The complex genetic landscape of familial MDS and AML reveals pathogenic germline variants
NATURE COMMUNICATIONS
Authors: Rio-Machin, Ana; Vulliamy, Tom; Hug, Nele; Walne, Amanda; Tawana, Kiran; Cardoso, Shirleny; Ellison, Alicia; Pontikos, Nikolas; Wang, Jun; Tummala, Hemanth; Al Seraihi, Ahad Fahad H.; Alnajar, Jenna; Bewicke-Copley, Findlay; Armes, Hannah; Barnett, Michael; Bloor, Adrian; Bodor, Csaba; Bowen, David; Fenaux, Pierre; Green, Andrew; Hallahan, Andrew; Hjorth-Hansen, Henrik; Hossain, Upal; Killick, Sally; Lawson, Sarah; Layton, Mark; Male, Alison M.; Marsh, Judith; Mehta, Priyanka; Mous, Rogier; Nomdedeu, Josep F.; Owen, Carolyn; Pavlu, Jiri; Payne, Elspeth M.; Protheroe, Rachel E.; Preudhomme, Claude; Pujol-Moix, Nuria; Renneville, Aline; Russell, Nigel; Saggar, Anand; Sciuccati, Gabriela; Taussig, David; Toze, Cynthia L.; Uyttebroeck, Anne; Vandenberghe, Peter; Schlegelberger, Brigitte; Ripperger, Tim; Steinemann, Doris; Wu, John; Mason, Joanne; Page, Paula; Akiki, Susanna; Reay, Kim; Cavenagh, Jamie D.; Plagnol, Vincent; Caceres, Javier F.; Fitzgibbon, Jude; Dokal, Inderjeet
Abstract
The inclusion of familial myeloid malignancies as a separate disease entity in the revised WHO classification has renewed efforts to improve the recognition and management of this group of at risk individuals. Here we report a cohort of 86 acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS) families with 49 harboring germline variants in 16 previously defined loci (57%). Whole exome sequencing in a further 37 uncharacterized families (43%) allowed us to rationalize 65 new candidate loci, including genes mutated in rare hematological syndromes (ADA, GP6, IL17RA, PRF1 and SEC23B), reported in prior MDS/AML or inherited bone marrow failure series (DNAH9, NAPRT1 and SH2B3) or variants at novel loci (DHX34) that appear specific to inherited forms of myeloid malignancies. Altogether, our series of MDS/AML families offer novel insights into the etiology of myeloid malignancies and provide a framework to prioritize variants for inclusion into routine diagnostics and patient management.
Inflammatory, regulatory, and autophagy co-expression modules and hub genes underlie the peripheral immune response to human intracerebral hemorrhage
JOURNAL OF NEUROINFLAMMATION
Authors: Durocher, Marc; Ander, Bradley P.; Jickling, Glen; Hamade, Farah; Hull, Heather; Knepp, Bodie; Liu, Da Zhi; Zhan, Xinhua; Anh Tran; Cheng, Xiyuan; Ng, Kwan; Yee, Alan; Sharp, Frank R.; Stamova, Boryana
Abstract
BackgroundIntracerebral hemorrhage (ICH) has a high morbidity and mortality. The peripheral immune system and cross-talk between peripheral blood and brain have been implicated in the ICH immune response. Thus, we delineated the gene networks associated with human ICH in the peripheral blood transcriptome. We also compared the differentially expressed genes in blood following ICH to a prior human study of perihematomal brain tissue.MethodsWe performed peripheral blood whole-transcriptome analysis of ICH and matched vascular risk factor control subjects (n=66). Gene co-expression network analysis identified groups of co-expressed genes (modules) associated with ICH and their most interconnected genes (hubs). Mixed-effects regression identified differentially expressed genes in ICH compared to controls.ResultsOf seven ICH-associated modules, six were enriched with cell-specific genes: one neutrophil module, one neutrophil plus monocyte module, one T cell module, one Natural Killer cell module, and two erythroblast modules. The neutrophil/monocyte modules were enriched in inflammatory/immune pathways; the T cell module in T cell receptor signaling genes; and the Natural Killer cell module in genes regulating alternative splicing, epigenetic, and post-translational modifications. One erythroblast module was enriched in autophagy pathways implicated in experimental ICH, and NRF2 signaling implicated in hematoma clearance. Many hub genes or module members, such as IARS, mTOR, S1PR1, LCK, FYN, SKAP1, ITK, AMBRA1, NLRC4, IL6R, IL17RA, GAB2, MXD1, PIK3CD, NUMB, MAPK14, DDX24, EVL, TDP1, ATG3, WDFY3, GSK3B, STAT3, STX3, CSF3R, PIP4K2A, ANXA3, DGAT2, LRP10, FLOT2, ANK1, CR1, SLC4A1, and DYSF, have been implicated in neuroinflammation, cell death, transcriptional regulation, and some as experimental ICH therapeutic targets. Gene-level analysis revealed 1225 genes (FDR p<0.05, fold-change > |1.2|) have altered expression in ICH in peripheral blood. There was significant overlap of the 1225 genes with dysregulated genes in human perihematomal brain tissue (p=7x10(-3)). Overlapping genes were enriched for neutrophil-specific genes (p=6.4x10(-08)) involved in interleukin, neuroinflammation, apoptosis, and PPAR signaling.ConclusionsThis study delineates key processes underlying ICH pathophysiology, complements experimental ICH findings, and the hub genes significantly expand the list of novel ICH therapeutic targets. The overlap between blood and brain gene responses underscores the importance of examining blood-brain interactions in human ICH.