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.
The Enteric Nervous System Relays Phsychological Stress to Intestinal Inflammation
. Cell. 2023; 186(13):2823-2838.e20.
Kindschuh W, Baldini F, Liu M, Liao J, Meydan Y, Lee H, Heinken A, Thiele I, Thaiss C, Levy M, Korem T. Preterm Birth is Associated with Xenobiotics and Predicted by the Vaginal Metabolome . Nat Microbiol. 2023; 8(2):246-259.
Dmitrieva-Posocco O, Wong A, Lundgren P, Golos A, Descamps H, Dohnalova L, Cramer Z, Tian Y… Katona B, Grivennikov S, Thaiss C,
Levy M.
Beta-Hydroxybutyrate Suppresses Colorectal Cancer. Nature. 2022; 605(7908):160-165.

Peter Miller, MD, PhD
Project
Dissecting the Role of PPM1D in Leukemia Development and Treatment Resistance
Topic Area
Blood Cancer
Highlighted Publications
Miller PG*, Sathappa M*, Moroco JA*, Jiang W, Qian Y, Iqbal S, Guo Q, Giacomelli AO…Root DE, Garvie CW, Ebert BL.
Allosteric Inhibition of PPM1D Serine/Theonine Phosphatase via An Altered Conformational State
. Nature Communications. 2022; 13(1):3778. *Authors Contributed Equally to This Work.
BoettcherS, Miller PG, Sharma R, McConkey M, Leventhal M, Krivtsov AV, Giacomelli AO, Wong W, Kim J… Armstrong SA, Ebert BL . A Dominant-Negative Effect Drives Selection of TP53 Missense Mutations in Myeloid Malignancies . Science. 2019; 365(6453):599-604.
Miller PG*, Qiao D*, Rojas-Quintero J, Honigberg MC, Sperling AS, Gibson CJ, Bick AG…Cho MH, Ebert BL
.
Association of Clonal Hematopoiesis with Chronic Obstructive Pulmonary Disease
. Blood. 2022; 139(3):357-368. *Authors Contributed Equally to This Work
Gibson CJ, Fell G, Sella T, Sperling AS, Snow C, Rosenberg SM, Kirkner G, Patel A, Dillon D, Bick AG, Neuberg D, Patridge AH, Miller PG
.
Clonal Hematopoiesis in Young Women Treated for Breast Cancer
. Clinical Cancer Research. 2023. 29(13):2551-2558.

Kacper Rogala, PhD
Project
Targeting Unusual Nutrient Acquisition Routes of Nutrient-Deprived Cancers
Topic Area
Bladder Cancer
Highlighted Publications
Valenstein ML*, Rogala KB*, Lalgudi PV, Brignole EJ, Gu X, Saxton RA, Chantranupong L, Kolibius J, Quast JP, Sabatini DM.
Structure of the Nutrient-Sensing Hub GATOR2
. Nature. 2022; 607(7919):610-616. *Co-first and Co-corresponding Author.
Rogala KB, Gu X, Kedir JF, Abu-Remaileh M, Bianchi LF, Bottino AMS, Dueholm R, Niehaus A, Overwijn D, Fils AP, Zhou SX, Leary D, Laqtom NN, Brignole EJ, Sabatini DM . Structural Basis for the Docking of mTORC1 on the Lysosomal Surface . Science. 2019; 366(6464):468-475.
Shen K*, Rogala KB*, Chou HT, Huang RK, Yu Z, Sabatini DM.
Cryo-EM Structure of the Human FLCN-FNIP2-Rag-Ragulator Complex
. Cell. 2019; 179(6):1319-1329.e8. *Co-first Author

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, Meredith D, Marostica E, Ligon K, Golden J, Yu K. Machine Learning for Cryosection Pathology Predicts the 2021 WHO Classification of Glioma . Med. 2023;S2666-6340(23)00189-7 (in press).
Tsai P, Lee T, Kuo, K, Su F, Lee T, 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 J, Nowak J, Ogino S, Yu K. Histology Images Predict Multi-omics Aberrations and Prognoses in Colorectal Cancer Patients . Nature Communications. 2023;14(1):2102.
Marostica E, Barber R, Denize T, Kohane I, Signoretti S, Golden J, Yu K . Development of a Histopathology Informatics Pipeline for Classification and Prediction of Clinical Outcomes in Subtypes of Renal Cell Carcinoma . Clinical Cancer Research. 2021;27(10):2868-2878.
Yu K, Beam A, Kohane I.
Artificial Intelligence in Healthcare
. Nature Biomedical Engineering. 2018;2(10):719-731.