Category: CosMx SMI

January 2, 2024 / Nat Cancer

  • Li Z, Pai R, Gupta S, … Chow PKH, Ginhoux F, Sharma A
Onco-fetal reprogramming of the tumor ecosystem induces fetal developmental signatures in the tumor microenvironment, leading to immunosuppressive features. Here, we employed single-cell RNA sequencing, spatial transcriptomics and bulk RNA sequencing…
December 20, 2023 / Nat Med

  • Sankowski R, Süß P, Benkendorff A, Böttcher C, Fernandez-Zapata C, Chhatbar C, Cahueau J, Monaco G, Gasull AD, Khavaran A, Grauvogel J, Scheiwe C, Shah MJ, Heiland DH, Schnell O, Markfeld-Erol F, Kunze M, Zeiser R, Priller J, Prinz M
The innate immune compartment of the human central nervous system (CNS) is highly diverse and includes several immune-cell populations such as macrophages that are frequent in the brain parenchyma (microglia)…
December 8, 2023 / Nat Genet

  • Varrone M, Tavernari D, Santamaria-Martínez A, Walsh LA, Ciriello G
Tissues are organized in cellular niches, the composition and interactions of which can be investigated using spatial omics technologies. However, systematic analyses of tissue composition are challenged by the scale…
November 28, 2023 / BMC Genomics

  • Dezem FS, Marção M, Ben-Cheikh B, Nikulina N, Omotoso A, Burnett D, Coelho P, Hurley J, Gomez C, Phan-Everson T, Ong G, Martelotto L, Lewis ZR, George S, Braubach O, Malta TM, Plummer J
Cell annotation is a crucial methodological component to interpreting single cell and spatial omics data. These approaches were developed for single cell analysis but are often biased, manually curated and…
November 1, 2023 / Neuro-oncol adv

  • Moffet JJD, Oluwaseun E Fatunla, Lutz Freytag, Jurgen Kriel, Jordan J Jones, Samuel J Roberts-Thomson, Anna Pavenko, David K Scoville, Liang Zhang, Yan Liang, Andrew P Morokoff, James R Whittle, Saskia Freytag, Sarah A Best
Background: High-grade gliomas (HGG) are aggressive primary brain cancers with poor response to standard regimens, driven by immense heterogeneity. In isocitrate dehydrogenase (IDH) wild-type high-grade glioma (glioblastoma, GBM), increased intra-tumoral…
October 10, 2023 / Cell Rep

  • Tsubosaka A, Komura D, Kakiuchi M, Katoh H, Onoyama T, Yamamoto A, Abe H, Seto Y, Ushiku T, Ishikawa S
The stomach is an important digestive organ with various biological functions. However, because of the complexity of its cellular and glandular composition, its precise cellular biology has yet to be…
October 5, 2023 / Brief Bioinform

  • Tang Z, Liu X, Li Z, Zhang T, Yang B, Su J, Song Q
Spatial cellular authors heterogeneity contributes to differential drug responses in a tumor lesion and potential therapeutic resistance. Recent emerging spatial technologies such as CosMx, MERSCOPE and Xenium delineate the spatial…
September 15, 2023 / Oncol Res

  • Xie F, Xi N, Han Z, Luo W, Shen J, Luo J, Tang X, Pang T, Lv Y, Liang J, Liao L, Zhang H, Jiang Y, Li Y, He J
Spatial omics technology integrates the concept of space into omics research and retains the spatial information of tissues or organs while obtaining molecular information. It is characterized by the ability…
September 12, 2023 / Nat Commun

  • Tang Z, Li Z, Hou T, Zhang T, Yang B, Su J, Song Q
Recent advances in high-throughput molecular imaging have pushed spatial transcriptomics technologies to subcellular resolution, which surpasses the limitations of both single-cell RNA-seq and array-based spatial profiling. The multichannel immunohistochemistry images…
September 4, 2023 / Int J Biol Sci

  • Du J, An ZJ, Huang ZF, Yang YC, Zhang MH, Fu XH, Shi WY, Hou J
Since its first application in 2016, spatial transcriptomics has become a rapidly evolving technology in recent years. Spatial transcriptomics enables transcriptomic data to be acquired from intact tissue sections and…
September 2, 2023 / Bioinformatics

  • Peters Couto BZ, Robertson N, Patrick E, Ghazanfar S
Motivation: Imaging-based spatial transcriptomics (ST) technologies have achieved subcellular resolution, enabling detection of individual molecules in their native tissue context. Data associated with these technologies promise unprecedented opportunity toward understanding…
August 12, 2023 / Immunol Cell Biol

  • Kulasinghe A, Wood F, Belz G
Spatial biology is a rapidly developing field which enables the visualization of protein and transcriptomic data while preserving tissue context and architecture. Initially used in discovery, there is growing promise…