Daniel J. Weisenberger, PhD

Associate Professor of Research Biochemistry & Molecular Medicine

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Publications

  • Albumin levels predict prognosis in advanced renal cell carcinoma treated with tyrosine kinase inhibitors: a systematic review and meta-analysisUrol Oncol. 2022 01; 40(1):12. e13-12. e22. . View in PubMed
  • Single cell transcriptomics reveals early photoreceptor states, cell-specific transcript isoforms, and cancer-predisposing features bioRxiv. 2024 Jun 13. . View in PubMed
  • Generic design principles for antibody-based tumour necrosis factor (TNF) receptor 2 (TNFR2) agonists with Fc? R-independent agonism. Theranostics. 2024; 14(2):496-509.. View in PubMed
  • Integrated DNA Methylation/RNA Profiling in Middle Temporal Gyrus of Alzheimer’s Disease Cell Mol Neurobiol. 2023 Jul; 43(5):2289-2307. . View in PubMed
  • Potential role of fructose on human colon DNA methylation in racial disparities observed for colorectal cancer risk medRxiv. 2023 Jun 04. . View in PubMed
  • A Multi-Omics Overview of Colorectal Cancer to Address Mechanisms of Disease, Metastasis, Patient Disparities and Outcomes Cancers (Basel). 2023 May 26; 15(11). . View in PubMed
  • Reversal of dual epigenetic repression of non-canonical Wnt-5a normalises diabetic corneal epithelial wound healing and stem cells Diabetologia. 2023 10; 66(10):1943-1958. . View in PubMed
  • Multi-omic analysis in normal colon organoids highlights MSH4 as a novel marker of defective mismatch repair in Lynch syndrome and microsatellite instability Cancer Med. 2023 06; 12(12):13551-13572. . View in PubMed
  • Detection of diagnostic and prognostic methylation-based signatures in liquid biopsy specimens from patients with meningiomas Nat Commun. 2023 09 13; 14(1):5669. . View in PubMed
  • Analysis of Pregnancy Complications and Epigenetic Gestational Age of Newborns JAMA Netw Open. 2023 02 01; 6(2):e230672. . View in PubMed
  • RNA mis-splicing drives viral mimicry response after DNMTi therapy in SETD2-mutant kidney cancer Cell Rep. 2023 01 31; 42(1):112016. . View in PubMed
  • SETD2 Deficiency Confers Sensitivity to Dual Inhibition of DNA Methylation and PARP in Kidney Cancer Cancer Res. 2023 11 15; 83(22):3813-3826. . View in PubMed
  • A Race-Specific, DNA Methylation Analysis of Aging in Normal Rectum: Implications for the Biology of Aging and Its Relationship to Rectal Cancer Cancers (Basel). 2022 Dec 22; 15(1). . View in PubMed
  • Genes regulated by DNA methylation are involved in distinct phenotypes during melanoma progression and are prognostic factors for patients Mol Oncol. 2022 05; 16(9):1913-1930. . View in PubMed
  • Fluctuating methylation clocks for cell lineage tracing at high temporal resolution in human tissues Nat Biotechnol. 2022 05; 40(5):720-730. . View in PubMed
  • DNMT and EZH2 inhibitors synergize to activate therapeutic targets in hepatocellular carcinoma Cancer Lett. 2022 11 01; 548:215899. . View in PubMed
  • The Multi-Omic Landscape of Primary Breast Tumors and Their Metastases: Expanding the Efficacy of Actionable Therapeutic Targets Genes (Basel). 2022 08 29; 13(9). . View in PubMed
  • The Role of DNA Methylation and DNA Methyltransferases in Cancer Adv Exp Med Biol. 2022; 1389:317-348. . View in PubMed
  • Epigenetic dysregulation in meningiomas Neurooncol Adv. 2022 Jan-Dec; 4(1):vdac084. . View in PubMed
  • Characterizing DNA methylation signatures of retinoblastoma using aqueous humor liquid biopsy Nat Commun. 2022 09 21; 13(1):5523. . View in PubMed
  • Racial Disparities in Epigenetic Aging of the Right vs Left Colon J Natl Cancer Inst. 2021 Nov 29; 113(12):1779-1782. . View in PubMed
  • A Novel DNA Methylation Signature as an Independent Prognostic Factor in Muscle-Invasive Bladder Cancer Front Oncol. 2021; 11:614927. . View in PubMed
  • Characterizing DNA methylation signatures and their potential functional roles in Merkel cell carcinoma Genome Med. 2021 08 16; 13(1):130. . View in PubMed
  • Exploring the evidence for epigenetic regulation of environmental influences on child health across generations Commun Biol. 2021 06 22; 4(1):769. . View in PubMed
  • Author Correction: Aberrant DNA methylation of miRNAs in Fuchs endothelial corneal dystrophy Sci Rep. 2020 Feb 06; 10(1):2395. . View in PubMed
  • Immunogenic cell death pathway polymorphisms for predicting oxaliplatin efficacy in metastatic colorectal cancer J Immunother Cancer. 2020 11; 8(2). . View in PubMed
  • Cell death and survival pathways in Alzheimer’s disease: an integrative hypothesis testing approach utilizing -omic data sets Neurobiol Aging. 2020 11; 95:15-25. . View in PubMed
  • Differences in Genome-wide DNA Methylation Profiles in Breast Milk by Race and Lactation Duration Cancer Prev Res (Phila). 2019 11; 12(11):781-790. . 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
  • Impact of polymorphisms within genes involved in regulating DNA methylation in patients with metastatic colorectal cancer enrolled in three independent, randomised, open-label clinical trials: a meta-analysis from TRIBE, MAVERICC and FIRE-3 Eur J Cancer. 2019 04; 111:138-147. . View in PubMed
  • The Roles of Human DNA Methyltransferases and Their Isoforms in Shaping the Epigenome Genes (Basel). 2019 02 23; 10(2). . View in PubMed
  • Aberrant DNA methylation of miRNAs in Fuchs endothelial corneal dystrophy Sci Rep. 2019 11 08; 9(1):16385. . View in PubMed
  • AMPK variant, a candidate of novel predictor for chemotherapy in metastatic colorectal cancer: A meta-analysis using TRIBE, MAVERICC and FIRE3 Int J Cancer. 2019 10 15; 145(8):2082-2090. . View in PubMed
  • Integrative Epigenetic Analysis Reveals Therapeutic Targets to the DNA Methyltransferase Inhibitor Guadecitabine (SGI-110) in Hepatocellular Carcinoma Hepatology. 2018 10; 68(4):1412-1428. . View in PubMed
  • DNA methylation loss in late-replicating domains is linked to mitotic cell division Nat Genet. 2018 04; 50(4):591-602. . View in PubMed
  • Rewiring of cisplatin-resistant bladder cancer cells through epigenetic regulation of genes involved in amino acid metabolism Theranostics. 2018; 8(16):4520-4534. . View in PubMed
  • DNA methylation aberrancies delineate clinically distinct subsets of colorectal cancer and provide novel targets for epigenetic therapies Oncogene. 2018 02 01; 37(5):566-577. . View in PubMed
  • MethyLight and Digital MethyLight Methods Mol Biol. 2018; 1708:497-513. . View in PubMed
  • Combination Epigenetic Therapy in Advanced Breast Cancer with 5-Azacitidine and Entinostat: A Phase II National Cancer Institute/Stand Up to Cancer Study Clin Cancer Res. 2017 Jun 01; 23(11):2691-2701. . View in PubMed
  • Combination epigenetic therapy in metastatic colorectal cancer (mCRC) with subcutaneous 5-azacitidine and entinostat: a phase 2 consortium/stand up 2 cancer study Oncotarget. 2017 May 23; 8(21):35326-35338. . View in PubMed
  • Improving needle biopsy accuracy in small renal mass using tumor-specific DNA methylation markers Oncotarget. 2017 Jan 17; 8(3):5439-5448. . View in PubMed
  • A Clinically Distinct and ‘Atypical’ Subgroup of Head and Neck Cancers Positive for a CpG Island Methylator Phenotype EBioMedicine. 2017 03; 17:22-23. . View in PubMed
  • DNA methylation aberrancies as a guide for surveillance and treatment of human cancers Epigenetics. 2017 06 03; 12(6):416-432. . View in PubMed
  • Identifying aggressive prostate cancer foci using a DNA methylation classifier Genome Biol. 2017 01 12; 18(1):3. . View in PubMed
  • The genomic landscape of tuberous sclerosis complex Nat Commun. 2017 06 15; 8:15816. . View in PubMed
  • Comprehensive characterization of DNA methylation changes in Fuchs endothelial corneal dystrophy PLoS One. 2017; 12(4):e0175112. . View in PubMed
  • Genetic and Epigenetic Alterations in Bladder Cancer Int Neurourol J. 2016 Nov; 20(Suppl 2):S84-94. . View in PubMed
  • Effects of folylpolyglutamate synthase modulation on global and gene-specific DNA methylation and gene expression in human colon and breast cancer cells J Nutr Biochem. 2016 Mar; 29:27-35. . View in PubMed
  • Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma N Engl J Med. 2016 Jan 14; 374(2):135-45. . View in PubMed
  • Promoter Methylation Analysis Reveals That KCNA5 Ion Channel Silencing Supports Ewing Sarcoma Cell Proliferation Mol Cancer Res. 2016 Jan; 14(1):26-34. . View in PubMed
  • Clinicopathologic Risk Factor Distributions for MLH1 Promoter Region Methylation in CIMP-Positive Tumors Cancer Epidemiol Biomarkers Prev. 2016 Jan; 25(1):68-75. . View in PubMed
  • Identification of DNA Methylation-Independent Epigenetic Events Underlying Clear Cell Renal Cell Carcinoma Cancer Res. 2016 04 01; 76(7):1954-64. . View in PubMed
  • Insights into the Pathogenesis of Anaplastic Large-Cell Lymphoma through Genome-wide DNA Methylation Profiling Cell Rep. 2016 10 04; 17(2):596-608. . View in PubMed
  • Tumor Budding in Colorectal Carcinoma: Confirmation of Prognostic Significance and Histologic Cutoff in a Population-based Cohort Am J Surg Pathol. 2015 Oct; 39(10):1340-6. . 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
  • Association of the colorectal CpG island methylator phenotype with molecular features, risk factors, and family history Cancer Epidemiol Biomarkers Prev. 2015 Mar; 24(3):512-519. . View in PubMed
  • Association between molecular subtypes of colorectal cancer and patient survivalGastroenterology. 2015 Jan; 148(1):77-87. e2. . View in PubMed
  • Characterizing DNA methylation alterations from The Cancer Genome Atlas J Clin Invest. 2014 Jan; 124(1):17-23. . View in PubMed
  • A pilot genome-scale profiling of DNA methylation in sporadic pituitary macroadenomas: association with tumor invasion and histopathological subtype PLoS One. 2014; 9(4):e96178. . View in PubMed
  • Genomic and transcriptome analysis revealing an oncogenic functional module in meningiomas Neurosurg Focus. 2013 Dec; 35(6):E3. . View in PubMed
  • Alterations of immune response of Non-Small Cell Lung Cancer with Azacytidine Oncotarget. 2013 Nov; 4(11):2067-79. . View in PubMed
  • The somatic genomic landscape of glioblastoma Cell. 2013 Oct 10; 155(2):462-77. . View in PubMed
  • Associations between colorectal cancer molecular markers and pathways with clinicopathologic features in older womenGastroenterology. 2013 Aug; 145(2):348-56. e1-2. . View in PubMed
  • Alterations in deoxyribonucleic acid (DNA) methylation patterns of Calca, Timp3, Mmp2, and Igf2r are associated with chronic cystitis in a cyclophosphamide-induced mouse modelUrology. 2013 Jul; 82(1):253. e9-15. . View in PubMed
  • Integrated analysis of genome-wide copy number alterations and gene expression in microsatellite stable, CpG island methylator phenotype-negative colon cancer Genes Chromosomes Cancer. 2013 May; 52(5):450-66. . View in PubMed
  • Low-level processing of Illumina Infinium DNA Methylation BeadArrays Nucleic Acids Res. 2013 Apr; 41(7):e90. . View in PubMed
  • 3-D DNA methylation phenotypes correlate with cytotoxicity levels in prostate and liver cancer cell models BMC Pharmacol Toxicol. 2013 Feb 11; 14:11. . View in PubMed
  • DNA methylation in the malignant transformation of meningiomas PLoS One. 2013; 8(1):e54114. . View in PubMed
  • Postmenopausal hormone therapy and colorectal cancer risk by molecularly defined subtypes among older women Gut. 2012 Sep; 61(9):1299-305. . View in PubMed
  • Cancer risks for the relatives of colorectal cancer cases with a methylated MLH1 promoter region: data from the Colorectal Cancer Family Registry Cancer Prev Res (Phila). 2012 Feb; 5(2):328-35. . View in PubMed
  • Genome-scale analysis of aberrant DNA methylation in colorectal cancer Genome Res. 2012 Feb; 22(2):271-82. . View in PubMed
  • cis-Expression QTL analysis of established colorectal cancer risk variants in colon tumors and adjacent normal tissue PLoS One. 2012; 7(2):e30477. . View in PubMed
  • Genome-scale discovery of DNA-methylation biomarkers for blood-based detection of colorectal cancer PLoS One. 2012; 7(11):e50266. . View in PubMed
  • Associations between intake of folate and related micronutrients with molecularly defined colorectal cancer risks in the Iowa Women’s Health Study Nutr Cancer. 2012; 64(7):899-910. . View in PubMed
  • Alcohol intake and colorectal cancer risk by molecularly defined subtypes in a prospective study of older women Cancer Prev Res (Phila). 2011 Dec; 4(12):2035-43. . View in PubMed
  • Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains Nat Genet. 2011 Nov 27; 44(1):40-6. . View in PubMed
  • Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage Nat Biotechnol. 2011 Nov 27; 29(12):1132-44. . View in PubMed
  • Modeling measurement error in tumor characterization studies BMC Bioinformatics. 2011 Jul 13; 12:284. . View in PubMed
  • Frequency of deletions of EPCAM (TACSTD1) in MSH2-associated Lynch syndrome cases J Mol Diagn. 2011 Jan; 13(1):93-9. . View in PubMed
  • Epigenetic subgroups of esophageal and gastric adenocarcinoma with differential GATA5 DNA methylation associated with clinical and lifestyle factors PLoS One. 2011; 6(10):e25985. . View in PubMed
  • Unique DNA methylation patterns distinguish noninvasive and invasive urothelial cancers and establish an epigenetic field defect in premalignant tissue Cancer Res. 2010 Oct 15; 70(20):8169-78. . View in PubMed
  • Cigarette smoking and colorectal cancer risk by molecularly defined subtypes J Natl Cancer Inst. 2010 Jul 21; 102(14):1012-22. . View in PubMed
  • Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma Cancer Cell. 2010 May 18; 17(5):510-22. . View in PubMed
  • Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer Genome Res. 2010 Apr; 20(4):440-6. . View in PubMed
  • Analysis of the association between CIMP and BRAF in colorectal cancer by DNA methylation profiling PLoS One. 2009 Dec 21; 4(12):e8357. . View in PubMed
  • Epigenetic profiling of somatic tissues from human autopsy specimens identifies tissue- and individual-specific DNA methylation patterns Hum Mol Genet. 2009 Dec 15; 18(24):4808-17. . View in PubMed
  • The relationship of DNA methylation with age, gender and genotype in twins and healthy controls PLoS One. 2009 Aug 26; 4(8):e6767. . View in PubMed
  • The methylenetetrahydrofolate reductase C677T mutation induces cell-specific changes in genomic DNA methylation and uracil misincorporation: a possible molecular basis for the site-specific cancer risk modification Int J Cancer. 2009 May 01; 124(9):1999-2005. . View in PubMed
  • Locking in on the human methylome Nat Biotechnol. 2009 Apr; 27(4):341-2. . View in PubMed
  • MethyLight Methods Mol Biol. 2009; 507:325-37. . View in PubMed
  • Molecular characterization of MSI-H colorectal cancer by MLHI promoter methylation, immunohistochemistry, and mismatch repair germline mutation screening Cancer Epidemiol Biomarkers Prev. 2008 Nov; 17(11):3208-15. . View in PubMed
  • DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight Nucleic Acids Res. 2008 Aug; 36(14):4689-98. . View in PubMed
  • Identification of a panel of sensitive and specific DNA methylation markers for squamous cell lung cancer Mol Cancer. 2008 Jul 10; 7:62. . View in PubMed
  • DNA methylation profiles in diffuse large B-cell lymphoma and their relationship to gene expression status Leukemia. 2008 May; 22(5):1035-43. . View in PubMed
  • DNA methylation profiles of gastric carcinoma characterized by quantitative DNA methylation analysis Lab Invest. 2008 Feb; 88(2):161-70. . View in PubMed
  • DNA methylation in the human cerebral cortex is dynamically regulated throughout the life span and involves differentiated neurons PLoS One. 2007 Sep 19; 2(9):e895. . View in PubMed
  • Epigenetic stem cell signature in cancer Nat Genet. 2007 Feb; 39(2):157-8. . View in PubMed
  • CpG island methylator phenotype (CIMP) of colorectal cancer is best characterised by quantitative DNA methylation analysis and prospective cohort studies Gut. 2006 Jul; 55(7):1000-6. . View in PubMed
  • CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer Nat Genet. 2006 Jul; 38(7):787-93. . View in PubMed
  • Precision and performance characteristics of bisulfite conversion and real-time PCR (MethyLight) for quantitative DNA methylation analysis J Mol Diagn. 2006 May; 8(2):209-17. . View in PubMed
  • Quantitative analysis of associations between DNA hypermethylation, hypomethylation, and DNMT RNA levels in ovarian tumors Oncogene. 2006 Apr 27; 25(18):2636-45. . View in PubMed
  • DNA methylation profiles of female steroid hormone-driven human malignancies Curr Top Microbiol Immunol. 2006; 310:141-78. . View in PubMed
  • Footprinting of mammalian promoters: use of a CpG DNA methyltransferase revealing nucleosome positions at a single molecule level Nucleic Acids Res. 2005 Nov 27; 33(20):e176. . View in PubMed
  • Prognostic relevance of methylation markers in patients with non-muscle invasive bladder carcinoma Eur J Cancer. 2005 Nov; 41(17):2769-78. . View in PubMed
  • Gene-specific methylation and subsequent risk of colorectal adenomas among participants of the polyp prevention trial Cancer Epidemiol Biomarkers Prev. 2005 May; 14(5):1219-23. . View in PubMed
  • Analysis of repetitive element DNA methylation by MethyLight Nucleic Acids Res. 2005; 33(21):6823-36. . View in PubMed
  • Detection of methylated apoptosis-associated genes in urine sediments of bladder cancer patients Clin Cancer Res. 2004 Nov 15; 10(22):7457-65. . View in PubMed
  • Preferential response of cancer cells to zebularine Cancer Cell. 2004 Aug; 6(2):151-8. . View in PubMed
  • Distinct localization of histone H3 acetylation and H3-K4 methylation to the transcription start sites in the human genome Proc Natl Acad Sci U S A. 2004 May 11; 101(19):7357-62. . View in PubMed
  • Continuous zebularine treatment effectively sustains demethylation in human bladder cancer cells Mol Cell Biol. 2004 Feb; 24(3):1270-8. . View in PubMed
  • Role of the DNA methyltransferase variant DNMT3b3 in DNA methylation Mol Cancer Res. 2004 Jan; 2(1):62-72. . View in PubMed
  • Comparison of multitarget fluorescence in situ hybridization in urine with other noninvasive tests for detecting bladder cancer BJU Int. 2003 Dec; 92(9):911-4. . View in PubMed
  • Histone H3-lysine 9 methylation is associated with aberrant gene silencing in cancer cells and is rapidly reversed by 5-aza-2′-deoxycytidine Cancer Res. 2002 Nov 15; 62(22):6456-61. . View in PubMed
  • Identification and characterization of alternatively spliced variants of DNA methyltransferase 3a in mammalian cells Gene. 2002 Sep 18; 298(1):91-9. . View in PubMed
  • Cell division is required for de novo methylation of CpG islands in bladder cancer cells Cancer Res. 2002 Apr 15; 62(8):2378-84. . View in PubMed
  • Cytosine methylation in a CpG sequence leads to enhanced reactivity with Benzo[a]pyrene diol epoxide that correlates with a conformational change J Biol Chem. 1999 Aug 20; 274(34):23948-55. . View in PubMed