Fig. 1

Examples of related findings and troubleshooting in spatial proteomics. From left to right, the figure illustrates: spatial proteome mapping, microenvironment and disease, cell–cell interaction, biomarker discovery, drug target development, and tumor heterogeneity research. Spatial Proteome Mapping: A high-resolution 3D reference atlas of the human kidney has been constructed, encompassing cellular, pathway, and genetic elements. This atlas reveals the cell types, functions, and molecular characteristics of a healthy kidney, facilitating the understanding of kidney disease classification and pathogenesis (refer to reference [3]). Microenvironment and Disease: In ovarian cancer (OC), non-enzymatic methyltransferase (NNMT) is upregulated in the tumor microenvironment and has been identified as a regulator promoting metastasis. Experimental validation shows that NNMT expression correlates with shorter survival periods, and inhibiting its activity can effectively suppress cancer metastasis. This research elucidates the relationship between NNMT and OC metastasis, enhancing the understanding of OC metastasis mechanisms (reference [4]). Cell–Cell Interaction: In hepatocellular carcinoma (HCC), cancer-associated fibroblasts (CAFs) and their protein expression differences were studied. It was found that proteins released by CAFs interact with the TLR2 receptor on HCC cancer cells, influencing HCC progression. This study addresses the challenge of isolating proteins from specific cells and reveals cell communication mechanisms in liver cancer progression (reference [5]).Biomarker Discovery: In endometrial cancer (EC), five proteins—PRSS3, PTX3, ASS1, ALDH2, and ANXA1—were identified in sentinel lymph nodes (SLNs) of EC patients. Their expression is significantly correlated with tumor grading, providing insights for early diagnosis and grading of EC (reference [6]). Drug Target Development: In toxic epidermal necrolysis (TEN), research has shown that interferon signaling pathways are active and pSTAT1 is activated in immune cells and keratin-forming cells of TEN patients. This supports the safety of using JAK inhibitors (JAKi) to treat TEN, highlighting their potential as drug targets (reference [7]).Tumor Heterogeneity: In melanoma heterogeneity research, specific proteins such as DMBT1 and MARCKS exhibit varied expression in squamous, papillary, acinar, and solid regions of tumors and are associated with recurrence risk. Immunosuppressive cells increase in the core region of solid tumors. This study addresses the challenge of understanding melanoma tumor heterogeneity, clarifying its internal molecular characteristics and immune cell distribution.(reference [8])