bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from An Empirical Antigen Selection Method Identifies Neoantigens That Either Elicit Broad Antitumor T-cell Responses or Drive Tumor Growth
Authors: Lam Hubert , McNeil Lisa K. , Starobinets Hanna , DeVault Victoria L. , Cohen Roger B. , Twardowski Przemyslaw , Johnson Melissa L. , Gillison Maura L. , Stein Mark N. , Vaishampayan Ulka N. , DeCillis Arthur P. , Foti James J. , Vemulapalli Vijetha , Tjon Emily , Ferber Kyle , DeOliveira Daniel B. , Broom Wendy , Agnihotri Parul , Jaffee Elizabeth M. , Wong Kwok-Kin , Drake Charles G. , Carroll Pamela M. , Davis Thomas A. , Flechtner Jessica Baker
Published: April 2023

Abstract
Neoantigens are critical targets of antitumor T-cell responses. The ATLAS bioassay was developed to identify neoantigens empirically by expressing each unique patient-specific tumor mutation individually in Escherichia coli, pulsing autologous dendritic cells in an ordered array, and testing the patient's T cells for recognition in an overnight assay. Profiling of T cells from patients with lung cancer revealed both stimulatory and inhibitory responses to individual neoantigens. In the murine B16F10 melanoma model, therapeutic immunization with ATLAS-identified stimulatory neoantigens protected animals, whereas immunization with peptides associated with inhibitory ATLAS responses resulted in accelerated tumor growth and abolished efficacy of an otherwise protective vaccine. A planned interim analysis of a clinical study testing a poly-ICLC adjuvanted personalized vaccine containing ATLAS-identified stimulatory neoantigens showed that it is well tolerated. In an adjuvant setting, immunized patients generated both CD4+ and CD8+ T-cell responses, with immune responses to 99% of the vaccinated peptide antigens.
Significance:
Predicting neoantigens in silico has progressed, but empirical testing shows that T-cell responses are more nuanced than straightforward MHC antigen recognition. The ATLAS bioassay screens tumor mutations to uncover preexisting, patient-relevant neoantigen T-cell responses and reveals a new class of putatively deleterious responses that could affect cancer immunotherapy design.

This article is highlighted in the In This Issue feature, p. 521
Data from Clonal Selection with RAS Pathway Activation Mediates Secondary Clinical Resistance to Selective FLT3 Inhibition in Acute Myeloid Leukemia
Authors: McMahon Christine M. , Ferng Timothy , Canaani Jonathan , Wang Eunice S. , Morrissette Jennifer J.D. , Eastburn Dennis J. , Pellegrino Maurizio , Durruthy-Durruthy Robert , Watt Christopher D. , Asthana Saurabh , Lasater Elisabeth A. , DeFilippis RosaAnna , Peretz Cheryl A.C. , McGary Lisa H.F. , Deihimi Safoora , Logan Aaron C. , Luger Selina M. , Shah Neil P. , Carroll Martin , Smith Catherine C. , Perl Alexander E.
Published: April 2023

Abstract
Gilteritinib is a potent and selective FLT3 kinase inhibitor with single-agent clinical efficacy in relapsed/refractory FLT3-mutated acute myeloid leukemia (AML). In this context, however, gilteritinib is not curative, and response duration is limited by the development of secondary resistance. To evaluate resistance mechanisms, we analyzed baseline and progression samples from patients treated on clinical trials of gilteritinib. Targeted next-generation sequencing at the time of AML progression on gilteritinib identified treatment-emergent mutations that activate RAS/MAPK pathway signaling, most commonly in NRAS or KRAS. Less frequently, secondary FLT3-F691L gatekeeper mutations or BCR–ABL1 fusions were identified at progression. Single-cell targeted DNA sequencing revealed diverse patterns of clonal selection and evolution in response to FLT3 inhibition, including the emergence of RAS mutations in FLT3-mutated subclones, the expansion of alternative wild-type FLT3 subclones, or both patterns simultaneously. These data illustrate dynamic and complex changes in clonal architecture underlying response and resistance to mutation-selective tyrosine kinase inhibitor therapy in AML.
Significance:
Comprehensive serial genotyping of AML specimens from patients treated with the selective FLT3 inhibitor gilteritinib demonstrates that complex, heterogeneous patterns of clonal selection and evolution mediate clinical resistance to tyrosine kinase inhibition in FLT3-mutated AML. Our data support the development of combinatorial targeted therapeutic approaches for advanced AML.

See related commentary by Wei and Roberts, p. 998.

This article is highlighted in the In This Issue feature, p. 983
Data from RBMS1 Suppresses Colon Cancer Metastasis through Targeted Stabilization of Its mRNA Regulon
Authors: Yu Johnny , Navickas Albertas , Asgharian Hosseinali , Culbertson Bruce , Fish Lisa , Garcia Kristle , Olegario John Paolo , Dermit Maria , Dodel Martin , Hänisch Benjamin , Luo Yikai , Weinberg Ethan M. , Dienstmann Rodrigo , Warren Robert S. , Mardakheh Faraz K. , Goodarzi Hani
Published: April 2023

Abstract
Identifying master regulators that drive pathologic gene expression is a key challenge in precision oncology. Here, we have developed an analytic framework, named PRADA, that identifies oncogenic RNA-binding proteins through the systematic detection of coordinated changes in their target regulons. Application of this approach to data collected from clinical samples, patient-derived xenografts, and cell line models of colon cancer metastasis revealed the RNA-binding protein RBMS1 as a suppressor of colon cancer progression. We observed that silencing RBMS1 results in increased metastatic capacity in xenograft mouse models, and that restoring its expression blunts metastatic liver colonization. We have found that RBMS1 functions as a posttranscriptional regulator of RNA stability by directly binding its target mRNAs. Together, our findings establish a role for RBMS1 as a previously unknown regulator of RNA stability and as a suppressor of colon cancer metastasis with clinical utility for risk stratification of patients.
Significance:
By applying a new analytic approach to transcriptomic data from clinical samples and models of colon cancer progression, we have identified RBMS1 as a suppressor of metastasis and as a post-transcriptional regulator of RNA stability. Notably, RBMS1 silencing and downregulation of its targets are negatively associated with patient survival.

See related commentary by Carter, p. 1261.

This article is highlighted in the In This Issue feature, p. 1241
Data from V211D Mutation in MEK1 Causes Resistance to MEK Inhibitors in Colon Cancer
Authors: Gao Yijun , Maria Ann , Na Na , da Cruz Paula Arnaud , Gorelick Alexander N. , Hechtman Jaclyn F. , Carson Julianne , Lefkowitz Robert A. , Weigelt Britta , Taylor Barry S. , Zhao HuiYong , Reis-Filho Jorge S. , de Stanchina Elisa , Rosen Neal , Yao Zhan , Yaeger Rona
Published: April 2023

Abstract
We report the emergence of the novel MEK1V211D gatekeeper mutation in a patient with BRAFK601E colon cancer treated with the allosteric MEK inhibitor binimetinib and the anti-EGFR antibody panitumumab. The MEK1V211D mutation concurrently occurs in the same cell with BRAFK601E and leads to RAF-independent activity but remains regulated by RAF. The V211D mutation causes resistance to binimetinib by both increasing the catalytic activity of MEK1 and reducing its affinity for the drug. Moreover, the mutant exhibits reduced sensitivity to all the allosteric MEK inhibitors tested. Thus, this mutation serves as a general resistance mutation for current MEK inhibitors; however, it is sensitive to a newly reported ATP-competitive MEK inhibitor, which therefore could be used to overcome drug resistance.
Significance:
We report a resistance mechanism to allosteric MEK inhibitors in the clinic. A MEK1V211D mutation developed in a patient with BRAFK601E colon cancer on MEK and EGFR inhibitors. This mutant increases the catalytic activity of MEK1 and reduces its affinity for binimetinib, but remains sensitive to ATP-competitive MEK inhibitors.

This article is highlighted in the In This Issue feature, p. 1143
Data from Immune Surveillance in Clinical Regression of Preinvasive Squamous Cell Lung Cancer
Authors: Pennycuick Adam , Teixeira Vitor H. , AbdulJabbar Khalid , Raza Shan E. Ahmed , Lund Tom , Akarca Ayse U. , Rosenthal Rachel , Kalinke Lukas , Chandrasekharan Deepak P. , Pipinikas Christodoulos P. , Lee-Six Henry , Hynds Robert E. , Gowers Kate H.C. , Henry Jake Y. , Millar Fraser R. , Hagos Yeman B. , Denais Celine , Falzon Mary , Moore David A. , Antoniou Sophia , Durrenberger Pascal F. , Furness Andrew J. , Carroll Bernadette , Marceaux Claire , Asselin-Labat Marie-Liesse , Larson William , Betts Courtney , Coussens Lisa M. , Thakrar Ricky M. , George Jeremy , Swanton Charles , Thirlwell Christina , Campbell Peter J. , Marafioti Teresa , Yuan Yinyin , Quezada Sergio A. , McGranahan Nicholas , Janes Sam M.
Published: April 2023

Abstract
Before squamous cell lung cancer develops, precancerous lesions can be found in the airways. From longitudinal monitoring, we know that only half of such lesions become cancer, whereas a third spontaneously regress. Although recent studies have described the presence of an active immune response in high-grade lesions, the mechanisms underpinning clinical regression of precancerous lesions remain unknown. Here, we show that host immune surveillance is strongly implicated in lesion regression. Using bronchoscopic biopsies from human subjects, we find that regressive carcinoma in situ lesions harbor more infiltrating immune cells than those that progress to cancer. Moreover, molecular profiling of these lesions identifies potential immune escape mechanisms specifically in those that progress to cancer: antigen presentation is impaired by genomic and epigenetic changes, CCL27–CCR10 signaling is upregulated, and the immunomodulator TNFSF9 is downregulated. Changes appear intrinsic to the carcinoma in situ lesions, as the adjacent stroma of progressive and regressive lesions are transcriptomically similar.
Significance:
Immune evasion is a hallmark of cancer. For the first time, this study identifies mechanisms by which precancerous lesions evade immune detection during the earliest stages of carcinogenesis and forms a basis for new therapeutic strategies that treat or prevent early-stage lung cancer.

See related commentary by Krysan et al., p. 1442.

This article is highlighted in the In This Issue feature, p. 1426
Data from Antitumor T-cell Homeostatic Activation Is Uncoupled from Homeostatic Inhibition by Checkpoint Blockade
Authors: Marshall Netonia , Hutchinson Keino , Marron Thomas U. , Aleynick Mark , Hammerich Linda , Upadhyay Ranjan , Svensson-Arvelund Judit , Brown Brian D. , Merad Miriam , Brody Joshua D.
Published: April 2023

Abstract
T-cell transfer into lymphodepleted recipients induces homeostatic activation and potentiates antitumor efficacy. In contrast to canonical T-cell receptor–induced activation, homeostatic activation yields a distinct phenotype and memory state whose regulatory mechanisms are poorly understood. Here, we show in patients and murine models that, following transfer into lymphodepleted bone marrow transplant (BMT) recipients, CD8+ T cells undergo activation but also simultaneous homeostatic inhibition manifested by upregulation of immune-checkpoint molecules and functional suppression. T cells transferred into BMT recipients were protected from homeostatic inhibition by PD-1/CTLA4 dual checkpoint blockade (dCB). This combination of dCB and BMT—”immunotransplant”—increased T-cell homeostatic activation and antitumor T-cell responses by an order of magnitude. Like homeostatic activation, homeostatic inhibition is IL7/IL15-dependent, revealing mechanistic coupling of these two processes. Marked similarity in ex vivo modulation of post-BMT T cells in mice and patients is promising for the clinical translation of immunotransplant (NCT03305445) and for addressing homeostatic inhibition in T-cell therapies.
Significance:
For optimal anticancer effect, T-cell therapies including chimeric antigen receptor T-cell, tumor-infiltrating lymphocyte, and transgenic T-cell therapies require transfer into lymphodepleted recipients and homeostatic activation; however, concomitant homeostatic inhibition mitigates T-cell therapies' efficacy. Checkpoint blockade uncouples homeostatic inhibition from activation, amplifying T-cell responses. Conversely, tumors nonresponsive to checkpoint blockade or BMT are treatable with immunotransplant.

See related commentary by Ansell, p. 1487.

This article is highlighted in the In This Issue feature, p. 1469
Data from Ontogenic Changes in Hematopoietic Hierarchy Determine Pediatric Specificity and Disease Phenotype in Fusion Oncogene–Driven Myeloid Leukemia
Authors: Lopez Cécile K. , Noguera Esteve , Stavropoulou Vaia , Robert Elie , Aid Zakia , Ballerini Paola , Bilhou-Nabera Chrystèle , Lapillonne Hélène , Boudia Fabien , Thirant Cécile , Fagnan Alexandre , Arcangeli Marie-Laure , Kinston Sarah J. , Diop M'Boyba , Job Bastien , Lecluse Yann , Brunet Erika , Babin Loélia , Villeval Jean Luc , Delabesse Eric , Peters Antoine H.F.M. , Vainchenker William , Gaudry Muriel , Masetti Riccardo , Locatelli Franco , Malinge Sébastien , Nerlov Claus , Droin Nathalie , Lobry Camille , Godin Isabelle , Bernard Olivier A. , Göttgens Berthold , Petit Arnaud , Pflumio Françoise , Schwaller Juerg , Mercher Thomas
Published: April 2023

Abstract
Fusion oncogenes are prevalent in several pediatric cancers, yet little is known about the specific associations between age and phenotype. We observed that fusion oncogenes, such as ETO2–GLIS2, are associated with acute megakaryoblastic or other myeloid leukemia subtypes in an age-dependent manner. Analysis of a novel inducible transgenic mouse model showed that ETO2–GLIS2 expression in fetal hematopoietic stem cells induced rapid megakaryoblastic leukemia whereas expression in adult bone marrow hematopoietic stem cells resulted in a shift toward myeloid transformation with a strikingly delayed in vivo leukemogenic potential. Chromatin accessibility and single-cell transcriptome analyses indicate ontogeny-dependent intrinsic and ETO2–GLIS2-induced differences in the activities of key transcription factors, including ERG, SPI1, GATA1, and CEBPA. Importantly, switching off the fusion oncogene restored terminal differentiation of the leukemic blasts. Together, these data show that aggressiveness and phenotypes in pediatric acute myeloid leukemia result from an ontogeny-related differential susceptibility to transformation by fusion oncogenes.
Significance:
This work demonstrates that the clinical phenotype of pediatric acute myeloid leukemia is determined by ontogeny-dependent susceptibility for transformation by oncogenic fusion genes. The phenotype is maintained by potentially reversible alteration of key transcription factors, indicating that targeting of the fusions may overcome the differentiation blockage and revert the leukemic state.

See related commentary by Cruz Hernandez and Vyas, p. 1653.

This article is highlighted in the In This Issue feature, p. 1631
Data from SWI/SNF Complex Mutations Promote Thyroid Tumor Progression and Insensitivity to Redifferentiation Therapies
Authors: Saqcena Mahesh , Leandro-Garcia Luis Javier , Maag Jesper L.V. , Tchekmedyian Vatche , Krishnamoorthy Gnana P. , Tamarapu Prasanna P. , Tiedje Vera , Reuter Vincent , Knauf Jeffrey A. , de Stanchina Elisa , Xu Bin , Liao Xiao-Hui , Refetoff Samuel , Ghossein Ronald , Chi Ping , Ho Alan L. , Koche Richard P. , Fagin James A.
Published: April 2023

Abstract
Mutations of subunits of the SWI/SNF chromatin remodeling complexes occur commonly in cancers of different lineages, including advanced thyroid cancers. Here we show that thyroid-specific loss of Arid1a, Arid2, or Smarcb1 in mouse BRAFV600E-mutant tumors promotes disease progression and decreased survival, associated with lesion-specific effects on chromatin accessibility and differentiation. As compared with normal thyrocytes, BRAFV600E-mutant mouse papillary thyroid cancers have decreased lineage transcription factor expression and accessibility to their target DNA binding sites, leading to impairment of thyroid-differentiated gene expression and radioiodine incorporation, which is rescued by MAPK inhibition. Loss of individual SWI/SNF subunits in BRAF tumors leads to a repressive chromatin state that cannot be reversed by MAPK pathway blockade, rendering them insensitive to its redifferentiation effects. Our results show that SWI/SNF complexes are central to the maintenance of differentiated function in thyroid cancers, and their loss confers radioiodine refractoriness and resistance to MAPK inhibitor–based redifferentiation therapies.
Significance:
Reprogramming cancer differentiation confers therapeutic benefit in various disease contexts. Oncogenic BRAF silences genes required for radioiodine responsiveness in thyroid cancer. Mutations in SWI/SNF genes result in loss of chromatin accessibility at thyroid lineage specification genes in BRAF-mutant thyroid tumors, rendering them insensitive to the redifferentiation effects of MAPK blockade.

This article is highlighted in the In This Issue feature, p. 995
Data from Tumor Immunity and Immunotherapy for HPV-Related Cancers
Authors: Shamseddine Achraf A. , Burman Bharat , Lee Nancy Y. , Zamarin Dmitriy , Riaz Nadeem
Published: April 2023

Abstract
Human papillomavirus (HPV) infection drives tumorigenesis in the majority of cervical, oropharyngeal, anal, and vulvar cancers. Genetic and epidemiologic evidence has highlighted the role of immunosuppression in the oncogenesis of HPV-related malignancies. Here we review how HPV modulates the immune microenvironment and subsequent therapeutic implications. We describe the landscape of immunotherapies for these cancers with a focus on findings from early-phase studies exploring antigen-specific treatments, and discuss future directions. Although responses across these studies have been modest to date, a deeper understanding of HPV-related tumor biology and immunology may prove instrumental for the development of more efficacious immunotherapeutic approaches.
Significance:
HPV modulates the microenvironment to create a protumorigenic state of immune suppression and evasion. Our understanding of these mechanisms has led to the development of immunomodulatory treatments that have shown early clinical promise in patients with HPV-related malignancies. This review summarizes our current understanding of the interactions of HPV and its microenvironment and provides insight into the progress and challenges of developing immunotherapies for HPV-related malignancies.
Data from Overcoming Resistance to Tumor-Targeted and Immune-Targeted Therapies
Authors: Aldea Mihaela , Andre Fabrice , Marabelle Aurelien , Dogan Semih , Barlesi Fabrice , Soria Jean-Charles
Published: April 2023

Abstract
Resistance to anticancer therapies includes primary resistance, usually related to lack of target dependency or presence of additional targets, and secondary resistance, mostly driven by adaptation of the cancer cell to the selection pressure of treatment. Resistance to targeted therapy is frequently acquired, driven by on-target, bypass alterations, or cellular plasticity. Resistance to immunotherapy is often primary, orchestrated by sophisticated tumor–host–microenvironment interactions, but could also occur after initial efficacy, mostly when only partial responses are obtained. Here, we provide an overview of resistance to tumor and immune-targeted therapies and discuss challenges of overcoming resistance, and current and future directions of development.
Significance:
A better and earlier identification of cancer-resistance mechanisms could avoid the use of ineffective drugs in patients not responding to therapy and provide the rationale for the administration of personalized drug associations. A clear description of the molecular interplayers is a prerequisite to the development of novel and dedicated anticancer drugs. Finally, the implementation of such cancer molecular and immunologic explorations in prospective clinical trials could de-risk the demonstration of more effective anticancer strategies in randomized registration trials, and bring us closer to the promise of cure.
Data from Resolving the Spatial and Cellular Architecture of Lung Adenocarcinoma by Multiregion Single-Cell Sequencing
Authors: Sinjab Ansam , Han Guangchun , Treekitkarnmongkol Warapen , Hara Kieko , Brennan Patrick M. , Dang Minghao , Hao Dapeng , Wang Ruiping , Dai Enyu , Dejima Hitoshi , Zhang Jiexin , Bogatenkova Elena , Sanchez-Espiridion Beatriz , Chang Kyle , Little Danielle R. , Bazzi Samer , Tran Linh M. , Krysan Kostyantyn , Behrens Carmen , Duose Dzifa Y. , Parra Edwin R. , Raso Maria Gabriela , Solis Luisa M. , Fukuoka Junya , Zhang Jianjun , Sepesi Boris , Cascone Tina , Byers Lauren Averett , Gibbons Don L. , Chen Jichao , Moghaddam Seyed Javad , Ostrin Edwin J. , Rosen Daniel , Heymach John V. , Scheet Paul , Dubinett Steven M. , Fujimoto Junya , Wistuba Ignacio I. , Stevenson Christopher S. , Spira Avrum , Wang Linghua , Kadara Humam
Published: April 2023

Abstract
Little is known of the geospatial architecture of individual cell populations in lung adenocarcinoma (LUAD) evolution. Here, we perform single-cell RNA sequencing of 186,916 cells from five early-stage LUADs and 14 multiregion normal lung tissues of defined spatial proximities from the tumors. We show that cellular lineages, states, and transcriptomic features geospatially evolve across normal regions to LUADs. LUADs also exhibit pronounced intratumor cell heterogeneity within single sites and transcriptional lineage-plasticity programs. T regulatory cell phenotypes are increased in normal tissues with proximity to LUAD, in contrast to diminished signatures and fractions of cytotoxic CD8+ T cells, antigen-presenting macrophages, and inflammatory dendritic cells. We further find that the LUAD ligand–receptor interactome harbors increased expression of epithelial CD24, which mediates protumor phenotypes. These data provide a spatial atlas of LUAD evolution, and a resource for identification of targets for its treatment.
Significance:
The geospatial ecosystem of the peripheral lung and early-stage LUAD is not known. Our multiregion single-cell sequencing analyses unravel cell populations, states, and phenotypes in the spatial and ecologic evolution of LUAD from the lung that comprise high-potential targets for early interception.

This article is highlighted in the In This Issue feature, p. 2355
Data from FGFR2 Extracellular Domain In-Frame Deletions Are Therapeutically Targetable Genomic Alterations That Function as Oncogenic Drivers in Cholangiocarcinoma
Authors: Cleary James M. , Raghavan Srivatsan , Wu Qibiao , Li Yvonne Y. , Spurr Liam F. , Gupta Hersh V. , Rubinson Douglas A. , Fetter Isobel J. , Hornick Jason L. , Nowak Jonathan A. , Siravegna Giulia , Goyal Lipika , Shi Lei , Brais Lauren K. , Loftus Maureen , Shinagare Atul B. , Abrams Thomas A. , Clancy Thomas E. , Wang Jiping , Patel Anuj K. , Brichory Franck , Vaslin Chessex Anne , Sullivan Ryan J. , Keller Rachel B. , Denning Sarah , Hill Emma R. , Shapiro Geoffrey I. , Pokorska-Bocci Anna , Zanna Claudio , Ng Kimmie , Schrag Deborah , Jänne Pasi A. , Hahn William C. , Cherniack Andrew D. , Corcoran Ryan B. , Meyerson Matthew , Daina Antoine , Zoete Vincent , Bardeesy Nabeel , Wolpin Brian M.
Published: April 2023

Abstract
We conducted next-generation DNA sequencing on 335 biliary tract cancers and characterized the genomic landscape by anatomic site within the biliary tree. In addition to frequent FGFR2 fusions among patients with intrahepatic cholangiocarcinoma (IHCC), we identified FGFR2 extracellular domain in-frame deletions (EID) in 5 of 178 (2.8%) patients with IHCC, including two patients with FGFR2 p.H167_N173del. Expression of this FGFR2 EID in NIH3T3 cells resulted in constitutive FGFR2 activation, oncogenic transformation, and sensitivity to FGFR inhibitors. Three patients with FGFR2 EIDs were treated with Debio 1347, an oral FGFR1/2/3 inhibitor, and all showed partial responses. One patient developed an acquired L618F FGFR2 kinase domain mutation at disease progression and experienced a further partial response for 17 months to an irreversible FGFR2 inhibitor, futibatinib. Together, these findings reveal FGFR2 EIDs as an alternative mechanism of FGFR2 activation in IHCC that predicts sensitivity to FGFR inhibitors in the clinic.
Significance:
FGFR2 EIDs are transforming genomic alterations that occur predominantly in patients with IHCC. These FGFR2 EIDs are sensitive to FGFR inhibition in vitro, and patients with these alterations benefited from treatment with FGFR inhibitors in the clinic.

This article is highlighted in the In This Issue feature, p. 2355
Data from Intrinsic Immunogenicity of Small Cell Lung Carcinoma Revealed by Its Cellular Plasticity
Authors: Mahadevan Navin R. , Knelson Erik H. , Wolff Jacquelyn O. , Vajdi Amir , Saigí Maria , Campisi Marco , Hong Deli , Thai Tran C. , Piel Brandon , Han Saemi , Reinhold Bruce B. , Duke-Cohan Jonathan S. , Poitras Michael J. , Taus Luke J. , Lizotte Patrick H. , Portell Andrew , Quadros Victor , Santucci Alison D. , Murayama Takahiko , Cañadas Israel , Kitajima Shunsuke , Akitsu Aoi , Fridrikh Maya , Watanabe Hideo , Reardon Brendan , Gokhale Prafulla C. , Paweletz Cloud P. , Awad Mark M. , Van Allen Eliezer M. , Lako Ana , Wang Xi-Tao , Chen Benjamin , Hong Fangxin , Sholl Lynette M. , Tolstorukov Michael Y. , Pfaff Kathleen , Jänne Pasi A. , Gjini Evisa , Edwards Robin , Rodig Scott , Reinherz Ellis L. , Oser Matthew G. , Barbie David A.
Published: April 2023

Abstract
Small cell lung carcinoma (SCLC) is highly mutated, yet durable response to immune checkpoint blockade (ICB) is rare. SCLC also exhibits cellular plasticity, which could influence its immunobiology. Here we discover that a distinct subset of SCLC uniquely upregulates MHC I, enriching for durable ICB benefit. In vitro modeling confirms epigenetic recovery of MHC I in SCLC following loss of neuroendocrine differentiation, which tracks with derepression of STING. Transient EZH2 inhibition expands these nonneuroendocrine cells, which display intrinsic innate immune signaling and basally restored antigen presentation. Consistent with these findings, murine nonneuroendocrine SCLC tumors are rejected in a syngeneic model, with clonal expansion of immunodominant effector CD8 T cells. Therapeutically, EZH2 inhibition followed by STING agonism enhances T-cell recognition and rejection of SCLC in mice. Together, these data identify MHC I as a novel biomarker of SCLC immune responsiveness and suggest novel immunotherapeutic approaches to co-opt SCLC's intrinsic immunogenicity.
Significance:
SCLC is poorly immunogenic, displaying modest ICB responsiveness with rare durable activity. In profiling its plasticity, we uncover intrinsically immunogenic MHC Ihi subpopulations of nonneuroendocrine SCLC associated with durable ICB benefit. We also find that combined EZH2 inhibition and STING agonism uncovers this cell state, priming cells for immune rejection.

This article is highlighted in the In This Issue feature, p. 1861
Data from Induction of APOBEC3 Exacerbates DNA Replication Stress and Chromosomal Instability in Early Breast and Lung Cancer Evolution
Authors: Venkatesan Subramanian , Angelova Mihaela , Puttick Clare , Zhai Haoran , Caswell Deborah R. , Lu Wei-Ting , Dietzen Michelle , Galanos Panagiotis , Evangelou Konstantinos , Bellelli Roberto , Lim Emilia L. , Watkins Thomas B.K. , Rowan Andrew , Teixeira Vitor H. , Zhao Yue , Chen Haiquan , Ngo Bryan , Zalmas Lykourgos-Panagiotis , Al Bakir Maise , Hobor Sebastijan , Grönroos Eva , Pennycuick Adam , Nigro Ersilia , Campbell Brittany B. , Brown William L. , Akarca Ayse U. , Marafioti Teresa , Wu Mary Y. , Howell Michael , Boulton Simon J. , Bertoli Cosetta , Fenton Tim R. , de Bruin Robertus A.M. , Maya-Mendoza Apolinar , Santoni-Rugiu Eric , Hynds Robert E. , Gorgoulis Vassilis G. , Jamal-Hanjani Mariam , McGranahan Nicholas , Harris Reuben S. , Janes Sam M. , Bartkova Jirina , Bakhoum Samuel F. , Bartek Jiri , Kanu Nnennaya , Swanton Charles
Published: April 2023

Abstract
APOBEC3 enzymes are cytosine deaminases implicated in cancer. Precisely when APOBEC3 expression is induced during cancer development remains to be defined. Here we show that specific APOBEC3 genes are upregulated in breast ductal carcinoma in situ, and in preinvasive lung cancer lesions coincident with cellular proliferation. We observe evidence of APOBEC3-mediated subclonal mutagenesis propagated from TRACERx preinvasive to invasive non–small cell lung cancer (NSCLC) lesions. We find that APOBEC3B exacerbates DNA replication stress and chromosomal instability through incomplete replication of genomic DNA, manifested by accumulation of mitotic ultrafine bridges and 53BP1 nuclear bodies in the G1 phase of the cell cycle. Analysis of TRACERx NSCLC clinical samples and mouse lung cancer models revealed APOBEC3B expression driving replication stress and chromosome missegregation. We propose that APOBEC3 is functionally implicated in the onset of chromosomal instability and somatic mutational heterogeneity in preinvasive disease, providing fuel for selection early in cancer evolution.
Significance:
This study reveals the dynamics and drivers of APOBEC3 gene expression in preinvasive disease and the exacerbation of cellular diversity by APOBEC3B through DNA replication stress to promote chromosomal instability early in cancer evolution.

This article is highlighted in the In This Issue feature, p. 2355
Data from An In Vivo CRISPR Screening Platform for Prioritizing Therapeutic Targets in AML
Authors: Lin Shan , Larrue Clément , Scheidegger Nastassja K. , Seong Bo Kyung A. , Dharia Neekesh V. , Kuljanin Miljan , Wechsler Caroline S. , Kugener Guillaume , Robichaud Amanda L. , Conway Amy Saur , Mashaka Thelma , Mouche Sarah , Adane Biniam , Ryan Jeremy A. , Mancias Joseph D. , Younger Scott T. , Piccioni Federica , Lee Lynn H. , Wunderlich Mark , Letai Anthony , Tamburini Jérôme , Stegmaier Kimberly
Published: April 2023

Abstract
CRISPR–Cas9-based genetic screens have successfully identified cell type–dependent liabilities in cancer, including acute myeloid leukemia (AML), a devastating hematologic malignancy with poor overall survival. Because most of these screens have been performed in vitro using established cell lines, evaluating the physiologic relevance of these targets is critical. We have established a CRISPR screening approach using orthotopic xenograft models to validate and prioritize AML-enriched dependencies in vivo, including in CRISPR-competent AML patient-derived xenograft (PDX) models tractable for genome editing. Our integrated pipeline has revealed several targets with translational value, including SLC5A3 as a metabolic vulnerability for AML addicted to exogenous myo-inositol and MARCH5 as a critical guardian to prevent apoptosis in AML. MARCH5 repression enhanced the efficacy of BCL2 inhibitors such as venetoclax, further highlighting the clinical potential of targeting MARCH5 in AML. Our study provides a valuable strategy for discovery and prioritization of new candidate AML therapeutic targets.
Significance:
There is an unmet need to improve the clinical outcome of AML. We developed an integrated in vivo screening approach to prioritize and validate AML dependencies with high translational potential. We identified SLC5A3 as a metabolic vulnerability and MARCH5 as a critical apoptosis regulator in AML, both of which represent novel therapeutic opportunities.

This article is highlighted in the In This Issue feature, p. 275
Data from Characterization of the Genomic and Immunologic Diversity of Malignant Brain Tumors through Multisector Analysis
Authors: Schaettler Maximilian O. , Richters Megan M. , Wang Anthony Z. , Skidmore Zachary L. , Fisk Bryan , Miller Katherine E. , Vickery Tammi L. , Kim Albert H. , Chicoine Michael R. , Osbun Joshua W. , Leuthardt Eric C. , Dowling Joshua L. , Zipfel Gregory J. , Dacey Ralph G. , Lu Hsiang-Chih , Johanns Tanner M. , Griffith Obi L. , Mardis Elaine R. , Griffith Malachi , Dunn Gavin P.
Published: April 2023

Abstract
Despite some success in secondary brain metastases, targeted or immune-based therapies have shown limited efficacy against primary brain malignancies such as glioblastoma (GBM). Although the intratumoral heterogeneity of GBM is implicated in treatment resistance, it remains unclear whether this diversity is observed within brain metastases and to what extent cancer cell–intrinsic heterogeneity sculpts the local immune microenvironment. Here, we profiled the immunogenomic state of 93 spatially distinct regions from 30 malignant brain tumors through whole-exome, RNA, and T-cell receptor sequencing. Our analyses identified differences between primary and secondary malignancies, with gliomas displaying more spatial heterogeneity at the genomic and neoantigen levels. In addition, this spatial diversity was recapitulated in the distribution of T-cell clones in which some gliomas harbored highly expanded but spatially restricted clonotypes. This study defines the immunogenomic landscape across a cohort of malignant brain tumors and contains implications for the design of targeted and immune-based therapies against intracranial malignancies.
Significance:
This study describes the impact of spatial heterogeneity on genomic and immunologic characteristics of gliomas and brain metastases. The results suggest that gliomas harbor significantly greater intratumoral heterogeneity of genomic alterations, neoantigens, and T-cell clones than brain metastases, indicating the importance of multisector analysis for clinical or translational studies.

This article is highlighted in the In This Issue feature, p. 1
Data from Identification and Therapeutic Targeting of GPR20, Selectively Expressed in Gastrointestinal Stromal Tumors, with DS-6157a, a First-in-Class Antibody–Drug Conjugate
Authors: Iida Kenji , Abdelhamid Ahmed Amr H. , Nagatsuma Akiko Kawano , Shibutani Tomoko , Yasuda Satoru , Kitamura Michiko , Hattori Chiharu , Abe Manabu , Hasegawa Jun , Iguchi Takuma , Karibe Tsuyoshi , Nakada Takashi , Inaki Koichiro , Kamei Reiko , Abe Yuki , Nomura Taisei , Andersen Jessica L. , Santagata Sandro , Hemming Matthew L. , George Suzanne , Doi Toshihiko , Ochiai Atsushi , Demetri George D. , Agatsuma Toshinori
Published: April 2023

Abstract
Currently, the only approved treatments for gastrointestinal stromal tumor (GIST) are tyrosine kinase inhibitors (TKI), which eventually lead to the development of secondary resistance mutations in KIT or PDGFRA and disease progression. Herein, we identified G protein–coupled receptor 20 (GPR20) as a novel non–tyrosine kinase target in GIST, developed new GPR20 IHC, and assessed GPR20 expression in cell lines, patient-derived xenografts, and clinical samples from two institutes (United States and Japan). We studied GPR20 expression stratified by treatment line, KIT expression, GIST molecular subtype, and primary tumor location. We produced DS-6157a, an anti-GPR20 antibody–drug conjugate with a novel tetrapeptide-based linker and DNA topoisomerase I inhibitor exatecan derivative (DXd). DS-6157a exhibited GPR20 expression–dependent antitumor activity in GIST xenograft models including a GIST model resistant to imatinib, sunitinib, and regorafenib. Preclinical pharmacokinetics and safety profile of DS-6157a support its clinical development as a potential novel GIST therapy in patients who are refractory or have resistance or intolerance to approved TKIs.
Significance:
GPR20 is selectively expressed in GIST across all treatment lines, regardless of KIT/PDGFRA genotypes. We generated DS-6157a, a DXd-based antibody–drug conjugate that exhibited antitumor activity in GIST models by a different mode of action than currently approved TKIs, showing favorable pharmacokinetics and safety profiles.

This article is highlighted in the In This Issue feature, p. 1307
Data from Live-Cell Imaging Shows Uneven Segregation of Extrachromosomal DNA Elements and Transcriptionally Active Extrachromosomal DNA Hubs in Cancer
Authors: Yi Eunhee , Gujar Amit D. , Guthrie Molly , Kim Hoon , Zhao Dacheng , Johnson Kevin C. , Amin Samirkumar B. , Costa Megan L. , Yu Qianru , Das Sunit , Jillette Nathaniel , Clow Patricia A. , Cheng Albert W. , Verhaak Roel G.W.
Published: April 2023

Abstract
Oncogenic extrachromosomal DNA elements (ecDNA) play an important role in tumor evolution, but our understanding of ecDNA biology is limited. We determined the distribution of single-cell ecDNA copy number across patient tissues and cell line models and observed how cell-to-cell ecDNA frequency varies greatly. The exceptional intratumoral heterogeneity of ecDNA suggested ecDNA-specific replication and propagation mechanisms. To evaluate the transfer of ecDNA genetic material from parental to offspring cells during mitosis, we established the CRISPR-based ecTag method. ecTag leverages ecDNA-specific breakpoint sequences to tag ecDNA with fluorescent markers in living cells. Applying ecTag during mitosis revealed disjointed ecDNA inheritance patterns, enabling rapid ecDNA accumulation in individual cells. After mitosis, ecDNAs clustered into ecDNA hubs, and ecDNA hubs colocalized with RNA polymerase II, promoting transcription of cargo oncogenes. Our observations provide direct evidence for uneven segregation of ecDNA and shed new light on mechanisms through which ecDNAs contribute to oncogenesis.
Significance:
ecDNAs are vehicles for oncogene amplification. The circular nature of ecDNA affords unique properties, such as mobility and ecDNA-specific replication and segregation behavior. We uncovered fundamental ecDNA properties by tracking ecDNAs in live cells, highlighting uneven and random segregation and ecDNA hubs that drive cargo gene transcription.

See related commentary by Henssen, p. 293.

This article is highlighted in the In This Issue feature, p. 275
Data from Early Tumor–Immune Microenvironmental Remodeling and Response to First-Line Fluoropyrimidine and Platinum Chemotherapy in Advanced Gastric Cancer
Authors: Kim Ryul , An Minae , Lee Hyuk , Mehta Arnav , Heo You Jeong , Kim Kyoung-Mee , Lee Song-Yi , Moon Jeonghyeon , Kim Seung Tae , Min Byung-Hoon , Kim Tae Jun , Rha Sun Young , Kang Won Ki , Park Woong-Yang , Klempner Samuel J. , Lee Jeeyun
Published: April 2023

Abstract
Chemotherapy is ubiquitous in first-line treatment of advanced gastric cancer, yet responses are heterogeneous, and little is known about mediators of chemotherapy response. To move forward, an understanding of the effects of standard chemotherapy on the tumor–immune microenvironment (TME) is needed. Coupling whole-exome sequencing, bulk RNA and single-cell transcriptomics from paired pretreatment and on-treatment samples in treatment-naïve patients with HER2-positive and HER2-negative gastric cancer, we define features associated with response to platinum-based chemotherapy. Response was associated with on-treatment TME remodeling including natural killer (NK) cell recruitment, decreased tumor-associated macrophages, M1-macrophage repolarization, and increased effector T-cell infiltration. Among chemotherapy nonresponders, we observed low/absent PD-L1 expression or modulation, on-treatment increases in Wnt signaling, B-cell infiltration, and LAG3-expressing T cells coupled to an exodus of dendritic cells. We did not observe significant genomic changes in early on-treatment sampling. We provide a map of on-treatment TME modulation with standard chemotherapy and nominate candidate future approaches.
Significance:
Using paired pretreatment and on-treatment samples during standard first-line chemotherapy, we identify chemotherapy-induced NK-cell infiltration, macrophage repolarization, and increased antigen presentation among responders. Increased LAG3 expression and decreased dendritic cell abundance were seen in nonresponders, emphasizing remodeling of the TME during chemotherapy response and resistance.

This article is highlighted in the In This Issue feature, p. 873
Data from Vitamin E Enhances Cancer Immunotherapy by Reinvigorating Dendritic Cells via Targeting Checkpoint SHP1
Authors: Yuan Xiangliang , Duan Yimin , Xiao Yi , Sun Kai , Qi Yutao , Zhang Yuan , Ahmed Zamal , Moiani Davide , Yao Jun , Li Hongzhong , Zhang Lin , Yuzhalin Arseniy E. , Li Ping , Zhang Chenyu , Badu-Nkansah Akosua , Saito Yohei , Liu Xianghua , Kuo Wen-Ling , Ying Haoqiang , Sun Shao-Cong , Chang Jenny C. , Tainer John A. , Yu Dihua
Published: April 2023

Abstract
Despite the popular use of dietary supplements during conventional cancer treatments, their impacts on the efficacies of prevalent immunotherapies, including immune-checkpoint therapy (ICT), are unknown. Surprisingly, our analyses of electronic health records revealed that ICT-treated patients with cancer who took vitamin E (VitE) had significantly improved survival. In mouse models, VitE increased ICT antitumor efficacy, which depended on dendritic cells (DC). VitE entered DCs via the SCARB1 receptor and restored tumor-associated DC functionality by directly binding to and inhibiting protein tyrosine phosphatase SHP1, a DC-intrinsic checkpoint. SHP1 inhibition, genetically or by VitE treatment, enhanced tumor antigen cross-presentation by DCs and DC-derived extracellular vesicles (DC-EV), triggering systemic antigen-specific T-cell antitumor immunity. Combining VitE with DC-recruiting cancer vaccines or immunogenic chemotherapies greatly boosted ICT efficacy in animals. Therefore, combining VitE supplement or SHP1-inhibited DCs/DC-EVs with DC-enrichment therapies could substantially augment T-cell antitumor immunity and enhance the efficacy of cancer immunotherapies.
Significance:
The impacts of nutritional supplements on responses to immunotherapies remain unexplored. Our study revealed that dietary vitamin E binds to and inhibits DC checkpoint SHP1 to increase antigen presentation, prime antitumor T-cell immunity, and enhance immunotherapy efficacy. VitE-treated or SHP1-silenced DCs/DC-EVs could be developed as potent immunotherapies.

This article is highlighted in the In This Issue feature, p. 1599
Data from Enhancing PD-L1 Degradation by ITCH during MAPK Inhibitor Therapy Suppresses Acquired Resistance
Authors: Yang Zhentao , Wang Yan , Liu Sixue , Deng Weixian , Lomeli Shirley H. , Moriceau Gatien , Wohlschlegel James , Piva Marco , Lo Roger S.
Published: April 2023

Abstract
MAPK inhibitor (MAPKi) therapy in melanoma leads to the accumulation of tumor-surface PD-L1/L2, which may evade antitumor immunity and accelerate acquired resistance. Here, we discover that the E3 ligase ITCH binds, ubiquitinates, and downregulates tumor-surface PD-L1/L2 in MAPKi-treated human melanoma cells, thereby promoting T-cell activation. During MAPKi therapy in vivo, melanoma cell–intrinsic ITCH knockdown induced tumor-surface PD-L1, reduced intratumoral cytolytic CD8+ T cells, and accelerated acquired resistance only in immune-competent mice. Conversely, tumor cell–intrinsic ITCH overexpression reduced MAPKi-elicited PD-L1 accumulation, augmented intratumoral cytolytic CD8+ T cells, and suppressed acquired resistance in BrafV600MUT, NrasMUT, or Nf1MUT melanoma and KrasMUT-driven cancers. CD8+ T-cell depletion and tumor cell–intrinsic PD-L1 overexpression nullified the phenotype of ITCH overexpression, thereby supporting an in vivo ITCH–PD-L1–T-cell regulatory axis. Moreover, we identify a small-molecular ITCH activator that suppresses acquired MAPKi resistance in vivo. Thus, MAPKi-induced PD-L1 accelerates resistance, and a PD-L1–degrading ITCH activator prolongs antitumor response.
Significance:
MAPKi induces tumor cell–surface PD-L1 accumulation, which promotes immune evasion and therapy resistance. ITCH degrades PD-L1, optimizing antitumor T-cell immunity. We propose degrading tumor cell–surface PD-L1 and/or activating tumor-intrinsic ITCH as strategies to overcome MAPKi resistance.

This article is highlighted in the In This Issue feature, p. 1825
Data from The Spatial Landscape of Progression and Immunoediting in Primary Melanoma at Single-Cell Resolution
Authors: Nirmal Ajit J. , Maliga Zoltan , Vallius Tuulia , Quattrochi Brian , Chen Alyce A. , Jacobson Connor A. , Pelletier Roxanne J. , Yapp Clarence , Arias-Camison Raquel , Chen Yu-An , Lian Christine G. , Murphy George F. , Santagata Sandro , Sorger Peter K.
Published: April 2023

Abstract
Cutaneous melanoma is a highly immunogenic malignancy that is surgically curable at early stages but life-threatening when metastatic. Here we integrate high-plex imaging, 3D high-resolution microscopy, and spatially resolved microregion transcriptomics to study immune evasion and immunoediting in primary melanoma. We find that recurrent cellular neighborhoods involving tumor, immune, and stromal cells change significantly along a progression axis involving precursor states, melanoma in situ, and invasive tumor. Hallmarks of immunosuppression are already detectable in precursor regions. When tumors become locally invasive, a consolidated and spatially restricted suppressive environment forms along the tumor–stromal boundary. This environment is established by cytokine gradients that promote expression of MHC-II and IDO1, and by PD1–PDL1-mediated cell contacts involving macrophages, dendritic cells, and T cells. A few millimeters away, cytotoxic T cells synapse with melanoma cells in fields of tumor regression. Thus, invasion and immunoediting can coexist within a few millimeters of each other in a single specimen.
Significance:
The reorganization of the tumor ecosystem in primary melanoma is an excellent setting in which to study immunoediting and immune evasion. Guided by classic histopathology, spatial profiling of proteins and mRNA reveals recurrent morphologic and molecular features of tumor evolution that involve localized paracrine cytokine signaling and direct cell–cell contact.

This article is highlighted in the In This Issue feature, p. 1397
Data from Single-Cell Atlas of Lineage States, Tumor Microenvironment, and Subtype-Specific Expression Programs in Gastric Cancer
Authors: Kumar Vikrant , Ramnarayanan Kalpana , Sundar Raghav , Padmanabhan Nisha , Srivastava Supriya , Koiwa Mayu , Yasuda Tadahito , Koh Vivien , Huang Kie Kyon , Tay Su Ting , Ho Shamaine Wei Ting , Tan Angie Lay Keng , Ishimoto Takatsugu , Kim Guowei , Shabbir Asim , Chen Qingfeng , Zhang Biyan , Xu Shengli , Lam Kong-Peng , Lum Huey Yew Jeffrey , Teh Ming , Yong Wei Peng , So Jimmy Bok Yan , Tan Patrick
Published: April 2023

Abstract
Gastric cancer heterogeneity represents a barrier to disease management. We generated a comprehensive single-cell atlas of gastric cancer (>200,000 cells) comprising 48 samples from 31 patients across clinical stages and histologic subtypes. We identified 34 distinct cell-lineage states including novel rare cell populations. Many lineage states exhibited distinct cancer-associated expression profiles, individually contributing to a combined tumor-wide molecular collage. We observed increased plasma cell proportions in diffuse-type tumors associated with epithelial-resident KLF2 and stage-wise accrual of cancer-associated fibroblast subpopulations marked by high INHBA and FAP coexpression. Single-cell comparisons between patient-derived organoids (PDO) and primary tumors highlighted inter- and intralineage similarities and differences, demarcating molecular boundaries of PDOs as experimental models. We complemented these findings by spatial transcriptomics, orthogonal validation in independent bulk RNA-sequencing cohorts, and functional demonstration using in vitro and in vivo models. Our results provide a high-resolution molecular resource of intra- and interpatient lineage states across distinct gastric cancer subtypes.
Significance:
We profiled gastric malignancies at single-cell resolution and identified increased plasma cell proportions as a novel feature of diffuse-type tumors. We also uncovered distinct cancer-associated fibroblast subtypes with INHBA–FAP-high cell populations as predictors of poor clinical prognosis. Our findings highlight potential origins of deregulated cell states in the gastric tumor ecosystem.

This article is highlighted in the In This Issue feature, p. 587