1
|
Towler WI, Zhang J, Ransburgh DJR, Toland AE, Ishioka C, Chiba N, Parvin JD. Analysis of BRCA1 variants in double-strand break repair by homologous recombination and single-strand annealing. Hum Mutat 2012; 34:439-45. [PMID: 23161852 DOI: 10.1002/humu.22251] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/24/2012] [Indexed: 01/13/2023]
Abstract
Missense substitutions of uncertain clinical significance in the BRCA1 gene are a vexing problem in genetic counseling for women who have a family history of breast cancer. In this study, we evaluated the functions of 29 missense substitutions of BRCA1 in two DNA repair pathways. Repair of double-strand breaks by homology-directed recombination (HDR) had been previously analyzed for 16 of these BRCA1 variants, and 13 more variants were analyzed in this study. All 29 variants were also analyzed for function in double-strand break repair by the single-strand annealing (SSA) pathway. We found that among the pathogenic mutations in BRCA1, all were defective for DNA repair by either pathway. The HDR assay was accurate because all pathogenic mutants were defective for HDR, and all nonpathogenic variants were fully functional for HDR. Repair by SSA accurately identified pathogenic mutants, but several nonpathogenic variants were scored as defective or partially defective. These results indicated that specific amino acid residues of the BRCA1 protein have different effects in the two related DNA repair pathways, and these results validate the HDR assay as highly correlative with BRCA1-associated breast cancer.
Collapse
Affiliation(s)
- William I Towler
- Department of Biomedical Informatics and the Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA
| | | | | | | | | | | | | |
Collapse
|
2
|
Cousins MM, Laeyendecker O, Beauchamp G, Brookmeyer R, Towler WI, Hudelson SE, Khaki L, Koblin B, Chesney M, Moore RD, Kelen GD, Coates T, Celum C, Buchbinder SP, Seage GR, Quinn TC, Donnell D, Eshleman SH. Use of a high resolution melting (HRM) assay to compare gag, pol, and env diversity in adults with different stages of HIV infection. PLoS One 2011; 6:e27211. [PMID: 22073290 PMCID: PMC3206918 DOI: 10.1371/journal.pone.0027211] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 10/11/2011] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Cross-sectional assessment of HIV incidence relies on laboratory methods to discriminate between recent and non-recent HIV infection. Because HIV diversifies over time in infected individuals, HIV diversity may serve as a biomarker for assessing HIV incidence. We used a high resolution melting (HRM) diversity assay to compare HIV diversity in adults with different stages of HIV infection. This assay provides a single numeric HRM score that reflects the level of genetic diversity of HIV in a sample from an infected individual. METHODS HIV diversity was measured in 203 adults: 20 with acute HIV infection (RNA positive, antibody negative), 116 with recent HIV infection (tested a median of 189 days after a previous negative HIV test, range 14-540 days), and 67 with non-recent HIV infection (HIV infected >2 years). HRM scores were generated for two regions in gag, one region in pol, and three regions in env. RESULTS Median HRM scores were higher in non-recent infection than in recent infection for all six regions tested. In multivariate models, higher HRM scores in three of the six regions were independently associated with non-recent HIV infection. CONCLUSIONS The HRM diversity assay provides a simple, scalable method for measuring HIV diversity. HRM scores, which reflect the genetic diversity in a viral population, may be useful biomarkers for evaluation of HIV incidence, particularly if multiple regions of the HIV genome are examined.
Collapse
Affiliation(s)
- Matthew M. Cousins
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Oliver Laeyendecker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Geetha Beauchamp
- Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Ronald Brookmeyer
- Department of Biostatistics, University of California Los Angeles, Los Angeles, California, United States of America
| | - William I. Towler
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Sarah E. Hudelson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Leila Khaki
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Beryl Koblin
- Laboratory of Infectious Disease Prevention, New York Blood Center, New York, New York, United States of America
| | - Margaret Chesney
- University of California San Francisco, San Francisco, California, United States of America
| | - Richard D. Moore
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Gabor D. Kelen
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Thomas Coates
- Program in Global Health, University of California Los Angeles, Los Angeles, California, United States of America
| | - Connie Celum
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Susan P. Buchbinder
- University of California San Francisco, San Francisco, California, United States of America
- San Francisco Department of Public Health, San Francisco, California, United States of America
| | - George R. Seage
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Thomas C. Quinn
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Deborah Donnell
- Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Susan H. Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| |
Collapse
|
3
|
James MM, Wang L, Musoke P, Donnell D, Fogel J, Towler WI, Khaki L, Nakabiito C, Jackson JB, Eshleman SH. Association of HIV diversity and survival in HIV-infected Ugandan infants. PLoS One 2011; 6:e18642. [PMID: 21533179 PMCID: PMC3077388 DOI: 10.1371/journal.pone.0018642] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 03/13/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The level of viral diversity in an HIV-infected individual can change during the course of HIV infection, reflecting mutagenesis during viral replication and selection of viral variants by immune and other selective pressures. Differences in the level of viral diversity in HIV-infected infants may reflect differences in viral dynamics, immune responses, or other factors that may also influence HIV disease progression. We used a novel high resolution melting (HRM) assay to measure HIV diversity in Ugandan infants and examined the relationship between diversity and survival through 5 years of age. METHODS Plasma samples were obtained from 31 HIV-infected infants (HIVNET 012 trial). The HRM assay was used to measure diversity in two regions in the gag gene (Gag1 and Gag2) and one region in the pol gene (Pol). RESULTS HRM scores in all three regions increased with age from 6-8 weeks to 12-18 months (for Gag1: P = 0.005; for Gag2: P = 0.006; for Pol: P = 0.016). Higher HRM scores at 6-8 weeks of age (scores above the 75(th) percentile) were associated with an increased risk of death by 5 years of age (for Pol: P = 0.005; for Gag1/Gag2 (mean of two scores): P = 0.003; for Gag1/Gag2/Pol (mean of three scores): P = 0.002). We did not find an association between HRM scores and other clinical and laboratory variables. CONCLUSIONS Genetic diversity in HIV gag and pol measured using the HRM assay was typically low near birth and increased over time. Higher HIV diversity in these regions at 6-8 weeks of age was associated with a significantly increased risk of death by 5 years of age.
Collapse
Affiliation(s)
- Maria M. James
- Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Lei Wang
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Philippa Musoke
- Makerere University-Johns Hopkins University Research Collaboration (MU-JHU), Baltimore, Maryland, United States of America, and Kampala, Uganda
- Makerere University School of Medicine, Kampala, Uganda
| | - Deborah Donnell
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jessica Fogel
- Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - William I. Towler
- Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Leila Khaki
- Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Clemensia Nakabiito
- Makerere University-Johns Hopkins University Research Collaboration (MU-JHU), Baltimore, Maryland, United States of America, and Kampala, Uganda
- Makerere University School of Medicine, Kampala, Uganda
| | - J. Brooks Jackson
- Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Susan H. Eshleman
- Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| |
Collapse
|
4
|
Towler WI, James MM, Ray SC, Wang L, Donnell D, Mwatha A, Guay L, Nakabiito C, Musoke P, Jackson JB, Eshleman S. Analysis of HIV diversity using a high-resolution melting assay. AIDS Res Hum Retroviruses 2010; 26:913-8. [PMID: 20666583 DOI: 10.1089/aid.2009.0259] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV viruses are usually genetically homogeneous shortly after infection, and become more heterogeneous over time. We developed a high-resolution melting (HRM) assay to analyze HIV diversity without sequencing. Plasma samples from the HIVNET 012 trial were obtained from nine Ugandan mother-infant pairs. DNA amplified from the HIV gag region was analyzed to determine the number of degrees over which the DNA melted (HRM score). HRM gag DNA was also cloned and sequenced (50 clones/mother; 20 clones/infant). The median HRM score for infants (4.3, range 4.2-5.3) was higher than that for control plasmids (3.4, range 3.2-3.8, p < 0.001) and lower than that for mothers (5.7, range 4.4-7.7, p = 0.005, exact Wilcoxon rank sum test). The intraclass correlation coefficient reflecting assay reproducibility was 94% (95% CI: 89-98%). HRM scores were also compared to sequenced-based measures of HIV diversity; higher HRM scores were associated with higher genetic diversity (p < 0.001), complexity (p = 0.009), and Shannon entropy (p = 0.022), but not with length variation (p = 0.111). The HRM assay provides a novel, rapid method for assessing HIV diversity without sequencing. This assay could be applied to any region of the HIV genome or to other genetic systems that exhibit DNA diversity.
Collapse
Affiliation(s)
| | - Maria M. James
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Stuart C. Ray
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lei Wang
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - Anthony Mwatha
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Laura Guay
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Clemensia Nakabiito
- Makerere University–Johns Hopkins University (MUJHU) Research Collaboration, Kampala, Uganda
| | - Philippa Musoke
- Makerere University–Johns Hopkins University (MUJHU) Research Collaboration, Kampala, Uganda
- Makerere University School of Medicine, Kampala, Uganda
| | | | - Susan Eshleman
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| |
Collapse
|
5
|
Towler WI, Barlow-Mosha L, Church JD, Bagenda D, Ajuna P, Mubiru M, Musoke P, Eshleman SH. Analysis of drug resistance in children receiving antiretroviral therapy for treatment of HIV-1 infection in Uganda. AIDS Res Hum Retroviruses 2010; 26:563-8. [PMID: 20455758 DOI: 10.1089/aid.2009.0164] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We analyzed drug resistance in HIV-infected Ugandan children who received antiretroviral therapy in a prospective, observational study (2004-2006); some children had prior single-dose nevirapine (sdNVP) exposure. Children received stavudine (d4T), lamivudine (3TC), and nevirapine (NVP); treatment was continued if they were clinically and immunologically stable. Samples with >1,000 copies/ml HIV RNA were analyzed by using the ViroSeq HIV Genotyping System (ViroSeq). Subtype A and D pretreatment samples also were analyzed with the LigAmp assay (for K103N, Y181C, and G190A). ViroSeq results were obtained for 74 pretreatment samples (35 from sdNVP-exposed children (median age, 19 months) and 39 from sdNVP-unexposed children (median age, 84 months). This included 39 subtype A, 22 subtype D, 1 subtype C, and 12 inter-subtype recombinant samples. One sample had nonnucleoside reverse transcriptase inhibitor (NNRTI) resistance, one had nucleoside reverse transcriptase inhibitor (NRTI) resistance, and three had protease inhibitor (PI) resistance. Y181C was detected by using LigAmp in five pretreatment samples [four (14.8%) of 37 samples from sdNVP-exposed children, one (4.2%) of 24 samples from children without prior sdNVP exposure; p = 0.35]. Among children who were not virally suppressed at 48 weeks of treatment, all 12 tested had NNRTI resistance, as well as resistance to 3TC and emtricitibine (FTC); three had resistance to other NRTIs. Seven of those children had a ViroSeq result at 96 weeks of treatment; four of the seven acquired resistance to additional NRTIs by 96 weeks. In Uganda, clinically and immunologically stable children receiving nonsuppressive antiretroviral treatment regimens are at risk for development of drug resistance.
Collapse
Affiliation(s)
- William I. Towler
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Linda Barlow-Mosha
- Makerere University-Johns Hopkins University Research Collaboration (MU-JHU), Baltimore, Maryland and Kampala, Uganda
| | - Jessica D. Church
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Danstan Bagenda
- Makerere University-Johns Hopkins University Research Collaboration (MU-JHU), Baltimore, Maryland and Kampala, Uganda
- Makerere University School of Public Health, Kampala, Uganda
| | - Patrick Ajuna
- Makerere University-Johns Hopkins University Research Collaboration (MU-JHU), Baltimore, Maryland and Kampala, Uganda
| | - Micheal Mubiru
- Makerere University-Johns Hopkins University Research Collaboration (MU-JHU), Baltimore, Maryland and Kampala, Uganda
| | - Philippa Musoke
- Makerere University-Johns Hopkins University Research Collaboration (MU-JHU), Baltimore, Maryland and Kampala, Uganda
- Department of Paediatrics, Makerere University, Mulago, Kampala, Uganda
| | - Susan H. Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| |
Collapse
|
6
|
Church JD, Towler WI, Hoover DR, Hudelson SE, Kumwenda N, Taha TE, Eshleman JR, Eshleman SH. Comparison of LigAmp and an ASPCR assay for detection and quantification of K103N-containing HIV variants. AIDS Res Hum Retroviruses 2008; 24:595-605. [PMID: 18370589 DOI: 10.1089/aid.2007.0224] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We compared the ability of the LigAmp assay and an ASPCR assay to detect and quantify K103N-containing HIV variants in samples from 63 women who received single-dose nevirapine in a clinical trial. Samples were first analyzed with the ViroSeq HIV Genotyping system, and ViroSeq PCR products were used as templates for the LigAmp and ASPCR assays. A cutoff of 0.5% K103N for detection of K103N was used for both assays. Results for the percentage K103N were similar for the two assays (R(2) = 0.92). Forty-six samples (73.0%) were positive for K103N by both assays and 13 samples (20.6%) were negative by both assays. Four samples (6.3%) were positive by ASPCR only. No samples were positive by LigAmp only. Eight discordant samples were analyzed in more detail. Sequence polymorphisms near oligonucleotide binding sites provided a possible explanation for the discordance in four of eight samples. The percentage K103N was also determined by analyzing 40 HIV clones from each of these eight samples, using a combined amplification/sequencing method (AmpliSeq). The percentage K103N determined by clonal analysis was consistent with the LigAmp result for five of eight samples, and was consistent with the ASPCR result for three of eight samples. Among 320 clones analyzed, we identified eight different codons at position 103 (mean = 3.8 codons/sample), which encoded six different amino acids, illustrating the extensive genetic diversity in HIV. Further studies are needed to compare performance of assays for detection and quantification of HIV drug resistance mutations in clinical samples.
Collapse
Affiliation(s)
| | | | | | | | | | - Taha E. Taha
- Johns Hopkins University, Baltimore, Maryland 21205
| | | | | |
Collapse
|
7
|
Peles JD, Towler WI, Guttman SI. Population genetic structure of earthworms (Lumbricus rubellus) in soils contaminated by heavy metals. Ecotoxicology 2003; 12:379-386. [PMID: 14649420 DOI: 10.1023/a:1026269804938] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The genetic structure of earthworm (Lumbricus rubellus) populations from plots (N = 3) contaminated by sewage sludge (containing Cd, Cu, Pb, Zn) and reference plots (N = 3) was compared. Earthworms (N = 30-40 per plot) were collected during May 2000 and electrophoretic analyses were used to assess genetic variation at three polymorphic loci (GPI, LAP, PGM). Allele and genotype frequencies for GPI and PGM differed significantly between sludge and reference populations. Sludge populations were characterized by a reduced frequency of the most common genotype and allele at these loci, and the presence of alleles not found in the reference population. Allele and genotype frequencies did not differ significantly among individual plots within the sludge or the reference population. These results suggest that certain alleles and genotypes may be more sensitive to the effects of heavy metals. Multi-locus heterozygosity was significantly higher in the sludge population compared to the reference population; the proportion of individuals heterozygous at two or more loci was more than 15% higher in the sludge population. Results demonstrate that measures of population genetic structure in earthworms may represent useful biological indicators for the assessment of impacted terrestrial habitats.
Collapse
Affiliation(s)
- John D Peles
- Pennsylvania State University McKeesport, 4000 University Drive, McKeesport, PA 15132, USA.
| | | | | |
Collapse
|