Mass Spec Molecular Oncology Charpentier et al., 2021

These files contain the full analysed mass spec data of the results presented in Charpentier et al., 2021 Molecular Oncology. We focused on MELOE-1, a melanoma neoantigen whose expression is restricted to tumor cells as a result of lineage-specific transcription and tumor-specific IRES-dependent translation of the polycistronic meloe RNA (Godet et al., 2008 and Bobinet et al., 2013). Our previous study on MELOE-1 translation reported the presence of an IRES activity located around 250nt upstream of MELOE-1 ORF (Carbonnelle et al., 2013). In the present work, we looked for the ITAF(s) that could bind to this region. To this aim, we in vitro transcribed the 275nt RNA sequence upstream of MELOE-1 ORF, biotinylated it and coupled it to a streptavidin BIAcore chip. We then prepared whole cell lysates from three melanoma cell-lines M117, M134 and M170, ran them on the RNA-coated BIAcore chip (40 rounds of 5 min injections) and then recovered the eluted material for mass spectrometry analysis. references: Godet Y et al. MELOE-1 is a new antigen overexpressed in melanomas and involved in adoptive T cell transfer efficiency. J Exp Med 2008;205(11):2673–2682. Bobinet M et al. Overexpression of Meloe Gene in Melanomas Is Controlled Both by Specific Transcription Factors and Hypomethylation. PLoS ONE 2013;8(9):e75421. Carbonnelle D et al. The Melanoma Antigens MELOE-1 and MELOE-2 Are Translated from a Bona Fide Polycistronic mRNA Containing Functional IRES Sequences. PLoS ONE 2013;8(9).

本数据集包含Charpentier等人2021年发表于《Molecular Oncology》的研究中所呈现的全部经分析的质谱（mass spectrometry, MS）数据。本研究聚焦于MELOE-1——一种黑色素瘤新抗原，其表达仅局限于肿瘤细胞，这源于多顺反子meloe RNA的谱系特异性转录以及肿瘤特异性的内部核糖体进入位点（Internal Ribosome Entry Site, IRES）依赖型翻译（Godet等人，2008；Bobinet等人，2013）。我们此前关于MELOE-1翻译的研究表明，在MELOE-1开放阅读框（Open Reading Frame, ORF）上游约250个核苷酸（nucleotide, nt）处存在IRES活性（Carbonnelle等人，2013）。
在本研究中，我们旨在筛选可结合该区域的IRES反式作用因子（IRES trans-acting factors, ITAF）。为此，我们体外转录了MELOE-1 ORF上游的275nt RNA序列，对其进行生物素标记后偶联至链霉亲和素BIAcore芯片。随后，我们从3株黑色素瘤细胞系M117、M134及M170中制备全细胞裂解液，将其上样至包被有RNA的BIAcore芯片（进行40轮、每轮5分钟的注射洗脱），之后收集洗脱组分用于质谱分析。
参考文献：
1. Godet Y等. MELOE-1是一种在黑色素瘤中高表达并参与调控过继性T细胞转输效率的新型抗原. 《实验医学杂志》, 2008, 205(11):2673–2682.
2. Bobinet M等. 黑色素瘤中Meloe基因的过表达受特异性转录因子与低甲基化共同调控. 《公共科学图书馆·综合》, 2013, 8(9):e75421.
3. Carbonnelle D等. 黑色素瘤抗原MELOE-1与MELOE-2源自携带功能性IRES序列的天然多顺反子mRNA. 《公共科学图书馆·综合》, 2013, 8(9).