• Matthew J Christopher, Allegra A Petti, Michael P Rettig, Christopher A Miller, Ezhilarasi Chendamarai, Eric J Duncavage, Jeffery M Klco, Nicole M Helton, Michelle O'Laughlin, Catrina C Fronick, Robert S Fulton, Richard K Wilson, Lukas D Wartman, John S Welch, Sharon E Heath, Jack D Baty, Jacqueline E Payton, Timothy A Graubert, Daniel C Link, Matthew J Walter, Peter Westervelt, Timothy J Ley, and John F DiPersio.
• From the Division of Oncology, Department of Internal Medicine (M.J.C., A.A.P., M.P.R., C.A.M., E.C., N.M.H., L.D.W., J.S.W., S.E.H., D.C.L., M.J.W., P.W., T.J.L., J.F.D.), the McDonnell Genome Institute (A.A.P., C.A.M., M.O., C.C.F., R.S.F., L.D.W., T.J.L.), the Department of Pathology and Immunology (E.J.D., J.E.P.), and the Division of Biostatistics (J.D.B.), Washington University in St. Louis, St. Louis; the Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN (J.M.K.); the Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH (R.K.W.); and the Center for Cancer Research, Massachusetts General Hospital, Boston (T.A.G.).
• N. Engl. J. Med. 2018 Dec 13; 379 (24): 2330-2341.

BackgroundAs consolidation therapy for acute myeloid leukemia (AML), allogeneic hematopoietic stem-cell transplantation provides a benefit in part by means of an immune-mediated graft-versus-leukemia effect. We hypothesized that the immune-mediated selective pressure imposed by allogeneic transplantation may cause distinct patterns of tumor evolution in relapsed disease.MethodsWe performed enhanced exome sequencing on paired samples obtained at initial presentation with AML and at relapse from 15 patients who had a relapse after hematopoietic stem-cell transplantation (with transplants from an HLA-matched sibling, HLA-matched unrelated donor, or HLA-mismatched unrelated donor) and from 20 patients who had a relapse after chemotherapy. We performed RNA sequencing and flow cytometry on a subgroup of these samples and on additional samples for validation.ResultsOn exome sequencing, the spectrum of gained and lost mutations observed with relapse after transplantation was similar to the spectrum observed with relapse after chemotherapy. Specifically, relapse after transplantation was not associated with the acquisition of previously unknown AML-specific mutations or structural variations in immune-related genes. In contrast, RNA sequencing of samples obtained at relapse after transplantation revealed dysregulation of pathways involved in adaptive and innate immunity, including down-regulation of major histocompatibility complex (MHC) class II genes ( HLA-DPA1, HLA-DPB1, HLA-DQB1, and HLA-DRB1) to levels that were 3 to 12 times lower than the levels seen in paired samples obtained at presentation. Flow cytometry and immunohistochemical analysis confirmed decreased expression of MHC class II at relapse in 17 of 34 patients who had a relapse after transplantation. Evidence suggested that interferon-γ treatment could rapidly reverse this phenotype in AML blasts in vitro.ConclusionsAML relapse after transplantation was not associated with the acquisition of relapse-specific mutations in immune-related genes. However, it was associated with dysregulation of pathways that may influence immune function, including down-regulation of MHC class II genes, which are involved in antigen presentation. These epigenetic changes may be reversible with appropriate therapy. (Funded by the National Cancer Institute and others.).

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