Genome-Wide CRISPR-Cas9 Screen Reveals Selective Vulnerability of ATRX-Mutant Cancers to WEE1 Inhibition

Abstract

The tumor suppressor gene ATRX is frequently mutated in a variety of tumors including gliomas and liver cancers, which are highly unresponsive to current therapies. Here, we performed a genomewide synthetic lethal screen, using CRISPR-Cas9 genome editing, to identify potential therapeutic targets specific for ATRX-mutated cancers. In isogenic hepatocellular carcinoma (HCC) cell lines engineered for ATRX loss, we identified 58 genes, including the checkpoint kinase WEE1, uniquely required for the cell growth of ATRX null cells. Treatment with the WEE1 inhibitor AZD1775 robustly inhibited the growth of several ATRX-deficient HCC cell lines in vitro, as well as xenografts in vivo. The increased sensitivity to the WEE1 inhibitor was caused by accumulated DNA damage-induced apoptosis. AZD1775 also selectively inhibited the proliferation of patient-derived primary cell lines from gliomas with naturally occurring ATRX mutations, indicating that the synthetic lethal relationship between WEE1 and ATRX could be exploited in a broader spectrum of human tumors. As WEE1 inhibitors have been investigated in several phase II clinical trials, our discovery provides the basis for an easily clinically testable therapeutic strategy specific for cancers deficient in ATRX.Significance: ATRX-mutant cancer cells depend on WEE1, which provides a basis for therapeutically targeting WEE1 in ATRX-deficient cancers.See related commentary by Cole, p. 375

Tousled-Like Kinases Suppress Innate Immune Signaling Triggered by Alternative Lengthening of Telomeres

“…In addition, ECTRs generated by ALT induce the cGAS-STING pathway and were proposed to provide selective pressure for the epigenetic silencing of STING to suppress potentially cytostatic innate immune signaling ( Chen et al., 2017 ). ALT+ cells deficient in ATRX may also have a higher dependency on ASF1 and, thus, TLK activity, to support H3.3 deposition and heterochromatin maintenance ( Liang et al., 2020 ; Lovejoy et al., 2012 ). This is consistent with previous work that showed redundancy in the histone chaperone network that can mitigate deleterious effects arising upon histone pool or histone chaperone imbalances ( Drané et al., 2010 ; Lacoste et al., 2014 ).…”

“…ALT+ tumors are frequently characterized by inactivation of the Alpha thalassemia/mental retardation syndrome X-linked (ATRX)-Death-domain associated protein (DAXX) complex, which controls histone H3.3 deposition and maintenance of pericentromeric and telomeric heterochromatin. ASF1 facilitates H3.3 deposition through the Histone Cell Cycle Regulation Defective Homolog A (HIRA) or Chromatin Assembly Factor 1 (CAF1) chaperones and may compensate for a lack of ATRX-DAXX in ALT+ tumors ( Clément et al., 2018 ; Liang et al., 2020 ; Lovejoy et al., 2012 ).…”

Telomere Maintenance Associated Mutations in the Genetic Landscape of Gynecological Mucosal Melanoma

“…Recently, Liang et al found treatment with the AZD1775, a WEE1 inhibitor, robustly inhibited the growth of several ATRX -deficient cancer cell lines in vitro , as well as xenografts in vivo . AZD1775 also selectively inhibited the proliferation of patient-derived primary cell lines from gliomas with naturally occurring ATRX mutations ( 34 ). In our research, we found ATRX protein loss in 82.1% (23/28) of ALT-positive patients.…”

Advances in synthetic lethality for cancer therapy: cellular mechanism and clinical translation

“…Several preclinical studies confirmed that WEE1 inhibitors cause mitotic lethality, making p53-deficient cells sensitive to radiation and DNA damaging agents [ 124 , 125 ]. For instance, Liang et al [ 126 ] reported that apoptosis induced by accumulated DNA damage increases the sensitivity of cancer cells to WEE1 inhibitors. WEE1 inhibitor can selectively inhibit the proliferation of glioma and hepatocellular carcinoma cells with ATRX mutations, which indicates that the synthetic lethal interaction between ATRX and WEE1 can be applied in an extensive range of tumors.…”