bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from CRISPR-GEMM Pooled Mutagenic Screening Identifies KMT2D as a Major Modulator of Immune Checkpoint Blockade
Authors: Wang Guangchuan , Chow Ryan D. , Zhu Lvyun , Bai Zhigang , Ye Lupeng , Zhang Feifei , Renauer Paul A. , Dong Matthew B. , Dai Xiaoyun , Zhang Xiaoya , Du Yaying , Cheng Yujing , Niu Leilei , Chu Zhiyuan , Kim Kristin , Liao Cun , Clark Paul , Errami Youssef , Chen Sidi
Published: March 2024

Abstract
Immune checkpoint blockade (ICB) has shown remarkable clinical efficacy in several cancer types. However, only a fraction of patients will respond to ICB. Here, we performed pooled mutagenic screening with CRISPR-mediated genetically engineered mouse models (CRISPR-GEMM) in ICB settings, and identified KMT2D as a major modulator of ICB response across multiple cancer types. KMT2D encodes a histone H3K4 methyltransferase and is among the most frequently mutated genes in patients with cancer. Kmt2d loss led to increased DNA damage and mutation burden, chromatin remodeling, intron retention, and activation of transposable elements. In addition, Kmt2d-mutant cells exhibited increased protein turnover and IFNγ-stimulated antigen presentation. In turn, Kmt2d-mutant tumors in both mouse and human were characterized by increased immune infiltration. These data demonstrate that Kmt2d deficiency sensitizes tumors to ICB by augmenting tumor immunogenicity, and also highlight the power of CRISPR-GEMMs for interrogating complex molecular landscapes in immunotherapeutic contexts that preserve the native tumor microenvironment.
Significance:
ICB is ineffective in the majority of patients. Through direct in vivo CRISPR mutagenesis screening in GEMMs of cancer, we find Kmt2d deficiency sensitizes tumors to ICB. Considering the prevalence of KMT2D mutations, this finding potentially has broad implications for patient stratification and clinical decision-making.

This article is highlighted in the In This Issue feature, p. 1775
Data from Triplet Therapy with Palbociclib, Taselisib, and Fulvestrant in PIK3CA-Mutant Breast Cancer and Doublet Palbociclib and Taselisib in Pathway-Mutant Solid Cancers
Authors: Pascual Javier , Lim Joline S.J. , Macpherson Iain R. , Armstrong Anne C. , Ring Alistair , Okines Alicia F.C. , Cutts Rosalind J. , Herrera-Abreu Maria Teresa , Garcia-Murillas Isaac , Pearson Alex , Hrebien Sarah , Gevensleben Heidrun , Proszek Paula Z. , Hubank Michael , Hills Margaret , King Jenny , Parmar Mona , Prout Toby , Finneran Laura , Malia Jason , Swales Karen E. , Ruddle Ruth , Raynaud Florence I. , Turner Alison , Hall Emma , Yap Timothy A. , Lopez Juanita S. , Turner Nicholas C.
Published: March 2024

Abstract
Cyclin-dependent kinase 4/6 (CDK4/6) and PI3K inhibitors synergize in PIK3CA-mutant ER-positive HER2-negative breast cancer models. We conducted a phase Ib trial investigating the safety and efficacy of doublet CDK4/6 inhibitor palbociclib plus selective PI3K inhibitor taselisib in advanced solid tumors, and triplet palbociclib plus taselisib plus fulvestrant in 25 patients with PIK3CA-mutant, ER-positive HER2-negative advanced breast cancer. The triplet therapy response rate in PIK3CA-mutant, ER-positive HER2-negative cancer was 37.5% [95% confidence interval (CI), 18.8–59.4]. Durable disease control was observed in PIK3CA-mutant ER-negative breast cancer and other solid tumors with doublet therapy. Both combinations were well tolerated at pharmacodynamically active doses. In the triplet group, high baseline cyclin E1 expression associated with shorter progression-free survival (PFS; HR = 4.2; 95% CI, 1.3–13.1; P = 0.02). Early circulating tumor DNA (ctDNA) dynamics demonstrated high on-treatment ctDNA association with shorter PFS (HR = 5.2; 95% CI, 1.4–19.4; P = 0.04). Longitudinal plasma ctDNA sequencing provided genomic evolution evidence during triplet therapy.
SIGNIFICANCE:
The triplet of palbociclib, taselisib, and fulvestrant has promising efficacy in patients with heavily pretreated PIK3CA-mutant ER-positive HER2-negative advanced breast cancer. A subset of patients with PIK3CA-mutant triple-negative breast cancer derived clinical benefit from palbociclib and taselisib doublet, suggesting a potential nonchemotherapy targeted approach for this population.

This article is highlighted in the In This Issue feature, p. 1
Data from Overcoming Genetically Based Resistance Mechanisms to PD-1 Blockade
Authors: Torrejon Davis Y. , Abril-Rodriguez Gabriel , Champhekar Ameya S. , Tsoi Jennifer , Campbell Katie M. , Kalbasi Anusha , Parisi Giulia , Zaretsky Jesse M. , Garcia-Diaz Angel , Puig-Saus Cristina , Cheung-Lau Gardenia , Wohlwender Thomas , Krystofinski Paige , Vega-Crespo Agustin , Lee Christopher M. , Mascaro Pau , Grasso Catherine S. , Berent-Maoz Beata , Comin-Anduix Begoña , Hu-Lieskovan Siwen , Ribas Antoni
Published: March 2024

Abstract
Mechanism-based strategies to overcome resistance to PD-1 blockade therapy are urgently needed. We developed genetic acquired resistant models of JAK1, JAK2, and B2M loss-of-function mutations by gene knockout in human and murine cell lines. Human melanoma cell lines with JAK1/2 knockout became insensitive to IFN-induced antitumor effects, while B2M knockout was no longer recognized by antigen-specific T cells and hence was resistant to cytotoxicity. All of these mutations led to resistance to anti–PD-1 therapy in vivo. JAK1/2-knockout resistance could be overcome with the activation of innate and adaptive immunity by intratumoral Toll-like receptor 9 agonist administration together with anti–PD-1, mediated by natural killer (NK) and CD8 T cells. B2M-knockout resistance could be overcome by NK-cell and CD4 T-cell activation using the CD122 preferential IL2 agonist bempegaldesleukin. Therefore, mechanistically designed combination therapies can overcome genetic resistance to PD-1 blockade therapy.
Significance:
The activation of IFN signaling through pattern recognition receptors and the stimulation of NK cells overcome genetic mechanisms of resistance to PD-1 blockade therapy mediated through deficient IFN receptor and antigen presentation pathways. These approaches are being tested in the clinic to improve the antitumor activity of PD-1 blockade therapy.

This article is highlighted in the In This Issue feature, p. 1079
Data from Harnessing CAR T-cell Insights to Develop Treatments for Hyperinflammatory Responses in Patients with COVID-19
Authors: Agarwal Sangya , June Carl H.
Published: March 2024

AbstractSummary:
Cytokine release and macrophage activation contribute to immunopathology after SARS-CoV-2 infection. We discuss approaches to decrease the morbidity and mortality in patients with COVID-19 by repurposing existing drugs previously developed for cancer therapy.
Data from Genetic Ancestry Contributes to Somatic Mutations in Lung Cancers from Admixed Latin American Populations
Authors: Carrot-Zhang Jian , Soca-Chafre Giovanny , Patterson Nick , Thorner Aaron R. , Nag Anwesha , Watson Jacqueline , Genovese Giulio , Rodriguez July , Gelbard Maya K. , Corrales-Rodriguez Luis , Mitsuishi Yoichiro , Ha Gavin , Campbell Joshua D. , Oxnard Geoffrey R. , Arrieta Oscar , Cardona Andres F. , Gusev Alexander , Meyerson Matthew
Published: March 2024

Abstract
Inherited lung cancer risk, particularly in nonsmokers, is poorly understood. Genomic and ancestry analysis of 1,153 lung cancers from Latin America revealed striking associations between Native American ancestry and their somatic landscape, including tumor mutational burden, and specific driver mutations in EGFR, KRAS, and STK11. A local Native American ancestry risk score was more strongly correlated with EGFR mutation frequency compared with global ancestry correlation, suggesting that germline genetics (rather than environmental exposure) underlie these disparities.
Significance:
The frequency of somatic EGFR and KRAS mutations in lung cancer varies by ethnicity, but we do not understand why. Our study suggests that the variation in EGFR and KRAS mutation frequency is associated with genetic ancestry and suggests further studies to identify germline alleles that underpin this association.

See related commentary by Gomez et al., p. 534.

This article is highlighted in the In This Issue feature, p. 521
Data from Deep Learning to Estimate RECIST in Patients with NSCLC Treated with PD-1 Blockade
Authors: Arbour Kathryn C. , Luu Anh Tuan , Luo Jia , Rizvi Hira , Plodkowski Andrew J. , Sakhi Mustafa , Huang Kevin B. , Digumarthy Subba R. , Ginsberg Michelle S. , Girshman Jeffrey , Kris Mark G. , Riely Gregory J. , Yala Adam , Gainor Justin F. , Barzilay Regina , Hellmann Matthew D.
Published: March 2024

Abstract
Real-world evidence (RWE), conclusions derived from analysis of patients not treated in clinical trials, is increasingly recognized as an opportunity for discovery, to reduce disparities, and to contribute to regulatory approval. Maximal value of RWE may be facilitated through machine-learning techniques to integrate and interrogate large and otherwise underutilized datasets. In cancer research, an ongoing challenge for RWE is the lack of reliable, reproducible, scalable assessment of treatment-specific outcomes. We hypothesized a deep-learning model could be trained to use radiology text reports to estimate gold-standard RECIST-defined outcomes. Using text reports from patients with non–small cell lung cancer treated with PD-1 blockade in a training cohort and two test cohorts, we developed a deep-learning model to accurately estimate best overall response and progression-free survival. Our model may be a tool to determine outcomes at scale, enabling analyses of large clinical databases.
Significance:
We developed and validated a deep-learning model trained on radiology text reports to estimate gold-standard objective response categories used in clinical trial assessments. This tool may facilitate analysis of large real-world oncology datasets using objective outcome metrics determined more reliably and at greater scale than currently possible.

This article is highlighted in the In This Issue feature, p. 1
Data from The Hepatic Microenvironment Uniquely Protects Leukemia Cells through Induction of Growth and Survival Pathways Mediated by LIPG
Authors: Ye Haobin , Minhajuddin Mohammad , Krug Anna , Pei Shanshan , Chou Chih-Hsing , Culp-Hill Rachel , Ponder Jessica , De Bloois Erik , Schniedewind Björn , Amaya Maria L. , Inguva Anagha , Stevens Brett M. , Pollyea Daniel A. , Christians Uwe , Grimes H. Leighton , D'Alessandro Angelo , Jordan Craig T.
Published: March 2024

Abstract
Due to the disseminated nature of leukemia, malignant cells are exposed to many different tissue microenvironments, including a variety of extramedullary sites. In the present study, we demonstrate that leukemic cells residing in the liver display unique biological properties and also contribute to systemic changes that influence physiologic responses to chemotherapy. Specifically, the liver microenvironment induces metabolic adaptations via upregulating expression of endothelial lipase in leukemia cells, which not only stimulates tumor cell proliferation through polyunsaturated fatty acid–mediated pathways, but also promotes survival by stabilizing antiapoptotic proteins. Additionally, hepatic infiltration and tissue damage caused by malignant cells induces release of liver-derived enzymes capable of degrading chemotherapy drugs, an event that further protects leukemia cells from conventional therapies. Together, these studies demonstrate a unique role for liver in modulating the pathogenesis of leukemic disease and suggest that the hepatic microenvironment may protect leukemia cells from chemotherapeutic challenge.
Significance:
The studies presented herein demonstrate that the liver provides a microenvironment in which leukemia cells acquire unique metabolic properties. The adaptations that occur in the liver confer increased resistance to chemotherapy. Therefore, we propose that therapies designed to overcome liver-specific metabolic changes will yield improved outcomes for patients with leukemia.

This article is highlighted in the In This Issue feature, p. 211
Data from Utilization of COVID-19 Treatments and Clinical Outcomes among Patients with Cancer: A COVID-19 and Cancer Consortium (CCC19) Cohort Study
Authors: Rivera Donna R. , Peters Solange , Panagiotou Orestis A. , Shah Dimpy P. , Kuderer Nicole M. , Hsu Chih-Yuan , Rubinstein Samuel M. , Lee Brendan J. , Choueiri Toni K. , de Lima Lopes Gilberto , Grivas Petros , Painter Corrie A. , Rini Brian I. , Thompson Michael A. , Arcobello Jonathan , Bakouny Ziad , Doroshow Deborah B. , Egan Pamela C. , Farmakiotis Dimitrios , Fecher Leslie A. , Friese Christopher R. , Galsky Matthew D. , Goel Sanjay , Gupta Shilpa , Halfdanarson Thorvardur R. , Halmos Balazs , Hawley Jessica E. , Khaki Ali Raza , Lemmon Christopher A. , Mishra Sanjay , Olszewski Adam J. , Pennell Nathan A. , Puc Matthew M. , Revankar Sanjay G. , Schapira Lidia , Schmidt Andrew , Schwartz Gary K. , Shah Sumit A. , Wu Julie T. , Xie Zhuoer , Yeh Albert C. , Zhu Huili , Shyr Yu , Lyman Gary H. , Warner Jeremy L.
Published: March 2024

Abstract
Among 2,186 U.S. adults with invasive cancer and laboratory-confirmed SARS-CoV-2 infection, we examined the association of COVID-19 treatments with 30-day all-cause mortality and factors associated with treatment. Logistic regression with multiple adjustments (e.g., comorbidities, cancer status, baseline COVID-19 severity) was performed. Hydroxychloroquine with any other drug was associated with increased mortality versus treatment with any COVID-19 treatment other than hydroxychloroquine or untreated controls; this association was not present with hydroxychloroquine alone. Remdesivir had numerically reduced mortality versus untreated controls that did not reach statistical significance. Baseline COVID-19 severity was strongly associated with receipt of any treatment. Black patients were approximately half as likely to receive remdesivir as white patients. Although observational studies can be limited by potential unmeasured confounding, our findings add to the emerging understanding of patterns of care for patients with cancer and COVID-19 and support evaluation of emerging treatments through inclusive prospective controlled trials.
Significance:
Evaluating the potential role of COVID-19 treatments in patients with cancer in a large observational study, there was no statistically significant 30-day all-cause mortality benefit with hydroxychloroquine or high-dose corticosteroids alone or in combination; remdesivir showed potential benefit. Treatment receipt reflects clinical decision-making and suggests disparities in medication access.

This article is highlighted in the In This Issue feature, p. 1426
Data from Infiltrating Myeloid Cells Drive Osteosarcoma Progression via GRM4 Regulation of IL23
Authors: Kansara Maya , Thomson Kristian , Pang Puiyi , Dutour Aurelie , Mirabello Lisa , Acher Francine , Pin Jean-Philippe , Demicco Elizabeth G. , Yan Juming , Teng Michele W.L. , Smyth Mark J. , Thomas David M.
Published: March 2024

Abstract
The glutamate metabotropic receptor 4 (GRM4) locus is linked to susceptibility to human osteosarcoma, through unknown mechanisms. We show that Grm4−/− gene–targeted mice demonstrate accelerated radiation-induced tumor development to an extent comparable with Rb1+/− mice. GRM4 is expressed in myeloid cells, selectively regulating expression of IL23 and the related cytokine IL12. Osteosarcoma-conditioned media induce myeloid cell Il23 expression in a GRM4-dependent fashion, while suppressing the related cytokine Il12. Both human and mouse osteosarcomas express an increased IL23:IL12 ratio, whereas higher IL23 expression is associated with worse survival in humans. Consistent with an oncogenic role, Il23−/− mice are strikingly resistant to osteosarcoma development. Agonists of GRM4 or a neutralizing antibody to IL23 suppressed osteosarcoma growth in mice. These findings identify a novel, druggable myeloid suppressor pathway linking GRM4 to the proinflammatory IL23/IL12 axis.
Significance:
Few novel systemic therapies targeting osteosarcoma have emerged in the last four decades. Using insights gained from a genome-wide association study and mouse modeling, we show that GRM4 plays a role in driving osteosarcoma via a non–cell-autonomous mechanism regulating IL23, opening new avenues for therapeutic intervention.

See related commentary by Jones, p. 1484.

This article is highlighted in the In This Issue feature, p. 1469
Data from TRK xDFG Mutations Trigger a Sensitivity Switch from Type I to II Kinase Inhibitors
Authors: Cocco Emiliano , Lee Ji Eun , Kannan Srinivasaraghavan , Schram Alison M. , Won Helen H. , Shifman Sophie , Kulick Amanda , Baldino Laura , Toska Eneda , Arruabarrena-Aristorena Amaia , Kittane Srushti , Wu Fan , Cai Yanyan , Arena Sabrina , Mussolin Benedetta , Kannan Ram , Vasan Neil , Gorelick Alexander N. , Berger Michael F. , Novoplansky Ofra , Jagadeeshan Sankar , Liao Yi , Rix Uwe , Misale Sandra , Taylor Barry S. , Bardelli Alberto , Hechtman Jaclyn F. , Hyman David M. , Elkabets Moshe , de Stanchina Elisa , Verma Chandra S. , Ventura Andrea , Drilon Alexander , Scaltriti Maurizio
Published: March 2024

Abstract
On-target resistance to next-generation TRK inhibitors in TRK fusion–positive cancers is largely uncharacterized. In patients with these tumors, we found that TRK xDFG mutations confer resistance to type I next-generation TRK inhibitors designed to maintain potency against several kinase domain mutations. Computational modeling and biochemical assays showed that TRKAG667 and TRKCG696 xDFG substitutions reduce drug binding by generating steric hindrance. Concurrently, these mutations stabilize the inactive (DFG-out) conformations of the kinases, thus sensitizing these kinases to type II TRK inhibitors. Consistently, type II inhibitors impede the growth and TRK-mediated signaling of xDFG-mutant isogenic and patient-derived models. Collectively, these data demonstrate that adaptive conformational resistance can be abrogated by shifting kinase engagement modes. Given the prior identification of paralogous xDFG resistance mutations in other oncogene-addicted cancers, these findings provide insights into rational type II drug design by leveraging inhibitor class affinity switching to address recalcitrant resistant alterations.
Significance:
In TRK fusion–positive cancers, TRK xDFG substitutions represent a shared liability for type I TRK inhibitors. In contrast, they represent a potential biomarker of type II TRK inhibitor activity. As all currently available type II agents are multikinase inhibitors, rational drug design should focus on selective type II inhibitor creation.

This article is highlighted in the In This Issue feature, p. 1
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: March 2024

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 Mechanisms of Lymphoma Clearance Induced by High-Dose Alkylating Agents
Authors: Lossos Chen , Liu Yunpeng , Kolb Kellie E. , Christie Amanda L. , Van Scoyk Alexandria , Prakadan Sanjay M. , Shigemori Kay , Stevenson Kristen E. , Morrow Sara , Plana Olivia D. , Fraser Cameron , Jones Kristen L. , Liu Huiyun , Pallasch Christian P. , Modiste Rebecca , Nguyen Quang-De , Craig Jeffrey W. , Morgan Elizabeth A. , Vega Francisco , Aster Jon C. , Sarosiek Kristopher A. , Shalek Alex K. , Hemann Michael T. , Weinstock David M.
Published: March 2024

Abstract
The extraordinary activity of high-dose cyclophosphamide against some high-grade lymphomas was described nearly 60 years ago. Here we address mechanisms that mediate cyclophosphamide activity in bona fide human double-hit lymphoma. We show that antibody resistance within the bone marrow (BM) is not present upon early engraftment but develops during lymphoma progression. This resistance required a high tumor:macrophage ratio, was recapitulated in spleen by partial macrophage depletion, and was overcome by multiple, high-dose alkylating agents. Cyclophosphamide induced endoplasmic reticulum (ER) stress in BM-resident lymphoma cells in vivo that resulted in ATF4-mediated paracrine secretion of VEGFA, massive macrophage infiltration, and clearance of alemtuzumab-opsonized cells. BM macrophages isolated after cyclophosphamide treatment had increased phagocytic capacity that was reversed by VEGFA blockade or SYK inhibition. Single-cell RNA sequencing of these macrophages identified a “super-phagocytic” subset that expressed CD36/FCGR4. Together, these findings define a novel mechanism through which high-dose alkylating agents promote macrophage-dependent lymphoma clearance.
Significance:
mAbs are effective against only a small subset of cancers. Herein, we recapitulate compartment-specific antibody resistance and define an ER stress–dependent mechanism induced by high-dose alkylating agents that promotes phagocytosis of opsonized tumor cells. This approach induces synergistic effects with mAbs and merits testing across additional tumor types.

See related commentary by Duval and De Palma, p. 834.

This article is highlighted in the In This Issue feature, p. 813
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: March 2024

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 A Procarcinogenic Colon Microbe Promotes Breast Tumorigenesis and Metastatic Progression and Concomitantly Activates Notch and β-Catenin Axes
Authors: Parida Sheetal , Wu Shaoguang , Siddharth Sumit , Wang Guannan , Muniraj Nethaji , Nagalingam Arumugam , Hum Christina , Mistriotis Panagiotis , Hao Haiping , Talbot C. Conover , Konstantopoulos Konstantinos , Gabrielson Kathleen L. , Sears Cynthia L. , Sharma Dipali
Published: March 2024

Abstract
The existence of distinct breast microbiota has been recently established, but their biological impact in breast cancer remains elusive. Focusing on the shift in microbial community composition in diseased breast compared with normal breast, we identified the presence of Bacteroides fragilis in cancerous breast. Mammary gland as well as gut colonization with enterotoxigenic Bacteroides fragilis (ETBF), which secretes B. fragilis toxin (BFT), rapidly induces epithelial hyperplasia in the mammary gland. Breast cancer cells exposed to BFT exhibit “BFT memory” from the initial exposure. Intriguingly, gut or breast duct colonization with ETBF strongly induces growth and metastatic progression of tumor cells implanted in mammary ducts, in contrast to nontoxigenic Bacteroides fragilis. This work sheds light on the oncogenic impact of a procarcinogenic colon bacterium ETBF on breast cancer progression, implicates the β-catenin and Notch1 axis as its functional mediators, and proposes the concept of “BFT memory” that can have far-reaching biological implications after initial exposure to ETBF.
Significance:
B. fragilis is an inhabitant of breast tissue, and gut or mammary duct colonization with ETBF triggers epithelial hyperplasia and augments breast cancer growth and metastasis. Short-term exposure to BFT elicits a “BFT memory” with long-term implications, functionally mediated by the β-catenin and Notch1 pathways.

This article is highlighted in the In This Issue feature, p. 995
Data from Preexisting and Post–COVID-19 Immune Responses to SARS-CoV-2 in Patients with Cancer
Authors: Bilich Tatjana , Roerden Malte , Maringer Yacine , Nelde Annika , Heitmann Jonas S. , Dubbelaar Marissa L. , Peter Andreas , Hörber Sebastian , Bauer Jens , Rieth Jonas , Wacker Marcel , Berner Fiamma , Flatz Lukas , Held Stefanie , Brossart Peter , Märklin Melanie , Wagner Philipp , Erne Eva , Klein Reinhild , Rammensee Hans-Georg , Salih Helmut R. , Walz Juliane S.
Published: March 2024

Abstract
Patients with cancer, in particular patients with hematologic malignancies, are at increased risk for critical illness upon COVID-19. We here assessed antibody as well as CD4+ and CD8+ T-cell responses in unexposed and SARS-CoV-2–infected patients with cancer to characterize SARS-CoV-2 immunity and to identify immunologic parameters contributing to COVID-19 outcome. Unexposed patients with hematologic malignancies presented with reduced prevalence of preexisting SARS-CoV-2 cross-reactive CD4+ T-cell responses and signs of T-cell exhaustion compared with patients with solid tumors and healthy volunteers. Whereas SARS-CoV-2 antibody responses did not differ between patients with COVID-19 and cancer and healthy volunteers, intensity, expandability, and diversity of SARS-CoV-2 T-cell responses were profoundly reduced in patients with cancer, and the latter associated with a severe course of COVID-19. This identifies impaired SARS-CoV-2 T-cell immunity as a potential determinant for dismal outcome of COVID-19 in patients with cancer.
Significance:
This first comprehensive analysis of SARS-CoV-2 immune responses in patients with cancer reports on the potential implications of impaired SARS-CoV-2 T-cell responses for understanding pathophysiology and predicting severity of COVID-19, which in turn might allow for the development of therapeutic measures and vaccines for this vulnerable patient population.

See related commentary by Salomé and Horowitz, p. 1877.

This article is highlighted in the In This Issue feature, p. 1861
Data from Splicing Patterns in SF3B1-Mutated Uveal Melanoma Generate Shared Immunogenic Tumor-Specific Neoepitopes
Authors: Bigot Jeremy , Lalanne Ana I. , Lucibello Francesca , Gueguen Paul , Houy Alexandre , Dayot Stephane , Ganier Olivier , Gilet Jules , Tosello Jimena , Nemati Fariba , Pierron Gaelle , Waterfall Joshua J. , Barnhill Raymond , Gardrat Sophie , Piperno-Neumann Sophie , Popova Tatiana , Masson Vanessa , Loew Damarys , Mariani Pascale , Cassoux Nathalie , Amigorena Sebastian , Rodrigues Manuel , Alsafadi Samar , Stern Marc-Henri , Lantz Olivier
Published: March 2024

Abstract
Disruption of splicing patterns due to mutations of genes coding splicing factors in tumors represents a potential source of tumor neoantigens, which would be both public (shared between patients) and tumor-specific (not expressed in normal tissues). In this study, we show that mutations of the splicing factor SF3B1 in uveal melanoma generate such immunogenic neoantigens. Memory CD8+ T cells specific for these neoantigens are preferentially found in 20% of patients with uveal melanoma bearing SF3B1-mutated tumors. Single-cell analyses of neoepitope-specific T cells from the blood identified large clonal T-cell expansions, with distinct effector transcription patterns. Some of these expanded T-cell receptors are also present in the corresponding tumors. CD8+ T-cell clones specific for the neoepitopes specifically recognize and kill SF3B1-mutated tumor cells, supporting the use of this new family of neoantigens as therapeutic targets.
Significance:
Mutations of the splicing factor SF3B1 in uveal melanoma generate shared neoantigens that are uniquely expressed by tumor cells, leading to recognition and killing by specific CD8 T cells. Mutations in splicing factors can be sources of new therapeutic strategies applicable to diverse tumors.

This article is highlighted in the In This Issue feature, p. 1861
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: March 2024

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 Genomic and Transcriptomic Analyses of Breast Cancer Primaries and Matched Metastases in AURORA, the Breast International Group (BIG) Molecular Screening Initiative
Authors: Aftimos Philippe , Oliveira Mafalda , Irrthum Alexandre , Fumagalli Debora , Sotiriou Christos , Gal-Yam Einav Nili , Robson Mark E. , Ndozeng Justin , Di Leo Angelo , Ciruelos Eva M. , de Azambuja Evandro , Viale Giuseppe , Scheepers Elsemieke D. , Curigliano Giuseppe , Bliss Judith M. , Reis-Filho Jorge S. , Colleoni Marco , Balic Marija , Cardoso Fatima , Albanell Joan , Duhem Caroline , Marreaud Sandrine , Romagnoli Dario , Rojas Beatriz , Gombos Andrea , Wildiers Hans , Guerrero-Zotano Angel , Hall Peter , Bonetti Andrea , Larsson Karolina Fs , Degiorgis Martina , Khodaverdi Silvia , Greil Richard , Sverrisdóttir Ásgerdur , Paoli Marta , Seyll Ethel , Loibl Sibylle , Linderholm Barbro , Zoppoli Gabriele , Davidson Nancy E. , Johannsson Oskar Th , Bedard Philippe L. , Loi Sherene , Knox Susan , Cameron David A. , Harbeck Nadia , Montoya Maite Lasa , Brandão Mariana , Vingiani Andrea , Caballero Carmela , Hilbers Florentine S. , Yates Lucy R. , Benelli Matteo , Venet David , Piccart Martine J.
Published: March 2024

Abstract
AURORA aims to study the processes of relapse in metastatic breast cancer (MBC) by performing multi-omics profiling on paired primary tumors and early-course metastases. Among 381 patients (primary tumor and metastasis pairs: 252 targeted gene sequencing, 152 RNA sequencing, 67 single nucleotide polymorphism arrays), we found a driver role for GATA1 and MEN1 somatic mutations. Metastases were enriched in ESR1, PTEN, CDH1, PIK3CA, and RB1 mutations; MDM4 and MYC amplifications; and ARID1A deletions. An increase in clonality was observed in driver genes such as ERBB2 and RB1. Intrinsic subtype switching occurred in 36% of cases. Luminal A/B to HER2-enriched switching was associated with TP53 and/or PIK3CA mutations. Metastases had lower immune score and increased immune-permissive cells. High tumor mutational burden correlated to shorter time to relapse in HR+/HER2− cancers. ESCAT tier I/II alterations were detected in 51% of patients and matched therapy was used in 7%. Integration of multi-omics analyses in clinical practice could affect treatment strategies in MBC.
Significance:
The AURORA program, through the genomic and transcriptomic analyses of matched primary and metastatic samples from 381 patients with breast cancer, coupled with prospectively collected clinical data, identified genomic alterations enriched in metastases and prognostic biomarkers. ESCAT tier I/II alterations were detected in more than half of the patients.

This article is highlighted in the In This Issue feature, p. 2659
Data from TNIK Is a Therapeutic Target in Lung Squamous Cell Carcinoma and Regulates FAK Activation through Merlin
Authors: Torres-Ayuso Pedro , An Elvira , Nyswaner Katherine M. , Bensen Ryan C. , Ritt Daniel A. , Specht Suzanne I. , Das Sudipto , Andresson Thorkell , Cachau Raul E. , Liang Roger J. , Ries Amy L. , Robinson Christina M. , Difilippantonio Simone , Gouker Brad , Bassel Laura , Karim Baktiar O. , Miller Chad J. , Turk Benjamin E. , Morrison Deborah K. , Brognard John
Published: March 2024

Abstract
Lung squamous cell carcinoma (LSCC) is the second most prevalent type of lung cancer. Despite extensive genomic characterization, no targeted therapies are approved for the treatment of LSCC. Distal amplification of the 3q chromosome is the most frequent genomic alteration in LSCC, and there is an urgent need to identify efficacious druggable targets within this amplicon. We identify the protein kinase TNIK as a therapeutic target in LSCC. TNIK is amplified in approximately 50% of LSCC cases. TNIK genetic depletion or pharmacologic inhibition reduces the growth of LSCC cells in vitro and in vivo. In addition, TNIK inhibition showed antitumor activity and increased apoptosis in established LSCC patient-derived xenografts. Mechanistically, we identified the tumor suppressor Merlin/NF2 as a novel TNIK substrate and showed that TNIK and Merlin are required for the activation of focal adhesion kinase. In conclusion, our data identify targeting TNIK as a potential therapeutic strategy in LSCC.
Significance:
Targeted therapies have not yet been approved for the treatment of LSCC, due to lack of identification of actionable cancer drivers. We define TNIK catalytic activity as essential for maintaining LSCC viability and validate the antitumor efficacy of TNIK inhibition in preclinical models of LSCC.

This article is highlighted in the In This Issue feature, p. 1307
Data from Cross-Talk between Myeloid-Derived Suppressor Cells and Mast Cells Mediates Tumor-Specific Immunosuppression in Prostate Cancer
Authors: Jachetti Elena , Cancila Valeria , Rigoni Alice , Bongiovanni Lucia , Cappetti Barbara , Belmonte Beatrice , Enriquez Claudia , Casalini Patrizia , Ostano Paola , Frossi Barbara , Sangaletti Sabina , Chiodoni Claudia , Chiorino Giovanna , Pucillo Carlo E. , Tripodo Claudio , Colombo Mario P.
Published: March 2024

Abstract
Immunotherapy, including the use of checkpoint inhibitors, is a potent therapeutic approach for some cancers, but has limited success with prostate tumors, in which immune suppression is instigated by the tumor. The immunosuppressive capacity of mast cells, which promote adenocarcinoma development in the prostate, prompted our investigation on whether mast cells promote tolerance to SV40 Large-T antigen, the transforming oncogene in transgenic adenocarcinoma of the mouse prostate (TRAMP) mice. The incidence of adenocarcinoma was reduced in the offspring of a cross between TRAMP mice and mast cell–deficient KitWsh mice. TRAMP mice are tolerant to the SV40 Large T antigen, which is otherwise immunogenic in normal syngeneic B6 mice. Genetic ablation of mast cells in TRAMP mice restored their ability to mount a tumor-specific cytotoxic T-cell response. In KitWsh-TRAMP mice, the restored T-cell immunity correlated with the reduced activity of polymorphonuclear myeloid-derived suppressor cells (PMN-MDSC), along with their reduced expression of Arg1, Nos2, and Stat3. Having found that CD40L-expressing mast cells can interact in vivo with CD40-expressing PMN-MDSC, we then determined that only KitWsh-TRAMP mice reconstituted with mast cells expressing CD40L could restore PMN-MDSCs suppressive functions, T-cell unresponsiveness and adenocarcinoma development. Thus, mast cells have an immunoregulatory effect on PMN-MDSCs activity through CD40L-CD40 interaction, favoring immunosuppression and tumor onset. In prostate cancer patients, in silico analyses correlated poor clinical outcomes with high expression of genes related to mast cells and PMN-MDSCs. Cancer Immunol Res; 6(5); 552–65. ©2018 AACR.
Data from Treg Depletion Licenses T Cell–Driven HEV Neogenesis and Promotes Tumor Destruction
Authors: Colbeck Emily J. , Jones Emma , Hindley James P. , Smart Kathryn , Schulz Ralph , Browne Molly , Cutting Scott , Williams Anwen , Parry Lee , Godkin Andrew , Ware Carl F. , Ager Ann , Gallimore Awen
Published: March 2024

Abstract
T-cell infiltration into tumors represents a critical bottleneck for immune-mediated control of cancer. We previously showed that this bottleneck can be overcome by depleting immunosuppressive Foxp3+ regulatory T cells (Tregs), a process that can increase frequencies of tumor-infiltrating lymphocytes through promoting the development of specialized portals for lymphocyte entry, namely high endothelial venules (HEVs). In this paper, we used a carcinogen-induced tumor model that allows for coevolution of the tumor microenvironment and the immune response to demonstrate that Treg depletion not only results in widespread disruption to HEV networks in lymph nodes (LNs) but also activates CD8+ T cells, which then drive intratumoral HEV development. Formation of these vessels contrasts with ontogenic HEV development in LNs in that the process is dependent on the TNF receptor and independent of lymphotoxin β receptor–mediated signaling. These intratumoral HEVs do not express the chemokine CCL21, revealing a previously undescribed intratumoral blood vessel phenotype. We propose a model where Treg depletion enables a self-amplifying loop of T-cell activation, which promotes HEV development, T-cell infiltration, and ultimately, tumor destruction. The findings point to a need to test for HEV development as part of ongoing clinical studies in patients with cancer. Cancer Immunol Res; 5(11); 1005–15. ©2017 AACR.
Data from Urinary Bladder Cancer Tregs Suppress MMP2 and Potentially Regulate Invasiveness
Authors: Winerdal Malin E. , Krantz David , Hartana Ciputra A. , Zirakzadeh Ali A. , Linton Ludvig , Bergman Emma A. , Rosenblatt Robert , Vasko Janos , Alamdari Farhood , Hansson Johan , Holmström Benny , Johansson Markus , Winerdal Max , Marits Per , Sherif Amir , Winqvist Ola
Published: March 2024

Abstract
Regulatory T cells (Treg) have long been considered one-sided suppressors of antitumor immune responses and hence associated with poor patient outcome in cancer. However, evidence is mounting of a paradoxical positive prognostic effect of Tregs on certain malignancies, including urinary bladder cancer (UBC). This discrepancy has partly been attributed to the shear misidentification of Tregs, but also to the inflammatory profile of the tumor. Our aim was to determine whether tumor-infiltrating Forkhead box P3+ (FOXP3+) cells confer a stable Treg phenotype and to investigate putative beneficial Treg functions, focusing on tumor-promoting inflammatory pathways in UBC. Patients (n = 52) with suspected UBC were prospectively included. We show, by using a broad range of analytical approaches, that tumor-infiltrating CD4+FOXP3+ T cells in UBC phenotypically, functionally, and epigenetically represent a true Treg population. At the invasive front of UBC tumors, we found an inverse relationship between Treg frequency and expression of matrix metalloproteinase 2 (MMP2), a key proinvasive factor induced by tumor-promoting inflammation. Correspondingly, a significant, dose-dependent Treg-mediated downregulation of MMP2 protein and mRNA expression was observed in both macrophages and UBC cells. Also, we found that Treg frequency specifically at the invasive front positively correlated with survival. Thus, we identify Treg-mediated suppression of MMP2 in the tumor microenvironment as a mechanism explaining the paradoxical positive prognostic impact of tumor-infiltrating Tregs in UBC. Cancer Immunol Res; 6(5); 528–38. ©2018 AACR.
Data from Baseline Cytokine Profiles of Tuberculin-Specific CD4+ T Cells in Non–Muscle-Invasive Bladder Cancer May Predict Outcomes of BCG Immunotherapy
Authors: Jallad Samer , Thomas Philip , Newport Melanie J. , Kern Florian
Published: March 2024

Abstract
Intravesical Bacillus Calmette-Guérin (BCG) immunotherapy preserves the bladder after resection of high-risk non–muscle-invasive bladder cancer (NMIBC). About 30% of patients experience treatment failure, which cannot be predicted a priori and carries a high risk of disease progression. We examined the in vitro tuberculin responsiveness of CD4+ T cells before BCG immunotherapy in 42 patients with high-risk NMIBC. The frequencies and functionalities of cytokine-expressing CD4+ T cells immediately before and after BCG immunotherapy induction were assessed by flow cytometry after overnight tuberculin stimulation. Tuberculin-induced secreted mediators were measured by electrochemiluminescence. We correlated the results with recurrence-free patient survival 6 months after induction. A tuberculin-induced, secreted, IL2 concentration > 250 pg/mL was the best predictor of recurrence-free survival, providing 79% sensitivity, 86% specificity (AUC = 0.852, P = 0.000), and overall correct classification in 78.6% of cases. In 50% of patients later experiencing recurrence, but not in any of the recurrence-free survivors, IL2 secretion was < 120 pg/mL. Other parameters predicting recurrence-free survival included secreted IFNγ (AUC = 0.796, P = 0.002) and the frequencies of TNF-producing (TNF+) CD4+ T cells (AUC = 0.745, P = 0.010). “Polyfunctional” CD4+ T cells (IFNγ+/IL2+/TNF+) were significantly associated with recurrence-free survival (AUC = 0.801, P = 0.002). Thus, the amount of IL2 secretion from CD4+ T cells after overnight in vitro incubation with tuberculin predicted the outcome of BCG immunotherapy. As many as half of potential BCG failures could be identified before induction therapy is begun, enabling better choices regarding treatment. Cancer Immunol Res; 6(10); 1212–9. ©2018 AACR.
Data from T Cells Specific for an Unconventional Natural Antigen Fail to Recognize Leukemic Cells
Authors: Pont Margot J. , Oostvogels Rimke , van Bergen Cornelis A.M. , van der Meijden Edith D. , Honders Maria W. , Bliss Sophie , Jongsma Marlieke L.M. , Lokhorst Henk M. , Falkenburg J.H. Frederik , Mutis Tuna , Griffioen Marieke , Spaapen Robbert M.
Published: March 2024

Abstract
MHC-bound peptides from aberrant proteins may be a specific immunotherapeutic target on cancer cells. Because of difficulties in identifying such antigens, viral or model antigens have so far been used to study their biological relevance. We here identify a naturally existing human T-cell epitope derived from a truncated protein. The antigenic peptide is derived from the gene TTK only through an alternative transcript containing a premature termination codon that may target the transcript for nonsense-mediated decay (NMD). This antigen is recognized by HLA-A*02:01–restricted CD8+ T cells derived from an allotransplanted leukemia patient. Functional analyses showed that these T cells failed to recognize several HLA-matched primary leukemic cells that expressed the alternative TTK transcript. Conventional antigen processing and presentation were not affected, suggesting that leukemic cells modify the generation of antigens processed from aberrant proteins. This natural TTK epitope provides insights in the source of transcripts producing antigenic epitopes in healthy and leukemic cells. Our data underscore potential pitfalls of targeting NMD-derived or other unconventionally generated epitopes as immunotherapeutic approach.