The Imaging and Molecular Annotation of Xenografts and Tumours (IMAXT) High Throughput Data and Analysis Infrastructure

Ea, González-Solares; Dariush, A.; González-Fernández, C.; Ak, Yoldaş; Ma, Sa’d; Millar, Neil; Whitmarsh, Tristan; Chornay, Nicholas; Falciatori, Ilaria; Fatemi, Ali; Goodwin, Daniel; Laura, Kuett; Mulvey, Claire M.; M, Páez Ribes; Qosaj, Fatime; Roth, Anastasia; Vázquez-García, Ignacio; Ss, Watson; Windhager, Jonas; Aparicio, Samuel; Bodenmiller, Bernd; Boyden, Edward S.; Caldas, Carlos; Harris, Olivia B; Sp, Shah; Tavaré, Simon; Bressan, Dario; Gj, Hannon; Na, Walton

doi:10.1101/2021.06.22.448403

Cited by 3 publications

(1 citation statement)

References 25 publications

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“…Slides were then imaged using the Hyperion Imaging Mass Cytometer (Fluidigm). IMC datasets, saved by the Hyperion instrument as .mcd files, were initially converted to the Zarrformat, preserving the entire signal dynamic range and metadata, using a custom python script described previously 71 and available at https://github.com/IMAXT/imc-nuclearsegmentation. The resulting zarr datasets were visualized using a custom-made IMC viewer tool, also written in python, operating on a jupyter notebook instance (also described in the same publication and available at https://github.com/IMAXT/imaxt-image).…”

Section: Imaging Mass Cytometry (Imc)mentioning

confidence: 99%

Creating a ‘Timeline’ of ductal carcinoma in situ to identify processes and biomarkers for progression towards invasive ductal carcinoma

Rebbeck

Jian

Bornelöv

et al. 2022

Preprint

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Ductal carcinoma in situ (DCIS) is considered a non-invasive precursor to breast cancer, and although associated with an increased risk of developing invasive disease, many women with DCIS will never progress beyond their in situ diagnosis. The path from normal duct to invasive disease is not well understood, and efforts to do so are hampered by the substantial heterogeneity that exists between patients and even within patients. Using gene expression analysis, we have generated a ‘Timeline’ of disease progression, utilising the variability within patients and combining >2,000 individually micro-dissected ductal lesions from 145 patients into one continuous trajectory. Using this Timeline we show there is a progressive loss in basal layer integrity, coupled with two epithelial to mesenchymal transitions (EMT), one early in the timeline and a second just prior to cells leaving the duct. We identify early processes and potential biomarkers, including CAMK2N1, MNX1, ADCY5, HOXC11 and ANKRD22, whose reduced expression is associated with the progression of DCIS to invasive breast cancer.

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Section: Imaging Mass Cytometry (Imc)mentioning

confidence: 99%

Creating a ‘Timeline’ of ductal carcinoma in situ to identify processes and biomarkers for progression towards invasive ductal carcinoma

Rebbeck

Jian

Bornelöv

et al. 2022

Preprint

Self Cite

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show abstract

Gene expression signatures of individual ductal carcinoma in situ lesions identify processes and biomarkers associated with progression towards invasive ductal carcinoma

et al. 2022

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Ductal carcinoma in situ (DCIS) is considered a non-invasive precursor to breast cancer, and although associated with an increased risk of developing invasive disease, many women with DCIS will never progress beyond their in situ diagnosis. The path from normal duct to invasive ductal carcinoma (IDC) is not well understood, and efforts to do so are hampered by the substantial heterogeneity that exists between patients, and even within patients. Here we show gene expression analysis from > 2,000 individually micro-dissected ductal lesions representing 145 patients. Combining all samples into one continuous trajectory we show there is a progressive loss in basal layer integrity heading towards IDC, coupled with two epithelial to mesenchymal transitions, one early and a second coinciding with the convergence of DCIS and IDC expression profiles. We identify early processes and potential biomarkers, including CAMK2N1, MNX1, ADCY5, HOXC11 and ANKRD22, whose reduced expression is associated with the progression of DCIS to invasive breast cancer.

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The dawn of spatial omics

Bressan

Battistoni

Hannon

2023

Science

187

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Spatial omics has been widely heralded as the new frontier in life sciences. This term encompasses a wide range of techniques that promise to transform many areas of biology and eventually revolutionize pathology by measuring physical tissue structure and molecular characteristics at the same time. Although the field came of age in the past 5 years, it still suffers from some growing pains: barriers to entry, robustness, unclear best practices for experimental design and analysis, and lack of standardization. In this Review, we present a systematic catalog of the different families of spatial omics technologies; highlight their principles, power, and limitations; and give some perspective and suggestions on the biggest challenges that lay ahead in this incredibly powerful—but still hard to navigate—landscape.

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The Imaging and Molecular Annotation of Xenografts and Tumours (IMAXT) High Throughput Data and Analysis Infrastructure

Cited by 3 publications

References 25 publications

Creating a ‘Timeline’ of ductal carcinoma in situ to identify processes and biomarkers for progression towards invasive ductal carcinoma

Creating a ‘Timeline’ of ductal carcinoma in situ to identify processes and biomarkers for progression towards invasive ductal carcinoma

Gene expression signatures of individual ductal carcinoma in situ lesions identify processes and biomarkers associated with progression towards invasive ductal carcinoma

The dawn of spatial omics

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