MetaTiME integrates single-cell gene expression to characterize the meta-components of the tumor immune microenvironment
Author
Abstract
Suggested Citation
DOI: 10.1038/s41467-023-38333-8
Download full text from publisher
References listed on IDEAS
- Omar Khan & Josephine R. Giles & Sierra McDonald & Sasikanth Manne & Shin Foong Ngiow & Kunal P. Patel & Michael T. Werner & Alexander C. Huang & Katherine A. Alexander & Jennifer E. Wu & John Attanas, 2019. "TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion," Nature, Nature, vol. 571(7764), pages 211-218, July.
- Massimo Andreatta & Jesus Corria-Osorio & Sören Müller & Rafael Cubas & George Coukos & Santiago J. Carmona, 2021. "Interpretation of T cell states from single-cell transcriptomics data using reference atlases," Nature Communications, Nature, vol. 12(1), pages 1-19, December.
Citations
Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
Cited by:
- Lulu Shang & Peijun Wu & Xiang Zhou, 2025. "Statistical identification of cell type-specific spatially variable genes in spatial transcriptomics," Nature Communications, Nature, vol. 16(1), pages 1-20, December.
- Xin Yuan & Yanran Ma & Ruitian Gao & Shuya Cui & Yifan Wang & Botao Fa & Shiyang Ma & Ting Wei & Shuangge Ma & Zhangsheng Yu, 2024. "HEARTSVG: a fast and accurate method for identifying spatially variable genes in large-scale spatial transcriptomics," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- Moujtaba Y. Kasmani & Paytsar Topchyan & Ashley K. Brown & Ryan J. Brown & Xiaopeng Wu & Yao Chen & Achia Khatun & Donia Alson & Yue Wu & Robert Burns & Chien-Wei Lin & Matthew R. Kudek & Jie Sun & We, 2023. "A spatial sequencing atlas of age-induced changes in the lung during influenza infection," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
- Hao Wu & Xiufeng Zhao & Sophia M. Hochrein & Miriam Eckstein & Gabriela F. Gubert & Konrad Knöpper & Ana Maria Mansilla & Arman Öner & Remi Doucet-Ladevèze & Werner Schmitz & Bart Ghesquière & Sebasti, 2023. "Mitochondrial dysfunction promotes the transition of precursor to terminally exhausted T cells through HIF-1α-mediated glycolytic reprogramming," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
- Víctor Albarrán-Fernández & Laura Angelats & Julio Delgado & Alena Gros & Álvaro Urbano-Ispizua & Sònia Guedan & Aleix Prat, 2025. "Unlocking the potential of engineered immune cell therapy for solid tumors," Nature Communications, Nature, vol. 16(1), pages 1-5, December.
- Emily N. Neubert & Julia M. DeRogatis & Sloan A. Lewis & Karla M. Viramontes & Pedro Ortega & Monique L. Henriquez & Rémi Buisson & Ilhem Messaoudi & Roberto Tinoco, 2023. "HMGB2 regulates the differentiation and stemness of exhausted CD8+ T cells during chronic viral infection and cancer," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
- Kateryna Onyshchenko & Ren Luo & Elena Guffart & Simone Gaedicke & Anca-Ligia Grosu & Elke Firat & Gabriele Niedermann, 2023. "Expansion of circulating stem-like CD8+ T cells by adding CD122-directed IL-2 complexes to radiation and anti-PD1 therapies in mice," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
- Yi Liu & Brian Debo & Mingfeng Li & Zhennan Shi & Wanqiang Sheng & Yang Shi, 2021. "LSD1 inhibition sustains T cell invigoration with a durable response to PD-1 blockade," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
- Carmen Oi Ning Leung & Yang Yang & Rainbow Wing Hei Leung & Karl Kam Hei So & Hai Jun Guo & Martina Mang Leng Lei & Gregory Kenneth Muliawan & Yuan Gao & Qian Qian Yu & Jing Ping Yun & Stephanie Ma & , 2023. "Broad-spectrum kinome profiling identifies CDK6 upregulation as a driver of lenvatinib resistance in hepatocellular carcinoma," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
- Leticia Laura Niborski & Paul Gueguen & Mengliang Ye & Allan Thiolat & Rodrigo Nalio Ramos & Pamela Caudana & Jordan Denizeau & Ludovic Colombeau & Raphaël Rodriguez & Christel Goudot & Jean-Michel Lu, 2022. "CD8+T cell responsiveness to anti-PD-1 is epigenetically regulated by Suv39h1 in melanomas," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
- Massimo Andreatta & Léonard Hérault & Paul Gueguen & David Gfeller & Ariel J. Berenstein & Santiago J. Carmona, 2024. "Semi-supervised integration of single-cell transcriptomics data," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
- Raphael Lutz & Florian Grünschläger & Malte Simon & Mohamed H. S. Awwad & Marcus Bauer & Schayan Yousefian & Niklas Beumer & Lea Jopp-Saile & Anastasia Sedlmeier & Llorenç Solé-Boldo & Bogdan Avanesya, 2024. "Multiple myeloma long-term survivors exhibit sustained immune alterations decades after first-line therapy," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
- Matthew A. Cottam & Heather L. Caslin & Nathan C. Winn & Alyssa H. Hasty, 2022. "Multiomics reveals persistence of obesity-associated immune cell phenotypes in adipose tissue during weight loss and weight regain in mice," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
- Tina Sarén & Giulia Saronio & Paula Marti Torrell & Xu Zhu & Josefin Thelander & Yasmin Andersson & Camilla Hofström & Marika Nestor & Anna Dimberg & Helena Persson & Mohanraj Ramachandran & Di Yu & M, 2023. "Complementarity-determining region clustering may cause CAR-T cell dysfunction," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
- Sonali Jindal & Nathan D. Pennock & Duanchen Sun & Wesley Horton & Michelle K. Ozaki & Jayasri Narasimhan & Alexandra Q. Bartlett & Sheila Weinmann & Paul E. Goss & Virginia F. Borges & Zheng Xia & Pe, 2021. "Postpartum breast cancer has a distinct molecular profile that predicts poor outcomes," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
- Anja Fischer & Thomas K. Albert & Natalia Moreno & Marta Interlandi & Jana Mormann & Selina Glaser & Paurnima Patil & Flavia W. Faria & Mathis Richter & Archana Verma & Sebastian T. Balbach & Rabea Wa, 2024. "Lack of SMARCB1 expression characterizes a subset of human and murine peripheral T-cell lymphomas," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
- Anneke L. Eerkens & Koen Brummel & Annegé Vledder & Sterre T. Paijens & Marta Requesens & Dominik Loiero & Nienke Rooij & Annechien Plat & Floris-Jan Haan & Patty Klok & Refika Yigit & Thijs Roelofsen, 2024. "Neoadjuvant immune checkpoint blockade in women with mismatch repair deficient endometrial cancer: a phase I study," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
- Marina T. Broz & Emily Y. Ko & Kristin Ishaya & Jinfen Xiao & Marco Simone & Xen Ping Hoi & Roberta Piras & Basia Gala & Fernando H. G. Tessaro & Anja Karlstaedt & Sandra Orsulic & Amanda W. Lund & Ke, 2024. "Metabolic targeting of cancer associated fibroblasts overcomes T-cell exclusion and chemoresistance in soft-tissue sarcomas," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
- Hideki Ogura & Jin Gohda & Xiuyuan Lu & Mizuki Yamamoto & Yoshio Takesue & Aoi Son & Sadayuki Doi & Kazuyuki Matsushita & Fumitaka Isobe & Yoshihiro Fukuda & Tai-Ping Huang & Takamasa Ueno & Naomi Mam, 2022. "Dysfunctional Sars-CoV-2-M protein-specific cytotoxic T lymphocytes in patients recovering from severe COVID-19," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
- Xiaofeng Liao & Wenxue Li & Hongyue Zhou & Barani Kumar Rajendran & Ao Li & Jingjing Ren & Yi Luan & David A. Calderwood & Benjamin Turk & Wenwen Tang & Yansheng Liu & Dianqing Wu, 2024. "The CUL5 E3 ligase complex negatively regulates central signaling pathways in CD8+ T cells," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
- Feng Xie & Xiaoxue Zhou & Peng Su & Heyu Li & Yifei Tu & Jinjin Du & Chen Pan & Xiang Wei & Min Zheng & Ke Jin & Liyan Miao & Chao Wang & Xuli Meng & Hans Dam & Peter Dijke & Long Zhang & Fangfang Zho, 2022. "Breast cancer cell-derived extracellular vesicles promote CD8+ T cell exhaustion via TGF-β type II receptor signaling," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
- Ahmed E. I. Hamouda & Jessica Filtjens & Elisabeth Brabants & Daliya Kancheva & Ayla Debraekeleer & Jan Brughmans & Lotte Jacobs & Pauline M. R. Bardet & Elisabeth Knetemann & Pierre Lefesvre & Lize A, 2024. "Intratumoral delivery of lipid nanoparticle-formulated mRNA encoding IL-21, IL-7, and 4-1BBL induces systemic anti-tumor immunity," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-38333-8. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.