Results 21 to 30 of about 3,823 (146)

STAID: A Self‐Refining Deep Learning Framework for Spatial Cell‐Type Deconvolution with Biologically Informed Modeling

Advanced Science, EarlyView.
STAID is a unified deep learning framework that couples iterative pseudo‐spot refinement with neural network training through a feedback loop and exploits gene co‐expression information to model higher‐order interactions, achieving accurate and robust cell‐type deconvolution in spatial transcriptomics.
Jixin Liu, Shuli Sun, Zhengliang Lv, Xinyu Liu, Yihua Wang, Bingqiang Liu   +5 more
wiley   +1 more source

SSR4 sustains Tertiary Lymphoid Structures by Regulation Quality Control of N‐linked Glycosylation During B‐cell Differentiation Into Plasmacyte in Colorectal Cancer

Advanced Science, EarlyView.
SSR4, a TRAP component induced in B cells, governs BAFFR N‐glycosylation via DDOST to sustain NF‐κB signaling, B‐cell differentiation, and TLS maturation. Its loss impairs anti‐tumor immunity, while overexpression improves antibody glycosylation and ADCC, revealing a critical regulator for cancer immunotherapy.
Wei Zhao, Youcai Zhao, Haiyang Li, Bowen Yang, Siyan Lu, Xueting Fu, Caixia Zhang, Yirong Chen, Xiaofeng Bian, Xinghua Ma, Xiaobing Yang, Bin Wang, Yuan Fang, Lulu Yang, Yelin Zhao, Shuli Zhao   +15 more
wiley   +1 more source

Automated classification of tertiary lymphoid structures in colorectal cancer using TLS-PAT artificial intelligence tool

Scientific Reports
Abstract Colorectal cancer (CRC) ranks as the third most common and second deadliest cancer worldwide. The immune system, particularly tertiary lymphoid structures (TLS), significantly influences CRC progression and prognosis. TLS maturation, especially in the presence of germinal centers, correlates with improved patient outcomes; however ...
Le Rochais, Marion, Brahim, Ikram, Zeghlache, Rachid, Redoulez, Geoffroy, Guillard, Matthieu, Le Noac’h, Pierre, Castillon, Marine, Bourhis, Amélie, Uguen, Arnaud   +8 more
openaire   +4 more sources

SPADE: A Deep Learning Framework for Spatial Mapping and Quantitative Cell–Cell Interaction Inference

Advanced Science, EarlyView.
SPADE integrates spatial transcriptomics with single‐cell RNA sequencing by using cell–cell communications (CCC) as a guide for spatial mapping. It improves cell‐type localization, enhances sparse gene‐expression signals, and reveals CCC programs at single‐spot resolution.
Xinyi Li, Ning Zhang, Zijie Jin
wiley   +1 more source

Stromal Regulation of Tumor Perineural Invasion: A Multicellular and Neuro‐Ecological Perspective

Advanced Science, EarlyView.
This review reframes perineural invasion (PNI) as a dynamic, multicellular process within the tumor–nerve–stromal ecosystem. The authors delineate how cancer‐associated fibroblasts, Schwann cells, and immune cells remodel the neural niche to facilitate tumor spread.
Xiaoyang Lin, Yingqiao Liu, Haitao Lin, Kang Feng, Xiqiang Liu   +4 more
wiley   +1 more source

An Integrated and Robust Deep Learning Framework for Denoising and Analyzing Single‐Cell Spatial Transcriptomics

Advanced Intelligent Systems, EarlyView.
Single‐cell Spatial Transcriptomics Analysis and Denoising Engine is introduced as a unified deep learning framework that jointly performs denoising, clustering, and gene prioritization in spatial transcriptomics. By integrating linear and nonlinear representations within a dual‐channel architecture, it improves robustness and accuracy, uncovers ...
Yaxuan Cui, Yang Cui, Ruheng Wang, Xin Zeng, Zheyong Zhu, Ding Yi, Ruihua Guo, Tetsuya Sakurai, Kenta Nakai, Xiucai Ye, Leyi Wei, Yong Chen   +11 more
wiley   +1 more source

Tumor‐Regional Immune Microenvironment: A Critical Factor in the Design of Radiotherapy–Immunotherapy Combination Trials

International Journal of Cancer, EarlyView.
ABSTRACT Clinical trials combining radiotherapy (RT) with immune checkpoint blockade (ICB) have shown improved outcomes in only a fraction of patients, and optimal strategies for integrating these modalities remain under intense investigation. With a few exceptions, phase III combination trials have yielded disappointing results.
Xuanwei Zhang, Hui Wang, Weiyan Tang, Kai Kang, Kateryna Onyshchenko, Taotao Huang, Dan Liu, Jianxin Xue, You Lu, Gabriele Niedermann, Ren Luo   +10 more
wiley   +1 more source

Spatial Transcriptomics and Bulk RNA‐Seq Analysis Revealed Molecular Classification of Invasive Lobular Carcinoma

Cancer Science, EarlyView.
Spatial transcriptomics and bulk RNA‐seq data analysis revealed the molecular characteristics of invasive lobular carcinoma (ILC). ILC was classified into three clusters: proliferative, immunoreactive, and stromal‐rich, with different prognoses. ABSTRACT Invasive lobular carcinoma (ILC) is a special type of breast cancer.
Momoko Tokura, Jun Nakayama, Hironori Suzuki, Mieko Ochi, Miyaka Umemori, Sho Shiino, Masayuki Yoshida, Shin Takayama, Yasushi Yatabe, Yusuke Yamamoto   +9 more
wiley   +1 more source

Organ‐Specific Cancer‐Associated Fibroblast Subtypes Across the Digestive System Linked to Cancer Hallmarks

Cancer Science, EarlyView.
We integrated 14 single‐cell RNA‐seq datasets and 18 bulk cohorts to define eight CAF subtypes in GI cancers. myCAF1 and myCAF2 promoted immunosuppressive, poor‐prognosis niches, whereas iCAF1 was linked to favorable prognosis and antitumor immunity.
Huaitao Wang, Takashi Semba, Atsuko Yonemura, Hiroshi Naito, Lingfeng Fu, Takuya Tajiri, Masaaki Iwatsuki, Takatsugu Ishimoto   +7 more
wiley   +1 more source

The Prognostic Significance of Tertiary Lymphoid Structures in Head and Neck Cancers: A Systematic Review and Meta‐Analysis

Journal of Oral Pathology &Medicine, EarlyView.
ABSTRACT Background Head and neck squamous cell carcinoma (HNSCC), particularly oral squamous cell carcinoma (OSCC), is associated with poor survival despite therapeutic advances. Tertiary lymphoid structures (TLSs) are emerging components of the tumor microenvironment, but their prognostic significance in HNSCC remains unclear.
Everton Freitas de Morais, Bruno Cesar da Costa, Antti Mäkitie, Ricardo D. Coletta, Alhadi Almangush   +4 more
wiley   +1 more source