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| Open AccessFragment-sequencing unveils local tissue microenvironments at single-cell resolution
Experimentally preserving tissue microenvironments remains challenging for single-cell sequencing methods. Here, the authors introduce fragment-sequencing, a method that can preserve three-dimensional microenvironments in single-cell RNA-seq, thus allowing the reconstruction of spatial tissue niches.
- Kristina Handler
- , Karsten Bach
- & Andreas E. Moor
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Article
| Open AccessRobust mapping of spatiotemporal trajectories and cell–cell interactions in healthy and diseased tissues
The integration of spatial, imaging, and sequencing information enables the mapping of cellular dynamics within a tissue. Here, authors show three algorithms in stLearn software to accurately reveal spatial trajectory, detect cell-cell interactions, and impute missing data.
- Duy Pham
- , Xiao Tan
- & Quan H. Nguyen
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Article
| Open Access3D bioprinted multilayered cerebrovascular conduits to study cancer extravasation mechanism related with vascular geometry
Geometrical complexities of blood vessels alter biophysical behaviors of circulating tumor cells, influencing cancer metastasis. Here, the authors develop a 3D bioprinted in vitro brain blood vessel-on-a-chip to investigate continuities between vascular geometry and metastatic cancer development.
- Wonbin Park
- , Jae-Seong Lee
- & Dong-Woo Cho
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Article
| Open AccessID1 expressing macrophages support cancer cell stemness and limit CD8+ T cell infiltration in colorectal cancer
Inhibitor of differentiation 1 (ID1) has been described as a cancer-promoting factor and also involved in the formation of an immunosuppressive tumor microenvironment. Here the authors report that ID1-expressing tumor associated macrophages favor colorectal cancer progression by promoting cancer cell stemness and CD8+ T cell exclusion.
- Shuang Shang
- , Chen Yang
- & Fang Hua
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Article
| Open AccessCDC7 inhibition induces replication stress-mediated aneuploid cells with an inflammatory phenotype sensitizing tumors to immune checkpoint blockade
TAK-931 is a selective CDC7 inhibitor and can induce replication stress (RS)-mediated chromosomal instability with antitumoral activity. Here the authors show that TAK-931-induced RS generates aneuploid cells with an inflammatory phenotype, rendering tumors sensitive to immune-checkpoint blockade.
- Tomoko Yamamori Morita
- , Jie Yu
- & Akihiro Ohashi
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| Open AccessSimultaneous selection of nanobodies for accessible epitopes on immune cells in the tumor microenvironment
INSPIREseq discovers accessible epitopes in complex environments and leads to nanobodies targeting thousands of epitopes. This in vivo diversity selection identifies selective nanobodies, potentially expediting target discovery and drug development.
- Thillai V. Sekar
- , Eslam A. Elghonaimy
- & Todd A. Aguilera
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| Open AccessMoving closer towards a comprehensive view of tumor biology and microarchitecture using spatial transcriptomics
Spatial transcriptomic profiling of cancer has enabled spatial delineation of malignant transcriptional heterogeneity, intercellular communication, and organization of microanatomical structures within the tumor microenvironment. This technical breakthrough paves the way for the development of precision diagnostic methods and targeted therapies.
- Young Min Park
- & De-Chen Lin
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Article
| Open AccessCancer-associated fibroblasts actively compress cancer cells and modulate mechanotransduction
Cancer-associated fibroblasts (CAFs) can produce ECM and form a physical barrier around the tumour. Here, the authors show in transgenic mouse models and in vitro systems that CAFs are able to actively compress cancer cells using actomyosin contractility and this leads to a modulation of cancer cell mechanosensing and tumour reorganisation.
- Jorge Barbazan
- , Carlos Pérez-González
- & Danijela Matic Vignjevic
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Article
| Open AccessThe Lin28b/Wnt5a axis drives pancreas cancer through crosstalk between cancer associated fibroblasts and tumor epithelium
Crosstalk between tumor cells and the microenvironment is essential for tumor progression. Here, the authors show Pancreatic ductal adenocarcinoma (PDAC) epithelial cells with high level of Lin28b secrete Wnt5a to upregulate Lin28b expression in cancer-associated fibroblasts, which in turn promote growth of PDAC cells via production of PCSK9.
- Zhaoqi Shu
- , Minghe Fan
- & Ying Zhao
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Article
| Open AccessGlycerol-weighted chemical exchange saturation transfer nanoprobes allow 19F/1H dual-modality magnetic resonance imaging-guided cancer radiotherapy
Radiotherapy (RT) sensitizers have been used to overcome tumor hypoxia and improve response to RT. Here the authors design and characterize a pH and oxygen sensitive nano-molecular probe for imaging-guided cancer radiotherapy.
- Rong A
- , Haoyu Wang
- & Xilin Sun
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Article
| Open AccessIntegrin signaling is critical for myeloid-mediated support of T-cell acute lymphoblastic leukemia
Tumor-associated myeloid cells directly support progression of T-cell acute lymphoblastic leukemia (TALL). Here, the authors show that T-ALL cells must contact myeloid cells and activate integrin signaling and downstream FAK/PYK2 kinases to survive.
- Aram Lyu
- , Ryan S. Humphrey
- & Lauren I. R. Ehrlich
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Article
| Open AccessDistinct and targetable role of calcium-sensing receptor in leukaemia
Several parameters in the bone marrow (BM) niche regulate leukaemic stem cell status and disease progression. Here, the authors show that calcium-sensing receptor affects the location of acute myeloid leukaemia (AML) cells in the BM niche which influences self-renewal of leukaemic stem cells and AML development
- Raquel S. Pereira
- , Rahul Kumar
- & Daniela S. Krause
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| Open AccessSingle-cell analysis reveals altered tumor microenvironments of relapse- and remission-associated pediatric acute myeloid leukemia
Single-cell RNA-seq could help identify acute myeloid leukaemia (AML) patients at high risk of relapse after therapy. Here, the authors use single-cell RNA-seq from paediatric AML samples to construct a 7-gene signature that can identify malignant cells at diagnosis, which are distinctly associated with relapse or complete remission.
- Hope Mumme
- , Beena E. Thomas
- & Manoj Bhasin
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Article
| Open AccessTHBS1-producing tumor-infiltrating monocyte-like cells contribute to immunosuppression and metastasis in colorectal cancer
Thrombospondin-1 (THBS1) is a matricellular protein highly expressed in inflammatory processes, including cancer. Here the authors show that bone-marrow derived monocyte-like cells are the primary source of THBS1 in colorectal cancer, associated with mesenchymal characteristics, immunosuppression and a poor prognosis.
- Mayuki Omatsu
- , Yuki Nakanishi
- & Hiroshi Seno
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Article
| Open AccessCritical requirement of SOS1 for tumor development and microenvironment modulation in KRASG12D-driven lung adenocarcinoma
Critical regulators of RAS signaling pathways in oncogenic RAS-driven tumors remain to be explored. Here, the authors show the development of KRAS(G12D)-driven lung adenocarcinoma is dependent on SOS1, with dual roles in both tumor and stroma.
- Fernando C. Baltanás
- , Rósula García-Navas
- & Eugenio Santos
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Article
| Open AccessThe tumor microenvironment shows a hierarchy of cell-cell interactions dominated by fibroblasts
The tumor microenvironment (TME) is complex and heterogenous, with cancer cells and diverse non-malignant cells interacting with each other. Here the authors define the network of interactions between different cell types in the TME of breast cancer, identifying and characterizing a two-cell circuit of cancer associated fibroblasts and macrophages.
- Shimrit Mayer
- , Tomer Milo
- & Ruth Scherz-Shouval
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| Open AccessIntracellular Fusobacterium nucleatum infection attenuates antitumor immunity in esophageal squamous cell carcinoma
Fusobacterium nucleatum (Fn) is an oncogenic bacterium reported to promote esophageal squamous cell carcinoma (ESCC). Here the authors show that the virulence factor of Fn, Fn-Dps upregulates PD-L1 and that Fn promotes cell death in T-cells, hence, limiting the efficacy of immunotherapy in ESCC.
- Yiqiu Li
- , Shan Xing
- & Ge Zhang
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Article
| Open AccessPerformance of tumour microenvironment deconvolution methods in breast cancer using single-cell simulated bulk mixtures
Multiple computational approaches have been developed for the deconvolution of cells in the tumour microenvironment (TME) using bulk RNA-seq data. Here, the authors use breast cancer single-cell RNA-seq data to produce simulated bulk data, with which they compare the performance of nine TME deconvolution methods.
- Khoa A. Tran
- , Venkateswar Addala
- & Nicola Waddell
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| Open AccessStressed target cancer cells drive nongenetic reprogramming of CAR T cells and solid tumor microenvironment
The emergency of a high frequency of early memory T cells has been associated with clinical success of CAR T cell therapy. Here the authors show that target cancer cells stressed by disulfiram/copper complexes and ionizing radiation favour the reprogramming of CAR T cells that acquire memory-like characteristics, associated with prolonged anti-tumor response in preclinical solid tumor models.
- Yufeng Wang
- , David L. Drum
- & Xinhui Wang
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Article
| Open AccessStromal heterogeneity may explain increased incidence of metaplastic breast cancer in women of African descent
Breast cancer patients of African ancestry face worse clinical outcomes, so understanding related cellular and molecular features remains critical. Here, the authors show that stromal cells that are particularly enriched in breast cancer patients with African ancestry can trans-differentiate into different lineages and can be transformed into metaplastic carcinoma.
- Brijesh Kumar
- , Aditi S. Khatpe
- & Harikrishna Nakshatri
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Article
| Open AccessFunctionally distinct cancer-associated fibroblast subpopulations establish a tumor promoting environment in squamous cell carcinoma
During the progression of cutaneous squamous cell carcinoma (cSCC), dermal fibroblasts become activated into cancer-associated fibroblasts (CAFs) which are pro-tumorigenic. Here, using single-cell RNA sequencing of patients’ samples at different stages of cSCC progression, the authors identify two main CAF subsets and deduce their potential functions using bioinformatics.
- Sabrina Schütz
- , Llorenç Solé-Boldo
- & Frank Lyko
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Article
| Open AccessImmunophenotypic correlates of sustained MRD negativity in patients with multiple myeloma
How the immune response is involved in the response to multiple myeloma after treatment is not fully understood. Here the authors investigate how lenalidomide treatment in newly diagnosed MM patients affects the immune microenvironment in the blood and bone marrow and compare between responses to treatment.
- David G. Coffey
- , Francesco Maura
- & Ola Landgren
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| Open AccessLow-dose carboplatin modifies the tumor microenvironment to augment CAR T cell efficacy in human prostate cancer models
Although CAR T therapy has greatly improved the therapeutic prospects for haematological malignancies, it is not yet widely used for solid tumors, such as prostate cancer. Here, using prostate cancer patient-derived xenografts, the authors demonstrate the efficacy of CAR T cells specific for Lewis Y antigen when combined with low-dose carboplatin.
- L. H. Porter
- , J. J. Zhu
- & G. P. Risbridger
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Article
| Open AccessCoordinated single-cell tumor microenvironment dynamics reinforce pancreatic cancer subtype
Multiple studies have characterised the tumour microenvironment (TME) of pancreatic ductal adenocarcinoma (PDAC) using single-cell RNA-seq. Here, the authors integrate the data from such single-cell studies to provide a cohesive analysis of the PDAC TME, revealing cell types and interactions that are associated with PDAC phenotypes.
- Ki Oh
- , Yun Jae Yoo
- & Richard A. Moffitt
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Article
| Open AccessSingle cell transcriptomic analyses implicate an immunosuppressive tumor microenvironment in pancreatic cancer liver metastasis
The metastatic tumour microenvironment in pancreatic ductal adenocarcinoma (PDAC) remains to be explored. Here, the authors perform single cell RNA sequencing analysis for synchronously resected PDAC primary tumours and matched liver metastases and find differences in cellular composition.
- Shu Zhang
- , Wen Fang
- & Ying Lv
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Article
| Open AccessDesmoplastic stroma restricts T cell extravasation and mediates immune exclusion and immunosuppression in solid tumors
Tumor stroma is a key component of the immunosuppressive tumor microenvironment in pancreatic ductal adenocarcinoma (PDAC). Here, in preclinical PDAC models, the authors show that depletion of FAP-expressing cancer associated fibroblasts with FAP-targeted CAR T cells results in a loss of the integrity of the desmoplastic matrix, rendering tumors more susceptible to sequential treatment with mesothelin-targeted CAR-T cells.
- Zebin Xiao
- , Leslie Todd
- & Ellen Puré
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Article
| Open AccessResolving the spatial architecture of myeloma and its microenvironment at the single-cell level
The spatial architecture of multiple myeloma remains to be explored. Here, the authors perform bulk and single cell sequencing for samples from newly diagnosed patients and reveal gene signatures associated with focal lesions and spatial heterogeneity in the tumour microenvironment.
- Lukas John
- , Alexandra M. Poos
- & Niels Weinhold
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Article
| Open AccessCombined PD-L1/TGFβ blockade allows expansion and differentiation of stem cell-like CD8 T cells in immune excluded tumors
It has been previously shown that combining immune checkpoint inhibitors with TGFβ blockade potentiates anti-tumor immune responses. Here the authors show that, in an immune excluded preclinical tumor model, combining therapeutic anti-PD-L1 with anti-TGFβ treatment promotes expansion and differentiation of stem-cell like CD8 + T cells.
- Alessandra Castiglioni
- , Yagai Yang
- & Sören Müller
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Article
| Open AccessTargeting of SLC25A22 boosts the immunotherapeutic response in KRAS-mutant colorectal cancer
KRAS mutations are associated with an immunosuppressive microenvironment in patients with colorectal cancer (CRC). Here the authors show that knockout of SLC25A22, a mitochondrial glutamate carrier, reverts KRAS-mediated immunosuppression in preclinical CRC models, by suppressing CXCL1 production and impairing MDSC recruitment.
- Qiming Zhou
- , Yao Peng
- & Chi Chun Wong
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Article
| Open AccessSchwann cells regulate tumor cells and cancer-associated fibroblasts in the pancreatic ductal adenocarcinoma microenvironment
The effects of Schwann cells on the neuro-stroma niche in pancreatic ductal adenocarcinoma (PDAC) remain to be explored. Here, single-cell RNA-sequencing and spatial transcriptome analysis of PDAC tissues reveal that Schwann cells induce malignant subtypes of tumour cells and cancer associated fibroblasts.
- Meilin Xue
- , Youwei Zhu
- & Hao Chen
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Article
| Open AccessChemically programmed STING-activating nano-liposomal vesicles improve anticancer immunity
Agonists of the cytosolic DNA-sensing STING pathway potently remodel the tumour immune microenvironment to support anti-tumour adaptive immunity, but at the expense of adverse systemic inflammation. Here authors exchange the STING agonist MSA-2 with its prodrugs that are suitable for nano-liposomal delivery and thus achieve increased efficiency and decreased toxicity.
- Xiaona Chen
- , Fanchao Meng
- & Hangxiang Wang
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Article
| Open AccessMAPK inhibitor sensitivity scores predict sensitivity driven by the immune infiltration in pediatric low-grade gliomas
The MAPK pathway is a key driver of pediatric low-grade gliomas (pLGG); however, response to MAPK inhibitors (MAPKi) in pLGG patients is not consistent. Here, the authors develop MAPKi sensitivity scores (MSS) to predict response to MAPKi and apply them to bulk and single-cell sequencing datasets from pLGG patients and preclinical models.
- Romain Sigaud
- , Thomas K. Albert
- & Till Milde
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Article
| Open AccessOncolytic viruses engineered to enforce cholesterol efflux restore tumor-associated macrophage phagocytosis and anti-tumor immunity in glioblastoma
Glioblastoma (GBM) cells are metabolically dependent on exogenous cholesterol uptake and targeting cholesterol metabolism has been proposed as a therapeutic option for GBM. Here the authors show that cholesterol promotes phagocytic dysfunction in tumor associated macrophages and they develop an Apo-A1 armed oncolytic adenovirus restoring anti-tumor immunity in GBM preclinical models.
- Wang Shiqun
- , Yan Wei
- & Wei Jiwu
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Article
| Open AccessTumor-derived GDF-15 blocks LFA-1 dependent T cell recruitment and suppresses responses to anti-PD-1 treatment
Here authors show that GDF15, a cytokine that is produced by cancer cells, prevents T cells from extravasation into the tumour microenvironment. Low availability of T cells in GDF-15-expressing tumours thus precludes effective immune therapy.
- Markus Haake
- , Beatrice Haack
- & Jörg Wischhusen
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Article
| Open AccessCellSighter: a neural network to classify cells in highly multiplexed images
Identification and classification of cells in multiplexed microscopy remain challenging. Here, the authors propose CellSighter, which uses neural networks to perform cell classification directly on multiplexed images, thus leveraging the spatial expression characteristics of proteins.
- Yael Amitay
- , Yuval Bussi
- & Leeat Keren
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Article
| Open AccessCancer-associated fibroblast classification in single-cell and spatial proteomics data
Cancer-associated fibroblasts (CAFs) have different subtypes and play diverse roles in the tumour microenvironment. Here, the authors use single-cell RNA-seq and multiplex imaging mass cytometry data to propose a CAF classification scheme of nine subtypes across different cancer types.
- Lena Cords
- , Sandra Tietscher
- & Bernd Bodenmiller
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Article
| Open AccessThe checkpoint inhibitor PD-1H/VISTA controls osteoclast-mediated multiple myeloma bone disease
Multiple myeloma bone disease is characterized by the development of osteolytic bone lesions. Here, the authors demonstrate that the checkpoint inhibitor PD-1H functions as a potential MMP-13 receptor on osteoclasts, mediating MMP-13 induced cytoskeleton reorganization, fusogenesis and bone resorption and further regulating osteolytic lesions.
- Jing Fu
- , Shirong Li
- & Suzanne Lentzsch
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Article
| Open AccessIL1R1+ cancer-associated fibroblasts drive tumor development and immunosuppression in colorectal cancer
IL1 signalling pathway has been shown to shape cancer associated fibroblast (CAF) heterogeneity. Here the authors identify a pro-tumorigenic CAF subtype in colorectal cancer characterized by high IL1R1 expression and associated with an immunosuppressive tumor microenvironment.
- E. Koncina
- , M. Nurmik
- & E. Letellier
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Article
| Open AccessmRNA lipid nanoparticle-mediated pyroptosis sensitizes immunologically cold tumors to checkpoint immunotherapy
mRNA nanomedicine-based gene therapy may offer opportunities for cancer treatment. Here the authors show that mRNA lipid nanoparticles encoding the N-terminal domain of gasdermin B trigger pyroptosis and promote anti-tumor immune responses in preclinical cancer models.
- Fengqiao Li
- , Xue-Qing Zhang
- & Xiaoyang Xu
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Article
| Open AccessLoss of PHF8 induces a viral mimicry response by activating endogenous retrotransposons
The role of PHD finger protein 8 (PHF8) in anti-tumour immunity remains to be investigated. Here, the authors suggest PHF8 as an epigenetic checkpoint and show that targeting PHF8 induces a viral mimicry response enhancing anti-tumour immunity in colorectal cancer.
- Yanan Liu
- , Longmiao Hu
- & Xiufeng Pang
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Article
| Open AccessDeciphering intercellular signaling complexes by interaction-guided chemical proteomics
Systematic profiling of the indirect cell–cell interactions remains challenging. Here, the authors report a chemical proteomics method to identify ligand-receptor complexes formed between cell surface receptors and secreted proteins from neighboring cells.
- Jiangnan Zheng
- , Zhendong Zheng
- & Ruijun Tian
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Article
| Open AccessIncreased glucose availability sensitizes pancreatic cancer to chemotherapy
Response to chemotherapy in patients with pancreatic ductal adenocarcinoma (PDAC) is often limited. Here, the authors report improved response to chemotherapy in PDAC patients with hyperglycaemia and investigate the underlying mechanism via glucose-mediated disruption of redox metabolism
- Ali Vaziri-Gohar
- , Jonathan J. Hue
- & Jordan M. Winter
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Article
| Open AccessSingle-cell transcriptomics and epigenomics unravel the role of monocytes in neuroblastoma bone marrow metastasis
The bone marrow is a common site of metastasis for neuroblastoma patients. Here, the authors perform single cell RNA-seq and ATAC-seq of bone marrow aspirates from 16 subjects and show conservation of tumor cell plasticity in metastases and identify tumor-to-bone marrow cell signals that trigger tumor promoting monocytes.
- Irfete S. Fetahu
- , Wolfgang Esser-Skala
- & Sabine Taschner-Mandl
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Article
| Open AccessNanovesicles loaded with a TGF-β receptor 1 inhibitor overcome immune resistance to potentiate cancer immunotherapy
Targeting the TGF-β signaling pathway has been exploited to relieve immunosuppression in the tumor microenvironment. Here the authors describe the design of a nanoplatform integrating the TGF-β receptor 1 inhibitor LY2157299 and the ROS-responsive JQ1 pro-drug, promoting anti-tumor immune responses in preclinical cancer models.
- Mengxue Zhou
- , Jiaxin Wang
- & Haijun Yu
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Comment
| Open AccessBioengineering of bacteria for cancer immunotherapy
Here, we provide a brief overview of the approaches and strategies underlying bacteria-based cancer immunotherapy (BCiT). We also describe and summarize research in the field of synthetic biology, which aims to regulate bacterial growth and gene expression for immunotherapeutic use. Finally, we discuss the current clinical status and limitations of BCiT.
- Dinh-Huy Nguyen
- , Ari Chong
- & Jung-Joon Min
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Article
| Open AccessEvaluation of therapeutic PD-1 antibodies by an advanced single-molecule imaging system detecting human PD-1 microclusters
Immune checkpoint inhibitors are now routinely used in cancer therapy, however, the dosage and integration into conventional cancer therapy is determined via empirical experience rather than mechanistic rationale. Here authors establish an advanced single-molecule imaging method, by with which they are directly monitoring and evaluating the effect of immune checkpoint inhibitors on T cell signaling.
- Wataru Nishi
- , Ei Wakamatsu
- & Tadashi Yokosuka
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Article
| Open AccessSingle-cell transcriptomics reveals immune suppression and cell states predictive of patient outcomes in rhabdomyosarcoma
The cellular differentiation states of paediatric rhabdomyosarcoma (RMS) remain to be explored. Here, single-cell RNA sequencing analysis of RMS tumours reveals an immunosuppressive microenvironment and distinct transcriptional programs predictive of patient outcomes.
- Jeff DeMartino
- , Michael T. Meister
- & Jarno Drost
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Article
| Open AccessTRABID inhibition activates cGAS/STING-mediated anti-tumor immunity through mitosis and autophagy dysregulation
cGAS/STING activation is linked to the induction of anti-tumor immune responses. Here the authors report a role for the deubiquitinating enzyme TRABID in regulating mitotic cell division and suppressing anti-tumor immunity, suggesting that TRABID inhibition induces micronuclei and activates cGAS/STING pathway.
- Yu-Hsuan Chen
- , Han-Hsiun Chen
- & Ruey-Hwa Chen
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Article
| Open AccessSingle-cell analysis of gastric signet ring cell carcinoma reveals cytological and immune microenvironment features
The tumour microenvironment in signet ring cell carcinoma (SRCC) remains to be characterised. Here, the authors perform single-cell RNA sequencing and reveal distinct features compared to moderately/poorly differentiated adenocarcinoma.
- Weizhu Zhao
- , Yanfei Jia
- & Jie Chai