Search Results - "Spatial Transcriptomics"

Integration of TWAS with single-cell and spatial transcriptomics identifies TLR1 as a susceptibility gene and therapeutic target in the breast cancer tumor microenvironment by Zhang, Jingmei, Chen, Zhiting

“…Breast cancer is a common malignant tumor with a complex pathogenesis, and while genome-wide association studies (GWAS) have identified multiple risk loci,…”
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Spatial profiling technologies illuminate the tumor microenvironment by Elhanani, Ofer, Ben-Uri, Raz, Keren, Leeat

“…The tumor microenvironment (TME) is composed of many different cellular and acellular components that together drive tumor growth, invasion, metastasis, and…”
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Immune mechanisms linking metabolic injury to inflammation and fibrosis in fatty liver disease – novel insights into cellular communication circuits by Peiseler, Moritz, Schwabe, Robert, Hampe, Jochen, Kubes, Paul, Heikenwälder, Mathias, Tacke, Frank

“…Non-alcoholic fatty liver disease (NAFLD) is the most prevalent chronic liver disease and is emerging as the leading cause of cirrhosis, liver transplantation…”
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Soluble TREM2 levels reflect the recruitment and expansion of TREM2+ macrophages that localize to fibrotic areas and limit NASH by Hendrikx, Tim, Porsch, Florentina, Kiss, Máté G., Rajcic, Dragana, Papac-Miličević, Nikolina, Hoebinger, Constanze, Goederle, Laura, Hladik, Anastasiya, Shaw, Lisa E., Horstmann, Hauke, Knapp, Sylvia, Derdak, Sophia, Bilban, Martin, Heintz, Lena, Krawczyk, Marcin, Paternostro, Rafael, Trauner, Michael, Farlik, Matthias, Wolf, Dennis, Binder, Christoph J.

“…Previous single-cell RNA-sequencing analyses have shown that Trem2-expressing macrophages are present in the liver during obesity, non-alcoholic…”
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Spatially resolved transcriptomics identifies tumor-stroma-immune networks and therapeutic targets in endocrine-resistant advanced breast cancer treated with Everolimus+Letrozole: insights from the MIRACLE trial by Xue, Xuemin, Ji, Danyang, Xue, Liyan, Tan, Yujing, Wang, Bingzhi, Wang, Jiayu, Ma, Fei, Luo, Yang, Lan, Bo, Chen, Shanshan, Ying, Jianming, Xu, Binghe, Fan, Ying

“…Breast cancer is the most commonly diagnosed cancer in women globally. Our previous MIRACLE trial (NCT02313051) demonstrated that everolimus plus letrozole…”
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Cell interactions inference for single-cell spatial transcriptomes with GraphCIM by Huo, Weiliang, Zhang, Qingchen

“…The continuous advancement of spatial transcriptomics technology has enabled the analysis of tissue microenvironments at a single-cell resolution. As the gene…”
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Single-cell and spatial transcriptomics implicate vascular cell orchestration of inflammatory changes after UV light exposure in skin by An, Jie, Bogle, Rachael, Najjar, Rayan, Tsoi, Lam C, Kahlenberg, J Michelle, Anufrieva, Ksenia, Theisen, Erin, Wei, Kevin, Gudjonsson, Johann E, Elkon, Keith B

“…To elucidate the complex effects of acute UVR on the skin, we exposed mouse skin to UVB and performed transcriptomic profiling of the epidermis, deep dermis,…”
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High-resolution Spatial Transcriptomic Characterization of Syncytial Variant of Nodular Sclerosis Classical Hodgkin Lymphoma by Xiao, Xiaoyue, Dong, Jiyan, Sun, Xujie, Jiang, Kang, Wang, Long, Nong, Lin, Xue, Xuemin, Feng, Xiaoli

“…The syncytial variant of nodular sclerosis classical Hodgkin Lymphoma (SV-NSCHL) is associated with inferior outcomes. However, the complexity of tumor…”
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Spatial Molecular Plasticity Underpins Lethal Morphologies in Lung Adenocarcinoma by Williams, Hannah L, Poulain, Nicolas, Powley, Ian, Martinelli, Silvia, Bielik, Robert, Leslie, Holly, Nixon, Colin, Wilson, Claire R, Sereno, Marco, He, Zhangyi, Officer-Jones, Leah, Ballantyne, Fiona, Pennie, Rachel, Wood, Colin S, Lewis, David Y, Jamieson, Nigel B, Le Quesne, John

“…Adenocarcinoma of the lung (LUAD) is common and highly lethal. Clinical grading of LUAD strongly predicts recurrence and survival after surgery and is…”
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Integrating Multiomic Mendelian Randomization, Microarray, Single-Cell RNA Sequencing, and Spatial RNA Sequencing to Identify Potential Therapeutic Targets for Vitiligo by Huang, Jiangfeng, Hu, Yibo, Zhang, Yushan, Jiang, Ling, Fu, Chuhan, Zhang, Keyi, Wen, Yaqing, Zhou, Shu, Huang, Jinhua, Chen, Jing, Zeng, Qinghai

“…Vitiligo is a chronic skin disorder characterized by the selective destruction of melanocytes. Current treatments, such as topical steroids, tacrolimus,…”
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An image-based transcriptomics atlas reveals the regional and microbiota-dependent molecular, cellular, and spatial structure of the murine gut by Xu, Rosalind J, Zhang, Hao, Cadinu, Paolo, Nicol, Phillip B, Herrmann, Uli S, Lee, Tyrone, Geistlinger, Ludwig, Irizarry, Rafael A, Moffitt, Jeffrey R

“…The gastrointestinal environment is home to a massive diversity of diet-, host-, and microbiota-derived small molecules, collectively sensed by a remarkable…”
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Spatial Transcriptomics Reveals Differential Inflammatory Pathways in Discoid Lupus Erythematosus and Lichen Planus by Kidacki, Michal, Cho, Christina, Lopez-Giraldez, Francesc, Breidbart, Rachel, Jaiswal, Anjali, Lee, Morten, Chowdhury, Shanin, Damsky, William, Chen, Lieping, Vesely, Matthew D

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Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays by Chen, Ao, Liao, Sha, Cheng, Mengnan, Ma, Kailong, Wu, Liang, Lai, Yiwei, Qiu, Xiaojie, Yang, Jin, Xu, Jiangshan, Hao, Shijie, Wang, Xin, Lu, Huifang, Chen, Xi, Liu, Xing, Huang, Xin, Li, Zhao, Hong, Yan, Jiang, Yujia, Peng, Jian, Liu, Shuai, Shen, Mengzhe, Liu, Chuanyu, Li, Quanshui, Yuan, Yue, Wei, Xiaoyu, Zheng, Huiwen, Feng, Weimin, Wang, Zhifeng, Liu, Yang, Wang, Zhaohui, Yang, Yunzhi, Xiang, Haitao, Han, Lei, Qin, Baoming, Guo, Pengcheng, Lai, Guangyao, Muñoz-Cánoves, Pura, Maxwell, Patrick H, Thiery, Jean Paul, Wu, Qing-Feng, Zhao, Fuxiang, Chen, Bichao, Li, Mei, Dai, Xi, Wang, Shuai, Kuang, Haoyan, Hui, Junhou, Wang, Liqun, Fei, Ji-Feng, Wang, Ou, Wei, Xiaofeng, Lu, Haorong, Wang, Bo, Liu, Shiping, Gu, Ying, Ni, Ming, Zhang, Wenwei, Mu, Feng, Yin, Ye, Yang, Huanming, Lisby, Michael, Cornall, Richard J, Mulder, Jan, Uhlén, Mathias, Esteban, Miguel A, Li, Yuxiang, Liu, Longqi, Xu, Xun, Wang, Jian

“…Spatially resolved transcriptomic technologies are promising tools to study complex biological processes such as mammalian embryogenesis. However, the…”
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Principles of Spatial Transcriptomics Analysis: A Practical Walk-Through in Kidney Tissue by Noel, Teia, Wang, Qingbo S., Greka, Anna, Marshall, Jamie L.

“…Spatial transcriptomic technologies capture genome-wide readouts across biological tissue space. Moreover, recent advances in this technology, including…”
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PH2ST: Prompt-guided hypergraph learning for spatial transcriptomics prediction in whole slide images by Niu, Yi, Liu, Jiashuai, Zhan, Yingkang, Shi, Jiangbo, Zhang, Di, Reinius, Marika, Machado, Ines, Crispin-Ortuzar, Mireia, Wu, Jialun, Li, Chen, Gao, Zeyu

“…•Redefined spatial transcriptomics (ST) prediction as an inference-time prompting task.•A novel framework using limited ST prompts to guide spatial gene…”
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Mechanisms of kidney fibrosis and routes towards therapy by Yamashita, Noriyuki, Kramann, Rafael

“…Single-cell genomic studies have shed light on the complex cellular and molecular mechanisms that initiate and drive kidney fibrosis, as well as on the origin…”
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Multiomic analysis reveals conservation of cancer-associated fibroblast phenotypes across species and tissue of origin by Foster, Deshka S, Januszyk, Michael, Delitto, Daniel, Yost, Kathryn E, Griffin, Michelle, Guo, Jason, Guardino, Nicholas, Delitto, Andrea E, Chinta, Malini, Burcham, Austin R, Nguyen, Alan T, Bauer-Rowe, Khristian E, Titan, Ashley L, Salhotra, Ankit, Jones, R Ellen, da Silva, Oscar, Lindsay, Hunter G, Berry, Charlotte E, Chen, Kellen, Henn, Dominic, Mascharak, Shamik, Talbott, Heather E, Kim, Alexia, Nosrati, Fatemeh, Sivaraj, Dharshan, Ransom, R Chase, Matthews, Michael, Khan, Anum, Wagh, Dhananjay, Coller, John, Gurtner, Geoffrey C, Wan, Derrick C, Wapnir, Irene L, Chang, Howard Y, Norton, Jeffrey A, Longaker, Michael T

“…Cancer-associated fibroblasts (CAFs) are integral to the solid tumor microenvironment. CAFs were once thought to be a relatively uniform population of…”
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Tertiary lymphoid structures generate and propagate anti-tumor antibody-producing plasma cells in renal cell cancer by Meylan, Maxime, Petitprez, Florent, Becht, Etienne, Bougoüin, Antoine, Pupier, Guilhem, Calvez, Anne, Giglioli, Ilenia, Verkarre, Virginie, Lacroix, Guillaume, Verneau, Johanna, Sun, Chen-Ming, Laurent-Puig, Pierre, Vano, Yann-Alexandre, Elaïdi, Reza, Méjean, Arnaud, Sanchez-Salas, Rafaël, Barret, Eric, Cathelineau, Xavier, Oudard, Stephane, Reynaud, Claude-Agnès, de Reyniès, Aurélien, Sautès-Fridman, Catherine, Fridman, Wolf Herman

“…The presence of intratumoral tertiary lymphoid structures (TLS) is associated with positive clinical outcomes and responses to immunotherapy in cancer. Here,…”
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Integrating histology and spatial transcriptomics via multimodal transformers and contrastive representation learning for accurate gene expression prediction by Wang, Kai, Shi, Liuming, Li, Xue, Li, Wei, Wang, Bin, Zhou, Shihua, Cao, Ben, Zheng, Pan

“…Predicting spatial gene expression from Histological images is a fundamental task in understanding tissue organization and molecular phenotypes. However,…”
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Spatial Reconstruction of Single Enterocytes Uncovers Broad Zonation along the Intestinal Villus Axis by Moor, Andreas E, Harnik, Yotam, Ben-Moshe, Shani, Massasa, Efi E, Rozenberg, Milena, Eilam, Raya, Bahar Halpern, Keren, Itzkovitz, Shalev

“…The intestinal epithelium is a highly structured tissue composed of repeating crypt-villus units. Enterocytes perform the diverse tasks of absorbing a wide…”
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