bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from Single and Dual Targeting of Mutant EGFR with an Allosteric Inhibitor
Authors: To Ciric , Jang Jaebong , Chen Ting , Park Eunyoung , Mushajiang Mierzhati , De Clercq Dries J.H. , Xu Man , Wang Stephen , Cameron Michael D. , Heppner David E. , Shin Bo Hee , Gero Thomas W. , Yang Annan , Dahlberg Suzanne E. , Wong Kwok-Kin , Eck Michael J. , Gray Nathanael S. , Jänne Pasi A.
Published: April 2023

Abstract
Allosteric kinase inhibitors offer a potentially complementary therapeutic strategy to ATP-competitive kinase inhibitors due to their distinct sites of target binding. In this study, we identify and study a mutant-selective EGFR allosteric inhibitor, JBJ-04-125-02, which as a single agent can inhibit cell proliferation and EGFRL858R/T790M/C797S signaling in vitro and in vivo. However, increased EGFR dimer formation limits treatment efficacy and leads to drug resistance. Remarkably, osimertinib, an ATP-competitive covalent EGFR inhibitor, uniquely and significantly enhances the binding of JBJ-04-125-02 for mutant EGFR. The combination of osimertinib and JBJ-04-125-02 results in an increase in apoptosis, a more effective inhibition of cellular growth, and an increased efficacy in vitro and in vivo compared with either single agent alone. Collectively, our findings suggest that the combination of a covalent mutant–selective ATP-competitive inhibitor and an allosteric EGFR inhibitor may be an effective therapeutic approach for patients with EGFR-mutant lung cancer.
Significance:
The clinical efficacy of EGFR tyrosine kinase inhibitors (TKI) in EGFR-mutant lung cancer is limited by acquired drug resistance, thus highlighting the need for alternative strategies to inhibit EGFR. Here, we identify a mutant EGFR allosteric inhibitor that is effective as a single agent and in combination with the EGFR TKI osimertinib.

This article is highlighted in the In This Issue feature, p. 813
Data from Antitumor Activity Associated with Prolonged Persistence of Adoptively Transferred NY-ESO-1 c259T Cells in Synovial Sarcoma
Authors: D'Angelo Sandra P. , Melchiori Luca , Merchant Melinda S. , Bernstein Donna , Glod John , Kaplan Rosandra , Grupp Stephan , Tap William D. , Chagin Karen , Binder Gwendolyn K. , Basu Samik , Lowther Daniel E. , Wang Ruoxi , Bath Natalie , Tipping Alex , Betts Gareth , Ramachandran Indu , Navenot Jean-Marc , Zhang Hua , Wells Daniel K. , Van Winkle Erin , Kari Gabor , Trivedi Trupti , Holdich Tom , Pandite Lini , Amado Rafael , Mackall Crystal L.
Published: April 2023

Abstract
We evaluated the safety and activity of autologous T cells expressing NY-ESO-1c259, an affinity-enhanced T-cell receptor (TCR) recognizing an HLA-A2–restricted NY-ESO-1/LAGE1a–derived peptide, in patients with metastatic synovial sarcoma (NY-ESO-1c259T cells). Confirmed antitumor responses occurred in 50% of patients (6/12) and were characterized by tumor shrinkage over several months. Circulating NY-ESO-1c259T cells were present postinfusion in all patients and persisted for at least 6 months in all responders. Most of the infused NY-ESO-1c259T cells exhibited an effector memory phenotype following ex vivo expansion, but the persisting pools comprised largely central memory and stem-cell memory subsets, which remained polyfunctional and showed no evidence of T-cell exhaustion despite persistent tumor burdens. Next-generation sequencing of endogenous TCRs in CD8+ NY-ESO-1c259T cells revealed clonal diversity without contraction over time. These data suggest that regenerative pools of NY-ESO-1c259T cells produced a continuing supply of effector cells to mediate sustained, clinically meaningful antitumor effects.

Significance: Metastatic synovial sarcoma is incurable with standard therapy. We employed engineered T cells targeting NY-ESO-1, and the data suggest that robust, self-regenerating pools of CD8+ NY-ESO-1c259T cells produce a continuing supply of effector cells over several months that mediate clinically meaningful antitumor effects despite prolonged exposure to antigen. Cancer Discov; 8(8); 944–57. ©2018 AACR.

See related commentary by Keung and Tawbi, p. 914.

This article is highlighted in the In This Issue feature, p. 899
Data from An Empirical Approach Leveraging Tumorgrafts to Dissect the Tumor Microenvironment in Renal Cell Carcinoma Identifies Missing Link to Prognostic Inflammatory Factors
Authors: Wang Tao , Lu Rong , Kapur Payal , Jaiswal Bijay S. , Hannan Raquibul , Zhang Ze , Pedrosa Ivan , Luke Jason J. , Zhang He , Goldstein Leonard D. , Yousuf Qurratulain , Gu Yi-Feng , McKenzie Tiffani , Joyce Allison , Kim Min S. , Wang Xinlei , Luo Danni , Onabolu Oreoluwa , Stevens Christina , Xie Zhiqun , Chen Mingyi , Filatenkov Alexander , Torrealba Jose , Luo Xin , Guo Wenbin , He Jingxuan , Stawiski Eric , Modrusan Zora , Durinck Steffen , Seshagiri Somasekar , Brugarolas James
Published: April 2023

Abstract
By leveraging tumorgraft (patient-derived xenograft) RNA-sequencing data, we developed an empirical approach, DisHet, to dissect the tumor microenvironment (eTME). We found that 65% of previously defined immune signature genes are not abundantly expressed in renal cell carcinoma (RCC) and identified 610 novel immune/stromal transcripts. Using eTME, genomics, pathology, and medical record data involving >1,000 patients, we established an inflamed pan-RCC subtype (IS) enriched for regulatory T cells, natural killer cells, TH1 cells, neutrophils, macrophages, B cells, and CD8+ T cells. IS is enriched for aggressive RCCs, including BAP1-deficient clear-cell and type 2 papillary tumors. The IS subtype correlated with systemic manifestations of inflammation such as thrombocytosis and anemia, which are enigmatic predictors of poor prognosis. Furthermore, IS was a strong predictor of poor survival. Our analyses suggest that tumor cells drive the stromal immune response. These data provide a missing link between tumor cells, the TME, and systemic factors.

Significance: We undertook a novel empirical approach to dissect the renal cell carcinoma TME by leveraging tumorgrafts. The dissection and downstream analyses uncovered missing links between tumor cells, the TME, systemic manifestations of inflammation, and poor prognosis. Cancer Discov; 8(9); 1142–55. ©2018 AACR.

This article is highlighted in the In This Issue feature, p. 1047
Data from Multidimensional Analyses of Donor Memory-Like NK Cells Reveal New Associations with Response after Adoptive Immunotherapy for Leukemia
Authors: Berrien-Elliott Melissa M. , Cashen Amanda F. , Cubitt Celia C. , Neal Carly C. , Wong Pamela , Wagner Julia A. , Foster Mark , Schappe Timothy , Desai Sweta , McClain Ethan , Becker-Hapak Michelle , Foltz Jennifer A. , Cooper Matthew L. , Jaeger Natalia , Srivatsan Sridhar Nonavinkere , Gao Feng , Romee Rizwan , Abboud Camille N. , Uy Geoffrey L. , Westervelt Peter , Jacoby Meagan A. , Pusic Iskra , Stockerl-Goldstein Keith E. , Schroeder Mark A. , DiPersio John , Fehniger Todd A.
Published: April 2023

Abstract
Natural killer (NK) cells are an emerging cancer cellular therapy and potent mediators of antitumor immunity. Cytokine-induced memory-like (ML) NK cellular therapy is safe and induces remissions in patients with acute myeloid leukemia (AML). However, the dynamic changes in phenotype that occur after NK-cell transfer that affect patient outcomes remain unclear. Here, we report comprehensive multidimensional correlates from ML NK cell–treated patients with AML using mass cytometry. These data identify a unique in vivo differentiated ML NK–cell phenotype distinct from conventional NK cells. Moreover, the inhibitory receptor NKG2A is a dominant, transcriptionally induced checkpoint important for ML, but not conventional NK-cell responses to cancer. The frequency of CD8α+ donor NK cells is negatively associated with AML patient outcomes after ML NK therapy. Thus, elucidating the multidimensional dynamics of donor ML NK cells in vivo revealed critical factors important for clinical response, and new avenues to enhance NK-cell therapeutics.
Significance:
Mass cytometry reveals an in vivo memory-like NK-cell phenotype, where NKG2A is a dominant checkpoint, and CD8α is associated with treatment failure after ML NK–cell therapy. These findings identify multiple avenues for optimizing ML NK–cell immunotherapy for cancer and define mechanisms important for ML NK–cell function.

This article is highlighted in the In This Issue feature, p. 1775
Data from H3.3 G34W Promotes Growth and Impedes Differentiation of Osteoblast-Like Mesenchymal Progenitors in Giant Cell Tumor of Bone
Authors: Khazaei Sima , De Jay Nicolas , Deshmukh Shriya , Hendrikse Liam D. , Jawhar Wajih , Chen Carol C.L. , Mikael Leonie G. , Faury Damien , Marchione Dylan M. , Lanoix Joel , Bonneil Éric , Ishii Takeaki , Jain Siddhant U. , Rossokhata Kateryna , Sihota Tianna S. , Eveleigh Robert , Lisi Véronique , Harutyunyan Ashot S. , Jung Sungmi , Karamchandani Jason , Dickson Brendan C. , Turcotte Robert , Wunder Jay S. , Thibault Pierre , Lewis Peter W. , Garcia Benjamin A. , Mack Stephen C. , Taylor Michael D. , Garzia Livia , Kleinman Claudia L. , Jabado Nada
Published: April 2023

Abstract
Glycine 34-to-tryptophan (G34W) substitutions in H3.3 arise in approximately 90% of giant cell tumor of bone (GCT). Here, we show H3.3 G34W is necessary for tumor formation. By profiling the epigenome, transcriptome, and secreted proteome of patient samples and tumor-derived cells CRISPR–Cas9-edited for H3.3 G34W, we show that H3.3K36me3 loss on mutant H3.3 alters the deposition of the repressive H3K27me3 mark from intergenic to genic regions, beyond areas of H3.3 deposition. This promotes redistribution of other chromatin marks and aberrant transcription, altering cell fate in mesenchymal progenitors and hindering differentiation. Single-cell transcriptomics reveals that H3.3 G34W stromal cells recapitulate a neoplastic trajectory from a SPP1+ osteoblast-like progenitor population toward an ACTA2+ myofibroblast-like population, which secretes extracellular matrix ligands predicted to recruit and activate osteoclasts. Our findings suggest that H3.3 G34W leads to GCT by sustaining a transformed state in osteoblast-like progenitors, which promotes neoplastic growth, pathologic recruitment of giant osteoclasts, and bone destruction.
Significance:
This study shows that H3.3 G34W drives GCT tumorigenesis through aberrant epigenetic remodeling, altering differentiation trajectories in mesenchymal progenitors. H3.3 G34W promotes in neoplastic stromal cells an osteoblast-like progenitor state that enables undue interactions with the tumor microenvironment, driving GCT pathogenesis. These epigenetic changes may be amenable to therapeutic targeting in GCT.

See related commentary by Licht, p. 1794.

This article is highlighted in the In This Issue feature, p. 1775
Data from Somatic Tissue Engineering in Mouse Models Reveals an Actionable Role for WNT Pathway Alterations in Prostate Cancer Metastasis
Authors: Leibold Josef , Ruscetti Marcus , Cao Zhen , Ho Yu-Jui , Baslan Timour , Zou Min , Abida Wassim , Feucht Judith , Han Teng , Barriga Francisco M. , Tsanov Kaloyan M. , Zamechek Leah , Kulick Amanda , Amor Corina , Tian Sha , Rybczyk Katarzyna , Salgado Nelson R. , Sánchez-Rivera Francisco J. , Watson Philip A. , de Stanchina Elisa , Wilkinson John E. , Dow Lukas E. , Abate-Shen Cory , Sawyers Charles L. , Lowe Scott W.
Published: April 2023

Abstract
To study genetic factors influencing the progression and therapeutic responses of advanced prostate cancer, we developed a fast and flexible system that introduces genetic alterations relevant to human disease directly into the prostate glands of mice using tissue electroporation. These electroporation-based genetically engineered mouse models (EPO-GEMM) recapitulate features of traditional germline models and, by modeling genetic factors linked to late-stage human disease, can produce tumors that are metastatic and castration-resistant. A subset of tumors with Trp53 alterations acquired spontaneous WNT pathway alterations, which are also associated with metastatic prostate cancer in humans. Using the EPO-GEMM approach and an orthogonal organoid-based model, we show that WNT pathway activation drives metastatic disease that is sensitive to pharmacologic WNT pathway inhibition. Thus, by leveraging EPO-GEMMs, we reveal a functional role for WNT signaling in driving prostate cancer metastasis and validate the WNT pathway as therapeutic target in metastatic prostate cancer.
Significance:
Our understanding of the factors driving metastatic prostate cancer is limited by the paucity of models of late-stage disease. Here, we develop EPO-GEMMs of prostate cancer and use them to identify and validate the WNT pathway as an actionable driver of aggressive metastatic disease.

This article is highlighted in the In This Issue feature, p. 890
Data from Oncogenic KRAS-Driven Metabolic Reprogramming in Pancreatic Cancer Cells Utilizes Cytokines from the Tumor Microenvironment
Authors: Dey Prasenjit , Li Jun , Zhang Jianhua , Chaurasiya Surendra , Strom Anders , Wang Huamin , Liao Wen-Ting , Cavallaro Frederick , Denz Parker , Bernard Vincent , Yen Er-Yen , Genovese Giannicola , Gulhati Pat , Liu Jielin , Chakravarti Deepavali , Deng Pingna , Zhang Tingxin , Carbone Federica , Chang Qing , Ying Haoqiang , Shang Xiaoying , Spring Denise J. , Ghosh Bidyut , Putluri Nagireddy , Maitra Anirban , Wang Y. Alan , DePinho Ronald A.
Published: April 2023

Abstract
A hallmark of pancreatic ductal adenocarcinoma (PDAC) is an exuberant stroma comprised of diverse cell types that enable or suppress tumor progression. Here, we explored the role of oncogenic KRAS in protumorigenic signaling interactions between cancer cells and host cells. We show that KRAS mutation (KRAS*) drives cell-autonomous expression of type I cytokine receptor complexes (IL2rγ–IL4rα and IL2rγ–IL13rα1) in cancer cells that in turn are capable of receiving cytokine growth signals (IL4 or IL13) provided by invading Th2 cells in the microenvironment. Early neoplastic lesions show close proximity of cancer cells harboring KRAS* and Th2 cells producing IL4 and IL13. Activated IL2rγ–IL4rα and IL2rγ–IL13rα1 receptors signal primarily via JAK1–STAT6. Integrated transcriptomic, chromatin occupancy, and metabolomic studies identified MYC as a direct target of activated STAT6 and that MYC drives glycolysis. Thus, paracrine signaling in the tumor microenvironment plays a key role in the KRAS*-driven metabolic reprogramming of PDAC.
Significance:
Type II cytokines, secreted by Th2 cells in the tumor microenvironment, can stimulate cancer cell–intrinsic MYC transcriptional upregulation to drive glycolysis. This KRAS*-driven heterotypic signaling circuit in the early and advanced tumor microenvironment enables cooperative protumorigenic interactions, providing candidate therapeutic targets in the KRAS* pathway for this intractable disease.
Data from Efficacy and Determinants of Response to HER Kinase Inhibition in HER2-Mutant Metastatic Breast Cancer
Authors: Smyth Lillian M. , Piha-Paul Sarina A. , Won Helen H. , Schram Alison M. , Saura Cristina , Loi Sherene , Lu Janice , Shapiro Geoffrey I. , Juric Dejan , Mayer Ingrid A. , Arteaga Carlos L. , de la Fuente Macarena I. , Brufksy Adam M. , Spanggaard Iben , Mau-Sørensen Morten , Arnedos Monica , Moreno Victor , Boni Valentina , Sohn Joohyuk , Schwartzberg Lee S. , Gonzàlez-Farré Xavier , Cervantes Andrés , Bidard François-Clement , Gorelick Alexander N. , Lanman Richard B. , Nagy Rebecca J. , Ulaner Gary A. , Chandarlapaty Sarat , Jhaveri Komal , Gavrila Elena I. , Zimel Catherine , Selcuklu S. Duygu , Melcer Myra , Samoila Aliaksandra , Cai Yanyan , Scaltriti Maurizio , Mann Grace , Xu Feng , Eli Lisa D. , Dujka Melanie , Lalani Alshad S. , Bryce Richard , Baselga José , Taylor Barry S. , Solit David B. , Meric-Bernstam Funda , Hyman David M.
Published: April 2023

Abstract
HER2 mutations define a subset of metastatic breast cancers with a unique mechanism of oncogenic addiction to HER2 signaling. We explored activity of the irreversible pan-HER kinase inhibitor neratinib, alone or with fulvestrant, in 81 patients with HER2-mutant metastatic breast cancer. Overall response rate was similar with or without estrogen receptor (ER) blockade. By comparison, progression-free survival and duration of response appeared longer in ER+ patients receiving combination therapy, although the study was not designed for direct comparison. Preexistent concurrent activating HER2 or HER3 alterations were associated with poor treatment outcome. Similarly, acquisition of multiple HER2-activating events, as well as gatekeeper alterations, were observed at disease progression in a high proportion of patients deriving clinical benefit from neratinib. Collectively, these data define HER2 mutations as a therapeutic target in breast cancer and suggest that coexistence of additional HER signaling alterations may promote both de novo and acquired resistance to neratinib.
Significance:
HER2 mutations define a targetable breast cancer subset, although sensitivity to irreversible HER kinase inhibition appears to be modified by the presence of concurrent activating genomic events in the pathway. These findings have implications for potential future combinatorial approaches and broader therapeutic development for this genomically defined subset of breast cancer.

This article is highlighted in the In This Issue feature, p. 161
Data from Gain-of-Function Genetic Alterations of G9a Drive Oncogenesis
Authors: Kato Shinichiro , Weng Qing Yu , Insco Megan L. , Chen Kevin Y. , Muralidhar Sathya , Pozniak Joanna , Diaz Joey Mark S. , Drier Yotam , Nguyen Nhu , Lo Jennifer A. , van Rooijen Ellen , Kemeny Lajos V. , Zhan Yao , Feng Yang , Silkworth Whitney , Powell C. Thomas , Liau Brian B. , Xiong Yan , Jin Jian , Newton-Bishop Julia , Zon Leonard I. , Bernstein Bradley E. , Fisher David E.
Published: April 2023

Abstract
Epigenetic regulators, when genomically altered, may become driver oncogenes that mediate otherwise unexplained pro-oncogenic changes lacking a clear genetic stimulus, such as activation of the WNT/β-catenin pathway in melanoma. This study identifies previously unrecognized recurrent activating mutations in the G9a histone methyltransferase gene, as well as G9a genomic copy gains in approximately 26% of human melanomas, which collectively drive tumor growth and an immunologically sterile microenvironment beyond melanoma. Furthermore, the WNT pathway is identified as a key tumorigenic target of G9a gain-of-function, via suppression of the WNT antagonist DKK1. Importantly, genetic or pharmacologic suppression of mutated or amplified G9a using multiple in vitro and in vivo models demonstrates that G9a is a druggable target for therapeutic intervention in melanoma and other cancers harboring G9a genomic aberrations.
Significance:
Oncogenic G9a abnormalities drive tumorigenesis and the “cold” immune microenvironment by activating WNT signaling through DKK1 repression. These results reveal a key druggable mechanism for tumor development and identify strategies to restore “hot” tumor immune microenvironments.

This article is highlighted in the In This Issue feature, p. 890
Data from The Meningioma Enhancer Landscape Delineates Novel Subgroups and Drives Druggable Dependencies
Authors: Prager Briana C. , Vasudevan Harish N. , Dixit Deobrat , Bernatchez Jean A. , Wu Qiulian , Wallace Lisa C. , Bhargava Shruti , Lee Derrick , King Bradley H. , Morton Andrew R. , Gimple Ryan C. , Pekmezci Melike , Zhu Zhe , Siqueira-Neto Jair L. , Wang Xiuxing , Xie Qi , Chen Clark , Barnett Gene H. , Vogelbaum Michael A. , Mack Stephen C. , Chavez Lukas , Perry Arie , Raleigh David R. , Rich Jeremy N.
Published: April 2023

Abstract
Meningiomas are the most common primary intracranial tumor with current classification offering limited therapeutic guidance. Here, we interrogated meningioma enhancer landscapes from 33 tumors to stratify patients based upon prognosis and identify novel meningioma-specific dependencies. Enhancers robustly stratified meningiomas into three biologically distinct groups (adipogenesis/cholesterol, mesodermal, and neural crest) distinguished by distinct hormonal lineage transcriptional regulators. Meningioma landscapes clustered with intrinsic brain tumors and hormonally responsive systemic cancers with meningioma subgroups, reflecting progesterone or androgen hormonal signaling. Enhancer classification identified a subset of tumors with poor prognosis, irrespective of histologic grading. Superenhancer signatures predicted drug dependencies with superior in vitro efficacy to treatment based upon the NF2 genomic profile. Inhibition of DUSP1, a novel and druggable meningioma target, impaired tumor growth in vivo. Collectively, epigenetic landscapes empower meningioma classification and identification of novel therapies.
Significance:
Enhancer landscapes inform prognostic classification of aggressive meningiomas, identifying tumors at high risk of recurrence, and reveal previously unknown therapeutic targets. Druggable dependencies discovered through epigenetic profiling potentially guide treatment of intractable meningiomas.

This article is highlighted in the In This Issue feature, p. 1611
Data from Mutations in the RNA Splicing Factor SF3B1 Promote Tumorigenesis through MYC Stabilization
Authors: Liu Zhaoqi , Yoshimi Akihide , Wang Jiguang , Cho Hana , Chun-Wei Lee Stanley , Ki Michelle , Bitner Lillian , Chu Timothy , Shah Harshal , Liu Bo , Mato Anthony R. , Ruvolo Peter , Fabbri Giulia , Pasqualucci Laura , Abdel-Wahab Omar , Rabadan Raul
Published: April 2023

Abstract
Although mutations in the gene encoding the RNA splicing factor SF3B1 are frequent in multiple cancers, their functional effects and therapeutic dependencies are poorly understood. Here, we characterize 98 tumors and 12 isogenic cell lines harboring SF3B1 hotspot mutations, identifying hundreds of cryptic 3′ splice sites common and specific to different cancer types. Regulatory network analysis revealed that the most common SF3B1 mutation activates MYC via effects conserved across human and mouse cells. SF3B1 mutations promote decay of transcripts encoding the protein phosphatase 2A (PP2A) subunit PPP2R5A, increasing MYC S62 and BCL2 S70 phosphorylation which, in turn, promotes MYC protein stability and impair apoptosis, respectively. Genetic PPP2R5A restoration or pharmacologic PP2A activation impaired SF3B1-mutant tumorigenesis, elucidating a therapeutic approach to aberrant splicing by mutant SF3B1.
Significance:
Here, we identify that mutations in SF3B1, the most commonly mutated splicing factor gene across cancers, alter splicing of a specific subunit of the PP2A serine/threonine phosphatase complex to confer post-translational MYC and BCL2 activation, which is therapeutically intervenable using an FDA-approved drug.

See related commentary by O'Connor and Narla, p. 765.

This article is highlighted in the In This Issue feature, p. 747
Data from PRMT5 Inhibition Modulates E2F1 Methylation and Gene-Regulatory Networks Leading to Therapeutic Efficacy in JAK2V617F-Mutant MPN
Authors: Pastore Friederike , Bhagwat Neha , Pastore Alessandro , Radzisheuskaya Aliaksandra , Karzai Abdul , Krishnan Aishwarya , Li Bing , Bowman Robert L. , Xiao Wenbin , Viny Aaron D. , Zouak Anouar , Park Young C. , Cordner Keith B. , Braunstein Stephanie , Maag Jesper L. , Grego Alexander , Mehta Jaanvi , Wang Min , Lin Hong , Durham Benjamin H. , Koche Richard P. , Rampal Raajit K. , Helin Kristian , Scherle Peggy , Vaddi Kris , Levine Ross L.
Published: April 2023

Abstract
We investigated the role of PRMT5 in myeloproliferative neoplasm (MPN) pathogenesis and aimed to elucidate key PRMT5 targets contributing to MPN maintenance. PRMT5 is overexpressed in primary MPN cells, and PRMT5 inhibition potently reduced MPN cell proliferation ex vivo. PRMT5 inhibition was efficacious at reversing elevated hematocrit, leukocytosis, and splenomegaly in a model of JAK2V617F+ polycythemia vera and leukocyte and platelet counts, hepatosplenomegaly, and fibrosis in the MPLW515L model of myelofibrosis. Dual targeting of JAK and PRMT5 was superior to JAK or PRMT5 inhibitor monotherapy, further decreasing elevated counts and extramedullary hematopoiesis in vivo. PRMT5 inhibition reduced expression of E2F targets and altered the methylation status of E2F1 leading to attenuated DNA damage repair, cell-cycle arrest, and increased apoptosis. Our data link PRMT5 to E2F1 regulatory function and MPN cell survival and provide a strong mechanistic rationale for clinical trials of PRMT5 inhibitors in MPN.
Significance:
Expression of PRMT5 and E2F targets is increased in JAK2V617F+ MPN. Pharmacologic inhibition of PRMT5 alters the methylation status of E2F1 and shows efficacy in JAK2V617F/MPLW515L MPN models and primary samples. PRMT5 represents a potential novel therapeutic target for MPN, which is now being clinically evaluated.

This article is highlighted in the In This Issue feature, p. 1611
Data from Tumor Microenvironment Remodeling Enables Bypass of Oncogenic KRAS Dependency in Pancreatic Cancer
Authors: Hou Pingping , Kapoor Avnish , Zhang Qiang , Li Jiexi , Wu Chang-Jiun , Li Jun , Lan Zhengdao , Tang Ming , Ma Xingdi , Ackroyd Jeffrey J. , Kalluri Raghu , Zhang Jianhua , Jiang Shan , Spring Denise J. , Wang Y. Alan , DePinho Ronald A.
Published: April 2023

Abstract
Oncogenic KRAS (KRAS*) is a key tumor maintenance gene in pancreatic ductal adenocarcinoma (PDAC), motivating pharmacologic targeting of KRAS* and its effectors. Here, we explored mechanisms involving the tumor microenvironment (TME) as a potential basis for resistance to targeting KRAS*. Using the inducible KrasG12D;Trp53−/− PDAC mouse model, gain-of-function screens of epigenetic regulators identified HDAC5 as the top hit enabling KRAS* independent tumor growth. HDAC5-driven escaper tumors showed a prominent neutrophil-to-macrophage switch relative to KRAS*-driven tumors. Mechanistically, HDAC5 represses Socs3, a negative regulator of chemokine CCL2, resulting in increased CCL2, which recruits CCR2+ macrophages. Correspondingly, enforced Ccl2 promotes macrophage recruitment into the TME and enables tumor recurrence following KRAS* extinction. These tumor-associated macrophages in turn provide cancer cells with trophic support including TGFβ to enable KRAS* bypass in a SMAD4-dependent manner. Our work uncovers a KRAS* resistance mechanism involving immune cell remodeling of the PDAC TME.
Significance:
Although KRAS* is required for PDAC tumor maintenance, tumors can recur following KRAS* extinction. The capacity of PDAC cancer cells to alter the TME myeloid cell composition to support KRAS*-independent tumor growth illuminates novel therapeutic targets that may enhance the effectiveness of therapies targeting KRAS* and its pathway components.

See related commentary by Carr and Fernandez-Zapico, p. 910.

This article is highlighted in the In This Issue feature, p. 890
Data from Polyunsaturated Fatty Acids from Astrocytes Activate PPARγ Signaling in Cancer Cells to Promote Brain Metastasis
Authors: Zou Yongkang , Watters Andrea , Cheng Nan , Perry Caroline E. , Xu Ke , Alicea Gretchen M. , Parris Joshua L.D. , Baraban Ezra , Ray Pulak , Nayak Anupma , Xu Xiaowei , Herlyn Meenhard , Murphy Maureen E. , Weeraratna Ashani T. , Schug Zachary T. , Chen Qing
Published: April 2023

Abstract
Brain metastasis, the most lethal form of melanoma and carcinoma, is the consequence of favorable interactions between the invading cancer cells and the brain cells. Peroxisome proliferator–activated receptor γ (PPARγ) has ambiguous functions in cancer development, and its relevance in advanced brain metastasis remains unclear. Here, we demonstrate that astrocytes, the unique brain glial cells, activate PPARγ in brain metastatic cancer cells. PPARγ activation enhances cell proliferation and metastatic outgrowth in the brain. Mechanistically, astrocytes have a high content of polyunsaturated fatty acids that act as “donors” of PPARγ activators to the invading cancer cells. In clinical samples, PPARγ signaling is significantly higher in brain metastatic lesions. Notably, systemic administration of PPARγ antagonists significantly reduces brain metastatic burden in vivo. Our study clarifies a prometastatic role for PPARγ signaling in cancer metastasis in the lipid-rich brain microenvironment and argues for the use of PPARγ blockade to treat brain metastasis.
Significance:
Brain-tropic cancer cells take advantage of the lipid-rich brain microenvironment to facilitate their proliferation by activating PPARγ signaling. This protumor effect of PPARγ in advanced brain metastases is in contrast to its antitumor function in carcinogenesis and early metastatic steps, indicating that PPARγ has diverse functions at different stages of cancer development.

This article is highlighted in the In This Issue feature, p. 1631
Data from β-Catenin Activation Promotes Immune Escape and Resistance to Anti–PD-1 Therapy in Hepatocellular Carcinoma
Authors: Ruiz de Galarreta Marina , Bresnahan Erin , Molina-Sánchez Pedro , Lindblad Katherine E. , Maier Barbara , Sia Daniela , Puigvehi Marc , Miguela Verónica , Casanova-Acebes María , Dhainaut Maxime , Villacorta-Martin Carlos , Singhi Aatur D. , Moghe Akshata , von Felden Johann , Tal Grinspan Lauren , Wang Shuang , Kamphorst Alice O. , Monga Satdarshan P. , Brown Brian D. , Villanueva Augusto , Llovet Josep M. , Merad Miriam , Lujambio Amaia
Published: April 2023

Abstract
PD-1 immune checkpoint inhibitors have produced encouraging results in patients with hepatocellular carcinoma (HCC). However, what determines resistance to anti–PD-1 therapies is unclear. We created a novel genetically engineered mouse model of HCC that enables interrogation of how different genetic alterations affect immune surveillance and response to immunotherapies. Expression of exogenous antigens in MYC;Trp53−/− HCCs led to T cell–mediated immune surveillance, which was accompanied by decreased tumor formation and increased survival. Some antigen-expressing MYC;Trp53−/− HCCs escaped the immune system by upregulating the β-catenin (CTNNB1) pathway. Accordingly, expression of exogenous antigens in MYC;CTNNB1 HCCs had no effect, demonstrating that β-catenin promoted immune escape, which involved defective recruitment of dendritic cells and consequently impaired T-cell activity. Expression of chemokine CCL5 in antigen-expressing MYC;CTNNB1 HCCs restored immune surveillance. Finally, β-catenin–driven tumors were resistant to anti–PD-1. In summary, β-catenin activation promotes immune escape and resistance to anti–PD-1 and could represent a novel biomarker for HCC patient exclusion.
Significance:
Determinants of response to anti–PD-1 immunotherapies in HCC are poorly understood. Using a novel mouse model of HCC, we show that β-catenin activation promotes immune evasion and resistance to anti–PD-1 therapy and could potentially represent a novel biomarker for HCC patient exclusion.

See related commentary by Berraondo et al., p. 1003.

This article is highlighted in the In This Issue feature, p. 983
Data from Loss of EZH2 Reprograms BCAA Metabolism to Drive Leukemic Transformation
Authors: Gu Zhimin , Liu Yuxuan , Cai Feng , Patrick McKenzie , Zmajkovic Jakub , Cao Hui , Zhang Yuannyu , Tasdogan Alpaslan , Chen Mingyi , Qi Le , Liu Xin , Li Kailong , Lyu Junhua , Dickerson Kathryn E. , Chen Weina , Ni Min , Merritt Matthew E. , Morrison Sean J. , Skoda Radek C. , DeBerardinis Ralph J. , Xu Jian
Published: April 2023

Abstract
Epigenetic gene regulation and metabolism are highly intertwined, yet little is known about whether altered epigenetics influence cellular metabolism during cancer progression. Here, we show that EZH2 and NRASG12D mutations cooperatively induce progression of myeloproliferative neoplasms to highly penetrant, transplantable, and lethal myeloid leukemias in mice. EZH1, an EZH2 homolog, is indispensable for EZH2-deficient leukemia-initiating cells and constitutes an epigenetic vulnerability. BCAT1, which catalyzes the reversible transamination of branched-chain amino acids (BCAA), is repressed by EZH2 in normal hematopoiesis and aberrantly activated in EZH2-deficient myeloid neoplasms in mice and humans. BCAT1 reactivation cooperates with NRASG12D to sustain intracellular BCAA pools, resulting in enhanced mTOR signaling in EZH2-deficient leukemia cells. Genetic and pharmacologic inhibition of BCAT1 selectively impairs EZH2-deficient leukemia-initiating cells and constitutes a metabolic vulnerability. Hence, epigenetic alterations rewire intracellular metabolism during leukemic transformation, causing epigenetic and metabolic vulnerabilities in cancer-initiating cells.
Significance:
EZH2 inactivation and oncogenic NRAS cooperate to induce leukemic transformation of myeloproliferative neoplasms by activating BCAT1 to enhance BCAA metabolism and mTOR signaling. We uncover a mechanism by which epigenetic alterations rewire metabolism during cancer progression, causing epigenetic and metabolic liabilities in cancer-initiating cells that may be exploited as potential therapeutics.

See related commentary by Li and Melnick, p. 1158.

This article is highlighted in the In This Issue feature, p. 1143
Data from Rational Targeting of Cooperating Layers of the Epigenome Yields Enhanced Therapeutic Efficacy against AML
Authors: Duy Cihangir , Teater Matt , Garrett-Bakelman Francine E. , Lee Tak C. , Meydan Cem , Glass Jacob L. , Li Meng , Hellmuth Johannes C. , Mohammad Helai P. , Smitheman Kimberly N. , Shih Alan H. , Abdel-Wahab Omar , Tallman Martin S. , Guzman Monica L. , Muench David , Grimes H. Leighton , Roboz Gail J. , Kruger Ryan G. , Creasy Caretha L. , Paietta Elisabeth M. , Levine Ross L. , Carroll Martin , Melnick Ari M.
Published: April 2023

Abstract
Disruption of epigenetic regulation is a hallmark of acute myeloid leukemia (AML), but epigenetic therapy is complicated by the complexity of the epigenome. Herein, we developed a long-term primary AML ex vivo platform to determine whether targeting different epigenetic layers with 5-azacytidine and LSD1 inhibitors would yield improved efficacy. This combination was most effective in TET2mut AML, where it extinguished leukemia stem cells and particularly induced genes with both LSD1-bound enhancers and cytosine-methylated promoters. Functional studies indicated that derepression of genes such as GATA2 contributes to drug efficacy. Mechanistically, combination therapy increased enhancer–promoter looping and chromatin-activating marks at the GATA2 locus. CRISPRi of the LSD1-bound enhancer in patient-derived TET2mut AML was associated with dampening of therapeutic GATA2 induction. TET2 knockdown in human hematopoietic stem/progenitor cells induced loss of enhancer 5-hydroxymethylation and facilitated LSD1-mediated enhancer inactivation. Our data provide a basis for rational targeting of cooperating aberrant promoter and enhancer epigenetic marks driven by mutant epigenetic modifiers.
Significance:
Somatic mutations of genes encoding epigenetic modifiers are a hallmark of AML and potentially disrupt many components of the epigenome. Our study targets two different epigenetic layers at promoters and enhancers that cooperate to aberrant gene silencing, downstream of the actions of a mutant epigenetic regulator.

This article is highlighted in the In This Issue feature, p. 813
Data from TAS-120 Overcomes Resistance to ATP-Competitive FGFR Inhibitors in Patients with FGFR2 Fusion–Positive Intrahepatic Cholangiocarcinoma
Authors: Goyal Lipika , Shi Lei , Liu Leah Y. , Fece de la Cruz Ferran , Lennerz Jochen K. , Raghavan Srivatsan , Leschiner Ignaty , Elagina Liudmila , Siravegna Giulia , Ng Raymond W.S. , Vu Phuong , Patra Krushna C. , Saha Supriya K. , Uppot Raul N. , Arellano Ron , Reyes Stephanie , Sagara Takeshi , Otsuki Sachie , Nadres Brandon , Shahzade Heather A. , Dey-Guha Ipsita , Fetter Isobel J. , Baiev Islam , Van Seventer Emily E. , Murphy Janet E. , Ferrone Cristina R. , Tanabe Kenneth K. , Deshpande Vikram , Harding James J. , Yaeger Rona , Kelley Robin K. , Bardelli Alberto , Iafrate A. John , Hahn William C. , Benes Cyril H. , Ting David T. , Hirai Hiroshi , Getz Gad , Juric Dejan , Zhu Andrew X. , Corcoran Ryan B. , Bardeesy Nabeel
Published: April 2023

Abstract
ATP-competitive fibroblast growth factor receptor (FGFR) kinase inhibitors, including BGJ398 and Debio 1347, show antitumor activity in patients with intrahepatic cholangiocarcinoma (ICC) harboring activating FGFR2 gene fusions. Unfortunately, acquired resistance develops and is often associated with the emergence of secondary FGFR2 kinase domain mutations. Here, we report that the irreversible pan-FGFR inhibitor TAS-120 demonstrated efficacy in 4 patients with FGFR2 fusion–positive ICC who developed resistance to BGJ398 or Debio 1347. Examination of serial biopsies, circulating tumor DNA (ctDNA), and patient-derived ICC cells revealed that TAS-120 was active against multiple FGFR2 mutations conferring resistance to BGJ398 or Debio 1347. Functional assessment and modeling the clonal outgrowth of individual resistance mutations from polyclonal cell pools mirrored the resistance profiles observed clinically for each inhibitor. Our findings suggest that strategic sequencing of FGFR inhibitors, guided by serial biopsy and ctDNA analysis, may prolong the duration of benefit from FGFR inhibition in patients with FGFR2 fusion–positive ICC.
Significance:
ATP-competitive FGFR inhibitors (BGJ398, Debio 1347) show efficacy in FGFR2-altered ICC; however, acquired FGFR2 kinase domain mutations cause drug resistance and tumor progression. We demonstrate that the irreversible FGFR inhibitor TAS-120 provides clinical benefit in patients with resistance to BGJ398 or Debio 1347 and overcomes several FGFR2 mutations in ICC models.

This article is highlighted in the In This Issue feature, p. 983
Data from Integrative Bulk and Single-Cell Profiling of Premanufacture T-cell Populations Reveals Factors Mediating Long-Term Persistence of CAR T-cell Therapy
Authors: Chen Gregory M. , Chen Changya , Das Rajat K. , Gao Peng , Chen Chia-Hui , Bandyopadhyay Shovik , Ding Yang-Yang , Uzun Yasin , Yu Wenbao , Zhu Qin , Myers Regina M. , Grupp Stephan A. , Barrett David M. , Tan Kai
Published: April 2023

Abstract
The adoptive transfer of chimeric antigen receptor (CAR) T cells represents a breakthrough in clinical oncology, yet both between- and within-patient differences in autologously derived T cells are a major contributor to therapy failure. To interrogate the molecular determinants of clinical CAR T-cell persistence, we extensively characterized the premanufacture T cells of 71 patients with B-cell malignancies on trial to receive anti-CD19 CAR T-cell therapy. We performed RNA-sequencing analysis on sorted T-cell subsets from all 71 patients, followed by paired Cellular Indexing of Transcriptomes and Epitopes (CITE) sequencing and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) on T cells from six of these patients. We found that chronic IFN signaling regulated by IRF7 was associated with poor CAR T-cell persistence across T-cell subsets, and that the TCF7 regulon not only associates with the favorable naïve T-cell state, but is maintained in effector T cells among patients with long-term CAR T-cell persistence. These findings provide key insights into the underlying molecular determinants of clinical CAR T-cell function.
Significance:
To improve clinical outcomes for CAR T-cell therapy, there is a need to understand the molecular determinants of CAR T-cell persistence. These data represent the largest clinically annotated molecular atlas in CAR T-cell therapy to date, and significantly advance our understanding of the mechanisms underlying therapeutic efficacy.

This article is highlighted in the In This Issue feature, p. 2113
Data from Targeting the p300/CBP Axis in Lethal Prostate Cancer
Authors: Welti Jonathan , Sharp Adam , Brooks Nigel , Yuan Wei , McNair Christopher , Chand Saswati N. , Pal Abhijit , Figueiredo Ines , Riisnaes Ruth , Gurel Bora , Rekowski Jan , Bogdan Denisa , West William , Young Barbara , Raja Meera , Prosser Amy , Lane Jordan , Thomson Stuart , Worthington Jenny , Onions Stuart , Shannon Jonathan , Paoletta Silvia , Brown Richard , Smyth Don , Harbottle Gareth W. , Gil Veronica S. , Miranda Susana , Crespo Mateus , Ferreira Ana , Pereira Rita , Tunariu Nina , Carreira Suzanne , Neeb Antje J. , Ning Jian , Swain Amanda , Taddei David , Schiewer Matthew J. , Knudsen Karen E. , Pegg Neil , de Bono Johann S.
Published: April 2023

Abstract
Resistance to androgen receptor (AR) blockade in castration-resistant prostate cancer (CRPC) is associated with sustained AR signaling, including through alternative splicing of AR (AR-SV). Inhibitors of transcriptional coactivators that regulate AR activity, including the paralog histone acetyltransferase proteins p300 and CBP, are attractive therapeutic targets for lethal prostate cancer. Herein, we validate targeting p300/CBP as a therapeutic strategy for lethal prostate cancer and describe CCS1477, a novel small-molecule inhibitor of the p300/CBP conserved bromodomain. We show that CCS1477 inhibits cell proliferation in prostate cancer cell lines and decreases AR- and C-MYC–regulated gene expression. In AR-SV–driven models, CCS1477 has antitumor activity, regulating AR and C-MYC signaling. Early clinical studies suggest that CCS1477 modulates KLK3 blood levels and regulates CRPC biopsy biomarker expression. Overall, CCS1477 shows promise for the treatment of patients with advanced prostate cancer.
Significance:
Treating CRPC remains challenging due to persistent AR signaling. Inhibiting transcriptional AR coactivators is an attractive therapeutic strategy. CCS1477, an inhibitor of p300/CBP, inhibits growth and AR activity in CRPC models, and can affect metastatic CRPC target expression in serial clinical biopsies.

See related commentary by Rasool et al., p. 1011.

This article is highlighted in the In This Issue feature, p. 995
Data from CRISPR Screening of CAR T Cells and Cancer Stem Cells Reveals Critical Dependencies for Cell-Based Therapies
Authors: Wang Dongrui , Prager Briana C. , Gimple Ryan C. , Aguilar Brenda , Alizadeh Darya , Tang Hongzhen , Lv Deguan , Starr Renate , Brito Alfonso , Wu Qiulian , Kim Leo J.Y. , Qiu Zhixin , Lin Peng , Lorenzini Michael H. , Badie Behnam , Forman Stephen J. , Xie Qi , Brown Christine E. , Rich Jeremy N.
Published: April 2023

Abstract
Glioblastoma (GBM) contains self-renewing GBM stem cells (GSC) potentially amenable to immunologic targeting, but chimeric antigen receptor (CAR) T-cell therapy has demonstrated limited clinical responses in GBM. Here, we interrogated molecular determinants of CAR-mediated GBM killing through whole-genome CRISPR screens in both CAR T cells and patient-derived GSCs. Screening of CAR T cells identified dependencies for effector functions, including TLE4 and IKZF2. Targeted knockout of these genes enhanced CAR antitumor efficacy. Bulk and single-cell RNA sequencing of edited CAR T cells revealed transcriptional profiles of superior effector function and inhibited exhaustion responses. Reciprocal screening of GSCs identified genes essential for susceptibility to CAR-mediated killing, including RELA and NPLOC4, the knockout of which altered tumor–immune signaling and increased responsiveness of CAR therapy. Overall, CRISPR screening of CAR T cells and GSCs discovered avenues for enhancing CAR therapeutic efficacy against GBM, with the potential to be extended to other solid tumors.
Significance:
Reciprocal CRISPR screening identified genes in both CAR T cells and tumor cells regulating the potency of CAR T-cell cytotoxicity, informing molecular targeting strategies to potentiate CAR T-cell antitumor efficacy and elucidate genetic modifications of tumor cells in combination with CAR T cells to advance immuno-oncotherapy.

This article is highlighted in the In This Issue feature, p. 995
Data from Comprehensive Genomic and Transcriptomic Analysis for Guiding Therapeutic Decisions in Patients with Rare Cancers
Authors: Horak Peter , Heining Christoph , Kreutzfeldt Simon , Hutter Barbara , Mock Andreas , Hüllein Jennifer , Fröhlich Martina , Uhrig Sebastian , Jahn Arne , Rump Andreas , Gieldon Laura , Möhrmann Lino , Hanf Dorothea , Teleanu Veronica , Heilig Christoph E. , Lipka Daniel B. , Allgäuer Michael , Ruhnke Leo , Laßmann Andreas , Endris Volker , Neumann Olaf , Penzel Roland , Beck Katja , Richter Daniela , Winter Ulrike , Wolf Stephan , Pfütze Katrin , Geörg Christina , Meißburger Bettina , Buchhalter Ivo , Augustin Marinela , Aulitzky Walter E. , Hohenberger Peter , Kroiss Matthias , Schirmacher Peter , Schlenk Richard F. , Keilholz Ulrich , Klauschen Frederick , Folprecht Gunnar , Bauer Sebastian , Siveke Jens Thomas , Brandts Christian H. , Kindler Thomas , Boerries Melanie , Illert Anna L. , von Bubnoff Nikolas , Jost Philipp J. , Spiekermann Karsten , Bitzer Michael , Schulze-Osthoff Klaus , von Kalle Christof , Klink Barbara , Brors Benedikt , Stenzinger Albrecht , Schröck Evelin , Hübschmann Daniel , Weichert Wilko , Glimm Hanno , Fröhling Stefan
Published: April 2023

Abstract
The clinical relevance of comprehensive molecular analysis in rare cancers is not established. We analyzed the molecular profiles and clinical outcomes of 1,310 patients (rare cancers, 75.5%) enrolled in a prospective observational study by the German Cancer Consortium that applies whole-genome/exome and RNA sequencing to inform the care of adults with incurable cancers. On the basis of 472 single and six composite biomarkers, a cross-institutional molecular tumor board provided evidence-based management recommendations, including diagnostic reevaluation, genetic counseling, and experimental treatment, in 88% of cases. Recommended therapies were administered in 362 of 1,138 patients (31.8%) and resulted in significantly improved overall response and disease control rates (23.9% and 55.3%) compared with previous therapies, translating into a progression-free survival ratio >1.3 in 35.7% of patients. These data demonstrate the benefit of molecular stratification in rare cancers and represent a resource that may promote clinical trial access and drug approvals in this underserved patient population.
Significance:
Rare cancers are difficult to treat; in particular, molecular pathogenesis–oriented medical therapies are often lacking. This study shows that whole-genome/exome and RNA sequencing enables molecularly informed treatments that lead to clinical benefit in a substantial proportion of patients with advanced rare cancers and paves the way for future clinical trials.

See related commentary by Eggermont et al., p. 2677.

This article is highlighted in the In This Issue feature, p. 2659