Thermal proteome profiling of childhood ALL cell lines for proteoform detection

The complexity of the functional proteome extends significantly beyond the protein coding genome resulting in millions of proteoforms. Investigation of proteoforms and their functional roles is important to understand cellular physiology and its deregulation in diseases, but challenging to perform systematically. Here, we apply thermal proteome profiling with deep peptide coverage to detect functional proteoforms in acute lymphoblastic leukemia cell lines with different cytogenetic aberrations. We detect 15,846 proteoforms, capturing differently spliced, post-translationally modified, and cleaved proteins expressed from 9,290 genes. We identify differential coaggregation of proteoform pairs and establish links to disease biology and drug sensitivity specific biomarkers. This approach provides a powerful and unique tool for systematic detection and functional annotation of proteoform groups.

功能蛋白质组的复杂度远高于编码蛋白质的基因组，可产生数百万种蛋白质变体（proteoforms）。对蛋白质变体及其功能作用的研究，对于理解细胞生理学及其在疾病中的失调机制至关重要，但系统性开展此类研究极具挑战。本研究将具备深度肽段覆盖度的热蛋白质组分析（thermal proteome profiling）应用于携带不同细胞遗传学异常的急性淋巴细胞白血病细胞系，以检测其中的功能蛋白质变体。本研究共鉴定到15846种蛋白质变体，涵盖了由9290个基因表达的不同剪接形式、翻译后修饰形式及剪切形式的蛋白质。我们鉴定出蛋白质变体对的差异共聚集现象，并明确了其与疾病生物学及药物敏感性特异性生物标志物的关联。该方法为蛋白质变体群体的系统性检测与功能注释提供了一款强大且独特的研究工具。