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We recapitulated two major continuum states during inflammation-driven epithelial carcinogenesis: (1) genomic stable stage (CNV –/low) with inflammatory adaptation 58; (2) genomic unstable (CNV high) stage with inflammatory reprogramming 7, as epitomized by the convergence of epithelial plasticity between inflamed and malignant gallbladder epithelium. Two PBM-associated benign EPC subsets (nEPC05–06), awash with regurgitated pancreatic juice, exhibited gastrointestinal metaplastic signatures. Cluster nEPC05 largely arose from tumor samples, likely implying a pre-malignant stage with not yet developed genomic instability. Another two XGC-associated clusters displayed EMP signatures, which accounted for the associated gallbladder wall destruction and inflammatory liver invasion (CC6). Unexpectedly, we captured genomic instability in a small fraction of epithelial cells from the histologically inflamed gallbladder (CC1), implying that CNV potentially occurred early and heralded morphologically malignant transformation, mirrored by previous pan-cancer evidence 59, and meanwhile suggesting fluid boundaries between chronic inflammation and tumorigenesis stages, presumably with a transitional zone of field cancerization 60. Of note, based on IHC validation and experimental exploration, we corroborated that elevated expression of PLA2G2A was associated with GBC initiation, corresponding with the notion that PLA2G2A may display an initial beneficial effect against gastrointestinal mucosal inflammation whereas face the tradeoff of increased cancer risk 22. In such a way, PLA2G2A potentially wires long-term chronic cholecystitis up to GBC. Hernandez-Fernaud, J. R. et al. Secreted CLIC3 drives cancer progression through its glutathione-dependent oxidoreductase activity. Nat. Commun. 8, 14206 (2017). Lee SK, Yi Y, Kim YH, Kim HI, Chow P, Xiao Y, Eng P, Shen G. Lee SK, et al. Sci Adv. 2023 May 19;9(20):eadg4159. doi: 10.1126/sciadv.adg4159. Epub 2023 May 19. Sci Adv. 2023. PMID: 37205753 Free PMC article. Both invasion and migration assays were conducted by using 8.0 mm Boyden chambers (BD Biosciences). For invasion assay, the Boyden chambers were covered with 200 μL of phenol-red-free matrigel mix which was diluted 1:40 portions with DMEM. Thereafter, these chambers were placed in a 24-well plate and were incubated for 20 mins at 37 °C. For invasion and migration assays of GBC cells, the wells of the lower chamber were filled with medium containing 10% FBS. GBC cells (2 × 10 4) were seeded in the upper compartment in serum-free medium for 24 h. At the end of assay, filters were removed and fixed. The invasion and migration were determined by counting the cells that migrated to the lower side of the filter. For invasion and migration assays in co-culture system, GBC-SD cells (2 × 10 4) labeling GFP were platted under the serum-starved condition in the upper chambers, while in the lower chambers, HFL-1 cells (2 × 10 4) that co-cultured with medium supernatant of GBC-SD cells for 0, 3, 6, and 9 days were seeded. The experiment was stopped after 24 h of incubation. An equal number of cells were seeded in wells underneath to normalize the invasion and migration assay to cell proliferation. Primers and antibodies Benson, A. B. et al. Hepatobiliary cancers, version 2.2021, NCCN clinical practice guidelines in oncology. J. Natl. Compr.Canc. Netw. 19, 541–565 (2021).

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Li H, Yang Y, Dai Y, Bai J, Yu S, Xiang Y (2017) Achieving secure and efficient dynamic searchable symmetric encryption over medical cloud data. IEEE Trans Cloud Comput PP(99):1–1 This article is part of the Topical Collection: Special Issue on Big Data and Smart Computing in Network Systems York, A. G. et al. Limiting cholesterol biosynthetic flux spontaneously engages type I IFN signaling. Cell 163, 1716–1729 (2015). Talevich, E., Shain, A. H., Botton, T. & Bastian, B. C. CNVkit: genome-wide copy number detection and visualization from targeted DNA sequencing. PLoS Comput. Biol. 12, e1004873 (2016). Puisieux, A., Pommier, R. M., Morel, A. P. & Lavial, F. Cellular pliancy and the multistep process of tumorigenesis. Cancer Cell 33, 164–172 (2018).Deczkowska, A., Weiner, A. & Amit, I. The physiology, pathology, and potential therapeutic applications of the TREM2 signaling pathway. Cell 181, 1207–1217 (2020). Telgerd MD, Sadeghinia M, Birhanu G, Daryasari MP, Zandi-Karimi A, Sadeghinia A, Akbarijavar H, Karami MH, Seyedjafari E. Telgerd MD, et al. J Biomed Mater Res A. 2019 Aug;107(8):1841-1848. doi: 10.1002/jbm.a.36707. Epub 2019 May 24. J Biomed Mater Res A. 2019. PMID: 31033136

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Roa, I. et al. Preneoplastic lesions and gallbladder cancer: an estimate of the period required for progression. Gastroenterology 111, 232–236 (1996). Neyaz, A. et al. Clinical relevance of PD-L1 expression in gallbladder cancer: a potential target for therapy. Histopathology 73, 622–633 (2018). Ding LP, Kuang XY, Shao P, Huang XF. Ding LP, et al. Inorg Chem. 2014 Apr 7;53(7):3471-9. doi: 10.1021/ic402913k. Epub 2014 Mar 7. Inorg Chem. 2014. PMID: 24605919Vora A, Nesterenko M (2006) Secure location verification using radio broadcast. IEEE Trans Dependable Sec Comput 3(4):377–385 In terms of GBO lentivirus infection, the organoids were resuspended in a 500 μL growth medium after trypsinization for 5 min at 37 °C. Then cells were seeded into 48-well plates at 80%–90% confluence and were infected with lentivirus of NC labeling GFP and KRAS G12D labeling GFP according to standard procedures 107. Three days after infection, the growth medium was exchanged with medium containing puromycin at a concentration of 5 μg/mL for selection for two weeks. Co-culture experiment and senescence-associated β-galactosidase (SA-β-gal) assay Genomic DNA of samples was extracted by QIAamp DNA Mini Kit (Qiagen) and then captured with an Agilent SureSelect Human All Exon Kit V6 (Agilent). DNA libraries were generated following the protocols provided by Illumina. DNA libraries were sequenced with the Illumina NovaSeq 6000 System (Illumina), yielding 150 bp of paired-end sequence, and FASTQ files were generated. The WES sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China). Single-cell RNA-seq data processing

Single-cell dissection of remodeled inflammatory ecosystem in

Wang, X., Liu, C., Chen, J. et al. Single-cell dissection of remodeled inflammatory ecosystem in primary and metastatic gallbladder carcinoma. Baker, S. et al. Cancer Hallmarks Analytics Tool (CHAT): a text mining approach to organize and evaluate scientific literature on cancer. Bioinformatics 33, 3973–3981 (2017).Macro01 was preferentially enriched in metastatic lesions (Fig. 4c; Supplementary Fig. S11a) and was mapped to tumor-associated macrophages (TAMs) (Fig. 4g; Supplementary Table S10), with extensive upregulation of ISGs (e.g., ISG15, GPNMB, IFI6) and lipid metabolism genes (e.g., APOC1, CTSD, PLA2G7) (Fig. 4b, f; Supplementary Table S9), conceivably implying its immunosuppressive role conferred by IFN-stimulated lipid reprogramming 29, 30. The S100A8 + THBS1 + Macro02 subset, rich in S100A family genes ( S100A8, S100A9, S100A12, VCAN, and FCN1), typically mapped to myeloid-derived suppressor cell-like (MDSC-like) macrophages (Fig. 4f, g) 31, 32, 33. Apart from its affluence in inflamed gallbladders akin to other chronic infections (Fig. 4c) 34, several GBC patients, especially one advanced case (GBC9), showed pronounced enrichment (Supplementary Fig. S11a), whereby this subset conceivably induced an immunocompromised state through regulating cytokine production and leukocyte chemotaxis (Fig. 4i). Macro03 ( FCGBP + CX3CR1 + C3 +) was enriched in GBCs (Fig. 4c), especially in two early cases (GBC1-2) (Supplementary Fig. S11a), typically expressing the tumor-promoting marker TREM2 (Fig. 4b, e, f) 35. It behaved as an immunosuppressive TAM subset by regulating leukocyte migration, differentiation, and chemotaxis (Fig. 4i). With marked patient occupancy (GBC6) (Fig. 4c; Supplementary Fig. S11a), Macro04 exhibited versatile tumor-promoting roles, including cytokine production (e.g., TNFAIP3, CXCL3), pro-angiogenesis (e.g., VEGFA), and ECM remodeling (e.g., SPP1) (Fig. 4e–g, j) 28, 36, 37. Macro05 displayed prominently active proliferation features ( MKI67 + STMN1 +) (Fig. 4b, f), likely serving as self-renewal gallbladder-resident macrophages 38. This subcluster was frequently found within GBCs (Supplementary Fig. S11a); however, a benign outlier (CC6 with XGC) was noted, whereby proliferating macrophages probably contributed to the shaping of ‘foamy’ macrophage milieu in XGC-related destructive inflammation. Predominantly residing in PTs (Fig. 4c), Macro06 synchronously behaved as M2-like TAMs (e.g., LYVE1, SEPP1, MRC1, FOLR2) 39, as well as perivascular TAMs (e.g., MRC1, VCAM1, SLC40A1) (Fig. 4f, g), which probably facilitated vascular development and cancer cell intravasation (Fig. 4c–g) 32, 40. Collectively, tumor-derived macrophages displayed more prominent M2- and TAM-like traits, together with boosted angiogenesis and phagocytosis processes. In contrast, their benign counterparts behaved more like M1- or MDSC-like macrophages (Fig. 4h). As for different epithelial subtypes, subtype II exhibited more active crosstalk with macrophages (Supplementary Fig. S11b). Cancer cell-derived MIF or COPA potentially dictated the crosstalk with macrophages through CD74-related signaling pathways and, reciprocally, macrophage-secreted granulin (GRN) might send tumor-promoting signals to cancer cells via TNF receptors (Supplementary Fig. S11c, d). Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015).

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Imielinski, M. et al. Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell 150, 1107–1120 (2012). Martinez, F. O. & Gordon, S. The M1 and M2 paradigm of macrophage activation: time for reassessment. F1000Prime Rep. 6, 13 (2014). The transverse momentum conservation diagram; the y axis is the cathode surface-vacuum interface, and the z axis is the direction of electron emission. There is a maximum value for θ In for the electrons to be emitted out. Reuse & PermissionsDepartment of General Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, People's Republic of China. López-Soto, A., Gonzalez, S., Smyth, M. J. & Galluzzi, L. Control of metastasis by NK cells. Cancer Cell 32, 135–154 (2017). Key Laboratory of Nuclear Physics and Technology, Institute of Heavy Ion Physics, Peking University, Beijing 100871, China Chandran N, Goyal V, Moriarty R, Ostrovsky R (2014) Position-based cryptography. SIAM J Comput 43(4):1291–1341. https://doi.org/10.1137/100805005 Electron source, DC guns, Beam dynamics simulation, Energy recovery LINAC ,Beamline commissioning, Electron cooling ,and SRF gun Research Activities