Proteogenomics Reveal the Overexpression of HLA‑I in Cancer

An accurate quantification of HLA class I gene expression
is important
in understanding the interplay with the tumor microenvironment of
antitumor cytotoxic T cell activities. Because HLA-I sequences are
highly variable, standard RNAseq and mass spectrometry-based quantification
workflows using common genome and protein sequence references do not
provide HLA-I allele specific quantifications. Here, we used personalized
HLA-I nucleotide and protein reference sequences based on the subjects’
HLA-I genotypes and surveyed tumor and adjacent normal samples from
patients across nine cancer types. Mass spectrometry using data dependent
acquisition data was validated to be sufficient to estimate HLA-A
protein expression at the allele level. We found that HLA-I proteins
were present in significantly higher levels in tumors compared to
adjacent normal tissues from 41 to 63% of head and neck squamous cell
carcinoma, uterine corpus endometrial carcinoma, and clear cell renal
cell carcinoma patients, and this was driven by increased levels of
HLA-I gene transcripts. Most immune cell types are universally enriched
in HLA-I high tumors, while endothelial and neuronal cells showed
divergent relationships with HLA-I. Pathway analysis revealed that
tumor senescence and autophagy activity influence the level of HLA-I
proteins in glioblastoma. Genes correlated to HLA-I protein expression
are mostly the ones directly involved in HLA-I function in immune
response and cell death, while glycosylation genes are exclusively
co-expressed with HLA-I at the protein level.

精确量化HLA I类基因表达对于理解肿瘤微环境与抗肿瘤细胞毒性T细胞活动之间的相互作用至关重要。鉴于HLA-I序列的高度变异性，基于通用基因组及蛋白质序列参考的标准化RNA测序及质谱分析工作流程无法提供HLA-I等位基因特异性量化。在本研究中，我们依据受试者的HLA-I基因型，采用个性化的HLA-I核酸和蛋白质参考序列，对来自九种不同癌症类型的肿瘤及邻近正常组织样本进行了调查。通过数据依赖性采集数据的质谱分析被验证为足以估算HLA-A蛋白质在等位基因水平的表达。我们发现，在头颈鳞状细胞癌、子宫体子宫内膜癌和透明细胞肾细胞癌患者中，与邻近正常组织相比，肿瘤中HLA-I蛋白质的水平显著升高，这一现象由HLA-I基因转录本水平的增加所驱动。大多数免疫细胞类型在HLA-I高表达肿瘤中普遍富集，而内皮细胞和神经元细胞与HLA-I的关系则表现出差异性。通路分析揭示了肿瘤衰老和自噬活性影响胶质母细胞瘤中HLA-I蛋白质的水平。与HLA-I蛋白质表达相关的基因大多直接参与HLA-I在免疫应答和细胞死亡中的功能，而糖基化基因则仅在蛋白质水平上与HLA-I共表达。