2022 SPORE Advances

Tracy T. Batchelor, MD - Brigham and Women's Hospital

De novo pyrimidine synthesis is a targetable vulnerability in IDH mutant glioma

Mutations affecting isocitrate dehydrogenase (IDH) enzymes are prevalent in glioma, leukemia, and other cancers. Although mutant IDH inhibitors are effective against leukemia, they seem to be less active in aggressive glioma, underscoring the need for alternative treatment strategies. Through a chemical synthetic lethality screen, we discovered that IDH1-mutant glioma cells are hypersensitive to drugs targeting enzymes in the de novo pyrimidine nucleotide synthesis pathway, including dihydroorotate dehydrogenase (DHODH). We developed a genetically engineered mouse model of mutant IDH1-driven astrocytoma and used it and multiple patient-derived models to show that the brain-penetrant DHODH inhibitor BAY 2402234 displays monotherapy efficacy against IDH-mutant gliomas. Mechanistically, this reflects an obligate dependence of glioma cells on the de novo pyrimidine synthesis pathway and mutant IDH's ability to sensitize to DNA damage upon nucleotide pool imbalance. Our work outlines a tumor-selective, biomarker-guided therapeutic strategy that is poised for clinical translation.

Citation:
Diana D Shi, Milan R Savani, Michael M Levitt, Adam C Wang, Jennifer E Endress, Cylaina E Bird, Joseph Buehler, Sylwia A Stopka, Michael S Regan, Yu-Fen Lin, Vinesh T Puliyappadamba, Wenhua Gao, Januka Khanal, Laura Evans, Joyce H Lee, Lei Guo, Yi Xiao, Min Xu, Bofu Huang, Rebecca B Jennings, Dennis M Bonal, Misty S Martin-Sandoval, Tammie Dang, Lauren C Gattie, Amy B Cameron, Sungwoo Lee, John M Asara, Harley I Kornblum, Tak W Mak, Ryan E Looper, Quang-De Nguyen, Sabina Signoretti, Stefan Gradl, Andreas Sutter, Michael Jeffers, Andreas Janzer, Mark A Lehrman, Lauren G Zacharias, Thomas P Mathews, Julie-Aurore Losman, Timothy E Richardson, Daniel P Cahill, Ralph J DeBerardinis, Keith L Ligon, Lin Xu, Peter Ly, Nathalie Y R Agar, Kalil G Abdullah, Isaac S Harris, William G Kaelin Jr, Samuel K McBrayer. PMID: 35985343. PMCID: PMC9515386. DOI: 10.1016/j.ccell.2022.07.011.

Kornelia Polyak, MD, PhD, Nancy Lin, MD, & Geoffrey Shapiro, MD, PhD - Dana-Farber/Harvard Cancer Center SPORE

Quiescent cancer cells resist T cell attack by forming an immunosuppressive niche

Immunotherapy is a promising treatment for triple-negative breast cancer (TNBC), but patients relapse, highlighting the need to understand the mechanisms of resistance. We discovered that in primary breast cancer, tumor cells that resist T cell attack are quiescent. Quiescent cancer cells (QCCs) form clusters with reduced immune infiltration. They also display superior tumorigenic capacity and higher expression of chemotherapy resistance and stemness genes. We adapted single-cell RNA-sequencing with precise spatial resolution to profile infiltrating cells inside and outside the QCC niche. This transcriptomic analysis revealed hypoxia-induced programs and identified more exhausted T cells, tumor-protective fibroblasts, and dysfunctional dendritic cells inside clusters of QCCs. This uncovered differential phenotypes in infiltrating cells based on their intra-tumor location. Thus, QCCs constitute immunotherapy-resistant reservoirs by orchestrating a local hypoxic immune-suppressive milieu that blocks T cell function. Eliminating QCCs holds the promise to counteract immunotherapy resistance and prevent disease recurrence in TNBC.

Citation:
Pilar Baldominos, Alex Barbera-Mourelle, Olga Barreiro, Yu Huang, Andrew Wight, Jae-Won Cho, Xi Zhao, Guillem Estivill, Isam Adam, Xavier Sanchez, Shannon McCarthy, Julien Schaller, Zara Khan, Albert Ruzo, Ricardo Pastorello, Edward T Richardson, Deborah Dillon, Paula Montero-Llopis, Romualdo Barroso-Sousa, Juliet Forman, Sachet A Shukla, Sara M Tolaney, Elizabeth A Mittendorf, Ulrich H von Andrian, Kai W Wucherpfennig, Martin Hemberg, Judith Agudo. PMID: 35447074. DOI: 10.1016/j.cell.2022.03.033.

Brian Wolpin, MD, & Nabeel Bardeesy, PhD - Dana-Farber/Harvard Cancer Center SPORE

KRASG12C-independent feedback activation of wild-type RAS constrains KRASG12C inhibitor

Although KRAS has long been considered undruggable, direct KRASG12C inhibitors have shown promising initial clinical efficacy. However, the majority of patients still fail to respond. Adaptive feedback reactivation of RAS-mitogen-activated protein kinase (MAPK) signaling has been proposed by our group and others as a key mediator of resistance, but the exact mechanism driving reactivation and the therapeutic implications are unclear. We find that upstream feedback activation of wild-type RAS, as opposed to a shift in KRASG12C to its active guanosine triphosphate (GTP)-bound state, is sufficient to drive RAS-MAPK reactivation in a KRASG12C-independent manner. Moreover, multiple receptor tyrosine kinases (RTKs) can drive feedback reactivation, potentially necessitating targeting of convergent signaling nodes for more universal efficacy. Even in colorectal cancer, where feedback is thought to be primarily epidermal growth factor receptor (EGFR)-mediated, alternative RTKs drive pathway reactivation and limit efficacy, but convergent upstream or downstream signal blockade can enhance activity. Overall, these data provide important mechanistic insight to guide therapeutic strategies targeting KRAS.

Citation:
Meagan B Ryan, Oluwadara Coker, Alexey Sorokin, Katerina Fella, Haley Barnes, Edmond Wong, Preeti Kanikarla, Fengqin Gao, Youyan Zhang, Lian Zhou, Scott Kopetz, Ryan B Corcoran. PMID: 35732135. PMCID: PMC9809542. DOI: 10.1016/j.celrep.2022.110993.

Brian Wolpin, MD, & Nabeel Bardeesy, PhD - Dana-Farber/Harvard Cancer Center SPORE

EGFR Inhibition Potentiates FGFR Inhibitor Therapy and Overcomes Resistance in FGFR2 Fusion-Positive Cholangiocarcinoma

FGFR inhibitors are approved for the treatment of advanced cholangiocarcinoma harboring FGFR2 fusions. However, the response rate is moderate, and resistance emerges rapidly due to acquired secondary FGFR2 mutations or due to other less-defined mechanisms. Here, we conducted high-throughput combination drug screens, biochemical analysis, and therapeutic studies using patient-derived models of FGFR2 fusion-positive cholangiocarcinoma to gain insight into these clinical profiles and uncover improved treatment strategies. We found that feedback activation of EGFR signaling limits FGFR inhibitor efficacy, restricting cell death induction in sensitive models and causing resistance in insensitive models lacking secondary FGFR2 mutations. Inhibition of wild-type EGFR potentiated responses to FGFR inhibitors in both contexts, durably suppressing MEK/ERK and mTOR signaling, increasing apoptosis, and causing marked tumor regressions in vivo. Our findings reveal EGFR-dependent adaptive signaling as an important mechanism limiting FGFR inhibitor efficacy and driving resistance and support clinical testing of FGFR/EGFR inhibitor therapy for FGFR2 fusion-positive cholangiocarcinoma.

Citation:
Qibiao Wu, Yuanli Zhen, Lei Shi, Phuong Vu, Patricia Greninger, Ramzi Adil, Joshua Merritt, Regina Egan, Meng-Ju Wu, Xunqin Yin, Cristina R Ferrone, Vikram Deshpande, Islam Baiev, Christopher J Pinto, Daniel E McLoughlin, Charlotte S Walmsley, James R Stone, John D Gordan, Andrew X Zhu, Dejan Juric, Lipika Goyal, Cyril H Benes, Nabeel Bardeesy. PMID: 35420673. PMCID: PMC9064956. DOI: 10.1158/2159-8290.CD-21-1168.

Marina Konopleva, MD, PhD, & Elizabeth Shpall, MD - The University of Texas MD Anderson Cancer Center Leukemia SPORE

KIR-based inhibitory CARs overcome CAR-NK cell trogocytosis-mediated fratricide and tumor escape

Trogocytosis is an active process that transfers surface material from targeted to effector cells. Using multiple in vivo tumor models and clinical data, we report that chimeric antigen receptor (CAR) activation in natural killer (NK) cells promoted transfer of the CAR cognate antigen from tumor to NK cells, resulting in (1) lower tumor antigen density, thus impairing the ability of CAR-NK cells to engage with their target, and (2) induced self-recognition and continuous CAR-mediated engagement, resulting in fratricide of trogocytic antigen-expressing NK cells (NKTROG+) and NK cell hyporesponsiveness. This phenomenon could be offset by a dual-CAR system incorporating both an activating CAR against the cognate tumor antigen and an NK self-recognizing inhibitory CAR that transferred a 'don't kill me' signal to NK cells upon engagement with their TROG+ siblings. This system prevented trogocytic antigen-mediated fratricide, while sparing activating CAR signaling against the tumor antigen, and resulted in enhanced CAR-NK cell activity.

Citation:
Ye Li 1, Rafet Basar, Guohui Wang, Enli Liu, Judy S Moyes, Li Li, Lucila N Kerbauy, Nadima Uprety, Mohsen Fathi, Ali Rezvan, Pinaki P Banerjee, Luis Muniz-Feliciano, Tamara J Laskowski, Emily Ensley, May Daher, Mayra Shanley, Mayela Mendt, Sunil Acharya, Bin Liu, Alexander Biederstädt, Hind Rafei, Xingliang Guo, Luciana Melo Garcia, Paul Lin, Sonny Ang, David Marin, Ken Chen, Laura Bover, Richard E Champlin, Navin Varadarajan, Elizabeth J Shpall, Katayoun Rezvani. PMID: 36175679. DOI: 10.1038/s41591-022-02003-x.

John Minna, MD, & John Heymach, MD, PhD - University of Texas Southwestern Medical Center/University of Texas MD Anderson Cancer Center SPORE

Structure-based classification predicts drug response in EGFR-mutant NSCLC

Epidermal growth factor receptor (EGFR) mutations typically occur in exons 18-21 and are established driver mutations in non-small cell lung cancer (NSCLC). Targeted therapies are approved for patients with 'classical' mutations and a small number of other mutations. However, effective therapies have not been identified for additional EGFR mutations. Furthermore, the frequency and effects of atypical EGFR mutations on drug sensitivity are unknown. Here we characterize the mutational landscape in 16,715 patients with EGFR-mutant NSCLC, and establish the structure-function relationship of EGFR mutations on drug sensitivity. We found that EGFR mutations can be separated into four distinct subgroups on the basis of sensitivity and structural changes that retrospectively predict patient outcomes following treatment with EGFR inhibitors better than traditional exon-based groups. Together, these data delineate a structure-based approach for defining functional groups of EGFR mutations that can effectively guide treatment and clinical trial choices for patients with EGFR-mutant NSCLC and suggest that a structure-function-based approach may improve the prediction of drug sensitivity to targeted therapies in oncogenes with diverse mutations.

Citation:
Jacqulyne P Robichaux, Xiuning Le, R S K Vijayan, J Kevin Hicks, Simon Heeke, Yasir Y Elamin, Heather Y Lin, Hibiki Udagawa, Ferdinandos Skoulidis, Hai Tran, Susan Varghese, Junqin He, Fahao Zhang, Monique B Nilsson, Lemei Hu, Alissa Poteete, Waree Rinsurongkawong, Xiaoshan Zhang, Chenghui Ren, Xiaoke Liu, Lingzhi Hong, Jianjun Zhang, Lixia Diao, Russell Madison, Alexa B Schrock, Jennifer Saam, Victoria Raymond, Bingliang Fang, Jing Wang, Min Jin Ha, Jason B Cross, Jhanelle E Gray, John V Heymach. PMID: 34526717. PMCID: PMC8481125. DOI: 10.1038/s41586-021-03898-1.

Marcus Bosenberg, MD, PhD, & Harriet Kluger, MD - Yale University SPORE

KDM5B promotes immune evasion by recruiting SETDB1 to silence retroelements

Tumours use various strategies to evade immune surveillance. Immunotherapies targeting tumour immune evasion such as immune checkpoint blockade have shown considerable efficacy on multiple cancers but are ineffective for most patients due to primary or acquired resistance. Recent studies showed that some epigenetic regulators suppress anti-tumour immunity, suggesting that epigenetic therapies could boost anti-tumour immune responses and overcome resistance to current immunotherapies. Here we show that, in mouse melanoma models, depletion of KDM5B-an H3K4 demethylase that is critical for melanoma maintenance and drug resistance-induces robust adaptive immune responses and enhances responses to immune checkpoint blockade. Mechanistically, KDM5B recruits the H3K9 methyltransferase SETDB1 to repress endogenous retroelements such as MMVL30 in a demethylase-independent manner. Derepression of these retroelements activates cytosolic RNA-sensing and DNA-sensing pathways and the subsequent type-I interferon response, leading to tumour rejection and induction of immune memory. Our results demonstrate that KDM5B suppresses anti-tumour immunity by epigenetic silencing of retroelements. We therefore reveal roles of KDM5B in heterochromatin regulation and immune evasion in melanoma, opening new paths for the development of KDM5B-targeting and SETDB1-targeting therapies to enhance tumour immunogenicity and overcome immunotherapy resistance.

Citation:
Shang-Min Zhang, Wesley L Cai, Xiaoni Liu, Durga Thakral, Jiesi Luo, Lok Hei Chan, Meaghan K McGeary, Eric Song, Kim R M Blenman, Goran Micevic, Shlomit Jessel, Yangyi Zhang, Mingzhu Yin, Carmen J Booth, Lucia B Jilaveanu, William Damsky, Mario Sznol, Harriet M Kluger, Akiko Iwasaki, Marcus W Bosenberg, Qin Yan. PMID: 34671158. PMCID: PMC8555464. DOI: 10.1038/s41586-021-03994-2.