Our lab studies the immune microenvironment in various pediatric central nervous system (CNS) tumors including medulloblastoma, glioblastoma, and others. Specifically, our lab utilizes advanced, next-generation sequencing technologies like single cell RNA-sequencing and spatial transcriptomic profiling to better understand the composition of immune cells present in CNS tumors.
Publications
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Macke EL, Miller AR, Colwell CM, Gonzalez MH, Hunter J, Venkata LPR, Walker L, Wheeler G, Wilson RK, Mardis ER, Miller KE, Mathew MT, Chaudhari BP, Akkari Y. Optical Genome Mapping (OGM) Identifies Multiple Structural Variants in a Case With Atypical Phelan-McDermid Syndrome. Am J Med Genet A. 2024 Nov 13; e63929.
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Wedemeyer MA, Ding T, Garfinkle EAR, Westfall JJ, Navarro JB, Hernandez Gonzalez ME, Varga EA, Witman P, Mardis ER, Cottrell CE, Miller AR, Miller KE. Defining the transcriptome of PIK3CA-altered cells in a human capillary malformation using single cell long-read sequencing. Sci Rep. 2024 Oct 25; 14: 25440.
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Stiff A, Fornerod M, Kain BN, Nicolet D, Kelly BJ, Miller KE, Mrózek K, Boateng I, Bollas A, Garfinkle EAR, Momoh O, Fasola FA, Olawumi HO, Mencia-Trinchant N, Kloppers JF, van Marle AC, Hu E, Wijeratne S, Wheeler G, Walker CJ, Buss J, Heyrosa A, Desai H, Laganson A, Hamp E, Abu-Shihab Y, Abaza H, Kronen P, Sen S, Johnstone ME, Quinn K, Wronowski B, Hertlein E, Miles LA, Mims AS, Oakes CC, Blachly JS, Larkin KT, Mundy-Bosse B, Carroll AJ, Powell BL, Kolitz JE, Stone RM, Duarte C, Abbott D, Amaya ML, Jordan CT, Uy GL, Stock W, Archer KJ, Paskett ED, Guzman ML, Levine RL, Menghrajani K, Chakravarty D, Berger MF, Bottomly D, McWeeney SK, Tyner JW, Byrd JC, Salomonis N, Grimes HL, Mardis ER, Eisfeld AK. Multiomic profiling identifies predictors of survival in African American patients with acute myeloid leukemia. Nat Genet. 2024 Oct 4;
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Goda C, Kulkarni R, Bustos Y, Li W, Rudich A, Balcioglu O, Chidester S, Urs AP, Karunasiri M, Al-Marrawi Y, Korn E, Kanna S, Garfinkle EAR, Shah N, Wooten A, Mundy-Bosse B, Sehgal L, Zhang B, Marcucci G, Mardis ER, Garzon R, Bowman RL, Viny AD, Miles LA, Miller KE, Dorrance AM. Cellular taxonomy of the preleukemic bone marrow niche of acute myeloid leukemia. Leukemia. 2024 Oct 2;
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Luo W, Hoang H, Zhu H, Miller K, Mo X, Eguchi S, Tian M, Liao Y, Ayello J, Rosenblum JM, Marcondes M, Currier M, Mardis E, Cripe T, Lee D, Cairo MS. Circumventing resistance within the Ewing sarcoma microenvironment by combinatorial innate immunotherapy. J Immunother Cancer. 2024 Sep 12; 12:
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Luo W, Hoang H, Miller KE, Zhu H, Xu S, Mo X, Garfinkle EAR, Costello H, Wijeratne S, Chemnitz W, Gandhi R, Liao Y, Ayello J, Gardenswartz A, Rosenblum JM, Cassady KA, Mardis ER, Lee DA, Cripe TP, Cairo MS. Combinatorial macrophage induced innate immunotherapy against Ewing sarcoma: Turning "Two Keys" simultaneously. J Exp Clin Cancer Res. 2024 Jul 11; 43: 193.
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Johanns TM, Garfinkle EAR, Miller KE, Livingstone AJ, Roberts KF, Rao Venkata LP, Dowling JL, Chicoine MR, Dacey RG, Zipfel GJ, Kim AH, Mardis ER, Dunn GP. Integrating multisector molecular characterization into personalized peptide vaccine design for patients with newly diagnosed glioblastoma. Clin Cancer Res. 2024 Apr 19;
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Wijeratne S, Gonzalez MEH, Roach K, Miller KE, Schieffer KM, Fitch JR, Leonard J, White P, Kelly BJ, Cottrell CE, Mardis ER, Wilson RK, Miller AR. Full-length isoform concatenation sequencing to resolve cancer transcriptome complexity. BMC Genomics. 2024 Jan 29; 25: 122.
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Mardis ER, Potter SL, Schieffer KM, Varga EA, Mathew MT, Costello HM, Wheeler G, Kelly BJ, Miller KE, Garfinkle EAR, Wilson RK, Cottrell CE. Germline susceptibility from broad genomic profiling of pediatric brain cancers. Neurooncol Adv. 2024 Jan-Dec; 6: vdae099.
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Shatara M, Schieffer KM, Melas M, Varga EA, Thomas D, Bucknor BA, Costello HM, Wheeler G, Kelly BJ, Miller KE, Rodriguez DP, Mathew MT, Lee K, Crotty E, Leary S, Paulson VA, Cole B, Abdelbaki MS, Finlay JL, Lazow MA, Salloum R, Fouladi M, Boué DR, Mardis ER, Cottrell CE. Molecular characterization of gliomas and glioneuronal tumors amid Noonan syndrome: cancer predisposition examined. Front Oncol. 2024; 14: 1453309.
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Kebede AM, Garfinkle EAR, Mathew MT, Varga E, Colace SI, Wheeler G, Kelly BJ, Schieffer KM, Miller KE, Mardis ER, Cottrell CE, Potter SL. Comprehensive genomic characterization of hematologic malignancies at a pediatric tertiary care center. Front Oncol. 2024; 14: 1498409.
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Miller KE, Rivaldi AC, Shinagawa N, Sran S, Navarro JB, Westfall JJ, Miller AR, Roberts RD, Akkari Y, Supinger R, Hester ME, Marhabaie M, Gade M, Lu J, Rodziyevska O, Bhattacharjee MB, Von Allmen GK, Yang E, Lidov HGW, Harini C, Shah MN, Leonard J, Pindrik J, Shaikhouni A, Goldman JE, Pierson CR, Thomas DL, Boué DR, Ostendorf AP, Mardis ER, Poduri A, Koboldt DC, Heinzen EL, Bedrosian TA. Post-zygotic rescue of meiotic errors causes brain mosaicism and focal epilepsy. Nat Genet. 2023 Nov; 55: 1920-1928.
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Hedberg J, Studebaker A, Smith L, Chen CY, Westfall JJ, Cam M, Gross A, Hernandez-Aguirre I, Martin A, Kim D, Dhital R, Kim Y, Roberts RD, Cripe TP, Mardis ER, Cassady KA, Leonard J, Miller KE. Oncolytic virus-driven immune remodeling revealed in mouse medulloblastomas at single cell resolution. Mol Ther Oncolytics. 2023 Sep 21; 30: 39-55.
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Mayoh C, Gifford AJ, Terry R, Lau LMS, Wong M, Rao P, Shai-Hee T, Saletta F, Khuong-Quang DA, Qin V, Mateos MK, Meyran D, Miller KE, Yuksel A, Mould EVA, Bowen-James R, Govender D, Senapati A, Zhukova N, Omer N, Dholaria H, Alvaro F, Tapp H, Diamond Y, Pozza LD, Moore AS, Nicholls W, Gottardo NG, McCowage G, Hansford JR, Khaw SL, Wood PJ, Catchpoole D, Cottrell CE, Mardis ER, Marshall GM, Tyrrell V, Haber M, Ziegler DS, Vittorio O, Trapani JA, Cowley MJ, Neeson PJ, Ekert PG. A novel transcriptional signature identifies T-cell infiltration in high-risk paediatric cancer. Genome Med. 2023 Apr 3; 15: 20.
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Townsend SE, Westfall JJ, Navarro JB, Koboldt DC, Mardis ER, Miller KE, Bedrosian TA. Single-nuclei transcriptomics enable detection of somatic variants in patient brain tissue. Sci Rep. 2023 Jan 11; 13: 527.
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Miller AR, Wijeratne S, McGrath SD, Schieffer KM, Miller KE, Lee K, Mathew M, LaHaye S, Fitch JR, Kelly BJ, White P, Mardis ER, Wilson RK, Cottrell CE, Magrini V. Pacific Biosciences Fusion and Long Isoform Pipeline for Cancer Transcriptome-Based Resolution of Isoform Complexity. J Mol Diagn. 2022 Dec; 24: 1292-1306.
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Westfall JJ, Schwind WN, Sran S, Navarro JB, Leonard J, Pindrik JA, Pierson CR, Boué DR, Koboldt DC, Ostendorf AP, Wilson RK, Mardis ER, Miller KE, Bedrosian TA. Molecular and spatial heterogeneity of microglia in Rasmussen encephalitis. Acta Neuropathol Commun. 2022 Nov 21; 10: 168.
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Bedrosian TA, Miller KE, Grischow OE, Schieffer KM, LaHaye S, Yoon H, Miller AR, Navarro J, Westfall J, Leraas K, Choi S, Williamson R, Fitch J, Kelly BJ, White P, Lee K, McGrath S, Cottrell CE, Magrini V, Leonard J, Pindrik J, Shaikhouni A, Boué DR, Thomas DL, Pierson CR, Wilson RK, Ostendorf AP, Mardis ER, Koboldt DC. Detection of brain somatic variation in epilepsy-associated developmental lesions. Epilepsia. 2022 Aug; 63: 1981-1997.
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Larkin K, Nicolet D, Kelly BJ, Mrózek K, LaHaye S, Miller KE, Wijeratne S, Wheeler GL, Kohlschmidt J, Blachly JS, Mims AS, Walker C, Oakes CC, Orwick S, Boateng I, Buss J, Heyrosa A, Desai H, Carroll AJ, Blum W, Powell BL, Kolitz JE, Moore JO, Mayer RJ, Larson RA, Stone RM, Paskett ED, Byrd JC, Mardis E, Eisfeld AK. High early death rates, treatment resistance, and short survival of Black adolescents and young adults with AML. Blood Adv. 2022 Jul 5;
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Miller KE, Mardis ER. Pediatric CNS cancer genomics and immunogenomics. Curr Opin Genet Dev. 2022 May 23; 75: 101918.
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Miller KE, Cassady KA, Roth JC, Clements J, Schieffer KM, Leraas K, Miller AR, Prasad N, Leavenworth JW, Aban IB, Whitley RJ, Gillespie GY, Mardis ER, Markert JM. Immune Activity and Response Differences of Oncolytic Viral Therapy in Recurrent Glioblastoma: Gene Expression Analyses of a Phase IB Study. Clin Cancer Res. 2022 Feb 1; 28: 498-506.
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Schaettler MO, Richters MM, Wang AZ, Skidmore ZL, Fisk B, Miller KE, Vickery TL, Kim AH, Chicoine MR, Osbun JW, Leuthardt EC, Dowling JL, Zipfel GJ, Dacey RG, Lu HC, Johanns TM, Griffith OL, Mardis ER, Griffith M, Dunn GP. Characterization of the Genomic and Immunologic Diversity of Malignant Brain Tumors through Multisector Analysis. Cancer Discov. 2022 Jan; 12: 154-171.
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Miller KE, MacDonald JP, Sullivan L, Venkata LPR, Shi J, Yeates KO, Chen S, Alshaikh E, Taylor HG, Hautmann A, Asa N, Cohen DM, Pommering TL, Mardis ER, Yang J, NCH Concussion Research Group.. Salivary miRNA Expression in Children With Persistent Post-concussive Symptoms. Front Public Health. 2022; 10: 890420.
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Miller KE, Wheeler G, LaHaye S, Schieffer KM, Cearlock S, Venkata LPR, Bravo AO, Grischow OE, Kelly BJ, White P, Pierson CR, Boué DR, Koo SC, Klawinski D, Ranalli MA, Shaikhouni A, Salloum R, Shatara M, Leonard JR, Wilson RK, Cottrell CE, Mardis ER, Koboldt DC. Molecular Heterogeneity in Pediatric Malignant Rhabdoid Tumors in Patients With Multi-Organ Involvement. Front Oncol. 2022; 12: 932337.
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Ronsley R, Boué DR, Venkata LPR, Scott S, Shaikhouni A, Jones J, Schieffer KM, Cottrell CE, Mardis ER, Olshefski R, Salloum R, Miller KE. An unusual case of atypical teratoid/rhabdoid tumor, initially diagnosed as atypical pituitary adenoma in a 13-year-old male patient. Neurooncol Adv. 2022 Jan-Dec; 4: vdac121.
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LaHaye S, Fitch JR, Voytovich KJ, Herman AC, Kelly BJ, Lammi GE, Arbesfeld JA, Wijeratne S, Franklin SJ, Schieffer KM, Bir N, McGrath SD, Miller AR, Wetzel A, Miller KE, Bedrosian TA, Leraas K, Varga EA, Lee K, Gupta A, Setty B, Boué DR, Leonard JR, Finlay JL, Abdelbaki MS, Osorio DS, Koo SC, Koboldt DC, Wagner AH, Eisfeld AK, Mrózek K, Magrini V, Cottrell CE, Mardis ER, Wilson RK, White P. Discovery of clinically relevant fusions in pediatric cancer. BMC Genomics. 2021 Dec 4; 22: 872.
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Marhabaie M, Hickey SE, Miller K, Grischow O, Schieffer KM, Franklin SJ, Gordon DM, Choi S, Mihalic Mosher T, White P, Koboldt DC, Wilson RK. Maternal mosaicism for a missense variant in the SMS gene that causes Snyder-Robinson syndrome. Cold Spring Harb Mol Case Stud. 2021 Dec; 7:
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Ghonime MG, Saini U, Kelly MC, Roth JC, Wang PY, Chen CY, Miller K, Hernandez-Aguirre I, Kim Y, Mo X, Stanek JR, Cripe T, Mardis E, Cassady KA. Eliciting an immune-mediated antitumor response through oncolytic herpes simplex virus-based shared antigen expression in tumors resistant to viroimmunotherapy. J Immunother Cancer. 2021 Oct; 9:
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Wedekind MF, Miller KE, Chen CY, Wang PY, Hutzen BJ, Currier MA, Nartker B, Roberts RD, Boon L, Conner J, LaHaye S, Kelly BJ, Gordon D, White P, Mardis ER, Cripe TP. Endogenous retrovirus envelope as a tumor-associated immunotherapeutic target in murine osteosarcoma. iScience. 2021 Jul 23; 24: 102759.
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Koboldt DC, Miller KE, Miller AR, Bush JM, McGrath S, Leraas K, Crist E, Fair S, Schwind W, Wijeratne S, Fitch J, Leonard J, Shaikhouni A, Hester ME, Magrini V, Ho ML, Pierson CR, Wilson RK, Ostendorf AP, Mardis ER, Bedrosian TA. PTEN somatic mutations contribute to spectrum of cerebral overgrowth. Brain. 2021 May 28;
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Miller KE, Schieffer KM, Grischow O, Rodriguez DP, Cottrell CE, Leonard JR, Finlay JL, Mardis ER. Clinical response to dabrafenib plus trametinib in a pediatric ganglioglioma with BRAF p.T599dup mutation. Cold Spring Harb Mol Case Stud. 2021 Apr; 7:
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Miller KE, Koboldt DC, Schieffer KM, Bedrosian TA, Crist E, Sheline A, Leraas K, Magrini V, Zhong H, Brennan P, Bush J, Fitch J, Bir N, Miller AR, Cottrell CE, Leonard J, Pindrik JA, Rusin JA, Shah SH, White P, Wilson RK, Mardis ER, Pierson CR, Ostendorf AP. Somatic SLC35A2 mosaicism correlates with clinical findings in epilepsy brain tissue. Neurol Genet. 2020 Aug; 6: e460.
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Wang Y, Liyanarachchi S, Miller KE, Nieminen TT, Comiskey DF Jr, Li W, Brock P, Symer DE, Akagi K, DeLap KE, He H, Koboldt DC, de la Chapelle A. Identification of Rare Variants Predisposing to Thyroid Cancer. Thyroid. 2019 Jul; 29: 946-955.
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