About

Richard Kolodner is a Professor of Cellular and Molecular Medicine at UC San Diego. His laboratory studies the genetic and biochemical mechanisms of genetic recombination, DNA repair, and suppression of spontaneous mutations, primarily using Saccharomyces cerevisiae as a model system. His research focuses on analyzing the proteins and genes involved in DNA mismatch repair and elucidating pathways that prevent translocations and other types of gross chromosomal rearrangements. Additionally, he investigates the genetics of cancer susceptibility and development, particularly in relation to Lynch Syndrome, a common cancer susceptibility syndrome caused by inherited defects in DNA mismatch repair genes. His work aims to understand whether genes that prevent genome instability act as tumor suppressors in humans and whether defects in these genes can be targeted therapeutically.

Research topics

• Biology
• Cancer research
• Genetics
• Molecular biology

Selected publications

• Abstract 5690: Mechanisms of efficacy of endonuclease FEN1 inhibition in neuroblastoma

  Cancer Research · 2026-04-03

  article

  Abstract Background: Children with high-risk and relapsed neuroblastoma (NB) need improved therapies, and recurrent cytogenetic abnormalities, such as MYCN oncogene amplification, represent candidate therapeutic targets. MYCN amplification and increased MYCN expression drive deregulated hyper-transcription that leads to development and growth of NB tumors, and MYCN amplifications, which can be found both within the linear genome (HSR) and on circular extrachromosomal DNA (ecDNA), are associated with significantly worse survival rates for children with NB. MYCN overexpression has been linked to an increase in replication stress (RS), and RS and subsequent genome instability are important drivers of tumor initiation and progression. Flap Endonuclease 1 (FEN1), a non-essential DNA replication enzyme, was identified as a synthetic lethal target in BRCA1/2-deficient cancers via induction of RS. Recent success of targeting RS-elevated cancers with replication enzyme inhibitors opens a new avenue to target MYCN-amplified NB. Methods: The efficacy of FEN1 inhibition was assessed using live cell imaging and cell viability assays, comparing results in MYCN-amplified to -nonamplified NB cells and in NB cells with inducible MYCN expression and repression. Mechanisms of cell death and impacts on replication stress in cells treated with FEN1 inhibitors were evaluated by Western blots. Results: FEN1 inhibition was effective against NB cells and was significantly more effective in MYCN-amplified NB cells causing reduced cell growth and viability. Increased MYCN expression also led to increased sensitivity to FEN1 inhibition, and reduced MYCN expression reduced sensitivity. FEN1 inhibition led to the induction of apoptosis and responses to FEN1 inhibition were associated with markers of replication stress. Conclusions: We have discovered that MYCN-amplified NB cells are hypersensitive to FEN1 inhibition, suggesting that FEN1 inhibition may be a promising therapeutic strategy for children with high-risk and relapsed neuroblastoma. Citation Format: Carla S. Sampaio, Eric Wu, Madison Cinelli, Erica Steen, Andrew Shiau, Richard Kolodner, Jean Wang, Peter E. Zage. Mechanisms of efficacy of endonuclease FEN1 inhibition in neuroblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 5690.

  PublisherDOI

• DNA mismatch repair mediated by Mlh1-Pms1 endonuclease-catalyzed mispair excision.

  UNC Libraries · 2026-01-09

  articleOpen accessSenior author

  Eukaryotic DNA mismatch repair (MMR) involves several excision pathways, including those mediated by exonuclease 1 (Exo1) and by the flap endonuclease Rad27 (human FEN1) coupled with DNA polymerase &delta;. Simultaneous inactivation of both excision mechanisms causes an MMR defect that is at most 5 to 13% of that caused by complete inactivation of MMR. Here, we reconstituted nicked-strand-specific MMR with the <em><em>Saccharomyces cerevisiae</em></em> proteins Msh2-Msh6 or Msh2-Msh3, DNA polymerase &epsilon;, RFC, PCNA, RPA, and Mlh1-Pms1 (human Mlh1-Pms2) under conditions lacking Exo1, Rad27, or strand-displacement synthesis by DNA polymerase &delta;. These reactions required the Mlh1-Pms1 endonuclease activity, its activation by RFC and PCNA, and its recruitment by Msh2-Msh6 or Msh2-Msh3. MMR was mediated by nicked-strand-specific excision by Mlh1-Pms1 through formation of single-strand DNA gaps having a broad range of sizes. This reaction is consistent with genetic data demonstrating redundancy between the Exo1, Rad27, and Mlh1-Pms1 excision pathways in MMR.

  PublisherDOI

• Mechanisms of efficacy of endonuclease inhibition in neuroblastoma.

  Journal of Clinical Oncology · 2025-05-28

  article

  e15108 Background: Children with high-risk and relapsed neuroblastoma (NB) need improved therapies, and recurrent cytogenetic abnormalities, such as MYCN oncogene amplification, represent candidate therapeutic targets. MYCN amplification and increased MYCN expression drive deregulated hyper-transcription that leads to development and growth of NB tumors, and MYCN amplifications, which can be found both within the linear genome (HSR) and on circular extrachromosomal DNA (ecDNA), are associated with significantly worse survival rates for children with NB. MYCN overexpression has been linked to an increase in replication stress (RS), and RS and subsequent genome instability are important drivers of tumor initiation and progression. Flap Endonuclease 1 (FEN1), a non-essential DNA replication enzyme, was identified as a synthetic lethal target in BRCA1 / 2 -deficient cancers via induction of RS. Recent success of targeting RS-elevated cancers with replication enzyme inhibitors opens a new avenue to target MYCN -amplified NB. Methods: Associations of gene expression with patient survival and prognostic features were performed on available neuroblastoma tumor databases using the R2 Genomics Analysis and Visualization Platform. The efficacy of FEN1 inhibition was assessed using live cell imaging and cell viability assays, comparing results in MYCN -amplified to -nonamplified NB cells and in NB cells with inducible MYCN expression and repression. Mechanisms of cell death and impacts on replication stress in cells treated with FEN1 inhibitors were evaluated by Western blots. Results: We have found that FEN1 expression levels are associated wtih NB patient outcomes and with features of high-risk disease, including tumor stage and MYCN amplification. FEN1 inhibition was effective against NB cells and was significantly more effective in MYCN -amplified NB cells causing reduced cell growth and viability. Increased MYCN expression also led to increased sensitivity to FEN1 inhibition, and reduced MYCN expression reduced sensitivity. FEN1 inhibition led to the induction of apoptosis but not necroptosis in NB cells and responses to FEN1 inhibition were associated with markers of replication stress, including activation of the ATR-CHK1 and ATM-CHK2 pathways. Conclusions: We have discovered that MYCN -amplified NB cells are hypersensitive to FEN1 inhibition, suggesting that FEN1 inhibition may be a promising therapeutic strategy for children with high-risk and relapsed neuroblastoma.

  PublisherDOI

• DNA mismatch repair mediated by Mlh1–Pms1 endonuclease-catalyzed mispair excision

  Proceedings of the National Academy of Sciences · 2025-12-24

  articleOpen accessSenior authorCorresponding

  Eukaryotic DNA mismatch repair (MMR) involves several excision pathways, including those mediated by exonuclease 1 (Exo1) and by the flap endonuclease Rad27 (human FEN1) coupled with DNA polymerase δ. Simultaneous inactivation of both excision mechanisms causes an MMR defect that is at most 5 to 13% of that caused by complete inactivation of MMR. Here, we reconstituted nicked-strand-specific MMR with the Saccharomyces cerevisiae proteins Msh2-Msh6 or Msh2-Msh3, DNA polymerase ε, RFC, PCNA, RPA, and Mlh1-Pms1 (human Mlh1-Pms2) under conditions lacking Exo1, Rad27, or strand-displacement synthesis by DNA polymerase δ. These reactions required the Mlh1-Pms1 endonuclease activity, its activation by RFC and PCNA, and its recruitment by Msh2-Msh6 or Msh2-Msh3. MMR was mediated by nicked-strand-specific excision by Mlh1-Pms1 through formation of single-strand DNA gaps having a broad range of sizes. This reaction is consistent with genetic data demonstrating redundancy between the Exo1, Rad27, and Mlh1-Pms1 excision pathways in MMR.

  PublisherOA PDFDOI

• Identification of different classes of genome instability suppressor genes through analysis of DNA damage response markers

  G3 Genes Genomes Genetics · 2024-03-25 · 3 citations

  articleOpen access

  Cellular pathways that detect DNA damage are useful for identifying genes that suppress DNA damage, which can cause genome instability and cancer predisposition syndromes when mutated. We identified 199 high-confidence and 530 low-confidence DNA damage-suppressing (DDS) genes in Saccharomyces cerevisiae through a whole-genome screen for mutations inducing Hug1 expression, a focused screen for mutations inducing Ddc2 foci, and data from previous screens for mutations causing Rad52 foci accumulation and Rnr3 induction. We also identified 286 high-confidence and 394 low-confidence diverse genome instability-suppressing (DGIS) genes through a whole-genome screen for mutations resulting in increased gross chromosomal rearrangements and data from previous screens for mutations causing increased genome instability as assessed in a diversity of genome instability assays. Genes that suppress both pathways (DDS+ DGIS+) prevent or repair DNA replication damage and likely include genes preventing collisions between the replication and transcription machineries. DDS+ DGIS- genes, including many transcription-related genes, likely suppress damage that is normally repaired properly or prevent inappropriate signaling, whereas DDS- DGIS+ genes, like PIF1, do not suppress damage but likely promote its proper, nonmutagenic repair. Thus, induction of DNA damage markers is not a reliable indicator of increased genome instability, and the DDS and DGIS categories define mechanistically distinct groups of genes.

  PublisherOA PDFDOI

• Insights into DNA cleavage by MutL homologs from analysis of conserved motifs in eukaryotic Mlh1

  BioEssays · 2023-07-09 · 3 citations

  articleOpen accessSenior author

  MutL family proteins contain an N-terminal ATPase domain (NTD), an unstructured interdomain linker, and a C-terminal domain (CTD), which mediates constitutive dimerization between subunits and often contains an endonuclease active site. Most MutL homologs direct strand-specific DNA mismatch repair by cleaving the error-containing daughter DNA strand. The strand cleavage reaction is poorly understood; however, the structure of the endonuclease active site is consistent with a two- or three-metal ion cleavage mechanism. A motif required for this endonuclease activity is present in the unstructured linker of Mlh1 and is conserved in all eukaryotic Mlh1 proteins, except those from metamonads, which also lack the almost absolutely conserved Mlh1 C-terminal phenylalanine-glutamate-arginine-cysteine (FERC) sequence. We hypothesize that the cysteine in the FERC sequence is autoinhibitory, as it sequesters the active site. We further hypothesize that the evolutionary co-occurrence of the conserved linker motif with the FERC sequence indicates a functional interaction, possibly by linker motif-mediated displacement of the inhibitory cysteine. This role is consistent with available data for interactions between the linker motif with DNA and the CTDs in the vicinity of the active site.

  PublisherOA PDFDOI

• Identification of Different Classes of Genome Instability Suppressor Genes Through Analysis of DNA Damage Response Markers

  SSRN Electronic Journal · 2022-01-01

  articleOpen access
  PublisherDOI

• Mlh1 interacts with both Msh2 and Msh6 for recruitment during mismatch repair

  DNA repair · 2022-09-14 · 12 citations

  articleOpen access

  Eukaryotic DNA mismatch repair (MMR) initiates through mispair recognition by the MutS homologs Msh2-Msh6 and Msh2-Msh3 and subsequent recruitment of the MutL homologs Mlh1-Pms1 (human MLH1-PMS2). In bacteria, MutL is recruited by interactions with the connector domain of one MutS subunit and the ATPase and core domains of the other MutS subunit. Analysis of the S. cerevisiae and human homologs have only identified an interaction between the Msh2 connector domain and Mlh1. Here we investigated whether a conserved Msh6 ATPase/core domain-Mlh1 interaction and an Msh2-Msh6 interaction with Pms1 also act in MMR. Mutations in MLH1 affecting interactions with both the Msh2 and Msh6 interfaces caused MMR defects, whereas equivalent pms1 mutations did not cause MMR defects. Mutant Mlh1-Pms1 complexes containing Mlh1 amino acid substitutions were defective for recruitment to mispaired DNA by Msh2-Msh6, did not support MMR in reconstituted Mlh1-Pms1-dependent MMR reactions in vitro, but were proficient in Msh2-Msh6-independent Mlh1-Pms1 endonuclease activity. These results indicate that Mlh1, the common subunit of the Mlh1-Pms1, Mlh1-Mlh2, and Mlh1-Mlh3 complexes, but not Pms1, is recruited by Msh2-Msh6 through interactions with both of its subunits.

  PublisherDOI

• Rad5 and Its Human Homologs, HLTF and SHPRH, Are Novel Interactors of Mismatch Repair

  Frontiers in Cell and Developmental Biology · 2022-06-16 · 9 citations

  articleOpen access

  DNA mismatch repair (MMR) repairs replication errors, and MMR defects play a role in both inherited cancer predisposition syndromes and in sporadic cancers. MMR also recognizes mispairs caused by environmental and chemotherapeutic agents; however, in these cases mispair recognition leads to apoptosis and not repair. Although mutation avoidance by MMR is fairly well understood, MMR-associated proteins are still being identified. We performed a bioinformatic analysis that implicated Saccharomyces cerevisiae Rad5 as a candidate for interacting with the MMR proteins Msh2 and Mlh1. Rad5 is a DNA helicase and E3 ubiquitin ligase involved in post-replicative repair and damage tolerance. We confirmed both interactions and found that the Mlh1 interaction is mediated by a conserved Mlh1-interacting motif (MIP box). Despite this, we did not find a clear role for Rad5 in the canonical MMR mutation avoidance pathway. The interaction of Rad5 with Msh2 and Mlh1 is conserved in humans, although each of the Rad5 human homologs, HLTF and SHPRH, shared only one of the interactions: HLTF interacts with MSH2, and SHPRH interacts with MLH1. Moreover, depletion of SHPRH, but not HLTF, results in a mild increase in resistance to alkylating agents although not as strong as loss of MMR, suggesting gene duplication led to specialization of the MMR-protein associated roles of the human Rad5 homologs. These results provide insights into how MMR accessory factors involved in the MMR-dependent apoptotic response interact with the core MMR machinery and have important health implications into how human cells respond to environmental toxins, tumor development, and treatment choices of tumors with defects in Rad5 homologs.

  PublisherDOI

• Identification of different classes of genome instability suppressor genes through analysis of DNA damage response markers

  bioRxiv (Cold Spring Harbor Laboratory) · 2022-03-01 · 1 citations

  preprintOpen access

  ABSTRACT Genetic studies in Saccharomyces cerevisiae have identified 266 genes and predicted an additional 38 genes that suppress the accumulation of spontaneous gross chromosomal rearrangements (GCRs). Here we identified mutations that induce two DNA damage response (DDR) markers, Hug1 expression and Ddc2 foci, and combined these data with other published screens identifying mutations inducing other DDR markers, including Rad52 foci and Rnr3 expression. Together, these data identify four categories of mutations: most mutations were DDR- GCR-, 356 were DDR+ GCR-, 72 were DDR- GCR+, and 157 were DDR+ GCR+. These results indicate that induction of DDR markers alone, while allowing DDR analysis, is not a reliable indicator of increased genome instability. They also guide further analysis of mechanistically distinct groups of GCR-inducing mutations, such as mutations that increase levels of GCR-inducing DNA damage and mutations that result in mis-repair of normal levels of DNA damage resulting in GCRs.

  PublisherOA PDFDOI

Recent grants

• NIH Grant T32CA009361

  NIH · $13.0M · 2017

• NIH Grant R01HG000305

  NIH · $619k · 1994

• Enzymatic Mechanisms of Genetic Recombination

  NIH · $11.4M · 1978–2027

• NIH Grant R37GM026017

  NIH · $3.2M · 2002

• NIH Grant P01CA044704

  NIH · $5.2M · 2000

Frequent coauthors

• Bert Vogelstein

  Howard Hughes Medical Institute

  195 shared

• Christopher D. Putnam

  Ludwig Cancer Research

  193 shared

• Annika Lindblom

  Karolinska University Hospital

  175 shared

• Païvi Peltomäki

  University of Helsinki

  171 shared

• K. W. Kinzler

  Johns Hopkins University

  170 shared

• Jana Vandrovcová

  University College London

  169 shared

• T. Liu

  University of Helsinki

  169 shared

• Mef Nilbert

  Lund University

  169 shared

Education

• Ph.D., Molecular Biology

  University of California, San Diego

  1983

• M.S., Molecular Biology

  University of California, San Diego

  1979

• B.S., Biology

  University of California, San Diego

  1977