Faculty

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Michael R. Lieber, MD, PhD
Professor of Pathology
Rita and Edward Polusky Chair in Basic Cancer Research
Pathology
NOR 5428 Health Sciences Campus Los Angeles
+1 323 865 0568

Overview

The web page for the Lieber lab is: lieber.usc.edu

The following overview of research at the Lieber lab is taken from lieber.usc.edu.

DNA double-strand breaks occur as part of the physiologic development of the immune repertoire in B and T lymphocytes. We study the manner in which these breaks are generated in a process called V(D)J recombination. Defects in the normal enzymes that generate these breaks can result in inherited forms of human severe combined immune deficiency (SCID). We study the biochemistry of how these proteins function, and we study how mutations in them result in SCID. Once DNA breaks are generated, they must be repaired. All cells of the body possess the ability to repair double-strand DNA breaks because all cells must deal with pathologic breaks in DNA that arise due to external radiation or due to free radicals of oxidative metabolism. The major pathway for repairing double-strand breaks in mammalian cells is called nonhomologous DNA end joining (NHEJ). If this pathway is defective in lymphocytes, then the breaks generated can not be repaired. Such defects also result in SCID. If the NHEJ pathway is defectve in all cells of the body, not only is the immune system affected, but the entire body is extremely vulnerable to ionizing radiation. Our laboratory has made substantial progress in defining proteins important in the NHEJ pathway. The first protein in the NHEJ pathway, Ku, binds at the broken DNA ends. The Artemis:DNA-PKcs complex is recruited to the DNA end by Ku. This binding activates the protein kinase activity of DNA-PKcs, which then phosphorylates Artemis and makes the Artemis:DNA-PKcs complex a potent nuclease for trimming DNA ends. Polymerase mu and lambda fill-in gaps, and polymerase mu can add nucleotides template-indepenently, like TdT. Finally, DNA ligase IV, XRCC4, and XLF form the ligation complex which ligates the double-strand break. We are interested in how all of these proteins carry out their functions and how their structure is important for this, and we are interested in identifying any other proteins that might be in th is pathway. We are also interested in how chromatin structure affects these proteins as they repair DNA breaks. The process of NHEJ is intrinsically imprecise. We suspect that this imprecision may contribute to the aging of somatic cells over time as well as to cancer. We are currently investigating this possibility using cell culture models, animal models, and analysis of human cells. Identification of inhibitors of NHEJ would be useful in cancer therapy and in improving gene targeting in human stem cells, and hence, we are trying to identify inhibitors of the pathway and individual components.

Mistakes of V(D)J recombination account for about 40% of nonHodgkin's lymphoma. We study how the normal V(D)J recombination process goes awry. Specifically, why do some ends fail to join properly, and why do some sites adjacent to oncogenes get cleaved inadvertently. The inadvertent cleavage of some sites may be due to an altered DNA structure at those sites. We are trying to understand the extent to which such DNA structural deviations contribute to the fragility of such common chromosomal translocation hotspots.

Class switch recombination is a second developmentally programmed gene rearrangement process in the vertebrate immune system, and it occurs in B cells at the Ig heavy chain locus. Class switching is the process that results in IgM being converted to IgG, IgA, or IgE. Humans borne with defects in class switching die early in life because they can not make IgA for protection of their lungs. The enzyme that initiates the class switch gene rearrangement process is a cytidine deaminase, called AID, that only functions on single-stranded DNA. We have focused on how the class switch recombination regions become single-stranded. Upon transcription, the RNA remains associated with the template DNA strand, resulting in an R-loop structure. The R-loop structure provides a substantial amount of single-stranded DNA at which the AID enzyme can act. We are interested in determining the factors that favor R-loop formation. In some lymphomas, the class switch recombination process goes awry, just as in V(D)J recombination. We are also studying these events.

In summary, the Lieber lab focuses on how physiologic and pathologic gene rearrangements function in the immune system and in cancer and aging.

Publications

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Bridging of double-stranded breaks by the nonhomologous end-joining ligation complex is modulated by DNA end chemistry. Nucleic Acids Res. 2016 Dec 06. View in: PubMed

Real-time analysis of RAG complex activity in V(D)J recombination. Proc Natl Acad Sci U S A. 2016 Oct 4. View in: PubMed

SCR7 is neither a selective nor a potent inhibitor of human DNA ligase IV. DNA Repair (Amst). 2016 Jul; 43:18-23. View in: PubMed

Mechanisms of human lymphoid chromosomal translocations. Nat Rev Cancer. 2016 May 25; 16(6):387-98. View in: PubMed

Dissecting the Roles of Divergent and Convergent Transcription in Chromosome Instability. Cell Rep. 2016 Feb 9; 14(5):1025-31. View in: PubMed

Unifying the DNA End-processing Roles of the Artemis Nuclease: KU-DEPENDENT ARTEMIS RESECTION AT BLUNT DNA ENDS. J Biol Chem. 2015 Oct 2; 290(40):24036-50. View in: PubMed

Convergent BCL6 and lncRNA promoters demarcate the major breakpoint region for BCL6 translocations. Blood. 2015 Oct 1; 126(14):1730-1. View in: PubMed

The repetitive portion of the Xenopus IgH Mu switch region mediates orientation-dependent class switch recombination. Mol Immunol. 2015 Oct; 67(2 Pt B):524-31. View in: PubMed

Effect of CpG dinucleotides within IgH switch region repeats on immunoglobulin class switch recombination. Mol Immunol. 2015 Aug; 66(2):284-9. View in: PubMed

Organization and dynamics of the nonhomologous end-joining machinery during DNA double-strand break repair. Proc Natl Acad Sci U S A. 2015 May 19; 112(20):E2575-84. View in: PubMed

Human lymphoid translocation fragile zones are hypomethylated and have accessible chromatin. Mol Cell Biol. 2015 Apr 1; 35(7):1209-22. View in: PubMed

Complexities due to single-stranded RNA during antibody detection of genomic rna:dna hybrids. BMC Res Notes. 2015; 8(1):127. View in: PubMed

The role of G-density in switch region repeats for immunoglobulin class switch recombination. Nucleic Acids Res. 2014 Dec 1; 42(21):13186-93. View in: PubMed

Histone methylation and V(D)J recombination. Int J Hematol. 2014 Sep; 100(3):230-7. View in: PubMed

The Strength of an Ig Switch Region Is Determined by Its Ability to Drive R Loop Formation and Its Number of WGCW Sites. Cell Rep. 2014 Jul 24; 8(2):557-69. View in: PubMed

Non-homologous end joining often uses microhomology: Implications for alternative end joining. DNA Repair (Amst). 2014 May; 17:74-80. View in: PubMed

Modeling of the RAG Reaction Mechanism. Cell Rep. 2014 Apr 24; 7(2):307-15. View in: PubMed

Evidence That the DNA Endonuclease ARTEMIS also Has Intrinsic 5'-Exonuclease Activity. J Biol Chem. 2014 Mar 14; 289(11):7825-34. View in: PubMed

Detection and characterization of R-loops at the murine immunoglobulin Sa region. Mol Immunol. 2013 Jun; 54(2):208-16. View in: PubMed

BCL6 breaks occur at different AID sequence motifs in Ig-BCL6 and non-Ig-BCL6 rearrangements. Blood. 2013 May 30; 121(22):4551-4. View in: PubMed

Large chromosome deletions, duplications, and gene conversion events accumulate with age in normal human colon crypts. Aging Cell. 2013 Apr; 12(2):269-79. View in: PubMed

Both CpG methylation and activation-induced deaminase are required for the fragility of the human bcl-2 major breakpoint region: implications for the timing of the breaks in the t(14;18) translocation. Mol Cell Biol. 2013 Mar; 33(5):947-57. View in: PubMed

A noncatalytic function of the ligation complex during nonhomologous end joining. J Cell Biol. 2013 Jan 21; 200(2):173-86. View in: PubMed

Reproducibility and reliability of SNP analysis using human cellular DNA at or near nanogram levels. BMC Res Notes. 2013; 6:515. View in: PubMed

IgH partner breakpoint sequences provide evidence that AID initiates t(11;14) and t(8;14) chromosomal breaks in mantle cell and Burkitt lymphomas. Blood. 2012 Oct 4; 120(14):2864-7. View in: PubMed

Mechanistic Basis for RAG Discrimination between Recombination Sites and the Off-Target Sites of Human Lymphomas. Mol Cell Biol. 2012 Jan; 32(2):365-75. View in: PubMed

Polynucleotide kinase and aprataxin-like forkhead-associated protein (PALF) acts as both a single-stranded DNA endonuclease and a single-stranded DNA 3' exonuclease and can participate in DNA end joining in a biochemical system. J Biol Chem. 2011 Oct 21; 286(42):36368-77. View in: PubMed

Formation of a G-quadruplex at the BCL2 major breakpoint region of the t(14;18) translocation in follicular lymphoma. Nucleic Acids Res. 2011 Feb; 39(3):936-48. View in: PubMed

t(X;14)(p22;q32)/t(Y;14)(p11;q32) CRLF2-IGH translocations from human B-lineage ALLs involve CpG-type breaks at CRLF2, but CRLF2/P2RY8 intrachromosomal deletions do not. Blood. 2010 Sep 16; 116(11):1993-4. View in: PubMed

SnapShot: Nonhomologous DNA end joining (NHEJ). Cell. 2010 Aug 6; 142(3):496-496. e1. View in: PubMed

Is there any genetic instability in human cancer? DNA Repair (Amst). Is there any genetic instability in human cancer? DNA Repair (Amst). 2010 Aug 5; 9(8):858; discussion 859-60. View in: PubMed

The t(14;18)(q32;q21)/IGH-MALT1 translocation in MALT lymphomas is a CpG-type translocation, but the t(11;18)(q21;q21)/API2-MALT1 translocation in MALT lymphomas is not. Blood. 2010 Apr 29; 115(17):3640-1; author reply 3641-2. View in: PubMed

DNA-PKcs regulates a single-stranded DNA endonuclease activity of Artemis. DNA Repair (Amst). 2010 Apr 4; 9(4):429-37. View in: PubMed

NHEJ and its backup pathways in chromosomal translocations. Nat Struct Mol Biol. 2010 Apr; 17(4):393-5. View in: PubMed

Cytosines, but not purines, determine recombination activating gene (RAG)-induced breaks on heteroduplex DNA structures: implications for genomic instability. J Biol Chem. 2010 Mar 5; 285(10):7587-97. View in: PubMed

Successful treatment of calcific uremic arteriolopathy in a pediatric dialysis patient. Pediatr Nephrol. 2010 Feb; 25(2):357-62. View in: PubMed

Competition between the RNA transcript and the nontemplate DNA strand during R-loop formation in vitro: a nick can serve as a strong R-loop initiation site. Mol Cell Biol. 2010 Jan; 30(1):146-59. View in: PubMed

Nonhomologous DNA end joining (NHEJ) and chromosomal translocations in humans. Subcell Biochem. 2010; 50:279-96. View in: PubMed

The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu Rev Biochem. 2010; 79:181-211. View in: PubMed

Mechanisms of chromosomal rearrangement in the human genome. BMC Genomics. 2010; 11 Suppl 1:S1. View in: PubMed

The B cell mutator AID promotes B lymphoid blast crisis and drug resistance in chronic myeloid leukemia. Cancer Cell. 2009 Sep 8; 16(3):232-45. View in: PubMed

H3K4me3 stimulates the V(D)J RAG complex for both nicking and hairpinning in trans in addition to tethering in cis: implications for translocations. Mol Cell. 2009 Jun 12; 34(5):535-44. View in: PubMed

G clustering is important for the initiation of transcription-induced R-loops in vitro, whereas high G density without clustering is sufficient thereafter. Mol Cell Biol. 2009 Jun; 29(11):3124-33. View in: PubMed

Conformational variants of duplex DNA correlated with cytosine-rich chromosomal fragile sites. J Biol Chem. 2009 Mar 13; 284(11):7157-64. View in: PubMed

A histidine in the beta-CASP domain of Artemis is critical for its full in vitro and in vivo functions. DNA Repair (Amst). 2009 Feb 1; 8(2):202-8. View in: PubMed

Human chromosomal translocations at CpG sites and a theoretical basis for their lineage and stage specificity. Cell. 2008 Dec 12; 135(6):1130-42. View in: PubMed

Unexpected complexity at breakpoint junctions in phenotypically normal individuals and mechanisms involved in generating balanced translocations t(1;22)(p36;q13). Genome Res. 2008 Nov; 18(11):1733-42. View in: PubMed

Turning anti-ageing genes against cancer. Nat Rev Mol Cell Biol. 2008 Nov; 9(11):903-10. View in: PubMed

A biochemically defined system for coding joint formation in V(D)J recombination. Mol Cell. 2008 Aug 22; 31(4):485-97. View in: PubMed

FACT-mediated exchange of histone variant H2AX regulated by phosphorylation of H2AX and ADP-ribosylation of Spt16. Mol Cell. 2008 Apr 11; 30(1):86-97. View in: PubMed

DNA-PKcs at 7 angstrom: insights for DNA repair. Structure. 2008 Mar; 16(3):334-6. View in: PubMed

RAGs found "not guilty": cleared by DNA evidence. Blood. 2008 Feb 15; 111(4):1750. View in: PubMed

Mechanistic flexibility as a conserved theme across 3 billion years of nonhomologous DNA end-joining. Genes Dev. 2008 Feb 15; 22(4):411-5. View in: PubMed

The mechanism of human nonhomologous DNA end joining. J Biol Chem. 2008 Jan 4; 283(1):1-5. View in: PubMed

Flexibility in the order of action and in the enzymology of the nuclease, polymerases, and ligase of vertebrate non-homologous DNA end joining: relevance to cancer, aging, and the immune system. Cell Res. 2008 Jan; 18(1):125-33. View in: PubMed

Mechanistic aspects of lymphoid chromosomal translocations. J Natl Cancer Inst Monogr. 2008; (39):8-11. View in: PubMed

Mechanism of R-loop formation at immunoglobulin class switch sequences. Mol Cell Biol. 2008 Jan; 28(1):50-60. View in: PubMed

Sequence dependence of chromosomal R-loops at the immunoglobulin heavy-chain Smu class switch region. Mol Cell Biol. 2007 Aug; 27(16):5921-32. View in: PubMed

The structure-specific nicking of small heteroduplexes by the RAG complex: implications for lymphoid chromosomal translocations. DNA Repair (Amst). 2007 Jun 1; 6(6):751-9. View in: PubMed

Length-dependent binding of human XLF to DNA and stimulation of XRCC4. DNA ligase IV activity. J Biol Chem. 2007 Apr 13; 282(15):11155-62. View in: PubMed

XRCC4:DNA ligase IV can ligate incompatible DNA ends and can ligate across gaps. EMBO J. 2007 Feb 21; 26(4):1010-23. View in: PubMed

DNA structure and human diseases. Front Biosci. 2007; 12:4402-8. View in: PubMed

Single-stranded DNA ligation and XLF-stimulated incompatible DNA end ligation by the XRCC4-DNA ligase IV complex: influence of terminal DNA sequence. Nucleic Acids Res. 2007; 35(17):5755-62. View in: PubMed

Extent to which hairpin opening by the Artemis:DNA-PKcs complex can contribute to junctional diversity in V(D)J recombination. Nucleic Acids Res. 2007; 35(20):6917-23. View in: PubMed

DNA-PKcs dependence of Artemis endonucleolytic activity, differences between hairpins and 5' or 3' overhangs. J Biol Chem. 2006 Nov 10; 281(45):33900-9. View in: PubMed

Roles of nonhomologous DNA end joining, V(D)J recombination, and class switch recombination in chromosomal translocations. DNA Repair (Amst). 2006 Sep 8; 5(9-10):1234-45. View in: PubMed

The polymerases for V(D)J recombination. Immunity. 2006 Jul; 25(1):7-9. View in: PubMed

DNA structures at chromosomal translocation sites. Bioessays. 2006 May; 28(5):480-94. View in: PubMed

Downstream boundary of chromosomal R-loops at murine switch regions: implications for the mechanism of class switch recombination. Proc Natl Acad Sci U S A. 2006 Mar 28; 103(13):5030-5. View in: PubMed

Hybrid joint formation in human V(D)J recombination requires nonhomologous DNA end joining. DNA Repair (Amst). 2006 Feb 3; 5(2):278-85. View in: PubMed

Analysis of non-B DNA structure at chromosomal sites in the mammalian genome. Methods Enzymol. 2006; 409:301-16. View in: PubMed

Severe combined immunodeficiency and microcephaly in siblings with hypomorphic mutations in DNA ligase IV. Eur J Immunol. 2006 Jan; 36(1):224-35. View in: PubMed

In vitro nonhomologous DNA end joining system. Methods Enzymol. 2006; 408:502-10. View in: PubMed

Detection and structural analysis of R-loops. Methods Enzymol. 2006; 409:316-29. View in: PubMed

The DNA-dependent protein kinase catalytic subunit phosphorylation sites in human Artemis. J Biol Chem. 2005 Oct 7; 280(40):33839-46. View in: PubMed

Repair of double-strand DNA breaks by the human nonhomologous DNA end joining pathway: the iterative processing model. Cell Cycle. 2005 Sep; 4(9):1193-200. View in: PubMed

Both V(D)J coding ends but neither signal end can recombine at the bcl-2 major breakpoint region, and the rejoining is ligase IV dependent. Mol Cell Biol. 2005 Aug; 25(15):6475-84. View in: PubMed

The Artemis:DNA-PKcs endonuclease cleaves DNA loops, flaps, and gaps. DNA Repair (Amst). 2005 Jul 12; 4(7):845-51. View in: PubMed

Double-strand break formation by the RAG complex at the bcl-2 major breakpoint region and at other non-B DNA structures in vitro. Mol Cell Biol. 2005 Jul; 25(14):5904-19. View in: PubMed

Evidence for a triplex DNA conformation at the bcl-2 major breakpoint region of the t(14;18) translocation. J Biol Chem. 2005 Jun 17; 280(24):22749-60. View in: PubMed

Omenn syndrome due to ARTEMIS mutations. Blood. 2005 Jun 1; 105(11):4179-86. View in: PubMed

Fine-structure analysis of activation-induced deaminase accessibility to class switch region R-loops. Mol Cell Biol. 2005 Mar; 25(5):1730-6. View in: PubMed

Generation and characterization of endonuclease G null mice. Mol Cell Biol. 2005 Jan; 25(1):294-302. View in: PubMed

Genetic interactions between BLM and DNA ligase IV in human cells. J Biol Chem. 2004 Dec 31; 279(53):55433-42. View in: PubMed

A biochemically defined system for mammalian nonhomologous DNA end joining. Mol Cell. 2004 Dec 3; 16(5):701-13. View in: PubMed

The efficacy of hyperbaric oxygen therapy in the treatment of radiation-induced late side effects. Int J Radiat Oncol Biol Phys. 2004 Nov 1; 60(3):871-8. View in: PubMed

Stability and strand asymmetry in the non-B DNA structure at the bcl-2 major breakpoint region. J Biol Chem. 2004 Oct 29; 279(44):46213-25. View in: PubMed

The mechanism of vertebrate nonhomologous DNA end joining and its role in V(D)J recombination. DNA Repair (Amst). 2004 Aug-Sep; 3(8-9):817-26. View in: PubMed

Chromosomal translocations and non-B DNA structures in the human genome. Cell Cycle. 2004 Jun; 3(6):762-8. View in: PubMed

DNA damage and aging. Mech Ageing Dev. 2004 Jun; 125(6):405-16. View in: PubMed

Functional and biochemical dissection of the structure-specific nuclease ARTEMIS. EMBO J. 2004 May 5; 23(9):1987-97. View in: PubMed

A non-B-DNA structure at the Bcl-2 major breakpoint region is cleaved by the RAG complex. Nature. 2004 Mar 4; 428(6978):88-93. View in: PubMed

DNA substrate length and surrounding sequence affect the activation-induced deaminase activity at cytidine. J Biol Chem. 2004 Feb 20; 279(8):6496-500. View in: PubMed

Kinetic analysis of the nicking and hairpin formation steps in V(D)J recombination. DNA Repair (Amst). 2004 Jan 5; 3(1):67-75. View in: PubMed

Ageing, repetitive genomes and DNA damage. Nat Rev Mol Cell Biol. 2004 Jan; 5(1):69-75. View in: PubMed

Developmental retinal apoptosis in Ku86-/- mice. DNA Repair (Amst). 2003 Dec 9; 2(12):1429-34. View in: PubMed

Nucleic acid structures and enzymes in the immunoglobulin class switch recombination mechanism. DNA Repair (Amst). 2003 Nov 21; 2(11):1163-74. View in: PubMed

Human severe combined immune deficiency and DNA repair. Bioessays. 2003 Nov; 25(11):1061-70. View in: PubMed

Mechanism and regulation of human non-homologous DNA end-joining. Nat Rev Mol Cell Biol. 2003 Sep; 4(9):712-20. View in: PubMed

R-loops at immunoglobulin class switch regions in the chromosomes of stimulated B cells. Nat Immunol. 2003 May; 4(5):442-51. View in: PubMed

Impact of DNA ligase IV on the fidelity of end joining in human cells. Nucleic Acids Res. 2003 Apr 15; 31(8):2157-67. View in: PubMed

Overexpression of Cu/Zn superoxide dismutase is lethal for mice lacking double-strand break repair. DNA Repair (Amst). 2003 Mar 1; 2(3):285-94. View in: PubMed

The DNA methyltransferase-like protein DNMT3L stimulates de novo methylation by Dnmt3a. Proc Natl Acad Sci U S A. 2002 Dec 24; 99(26):16916-21. View in: PubMed

The embryonic lethality in DNA ligase IV-deficient mice is rescued by deletion of Ku: implications for unifying the heterogeneous phenotypes of NHEJ mutants. DNA Repair (Amst). 2002 Dec 5; 1(12):1017-26. View in: PubMed

Prevalent involvement of illegitimate V(D)J recombination in chromosome 9p21 deletions in lymphoid leukemia. J Biol Chem. 2002 Nov 29; 277(48):46289-97. View in: PubMed

Bidirectional gene organization: a common architectural feature of the human genome. Cell. 2002 Jun 28; 109(7):807-9. View in: PubMed

Binding of inositol hexakisphosphate (IP6) to Ku but not to DNA-PKcs. J Biol Chem. 2002 Mar 29; 277(13):10756-9. View in: PubMed

Hairpin opening and overhang processing by an Artemis/DNA-dependent protein kinase complex in nonhomologous end joining and V(D)J recombination. Cell. 2002 Mar 22; 108(6):781-94. View in: PubMed

Oxygen metabolism causes chromosome breaks and is associated with the neuronal apoptosis observed in DNA double-strand break repair mutants. Curr Biol. 2002 Mar 5; 12(5):397-402. View in: PubMed

The cleavage efficiency of the human immunoglobulin heavy chain VH elements by the RAG complex: implications for the immune repertoire. J Biol Chem. 2002 Feb 15; 277(7):5040-6. View in: PubMed

Analysis of the kinetic and equilibrium binding of Ku protein to DNA. J Theor Biol. 2002 Jan 7; 214(1):85-97. View in: PubMed

Two overlapping divergent transcription units in the human genome: the FEN1/C11orf10 locus. OMICS. 2002; 6(3):273-9. View in: PubMed

Antibody diversity: a link between switching and hypermutation. Curr Biol. 2000 Nov 2; 10(21):R798-800. View in: PubMed

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