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Atlas of Genetics and Cytogenetics in Oncology and Haematology INIST-CNRS OPEN ACCESS JOURNAL Gene Section Review PRAME (preferentially expressed antigen in melanoma) Joel Fulton, David M Heery Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK (JF, DMH) Published in Atlas Database: April 2014 Online updated version : http://AtlasGeneticsOncology.org/Genes/PRAMEID41828ch22q11.html DOI: 10.4267/2042/54374 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2014 Atlas of Genetics and Cytogenetics in Oncology and Haematology gene segments which code for production of l light chains during B cell development and several other non-immunoglobulin genes, for example, tandem Suppressor of Hairy Wing genes (SUHW1/ZNF280A and SUHW2/ZNF280B) and a gene encoding a putative membrane glycoprotein (POM121L1). Abstract Review on PRAME, with data on DNA/RNA, on the protein encoded and where the gene is implicated. Identity Transcription Other names: CT130, MAPE, OIP-4, OIP4 HGNC (Hugo): PRAME Location: 22q11.22 The NCBI database annotates five PRAME mRNA transcripts ranging from 2.1-2.7 kb in length (2141, 2162, 2197, 2220, 2776 bases) which encode the same protein. Transcript (Including UTRs): - Position: chr22:22890123-22896603, Size: 6481, Total exon count: 4 - Strand: Coding region: - Position: chr22:22890489-22893484, Size: 2996, Coding exon count: 3 DNA/RNA Note PRAME is a member of a multigene family present in humans and other mammals. It was originally identified as a gene encoding a novel cancer-testis antigen that is over expressed in melanoma (Ikeda et al., 1997). Its evolution is consistent with adaptive (positive) selection similar to gene clusters involved in immunity and reproduction, such as the NALP family (Tian et al., 2009). Expression of PRAME has been shown to be regulated by hypomethylation of its promoter in AML and CML (Ortmann et al., 2008; Roman-Gomez et al., 2007). Pseudogene The gene seems to have undergone multiple duplications during hominid evolution, and at least 22 PRAME-like genes and 10 pseudogenes have been identified in the human genome (Birtle et al., 2005). Description Protein The gene is encoded on the reverse strand of chromosome 22 (22q11.22) covering a region of approximately 12 kilobases and is within the human immunoglobulin lambda gene locus (Kawasaki et al., 1997). This locus contains a large number of Vl Atlas Genet Cytogenet Oncol Haematol. 2014; 18(12) Note PRAME is a leucine-rich protein of which 21.8% of residues are leucine or isoleucine. 941 PRAME (preferentially expressed antigen in melanoma) Fulton J, Heery DM Predicted domain structure of the human PRAME sequence highlighting Leucine Rich Repeats (LRRs). The LRRs are numbered and indicated by the blue arrows; residues conserved in typical LRRs are highlighted in bold. The black boxes indicate regions predicted to have a high probability of α-helicity, and two predicted NLS sequences are underlined. The boxed area in red is a region implicated in interaction with retinoic acid receptors (Wadelin et al., 2010). Description Homology NP_006106 : Predicted 509 amino acid, 58 kDa protein. Sequence homology and structural predictions suggest that PRAME is related to the leucine-rich repeat (LRR) family of proteins such as the Tolllike receptors. The Oogenesins 1-4 also show considerable homology to PRAME and PRAME family members (Dade et al., 2003). Expression PRAME is expressed at low levels in a few normal tissues, at intermediate level in adrenals, ovary, and endometrium and at high level in the testes. It has been shown to be overexpressed in malignant cells including the vast majority of primary and metastatic melanomas and is recognized by cytolytic T lymphocytes (Haqq et al., 2005). In PRAME-negative leukaemias the gene can be induced by demethylating agents (Sigalotti et al., 2004). Mutations Note Some listed in COSMIC. Implicated in Melanoma Localisation Note High levels of PRAME mRNA are present in the majority of primary and metastatic melanomas (88% and 95% respectively) (Haqq et al., 2005), while being absent in normal haematopoietic tissues including bone marrow (Oehler et al., 2009; Radich et al., 2006; Steinbach et al., 2002; van Baren et al., 1998). The protein has been observed to localise to both the nucleus and perinuclear regions (Tajeddine et al., 2005). PRAME contains several candidate nuclear localisation signal (NLS) sequences (See Figure). Function Human PRAME and its paralogues are related to LRR family proteins, some of which are known to have functions in cell immunity and signal transduction. It has been suggested that, like TLRs, PRAME may be upregulated in response to encounters with microbial pathogens, and may be involved in targeting intracellular PAMPs to the Golgi for ubiquitylation and processing. (Wadelin et al., 2013). PRAME has been reported to function as a repressor of retinoic acid (RA) signalling through interactions with retinoic acid receptors (RARs) and repression of the RARb2 gene (Epping et al., 2005; Epping et al., 2007). Atlas Genet Cytogenet Oncol Haematol. 2014; 18(12) Acute and chronic leukaemia, non Hodgkins lymphomas Note Numerous studies have reported highly elevated levels of PRAME in both acute and chronic leukaemias and non Hodgkin's lymphomas (van Baren et al., 1998; Matsushita et al., 2001; Oehler et al., 2009; Qin et al., 2009; Radich et al., 2006; Santamaria et al., 2008). PRAME expression has been suggested to be predicator for a good clinical outcome in childhood acute lymphoblastic 942 PRAME (preferentially expressed antigen in melanoma) Fulton J, Heery DM cytolytic T cells, is expressed in acute leukaemia cells. Br J Haematol. 1998 Sep;102(5):1376-9 leukemia in addition to being a target for immunotherapy, and biomarker for the monitoring of minimal residual disease (Abdelmalak et al., 2014). Matsushita M, Ikeda H, Kizaki M, Okamoto S, Ogasawara M, Ikeda Y, Kawakami Y. Quantitative monitoring of the PRAME gene for the detection of minimal residual disease in leukaemia. Br J Haematol. 2001 Mar;112(4):916-26 Neuroblastoma Note PRAME is expressed in high-stage neuroblastoma and associated with poor outcome (Oberthuer et al., 2004). Steinbach D, Viehmann S, Zintl F, Gruhn B. PRAME gene expression in childhood acute lymphoblastic leukemia. Cancer Genet Cytogenet. 2002 Oct 1;138(1):89-91 Boon K, Edwards JB, Siu IM, Olschner D, Eberhart CG, Marra MA, Strausberg RL, Riggins GJ. Comparison of medulloblastoma and normal neural transcriptomes identifies a restricted set of activated genes. Oncogene. 2003 Oct 23;22(48):7687-94 Breast cancer Note PRAME is expressed in advanced breast cancer and has been shown to be an independent prognostic factor for shortened disease-free survival (Doolan et al., 2008). Dadé S, Callebaut I, Mermillod P, Monget P. Identification of a new expanding family of genes characterized by atypical LRR domains. Localization of a cluster preferentially expressed in oocyte. FEBS Lett. 2003 Dec 18;555(3):533-8 Ovarian adenocarcinoma Oberthuer A, Hero B, Spitz R, Berthold F, Fischer M. The tumor-associated antigen PRAME is universally expressed in high-stage neuroblastoma and associated with poor outcome. Clin Cancer Res. 2004 Jul 1;10(13):4307-13 Note PRAME was found to be a biomarker and prognostic factor for patients with stage III serous ovarian adenocarcinomas (Partheen et al., 2008). Sigalotti L, Fratta E, Coral S, Tanzarella S, Danielli R, Colizzi F, Fonsatti E, Traversari C, Altomonte M, Maio M. Intratumor heterogeneity of cancer/testis antigens expression in human cutaneous melanoma is methylationregulated and functionally reverted by 5-aza-2'deoxycytidine. Cancer Res. 2004 Dec 15;64(24):9167-71 Lung squamous cell carcinoma Note Northern blot analysis demonstrated that high proportion of positive tumours were shown to express PRAME (Ikeda et al., 1997). Birtle Z, Goodstadt L, Ponting C. Duplication and positive selection among hominin-specific PRAME genes. BMC Genomics. 2005 Sep 13;6:120 Head and neck cancer Epping MT, Wang L, Edel MJ, Carlée L, Hernandez M, Bernards R. The human tumor antigen PRAME is a dominant repressor of retinoic acid receptor signaling. Cell. 2005 Sep 23;122(6):835-47 Note Reverse-transcriptase polymerase chain reaction (RT-PCR) showed high expression of the gene coding for the tumor antigen PRAME in surgical samples of the tumors, margins, and lymph nodes from patients with a diagnosis of head and neck carcinoma (Figueiredo et al., 2006). Haqq C, Nosrati M, Sudilovsky D, Crothers J, Khodabakhsh D, Pulliam BL, Federman S, Miller JR 3rd, Allen RE, Singer MI, Leong SP, Ljung BM, Sagebiel RW, Kashani-Sabet M. The gene expression signatures of melanoma progression. Proc Natl Acad Sci U S A. 2005 Apr 26;102(17):6092-7 Neurological neoplasms Tajeddine N, Gala JL, Louis M, Van Schoor M, Tombal B, Gailly P. Tumor-associated antigen preferentially expressed antigen of melanoma (PRAME) induces caspase-independent cell death in vitro and reduces tumorigenicity in vivo. Cancer Res. 2005 Aug 15;65(16):7348-55 Note PRAME has been identified as a potential CT antigen for medulloblastoma (Boon et al., 2003) and is universally expressed in high-stage neuroblastoma, and has been associated with poor outcome (Oberthuer et al., 2004). Figueiredo DL, Mamede RC, Proto-Siqueira R, Neder L, Silva WA Jr, Zago MA. Expression of cancer testis antigens in head and neck squamous cell carcinomas. Head Neck. 2006 Jul;28(7):614-9 References Ikeda H, Lethé B, Lehmann F, van Baren N, Baurain JF, de Smet C, Chambost H, Vitale M, Moretta A, Boon T, Coulie PG. Characterization of an antigen that is recognized on a melanoma showing partial HLA loss by CTL expressing an NK inhibitory receptor. Immunity. 1997 Feb;6(2):199-208 Radich JP, Dai H, Mao M, Oehler V, Schelter J, Druker B, Sawyers C, Shah N, Stock W, Willman CL, Friend S, Linsley PS. Gene expression changes associated with progression and response in chronic myeloid leukemia. Proc Natl Acad Sci U S A. 2006 Feb 21;103(8):2794-9 Kawasaki K, Minoshima S, Nakato E, Shibuya K, Shintani A, Schmeits JL, Wang J, Shimizu N. One-megabase sequence analysis of the human immunoglobulin lambda gene locus. Genome Res. 1997 Mar;7(3):250-61 Epping MT, Wang L, Plumb JA, Lieb M, Gronemeyer H, Brown R, Bernards R. A functional genetic screen identifies retinoic acid signaling as a target of histone deacetylase inhibitors. Proc Natl Acad Sci U S A. 2007 Nov 6;104(45):17777-82 van Baren N, Chambost H, Ferrant A, Michaux L, Ikeda H, Millard I, Olive D, Boon T, Coulie PG. PRAME, a gene encoding an antigen recognized on a human melanoma by Roman-Gomez J, Jimenez-Velasco A, Agirre X, Castillejo JA, Navarro G, Jose-Eneriz ES, Garate L, Cordeu L, Atlas Genet Cytogenet Oncol Haematol. 2014; 18(12) 943 PRAME (preferentially expressed antigen in melanoma) Fulton J, Heery DM Cervantes F, Prosper F, Heiniger A, Torres A. Epigenetic regulation of PRAME gene in chronic myeloid leukemia. Leuk Res. 2007 Nov;31(11):1521-8 hematopoietic and leukemic progenitor cells. Blood. 2009 Oct 8;114(15):3299-308 Qin Y, Zhu H, Jiang B, Li J, Lu X, Li L, Ruan G, Liu Y, Chen S, Huang X. Expression patterns of WT1 and PRAME in acute myeloid leukemia patients and their usefulness for monitoring minimal residual disease. Leuk Res. 2009 Mar;33(3):384-90 Doolan P, Clynes M, Kennedy S, Mehta JP, Crown J, O'Driscoll L. Prevalence and prognostic and predictive relevance of PRAME in breast cancer. Breast Cancer Res Treat. 2008 May;109(2):359-65 Ortmann CA, Eisele L, Nückel H, Klein-Hitpass L, Führer A, Dührsen U, Zeschnigk M. Aberrant hypomethylation of the cancer-testis antigen PRAME correlates with PRAME expression in acute myeloid leukemia. Ann Hematol. 2008 Oct;87(10):809-18 Tian X, Pascal G, Monget P. Evolution and functional divergence of NLRP genes in mammalian reproductive systems. BMC Evol Biol. 2009 Aug 14;9:202 Wadelin F, Fulton J, McEwan PA, Spriggs KA, Emsley J, Heery DM. Leucine-rich repeat protein PRAME: expression, potential functions and clinical implications for leukaemia. Mol Cancer. 2010 Aug 27;9:226 Partheen K, Levan K, Osterberg L, Claesson I, Fallenius G, Sundfeldt K, Horvath G. Four potential biomarkers as prognostic factors in stage III serous ovarian adenocarcinomas. Int J Cancer. 2008 Nov 1;123(9):2130-7 Wadelin FR, Fulton J, Collins HM, Tertipis N, Bottley A, Spriggs KA, Falcone FH, Heery DM. PRAME is a golgitargeted protein that associates with the Elongin BC complex and is upregulated by interferon-gamma and bacterial PAMPs. PLoS One. 2013;8(2):e58052 Santamaría C, Chillón MC, García-Sanz R, Balanzategui A, Sarasquete ME, Alcoceba M, Ramos F, Bernal T, Queizán JA, Peñarrubia MJ, Giraldo P, San Miguel JF, Gonzalez M. The relevance of preferentially expressed antigen of melanoma (PRAME) as a marker of disease activity and prognosis in acute promyelocytic leukemia. Haematologica. 2008 Dec;93(12):1797-805 Abdelmalak CA, Yahya RS, Elghannam DM, El-Khadragy AE, Abd El Messih HM. PRAME gene expression in childhood acute lymphoblastic leukemia: impact on prognosis. Clin Lab. 2014;60(1):55-61 Oehler VG, Guthrie KA, Cummings CL, Sabo K, Wood BL, Gooley T, Yang T, Epping MT, Shou Y, PogosovaAgadjanyan E, Ladne P, Stirewalt DL, Abkowitz JL, Radich JP. The preferentially expressed antigen in melanoma (PRAME) inhibits myeloid differentiation in normal Atlas Genet Cytogenet Oncol Haematol. 2014; 18(12) This article should be referenced as such: Fulton J, Heery DM. PRAME (preferentially expressed antigen in melanoma). Atlas Genet Cytogenet Oncol Haematol. 2014; 18(12):941-944. 944