OLD Category: CosMx SMI

April 3, 2024 / Nat Commun

  • Denisenko E, de Kock L, Tan A, Beasley AB, Beilin M, Jones ME, Hou R, Muirí DÓ, Bilic S, Mohan GRKA, Salfinger S, Fox S, Hmon KPW, Yeow Y, Kim Y, John R, Gilderman TS, Killingbeck E, Gray ES, Cohen PA, Yu Y, Forrest ARR
High-grade serous ovarian carcinoma (HGSOC) is genetically unstable and characterised by the presence of subclones with distinct genotypes. Intratumoural heterogeneity is linked to recurrence, chemotherapy resistance, and poor prognosis. Here,…
March 28, 2024 / Cancer Discov

  • Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidzinski L, Zhu S, Colburg DRC, Luca B, Phillips DJ, Brubaker SW, Charville GW, Shen J, Loh KM, Okwan-Duodu DK, Nolan GP, Newman AM, West RB, van de Rijn M
Tumor-associated macrophages are transcriptionally heterogeneous, but the spatial distribution and cell interactions that shape macrophage tissue roles remain poorly characterized. Here, we spatially resolve five distinct human macrophage populations in…
March 26, 2024 / Nat Commun

  • Goralski TM, Meyerdirk L, Breton L, Brasseur L, Kurgat K, DeWeerd D, Turner L, Becker K, Adams M, Newhouse DJ, Henderson MX
A key hallmark of Parkinson’s disease (PD) is Lewy pathology. Composed of α-synuclein, Lewy pathology is found both in dopaminergic neurons that modulate motor function, and cortical regions that control…
February 27, 2024 / Nat Genet

  • Singhal V, Chou N, Lee J, Yue Y, Liu J, Chock WK, Lin L, Chang YC, Teo EML, Aow J, Lee HK, Chen KH, Prabhakar S
Spatial omics data are clustered to define both cell types and tissue domains. We present Building Aggregates with a Neighborhood Kernel and Spatial Yardstick (BANKSY), an algorithm that unifies these…
February 19, 2024 / Nat Commun

  • Mennillo E, Kim YJ, Lee G, Rusu I, Patel RK, Dorman LC, Flynn E, Li S, Bain JL, Andersen C, Rao A, Tamaki S, Tsui J, Shen A, Lotstein ML, Rahim M, Naser M, Bernard-Vazquez F, Eckalbar W, Cho Sj, Beck K, El-Nachef N, Lewin S, Selvig DR, Terdiman JP, Mahadevan U, Oh DY, Fragiadakis GK, Pisco A, Combes AJ, Kattah MG
Ulcerative colitis (UC) is driven by immune and stromal subsets, culminating in epithelial injury. Vedolizumab (VDZ) is an anti-integrin antibody that is effective for treating UC. VDZ is known to…
February 18, 2024 / eBioMedicine

  • Tan CW, Jinjin Chen, Ning Liu, Dharmesh D. Bhuva, Tony Blick, James Monkman, Caroline Cooper, Malvika Kharbanda, Kristen Feher, Belinda Phipson, Emily E. Killingbeck, Liuliu Pan, Youngmi Kim, Yan Liang, Andy Nam, Michael Leon, Paulo Souza-Fonseca-Guimaraes, Seigo Nagashima, Ana Paula Camargo Martins, Cleber Machado-Souza, Lucia de Noronha, Benjamin Tang, Kirsty Short, John Fraser, Gabrielle T. Belz, Fernando Souza-Fonseca-Guimaraes, Arutha Kulasinghe, Melissa J. Davis
The utilization of single-cell resolved spatial transcriptomics to delineate immune responses during SARS-CoV-2 infection was able to identify M1 macrophages to have elevated expression of IFI27 in areas of infection.…
January 13, 2024 / Nat Commun

  • Fu X, Lin Y, Lin DM, Mechtersheimer D, Wang C, Ameen F, Ghazanfar S, Patrick E, Kim J, Yang JYH
Recent advances in subcellular imaging transcriptomics platforms have enabled high-resolution spatial mapping of gene expression, while also introducing significant analytical challenges in accurately identifying cells and assigning transcripts. Existing methods…
January 12, 2024 / Genome Biol

  • Mason K, Sathe A, Hess PR, Rong J, Wu CY, Furth E, Susztak K, Levinsohn J, Ji HP, Zhang N
Existing methods for analysis of spatial transcriptomic data focus on delineating the global gene expression variations of cell types across the tissue, rather than local gene expression changes driven by…
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…