ABSTRACT
Neoantigens arise from mutations in cancer cells and are important targets of T cell-mediated anti-tumor immunity. Here, we report the first open-label, phase Ib clinical trial of a personalized neoantigen-based vaccine, NEO-PV-01, in combination with PD-1 blockade in patients with advanced melanoma, non-small cell lung cancer, or bladder cancer. This analysis of 82 patients demonstrated that the regimen was safe, with no treatment-related serious adverse events observed. De novo neoantigen-specific CD4+ and CD8+ T cell responses were observed post-vaccination in all of the patients. The vaccine-induced T cells had a cytotoxic phenotype and were capable of trafficking to the tumor and mediating cell killing. In addition, epitope spread to neoantigens not included in the vaccine was detected post-vaccination. These data support the safety and immunogenicity of this regimen in patients with advanced solid tumors (Clinicaltrials.gov: NCT02897765).
Subject(s)
Cancer Vaccines/immunology , Immunotherapy/methods , Precision Medicine/methods , Aged , Antigens, Neoplasm/genetics , Antigens, Neoplasm/immunology , CD8-Positive T-Lymphocytes/immunology , Cancer Vaccines/genetics , Carcinoma, Non-Small-Cell Lung/drug therapy , Carcinoma, Non-Small-Cell Lung/immunology , Female , Humans , Kaplan-Meier Estimate , Male , Melanoma/drug therapy , Melanoma/immunology , Middle Aged , Mutation , Nivolumab/therapeutic use , Programmed Cell Death 1 Receptor/immunology , Programmed Cell Death 1 Receptor/metabolism , Urinary Bladder Neoplasms/drug therapy , Urinary Bladder Neoplasms/immunologyABSTRACT
Accurate prediction of long-term outcomes remains a challenge in the care of cancer patients. Due to the difficulty of serial tumor sampling, previous prediction tools have focused on pretreatment factors. However, emerging non-invasive diagnostics have increased opportunities for serial tumor assessments. We describe the Continuous Individualized Risk Index (CIRI), a method to dynamically determine outcome probabilities for individual patients utilizing risk predictors acquired over time. Similar to "win probability" models in other fields, CIRI provides a real-time probability by integrating risk assessments throughout a patient's course. Applying CIRI to patients with diffuse large B cell lymphoma, we demonstrate improved outcome prediction compared to conventional risk models. We demonstrate CIRI's broader utility in analogous models of chronic lymphocytic leukemia and breast adenocarcinoma and perform a proof-of-concept analysis demonstrating how CIRI could be used to develop predictive biomarkers for therapy selection. We envision that dynamic risk assessment will facilitate personalized medicine and enable innovative therapeutic paradigms.
Subject(s)
Biomarkers, Tumor/metabolism , Breast Neoplasms/pathology , Lymphoma, Large B-Cell, Diffuse/pathology , Precision Medicine , Algorithms , Antineoplastic Agents/therapeutic use , Biomarkers, Tumor/blood , Breast Neoplasms/drug therapy , Breast Neoplasms/mortality , Circulating Tumor DNA/blood , Female , Humans , Kaplan-Meier Estimate , Lymphoma, Large B-Cell, Diffuse/drug therapy , Lymphoma, Large B-Cell, Diffuse/mortality , Neoadjuvant Therapy , Prognosis , Progression-Free Survival , Proportional Hazards Models , Risk Assessment , Treatment OutcomeABSTRACT
New opportunities are needed to increase immune checkpoint blockade (ICB) benefit. Whereas the interferon (IFN)γ pathway harbors both ICB resistance factors and therapeutic opportunities, this has not been systematically investigated for IFNγ-independent signaling routes. A genome-wide CRISPR/Cas9 screen to sensitize IFNγ receptor-deficient tumor cells to CD8 T cell elimination uncovered several hits mapping to the tumor necrosis factor (TNF) pathway. Clinically, we show that TNF antitumor activity is only limited in tumors at baseline and in ICB non-responders, correlating with its low abundance. Taking advantage of the genetic screen, we demonstrate that ablation of the top hit, TRAF2, lowers the TNF cytotoxicity threshold in tumors by redirecting TNF signaling to favor RIPK1-dependent apoptosis. TRAF2 loss greatly enhanced the therapeutic potential of pharmacologic inhibition of its interaction partner cIAP, another screen hit, thereby cooperating with ICB. Our results suggest that selective reduction of the TNF cytotoxicity threshold increases the susceptibility of tumors to immunotherapy.
Subject(s)
CD8-Positive T-Lymphocytes/immunology , Immunotherapy , Tumor Necrosis Factor-alpha/metabolism , Animals , Apoptosis/drug effects , CD8-Positive T-Lymphocytes/cytology , CD8-Positive T-Lymphocytes/metabolism , Cell Line, Tumor , Humans , Inhibitor of Apoptosis Proteins/metabolism , Interferon-gamma/metabolism , Kaplan-Meier Estimate , Male , Mice , Mice, Inbred C57BL , Neoplasms/mortality , Neoplasms/therapy , RNA, Guide, Kinetoplastida/metabolism , Receptor-Interacting Protein Serine-Threonine Kinases/metabolism , Receptors, Interferon/deficiency , Receptors, Interferon/genetics , Signal Transduction/drug effects , TNF Receptor-Associated Factor 2/deficiency , TNF Receptor-Associated Factor 2/genetics , Tumor Necrosis Factor-alpha/pharmacology , Interferon gamma ReceptorABSTRACT
Neutrophils are a component of the tumor microenvironment and have been predominantly associated with cancer progression. Using a genetic approach complemented by adoptive transfer, we found that neutrophils are essential for resistance against primary 3-methylcholantrene-induced carcinogenesis. Neutrophils were essential for the activation of an interferon-γ-dependent pathway of immune resistance, associated with polarization of a subset of CD4- CD8- unconventional αß T cells (UTCαß). Bulk and single-cell RNA sequencing (scRNA-seq) analyses unveiled the innate-like features and diversity of UTCαß associated with neutrophil-dependent anti-sarcoma immunity. In selected human tumors, including undifferentiated pleomorphic sarcoma, CSF3R expression, a neutrophil signature and neutrophil infiltration were associated with a type 1 immune response and better clinical outcome. Thus, neutrophils driving UTCαß polarization and type 1 immunity are essential for resistance against murine sarcomas and selected human tumors.
Subject(s)
Disease Resistance , Neoplasms/pathology , Neutrophils/immunology , Sarcoma/pathology , T-Lymphocytes/metabolism , Animals , Chromones/toxicity , Disease Resistance/immunology , Humans , Immunity, Innate , Interferon-gamma/genetics , Interferon-gamma/metabolism , Interleukin-12/genetics , Interleukin-12/metabolism , Kaplan-Meier Estimate , Macrophages/immunology , Macrophages/metabolism , Male , Mice , Mice, Inbred C57BL , Mice, Knockout , Neoplasms/immunology , Neoplasms/mortality , Neutrophil Infiltration , Neutrophils/cytology , Neutrophils/metabolism , Receptors, Colony-Stimulating Factor/metabolism , Sarcoma/chemically induced , Sarcoma/immunology , T-Lymphocytes/cytology , T-Lymphocytes/immunology , Tumor MicroenvironmentABSTRACT
For tumors to progress efficiently, cancer cells must overcome barriers of oxidative stress. Although dietary antioxidant supplementation or activation of endogenous antioxidants by NRF2 reduces oxidative stress and promotes early lung tumor progression, little is known about its effect on lung cancer metastasis. Here, we show that long-term supplementation with the antioxidants N-acetylcysteine and vitamin E promotes KRAS-driven lung cancer metastasis. The antioxidants stimulate metastasis by reducing levels of free heme and stabilizing the transcription factor BACH1. BACH1 activates transcription of Hexokinase 2 and Gapdh and increases glucose uptake, glycolysis rates, and lactate secretion, thereby stimulating glycolysis-dependent metastasis of mouse and human lung cancer cells. Targeting BACH1 normalized glycolysis and prevented antioxidant-induced metastasis, while increasing endogenous BACH1 expression stimulated glycolysis and promoted metastasis, also in the absence of antioxidants. We conclude that BACH1 stimulates glycolysis-dependent lung cancer metastasis and that BACH1 is activated under conditions of reduced oxidative stress.
Subject(s)
Antioxidants/pharmacology , Basic-Leucine Zipper Transcription Factors/metabolism , Glycolysis/drug effects , Lung Neoplasms/pathology , Animals , Antioxidants/administration & dosage , Basic-Leucine Zipper Transcription Factors/genetics , Cell Movement/drug effects , Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating)/metabolism , Heme/metabolism , Hexokinase/antagonists & inhibitors , Hexokinase/genetics , Hexokinase/metabolism , Humans , Kaplan-Meier Estimate , Lung Neoplasms/drug therapy , Lung Neoplasms/mortality , Mice , Mice, Inbred NOD , Mice, Knockout , Mice, SCID , NF-E2-Related Factor 2/metabolism , Neoplasm Metastasis , RNA Interference , RNA, Small Interfering/metabolism , Reactive Oxygen Species/metabolismABSTRACT
Approximately 30% of human lung cancers acquire mutations in either Keap1 or Nfe2l2, resulting in the stabilization of Nrf2, the Nfe2l2 gene product, which controls oxidative homeostasis. Here, we show that heme triggers the degradation of Bach1, a pro-metastatic transcription factor, by promoting its interaction with the ubiquitin ligase Fbxo22. Nrf2 accumulation in lung cancers causes the stabilization of Bach1 by inducing Ho1, the enzyme catabolizing heme. In mouse models of lung cancers, loss of Keap1 or Fbxo22 induces metastasis in a Bach1-dependent manner. Pharmacological inhibition of Ho1 suppresses metastasis in a Fbxo22-dependent manner. Human metastatic lung cancer display high levels of Ho1 and Bach1. Bach1 transcriptional signature is associated with poor survival and metastasis in lung cancer patients. We propose that Nrf2 activates a metastatic program by inhibiting the heme- and Fbxo22-mediated degradation of Bach1, and that Ho1 inhibitors represent an effective therapeutic strategy to prevent lung cancer metastasis.
Subject(s)
Basic-Leucine Zipper Transcription Factors/metabolism , Lung Neoplasms/pathology , NF-E2-Related Factor 2/metabolism , Animals , Basic-Leucine Zipper Transcription Factors/antagonists & inhibitors , Basic-Leucine Zipper Transcription Factors/genetics , Cell Line, Tumor , Cell Movement , F-Box Proteins/antagonists & inhibitors , F-Box Proteins/genetics , F-Box Proteins/metabolism , Female , Heme Oxygenase-1/antagonists & inhibitors , Heme Oxygenase-1/genetics , Heme Oxygenase-1/metabolism , Humans , Kaplan-Meier Estimate , Kelch-Like ECH-Associated Protein 1/antagonists & inhibitors , Kelch-Like ECH-Associated Protein 1/genetics , Kelch-Like ECH-Associated Protein 1/metabolism , Lung Neoplasms/metabolism , Lung Neoplasms/mortality , Male , Mice , Mice, Inbred C57BL , Mice, Knockout , NF-E2-Related Factor 2/genetics , Neoplasm Metastasis , RNA Interference , RNA, Small Interfering/metabolism , Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors , Receptors, Cytoplasmic and Nuclear/genetics , Receptors, Cytoplasmic and Nuclear/metabolism , Transcriptional ActivationABSTRACT
Although the pathological significance of tumor-associated macrophage (TAM) heterogeneity is still poorly understood, TAM reprogramming is viewed as a promising anticancer therapy. Here we show that a distinct subset of TAMs (F4/80hiCD115hiC3aRhiCD88hi), endowed with high rates of heme catabolism by the stress-responsive enzyme heme oxygenase-1 (HO-1), plays a critical role in shaping a prometastatic tumor microenvironment favoring immunosuppression, angiogenesis and epithelial-to-mesenchymal transition. This population originates from F4/80+HO-1+ bone marrow (BM) precursors, accumulates in the blood of tumor bearers and preferentially localizes at the invasive margin through a mechanism dependent on the activation of Nrf2 and coordinated by the NF-κB1-CSF1R-C3aR axis. Inhibition of F4/80+HO-1+ TAM recruitment or myeloid-specific deletion of HO-1 blocks metastasis formation and improves anticancer immunotherapy. Relative expression of HO-1 in peripheral monocyte subsets, as well as in tumor lesions, discriminates survival among metastatic melanoma patients. Overall, these results identify a distinct cancer-induced HO-1+ myeloid subgroup as a new antimetastatic target and prognostic blood marker.
Subject(s)
Biomarkers, Tumor/metabolism , Heme Oxygenase-1/metabolism , Lung Neoplasms/immunology , Melanoma/immunology , Skin Neoplasms/immunology , Tumor-Associated Macrophages/immunology , Animals , Antineoplastic Agents, Immunological/pharmacology , Antineoplastic Agents, Immunological/therapeutic use , Biomarkers, Tumor/antagonists & inhibitors , Biomarkers, Tumor/blood , Cell Line, Tumor/transplantation , Chemotherapy, Adjuvant/methods , Disease Models, Animal , Epithelial-Mesenchymal Transition/immunology , Female , Heme/metabolism , Heme Oxygenase-1/antagonists & inhibitors , Heme Oxygenase-1/blood , Heme Oxygenase-1/genetics , Humans , Kaplan-Meier Estimate , Lung Neoplasms/mortality , Lung Neoplasms/secondary , Lung Neoplasms/therapy , Male , Melanoma/mortality , Melanoma/secondary , Melanoma/therapy , Membrane Proteins/antagonists & inhibitors , Membrane Proteins/genetics , Membrane Proteins/metabolism , Mice , Mice, Transgenic , Myeloid Progenitor Cells/immunology , Myeloid Progenitor Cells/metabolism , Skin Neoplasms/mortality , Skin Neoplasms/pathology , Skin Neoplasms/therapy , Tumor Escape/drug effects , Tumor Microenvironment/drug effects , Tumor Microenvironment/immunology , Tumor-Associated Macrophages/metabolismABSTRACT
Regulatory T (Treg) cells are a barrier for tumor immunity and a target for immunotherapy. Using single-cell transcriptomics, we found that CD4+ T cells infiltrating primary and metastatic colorectal cancer and non-small-cell lung cancer are highly enriched for two subsets of comparable size and suppressor function comprising forkhead box protein P3+ Treg and eomesodermin homolog (EOMES)+ type 1 regulatory T (Tr1)-like cells also expressing granzyme K and chitinase-3-like protein 2. EOMES+ Tr1-like cells, but not Treg cells, were clonally related to effector T cells and were clonally expanded in primary and metastatic tumors, which is consistent with their proliferation and differentiation in situ. Using chitinase-3-like protein 2 as a subset signature, we found that the EOMES+ Tr1-like subset correlates with disease progression but is also associated with response to programmed cell death protein 1-targeted immunotherapy. Collectively, these findings highlight the heterogeneity of Treg cells that accumulate in primary tumors and metastases and identify a new prospective target for cancer immunotherapy.
Subject(s)
Carcinoma, Non-Small-Cell Lung/immunology , Clonal Hematopoiesis/immunology , Colorectal Neoplasms/immunology , Lung Neoplasms/immunology , T-Lymphocytes, Regulatory/immunology , Adult , Aged , Aged, 80 and over , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/secondary , Carcinoma, Non-Small-Cell Lung/therapy , Cell Differentiation/genetics , Cell Differentiation/immunology , Cell Proliferation/genetics , Chemotherapy, Adjuvant/methods , Chitinases/metabolism , Colectomy , Colon/pathology , Colon/surgery , Colorectal Neoplasms/genetics , Colorectal Neoplasms/pathology , Colorectal Neoplasms/therapy , Datasets as Topic , Disease Progression , Drug Resistance, Neoplasm/immunology , Female , Flow Cytometry , Forkhead Transcription Factors/metabolism , Gene Expression Regulation, Neoplastic/immunology , Granzymes/metabolism , Humans , Immune Checkpoint Inhibitors/pharmacology , Immune Checkpoint Inhibitors/therapeutic use , Kaplan-Meier Estimate , Lung Neoplasms/genetics , Lung Neoplasms/pathology , Lung Neoplasms/therapy , Male , Middle Aged , Primary Cell Culture , Programmed Cell Death 1 Receptor/antagonists & inhibitors , RNA-Seq , Single-Cell Analysis , T-Box Domain Proteins/metabolism , T-Lymphocytes, Regulatory/metabolismABSTRACT
For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale.
Subject(s)
Neoplasms/pathology , Databases, Genetic , Genomics , Humans , Kaplan-Meier Estimate , Neoplasms/genetics , Neoplasms/mortality , Proportional Hazards ModelsABSTRACT
The immune system is critical in modulating cancer progression, but knowledge of immune composition, phenotype, and interactions with tumor is limited. We used multiplexed ion beam imaging by time-of-flight (MIBI-TOF) to simultaneously quantify in situ expression of 36 proteins covering identity, function, and immune regulation at sub-cellular resolution in 41 triple-negative breast cancer patients. Multi-step processing, including deep-learning-based segmentation, revealed variability in the composition of tumor-immune populations across individuals, reconciled by overall immune infiltration and enriched co-occurrence of immune subpopulations and checkpoint expression. Spatial enrichment analysis showed immune mixed and compartmentalized tumors, coinciding with expression of PD1, PD-L1, and IDO in a cell-type- and location-specific manner. Ordered immune structures along the tumor-immune border were associated with compartmentalization and linked to survival. These data demonstrate organization in the tumor-immune microenvironment that is structured in cellular composition, spatial arrangement, and regulatory-protein expression and provide a framework to apply multiplexed imaging to immune oncology.
Subject(s)
Lymphocytes/immunology , Mass Spectrometry , Triple Negative Breast Neoplasms/pathology , Tumor Microenvironment/immunology , Antigens, CD/metabolism , B7-H1 Antigen/metabolism , Cluster Analysis , Female , Humans , Indoleamine-Pyrrole 2,3,-Dioxygenase/metabolism , Kaplan-Meier Estimate , Lymphocytes/cytology , Lymphocytes/metabolism , Machine Learning , Principal Component Analysis , Programmed Cell Death 1 Receptor/metabolism , Spatial Analysis , Triple Negative Breast Neoplasms/diagnostic imaging , Triple Negative Breast Neoplasms/immunology , Triple Negative Breast Neoplasms/mortality , Lymphocyte Activation Gene 3 ProteinABSTRACT
Most high-grade serous ovarian cancer (HGSOC) patients develop resistance to platinum-based chemotherapy and recur, but 15% remain disease free over a decade. To discover drivers of long-term survival, we quantitatively analyzed the proteomes of platinum-resistant and -sensitive HGSOC patients from minute amounts of formalin-fixed, paraffin-embedded tumors. This revealed cancer/testis antigen 45 (CT45) as an independent prognostic factor associated with a doubling of disease-free survival in advanced-stage HGSOC. Phospho- and interaction proteomics tied CT45 to DNA damage pathways through direct interaction with the PP4 phosphatase complex. In vitro, CT45 regulated PP4 activity, and its high expression led to increased DNA damage and platinum sensitivity. CT45-derived HLA class I peptides, identified by immunopeptidomics, activate patient-derived cytotoxic T cells and promote tumor cell killing. This study highlights the power of clinical cancer proteomics to identify targets for chemo- and immunotherapy and illuminate their biological roles.
Subject(s)
Antigens, Neoplasm/physiology , Drug Resistance, Neoplasm/genetics , Proteomics/methods , Aged , Amino Acid Sequence/genetics , Antineoplastic Agents/therapeutic use , DNA Methylation/drug effects , Female , Gene Expression Regulation, Neoplastic/genetics , Humans , Immunotherapy/methods , Kaplan-Meier Estimate , Middle Aged , Neoplasm Recurrence, Local/drug therapy , Ovarian Neoplasms/drug therapy , Phosphoprotein Phosphatases/metabolism , Phosphoprotein Phosphatases/physiology , PrognosisABSTRACT
Extracellular proTGF-ß is covalently linked to "milieu" molecules in the matrix or on cell surfaces and is latent until TGF-ß is released by integrins. Here, we show that LRRC33 on the surface of microglia functions as a milieu molecule and enables highly localized, integrin-αVß8-dependent TGF-ß activation. Lrrc33-/- mice lack CNS vascular abnormalities associated with deficiency in TGF-ß-activating integrins but have microglia with a reactive phenotype and after 2 months develop ascending paraparesis with loss of myelinated axons and death by 5 months. Whole bone marrow transplantation results in selective repopulation of Lrrc33-/- brains with WT microglia and halts disease progression. The phenotypes of WT and Lrrc33-/- microglia in the same brain suggest that there is little spreading of TGF-ß activated from one microglial cell to neighboring microglia. Our results suggest that interactions between integrin-bearing cells and cells bearing milieu molecule-associated TGF-ß provide localized and selective activation of TGF-ß.
Subject(s)
Carrier Proteins/metabolism , Microglia/metabolism , Nervous System/metabolism , Transforming Growth Factor beta/metabolism , Animals , Axons/metabolism , Bone Marrow Transplantation , Brain/metabolism , Carrier Proteins/classification , Carrier Proteins/genetics , Cells, Cultured , Integrins/metabolism , Kaplan-Meier Estimate , Macrophages/cytology , Macrophages/immunology , Macrophages/metabolism , Mice , Mice, Inbred C57BL , Mice, Knockout , Microglia/cytology , Mutagenesis, Site-Directed , Neurodegenerative Diseases/mortality , Neurodegenerative Diseases/pathology , Neurodegenerative Diseases/therapy , Phylogeny , Protein Binding , Protein Precursors/genetics , Protein Precursors/metabolism , Transforming Growth Factor beta/geneticsABSTRACT
Genetic drivers of cancer can be dysregulated through epigenetic modifications of DNA. Although the critical role of DNA 5-methylcytosine (5mC) in the regulation of transcription is recognized, the functions of other non-canonical DNA modifications remain obscure. Here, we report the identification of novel N6-methyladenine (N6-mA) DNA modifications in human tissues and implicate this epigenetic mark in human disease, specifically the highly malignant brain cancer glioblastoma. Glioblastoma markedly upregulated N6-mA levels, which co-localized with heterochromatic histone modifications, predominantly H3K9me3. N6-mA levels were dynamically regulated by the DNA demethylase ALKBH1, depletion of which led to transcriptional silencing of oncogenic pathways through decreasing chromatin accessibility. Targeting the N6-mA regulator ALKBH1 in patient-derived human glioblastoma models inhibited tumor cell proliferation and extended the survival of tumor-bearing mice, supporting this novel DNA modification as a potential therapeutic target for glioblastoma. Collectively, our results uncover a novel epigenetic node in cancer through the DNA modification N6-mA.
Subject(s)
Adenine/analogs & derivatives , Brain Neoplasms/pathology , DNA Methylation , Glioblastoma/pathology , Adenine/analysis , Adenine/chemistry , Adult , Aged , AlkB Homolog 1, Histone H2a Dioxygenase/antagonists & inhibitors , AlkB Homolog 1, Histone H2a Dioxygenase/genetics , AlkB Homolog 1, Histone H2a Dioxygenase/metabolism , Animals , Astrocytes/cytology , Astrocytes/metabolism , Brain Neoplasms/metabolism , Brain Neoplasms/mortality , Cell Hypoxia , Child , Epigenomics , Female , Glioblastoma/metabolism , Glioblastoma/mortality , Heterochromatin/metabolism , Histones/metabolism , Humans , Kaplan-Meier Estimate , Male , Mice , Middle Aged , Neoplastic Stem Cells/cytology , Neoplastic Stem Cells/metabolism , RNA Interference , RNA, Small Interfering/metabolism , Tumor Suppressor Protein p53/metabolismABSTRACT
The fusion oncoprotein CBFß-SMMHC, expressed in leukemia cases with chromosome 16 inversion, drives leukemia development and maintenance by altering the activity of the transcription factor RUNX1. Here, we demonstrate that CBFß-SMMHC maintains cell viability by neutralizing RUNX1-mediated repression of MYC expression. Upon pharmacologic inhibition of the CBFß-SMMHC/RUNX1 interaction, RUNX1 shows increased binding at three MYC distal enhancers, where it represses MYC expression by mediating the replacement of the SWI/SNF complex component BRG1 with the polycomb-repressive complex component RING1B, leading to apoptosis. Combining the CBFß-SMMHC inhibitor with the BET inhibitor JQ1 eliminates inv(16) leukemia in human cells and a mouse model. Enhancer-interaction analysis indicated that the three enhancers are physically connected with the MYC promoter, and genome-editing analysis demonstrated that they are functionally implicated in deregulation of MYC expression. This study reveals a mechanism whereby CBFß-SMMHC drives leukemia maintenance and suggests that inhibitors targeting chromatin activity may prove effective in inv(16) leukemia therapy.
Subject(s)
Apoptosis , Chromatin/metabolism , Oncogene Proteins, Fusion/antagonists & inhibitors , Proto-Oncogene Proteins c-myc/metabolism , Animals , Apoptosis/drug effects , Azepines/pharmacology , Azepines/therapeutic use , Benzimidazoles/pharmacology , Benzimidazoles/therapeutic use , Cell Line, Tumor , Chromosomal Proteins, Non-Histone/chemistry , Chromosomal Proteins, Non-Histone/metabolism , Chromosome Inversion/drug effects , Core Binding Factor Alpha 2 Subunit/chemistry , Core Binding Factor Alpha 2 Subunit/metabolism , DNA/chemistry , DNA/metabolism , DNA Helicases/metabolism , Disease Models, Animal , Humans , Kaplan-Meier Estimate , Leukemia, Myeloid, Acute/drug therapy , Leukemia, Myeloid, Acute/mortality , Leukemia, Myeloid, Acute/pathology , Mice , Mice, Inbred C57BL , Nuclear Proteins/metabolism , Oncogene Proteins, Fusion/metabolism , Polycomb Repressive Complex 1/metabolism , Promoter Regions, Genetic , Protein Binding , Proto-Oncogene Proteins c-myc/genetics , Transcription Factors/chemistry , Transcription Factors/metabolism , Triazoles/pharmacology , Triazoles/therapeutic useABSTRACT
Deconvolution of regulatory mechanisms that drive transcriptional programs in cancer cells is key to understanding tumor biology. Herein, we present matched transcriptome (scRNA-seq) and chromatin accessibility (scATAC-seq) profiles at single-cell resolution from human ovarian and endometrial tumors processed immediately following surgical resection. This dataset reveals the complex cellular heterogeneity of these tumors and enabled us to quantitatively link variation in chromatin accessibility to gene expression. We show that malignant cells acquire previously unannotated regulatory elements to drive hallmark cancer pathways. Moreover, malignant cells from within the same patients show substantial variation in chromatin accessibility linked to transcriptional output, highlighting the importance of intratumoral heterogeneity. Finally, we infer the malignant cell type-specific activity of transcription factors. By defining the regulatory logic of cancer cells, this work reveals an important reliance on oncogenic regulatory elements and highlights the ability of matched scRNA-seq/scATAC-seq to uncover clinically relevant mechanisms of tumorigenesis in gynecologic cancers.
Subject(s)
Ovarian Neoplasms/genetics , Ovarian Neoplasms/metabolism , RNA, Small Cytoplasmic/genetics , Aged , Carcinogenesis , Chromatin/metabolism , Enhancer Elements, Genetic , Epithelial-Mesenchymal Transition , Female , Gastrointestinal Stromal Tumors/genetics , Gene Library , Genetic Techniques , Genomics , Humans , Kaplan-Meier Estimate , Middle Aged , Oncogenes , Ovary/metabolism , Proteomics , RNA-Seq , Regulatory Elements, Transcriptional , Transcription Factors/metabolism , TranscriptomeABSTRACT
Graft-versus-host disease (GVHD) in the gastrointestinal (GI) tract is the principal determinant of lethality following allogeneic bone marrow transplantation (BMT). Here, we examined the mechanisms that initiate GVHD, including the relevant antigen-presenting cells. MHC class II was expressed on intestinal epithelial cells (IECs) within the ileum at steady state but was absent from the IECs of germ-free mice. IEC-specific deletion of MHC class II prevented the initiation of lethal GVHD in the GI tract. MHC class II expression on IECs was absent from mice deficient in the TLR adaptors MyD88 and TRIF and required IFNγ secretion by lamina propria lymphocytes. IFNγ responses are characteristically driven by IL-12 secretion from myeloid cells. Antibiotic-mediated depletion of the microbiota inhibited IL-12/23p40 production by ileal macrophages. IL-12/23p40 neutralization prevented MHC class II upregulation on IECs and initiation of lethal GVHD in the GI tract. Thus, MHC class II expression by IECs in the ileum initiates lethal GVHD, and blockade of IL-12/23p40 may represent a readily translatable therapeutic strategy.
Subject(s)
Antigen Presentation/immunology , Antigen-Presenting Cells/immunology , Gastrointestinal Microbiome/immunology , Graft vs Host Disease/etiology , Histocompatibility Antigens Class II/immunology , Intestinal Mucosa/immunology , Animals , Antigen-Presenting Cells/metabolism , Biomarkers , Cytokines/metabolism , Disease Susceptibility , Female , Gene Expression , Graft vs Host Disease/mortality , Histocompatibility Antigens Class II/genetics , Ileum/metabolism , Intestinal Mucosa/metabolism , Intestinal Mucosa/microbiology , Kaplan-Meier Estimate , Lymphocyte Subsets/immunology , Lymphocyte Subsets/metabolism , Male , Mice , Mice, Transgenic , Prognosis , Promoter Regions, Genetic , Signal TransductionABSTRACT
BACKGROUND: The Resynchronization-Defibrillation for Ambulatory Heart Failure Trial (RAFT) showed a greater benefit with respect to mortality at 5 years among patients who received cardiac-resynchronization therapy (CRT) than among those who received implantable cardioverter-defibrillators (ICDs). However, the effect of CRT on long-term survival is not known. METHODS: We randomly assigned patients with New York Heart Association (NYHA) class II or III heart failure, a left ventricular ejection fraction of 30% or less, and an intrinsic QRS duration of 120 msec or more (or a paced QRS duration of 200 msec or more) to receive either an ICD alone or a CRT defibrillator (CRT-D). We assessed long-term outcomes among patients at the eight highest-enrolling participating sites. The primary outcome was death from any cause; the secondary outcome was a composite of death from any cause, heart transplantation, or implantation of a ventricular assist device. RESULTS: The trial enrolled 1798 patients, of whom 1050 were included in the long-term survival trial; the median duration of follow-up for the 1050 patients was 7.7 years (interquartile range, 3.9 to 12.8), and the median duration of follow-up for those who survived was 13.9 years (interquartile range, 12.8 to 15.7). Death occurred in 405 of 530 patients (76.4%) assigned to the ICD group and in 370 of 520 patients (71.2%) assigned to the CRT-D group. The time until death appeared to be longer for those assigned to receive a CRT-D than for those assigned to receive an ICD (acceleration factor, 0.80; 95% confidence interval, 0.69 to 0.92; P = 0.002). A secondary-outcome event occurred in 412 patients (77.7%) in the ICD group and in 392 (75.4%) in the CRT-D group. CONCLUSIONS: Among patients with a reduced ejection fraction, a widened QRS complex, and NYHA class II or III heart failure, the survival benefit associated with receipt of a CRT-D as compared with ICD appeared to be sustained during a median of nearly 14 years of follow-up. (RAFT ClinicalTrials.gov number, NCT00251251.).
Subject(s)
Cardiac Resynchronization Therapy , Defibrillators, Implantable , Heart Failure , Humans , Heart Failure/mortality , Heart Failure/physiopathology , Heart Failure/therapy , Kaplan-Meier Estimate , Stroke Volume , Treatment Outcome , Ventricular Function, Left , Electrocardiography , Follow-Up Studies , Time FactorsABSTRACT
BACKGROUND: Patients with severe aortic stenosis and a small aortic annulus are at risk for impaired valvular hemodynamic performance and associated adverse cardiovascular clinical outcomes after transcatheter aortic-valve replacement (TAVR). METHODS: We randomly assigned patients with symptomatic severe aortic stenosis and an aortic-valve annulus area of 430 mm2 or less in a 1:1 ratio to undergo TAVR with either a self-expanding supraannular valve or a balloon-expandable valve. The coprimary end points, each assessed through 12 months, were a composite of death, disabling stroke, or rehospitalization for heart failure (tested for noninferiority) and a composite end point measuring bioprosthetic-valve dysfunction (tested for superiority). RESULTS: A total of 716 patients were treated at 83 sites in 13 countries (mean age, 80 years; 87% women; mean Society of Thoracic Surgeons Predicted Risk of Mortality, 3.3%). The Kaplan-Meier estimate of the percentage of patients who died, had a disabling stroke, or were rehospitalized for heart failure through 12 months was 9.4% with the self-expanding valve and 10.6% with the balloon-expandable valve (difference, -1.2 percentage points; 90% confidence interval [CI], -4.9 to 2.5; P<0.001 for noninferiority). The Kaplan-Meier estimate of the percentage of patients with bioprosthetic-valve dysfunction through 12 months was 9.4% with the self-expanding valve and 41.6% with the balloon-expandable valve (difference, -32.2 percentage points; 95% CI, -38.7 to -25.6; P<0.001 for superiority). The aortic-valve mean gradient at 12 months was 7.7 mm Hg with the self-expanding valve and 15.7 mm Hg with the balloon-expandable valve, and the corresponding values for additional secondary end points through 12 months were as follows: mean effective orifice area, 1.99 cm2 and 1.50 cm2; percentage of patients with hemodynamic structural valve dysfunction, 3.5% and 32.8%; and percentage of women with bioprosthetic-valve dysfunction, 10.2% and 43.3% (all P<0.001). Moderate or severe prosthesis-patient mismatch at 30 days was found in 11.2% of the patients in the self-expanding valve group and 35.3% of those in the balloon-expandable valve group (P<0.001). Major safety end points appeared to be similar in the two groups. CONCLUSIONS: Among patients with severe aortic stenosis and a small aortic annulus who underwent TAVR, a self-expanding supraannular valve was noninferior to a balloon-expandable valve with respect to clinical outcomes and was superior with respect to bioprosthetic-valve dysfunction through 12 months. (Funded by Medtronic; SMART ClinicalTrials.gov number, NCT04722250.).
Subject(s)
Aortic Valve Stenosis , Aortic Valve , Bioprosthesis , Heart Valve Prosthesis , Transcatheter Aortic Valve Replacement , Aged , Aged, 80 and over , Female , Humans , Male , Aortic Valve/surgery , Aortic Valve Stenosis/surgery , Aortic Valve Stenosis/complications , Bioprosthesis/adverse effects , Heart Failure , Kaplan-Meier Estimate , Postoperative Complications/etiology , Prosthesis Design , Prosthesis Failure , Stroke/etiology , Transcatheter Aortic Valve Replacement/adverse effectsABSTRACT
BACKGROUND: Recurrent cervical cancer is a life-threatening disease, with limited treatment options available when disease progression occurs after first-line combination therapy. METHODS: We conducted a phase 3, multinational, open-label trial of tisotumab vedotin as second- or third-line therapy in patients with recurrent or metastatic cervical cancer. Patients were randomly assigned, in a 1:1 ratio, to receive tisotumab vedotin monotherapy (2.0 mg per kilogram of body weight every 3 weeks) or the investigator's choice of chemotherapy (topotecan, vinorelbine, gemcitabine, irinotecan, or pemetrexed). The primary end point was overall survival. RESULTS: A total of 502 patients underwent randomization (253 were assigned to the tisotumab vedotin group and 249 to the chemotherapy group); the groups were similar with respect to demographic and disease characteristics. The median overall survival was significantly longer in the tisotumab vedotin group than in the chemotherapy group (11.5 months [95% confidence interval {CI}, 9.8 to 14.9] vs. 9.5 months [95% CI, 7.9 to 10.7]), results that represented a 30% lower risk of death with tisotumab vedotin than with chemotherapy (hazard ratio, 0.70; 95% CI, 0.54 to 0.89; two-sided P = 0.004). The median progression-free survival was 4.2 months (95% CI, 4.0 to 4.4) with tisotumab vedotin and 2.9 months (95% CI, 2.6 to 3.1) with chemotherapy (hazard ratio, 0.67; 95% CI, 0.54 to 0.82; two-sided P<0.001). The confirmed objective response rate was 17.8% in the tisotumab vedotin group and 5.2% in the chemotherapy group (odds ratio, 4.0; 95% CI, 2.1 to 7.6; two-sided P<0.001). A total of 98.4% of patients in the tisotumab vedotin group and 99.2% in the chemotherapy group had at least one adverse event that occurred during the treatment period (defined as the period from day 1 of dose 1 until 30 days after the last dose); grade 3 or greater events occurred in 52.0% and 62.3%, respectively. A total of 14.8% of patients stopped tisotumab vedotin treatment because of toxic effects. CONCLUSIONS: In patients with recurrent cervical cancer, second- or third-line treatment with tisotumab vedotin resulted in significantly greater efficacy than chemotherapy. (Funded by Genmab and Seagen [acquired by Pfizer]; innovaTV 301 ClinicalTrials.gov number, NCT04697628.).
Subject(s)
Antineoplastic Combined Chemotherapy Protocols , Neoplasm Recurrence, Local , Uterine Cervical Neoplasms , Humans , Female , Uterine Cervical Neoplasms/drug therapy , Uterine Cervical Neoplasms/mortality , Middle Aged , Neoplasm Recurrence, Local/drug therapy , Adult , Aged , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Antineoplastic Combined Chemotherapy Protocols/adverse effects , Kaplan-Meier Estimate , Antibodies, Monoclonal/therapeutic use , Antibodies, Monoclonal/adverse effects , Antibodies, Monoclonal/administration & dosage , Survival Analysis , Progression-Free Survival , Aged, 80 and overABSTRACT
BACKGROUND: Belantamab mafodotin had single-agent activity in patients with relapsed or refractory multiple myeloma, a finding that supports further evaluation of the agent in combination with standard-care therapies. METHODS: In this phase 3, open-label, randomized trial, we evaluated belantamab mafodotin, bortezomib, and dexamethasone (BVd), as compared with daratumumab, bortezomib, and dexamethasone (DVd), in patients who had progression of multiple myeloma after at least one line of therapy. The primary end point was progression-free survival. Key secondary end points were overall survival, response duration, and minimal residual disease (MRD)-negative status. RESULTS: In total, 494 patients were randomly assigned to receive BVd (243 patients) or DVd (251 patients). At a median follow-up of 28.2 months (range, 0.1 to 40.0), median progression-free survival was 36.6 months (95% confidence interval [CI], 28.4 to not reached) in the BVd group and 13.4 months (95% CI, 11.1 to 17.5) in the DVd group (hazard ratio for disease progression or death, 0.41; 95% CI, 0.31 to 0.53; P<0.001). Overall survival at 18 months was 84% in the BVd group and 73% in the DVd group. An analysis of the restricted mean response duration favored BVd over DVd (P<0.001). A complete response or better plus MRD-negative status occurred in 25% of the patients in the BVd group and 10% of those in the DVd group. Grade 3 or higher adverse events occurred in 95% of the patients in the BVd group and 78% of those in the DVd group. Ocular events were more common in the BVd group than in the DVd group (79% vs. 29%); such events were managed with dose modifications, and events of worsening visual acuity mostly resolved. CONCLUSIONS: As compared with DVd therapy, BVd therapy conferred a significant benefit with respect to progression-free survival among patients who had relapsed or refractory multiple myeloma after at least one line of therapy. Most patients had grade 3 or higher adverse events. (Funded by GSK; DREAMM-7 ClinicalTrials.gov number, NCT04246047; EudraCT number, 2018-003993-29.).