In This Issue

See article, p. 1087

The genetic landscape of pancreatic ductal adenocarcinoma (PDAC) in younger patients remains poorly understood. Heining, Horak, Uhrig, and colleagues performed whole-exome or whole-genome sequencing of 17 young patients with PDAC (aged 24–49) enrolled in a genomics-guided precision oncology program. The tumors harbored a range of nonsynonymous point mutations, small insertions/deletions, and DNA copy-number aberrations. KRAS mutations occurred in 13 of 17 (76.5%) samples, most of which also harbored point mutations in TP53 and deletions affecting CDKN2A/B, whereas the 4 KRAS wild-type tumors lacked TP53 mutations. Three patients had pathologic germline variants in DNA-repair genes, and 5 additional patients had germline variants of uncertain significance in genes involved in DNA repair. The 4 KRAS wild-type patients harbored complex structural rearrangements that resulted in oncogenic gene fusions involving NRG1, which were absent in KRAS-mutant tumors. NRG1 fusion partners included APP, CDH6, SARAF, and ATP1B1. Overexpressing ATP1B1–NRG1 in a human pancreatic epithelial cell line increased proliferation and AKT and ERK phosphorylation in vitro and promoted tumor formation in vivo, supporting an oncogenic role for these NRG1 fusions. NRG1 rearrangements are predicted to drive PDAC via aberrant ERBB signaling. Thus, two of the patients with NRG1 rearrangements were treated with the ERBB inhibitor afatinib, which resulted in clinical benefit and remission of liver metastases. Collectively, these findings indicate that oncogenic gene rearrangements are potential therapeutic targets in a sizeable fraction of young patients with KRAS wild-type PDAC.

See article, p. 1096

Pancreatic ductal adenocarcinoma (PDAC) can be classified into subtypes based on genetic and molecular characterization, but methods are needed to efficiently utilize genomic information to facilitate precision medicine in patients with PDAC. To this end, Aguirre, Nowak, Camarda, and colleagues developed a rapid biopsy protocol (PancSeq) for time-sensitive whole-exome and RNA sequencing of patients with PDAC. In total, 79 patients underwent biopsy on the PancSeq protocol, the majority of whom had treatment-naïve metastatic disease. This approach revealed clinically relevant genomic alterations in 34 of 71 patients (48%) that could confer eligibility for a clinical trial or support off-label use of an approved agent. Overall, the PancSeq data resulted in changes in clinical management in 21 of 71 (30%) patients. Further, 64 of 71 (90%) patients harbored KRAS mutations, and 13 of 71 (18%) patients had germline alterations suspected to be pathogenic. Mutations in DNA damage repair genes occurred in 31 of 71 (44%) patients, and these mutations may identify patients susceptible to PARP inhibitors or other DNA-damaging agents. Two patients harbored in-frame BRAF deletions expected to activate MAPK signaling, and one of these patients was treated with a MEK1/2 inhibitor and achieved a significant response. Taken together, these findings suggest that a rapid biopsy program may be feasible to facilitate real-time genomic characterization of tumors in patients with advanced PDAC, and these findings may guide the use of molecularly targeted therapies.

See article, p. 1112

In patients with pancreatic ductal adenocarcinoma (PDAC) there is an unmet clinical need for methods to determine the most effective therapeutic regimen for each patient. To this end, Tiriac and colleagues developed a pancreatic cancer patient-derived organoid (PDO) library. A total of 114 PDO cultures were generated from 101 patients, representing a generation efficiency of 75%. A subset of the PDO cultures underwent whole-exome sequencing, whole-genome sequencing, KRAS mutation profiling, or RNA sequencing, and the PDOs recapitulated the genetic and transcriptomic subtypes present in primary pancreatic cancer, suggesting the potential utility of PDO cultures in precision medicine strategies for identification of actionable alterations and evaluation of candidate therapies. Therapeutic profiling or “pharmacotyping” of 66 PDOs, evaluating 5 chemotherapeutics commonly used to treat PDAC, revealed substantial interpatient variability in response. The PDO therapeutic profiles corresponded to treatment response in patients. This approach allowed longitudinal profiling of chemosensitivity and the potential for nomination of effective therapeutics in chemoresistant PDOs. PDO gene expression signatures associated with chemosensitivity identified groups of patients who best responded to these chemotherapies in both the adjuvant and advanced disease settings. Taken together, these findings suggest that combined genomic, transcriptomic, and therapeutic profiling of PDOs may predict therapeutic response and enable therapeutic selection to facilitate precision medicine in patients with PDAC.

See article, p. 1130

The efficacy of RAF kinase inhibitors in BRAF^V600E -mutant tumors is limited by the acquisition of resistance mechanisms that promote RAS activation or induce RAS-independent BRAF dimerization. However, it remains unclear whether second-site mutations in BRAF drive clinical resistance to RAF inhibitor therapy. Using whole-exome and transcriptome sequencing, Wang and colleagues identified a secondary BRAF point mutation that emerged at progression following an initial response to dabrafenib treatment in a pediatric patient with a BRAF^V600E -mutant brain tumor. The BRAF^L514V mutation was present in cis with the V600E mutation and was detected in the post-dabrafenib resistant tumor but not in pre-dabrafenib tumor samples. Functional studies demonstrated that expression of double-mutant BRAF ^V600E/L514V was sufficient to confer acquired resistance to RAF inhibitors in vitro and that the L514V mutation mediated resistance via a mechanism distinct from conventional gatekeeper mutations by promoting RAF dimerization and subsequent activation of ERK signaling. Although MEK inhibition was not fully capable of overcoming BRAF ^V600E/L514V -mediated resistance, BRAF^V600E/L514V dimers retained sensitivity to treatment with more recently developed RAF dimer inhibitors or an ERK1/2 kinase inhibitor. These findings identify emergence of a second-site BRAF mutation as a previously unidentified mechanism of acquired RAF inhibitor resistance and suggest potential therapeutic strategies to overcome this resistance in patients whose tumors harbor this mutation.

See article, p. 1142

Interactions between the tumor and its microenvironment influence tumorigenesis, but these tumor–microenvironment interactions have not been fully characterized. Wang and colleagues developed an algorithm for dissection of tumors, DisHet, to evaluate the tumor microenvironment in renal cellcarcinoma (RCC) using patient-derived xenografts (or tumorgrafts). DisHet was used to subtract human tumorgraft expression data from the corresponding patient tumor to generate an empirically defined tumor microenvironment signature (eTME). DisHet analyses uncovered 610 genes not previously linked to the RCC tumor microenvironment and found that half of the previously designated immune signature genes are not expressed in the RCC tumor microenvironment. Using data from The Cancer Genome Atlas, eTME analyses characterized a highly inflamed RCC subtype (termed IS) that exhibited enrichment of regulatory T cells, natural killer cells, T_H1 cells, neutrophils, macrophages, B cells, and CD8⁺ T cells. The IS subtype was associated with aggressive disease, including BAP1-deficient clear-cell RCC and type 2 papillary tumors, and predicted poor survival in patients with RCC. Further, the IS subtype was associated with systemic inflammation, such as thrombocytosis and anemia, which are indicators of poor prognosis. In addition to developing an algorithm and an immune signature gene set to dissect the RCC tumor microenvironment, these findings provide a link between tumor and systemic prognostic factors.

See article, p. 1156

Immune checkpoint blockade targeting PD-1 and its ligand PD-L1 has shown significant clinical responses in a subset of patients with cancer; however, various tumor cell–intrinsic and –extrinsic mechanisms have been implicated in therapeutic resistance and disease progression. To further understand the molecular mechanisms underlying immunotherapy resistance, Chen and colleagues analyzed gene expression profiles derived from mouse models of lung cancer and melanoma treated with anti–PD-1/PD-L1 and identified CD38 upregulation in resistant tumor cells. This increase in CD38 expression was induced by ATRA and IFNβ in the inflammatory tumor microenvironment in response to anti–PD-1/PD-L1 therapy. Upregulation of CD38 inhibited the proliferation and function of CD8⁺ T cells by enhancing adenosine production and downstream activation of immunosuppressive adenosine receptor signaling on T cells, suggesting that CD38 contributes to resistance by promoting tumor immune escape. Consistent with this idea, CD38 expression was increased in patients with melanoma in response to anti–PD-1 treatment, and high levels of CD38 were associated with an active intratumoral immune infiltrate in human melanoma and lung cancer. Combined treatment with anti–PD-L1 and a CD38-blocking antibody or adenosine receptor antagonists augmented CD8⁺ effector T-cell infiltration and improved suppression of tumor growth compared with single-agent treatment. These results implicate CD38 upregulation as a mechanism of acquired resistance to anti–PD-1/PD-L1 therapy and suggest that inhibition of CD38-mediated adenosine signaling may increase the efficacy of immune checkpoint blockade.

See article, p. 1176

The majority of breast cancers express the estrogen receptor alpha (ERα), which can be therapeutically targeted by several classes of drugs. However, acquired resistance can develop by multiple mechanisms including the acquisition of ERα mutations (ERα^MUT) that drive ligand-independent activation of the ERα pathway. To potentially overcome resistance mediated by ERα^MUT, Puyang, Furman, Zheng, and colleagues developed a small-molecule inhibitor, H3B-5942, that inhibits both ERα^MUT and wild-type ERα (ERα^WT). H3B-5942 is a selective estrogen receptor covalent antagonist that covalently targets a cysteine residue at the 530 position to enforce the antagonistic conformation of both mutant and wild-type ERα. In vitro, H3B-5942 was more active against ERα^MUT and ERα^WT breast cancer cells than standard-of-care therapies without inducing selective ER modulator (SERM)-like activity, whereas the SERM 4-hydroxytamoxifen did. In vivo, H3B-5942 monotherapy potently suppressed the growth of ERα^MUT and ERα^WT breast tumors in xenograft and patient-derived xenograft models. To identify drugs that might be effective in combination with H3B-5942, a screen of 1,356 small-molecule inhibitors was performed. This screen identified several CDK4/6 inhibitors and mTOR inhibitors that were highly synergistic with H3B-5942 in vitro. Consistent with these data, adding the CDK4/6 inhibitor palbociclib enhanced the efficacy of H3B-5942 against ERα^MUT and ERα^WT breast cancer cells in vitro and in vivo. These findings indicate that H3B-5942 has activity against ERα^MUT and ERα^WT breast tumors and may overcome endocrine therapy resistance. Further, the efficacy of H3B-5942 may be enhanced by combination with CDK4/6 or mTOR inhibitors.

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