq) technologies can simultaneously quantify gene expression in thousands of cells across the genome. However, the majority of the noncoding RNAs, such as microRNAs (miRNAs), cannot currently be profiled at the same scale. MiRNAs are a class of small noncoding RNAs and play an important role in gene regulation. MiRNAs originate from the processing of primary transcripts, known as primary-microRNAs (pri-miRNAs). The pri-miRNA transcripts, independent of their cognate miRNAs, can also function as long noncoding RNAs, code for micropeptides or even interact with DNA, acting like enhancers. Therefore, it is apparent that the significance of scRNA-seq pri-miRNA profiling expands beyond using pri-miRNA as proxies of mature miRNAs. However, there are no computational methods that allow profiling and quantification of pri-miRNAs at the single-cell-type resolution. RESULTS We have developed a simple yet effective computational framework to profile pri-MiRNAs from single-cell RNA-sequencing datasets (PPMS). Based on user input, PPMS can profile pri-miRNAs at cell-type resolution. PPMS can be applied to both newly produced and publicly available datasets obtained via single cell or single-nuclei RNA-seq. It allows users to (i) investigate the distribution of pri-miRNAs across cell types and cell states and (ii) establish a relationship between the number of cells/reads sequenced and the detection of pri-miRNAs. Here, to demonstrate its efficacy, we have applied PPMS to publicly available scRNA-seq data generated from (i) individual chambers (ventricles and atria) of the human heart, (ii) human pluripotent stem cells during their differentiation into cardiomyocytes (the heart beating cells) and (iii) hiPSCs-derived cardiomyocytes infected with severe acute respiratory syndrome coronavirus 2.
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Affiliation(s)
- Jiahui Ji
- National Heart and Lung Institute, Imperial College London, UK
| | - Maryam Anwar
- National Heart and Lung Institute, Imperial College London, UK
| | - Enrico Petretto
- London Institute of Medical Sciences, MRC, UK
- Duke-NUS Medical School, Singapore
- Institute of Big Data and Artificial Intelligence, China Pharmaceutical University (CPU), 211198 Nanjing, China
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12
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Lee LM, Christodoulou EG, Shyamsunder P, Chen BJ, Lee KL, Fung TK, So CWE, Wong GC, Petretto E, Rackham OJL, Tiong Ong S. A novel network pharmacology approach for leukaemia differentiation therapy using Mogrify ®. Oncogene 2022; 41:5160-5175. [PMID: 36271030 DOI: 10.1038/s41388-022-02505-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 11/09/2022]
Abstract
Acute myeloid leukaemia (AML) is a rapidly fatal blood cancer that is characterised by the accumulation of immature myeloid cells in the blood and bone marrow as a result of blocked differentiation. Methods which identify master transcriptional regulators of AML subtype-specific leukaemia cell states and their combinations could be critical for discovering novel differentiation-inducing therapies. In this proof-of-concept study, we demonstrate a novel utility of the Mogrify® algorithm in identifying combinations of transcription factors (TFs) and drugs, which recapitulate granulocytic differentiation of the NB4 acute promyelocytic leukaemia (APL) cell line, using two different approaches. In the first approach, Connectivity Map (CMAP) analysis of these TFs and their target networks outperformed standard approaches, retrieving ATRA as the top hit. We identify dimaprit and mebendazole as a drug combination which induces myeloid differentiation. In the second approach, we show that genetic manipulation of specific Mogrify®-identified TFs (MYC and IRF1) leads to co-operative induction of APL differentiation, as does pharmacological targeting of these TFs using currently available compounds. We also show that loss of IRF1 blunts ATRA-mediated differentiation, and that MYC represses IRF1 expression through recruitment of PML-RARα, the driver fusion oncoprotein in APL, to the IRF1 promoter. Finally, we demonstrate that these drug combinations can also induce differentiation of primary patient-derived APL cells, and highlight the potential of targeting MYC and IRF1 in high-risk APL. Thus, these results suggest that Mogrify® could be used for drug discovery or repositioning in leukaemia differentiation therapy for other subtypes of leukaemia or cancers.
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MESH Headings
- Humans
- Tretinoin/pharmacology
- Tretinoin/therapeutic use
- Network Pharmacology
- Leukemia, Promyelocytic, Acute/drug therapy
- Leukemia, Promyelocytic, Acute/genetics
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Cell Differentiation/genetics
- Transcription Factors/genetics
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Affiliation(s)
- Lin Ming Lee
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Eleni G Christodoulou
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Pavithra Shyamsunder
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Bei Jun Chen
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Kian Leong Lee
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Tsz Kan Fung
- Comprehensive Cancer Centre, King's College London, London, UK
- Department of Haematological Medicine, King's College Hospital, London, UK
| | - Chi Wai Eric So
- Comprehensive Cancer Centre, King's College London, London, UK
- Department of Haematological Medicine, King's College Hospital, London, UK
| | - Gee Chuan Wong
- Department of Haematology, Singapore General Hospital, Singapore, Singapore
| | - Enrico Petretto
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore.
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore.
- MRC London Institute of Medical Sciences (LMC), Imperial College London, Faculty of Medicine, London, UK.
- Institute for Big Data and Artificial Intelligence in Medicine, School of Science, China Pharmaceutical University (CPU), Nanjing, China.
| | - Owen J L Rackham
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore.
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore.
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - S Tiong Ong
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore.
- Department of Haematology, Singapore General Hospital, Singapore, Singapore.
- Department of Medical Oncology, National Cancer Centre, Singapore, Singapore.
- Department of Medicine, Duke University Medical Center, Durham, NC, USA.
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13
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Muralidharan S, Torta F, Lin MK, Olona A, Bagnati M, Moreno-Moral A, Ko JH, Ji S, Burla B, Wenk MR, Rodrigues HG, Petretto E, Behmoaras J. Immunolipidomics Reveals a Globoside Network During the Resolution of Pro-Inflammatory Response in Human Macrophages. Front Immunol 2022; 13:926220. [PMID: 35844525 PMCID: PMC9280915 DOI: 10.3389/fimmu.2022.926220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Toll-like receptor 4 (TLR4)-mediated changes in macrophages reshape intracellular lipid pools to coordinate an effective innate immune response. Although this has been previously well-studied in different model systems, it remains incompletely understood in primary human macrophages. Here we report time-dependent lipidomic and transcriptomic responses to lipopolysaccharide (LPS) in primary human macrophages from healthy donors. We grouped the variation of ~200 individual lipid species measured by LC-MS/MS into eight temporal clusters. Among all other lipids, glycosphingolipids (glycoSP) and cholesteryl esters (CE) showed a sharp increase during the resolution phase (between 8h or 16h post LPS). GlycoSP, belonging to the globoside family (Gb3 and Gb4), showed the greatest inter-individual variability among all lipids quantified. Integrative network analysis between GlycoSP/CE levels and genome-wide transcripts, identified Gb4 d18:1/16:0 and CE 20:4 association with subnetworks enriched for T cell receptor signaling (PDCD1, CD86, PTPRC, CD247, IFNG) and DC-SIGN signaling (RAF1, CD209), respectively. Our findings reveal Gb3 and Gb4 globosides as sphingolipids associated with the resolution phase of inflammatory response in human macrophages.
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Affiliation(s)
- Sneha Muralidharan
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore,Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India
| | - Federico Torta
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore,Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore,*Correspondence: Jacques Behmoaras, ; Federico Torta,
| | - Michelle K. Lin
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Antoni Olona
- Program in Cardiovascular and Metabolic Disorders (CVMD) and Center for Computational Biology (CCB), Duke NUS Graduate Medical School, Singapore, Singapore
| | - Marta Bagnati
- Department of Immunology and Inflammation, Centre for Inflammatory Disease, Imperial College London, London, United Kingdom
| | - Aida Moreno-Moral
- Program in Cardiovascular and Metabolic Disorders (CVMD) and Center for Computational Biology (CCB), Duke NUS Graduate Medical School, Singapore, Singapore
| | - Jeong-Hun Ko
- Department of Immunology and Inflammation, Centre for Inflammatory Disease, Imperial College London, London, United Kingdom
| | - Shanshan Ji
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Bo Burla
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Markus R. Wenk
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore,Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Hosana G. Rodrigues
- Laboratory of Nutrients and Tissue Repair, School of Applied Sciences, University of Campinas, Limeira, Brazil
| | - Enrico Petretto
- Program in Cardiovascular and Metabolic Disorders (CVMD) and Center for Computational Biology (CCB), Duke NUS Graduate Medical School, Singapore, Singapore,MRC London Institute of Medical Sciences (LMC), Imperial College, London, United Kingdom,Institute for Big Data and Artificial Intelligence in Medicine, School of Science, China Pharmaceutical University, Nanjing, China
| | - Jacques Behmoaras
- Program in Cardiovascular and Metabolic Disorders (CVMD) and Center for Computational Biology (CCB), Duke NUS Graduate Medical School, Singapore, Singapore,Department of Immunology and Inflammation, Centre for Inflammatory Disease, Imperial College London, London, United Kingdom,*Correspondence: Jacques Behmoaras, ; Federico Torta,
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14
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Kumar P, Lim A, Hazirah SN, Chua CJH, Ngoh A, Poh SL, Yeo TH, Lim J, Ling S, Sutamam NB, Petretto E, Low DCY, Zeng L, Tan EK, Arkachaisri T, Yeo JG, Ginhoux F, Chan D, Albani S. Single-cell transcriptomics and surface epitope detection in human brain epileptic lesions identifies pro-inflammatory signaling. Nat Neurosci 2022; 25:956-966. [PMID: 35739273 PMCID: PMC9276529 DOI: 10.1038/s41593-022-01095-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 05/12/2022] [Indexed: 12/31/2022]
Abstract
Epileptogenic triggers are multifactorial and not well understood. Here we aimed to address the hypothesis that inappropriate pro-inflammatory mechanisms contribute to the pathogenesis of refractory epilepsy (non-responsiveness to antiepileptic drugs) in human patients. We used single-cell cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) to reveal the immunotranscriptome of surgically resected epileptic lesion tissues. Our approach uncovered a pro-inflammatory microenvironment, including extensive activation of microglia and infiltration of other pro-inflammatory immune cells. These findings were supported by ligand–receptor (LR) interactome analysis, which demonstrated potential mechanisms of infiltration and evidence of direct physical interactions between microglia and T cells. Together, these data provide insight into the immune microenvironment in epileptic tissue, which may aid the development of new therapeutics. Single-cell analysis of immune cells from surgically resected human epileptic brain tissues showed heterogeneity and pro-inflammatory signaling in microglia and evidence for direct interaction of microglia with T cells.
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Affiliation(s)
- Pavanish Kumar
- Translational Immunology Institute, SingHealth/Duke-NUS Academic Medical Centre, Singapore, Singapore. .,Paediatrics Academic Clinical Programme, KK Women's and Children's Hospital, Singapore, Singapore.
| | - Amanda Lim
- Translational Immunology Institute, SingHealth/Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Sharifah Nur Hazirah
- Translational Immunology Institute, SingHealth/Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Camillus Jian Hui Chua
- Translational Immunology Institute, SingHealth/Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Adeline Ngoh
- Duke-NUS Medical School and Paediatric Neurology Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - Su Li Poh
- Translational Immunology Institute, SingHealth/Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Tong Hong Yeo
- Duke-NUS Medical School and Paediatric Neurology Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - Jocelyn Lim
- Duke-NUS Medical School and Paediatric Neurology Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - Simon Ling
- Duke-NUS Medical School and Paediatric Neurology Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - Nursyuhadah Binte Sutamam
- Translational Immunology Institute, SingHealth/Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Enrico Petretto
- Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Singapore, Singapore
| | - David Chyi Yeu Low
- Duke-NUS Medical School and Neurosurgical Service, KK Women's and Children's Hospital, Singapore, Singapore.,Research Department, National Neuroscience Institute, Singapore, Singapore
| | - Li Zeng
- Department of Neurology, National Neuroscience Institute, Singapore, Singapore.,Neuroscience & Behavioral Disorders Program, DUKE-NUS Medical School, Singapore, Singapore
| | - Eng-King Tan
- Department of Neurology, National Neuroscience Institute, Singapore, Singapore.,Neuroscience & Behavioral Disorders Program, DUKE-NUS Medical School, Singapore, Singapore
| | - Thaschawee Arkachaisri
- Paediatrics Academic Clinical Programme, KK Women's and Children's Hospital, Singapore, Singapore.,Duke-NUS Medical School and Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - Joo Guan Yeo
- Translational Immunology Institute, SingHealth/Duke-NUS Academic Medical Centre, Singapore, Singapore.,Paediatrics Academic Clinical Programme, KK Women's and Children's Hospital, Singapore, Singapore.,Duke-NUS Medical School and Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - Florent Ginhoux
- Translational Immunology Institute, SingHealth/Duke-NUS Academic Medical Centre, Singapore, Singapore.,Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Derrick Chan
- Paediatrics Academic Clinical Programme, KK Women's and Children's Hospital, Singapore, Singapore.,Duke-NUS Medical School and Paediatric Neurology Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - Salvatore Albani
- Translational Immunology Institute, SingHealth/Duke-NUS Academic Medical Centre, Singapore, Singapore.,Paediatrics Academic Clinical Programme, KK Women's and Children's Hospital, Singapore, Singapore.,Duke-NUS Medical School and Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore, Singapore
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15
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GUO J, Nguyen M, Yamaji T, Azushima K, Gurley S, Petretto E, Coffman M. T. POS-367 UNDERSTANDING GENETIC MECHANISMS OF DIABETIC NEPHROPATHY AT THE SINGLE CELL LEVEL. Kidney Int Rep 2022. [DOI: 10.1016/j.ekir.2022.01.389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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16
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Huang KY, Petretto E. Cross-species integration of single-cell RNA-seq resolved alveolar-epithelial transitional states in idiopathic pulmonary fibrosis. Am J Physiol Lung Cell Mol Physiol 2021; 321:L491-L506. [PMID: 34132117 DOI: 10.1152/ajplung.00594.2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Single-cell transcriptomics analyses of the fibrotic lung uncovered two cell states critical to lung injury recovery in the alveolar epithelium-a reparative transitional cell state in the mouse and a disease-specific cell state (KRT5-/KRT17+) in human idiopathic pulmonary fibrosis (IPF). The murine transitional cell state lies between the differentiation from type 2 (AT2) to type 1 pneumocyte (AT1), and the human KRT5-/KRT17+ cell state may arise from the dysregulation of this differentiation process. We review major findings of single-cell transcriptomics analyses of the fibrotic lung and reanalyzed data from seven single-cell RNA sequencing studies of human and murine models of IPF, focusing on the alveolar epithelium. Our comparative and cross-species single-cell transcriptomics analyses allowed us to further delineate the differentiation trajectories from AT2 to AT1 and AT2 to the KRT5-/KRT17+ cell state. We observed AT1 cells in human IPF retain the transcriptional signature of the murine transitional cell state. Using pseudotime analysis, we recapitulated the differentiation trajectories from AT2 to AT1 and from AT2 to KRT5-/KRT17+ cell state in multiple human IPF studies. We further delineated transcriptional programs underlying cell-state transitions and determined the molecular phenotypes at terminal differentiation. We hypothesize that in addition to the reactivation of developmental programs (SOX4, SOX9), senescence (TP63, SOX4) and the Notch pathway (HES1) are predicted to steer intermediate progenitors to the KRT5-/KRT17+ cell state. Our analyses suggest that activation of SMAD3 later in the differentiation process may explain the fibrotic molecular phenotype typical of KRT5-/KRT17+ cells.
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Affiliation(s)
- Kevin Y Huang
- Program in Cardiovascular and Metabolic Disorders (CVMD) and Center for Computational Biology (CCB), Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Enrico Petretto
- Program in Cardiovascular and Metabolic Disorders (CVMD) and Center for Computational Biology (CCB), Duke-NUS Medical School, Singapore, Republic of Singapore
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17
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Ciconte G, Monasky MM, Santinelli V, Micaglio E, Vicedomini G, Anastasia L, Negro G, Borrelli V, Giannelli L, Santini F, de Innocentiis C, Rondine R, Locati ET, Bernardini A, Mazza BC, Mecarocci V, Ćalović Ž, Ghiroldi A, D'Imperio S, Benedetti S, Di Resta C, Rivolta I, Casari G, Petretto E, Pappone C. Brugada syndrome genetics is associated with phenotype severity. Eur Heart J 2021; 42:1082-1090. [PMID: 33221895 PMCID: PMC7955973 DOI: 10.1093/eurheartj/ehaa942] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/02/2020] [Accepted: 11/02/2020] [Indexed: 12/14/2022] Open
Abstract
Aims Brugada syndrome (BrS) is associated with an increased risk of sudden cardiac death due to ventricular tachycardia/fibrillation (VT/VF) in young, otherwise healthy individuals. Despite SCN5A being the most commonly known mutated gene to date, the genotype–phenotype relationship is poorly understood and remains uncertain. This study aimed to elucidate the genotype–phenotype correlation in BrS. Methods and results Brugada syndrome probands deemed at high risk of future arrhythmic events underwent genetic testing and phenotype characterization by the means of epicardial arrhythmogenic substrate (AS) mapping, and were divided into two groups according to the presence or absence of SCN5A mutation. Two-hundred probands (160 males, 80%; mean age 42.6 ± 12.2 years) were included in this study. Patients harbouring SCN5A mutations exhibited a spontaneous type 1 pattern and experienced aborted cardiac arrest or spontaneous VT/VF more frequently than the other subjects. SCN5A-positive patients exhibited a larger epicardial AS area, more prolonged electrograms and more frequently observed non-invasive late potentials. The presence of an SCN5A mutation explained >26% of the variation in the epicardial AS area and was the strongest predictor of a large epicardial area. Conclusion In BrS, the genetic background is the main determinant for the extent of the electrophysiological abnormalities. SCN5A mutation carriers exhibit more pronounced epicardial electrical abnormalities and a more aggressive clinical presentation. These results contribute to the understanding of the genetic determinants of the BrS phenotypic expression and provide possible explanations for the varying degrees of disease expression. ![]()
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Affiliation(s)
- Giuseppe Ciconte
- Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, Piazza E. Malan 1, 20097 San Donato Milanese, Milano, Italy
| | - Michelle M Monasky
- Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, Piazza E. Malan 1, 20097 San Donato Milanese, Milano, Italy
| | - Vincenzo Santinelli
- Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, Piazza E. Malan 1, 20097 San Donato Milanese, Milano, Italy
| | - Emanuele Micaglio
- Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, Piazza E. Malan 1, 20097 San Donato Milanese, Milano, Italy
| | - Gabriele Vicedomini
- Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, Piazza E. Malan 1, 20097 San Donato Milanese, Milano, Italy
| | - Luigi Anastasia
- Stem Cells for Tissue Engineering Laboratory, IRCCS Policlinico San Donato, piazza Malan 2, 20097 San Donato Milanese, Milan, Italy.,Vita-Salute San Raffaele University, Milan, Italy
| | - Gabriele Negro
- Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, Piazza E. Malan 1, 20097 San Donato Milanese, Milano, Italy
| | - Valeria Borrelli
- Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, Piazza E. Malan 1, 20097 San Donato Milanese, Milano, Italy
| | - Luigi Giannelli
- Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, Piazza E. Malan 1, 20097 San Donato Milanese, Milano, Italy
| | - Francesca Santini
- Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, Piazza E. Malan 1, 20097 San Donato Milanese, Milano, Italy
| | - Carlo de Innocentiis
- Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, Piazza E. Malan 1, 20097 San Donato Milanese, Milano, Italy
| | - Roberto Rondine
- Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, Piazza E. Malan 1, 20097 San Donato Milanese, Milano, Italy
| | - Emanuela T Locati
- Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, Piazza E. Malan 1, 20097 San Donato Milanese, Milano, Italy
| | - Andrea Bernardini
- Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, Piazza E. Malan 1, 20097 San Donato Milanese, Milano, Italy
| | - Beniamino C Mazza
- Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, Piazza E. Malan 1, 20097 San Donato Milanese, Milano, Italy
| | - Valerio Mecarocci
- Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, Piazza E. Malan 1, 20097 San Donato Milanese, Milano, Italy
| | - Žarko Ćalović
- Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, Piazza E. Malan 1, 20097 San Donato Milanese, Milano, Italy
| | - Andrea Ghiroldi
- Stem Cells for Tissue Engineering Laboratory, IRCCS Policlinico San Donato, piazza Malan 2, 20097 San Donato Milanese, Milan, Italy
| | - Sara D'Imperio
- Stem Cells for Tissue Engineering Laboratory, IRCCS Policlinico San Donato, piazza Malan 2, 20097 San Donato Milanese, Milan, Italy
| | - Sara Benedetti
- Clinical Genomics - SMEL, IRCCS San Raffaele Hospital, Milan, Italy
| | - Chiara Di Resta
- Vita-Salute San Raffaele University, Milan, Italy.,Clinical Genomics - SMEL, IRCCS San Raffaele Hospital, Milan, Italy
| | - Ilaria Rivolta
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Giorgio Casari
- Vita-Salute San Raffaele University, Milan, Italy.,Clinical Genomics - SMEL, IRCCS San Raffaele Hospital, Milan, Italy
| | - Enrico Petretto
- Programme in Cardiovascular and Metabolic Disorders and Centre for Computational Biology, Duke-NUS Medical School Singapore, Republic of Singapore
| | - Carlo Pappone
- Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, Piazza E. Malan 1, 20097 San Donato Milanese, Milano, Italy.,Vita-Salute San Raffaele University, Milan, Italy
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18
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Kaur A, Lim JYS, Sepramaniam S, Patnaik S, Harmston N, Lee MA, Petretto E, Virshup DM, Madan B. WNT inhibition creates a BRCA-like state in Wnt-addicted cancer. EMBO Mol Med 2021; 13:e13349. [PMID: 33660437 PMCID: PMC8033517 DOI: 10.15252/emmm.202013349] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 01/25/2021] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
Wnt signaling maintains diverse adult stem cell compartments and is implicated in chemotherapy resistance in cancer. PORCN inhibitors that block Wnt secretion have proven effective in Wnt-addicted preclinical cancer models and are in clinical trials. In a survey for potential combination therapies, we found that Wnt inhibition synergizes with the PARP inhibitor olaparib in Wnt-addicted cancers. Mechanistically, we find that multiple genes in the homologous recombination and Fanconi anemia repair pathways, including BRCA1, FANCD2, and RAD51, are dependent on Wnt/β-catenin signaling in Wnt-high cancers, and treatment with a PORCN inhibitor creates a BRCA-like state. This coherent regulation of DNA repair genes occurs in part via a Wnt/β-catenin/MYBL2 axis. Importantly, this pathway also functions in intestinal crypts, where high expression of BRCA and Fanconi anemia genes is seen in intestinal stem cells, with further upregulation in Wnt-high APCmin mutant polyps. Our findings suggest a general paradigm that Wnt/β-catenin signaling enhances DNA repair in stem cells and cancers to maintain genomic integrity. Conversely, interventions that block Wnt signaling may sensitize cancers to radiation and other DNA damaging agents.
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Affiliation(s)
- Amanpreet Kaur
- Program in Cancer and Stem Cell BiologyDuke‐NUS Medical SchoolSingaporeSingapore
| | - Jun Yi Stanley Lim
- Program in Cancer and Stem Cell BiologyDuke‐NUS Medical SchoolSingaporeSingapore
| | | | - Siddhi Patnaik
- Program in Cancer and Stem Cell BiologyDuke‐NUS Medical SchoolSingaporeSingapore
| | - Nathan Harmston
- Program in Cancer and Stem Cell BiologyDuke‐NUS Medical SchoolSingaporeSingapore
- Science DivisionYale‐NUS CollegeSingaporeSingapore
| | - May Ann Lee
- Experimental Drug Development CentreA*StarSingaporeSingapore
| | - Enrico Petretto
- Center for Computational Biology and Program in Cardiovascular and Metabolic DisordersDuke‐NUS Medical SchoolSingaporeSingapore
| | - David M Virshup
- Program in Cancer and Stem Cell BiologyDuke‐NUS Medical SchoolSingaporeSingapore
- Department of PediatricsDuke University School of MedicineDurhamNCUSA
| | - Babita Madan
- Program in Cancer and Stem Cell BiologyDuke‐NUS Medical SchoolSingaporeSingapore
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19
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Lovisari F, Roncon P, Soukoupova M, Paolone G, Labasque M, Ingusci S, Falcicchia C, Marino P, Johnson M, Rossetti T, Petretto E, Leclercq K, Kaminski RM, Moyon B, Webster Z, Simonato M, Zucchini S. Implication of sestrin3 in epilepsy and its comorbidities. Brain Commun 2021; 3:fcaa130. [PMID: 33758823 PMCID: PMC7966953 DOI: 10.1093/braincomms/fcaa130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 06/30/2020] [Accepted: 07/13/2020] [Indexed: 12/21/2022] Open
Abstract
Epilepsy is a serious neurological disorder affecting about 1% of the population worldwide. Epilepsy may arise as a result of acquired brain injury, or as a consequence of genetic predisposition. To date, genome-wide association studies and exome sequencing approaches have provided limited insights into the mechanisms of acquired brain injury. We have previously reported a pro-epileptic gene network, which is conserved across species, encoding inflammatory processes and positively regulated by sestrin3 (SESN3). In this study, we investigated the phenotype of SESN3 knock-out rats in terms of susceptibility to seizures and observed a significant delay in status epilepticus onset in SESN3 knock-out compared to control rats. This finding confirms previous in vitro and in vivo evidence indicating that SESN3 may favour occurrence and/or severity of seizures. We also analysed the phenotype of SESN3 knock-out rats for common comorbidities of epilepsy, i.e., anxiety, depression and cognitive impairment. SESN3 knock-out rats proved less anxious compared to control rats in a selection of behavioural tests. Taken together, the present results suggest that SESN3 may regulate mechanisms involved in the pathogenesis of epilepsy and its comorbidities.
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Affiliation(s)
- Francesca Lovisari
- Department of Medical Sciences, Section of Pharmacology, University of Ferrara, Italy
| | - Paolo Roncon
- Division of Neuroscience, School of Medicine, University Vita-Salute San Raffaele, Milan, Italy
| | - Marie Soukoupova
- Department of Medical Sciences, Section of Pharmacology, University of Ferrara, Italy
| | - Giovanna Paolone
- Department of Medical Sciences, Section of Pharmacology, University of Ferrara, Italy
| | - Marilyne Labasque
- Department of Medical Sciences, Section of Pharmacology, University of Ferrara, Italy
| | - Selene Ingusci
- Department of Medical Sciences, Section of Pharmacology, University of Ferrara, Italy
| | - Chiara Falcicchia
- Department of Medical Sciences, Section of Pharmacology, University of Ferrara, Italy
| | - Pietro Marino
- Department of Medical Sciences, Section of Pharmacology, University of Ferrara, Italy
| | | | | | - Enrico Petretto
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore.,MRC London Institute of Medical Sciences (LMC), Imperial College London, UK
| | - Karine Leclercq
- Neuroscience TA, UCB Biopharma SPRL, Braine l'Alleud, Belgium
| | | | - Ben Moyon
- Es Cell and Transgenics, Medical Research Council, Imperial College London, UK
| | - Zoe Webster
- Es Cell and Transgenics, Medical Research Council, Imperial College London, UK
| | - Michele Simonato
- Department of Medical Sciences, Section of Pharmacology, University of Ferrara, Italy.,Division of Neuroscience, School of Medicine, University Vita-Salute San Raffaele, Milan, Italy
| | - Silvia Zucchini
- Department of Medical Sciences, Section of Pharmacology, University of Ferrara, Italy
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20
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Harmston N, Lim JYS, Arqués O, Palmer HG, Petretto E, Virshup DM, Madan B. Widespread Repression of Gene Expression in Cancer by a Wnt/β-Catenin/MAPK Pathway. Cancer Res 2020; 81:464-475. [PMID: 33203702 DOI: 10.1158/0008-5472.can-20-2129] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 10/06/2020] [Accepted: 11/12/2020] [Indexed: 11/16/2022]
Abstract
Aberrant Wnt signaling drives a number of cancers through regulation of diverse downstream pathways. Wnt/β-catenin signaling achieves this in part by increasing the expression of proto-oncogenes such as MYC and cyclins. However, global assessment of the Wnt-regulated transcriptome in vivo in genetically distinct cancers demonstrates that Wnt signaling suppresses the expression of as many genes as it activates. In this study, we examined the set of genes that are upregulated upon inhibition of Wnt signaling in Wnt-addicted pancreatic and colorectal cancer models. Decreasing Wnt signaling led to a marked increase in gene expression by activating ERK and JNK; these changes in gene expression could be mitigated in part by concurrent inhibition of MEK. These findings demonstrate that increased Wnt signaling in cancer represses MAPK activity, preventing RAS-mediated senescence while allowing cancer cells to proliferate. These results shift the paradigm from Wnt/β-catenin primarily as an activator of transcription to a more nuanced view where Wnt/β-catenin signaling drives both widespread gene repression and activation. SIGNIFICANCE: These findings show that Wnt/β-catenin signaling causes widespread gene repression via inhibition of MAPK signaling, thus fine tuning the RAS-MAPK pathway to optimize proliferation in cancer.
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Affiliation(s)
- Nathan Harmston
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore.,Science Division, Yale-NUS College, Singapore
| | - Jun Yi Stanley Lim
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Oriol Arqués
- Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), CIBERONC, Barcelona, Spain
| | - Héctor G Palmer
- Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), CIBERONC, Barcelona, Spain
| | - Enrico Petretto
- Center for Computational Biology and Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - David M Virshup
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore. .,Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina
| | - Babita Madan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore.
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21
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Kamaraj US, Chen J, Katwadi K, Ouyang JF, Yang Sun YB, Lim YM, Liu X, Handoko L, Polo JM, Petretto E, Rackham OJ. EpiMogrify Models H3K4me3 Data to Identify Signaling Molecules that Improve Cell Fate Control and Maintenance. Cell Syst 2020; 11:509-522.e10. [DOI: 10.1016/j.cels.2020.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 04/30/2020] [Accepted: 09/14/2020] [Indexed: 12/14/2022]
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22
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Liu S, Harmston N, Glaser TL, Wong Y, Zhong Z, Madan B, Virshup DM, Petretto E. Wnt-regulated lncRNA discovery enhanced by in vivo identification and CRISPRi functional validation. Genome Med 2020; 12:89. [PMID: 33092630 PMCID: PMC7580003 DOI: 10.1186/s13073-020-00788-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 10/02/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Wnt signaling is an evolutionarily conserved developmental pathway that is frequently hyperactivated in cancer. While multiple protein-coding genes regulated by Wnt signaling are known, the functional lncRNAs regulated by Wnt signaling have not been systematically characterized. METHODS We comprehensively mapped Wnt-regulated lncRNAs from an orthotopic Wnt-addicted pancreatic cancer model and examined the response of lncRNAs to Wnt inhibition between in vivo and in vitro cancer models. We further annotated and characterized these Wnt-regulated lncRNAs using existing genomic classifications (using data from FANTOM5) in the context of Wnt signaling and inferred their role in cancer pathogenesis (using GWAS and expression data from the TCGA). To functionally validate Wnt-regulated lncRNAs, we performed CRISPRi screens to assess their role in cancer cell proliferation both in vivo and in vitro. RESULTS We identified 3633 lncRNAs, of which 1503 were regulated by Wnt signaling in an orthotopic Wnt-addicted pancreatic cancer model. These lncRNAs were much more sensitive to changes in Wnt signaling in xenografts than in cultured cells. Our analysis suggested that Wnt signaling inhibition could influence the co-expression relationship of Wnt-regulated lncRNAs and their eQTL-linked protein-coding genes. Wnt-regulated lncRNAs were also implicated in specific gene networks involved in distinct biological processes that contribute to the pathogenesis of cancers. Consistent with previous genome-wide lncRNA CRISPRi screens, around 1% (13/1503) of the Wnt-regulated lncRNAs were found to modify cancer cell growth in vitro. This included CCAT1 and LINC00263, previously reported to regulate cancer growth. Using an in vivo CRISPRi screen, we doubled the discovery rate, identifying twice as many Wnt-regulated lncRNAs (25/1503) that had a functional effect on cancer cell growth. CONCLUSIONS Our study demonstrates the value of studying lncRNA functions in vivo, provides a valuable resource of lncRNAs regulated by Wnt signaling, and establishes a framework for systematic discovery of functional lncRNAs.
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Affiliation(s)
- Shiyang Liu
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | | | - Trudy Lee Glaser
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Yunka Wong
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Zheng Zhong
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Babita Madan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - David M Virshup
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore.
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA.
| | - Enrico Petretto
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore.
- MRC London Institute of Medical Sciences, Imperial College London, London, UK.
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23
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Pereira M, Ko JH, Logan J, Protheroe H, Kim KB, Tan ALM, Croucher PI, Park KS, Rotival M, Petretto E, Bassett JD, Williams GR, Behmoaras J. A trans-eQTL network regulates osteoclast multinucleation and bone mass. eLife 2020; 9:55549. [PMID: 32553114 PMCID: PMC7351491 DOI: 10.7554/elife.55549] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 06/12/2020] [Indexed: 12/11/2022] Open
Abstract
Functional characterisation of cell-type-specific regulatory networks is key to establish a causal link between genetic variation and phenotype. The osteoclast offers a unique model for interrogating the contribution of co-regulated genes to in vivo phenotype as its multinucleation and resorption activities determine quantifiable skeletal traits. Here we took advantage of a trans-regulated gene network (MMnet, macrophage multinucleation network) which we found to be significantly enriched for GWAS variants associated with bone-related phenotypes. We found that the network hub gene Bcat1 and seven other co-regulated MMnet genes out of 13, regulate bone function. Specifically, global (Pik3cb-/-, Atp8b2+/-, Igsf8-/-, Eml1-/-, Appl2-/-, Deptor-/-) and myeloid-specific Slc40a1 knockout mice displayed abnormal bone phenotypes. We report opposing effects of MMnet genes on bone mass in mice and osteoclast multinucleation/resorption in humans with strong correlation between the two. These results identify MMnet as a functionally conserved network that regulates osteoclast multinucleation and bone mass.
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Affiliation(s)
- Marie Pereira
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Hammersmith Hospital, Imperial College London, London, United Kingdom.,Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Hammersmith Hospital, Imperial College London, London, United Kingdom
| | - Jeong-Hun Ko
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Hammersmith Hospital, Imperial College London, London, United Kingdom.,Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Hammersmith Hospital, Imperial College London, London, United Kingdom
| | - John Logan
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Hammersmith Hospital, Imperial College London, London, United Kingdom
| | - Hayley Protheroe
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Hammersmith Hospital, Imperial College London, London, United Kingdom
| | - Kee-Beom Kim
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, United States
| | | | - Peter I Croucher
- The Garvan Institute of Medical Research and St. Vincent's Clinical School, University of NewSouth Wales Medicine, Sydney, Australia
| | - Kwon-Sik Park
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, United States
| | - Maxime Rotival
- Human Evolutionary Genetics Unit, Institut Pasteur, Centre National de la Recherche Scientifique, UMR 2000, Paris, France
| | | | - Jh Duncan Bassett
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Hammersmith Hospital, Imperial College London, London, United Kingdom
| | - Graham R Williams
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Hammersmith Hospital, Imperial College London, London, United Kingdom
| | - Jacques Behmoaras
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Hammersmith Hospital, Imperial College London, London, United Kingdom
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24
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Yap L, Wang JW, Moreno-Moral A, Chong LY, Sun Y, Harmston N, Wang X, Chong SY, Vanezis K, Öhman MK, Wei H, Bunte R, Gosh S, Cook S, Hovatta O, de Kleijn DPV, Petretto E, Tryggvason K. In Vivo Generation of Post-infarct Human Cardiac Muscle by Laminin-Promoted Cardiovascular Progenitors. Cell Rep 2020; 31:107714. [PMID: 32460024 DOI: 10.1016/j.celrep.2020.107714] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Lynn Yap
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Jiong-Wei Wang
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore; Cardiovascular Research Institute, National University Heart Centre, Singapore 117599, Singapore
| | - Aida Moreno-Moral
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Li Yen Chong
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Yi Sun
- BioLamina AB, Lö fströ ms Allé 5A, Sundbyberg 17266, Sweden
| | - Nathan Harmston
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Xiaoyuan Wang
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Cardiovascular Research Institute, National University Heart Centre, Singapore 117599, Singapore
| | - Suet Yen Chong
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Cardiovascular Research Institute, National University Heart Centre, Singapore 117599, Singapore
| | - Konstantinos Vanezis
- Cardiovascular Genetics and Genomics Group, MRC London Institute of Medical Sciences, Imperial Centre for Translational and Experimental Medicine, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Miina K Öhman
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Heming Wei
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore; National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore 169609, Singapore
| | - Ralph Bunte
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Sujoy Gosh
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Stuart Cook
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore; National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore 169609, Singapore; National Heart & Lung Institute, Imperial College London, Cale Street, London SW3 6LY, UK
| | - Outi Hovatta
- Division of Obstetrics and Gynecology, Department of Clinical Sciences, Intervention and Technology, Karolinska Institute and Karolinska University Hospital, Huddinge, Stockholm 141 86, Sweden
| | - Dominique P V de Kleijn
- Cardiovascular Research Institute, National University Heart Centre, Singapore 117599, Singapore; University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Enrico Petretto
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Karl Tryggvason
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore; Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77 Stockholm, Sweden.
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25
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Yap L, Wang JW, Moreno-Moral A, Chong LY, Sun Y, Harmston N, Wang X, Chong SY, Vanezis K, Öhman MK, Wei H, Bunte R, Gosh S, Cook S, Hovatta O, de Kleijn DPV, Petretto E, Tryggvason K. In Vivo Generation of Post-infarct Human Cardiac Muscle by Laminin-Promoted Cardiovascular Progenitors. Cell Rep 2020; 26:3231-3245.e9. [PMID: 30893597 DOI: 10.1016/j.celrep.2019.02.083] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 01/15/2019] [Accepted: 02/21/2019] [Indexed: 12/25/2022] Open
Abstract
Regeneration of injured human heart muscle is limited and an unmet clinical need. There are no methods for the reproducible generation of clinical-quality stem cell-derived cardiovascular progenitors (CVPs). We identified laminin-221 (LN-221) as the most likely expressed cardiac laminin. We produced it as human recombinant protein and showed that LN-221 promotes differentiation of pluripotent human embryonic stem cells (hESCs) toward cardiomyocyte lineage and downregulates pluripotency and teratoma-associated genes. We developed a chemically defined, xeno-free laminin-based differentiation protocol to generate CVPs. We show high reproducibility of the differentiation protocol using time-course bulk RNA sequencing developed from different hESC lines. Single-cell RNA sequencing of CVPs derived from hESC lines supported reproducibility and identified three main progenitor subpopulations. These CVPs were transplanted into myocardial infarction mice, where heart function was measured by echocardiogram and human heart muscle bundle formation was identified histologically. This method may provide clinical-quality cells for use in regenerative cardiology.
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Affiliation(s)
- Lynn Yap
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Jiong-Wei Wang
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore; Cardiovascular Research Institute, National University Heart Centre, Singapore 117599, Singapore
| | - Aida Moreno-Moral
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Li Yen Chong
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Yi Sun
- BioLamina AB, Löfströms Allé 5A, Sundbyberg 17266, Sweden
| | - Nathan Harmston
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Xiaoyuan Wang
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Cardiovascular Research Institute, National University Heart Centre, Singapore 117599, Singapore
| | - Suet Yen Chong
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Cardiovascular Research Institute, National University Heart Centre, Singapore 117599, Singapore
| | - Konstantinos Vanezis
- Cardiovascular Genetics and Genomics Group MRC London Institute of Medical Sciences, Imperial Centre for Translational and Experimental Medicine, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Miina K Öhman
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Heming Wei
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore; National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore 169609, Singapore
| | - Ralph Bunte
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Sujoy Gosh
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Stuart Cook
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore; National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore 169609, Singapore; National Heart & Lung Institute, Imperial College London, Cale Street, London SW3 6LY, UK
| | - Outi Hovatta
- Division of Obstetrics and Gynecology, Department of Clinical Sciences, Intervention and Technology, Karolinska Institute and Karolinska University Hospital, Huddinge, Stockholm 141 86, Sweden
| | - Dominique P V de Kleijn
- Cardiovascular Research Institute, National University Heart Centre, Singapore 117599, Singapore; University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Enrico Petretto
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Karl Tryggvason
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore; Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77 Stockholm, Sweden.
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26
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Jupp B, Pitzoi S, Petretto E, Mar AC, Oliver YP, Jordan ER, Taylor S, Atanur SS, Srivastava PK, Saar K, Hubner N, Sommer WH, Staehlin O, Spanagel R, Robinson ES, Schumann G, Moreno M, Everitt BJ, Robbins TW, Aitman TJ, Dalley JW. Impulsivity is a heritable trait in rodents and associated with a novel quantitative trait locus on chromosome 1. Sci Rep 2020; 10:6684. [PMID: 32317713 PMCID: PMC7174407 DOI: 10.1038/s41598-020-63646-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/01/2020] [Indexed: 12/30/2022] Open
Abstract
Impulsivity describes the tendency to act prematurely without appropriate foresight and is symptomatic of a number of neuropsychiatric disorders. Although a number of genes for impulsivity have been identified, no study to date has carried out an unbiased, genome-wide approach to identify genetic markers associated with impulsivity in experimental animals. Herein we report a linkage study of a six-generational pedigree of adult rats phenotyped for one dimension of impulsivity, namely premature responding on the five-choice serial reaction time task, combined with genome wide sequencing and transcriptome analysis to identify candidate genes associated with the expression of the impulsivity trait. Premature responding was found to be heritable (h2 = 13-16%), with significant linkage (LOD 5.2) identified on chromosome 1. Fine mapping of this locus identified a number of polymorphic candidate genes, however only one, beta haemoglobin, was differentially expressed in both the founder strain and F6 generation. These findings provide novel insights into the genetic substrates and putative neurobiological mechanisms of impulsivity with broader translational relevance for impulsivity-related disorders in humans.
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Affiliation(s)
- Bianca Jupp
- 0000000121885934grid.5335.0Department of Psychology and Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge, UK
| | - Silvia Pitzoi
- 0000 0001 2113 8111grid.7445.2MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, UK
| | - Enrico Petretto
- 0000 0001 2113 8111grid.7445.2MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, UK ,0000 0004 0385 0924grid.428397.3Duke-NUS Medical School, Singapore, Singapore
| | - Adam C. Mar
- 0000000121885934grid.5335.0Department of Psychology and Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge, UK ,0000 0004 1936 8753grid.137628.9NYU School of Medicine, New York, USA
| | - Yolanda Pena Oliver
- 0000 0004 1936 7590grid.12082.39School of Psychology, University of Sussex, Brighton, UK
| | - Emily R. Jordan
- 0000000121885934grid.5335.0Department of Psychology and Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge, UK
| | - Stephanie Taylor
- 0000000121885934grid.5335.0Department of Psychology and Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge, UK
| | - Santosh S. Atanur
- 0000 0001 2113 8111grid.7445.2MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, UK
| | - Prashant K. Srivastava
- 0000 0001 2113 8111grid.7445.2MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, UK
| | - Kathrin Saar
- 0000 0001 1014 0849grid.419491.0Max Delbruck Centre for Molecular Medicine, Berlin, Germany
| | - Norbert Hubner
- 0000 0001 1014 0849grid.419491.0Max Delbruck Centre for Molecular Medicine, Berlin, Germany
| | - Wolfgang H. Sommer
- 0000 0004 0477 2235grid.413757.3Institute of Psychopharmacology, Central Institute of Mental Health, Faculty of Medicine Mannheim, University of Heidelberg, Mannheim, Germany
| | - Oliver Staehlin
- 0000 0004 0477 2235grid.413757.3Institute of Psychopharmacology, Central Institute of Mental Health, Faculty of Medicine Mannheim, University of Heidelberg, Mannheim, Germany
| | - Rainer Spanagel
- 0000 0004 0477 2235grid.413757.3Institute of Psychopharmacology, Central Institute of Mental Health, Faculty of Medicine Mannheim, University of Heidelberg, Mannheim, Germany
| | - Emma S. Robinson
- 0000 0004 1936 7603grid.5337.2School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
| | - Gunter Schumann
- 0000 0001 2322 6764grid.13097.3cCentre for Population Neuroscience and Stratified Medicine, Institute of Psychiatry, Psychology and Neuroscience, King¹s College, London, UK
| | - Margarita Moreno
- 0000000101969356grid.28020.38Department of Psychology & Health Research Centre (CEINSA), University of Almería, Almería, Spain
| | - Barry J. Everitt
- 0000000121885934grid.5335.0Department of Psychology and Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge, UK
| | - Trevor W. Robbins
- 0000000121885934grid.5335.0Department of Psychology and Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge, UK
| | - Timothy J. Aitman
- 0000 0004 1936 7988grid.4305.2Centre for Genomics and Experimental Medicine, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Jeffrey W. Dalley
- 0000000121885934grid.5335.0Department of Psychology and Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge, UK ,0000000121885934grid.5335.0Department of Psychiatry, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
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27
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Guo J, Rackham OJL, Sandholm N, He B, Österholm AM, Valo E, Harjutsalo V, Forsblom C, Toppila I, Parkkonen M, Li Q, Zhu W, Harmston N, Chothani S, Öhman MK, Eng E, Sun Y, Petretto E, Groop PH, Tryggvason K. Whole-Genome Sequencing of Finnish Type 1 Diabetic Siblings Discordant for Kidney Disease Reveals DNA Variants associated with Diabetic Nephropathy. J Am Soc Nephrol 2020; 31:309-323. [PMID: 31919106 DOI: 10.1681/asn.2019030289] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 10/19/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Several genetic susceptibility loci associated with diabetic nephropathy have been documented, but no causative variants implying novel pathogenetic mechanisms have been elucidated. METHODS We carried out whole-genome sequencing of a discovery cohort of Finnish siblings with type 1 diabetes who were discordant for the presence (case) or absence (control) of diabetic nephropathy. Controls had diabetes without complications for 15-37 years. We analyzed and annotated variants at genome, gene, and single-nucleotide variant levels. We then replicated the associated variants, genes, and regions in a replication cohort from the Finnish Diabetic Nephropathy study that included 3531 unrelated Finns with type 1 diabetes. RESULTS We observed protein-altering variants and an enrichment of variants in regions associated with the presence or absence of diabetic nephropathy. The replication cohort confirmed variants in both regulatory and protein-coding regions. We also observed that diabetic nephropathy-associated variants, when clustered at the gene level, are enriched in a core protein-interaction network representing proteins essential for podocyte function. These genes include protein kinases (protein kinase C isoforms ε and ι) and protein tyrosine kinase 2. CONCLUSIONS Our comprehensive analysis of a diabetic nephropathy cohort of siblings with type 1 diabetes who were discordant for kidney disease points to variants and genes that are potentially causative or protective for diabetic nephropathy. This includes variants in two isoforms of the protein kinase C family not previously linked to diabetic nephropathy, adding support to previous hypotheses that the protein kinase C family members play a role in diabetic nephropathy and might be attractive therapeutic targets.
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Affiliation(s)
- Jing Guo
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Cardiovascular and Metabolic Disorders Programme, Duke-National University of Singapore Medical School, Singapore
| | - Owen J L Rackham
- Cardiovascular and Metabolic Disorders Programme, Duke-National University of Singapore Medical School, Singapore
| | - Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Centre, Helsinki, Finland.,Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Bing He
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Anne-May Österholm
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Cardiovascular and Metabolic Disorders Programme, Duke-National University of Singapore Medical School, Singapore
| | - Erkka Valo
- Folkhälsan Institute of Genetics, Folkhälsan Research Centre, Helsinki, Finland.,Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Valma Harjutsalo
- Folkhälsan Institute of Genetics, Folkhälsan Research Centre, Helsinki, Finland.,Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Chronic Disease Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Carol Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Centre, Helsinki, Finland.,Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Iiro Toppila
- Folkhälsan Institute of Genetics, Folkhälsan Research Centre, Helsinki, Finland.,Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Maija Parkkonen
- Folkhälsan Institute of Genetics, Folkhälsan Research Centre, Helsinki, Finland.,Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Qibin Li
- Complex Disease Research Center, BGI Genomics, Shenzhen, China
| | - Wenjuan Zhu
- Complex Disease Research Center, BGI Genomics, Shenzhen, China
| | - Nathan Harmston
- Cardiovascular and Metabolic Disorders Programme, Duke-National University of Singapore Medical School, Singapore.,Science Division, Yale-National University of Singapore College, National University of Singapore, Singapore
| | - Sonia Chothani
- Cardiovascular and Metabolic Disorders Programme, Duke-National University of Singapore Medical School, Singapore
| | - Miina K Öhman
- Cardiovascular and Metabolic Disorders Programme, Duke-National University of Singapore Medical School, Singapore
| | - Eudora Eng
- Cardiovascular and Metabolic Disorders Programme, Duke-National University of Singapore Medical School, Singapore
| | - Yang Sun
- Cardiovascular and Metabolic Disorders Programme, Duke-National University of Singapore Medical School, Singapore
| | - Enrico Petretto
- Cardiovascular and Metabolic Disorders Programme, Duke-National University of Singapore Medical School, Singapore; .,MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Centre, Helsinki, Finland; .,Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia; and
| | - Karl Tryggvason
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden; .,Cardiovascular and Metabolic Disorders Programme, Duke-National University of Singapore Medical School, Singapore.,Division of Nephrology, Department of Medicine, Duke University, Durham, North Carolina
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28
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Idris M, Harmston N, Petretto E, Madan B, Virshup DM. Broad regulation of gene isoform expression by Wnt signaling in cancer. RNA 2019; 25:1696-1713. [PMID: 31506381 PMCID: PMC6859862 DOI: 10.1261/rna.071506.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/06/2019] [Indexed: 05/08/2023]
Abstract
Differential gene isoform expression is a ubiquitous mechanism to enhance proteome diversity and maintain cell homeostasis. Mechanisms such as splicing that drive gene isoform variability are highly dynamic and responsive to changes in cell signaling pathways. Wnt/β-catenin signaling has profound effects on cell activity and cell fate and is known to modify several splicing events by altering the expression of individual splicing factors. However, a global assessment of how extensively Wnt signaling regulates splicing and other mechanisms that determine mRNA isoform composition in cancer is lacking. We used deep time-resolved RNA-seq in two independent in vivo Wnt-addicted tumor models during treatment with the potent Wnt inhibitor ETC-159 and examined Wnt regulated splicing events and splicing regulators. We found 1025 genes that underwent Wnt regulated variable exon usage leading to isoform expression changes. This was accompanied by extensive Wnt regulated changes in the expression of splicing regulators. Many of these Wnt regulated events were conserved in multiple human cancers, and many were linked to previously defined cancer-associated splicing quantitative trait loci. This suggests that the Wnt regulated splicing events are components of fundamental oncogenic processes. These findings demonstrate the wide-ranging effects of Wnt signaling on the isoform composition of the cell and provides an extensive resource of expression changes of splicing regulators and gene isoforms regulated by Wnt signaling.
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Affiliation(s)
- Muhammad Idris
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857
| | - Nathan Harmston
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857
- Centre for Computational Biology and Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857
- Science Division, Yale-NUS College, Singapore, 138527
| | - Enrico Petretto
- Centre for Computational Biology and Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857
| | - Babita Madan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857
| | - David M Virshup
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina 27705, USA
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29
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Grubman A, Chew G, Ouyang JF, Sun G, Choo XY, McLean C, Simmons RK, Buckberry S, Vargas-Landin DB, Poppe D, Pflueger J, Lister R, Rackham OJL, Petretto E, Polo JM. A single-cell atlas of entorhinal cortex from individuals with Alzheimer's disease reveals cell-type-specific gene expression regulation. Nat Neurosci 2019; 22:2087-2097. [PMID: 31768052 DOI: 10.1038/s41593-019-0539-4] [Citation(s) in RCA: 434] [Impact Index Per Article: 86.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There is currently little information available about how individual cell types contribute to Alzheimer's disease. Here we applied single-nucleus RNA sequencing to entorhinal cortex samples from control and Alzheimer's disease brains (n = 6 per group), yielding a total of 13,214 high-quality nuclei. We detail cell-type-specific gene expression patterns, unveiling how transcriptional changes in specific cell subpopulations are associated with Alzheimer's disease. We report that the Alzheimer's disease risk gene APOE is specifically repressed in Alzheimer's disease oligodendrocyte progenitor cells and astrocyte subpopulations and upregulated in an Alzheimer's disease-specific microglial subopulation. Integrating transcription factor regulatory modules with Alzheimer's disease risk loci revealed drivers of cell-type-specific state transitions towards Alzheimer's disease. For example, transcription factor EB, a master regulator of lysosomal function, regulates multiple disease genes in a specific Alzheimer's disease astrocyte subpopulation. These results provide insights into the coordinated control of Alzheimer's disease risk genes and their cell-type-specific contribution to disease susceptibility. These results are available at http://adsn.ddnetbio.com.
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Affiliation(s)
- Alexandra Grubman
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Gabriel Chew
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Guizhi Sun
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Xin Yi Choo
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
- Department of Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Catriona McLean
- Victorian Brain Bank, Florey Institute of Neurosciences, Parkville, Victoria, Australia
| | - Rebecca K Simmons
- ARC Center of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Sam Buckberry
- ARC Center of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Dulce B Vargas-Landin
- ARC Center of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Daniel Poppe
- ARC Center of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Jahnvi Pflueger
- ARC Center of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Ryan Lister
- ARC Center of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore.
| | - Enrico Petretto
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore.
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia.
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia.
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30
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Adriaens ME, Lodder EM, Moreno‐Moral A, Šilhavý J, Heinig M, Glinge C, Belterman C, Wolswinkel R, Petretto E, Pravenec M, Remme CA, Bezzina CR. Systems Genetics Approaches in Rat Identify Novel Genes and Gene Networks Associated With Cardiac Conduction. J Am Heart Assoc 2019; 7:e009243. [PMID: 30608189 PMCID: PMC6404199 DOI: 10.1161/jaha.118.009243] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Background Electrocardiographic (ECG) parameters are regarded as intermediate phenotypes of cardiac arrhythmias. Insight into the genetic underpinnings of these parameters is expected to contribute to the understanding of cardiac arrhythmia mechanisms. Here we used HXB/BXH recombinant inbred rat strains to uncover genetic loci and candidate genes modulating ECG parameters. Methods and Results RR interval, PR interval, QRS duration, and QTc interval were measured from ECGs obtained in 6 male rats from each of the 29 available HXB/BXH recombinant inbred strains. Genes at loci displaying significant quantitative trait loci (QTL) effects were prioritized by assessing the presence of protein‐altering variants, and by assessment of cis expression QTL (eQTL) effects and correlation of transcript abundance to the respective trait in the heart. Cardiac RNA‐seq data were additionally used to generate gene co‐expression networks. QTL analysis of ECG parameters identified 2 QTL for PR interval, respectively, on chromosomes 10 and 17. At the chromosome 10 QTL, cis‐eQTL effects were identified for Acbd4, Cd300lg, Fam171a2, and Arhgap27; the transcript abundance in the heart of these 4 genes was correlated with PR interval. At the chromosome 17 QTL, a cis‐eQTL was uncovered for Nhlrc1 candidate gene; the transcript abundance of this gene was also correlated with PR interval. Co‐expression analysis furthermore identified 50 gene networks, 6 of which were correlated with PR interval or QRS duration, both parameters of cardiac conduction. Conclusions These newly identified genetic loci and gene networks associated with the ECG parameters of cardiac conduction provide a starting point for future studies with the potential of identifying novel mechanisms underlying cardiac electrical function.
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Affiliation(s)
- Michiel E. Adriaens
- Department of Experimental CardiologyHeart CentreAcademic Medical Center AmsterdamAmsterdamThe Netherlands
- Maastricht Centre for Systems BiologyMaastricht UniversityMaastrichtThe Netherlands
| | - Elisabeth M. Lodder
- Department of Experimental CardiologyHeart CentreAcademic Medical Center AmsterdamAmsterdamThe Netherlands
| | | | - Jan Šilhavý
- Institute of PhysiologyAcademy of Sciences of the Czech RepublicPragueCzech Republic
| | - Matthias Heinig
- Institute of Computational BiologyHelmholtz Zentrum MünchenMünchenGermany
| | - Charlotte Glinge
- Department of Experimental CardiologyHeart CentreAcademic Medical Center AmsterdamAmsterdamThe Netherlands
| | - Charly Belterman
- Department of Experimental CardiologyHeart CentreAcademic Medical Center AmsterdamAmsterdamThe Netherlands
| | - Rianne Wolswinkel
- Department of Experimental CardiologyHeart CentreAcademic Medical Center AmsterdamAmsterdamThe Netherlands
| | - Enrico Petretto
- The MRC London Institute of Medical SciencesImperial College LondonLondonUnited Kingdom
- Duke‐NUS Medical SchoolSingapore
| | - Michal Pravenec
- Institute of PhysiologyAcademy of Sciences of the Czech RepublicPragueCzech Republic
| | - Carol Ann Remme
- Department of Experimental CardiologyHeart CentreAcademic Medical Center AmsterdamAmsterdamThe Netherlands
| | - Connie R. Bezzina
- Department of Experimental CardiologyHeart CentreAcademic Medical Center AmsterdamAmsterdamThe Netherlands
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31
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Chew G, Petretto E. Transcriptional Networks of Microglia in Alzheimer's Disease and Insights into Pathogenesis. Genes (Basel) 2019; 10:E798. [PMID: 31614849 PMCID: PMC6826883 DOI: 10.3390/genes10100798] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/30/2019] [Accepted: 10/11/2019] [Indexed: 02/07/2023] Open
Abstract
Microglia, the main immune cells of the central nervous system, are increasingly implicated in Alzheimer's disease (AD). Manifold transcriptomic studies in the brain have not only highlighted microglia's role in AD pathogenesis, but also mapped crucial pathological processes and identified new therapeutic targets. An important component of many of these transcriptomic studies is the investigation of gene expression networks in AD brain, which has provided important new insights into how coordinated gene regulatory programs in microglia (and other cell types) underlie AD pathogenesis. Given the rapid technological advancements in transcriptional profiling, spanning from microarrays to single-cell RNA sequencing (scRNA-seq), tools used for mapping gene expression networks have evolved to keep pace with the unique features of each transcriptomic platform. In this article, we review the trajectory of transcriptomic network analyses in AD from brain to microglia, highlighting the corresponding methodological developments. Lastly, we discuss examples of how transcriptional network analysis provides new insights into AD mechanisms and pathogenesis.
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Affiliation(s)
- Gabriel Chew
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, 69857 Singapore, Singapore.
| | - Enrico Petretto
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, 69857 Singapore, Singapore.
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32
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Dixit P, Anwar M, Saif J, Chamorro-Jorganes A, Dumas M, Angelini G, Punjabi P, Srivastava P, Katare R, Petretto E, Emanueli C. P6309Impaired secretion of clusterin in pericardial fluid of diabetics, a deleterious outcome for the cardiac micro-vasculature. Eur Heart J 2019. [DOI: 10.1093/eurheartj/ehz746.0906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Extracellular vesicles are vital mediators of cell-to-cell communications. We previously demonstrated that in the adult heart, exosomes released in the pericardial fluid (PF) have the functional capability to induce cell survival and angiogenesis in recipient endothelial cells. It has previously been shown that PF exosomes from patients with an existing myocardial infarction (MI) contain clusterin (CLU). Remarkably, secreted CLU is cardio-protective as evidenced by enhanced arteriogenesis and reduced apoptosis in animal models of MI. We hypothesize that type 2 Diabetes Mellitus (T2DM) along with ischemic heart disease (IHD) alters PF EV content impairing its reparative angiogenic potential.
Aim
To investigate the role of T2DM in modulating human PF exosomal content and its vascular action.
Methods and results
PF samples were collected from 3 different groups of patients (N=3): 1) Ischemic heart disease (IHD) with or 2) without T2DM, and 3) non-ischaemic, non-diabetic controls operated for mitral valve repair.
The impact of PF exosomes on human coronary microvascular ECs (HCMECs) was evaluated by cell based functional assays for measuring apoptosis, proliferation and angiogenesis. Interestingly, unlike PF exosomes from control patients, PF exosomes from DM patients with IHD promoted EC apoptosis and impaired angiogenesis.
To investigate the effect of T2DM on PF content, we performed high throughput proteomic and metabolomic analysis of whole PF and PF EVs. We identified proteins and metabolites that were differentially expressed under T2DM condition by using the R package Limma. Employing a network approach, protein and metabolic data were integrated by using our newly developed inhouse R package Metabosignal. This networks approach revealed an interesting interaction circuit involving protein CLU. The T2DM-associated reduction of CLU level in the PF, identified from the “omics” analyses was confirmed by ELISA (n=8 patients per group).
To examine the effects of DM and ischemia on CLU intracellular expression and secretion, HCMECs were exposed to high D-glucose (HG, 25 mM) and hypoxia (1%O2). In line with our PF data, HCMECs exposed to HG and hypoxia showed lower levels of both CLU mRNA and secreted CLU (ELISA). Importantly, recombinant CLU (rCLU) treatment on HCMECs rescued their angiogenic potential, induced cell proliferation and protected them from apoptosis under both HG and hypoxia conditions. In addition, silencing of endogenous levels of CLU in HCMECs impaired angiogenesis, suggesting that CLU might be an inherent component of the angiogenesis machinery in ECs.
Conclusions
This study suggests that DM reduces the level of secreted CLU in the PF, depriving myocardial micro-vessels of this protective and regenerative mediator. Restoring diminished CLU levels in the diabetic heart could be a possible therapeutic approach for contrasting diabetic micro-angiopathy.
Acknowledgement/Funding
British Heart Foundation Program Grant
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Affiliation(s)
- P Dixit
- Imperial College London, London, United Kingdom
| | - M Anwar
- Imperial College London, London, United Kingdom
| | - J Saif
- Imperial College London, London, United Kingdom
| | | | - M Dumas
- Imperial College London, London, United Kingdom
| | - G Angelini
- Bristol Heart Institute, Bristol, United Kingdom
| | - P Punjabi
- Imperial College London, London, United Kingdom
| | | | - R Katare
- University of Otago, Physiology, Dunedin, New Zealand
| | - E Petretto
- Duke-NUS Graduate Medical School Singapore, Singapore, Singapore
| | - C Emanueli
- Imperial College London, London, United Kingdom
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33
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Chen H, Moreno-Moral A, Pesce F, Devapragash N, Mancini M, Heng EL, Rotival M, Srivastava PK, Harmston N, Shkura K, Rackham OJL, Yu WP, Sun XM, Tee NGZ, Tan ELS, Barton PJR, Felkin LE, Lara-Pezzi E, Angelini G, Beltrami C, Pravenec M, Schafer S, Bottolo L, Hubner N, Emanueli C, Cook SA, Petretto E. Author Correction: WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling. Nat Commun 2019; 10:4085. [PMID: 31501434 PMCID: PMC6733793 DOI: 10.1038/s41467-019-12060-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Huimei Chen
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Aida Moreno-Moral
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Francesco Pesce
- Department of Emergency and Organ Transplantation (DETO), University of Bari, 70124, Bari, Italy
| | - Nithya Devapragash
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Massimiliano Mancini
- SOC di Anatomia Patologica, Ospedale San Giovanni di Dio, 50123, Florence, Italy
| | - Ee Ling Heng
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Maxime Rotival
- Unit of Human Evolutionary Genetics, Institute Pasteur, 75015, Paris, France
| | - Prashant K Srivastava
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, W12 0NN, UK
| | - Nathan Harmston
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Kirill Shkura
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, W12 0NN, UK
| | - Owen J L Rackham
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Wei-Ping Yu
- Animal Gene Editing Laboratory, BRC, A*STAR20 Biopolis Way, Singapore, 138668, Republic of Singapore
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Drive, Singapore, 138673, Republic of Singapore
| | - Xi-Ming Sun
- MRC London Institute of Medical Sciences (LMC), Imperial College, London, W12 0NN, UK
| | | | - Elisabeth Li Sa Tan
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Paul J R Barton
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS Trust, London, SW3 6NP, UK
| | - Leanne E Felkin
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS Trust, London, SW3 6NP, UK
| | - Enrique Lara-Pezzi
- Centro Nacional de Investigaciones Cardiovasculares - CNIC, 28029, Madrid, Spain
| | - Gianni Angelini
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Bristol Heart Institute, Bristol Medical School, University of Bristol, Bristol, BS2 89HW, UK
| | - Cristina Beltrami
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences, 142 00, Praha 4, Czech Republic
| | - Sebastian Schafer
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
- National Heart Centre Singapore, Singapore, 169609, Republic of Singapore
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- The Alan Turing Institute, London, NW1 2DB, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347, Berlin, Germany
- Charité-Universitätsmedizin, 10117, Berlin, Germany
- Berlin Institute of Health (BIH), 10178, Berlin, Germany
| | - Costanza Emanueli
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS Trust, London, SW3 6NP, UK
| | - Stuart A Cook
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
- MRC London Institute of Medical Sciences (LMC), Imperial College, London, W12 0NN, UK
- National Heart Centre Singapore, Singapore, 169609, Republic of Singapore
| | - Enrico Petretto
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore.
- MRC London Institute of Medical Sciences (LMC), Imperial College, London, W12 0NN, UK.
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Besnier M, Shantikumar S, Anwar M, Dixit P, Chamorro-Jorganes A, Sweaad W, Sala-Newby G, Madeddu P, Thomas AC, Howard L, Mushtaq S, Petretto E, Caporali A, Emanueli C. miR-15a/-16 Inhibit Angiogenesis by Targeting the Tie2 Coding Sequence: Therapeutic Potential of a miR-15a/16 Decoy System in Limb Ischemia. Mol Ther Nucleic Acids 2019; 17:49-62. [PMID: 31220779 PMCID: PMC6586592 DOI: 10.1016/j.omtn.2019.05.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 04/09/2019] [Accepted: 05/05/2019] [Indexed: 12/13/2022]
Abstract
MicroRNA-15a (miR-15a) and miR-16, which are transcribed from the miR-15a/miR-16-1 cluster, inhibit post-ischemic angiogenesis. MicroRNA (miRNA) binding to mRNA coding sequences (CDSs) is a newly emerging mechanism of gene expression regulation. We aimed to (1) identify new mediators of the anti-angiogenic action of miR-15a and -16, (2) develop an adenovirus (Ad)-based miR-15a/16 decoy system carrying a luciferase reporter (Luc) to both sense and inhibit miR-15a/16 activity, and (3) investigate Ad.Luc-Decoy-15a/16 therapeutic potential in a mouse limb ischemia (LI) model. LI increased miR-15a and -16 expression in mouse muscular endothelial cells (ECs). The miRNAs also increased in cultured human umbilical vein ECs (HUVECs) exposed to serum starvation, but not hypoxia. Using bioinformatic tools and luciferase activity assays, we characterized miR-15a and -16 binding to Tie2 CDS. In HUVECs, miR-15a or -16 overexpression reduced Tie2 at the protein, but not the mRNA, level. Conversely, miR-15a or -16 inhibition improved angiogenesis in a Tie2-dependent manner. Local Ad.Luc-Decoy-15a/16 delivery increased Tie2 levels in ischemic skeletal muscle and improved post-LI angiogenesis and perfusion recovery, with reduced toe necrosis. Bioluminescent imaging (in vivo imaging system [IVIS]) provided evidence that the Ad.Luc-Decoy-15a/16 system responds to miR-15a/16 increases. In conclusion, we have provided novel mechanistic evidence of the therapeutic potential of local miR-15a/16 inhibition in LI.
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Affiliation(s)
- Marie Besnier
- Bristol Heart Institute, University of Bristol, Bristol, UK
| | | | - Maryam Anwar
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Parul Dixit
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Walid Sweaad
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Paolo Madeddu
- Bristol Heart Institute, University of Bristol, Bristol, UK
| | - Anita C Thomas
- Bristol Heart Institute, University of Bristol, Bristol, UK
| | - Lynsey Howard
- Bristol Heart Institute, University of Bristol, Bristol, UK
| | - Sobia Mushtaq
- Bristol Heart Institute, University of Bristol, Bristol, UK
| | - Enrico Petretto
- Institute of Clinical Sciences, Imperial College London, London, UK; Cardiovascular & Metabolic Disorders Programme, Centre for Computational Biology, Duke NUS Medical School, Singapore, Singapore
| | - Andrea Caporali
- Bristol Heart Institute, University of Bristol, Bristol, UK; BHF Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
| | - Costanza Emanueli
- Bristol Heart Institute, University of Bristol, Bristol, UK; National Heart and Lung Institute, Imperial College London, London, UK.
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35
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Laaniste L, Srivastava PK, Stylianou J, Syed N, Cases-Cunillera S, Shkura K, Zeng Q, Rackham OJL, Langley SR, Delahaye-Duriez A, O'Neill K, Williams M, Becker A, Roncaroli F, Petretto E, Johnson MR. Integrated systems-genetic analyses reveal a network target for delaying glioma progression. Ann Clin Transl Neurol 2019; 6:1616-1638. [PMID: 31420939 PMCID: PMC6764637 DOI: 10.1002/acn3.50850] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/27/2019] [Accepted: 06/28/2019] [Indexed: 12/12/2022] Open
Abstract
Objective To identify a convergent, multitarget proliferation characteristic for astrocytoma transformation that could be targeted for therapy discovery. Methods Using an integrated functional genomics approach, we prioritized networks associated with astrocytoma progression using the following criteria: differential co‐expression between grade II and grade III IDH1‐mutated and 1p/19q euploid astrocytomas, preferential enrichment for genetic risk to cancer, association with patient survival and sample‐level genomic features. Drugs targeting the identified multitarget network characteristic for astrocytoma transformation were computationally predicted using drug transcriptional perturbation data and validated using primary human astrocytoma cells. Results A single network, M2, consisting of 177 genes, was associated with glioma progression on the basis of the above criteria. Functionally, M2 encoded physically interacting proteins regulating cell cycle processes and analysis of genome‐wide gene‐regulatory interactions using mutual information and DNA–protein interactions revealed the known regulators of cell cycle processes FoxM1, B‐Myb, and E2F2 as key regulators of M2. These results suggest functional disruption of M2 via gene mutation or altered expression as a convergent pathway regulating astrocytoma transformation. By considering M2 as a multitarget drug target regulating astrocytoma transformation, we identified several drugs that are predicted to restore M2 expression in anaplastic astrocytoma toward its low‐grade profile and of these, we validated the known antiproliferative drug resveratrol as down‐regulating multiple nodes of M2 including at nanomolar concentrations achievable in human cerebrospinal fluid by oral dosing. Interpretation Our results identify M2 as a multitarget network characteristic for astrocytoma progression and encourage M2‐based drug screening to identify new compounds for preventing glioma transformation.
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Affiliation(s)
- Liisi Laaniste
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | | | - Julianna Stylianou
- John Fulcher Neuro-oncology Laboratory, Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | - Nelofer Syed
- John Fulcher Neuro-oncology Laboratory, Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | | | - Kirill Shkura
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | - Qingyu Zeng
- John Fulcher Neuro-oncology Laboratory, Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | | | - Sarah R Langley
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK.,Duke-NUS Medical School, Singapore
| | - Andree Delahaye-Duriez
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK.,PROTECT, INSERM, Université Paris Diderot, Sorbonne Paris Cité, France
| | - Kevin O'Neill
- Department of Neurosurgery, Imperial College Healthcare NHS Trust, London, UK
| | - Matthew Williams
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Albert Becker
- Department of Neuropathology, University of Bonn Medical Centre, Bonn, Germany
| | - Federico Roncaroli
- Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Enrico Petretto
- Duke-NUS Medical School, Singapore.,MRC London Institute of Medical Sciences (LMS), Imperial College London, London, UK
| | - Michael R Johnson
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
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36
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Chen H, Moreno-Moral A, Pesce F, Devapragash N, Mancini M, Heng EL, Rotival M, Srivastava PK, Harmston N, Shkura K, Rackham OJL, Yu WP, Sun XM, Tee NGZ, Tan ELS, Barton PJR, Felkin LE, Lara-Pezzi E, Angelini G, Beltrami C, Pravenec M, Schafer S, Bottolo L, Hubner N, Emanueli C, Cook SA, Petretto E. WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling. Nat Commun 2019; 10:3616. [PMID: 31399586 PMCID: PMC6689010 DOI: 10.1038/s41467-019-11551-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 07/19/2019] [Indexed: 01/03/2023] Open
Abstract
Cardiac fibrosis is a final common pathology in inherited and acquired heart diseases that causes cardiac electrical and pump failure. Here, we use systems genetics to identify a pro-fibrotic gene network in the diseased heart and show that this network is regulated by the E3 ubiquitin ligase WWP2, specifically by the WWP2-N terminal isoform. Importantly, the WWP2-regulated pro-fibrotic gene network is conserved across different cardiac diseases characterized by fibrosis: human and murine dilated cardiomyopathy and repaired tetralogy of Fallot. Transgenic mice lacking the N-terminal region of the WWP2 protein show improved cardiac function and reduced myocardial fibrosis in response to pressure overload or myocardial infarction. In primary cardiac fibroblasts, WWP2 positively regulates the expression of pro-fibrotic markers and extracellular matrix genes. TGFβ1 stimulation promotes nuclear translocation of the WWP2 isoforms containing the N-terminal region and their interaction with SMAD2. WWP2 mediates the TGFβ1-induced nucleocytoplasmic shuttling and transcriptional activity of SMAD2.
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Affiliation(s)
- Huimei Chen
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Aida Moreno-Moral
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Francesco Pesce
- Department of Emergency and Organ Transplantation (DETO), University of Bari, 70124, Bari, Italy
| | - Nithya Devapragash
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Massimiliano Mancini
- SOC di Anatomia Patologica, Ospedale San Giovanni di Dio, 50123, Florence, Italy
| | - Ee Ling Heng
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Maxime Rotival
- Unit of Human Evolutionary Genetics, Institute Pasteur, 75015, Paris, France
| | - Prashant K Srivastava
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, W12 0NN, UK
| | - Nathan Harmston
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Kirill Shkura
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, W12 0NN, UK
| | - Owen J L Rackham
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Wei-Ping Yu
- Animal Gene Editing Laboratory, BRC, A*STAR20 Biopolis Way, Singapore, 138668, Republic of Singapore
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Drive, Singapore, 138673, Republic of Singapore
| | - Xi-Ming Sun
- MRC London Institute of Medical Sciences (LMC), Imperial College, London, W12 0NN, UK
| | | | - Elisabeth Li Sa Tan
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Paul J R Barton
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS Trust, London, SW3 6NP, UK
| | - Leanne E Felkin
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS Trust, London, SW3 6NP, UK
| | - Enrique Lara-Pezzi
- Centro Nacional de Investigaciones Cardiovasculares - CNIC, 28029, Madrid, Spain
| | - Gianni Angelini
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Bristol Heart Institute, Bristol Medical School, University of Bristol, Bristol, BS2 89HW, UK
| | - Cristina Beltrami
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences, 142 00, Praha 4, Czech Republic
| | - Sebastian Schafer
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
- National Heart Centre Singapore, Singapore, 169609, Republic of Singapore
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- The Alan Turing Institute, London, NW1 2DB, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347, Berlin, Germany
- Charité-Universitätsmedizin, 10117, Berlin, Germany
- Berlin Institute of Health (BIH), 10178, Berlin, Germany
| | - Costanza Emanueli
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS Trust, London, SW3 6NP, UK
| | - Stuart A Cook
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
- MRC London Institute of Medical Sciences (LMC), Imperial College, London, W12 0NN, UK
- National Heart Centre Singapore, Singapore, 169609, Republic of Singapore
| | - Enrico Petretto
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore.
- MRC London Institute of Medical Sciences (LMC), Imperial College, London, W12 0NN, UK.
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37
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Aday S, Halevy I, Anwar M, Madeddu P, Sahoo S, Petretto E, Peer D, Emanueli C. Abstract 130: Development of Bioinspired Synthetic Exosomes With Proangiogenic Potential. Circ Res 2019. [DOI: 10.1161/res.125.suppl_1.130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Exosomes with variable microRNA cargos are released from different cell types and stimulate angiogenesis in animal models. Therefore, exosomes are currently considered for their potential to represent a safer and easier biological-based alternative to stem cell therapies. However, the limited amount of exosomes that can be reproducibly prepared from cultured stem cells and the complexity of the cargo of endogenous exosomes make them difficult to develop as off-the-shelf “pharmaceutical products” and limit their clinical potential. These issues could be surpassed by the use of artificial (i.e. nanoparticles mimicking the natural product) exosomes carrying a therapeutic cargo. In consideration of the possibility that not all cargo components of exosomes are required for their therapeutic functions, we reasoned that bioinspired artificial exosomes (AEs) incorporating key therapeutically relevant molecules and devoid of potentially negative or indifferent factors could further improve their therapeutic potential. Therefore, we developed and tested AEs containing exosomal proangiogenic miRNAs as a “proof-of-concept” for therapeutic angiogenesis. In order to achieve this, we: (1) characterized the common microRNA cargo of endogenous proangiogenic exosomes (from stem cells, pericytes and pericardial fluid) using bioinformatics, (2) exploited this knowledge to develop off-the-shelf artificial exosomes (AEs) with proangiogenic capacities, (3) validated the angiogenic potential of the bioinspired AEs. Bioinformatics analyses integrating data of miRNA arrays and panels of proangiogenic exosomes confirmed the enrichment of let-7 family in these exosomes. After testing the angiogenic potential of different members of let-7 family, we produced AEs containing let-7b (the most potent in the family) by microfluidic micromixing. The AEs were uptaken by human ECs cultured under hypoxic conditions, without causing toxicity. let-7b-AEs transferred functional let-7b, thus decreased the expression of validated targets of let-7b in recipient cells. let-7b-AEs improved EC survival, proliferation and angiogenesis
in vitro
and
in vivo
. These data suggest the therapeutic potential of bioinspired AEs containing let-7b.
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Baliga NS, Björkegren JLM, Boeke JD, Boutros M, Crawford NPS, Dudley AM, Farber CR, Jones A, Levey AI, Lusis AJ, Mak HC, Nadeau JH, Noyes MB, Petretto E, Seyfried NT, Steinmetz LM, Vonesch SC. The State of Systems Genetics in 2017. Cell Syst 2019; 4:7-15. [PMID: 28125793 DOI: 10.1016/j.cels.2017.01.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cell Systems invited 16 experts to share their views on the field of systems genetics. In questions repeated in the headings, we asked them to define systems genetics, highlight its relevance to researchers outside the field, discuss what makes a strong systems genetics paper, and paint a picture of where the field is heading in the coming years. Their responses, ordered by the journal but otherwise unedited, make it clear that deciphering genotype to phenotype relationships is a central challenge of systems genetics and will require understanding how networks and higher-order properties of biological systems underlie complex traits. In addition, our experts illuminate the applications and relevance of systems genetics to human disease, the gut microbiome, development of tools that connect the global research community, sustainability, drug discovery, patient-specific disease and network models, and personalized treatments. Finally, a table of suggested reading provides a sample of influential work in the field.
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Affiliation(s)
| | - Johan L M Björkegren
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Department of Medical Biochemistry and Biophysics, Vascular Biology Unit, Karolinska Institutet, Stockholm, Sweden; Department of Physiology, Institute of Biomedicine and Translation Medicine, University of Tartu, Estonia
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Medical Center, New York, NY, USA
| | - Michael Boutros
- German Cancer Research Center (DKFZ) and Heidelberg University, Germany
| | | | - Aimée M Dudley
- Pacific Northwest Research Institute, Seattle, Washington, USA
| | - Charles R Farber
- Departments of Public Health Sciences and Biochemistry and Molecular Genetics, Center for Public Health Genomics, University of Virginia, Charlottesville VA, 22908, USA
| | - Allan Jones
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Allan I Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Aldons J Lusis
- Department of Medicine; Department of Microbiology, Immunology and Molecular Genetics; Department of Human Genetics, University of California Los Angeles, California, USA
| | - H Craig Mak
- Cell Systems, Cell Press, Cambridge, MA, USA.
| | - Joseph H Nadeau
- Pacific Northwest Research Institute, Seattle, Washington, USA
| | - Marcus B Noyes
- Institute for Systems Genetics, NYU Langone Medical Center, New York, NY, USA
| | - Enrico Petretto
- Cardiovascular & Metabolic Disorders Program and Centre for Computational Biology, Duke-National University of Singapore (NUS) Medical School, Singapore
| | - Nicholas T Seyfried
- Department of Biochemistry and Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany; Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sibylle C Vonesch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
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Douros JD, Niu J, Sdao S, Gregg T, Fisher-Wellman K, Bharadwaj M, Molina A, Arumugam R, Martin M, Petretto E, Merrins MJ, Herman MA, Tong J, Campbell J, D’Alessio D. Sleeve gastrectomy rapidly enhances islet function independently of body weight. JCI Insight 2019; 4:126688. [PMID: 30777938 PMCID: PMC6483064 DOI: 10.1172/jci.insight.126688] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/11/2019] [Indexed: 12/14/2022] Open
Abstract
Bariatric surgeries including vertical sleeve gastrectomy (VSG) ameliorate obesity and diabetes. Weight loss and accompanying increases to insulin sensitivity contribute to improved glycemia after surgery; however, studies in humans also suggest weight-independent actions of bariatric procedures to lower blood glucose, possibly by improving insulin secretion. To evaluate this hypothesis, we compared VSG-operated mice with pair-fed, sham-surgical controls (PF-Sham) 2 weeks after surgery. This paradigm yielded similar postoperative body weight and insulin sensitivity between VSG and calorically restricted PF-Sham animals. However, VSG improved glucose tolerance and markedly enhanced insulin secretion during oral nutrient and i.p. glucose challenges compared with controls. Islets from VSG mice displayed a unique transcriptional signature enriched for genes involved in Ca2+ signaling and insulin secretion pathways. This finding suggests that bariatric surgery leads to intrinsic changes within the islet that alter function. Indeed, islets isolated from VSG mice had increased glucose-stimulated insulin secretion and a left-shifted glucose sensitivity curve compared with islets from PF-Sham mice. Isolated islets from VSG animals showed corresponding increases in the pulse duration of glucose-stimulated Ca2+ oscillations. Together, these findings demonstrate a weight-independent improvement in glycemic control following VSG, which is, in part, driven by improved insulin secretion and associated with substantial changes in islet gene expression. These results support a model in which β cells play a key role in the adaptation to bariatric surgery and the improved glucose tolerance that is typical of these procedures.
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Affiliation(s)
- Jonathan D. Douros
- Division of Endocrinology, Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | - Jingjing Niu
- Division of Endocrinology, Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | - Sophia Sdao
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Trillian Gregg
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kelsey Fisher-Wellman
- Division of Endocrinology, Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | - Manish Bharadwaj
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Anthony Molina
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Ramamani Arumugam
- Division of Endocrinology, Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | - MacKenzie Martin
- Division of Endocrinology, Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | - Enrico Petretto
- Centre for Computational Biology, Duke-NUS Medical School, Singapore
| | - Matthew J. Merrins
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mark A. Herman
- Division of Endocrinology, Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | - Jenny Tong
- Division of Endocrinology, Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | - Jonathan Campbell
- Division of Endocrinology, Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | - David D’Alessio
- Division of Endocrinology, Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
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40
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Ford KL, Anwar M, Heys R, Ahmed EM, Caputo M, Game L, Reeves BC, Punjabi PP, Angelini GD, Petretto E, Emanueli C. Optimisation of laboratory methods for whole transcriptomic RNA analyses in human left ventricular biopsies and blood samples of clinical relevance. PLoS One 2019; 14:e0213685. [PMID: 30870483 PMCID: PMC6417664 DOI: 10.1371/journal.pone.0213685] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 02/18/2019] [Indexed: 01/08/2023] Open
Abstract
This study aimed to optimise techniques for whole transcriptome and small RNA analyses on clinical tissue samples from patients with cardiovascular disease. Clinical samples often represent a particular challenge to extracting RNA of sufficient quality for robust RNA sequencing analysis, and due to availability, it is rarely possible to optimise techniques on the samples themselves. Therefore, we have used equivalent samples from pigs undergoing cardiopulmonary bypass surgery to test different protocols for optimal RNA extraction, and then validated the protocols in human samples. Here we present an assessment of the quality and quantity of RNA obtained using a variety of commercially-available RNA extraction kits on both left ventricular biopsies and blood plasma. RNA extraction from these samples presents different difficulties; left ventricular biopsies are small and fibrous, while blood plasma has a low RNA content. We have validated our optimised extraction techniques on human clinical samples collected as part of the ARCADIA (Association of non-coding RNAs with Coronary Artery Disease and type 2 Diabetes) cohort study, resulting in successful whole transcriptome and small RNA sequencing of human left ventricular tissue.
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Affiliation(s)
- Kerrie L. Ford
- National Heart and Lung Institute, ICTEM, The Hammersmith Hospital, Imperial College London, London, United Kingdom
- Bristol Heart Institute, School of Translational Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Maryam Anwar
- National Heart and Lung Institute, ICTEM, The Hammersmith Hospital, Imperial College London, London, United Kingdom
| | - Rachael Heys
- Clinical Trials and Evaluation Unit, Bristol Trials Centre, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Eltayeb Mohamed Ahmed
- Bristol Heart Institute, School of Translational Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Massimo Caputo
- Bristol Heart Institute, School of Translational Health Sciences, University of Bristol, Bristol, United Kingdom
- University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Laurence Game
- MRC London Institute of Medical Sciences, The Hammersmith Hospital, Imperial College London, London, United Kingdom
| | - Barnaby C. Reeves
- Clinical Trials and Evaluation Unit, Bristol Trials Centre, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Prakash P. Punjabi
- National Heart and Lung Institute, ICTEM, The Hammersmith Hospital, Imperial College London, London, United Kingdom
- Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Gianni D. Angelini
- Bristol Heart Institute, School of Translational Health Sciences, University of Bristol, Bristol, United Kingdom
- University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Enrico Petretto
- MRC London Institute of Medical Sciences, The Hammersmith Hospital, Imperial College London, London, United Kingdom
- Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Costanza Emanueli
- National Heart and Lung Institute, ICTEM, The Hammersmith Hospital, Imperial College London, London, United Kingdom
- Bristol Heart Institute, School of Translational Health Sciences, University of Bristol, Bristol, United Kingdom
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41
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Tan ALM, Langley SR, Tan CF, Chai JF, Khoo CM, Leow MKS, Khoo EYH, Moreno-Moral A, Pravenec M, Rotival M, Sadananthan SA, Velan SS, Venkataraman K, Chong YS, Lee YS, Sim X, Stunkel W, Liu MH, Tai ES, Petretto E. Ethnicity-Specific Skeletal Muscle Transcriptional Signatures and Their Relevance to Insulin Resistance in Singapore. J Clin Endocrinol Metab 2019; 104:465-486. [PMID: 30137523 DOI: 10.1210/jc.2018-00309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 08/14/2018] [Indexed: 11/19/2022]
Abstract
CONTEXT Insulin resistance (IR) and obesity differ among ethnic groups in Singapore, with the Malays more obese yet less IR than Asian-Indians. However, the molecular basis underlying these differences is not clear. OBJECTIVE As the skeletal muscle (SM) is metabolically relevant to IR, we investigated molecular pathways in SM that are associated with ethnic differences in IR, obesity, and related traits. DESIGN, SETTING, AND MAIN OUTCOME MEASURES We integrated transcriptomic, genomic, and phenotypic analyses in 156 healthy subjects representing three major ethnicities in the Singapore Adult Metabolism Study. PATIENTS This study contains Chinese (n = 63), Malay (n = 51), and Asian-Indian (n = 42) men, aged 21 to 40 years, without systemic diseases. RESULTS We found remarkable diversity in the SM transcriptome among the three ethnicities, with >8000 differentially expressed genes (40% of all genes expressed in SM). Comparison with blood transcriptome from a separate Singaporean cohort showed that >95% of SM expression differences among ethnicities were unique to SM. We identified a network of 46 genes that were specifically downregulated in Malays, suggesting dysregulation of components of cellular respiration in SM of Malay individuals. We also report 28 differentially expressed gene clusters, four of which were also enriched for genes that were found in genome-wide association studies of metabolic traits and disease and correlated with variation in IR, obesity, and related traits. CONCLUSION We identified extensive gene-expression changes in SM among the three Singaporean ethnicities and report specific genes and molecular pathways that might underpin and explain the differences in IR among these ethnic groups.
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Affiliation(s)
- Amelia Li Min Tan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Duke-National University of Singapore Medical School, Singapore
| | - Sarah R Langley
- Duke-National University of Singapore Medical School, Singapore
- National Heart Centre Singapore, Singapore
| | - Chee Fan Tan
- Nanyang Institute of Technology in Health and Medicine, Nanyang Technological University, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Jin Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Chin Meng Khoo
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Duke-National University of Singapore Medical School, Singapore
- Division of Endocrinology, Department of Medicine, National University Health System, Singapore
| | - Melvin Khee-Shing Leow
- Duke-National University of Singapore Medical School, Singapore
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore
- Department of Endocrinology, Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Eric Yin Hao Khoo
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Division of Endocrinology, Department of Medicine, National University Health System, Singapore
| | | | - Michal Pravenec
- Institute Of Physiology, Czech Academy Of Sciences, Prague, Czech Republic
| | - Maxime Rotival
- Unit of Human Evolutionary Genetics, Institut Pasteur, Paris, France
| | - Suresh Anand Sadananthan
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore
| | - S Sendhil Velan
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore
- Singapore Bioimaging Consortium, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Kavita Venkataraman
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Yap Seng Chong
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yung Seng Lee
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Division of Paediatrics Endocrinology, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Walter Stunkel
- Experimental Biotherapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Mei Hui Liu
- Department of Chemistry, Food Science & Technology Programme, National University of Singapore, Singapore
| | - E Shyong Tai
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Duke-National University of Singapore Medical School, Singapore
- Division of Endocrinology, Department of Medicine, National University Health System, Singapore
| | - Enrico Petretto
- Duke-National University of Singapore Medical School, Singapore
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42
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Ooi J, Langley SR, Xu X, Utami KH, Sim B, Huang Y, Harmston NP, Tay YL, Ziaei A, Zeng R, Low D, Aminkeng F, Sobota RM, Ginhoux F, Petretto E, Pouladi MA. Unbiased Profiling of Isogenic Huntington Disease hPSC-Derived CNS and Peripheral Cells Reveals Strong Cell-Type Specificity of CAG Length Effects. Cell Rep 2019; 26:2494-2508.e7. [DOI: 10.1016/j.celrep.2019.02.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/17/2018] [Accepted: 02/01/2019] [Indexed: 02/02/2023] Open
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43
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Bagnati M, Moreno-Moral A, Ko JH, Nicod J, Harmston N, Imprialou M, Game L, Gil J, Petretto E, Behmoaras J. Systems genetics identifies a macrophage cholesterol network associated with physiological wound healing. JCI Insight 2019; 4:e125736. [PMID: 30674726 PMCID: PMC6413785 DOI: 10.1172/jci.insight.125736] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 12/18/2018] [Indexed: 01/18/2023] Open
Abstract
Among other cells, macrophages regulate the inflammatory and reparative phases during wound healing but genetic determinants and detailed molecular pathways that modulate these processes are not fully elucidated. Here, we took advantage of normal variation in wound healing in 1,378 genetically outbred mice, and carried out macrophage RNA-sequencing profiling of mice with extreme wound healing phenotypes (i.e., slow and fast healers, n = 146 in total). The resulting macrophage coexpression networks were genetically mapped and led to the identification of a unique module under strong trans-acting genetic control by the Runx2 locus. This macrophage-mediated healing network was specifically enriched for cholesterol and fatty acid biosynthetic processes. Pharmacological blockage of fatty acid synthesis with cerulenin resulted in delayed wound healing in vivo, and increased macrophage infiltration in the wounded skin, suggesting the persistence of an unresolved inflammation. We show how naturally occurring sequence variation controls transcriptional networks in macrophages, which in turn regulate specific metabolic pathways that could be targeted in wound healing.
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Affiliation(s)
- Marta Bagnati
- Centre for Inflammatory Disease, Imperial College London, Hammersmith Hospital, London, United Kingdom (UK)
| | | | - Jeong-Hun Ko
- Centre for Inflammatory Disease, Imperial College London, Hammersmith Hospital, London, United Kingdom (UK)
| | - Jérôme Nicod
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Martha Imprialou
- Centre for Inflammatory Disease, Imperial College London, Hammersmith Hospital, London, United Kingdom (UK)
| | - Laurence Game
- Genomics Laboratory, Medical Research Council (MRC) London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital, London, UK
| | - Jesus Gil
- Cell Proliferation Group, MRC London Institute of Medical Sciences (LMS), London, UK
| | - Enrico Petretto
- Duke-NUS Medical School, Singapore, Singapore
- MRC London Institute of Medical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Jacques Behmoaras
- Centre for Inflammatory Disease, Imperial College London, Hammersmith Hospital, London, United Kingdom (UK)
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44
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Rodriguez-Martinez A, Posma JM, Ayala R, Neves AL, Anwar M, Petretto E, Emanueli C, Gauguier D, Nicholson JK, Dumas ME. MWASTools: an R/bioconductor package for metabolome-wide association studies. Bioinformatics 2018; 34:890-892. [PMID: 28961702 PMCID: PMC6049002 DOI: 10.1093/bioinformatics/btx477] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 07/24/2017] [Indexed: 12/14/2022] Open
Abstract
Summary MWASTools is an R package designed to provide an integrated pipeline to analyse metabonomic data in large-scale epidemiological studies. Key functionalities of our package include: quality control analysis; metabolome-wide association analysis using various models (partial correlations, generalized linear models); visualization of statistical outcomes; metabolite assignment using statistical total correlation spectroscopy (STOCSY); and biological interpretation of metabolome-wide association studies results. Availability and implementation The MWASTools R package is implemented in R (version > =3.4) and is available from Bioconductor: https://bioconductor.org/packages/MWASTools/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Joram M Posma
- Department of Surgery and Cancer, Computational and Systems Medicine, Imperial College London, UK
| | - Rafael Ayala
- Department of Surgery and Cancer, Computational and Systems Medicine, Imperial College London, UK
| | - Ana L Neves
- Department of Surgery and Cancer, Computational and Systems Medicine, Imperial College London, UK
| | - Maryam Anwar
- Division of Myocardial Function, National Heart and Lung Institute, Imperial College London, UK
| | | | - Costanza Emanueli
- Division of Myocardial Function, National Heart and Lung Institute, Imperial College London, UK.,Bristol Heart Institute, University of Bristol, UK
| | - Dominique Gauguier
- Department of Surgery and Cancer, Computational and Systems Medicine, Imperial College London, UK
| | - Jeremy K Nicholson
- Department of Surgery and Cancer, Computational and Systems Medicine, Imperial College London, UK
| | - Marc-Emmanuel Dumas
- Department of Surgery and Cancer, Computational and Systems Medicine, Imperial College London, UK
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45
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Madan B, Harmston N, Nallan G, Montoya A, Faull P, Petretto E, Virshup DM. Temporal dynamics of Wnt-dependent transcriptome reveal an oncogenic Wnt/MYC/ribosome axis. J Clin Invest 2018; 128:5620-5633. [PMID: 30300142 DOI: 10.1172/jci122383] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 10/02/2018] [Indexed: 12/18/2022] Open
Abstract
Activating mutations in the Wnt pathway drive a variety of cancers, but the specific targets and pathways activated by Wnt ligands are not fully understood. To bridge this knowledge gap, we performed a comprehensive time-course analysis of Wnt-dependent signaling pathways in an orthotopic model of Wnt-addicted pancreatic cancer, using a porcupine (PORCN) inhibitor currently in clinical trials, and validated key results in additional Wnt-addicted models. The temporal analysis of the drug-perturbed transcriptome demonstrated direct and indirect regulation of more than 3,500 Wnt-activated genes (23% of the transcriptome). Regulation was both via Wnt/β-catenin and through the modulation of protein abundance of important transcription factors, including MYC, via Wnt-dependent stabilization of proteins (Wnt/STOP). Our study identifies a central role of Wnt/β-catenin and Wnt/STOP signaling in controlling ribosome biogenesis, a key driver of cancer proliferation.
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Affiliation(s)
- Babita Madan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Nathan Harmston
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore.,Centre for Computational Biology and Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Gahyathiri Nallan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Alex Montoya
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Peter Faull
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Enrico Petretto
- Centre for Computational Biology and Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore.,MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - David M Virshup
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore.,Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
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46
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Tjin MS, Chua AWC, Moreno-Moral A, Chong LY, Tang PY, Harmston NP, Cai Z, Petretto E, Tan BK, Tryggvason K. Biologically relevant laminin as chemically defined and fully human platform for human epidermal keratinocyte culture. Nat Commun 2018; 9:4432. [PMID: 30377295 PMCID: PMC6207750 DOI: 10.1038/s41467-018-06934-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 09/27/2018] [Indexed: 12/18/2022] Open
Abstract
The current expansion of autologous human keratinocytes to resurface severe wound defects still relies on murine feeder layer and calf serum in the cell culture system. Through our characterization efforts of the human skin basement membrane and murine feeder layer 3T3-J2, we identified two biologically relevant recombinant laminins-LN-511 and LN-421- as potential candidates to replace the murine feeder. Herein, we report a completely xeno-free and defined culture system utilizing these laminins which enables robust expansion of adult human skin keratinocytes. We demonstrate that our laminin system is comparable to the 3T3-J2 co-culture system in terms of basal markers' profile, colony-forming efficiency and the ability to form normal stratified epidermal structure in both in vitro and in vivo models. These results show that the proposed system may not only provide safer keratinocyte use in the clinics, but also facilitate the broader use of other cultured human epithelial cells in regenerative medicine.
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Affiliation(s)
- Monica Suryana Tjin
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Alvin Wen Choong Chua
- Department of Plastic Reconstructive & Aesthetic Surgery, Singapore General Hospital, 20 College Road, Singapore, 169856, Singapore.
- Skin Bank Unit, Singapore General Hospital, Singapore, 169608, Singapore.
| | - Aida Moreno-Moral
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Li Yen Chong
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Po Yin Tang
- Department of Anatomical Pathology, Singapore General Hospital, 20 College Road, Singapore, 169856, Singapore
| | - Nathan Peter Harmston
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Zuhua Cai
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Enrico Petretto
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Bien Keem Tan
- Department of Plastic Reconstructive & Aesthetic Surgery, Singapore General Hospital, 20 College Road, Singapore, 169856, Singapore
- Skin Bank Unit, Singapore General Hospital, Singapore, 169608, Singapore
| | - Karl Tryggvason
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17771, Stockholm, Sweden.
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47
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Srivastava PK, van Eyll J, Godard P, Mazzuferi M, Delahaye-Duriez A, Van Steenwinckel J, Gressens P, Danis B, Vandenplas C, Foerch P, Leclercq K, Mairet-Coello G, Cardenas A, Vanclef F, Laaniste L, Niespodziany I, Keaney J, Gasser J, Gillet G, Shkura K, Chong SA, Behmoaras J, Kadiu I, Petretto E, Kaminski RM, Johnson MR. A systems-level framework for drug discovery identifies Csf1R as an anti-epileptic drug target. Nat Commun 2018; 9:3561. [PMID: 30177815 PMCID: PMC6120885 DOI: 10.1038/s41467-018-06008-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/03/2018] [Indexed: 01/14/2023] Open
Abstract
The identification of drug targets is highly challenging, particularly for diseases of the brain. To address this problem, we developed and experimentally validated a general computational framework for drug target discovery that combines gene regulatory information with causal reasoning (“Causal Reasoning Analytical Framework for Target discovery”—CRAFT). Using a systems genetics approach and starting from gene expression data from the target tissue, CRAFT provides a predictive framework for identifying cell membrane receptors with a direction-specified influence over disease-related gene expression profiles. As proof of concept, we applied CRAFT to epilepsy and predicted the tyrosine kinase receptor Csf1R as a potential therapeutic target. The predicted effect of Csf1R blockade in attenuating epilepsy seizures was validated in three pre-clinical models of epilepsy. These results highlight CRAFT as a systems-level framework for target discovery and suggest Csf1R blockade as a novel therapeutic strategy in epilepsy. CRAFT is applicable to disease settings other than epilepsy. The identification of new drug targets is highly challenging, particularly for diseases of the brain. This study describes a general computational gene regulatory framework called CRAFT for drug target discovery, and the authors use CRAFT to identify the microglial membrane receptor Csf1R as a potential therapeutic target for epilepsy.
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Affiliation(s)
| | - Jonathan van Eyll
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Patrice Godard
- Clarivate Analytics (formerly the IP & Science Business of Thomson Reuters), 5901 Priestly Drive, #200, Carlsbad, CA, 92008, USA
| | - Manuela Mazzuferi
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Andree Delahaye-Duriez
- Division of Brain Sciences, Imperial College London, London, W12 0NN, UK.,UFR de Santé, Médecine et Biologie Humaine, Sorbonne Paris Cité, Université Paris 13, Bobigny, France.,PROTECT, INSERM, Sorbonne Paris Cité, Université Paris Diderot, Paris, France
| | | | - Pierre Gressens
- PROTECT, INSERM, Sorbonne Paris Cité, Université Paris Diderot, Paris, France.,School of Biomedical Engineering & Imaging Sciences, Centre for the Developing Brain, King's College London, St. Thomas' Hospital, London, SE1 7EH, UK
| | - Benedicte Danis
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | | | - Patrik Foerch
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Karine Leclercq
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | | | - Alvaro Cardenas
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Frederic Vanclef
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Liisi Laaniste
- Division of Brain Sciences, Imperial College London, London, W12 0NN, UK
| | | | - James Keaney
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Julien Gasser
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Gaelle Gillet
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Kirill Shkura
- Division of Brain Sciences, Imperial College London, London, W12 0NN, UK
| | - Seon-Ah Chong
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Jacques Behmoaras
- Centre for Complement and Inflammation Research, Imperial College London, London, W12 0NN, UK
| | - Irena Kadiu
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Enrico Petretto
- Duke-NUS Medical School, Centre for Computational Biology, 8 College Road, Singapore, 169857, Republic of Singapore. .,Faculty of Medicine, MRC Clinical Sciences Centre, Imperial College London, London, W12 0NN, UK.
| | - Rafal M Kaminski
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium.
| | - Michael R Johnson
- Division of Brain Sciences, Imperial College London, London, W12 0NN, UK.
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48
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Cuartero S, Weiss FD, Dharmalingam G, Guo Y, Ing-Simmons E, Masella S, Robles-Rebollo I, Xiao X, Wang YF, Barozzi I, Djeghloul D, Amano MT, Niskanen H, Petretto E, Dowell RD, Tachibana K, Kaikkonen MU, Nasmyth KA, Lenhard B, Natoli G, Fisher AG, Merkenschlager M. Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation. Nat Immunol 2018; 19:932-941. [PMID: 30127433 PMCID: PMC6195188 DOI: 10.1038/s41590-018-0184-1] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 07/17/2018] [Indexed: 02/07/2023]
Abstract
Cohesin is important for 3D genome organization. Nevertheless, even the complete removal of cohesin has surprisingly little impact on steady-state gene transcription and enhancer activity. Here we show that cohesin is required for the core transcriptional response of primary macrophages to microbial signals, and for inducible enhancer activity that underpins inflammatory gene expression. Consistent with a role for inflammatory signals in promoting myeloid differentiation of hematopoietic stem and progenitor cells (HPSCs), cohesin mutations in HSPCs led to reduced inflammatory gene expression and increased resistance to differentiation-inducing inflammatory stimuli. These findings uncover an unexpected dependence of inducible gene expression on cohesin, link cohesin with myeloid differentiation, and may help explain the prevalence of cohesin mutations in human acute myeloid leukemia.
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Affiliation(s)
- Sergi Cuartero
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Felix D Weiss
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Gopuraja Dharmalingam
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Ya Guo
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Elizabeth Ing-Simmons
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Computational Regulatory Genomics Group, Integrative Biology Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
| | - Silvia Masella
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Irene Robles-Rebollo
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Xiaolin Xiao
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Yi-Fang Wang
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Iros Barozzi
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
- Department of Surgery and Cancer, Department of Medicine, Imperial College London, London, UK
| | - Dounia Djeghloul
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Mariane T Amano
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Hospital Sírio-Libanês, Sao Paulo, Brazil
| | - Henri Niskanen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Enrico Petretto
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Robin D Dowell
- BioFrontiers Institute and Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Kikuë Tachibana
- Department of Biochemistry, University of Oxford, Oxford, UK
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Minna U Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Kim A Nasmyth
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Boris Lenhard
- Computational Regulatory Genomics Group, Integrative Biology Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Gioacchino Natoli
- Humanitas Clinical and Research Center, Milan, Italy
- Humanitas University, Milan, Italy
| | - Amanda G Fisher
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Matthias Merkenschlager
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
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49
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Sigmundsson K, Ojala JR, Öhman MK, Österholm AM, Moreno-Moral A, Domogatskaya A, Chong LY, Sun Y, Chai X, Steele JA, George B, Patarroyo M, Nilsson AS, Rodin S, Ghosh S, Stevens MM, Petretto E, Tryggvason K. Culturing functional pancreatic islets on α5-laminins and curative transplantation to diabetic mice. Matrix Biol 2018; 70:5-19. [DOI: 10.1016/j.matbio.2018.03.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/22/2018] [Accepted: 03/22/2018] [Indexed: 12/15/2022]
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50
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Pereira M, Petretto E, Gordon S, Bassett JHD, Williams GR, Behmoaras J. Common signalling pathways in macrophage and osteoclast multinucleation. J Cell Sci 2018; 131:131/11/jcs216267. [PMID: 29871956 DOI: 10.1242/jcs.216267] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Macrophage cell fusion and multinucleation are fundamental processes in the formation of multinucleated giant cells (MGCs) in chronic inflammatory disease and osteoclasts in the regulation of bone mass. However, this basic cell phenomenon is poorly understood despite its pathophysiological relevance. Granulomas containing multinucleated giant cells are seen in a wide variety of complex inflammatory disorders, as well as in infectious diseases. Dysregulation of osteoclastic bone resorption underlies the pathogenesis of osteoporosis and malignant osteolytic bone disease. Recent reports have shown that the formation of multinucleated giant cells and osteoclast fusion display a common molecular signature, suggesting shared genetic determinants. In this Review, we describe the background of cell-cell fusion and the similar origin of macrophages and osteoclasts. We specifically focus on the common pathways involved in osteoclast and MGC fusion. We also highlight potential approaches that could help to unravel the core mechanisms underlying bone and granulomatous disorders in humans.
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Affiliation(s)
- Marie Pereira
- Centre for Inflammatory Disease, Imperial College London, London W12 0NN, UK
| | - Enrico Petretto
- Duke-NUS Medical School, Singapore 169857, Republic of Singapore
| | - Siamon Gordon
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan City 33302, Taiwan.,Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - J H Duncan Bassett
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Graham R Williams
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Jacques Behmoaras
- Centre for Inflammatory Disease, Imperial College London, London W12 0NN, UK
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