{"id":242552,"date":"2026-01-17T05:49:08","date_gmt":"2026-01-17T05:49:08","guid":{"rendered":"https:\/\/www.newsbeep.com\/il\/242552\/"},"modified":"2026-01-17T05:49:08","modified_gmt":"2026-01-17T05:49:08","slug":"hacca-multi-module-integration-of-spot-based-spatial-transcriptomes-and-metabolomes","status":"publish","type":"post","link":"https:\/\/www.newsbeep.com\/il\/242552\/","title":{"rendered":"haCCA: multi-module Integration of spot-based spatial transcriptomes and metabolomes"},"content":{"rendered":"

Vandereyken, K. et al. Methods and applications for single-cell and spatial multi-omics. Nat. Rev. Genet. 24, 494\u2013515 (2023).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Vicari, M.M. et al. Spatial Multimodal Analysis of Transcriptomes and Metabolomes in Tissues Mendeley Data, V1, https:\/\/doi.org\/10.17632\/w7nw4km7xd.1<\/a> (2023).<\/p>\n

Argelaguet, R. et al. Computational principles and challenges in single-cell data integration. Nat. Biotechnol. 39, 1202\u20131215 (2021).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Vicari, M. et al. Spatial multimodal analysis of transcriptomes and metabolomes in tissues. Nat. Biotechnol. 42, 1046\u20131050 (2023).<\/p>\n

Ravi, V. M. et al. Spatially resolved multi-omics deciphers bidirectional tumor-host interdependence in glioblastoma. Cancer Cell 40, 639\u2013655 e13 (2022).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Sun, C. et al. Spatially resolved multi-omics highlights cell-specific metabolic remodeling and interactions in gastric cancer. Nat. Commun. 14, 2692 (2023).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Zhi, Y. et al. Spatial transcriptomic and metabolomic landscapes of oral submucous fibrosis-derived oral squamous cell carcinoma and its tumor microenvironment. Adv. Sci. 11, e2306515 (2024).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Zheng, P. et al. Integrated spatial transcriptome and metabolism study reveals metabolic heterogeneity in human injured brain. Cell Rep. Med. 4, 101057 (2023).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Stuart, T. et al. Comprehensive Integration of single-cell Data. Cell 177, 1888\u20131902 e21 (2019).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Liu, J. et al. Jointly defining cell types from multiple single-cell datasets using LIGER. Nat. Protoc. 15, 3632\u20133662 (2020).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Argelaguet, R. et al. MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data. Genome Biol. 21, 111 (2020).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Singh, S. et al. Integrative metabolomics and transcriptomics identifies itaconate as an adjunct therapy to treat ocular bacterial infection. Cell Rep. Med. 2, 100277 (2021).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Iturria-Medina, Y. et al. Unified epigenomic, transcriptomic, proteomic, and metabolomic taxonomy of Alzheimer\u2019s disease progression and heterogeneity. Sci. Adv. 8, eabo6764 (2022).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Wolf, F. A., Angerer, P. & Theis, F. J. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 19, 15 (2018).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Zeira, R. et al. Alignment and integration of spatial transcriptomics data. Nat. Methods 19, 567\u2013575 (2022).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Clifton, K. et al. STalign: alignment of spatial transcriptomics data using diffeomorphic metric mapping. Nat. Commun. 14, 8123 (2023).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Dong, L. et al. Proteogenomic characterization identifies clinically relevant subgroups of intrahepatic cholangiocarcinoma. Cancer Cell 40, 70\u201387 e15 (2022).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Zhang, M. et al. An inflammatory checkpoint generated by IL1RN splicing offers therapeutic opportunity for KRAS-mutant intrahepatic cholangiocarcinoma. Cancer Discov. 13, 2248\u20132269 (2023).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Yang, L. Y. et al. Increased neutrophil extracellular traps promote metastasis potential of hepatocellular carcinoma via provoking tumorous inflammatory response. J. Hematol. Oncol. 13, 3 (2020).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Shen, X. T. et al. Pan-cancer analysis reveals a distinct neutrophil extracellular trap-associated regulatory pattern. Front. Immunol. 13, 798022 (2022).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Xiong, S., Dong, L. & Cheng, L. Neutrophils in cancer carcinogenesis and metastasis. J. Hematol. Oncol. 14, 173 (2021).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Yazdani, H. O. et al. Neutrophil extracellular traps drive mitochondrial homeostasis in tumors to augment growth. Cancer Res. 79, 5626\u20135639 (2019).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

van der Windt, D. J. et al. Neutrophil extracellular traps promote inflammation and development of hepatocellular carcinoma in nonalcoholic steatohepatitis. Hepatology 68, 1347\u20131360 (2018).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Pang, Z. et al. MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation. Nucleic Acids Res. 52, W398\u2013W406 (2024).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Huang, F. et al. Active AKT2 stimulation of SREBP1\/SCD1-mediated lipid metabolism boosts hepatosteatosis and cancer. Transl. Res. 268, 51\u201362 (2024).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Piccinin, E. et al. Role of oleic acid in the gut-liver axis: from diet to the regulation of its synthesis via stearoyl-CoA desaturase 1 (SCD1). Nutrients 11, 2283 (2019).<\/p>\n

Caron-Jobin, M. et al. Stearic acid content of abdominal adipose tissues in obese women. Nutr. Diab 2, e23 (2012).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Guo, T. et al. SPIRAL: integrating and aligning spatially resolved transcriptomics data across different experiments, conditions, and technologies. Genome Biol. 24, 241 (2023).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Liu, X., Zeira, R. & Raphael, B. J. Partial alignment of multislice spatially resolved transcriptomics data. Genome Res. 33, 1124\u20131132 (2023).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

De Vleeschauwer, S. I. et al. OBSERVE: guidelines for the refinement of rodent cancer models. Nat. Protoc. 19, 2571\u20132596 (2024).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Xiaoyun Zhang, B. LittleLittleCloud\/haCCA: DOI (v0.0.4-DOI). Zenodo https:\/\/doi.org\/10.5281\/zenodo.17785970<\/a> (2025).<\/p>\n","protected":false},"excerpt":{"rendered":"Vandereyken, K. et al. Methods and applications for single-cell and spatial multi-omics. Nat. Rev. Genet. 24, 494\u2013515 (2023).…\n","protected":false},"author":2,"featured_media":242553,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[7],"tags":[9187,118355,3181,85,46,3183,17967,141],"class_list":["post-242552","post","type-post","status-publish","format-standard","has-post-thumbnail","category-science","tag-chemical-biology","tag-data-integration","tag-general","tag-il","tag-israel","tag-life-sciences","tag-metabolomics","tag-science"],"_links":{"self":[{"href":"https:\/\/www.newsbeep.com\/il\/wp-json\/wp\/v2\/posts\/242552","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.newsbeep.com\/il\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.newsbeep.com\/il\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/il\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/il\/wp-json\/wp\/v2\/comments?post=242552"}],"version-history":[{"count":0,"href":"https:\/\/www.newsbeep.com\/il\/wp-json\/wp\/v2\/posts\/242552\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/il\/wp-json\/wp\/v2\/media\/242553"}],"wp:attachment":[{"href":"https:\/\/www.newsbeep.com\/il\/wp-json\/wp\/v2\/media?parent=242552"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.newsbeep.com\/il\/wp-json\/wp\/v2\/categories?post=242552"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.newsbeep.com\/il\/wp-json\/wp\/v2\/tags?post=242552"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}