bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from A Genetic Mouse Model Recapitulates Immune Checkpoint Inhibitor–Associated Myocarditis and Supports a Mechanism-Based Therapeutic Intervention
Authors: Wei Spencer C. , Meijers Wouter C. , Axelrod Margaret L. , Anang Nana-Ama A.S. , Screever Elles M. , Wescott Elizabeth C. , Johnson Douglas B. , Whitley Elizabeth , Lehmann Lorenz , Courand Pierre-Yves , Mancuso James J. , Himmel Lauren E. , Lebrun-Vignes Benedicte , Wleklinski Matthew J. , Knollmann Bjorn C. , Srinivasan Jayashree , Li Yu , Atolagbe Oluwatomisin T. , Rao Xiayu , Zhao Yang , Wang Jing , Ehrlich Lauren I.R. , Sharma Padmanee , Salem Joe-Elie , Balko Justin M. , Moslehi Javid J. , Allison James P.
Published: April 2023

Abstract
Immune checkpoint inhibitors (ICI) targeting CTLA4 or PD-1/PD-L1 have transformed cancer therapy but are associated with immune-related adverse events, including myocarditis. Here, we report a robust preclinical mouse model of ICI-associated myocarditis in which monoallelic loss of Ctla4 in the context of complete genetic absence of Pdcd1 leads to premature death in approximately half of mice. Premature death results from myocardial infiltration by T cells and macrophages and severe ECG abnormalities, closely recapitulating the clinical and pathologic hallmarks of ICI-associated myocarditis observed in patients. Using this model, we show that Ctla4 and Pdcd1 functionally interact in a gene dosage–dependent manner, providing a mechanism by which myocarditis arises with increased frequency in the setting of combination ICI therapy. We demonstrate that intervention with CTLA4–Ig (abatacept) is sufficient to ameliorate disease progression and additionally provide a case series of patients in which abatacept mitigates the fulminant course of ICI myocarditis.
Significance:
We provide a preclinical model of ICI-associated myocarditis which recapitulates this clinical syndrome. Using this model, we demonstrate that CTLA4 and PD-1 (ICI targets) functionally interact for myocarditis development and that intervention with CTLA4–Ig (abatacept) attenuates myocarditis, providing mechanistic rationale and preclinical support for therapeutic clinical studies.

See related commentary by Young and Bluestone, p. 537.

This article is highlighted in the In This Issue feature, p. 521
Data from Genetically Defined Syngeneic Mouse Models of Ovarian Cancer as Tools for the Discovery of Combination Immunotherapy
Authors: Iyer Sonia , Zhang Shuang , Yucel Simge , Horn Heiko , Smith Sean G. , Reinhardt Ferenc , Hoefsmit Esmee , Assatova Bimarzhan , Casado Julia , Meinsohn Marie-Charlotte , Barrasa M. Inmaculada , Bell George W. , Pérez-Villatoro Fernando , Huhtinen Kaisa , Hynninen Johanna , Oikkonen Jaana , Galhenage Pamoda M. , Pathania Shailja , Hammond Paula T. , Neel Benjamin G. , Farkkila Anniina , Pépin David , Weinberg Robert A.
Published: April 2023

Abstract
Despite advances in immuno-oncology, the relationship between tumor genotypes and response to immunotherapy remains poorly understood, particularly in high-grade serous tubo-ovarian carcinomas (HGSC). We developed a series of mouse models that carry genotypes of human HGSCs and grow in syngeneic immunocompetent hosts to address this gap. We transformed murine-fallopian tube epithelial cells to phenocopy homologous recombination–deficient tumors through a combined loss of Trp53, Brca1, Pten, and Nf1 and overexpression of Myc and Trp53R172H, which was contrasted with an identical model carrying wild-type Brca1. For homologous recombination–proficient tumors, we constructed genotypes combining loss of Trp53 and overexpression of Ccne1, Akt2, and Trp53R172H, and driven by KRASG12V or Brd4 or Smarca4 overexpression. These lines form tumors recapitulating human disease, including genotype-driven responses to treatment, and enabled us to identify follistatin as a driver of resistance to checkpoint inhibitors. These data provide proof of concept that our models can identify new immunotherapy targets in HGSC.
Significance:
We engineered a panel of murine fallopian tube epithelial cells bearing mutations typical of HGSC and capable of forming tumors in syngeneic immunocompetent hosts. These models recapitulate tumor microenvironments and drug responses characteristic of human disease. In a Ccne1-overexpressing model, immune-checkpoint resistance was driven by follistatin.

This article is highlighted in the In This Issue feature, p. 211
Data from The Phenotypes of Proliferating Glioblastoma Cells Reside on a Single Axis of Variation
Authors: Wang Lin , Babikir Husam , Müller Sören , Yagnik Garima , Shamardani Karin , Catalan Francisca , Kohanbash Gary , Alvarado Beatriz , Di Lullo Elizabeth , Kriegstein Arnold , Shah Sumedh , Wadhwa Harsh , Chang Susan M. , Phillips Joanna J. , Aghi Manish K. , Diaz Aaron A.
Published: April 2023

Abstract
Although tumor-propagating cells can be derived from glioblastomas (GBM) of the proneural and mesenchymal subtypes, a glioma stem-like cell (GSC) of the classic subtype has not been identified. It is unclear whether mesenchymal GSCs (mGSC) and/or proneural GSCs (pGSC) alone are sufficient to generate the heterogeneity observed in GBM. We performed single-cell/single-nucleus RNA sequencing of 28 gliomas, and single-cell ATAC sequencing for 8 cases. We found that GBM GSCs reside on a single axis of variation, ranging from proneural to mesenchymal. In silico lineage tracing using both transcriptomics and genetics supports mGSCs as the progenitors of pGSCs. Dual inhibition of pGSC-enriched and mGSC-enriched growth and survival pathways provides a more complete treatment than combinations targeting one GSC phenotype alone. This study sheds light on a long-standing debate regarding lineage relationships among GSCs and presents a paradigm by which personalized combination therapies can be derived from single-cell RNA signatures, to overcome intratumor heterogeneity.
Significance:
Tumor-propagating cells can be derived from mesenchymal and proneural glioblastomas. However, a stem cell of the classic subtype has yet to be demonstrated. We show that classic-subtype gliomas are comprised of proneural and mesenchymal cells. This study sheds light on a long-standing debate regarding lineage relationships between glioma cell types.

See related commentary by Fine, p. 1650.

This article is highlighted in the In This Issue feature, p. 1631
Data from Clinical BRCA1/2 Reversion Analysis Identifies Hotspot Mutations and Predicted Neoantigens Associated with Therapy Resistance
Authors: Pettitt Stephen J. , Frankum Jessica R. , Punta Marco , Lise Stefano , Alexander John , Chen Yi , Yap Timothy A. , Haider Syed , Tutt Andrew N.J. , Lord Christopher J.
Published: April 2023

Abstract
Reversion mutations in BRCA1 or BRCA2 are associated with resistance to PARP inhibitors and platinum. To better understand the nature of these mutations, we collated, codified, and analyzed more than 300 reversions. This identified reversion “hotspots” and “deserts” in regions encoding the N and C terminus, respectively, of BRCA2, suggesting that pathogenic mutations in these regions may be at higher or lower risk of reversion. Missense and splice-site pathogenic mutations in BRCA1/2 also appeared less likely to revert than truncating mutations. Most reversions were <100 bp deletions. Although many deletions exhibited microhomology, this was not universal, suggesting that multiple DNA-repair processes cause reversion. Finally, we found that many reversions were predicted to encode immunogenic neopeptides, suggesting a route to the treatment of reverted disease. As well as providing a freely available database for the collation of future reversion cases, these observations have implications for how drug resistance might be managed in BRCA-mutant cancers.
Significance:
Reversion mutations in BRCA genes are a major cause of clinical platinum and PARP inhibitor resistance. This analysis of all reported clinical reversions suggests that the position of BRCA2 mutations affects the risk of reversion. Many reversions are also predicted to encode tumor neoantigens, providing a potential route to targeting resistance.

This article is highlighted in the In This Issue feature, p. 1426
Data from Oral Mucosal Organoids as a Potential Platform for Personalized Cancer Therapy
Authors: Driehuis Else , Kolders Sigrid , Spelier Sacha , Lõhmussaar Kadi , Willems Stefan M. , Devriese Lot A. , de Bree Remco , de Ruiter Emma J. , Korving Jeroen , Begthel Harry , van Es Johan H. , Geurts Veerle , He Gui-Wei , van Jaarsveld Richard H. , Oka Rurika , Muraro Mauro J. , Vivié Judith , Zandvliet Maurice M.J.M. , Hendrickx Antoni P.A. , Iakobachvili Nino , Sridevi Priya , Kranenburg Onno , van Boxtel Ruben , Kops Geert J.P.L. , Tuveson David A. , Peters Peter J. , van Oudenaarden Alexander , Clevers Hans
Published: April 2023

Abstract
Previous studies have described that tumor organoids can capture the diversity of defined human carcinoma types. Here, we describe conditions for long-term culture of human mucosal organoids. Using this protocol, a panel of 31 head and neck squamous cell carcinoma (HNSCC)–derived organoid lines was established. This panel recapitulates genetic and molecular characteristics previously described for HNSCC. Organoids retain their tumorigenic potential upon xenotransplantation. We observe differential responses to a panel of drugs including cisplatin, carboplatin, cetuximab, and radiotherapy in vitro. Additionally, drug screens reveal selective sensitivity to targeted drugs that are not normally used in the treatment of patients with HNSCC. These observations may inspire a personalized approach to the management of HNSCC and expand the repertoire of HNSCC drugs.
Significance:
This work describes the culture of organoids derived from HNSCC and corresponding normal epithelium. These tumoroids recapitulate the disease genetically, histologically, and functionally. In vitro drug screening of tumoroids reveals responses to therapies both currently used in the treatment of HNSCC and those not (yet) used in clinical practice.

See related commentary by Hill and D'Andrea, p. 828.

This article is highlighted in the In This Issue feature, p. 813
Data from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts
Authors: Elyada Ela , Bolisetty Mohan , Laise Pasquale , Flynn William F. , Courtois Elise T. , Burkhart Richard A. , Teinor Jonathan A. , Belleau Pascal , Biffi Giulia , Lucito Matthew S. , Sivajothi Santhosh , Armstrong Todd D. , Engle Dannielle D. , Yu Kenneth H. , Hao Yuan , Wolfgang Christopher L. , Park Youngkyu , Preall Jonathan , Jaffee Elizabeth M. , Califano Andrea , Robson Paul , Tuveson David A.
Published: April 2023

Abstract
Cancer-associated fibroblasts (CAF) are major players in the progression and drug resistance of pancreatic ductal adenocarcinoma (PDAC). CAFs constitute a diverse cell population consisting of several recently described subtypes, although the extent of CAF heterogeneity has remained undefined. Here we use single-cell RNA sequencing to thoroughly characterize the neoplastic and tumor microenvironment content of human and mouse PDAC tumors. We corroborate the presence of myofibroblastic CAFs and inflammatory CAFs and define their unique gene signatures in vivo. Moreover, we describe a new population of CAFs that express MHC class II and CD74, but do not express classic costimulatory molecules. We term this cell population “antigen-presenting CAFs” and find that they activate CD4+ T cells in an antigen-specific fashion in a model system, confirming their putative immune-modulatory capacity. Our cross-species analysis paves the way for investigating distinct functions of CAF subtypes in PDAC immunity and progression.
Significance:
Appreciating the full spectrum of fibroblast heterogeneity in pancreatic ductal adenocarcinoma is crucial to developing therapies that specifically target tumor-promoting CAFs. This work identifies MHC class II–expressing CAFs with a capacity to present antigens to CD4+ T cells, and potentially to modulate the immune response in pancreatic tumors.

See related commentary by Belle and DeNardo, p. 1001.

This article is highlighted in the In This Issue feature, p. 983
Data from Radiotherapy and Immunotherapy Promote Tumoral Lipid Oxidation and Ferroptosis via Synergistic Repression of SLC7A11
Authors: Lang Xueting , Green Michael D. , Wang Weimin , Yu Jiali , Choi Jae Eun , Jiang Long , Liao Peng , Zhou Jiajia , Zhang Qiang , Dow Ania , Saripalli Anjali L. , Kryczek Ilona , Wei Shuang , Szeliga Wojciech , Vatan Linda , Stone Everett M. , Georgiou George , Cieslik Marcin , Wahl Daniel R. , Morgan Meredith A. , Chinnaiyan Arul M. , Lawrence Theodore S. , Zou Weiping
Published: April 2023

Abstract
A challenge in oncology is to rationally and effectively integrate immunotherapy with traditional modalities, including radiotherapy. Here, we demonstrate that radiotherapy induces tumor-cell ferroptosis. Ferroptosis agonists augment and ferroptosis antagonists limit radiotherapy efficacy in tumor models. Immunotherapy sensitizes tumors to radiotherapy by promoting tumor-cell ferroptosis. Mechanistically, IFNγ derived from immunotherapy-activated CD8+ T cells and radiotherapy-activated ATM independently, yet synergistically, suppresses SLC7A11, a unit of the glutamate–cystine antiporter xc−, resulting in reduced cystine uptake, enhanced tumor lipid oxidation and ferroptosis, and improved tumor control. Thus, ferroptosis is an unappreciated mechanism and focus for the development of effective combinatorial cancer therapy.
Significance:
This article describes ferroptosis as a previously unappreciated mechanism of action for radiotherapy. Further, it shows that ferroptosis is a novel point of synergy between immunotherapy and radiotherapy. Finally, it nominates SLC7A11, a critical regulator of ferroptosis, as a mechanistic determinant of synergy between radiotherapy and immunotherapy.

This article is highlighted in the In This Issue feature, p. 1631
Data from Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia
Authors: Adelman Emmalee R. , Huang Hsuan-Ting , Roisman Alejandro , Olsson André , Colaprico Antonio , Qin Tingting , Lindsley R. Coleman , Bejar Rafael , Salomonis Nathan , Grimes H. Leighton , Figueroa Maria E.
Published: April 2023

Abstract
Aging is associated with functional decline of hematopoietic stem cells (HSC) as well as an increased risk of myeloid malignancies. We performed an integrative characterization of epigenomic and transcriptomic changes, including single-cell RNA sequencing, during normal human aging. Lineage−CD34+CD38− cells [HSC-enriched (HSCe)] undergo age-associated epigenetic reprogramming consisting of redistribution of DNA methylation and reductions in H3K27ac, H3K4me1, and H3K4me3. This reprogramming of aged HSCe globally targets developmental and cancer pathways that are comparably altered in acute myeloid leukemia (AML) of all ages, encompassing loss of 4,646 active enhancers, 3,091 bivalent promoters, and deregulation of several epigenetic modifiers and key hematopoietic transcription factors, such as KLF6, BCL6, and RUNX3. Notably, in vitro downregulation of KLF6 results in impaired differentiation, increased colony-forming potential, and changes in expression that recapitulate aging and leukemia signatures. Thus, age-associated epigenetic reprogramming may form a predisposing condition for the development of age-related AML.
Significance:
AML, which is more frequent in the elderly, is characterized by epigenetic deregulation. We demonstrate that epigenetic reprogramming of human HSCs occurs with age, affecting cancer and developmental pathways. Downregulation of genes epigenetically altered with age leads to impairment in differentiation and partially recapitulates aging phenotypes.

This article is highlighted in the In This Issue feature, p. 983
Data from Targeting CD39 in Cancer Reveals an Extracellular ATP- and Inflammasome-Driven Tumor Immunity
Authors: Li Xian-Yang , Moesta Achim K. , Xiao Christos , Nakamura Kyohei , Casey Mika , Zhang Haiyan , Madore Jason , Lepletier Ailin , Aguilera Amelia Roman , Sundarrajan Ashmitha , Jacoberger-Foissac Celia , Wong Clifford , dela Cruz Tracy , Welch Megan , Lerner Alana G. , Spatola Bradley N. , Soros Vanessa B. , Corbin John , Anderson Ana C. , Effern Maike , Hölzel Michael , Robson Simon C. , Johnston Rebecca L. , Waddell Nicola , Smith Corey , Bald Tobias , Geetha Nishamol , Beers Courtney , Teng Michele W. L. , Smyth Mark J.
Published: April 2023

Abstract
We explored the mechanism of action of CD39 antibodies that inhibit ectoenzyme CD39 conversion of extracellular ATP (eATP) to AMP and thus potentially augment eATP–P2-mediated proinflammatory responses. Using syngeneic and humanized tumor models, we contrast the potency and mechanism of anti-CD39 mAbs with other agents targeting the adenosinergic pathway. We demonstrate the critical importance of an eATP–P2X7–ASC–NALP3-inflammasome–IL18 pathway in the antitumor activity mediated by CD39 enzyme blockade, rather than simply reducing adenosine as mechanism of action. Efficacy of anti-CD39 activity was underpinned by CD39 and P2X7 coexpression on intratumor myeloid subsets, an early signature of macrophage depletion, and active IL18 release that facilitated the significant expansion of intratumor effector T cells. More importantly, anti-CD39 facilitated infiltration into T cell–poor tumors and rescued anti–PD-1 resistance. Anti-human CD39 enhanced human T-cell proliferation and Th1 cytokine production and suppressed human B-cell lymphoma in the context of autologous Epstein–Barr virus–specific T-cell transfer.
Significance:
Overall, these data describe a potent and novel mechanism of action of antibodies that block mouse or human CD39, triggering an eATP–P2X7–inflammasome–IL18 axis that reduces intratumor macrophage number, enhances intratumor T-cell effector function, overcomes anti–PD-1 resistance, and potentially enhances the efficacy of adoptive T-cell transfer.

This article is highlighted in the In This Issue feature, p. 1631
Data from Cross-Species Genomics Reveals Oncogenic Dependencies in ZFTA/C11orf95 Fusion–Positive Supratentorial Ependymomas
Authors: Zheng Tuyu , Ghasemi David R. , Okonechnikov Konstantin , Korshunov Andrey , Sill Martin , Maass Kendra K. , Benites Goncalves da Silva Patricia , Ryzhova Marina , Gojo Johannes , Stichel Damian , Arabzade Amir , Kupp Robert , Benzel Julia , Taya Shinichiro , Adachi Toma , Shiraishi Ryo , Gerber Nicolas U. , Sturm Dominik , Ecker Jonas , Sievers Philipp , Selt Florian , Chapman Rebecca , Haberler Christine , Figarella-Branger Dominique , Reifenberger Guido , Fleischhack Gudrun , Rutkowski Stefan , Donson Andrew M. , Ramaswamy Vijay , Capper David , Ellison David W. , Herold-Mende Christel C. , Schüller Ulrich , Brandner Sebastian , Driever Pablo Hernáiz , Kros Johan M. , Snuderl Matija , Milde Till , Grundy Richard G. , Hoshino Mikio , Mack Stephen C. , Gilbertson Richard J. , Jones David T.W. , Kool Marcel , von Deimling Andreas , Pfister Stefan M. , Sahm Felix , Kawauchi Daisuke , Pajtler Kristian W.
Published: April 2023

Abstract
Molecular groups of supratentorial ependymomas comprise tumors with ZFTA–RELA or YAP1-involving fusions and fusion-negative subependymoma. However, occasionally supratentorial ependymomas cannot be readily assigned to any of these groups due to lack of detection of a typical fusion and/or ambiguous DNA methylation–based classification. An unbiased approach with a cohort of unprecedented size revealed distinct methylation clusters composed of tumors with ependymal but also various other histologic features containing alternative translocations that shared ZFTA as a partner gene. Somatic overexpression of ZFTA-associated fusion genes in the developing cerebral cortex is capable of inducing tumor formation in vivo, and cross-species comparative analyses identified GLI2 as a key downstream regulator of tumorigenesis in all tumors. Targeting GLI2 with arsenic trioxide caused extended survival of tumor-bearing animals, indicating a potential therapeutic vulnerability in ZFTA fusion–positive tumors.
Significance:
ZFTA–RELA fusions are a hallmark feature of supratentorial ependymoma. We find that ZFTA acts as a partner for alternative transcriptional activators in oncogenic fusions of supratentorial tumors with various histologic characteristics. Establishing representative mouse models, we identify potential therapeutic targets shared by ZFTA fusion–positive tumors, such as GLI2.

This article is highlighted in the In This Issue feature, p. 2113
Data from IFNγ Is Critical for CAR T Cell–Mediated Myeloid Activation and Induction of Endogenous Immunity
Authors: Alizadeh Darya , Wong Robyn A. , Gholamin Sharareh , Maker Madeleine , Aftabizadeh Maryam , Yang Xin , Pecoraro Joseph R. , Jeppson John D. , Wang Dongrui , Aguilar Brenda , Starr Renate , Larmonier Claire B. , Larmonier Nicolas , Chen Min-Hsuan , Wu Xiwei , Ribas Antoni , Badie Behnam , Forman Stephen J. , Brown Christine E.
Published: April 2023

Abstract
Chimeric antigen receptor (CAR) T cells mediate potent antigen-specific antitumor activity; however, their indirect effects on the endogenous immune system are not well characterized. Remarkably, we demonstrate that CAR T-cell treatment of mouse syngeneic glioblastoma (GBM) activates intratumoral myeloid cells and induces endogenous T-cell memory responses coupled with feed-forward propagation of CAR T-cell responses. IFNγ production by CAR T cells and IFNγ responsiveness of host immune cells are critical for tumor immune landscape remodeling to promote a more activated and less suppressive tumor microenvironment. The clinical relevance of these observations is supported by studies showing that human IL13Rα2–CAR T cells activate patient-derived endogenous T cells and monocytes/macrophages through IFNγ signaling and induce the generation of tumor-specific T-cell responses in a responding patient with GBM. These studies establish that CAR T-cell therapy has the potential to shape the tumor microenvironment, creating a context permissible for eliciting endogenous antitumor immunity.
Significance:
Our findings highlight the critical role of IFNγ signaling for a productive CAR T-cell therapy in GBM. We establish that CAR T cells can activate resident myeloid populations and promote endogenous T-cell immunity, emphasizing the importance of host innate and adaptive immunity for CAR T-cell therapy of solid tumors.

This article is highlighted in the In This Issue feature, p. 2113
Data from Tilsotolimod with Ipilimumab Drives Tumor Responses in Anti–PD-1 Refractory Melanoma
Authors: Haymaker Cara , Johnson Daniel H. , Murthy Ravi , Bentebibel Salah-Eddine , Uemura Marc I. , Hudgens Courtney W. , Safa Houssein , James Marihella , Andtbacka Robert H.I. , Johnson Douglas B. , Shaheen Montaser , Davies Michael A. , Rahimian Shah , Chunduru Srinivas K. , Milton Denái R. , Tetzlaff Michael T. , Overwijk Willem W. , Hwu Patrick , Gabrail Nashat , Agrawal Sudhir , Doolittle Gary , Puzanov Igor , Markowitz Joseph , Bernatchez Chantale , Diab Adi
Published: April 2023

Abstract
Many patients with advanced melanoma are resistant to immune checkpoint inhibition. In the ILLUMINATE-204 phase I/II trial, we assessed intratumoral tilsotolimod, an investigational Toll-like receptor 9 agonist, with systemic ipilimumab in patients with anti–PD-1– resistant advanced melanoma. In all patients, 48.4% experienced grade 3/4 treatment-emergent adverse events. The overall response rate at the recommended phase II dose of 8 mg was 22.4%, and an additional 49% of patients had stable disease. Responses in noninjected lesions and in patients expected to be resistant to ipilimumab monotherapy were observed. Rapid induction of a local IFNα gene signature, dendritic cell maturation and enhanced markers of antigen presentation, and T-cell clonal expansion correlated with clinical response. A phase III clinical trial with this combination (NCT03445533) is ongoing.
Significance:
Despite recent developments in advanced melanoma therapies, most patients do not experience durable responses. Intratumoral tilsotolimod injection elicits a rapid, local type 1 IFN response and, in combination with ipilimumab, activates T cells to promote clinical activity, including in distant lesions and patients not expected to respond to ipilimumab alone.

This article is highlighted in the In This Issue feature, p. 1861
Data from Integrated Genomic Analysis Identifies Driver Genes and Cisplatin-Resistant Progenitor Phenotype in Pediatric Liver Cancer
Authors: Hirsch Theo Z. , Pilet Jill , Morcrette Guillaume , Roehrig Amélie , Monteiro Benedict J.E. , Molina Laura , Bayard Quentin , Trépo Eric , Meunier Léa , Caruso Stefano , Renault Victor , Deleuze Jean-François , Fresneau Brice , Chardot Christophe , Gonzales Emmanuel , Jacquemin Emmanuel , Guerin Florent , Fabre Monique , Aerts Isabelle , Taque Sophie , Laithier Véronique , Branchereau Sophie , Guettier Catherine , Brugières Laurence , Rebouissou Sandra , Letouzé Eric , Zucman-Rossi Jessica
Published: April 2023

Abstract
Pediatric liver cancers (PLC) comprise diverse diseases affecting infants, children, and adolescents. Despite overall good prognosis, PLCs display heterogeneous response to chemotherapy. Integrated genomic analysis of 126 pediatric liver tumors showed a continuum of driver mechanisms associated with patient age, including new targetable oncogenes. In 10% of patients with hepatoblastoma, all before three years old, we identified a mosaic premalignant clonal expansion of cells altered at the 11p15.5 locus. Analysis of spatial and longitudinal heterogeneity revealed an important plasticity between “hepatocytic,” “liver progenitor,” and “mesenchymal” molecular subgroups of hepatoblastoma. We showed that during chemotherapy, “liver progenitor” cells accumulated massive loads of cisplatin-induced mutations with a specific mutational signature, leading to the development of heavily mutated relapses and metastases. Drug screening in PLC cell lines identified promising targets for cisplatin-resistant progenitor cells, validated in mouse xenograft experiments. These data provide new insights into cisplatin resistance mechanisms in PLC and suggest alternative therapies.
Significance:
PLCs are deadly when they resist chemotherapy, with limited alternative treatment options. Using a multiomics approach, we identified PLC driver genes and the cellular phenotype at the origin of cisplatin resistance. We validated new treatments targeting these molecular features in cell lines and xenografts.

This article is highlighted in the In This Issue feature, p. 2355
Data from Leukocyte Heterogeneity in Pancreatic Ductal Adenocarcinoma: Phenotypic and Spatial Features Associated with Clinical Outcome
Authors: Liudahl Shannon M. , Betts Courtney B. , Sivagnanam Shamilene , Morales-Oyarvide Vicente , da Silva Annacarolina , Yuan Chen , Hwang Samuel , Grossblatt-Wait Alison , Leis Kenna R. , Larson William , Lavoie Meghan B. , Robinson Padraic , Dias Costa Andressa , Väyrynen Sara A. , Clancy Thomas E. , Rubinson Douglas A. , Link Jason , Keith Dove , Horton Wesley , Tempero Margaret A. , Vonderheide Robert H. , Jaffee Elizabeth M. , Sheppard Brett , Goecks Jeremy , Sears Rosalie C. , Park Byung S. , Mori Motomi , Nowak Jonathan A. , Wolpin Brian M. , Coussens Lisa M.
Published: April 2023

Abstract
Immunotherapies targeting aspects of T cell functionality are efficacious in many solid tumors, but pancreatic ductal adenocarcinoma (PDAC) remains refractory to these treatments. Deeper understanding of the PDAC immune ecosystem is needed to identify additional therapeutic targets and predictive biomarkers for therapeutic response and resistance monitoring. To address these needs, we quantitatively evaluated leukocyte contexture in 135 human PDACs at single-cell resolution by profiling density and spatial distribution of myeloid and lymphoid cells within histopathologically defined regions of surgical resections from treatment-naive and presurgically (neoadjuvant)–treated patients and biopsy specimens from metastatic PDAC. Resultant data establish an immune atlas of PDAC heterogeneity, identify leukocyte features correlating with clinical outcomes, and, through an in silico study, provide guidance for use of PDAC tissue microarrays to optimally measure intratumoral immune heterogeneity. Atlas data have direct applicability as a reference for evaluating immune responses to investigational neoadjuvant PDAC therapeutics where pretherapy baseline specimens are not available.
Significance:
We provide a phenotypic and spatial immune atlas of human PDAC identifying leukocyte composition at steady state and following standard neoadjuvant therapies. These data have broad utility as a resource that can inform on leukocyte responses to emerging therapies where baseline tissues were not acquired.

This article is highlighted in the In This Issue feature, p. 1861
Data from Anti-Inflammatory Drugs Remodel the Tumor Immune Environment to Enhance Immune Checkpoint Blockade Efficacy
Authors: Pelly Victoria S. , Moeini Agrin , Roelofsen Lisanne M. , Bonavita Eduardo , Bell Charlotte R. , Hutton Colin , Blanco-Gomez Adrian , Banyard Antonia , Bromley Christian P. , Flanagan Eimear , Chiang Shih-Chieh , Jørgensen Claus , Schumacher Ton N. , Thommen Daniela S. , Zelenay Santiago
Published: April 2023

Abstract
Identifying strategies to improve the efficacy of immune checkpoint blockade (ICB) remains a major clinical need. Here, we show that therapeutically targeting the COX2/PGE2/EP2-4 pathway with widely used nonsteroidal and steroidal anti-inflammatory drugs synergized with ICB in mouse cancer models. We exploited a bilateral surgery model to distinguish responders from nonresponders shortly after treatment and identified acute IFNγ-driven transcriptional remodeling in responder mice, which was also associated with patient benefit to ICB. Monotherapy with COX2 inhibitors or EP2-4 PGE2 receptor antagonists rapidly induced this response program and, in combination with ICB, increased the intratumoral accumulation of effector T cells. Treatment of patient-derived tumor fragments from multiple cancer types revealed a similar shift in the tumor inflammatory environment to favor T-cell activation. Our findings establish the COX2/PGE2/EP2-4 axis as an independent immune checkpoint and a readily translatable strategy to rapidly switch the tumor inflammatory profile from cold to hot.
Significance:
Through performing in-depth profiling of mice and human tumors, this study identifies mechanisms by which anti-inflammatory drugs rapidly alter the tumor immune landscape to enhance tumor immunogenicity and responses to immune checkpoint inhibitors.

See related commentary by Melero et al., p. 2372.

This article is highlighted in the In This Issue feature, p. 2355
Data from ZFTA–RELA Dictates Oncogenic Transcriptional Programs to Drive Aggressive Supratentorial Ependymoma
Authors: Arabzade Amir , Zhao Yanhua , Varadharajan Srinidhi , Chen Hsiao-Chi , Jessa Selin , Rivas Bryan , Stuckert Austin J. , Solis Minerva , Kardian Alisha , Tlais Dana , Golbourn Brian J. , Stanton Ann-Catherine J. , Chan Yuen San , Olson Calla , Karlin Kristen L. , Kong Kathleen , Kupp Robert , Hu Baoli , Injac Sarah G. , Ngo Madeline , Wang Peter R. , De León Luz A. , Sahm Felix , Kawauchi Daisuke , Pfister Stefan M. , Lin Charles Y. , Hodges H. Courtney , Singh Irtisha , Westbrook Thomas F. , Chintagumpala Murali M. , Blaney Susan M. , Parsons Donald W. , Pajtler Kristian W. , Agnihotri Sameer , Gilbertson Richard J. , Yi Joanna , Jabado Nada , Kleinman Claudia L. , Bertrand Kelsey C. , Deneen Benjamin , Mack Stephen C.
Published: April 2023

Abstract
More than 60% of supratentorial ependymomas harbor a ZFTA–RELA (ZRfus) gene fusion (formerly C11orf95–RELA). To study the biology of ZRfus, we developed an autochthonous mouse tumor model using in utero electroporation (IUE) of the embryonic mouse brain. Integrative epigenomic and transcriptomic mapping was performed on IUE-driven ZRfus tumors by CUT&RUN, chromatin immunoprecipitation sequencing, assay for transposase-accessible chromatin sequencing, and RNA sequencing and compared with human ZRfus-driven ependymoma. In addition to direct canonical NFκB pathway activation, ZRfus dictates a neoplastic transcriptional program and binds to thousands of unique sites across the genome that are enriched with PLAGL family transcription factor (TF) motifs. ZRfus activates gene expression programs through recruitment of transcriptional coactivators (Brd4, Ep300, Cbp, Pol2) that are amenable to pharmacologic inhibition. Downstream ZRfus target genes converge on developmental programs marked by PLAGL TF proteins, and activate neoplastic programs enriched in Mapk, focal adhesion, and gene imprinting networks.
Significance:
Ependymomas are aggressive brain tumors. Although drivers of supratentorial ependymoma (ZFTA- and YAP1-associated gene fusions) have been discovered, their functions remain unclear. Our study investigates the biology of ZFTA–RELA-driven ependymoma, specifically mechanisms of transcriptional deregulation and direct downstream gene networks that may be leveraged for potential therapeutic testing.

This article is highlighted in the In This Issue feature, p. 2113
Data from CARM1 Inhibition Enables Immunotherapy of Resistant Tumors by Dual Action on Tumor Cells and T Cells
Authors: Kumar Sushil , Zeng Zexian , Bagati Archis , Tay Rong En , Sanz Lionel A. , Hartono Stella R. , Ito Yoshinaga , Abderazzaq Fieda , Hatchi Elodie , Jiang Peng , Cartwright Adam N.R. , Olawoyin Olamide , Mathewson Nathan D. , Pyrdol Jason W. , Li Mamie Z. , Doench John G. , Booker Matthew A. , Tolstorukov Michael Y. , Elledge Stephen J. , Chédin Frédéric , Liu X. Shirley , Wucherpfennig Kai W.
Published: April 2023

Abstract
A number of cancer drugs activate innate immune pathways in tumor cells but unfortunately also compromise antitumor immune function. We discovered that inhibition of CARM1, an epigenetic enzyme and cotranscriptional activator, elicited beneficial antitumor activity in both cytotoxic T cells and tumor cells. In T cells, Carm1 inactivation substantially enhanced their antitumor function and preserved memory-like populations required for sustained antitumor immunity. In tumor cells, Carm1 inactivation induced a potent type 1 interferon response that sensitized resistant tumors to cytotoxic T cells. Substantially increased numbers of dendritic cells, CD8 T cells, and natural killer cells were present in Carm1-deficient tumors, and infiltrating CD8 T cells expressed low levels of exhaustion markers. Targeting of CARM1 with a small molecule elicited potent antitumor immunity and sensitized resistant tumors to checkpoint blockade. Targeting of this cotranscriptional regulator thus offers an opportunity to enhance immune function while simultaneously sensitizing resistant tumor cells to immune attack.
Significance:
Resistance to cancer immunotherapy remains a major challenge. Targeting of CARM1 enables immunotherapy of resistant tumors by enhancing T-cell functionality and preserving memory-like T-cell populations within tumors. CARM1 inhibition also sensitizes resistant tumor cells to immune attack by inducing a tumor cell–intrinsic type 1 interferon response.

This article is highlighted in the In This Issue feature, p. 1861
Data from Cancer Cells Retrace a Stepwise Differentiation Program during Malignant Progression
Authors: Saghafinia Sadegh , Homicsko Krisztian , Di Domenico Annunziata , Wullschleger Stephan , Perren Aurel , Marinoni Ilaria , Ciriello Giovanni , Michael Iacovos P. , Hanahan Douglas
Published: April 2023

Abstract
Pancreatic neuroendocrine tumors (PanNET) comprise two molecular subtypes, relatively benign islet tumors (IT) and invasive, metastasis-like primary (MLP) tumors. Until now, the origin of aggressive MLP tumors has been obscure. Herein, using multi-omics approaches, we revealed that MLP tumors arise from IT via dedifferentiation following a reverse trajectory along the developmental pathway of islet β cells, which results in the acquisition of a progenitor-like molecular phenotype. Functionally, the miR-181cd cluster induces the IT-to-MLP transition by suppressing expression of the Meis2 transcription factor, leading to upregulation of a developmental transcription factor, Hmgb3. Notably, the IT-to-MLP transition constitutes a distinct step of tumorigenesis and is separable from the classic proliferation-associated hallmark, temporally preceding accelerated proliferation of cancer cells. Furthermore, patients with PanNET with elevated HMGB3 expression and an MLP transcriptional signature are associated with higher-grade tumors and worse survival. Overall, our results unveil a new mechanism that modulates cancer cell plasticity to enable malignant progression.
Significance:
Dedifferentiation has long been observed as a histopathologic characteristic of many cancers, albeit inseparable from concurrent increases in cell proliferation. Herein, we demonstrate that dedifferentiation is a mechanistically and temporally separable step in the multistage tumorigenesis of pancreatic islet cells, retracing the developmental lineage of islet β cells.

This article is highlighted in the In This Issue feature, p. 2355
Data from Design and Efficacy of a Monovalent Bispecific PD-1/CTLA4 Antibody That Enhances CTLA4 Blockade on PD-1+ Activated T Cells
Authors: Dovedi Simon J. , Elder Matthew J. , Yang Chunning , Sitnikova Suzanne I. , Irving Lorraine , Hansen Anna , Hair James , Jones Des C. , Hasani Sumati , Wang Bo , Im Seock-Ah , Tran Ben , Subramaniam Deepa S. , Gainer Shelby D. , Vashisht Kapil , Lewis Arthur , Jin Xiaofang , Kentner Stacy , Mulgrew Kathy , Wang Yaya , Overstreet Michael G. , Dodgson James , Wu Yanli , Palazon Asis , Morrow Michelle , Rainey Godfrey J. , Browne Gareth J. , Neal Frances , Murray Thomas V. , Toloczko Aleksandra D. , Dall'Acqua William , Achour Ikbel , Freeman Daniel J. , Wilkinson Robert W. , Mazor Yariv
Published: April 2023

Abstract
The clinical benefit of PD-1 blockade can be improved by combination with CTLA4 inhibition but is commensurate with significant immune-related adverse events suboptimally limiting the doses of anti-CTLA4 mAb that can be used. MEDI5752 is a monovalent bispecific antibody designed to suppress the PD-1 pathway and provide modulated CTLA4 inhibition favoring enhanced blockade on PD-1+ activated T cells. We show that MEDI5752 preferentially saturates CTLA4 on PD-1+ T cells versus PD-1− T cells, reducing the dose required to elicit IL2 secretion. Unlike conventional PD-1/CTLA4 mAbs, MEDI5752 leads to the rapid internalization and degradation of PD-1. Moreover, we show that MEDI5752 preferentially localizes and accumulates in tumors providing enhanced activity when compared with a combination of mAbs targeting PD-1 and CTLA4 in vivo. Following treatment with MEDI5752, robust partial responses were observed in two patients with advanced solid tumors. MEDI5752 represents a novel immunotherapy engineered to preferentially inhibit CTLA4 on PD-1+ T cells.
Significance:
The unique characteristics of MEDI5752 represent a novel immunotherapy engineered to direct CTLA4 inhibition to PD-1+ T cells with the potential for differentiated activity when compared with current conventional mAb combination strategies targeting PD-1 and CTLA4. This molecule therefore represents a step forward in the rational design of cancer immunotherapy.

See related commentary by Burton and Tawbi, p. 1008.

This article is highlighted in the In This Issue feature, p. 995
Data from Microbiota-Centered Interventions: The Next Breakthrough in Immuno-Oncology?
Authors: Derosa Lisa , Routy Bertrand , Desilets Antoine , Daillère Romain , Terrisse Safae , Kroemer Guido , Zitvogel Laurence
Published: April 2023

Abstract
The cancer–immune dialogue subject to immuno-oncological intervention is profoundly influenced by microenvironmental factors. Indeed, the mucosal microbiota—and more specifically, the intestinal ecosystem—influences the tone of anticancer immune responses and the clinical benefit of immunotherapy. Antibiotics blunt the efficacy of immune checkpoint inhibitors (ICI), and fecal microbial transplantation may restore responsiveness of ICI-resistant melanoma. Here, we review the yin and yang of intestinal bacteria at the crossroads between the intestinal barrier, metabolism, and local or systemic immune responses during anticancer therapies. We discuss diagnostic tools to identify gut dysbiosis and the future prospects of microbiota-based therapeutic interventions.
Significance:
Given the recent proof of concept of the potential efficacy of fecal microbial transplantation in patients with melanoma primarily resistant to PD-1 blockade, it is timely to discuss how and why antibiotics compromise the efficacy of cancer immunotherapy, describe the balance between beneficial and harmful microbial species in play during therapies, and introduce the potential for microbiota-centered interventions for the future of immuno-oncology.
Data from Genetic Screens Identify a Context-Specific PI3K/p27Kip1 Node Driving Extrahepatic Biliary Cancer
Authors: Falcomatà Chiara , Bärthel Stefanie , Ulrich Angelika , Diersch Sandra , Veltkamp Christian , Rad Lena , Boniolo Fabio , Solar Myriam , Steiger Katja , Seidler Barbara , Zukowska Magdalena , Madej Joanna , Wang Mingsong , Öllinger Rupert , Maresch Roman , Barenboim Maxim , Eser Stefan , Tschurtschenthaler Markus , Mehrabi Arianeb , Roessler Stephanie , Goeppert Benjamin , Kind Alexander , Schnieke Angelika , Robles Maria S. , Bradley Allan , Schmid Roland M. , Schmidt-Supprian Marc , Reichert Maximilian , Weichert Wilko , Sansom Owen J. , Morton Jennifer P. , Rad Roland , Schneider Günter , Saur Dieter
Published: April 2023

Abstract
Biliary tract cancer ranks among the most lethal human malignancies, representing an unmet clinical need. Its abysmal prognosis is tied to an increasing incidence and a fundamental lack of mechanistic knowledge regarding the molecular basis of the disease. Here, we show that the Pdx1-positive extrahepatic biliary epithelium is highly susceptible toward transformation by activated PIK3CAH1047R but refractory to oncogenic KrasG12D. Using genome-wide transposon screens and genetic loss-of-function experiments, we discover context-dependent genetic interactions that drive extrahepatic cholangiocarcinoma (ECC) and show that PI3K signaling output strength and repression of the tumor suppressor p27Kip1 are critical context-specific determinants of tumor formation. This contrasts with the pancreas, where oncogenic Kras in concert with p53 loss is a key cancer driver. Notably, inactivation of p27Kip1 permits KrasG12D-driven ECC development. These studies provide a mechanistic link between PI3K signaling, tissue-specific tumor suppressor barriers, and ECC pathogenesis, and present a novel genetic model of autochthonous ECC and genes driving this highly lethal tumor subtype.
Significance:
We used the first genetically engineered mouse model for extrahepatic bile duct carcinoma to identify cancer genes by genome-wide transposon-based mutagenesis screening. Thereby, we show that PI3K signaling output strength and p27Kip1 function are critical determinants for context-specific ECC formation.

This article is highlighted in the In This Issue feature, p. 2945
Data from Systematic Profiling of DNMT3A Variants Reveals Protein Instability Mediated by the DCAF8 E3 Ubiquitin Ligase Adaptor
Authors: Huang Yung-Hsin , Chen Chun-Wei , Sundaramurthy Venkatasubramaniam , Słabicki Mikołaj , Hao Dapeng , Watson Caroline J. , Tovy Ayala , Reyes Jaime M. , Dakhova Olga , Crovetti Brielle R. , Galonska Christina , Lee Minjung , Brunetti Lorenzo , Zhou Yubin , Tatton-Brown Katrina , Huang Yun , Cheng Xiaodong , Meissner Alexander , Valk Peter J.M. , Van Maldergem Lionel , Sanders Mathijs A. , Blundell Jamie R. , Li Wei , Ebert Benjamin L. , Goodell Margaret A.
Published: April 2023

Abstract
Clonal hematopoiesis is a prevalent age-related condition associated with a greatly increased risk of hematologic disease; mutations in DNA methyltransferase 3A (DNMT3A) are the most common driver of this state. DNMT3A variants occur across the gene with some particularly associated with malignancy, but the functional relevance and mechanisms of pathogenesis of the majority of mutations are unknown. Here, we systematically investigated the methyltransferase activity and protein stability of 253 disease-associated DNMT3A mutations, and found that 74% were loss-of-function mutations. Half of these variants exhibited reduced protein stability and, as a class, correlated with greater clonal expansion and acute myeloid leukemia development. We investigated the mechanisms underlying the instability using a CRISPR screen and uncovered regulated destruction of DNMT3A mediated by the DCAF8 E3 ubiquitin ligase adaptor. We establish a new paradigm to classify novel variants that has prognostic and potential therapeutic significance for patients with hematologic disease.
Significance:
DNMT3A has emerged as the most important epigenetic regulator and tumor suppressor in the hematopoietic system. Our study represents a systematic and high-throughput method to characterize the molecular impact of DNMT3A missense mutations and the discovery of a regulated destruction mechanism of DNMT3A offering new prognostic and future therapeutic avenues.

See related commentary by Ma and Will, p. 23.

This article is highlighted in the In This Issue feature, p. 1
Data from Paradigms on Immunotherapy Combinations with Chemotherapy
Authors: Salas-Benito Diego , Pérez-Gracia José L. , Ponz-Sarvisé Mariano , Rodriguez-Ruiz María E. , Martínez-Forero Iván , Castañón Eduardo , López-Picazo José M. , Sanmamed Miguel F. , Melero Ignacio
Published: April 2023

Abstract
Checkpoint inhibitors are being added to standard-of-care chemotherapy in multiple clinical trials. Success has been reported in non–small and small cell lung carcinomas and urothelial, head and neck, gastric, and esophageal cancers, and promising results are already available in triple-negative breast and pancreatic malignancies. The potential mechanisms of synergy include immunogenic tumor cell death, antiangiogenesis, selective depletion of myeloid immunosuppressive cells, and lymphopenia, which reduces regulatory T cells and makes room for proliferation of effector T cells. However, chemotherapy regimens have not been optimized for such combinations, perhaps explaining some recent clinical trial disappointments. Approaches to make the most of chemoimmunotherapy include neoadjuvant and adjuvant schemes.

Significance: Immunotherapy of cancer based on PD-1/PD-L1 blockade has prompted a revolution in cancer clinical management. Evidence in phase III clinical trials already supports combinations of immunotherapy with standard-of-care chemotherapy for a number of malignant diseases. This review focuses on such evidence and provides an overview of the potential synergistic mechanisms of action and the opportunities to optimize chemoimmunotherapy regimens.