Data

Colorectal Cancer Atlas

The Colorectal Cancer atlas aims to advance our understanding of the complex spatial interactions that contribute to colorectal cancer. Colorectal cancers are complex assemblies of tumor, immune, and stromal cells that invade adjacent tissue and spread to distant sites. We use highly multiplexed tissue imaging, spatial statistics, and machine learning to identify cell types and states underlying morphological features of known diagnostic and prognostic significance in colorectal cancer.

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Publications

High-plex immunofluorescence imaging and traditional histology of the same tissue section for discovering image-based biomarkers.

Lin JR, Chen YA, Campton D, Cooper J, Coy S, Yapp C, Tefft JB, McCarty E, Ligon KL, Rodig SJ, Reese S, George T, Santagata S, Sorger PK (2023).

Nature Cancer https://doi.org/10.1038/s43018-023-00576-1

Multiplexed 3D atlas of state transitions and immune interactions in colorectal cancer.

Lin, J.-R., Wang, S., Coy, S., Tyler, M., Yapp, C., Chen, Y.-A., Heiser, C.N., Lau, K.S., Santagata, S., Sorger, P.K. (2023).

Cell, 186(19), 363-381.e19. https://doi.org/10.1016/j.cell.2022.12.028

Epigenetic and oncogenic inhibitors cooperatively drive differentiation and kill KRAS-mutant colorectal cancers

Loi P, Schade AE, Rodriguez CL, Krishnan A, Perurena N, Nguyen VTM, Xu Y, Watanabe M, Davis RA, Gardner A, Pilla NF, Mattioli K, Popow O, Gunduz N, Lannagan TRM, Fitzgerald S, Sicinska ET, Lin J-R, Tan W, Brais LK, Haigis KM, Giannakis M, Ng K, Santagata S, Helin K, Sansom OJ, Cichowski K. (2024).

Cancer Discovery https://doi.org/10.1158/2159-8290.CD-23-0866

PubMed

Narrated Minerva Stories

Narrated stories use multi-step narrations and annotations to walk a viewer through key features of the data. Narrated stories distill the multidisciplinary knowledge encompassed by each dataset into a single product that grounds the scientific analyses in the underlying data and metadata. Click the Minerva story icon for an interactive view of the full-resolution images.

Multimodal spatial profiling of colorectal cancer using Orion

Graphical Abstract - Multiplexed 3D atlas of state transitions and immune interactions in colorectal cancer

Pathological annotations - Multiplexed 3D atlas of state transitions and immune interactions in colorectal cancer - CRC01

Colorectal cancer pilot - CRC01

HSF1 phase transition mediates stress adaptation and cell fate decisions

Curated Minerva Stories

Curated stories provide access to images that have undergone a quality control step to remove failed markers, ensure appropriate channel intensity settings, and provide metadata about the underlying sample and image. Click the Minerva story icon for an interactive view of the full-resolution images.

All CyCIF sections of CRC01 (Z-stack)

All 25 CyCIF sections from CRC01 (array)

All 22 H&E sections from CRC01 (array)

Automated Minerva Stories

Automated stories provide basic image viewing with automatic rendering settings, enabling rapid, lightweight sharing of highly multiplexed images, without download. Click the Minerva story icon for an interactive view of the full-resolution images.

Orion CRC40 - overview - Lin, Chen, Campton et al., 2023

Orion CRC39 - overview - Lin, Chen, Campton et al., 2023

Orion CRC38 - overview - Lin, Chen, Campton et al., 2023

Orion CRC37 - overview - Lin, Chen, Campton et al., 2023

Orion CRC36 - overview - Lin, Chen, Campton et al., 2023

Orion CRC35 - overview - Lin, Chen, Campton et al., 2023

Orion CRC34 - overview - Lin, Chen, Campton et al., 2023

Orion CRC33_02 - overview - Lin, Chen, Campton et al., 2023

Orion CRC33_01 - overview - Lin, Chen, Campton et al., 2023

Orion CRC32 - overview - Lin, Chen, Campton et al., 2023

Orion CRC31 - overview - Lin, Chen, Campton et al., 2023

Orion CRC30 - overview - Lin, Chen, Campton et al., 2023

Orion CRC29 - overview - Lin, Chen, Campton et al., 2023

Orion CRC28 - overview - Lin, Chen, Campton et al., 2023

Orion CRC27 - overview - Lin, Chen, Campton et al., 2023

Orion CRC26 - overview - Lin, Chen, Campton et al., 2023

Orion CRC25 - overview - Lin, Chen, Campton et al., 2023

Orion CRC24 - overview - Lin, Chen, Campton et al., 2023

Orion CRC23 - overview - Lin, Chen, Campton et al., 2023

Orion CRC21 - overview - Lin, Chen, Campton et al., 2023

Orion CRC08 - overview - Lin, Chen, Campton et al., 2023

Orion CRC20 - overview - Lin, Chen, Campton et al., 2023

Orion CRC19 - overview - Lin, Chen, Campton et al., 2023

Orion CRC18 - overview - Lin, Chen, Campton et al., 2023

Orion CRC17 - overview - Lin, Chen, Campton et al., 2023

Orion CRC16 - overview - Lin, Chen, Campton et al., 2023

Orion CRC15 - overview - Lin, Chen, Campton et al., 2023

Orion CRC14 - overview - Lin, Chen, Campton et al., 2023

Orion CRC13 - overview - Lin, Chen, Campton et al., 2023

Orion CRC12 - overview - Lin, Chen, Campton et al., 2023

Orion CRC11 - overview - Lin, Chen, Campton et al., 2023

Orion CRC10 - overview - Lin, Chen, Campton et al., 2023

Orion CRC09 - overview - Lin, Chen, Campton et al., 2023

Orion CRC07 - overview - Lin, Chen, Campton et al., 2023

Orion CRC06 - overview - Lin, Chen, Campton et al., 2023

Orion CRC05 - overview - Lin, Chen, Campton et al., 2023

Orion CRC04 - overview - Lin, Chen, Campton et al., 2023

Orion CRC03 - overview - Lin, Chen, Campton et al., 2023

Orion CRC02 - overview - Lin, Chen, Campton et al., 2023

Orion CRC01 - overview - Lin, Chen, Campton et al., 2023

CRC18 - H&E - overview - Lin, Wang, Coy et al., 2021

CRC17 - overview - Lin, Wang, Coy et al., 2021

CRC17 - H&E - overview - Lin, Wang, Coy et al., 2021

CRC16 - overview - Lin, Wang, Coy et al., 2021

CRC16 - H&E - overview - Lin, Wang, Coy et al., 2021

CRC15 - overview - Lin, Wang, Coy et al., 2021

CRC15 - H&E - overview - Lin, Wang, Coy et al., 2021

CRC14 - overview - Lin, Wang, Coy et al., 2021

CRC14 - H&E - overview - Lin, Wang, Coy et al., 2021

CRC13 - overview - Lin, Wang, Coy et al., 2021

CRC13 - H&E - overview - Lin, Wang, Coy et al., 2021

CRC12 - overview - Lin, Wang, Coy et al., 2021

CRC12 - H&E - overview - Lin, Wang, Coy et al., 2021

CRC11 - overview - Lin, Wang, Coy et al., 2021

CRC11 - H&E - overview - Lin, Wang, Coy et al., 2021

CRC10 - overview - Lin, Wang, Coy et al., 2021

CRC10 - H&E - overview - Lin, Wang, Coy et al., 2021

CRC08 - overview - Lin, Wang, Coy et al., 2021

CRC09 - H&E - overview - Lin, Wang, Coy et al., 2021

CRC08 - overview - Lin, Wang, Coy et al., 2021

CRC08 - H&E - overview - Lin, Wang, Coy et al., 2021

CRC07 - overview - Lin, Wang, Coy et al., 2021

CRC07 - H&E - overview - Lin, Wang, Coy et al., 2021

CRC06 - overview - Lin, Wang, Coy et al., 2021

CRC06 - H&E - overview - Lin, Wang, Coy et al., 2021

CRC05 - overview - Lin, Wang, Coy et al., 2021

CRC05 - H&E - overview - Lin, Wang, Coy et al., 2021

CRC04 - overview - Lin, Wang, Coy et al., 2021

CRC04 - H&E - overview - Lin, Wang, Coy et al., 2021

CRC03 - overview - Lin, Wang, Coy et al., 2021

CRC03 - H&E - overview - Lin, Wang, Coy et al., 2021

CRC02 - overview - Lin, Wang, Coy et al., 2021

CRC02 - H&E - overview - Lin, Wang, Coy et al., 2021

Funding

This work has been funded by the NIH NCI Human Tumor Atlas Network, (Grant U2C-CA233262), the NCI Cancer Systems Biology Program (Grant U54-CA225088), an NIH NCI Research Specialist Award (Grant R50-CA274277), and the The Quadrangle Fund for Advancing and Seeding Translational Research at Harvard Medical School (QFASTR).