Timothy J Triche, MD, PhD

My research focuses on genetic aspects of cancer biology and their biologic consequences. Current research emphasizes whole genome approaches to gene expression profiling and genomic polymorphisms using DNA microarrays and software developed by our group to analyze this data. Laboratory studies typically utilize tumor cell lines expressing transfected genes, or with silenced genes. Gene targets and biologically active small molecules are often analyzed in biologic context by these same methods. Clinical correlative studies utilize tumor tissue with linked clinical data. Recently, these methods have been applied to studies of age related macular degeneration, as part of the Beckman Macular Research Center at the Doheny Eye Institute, Keck School of Medicine.

• BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies Nucleic Acids Res. 2024 Feb 27. . View in PubMed
• Structural variants involving MLLT10 fusion are associated with adverse outcomes in pediatric acute myeloid leukemia Blood Adv. 2024 Feb 02. . View in PubMed
• Validation of Myc-Associated Protein X (MAX) regulation in growth hormone secreting and nonfunctional pituitary adenoma PLoS One. 2023; 18(4):e0284949. . View in PubMed
• Long Noncoding RNA Expression Independently Predicts Outcome in Pediatric Acute Myeloid Leukemia J Clin Oncol. 2023 06 01; 41(16):2949-2962. . View in PubMed
• Non-Invasive Profiling of Advanced Prostate Cancer via Multi-Parametric Liquid Biopsy and Radiomic Analysis Int J Mol Sci. 2022 Feb 25; 23(5). . View in PubMed
• Integrated stem cell signature and cytomolecular risk determination in pediatric acute myeloid leukemia Nat Commun. 2022 09 19; 13(1):5487. . View in PubMed
• Rapidly emerging SARS-CoV-2 B1. 1. 7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. Emerg Microbes Infect. 2021 Dec; 10(1):1293-1299. . View in PubMed
• Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications Emerg Microbes Infect. 2021 Dec; 10(1):885-893. . View in PubMed
• A B-cell developmental gene regulatory network is activated in infant AML PLoS One. 2021; 16(11):e0259197. . View in PubMed
• Baseline Circulating Tumor Cell Count as a Prognostic Marker of PSA Response and Disease Progression in Metastatic Castrate-Sensitive Prostate Cancer (SWOG S1216) Clin Cancer Res. 2021 04 01; 27(7):1967-1973. . View in PubMed
• Distinctive epigenomic alterations in NF1-deficient cutaneous and plexiform neurofibromas drive differential MKK/p38 signaling Epigenetics Chromatin. 2021 01 13; 14(1):7. . View in PubMed
• Mithramycin induces promoter reprogramming and differentiation of rhabdoid tumor EMBO Mol Med. 2021 02 05; 13(2):e12640. . View in PubMed
• Comprehensive Transcriptome Profiling of Cryptic CBFA2T3-GLIS2 Fusion-Positive AML Defines Novel Therapeutic Options: A COG and TARGET Pediatric AML Study Clin Cancer Res. 2020 02 01; 26(3):726-737. . View in PubMed
• Mathematical Oncology Comes to the Clinic: A Data-Driven Treatment for Financial Toxicity? Cancer Res. 2020 06 01; 80(11):2083-2084.. View in PubMed
• Publisher Correction: The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions Nat Med. 2019 Mar; 25(3):530. . View in PubMed
• DNA methylation patterns of adult survivors of adolescent/young adult Hodgkin lymphoma compared to their unaffected monozygotic twin Leuk Lymphoma. 2019 06; 60(6):1429-1437. . View in PubMed
• Landscape of Germline and Somatic Mitochondrial DNA Mutations in Pediatric Malignancies Cancer Res. 2019 04 01; 79(7):1318-1330. . View in PubMed
• Integrated Epigenome, Exome, and Transcriptome Analyses Reveal Molecular Subtypes and Homeotic Transformation in Uterine FibroidsCell Rep. 2019 12 17; 29(12):4069-4085. e6. . View in PubMed
• Erratum: The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions Nat Med. 2018 Apr 10; 24(4):526. . View in PubMed
• Author Correction: Suppression of Transposable Elements in Leukemic Stem Cells Sci Rep. 2018 Mar 06; 8(1):4240. . View in PubMed
• OncoKids: A Comprehensive Next-Generation Sequencing Panel for Pediatric Malignancies J Mol Diagn. 2018 11; 20(6):765-776. . View in PubMed
• Senescent human hematopoietic progenitors show elevated expression of transposable elements and inflammatory genesExp Hematol. 2018 06; 62:33-38. e6. . View in PubMed
• The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions Nat Med. 2018 01; 24(1):103-112. . View in PubMed
• Methylome of human senescent hematopoietic progenitors Exp Hematol Oncol. 2018; 7:32. . View in PubMed
• SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions Nucleic Acids Res. 2018 11 16; 46(20):e123. . View in PubMed
• Lack of APC somatic mutation is associated with early-onset colorectal cancer in African Americans Carcinogenesis. 2018 12 13; 39(11):1331-1341. . View in PubMed
• A phase 1 study of azacitidine combined with chemotherapy in childhood leukemia: a report from the TACL consortium Blood. 2018 03 08; 131(10):1145-1148. . View in PubMed
• Transposable Element Expression in Acute Myeloid Leukemia Transcriptome and Prognosis Sci Rep. 2018 11 06; 8(1):16449. . View in PubMed
• EPHB4 is a therapeutic target in AML and promotes leukemia cell survival via AKT Blood Adv. 2017 Sep 12; 1(20):1635-1644. . View in PubMed
• Suppression of Transposable Elements in Leukemic Stem Cells Sci Rep. 2017 08 01; 7(1):7029. . View in PubMed
• GLI3 repressor determines Hedgehog pathway activation and is required for response to SMO antagonist glasdegib in AML Blood. 2017 06 29; 129(26):3465-3475. . View in PubMed
• A multicenter, randomized study of decitabine as epigenetic priming with induction chemotherapy in children with AML Clin Epigenetics. 2017; 9:108. . View in PubMed
• Response: Making “perfect” the enemy of good Blood. 2017 08 31; 130(9):1168-1169. . View in PubMed
• Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi Bioinformatics. 2017 02 15; 33(4):558-560. . View in PubMed
• A Rapid and Sensitive Next-Generation Sequencing Method to Detect RB1 Mutations Improves Care for Retinoblastoma Patients and Their Families J Mol Diagn. 2016 07; 18(4):480-93. . View in PubMed
• Insulin-like Growth Factor 2 Gene Expression Molecularly Differentiates Pleuropulmonary Blastoma and Embryonal Rhabdomyosarcoma J Pediatr Hematol Oncol. 2015 Aug; 37(6):e356-60. . View in PubMed
• Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas N Engl J Med. 2015 Jun 25; 372(26):2481-98. . View in PubMed
• Discovery and validation of novel expression signature for postcystectomy recurrence in high-risk bladder cancer J Natl Cancer Inst. 2014 Nov; 106(11). . View in PubMed
• Reprogramming of the human intestinal epigenome by surgical tissue transposition Genome Res. 2014 Apr; 24(4):545-53. . View in PubMed
• T lymphocyte abnormalities in juvenile systemic sclerosis patients Clin Immunol. 2013 Oct; 149(1):146-55. . View in PubMed
• A novel algorithm for simplification of complex gene classifiers in cancer Cancer Res. 2013 Sep 15; 73(18):5625-32. . View in PubMed
• Low-level processing of Illumina Infinium DNA Methylation BeadArrays Nucleic Acids Res. 2013 Apr; 41(7):e90. . View in PubMed
• Characterization and drug resistance patterns of Ewing’s sarcoma family tumor cell lines PLoS One. 2013; 8(12):e80060. . View in PubMed
• FOXM1 is an oncogenic mediator in Ewing Sarcoma PLoS One. 2013; 8(1):e54556. . View in PubMed
• Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia N Engl J Med. 2013 05 30; 368(22):2059-74. . View in PubMed
• An epigenomic mechanism in retinoblastoma: the end of the story? Genome Med. 2012 Feb 24; 4(2):15.. View in PubMed
• Influence of RNA labeling on expression profiling of microRNAs J Mol Diagn. 2012 Jan; 14(1):12-21. . View in PubMed
• Quantitative expression profiling in formalin-fixed paraffin-embedded samples by affymetrix microarrays J Mol Diagn. 2010 Jul; 12(4):409-17. . View in PubMed
• Prediction of human functional genetic networks from heterogeneous data using RVM-based ensemble learning Bioinformatics. 2010 Mar 15; 26(6):807-13. . View in PubMed
• Loss of CAK phosphorylation of RAR{alpha} mediates transcriptional control of retinoid-induced cancer cell differentiation FASEB J. 2010 Mar; 24(3):833-43. . View in PubMed
• Gene expression profiling for survival prediction in pediatric rhabdomyosarcomas: a report from the children’s oncology group J Clin Oncol. 2010 Mar 01; 28(7):1240-6. . View in PubMed
• Molecular classification of rhabdomyosarcoma–genotypic and phenotypic determinants of diagnosis: a report from the Children’s Oncology Group Am J Pathol. 2009 Feb; 174(2):550-64. . View in PubMed
• Sparse representation and Bayesian detection of genome copy number alterations from microarray data Bioinformatics. 2008 Feb 01; 24(3):309-18. . View in PubMed
• Hierarchical Bayes prioritization of marker associations from a genome-wide association scan for further investigation Genet Epidemiol. 2007 Dec; 31(8):871-82. . View in PubMed
• Experimental comparison and evaluation of the Affymetrix exon and U133Plus2 GeneChip arrays PLoS One. 2007 Sep 19; 2(9):e913. . View in PubMed
• Histone deacetylase 1 gene expression and sensitization of multidrug-resistant neuroblastoma cell lines to cytotoxic agents by depsipeptide J Natl Cancer Inst. 2007 Jul 18; 99(14):1107-19. . View in PubMed
• E-cadherin cell-cell adhesion in ewing tumor cells mediates suppression of anoikis through activation of the ErbB4 tyrosine kinase Cancer Res. 2007 Apr 01; 67(7):3094-105. . View in PubMed
• Population-based study of early age-related macular degeneration: role of the complement factor H Y402H polymorphism in bilateral but not unilateral disease Ophthalmology. 2007 Jan; 114(1):99-103. . View in PubMed
• Identification of a PAX-FKHR gene expression signature that defines molecular classes and determines the prognosis of alveolar rhabdomyosarcomas Cancer Res. 2006 Jul 15; 66(14):6936-46. . View in PubMed
• EWS-FLI1 fusion protein up-regulates critical genes in neural crest development and is responsible for the observed phenotype of Ewing’s family of tumors Cancer Res. 2005 Jun 01; 65(11):4633-44. . View in PubMed
• Retinoid-modulated MAT1 ubiquitination and CAK activity FASEB J. 2004 Nov; 18(14):1734-6. . View in PubMed
• Selective usage of D-Type cyclins by Ewing’s tumors and rhabdomyosarcomas Cancer Res. 2004 Sep 01; 64(17):6026-34. . View in PubMed
• MAT1-modulated cyclin-dependent kinase-activating kinase activity cross-regulates neuroblastoma cell G1 arrest and neurite outgrowth Cancer Res. 2004 May 01; 64(9):2977-83. . View in PubMed
• Presence of well-differentiated rhabdomyoblasts at the end of therapy for pelvic rhabdomyosarcoma: implications for the outcome J Pediatr Hematol Oncol. 2000 Mar-Apr; 22(2):106-11. . View in PubMed

• Lenz, Heinz-Josef
• Alonzo, Todd
• Berry, Jesse
• Biegel, Jaclyn
• Wiemels, Joseph
• Mascarenhas, Leo
• Zada, Gabriel
• Daneshmand, Siamak
• Alachkar, Houda