Microarray integrated spatial transcriptomics (MIST) for affordable and robust digital pathology by Juwayria, Priyansh Shrivastava, Kaustar Yadav, Sourabh Das, Shubham Mittal, Sunil Kumar, Deepali Jain, Prabhat Singh Malik, Ishaan Gupta

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Spatial Transcriptomics in Inflammatory Skin Diseases Using GeoMx Digital Spatial Profiling: A Practical Guide for Applications in Dermatology by Christina Cho, Nazgol-Sadat Haddadi, Michal Kidacki, Gavitt A. Woodard, Saeed Shakiba, Ümmügülsüm Yıldız-Altay, Jillian M. Richmond, Matthew D. Vesely

“…Overall, we hope to illustrate the potential of digital spatial profiling to dissect skin disease pathogenesis in a spatially resolved manner and provide a framework for other skin biology investigators using digital spatial profiling.…”
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Spatial transcriptomic analysis across histological subtypes reveals molecular heterogeneity and prognostic markers in early‐stage lung adenocarcinoma by Hua Geng, Wenhao Zhou, Haitao Luo, Jiaqian Wang, Shixiong Li, Congcong Song, Yujie Zhao, Meilin Xu

“…Methods Formalin‐fixed paraffin‐embedded (FFPE) samples were collected from patients with primary early‐stage lung adenocarcinoma, encompassing three histologic subtypes: well‐differentiated, moderately differentiated, and poorly differentiated. The GeoMx Digital Spatial Profiler platform was utilized to obtain spatial transcriptomic profiling. …”
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Spatial transcriptomic profiling of the human fallopian tube epithelium reveals region-specific gene expression patterns by Jared Sipes, Sagar Rayamajhi, Leonidas E. Bantis, Rashna Madan, Amrita Mitra, Rajni V. Puri, Mohammod Mahmudur Rahman, Foyez Ahmmed, Harsh B. Pathak, Andrew K. Godwin

“…Despite its importance, the spatial transcriptome of the FT’s distinct anatomical regions (fimbria, infundibulum, ampulla, and isthmus) remains underexplored. …”
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Spatial transcriptomic analysis of 4NQO-induced tongue cancer revealed cellular lineage diversity and evolutionary trajectory by Feng Liu, Feng Liu, Xiaojun Wu, Shaoqing Yu, Deqiang Cheng, Jun Pan, Xiaodong Wang, Guanzhen Yu, Guanzhen Yu, Chaofu Li

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Spatial gene expression profiling identifies prognostic features of residual tumors after neoadjuvant chemotherapy in triple-negative breast cancer by Hye Sung Won, Yong-Seok Kim, Kyung Jin Seo, Sun-Young Jun, Der Sheng Sun, Mihong Choi, Jung-Sook Yoon, Jae Ho Byun

“…We investigated genetic alterations related to recurrence using spatial transcriptomic analyses of residual tumors from patients who had and had not relapsed after NAC for early-stage TNBC.MethodsThirteen patients who underwent curative resection after NAC for early-stage TNBC, six of whom experienced recurrence, were included. …”
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PLXDC1+ Tumor‐Associated Pancreatic Stellate Cells Promote Desmoplastic and Immunosuppressive Niche in Pancreatic Ductal Adenocarcinoma by Yanhua Du, Yizhou Zhao, Judong Li, Jiaxin Wang, Shenglan You, Yao Zhang, Li Zhang, Jihong Yang, Hamid Alinejad‐Rokny, Shujie Cheng, Chenghao Shao, Duowu Zou, Youqiong Ye

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Elucidating the dynamic tumor microenvironment through deep transcriptomic analysis and therapeutic implication of MRE11 expression patterns in hepatocellular carcinoma by Ruiqiu Chen, Chaohui Xiao, Zizheng Wang, Guineng Zeng, Shaoming Song, Gong Zhang, Lin Zhu, Penghui Yang, Rong Liu

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The development of a high-plex spatial proteomic methodology for the characterisation of the head and neck tumour microenvironment by Chin Wee Tan, Naomi Berrell, Meg L. Donovan, James Monkman, Clara Lawler, Habib Sadeghirad, Vahid Yaghoubi Naei, Jinjin Chen, Alyssa Rossenbloom, Shilah Bonnett, Mark Conner, Brian Filanoski, Christine Kang, Joseph M. Beechem, John F. Fraser, Catherine Barnett, Rahul Ladwa, Brett G. M. Hughes, Arutha Kulasinghe

“…Here, we profiled 84 mucosal HNSCC tissue samples using next-generation ultra-high plex spatial protein profiling (580-proteins, Immuno-Oncology Proteome Atlas (IPA)) and spatial transcriptome mapping (18,000 mRNA, Whole Transcriptome Atlas (WTA)) from Bruker Spatial Biology. …”
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The future of immunohistochemistry: advancing precision medicine through artificial intelligence-driven spatial proteomics and multiplexed diagnostic technologies by Ruby Dhar, Arun Kumar, Subhradip Karmakar

“…The application of IHC is rapidly broadening beyond conventional single-marker analyses to include advanced multiplexed spatial proteomics techniques that allow for the detection of 40 or more protein markers simultaneously within intact tissue structures at subcellular precision, providing new insights into the tumor microenvironment and cellular interactions. …”
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Integrated spatial multi‐omics profiling of Fusobacterium nucleatum in breast cancer unveils its role in tumour microenvironment modulation and cancer progression by Feng Zhao, Rui An, Yilei Ma, Shaobo Yu, Yuzhen Gao, Yanzhong Wang, Haitao Yu, Xinyou Xie, Jun Zhang

“…GeoMx digital spatial profiling (DSP) revealed that regions colonized by F. nucleatum exhibit significant influence on the expression of RNAs and proteins involved in proliferation, migration and invasion. …”
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Induced collagen type‐I secretion by hepatocytes of the melanoma liver metastasis is associated with a reduction in tumour‐infiltrating lymphocytes by Shodai Mizuno, Matias A. Bustos, Yoshinori Hayashi, Kodai Abe, Satoru Furuhashi, Yalda Naeini, Xiaowei Xu, Anton J Bilchik, Dave S. B. Hoon

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Multiplex imaging analysis of the tumor immune microenvironment for guiding precision immunotherapy by Feng Liu, Feng Liu, Feng Liu, Guiqing Li, Guiqing Li, Yi Zheng, Yi Zheng, Yanxia Liu, Yanxia Liu, Kang Liu, Kang Liu

“…Despite current technical and analytical challenges, ongoing technological advancements and integration with emerging methods like spatial transcriptomics and super-resolution imaging promise broader clinical utility, ultimately improving patient outcomes in precision immunotherapy.…”
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Intercellular TIMP-1-CD63 signaling directs the evolution of immune escape and metastasis in KRAS-mutated pancreatic cancer cells by Chu-An Wang, Ya-Chin Hou, Yi-Kai Hong, Yu-Jing Tai, Chieh Shen, Pei-Chi Hou, Jhao-Lin Fu, Cheng-Lin Wu, Siao Muk Cheng, Daw-Yang Hwang, Yung-Yeh Su, Yan-Shen Shan, Shaw-Jenq Tsai

“…Clinical relevance was validated by digital spatial transcriptomic analysis of PDAC tumors. …”
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KDM1A epigenetically enhances RAD51 expression to suppress the STING-associated anti-tumor immunity in esophageal squamous cell carcinoma by Qingyuan Yang, Shiyin Wei, Cen Qiu, Chenjie Han, Zunguo Du, Ning Wu

“…Cell growth was assessed by colony formation assays in vitro and subcutaneous xenograft models in vivo. High-throughput transcriptomics and spatial immune proteomics were performed using bulk RNA sequencing and digital spatial profiling techniques, respectively. …”
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The dual role of CXCL9/SPP1 polarized tumor-associated macrophages in modulating anti-tumor immunity in hepatocellular carcinoma by Yu Gu, Zhihui Zhang, Hao Huang, Wenyong Zhu, Hongjia Liu, Rongxin Zhang, Nan Weng, Xiao Sun

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Attenuated immune surveillance during squamous cell transformation of pancreatic adenosquamous cancer defines new therapeutic opportunity for cancer interception by Jie Chen, Xianlong Chen, Xinyuan Chen, Shanyue Sun, Shuofeng Li, Shuangni Yu

“…Beyond differences in IC density, we observed closer spatial proximity of CD45RO+ and PD-1+CD3+CD8+ T cells to tumor cells within 10, 20 and 30 µm ranges in PASC compared with PDAC, with variations by histological subregion. …”
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3D printing-biomimetic local stiff niche enhances glycolysis to boost PDAC cell stem-like phenotype via N6-methyladenosine-suppressed YAP1 mRNA decay by Di Wu, Xiaoqi Guan, Tao Yang, Jiashuai Yan, Biwen Zhu, Junchao Zhou, Yibing Guo, Yuhua Lu

“…Bioinformatics, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, of CSCs identified from spatial transcriptomic and single-cell datasets of PDAC lesions exhibited activated mechanical and glycolytic pathways. …”
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Integrated multi-omics profiling characterizes the crucial role of human dental epithelium during tooth development by Ran Zhang, Zongshan Shen, Zhenni Zhao, Xiuge Gu, Tianxing Yan, Wei Wei, Chuan Wu, Jinxuan Xia, Yuanyuan Zhang, Suwen Chen, Linsha Ma, Dong Zhang, Xiaoshan Wu, Paul T. Sharpe, Songlin Wang

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Prediction of post-treatment recurrence in early-stage breast cancer using deep-learning with mid-infrared chemical histopathological imaging by Abigail Keogan, Thi Nguyet Que Nguyen, Pascaline Bouzy, Nicholas Stone, Karin Jirstrom, Arman Rahman, William M. Gallagher, Aidan D. Meade

“…Prognostic assays which utilize bulk transcriptomics ignore the spatial context of the cellular material and are, therefore, of limited value in the development of mechanistic models. …”
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