In This Issue

See article, p. 1529.

The EGFR tyrosine kinase inhibitor (TKI) osimertinib is now the standard first-line therapy for patients with EGFR-mutant non–small cell lung cancer (NSCLC). Osimertinib achieves high initial response rates, but acquired resistance limits the duration of response. To identify mechanisms of resistance to osimertinib, Piotrowska, Isozaki, and colleagues analyzed tumor tissue or circulating tumor DNA (ctDNA) from 41 patients with EGFR-mutant NSCLC who progressed on osimertinib. Identified acquired mutations included EGFR^C797S, EGFR^T790M, and MET amplification, and identified gene fusions included CCDC6–RET, TPM3–NTRK1, PCBP2–BRAF, and AGK–BRAF. Retrospective analysis of additional EGFR-mutant NSCLC biopsies identified two additional patients with RET fusions: CCDC6–RET and NCOA4–RET. Expression of CCDC6–RET in EGFR-mutant cell lines was sufficient to confer resistance to EGFR TKIs, indicating that RET fusions may confer acquired resistance to EGFR inhibition. Dual inhibition of CCDC6–RET, with the selective RET inhibitor BLU-667, and EGFR could overcome resistance to EGFR inhibition, completely suppressing phosphorylation of ERK and AKT and reducing cell viability. Similarly, cells harboring PCBP2–BRAF were sensitive to combined targeting of MEK and EGFR. Based on these findings, two patients with EGFR-mutant NSCLC who had progressed on afatinib and harbored a CCDC6–RET or NCOA4–RET fusion were treated with osimertinib plus BLU-667. This combination was well tolerated and produced a rapid response in both patients. Together, these findings demonstrate that RET fusions can confer resistance to EGFR inhibition, and therapeutic targeting of RET may overcome therapeutic resistance in patients with EGFR-mutant NSCLC.

See article, p. 1540.

Recurrent mutations in isocitrate dehydrogenase 1 (IDH1) and IDH2 occur in acute myeloid leukemia (AML) and some solid tumors that cause the abnormal conversion of α-ketoglutarate (αKG) to 2-hydroxyglutarate (2HG), which inhibits normal differentiation and drives tumorigenesis through the inhibition of αKG-dependent DNA and histone demethylases. Isoform-specific inhibitors of mutant IDH1 and IDH2 that block 2HG production, induce cellular differentiation, and suppress tumor growth in preclinical studies are being evaluated in patients with relapsed or refractory IDH-mutant cancers. Harding, Lowery, and colleagues describe two patients with IDH1-mutant AML and one patient with IDH1-mutant intrahepatic cholangiocarcinoma who initially responded to the mutant IDH1-selective inhibitor ivosidenib but had a detectable IDH2 mutation and increased serum 2HG at relapse, and a patient with IDH2-mutant AML who initially responded to the mutant IDH2-selective inhibitor enasidenib but had a detectable IDH1 mutation and increased serum 2HG at relapse. Expression of mutant IDH2 in IDH1-mutant chondrosarcoma cells restored 2HG production in the presence of ivosidenib, as did expression of mutant IDH1 in IDH2-mutant cells in the presence of enasidenib, but combined treatment with ivosidenib and enasidenib suppressed 2HG production. These observations suggest that mutant isoform switching may be a general mechanism of acquired resistance to IDH-targeted therapy in both hematologic and solid tumors and raise the possibility that coinhibition of IDH1 and IDH2 may circumvent or prevent resistance to IDH inhibition.

See article, p. 1548.

Copy-number loss and somatic mutations in several genes including BAP1, NF2, and CDKN2A have been previously identified in malignant pleural mesothelioma (MPM), a cancer arising from the mesothelial cells lining the pleural cavity. However, our understanding of the molecular landscape of MPM remains incomplete and effective molecularly targeted therapies have remained elusive. To address these issues, Hmeljak, Sanchez-Vega, and colleagues performed a comprehensive genomic analysis of 74 primary MPM samples as part of The Cancer Genome Atlas (TCGA). Whole-exome sequencing and copy-number analysis revealed a genomic landscape featuring a low mutation burden and many recurrent losses but no recurrent amplifications, and confirmed BAP1 as the most frequently mutated cancer gene in this MPM cohort, consistent with previous studies. This analysis also defined a previously unrecognized MPM subtype characterized by extensive loss of heterozygosity, termed genomic near-haploidization, usually followed by genome duplication, which co-occurred with mutations in TP53 and SETDB1; remarkably, unlike MPM in general, this subtype appears more common in women. Integrative multiplatform clustering analysis identified distinct molecular MPM subgroups, which were histology-independent and associated with significant differences in prognosis. Furthermore, the expression of the negative immune checkpoint gene VISTA showed markedly higher expression on tumor cells in the better-differentiated epithelioid subtype of MPM than any other solid tumor studied by TCGA. Together, these findings further define the genomics and biological subtypes of MPM and suggest potential therapeutic targets and strategies to improve risk stratification of patients with this disease.

See article, p. 1566.

Venetoclax, which inhibitsthe antiapoptotic protein BCL2, can induce apoptosis to achieve responses in acute myeloid leukemia (AML). However, the upregulation of alternative antiapoptotic proteins (such as MCL1 and BCL-xL) can lead to the development of resistance that limits the duration of response to venetoclax. Ramsey and colleagues used fragment-based methods and structure-based design to discover VU661013, a potent, selective small-molecule MCL1 inhibitor. In vitro, VU661013 suppressed the growth of AML cell lines. In vivo, VU661013 monotherapy reduced disease burden in a mouse model of disseminated AML. Although the initial effects of VU661013 were dramatic, the mice eventually developed resistance and succumbed to AML, and this resistance wasassociated with an increased dependence on BCL2. Thus, VU661013 was evaluated in combination with the BCL2 inhibitor venetoclax, and the inhibitors synergized to suppress AML in vivo with no apparent organ toxicity and a minimal impact on normal hematopoietic stem and progenitor cells. BH3 profiling predicted the response to MCL1 inhibition, and resistance to VU661013 was linked to a greater sensitivity to BCL2 inhibition and vice versa. Further, BH3 profiling in AML samples from patients along with ex vivo drug-sensitivity testing predicted sensitivity to MCL1 or BCL2 inhibition, with combination treatment demonstrating superior effects in patient-derived xenograft transplantation models. In addition to identifying a potent MCL1 inhibitor, these findings indicate that dual targeting of MCL1 and BCL2 may be an effective therapeutic strategy in patients with AML and potentially overcome venetoclax resistance.

See article, p. 1582.

Tumor cells frequently exhibit dysregulation of the BCL2 family proteins to evade apoptosis.The BCL2 family proteins include antiapoptotic proteins (such as BCL2, BCL-xL, and MCL1) and proapoptotic proteins (such as the BH3-only proteins BIM and BAD and the downstream effectors BAX and BAK). The BCL2 inhibitor venetoclax has demonstrated clinical activity in chronic lymphocytic leukemia but more modest response rates in other malignancies including acute myeloid leukemia (AML) and multiple myeloma, likely due to the activity of other antiapoptotic BCL2 family proteins. These findings suggest the potential for MCL1 inhibitors, but the shallow BH3-domain binding pocket has made their development challenging. Caenepeel and colleagues used small-molecule conformation restriction and optimization to identify AMG 176, an orally bioavailable selective MCL1 inhibitor. In a panel of 952 tumor cell lines, cells from hematologic malignancies including multiple myeloma, AML, and B-cell lymphoma were most sensitive to MCL1 inhibition, with a rapid commitment toward apoptosis. Cells with low expression of BCL-xL and high expression of BAK were most sensitive to MCL1 inhibition. In vivo, AMG 176 induced apoptosis and reduced tumor burden in xenograft models of multiple myeloma and AML, and efficacy was increased by its combination with venetoclax or other clinically relevant agents such as corticosteroids, proteasome inhibitors, or immunomodulatory drugs. Further, AMG 176 was well tolerated in human MCL1 knock-in mice. These data suggest that MCL1 inhibition is feasible and may be effective in a variety of hematologic malignancies, alone or in combination with other therapeutics including inhibitors of other BCL2 family proteins.

See article, p. 1598.

KRAS mutations occur frequently in non–small cell lung cancer (NSCLC) and activate RAS–MAPK signaling to drive tumorigenesis. Therapeutic targeting of downstream MAPK effectors has had limited clinical success, and strategies to simultaneously target multiple downstream pathways have been limited by toxicity. MEK inhibition promotes accumulation of the proapoptotic BH3 protein BIM. However, antiapoptotic BCL2 family members including MCL1 and BCL-xL can neutralize BIM, suggesting the potential for combined MCL1 and MEK inhibition. To identify drugs that may be beneficial in combination with MCL1 inhibition, Nangia, Siddiqui, and colleagues screened 187 compounds in combination with the MCL1 inhibitor AM-8621 in a panel of solid tumor cell lines. In cell lines with MAPK pathway activation, MAPK pathway inhibitors synergized with AM-8621. KRAS-mutant NSCLC cells that did not respond to inhibition of MEK plus BCL-xL were sensitive to inhibition of MEK and MCL1, indicating that MCL1 and BCL-xL each enhanced the effects of MEK inhibition in distinct but overlapping subsets of KRAS-mutant NSCLC. Specifically, BIM interacted with MCL1 and BCL-xL in the mitochondria, and the extent of binding determined sensitivity to MCL1 or BCL-xL inhibition. In vivo, combined inhibition of MEK and MCL1 induced tumor regression in NSCLC xenografts. Further, transient BCL-xL inhibition increased the dependence on MCL1, thereby sensitizing cells to subsequent MCL1 inhibition. Collectively, these findings suggest the potential for MCL1 inhibition in combination with MEK inhibition in KRAS-mutant NSCLC.

See article, p. 1614.

Deletion of chromosome 6q [del(6q)] is a recurrent event in T-cell acute lymphoblastic leukemia (T-ALL) that is associated with a poor prognosis, but the gene(s) targeted by this chromosomal alteration and how their loss contributes to T-ALL development remains an unanswered question in the field. Gachet, El-Chaar, Avran, Genesca, and colleagues determined that del(6q) was a late-stage event associated with leukemic progression, particularly the subtype characterized by TAL1 overexpression, and identified a common deleted region in del(6q) T-ALL that specifically led to decreased expression of two genes in the region, SYNCRIP and SNHG5. Combined silencing of both genes significantly accelerated development of Tal1-driven leukemia in mice, suggesting that these genes constitute a haploinsufficient tumor suppressor region that underlies the effects of del(6q) in T-ALL. Because SYNCRIP encodes a heterogeneous nuclear ribonucleoprotein and SNHG5 hosts small nucleolar RNAs (snoRNA), the effects of SYNCRIP–SNHG5 deletion on ribosome function were evaluated in human T-ALL cells. In SYNCRIP–SNHG5-deleted cells, altered 2′-O-methylation (caused by reduced snoRNA expression) and ribosome assembly specifically affected the translation efficacy of genes involved in oxidative phosphorylation, leading to reduced basal and maximal mitochondrial respiration. The changes to the metabolic state induced by co-deletion of SYNCRIP and SNHG5 significantly increased leukemic-initiating cell activity of T-ALL cells and could be phenocopied by inhibition of mitochondrial protein translation, providing further support for a role of reduced ribosomal and mitochondrial function caused by haploinsufficiency of SYNCRIP and SNHG5 in the pathogenesis of del(6q) T-ALL.

See article, p. 1632.

Approximately 10% of diffuse large B-cell lymphomas (DLBCL) harbor somatic mutations of TET2, but it is unknown whether this is a driver or passenger event in this disease. DLBCL originates from mature B-cells transiting through germinal centers (GC), where B cells normally undergo accelerated replication and somatic hypermutation to result in expression of high-affinity antigen-specific B-cell receptors that are required for exit from the GC reaction and differentiation into memory B cells and plasma cells. Dominguez, Ghamlouch, Rosikiewicz, and colleagues found that B cell–specific Tet2 deletion resulted in GC B-cell hyperplasia and impaired affinity maturation and plasma cell differentiation, suggesting that TET2 loss blocks B cells from exiting the GC stage of development, a hallmark of DLBCL. Consistent with these observations, Tet2-deficient B cells abnormally accumulated as centrocytes, and Tet2 deficiency promoted progression of GC B cells toward a preneoplastic phenotype and cooperated with the DLBCL oncogene Bcl6 to accelerate lymphomagenesis in mice. Loss of the TET2 methylcytosine dioxygenase function resulted in decreased cytosine hydroxymethylation at enhancers accompanied by reduced expression of the respective genes that are normally induced during GC exit. Histone acetylation at enhancers was also reduced, and the gene expression profile of Tet2-deficient GC B cells was similar to the signature induced by somatic loss-of-function mutations of the histone acetyltransferase gene CREBBP in DLBCL. In human DLBCL, TET2 and CREBBP mutations were largely mutually exclusive, suggesting they have overlapping functions and that TET2-mutant and CREBBP-mutant DLBCL may have shared therapeutic vulnerabilities.

Note: In This Issue is written by Cancer Discovery editorial staff. Readers are encouraged to consult the original articles for full details.