Integrative network analysis reveals USP7 haploinsufficiency inhibits E-protein activity in pediatric T-lineage acute lymphoblastic leukemia (T-ALL)

Abstract

USP7, which encodes a deubiquitylating enzyme, is among the most frequently mutated genes in pediatric T-ALL, with somatic heterozygous loss-of-function mutations (haploinsufficiency) predominantly affecting the subgroup that has aberrant TAL1 oncogene activation. Network analysis of > 200 T-ALL transcriptomes linked USP7 haploinsufficiency with decreased activities of E-proteins. E-proteins are also negatively regulated by TAL1, leading to concerted down-regulation of E-protein target genes involved in T-cell development. In T-ALL cell lines, we showed the physical interaction of USP7 with E-proteins and TAL1 by mass spectrometry and ChIP-seq. Haploinsufficient but not complete CRISPR knock-out of USP7 showed accelerated cell growth and validated transcriptional down-regulation of E-protein targets. Our study unveiled the synergistic effect of USP7 haploinsufficiency with aberrant TAL1 activation on T-ALL, implicating USP7 as a haploinsufficient tumor suppressor in T-ALL. Our findings caution against a universal oncogene designation for USP7 while emphasizing the dosage-dependent consequences of USP7 inhibitors currently under development as potential cancer therapeutics.

DRPPM-EASY: A Web-Based Framework for Integrative Analysis of Multi-Omics Cancer Datasets

“…A joint analysis of the transcriptome and proteome data was carried out by the DRPPM-EASY-Integration pipeline, identifying genes with altered protein abundance and unaltered mRNA levels, such as TRIM27, NOTCH2, UBR3, and USP22 ( Figure 3 B). Consistent with our previous observation, TRIM27, a known target of USP7 [ 27 ], observed decreased protein abundance in T-ALL cell lines with a haploinsufficient USP7 [ 21 ]. The altered abundance of UBR3 and USP22 suggests an altered ubiquitin ligase network.…”

“…By GSEA and single-sample GSEA, we found USP7 knockdown upregulated with MYC and TAL1 associated targets ( Figure 2 D,E) and found downregulated apoptotic gene signature from the Hallmark database ( Figure 2 F). Overall, the RNA-seq analysis supports our previous finding that USP7 is implicated in the negative regulation of TAL1-dependent leukemia growth [ 21 ].…”

“…We previously identified that USP7 knockdown in T-ALL reduces the activity of E-proteins in a TAL1 dependent manner [ 21 ]. To highlight the functions of the DRPPM-EASY application, we re-examined the RNA sequencing profiling data of Jurkat cells after USP7 shRNA silencing.…”

“…USP7 samples were prepared as described in Shaw et al [ 21 ]. Briefly, human T-ALL cell lines Jurkat (ATCC) cells were transduced with USP7 shRNA lentivirus and sorted for GFP positive cells or selected by puromycin.…”

Deubiquitinases in hematological malignancies

“…However, USP7 is frequently mutated in pediatric T-ALL, with somatic heterozygous loss-of-function mutations (haploinsufficiency) predominantly affecting the subgroup that has aberrant TAL1 oncogene activation. Haploinsufficiency of USP7 promotes cell growth and transcriptionally down-regulates E-proteins targets by interacting with TAL1 [ 113 ]. Specifically, USP7 interacts with p190 BCR-ABL in Philadelphia chromosome-positive (Ph+) ALL, and decreased USP7 activity is associated with p53 protein stability [ 114 ].…”