Program Official
Sudhir Srivastava, Ph.D., M.P.H.

Principal Investigator

Peter Karl
Sorger
Awardee Organization

Harvard Medical School
United States

Fiscal Year
2023
Activity Code
U2C
Early Stage Investigator Grants (ESI)
Not Applicable
Project End Date
Notice of Funding Opportunity
NIH RePORTER
For more information, see NIH RePORTER Project 3U2CCA233262-01S2

Pre-cancer atlases of cutaneous and hematologic origin (PATCH Center)

The overall aims of the Center for Pre-cancer Atlases of Cutaneous and Hematologic Origin (PATCH Center) will pivot in the supplemental year to focus on data analysis and dissemination. The Administration and Project Management team will focus on the scientific management of the Center, communicate with NCI staff and HTAN Centers, and ensure regular data deposition. They will guide the other Center members to focus on all activities related to the completion and dissemination of the Center atlas. We anticipate the biospecimen and clinical teams will focus on curating clinical and biospecimen metadata and participating in the interpretation of results for publication and other dissemination activities. Most characterization activities for the atlas and the SARDANA TNP will be completed prior to the initiation of the supplement, but additional characterization will be performed for quality assurance and follow up experimentation during the publication process. The bulk of the activities will be in data analysis, software development, and dissemination of complex image data. The Center will be working on 3D segmentation and visualization tools, improvements to the MCMICRO pipeline, and advancements to Minerva Story tools to accommodate 3D visualization as well as clinical and biospecimen metadata. Our Center will continue to work with the DCC to develop and optimize the process for sharing highly complex imaging data.

Publications

  • 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. Journal of open source software. 2020;5. (54). Epub 2020 Oct 15. PMID: 33768192
  • Muhlich JL, Chen YA, Yapp C, Russell D, Santagata S, Sorger PK. Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR. Bioinformatics (Oxford, England). 2022 Sep 30;38(19):4613-4621. PMID: 35972352
  • Prabhakaran S, Yapp C, Baker GJ, Beyer J, Chang YH, Creason AL, Krueger R, Muhlich J, Patterson NH, Sidak K, Sudar D, Taylor AJ, Ternes L, Troidl J, Xie Y, Sokolov A, Tyson DR, Cell Imaging Hackathon 2022 Participants. Addressing persistent challenges in digital image analysis of cancerous tissues. bioRxiv : the preprint server for biology. 2023 Jul 24. PMID: 37547011
  • Russell-Goldman E, Murphy GF. The Pathobiology of Skin Aging: New Insights into an Old Dilemma. The American journal of pathology. 2020 Jul;190(7):1356-1369. Epub 2020 Apr 1. PMID: 32246919
  • 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. Nature biomedical engineering. 2022 May;6(5):515-526. Epub 2021 Nov 8. PMID: 34750536
  • Coy S, Lee JS, Chan SJ, Woo T, Jones J, Alexandrescu S, Wen PY, Sorger PK, Ligon KL, Santagata S. Systematic characterization of antibody-drug conjugate targets in central nervous system tumors. Neuro-oncology. 2024 Mar 4;26(3):458-472. PMID: 37870091
  • 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, Abravanel DL, Achilefu S, Ademuyiwa FO, Adey AC, Aft R, Ahn KJ, Alikarami F, Alon S, Ashenberg O, Baker E, Baker GJ, Bandyopadhyay S, Bayguinov P, Beane J, Becker W, Bernt K, Betts CB, Bletz J, Blosser T, Boire A, Boland GM, Boyden ES, Bucher E, Bueno R, Cai Q, Cambuli F, Campbell J, Cao S, Caravan W, Chaligné R, Chan JM, Chasnoff S, Chatterjee D, Chen AA, Chen C, Chen CH, Chen B, Chen F, Chen S, Chheda MG, Chin K, Cho H, Chun J, Cisneros L, Coffey RJ, Cohen O, Colditz GA, Cole KA, Collins N, Cotter D, Coussens LM, Coy S, Creason AL, Cui Y, Zhou DC, Curtis C, Davies SR, Bruijn I, Delorey TM, Demir E, Denardo D, Diep D, Ding L, DiPersio J, Dubinett SM, Eberlein TJ, Eddy JA, Esplin ED, Factor RE, Fatahalian K, Feiler HS, Fernandez J, Fields A, Fields RC, Fitzpatrick JAJ, Ford JM, Franklin J, Fulton B, Gaglia G, Galdieri L, Ganesh K, Gao J, Gaudio BL, Getz G, Gibbs DL, Gillanders WE, Goecks J, Goodwin D, Gray JW, Greenleaf W, Grimm LJ, Gu Q, Guerriero JL, Guha T, Guimaraes AR, Gutierrez B, Hacohen N, Hanson CR, Harris CR, Hawkins WG, Heiser CN, Hoffer J, Hollmann TJ, Hsieh JJ, Huang J, Hunger SP, Hwang ES, Iacobuzio-Donahue C, Iglesia MD, Islam M, Izar B, Jacobson CA, Janes S, Jayasinghe RG, Jeudi T, Johnson BE, Johnson BE, Ju T, Kadara H, Karnoub ER, Karpova A, Khan A, Kibbe W, Kim AH, King LM, Kozlowski E, Krishnamoorthy P, Krueger R, Kundaje A, Ladabaum U, Laquindanum R, Lau C, Lau KSK, LeBoeuf NR, Lee H, Lenburg M, Leshchiner I, Levy R, Li Y, Lian CG, Liang WW, Lim KH, Lin Y, Liu D, Liu Q, Liu R, Lo J, Lo P, Longabaugh WJ, Longacre T, Luckett K, Ma C, Maher C, Maier A, Makowski D, Maley C, Maliga Z, Manoj P, Maris JM, Markham N, Marks JR, Martinez D, Mashl J, Masilionis I, Massague J, Mazurowski MA, McKinley ET, McMichael J, Meyerson M, Mills GB, Mitri ZI, Moorman A, Mudd J, Murphy GF, Deen NNA, Navin NE, Nawy T, Ness RM, Nevins S, Nirmal AJ, Novikov E, Oh ST, Oldridge DA, Owzar K, Pant SM, Park W, Patti GJ, Paul K, Pelletier R, Persson D, Petty C, Pfister H, Polyak K, Puram SV, Qiu Q, Villalonga ÁQ, Ramirez MA, Rashid R, Reeb AN, Reid ME, Remsik J, Riesterer JL, Risom T, Ritch CC, Rolong A, Rudin CM, Ryser MD, Sato K, Sears CL, Semenov YR, Shen J, Shoghi KI, Shrubsole MJ, Shyr Y, Sibley AB, Simmons AJ, Sinha A, Sivagnanam S, Song SK, Southar-Smith A, Spira AE, Cyr JS, Stefankiewicz S, Storrs EP, Stover EH, Strand SH, Straub C, Street C, Su T, Surrey LF, Suver C, Tan K, Terekhanova NV, Ternes L, Thadi A, Thomas G, Tibshirani R, Umeda S, Uzun Y, Vallius T, Van Allen ER, Vandekar S, Vega PN, Veis DJ, Vennam S, Verma A, Vigneau S, Wagle N, Wahl R, Walle T, Wang LB, Warchol S, Washington MK, Watson C, Weimer AK, Wendl MC, West RB, White S, Windon AL, Wu H, Wu CY, Wu Y, Wyczalkowski MA, Xu J, Yao L, Yu W, Zhang K, Zhu X. MITI minimum information guidelines for highly multiplexed tissue images. Nature methods. 2022 Mar;19(3):262-267. PMID: 35277708
  • Herzberger L, Hadwiger M, Kruger R, Sorger P, Pfister H, Groller E, Beyer J. Residency Octree: A Hybrid Approach for Scalable Web-Based Multi-Volume Rendering. IEEE transactions on visualization and computer graphics. 2024 Jan;30(1):1380-1390. Epub 2023 Dec 25. PMID: 37889813
  • Ternes L, Lin JR, Chen YA, Gray JW, Chang YH. Computational multiplex panel reduction to maximize information retention in breast cancer tissue microarrays. PLoS computational biology. 2022 Sep 30;18(9):e1010505. doi: 10.1371/journal.pcbi.1010505. eCollection 2022 Sep. PMID: 36178966
  • Coy S, Rashid R, Stemmer-Rachamimov A, Santagata S. An update on the CNS manifestations of neurofibromatosis type 2. Acta neuropathologica. 2020 Apr;139(4):643-665. Epub 2019 Jun 4. PMID: 31161239
  • Lecky E, Mukherji A, German R, Antonellis G, Lin JR, Yorsz M, McQueeney KE, Ryan J, Ng K, Sicinska E, Sorger PK, Letai A, Bhola PD. Sequential apoptotic and multiplexed proteomic evaluation of single cancer cells. Science advances. 2023 Jun 23;9(25):eadg4128. Epub 2023 Jun 23. PMID: 37352344
  • 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. Nature immunology. 2021 Dec;22(12):1515-1523. Epub 2021 Nov 22. PMID: 34811542
  • Du Z, Lin JR, Rashid R, Maliga Z, Wang S, Aster JC, Izar B, Sorger PK, Santagata S. Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging. Nature protocols. 2019 Oct;14(10):2900-2930. Epub 2019 Sep 18. PMID: 31534232
  • Nirmal AJ, Maliga Z, Vallius T, Quattrochi B, Chen AA, Jacobson CA, Pelletier RJ, Yapp C, Arias-Camison R, Chen YA, Lian CG, Murphy GF, Santagata S, Sorger PK. The Spatial Landscape of Progression and Immunoediting in Primary Melanoma at Single-Cell Resolution. Cancer discovery. 2022 Jun 2;12(6):1518-1541. PMID: 35404441
  • 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. Nature methods. 2022 Mar;19(3):311-315. Epub 2021 Nov 25. PMID: 34824477
  • 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. Scientific data. 2019 Dec 17;6(1):323. PMID: 31848351
  • Lin JR, Wang S, Coy S, Chen YA, Yapp C, Tyler M, Nariya MK, Heiser CN, Lau KS, Santagata S, Sorger PK. Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer. Cell. 2023 Jan 19;186(2):363-381.e19. PMID: 36669472
  • Gaglia G, Burger ML, Ritch CC, Rammos D, Dai Y, Crossland GE, Tavana SZ, Warchol S, Jaeger AM, Naranjo S, Coy S, Nirmal AJ, Krueger R, Lin JR, Pfister H, Sorger PK, Jacks T, Santagata S. Lymphocyte networks are dynamic cellular communities in the immunoregulatory landscape of lung adenocarcinoma. Cancer cell. 2023 May 8;41(5):871-886.e10. Epub 2023 Apr 13. PMID: 37059105
  • 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, Aberle D, Achilefu SI, Ademuyiwa FO, Adey AC, Aft RL, Agarwal R, Aguilar RA, Alikarami F, Allaj V, Amos C, Anders RA, Angelo MR, Anton K, Ashenberg O, Aster JC, Babur O, Bahmani A, Balsubramani A, Barrett D, Beane J, Bender DE, Bernt K, Berry L, Betts CB, Bletz J, Blise K, Boire A, Boland G, Borowsky A, Bosse K, Bott M, Boyden E, Brooks J, Bueno R, Burlingame EA, Cai Q, Campbell J, Caravan W, Cerami E, Chaib H, Chan JM, Chang YH, Chatterjee D, Chaudhary O, Chen AA, Chen B, Chen C, Chen CH, Chen F, Chen YA, Chheda MG, Chin K, Chiu R, Chu SK, Chuaqui R, Chun J, Cisneros L, Coffey RJ, Colditz GA, Cole K, Collins N, Contrepois K, Coussens LM, Creason AL, Crichton D, Curtis C, Davidsen T, Davies SR, de Bruijn I, Dellostritto L, De Marzo A, Demir E, DeNardo DG, Diep D, Ding L, Diskin S, Doan X, Drewes J, Dubinett S, Dyer M, Egger J, Eng J, Engelhardt B, Erwin G, Esplin ED, Esserman L, Felmeister A, Feiler HS, Fields RC, Fisher S, Flaherty K, Flournoy J, Ford JM, Fortunato A, Frangieh A, Frye JL, Fulton RS, Galipeau D, Gan S, Gao J, Gao L, Gao P, Gao VR, Geiger T, George A, Getz G, Ghosh S, Giannakis M, Gibbs DL, Gillanders WE, Goecks J, Goedegebuure SP, Gould A, Gowers K, Gray JW, Greenleaf W, Gresham J, Guerriero JL, Guha TK, Guimaraes AR, Guinney J, Gutman D, Hacohen N, Hanlon S, Hansen CR, Harismendy O, Harris KA, Hata A, Hayashi A, Heiser C, Helvie K, Herndon JM, Hirst G, Hodi F, Hollmann T, Horning A, Hsieh JJ, Hughes S, Huh WJ, Hunger S, Hwang SE, Iacobuzio-Donahue CA, Ijaz H, Izar B, Jacobson CA, Janes S, Jané-Valbuena J, Jayasinghe RG, Jiang L, Johnson BE, Johnson B, Ju T, Kadara H, Kaestner K, Kagan J, Kalinke L, Keith R, Khan A, Kibbe W, Kim AH, Kim E, Kim J, Kolodzie A, Kopytra M, Kotler E, Krueger R, Krysan K, Kundaje A, Ladabaum U, Lake BB, Lam H, Laquindanum R, Lau KS, Laughney AM, Lee H, Lenburg M, Leonard C, Leshchiner I, Levy R, Li J, Lian CG, Lim KH, Lin JR, Lin Y, Liu Q, Liu R, Lively T, Longabaugh WJR, Longacre T, Ma CX, Macedonia MC, Madison T, Maher CA, Maitra A, Makinen N, Makowski D, Maley C, Maliga Z, Mallo D, Maris J, Markham N, Marks J, Martinez D, Mashl RJ, Masilionais I, Mason J, Massagué J, Massion P, Mattar M, Mazurchuk R, Mazutis L, Mazzilli SA, McKinley ET, McMichael JF, Merrick D, Meyerson M, Miessner JR, Mills GB, Mills M, Mondal SB, Mori M, Mori Y, Moses E, Mosse Y, Muhlich JL, Murphy GF, Navin NE, Nawy T, Nederlof M, Ness R, Nevins S, Nikolov M, Nirmal AJ, Nolan G, Novikov E, Oberdoerffer P, O'Connell B, Offin M, Oh ST, Olson A, Ooms A, Ossandon M, Owzar K, Parmar S, Patel T, Patti GJ, Pe'er D, Pe'er I, Peng T, Persson D, Petty M, Pfister H, Polyak K, Pourfarhangi K, Puram SV, Qiu Q, Quintanal-Villalonga Á, Raj A, Ramirez-Solano M, Rashid R, Reeb AN, Regev A, Reid M, Resnick A, Reynolds SM, Riesterer JL, Rodig S, Roland JT, Rosenfield S, Rotem A, Roy S, Rozenblatt-Rosen O, Rudin CM, Ryser MD, Santagata S, Santi-Vicini M, Sato K, Schapiro D, Schrag D, Schultz N, Sears CL, Sears RC, Sen S, Sen T, Shalek A, Sheng J, Sheng Q, Shoghi KI, Shrubsole MJ, Shyr Y, Sibley AB, Siex K, Simmons AJ, Singer DS, Sivagnanam S, Slyper M, Snyder MP, Sokolov A, Song SK, Sorger PK, Southard-Smith A, Spira A, Srivastava S, Stein J, Storm P, Stover E, Strand SH, Su T, Sudar D, Sullivan R, Surrey L, Suvà M, Tan K, Terekhanova NV, Ternes L, Thammavong L, Thibault G, Thomas GV, Thorsson V, Todres E, Tran L, Tyler M, Uzun Y, Vachani A, Van Allen E, Vandekar S, Veis DJ, Vigneau S, Vossough A, Waanders A, Wagle N, Wang LB, Wendl MC, West R, Williams EH, Wu CY, Wu H, Wu HY, Wyczalkowski MA, Xie Y, Yang X, Yapp C, Yu W, Yuan Y, Zhang D, Zhang K, Zhang M, Zhang N, Zhang Y, Zhao Y, Zhou DC, Zhou Z, Zhu H, Zhu Q, Zhu X, Zhu Y, Zhuang X. The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution. Cell. 2020 Apr 16;181(2):236-249. PMID: 32302568
  • Yapp C, Novikov E, Jang WD, Vallius T, Chen YA, Cicconet M, Maliga Z, Jacobson CA, Wei D, Santagata S, Pfister H, Sorger PK. UnMICST: Deep learning with real augmentation for robust segmentation of highly multiplexed images of human tissues. Communications biology. 2022 Nov 18;5(1):1263. PMID: 36400937
  • 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 transactions on visualization and computer graphics. 2022 Jan;28(1):259-269. Epub 2021 Dec 24. PMID: 34606456
  • 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. High-plex immunofluorescence imaging and traditional histology of the same tissue section for discovering image-based biomarkers. Nature cancer. 2023 Jul;4(7):1036-1052. Epub 2023 Jun 22. PMID: 37349501
  • Yapp C, Nirmal AJ, Zhou F, Maliga Z, Llopis PM, Murphy GF, Lian CG, Danuser G, Santagata S, Sorger PK. Multiplexed 3D Analysis of Cell Plasticity and Immune Niches in Melanoma. bioRxiv : the preprint server for biology. 2023 Nov 28. PMID: 38014052
  • Coy S, Cheng B, Lee JS, Rashid R, Browning L, Xu Y, Chakrabarty SS, Yapp C, Chan S, Tefft JB, Scott E, Spektor A, Ligon KL, Baker GJ, Pellman D, Sorger PK, Santagata S. 2D and 3D multiplexed subcellular profiling of nuclear instability in human cancer. bioRxiv : the preprint server for biology. 2023 Nov 11. PMID: 37986801
  • Nirmal AJ, Yapp C, Santagata S, Sorger PK. Cell Spotter (CSPOT): A machine-learning approach to automated cell spotting and quantification of highly multiplexed tissue images. bioRxiv : the preprint server for biology. 2023 Nov 17. PMID: 38014110
  • Guerriero JL, Lin JR, Pastorello RG, Du Z, Chen YA, Townsend MG, Shimada K, Hughes ME, Ren S, Tayob N, Zheng K, Mei S, Patterson A, Taneja KL, Metzger O, Tolaney SM, Lin NU, Dillon DA, Schnitt SJ, Sorger PK, Mittendorf EA, Santagata S. Qualification of a multiplexed tissue imaging assay and detection of novel patterns of HER2 heterogeneity in breast cancer. NPJ breast cancer. 2024 Jan 2;10(1):2. PMID: 38167908
  • Baker GJ, Novikov E, Zhao Z, Vallius T, Davis JA, Lin JR, Muhlich JL, Mittendorf EA, Santagata S, Guerriero JL, Sorger PK. Quality Control for Single Cell Analysis of High-plex Tissue Profiles using CyLinter. bioRxiv : the preprint server for biology. 2024 Mar 22. PMID: 37961235
  • Haddox CL, Nathenson MJ, Mazzola E, Lin JR, Baginska J, Nau A, Weirather JL, Choy E, Marino-Enriquez A, Morgan JA, Cote GM, Merriam P, Wagner AJ, Sorger PK, Santagata S, George S. Phase II Study of Eribulin plus Pembrolizumab in Metastatic Soft-tissue Sarcomas: Clinical Outcomes and Biological Correlates. Clinical cancer research : an official journal of the American Association for Cancer Research. 2024 Apr 1;30(7):1281-1292. PMID: 38236580
  • Inde Z, Yapp C, Joshi GN, Spetz J, Fraser C, Deskin B, Ghelfi E, Sodhi C, Hackam DJ, Kobzik L, Croker BA, Brownfield D, Jia H, Sarosiek KA. Age-dependent regulation of SARS-CoV-2 cell entry genes and cell death programs correlates with COVID-19 disease severity. bioRxiv : the preprint server for biology. 2020 Sep 13. PMID: 32935109