bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from TGFβ and CIS Inhibition Overcomes NK-cell Suppression to Restore Antitumor Immunity
Authors: Souza-Fonseca-Guimaraes Fernando , Rossi Gustavo R. , Dagley Laura F. , Foroutan Momeneh , McCulloch Timothy R. , Yousef Jumana , Park Hae-Young , Gunter Jennifer H. , Beavis Paul A. , Lin Cheng-Yu , Hediyeh-Zadeh Soroor , Camilleri Tania , Davis Melissa J. , Huntington Nicholas D.
Published: April 2023

Abstract
Antibodies targeting “immune checkpoints” have revolutionized cancer therapy by reactivating tumor-resident cytotoxic lymphocytes, primarily CD8+ T cells. Interest in targeting analogous pathways in other cytotoxic lymphocytes is growing. Natural killer (NK) cells are key to cancer immunosurveillance by eradicating metastases and driving solid tumor inflammation. NK-cell antitumor function is dependent on the cytokine IL15. Ablation of the IL15 signaling inhibitor CIS (Cish) enhances NK-cell antitumor immunity by increasing NK-cell metabolism and persistence within the tumor microenvironment (TME). The TME has also been shown to impair NK-cell fitness via the production of immunosuppressive transforming growth factor β (TGFβ), a suppression which occurs even in the presence of high IL15 signaling. Here, we identified an unexpected interaction between CIS and the TGFβ signaling pathway in NK cells. Independently, Cish- and Tgfbr2-deficient NK cells are both hyperresponsive to IL15 and hyporesponsive to TGFβ, with dramatically enhanced antitumor immunity. Remarkably, when both these immunosuppressive genes are simultaneously deleted in NK cells, mice are largely resistant to tumor development, suggesting that combining suppression of these two pathways might represent a novel therapeutic strategy to enhance innate anticancer immunity.
Data from Preclinical Characterization and Phase I Study of an Anti–HER2-TLR7 Immune-Stimulator Antibody Conjugate in Patients with HER2+ Malignancies
Authors: Janku Filip , Han Sae-Won , Doi Toshihiko , Amatu Alessio , Ajani Jaffer A. , Kuboki Yasutoshi , Cortez Alex , Cellitti Susan E. , Mahling Ping C. , Subramanian Kulandayan , Schoenfeld Heidi A. , Choi Sarah M. , Iaconis Lori A. , Lee Lang Ho , Pelletier Marc R. , Dranoff Glenn , Askoxylakis Vasileios , Siena Salvatore
Published: April 2023

Abstract
Immune-stimulator antibody conjugates (ISAC) combining tumor-targeting monoclonal antibodies with immunostimulatory agents allow targeted delivery of immune activators into tumors. NJH395 is a novel, first-in-class ISAC comprising a Toll‐like receptor 7 (TLR7) agonist conjugated to an anti-HER2 antibody via a noncleavable linker payload. Preclinical characterization showed ISAC-mediated activation of myeloid cells in the presence of antigen-expressing cancer cells, with antigen targeting and TLR7 agonism contributing to antitumor activity. Safety, efficacy, immunogenicity, pharmacokinetics, and pharmacodynamics were investigated in a phase I, multicenter, open-label study in patients with HER2+ non-breast advanced malignancies (NCT03696771). Data from 18 patients enrolled in single ascending dose escalation demonstrated delivery of the TLR7-agonist payload in HER2+ tumor cells and induction of type I IFN responses, which correlated with immune modulation in the tumor microenvironment. Cytokine release syndrome was a common, but manageable, drug-related adverse event. Antidrug antibodies and neuroinflammation at high doses represented significant clinical challenges. Data provide proof-of-mechanism and critical insights for novel immunotherapies.
Data from Adenosine A2a Receptor Antagonism Restores Additive Cytotoxicity by Cytotoxic T Cells in Metabolically Perturbed Tumors
Authors: Slaats Jeroen , Wagena Esther , Smits Daan , Berends Annemarie A. , Peters Ella , Bakker Gert-Jan , van Erp Merijn , Weigelin Bettina , Adema Gosse J. , Friedl Peter
Published: April 2023

Abstract
Cytotoxic T lymphocytes (CTL) are antigen-specific effector cells with the ability to eradicate cancer cells in a contact-dependent manner. Metabolic perturbation compromises the CTL effector response in tumor subregions, resulting in failed cancer cell elimination despite the infiltration of tumor-specific CTLs. Restoring the functionality of these tumor-infiltrating CTLs is key to improve immunotherapy. Extracellular adenosine is an immunosuppressive metabolite produced within the tumor microenvironment. Here, by applying single-cell reporter strategies in 3D collagen cocultures in vitro and progressing tumors in vivo, we show that adenosine weakens one-to-one pairing of activated effector CTLs with target cells, thereby dampening serial cytotoxic hit delivery and cumulative death induction. Adenosine also severely compromised CTL effector restimulation and expansion. Antagonization of adenosine A2a receptor (ADORA2a) signaling stabilized and prolonged CTL–target cell conjugation and accelerated lethal hit delivery by both individual contacts and CTL swarms. Because adenosine signaling is a near-constitutive confounding parameter in metabolically perturbed tumors, ADORA2a targeting represents an orthogonal adjuvant strategy to enhance immunotherapy efficacy.
Data from Syntaphilin Regulates Neutrophil Migration in Cancer
Authors: Fu Shuyu , Deng Hui , Bertolini Irene , Perego Michela , Chen Eric S. , Sanseviero Emilio , Mostafa Ali , Alicea-Torres Kevin , Garcia-Gerique Laura , Stone Erica L. , Kossenkov Andrew V. , Schug Zachary T. , Nam Brian , Mulligan Charles , Altieri Dario C. , Nefedova Yulia , Gabrilovich Dmitry I.
Published: April 2023

Abstract
Pathologically activated neutrophils (PMN) with immunosuppressive activity, which are termed myeloid-derived suppressor cells (PMN-MDSC), play a critical role in regulating tumor progression. These cells have been implicated in promoting tumor metastases by contributing to premetastatic niche formation. This effect was facilitated by enhanced spontaneous migration of PMN from bone marrow to the premetastatic niches during the early-stage of cancer development. The molecular mechanisms underpinning this phenomenon remained unclear. In this study, we found that syntaphilin (SNPH), a cytoskeletal protein previously known for anchoring mitochondria to the microtubule in neurons and tumor cells, could regulate migration of PMN. Expression of SNPH was decreased in PMN from tumor-bearing mice and patients with cancer as compared with PMN from tumor-free mice and healthy donors, respectively. In Snph-knockout (SNPH-KO) mice, spontaneous migration of PMN was increased and the mice showed increased metastasis. Mechanistically, in SNPH-KO mice, the speed and distance travelled by mitochondria in PMN was increased, rates of oxidative phosphorylation and glycolysis were elevated, and generation of adenosine was increased. Thus, our study reveals a molecular mechanism regulating increased migratory activity of PMN during cancer progression and suggests a novel therapeutic targeting opportunity.
Data from Infiltration of Tumors Is Regulated by T cell–Intrinsic Nitric Oxide Synthesis
Authors: Cunha Pedro P. , Bargiela David , Minogue Eleanor , Krause Lena C.M. , Barbieri Laura , Brombach Carolin , Gojkovic Milos , Marklund Emilia , Pietsch Sandra , Foskolou Iosifina , Branco Cristina M. , Veliça Pedro , Johnson Randall S.
Published: April 2023

Abstract
Nitric oxide (NO) is a signaling molecule produced by NO synthases (NOS1–3) to control processes such as neurotransmission, vascular permeability, and immune function. Although myeloid cell–derived NO has been shown to suppress T-cell responses, the role of NO synthesis in T cells themselves is not well understood. Here, we showed that significant amounts of NO were synthesized in human and murine CD8+ T cells following activation. Tumor growth was significantly accelerated in a T cell–specific, Nos2-null mouse model. Genetic deletion of Nos2 expression in murine T cells altered effector differentiation, reduced tumor infiltration, and inhibited recall responses and adoptive cell transfer function. These data show that endogenous NO production plays a critical role in T cell–mediated tumor immunity.
Data from Characterization of Leukemic Resistance to CD19-Targeted CAR T-cell Therapy through Deep Genomic Sequencing
Authors: Chen Gregory M. , Chen Chia-Hui , Perazzelli Jessica , Grupp Stephan A. , Barrett David M. , Tan Kai
Published: April 2023

Abstract
Chimeric antigen receptor (CAR) T-cell therapy targeting CD19 has been a clinical breakthrough for pediatric B-cell acute lymphoblastic leukemia (B-ALL), and loss of the CD19 target antigen on leukemic cells represents a major mechanism of relapse. Previous studies have observed CD19 mutations specific to CD19− relapses, and we sought to clarify and strengthen this relationship using deep whole-exome sequencing in leukemic cells expanded in a patient-derived xenograft. By assessing pre-treatment and relapse cells from 13 patients treated with CAR T-cell therapy, 8 of whom developed CD19− relapse and 5 of whom developed CD19+ relapse, we demonstrate that relapse-specific single-nucleotide variants and small indels with high allele frequency combined with deletions in the CD19 gene in a manner specific to those patients with CD19− relapse. Before CAR T-cell infusion, one patient was found to harbor a pre-existing CD19 deletion in the context of genomic instability, which likely represented the first hit leading to the patient's subsequent CD19− relapse. Across patients, preexisting mutations and genomic instability were not significant predictors of subsequent CD19− relapse across patients, with sample size as a potential limiting factor. Together, our results clarify and strengthen the relationship between genomic events and CD19− relapse, demonstrating this intriguing mechanism of resistance to a targeted cancer immunotherapy.
Data from Antigen-Loaded Extracellular Vesicles Induce Responsiveness to Anti–PD-1 and Anti–PD-L1 Treatment in a Checkpoint Refractory Melanoma Model
Authors: Veerman Rosanne E. , Akpinar Gözde Güclüler , Offens Annemarijn , Steiner Loïc , Larssen Pia , Lundqvist Andreas , Karlsson Mikael C.I. , Gabrielsson Susanne
Published: April 2023

Abstract
Extracellular vesicles (EV) are important mediators of intercellular communication and are potential candidates for cancer immunotherapy. Immune checkpoint blockade, specifically targeting the programmed cell death protein 1 (PD-1)/programmed death-ligand 1 (PD-L1) axis, mitigates T-cell exhaustion, but is only effective in a subset of patients with cancer. Reasons for therapy resistance include low primary T-cell activation to cancer antigens, poor antigen presentation, and reduced T-cell infiltration into the tumor. Therefore, combination strategies have been extensively explored. Here, we investigated whether EV therapy could induce susceptibility to anti–PD-1 or anti–PD-L1 therapy in a checkpoint-refractory B16 melanoma model. Injection of dendritic cell–derived EVs, but not checkpoint blockade, induced a potent antigen-specific T-cell response and reduced tumor growth in tumor-bearing mice. Combination therapy of EVs and anti–PD-1 or anti–PD-L1 potentiated immune responses to ovalbumin- and α-galactosylceramide–loaded EVs in the therapeutic model. Moreover, combination therapy resulted in increased survival in a prophylactic tumor model. This demonstrates that EVs can induce potent antitumor immune responses in checkpoint refractory cancer and induce anti–PD-1 or anti–PD-L1 responses in a previously nonresponsive tumor model.
Data from VISTA Targeting of T-cell Quiescence and Myeloid Suppression Overcomes Adaptive Resistance
Authors: Schaafsma Evelien , Croteau Walburga , ElTanbouly Mohamed , Nowak Elizabeth C. , Smits Nicole C. , Deng Jie , Sarde Aurelien , Webber Cecilia A. , Rabadi Dina , Cheng Chao , Noelle Randolph , Lines J. Louise
Published: April 2023

Abstract
V domain immunoglobulin suppressor of T-cell activation (VISTA) is a premier target for cancer treatment due to its broad expression in many cancer types and enhanced expression upon development of adaptive immune checkpoint resistance. In the CT26 colorectal cancer model, monotherapy of small tumors with anti-VISTA resulted in slowed tumor growth. In a combination therapy setting, large CT26 tumors showed complete adaptive resistance to anti–PD-1/CTLA-4, but inclusion of anti-VISTA led to rejection of half the tumors. Mechanisms of enhanced antitumor immunity were investigated using single-cell RNA sequencing (scRNA-seq), multiplex image analysis, and flow cytometry of the tumor immune infiltrate. In both treatment models, anti-VISTA upregulated stimulated antigen presentation pathways and reduced myeloid-mediated suppression. Imaging revealed an anti-VISTA stimulated increase in contacts between T cells and myeloid cells, further supporting the notion of increased antigen presentation. scRNA-seq of tumor-specific CD8+ T cells revealed that anti-VISTA therapy induced T-cell pathways highly distinct from and complementary to those induced by anti–PD-1 therapy. Whereas anti–CTLA-4/PD-1 expanded progenitor exhausted CD8+ T-cell subsets, anti-VISTA promoted costimulatory genes and reduced regulators of T-cell quiescence. Notably, this is the first report of a checkpoint regulator impacting CD8+ T-cell quiescence, and the first indication that quiescence may be a target in the context of T-cell exhaustion and in cancer. This study builds a foundation for all future studies on the role of anti-VISTA in the development of antitumor immunity and provides important mechanistic insights that strongly support use of anti-VISTA to overcome the adaptive resistance seen in contemporary treatments involving PD-1 and/or CTLA-4.

See related Spotlight by Wei, p. 3
Data from Tumor-Associated CD19+CD39− B Regulatory Cells Deregulate Class-Switch Recombination to Suppress Antibody Responses
Authors: Pati Subhadip , Mukherjee Sumon , Dutta Saikat , Guin Aharna , Roy Dia , Bose Sayantan , Paul Silpita , Saha Sudipto , Bhattacharyya Sankar , Datta Pratyush , Chakraborty Jayati , Sarkar Diptendra K. , Sa Gaurisankar
Published: April 2023

Abstract
B cells are an essential component of humoral immunity. Their primary function is to mount antigen-specific antibody responses to eliminate pathogens. Despite an increase in B-cell number, we found that serum-IgG levels were low in patients with breast cancer. To solve this conundrum, we used high-dimensional flow cytometry to analyze the heterogeneity of B-cell populations and identified a tumor-specific CD19+CD24hiCD38hi IL10-producing B regulatory (Breg)–cell subset. Although IL10 is a Breg-cell marker, being an intracellular protein, it is of limited value for Breg-cell isolation. Highly expressed Breg-cell surface proteins CD24 and CD38 also impede the isolation of viable Breg cells. These are hurdles that limit understanding of Breg-cell functions. Our transcriptomic analysis identified, CD39-negativity as an exclusive, sorting-friendly surface marker for tumor-associated Breg cells. We found that the identified CD19+CD39‒IL10+ B-cell population was suppressive in nature as it limited T helper–cell proliferation, type-1 cytokine production, and T effector–cell survival, and augmented CD4+FOXP3+ regulatory T–cell generation. These tumor-associated Breg cells were also found to restrict autologous T follicular helper–cell expansion and IL21 secretion, thereby inhibiting germinal transcript formation and activation-induced cytidine deaminase expression involved in H-chain class-switch recombination (CSR). This isotype-switching abnormality was shown to hinder B-cell differentiation into class-switched memory B cells and subsequent high-affinity antibody-producing plasma B cells, which collectively led to the dampening of IgG-mediated antibody responses in patients with cancer. As low IgG is associated with poor prognosis in patients with cancer, Breg-cell depletion could be a promising future therapy for boosting plasma B cell–mediated antibody responses.
Data from High-Resolution Analysis of Mononuclear Phagocytes Reveals GPNMB as a Prognostic Marker in Human Colorectal Liver Metastasis
Authors: Cortese Nina , Carriero Roberta , Barbagallo Marialuisa , Putignano Anna Rita , Costa Guido , Giavazzi Fabio , Grizzi Fabio , Pasqualini Fabio , Peano Clelia , Basso Gianluca , Marchini Sergio , Colombo Federico Simone , Soldani Cristiana , Franceschini Barbara , Di Tommaso Luca , Terracciano Luigi , Donadon Matteo , Torzilli Guido , Kunderfranco Paolo , Mantovani Alberto , Marchesi Federica
Published: April 2023

Abstract
Patients with colorectal liver metastasis (CLM) present with heterogenous clinical outcomes and improved classification is needed to ameliorate the therapeutic output. Macrophages (Mϕ) hold promise as prognostic classifiers and therapeutic targets. Here, stemming from a single-cell analysis of mononuclear phagocytes infiltrating human CLM, we identified two Mϕ markers associated with distinct populations with opposite clinical relevance. The invasive margin of CLM was enriched in pro-inflammatory monocyte-derived Mϕ (MoMϕ) expressing the monocytic marker SERPINB2, and a more differentiated population, tumor-associated Mϕ (TAM), expressing glycoprotein nonmetastatic melanoma protein B (GPNMB). SERPINB2+ MoMϕ had an early inflammatory profile, whereas GPNMB+ TAMs were enriched in pathways of matrix degradation, angiogenesis, and lipid metabolism and were found closer to the tumor margin, as confirmed by spatial transcriptomics on CLM specimens. In a cohort of patients, a high infiltration of SERPINB2+ cells independently associated with longer disease-free survival (DFS; P = 0.033), whereas a high density of GPNMB+ cells correlated with shorter DFS (P = 0.012) and overall survival (P = 0.002). Cell–cell interaction analysis defined opposing roles for MoMϕ and TAMs, suggesting that SERPINB2+ and GPNMB+ cells are discrete populations of Mϕ and may be exploited for further translation to an immune-based stratification tool. This study provides evidence of how multi-omics approaches can identify nonredundant, clinically relevant markers for further translation to immune-based patient stratification tools and therapeutic targets. GPNMB has been shown to set Mϕ in an immunosuppressive mode. Our high dimensional analyses provide further evidence that GPNMB is a negative prognostic indicator and a potential player in the protumor function of Mϕ populations.
Supplementary Table 1 from A Method for Overcoming Plasma Protein Inhibition of Tyrosine Kinase Inhibitors
Authors: Young David J. , Nguyen Bao , Li Li , Higashimoto Tomoyasu , Levis Mark J. , Liu Jun O. , Small Donald
Published: April 2023

Validation cohort patient characteristics
Supplementary Discussion and Figures from A Method for Overcoming Plasma Protein Inhibition of Tyrosine Kinase Inhibitors
Authors: Young David J. , Nguyen Bao , Li Li , Higashimoto Tomoyasu , Levis Mark J. , Liu Jun O. , Small Donald
Published: April 2023

Mathematical treatment of drug-protein interactions and supplementary figures 1-4
Supplementary Data from BCOR and BCORL1 Mutations Drive Epigenetic Reprogramming and Oncogenic Signaling by Unlinking PRC1.1 from Target Genes
Authors: Schaefer Eva J. , Wang Helen C. , Karp Hannah Q. , Meyer Clifford A. , Cejas Paloma , Gearhart Micah D. , Adelman Emmalee R. , Fares Iman , Apffel Annie , Lim Klothilda , Xie Yingtian , Gibson Christopher J. , Schenone Monica , Murdock H. Moses , Wang Eunice S. , Gondek Lukasz P. , Carroll Martin P. , Vedula Rahul S. , Winer Eric S. , Garcia Jacqueline S. , Stone Richard M. , Luskin Marlise R. , Carr Steven A. , Long Henry W. , Bardwell Vivian J. , Figueroa Maria E. , Lindsley R. Coleman
Published: April 2023

Supplementary Data from BCOR and BCORL1 Mutations Drive Epigenetic Reprogramming and Oncogenic Signaling by Unlinking PRC1.1 from Target Genes
Supplementary Table from Perspectives on the Risk-Stratified Treatment of Multiple Myeloma
Authors: Davies Faith E. , Pawlyn Charlotte , Usmani Saad Z. , San-Miguel Jesus F. , Einsele Hermann , Boyle Eileen M. , Corre Jill , Auclair Daniel , Cho Hearn Jay , Lonial Sagar , Sonneveld Pieter , Stewart A. Keith , Bergsagel P. Leif , Kaiser Martin F. , Weisel Katja , Keats Jonathan J. , Mikhael Joseph R. , Morgan Kathryn E. , Ghobrial Irene M. , Orlowski Robert Z. , Landgren C. Ola , Gay Francesca , Caers Joseph , Chng Wee Joo , Chari Ajai , Walker Brian A. , Kumar Shaji K. , Costa Luciano J. , Anderson Kenneth C. , Morgan Gareth J.
Published: April 2023

Supplementary Table from Perspectives on the Risk-Stratified Treatment of Multiple Myeloma
Supplementary Figure from Clonal Hematopoiesis Is Associated with Increased Risk of Severe Neurotoxicity in Axicabtagene Ciloleucel Therapy of Large B-Cell Lymphoma
Authors: Saini Neeraj Y. , Swoboda David M. , Greenbaum Uri , Ma Junsheng , Patel Romil D. , Devashish Kartik , Das Kaberi , Tanner Mark R. , Strati Paolo , Nair Ranjit , Fayad Luis , Ahmed Sairah , Lee Hun Ju , Iyer Swaminathan P. , Steiner Raphael , Jain Nitin , Nastoupil Loretta , Loghavi Sanam , Tang Guilin , Bassett Roland L. , Jain Preetesh , Wang Michael , Westin Jason R. , Green Michael R. , Sallman David A. , Padron Eric , Davila Marco L. , Locke Frederick L. , Champlin Richard E. , Garcia-Manero Guillermo , Shpall Elizabeth J. , Kebriaei Partow , Flowers Christopher R. , Jain Michael D. , Wang Feng , Futreal Andrew P. , Gillis Nancy , Neelapu Sattva S. , Takahashi Koichi
Published: April 2023

Supplementary Figure from Clonal Hematopoiesis Is Associated with Increased Risk of Severe Neurotoxicity in Axicabtagene Ciloleucel Therapy of Large B-Cell Lymphoma
Supplementary Table from Transcriptional Plasticity Drives Leukemia Immune Escape
Authors: Eagle Kenneth , Harada Taku , Kalfon Jérémie , Perez Monika W. , Heshmati Yaser , Ewers Jazmin , Koren Jošt Vrabič , Dempster Joshua M. , Kugener Guillaume , Paralkar Vikram R. , Lin Charles Y. , Dharia Neekesh V. , Stegmaier Kimberly , Orkin Stuart H. , Pimkin Maxim
Published: April 2023

Supplementary Table from Transcriptional Plasticity Drives Leukemia Immune Escape
Supplementary Figure from PU.1-Dependent Enhancer Inhibition Separates Tet2-Deficient Hematopoiesis from Malignant Transformation
Authors: Aivalioti Maria M. , Bartholdy Boris A. , Pradhan Kith , Bhagat Tushar D. , Zintiridou Aliona , Jeong Jong Jin , Thiruthuvanathan Victor J. , Pujato Mario , Paranjpe Aditi , Zhang Chi , Levine Ross L. , Viny Aaron D. , Wickrema Amittha , Verma Amit , Will Britta
Published: April 2023

Supplementary Figure from PU.1-Dependent Enhancer Inhibition Separates Tet2-Deficient Hematopoiesis from Malignant Transformation
Supplementary Figure from Follicular Lymphoma Microenvironment Characteristics Associated with Tumor Cell Mutations and MHC Class II Expression
Authors: Han Guangchun , Deng Qing , Marques-Piubelli Mario L. , Dai Enyu , Dang Minghao , Ma Man Chun John , Li Xubin , Yang Haopeng , Henderson Jared , Kudryashova Olga , Meerson Mark , Isaev Sergey , Kotlov Nikita , Nomie Krystle J. , Bagaev Alexander , Parra Edwin R. , Solis Soto Luisa M. , Parmar Simrit , Hagemeister Fredrick B. , Ahmed Sairah , Iyer Swaminathan P. , Samaniego Felipe , Steiner Raphael , Fayad Luis , Lee Hun , Fowler Nathan H. , Flowers Christopher R. , Strati Paolo , Westin Jason R. , Neelapu Sattva S. , Nastoupil Loretta J. , Vega Francisco , Wang Linghua , Green Michael R.
Published: April 2023

Supplementary Figure from Follicular Lymphoma Microenvironment Characteristics Associated with Tumor Cell Mutations and MHC Class II Expression
Supplementary Table S4 from A Therapeutically Targetable NOTCH1–SIRT1–KAT7 Axis in T-cell Leukemia
Authors: Lancho Olga , Singh Amartya , da Silva-Diz Victoria , Aleksandrova Maya , Khatun Jesminara , Tottone Luca , Nunes Patricia Renck , Luo Shirley , Zhao Caifeng , Zheng Haiyan , Chiles Eric , Zuo Zhenyu , Rocha Pedro P. , Su Xiaoyang , Khiabanian Hossein , Herranz Daniel
Published: April 2023

H4K12ac ChIPseq results
Supplementary Table S2 from A Therapeutically Targetable NOTCH1–SIRT1–KAT7 Axis in T-cell Leukemia
Authors: Lancho Olga , Singh Amartya , da Silva-Diz Victoria , Aleksandrova Maya , Khatun Jesminara , Tottone Luca , Nunes Patricia Renck , Luo Shirley , Zhao Caifeng , Zheng Haiyan , Chiles Eric , Zuo Zhenyu , Rocha Pedro P. , Su Xiaoyang , Khiabanian Hossein , Herranz Daniel
Published: April 2023

Gene expression profiling results
Supplementary Figures from In Vivo Modeling of CLL Transformation to Richter Syndrome Reveals Convergent Evolutionary Paths and Therapeutic Vulnerabilities
Authors: ten Hacken Elisa , Sewastianik Tomasz , Yin Shanye , Hoffmann Gabriela Brunsting , Gruber Michaela , Clement Kendell , Penter Livius , Redd Robert A. , Ruthen Neil , Hergalant Sébastien , Sholokhova Alanna , Fell Geoffrey , Parry Erin M. , Broséus Julien , Guieze Romain , Lucas Fabienne , Hernández-Sánchez María , Baranowski Kaitlyn , Southard Jackson , Joyal Heather , Billington Leah , Regis Fara Faye D. , Witten Elizabeth , Uduman Mohamed , Knisbacher Binyamin A. , Li Shuqiang , Lyu Haoxiang , Vaisitti Tiziana , Deaglio Silvia , Inghirami Giorgio , Feugier Pierre , Stilgenbauer Stephan , Tausch Eugen , Davids Matthew S. , Getz Gad , Livak Kenneth J. , Bozic Ivana , Neuberg Donna S. , Carrasco Ruben D. , Wu Catherine J.
Published: April 2023

Supplementary file contains a PDF version of supplementary figures S1-S7 and associated figure legends.
Data from Cytotoxic Therapy–Induced Effects on Both Hematopoietic and Marrow Stromal Cells Promotes Therapy-Related Myeloid Neoplasms
Authors: Stoddart Angela , Wang Jianghong , Fernald Anthony A. , Davis Elizabeth M. , Johnson Camille R. , Hu Chunmei , Cheng Jason X. , McNerney Megan E. , Le Beau Michelle M.
Published: April 2023

Abstract
Therapy-related myeloid neoplasms (t-MN) following treatment with alkylating agents are characterized by a del(5q), complex karyotypes, alterations of TP53, and a dismal prognosis. To decipher the molecular pathway(s) leading to the pathogenesis of del(5q) t-MN and the effect(s) of cytotoxic therapy on the marrow microenvironment, we developed a mouse model with loss of two key del(5q) genes, EGR1 and APC, in hematopoietic cells. We used the well-characterized drug, N-ethyl-N-nitrosurea (ENU), to demonstrate that alkylating agent exposure of stromal cells in the microenvironment increases the incidence of myeloid disease. In addition, loss of Trp53 with Egr1 and Apc was required to drive the development of a transplantable leukemia, and accompanied by the acquisition of somatic mutations in DNA damage response genes. ENU treatment of mesenchymal stromal cells induced cellular senescence and led to the acquisition of a senescence-associated secretory phenotype, which may be a critical microenvironmental alteration in the pathogenesis of myeloid neoplasms.
Significance:
This study challenges the historic view that prior cytotoxic therapy targets only hematopoietic cells and shows that chemotherapy-induced alterations to the microenvironment contribute to myeloid neoplasms in a model of del(5q) t-MN. The DNA damage response in hematopoietic cells and senescence of stromal cells are identified as potential therapeutic targets.

See related commentary by Shannon and Link, p. 10.

This article is highlighted in the In This Issue feature, p. 5
Data from Mutation Signatures of Pediatric Acute Myeloid Leukemia and Normal Blood Progenitors Associated with Differential Patient Outcomes
Authors: Brandsma Arianne M. , Bertrums Eline J.M. , van Roosmalen Markus J. , Hofman Damon A. , Oka Rurika , Verheul Mark , Manders Freek , Ubels Joske , Belderbos Mirjam E. , van Boxtel Ruben
Published: April 2023

Abstract
Acquisition of oncogenic mutations with age is believed to be rate limiting for carcinogenesis. However, the incidence of leukemia in children is higher than in young adults. Here we compare somatic mutations across pediatric acute myeloid leukemia (pAML) patient-matched leukemic blasts and hematopoietic stem and progenitor cells (HSPC), as well as HSPCs from age-matched healthy donors. HSPCs in the leukemic bone marrow have limited genetic relatedness and share few somatic mutations with the cell of origin of the malignant blasts, suggesting polyclonal hematopoiesis in patients with pAML. Compared with normal HSPCs, a subset of pAML cases harbored more somatic mutations and a distinct composition of mutational process signatures. We hypothesize that these cases might have arisen from a more committed progenitor. This subset had better outcomes than pAML cases with mutation burden comparable with age-matched healthy HSPCs. Our study provides insights into the etiology and patient stratification of pAML.
Significance:
Genome-wide analysis of pAML and patient-matched HSPCs provides new insights into the etiology of the disease and shows the clinical potential of these analyses for patient stratification.

This article is highlighted in the In This Issue feature, p. 403
Data from Large-scale Identification of Clonal Hematopoiesis and Mutations Recurrent in Blood Cancers
Authors: Feusier Julie E. , Arunachalam Sasi , Tashi Tsewang , Baker Monika J. , VanSant-Webb Chad , Ferdig Amber , Welm Bryan E. , Rodriguez-Flores Juan L. , Ours Christopher , Jorde Lynn B. , Prchal Josef T. , Mason Clinton C.
Published: April 2023

Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) is characterized by detectable hematopoietic-associated gene mutations in a person without evidence of hematologic malignancy. We sought to identify additional cancer-presenting mutations usable for CHIP detection by performing a data mining analysis of 48 somatic mutation landscape studies reporting mutations at diagnoses of 7,430 adult and pediatric patients with leukemia or other hematologic malignancy. Following extraction of 20,141 protein-altering mutations, we identified 434 significantly recurrent mutation hotspots, 364 of which occurred at loci confidently assessable for CHIP. We then performed an additional large-scale analysis of whole-exome sequencing data from 4,538 persons belonging to three noncancer cohorts for clonal mutations. We found the combined cohort prevalence of CHIP with mutations identical to those reported at blood cancer mutation hotspots to be 1.8%, and that some of these CHIP mutations occurred in children. Our findings may help to improve CHIP detection and precancer surveillance for both children and adults.
Significance:
This study identifies frequently occurring mutations across several blood cancers that may drive hematologic malignancies and signal increased risk for cancer when detected in healthy persons. We find clonal mutations at these hotspots in a substantial number of individuals from noncancer cohorts, including children, showcasing potential for improved precancer surveillance.

See related commentary by Spitzer and Levine, p. 192.
Data from Phase II Trial of Pembrolizumab after High-Dose Cytarabine in Relapsed/Refractory Acute Myeloid Leukemia
Authors: Zeidner Joshua F. , Vincent Benjamin G. , Ivanova Anastasia , Moore Dominic , McKinnon Karen P. , Wilkinson Alec D. , Mukhopadhyay Rupkatha , Mazziotta Francesco , Knaus Hanna A. , Foster Matthew C. , Coombs Catherine C. , Jamieson Katarzyna , Van Deventer Hendrik , Webster Jonathan A. , Prince Gabrielle T. , DeZern Amy E. , Smith B. Douglas , Levis Mark J. , Montgomery Nathan D. , Luznik Leo , Serody Jonathan S. , Gojo Ivana
Published: April 2023

Abstract
Immune suppression, exhaustion, and senescence are frequently seen throughout disease progression in acute myeloid leukemia (AML). We conducted a phase II study of high-dose cytarabine followed by pembrolizumab 200 mg i.v. on day 14 to examine whether PD-1 inhibition improves clinical responses in relapsed/refractory (R/R) AML. Overall responders could receive pembrolizumab maintenance up to 2 years. Among 37 patients enrolled, the overall response rate, composite complete remission (CRc) rate (primary endpoint), and median overall survival (OS) were 46%, 38%, and 11.1 months, respectively. Patients with refractory/early relapse and those receiving treatment as first salvage had encouraging outcomes (median OS, 13.2 and 11.3 months, respectively). Grade ≥3 immune-related adverse events were rare (14%) and self-limiting. Patients who achieved CRc had a higher frequency of progenitor exhausted CD8+ T cells expressing TCF-1 in the bone marrow prior to treatment. A multifaceted correlative approach of genomic, transcriptomic, and immunophenotypic profiling offers insights on molecular correlates of response and resistance to pembrolizumab.
Significance:
Immune-checkpoint blockade with pembrolizumab was tolerable and feasible after high-dose cytarabine in R/R AML, with encouraging clinical activity, particularly in refractory AML and those receiving treatment as first salvage regimen. Further study of pembrolizumab and other immune-checkpoint blockade strategies after cytotoxic chemotherapy is warranted in AML.

See related commentary by Wei et al., p. 551.

This article is highlighted in the In This Issue feature, p. 549
Data from ROBO1 Promotes Homing, Dissemination, and Survival of Multiple Myeloma within the Bone Marrow Microenvironment
Authors: Bianchi Giada , Czarnecki Peter G. , Ho Matthew , Roccaro Aldo M. , Sacco Antonio , Kawano Yawara , Gullà Annamaria , Samur Anil Aktas , Chen Tianzeng , Wen Kenneth , Tai Yu-Tzu , Moscvin Maria , Wu Xinchen , Camci-Unal Gulden , Da Vià Matteo C. , Bolli Niccolo' , Sewastianik Tomasz , Carrasco Ruben D. , Ghobrial Irene M. , Anderson Kenneth C.
Published: April 2023

Abstract
The bone marrow (BM) microenvironment actively promotes multiple myeloma pathogenesis, and therapies targeting both cancer cells and the niche are highly effective. We were interested in identifying novel signaling pathways supporting multiple myeloma–BM cross-talk. Mutations in the transmembrane receptor Roundabout 1 (ROBO1) were recently identified in patients with multiple myeloma; however, their functional consequences are uncertain. Through protein structure–function studies, we discovered that ROBO1 is necessary for multiple myeloma adhesion to BM stromal and endothelial cells and that ROBO1 knockout (KO) compromises BM homing and engraftment in a disseminated mouse model. ROBO1 KO significantly decreases multiple myeloma proliferation in vitro and intra- and extramedullary tumor growth in vivo. Mechanistically, the ROBO1 C-terminus is cleaved in a ligand-independent fashion and is sufficient to promote multiple myeloma proliferation. Vice versa, mutants lacking the cytoplasmic domain, including the human-derived G674* truncation, act dominantly negative. Interactomic and RNA-sequencing studies suggest that ROBO1 may be involved in RNA processing, supporting further studies.
Significance:
ROBO1 is highly expressed in t(4;14) multiple myeloma and supports homing and dissemination to the BM niche. ROBO1 knockout causes reduced tumor growth in intramedullary and extramedullary myeloma animal models, while the ROBO1 C-terminus is cleaved in multiple fragments and it is necessary and sufficient to sustain myeloma proliferation.
Data from Avadomide Induces Degradation of ZMYM2 Fusion Oncoproteins in Hematologic Malignancies
Authors: Renneville Aline , Gasser Jessica A. , Grinshpun Daniel E. , Jean Beltran Pierre M. , Udeshi Namrata D. , Matyskiela Mary E. , Clayton Thomas , McConkey Marie , Viswanathan Kaushik , Tepper Alexander , Guirguis Andrew A. , Sellar Rob S. , Cotteret Sophie , Marzac Christophe , Saada Véronique , De Botton Stéphane , Kiladjian Jean-Jacques , Cayuela Jean-Michel , Rolfe Mark , Chamberlain Philip P. , Carr Steven A. , Ebert Benjamin L.
Published: April 2023

Abstract
Thalidomide analogues exert their therapeutic effects by binding to the CRL4CRBN E3 ubiquitin ligase, promoting ubiquitination and subsequent proteasomal degradation of specific protein substrates. Drug-induced degradation of IKZF1 and IKZF3 in B-cell malignancies demonstrates the clinical utility of targeting disease-relevant transcription factors for degradation. Here, we found that avadomide (CC-122) induces CRBN-dependent ubiquitination and proteasomal degradation of ZMYM2 (ZNF198), a transcription factor involved in balanced chromosomal rearrangements with FGFR1 and FLT3 in aggressive forms of hematologic malignancies. The minimal drug-responsive element of ZMYM2 is a zinc-chelating MYM domain and is contained in the N-terminal portion of ZMYM2 that is universally included in the derived fusion proteins. We demonstrate that avadomide has the ability to induce proteasomal degradation of ZMYM2–FGFR1 and ZMYM2–FLT3 chimeric oncoproteins, both in vitro and in vivo. Our findings suggest that patients with hematologic malignancies harboring these ZMYM2 fusion proteins may benefit from avadomide treatment.
Significance:
We extend the potential clinical scope of thalidomide analogues by the identification of a novel avadomide-dependent CRL4CRBN substrate, ZMYM2. Avadomide induces ubiquitination and degradation of ZMYM2–FGFR1 and ZMYM2–FLT3, two chimeric oncoproteins involved in hematologic malignancies, providing a proof of concept for drug-induced degradation of transcription factor fusion proteins by thalidomide analogues.
Data from Scalable Manufacturing of CAR T Cells for Cancer Immunotherapy
Authors: Abou-el-Enein Mohamed , Elsallab Magdi , Feldman Steven A. , Fesnak Andrew D. , Heslop Helen E. , Marks Peter , Till Brian G. , Bauer Gerhard , Savoldo Barbara
Published: April 2023

Abstract
As of April 2021, there are five commercially available chimeric antigen receptor (CAR) T cell therapies for hematologic malignancies. With the current transition of CAR T cell manufacturing from academia to industry, there is a shift toward Good Manufacturing Practice (GMP)–compliant closed and automated systems to ensure reproducibility and to meet the increased demand for patients with cancer. In this review, we describe current CAR T cell clinical manufacturing models and discuss emerging technologic advances that embrace scaling and production optimization. We summarize measures being used to shorten CAR T cell manufacturing times and highlight regulatory challenges to scaling production for clinical use.
Significance:
As the demand for CAR T cell cancer therapy increases, several closed and automated production platforms are being deployed, and others are in development. This review provides a critical appraisal of these technologies, which can be leveraged to scale and optimize the production of next-generation CAR T cells.

See related video:https://aacrjournals.org/content/webinar-car-t-cell-manufacturing
Data from Next-Generation Sequencing of Minimal Residual Disease for Predicting Relapse after Tisagenlecleucel in Children and Young Adults with Acute Lymphoblastic Leukemia
Authors: Pulsipher Michael A. , Han Xia , Maude Shannon L. , Laetsch Theodore W. , Qayed Muna , Rives Susana , Boyer Michael W. , Hiramatsu Hidefumi , Yanik Gregory A. , Driscoll Tim , Myers G. Doug , Bader Peter , Baruchel Andre , Buechner Jochen , Stefanski Heather E. , Kalfoglou Creton , Nguyen Kevin , Waldron Edward R. , Thudium Mueller Karen , Maier Harald J. , Kari Gabor , Grupp Stephan A.
Published: April 2023

Abstract
We assessed minimal residual disease (MRD) detection and B-cell aplasia after tisagenlecleucel therapy for acute lymphoblastic leukemia (ALL) to define biomarkers predictive of relapse (N = 143). Next-generation sequencing (NGS) MRD detection >0 in bone marrow (BM) was highly associated with relapse. B-cell recovery [signifying loss of functional chimeric antigen receptor (CAR) T cells] within the first year of treatment was associated with a hazard ratio (HR) for relapse of 4.5 [95% confidence interval (CI), 2.03–9.97; P < 0.001]. Multivariate analysis at day 28 showed independent associations of BMNGS-MRD >0 (HR = 4.87; 95% CI, 2.18–10.8; P < 0.001) and B-cell recovery (HR = 3.33; 95% CI, 1.44–7.69; P = 0.005) with relapse. By 3 months, the BMNGS-MRD HR increased to 12 (95% CI, 2.87–50; P < 0.001), whereas B-cell recovery was not independently predictive (HR = 1.27; 95% CI, 0.33–4.79; P = 0.7). Relapses occurring with persistence of B-cell aplasia were largely CD19− (23/25: 88%). Detectable BMNGS-MRD reliably predicts risk with sufficient time to consider approaches to relapse prevention such as hematopoietic cell transplantation (HCT) or second CAR-T cell infusion.
Significance:
Detectable disease by BMNGS-MRD with or without B-cell aplasia is highly predictive of relapse after tisagenlecleucel therapy for ALL. Clonotypic rearrangements used to follow NGS-MRD did not change after loss of CD19 or lineage switch. High-risk patients identified by these biomarkers may benefit from HCT or investigational cell therapies.

See related commentary by Ghorashian and Bartram, p. 2.

This article is highlighted in the In This Issue feature, p. 1
Data from BCOR and BCORL1 Mutations Drive Epigenetic Reprogramming and Oncogenic Signaling by Unlinking PRC1.1 from Target Genes
Authors: Schaefer Eva J. , Wang Helen C. , Karp Hannah Q. , Meyer Clifford A. , Cejas Paloma , Gearhart Micah D. , Adelman Emmalee R. , Fares Iman , Apffel Annie , Lim Klothilda , Xie Yingtian , Gibson Christopher J. , Schenone Monica , Murdock H. Moses , Wang Eunice S. , Gondek Lukasz P. , Carroll Martin P. , Vedula Rahul S. , Winer Eric S. , Garcia Jacqueline S. , Stone Richard M. , Luskin Marlise R. , Carr Steven A. , Long Henry W. , Bardwell Vivian J. , Figueroa Maria E. , Lindsley R. Coleman
Published: April 2023

Abstract
Polycomb repressive epigenetic complexes are recurrently dysregulated in cancer. Unlike polycomb repressive complex 2 (PRC2), the role of PRC1 in oncogenesis and therapy resistance is not well-defined. Here, we demonstrate that highly recurrent mutations of the PRC1 subunits BCOR and BCORL1 in leukemia disrupt assembly of a noncanonical PRC1.1 complex, thereby selectively unlinking the RING-PCGF enzymatic core from the chromatin-targeting auxiliary subcomplex. As a result, BCOR-mutated PRC1.1 is localized to chromatin but lacks repressive activity, leading to epigenetic reprogramming and transcriptional activation at target loci. We define a set of functional targets that drive aberrant oncogenic signaling programs in PRC1.1-mutated cells and primary patient samples. Activation of these PRC1.1 targets in BCOR-mutated cells confers acquired resistance to treatment while sensitizing to targeted kinase inhibition. Our study thus reveals a novel epigenetic mechanism that explains PRC1.1 tumor-suppressive activity and identifies a therapeutic strategy in PRC1.1-mutated cancer.
Significance:
We demonstrate that BCOR and BCORL1 mutations in leukemia unlink PRC1.1 repressive function from target genes, resulting in epigenetic reprogramming and activation of aberrant cell signaling programs that mediate treatment resistance. Our study provides mechanistic insights into the pathogenesis of PRC1.1-mutated leukemia that inform novel therapeutic approaches.

This article is highlighted in the In This Issue feature, p. 85
Data from Genetic and Transcriptional Contributions to Relapse in Normal Karyotype Acute Myeloid Leukemia
Authors: Petti Allegra A. , Khan Saad M. , Xu Ziheng , Helton Nichole , Fronick Catrina C. , Fulton Robert , Ramakrishnan Sai M. , Nonavinkere Srivatsan Sridhar , Heath Sharon E. , Westervelt Peter , Payton Jacqueline E. , Walter Matthew J. , Link Daniel C. , DiPersio John , Miller Christopher , Ley Timothy J.
Published: April 2023

Abstract
To better understand clonal and transcriptional adaptations after relapse in patients with acute myeloid leukemia (AML), we collected presentation and relapse samples from six normal karyotype AML cases. We performed enhanced whole-genome sequencing to characterize clonal evolution, and deep-coverage single-cell RNA sequencing on the same samples, which yielded 142,642 high-quality cells for analysis. Identifying expressed mutations in individual cells enabled us to discriminate between normal and AML cells, to identify coordinated changes in the genome and transcriptome, and to identify subclone-specific cell states. We quantified the coevolution of genetic and transcriptional heterogeneity during AML progression, and found that transcriptional changes were significantly correlated with genetic changes. However, transcriptional adaptation sometimes occurred independently, suggesting that clonal evolution does not represent all relevant biological changes. In three cases, we identified cells at diagnosis that likely seeded the relapse. Finally, these data revealed a conserved relapse-enriched leukemic cell state bearing markers of stemness, quiescence, and adhesion.
Significance:
These data enabled us to identify a relapse-enriched leukemic cell state with distinct transcriptional properties. Detailed case-by-case analyses elucidated the complex ways in which the AML genome, transcriptome, and immune microenvironment interact to evade chemotherapy. These analyses provide a blueprint for evaluating these factors in larger cohorts.

This article is highlighted in the In This Issue feature, p. 1
Data from Distinct Patterns of Clonal Evolution Drive Myelodysplastic Syndrome Progression to Secondary Acute Myeloid Leukemia
Authors: Guess Tiffany , Potts Chad R. , Bhat Pawan , Cartailler Justin A. , Brooks Austin , Holt Clinton , Yenamandra Ashwini , Wheeler Ferrin C. , Savona Michael R. , Cartailler Jean-Philippe , Ferrell P. Brent
Published: April 2023

Abstract
Clonal evolution in myelodysplastic syndrome (MDS) can result in clinical progression and secondary acute myeloid leukemia (sAML). To dissect changes in clonal architecture associated with this progression, we performed single-cell genotyping of paired MDS and sAML samples from 18 patients. Analysis of single-cell genotypes revealed patient-specific clonal evolution and enabled the assessment of single-cell mutational cooccurrence. We discovered that changes in clonal architecture proceed via distinct patterns, classified as static or dynamic, with dynamic clonal architectures having a more proliferative phenotype by blast count fold change. Proteogenomic analysis of a subset of patients confirmed that pathogenic mutations were primarily confined to primitive and mature myeloid cells, though we also identify rare but present mutations in lymphocyte subsets. Single-cell transcriptomic analysis of paired sample sets further identified gene sets and signaling pathways involved in two cases of progression. Together, these data define serial changes in the MDS clonal landscape with clinical and therapeutic implications.
Significance:
Precise clonal trajectories in MDS progression are made possible by single-cell genomic sequencing. Here we use this technology to uncover the patterns of clonal architecture and clonal evolution that drive the transformation to secondary AML. We further define the phenotypic and transcriptional changes of disease progression at the single-cell level.

See related article by Menssen et al., p. 330 (31).

See related commentary by Romine and van Galen, p. 270.

This article is highlighted in the In This Issue feature, p. 265