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.

Liu S, Devason A, Levy M. From intestinal metabolites to the brain: Investigating the mysteries of Long COVID. Clin Transl Med. 2024; 14:e1608. https://doi.org/10.1002/ctm2.1608.


Peter Miller, MD, PhD

Project

Dissecting the Role of PPM1D in Leukemia Development and Treatment Resistance

Topic Area

Blood Cancers

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.

Kindschuh WF*, Baldini F*, Liu MC*, Liao J, Meydan Y, Lee HH, Heinken A, Thiele I, Thaiss CA, Levy M* 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.


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 . Clonal Hematopoiesis in Young Women Treated for Breast Cancer . Clinical Cancer Research. 2023. 29(13):2551-2558.
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 . Cryo-EM Structure of the Human FLCN-FNIP2-Rag-Ragulator Complex . Cell. 2019; 179(6):1319-1329.e8. *Co-first Author

Decoupling Genetics, Lineages, and Microenvironment in IDH-Mutant Gliomas by Single-Cell RNA-Seq. Science. 2017;355(6332):eaai8478.

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 KMarostica E, Barber R, Denize T, Kohane I, Signoretti S, Golden J, Yu K . Artificial Intelligence in Healthcare . Nature Biomedical Engineering. 2018;2(10):719-731. Clinical Cancer Research. 2021;27(10):2868-2878.

Yu K, Beam A, Kohane I.. 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.