Lectures and seminars OnkPat Friday Seminar: Characterization of tumour heterogeneity using digital pathology and spatial omics

19-09-2025 12:30 pm Add to iCal
Karolinska University Hospital, Solna J3:14 Kerstin Hagenfeldt, BioClinicum, Solnavägen 30

Welcome to OnkPat Friday Seminar with David Fenyö, NYU Grossman School of Medicine, New York.

Host: Thuy Tran, Department of Oncology-Pathology.

Abstract

Currently there is a general shift towards digital pathology that enables the application of artificial intelligence as a tool for pathologists that promises to improve both accuracy and speed. At the same time there is a rapid technology development in spatial omics technologies that provide a detailed molecular understanding of the tumor microenvironment but the analysis of this complex data is challenging. Strategies for analyzing digital pathology and high-dimensional spatial tissue images will be discussed.

Selected references

Characterization of tumour heterogeneity through segmentation-free representation learning on multiplexed imaging data.
Tan J, Le H, Deng J, Liu Y, Hao Y, Hollenberg M, Liu W, Wang JM, Xia B, Ramaswami S, Mezzano V, Loomis C, Murrell N, Moreira AL, Cho K, Pass HI, Wong KK, Ban Y, Neel BG, Tsirigos A, Fenyö D
Nat Biomed Eng 2025 Mar;9(3):405-419

Proteogenomic insights suggest druggable pathways in endometrial carcinoma.
Dou Y, Katsnelson L, Gritsenko MA, Hu Y, Reva B, Hong R, Wang YT, Kolodziejczak I, Lu RJ, Tsai CF, Bu W, Liu W, Guo X, An E, Arend RC, Bavarva J, Chen L, Chu RK, Czekański A, Davoli T, Demicco EG, DeLair D, Devereaux K, Dhanasekaran SM, Dottino P, Dover B, Fillmore TL, Foxall M, Hermann CE, Hiltke T, Hostetter G, Jędryka M, Jewell SD, Johnson I, Kahn AG, Ku AT, Kumar-Sinha C, Kurzawa P, Lazar AJ, Lazcano R, Lei JT, Li Y, Liao Y, Lih TM, Lin TT, Martignetti JA, Masand RP, Matkowski R, McKerrow W, Mesri M, Monroe ME, Moon J, Moore RJ, Nestor MD, Newton C, Omelchenko T, Omenn GS, Payne SH, Petyuk VA, Robles AI, Rodriguez H, Ruggles KV, Rykunov D, Savage SR, Schepmoes AA, Shi T, Shi Z, Tan J, Taylor M, Thiagarajan M, Wang JM, Weitz KK, Wen B, Williams CM, Wu Y, Wyczalkowski MA, Yi X, Zhang X, Zhao R, Mutch D, Chinnaiyan AM, Smith RD, Nesvizhskii AI, Wang P, Wiznerowicz M, Ding L, Mani DR, Zhang H, Anderson ML, Rodland KD, Zhang B, Liu T, Fenyö D, 
Cancer Cell 2023 Sep;41(9):1586-1605.e15

LINE-1 expression in cancer correlates with p53 mutation, copy number alteration, and S phase checkpoint.
McKerrow W, Wang X, Mendez-Dorantes C, Mita P, Cao S, Grivainis M, Ding L, LaCava J, Burns KH, Boeke JD, Fenyö D
Proc Natl Acad Sci U S A 2022 Feb;119(8):

Predicting endometrial cancer subtypes and molecular features from histopathology images using multi-resolution deep learning models.
Hong R, Liu W, DeLair D, Razavian N, Fenyö D
Cell Rep Med 2021 Sep;2(9):100400

Proteogenomic Characterization of Endometrial Carcinoma.
Dou Y, Kawaler EA, Cui Zhou D, Gritsenko MA, Huang C, Blumenberg L, Karpova A, Petyuk VA, Savage SR, Satpathy S, Liu W, Wu Y, Tsai CF, Wen B, Li Z, Cao S, Moon J, Shi Z, Cornwell M, Wyczalkowski MA, Chu RK, Vasaikar S, Zhou H, Gao Q, Moore RJ, Li K, Sethuraman S, Monroe ME, Zhao R, Heiman D, Krug K, Clauser K, Kothadia R, Maruvka Y, Pico AR, Oliphant AE, Hoskins EL, Pugh SL, Beecroft SJI, Adams DW, Jarman JC, Kong A, Chang HY, Reva B, Liao Y, Rykunov D, Colaprico A, Chen XS, Czekański A, Jędryka M, Matkowski R, Wiznerowicz M, Hiltke T, Boja E, Kinsinger CR, Mesri M, Robles AI, Rodriguez H, Mutch D, Fuh K, Ellis MJ, DeLair D, Thiagarajan M, Mani DR, Getz G, Noble M, Nesvizhskii AI, Wang P, Anderson ML, Levine DA, Smith RD, Payne SH, Ruggles KV, Rodland KD, Ding L, Zhang B, Liu T, Fenyö D, 
Cell 2020 Feb;180(4):729-748.e26