Tumor genetic alterations and features of the immune microenvironment drive myelodysplastic syndrome escape and progression
The transformation and progression of myelodysplastic syndromes (MDS) to secondary acute myeloid leukemia (sAML) involve genetic, epigenetic, and microenvironmental factors. Driver mutations have emerged as valuable markers for defining risk groups and as candidates for targeted treatment approaches in MDS. It is also evident that the risk of transformation to sAML is increased by evasion of adaptive immune surveillance. This study was designed to explore the immune microenvironment, immunogenic tumor-intrinsic mechanisms (HLA and PD-L1 expression), and tumor genetic features (somatic mutations and altered karyotypes) in MDS patients and to determine their influence on the progression of the disease. We detected major alterations of the immune microenvironment in MDS patients, with a reduced count of CD4+ T cells, a more frequent presence of markers related to T cell exhaustion, a more frequent presence of myeloid-derived suppressor cells (MDSCs), and changes in the functional phenotype of NK cells. HLA Class I (HLA-I) expression was normally expressed in CD34+ blasts and during myeloid differentiation. Only two out of thirty-six patients with homozygosity for HLA-C groups acquired complete copy-neutral loss of heterozygosity in the HLA region. PD-L1 expression on the leukemic clone was also increased in MDS patients. Finally, no interplay was observed between the anti-tumor immune microenvironment and mutational genomic features. In summary, extrinsic and intrinsic immunological factors might severely impair immune surveillance and contribute to clonal immune escape. Genomic alterations appear to make an independent contribution to the clonal evolution and progression of MDS.
KeywordsMyelodysplastic syndrome (MDS) Immune microenvironment High molecular risk (HMR) mutations Loss of heterozygosity (LOH) Immune-evasion
HLA Class I
High molecular risk
International prognostic scoring system
International prognostic scoring system revised
- LOH HLA
Loss of heterozygosity in the HLA region
Loss of heterozygosity
- MDS del(5q)
MDS with isolated del(5q)
- MDS EB
MDS with excess blasts
Myeloid derived suppressor cells
MDS with multilineage dysplasia
MLD and ring sideroblasts
MDS with single lineage dysplasia
Secondary acute myeloid leukemia
The authors thank Victoria Calvo and María Corzo for technical assistance.
PM and LNC contributed to the immunophenotypic analysis of the tumor microenvironment. PM and MB contributed to sequencing and data analysis. FH and PG contributed to the diagnosis and classification of patients based on their clinical and hematological characteristics. ARG-R carried out the statistical analyses. PM, MB, PJ, MJ, FG, and FR-C were involved with all aspects of the study’s design and contributed to the manuscript preparation.
This work was supported by Grants from the Instituto de Salud Carlos III co-financed by FEDER funds (European Union) (PI 16/00752, PI 17/00197) and Junta de Andalucía in Spain (Group CTS-143, PI09/0382). This study is part of the doctoral thesis of Paola Montes, whose pre-doctoral fellowship was partially financed by Abbott, Becton–Dickinson, Beckman Coulter, and the Spanish MDS group.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
Ethical approval and ethical standards
The procedures with human samples were performed in accordance with the Declaration of Helsinki and the ethical standards of the Research Ethics Committee of Virgen de las Nieves Hospital in Granada, Spain, which approved the project on June 28 2016 (PEIBA code 0713-N-16 and PROYECTO code 555).
Written informed consent was provided by all patients at the time of their diagnosis and by healthy donors at routine analyses during the first few months of the study.
- 5.Greenberg PL, Tuechler H, Schanz J, Sanz G, Garcia-Manero G, Solé F, Bennett JM, Bowen D, Fenaux P, Dreyfus F, Kantarjian H, Kuendgen A, Levis A, Malcovati L, Cazzola M, Cermak J, Fonatsch C, Le Beau MM, Slovak ML, Krieger O, Luebbert M, Maciejewski J, Magalhaes SM, Miyazaki Y, Pfeilstöcker M, Sekeres M, Sperr WR, Stauder R, Tauro S, Valent P, Vallespi T, van de Loosdrecht AA, Germing U, Haase D (2012) Revised international prognostic scoring system for myelodysplastic syndromes. Blood 120:2454–2465. https://doi.org/10.1182/blood-2012-03-420489 CrossRefPubMedPubMedCentralGoogle Scholar
- 8.Papaemmanuil E, Gerstung M, Malcovati L, Tauro S, Gundem G, Van Loo P, Yoon CJ, Ellis P, Wedge DC, Pellagatti A, Shlien A, Groves MJ, Forbes SA, Raine K, Hinton J, Mudie LJ, McLaren S, Hardy C, Latimer C, Della Porta MG, O’Meara S, Ambaglio I, Galli A, Butler AP, Walldin G, Teague JW, Quek L, Sternberg A, Gambacorti-Passerini C, Cross NC, Green AR, Boultwood J, Vyas P, Hellstrom-Lindberg E, Bowen D, Cazzola M, Stratton MR, Campbell PJ (2013) Clinical and biological implications of driver mutations in myelodysplastic syndromes. Blood 122:3616–3627. https://doi.org/10.1182/blood-2013-08-518886 CrossRefPubMedPubMedCentralGoogle Scholar
- 14.Bouchliou I, Miltiades P, Nakou E, Spanoudakis E, Goutzouvelidis A, Vakalopoulou S, Garypidou V, Kotoula V, Bourikas G, Tsatalas C, Kotsianidis I (2011) Th17 and Foxp3(+) T regulatory cell dynamics and distribution in myelodysplastic syndromes. Clin Immunol 139:350–359. https://doi.org/10.1016/j.clim.2011.03.001 CrossRefPubMedGoogle Scholar
- 15.Aggarwal S, van de Loosdrecht AA, Alhan C, Ossenkoppele GJ, Westers TM, Bontkes HJ (2011) Role of immune responses in the pathogenesis of low-risk MDS and high-risk MDS: implications for immunotherapy. Br J Haematol 153:568–581. https://doi.org/10.1111/j.1365-2141.2011.08683x CrossRefPubMedGoogle Scholar
- 16.Epling-Burnette PK, Bai F, Painter JS, Rollison DE, Salih HR, Krusch M, Zou J, Ku E, Zhong B, Boulware D, Moscinski L, Wei S, Djeu JY, List AF (2007) Reduced natural killer (NK) function associated with high-risk myelodysplastic syndrome (MDS) and reduced expression of activating NK receptors. Blood 109:4816–4824CrossRefGoogle Scholar
- 19.Montes P, Kerick M, Bernal M, Hernández F, Jiménez P, Garrido P, Márquez A, Jurado M, Martin J, Garrido F, Ruiz-Cabello F (2018) Genomic loss of HLA alleles may affect the clinical outcome in low-risk myelodysplastic syndrome patients. Oncotarget 9:36929–36944. https://doi.org/10.18632/oncotarget.26405 CrossRefPubMedPubMedCentralGoogle Scholar
- 20.Del Mar Valenzuela-Membrives M, Perea-García F, Sanchez-Palencia A, Ruiz-Cabello F, Gómez-Morales M, Miranda-León MT, Galindo-Angel I, Fárez-Vidal ME (2016) Progressive changes in composition of lymphocytes in lung tissues from patients with non-small-cell lung cancer. Oncotarget 7:71608–71619. https://doi.org/10.18632/oncotarget.12264 CrossRefGoogle Scholar
- 21.Kittang AO, Kordasti S, Sand KE, Costantini B, Kramer AM, Perezabellan P, Seidl T, Rye KP, Hagen KM, Kulasekararaj A, Bruserud Ø, Mufti GJ (2015) Expansion of myeloid derived suppressor cells correlates with number of T regulatory cells and disease progression in myelodysplastic syndrome. Oncoimmunology 5:e1062208CrossRefGoogle Scholar
- 27.Canale FP, Ramello MC, Núñez N, Araujo Furlan CL, Bossio SN, Gorosito Serrán M, Tosello Boari J, Del Castillo A, Ledesma M, Sedlik C, Piaggio E, Gruppi A, Acosta Rodríguez EA, Montes CL (2018) CD39 expression defines cell exhaustion in tumor-infiltrating CD8(+) T cells. Cancer Res 78:115–128. https://doi.org/10.1158/0008-5472.can-16-2684 CrossRefPubMedGoogle Scholar
- 28.Perry C, Hazan-Halevy I, Kay S, Cipok M, Grisaru D, Deutsch V, Polliack A, Naparstek E, Herishanu Y (2012) Increased CD39 expression on CD4(+) T lymphocytes has clinical and prognostic significance in chronic lymphocytic leukemia. Ann Hematol 91:1271–1279. https://doi.org/10.1007/s00277-012-1425-2 CrossRefPubMedGoogle Scholar
- 29.Cichocki F, Schlums H, Theorell J, Tesi B, Miller JS, Ljunggren HG, Bryceson YT (2016) Diversification and functional specialization of human NK cell subsets. Curr Top Microbiol 395:63–93Google Scholar
- 33.Yang H, Bueso-Ramos C, DiNardo C, Estecio MR, Davanlou M, Geng QR, Fang Z, Nguyen M, Pierce S, Wei Y, Parmar S, Cortes J, Kantarjian H, Garcia-Manero G (2014) Expression of PD-L1, PD-L2, PD-1 and CTLA4 in myelodysplastic syndromes is enhanced by treatment with hypomethylating agents. Leukemia 28:1280–1288. https://doi.org/10.1038/leu.2013.355 CrossRefPubMedGoogle Scholar
- 34.Perea F, Bernal M, Sánchez-Palencia A, Carretero J, Torres C, Bayarri C, Gómez-Morales M, Garrido F, Ruiz-Cabello F (2017) The absence of HLA Class I expression in non-small cell lung cancer correlates with the tumor tissue structure and the pattern of T cell infiltration. Int J Cancer 140:888–899. https://doi.org/10.1002/ijc.30489 CrossRefPubMedGoogle Scholar
- 35.McGranahan N, Rosenthal R, Hiley CT, Rowan AJ, Watkins TBK, Wilson GA, Birkbak NJ, Veeriah S, Van Loo P, Herrero J, Swanton C (2017) Allele-specific HLA loss and immune escape in lung cancer evolution. Cell 171:1259–1271. https://doi.org/10.1016/j.cell.2017.10.001 CrossRefPubMedPubMedCentralGoogle Scholar
- 36.Carretero R, Romero JM, Ruiz-Cabello F, Maleno I, Rodriguez F, Camacho FM, Real LM, Garrido F, Cabrera T (2008) Analysis of HLA Class I expression in progressing and regressing metastatic melanoma lesions after immunotherapy. Immunogenetics 60:439–447. https://doi.org/10.1007/s00251-008-0303-5 CrossRefPubMedGoogle Scholar
- 37.Brouwer RE, van der Heiden P, Schreuder GM, Mulder A, Datema G, Anholts JD, Willemze R, Claas FH, Falkenburg JH (2002) Loss or downregulation of HLA Class I expression at the allelic level in acute leukemia is infrequent but functionally relevant and can be restored by interferon. Hum Immunol 63:200–210CrossRefGoogle Scholar
- 39.Abushok DV, Duke JL, Xie HM, Stanley N, Atienza J, Perdigones N, Nicholas P, Ferriola D, Li Y, Huang H, Ye W, Morrissette JJD, Kearns J, Porter DL, Podsakoff GM, Eisenlohr LC, Biegel JA, Chou ST, Monos DS, Bessler M, Olson TS (2017) Somatic HLA mutations expose the role of class I-mediated autoimmunity in aplastic anemia and its clonal complications. Blood Adv 1:1900–1910CrossRefGoogle Scholar
- 41.Perea F, Sánchez-Palencia A, Gómez-Morales M, Bernal M, Concha Á, García MM, González-Ramírez AR, Kerick M, Martin J, Garrido F, Ruiz-Cabello F, Aptsiauri N (2017) HLA class I loss and PD-L1 expression in lung cancer: impact on T-cell infiltration and immune escape. Oncotarget 9:4120–4133. https://doi.org/10.18632/oncotarget.23469 CrossRefPubMedPubMedCentralGoogle Scholar
- 42.Rosenthal R, Cadieux EL, Salgado R, Bakir MA, Moore DA, Hiley CT, Lund T, Tanić M, Reading JL, Joshi K, Henry JY, Ghorani E, Wilson GA, Birkbak NJ, Jamal-Hanjani M, Veeriah S, Szallasi Z, Loi S, Hellmann MD, Feber A, Chain B, Herrero J, Quezada SA, Demeulemeester J, Van Loo P, Beck S, McGranahan N, Swanton C (2019) Neoantigen-directed immune escape in lung cancer evolution. Nature 567:479–485. https://doi.org/10.1038/s41586-019-1032-7 CrossRefPubMedGoogle Scholar
- 43.Jordanova ES, Riemersma SA, Philippo K, Giphart-Gassler M, Schuuring E, Kluin PM (2002) Hemizygous deletions in the HLA region account for loss of heterozygosity in the majority of diffuse large B-cell lymphomas of the testis and the central nervous system. Genes Chromosom Cancer 35:38–48CrossRefGoogle Scholar
- 44.Sebastián E, Alcoceba M, Martín-García D, Blanco Ó, Sanchez-Barba M, Balanzategui A, Marín L, Montes-Moreno S, González-Barca E, Pardal E, Jiménez C, García-Álvarez M, Clot G, Carracedo Á, Gutiérrez NC, Sarasquete ME, Chillón C, Corral R, Prieto-Conde MI, Caballero MD, Salaverria I, García-Sanz R, González M (2016) High-resolution copy number analysis of paired normal-tumor samples from diffuse large B cell lymphoma. Ann Hematol 95:253–262. https://doi.org/10.1007/s00277-015-2552-3 CrossRefPubMedGoogle Scholar