COHORT 2

Floris Barthel, MD, PhD

Project

Genomic Dissection of Structural Mutations Following Telomere Dysfunction in Glioblastoma Cells and Patients

Topic Area

Brain Cancer

Highlighted Publications

Kocakavuk E, Anderson K, Varn F, Johnson K, Amin S, Sulman E, Lolkema M, Barthel FP (co-corresponding) , Verhaak RGW. Radiotherapy is Associated with a Deletion Signature That Contributes to Poor Outcomes in Patients with Cancer . Nature Genetics. 2021; 53, 1088-1096.

Barthel FP, Johnson K, Varn F, Moskalik A, Tanner G, Kocakavuk E, Anderson K, Abiola O, Aldape K, Alfaro K,…Bruns A, Bulsara K, Chakrabarty A, Chakravarti A, The GLASS Consortium. Longitudinal Molecular Trajectories of Diffuse Glioma in Adults . Nature. 2019;576, 112-120.

Barthel FP, Wesseling P, Verhaak R. Reconstructing the Molecular Life History of Gliomas . Acta Neuropathol. 2018: 135(5): 649-670.

Barthel FP, Wei W, Tang M, Martinez-Ledesma E, Hu X, Amin S, Akdemir K…Zhang J, Zheng S, Verhaak R. Systematic Analysis of Telomere Length and Somatic Alterations in 31 Cancer Types . Nature Genetics. 2017; 49, 349-357.ure G

Priya Dedhia, MD, PhD

Project

Metastatic Progression in Medullary Thyroid Cancer

Topic Area

Thyroid Cancer

Highlighted Publications

Dedhia PH, Sivakumar H, Rodriguez MA, Nairon KG, Zent J, Zheng X, Jones K, Popova L, Leight J, Skardal A. A 3D Adrenocortical Carcinoma Tumor Platform for Preclinical Modeling of Drug Response and Matrix Metalloproteinase Activity . Preprint available.

Dedhia PH, Saucke MA, Long KL, Doherty GM, Pitt SC. Physician Perspectives of Overdiagnosis and Overtreatment of Low-Risk Papillary Thyroid Cancer in the US . Jama Network Open. 2022;5(4):e228722.

Dedhia PH, Keeshan K, Uljon S, Xu L, Vega ME, Shestova O, Zaks-Zilberman M, Romany C, Blacklow SC, Pear WS. Differential Ability of Tribbles Family Members to Promote Degradation of C/EBP Alpha and Induce Acute Myelogenous Leukemia . Blood. 116(8): 1321-8. 2010.

Mayaan Levy, PhD

Project

Deciphering the Mechanisms Underlying Dietary Protection from Colorectal Cancer

Topic Area

Colorectal Cancer

Highlighted Publications

Schneider KM, Blank N, Alvarez Y, Thum K, Lundgren P, Litichevskiy L, Sleeman M…Bewtra M, Heuckeroth RO, Levy M, Thaiss CA. A Dominant-Negative Effect Drives Selection of TP53 Missense Mutations in Myeloid Malignancies . Science. 2019; 365(6453):599-604.

Kindschuh WF*, Baldini F*, Liu MC*, Liao J, Meydan Y, Lee HH, Heinken A, Thiele I, Thaiss CA, Levy M*, Korem T*. Preterm birth is associated with xenobiotics and predicted by the vaginal metabolome . Nature Microbiology. 2023.

Dmitrieva-Posocco O, Wong AC, Lundgren P, Golos AM, Descamps HC, Dohnalova L, Cramer Z, Tian Y, Yueh B…Katona BW, Grivennikov S, Thaiss CA, Levy M* . Beta-hydroxybutyrate suppresses colorectal cancer. Nature . 2022.


Peter Miller, MD, PhD

Project

Dissecting the Role of PPM1D in Leukemia Development and Treatment Resistance

Topic Area

Blood Cancers

Highlighted Publications

Gibson C, Fell G, Sella T, Sperling A, Snow C, Rosenberg S, Kirkner G, Patel A, Dillon D, Bick A, Neuberg D, Patridge A, Miller PG . Clonal Hematopoiesis in Young Women Treated for Breast Cancer . Clin Cancer Res. 2023 5;29(13):2551-2558.

Miller PG, Sathappa M, Moroco J, Jiang W, Qian Y, Iqbal S, Guo Q, Giacomelli A, Shaw S, Vernier C, Bajrami B, Yang X, Raffier C, Sperling A, et al. Allosteric Inhibition of PPM1D Serine/Threonine Phosphatase via an Altered Conformational State . Nat Commun. 2022 30;13(1):3778.

Miller PG, Qiao D, Rojas-Quintero J, Honigberg M, Sperling A, Gibson C, Bick A, Niroula A, McConkey M, Sandoval B, Miller B, Shi W, Viswanathan K, et al. Association of Clonal Hematopoiesis with Chronic Obstructive Pulmonary Disease . Blood. 2022 20;139(3):357-368.

Boettcher S, Miller PG, Sharma R, McConkey M, Leventhal M, Krivtsov A, Giacomelli A, Wong W, Kim J, Chao S, Kurppa K, Yang X, Milenkowic K, et al. A Dominant-Negative Effect Drives Selection of TP53 Missense Mutations in Myeloid Malignancies . Science. 2019 9; 365(6453):599-604.

Kacper Rogala, PhD

Project

Targeting Unusual Nutrient Acquisition Routes of Nutrient- Deprived Cancers

Topic Area

Bladder Cancer

Highlighted Publications

Valenstein M*, Rogala K*, Lalgudi P, Brignole E, Gu X, Saxton R, Chantranupong L, Kolibius J, Quast JP, Sabatini D. Structure of the Nutrient-Sensing Hub GATOR2 . Nature. 607, 610-616 (2022). *Co-first & Co-corresponding author.

Shen K*, Rogala K*, Chou HT, Huang R, Yu Z, Sabatini D. Cryo-EM Structure of the Human FLCN-FNIP2-Rag-Ragulator Complex . Cell. 2019 27;179(6): 1319-1329.e8. *Co-first author.

Rogala K, Gu X, Kedir J, Abu-Remaileh M, Bianchi L, Bottino A, Dueholm R, Niehaus A, Overwijn D, Fils AC, Zhou S, Leary D, Laqtom N, Brignole E, Sabatini D. Structural Basis for the Docking of mTORC1 on the Lysosomal Surface . Science. 2019 25;366(6464): 468-475.

Andrew Venteicher, MD, PhD

Project

Mapping Elements of DNA Architecture Responsible for Malignant Transformation in Craniospinal Sarcoma

Topic Area

Sarcoma

Highlighted Publications

Li J, Kaneda M, Ma J, Li M, Shepard R, Patel K, Koga T, Sarver A, Furnari F, Xu B, Dhawan S, Ning J, Zhu H, Wu A, You G, Jiang T,  Venteicher A, Rich J, Glass C, Varner J, Chen C. PI3Ky Inhibition Suppresses Microglia/TAM Accumulation in Glioblastoma Microenvironment to Promote Exceptional Temozolomide Response . Proceedings of the National Academy of Sciences. 2021;118(16):e2009290118.

Venteicher A, Tirosh I, Hebert C, Yizhak K, Neftel C, Filbin M, Hovestadt V, Escalante L, Shaw M, Rodman C, Gillespie S…Regev A, Suva M. Decoupling Genetics, Lineages, and Microenvironment in IDH-Mutant Gliomas by Single-Cell RNA-Seq . Science. 2017;355(6332):eaai8478.

Tirosh I, Venteicher A, Hebert C, Escalante L, Patel A, Neftel C, Yizhak K, Fisher J, Rodman C, Mount C, Filbin M, Neftel C…Regev A, Suva M. Single-Cell RNA-Seq Supports a Developmental Hierarchy in Human Oligodendroglioma . Nature. 2016;539(7628):309-313.

Kun-Hsing Yu, MD, PhD

Project

Optimizing Individualized Colorectal Cancer Treatment and Prognostic Prediction via Causal Machine Learning

Topic Area

Colorectal Cancer

Highlighted Publications

Nasrallah M, Zhao J, Tsai C, Mereditch D, Marostica E, Ligon K, Golden J, Yu KH. Machine Learning for Cryosection Pathology Predicts the 2021 WHO Classification of Glioma . Med. 2023; 4(8): 526-540.

Tsai PC, Lee TH, Kuo KC, Su FY, Lee TL, Marostica E, Ugai T, Zhao M, Lau M, Vayrynen J, Giannakis M, Takashima Y, Kahaki S, Wu K, Song M, Meyerhardt J, Chan A, Chiang JH, Nowak J, Ogino S, Yu KH. Histopathology Images Predict Multi-Omics Aberrations and Prognoses in Colorectal Cancer Patients . Nat Commun 14, 2102 (2023).

Yu KH, Beam A, Kohane I. Artificial Intelligence in Healthcare . Nat Biomedical Eng. 2, 719-731 (2018).

Wan G, Khattab S, Leung B, Zhang S, Nguyen N, Tran M, Lin C, Chang C, Alexander N, Jairath R, Phillipps J…Yu KH, Gusev A, Kwatra S, LeBoeuf N, Reynolds K, Semenov Y. Cancer Type and Histology Influence Cutaneous Immunotherapy Toxicities: A Multi-Institutional Cohort Study. Br J Dermatol. 2024 Jun 20;191(1):117-124. doi: 10.1093/bjd/ljae053. PMID: 38366637; PMCID: PMC11188738. **CSVCC Supported**

Pinto de Almeida, Janosi AJ, Hong R, et al. Mitochondrial dysfunction and immune suppression in BRAF V600E-mutated metastatic melanoma . Clin Transl Med. 2024 Jul;14(7)e1773. PMID: 39032005. PMCID: PMC11259597. **CSVCC Supported**

Wang X, Zhao J, Marostica E, Yuan W, Jin J, Zhang J, Li R, Tang H, Wang K, Li Y, Wang F, Peng Y, Zhu J, Zhang J, Jackson C, Zhang J, Dillon D, Lin N, Sholl L, Denize T, Mereditch D, Ligon M, Signoretti S, Ogino S, Golden J, Masrallah M, Han X, Yang S, Yu KH. A Pathology Foundation Model for Cancer Diagnosis and Prognosis Prediction. Nature (2024). PMID: 39232164. **CSVCC Supported**