Spatial proteomics: unveiling the multidimensional landscape of protein localization in human diseases

Authors: Mengyao Wu, Huihui Tao, Tiantian Xu, Xuejia Zheng, Chunmei Wen, Guoying Wang, Yali Peng, Yong Dai

Source: Proteome Science, Vol 22, Iss 1, Pp 1-15 (2024)

Subject Terms: Spatial proteomics, Mass spectrometry, Fluorescent antibody, Disease, DSP, Cytology, QH573-671

File Description: electronic resource

Relation: https://doaj.org/toc/1477-5956

Access URL: https://doaj.org/article/b11e53a94a344ee791941f580415afa4

Deciphering functional tumor-immune crosstalk through highly multiplexed imaging and deep visual proteomics

Authors: Zheng, Xiang ^{1, 2, ∗}, Mund, Andreas ^{1, 3}, Mann, Matthias ^{1, 4, 5, ∗∗}

Source: In Molecular Cell 6 March 2025 85(5):1008-1023

Profiling immune cell tissue niches in the spatial -omics era

Authors: Lee, Colin Y.C. ^{a, b}, McCaffrey, James ^{a, b, c}, McGovern, Dominic ^{a, b, c}, Clatworthy, Menna R. ^{a, b, c, ∗}

Source: In The Journal of Allergy and Clinical Immunology March 2025 155(3):663-677

Global organelle profiling reveals subcellular localization and remodeling at proteome scale

Authors: Hein, Marco Y. ^{1, 5, 6, 13, ∗}, Peng, Duo ^{1, 13, ∗∗}, Todorova, Verina ^{1, 13}, McCarthy, Frank ^{1, 13}, Kim, Kibeom ^{1, 7, 13}, Liu, Chad ^{1, 13}, Savy, Laura ^{1, 8}, Januel, Camille ¹, Baltazar-Nunez, Rodrigo ¹, Sekhar, Madhurya ¹, Vaid, Shivanshi ¹, Bax, Sophie ¹, Vangipuram, Madhuri ¹, Burgess, James ², Njoya, Leila ¹, Wang, Eileen ¹, Ivanov, Ivan E. ¹, Byrum, Janie R. ^{1, 9}, Pradeep, Soorya ¹, Gonzalez, Carlos G. ¹, Aniseia, Yttria ¹, Creery, Joseph S. ¹, McMorrow, Aidan H. ^{1, 10}, Sunshine, Sara ^{3, 11}, Yeung-Levy, Serena ^{1, 4}, DeFelice, Brian C. ¹, Mehta, Shalin B. ¹, Itzhak, Daniel N. ^{1, 12}, Elias, Joshua E. ^{1, ∗∗∗}, Leonetti, Manuel D. ^{1, 14, ∗∗∗∗}

Source: In Cell 20 February 2025 188(4):1137-1155

High-resolution spatially resolved proteomics of complex tissues based on microfluidics and transfer learning

Authors: Hu, Beiyu ^{1, 2, 6}, He, Ruiqiao ^{1, 3, 6}, Pang, Kun ^{1, 3, 6}, Wang, Guibin ^{4, 6}, Wang, Ning ^{1, 3}, Zhu, Wenzhuo ¹, Sui, Xin ⁵, Teng, Huajing ⁵, Liu, Tianxin ¹, Zhu, Junjie ^{1, 2}, Jiang, Zewen ¹, Zhang, Jinyang ¹, Zuo, Zhenqiang ¹, Wang, Weihu ⁵, Ji, Peifeng ^{1, ∗}, Zhao, Fangqing ^{1, 2, 3, 7, ∗∗}

Source: In Cell 6 February 2025 188(3):734-748

Predicting Protein Pathways Associated to Tumor Heterogeneity by Correlating Spatial Lipidomics and Proteomics: The Dry Proteomic Concept

Authors: Lagache, Laurine ^{1, ‡}, Zirem, Yanis ^{1, ‡}, Le Rhun, Émilie ^{1, 2}, Fournier, Isabelle ^{1, 3, ∗, ‡}, Salzet, Michel ^{1, 3, ∗, ‡}

Source: In Molecular & Cellular Proteomics January 2025 24(1)

Highly Multiplexed Immunofluorescence PhenoCycler Panel for Murine Formalin-Fixed Paraffin-Embedded Tissues Yields Insight Into Tumor Microenvironment Immunoengineering

Authors: Surwase, Sachin S. ^{a, b, c}, Zhou, Xin Ming M. ^d, Luly, Kathryn M. ^{a, b, c}, Zhu, Qingfeng ^{e, f, g}, Anders, Robert A. ^{e, f, g, h, i}, Green, Jordan J. ^{a, b, c, e, h, i, j, k, l, m, n}, Tzeng, Stephany Y. ^{a, b, c}, Sunshine, Joel C. ^{a, c, d, e, f, h, i, ∗}

Source: In Laboratory Investigation January 2025 105(1)

Current state and future prospects of spatial biology in colorectal cancer

Authors: Francisco G. Carranza, Fernando C. Diaz, Maria Ninova, Enrique Velazquez-Villarreal

Source: Frontiers in Oncology, Vol 14 (2024)

Subject Terms: colorectal cancer, spatial transcriptomics, spatial proteomics, bioinformatics, genomics, personalized medicine, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

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Relation: https://www.frontiersin.org/articles/10.3389/fonc.2024.1513821/full; https://doaj.org/toc/2234-943X

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How spatial omics approaches can be used to map the biological impacts of stress in psychiatric disorders: a perspective, overview and technical guide

Authors: Amber R. Curry, Lezanne Ooi, Natalie Matosin

Source: Stress, Vol 27, Iss 1 (2024)

Subject Terms: Stress, psychiatry, spatial, omics, spatial transcriptomics, spatial proteomics, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

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Relation: https://doaj.org/toc/1025-3890; https://doaj.org/toc/1607-8888

Access URL: https://doaj.org/article/8443cc0bec89435a8dff0f33be0a9a17

Novel Integration of Spatial and Single-Cell Omics Data Sets Enables Deeper Insights into IPF Pathogenesis

Authors: Fei Wang, Liang Jin, Xue Wang, Baoliang Cui, Yingli Yang, Lori Duggan, Annette Schwartz Sterman, Sarah M. Lloyd, Lisa A. Hazelwood, Neha Chaudhary, Bhupinder Bawa, Lucy A. Phillips, Yupeng He, Yu Tian

Source: Proteomes, Vol 13, Iss 1, p 3 (2025)

Subject Terms: Idiopathic pulmonary fibrosis, spatial transcriptomics, laser capture microdissection, spatial proteomics, mass spectrometry, scRNA-seq, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.mdpi.com/2227-7382/13/1/3; https://doaj.org/toc/2227-7382

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The burgeoning spatial multi-omics in human gastrointestinal cancers

Authors: Weizheng Liang, Zhenpeng Zhu, Dandan Xu, Peng Wang, Fei Guo, Haoshan Xiao, Chenyang Hou, Jun Xue, Xuejun Zhi, Rensen Ran

Source: PeerJ, Vol 12, p e17860 (2024)

Subject Terms: Spatial transcriptomics, Spatial proteomics, Spatial metabolomics, Esophageal cancer, Gastric cancer and colorectal cancer, Medicine, Biology (General), QH301-705.5

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Relation: https://peerj.com/articles/17860.pdf; https://peerj.com/articles/17860/; https://doaj.org/toc/2167-8359

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Modulation of hippocampal protein expression by a brain penetrant biologic TNF-α inhibitor in the 3xTg Alzheimer’s disease mice

Authors: Nataraj Jagadeesan, G. Chuli Roules, Devaraj V. Chandrashekar, Joshua Yang, Sanjana Kolluru, Rachita K. Sumbria

Source: Journal of Translational Medicine, Vol 22, Iss 1, Pp 1-18 (2024)

Subject Terms: Biologic TNF-α inhibitor, Transferrin receptor antibody, Spatial proteomics, Alzheimer’s disease, Tau, Amyloid beta, Medicine

File Description: electronic resource

Relation: https://doaj.org/toc/1479-5876

Access URL: https://doaj.org/article/9c7d4ce603b74672a7572a0c179d092c

Spatial multi-omics: novel tools to study the complexity of cardiovascular diseases

Authors: Paul Kiessling, Christoph Kuppe

Source: Genome Medicine, Vol 16, Iss 1, Pp 1-17 (2024)

Subject Terms: Spatial multi-omics, Spatial transcriptomics, In situ sequencing, Multiplex in situ FISH, MALDI, Spatial proteomics, Medicine, Genetics, QH426-470

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Relation: https://doaj.org/toc/1756-994X

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Using adjusted local assortativity with Molecular Pixelation unveils colocalization of membrane proteins with immunological significance

Authors: Jan Rhomberg-Kauert, Max Karlsson, Divya Thiagarajan, Tomasz Kallas, Filip Karlsson, Simon Fredriksson, Johan Dahlberg, Alvaro Martinez Barrio

Source: Frontiers in Immunology, Vol 15 (2024)

Subject Terms: molecular pixelation, single cell, spatial proteomics, graph theory, topological data analysis, local assortativity, Immunologic diseases. Allergy, RC581-607

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Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2024.1309916/full; https://doaj.org/toc/1664-3224

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The evolving landscape of spatial proteomics technologies in the AI age

Authors: Hu, Beiyu ^{a, b, 1}, Zhu, Junjie ^{a, b, 1}, Zhao, Fangqing ^{a, b, ⁎}

Source: In Fundamental Research November 2024

Dissecting the brain with spatially resolved multi-omics

Authors: Yijia Fangma, Mengting Liu, Jie Liao, Zhong Chen, Yanrong Zheng

Source: Journal of Pharmaceutical Analysis, Vol 13, Iss 7, Pp 694-710 (2023)

Subject Terms: Central nervous system disorders, Multi-omics, Spatial transcriptomics, Spatial proteomics, Spatial metabolomics, Therapeutics. Pharmacology, RM1-950

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2095177923000643; https://doaj.org/toc/2095-1779

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Spatial proteomic profiling of tumor and stromal compartments in non‐small‐cell lung cancer identifies signatures associated with overall survival

Authors: Vahid Yaghoubi Naei, James Monkman, Habib Sadeghirad, Ahmed Mehdi, Tony Blick, William Mullally, Ken O'Byrne, Majid Ebrahimi Warkiani, Arutha Kulasinghe

Source: Clinical & Translational Immunology, Vol 13, Iss 7, Pp n/a-n/a (2024)

Subject Terms: digital spatial profiling, non‐small‐cell lung cancer, spatial proteomics, tumor microenvironment, Immunologic diseases. Allergy, RC581-607

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Relation: https://doaj.org/toc/2050-0068

Access URL: https://doaj.org/article/71afaa1369b246e48af2b950a8616b55

Targeted spatial proteomic analysis of CD8+ T- and myeloid cells in tonsillar cancer

Authors: Can Altunbulakli, David G. Jimenez, David Askmyr, Aastha Sobti, Sabine Swoboda, Lennart Greiff, Malin Lindstedt

Source: Frontiers in Oncology, Vol 13 (2023)

Subject Terms: spatial proteomics, head and neck (H&N) cancer, tonsillar cancer, immune check point, cytotoxic T lymphocytes (CTL), myeloid cell, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fonc.2023.1253418/full; https://doaj.org/toc/2234-943X

Access URL: https://doaj.org/article/643e7ef3986b40e1a688bc064d957078

Molecular and spatial heterogeneity of microglia in Rasmussen encephalitis

Authors: Jesse J. Westfall, Wesley N. Schwind, Sahibjot Sran, Jason B. Navarro, Jeffrey Leonard, Jonathan A. Pindrik, Christopher R. Pierson, Daniel R. Boué, Daniel C. Koboldt, Adam P. Ostendorf, Richard K. Wilson, Elaine R. Mardis, Katherine E. Miller, Tracy A. Bedrosian

Source: Acta Neuropathologica Communications, Vol 10, Iss 1, Pp 1-16 (2022)

Subject Terms: Encephalitis, Microglial nodules, Epilepsy, Inflammation, Spatial proteomics, Single nucleus RNA-seq, Neurology. Diseases of the nervous system, RC346-429

File Description: electronic resource

Relation: https://doaj.org/toc/2051-5960

Access URL: https://doaj.org/article/7172266047244c74a00d43d4b08784a7

Spatial proteomics identifies a spectrum of immune dysregulation in acquired bone marrow failure syndromes

Authors: Rachel M. Koldej, Ashvind Prabahran, Chin Wee Tan, Mandy Ludford-Menting, Huw Morgan, Nicholas Holzwart, Melissa J. Davis, David S. Ritchie

Source: Frontiers in Immunology, Vol 14 (2023)

Subject Terms: aplastic anaemia, poor graft function, stem cell transplant, spatial proteomics, bone marrow, microenvironment, Immunologic diseases. Allergy, RC581-607

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Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2023.1213560/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/45a5cd1df5f84a9bbd3e900c61ca0bad