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Hilz S, Hong C, Jalbert L, Mazor T, Martin M, Kumar A, Shelton S, Wong K, Hayes J, Yu Y, Zhang M, Luks T, Olson M, Lafontaine M, Shai A, Bengtsson H, Olshen A, Molinaro A, McDermott M, Chang E, Hervey-Jumper S, Berger M, Lim D, Diaz A, Lupo J, Phillips J, Chang S, Nelson S, Oldham M, Costello J. GENE-47. A 3D ATLAS TO EVALUATE THE SPATIAL PATTERNING OF GENETIC ALTERATIONS AND TUMOR CELL STATES IN GLIOMA. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz175.449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
BACKGROUND
Previous studies of solid tumors have been restricted in their ability to map how heterogeneous cell populations evolved within the tumor in three-dimensional (3D) space due to insufficient sampling, typically one sample per tumor, and a lack of knowledge of where within the tumor the sample was obtained. Knowledge of the extensivity of heterogeneity and how it is spatially distributed is crucial for assessing whether a therapeutic target is truly tumor-wide, and for exploring how mutations relate to heterogeneity in the local microenvironment.
METHODS
We developed a novel platform to integrate and visualize in 3D multi-omics data generated from each of 8–10 spatially mapped samples per tumor. Together, the 171 samples collected using this approach from 16 adult diffuse glioma at diagnosis and recurrence form a novel resource – the 3D Glioma Atlas.
RESULTS
By maximally sampling the tumor geography without excluding samples based on low cancer cell fraction (CCF), we identify a subpopulation of glioblastoma with pervasively lower CCF likely excluded by other atlases, such as the TCGA, that used stringent CCF cutoffs. Exome sequencing of 3D-mapped samples from lower-grade tumors revealed that clonal expansions are typically spatially segregated, implying minimal tumor-wide intermixing of genetically heterogenous cells. Heterogeneity is less spatially segregated for faster-growing high-grade tumors, suggesting that cell populations expand in these tumors differently. Recurrent low-grade tumors have greater intratumoral mutational heterogeneity than newly diagnosed tumors, though this did not translate into greater dissimilarity in gene expression profiles for recurrent tumors, suggesting minimal functional impact of this additional mutational diversity on gene expression.
CONCLUSIONS
The delineation of spatial patterns of heterogeneity that our work provides enables more informed interpretation of biopsies and greater insight into the factors shaping intratumoral variation of gene expression patterns. Ongoing work is exploring the spatial patterning of amplification events and the tumor microenvironment.
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Affiliation(s)
- Stephanie Hilz
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Chibo Hong
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Llewellyn Jalbert
- Department of Radiology, University of California, San Francisco, San Francisco, CA, USA
| | - Tali Mazor
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Michael Martin
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Anupam Kumar
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Samuel Shelton
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Karen Wong
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Josie Hayes
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Yao Yu
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
| | - Michael Zhang
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
| | - Tracy Luks
- Department of Radiology, University of California, San Francisco, San Francisco, CA, USA
| | - Marram Olson
- Department of Radiology, University of California, San Francisco, San Francisco, CA, USA
| | - Marisa Lafontaine
- Department of Radiology, University of California, San Francisco, San Francisco, CA, USA
| | - Anny Shai
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Henrik Bengtsson
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, San Francisco, USA
| | - Adam Olshen
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, San Francisco, USA
| | - Annette Molinaro
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Michael McDermott
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Edward Chang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Shawn Hervey-Jumper
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Mitchel Berger
- University of California, San Francisco, San Francisco, CA, USA
| | - Daniel Lim
- University of California, San Francisco, San Francisco, CA, USA
| | - Aaron Diaz
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Janine Lupo
- Department of Radiology, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna Phillips
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Susan Chang
- University of California, San Francisco, San Francisco, CA, USA
| | - Sarah Nelson
- Department of Radiology, University of California, San Francisco, San Francisco, CA, USA
| | - Michael Oldham
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph Costello
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
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Moriera F, So K, Gould P, Kamnasaran D, Jensen RL, Hussain I, Gutmann DH, Gorovets D, Kastenhuber ER, Pentsova E, Nayak L, Huse JT, van den Bent MJ, Gravendeel LA, Gorlia T, Kros JM, Wesseling P, Teepen J, Idbaih A, Sanson M, Smitt PAS, French PJ, Zhang W, Zhang J, Hoadley K, Carter B, Li S, Kang C, You Y, Jiang C, Song S, Jiang T, Chen C, Grimm C, Weiler M, Claus R, Weichenhan D, Hartmann C, Plass C, Weller M, Wick W, Jenkins RB, Sicotte H, Xiao Y, Fridley BL, Decker PA, Kosel ML, Kollmeyer TM, Fink SR, Rynearson AL, Rice T, McCoy LS, Smirnov I, Tehan T, Hansen HM, Patoka JS, Prados MD, Chang SM, Berger MS, Lachance DH, Wiencke JK, Wiemels JL, Wrensch MR, Gephart MH, Lee E, Kyriazopoulou-Panagiotopoulou S, Milenkovic L, Xun X, Hou Y, Kui W, Edwards M, Batzoglou S, Jun W, Scott M, Hobbs JE, Tipton J, Zhou T, Kelleher NL, Chandler JP, Schwarzenberg J, Czernin J, Cloughesy T, Ellingson B, Geist C, Phelps M, Chen W, Nakada M, Hayashi Y, Obuchi W, Ohtsuki S, Watanabe T, Ikeda C, Misaki K, Kita D, Hayashi Y, Uchiyama N, Terasaki T, Hamada JI, Hiddingh L, Tops B, Hulleman E, Kaspers GJL, Vandertop WP, Wesseling P, Noske DP, Wurdinger T, Jeuken JW, See AP, Hwang T, Shin D, Shin JH, Gao Y, Lim M, Hutterer M, Michael M, Gerold U, Karin S, Ingrid G, Florian D, Armin M, Eugen T, Eberhard G, Gunther S, Cook RW, Oelschlager K, Sevim H, Chung L, Wheeler HT, Baxter RC, McDonald KL, Chaturbedi A, Yu L, Zhou YH, Chaturbedi A, Wong A, Fatuyi R, Linskey ME, Zhou YH, Lavon I, Shahar T, Zrihan D, Granit A, Ram Z, Siegal T, Brat DJ, Cooper LA, Gutman DA, Chisolm CS, Appin C, Kong J, Kurc T, Van Meir EG, Saltz JH, Moreno CS, Abuhusain HJ, McDonald KL, Don AS, Nagarajan RP, Johnson BE, Olshen AB, Smirnov I, Xie M, Wang J, Sundaram V, Paris P, Wang T, Costello JF, Sijben AE, Boots-Sprenger SH, Boogaarts J, Rijntjes J, Geitenbeek JM, van der Palen J, Bernsen HJ, Wesseling P, Jeuken JW, Schnell O, Adam SA, Eigenbrod S, Kretzschmar HA, Tonn JC, Schuller U, Schwarzenberg J, Cloughesy T, Czernin J, Geist C, Phelps M, Chen W, Sperduto PW, Kased N, Roberge D, Xu Z, Shanley R, Luo X, Sneed PK, Chao ST, Weil RJ, Suh J, Bhatt A, Jensen AW, Brown PD, Shih HA, Kirkpatrick J, Gaspar LE, Fiveash JB, Chiang V, Knisely JP, Sperduto CM, Lin N, Mehta MP, Kwatra MM, Porter TM, Brown KE, Herndon JE, Bigner DD, Dahlrot RH, Kristensen BW, Hansen S, Sulman EP, Cahill DP, Wang M, Won M, Hegi ME, Mehta MP, Aldape KD, Gilbert MR, Sadr ES, Tessier A, Sadr MS, Alshami J, Sabau C, Del Maestro R, Neal ML, Rockne R, Trister AD, Swanson KR, Maleki S, Back M, Buckland M, Brazier D, McDonald K, Cook R, Parker N, Wheeler H, Jalbert L, Elkhaled A, Phillips JJ, Yoshihara HA, Parvataneni R, Srinivasan R, Bourne G, Chang SM, Cha S, Nelson SJ, Aldape KD, Gilbert M, Cahill D, Wang M, Won M, Hegi M, Colman H, Mehta M, Sulman E, Elkhaled A, Jalbert L, Constantin A, Phillips J, Yoshihara H, Srinivasan R, Bourne G, Chang SM, Cha S, Nelson S, Gunn S, Reveles XT, Tirtorahardjo B, Strecker MN, Fichtel L. -OMICS AND PROGNOSTIC MARKERS. Neuro Oncol 2011. [DOI: 10.1093/neuonc/nor167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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