bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from Increased CaMKK2 Expression Is an Adaptive Response That Maintains the Fitness of Tumor-Infiltrating Natural Killer Cells
Authors: Juras Patrick K. , Racioppi Luigi , Mukherjee Debarati , Artham Sandeep , Gao Xia , Akullian D'Agostino Laura , Chang Ching-Yi , McDonnell Donald P.
Published: April 2023

Abstract
Calcium/calmodulin-dependent protein kinase kinase 2 (CaMKK2) is a key regulator of energy homeostasis in several cell types. Expression of this enzyme in tumor cells promotes proliferation and migration, and expression in tumor-associated immune cells facilitates M2 macrophage polarization and the development of myeloid-derived suppressor cells. Thus, there has been interest in developing CaMKK2 inhibitors as potential anticancer therapeutics. One impediment to clinical development of these agents is that the roles of CaMKK2 in other cellular compartments within the tumor immune microenvironment remain to be established. We report herein that CaMKK2 is expressed at low basal levels in natural killer (NK) cells but is upregulated in tumor-infiltrating NK cells where it suppresses apoptosis and promotes proliferation. NK cell–intrinsic deletion of CaMKK2 increased metastatic progression in several murine models, establishing a critical role for this enzyme in NK cell–mediated antitumor immunity. Ablation of the CaMKK2 protein, but not inhibition of its kinase activity, resulted in decreased NK-cell survival. These results indicate an important scaffolding function for CaMKK2 in NK cells and suggest that competitive CaMKK2 inhibitors and ligand-directed degraders (LDD) are likely to have distinct therapeutic utilities. Finally, we determined that intracellular lactic acid is a key driver of CaMKK2 expression, suggesting that upregulated expression of this enzyme is an adaptive mechanism by which tumor-infiltrating NK cells mitigate the deleterious effects of a lactic acid–rich tumor microenvironment. The findings of this study should inform strategies to manipulate the CaMKK2-signaling axis as a therapeutic approach in cancer.
Data from Protection of Regulatory T Cells from Fragility and Inactivation in the Tumor Microenvironment
Authors: Zhang Hongru , Tomar Vivek S. , Li Jinyang , Basavaraja Raghavendra , Yan Fangxue , Gui Jun , McBrearty Noreen , Costich Tara Lee , Beiting Daniel P. , Blanco M. Andres , Conejo-Garcia Jose R. , Saggu Gurpanna , Berger Allison , Nefedova Yulia , Gabrilovich Dmitry I. , Fuchs Serge Y.
Published: April 2023

Abstract
Fragility of regulatory T (Treg) cells manifested by the loss of neuropilin-1 (NRP1) and expression of IFNγ undermines the immune suppressive functions of Treg cells and contributes to the success of immune therapies against cancers. Intratumoral Treg cells somehow avoid fragility; however, the mechanisms by which Treg cells are protected from fragility in the tumor microenvironment are not well understood. Here, we demonstrate that the IFNAR1 chain of the type I IFN (IFN1) receptor was downregulated on intratumoral Treg cells. Downregulation of IFNAR1 mediated by p38α kinase protected Treg cells from fragility and maintained NRP1 levels, which were decreased in response to IFN1. Genetic or pharmacologic inactivation of p38α and stabilization of IFNAR1 in Treg cells induced fragility and inhibited their immune suppressive and protumorigenic activities. The inhibitor of sumoylation TAK981 (Subasumstat) upregulated IFNAR1, eliciting Treg fragility and inhibiting tumor growth in an IFNAR1-dependent manner. These findings describe a mechanism by which intratumoral Treg cells retain immunosuppressive activities and suggest therapeutic approaches for inducing Treg fragility and increasing the efficacy of immunotherapies.
Data from DKK1 Promotes Tumor Immune Evasion and Impedes Anti–PD-1 Treatment by Inducing Immunosuppressive Macrophages in Gastric Cancer
Authors: Shi Tao , Zhang Yipeng , Wang Yue , Song Xueru , Wang Hanbing , Zhou Xiaoyu , Liang Kaijie , Luo Yuting , Che Keying , Wang Xuan , Pan Yunfeng , Liu Fangcen , Yang Ju , Liu Qin , Yu Lixia , Liu Baorui , Wei Jia
Published: April 2023

Abstract
Tumor-associated macrophages (TAM) have key functions in promoting a suppressive tumor immune microenvironment (TIME) and immune evasion, which largely limit treatment effects of immune-checkpoint inhibitors (ICI) in different cancers, including gastric cancer. Dickkopf-1 (DKK1) is associated with tumor progression and has been shown to negatively regulate antitumor immunity, but the impact of DKK1 on the TIME remains incompletely understood. Here, we found that tumoral DKK1 expression is closely associated with worse survival and a suppressive TIME in gastric cancer patients. Results from in vitro coculture assays suggested that DKK1 induces macrophages to become immunosuppressive, thereby inhibiting antitumor responses of CD8+ T cells and natural killer (NK) cells. In vivo DKK1 blockade in syngeneic gastric cancer mouse models reprogramed TAMs to restore the immune activity in the TIME and triggered significant tumor regression. DKK1 blockade also directly reduced the growth of human gastric cancer tumors with high DKK1 expression in a xenograft model. Mechanistically, DKK1 interacted with cytoskeleton-associated protein 4 (CKAP4) on the macrophage surface and activated downstream PI3K–AKT signaling, which contributed to immune suppression. TAM reprogramming by DKK1 blockade also augmented the efficacy of programmed cell death protein-1 (PD-1) blockade in gastric cancer models. Therefore, our study provides novel insights into the role of DKK1 on tumor-intrinsic, innate, and adaptive antitumor immunity modulation and suggests that DKK1 is a promising immunotherapeutic target for enhanced PD-1 blockade therapy in gastric cancer.
Data from HRS Regulates Small Extracellular Vesicle PD-L1 Secretion and Is Associated with Anti–PD-1 Treatment Efficacy
Authors: Xiao Bo-Lin , Wang Xiao-Le , Xia Hou-Fu , Zhang Lin-Zhou , Wang Kui-Ming , Chen Zhuo-Kun , Zhong Ya-Hua , Jiang Huan-Gang , Zhou Fu-Xiang , Wang Wei , Chen Gai-Li , Chen Gang
Published: April 2023

Abstract
PD-L1 localized to immunosuppressive small extracellular vesicles (sEV PD-L1) contributes to tumor progression and is associated with resistance to immune-checkpoint blockade (ICB) therapy. Here, by establishing a screening strategy with a combination of tissue microarray (TMA), IHC staining, and measurement of circulating sEV PD-L1, we found that the endosomal sorting complex required for transport (ESCRT) member protein hepatocyte growth factor–regulated tyrosine kinase substrate (HRS) was the key regulator of circulating sEV PD-L1 in head and neck squamous cell carcinoma (HNSCC) patients. Increased HRS expression was found in tumor tissues and positively correlated with elevated circulating sEV PD-L1 in patients with HNSCC. The expression of HRS was also negatively correlated to the infiltration of CD8+ T cells. Knockdown of HRS markedly reduced PD-L1 expression in HNSCC cell–derived sEVs, and these sEVs from HRS knockdown cells showed decreased immunosuppressive effects on CD8+ T cells. Knockout of HRS inhibited tumor growth in immunocompetent mice together with PD-1 blockade. Moreover, a higher HRS expression was associated with a lower response rate to anti–PD-1 therapy in patients with HNSCC. In summary, our study reveals HRS, the core component of ESCRT-0, regulates sEV PD-L1 secretion, and is associated with the response to ICB therapy in patients with HNSCC, suggesting HRS is a promising target to improve cancer immunotherapy.
Data from Intratumoral Gene Transfer of mRNAs Encoding IL12 in Combination with Decoy-Resistant IL18 Improves Local and Systemic Antitumor Immunity
Authors: Cirella Assunta , Bolaños Elixabet , Di Trani Claudia Augusta , de Andrea Carlos E. , Sánchez-Gregorio Sandra , Etxeberria Iñaki , Gonzalez-Gomariz Jose , Olivera Irene , Brocco Davide , Glez-Vaz Javier , Luri-Rey Carlos , Azpilikueta Arantza , Rodríguez Inmaculada , Fernandez-Sendín Myriam , Egea Josune , Eguren Iñaki , Sanmamed Miguel F. , Palencia Belen , Teijeira Alvaro , Berraondo Pedro , Melero Ignacio
Published: April 2023

Abstract
IL12-based local gene therapy of cancer constitutes an active area of clinical research using plasmids, mRNAs, and viral vectors. To improve antitumor effects, we have experimentally tested the combination of mRNA constructs encoding IL12 and IL18. Moreover, we have used a form of IL18 [decoy-resistant IL18 (DR-18)] which has preserved bioactivity but does not bind to the IL18 binding protein decoy receptor. Both cytokines dramatically synergize to induce IFNγ release from mouse splenocytes, and, if systemically cotransferred to the liver, they mediate lethal toxicity. However, if given intratumorally to B16OVA tumor-bearing mice, the combination attains efficacy against the directly treated tumor and moderate tumor-delaying activity on distant noninjected lesions. Cotreatment was conducive to the presence of more activated CD8+ T cells in the treated and noninjected tumors. In keeping with these findings, the efficacy of treatment was contingent on the integrity of CD8+ T cells and cDC1 dendritic cells in the treated mice. Furthermore, efficacy of IL12 plus DR-18 local mRNA coinjection against distant concomitant tumors could be enhanced upon combination with anti–PD-1 mAb systemic treatment, thus defining a feasible synergistic immunotherapy strategy.
Data from Suppression of Tumor or Host Intrinsic CMTM6 Drives Antitumor Cytotoxicity in a PD-L1–Independent Manner
Authors: Long Yiru , Chen Runqiu , Yu Xiaolu , Tong Yongliang , Peng Xionghua , Li Fanglin , Hu Chao , Sun Jianhua , Gong Likun
Published: April 2023

Abstract
CKLF-like MARVEL transmembrane domain-containing protein 6 (CMTM6) is known to be a regulator of membranal programmed death ligand 1 (PD-L1) stability and a factor associated with malignancy progression, but the effects and mechanisms of CMTM6 on tumor growth, as well as its potential as a target for therapy, are still largely unknown. Here, we show that CMTM6 expression increased with tumor progression in both patients and mice. Ablation of CMTM6 significantly reduced human and murine tumor growth in a manner dependent on T-cell immunity. Tumor CMTM6 suppression broke resistance to immune-checkpoint inhibitors and remodeled the tumor immune microenvironment, as specific antitumor cytotoxicity was enhanced and contributed primarily to tumor inhibition. Without the PD-1/PD-L1 axis, CMTM6 suppression still significantly dampened tumor growth dependent on cytotoxic cells. Furthermore, we identified that CMTM6 was widely expressed on immune cells. T-cell CMTM6 levels increased with sustained immune activation and intratumoral immune exhaustion and affected T cell–intrinsic PD-L1 levels. Host CMTM6 knockout significantly restrained tumor growth in a manner dependent on CD8+ T cells and not entirely dependent on PD-L1. Thus, we developed and evaluated the antitumor efficacy of CMTM6-targeting adeno-associated virus (AAV), which effectively mobilized antitumor immunity and could be combined with various antitumor drugs. Our findings reveal that both tumor and host CMTM6 are involved in antitumor immunity with or without the PD-1/PD-L1 axis and that gene therapy targeting CMTM6 is a promising strategy for cancer immunotherapy.
Data from CD8+ T cell–Dependent Remodeling of the Tumor Microenvironment Overcomes Chemoresistance
Authors: Lao Liyan , Zeng Wenfeng , Huang Penghan , Chen Huiping , Jia Zishuo , Wang Pei , Huang Di , Chen Jianing , Nie Yan , Yang Linbin , Wu Wei , Liu Jiang
Published: April 2023

Abstract
The therapeutic efficacy of chemotherapy is in part a result of its ability to enhance adaptive antitumor immune responses. However, tumor cells exploit various evasion mechanisms to escape the immune attack and blunt chemosensitivity. Herein, we report that through single-cell profiling of the tumor immune microenvironment, we identified a subset of CD161-overexpressing CD8+ T cells enriched in chemoresistant tumors. CD161 engagement repressed the calcium influx and cytolytic capacity of CD8+ T cells through acid sphingomyelinase activation and ceramide generation. Targeting CD161 in adoptively transferred cytotoxic T lymphocytes enhanced antitumor immunity and reversed chemoresistance in patient-derived xenografts in vivo. Clinically, CD161 expression on CD8+ T cells was associated with chemoresistance and shortened patient survival. Our findings provide insights into novel immunosuppressive mechanisms in chemoresistance and highlight targeting CD161 as a potential therapeutic strategy.
Data from LEF1 Drives a Central Memory Program and Supports Antitumor Activity of Natural Killer T Cells
Authors: Ngai Ho , Barragan Gabriel A. , Tian Gengwen , Balzeau Julien C. , Zhang Chunchao , Courtney Amy N. , Guo Linjie , Xu Xin , Wood Michael S. , Drabek Janice M. , Demberg Thorsten , Sands Caroline M. , Chauvin-Fleurence Cynthia N. , Di Pierro Erica J. , Rosen Jeffrey M. , Metelitsa Leonid S.
Published: April 2023

Abstract
Vα24-invariant natural killer T cells (NKT) possess innate antitumor properties that can be exploited for cancer immunotherapy. We have shown previously that the CD62L+ central memory-like subset of these cells drives the in vivo antitumor activity of NKTs, but molecular mediators of NKT central memory differentiation remain unknown. Here, we demonstrate that relative to CD62L– cells, CD62L+ NKTs express a higher level of the gene encoding the Wnt/β-catenin transcription factor lymphoid enhancer binding factor 1 (LEF1) and maintain active Wnt/β-catenin signaling. CRISPR/Cas9-mediated LEF1 knockout reduced CD62L+ frequency after antigenic stimulation, whereas Wnt/β-catenin activator Wnt3a ligand increased CD62L+ frequency. LEF1 overexpression promoted NKT expansion and limited exhaustion following serial tumor challenge and was sufficient to induce a central memory–like transcriptional program in NKTs. In mice, NKTs expressing a GD2-specific chimeric-antigen receptor (CAR) with LEF1 demonstrated superior control of neuroblastoma xenograft tumors compared with control CAR-NKTs. These results identify LEF1 as a transcriptional activator of the NKT central memory program and advance development of NKT cell–based immunotherapy.

See related Spotlight by Van Kaer, p. 144
Figure S7 from Preneoplastic Alterations Define CLL DNA Methylome and Persist through Disease Progression and Therapy
Authors: Kretzmer Helene , Biran Anat , Purroy Noelia , Lemvigh Camilla K. , Clement Kendell , Gruber Michaela , Gu Hongcang , Rassenti Laura , Mohammad Arman W. , Lesnick Connie , Slager Susan L. , Braggio Esteban , Shanafelt Tait D. , Kay Neil E. , Fernandes Stacey M. , Brown Jennifer R. , Wang Lili , Li Shuqiang , Livak Kenneth J. , Neuberg Donna S. , Klages Sven , Timmermann Bernd , Kipps Thomas J. , Campo Elias , Gnirke Andreas , Wu Catherine J. , Meissner Alexander
Published: April 2023

Low count MBL already show signs of the altered DNA methylation landscape
Supplementary Figure S2 from Lysine Demethylase 5A Is Required for MYC-Driven Transcription in Multiple Myeloma
Authors: Ohguchi Hiroto , Park Paul M.C. , Wang Tingjian , Gryder Berkley E. , Ogiya Daisuke , Kurata Keiji , Zhang Xiaofeng , Li Deyao , Pei Chengkui , Masuda Takeshi , Johansson Catrine , Wimalasena Virangika K. , Kim Yong , Hino Shinjiro , Usuki Shingo , Kawano Yawara , Samur Mehmet K. , Tai Yu-Tzu , Munshi Nikhil C. , Matsuoka Masao , Ohtsuki Sumio , Nakao Mitsuyoshi , Minami Takashi , Lauberth Shannon , Khan Javed , Oppermann Udo , Durbin Adam D. , Anderson Kenneth C. , Hideshima Teru , Qi Jun
Published: April 2023

Supplementary Figure S2 shows the selectivity of JQKD82 against KDM5 in biochemical assay and in MM cells
Supplementary Figure S1 from Lysine Demethylase 5A Is Required for MYC-Driven Transcription in Multiple Myeloma
Authors: Ohguchi Hiroto , Park Paul M.C. , Wang Tingjian , Gryder Berkley E. , Ogiya Daisuke , Kurata Keiji , Zhang Xiaofeng , Li Deyao , Pei Chengkui , Masuda Takeshi , Johansson Catrine , Wimalasena Virangika K. , Kim Yong , Hino Shinjiro , Usuki Shingo , Kawano Yawara , Samur Mehmet K. , Tai Yu-Tzu , Munshi Nikhil C. , Matsuoka Masao , Ohtsuki Sumio , Nakao Mitsuyoshi , Minami Takashi , Lauberth Shannon , Khan Javed , Oppermann Udo , Durbin Adam D. , Anderson Kenneth C. , Hideshima Teru , Qi Jun
Published: April 2023

Supplementary Figure S1 shows that higher KDM5A expression is associated with poor prognosis in MM.
Supplementary Data from Reconstructing Complex Cancer Evolutionary Histories from Multiple Bulk DNA Samples Using Pairtree
Authors: Wintersinger Jeff A. , Dobson Stephanie M. , Kulman Ethan , Stein Lincoln D. , Dick John E. , Morris Quaid
Published: April 2023

Supplementary Data from Reconstructing Complex Cancer Evolutionary Histories from Multiple Bulk DNA Samples Using Pairtree
Supplementary Figure 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 Figure from Transcriptional Plasticity Drives Leukemia Immune Escape
Supplementary Data 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 Data from PU.1-Dependent Enhancer Inhibition Separates Tet2-Deficient Hematopoiesis from Malignant Transformation
Supplementary Data from Progenitor Hierarchy of Chronic Myelomonocytic Leukemia Identifies Inflammatory Monocytic-Biased Trajectory Linked to Worse Outcomes
Authors: Ferrall-Fairbanks Meghan C. , Dhawan Abhishek , Johnson Brian , Newman Hannah , Volpe Virginia , Letson Christopher , Ball Markus , Hunter Anthony M. , Balasis Maria E. , Kruer Traci , Ben-Crentsil Nana Adjoa , Kroeger Jodi L. , Balderas Robert , Komrokji Rami S. , Sallman David A. , Zhang Jing , Bejar Rafael , Altrock Philipp M. , Padron Eric
Published: April 2023

Supplementary Data from Progenitor Hierarchy of Chronic Myelomonocytic Leukemia Identifies Inflammatory Monocytic-Biased Trajectory Linked to Worse Outcomes
Supplementary Figure from Deep Morphology Learning Enhances Ex Vivo Drug Profiling-Based Precision Medicine
Authors: Heinemann Tim , Kornauth Christoph , Severin Yannik , Vladimer Gregory I. , Pemovska Tea , Hadzijusufovic Emir , Agis Hermine , Krauth Maria-Theresa , Sperr Wolfgang R. , Valent Peter , Jäger Ulrich , Simonitsch-Klupp Ingrid , Superti-Furga Giulio , Staber Philipp B. , Snijder Berend
Published: April 2023

Supplementary Figure from Deep Morphology Learning Enhances Ex Vivo Drug Profiling-Based Precision Medicine
Supplementary Table S3 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

GSEA analyses
Supplementary Tables S2-S4 from Impaired SARS-CoV-2 Variant Neutralization and CD8+ T-cell Responses Following 3 Doses of mRNA Vaccines in Myeloma: Correlation with Breakthrough Infections
Authors: Azeem Maryam I. , Nooka Ajay K. , Shanmugasundaram Uma , Cheedarla Narayanaiah , Potdar Sayalee , Manalo Renee Julia , Moreno Alberto , Switchenko Jeffrey M. , Cheedarla Suneethamma , Doxie Deon Bryant , Radzievski Roman , Ellis Madison Leigh , Manning Kelly E. , Wali Bushra , Valanparambil Rajesh M. , Maples Kathryn T. , Baymon Essence , Kaufman Jonathan L. , Hofmeister Craig C. , Joseph Nisha S. , Lonial Sagar , Roback John D. , Sette Alessandro , Ahmed Rafi , Suthar Mehul S. , Neish Andrew S. , Dhodapkar Madhav V. , Dhodapkar Kavita M.
Published: April 2023

Supplementary Table 2: Antibodies used for immune-phenotyping (CyTOF analysis). Supplementary Table 3: Antibodies used for flow cytometry. Supplementary Table 4: Antibodies used for AIM Assay (CyTOF analysis).
Data from A Tumor Suppressor Enhancer of PTEN in T-cell Development and Leukemia
Authors: Tottone Luca , Lancho Olga , Loh Jui-Wan , Singh Amartya , Kimura Shunsuke , Roels Juliette , Kuchmiy Anna , Strubbe Steven , Lawlor Matthew A. , da Silva-Diz Victoria , Luo Shirley , Gachet Stéphanie , García-Prieto Carlos A. , Hagelaar Rico , Esteller Manel , Meijerink Jules P.P. , Soulier Jean , Taghon Tom , Van Vlierberghe Pieter , Mullighan Charles G. , Khiabanian Hossein , Rocha Pedro P. , Herranz Daniel
Published: April 2023

Abstract
Long-range oncogenic enhancers play an important role in cancer. Yet, whether similar regulation of tumor suppressor genes is relevant remains unclear. Loss of expression of PTEN is associated with the pathogenesis of various cancers, including T-cell acute lymphoblastic leukemia (T-ALL). Here, we identify a highly conserved distal enhancer (PE) that interacts with the PTEN promoter in multiple hematopoietic populations, including T cells, and acts as a hub of relevant transcription factors in T-ALL. Consistently, loss of PE leads to reduced PTEN levels in T-ALL cells. Moreover, PE-null mice show reduced Pten levels in thymocytes and accelerated development of NOTCH1-induced T-ALL. Furthermore, secondary loss of PE in established leukemias leads to accelerated progression and a gene expression signature driven by Pten loss. Finally, we uncovered recurrent deletions encompassing PE in T-ALL, which are associated with decreased PTEN levels. Altogether, our results identify PE as the first long-range tumor suppressor enhancer directly implicated in cancer.
Significance:
Here, we identify a PTEN enhancer that is recurrently deleted in patients with T-ALL. Loss of this enhancer leads to reduced PTEN levels in T cells together with accelerated generation and progression of NOTCH1-induced leukemia in vivo. These results uncover long-range regulation of tumor suppressor genes as a relevant mechanism in cancer.

This article is highlighted in the In This Issue feature, p. 1
Data from Dissecting Clonal Hematopoiesis in Tissues of Patients with Classic Hodgkin Lymphoma
Authors: Venanzi Alessandra , Marra Andrea , Schiavoni Gianluca , Milner Sara G. , Limongello Roberto , Santi Alessia , Pettirossi Valentina , Ultimo Simona , Tasselli Luisa , Pucciarini Alessandra , Falini Lorenza , Sciabolacci Sofia , Martelli Maria Paola , Sportoletti Paolo , Ascani Stefano , Falini Brunangelo , Tiacci Enrico
Published: April 2023

Abstract
Clonal hematopoiesis predisposes to hematologic malignancies. However, clonal hematopoiesis is understudied in classic Hodgkin lymphoma (cHL), a mature B-cell neoplasm exhibiting the most abundant microenvironment. We analyzed clonal hematopoiesis in 40 cHL cases by sequencing microdissected tumor cells and matched normal cells from blood and/or lymph nodes. Five patients had blood and/or tissue clonal hematopoiesis. In three of five patients (all failing first-line therapy), clonal hematopoiesis spread through the tissue microenvironment extensively, and featured mutant DNMT3AR882H, KRASG60D, and DNMT3AR882H+TET2Q1274* in 33%, 92%, and 60% of nonneoplastic cells, respectively. In the latter case, DNMT3A/TET2-mutant clonal hematopoiesis seeded the neoplastic clone, which was infected by the Epstein–Barr virus and showed almost no other somatic mutations exome-wide. In the former case, DNMT3A-mutant clonal hematopoiesis did not originate the neoplastic clone despite dominating the blood and B-cell lineage (∼94% leukocytes; ∼96% mature blood B cells), yet led to NPM1-mutated acute myeloid leukemia 6 years after therapy for cHL. Our results expand to cHL the spectrum of hematologic malignancies associated with clonal hematopoiesis.
Significance:
Clonal hematopoiesis can be present in the cHL tissue, can give rise to the tumor clone, and can spread to large parts of its microenvironment. Even when massive, clonal hematopoiesis does not always give rise to the neoplastic clone of multiple myeloid and lymphoid neoplasms occurring in the same patient.
Data from Single-Cell Analysis of the Multicellular Ecosystem in Viral Carcinogenesis by HTLV-1
Authors: Koya Junji , Saito Yuki , Kameda Takuro , Kogure Yasunori , Yuasa Mitsuhiro , Nagasaki Joji , McClure Marni B. , Shingaki Sumito , Tabata Mariko , Tahira Yuki , Akizuki Keiichi , Kamiunten Ayako , Sekine Masaaki , Shide Kotaro , Kubuki Yoko , Hidaka Tomonori , Kitanaka Akira , Nakano Nobuaki , Utsunomiya Atae , Togashi Yosuke , Ogawa Seishi , Shimoda Kazuya , Kataoka Keisuke
Published: April 2023

Abstract
Premalignant clonal expansion of human T-cell leukemia virus type-1 (HTLV-1)–infected cells occurs before viral carcinogenesis. Here we characterize premalignant cells and the multicellular ecosystem in HTLV-1 infection with and without adult T-cell leukemia/lymphoma (ATL) by genome sequencing and single-cell simultaneous transcriptome and T/B-cell receptor sequencing with surface protein analysis. We distinguish malignant phenotypes caused by HTLV-1 infection and leukemogenesis and dissect clonal evolution of malignant cells with different clinical behavior. Within HTLV-1–infected cells, a regulatory T-cell phenotype associates with premalignant clonal expansion. We also delineate differences between virus- and tumor-related changes in the nonmalignant hematopoietic pool, including tumor-specific myeloid propagation. In a newly generated conditional knockout mouse model recapitulating T-cell–restricted CD274 (encoding PD-L1) gene lesions found in ATL, we demonstrate that PD-L1 overexpressed by T cells is transferred to surrounding cells, leading to their PD-L1 upregulation. Our findings provide insights into clonal evolution and immune landscape of multistep virus carcinogenesis.
Significance:
Our multimodal single-cell analyses comprehensively dissect the cellular and molecular alterations of the peripheral blood in HTLV-1 infection, with and without progression to leukemia. This study not only sheds light on premalignant clonal expansion in viral carcinogenesis, but also helps to devise novel diagnostic and therapeutic strategies for HTLV-1–related disorders.

This article is highlighted in the In This Issue feature, p. 403
Data from How to Provide the Needed Protection from COVID-19 to Patients with Hematologic Malignancies
Authors: Ribas Antoni , Dhodapkar Madhav V. , Campbell Katie M. , Davies Faith E. , Gore Steven D. , Levy Ronald , Greenberger Lee M.
Published: April 2023

AbstractSummary:
Patients with hematologic malignancies are particularly vulnerable to COVID-19 infections, and upon a pooled data analysis of 24 publications, there is evidence that they have suboptimal antibody responses to COVID-19 vaccination and boosters. To provide them the needed additional protection from COVID-19, it is imperative to achieve a 100% full immunization rate in health care workers and adult caretakers, and to foster research to test higher doses and repeated rounds of COVID-19 vaccines and the use of passive immune prophylaxis and therapy.
Data from Lysine Demethylase 5A Is Required for MYC-Driven Transcription in Multiple Myeloma
Authors: Ohguchi Hiroto , Park Paul M.C. , Wang Tingjian , Gryder Berkley E. , Ogiya Daisuke , Kurata Keiji , Zhang Xiaofeng , Li Deyao , Pei Chengkui , Masuda Takeshi , Johansson Catrine , Wimalasena Virangika K. , Kim Yong , Hino Shinjiro , Usuki Shingo , Kawano Yawara , Samur Mehmet K. , Tai Yu-Tzu , Munshi Nikhil C. , Matsuoka Masao , Ohtsuki Sumio , Nakao Mitsuyoshi , Minami Takashi , Lauberth Shannon , Khan Javed , Oppermann Udo , Durbin Adam D. , Anderson Kenneth C. , Hideshima Teru , Qi Jun
Published: April 2023

Abstract
Lysine demethylase 5A (KDM5A) is a negative regulator of histone H3 lysine 4 trimethy­lation (H3K4me3), a histone mark associated with activate gene transcription. We identify that KDM5A interacts with the P-TEFb complex and cooperates with MYC to control MYC-targeted genes in multiple myeloma cells. We develop a cell-permeable and selective KDM5 inhibitor, JQKD82, that increases H3K4me3 but paradoxically inhibits downstream MYC-driven transcriptional output in vitro and in vivo. Using genetic ablation together with our inhibitor, we establish that KDM5A supports MYC target gene transcription independent of MYC itself by supporting TFIIH (CDK7)- and P-TEFb (CDK9)–mediated phosphorylation of RNAPII. These data identify KDM5A as a unique vulnerability in multiple myeloma functioning through regulation of MYC target gene transcription and establish JQKD82 as a tool compound to block KDM5A function as a potential therapeutic strategy for multiple myeloma.
Significance:
We delineate the function of KDM5A in activating the MYC-driven transcriptional landscape. We develop a cell-permeable KDM5 inhibitor to define the activating role of KDM5A on MYC target gene expression and implicate the therapeutic potential of this compound in mouse models and multiple myeloma patient samples.

See related video from the AACR Annual Meeting 2021: https://vimeo.com/554896826
Data from Reconstructing Complex Cancer Evolutionary Histories from Multiple Bulk DNA Samples Using Pairtree
Authors: Wintersinger Jeff A. , Dobson Stephanie M. , Kulman Ethan , Stein Lincoln D. , Dick John E. , Morris Quaid
Published: April 2023

Abstract
Cancers are composed of genetically distinct subpopulations of malignant cells. DNA-sequencing data can be used to determine the somatic point mutations specific to each population and build clone trees describing the evolutionary relationships between them. These clone trees can reveal critical points in disease development and inform treatment. Pairtree is a new method that constructs more accurate and detailed clone trees than previously possible using variant allele frequency data from one or more bulk cancer samples. It does so by first building a Pairs Tensor that captures the evolutionary relationships between pairs of subpopulations, and then it uses these relations to constrain clone trees and infer violations of the infinite sites assumption. Pairtree can accurately build clone trees using up to 100 samples per cancer that contain 30 or more subclonal populations. On 14 B-progenitor acute lymphoblastic leukemias, Pairtree replicates or improves upon expert-derived clone tree reconstructions.
Significance:
Clone trees illustrate the evolutionary history of a cancer and can provide insights into how the disease changed through time (e.g., between diagnosis and relapse). Pairtree uses DNA-sequencing data from many samples of the same cancer to build more detailed and accurate clone trees than previously possible.

See related commentary by Miller, p. 176.

This article is highlighted in the In This Issue feature, p. 171.
Data from CD20-Targeted Therapy Ablates De Novo Antibody Response to Vaccination but Spares Preestablished Immunity
Authors: Shree Tanaya , Shankar Vishnu , Lohmeyer Julian J.K. , Czerwinski Debra K. , Schroers-Martin Joseph G. , Rodriguez Gladys M. , Beygi Sara , Kanegai Alyssa M. , Corbelli Karen S. , Gabriel Etelka , Kurtz David M. , Khodadoust Michael S. , Gupta Neel K. , Maeda Lauren S. , Advani Ranjana H. , Alizadeh Ash A. , Levy Ronald
Published: April 2023

Abstract
To obtain a deeper understanding of poor responses to COVID-19 vaccination in patients with lymphoma, we assessed blocking antibodies, total anti-spike IgG, and spike-specific memory B cells in the peripheral blood of 126 patients with lymphoma and 20 age-matched healthy controls 1 and 4 months after COVID-19 vaccination. Fifty-five percent of patients developed blocking antibodies postvaccination, compared with 100% of controls. When evaluating patients last treated from days to nearly 18 years prior to vaccination, time since last anti-CD20 was a significant independent predictor of vaccine response. None of 31 patients who had received anti-CD20 treatment within 6 months prior to vaccination developed blocking antibodies. In contrast, patients who initiated anti-CD20 treatment shortly after achieving a vaccine-induced antibody response tended to retain that response during treatment, suggesting a policy of immunizing prior to treatment whenever possible.
Significance:
In a large cohort of patients with B-cell lymphoma, time since anti-CD20 treatment was an independent predictor of neutralizing antibody response to COVID-19 vaccination. Comparing patients who received anti-CD20 treatment before or after vaccination, we demonstrate that vaccinating first can generate an antibody response that endures through anti-CD20–containing treatment.

This article is highlighted in the In This Issue feature, p. 85
Data from Convergent Clonal Evolution of Signaling Gene Mutations Is a Hallmark of Myelodysplastic Syndrome Progression
Authors: Menssen Andrew J. , Khanna Ajay , Miller Christopher A. , Nonavinkere Srivatsan Sridhar , Chang Gue Su , Shao Jin , Robinson Joshua , O'Laughlin Michele , Fronick Catrina C. , Fulton Robert S. , Brendel Kimberly , Heath Sharon E. , Saba Raya , Welch John S. , Spencer David H. , Payton Jacqueline E. , Westervelt Peter , DiPersio John F. , Link Daniel C. , Schuelke Matthew J. , Jacoby Meagan A. , Duncavage Eric J. , Ley Timothy J. , Walter Matthew J.
Published: April 2023

Abstract
Progression from myelodysplastic syndromes (MDS) to secondary acute myeloid leukemia (AML) is associated with the acquisition and expansion of subclones. Our understanding of subclone evolution during progression, including the frequency and preferred order of gene mutation acquisition, remains incomplete. Sequencing of 43 paired MDS and secondary AML samples identified at least one signaling gene mutation in 44% of MDS and 60% of secondary AML samples, often below the level of standard sequencing detection. In addition, 19% of MDS and 47% of secondary AML patients harbored more than one signaling gene mutation, almost always in separate, coexisting subclones. Signaling gene mutations demonstrated diverse patterns of clonal evolution during disease progression, including acquisition, expansion, persistence, and loss of mutations, with multiple patterns often coexisting in the same patient. Multivariate analysis revealed that MDS patients who had a signaling gene mutation had a higher risk of AML progression, potentially providing a biomarker for progression.
Significance:
Subclone expansion is a hallmark of progression from MDS to secondary AML. Subclonal signaling gene mutations are common at MDS (often at low levels), show complex and convergent patterns of clonal evolution, and are associated with future progression to secondary AML.

See related article by Guess et al., p. 316 (33).

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

This article is highlighted in the In This Issue feature, p. 265
Data from The Cell Type–Specific 5hmC Landscape and Dynamics of Healthy Human Hematopoiesis and TET2-Mutant Preleukemia
Authors: Nakauchi Yusuke , Azizi Armon , Thomas Daniel , Corces M. Ryan , Reinisch Andreas , Sharma Rajiv , Cruz Hernandez David , Köhnke Thomas , Karigane Daiki , Fan Amy , Martinez-Krams Daniel , Stafford Melissa , Kaur Satinder , Dutta Ritika , Phan Paul , Ediriwickrema Asiri , McCarthy Erin , Ning Yuhong , Phillips Tierney , Ellison Christopher K. , Guler Gulfem D. , Bergamaschi Anna , Ku Chin-Jen , Levy Samuel , Majeti Ravindra
Published: April 2023

Abstract
The conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) is a key step in DNA demethylation that is mediated by ten–eleven translocation (TET) enzymes, which require ascorbate/vitamin C. Here, we report the 5hmC landscape of normal hematopoiesis and identify cell type–specific 5hmC profiles associated with active transcription and chromatin accessibility of key hematopoietic regulators. We utilized CRISPR/Cas9 to model TET2 loss-of-function mutations in primary human hematopoietic stem and progenitor cells (HSPC). Disrupted cells exhibited increased colonies in serial replating, defective erythroid/megakaryocytic differentiation, and in vivo competitive advantage and myeloid skewing coupled with reduction of 5hmC at erythroid-associated gene loci. Azacitidine and ascorbate restored 5hmC abundance and slowed or reverted the expansion of TET2-mutant clones in vivo. These results demonstrate the key role of 5hmC in normal hematopoiesis and TET2-mutant phenotypes and raise the possibility of utilizing these agents to further our understanding of preleukemia and clonal hematopoiesis.
Significance:
We show that 5-hydroxymethylation profiles are cell type–specific and associated with transcriptional abundance and chromatin accessibility across human hematopoiesis. TET2 loss caused aberrant growth and differentiation phenotypes and disrupted 5hmC and transcriptional landscapes. Treatment of TET2 KO HSPCs with ascorbate or azacitidine reverted 5hmC profiles and restored aberrant phenotypes.

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

Abstract
Relapse of acute myeloid leukemia (AML) after allogeneic bone marrow transplantation has been linked to immune evasion due to reduced expression of major histocompatibility complex class II (MHCII) genes through unknown mechanisms. In this work, we developed CORENODE, a computational algorithm for genome-wide transcription network decomposition that identified a transcription factor (TF) tetrad consisting of IRF8, MYB, MEF2C, and MEIS1, regulating MHCII expression in AML cells. We show that reduced MHCII expression at relapse is transcriptionally driven by combinatorial changes in the expression of these TFs, where MYB and IRF8 play major opposing roles, acting independently of the IFNγ/CIITA pathway. Beyond the MHCII genes, MYB and IRF8 antagonistically regulate a broad genetic program responsible for cytokine signaling and T-cell stimulation that displays reduced expression at relapse. A small number of cells with altered TF abundance and silenced MHCII expression are present at the time of initial leukemia diagnosis, likely contributing to eventual relapse.
Significance:
Our findings point to an adaptive transcriptional mechanism of AML evolution after allogeneic transplantation whereby combinatorial fluctuations of TF expression under immune pressure result in the selection of cells with a silenced T-cell stimulation program.

This article is highlighted in the In This Issue feature, p. 369
Data from Anti-spike T-cell and Antibody Responses to SARS-CoV-2 mRNA Vaccines in Patients with Hematologic Malignancies
Authors: Greenberger Lee M. , Saltzman Larry A. , Gruenbaum Lore M. , Xu Jun , Reddy Sneha T. , Senefeld Jonathon W. , Johnson Patrick W. , Fields Paul A. , Sanders Catherine , DeGennaro Louis J. , Nichols Gwen L.
Published: April 2023

Abstract
The anti-spike T-cell and antibody responses to SARS-CoV-2 mRNA vaccines in patients with B-cell malignancies were examined in a real-world setting. A next-generation sequencing (NGS)–based molecular assay was used to assess SARS-CoV-2–specific T-cell responses. After the second dose, 58% (166/284) of seropositive and 45% (99/221) of seronegative patients display anti-spike T cells. The percentage of patients who displayed T-cell response was higher among patients receiving mRNA-1273 vaccines compared with those receiving BNT162b2 vaccines. After the third vaccination, 40% (137/342) of patients seroconverted, although only 22% displayed sufficient antibody levels associated with the production of neutralizing antibodies. 97% (717/738) of patients who were seropositive before the third dose had markedly elevated anti-spike antibody levels. Anti-spike antibody levels, but not T-cell responses, were depressed by B cell–directed therapies. Vaccinated patients with B-cell malignancies with a poor response to SARS-CoV-2 vaccines may remain vulnerable to COVID-19 infections.
Significance:
This study represents the first investigation of SARS-CoV-2–specific immune responses to vaccination in a patient registry using an NGS-based method for T-cell receptor repertoire–based analysis combined with anti-spike antibody assessments. Vaccinated patients with B cell–derived hematologic malignancies are likely at higher risk of infection or severe COVID-19.

This article is highlighted in the In This Issue feature, p. 476
Data from In Vivo Monitoring of Polycythemia Vera Development Reveals Carbonic Anhydrase 1 as a Potent Therapeutic Target
Authors: Murakami Shohei , Barroca Vilma , Perié Leïla , Bravard Anne , Bernardino-Sgherri Jacqueline , Tisserand Amandine , Devanand Caroline , Edmond Valérie , Magniez Aurélie , Tenreira Bento Sabrina , Torres Claire , Pasquier Florence , Plo Isabelle , Vainchenker William , Villeval Jean-Luc , Roméo Paul-Henri , Lewandowski Daniel
Published: April 2023

Abstract
Current murine models of myeloproliferative neoplasms (MPNs) cannot examine how MPNs progress from a single bone marrow source to the entire hematopoietic system. Thus, using transplantation of knock-in JAK2V617F hematopoietic cells into a single irradiated leg, we show development of polycythemia vera (PV) from a single anatomic site in immunocompetent mice. Barcode experiments reveal that grafted JAK2V617F stem/progenitor cells migrate from the irradiated leg to nonirradiated organs such as the contralateral leg and spleen, which is strictly required for development of PV. Mutant cells colonizing the nonirradiated leg efficiently induce PV in nonconditioned recipient mice and contain JAK2V617F hematopoietic stem/progenitor cells that express high levels of carbonic anhydrase 1 (CA1), a peculiar feature also found in CD34+ cells from patients with PV. Finally, genetic and pharmacologic inhibition of CA1 efficiently suppresses PV development and progression in mice and decreases PV patients’ erythroid progenitors, strengthening CA1 as a potent therapeutic target for PV.
Significance:
Follow-up of hematopoietic malignancies from their initiating anatomic site is crucial for understanding their development and discovering new therapeutic avenues. We developed such an approach, used it to characterize PV progression, and identified CA1 as a promising therapeutic target of PV.

This article is highlighted in the In This Issue feature, p. 265
Data from Targeting the EIF2AK1 Signaling Pathway Rescues Red Blood Cell Production in SF3B1-Mutant Myelodysplastic Syndromes With Ringed Sideroblasts
Authors: Adema Vera , Ma Feiyang , Kanagal-Shamanna Rashmi , Thongon Natthakan , Montalban-Bravo Guillermo , Yang Hui , Peslak Scott A. , Wang Feng , Acha Pamela , Sole Francesc , Lockyer Pamela , Cassari Margherita , Maciejewski Jaroslaw P. , Visconte Valeria , Gañán-Gómez Irene , Song Yuanbin , Bueso-Ramos Carlos , Pellegrini Matteo , Tan Tuyet M. , Bejar Rafael , Carew Jennifer S. , Halene Stephanie , Santini Valeria , Al-Atrash Gheath , Clise-Dwyer Karen , Garcia-Manero Guillermo , Blobel Gerd A. , Colla Simona
Published: April 2023

Abstract
SF3B1 mutations, which occur in 20% of patients with myelodysplastic syndromes (MDS), are the hallmarks of a specific MDS subtype, MDS with ringed sideroblasts (MDS-RS), which is characterized by the accumulation of erythroid precursors in the bone marrow and primarily affects the elderly population. Here, using single-cell technologies and functional validation studies of primary SF3B1-mutant MDS-RS samples, we show that SF3B1 mutations lead to the activation of the EIF2AK1 pathway in response to heme deficiency and that targeting this pathway rescues aberrant erythroid differentiation and enables the red blood cell maturation of MDS-RS erythroblasts. These data support the development of EIF2AK1 inhibitors to overcome transfusion dependency in patients with SF3B1-mutant MDS-RS with impaired red blood cell production.
Significance:
MDS-RS are characterized by significant anemia. Patients with MDS-RS die from a shortage of red blood cells and the side effects of iron overload due to their constant need for transfusions. Our study has implications for the development of therapies to achieve long-lasting hematologic responses.

This article is highlighted in the In This Issue feature, p. 476
Data from ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia
Authors: Kodgule Rohan , Goldman Joshua W. , Monovich Alexander C. , Saari Travis , Aguilar Athalee R. , Hall Cody N. , Rajesh Niharika , Gupta Juhi , Chu Shih-Chun A. , Ye Li , Gurumurthy Aishwarya , Iyer Ashwin , Brown Noah A. , Chiang Mark Y. , Cieslik Marcin P. , Ryan Russell J.H.
Published: April 2023

Abstract
Distal enhancers play critical roles in sustaining oncogenic gene-expression programs. We identify aberrant enhancer-like activation of GGAA tandem repeats as a characteristic feature of B-cell acute lymphoblastic leukemia (B-ALL) with genetic defects of the ETV6 transcriptional repressor, including ETV6–RUNX1+ and ETV6-null B-ALL. We show that GGAA repeat enhancers are direct activators of previously identified ETV6–RUNX1+/− like B-ALL “signature” genes, including the likely leukemogenic driver EPOR. When restored to ETV6-deficient B-ALL cells, ETV6 directly binds to GGAA repeat enhancers, represses their acetylation, downregulates adjacent genes, and inhibits B-ALL growth. In ETV6-deficient B-ALL cells, we find that the ETS transcription factor ERG directly binds to GGAA microsatellite enhancers and is required for sustained activation of repeat enhancer-activated genes. Together, our findings reveal an epigenetic gatekeeper function of the ETV6 tumor suppressor gene and establish microsatellite enhancers as a key mechanism underlying the unique gene-expression program of ETV6–RUNX1+/− like B-ALL.
Significance:
We find a unifying mechanism underlying a leukemia subtype-defining gene-expression signature that relies on repetitive elements with poor conservation between humans and rodents. The ability of ETV6 to antagonize promiscuous, nonphysiologic ERG activity may shed light on other roles of these key regulators in hematolymphoid development and human disease.

See related commentary by Mercher, p. 2.

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