Publications by authors named "Daniel D De Carvalho"

55Publications

The Transition from Quiescent to Activated States in Human Hematopoietic Stem Cells Is Governed by Dynamic 3D Genome Reorganization.

Cell Stem Cell 2020 Nov 17. Epub 2020 Nov 17.

Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.stem.2020.11.001DOI Listing
November 2020

Epigenetic therapy induces transcription of inverted SINEs and ADAR1 dependency.

Nature 2020 Dec 21;588(7836):169-173. Epub 2020 Oct 21.

Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41586-020-2844-1DOI Listing
December 2020

DNA Methylation Profiling of Premalignant Lesions as a Path to Ovarian Cancer Early Detection.

Clin Cancer Res 2020 Dec 28;26(23):6083-6085. Epub 2020 Sep 28.

Princess Margaret Cancer Centre, University Health Network. Toronto, Ontario, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/1078-0432.CCR-20-3331DOI Listing
December 2020

Dynamics of the cell-free DNA methylome of metastatic prostate cancer during androgen-targeting treatment.

Epigenomics 2020 Aug 1;12(15):1317-1332. Epub 2020 Sep 1.

Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.2217/epi-2020-0173DOI Listing
August 2020

Detection and discrimination of intracranial tumors using plasma cell-free DNA methylomes.

Nat Med 2020 07 22;26(7):1044-1047. Epub 2020 Jun 22.

Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41591-020-0932-2DOI Listing
July 2020

Using epigenetic data to estimate immune composition in admixed samples.

Methods Enzymol 2020 1;636:77-92. Epub 2019 Aug 1.

UHN Princess Margaret Cancer Centre, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/bs.mie.2019.07.004DOI Listing
August 2019

Methods to detect endogenous dsRNA induction and recognition.

Methods Enzymol 2019 3;629:35-51. Epub 2019 Sep 3.

Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/bs.mie.2019.07.002DOI Listing
June 2020

The role of DNA-demethylating agents in cancer therapy.

Pharmacol Ther 2020 01 15;205:107416. Epub 2019 Oct 15.

Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.pharmthera.2019.107416DOI Listing
January 2020

Preparation of cfMeDIP-seq libraries for methylome profiling of plasma cell-free DNA.

Nat Protoc 2019 10 30;14(10):2749-2780. Epub 2019 Aug 30.

Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41596-019-0202-2DOI Listing
October 2019

DNA Methylation as a Robust Classifier of Epithelial Ovarian Cancer.

Clin Cancer Res 2019 Oct 23;25(19):5729-5731. Epub 2019 Jul 23.

Princess Margaret Cancer Centre, University Health Network. Toronto, Ontario, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/1078-0432.CCR-19-1797DOI Listing
October 2019

Epigenetic therapy in immune-oncology.

Nat Rev Cancer 2019 03;19(3):151-161

Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41568-019-0109-9DOI Listing
March 2019

The Cancer Epigenome: Exploiting Its Vulnerabilities for Immunotherapy.

Trends Cell Biol 2019 01 25;29(1):31-43. Epub 2018 Aug 25.

Princess Margaret Cancer Centre, University Health Network, Toronto, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Canada. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S09628924183012
Publisher Site
http://dx.doi.org/10.1016/j.tcb.2018.07.006DOI Listing
January 2019

Deregulation of Retroelements as an Emerging Therapeutic Opportunity in Cancer.

Trends Cancer 2018 08 19;4(8):583-597. Epub 2018 Jun 19.

Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.trecan.2018.05.008DOI Listing
August 2018

LSD1 Ablation Stimulates Anti-tumor Immunity and Enables Checkpoint Blockade.

Cell 2018 07 21;174(3):549-563.e19. Epub 2018 Jun 21.

Division of Newborn Medicine and Epigenetics Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2018.05.052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6063761PMC
July 2018

Cell-free DNA as a post-treatment surveillance strategy: current status.

Semin Oncol 2017 10 3;44(5):330-346. Epub 2018 Feb 3.

Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1053/j.seminoncol.2018.01.009DOI Listing
October 2017

Drug-induced activation of "junk" DNA - A path to combat cancer therapy resistance?

Oncoscience 2017 Sep 1;4(9-10):115-116. Epub 2017 Oct 1.

Princess Margaret Cancer Centre, University Health Network, Toronto, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.18632/oncoscience.364DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5672890PMC
September 2017

O-Acetylation of Peptidoglycan Limits Helper T Cell Priming and Permits Staphylococcus aureus Reinfection.

Cell Host Microbe 2017 Oct 21;22(4):543-551.e4. Epub 2017 Sep 21.

Division of Pediatric Infectious Diseases, Cedars-Sinai Medical Center (CSMC), Los Angeles, CA 90048, USA; Research Division of Immunology, Department of Biomedical Sciences, CSMC, Los Angeles, CA 90048, USA; F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, CSMC, Los Angeles, CA 90048, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.chom.2017.08.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5679255PMC
October 2017

Epigenetic regulation of nitric oxide synthase 2, inducible (Nos2) by NLRC4 inflammasomes involves PARP1 cleavage.

Sci Rep 2017 02 2;7:41686. Epub 2017 Feb 2.

Centro de Terapia Celular e Molecular (CTC-Mol) e Departamento de Ciências Biológicas - Universidade Federal de São Paulo, São Paulo, Brazil.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/srep41686DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5288713PMC
February 2017

Early-life antibiotic treatment enhances the pathogenicity of CD4 T cells during intestinal inflammation.

J Leukoc Biol 2017 04 29;101(4):893-900. Epub 2016 Dec 29.

The Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia, Canada;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1189/jlb.3MA0716-334RRDOI Listing
April 2017

Integrated (epi)-Genomic Analyses Identify Subgroup-Specific Therapeutic Targets in CNS Rhabdoid Tumors.

Authors:
Jonathon Torchia Brian Golbourn Shengrui Feng King Ching Ho Patrick Sin-Chan Alexandre Vasiljevic Joseph D Norman Paul Guilhamon Livia Garzia Natalia R Agamez Mei Lu Tiffany S Chan Daniel Picard Pasqualino de Antonellis Dong-Anh Khuong-Quang Aline C Planello Constanze Zeller Dalia Barsyte-Lovejoy Lucie Lafay-Cousin Louis Letourneau Mathieu Bourgey Man Yu Deena M A Gendoo Misko Dzamba Mark Barszczyk Tiago Medina Alexandra N Riemenschneider A Sorana Morrissy Young-Shin Ra Vijay Ramaswamy Marc Remke Christopher P Dunham Stephen Yip Ho-Keung Ng Jian-Qiang Lu Vivek Mehta Steffen Albrecht Jose Pimentel Jennifer A Chan Gino R Somers Claudia C Faria Lucia Roque Maryam Fouladi Lindsey M Hoffman Andrew S Moore Yin Wang Seung Ah Choi Jordan R Hansford Daniel Catchpoole Diane K Birks Nicholas K Foreman Doug Strother Almos Klekner Laszló Bognár Miklós Garami Péter Hauser Tibor Hortobágyi Beverly Wilson Juliette Hukin Anne-Sophie Carret Timothy E Van Meter Eugene I Hwang Amar Gajjar Shih-Hwa Chiou Hideo Nakamura Helen Toledano Iris Fried Daniel Fults Takafumi Wataya Chris Fryer David D Eisenstat Katrin Scheinemann Adam J Fleming Donna L Johnston Jean Michaud Shayna Zelcer Robert Hammond Samina Afzal David A Ramsay Nongnuch Sirachainan Suradej Hongeng Noppadol Larbcharoensub Richard G Grundy Rishi R Lulla Jason R Fangusaro Harriet Druker Ute Bartels Ronald Grant David Malkin C Jane McGlade Theodore Nicolaides Tarik Tihan Joanna Phillips Jacek Majewski Alexandre Montpetit Guillaume Bourque Gary D Bader Alyssa T Reddy G Yancey Gillespie Monika Warmuth-Metz Stefan Rutkowski Uri Tabori Mathieu Lupien Michael Brudno Ulrich Schüller Torsten Pietsch Alexander R Judkins Cynthia E Hawkins Eric Bouffet Seung-Ki Kim Peter B Dirks Michael D Taylor Anat Erdreich-Epstein Cheryl H Arrowsmith Daniel D De Carvalho James T Rutka Nada Jabado Annie Huang

Cancer Cell 2016 Dec;30(6):891-908

Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G0A4, Canada; Department of Paediatrics, University of Toronto, Toronto, ON M5G0A4, Canada; Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ccell.2016.11.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5500911PMC
December 2016

Mutant IDH1 Downregulates ATM and Alters DNA Repair and Sensitivity to DNA Damage Independent of TET2.

Cancer Cell 2016 08 14;30(2):337-348. Epub 2016 Jul 14.

The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, ON M5G 2C1, Canada; The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ccell.2016.05.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5022794PMC
August 2016

Pharmacological DNA demethylation: Implications for cancer immunotherapy.

Oncoimmunology 2016 Mar 30;5(3):e1090077. Epub 2015 Nov 30.

Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1080/2162402X.2015.1090077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4839380PMC
March 2016

IL17 Promotes Mammary Tumor Progression by Changing the Behavior of Tumor Cells and Eliciting Tumorigenic Neutrophils Recruitment.

Cancer Res 2015 Sep 24;75(18):3788-99. Epub 2015 Jul 24.

Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/0008-5472.CAN-15-0054DOI Listing
September 2015

Aberrant DNA methylation reprogramming during induced pluripotent stem cell generation is dependent on the choice of reprogramming factors.

Cell Regen 2014 7;3(1). Epub 2014 Feb 7.

Ontario Institute for Cancer Research, Toronto, Ontario M4G 0A3 Canada ; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2 M9 Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/2045-9769-3-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4230737PMC
November 2014

Gene body methylation can alter gene expression and is a therapeutic target in cancer.

Cancer Cell 2014 Oct 25;26(4):577-90. Epub 2014 Sep 25.

Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ccr.2014.07.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4224113PMC
October 2014

Constitutive androstane receptor ligands modulate the anti-tumor efficacy of paclitaxel in non-small cell lung cancer cells.

PLoS One 2014 24;9(6):e99484. Epub 2014 Jun 24.

Laboratory of Experimental and Comparative Oncology, Department of Pathology, School of Veterinary Medicine and Animal Science of the University of São Paulo, Sao Paulo, Brazil.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0099484PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4069004PMC
November 2015

SNF5 is an essential executor of epigenetic regulation during differentiation.

PLoS Genet 2013 Apr 25;9(4):e1003459. Epub 2013 Apr 25.

Departments of Urology and Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angles, California, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1003459DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3636213PMC
April 2013

DNA methylation screening identifies driver epigenetic events of cancer cell survival.

Cancer Cell 2012 May;21(5):655-67

Department of Urology, Biochemistry and Molecular Biology, University of Southern California/Norris Comprehensive Cancer Center Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9181, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ccr.2012.03.045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3395886PMC
May 2012

Polycomb-repressed genes have permissive enhancers that initiate reprogramming.

Cell 2011 Dec;147(6):1283-94

Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2011.10.040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3240866PMC
December 2011

OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes.

Proc Natl Acad Sci U S A 2011 Aug 15;108(35):14497-502. Epub 2011 Aug 15.

Department of Urology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1111309108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3167525PMC
August 2011

Nucleosomes containing methylated DNA stabilize DNA methyltransferases 3A/3B and ensure faithful epigenetic inheritance.

PLoS Genet 2011 Feb 3;7(2):e1001286. Epub 2011 Feb 3.

Department of Urology, Biochemistry, and Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America.

View Article

Download full-text PDF

Source
https://dx.plos.org/10.1371/journal.pgen.1001286
Publisher Site
http://dx.doi.org/10.1371/journal.pgen.1001286DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3033376PMC
February 2011

Epigenetic modifications as therapeutic targets.

Nat Biotechnol 2010 Oct;28(10):1069-78

Departments of Urology and Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/nbt.1678
Publisher Site
http://dx.doi.org/10.1038/nbt.1678DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3022972PMC
October 2010

DNA methylation and cellular reprogramming.

Trends Cell Biol 2010 Oct 31;20(10):609-17. Epub 2010 Aug 31.

Department of Urology, University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.

View Article

Download full-text PDF

Source
http://linkinghub.elsevier.com/retrieve/pii/S096289241000153
Publisher Site
http://dx.doi.org/10.1016/j.tcb.2010.08.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981432PMC
October 2010