Regulation of homologous recombination in human cells

Christelle de Renty, Ph.D.
Kelvin Pond, M.S.
Mary Yagle - Lab Manager

Cells contain numerous systems that respond to DNA damage and maintain the integrity of the genome. When a component of one of these systems is mutated, either somatically or in the germline, cells accumulate mutations at an increased rate. When genomic integrity is compromised in the germline, susceptibility to cancer increases; when it is compromised in a somatic cell, carcinogenesis is empowered.

In mammalian cells, homologous recombination is a high-fidelity DNA repair pathway that maintains the stability and integrity of stressed or damaged replication forks and that is activated to repair DNA double-strand breaks when a closely apposite sister chromatid is available. Homologous recombination is carefully regulated to avoid genotoxic consequences of excess or inadequate activation. In the autosomal recessive disorder Bloom's syndrome, there is excess homologous recombination in somatic cells. The gene mutated in Bloom's syndrome is BLM. BLM is a DNA helicase of the RecQ family, and it plays multiple roles in controlling homologous recombination.

A major focus in the Ellis laboratory is to investigate how BLM regulates homologous recombination. BLM helps maintain replication fork stability during stalling events through its interaction with RPA and RAD51. BLM’s interactions with RPA and RAD51 are regulated by post-translational protein modification by SUMOs (small ubiquitin-related modifier). Unsumoylated BLM preferentially binds RPA and excludes the accumulation of RAD51 whereas sumoylated BLM promotes the recruitment and retention of RAD51 at the stalled fork. We have recently found that sumoylation of BLM is also important for normal replication dynamics of unperturbed replication forks, demonstrating for the first time the role of sumoylation is the normal replication process.

Another critical question relates to the E3 SUMO ligases that operate to sumoylate BLM and other substrates at stalled forks. We have determined that depletion of NSMCE2 reduces the amount of sumoylated BLM generated during fork stalling; however, the phenotypic effects of reduced BLM sumoylation – increased RPA and decreased RAD51 accumulation at stalled forks – were not observed. These experiments have opened an important window to understanding the regulation of homologous recombination.


1: Ouyang KJ, Yagle MK, Matunis MJ, Ellis NA. BLM SUMOylation regulates ssDNA accumulation at stalled replication forks. Front Genet. 2013 Sep 4;4:167. doi: 10.3389/fgene.2013.00167. eCollection 2013. PubMed PMID: 24027577; PubMed Central PMCID: PMC3761158.

2: Ouyang KJ, Woo LL, Zhu J, Huo D, Matunis MJ, Ellis NA. SUMO modification regulates BLM and RAD51 interaction at damaged replication forks. PLoS Biol. 2009 Dec;7(12):e1000252. doi: 10.1371/journal.pbio.1000252. Epub 2009 Dec 1. PubMed PMID: 19956565; PubMed Central PMCID: PMC2779653.

3: Zhu J, Zhu S, Guzzo CM, Ellis NA, Sung KS, Choi CY, Matunis MJ. Small ubiquitin-related modifier (SUMO) binding determines substrate recognition and paralog-selective SUMO modification. J Biol Chem. 2008 Oct 24;283(43):29405-15. doi: 10.1074/jbc.M803632200. Epub 2008 Aug 15. PubMed PMID: 18708356; PubMed Central PMCID: PMC2570875.

Genetic analysis of colorectal cancer susceptibility

Gaius Augustus, B.Sc.

Genetic risk factors play an important role in the development of colorectal cancer (CRC). Two hereditary CRC syndromes – Lynch syndrome and MYH-associated polyposis – feature defects in mismatch repair and base excision repair, respectively, demonstrating the importance of DNA repair in CRC susceptibility. Moreover, some of the environmental factors that are known to increase the risk of CRC development increase the levels of reactive oxygen species in colonic epithelial cells and cause increased DNA damage. While DNA damage and repair are clearly important, genetic factors that promote inflammatory signals and influence cell proliferation in the gut epithelium can also increase CRC risk. We are striving the understand the interplay of these diverse factors in CRC susceptibility and carcinogenesis.

Our research aims include (1) identification of clinically useful genetic risk factors that predict a person's risk of developing CRC, (2) elucidation of the genetic mechanisms by which these risk factors promote disease pathogenesis in determining CRC risk, and (3) characterization of gene x environment interactions in susceptibility and carcinogenesis by integrative analysis of the gut microbiome, inflammatory signals, and gut epithelial cell responses in the context of host diet and genetics.

Approaches to these aims include (i) performance of candidate gene and genome-wide association studies comparing CRC cases with cancer-free controls, (ii) metagenomic analysis of the gut microbiome in CRC cases and controls, (iii) exome, copy number, and transcriptomic analyses of CRCs, and (iv) analysis of inflammatory markers in epithelial and cancer tissues. We have established a multi-institutional collaboration to ascertain large numbers of CRC cases and healthy controls, including many African American (AA) patients. This study began with a patient base in Chicago and we are expanding our reach to other parts of the US, including Arizona and Connecticut. Because the AA population is enormously more diverse genetically than populations derived from Europe, we have conducted comparative studies to identify novel genetic risk factors and to better refine the map location of shared risk factors. Finally, our work with AA CRC patients also examines population-specific factors in CRC incidence and we hope these analyses will shed light on biological components underlying health disparities in this population.


1: Hulur I, Gamazon ER, Skol AD, Xicola RM, Llor X, Onel K, Ellis NA, Kupfer SS. Enrichment of inflammatory bowel disease and colorectal cancer risk variants in colon expression quantitative trait loci. BMC Genomics. 2015 Feb 27;16:138. doi: 10.1186/s12864-015-1292-z. PubMed PMID: 25766683; PubMed Central PMCID: PMC4351699.

2: Grimm WA, Messer JS, Murphy SF, Nero T, Lodolce JP, Weber CR, Logsdon MF, Bartulis S, Sylvester BE, Springer A, Dougherty U, Niewold TB, Kupfer SS, Ellis N, Huo D, Bissonnette M, Boone DL. The Thr300Ala variant in ATG16L1 is associated with improved survival in human colorectal cancer and enhanced production of type I interferon. Gut. 2015 Feb 2. pii: gutjnl-2014-308735. doi: 10.1136/gutjnl-2014-308735. [Epub ahead of print] PubMed PMID: 25645662.

3: Xicola RM, Gagnon M, Clark JR, Carroll T, Gao W, Fernandez C, Mijic D, Rawson JB, Janoski A, Pusatcioglu CK, Rajaram P, Gluskin AB, Regan M, Chaudhry V, Abcarian H, Blumetti J, Cintron J, Melson J, Xie H, Guzman G, Emmadi R, Alagiozian-Angelova V, Kupfer SS, Braunschweig C, Ellis NA, Llor X. Excess of proximal microsatellite-stable colorectal cancer in African Americans from a multiethnic study. Clin Cancer Res. 2014 Sep 15;20(18):4962-70. doi: 10.1158/1078-0432.CCR-14-0353. Epub 2014 Jul 10. PubMed PMID: 25013126; PubMed Central PMCID: PMC4167473.

4: Kupfer SS, Skol AD, Hong E, Ludvik A, Kittles RA, Keku TO, Sandler RS, Ellis NA. Shared and independent colorectal cancer risk alleles in TGFβ-related genes in African and European Americans. Carcinogenesis. 2014 Sep;35(9):2025-30. doi: 10.1093/carcin/bgu088. Epub 2014 Apr 21. PubMed PMID: 24753543; PubMed Central PMCID: PMC4146413.

5: Tuupanen S, Yan J, Turunen M, Gylfe AE, Kaasinen E, Li L, Eng C, Culver DA, Kalady MF, Pennison MJ, Pasche B, Manne U, de la Chapelle A, Hampel H, Henderson BE, Le Marchand L, Hautaniemi S, Askhtorab H, Smoot D, Sandler RS, Keku T, Kupfer SS, Ellis NA, Haiman CA, Taipale J, Aaltonen LA. Characterization of the colorectal cancer-associated enhancer MYC-335 at 8q24: the role of rs67491583. Cancer Genet. 2012 Jan-Feb;205(1-2):25-33. doi: 10.1016/j.cancergen.2012.01.005. PubMed PMID: 22429595; PubMed Central PMCID: PMC3770308.

6: Ellis NA, Offit K. Heterozygous mutations in DNA repair genes and hereditary breast cancer: a question of power. PLoS Genet. 2012 Sep;8(9):e1003008. doi: 10.1371/journal.pgen.1003008. Epub 2012 Sep 27. PubMed PMID: 23028381; PubMed Central PMCID: PMC3459983.

7: Theodoratou E, Campbell H, Tenesa A, Houlston R, Webb E, Lubbe S, Broderick P, Gallinger S, Croitoru EM, Jenkins MA, Win AK, Cleary SP, Koessler T, Pharoah PD, Küry S, Bézieau S, Buecher B, Ellis NA, Peterlongo P, Offit K, Aaltonen LA, Enholm S, Lindblom A, Zhou XL, Tomlinson IP, Moreno V, Blanco I, Capellà G, Barnetson R, Porteous ME, Dunlop MG, Farrington SM. A large-scale meta-analysis to refine colorectal cancer risk estimates associated with MUTYH variants. Br J Cancer. 2010 Dec 7;103(12):1875-84. doi: 10.1038/sj.bjc.6605966. Epub 2010 Nov 9. PubMed PMID: 21063410; PubMed Central PMCID: PMC3008602.

Genetic analysis of the vitamin D genes in AA CRC

There is a sizeable disparity in colorectal cancer (CRC) incidence and mortality between African Americans (AAs) and all other US racial groups. Differences in serum vitamin D levels could contribute to this disparity because vitamin D is thought to protect against CRC incidence, and AAs have lower serum vitamin D levels than other Americans. Single nucleotide polymorphisms (SNPs) in genes in the pathway that produce, deliver to cells, and degrade vitamin D (vitamin D pathway genes) have been previously associated with CRC. Because the enzymes of the vitamin D pathway play a critical role in controlling serum vitamin D levels, we have studied how SNPs in vitamin D pathway genes contribute to CRC risk, and whether or not they modify the association between serum vitamin D levels and CRC risk.


1: Pibiri F, Kittles RA, Sandler RS, Keku TO, Kupfer SS, Xicola RM, Llor X, Ellis NA. Genetic variation in vitamin D-related genes and risk of colorectal cancer in African Americans. Cancer Causes Control. 2014 May;25(5):561-70. doi: 10.1007/s10552-014-0361-y. Epub 2014 Feb 23. PubMed PMID: 24562971; PubMed Central PMCID: PMC3978221.

2: Kupfer SS, Anderson JR, Ludvik AE, Hooker S, Skol A, Kittles RA, Keku TO, Sandler RS, Ruiz-Ponte C, Castellvi-Bel S, Castells A, Carracedo A, Ellis NA. Genetic associations in the vitamin D receptor and colorectal cancer in African Americans and Caucasians. PLoS One. 2011;6(10):e26123. doi: 10.1371/journal.pone.0026123. Epub 2011 Oct 27. PubMed PMID: 22046258; PubMed Central PMCID: PMC3203108.