Looijenga LH, Stoop H, Biermann K. Testicular cancer: biology and biomarkers. Virchows Archiv : an international journal of pathology. 2014;464(3):301–13.
Article
CAS
Google Scholar
Huyghe E, Matsuda T, Thonneau P. Increasing incidence of testicular cancer worldwide: a review. The Journal of urology. 2003;170(1):5–11.
Article
PubMed
Google Scholar
Smolarek TA, Blough RI, Foster RS, Ulbright TM, Palmer CG, Heerema NA. Cytogenetic analyses of 85 testicular germ cell tumors: comparison of postchemotherapy and untreated tumors. Cancer genetics and cytogenetics. 1999;108(1):57–69.
Article
CAS
PubMed
Google Scholar
Skakkebaek NE. Possible carcinoma-in-situ of the testis. Lancet. 1972;2(7776):516–7.
Article
CAS
PubMed
Google Scholar
Horwich A, Shipley J, Huddart R. Testicular germ-cell cancer. The Lancet. 2006;367(9512):754–65.
Article
CAS
Google Scholar
Chung CC, Kanetsky PA, Wang Z, Hildebrandt MA, Koster R, Skotheim RI, Kratz CP, Turnbull C, Cortessis VK, Bakken AC, et al. Meta-analysis identifies four new loci associated with testicular germ cell tumor. Nature genetics. 2013;45(6):680–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Looijenga LH, Van Agthoven T, Biermann K. Development of malignant germ cells - the genvironmental hypothesis. The International journal of developmental biology. 2013;57(2-4):241–53.
Article
CAS
PubMed
Google Scholar
Reuter M, Berninger P, Chuma S, Shah H, Hosokawa M, Funaya C, Antony C, Sachidanandam R, Pillai RS. Miwi catalysis is required for piRNA amplification-independent LINE1 transposon silencing. Nature. 2011;480(7376):264–7.
Article
CAS
PubMed
Google Scholar
Goh WS, Falciatori I, Tam OH, Burgess R, Meikar O, Kotaja N, Hammell M, Hannon GJ. piRNA-directed cleavage of meiotic transcripts regulates spermatogenesis. Genes & development. 2015;29(10):1032–44.
Article
CAS
Google Scholar
Gou LT, Dai P, Yang JH, Xue Y, Hu YP, Zhou Y, Kang JY, Wang X, Li H, Hua MM, et al. Pachytene piRNAs instruct massive mRNA elimination during late spermiogenesis. Cell research. 2014;24(6):680–700.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lee JH, Schutte D, Wulf G, Fuzesi L, Radzun HJ, Schweyer S, Engel W, Nayernia K. Stem-cell protein Piwil2 is widely expressed in tumors and inhibits apoptosis through activation of Stat3/Bcl-XL pathway. Human molecular genetics. 2006;15(2):201–11.
Article
CAS
PubMed
Google Scholar
Ferreira HJ, Heyn H, Garcia del Muro X, Vidal A, Larriba S, Munoz C, Villanueva A, Esteller M. Epigenetic loss of the PIWI/piRNA machinery in human testicular tumorigenesis. Epigenetics : official journal of the DNA Methylation Society. 2014;9(1):113–8.
Article
CAS
Google Scholar
Rounge TB, Furu K, Skotheim RI, Haugen TB, Grotmol T, Enerly E. Profiling of the small RNA populations in human testicular germ cell tumors shows global loss of piRNAs. Mol Cancer. 2015;14:153.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gainetdinov IV, Kondratieva SA, Skvortsova YV, Zinovyeva MV, Stukacheva EA, Klimov A, Tryakin AA, Azhikina TL: Distinguishing epigenetic features of preneoplastic testis tissues adjacent to seminomas and nonseminomas. Oncotarget. 2016;7(16):22439–47. doi:https://doi.org/10.18632/oncotarget.7074. Published online 2016 Jan 29.
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome biology. 2009;10(3):R25.
Article
PubMed
PubMed Central
Google Scholar
Chou MT, Han BW, Hsiao CP, Zamore PD, Weng Z, Hung JH. Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs. Nucleic acids research. 2015;43(17):e109.
Article
PubMed
PubMed Central
Google Scholar
Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. Integrative genomics viewer. Nat Biotechnol. 2011;29(1):24–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pezic D, Manakov SA, Sachidanandam R, Aravin AA: piRNA pathway targets active LINE1 elements to establish the repressive H3K9me3 mark in germ cells. Genes & development 2014, 28(13):1410-1428.
Rosenkranz D, Zischler H. proTRAC--a software for probabilistic piRNA cluster detection, visualization and analysis. BMC Bioinformatics. 2012;13:5.
Article
PubMed
PubMed Central
Google Scholar
Rosenkranz D. piRNA cluster database: a web resource for piRNA producing loci. Nucleic acids research. 2016; 44(D1):D223–30.
Article
CAS
PubMed
Google Scholar
Chirn GW, Rahman R, Sytnikova YA, Matts JA, Zeng M, Gerlach D, Yu M, Berger B, Naramura M, Kile BT, et al. Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals. PLoS genetics. 2015;11(11):e1005652.
Article
PubMed
PubMed Central
Google Scholar
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28(5):511–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25(9):1105–11.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome biology. 2013;14(4):R36.
Article
PubMed
PubMed Central
Google Scholar
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature protocols 2012, 7(3):562-578.
Fogh J, Wright WC, Loveless JD. Absence of HeLa cell contamination in 169 cell lines derived from human tumors. Journal of the National Cancer Institute. 1977;58(2):209–14.
Article
CAS
PubMed
Google Scholar
Gushchanskaya ES, Artemov AV, Ulyanov SV, Logacheva MD, Penin AA, Kotova ES, Akopov SB, Nikolaev LG, Iarovaia OV, Sverdlov ED, et al. The clustering of CpG islands may constitute an important determinant of the 3D organization of interphase chromosomes. Epigenetics : official journal of the DNA Methylation Society. 2014;9(7):951–63.
Article
Google Scholar
Orlando V. Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation. Trends in biochemical sciences. 2000;25(3):99–104.
Article
CAS
PubMed
Google Scholar
Rangwala SH, Kazazian HH Jr. The L1 retrotransposition assay: a retrospective and toolkit. Methods. 2009;49(3):219–26.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lin YM, Chen CW, Sun HS, Tsai SJ, Hsu CC, Teng YN, Lin JS, Kuo PL. Expression patterns and transcript concentrations of the autosomal DAZL gene in testes of azoospermic men. Mol Hum Reprod. 2001;7(11):1015–22.
Article
CAS
PubMed
Google Scholar
Boellaard WPA, Stoop H, Gillis AJM, Oosterhuis JW, Looijenga LHJ. VASA mRNA (DDX4) detection is more specific than immunohistochemistry using poly- or monoclonal antibodies for germ cells in the male urogenital tract. Medicine. 2017;96(30):e7489.
Article
CAS
PubMed
PubMed Central
Google Scholar
Castrillon DH, Quade BJ, Wang TY, Quigley C, Crum CP. The human VASA gene is specifically expressed in the germ cell lineage. Proceedings of the National Academy of Sciences of the United States of America. 2000;97(17):9585–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rajpert-De Meyts E, Nielsen JE, Skakkebaek NE, Almstrup K. Diagnostic markers for germ cell neoplasms: from placental-like alkaline phosphatase to micro-RNAs. Folia Histochem Cytobiol. 2015;53(3):177–88.
Article
PubMed
Google Scholar
Jones TD, Ulbright TM, Eble JN, Cheng L. OCT4: A sensitive and specific biomarker for intratubular germ cell neoplasia of the testis. Clinical cancer research : an official journal of the American Association for Cancer Research. 2004;10(24):8544–7.
Article
CAS
Google Scholar
Jones TD, Ulbright TM, Eble JN, Baldridge LA, Cheng L. OCT4 staining in testicular tumors: a sensitive and specific marker for seminoma and embryonal carcinoma. The American journal of surgical pathology. 2004;28(7):935–40.
Article
PubMed
Google Scholar
Hart AH, Hartley L, Parker K, Ibrahim M, Looijenga LH, Pauchnik M, Chow CW, Robb L. The pluripotency homeobox gene NANOG is expressed in human germ cell tumors. Cancer. 2005;104(10):2092–8.
Article
CAS
PubMed
Google Scholar
Hoei-Hansen CE, Almstrup K, Nielsen JE, Brask Sonne S, Graem N, Skakkebaek NE, Leffers H, Rajpert-De Meyts E. Stem cell pluripotency factor NANOG is expressed in human fetal gonocytes, testicular carcinoma in situ and germ cell tumours. Histopathology. 2005;47(1):48–56.
Article
CAS
PubMed
Google Scholar
Consortium GT. The Genotype-Tissue Expression (GTEx) project. Nature genetics. 2013;45(6):580–5.
Article
Google Scholar
Williams Z, Morozov P, Mihailovic A, Lin C, Puvvula PK, Juranek S, Rosenwaks Z, Tuschl T. Discovery and Characterization of piRNAs in the Human Fetal Ovary. Cell Rep. 2015;13(4):854–63.
Article
CAS
PubMed
Google Scholar
Li XZ, Roy CK, Dong X, Bolcun-Filas E, Wang J, Han BW, Xu J, Moore MJ, Schimenti JC, Weng Z, et al. An ancient transcription factor initiates the burst of piRNA production during early meiosis in mouse testes. Molecular cell. 2013;50(1):67–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gainetdinov IV, Skvortsova YV, Stukacheva EA, Bychenko OS, Kondratieva SA, Zinovieva MV, Azhikina TL. Expression profiles of PIWIL2 short isoforms differ in testicular germ cell tumors of various differentiation subtypes. PloS one. 2014;9(11):e112528.
Article
PubMed
PubMed Central
Google Scholar
Vagin VV, Wohlschlegel J, Qu J, Jonsson Z, Huang X, Chuma S, Girard A, Sachidanandam R, Hannon GJ, Aravin AA. Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members. Genes & development. 2009;23(15):1749–62.
Article
CAS
Google Scholar
Kazazian HH Jr, Moran JV. Mobile DNA in Health and Disease. N Engl J Med. 2017;377(4):361–70.
Article
CAS
PubMed
Google Scholar
Kazazian HH Jr, Moran JV. The impact of L1 retrotransposons on the human genome. Nature genetics. 1998;19(1):19–24.
Article
CAS
PubMed
Google Scholar
Deininger P. Alu elements: know the SINEs. Genome biology. 2011;12(12):236.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hancks DC, Kazazian HH Jr. Active human retrotransposons: variation and disease. Current opinion in genetics & development. 2012;22(3):191–203.
Article
CAS
Google Scholar
Suzuki R, Honda S, Kirino Y. PIWI Expression and Function in Cancer. Frontiers in genetics. 2012;3:204.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ng KW, Anderson C, Marshall EA, Minatel BC, Enfield KS, Saprunoff HL, Lam WL, Martinez VD. Piwi-interacting RNAs in cancer: emerging functions and clinical utility. Mol Cancer. 2016;15:5.
Article
PubMed
PubMed Central
Google Scholar
Litwin M, Szczepanska-Buda A, Piotrowska A, Dziegiel P, Witkiewicz W. The meaning of PIWI proteins in cancer development. Oncol Lett. 2017;13(5):3354–62.
PubMed
PubMed Central
Google Scholar