Omic and Multidimensional Spatial (OMS) Human Tumor Atlas
A National Cancer Institute initiative
The Omic and Multidimensional Spatial (OMS) Atlas is one of several "U2C" Human Tumor Atlases (HTA) Research Centers of the National Cancer Institute (NCI) Human Tumor Atlas Network, which emerged out of the Beau Biden Cancer Moonshot Initiative. The purpose of the construction of these "atlases" is to provide a more comprehensive understanding of the "ecosystems of tumors at the macro- and micro-level" by describing changes in cellular, structural, and molecular characteristics of human cancers as they progress over time.
Multi-institutional collaboration
The OMS Atlas lead investigators are: Joe Gray, Ph.D., Gordon Mills, M.D., Ph.D., Jeremy Goecks, Ph.D., and George Thomas, M.D., and our team includes collaborators from Harvard Medical School and the MD Anderson Cancer Center, who will work together to develop "maps" of human metastatic breast cancers.
Utilizes SMMART program infrastructure and data
Newly established in fall of 2018, it will take advantage of the clinical infrastructure in the SMMART program and support extensive characterization of tissues collected therein.
Read more
- Generation of the Human Tumor Atlases, National Cancer Institute
- Cancer and the Human Tumor Atlas Network (infographic), National Cancer Institute
Inquiries
Please direct any inquiries regarding the Omic and Multidimensional Spatial (OMS) Human Tumor Atlas to Heidi Feiler, Scientific Program Manager, feiler@ohsu.edu.
News
- June 27-28, 2022: The OMS Atlas Center at OHSU will co-host the HTAN F2F in Portland, bringing consortium centers together for workshops and presentations on lung, pediatric, breast, and colon cancers as well as a diversity and inclusion discussion. (Registration is closed.)
- A member of our OMS Atlas Team (Nick Navin from MDACC) was interviewed by NCI. The story "Meticulous Reconstructions of Tumor Origins With Single-Cell DNA Sequencing: Researcher Interview with Nicholas Navin" posted to the NCI Insights & Innovations blog on November 27, 2018. View the transcript.
Publications
2022
2021
2020
2019
2018
- Rashid R, Chen YA, Hoffer J, Muhlich JL, Lin JR, Krueger R, Pfister H, Mitchell R, Santagata S, Sorger PK. Narrative online guides for the interpretation of digital-pathology images and tissue-atlas data. Nat Biomed Eng. 2022 May;6(5):515-526. doi: 10.1038/s41551-021-00789-8. Epub 2021 Nov 8. PMID: 34750536; PMCID: PMC9079188.
- Schapiro D, Yapp C, Sokolov A, Reynolds SM, Chen YA, Sudar D, Xie Y, Muhlich J, Arias-Camison R, Arena S, Taylor AJ, Nikolov M, Tyler M, Lin JR, Burlingame EA; Human Tumor Atlas Network, Chang YH, Farhi SL, Thorsson V, Venkatamohan N, Drewes JL, Pe'er D, Gutman DA, Herrmann MD, Gehlenborg N, Bankhead P, Roland JT, Herndon JM, Snyder MP, Angelo M, Nolan G, Swedlow JR, Schultz N, Merrick DT, Mazzili SA, Cerami E, Rodig SJ, Santagata S, Sorger PK. MITI minimum information guidelines for highly multiplexed tissue images. Nat Methods. 2022 Mar;19(3):262-267. doi: 10.1038/s41592-022-01415-4. PMID: 35277708; PMCID: PMC9009186.
- Taylor MH, Betts CB, Maloney L, Nadler E, Algazi A, Guarino MJ, Nemunaitis J, Jimeno A, Patel P, Munugalavadla V, Tao L, Adkins D, Goldschmidt JH, Cohen EEW, Coussens LM. Safety and Efficacy of Pembrolizumab in Combination with Acalabrutinib in Advanced Head and Neck Squamous Cell Carcinoma: Phase 2 Proof-of-Concept Study. Clin Cancer Res. 2022 Mar 1;28(5):903-914. doi: 10.1158/1078-0432.CCR-21-2547. PMID: 34862248.
- Ternes L, Dane M, Gross S, Labrie M, Mills G, Gray J, Heiser L, Chang YH. A multi-encoder variational autoencoder controls multiple transformational features in single-cell image analysis. Commun Biol. 2022 Mar 23;5(1):255. doi: 10.1038/s42003-022-03218-x. PMID: 35322205; PMCID: PMC8943013.
- Schapiro D, Sokolov A, Yapp C, Chen YA, Muhlich JL, Hess J, Creason AL, Nirmal AJ, Baker GJ, Nariya MK, Lin JR, Maliga Z, Jacobson CA, Hodgman MW, Ruokonen J, Farhi SL, Abbondanza D, McKinley ET, Persson D, Betts C, Sivagnanam S, Regev A, Goecks J, Coffey RJ, Coussens LM, Santagata S, Sorger PK. MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging. Nat Methods. 2022 Mar;19(3):311-315. doi: 10.1038/s41592-021-01308-y. Epub 2021 Nov 25. PMID: 34824477; PMCID: PMC8916956.
- Blise KE, Sivagnanam S, Banik GL, Coussens LM, Goecks J. Single-cell spatial architectures associated with clinical outcome in head and neck squamous cell carcinoma. NPJ Precis Oncol. 2022 Feb 25;6(1):10. doi: 10.1038/s41698-022-00253-z. PMID: 35217711; PMCID: PMC8881577.
- Johnson BE, Creason AL, Stommel JM, Keck JM, Parmar S, Betts CB, Blucher A, Boniface C, Bucher E, Burlingame E, Camp T, Chin K, Eng J, Estabrook J, Feiler HS, Heskett MB, Hu Z, Kolodzie A, Kong BL, Labrie M, Lee J, Leyshock P, Mitri S, Patterson J, Riesterer JL, Sivagnanam S, Somers J, Sudar D, Thibault G, Weeder BR, Zheng C, Nan X, Thompson RF, Heiser LM, Spellman PT, Thomas G, Demir E, Chang YH, Coussens LM, Guimaraes AR, Corless C, Goecks J, Bergan R, Mitri Z, Mills GB, Gray JW. An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer. Cell Rep Med. 2022 Feb 15;3(2):100525. doi: 10.1016/j.xcrm.2022.100525. PMID: 35243422; PMCID: PMC8861971.
- CSBC/PS-ON Image Analysis Working Group, Vizcarra JC, Burlingame EA, Hug CB, Goltsev Y, White BS, Tyson DR, Sokolov A. A community-based approach to image analysis of cells, tissues and tumors. Comput Med Imaging Graph. 2022 Jan;95:102013. doi: 10.1016/j.compmedimag.2021.102013. Epub 2021 Nov 19. PMID: 34864359; PMCID: PMC8761177.
- Jessup J, Krueger R, Warchol S, Hoffer J, Muhlich J, Ritch CC, Gaglia G, Coy S, Chen YA, Lin JR, Santagata S, Sorger PK, Pfister H. Scope2Screen: Focus+Context Techniques for Pathology Tumor Assessment in Multivariate Image Data. IEEE Trans Vis Comput Graph. 2022 Jan;28(1):259-269. doi: 10.1109/TVCG.2021.3114786. Epub 2021 Dec 24. PMID: 34606456; PMCID: PMC8805697.
- Gu JT, Claudio N, Betts C, Sivagnanam S, Geltzeiler M, Pucci F. Characterization of the tumor immune microenvironment of sinonasal squamous-cell carcinoma. Int Forum Allergy Rhinol. 2022 Jan;12(1):39-50. doi: 10.1002/alr.22867. Epub 2021 Sep 12. PMID: 34510766; PMCID: PMC8716469.
- Irvine EB, O'Neil A, Darrah PA, Shin S, Choudhary A, Li W, Honnen W, Mehra S, Kaushal D, Gideon HP, Flynn JL, Roederer M, Seder RA, Pinter A, Fortune S, Alter G. Robust IgM responses following intravenous vaccination with Bacille Calmette-Guérin associate with prevention of Mycobacterium tuberculosis infection in macaques. Nat Immunol. 2021 Dec;22(12):1515-1523. doi: 10.1038/s41590-021-01066-1. Epub 2021 Nov 22. PMID: 34811542; PMCID: PMC8642241.
- Hammer M, Huisman M, Rigano A, Boehm U, Chambers JJ, Gaudreault N, North AJ, Pimentel JA, Sudar D, Bajcsy P, Brown CM, Corbett AD, Faklaris O, Lacoste J, Laude A, Nelson G, Nitschke R, Farzam F, Smith CS, Grunwald D, Strambio-De-Castillia C. Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model. Nat Methods. 2021 Dec;18(12):1427-1440. doi: 10.1038/s41592-021-01327-9. Erratum in: Nat Methods. 2022 Feb;19(2):255. PMID: 34862501.
- Nelson G, Boehm U, Bagley S, Bajcsy P, Bischof J, Brown CM, Dauphin A, Dobbie IM, Eriksson JE, Faklaris O, Fernandez-Rodriguez J, Ferrand A, Gelman L, Gheisari A, Hartmann H, Kukat C, Laude A, Mitkovski M, Munck S, North AJ, Rasse TM, Resch-Genger U, Schuetz LC, Seitz A, Strambio-De-Castillia C, Swedlow JR, Alexopoulos I, Aumayr K, Avilov S, Bakker GJ, Bammann RR, Bassi A, Beckert H, Beer S, Belyaev Y, Bierwagen J, Birngruber KA, Bosch M, Breitlow J, Cameron LA, Chalfoun J, Chambers JJ, Chen CL, Conde-Sousa E, Corbett AD, Cordelieres FP, Nery ED, Dietzel R, Eismann F, Fazeli E, Felscher A, Fried H, Gaudreault N, Goh WI, Guilbert T, Hadleigh R, Hemmerich P, Holst GA, Itano MS, Jaffe CB, Jambor HK, Jarvis SC, Keppler A, Kirchenbuechler D, Kirchner M, Kobayashi N, Krens G, Kunis S, Lacoste J, Marcello M, Martins GG, Metcalf DJ, Mitchell CA, Moore J, Mueller T, Nelson MS, Ogg S, Onami S, Palmer AL, Paul-Gilloteaux P, Pimentel JA, Plantard L, Podder S, Rexhepaj E, Royon A, Saari MA, Schapman D, Schoonderwoert V, Schroth-Diez B, Schwartz S, Shaw M, Spitaler M, Stoeckl MT, Sudar D, Teillon J, Terjung S, Thuenauer R, Wilms CD, Wright GD, Nitschke R. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. J Microsc. 2021 Oct;284(1):56-73. doi: 10.1111/jmi.13041. Epub 2021 Aug 11. PMID: 34214188.
- Labrie M, Li A, Creason A, Betts C, Keck J, Johnson B, Sivagnanam S, Boniface C, Ma H, Blucher A, Chang YH, Chin K, Vuky J, Guimaraes AR, Downey M, Lim JY, Gao L, Siex K, Parmar S, Kolodzie A, Spellman PT, Goecks J, Coussens LM, Corless CL, Bergan R, Gray JW, Mills GB, Mitri ZI. Multiomics analysis of serial PARP inhibitor treated metastatic TNBC inform on rational combination therapies. NPJ Precis Oncol. 2021 Oct 19;5(1):92. doi: 10.1038/s41698-021-00232-w. PMID: 34667258; PMCID: PMC8526613.
- Liudahl SM, Betts CB, Sivagnanam S, Morales-Oyarvide V, da Silva A, Yuan C, Hwang S, Grossblatt-Wait A, Leis KR, Larson W, Lavoie MB, Robinson P, Dias Costa A, Väyrynen SA, Clancy TE, Rubinson DA, Link J, Keith D, Horton W, Tempero MA, Vonderheide RH, Jaffee EM, Sheppard B, Goecks J, Sears RC, Park BS, Mori M, Nowak JA, Wolpin BM, Coussens LM. Leukocyte Heterogeneity in Pancreatic Ductal Adenocarcinoma: Phenotypic and Spatial Features Associated with Clinical Outcome. Cancer Discov. 2021 Aug;11(8):2014-2031. doi: 10.1158/2159-8290.CD-20-0841. Epub 2021 Mar 16. PMID: 33727309; PMCID: PMC8338775.
- Byrne KT, Betts CB, Mick R, Sivagnanam S, Bajor DL, Laheru DA, Chiorean EG, O'Hara MH, Liudahl SM, Newcomb C, Alanio C, Ferreira AP, Park BS, Ohtani T, Huffman AP, Väyrynen SA, Dias Costa A, Kaiser JC, Lacroix AM, Redlinger C, Stern M, Nowak JA, Wherry EJ, Cheever MA, Wolpin BM, Furth EE, Jaffee EM, Coussens LM, Vonderheide RH. Neoadjuvant Selicrelumab, an Agonist CD40 Antibody, Induces Changes in the Tumor Microenvironment in Patients with Resectable Pancreatic Cancer. Clin Cancer Res. 2021 Aug 15;27(16):4574-4586. doi: 10.1158/1078-0432.CCR-21-1047. Epub 2021 Jun 10. PMID: 34112709; PMCID: PMC8667686.
- Burlingame EA, Eng J, Thibault G, Chin K, Gray JW, Chang YH. Toward reproducible, scalable, and robust data analysis across multiplex tissue imaging platforms. Cell Rep Methods. 2021 Aug 23;1(4):100053. doi: 10.1016/j.crmeth.2021.100053. Epub 2021 Jul 23. PMID: 34485971; PMCID: PMC8415641.
- Thomas PL, Groves SM, Zhang YK, Li J, Gonzalez-Ericsson P, Sivagnanam S, Betts CB, Chen HC, Liu Q, Lowe C, Chen H, Boyd KL, Kopparapu PR, Yan Y, Coussens LM, Quaranta V, Tyson DR, Iams W, Lovly CM. Beyond Programmed Death-Ligand 1: B7-H6 Emerges as a Potential Immunotherapy Target in SCLC. J Thorac Oncol. 2021 Jul;16(7):1211-1223. doi: 10.1016/j.jtho.2021.03.011. Epub 2021 Apr 8. PMID: 33839362; PMCID: PMC8222171.
- Gu Q, Kumar A, Bray S, Creason A, Khanteymoori A, Jalili V, Grüning B, Goecks J. Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine. PLoS Comput Biol. 2021 Jun 1;17(6):e1009014. doi: 10.1371/journal.pcbi.1009014. PMID: 34061826; PMCID: PMC8213174.
- Grzadkowski MR, Holly HD, Somers J, Demir E. Systematic interrogation of mutation groupings reveals divergent downstream expression programs within key cancer genes. BMC Bioinformatics. 2021 May 6;22(1):233. doi: 10.1186/s12859-021-04147-y. PMID: 33957863; PMCID: PMC8101181.
- Tognon CE, Sears RC, Mills GB, Gray JW, Tyner JW. Ex Vivo Analysis of Primary Tumor Specimens for Evaluation of Cancer Therapeutics. Annu Rev Cancer Biol. 2021 Mar;5:39-57. doi: 10.1146/annurev-cancerbio-043020-125955. Epub 2020 Dec 8. PMID: 34222745; PMCID: PMC8248658.
- Ternes L, Huang G, Lanciault C, Thibault G, Riggers R, Gray JW, Muschler J, Chang YH. VISTA: VIsual Semantic Tissue Analysis for pancreatic disease quantification in murine cohorts. Sci Rep. 2020 Dec 1;10(1):20904. doi: 10.1038/s41598-020-78061-3. PMID: 33262400; PMCID: PMC7708430.
- Shah VM, Sheppard BC, Sears RC, Alani AW. Hypoxia: Friend or Foe for drug delivery in Pancreatic Cancer. Cancer Lett. 2020 Nov 1;492:63-70. doi: 10.1016/j.canlet.2020.07.041. Epub 2020 Aug 18. PMID: 32822815; PMCID: PMC7879337.
- Burlingame EA, McDonnell M, Schau GF, Thibault G, Lanciault C, Morgan T, Johnson BE, Corless C, Gray JW, Chang YH. SHIFT: speedy histological-to-immunofluorescent translation of a tumor signature enabled by deep learning. Sci Rep. 2020 Oct 15;10(1):17507. doi: 10.1038/s41598-020-74500-3. PMID: 33060677; PMCID: PMC7566625.
- Hoffer J, Rashid R, Muhlich JL, Chen YA, Russell DPW, Ruokonen J, Krueger R, Pfister H, Santagata S, Sorger PK. Minerva: a light-weight, narrative image browser for multiplexed tissue images. J Open Source Softw. 2020;5(54):2579. doi: 10.21105/joss.02579. Epub 2020 Oct 15. PMID: 33768192; PMCID: PMC7989801.
- Pennycuick A, Teixeira VH, AbdulJabbar K, Raza SEA, Lund T, Akarca AU, Rosenthal R, Kalinke L, Chandrasekharan DP, Pipinikas CP, Lee-Six H, Hynds RE, Gowers KHC, Henry JY, Millar FR, Hagos YB, Denais C, Falzon M, Moore DA, Antoniou S, Durrenberger PF, Furness AJ, Carroll B, Marceaux C, Asselin-Labat ML, Larson W, Betts C, Coussens LM, Thakrar RM, George J, Swanton C, Thirlwell C, Campbell PJ, Marafioti T, Yuan Y, Quezada SA, McGranahan N, Janes SM. Immune Surveillance in Clinical Regression of Preinvasive Squamous Cell Lung Cancer. Cancer Discov. 2020 Oct;10(10):1489-1499. doi: 10.1158/2159-8290.CD-19-1366. Epub 2020 Jul 20. PMID: 32690541; PMCID: PMC7611527.
- Shah VM, English IA, Sears RC. Select Stabilization of a Tumor-Suppressive PP2A Heterotrimer. Trends Pharmacol Sci. 2020 Sep;41(9):595-597. doi: 10.1016/j.tips.2020.06.008. Epub 2020 Jul 2. PMID: 32624198; PMCID: PMC8106543.
- Rozenblatt-Rosen O, Regev A, Oberdoerffer P, Nawy T, Hupalowska A, Rood JE, Ashenberg O, Cerami E, Coffey RJ, Demir E, Ding L, Esplin ED, Ford JM, Goecks J, Ghosh S, Gray JW, Guinney J, Hanlon SE, Hughes SK, Hwang ES, Iacobuzio-Donahue CA, Jané-Valbuena J, Johnson BE, Lau KS, Lively T, Mazzilli SA, Pe'er D, Santagata S, Shalek AK, Schapiro D, Snyder MP, Sorger PK, Spira AE, Srivastava S, Tan K, West RB, Williams EH; Human Tumor Atlas Network. The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution. Cell. 2020 Apr 16;181(2):236-249. doi: 10.1016/j.cell.2020.03.053. PMID: 32302568; PMCID: PMC7376497.
- Goecks J, Jalili V, Heiser LM, Gray JW. https://pubmed.ncbi.nlm.nih.gov/32243801/How Machine Learning Will Transform Biomedicine. Cell. 2020 Apr 2;181(1):92-101. doi: 10.1016/j.cell.2020.03.022. PMID: 32243801; PMCID: PMC7141410.
- Riesterer JL, López CS, Stempinski ES, Williams M, Loftis K, Stoltz K, Thibault G, Lanicault C, Williams T, Gray JW. A workflow for visualizing human cancer biopsies using large-format electron microscopy. Methods Cell Biol. 2020;158:163-181. doi: 10.1016/bs.mcb.2020.01.005. Epub 2020 Mar 12. PMID: 32423648.
- Chang YH, Chin K, Thibault G, Eng J, Burlingame E, Gray JW. RESTORE: Robust intEnSiTy nORmalization mEthod for multiplexed imaging. Commun Biol. 2020 Mar 9;3(1):111. doi: 10.1038/s42003-020-0828-1. PMID: 32152447; PMCID: PMC7062831.
- Chang YH, Chin K, Thibault G, Eng J, Burlingame E, Gray JW. RESTORE: Robust intEnSiTy nORmalization mEthod for multiplexed imaging. Commun Biol. 2020 Mar 9;3(1):111. doi: 10.1038/s42003-020-0828-1. PMID: 32152447; PMCID: PMC7062831.
- Banik G, Betts CB, Liudahl SM, Sivagnanam S, Kawashima R, Cotechini T, Larson W, Goecks J, Pai SI, Clayburgh DR, Tsujikawa T, Coussens LM. High-dimensional multiplexed immunohistochemical characterization of immune contexture in human cancers. Methods Enzymol. 2020;635:1-20. doi: 10.1016/bs.mie.2019.05.039. Epub 2019 Jul 2. PMID: 32122539; PMCID: PMC7390987.
- Rashid R, Gaglia G, Chen YA, Lin JR, Du Z, Maliga Z, Schapiro D, Yapp C, Muhlich J, Sokolov A, Sorger P, Santagata S. Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer. Sci Data. 2019 Dec 17;6(1):323. doi: 10.1038/s41597-019-0332-y. PMID: 31848351; PMCID: PMC6917801.
- Heiser LM, Mills GB, Gray JW. Therapeutic Clues from an Integrated Omic Assessment of East Asian Triple Negative Breast Cancers. Cancer Cell. 2019 Mar 18;35(3):341-343. doi: 10.1016/j.ccell.2019.02.012. PMID: 30889376; PMCID: PMC6499473.
- Burlingame EA, Margolin AA, Gray JW, Chang YH. SHIFT: speedy histopathological-to-immunofluorescent translation of whole slide images using conditional generative adversarial networks. Proc SPIE Int Soc Opt Eng. 2018 Feb;10581:1058105. doi: 10.1117/12.2293249. Epub 2018 Mar 6. PMID: 30283195; PMCID: PMC6166432.