Publications Learn more about the work that we do in the Brat laboratory through our recent publications. View all publications by Dr. Daniel J. Brat listed in the National Library of Medicine. Human Mesenchymal glioblastomas are characterized by an increased immune cell presence compared to Proneural and Classical tumors. Kaffes I, Szulzewsky F, Chen Z, Herting CJ, Gabanic B, Velázquez Vega JE, Shelton J, Switchenko JM, Ross JL, McSwain LF, Huse JT, Westermark B, Nelander S, Forsberg-Nilsson K, Uhrbom L, Maturi NP, Cimino PJ, Holland EC, Kettenmann H, Brennan CW, Brat DJ, Hambardzumyan D. Oncoimmunology. 2019 Aug 22;8(11):e1655360. doi: 10.1080/2162402X.2019.1655360. eCollection 2019. PMID:31646100 Surfen-mediated blockade of extratumoral chondroitin sulfate glycosaminoglycans inhibits glioblastoma invasion. Logun MT, Wynens KE, Simchick G, Zhao W, Mao L, Zhao Q, Mukherjee S, Brat DJ, Karumbaiah L. FASEB J. 2019 Nov;33(11):11973-11992. doi: 10.1096/fj.201802610RR. Epub 2019 Aug 9.PMID:31398290 The medical necessity of advanced molecular testing in the diagnosis and treatment of brain tumor patients. Horbinski C, Ligon KL, Brastianos P, Huse JT, Venere M, Chang S, Buckner J, Cloughesy T, Jenkins RB, Giannini C, Nabors LB, Wen PY, Aldape KJ, Lukas RV, Galanis E, Eberhart CG, Brat DJ, Sarkaria JN. Neuro Oncol. 2019 Jul 4. pii: noz119. doi: 10.1093/neuonc/noz119. [Epub ahead of print] PMID:31276167 Data Sets for the Reporting of Tumors of the Central Nervous System. Louis DN, Wesseling P, Brandner S, Brat DJ, Ellison DW, Giangaspero F, Hattab EM, Hawkins C, Judge MJ, Kleinschmidt-DeMasters B, Komori T, McLean C, Paulus W, Perry A, Reifenberger G, Weller M, Rous B. Arch Pathol Lab Med. 2019 Jun 20. doi: 10.5858/arpa.2018-0565-OA. [Epub ahead of print] PMID:31219344 cIMPACT-NOW: a practical summary of diagnostic points from Round 1 updates. Louis DN, Ellison DW, Brat DJ, Aldape K, Capper D, Hawkins C, Paulus W, Perry A, Reifenberger G, Figarella-Branger D, von Deimling A, Wesseling P. Brain Pathol. 2019 Jul;29(4):469-472. doi: 10.1111/bpa.12732. Epub 2019 May 22. Review. PMID:31038238 Effective nuclei segmentation with sparse shape prior and dynamic occlusion constraint for glioblastoma pathology images. Zhang P, Wang F, Teodoro G, Liang Y, Roy M, Brat D, Kong J. J Med Imaging (Bellingham). 2019 Jan;6(1):017502. doi: 10.1117/1.JMI.6.1.017502. Epub 2019 Mar 14. PMID:30891467 What Every Neuropathologist Needs to Know: Update on cIMPACT-NOW. Yeaney GA, Brat DJ. J Neuropathol Exp Neurol. 2019 Apr 1;78(4):294-296. doi: 10.1093/jnen/nlz012. PMID:30830209 Occupational-like organophosphate exposure disrupts microglia and accelerates deficits in a rat model of Alzheimer’s disease. Voorhees JR, Remy MT, Erickson CM, Dutca LM, Brat DJ, Pieper AA. NPJ Aging Mech Dis. 2019 Jan 22;5:3. doi: 10.1038/s41514-018-0033-3. eCollection 2019. PMID:30701080 The impact of histopathology and NAB2-STAT6 fusion subtype in classification and grading of meningeal solitary fibrous tumor/hemangiopericytoma. Fritchie K, Jensch K, Moskalev EA, Caron A, Jenkins S, Link M, Brown PD, Rodriguez FJ, Guajardo A, Brat D, Velázquez Vega JE, Perry A, Wu A, Raleigh DR, Santagata S, Louis DN, Brastianos PK, Kaplan A, Alexander BM, Rossi S, Ferrarese F, Haller F, Giannini C. Acta Neuropathol. 2019 Feb;137(2):307-319. doi: 10.1007/s00401-018-1952-6. Epub 2018 Dec 24. PMID:30584643 Drak/STK17A Drives Neoplastic Glial Proliferation through Modulation of MRLC Signaling. Chen AS, Wardwell-Ozgo J, Shah NN, Wright D, Appin CL, Vigneswaran K, Brat DJ, Kornblum HI, Read RD. Cancer Res. 2019 Mar 15;79(6):1085-1097. doi: 10.1158/0008-5472.CAN-18-0482. Epub 2018 Dec 10. PMID:30530503 Inhibition of breast cancer metastasis to the lungs with UBS109. Shoji M, Qian WP, Nagaraju GP, Brat DJ, Pessolano D, Luzietti R, Chennamadhavuni S, Yamaguchi M, Yang L, Liotta DC. Oncotarget. 2018 Nov 16;9(90):36102-36109. doi: 10.18632/oncotarget.26302. eCollection 2018 Nov 16. PMID:30546830 Chordoma of the corpus callosum: case report. Rinaldo L, Priemer DS, Vortmeyer AO, Cohen-Gadol AA, Brat DJ, Mahajan A, Giannini C, Burns TC. Neurosurg. 2018 Nov 1:1-7. doi: 10.3171/2018.6.JNS181028. [Epub ahead of print] PMID:30497142 Analysis of Cellular Feature Differences of Astrocytomas with Distinct Mutational Profiles Using Digitized Histopathology Images. Roy M, Wang F, Teodoro G, Vega JV, Brat D, Kong J. Conf Proc IEEE Eng Med Biol Soc. 2018 Jul;2018:4644-4647. doi: 10.1109/EMBC.2018.8513157. PMID:30441386 Clumped Nuclei Segmentation with Adjacent Point Match and Local Shape-Based Intensity Analysis in Fluorescence Microscopy Images. Guo X, Yu H, Rossetti B, Teodoro G, Brat D, Kong J. Conf Proc IEEE Eng Med Biol Soc. 2018 Jul;2018:3410-3413. doi: 10.1109/EMBC.2018.8512961. PMID:30441120 Multi-faceted computational assessment of risk and progression in oligodendroglioma implicates NOTCH and PI3K pathways. Halani SH, Yousefi S, Vega JV, Rossi MR, Zhao Z, Amrollahi F, Holder CA, Baxter-Stoltzfus A, Eschbacher J, Griffith B, Olson JJ, Jiang T, Yates JR, Eberhart CG, Poisson LM, Cooper LAD, Brat DJ. NPJ Precis Oncol. 2018 Nov 6;2:24. doi: 10.1038/s41698-018-0067-9. eCollection 2018. PMID:30417117 cIMPACT-NOW update 3: recommended diagnostic criteria for “Diffuse astrocytic glioma, IDH-wildtype, with molecular features of glioblastoma, WHO grade IV”. Brat DJ, Aldape K, Colman H, Holland EC, Louis DN, Jenkins RB, Kleinschmidt-DeMasters BK, Perry A, Reifenberger G, Stupp R, von Deimling A, Weller M. Acta Neuropathol. 2018 Nov;136(5):805-810. doi: 10.1007/s00401-018-1913-0. Epub 2018 Sep 26. PMID:30259105 A Revised Diagnostic Classification of Canine Glioma: Towards Validation of the Canine Glioma Patient as a Naturally Occurring Preclinical Model for Human Glioma. Koehler JW, Miller AD, Miller CR, Porter B, Aldape K, Beck J, Brat D, Cornax I, Corps K, Frank C, Giannini C, Horbinski C, Huse JT, O’Sullivan MG, Rissi DR, Mark Simpson R, Woolard K, Shih JH, Mazcko C, Gilbert MR, LeBlanc AK. J Neuropathol Exp Neurol. 2018 Nov 1;77(11):1039-1054. doi: 10.1093/jnen/nly085. PMID:30239918 [18F]Fluciclovine PET discrimination between high- and low-grade gliomas. Parent EE, Benayoun M, Ibeanu I, Olson JJ, Hadjipanayis CG, Brat DJ, Adhikarla V, Nye J, Schuster DM, Goodman MM. EJNMMI Res. 2018 Jul 25;8(1):67. doi: 10.1186/s13550-018-0415-3. PMID:30046944 CDK5 Inhibition Resolves PKA/cAMP-Independent Activation of CREB1 Signaling in Glioma Stem Cells. Mukherjee S, Tucker-Burden C, Kaissi E, Newsam A, Duggireddy H, Chau M, Zhang C, Diwedi B, Rupji M, Seby S, Kowalski J, Kong J, Read R, Brat DJ. Cell Rep. 2018 May 8;23(6):1651-1664. doi: 10.1016/j.celrep.2018.04.016. PMID: 29742423 TASI: A software tool for spatial-temporal quantification of tumor spheroid dynamics. Hou Y, Konen J, Brat DJ, Marcus AI, Cooper LAD. Sci Rep. 2018 May 8;8(1):7248. doi: 10.1038/s41598-018-25337-4. PMID: 29739990 Predicting cancer outcomes from histology and genomics using convolutional networks. Mobadersany P, Yousefi S, Amgad M, Gutman DA, Barnholtz-Sloan JS, Velázquez Vega JE, Brat DJ, Cooper LAD. Proc Natl Acad Sci U S A. 2018 Mar 27;115(13):E2970-E2979. doi: 10.1073/pnas.1717139115. Epub 2018 Mar 12.PMID:29531073 Incorporating Advances in Molecular Pathology Into Brain Tumor Diagnostics. Velázquez Vega JE, Brat DJ. Adv Anat Pathol. 2018 May;25(3):143-171. doi: 10.1097/PAP.0000000000000186. PMID:29521646 A recurrent kinase domain mutation in PRKCA defines chordoid glioma of the third ventricle. Goode B, Mondal G, Hyun M, Ruiz DG, Lin YH, Van Ziffle J, Joseph NM, Onodera C, Talevich E, Grenert JP, Hewedi IH, Snuderl M, Brat DJ, Kleinschmidt-DeMasters BK, Rodriguez FJ, Louis DN, Yong WH, Lopes MB, Rosenblum MK, Butowski N, Tihan T, Bollen AW, Phillips JJ, Wiita AP, Yeh I, Jacobson MP, Bastian BC, Perry A, Solomon DA. Nat Commun. 2018 Feb 23;9(1):810. doi: 10.1038/s41467-018-02826-8. PMID:29476136 Glioma Through the Looking GLASS: Molecular Evolution of Diffuse Gliomas and the Glioma Longitudinal AnalySiS Consortium. Aldape K, Amin SB, Ashley DM, Barnholtz-Sloan JS, Bates AJ, Beroukhim R, Bock C, Brat DJ, Claus EB, Costello JF, de Groot JF, Finocchiaro G, French PJ, Gan HK, Griffith B, Herold-Mende CC, Horbinski C, Iavarone A, Kalkanis SN, Karabatsou K, Kim H, Kouwenhoven MCM, McDonald KL, Miletic H, Nam DH, Ng HK, Niclou SP, Noushmehr H, Ormond R, Poisson LM, Reifenberger G, Roncaroli F, Sa JK, Sillevis Smitt PAE, Smits M, Souza CF, Tabatabai G, Van Meir EG, Verhaak RGW, Watts C, Wesseling P, Woehrer A, Yung WKA, Jungk C, Hau AC, van Dyck E, Westerman BA, Yin J, Abiola O, Zeps N, Grimmond S, Buckland M, Khasraw M, Sulman EP, Muscat AM, Stead L; GLASS Consortium. Neuro Oncol. 2018 Feb 8. doi: 10.1093/neuonc/noy020. [Epub ahead of print] PMID:29432615 Practical Diagnostic Approach to the Presence of Hyphae in Neuropathology Specimens With Three Illustrative Cases. Chavez JA, Brat DJ, Hunter SB, Velazquez Vega J, Guarner J. Am J Clin Pathol. 2018 Jan 29;149(2):98-104. doi: 10.1093/ajcp/aqx144. PMID: 29365030 (-)-P7C3-S243 Protects a Rat Model of Alzheimer’s Disease From Neuropsychiatric Deficits and Neurodegeneration Without Altering Amyloid Deposition or Reactive Glia. Voorhees JR, Remy MT, Cintrón-Pérez CJ, El Rassi E, Khan MZ, Dutca LM, Yin TC, McDaniel LN, Williams NS, Brat DJ, Pieper AA. Biol Psychiatry. 2017 Nov 6. pii: S0006-3223(17)32145-5. doi: 10.1016/j.biopsych.2017.10.023. [Epub ahead of print] PMID:29246437 5-Aminolevulinic Acid Guided Sampling of Glioblastoma Microenvironments Identifies Pro-Survival Signaling at Infiltrative Margins. Ross JL, Cooper LAD, Kong J, Gutman D, Williams M, Tucker-Burden C, McCrary MR, Bouras A, Kaluzova M, Dunn WD Jr, Duong D, Hadjipanayis CG, Brat DJ. Sci Rep. 2017 Nov 15;7(1):15593. doi: 10.1038/s41598-017-15849-w. PMID: 29142297 Interactive phenotyping of large-scale histology imaging data with HistomicsML. Nalisnik M, Amgad M, Lee S, Halani SH, Velazquez Vega JE, Brat DJ, Gutman DA, Cooper LAD. Sci Rep. 2017 Nov 6;7(1):14588. doi: 10.1038/s41598-017-15092-3. PMID: 29109450 Predicting clinical outcomes from large scale cancer genomic profiles with deep survival models. Yousefi S, Amrollahi F, Amgad M, Dong C, Lewis JE, Song C, Gutman DA, Halani SH, Velazquez Vega JE, Brat DJ, Cooper LAD. Sci Rep. 2017 Sep 15;7(1):11707. doi: 10.1038/s41598-017-11817-6. PMID: 28916782 Progesterone improves neurocognitive outcomes following therapeutic cranial irradiation in mice. Yousuf S, Brat DJ, Shu HK, Wang Y, Stein DG, Atif F. Horm Behav. 2017 Nov;96:21-30. doi: 10.1016/j.yhbeh.2017.08.004. Epub 2017 Sep 18. PMID: 28866326 Meningioma With Tyrosine-Rich Crystalloids: A Case Report and Review of the Literature. Reinertsen E, Neill SG, Nael K, Brat DJ, Hadjipanayis CG. Int J Surg Pathol. 2018 Apr;26(2):157-160. doi: 10.1177/1066896917727100. Epub 2017 Aug 17. PMID: 28817996 Development of a Framework for Large Scale Three-Dimensional Pathology and Biomarker Imaging and Spatial Analytics. Liang Y, Wang F, Zhang P, Saltz JH, Brat DJ, Kong J. AMIA Jt Summits Transl Sci Proc. 2017 Jul 26;2017:75-84. eCollection 2017. PMID: 28815110 DYNAMIC REGISTRATION FOR GIGAPIXEL SERIAL WHOLE SLIDE IMAGES. Rossetti BJ, Wang F, Zhang P, Teodoro G, Brat DJ, Kong J. Proc IEEE Int Symp Biomed Imaging. 2017 Apr;2017:424-428. doi: 10.1109/ISBI.2017.7950552. Epub 2017 Jun 19. PMID: 28804569 T2-FLAIR Mismatch, an Imaging Biomarker for IDH and 1p/19q Status in Lower-grade Gliomas: A TCGA/TCIA Project. Patel SH, Poisson LM, Brat DJ, Zhou Y, Cooper L, Snuderl M, Thomas C, Franceschi AM, Griffith B, Flanders AE, Golfinos JG, Chi AS, Jain R. Clin Cancer Res. 2017 Oct 15;23(20):6078-6085. doi: 10.1158/1078-0432.CCR-17-0560. Epub 2017 Jul 27. PMID: 28751449 Molecular Programs Underlying Asymmetric Stem Cell Division and Their Disruption in Malignancy. Mukherjee S, Brat DJ. Results Probl Cell Differ. 2017;61:401-421. doi: 10.1007/978-3-319-53150-2_18. Review. PMID: 28409315 Robust Cell Segmentation for Histological Images of Glioblastoma. Kong J, Zhang P, Liang Y, Teodoro G, Brat DJ, Wang F. Proc IEEE Int Symp Biomed Imaging. 2016 Apr;2016:1041-1045. doi: 10.1109/ISBI.2016.7493444. Epub 2016 Jun 16. PMID: 28392891 Co-amplification of phosphoinositide 3-kinase enhancer A and cyclin-dependent kinase 4 triggers glioblastoma progression.Qi Q, Kang SS, Zhang S, Pham C, Fu H, Brat DJ, Ye K. Oncogene. 2017 Aug 10;36(32):4562-4572. doi: 10.1038/onc.2017.67. Epub 2017 Apr 3. PMID: 28368413 Chordoid glioma of the third ventricle: report of a rapidly progressive case. Erwood AA, Velazquez-Vega JE, Neill S, Solomon DA, Butowski N, Nowlan A, Dunbar E, Brat DJ. J Neurooncol. 2017 May;132(3):487-495. doi: 10.1007/s11060-017-2399-7. Epub 2017 Mar 18. PMID: 28315998 Genomic Analysis in the Practice of Surgical Neuropathology: The Emory Experience. Neill SG, Saxe DF, Rossi MR, Schniederjan MJ, Brat DJ. Arch Pathol Lab Med. 2017 Mar;141(3):355-365. doi: 10.5858/arpa.2016-0276-SAI. Review. PMID: 28234572 TRIM8 regulates stemness in glioblastoma through PIAS3-STAT3. Zhang C, Mukherjee S, Tucker-Burden C, Ross JL, Chau MJ, Kong J, Brat DJ. Mol Oncol. 2017 Mar;11(3):280-294. doi: 10.1002/1878-0261.12034. Epub 2017 Feb 15. PMID: 28100038
