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Soh PXY, Mmekwa N, Petersen DC, Gheybi K, van Zyl S, Jiang J, Patrick SM, Campbell R, Jaratlerdseri W, Mutambirwa SBA, Bornman MSR, Hayes VM. Prostate cancer genetic risk and associated aggressive disease in men of African ancestry. Nat Commun 2023; 14:8037. [PMID: 38052806 PMCID: PMC10697980 DOI: 10.1038/s41467-023-43726-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 11/17/2023] [Indexed: 12/07/2023] Open
Abstract
African ancestry is a significant risk factor for prostate cancer and advanced disease. Yet, genetic studies have largely been conducted outside the context of Sub-Saharan Africa, identifying 278 common risk variants contributing to a multiethnic polygenic risk score, with rare variants focused on a panel of roughly 20 pathogenic genes. Based on this knowledge, we are unable to determine polygenic risk or differentiate prostate cancer status interrogating whole genome data for 113 Black South African men. To further assess for potentially functional common and rare variant associations, here we interrogate 247,780 exomic variants for 798 Black South African men using a case versus control or aggressive versus non-aggressive study design. Notable genes of interest include HCP5, RFX6 and H3C1 for risk, and MKI67 and KLF5 for aggressive disease. Our study highlights the need for further inclusion across the African diaspora to establish African-relevant risk models aimed at reducing prostate cancer health disparities.
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Affiliation(s)
- Pamela X Y Soh
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Naledi Mmekwa
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Desiree C Petersen
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Kazzem Gheybi
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Smit van Zyl
- Faculty of Health Sciences, University of Limpopo, Turfloop Campus, South Africa
| | - Jue Jiang
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Sean M Patrick
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | | | - Weerachai Jaratlerdseri
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Shingai B A Mutambirwa
- Department of Urology, Sefako Makgatho Health Science University, Dr George Mukhari Academic Hospital, Medunsa, South Africa
| | - M S Riana Bornman
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Vanessa M Hayes
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia.
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa.
- Faculty of Health Sciences, University of Limpopo, Turfloop Campus, South Africa.
- Manchester Cancer Research Centre, University of Manchester, Manchester, M20 4GJ, UK.
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Gheybi K, Mmekwa N, Lebelo MT, Patrick SM, Campbell R, Nenzhelele M, Soh PXY, Obida M, Loda M, Shirindi J, Butler EN, Mutambirwa SBA, Bornman MSR, Hayes VM. Linking African ancestral substructure to prostate cancer health disparities. Sci Rep 2023; 13:20909. [PMID: 38017150 PMCID: PMC10684577 DOI: 10.1038/s41598-023-47993-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/21/2023] [Indexed: 11/30/2023] Open
Abstract
Prostate cancer (PCa) is a significant health burden in Sub-Saharan Africa, with mortality rates loosely linked to African ancestry. Yet studies aimed at identifying contributing risk factors are lacking within the continent and as such exclude for significant ancestral diversity. Here, we investigate a series of epidemiological demographic and lifestyle risk factors for 1387 men recruited as part of the multi-ethnic Southern African Prostate Cancer Study (SAPCS). We found poverty to be a decisive factor for disease grade and age at diagnosis, with other notably significant PCa associated risk factors including sexually transmitted diseases, erectile dysfunction, gynaecomastia, and vertex or complete pattern balding. Aligned with African American data, Black ethnicity showed significant risk for PCa diagnosis (OR = 1.44, 95% CI 1.05-2.00), and aggressive disease presentation (ISUP ≥ 4: OR = 2.25, 95% CI 1.49-3.40). New to this study, we demonstrate African ancestral population substructure associated PCa disparity, observing increased risk for advanced disease for the southern African Tsonga people (ISUP ≥ 4: OR = 3.43, 95% CI 1.62-7.27). Conversely, South African Coloured were less likely to be diagnosed with aggressive disease overall (ISUP ≥ 3: OR = 0.38, 95% 0.17-0.85). Understanding the basis for PCa health disparities calls for African inclusion, however, lack of available data has limited the power to begin discussions. Here, focusing on arguably the largest study of its kind for the African continent, we draw attention to the contribution of within African ancestral diversity as a contributing factor to PCa health disparities within the genetically diverse region of southern Africa.
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Affiliation(s)
- Kazzem Gheybi
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Naledi Mmekwa
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Maphuti Tebogo Lebelo
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Sean M Patrick
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | | | | | - Pamela X Y Soh
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Muvhulawa Obida
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weil Cornell Medicine, New York Presbyterian-Weill Cornell Campus, New York, NY, USA
| | - Joyce Shirindi
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Eboneé N Butler
- Department of Epidemiology, University of North Carolina at Chapel Hill, Gillings School of Global Public Health, Chapel Hill, NC, USA
| | - Shingai B A Mutambirwa
- Department of Urology, Sefako Makgatho Health Science University, Dr George Mukhari Academic Hospital, Medunsa, South Africa
| | - M S Riana Bornman
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Vanessa M Hayes
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia.
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa.
- Manchester Cancer Research Centre, University of Manchester, Manchester, M20 4GJ, UK.
- Faculty of Health Sciences, University of Limpopo, Turfloop Campus, Sovenga, Limpopo, South Africa.
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Craddock J, Jiang J, Patrick SM, Mutambirwa SBA, Stricker PD, Bornman MSR, Jaratlerdsiri W, Hayes VM. Alterations in the Epigenetic Machinery Associated with Prostate Cancer Health Disparities. Cancers (Basel) 2023; 15:3462. [PMID: 37444571 DOI: 10.3390/cancers15133462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Prostate cancer is driven by acquired genetic alterations, including those impacting the epigenetic machinery. With African ancestry as a significant risk factor for aggressive disease, we hypothesize that dysregulation among the roughly 656 epigenetic genes may contribute to prostate cancer health disparities. Investigating prostate tumor genomic data from 109 men of southern African and 56 men of European Australian ancestry, we found that African-derived tumors present with a longer tail of epigenetic driver gene candidates (72 versus 10). Biased towards African-specific drivers (63 versus 9 shared), many are novel to prostate cancer (18/63), including several putative therapeutic targets (CHD7, DPF3, POLR1B, SETD1B, UBTF, and VPS72). Through clustering of all variant types and copy number alterations, we describe two epigenetic PCa taxonomies capable of differentiating patients by ancestry and predicted clinical outcomes. We identified the top genes in African- and European-derived tumors representing a multifunctional "generic machinery", the alteration of which may be instrumental in epigenetic dysregulation and prostate tumorigenesis. In conclusion, numerous somatic alterations in the epigenetic machinery drive prostate carcinogenesis, but African-derived tumors appear to achieve this state with greater diversity among such alterations. The greater novelty observed in African-derived tumors illustrates the significant clinical benefit to be derived from a much needed African-tailored approach to prostate cancer healthcare aimed at reducing prostate cancer health disparities.
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Affiliation(s)
- Jenna Craddock
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria 0084, South Africa
| | - Jue Jiang
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2006, Australia
| | - Sean M Patrick
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria 0084, South Africa
| | - Shingai B A Mutambirwa
- Department of Urology, Sefako Makgatho Health Science University, Dr George Mukhari Academic Hospital, Medunsa 0208, South Africa
| | - Phillip D Stricker
- Department of Urology, St Vincent's Hospital, Darlinghurst, NSW 2010, Australia
| | - M S Riana Bornman
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria 0084, South Africa
| | - Weerachai Jaratlerdsiri
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2006, Australia
| | - Vanessa M Hayes
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria 0084, South Africa
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2006, Australia
- Manchester Cancer Research Centre, University of Manchester, Manchester M20 4GJ, UK
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Patrick SM, Bendiane MK, Kruger T, Harris BN, Riddin MA, Trehard H, de Jager C, Bornman R, Gaudart J. Household living conditions and individual behaviours associated with malaria risk: a community-based survey in the Limpopo River Valley, 2020, South Africa. Malar J 2023; 22:156. [PMID: 37189177 DOI: 10.1186/s12936-023-04585-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/09/2023] [Indexed: 05/17/2023] Open
Abstract
BACKGROUND Over the past decade, implementation of multiple malaria control strategies in most countries has largely contributed to advance the global malaria elimination agenda. Nevertheless, in some regions, seasonal epidemics may adversely affect the health of local populations. In South Africa, Plasmodium falciparum malaria is still present, with the Vhembe District experiencing an incidence rate of 3.79 cases/1000 person-years in 2018, particularly in the Limpopo River Valley, bordering Zimbabwe. To elucidate the complexity of the mechanisms involved in local regular malaria outbreaks, a community-based survey was implemented in 2020 that focused on the relationship between housing conditions and malaria risky behaviours. METHODS The community-based cross-sectional survey was conducted among the population of three study sites in the Vhembe District, which were selected based on malaria incidence rate, social and health characteristics of inhabitants. The household survey used a random sampling strategy, where data were collected through face-to-face questionnaires and field notes; to described the housing conditions (housing questionnaire), and focus on individual behaviours of household members. Statistical analyses were performed combining hierarchical classifications and logistic regressions. RESULTS In this study, 398 households were described, covering a population of 1681 inhabitants of all ages, and 439 adults who participated in community-based survey. The analysis of situations at risk of malaria showed that the influence of contextual factors, particularly those defined by the type of habitat, was significant. Housing conditions and poor living environments were factors of malaria exposure and history, regardless of site of investigation, individual preventive behaviours and personal characteristics of inhabitants. Multivariate models showed that, considering all personal characteristics or behaviours of inhabitants, housing conditions such as overcrowding pressures were significantly associated with individual malaria risk. CONCLUSIONS The results showed the overwhelming weight of social and contextual factors on risk situations. Considering the Fundamental Causes Theory, malaria control policies based on health behaviour prevention, should reinforce access to care or promoting health education actions. Overarching economic development interventions in targeted geographical areas and populations have to be implemented, so that malaria control and elimination strategies can be efficiently and effectively managed.
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Affiliation(s)
- Sean M Patrick
- UP Institute for Sustainable Malaria Control & MRC Collaborating Centre for Malaria Research, School of Health Systems and Public Health, University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa.
| | - Marc-Karim Bendiane
- Economics & Social Sciences Applied to Health & Medical Information Processing, Aix Marseille University, INSERM, IRD, ISSPAM, SESSTIM, 13005, Marseille, France
| | - Taneshka Kruger
- UP Institute for Sustainable Malaria Control & MRC Collaborating Centre for Malaria Research, School of Health Systems and Public Health, University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Bernice N Harris
- UP Institute for Sustainable Malaria Control & MRC Collaborating Centre for Malaria Research, School of Health Systems and Public Health, University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Megan A Riddin
- UP Institute for Sustainable Malaria Control & MRC Collaborating Centre for Malaria Research, School of Health Systems and Public Health, University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Helene Trehard
- Economics & Social Sciences Applied to Health & Medical Information Processing, Aix Marseille University, INSERM, IRD, ISSPAM, SESSTIM, 13005, Marseille, France
| | - Christiaan de Jager
- UP Institute for Sustainable Malaria Control & MRC Collaborating Centre for Malaria Research, School of Health Systems and Public Health, University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Riana Bornman
- UP Institute for Sustainable Malaria Control & MRC Collaborating Centre for Malaria Research, School of Health Systems and Public Health, University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Jean Gaudart
- Aix Marseille University, INSERM, IRD, APHM, ISSPAM, SESSTIM, UMR1252, Hospital La Timone, BioSTIC, Biostatistics & ICT, 13005, Marseille, France
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5
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Patrick SM, Cox SN, Guidera KE, Simon MJ, Kruger T, Bornman R. COVID-19 and the malaria elimination agenda in Africa: Re-shifting the focus. Glob Public Health 2022; 17:3981-3992. [PMID: 36194811 DOI: 10.1080/17441692.2022.2129729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The global Coronavirus disease 2019 (COVID-19) pandemic has resulted in public health, political, scientific and private sector response at an unprecedented scale. However, this shift in focus has caused widespread disruption to global health services and has the potential to reverse gains made in efforts to control malaria. If health systems are not able to maintain malaria control interventions while managing the response to the COVID-19 pandemic, malaria cases will increase, thereby placing even more strain on already overtaxed systems. Using a Narrative Review Approach, this commentary explores the impact of COVID-19 on progress made with malaria control and prevention strategies in Africa; and discusses possible mitigation steps to aid community resilience building, through proactive planning and implementation of integrated, inclusive and sustainable strategies to re-shift the focus to attain the malaria elimination goals. We propose strengthening community partnerships, where academia and communities should collaborate and these knowledge-sharing strategies be implemented in order for awareness and interventions to become more networked, inclusive, resilient and effective. Communities should be viewed as 'thought partners', who challenge conventional strategies and aid in developing innovative approaches to community resilience building.
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Affiliation(s)
- Sean M Patrick
- University of Pretoria Institute for Sustainable Malaria Control, School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Sarah N Cox
- Public Health, University of Washington, Seattle, WA, USA.,One Sun Health Inc., New York, USA & Mpumalanga, ZA
| | | | | | - Taneshka Kruger
- University of Pretoria Institute for Sustainable Malaria Control, School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Riana Bornman
- University of Pretoria Institute for Sustainable Malaria Control, School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
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Gong T, Jaratlerdsiri W, Jiang J, Willet C, Chew T, Patrick SM, Lyons RJ, Haynes AM, Pasqualim G, Brum IS, Stricker PD, Mutambirwa SBA, Sadsad R, Papenfuss AT, Bornman RMS, Chan EKF, Hayes VM. Genome-wide interrogation of structural variation reveals novel African-specific prostate cancer oncogenic drivers. Genome Med 2022; 14:100. [PMID: 36045381 PMCID: PMC9434886 DOI: 10.1186/s13073-022-01096-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/28/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND African ancestry is a significant risk factor for advanced prostate cancer (PCa). Mortality rates in sub-Saharan Africa are 2.5-fold greater than global averages. However, the region has largely been excluded from the benefits of whole genome interrogation studies. Additionally, while structural variation (SV) is highly prevalent, PCa genomic studies are still biased towards small variant interrogation. METHODS Using whole genome sequencing and best practice workflows, we performed a comprehensive analysis of SVs for 180 (predominantly Gleason score ≥ 8) prostate tumours derived from 115 African, 61 European and four ancestrally admixed patients. We investigated the landscape and relationship of somatic SVs in driving ethnic disparity (African versus European), with a focus on African men from southern Africa. RESULTS Duplication events showed the greatest ethnic disparity, with a 1.6- (relative frequency) to 2.5-fold (count) increase in African-derived tumours. Furthermore, we found duplication events to be associated with CDK12 inactivation and MYC copy number gain, and deletion events associated with SPOP mutation. Overall, African-derived tumours were 2-fold more likely to present with a hyper-SV subtype. In addition to hyper-duplication and deletion subtypes, we describe a new hyper-translocation subtype. While we confirm a lower TMPRSS2-ERG fusion-positive rate in tumours from African cases (10% versus 33%), novel African-specific PCa ETS family member and TMPRSS2 fusion partners were identified, including LINC01525, FBXO7, GTF3C2, NTNG1 and YPEL5. Notably, we found 74 somatic SV hotspots impacting 18 new candidate driver genes, with CADM2, LSAMP, PTPRD, PDE4D and PACRG having therapeutic implications for African patients. CONCLUSIONS In this first African-inclusive SV study for high-risk PCa, we demonstrate the power of SV interrogation for the identification of novel subtypes, oncogenic drivers and therapeutic targets. Identifying a novel spectrum of SVs in tumours derived from African patients provides a mechanism that may contribute, at least in part, to the observed ethnic disparity in advanced PCa presentation in men of African ancestry.
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Affiliation(s)
- Tingting Gong
- grid.1013.30000 0004 1936 834XAncestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW Australia ,grid.415306.50000 0000 9983 6924Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Darlinghurst, NSW Australia ,grid.8547.e0000 0001 0125 2443Human Phenome Institute, Fudan University, Shanghai, China
| | - Weerachai Jaratlerdsiri
- grid.1013.30000 0004 1936 834XAncestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW Australia ,grid.415306.50000 0000 9983 6924Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Darlinghurst, NSW Australia
| | - Jue Jiang
- grid.1013.30000 0004 1936 834XAncestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW Australia ,grid.415306.50000 0000 9983 6924Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Darlinghurst, NSW Australia
| | - Cali Willet
- grid.1013.30000 0004 1936 834XSydney Informatics Hub, University of Sydney, Sydney, NSW Australia
| | - Tracy Chew
- grid.1013.30000 0004 1936 834XSydney Informatics Hub, University of Sydney, Sydney, NSW Australia
| | - Sean M. Patrick
- grid.49697.350000 0001 2107 2298School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Ruth J. Lyons
- grid.415306.50000 0000 9983 6924Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Darlinghurst, NSW Australia
| | - Anne-Maree Haynes
- grid.415306.50000 0000 9983 6924Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Darlinghurst, NSW Australia
| | - Gabriela Pasqualim
- grid.8532.c0000 0001 2200 7498Endocrine and Tumor Molecular Biology Laboratory, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil ,grid.411598.00000 0000 8540 6536Laboratory of Genetics, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Ilma Simoni Brum
- grid.8532.c0000 0001 2200 7498Endocrine and Tumor Molecular Biology Laboratory, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Phillip D. Stricker
- grid.415306.50000 0000 9983 6924Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Darlinghurst, NSW Australia ,grid.437825.f0000 0000 9119 2677Department of Urology, St. Vincent’s Hospital, Darlinghurst, NSW Australia
| | - Shingai B. A. Mutambirwa
- grid.461049.eDepartment of Urology, Sefako Makgatho Health Science University, Dr George Mukhari Academic Hospital, Medunsa, Ga-Rankuwa, South Africa
| | - Rosemarie Sadsad
- grid.1013.30000 0004 1936 834XSydney Informatics Hub, University of Sydney, Sydney, NSW Australia
| | - Anthony T. Papenfuss
- grid.1042.70000 0004 0432 4889Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Melbourne, Victoria Australia
| | - Riana M. S. Bornman
- grid.49697.350000 0001 2107 2298School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Eva K. F. Chan
- grid.415306.50000 0000 9983 6924Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Darlinghurst, NSW Australia ,grid.416088.30000 0001 0753 1056NSW Health Pathology, Sydney, Australia
| | - Vanessa M. Hayes
- grid.1013.30000 0004 1936 834XAncestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW Australia ,grid.415306.50000 0000 9983 6924Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Darlinghurst, NSW Australia ,grid.49697.350000 0001 2107 2298School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa ,grid.411732.20000 0001 2105 2799Faculty of Health Sciences, University of Limpopo, Turfloop Campus, Mankweng, South Africa
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Feng Y, Jaratlerdsiri W, Patrick SM, Lyons RJ, Haynes A, Collins CC, Stricker PD, Bornman MR, Hayes VM. Metagenomic analysis reveals a rich bacterial content in high-risk prostate tumors from African men. Prostate 2019; 79:1731-1738. [PMID: 31454437 PMCID: PMC6790596 DOI: 10.1002/pros.23897] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 08/06/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND Inflammation is a hallmark of prostate cancer (PCa), yet no pathogenic agent has been identified. Men from Africa are at increased risk for both aggressive prostate disease and infection. We hypothesize that pathogenic microbes may be contributing, at least in part, to high-risk PCa presentation within Africa and in turn the observed ethnic disparity. METHODS Here we reveal through metagenomic analysis of host-derived whole-genome sequencing data, the microbial content within prostate tumor tissue from 22 men. What is unique about this study is that patients were separated by ethnicity, African vs European, and environments, Africa vs Australia. RESULTS We identified 23 common bacterial genera between the African, Australian, and Chinese prostate tumor samples, while nonbacterial microbes were notably absent. While the most abundant genera across all samples included: Escherichia, Propionibacterium, and Pseudomonas, the core prostate tumor microbiota was enriched for Proteobacteria. We observed a significant increase in the richness of the bacterial communities within the African vs Australian samples (t = 4.6-5.5; P = .0004-.001), largely driven by eight predominant genera. Considering core human gut microbiota, African prostate tissue samples appear enriched for Escherichia and Acidovorax, with an abundance of Eubacterium associated with host tumor hypermutation. CONCLUSIONS Our study provides suggestive evidence for the presence of a core, bacteria-rich, prostate microbiome. While unable to exclude for fecal contamination, the observed increased bacterial content and richness within the African vs non-African samples, together with elevated tumor mutational burden, suggests the possibility that bacterially-driven oncogenic transformation within the prostate microenvironment may be contributing to aggressive disease presentation in Africa.
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Affiliation(s)
- Ye Feng
- Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
- Institute of Translational MedicineZhejiang University School of MedicineHangzhouChina
| | - Weerachai Jaratlerdsiri
- Laboratory for Human Comparative and Prostate Cancer Genomics, Garvan Institute of Medical ResearchThe Kinghorn Cancer CentreDarlinghurstNew South WalesAustralia
| | - Sean M. Patrick
- School of Health Systems and Public HealthUniversity of PretoriaPretoriaSouth Africa
| | - Ruth J. Lyons
- Laboratory for Human Comparative and Prostate Cancer Genomics, Garvan Institute of Medical ResearchThe Kinghorn Cancer CentreDarlinghurstNew South WalesAustralia
| | - Anne‐Maree Haynes
- Laboratory for Human Comparative and Prostate Cancer Genomics, Garvan Institute of Medical ResearchThe Kinghorn Cancer CentreDarlinghurstNew South WalesAustralia
| | - Colin C. Collins
- Vancouver Prostate CentreVancouverCanada
- Department of UrologyUniversity of British ColumbiaVancouverCanada
| | - Phillip D. Stricker
- Department of UrologySt Vincent's Hospital SydneyDarlinghurstNew South WalesAustralia
| | - M.S. Riana Bornman
- School of Health Systems and Public HealthUniversity of PretoriaPretoriaSouth Africa
| | - Vanessa M. Hayes
- Laboratory for Human Comparative and Prostate Cancer Genomics, Garvan Institute of Medical ResearchThe Kinghorn Cancer CentreDarlinghurstNew South WalesAustralia
- School of Health Systems and Public HealthUniversity of PretoriaPretoriaSouth Africa
- St Vincent's Clinical SchoolUniversity of New South Wales SydneySydneyNew South WalesAustralia
- Central Clinical School, Faculty of Medicine and HealthUniversity of SydneyCamperdownNew South WalesAustralia
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Blackburn J, Vecchiarelli S, Heyer EE, Patrick SM, Lyons RJ, Jaratlerdsiri W, van Zyl S, Bornman MSR, Mercer TR, Hayes VM. TMPRSS2-ERG fusions linked to prostate cancer racial health disparities: A focus on Africa. Prostate 2019; 79:1191-1196. [PMID: 31090091 PMCID: PMC6617820 DOI: 10.1002/pros.23823] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/11/2019] [Accepted: 04/17/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND The androgen-regulated gene TMPRSS2 to the ETS transcription factor gene ERG fusion is the most common genomic alteration acquired during prostate tumorigenesis and biased toward men of European ancestry. In contrast, African American men present with more advanced disease, yet their tumors are less likely to acquire TMPRSS2-ERG. Data for Africa is scarce. METHODS RNA was made available for genomic analyses from 181 prostate tissue biopsy cores from Black South African men, 94 with and 87 without pathological evidence for prostate cancer. Reverse transcription polymerase chain reaction was used to screen for the TMPRSS2-ERG fusion, while transcript junction coordinates and isoform frequencies, including novel gene fusions, were determined using targeted RNA sequencing. RESULTS Here we report a frequency of 13% for TMPRSS2-ERG in tumors from Black South Africans. Present in 12/94 positive versus 1/87 cancer negative prostate tissue cores, this suggests a 92.62% predictivity for a positive cancer diagnosis (P = 0.0031). At a frequency of almost half that reported for African Americans and roughly a quarter of that reported for men of European ancestry, acquisition of TMPRSS2-ERG appears to be inversely associated with aggressive prostate cancer. Further support was provided by linking the presence of TMPRSS2-ERG to low-grade disease in younger patients (P = 0.0466), with higher expressing distal ERG fusion junction coordinates. CONCLUSIONS Only the second study of its kind for the African continent, we support a link between TMPRSS2-ERG status and prostate cancer racial health disparity beyond the borders of the United States. We call for urgent evaluation of androgen deprivation therapy within Africa.
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Affiliation(s)
- James Blackburn
- Garvan Institute of Medical ResearchThe Kinghorn Cancer CentreDarlinghurstAustralia
- St. Vincent's Clinical SchoolFaculty of Medicine, UNSWSydneyAustralia
| | - Stefano Vecchiarelli
- Garvan Institute of Medical ResearchThe Kinghorn Cancer CentreDarlinghurstAustralia
| | - Erin E. Heyer
- Garvan Institute of Medical ResearchThe Kinghorn Cancer CentreDarlinghurstAustralia
| | - Sean M. Patrick
- School of Health Systems and Public HealthUniversity of PretoriaGezinaSouth Africa
| | - Ruth J. Lyons
- Garvan Institute of Medical ResearchThe Kinghorn Cancer CentreDarlinghurstAustralia
| | | | - Smit van Zyl
- University of Limpopo, Turfloop CampusSovengaSouth Africa
| | - M. S. Riana Bornman
- School of Health Systems and Public HealthUniversity of PretoriaGezinaSouth Africa
| | - Tim R. Mercer
- Garvan Institute of Medical ResearchThe Kinghorn Cancer CentreDarlinghurstAustralia
- St. Vincent's Clinical SchoolFaculty of Medicine, UNSWSydneyAustralia
- Altius Institute for Biomedical SciencesSeattleWashington
| | - Vanessa M. Hayes
- Garvan Institute of Medical ResearchThe Kinghorn Cancer CentreDarlinghurstAustralia
- St. Vincent's Clinical SchoolFaculty of Medicine, UNSWSydneyAustralia
- School of Health Systems and Public HealthUniversity of PretoriaGezinaSouth Africa
- University of Limpopo, Turfloop CampusSovengaSouth Africa
- Sydney Medical SchoolUniversity of SydneyCamperdownAustralia
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9
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Bornman MS, Aneck-Hahn NH, de Jager C, Wagenaar GM, Bouwman H, Barnhoorn IEJ, Patrick SM, Vandenberg LN, Kortenkamp A, Blumberg B, Kimmins S, Jegou B, Auger J, DiGangi J, Heindel JJ. Endocrine Disruptors and Health Effects in Africa: A Call for Action. Environ Health Perspect 2017; 125:085005. [PMID: 28935616 PMCID: PMC5783641 DOI: 10.1289/ehp1774] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 05/22/2017] [Accepted: 05/24/2017] [Indexed: 06/01/2023]
Abstract
BACKGROUND Africa faces a number of unique environmental challenges. Unfortunately, it lacks the infrastructure needed to support the comprehensive environmental studies that could provide the scientific basis to inform environmental policies. There are a number of known sources of endocrine-disrupting chemicals (EDCs) and other hazardous chemicals in Africa. However, a coordinated approach to identify and monitor these contaminants and to develop strategies for public health interventions has not yet been made. OBJECTIVES This commentary summarizes the scientific evidence presented by experts at the First African Endocrine Disruptors meeting. We describe a "call to action" to utilize the available scientific knowledge to address the impact of EDCs on human and wildlife health in Africa. DISCUSSION We identify existing knowledge gaps about exposures to EDCs in Africa and describe how well-designed research strategies are needed to address these gaps. A lack of resources for research and a lag in policy implementation slows down intervention strategies and poses a challenge to advancing future health in Africa. CONCLUSION To address the many challenges posed by EDCs, we argue that Africans should take the lead in prioritization and evaluation of environmental hazards, including EDCs. We recommend the institution of education and training programs for chemical users, adoption of the precautionary principle, establishment of biomonitoring programs, and funding of community-based epidemiology and wildlife research programs led and funded by African institutes and private companies. https://doi.org/10.1289/EHP1774.
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Affiliation(s)
- Maria S Bornman
- Environmental and Occupational Health, School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
- Environmental Chemical Pollution and Health Research Unit, University of Pretoria, Pretoria, South Africa
| | - Natalie H Aneck-Hahn
- Environmental and Occupational Health, School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
- Environmental Chemical Pollution and Health Research Unit, University of Pretoria, Pretoria, South Africa
- Department of Urology, University of Pretoria , Pretoria, South Africa
| | - Christiaan de Jager
- Environmental and Occupational Health, School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
- Environmental Chemical Pollution and Health Research Unit, University of Pretoria, Pretoria, South Africa
| | - Gesina M Wagenaar
- Department of Zoology, University of Johannesburg , Johannesburg, South Africa
| | - Hindrik Bouwman
- Unit for Environmental Sciences and Management, North-West University , Potchefstroom, South Africa
| | | | - Sean M Patrick
- Environmental and Occupational Health, School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
- Environmental Chemical Pollution and Health Research Unit, University of Pretoria, Pretoria, South Africa
| | - Laura N Vandenberg
- Department of Environmental Health Sciences, University of Massachusetts Amherst School of Public Health and Health Sciences , Amherst, Massachusetts, USA
| | - Andreas Kortenkamp
- Institute of Environment, Health and Societies, Brunel University London , Uxbridge, UK
| | - Bruce Blumberg
- Department of Developmental and Cell Biology, University of California, Irvine , Irvine, California, USA
| | - Sarah Kimmins
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University , Montreal, Canada
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University , Montreal, Canada
| | - Bernard Jegou
- Institut de Recherche en Santé, Environnement et Travail (IRSET-INSERM UMR 1085 ), Institut national de la santé et de la recherche médicale (INSERM) , Rennes, France
- Ecole des Hautes Études en Santé Publique (EHESP) , Rennes, France
| | - Jacques Auger
- INSERM U1016, Equipe Génomique, Epigénétique et Physiologie de la Reproduction, Institut Cochin, Université Paris Descartes , Paris, France
| | - Joseph DiGangi
- International POPs Elimination Network (IPEN) , Gothenburg, Sweden
| | - Jerrold J Heindel
- Division of Extramural Research and Training, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services , Research Triangle Park, North Carolina, USA
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10
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Patrick SM, Bornman MS, Joubert AM, Pitts N, Naidoo V, de Jager C. Effects of environmental endocrine disruptors, including insecticides used for malaria vector control on reproductive parameters of male rats. Reprod Toxicol 2016; 61:19-27. [PMID: 26928317 DOI: 10.1016/j.reprotox.2016.02.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 02/21/2016] [Accepted: 02/23/2016] [Indexed: 12/12/2022]
Abstract
The male reproductive system is sensitive to endocrine disrupting chemicals (EDCs) during critical developmental windows. Male Sprague-Dawley rats were exposed in utero-, during lactation- and directly to 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane (DDT), 1,1,-dichloro-2,2-bis(p-chlorophenyl)ethylene (DDE) and a mixture of DDT, deltamethrin (DM), p-nonylphenol (p-NP) and phytoestrogens, at concentrations found in a malaria-area. After dosing for 104 days, histological assessments and reproductive-endpoints were assessed. The anogenital distance (AGD) (P=0.005) was shorter in the mixture-exposed group, while the prostate mass (P=0.018) was higher in the DDT-exposed group. A higher testicular mass and abnormal histology was observed in the DDT-(P=0.019), DDE-(P=0.047) and mixture-exposed (P<0.005) groups. This study shows that in utero-, lactational- and direct exposure to EDCs present in a malaria-area negatively affects male reproductive parameters in rats. These findings raise concerns to EDC-exposures to mothers living in malaria-areas and the reproductive health of their male offspring.
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Affiliation(s)
- Sean M Patrick
- School of Health Systems and Public Health, University of Pretoria, South Africa; University of Pretoria Center for Sustainable Malaria Control (UP CSMC), South Africa
| | - Maria S Bornman
- School of Health Systems and Public Health, University of Pretoria, South Africa; University of Pretoria Center for Sustainable Malaria Control (UP CSMC), South Africa
| | - Annie M Joubert
- Department of Physiology, University of Pretoria, South Africa
| | - Neville Pitts
- School of Physiology, University of the Witwatersrand, South Africa
| | - Vinny Naidoo
- University of Pretoria Center for Sustainable Malaria Control (UP CSMC), South Africa; Biomedical Research Centre, Faculty of Veterinary Science, University of Pretoria, South Africa
| | - Christiaan de Jager
- School of Health Systems and Public Health, University of Pretoria, South Africa; University of Pretoria Center for Sustainable Malaria Control (UP CSMC), South Africa.
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11
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Patrick SM, White E, Brill RW, Shiels HA. The effect of stimulation frequency on the transmural ventricular monophasic action potential in yellowfin tuna Thunnus albacares. J Fish Biol 2011; 78:651-658. [PMID: 21284642 DOI: 10.1111/j.1095-8649.2010.02869.x] [Citation(s) in RCA: 3] [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: 05/30/2023]
Abstract
Monophasic action potentials (MAPs) were recorded from the spongy and compact layers of the yellowfin tuna Thunnus albacares ventricle as stimulation frequency was increased. MAP duration decreased with increase in stimulation frequency in both the spongy and compact myocardial layers, but no significant difference in MAP duration was observed between the layers.
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Affiliation(s)
- S M Patrick
- Faculty of Life Sciences, University of Manchester, 46 Grafton Street, Core Technology Facility, Manchester, U.K
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12
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Patrick SM, Turchi JJ. Stopped-flow kinetic analysis of replication protein A-binding DNA: damage recognition and affinity for single-stranded DNA reveal differential contributions of k(on) and k(off) rate constants. J Biol Chem 2001; 276:22630-7. [PMID: 11278662 DOI: 10.1074/jbc.m010314200] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Replication protein A (RPA) is a heterotrimeric protein required for many DNA metabolic functions, including replication, recombination, and nucleotide excision repair (NER). We report the pre-steady-state kinetic analysis of RPA-binding DNA substrates using a stopped-flow assay to elucidate the kinetics of DNA damage recognition. The bimolecular association rate, k(on), for RPA binding to duplex DNA substrates is greatest for a 1,3d(GXG), intermediate for a 1,2d(GpG) cisplatin-DNA adduct, and least for an undamaged duplex DNA substrate. RPA displays a decreased k(on) and an increased k(off) for a single-stranded DNA substrate containing a single 1,2d(GpG) cisplatin-DNA adduct compared with an undamaged DNA substrate. The k(on) for RPA-binding single-stranded polypyrimidine sequences appears to be diffusion-limited. There is minimal difference in k(on) for varying length DNA substrates; therefore, the difference in equilibrium binding affinity is mainly attributed to the k(off). The k(on) for a purine-rich 30-base DNA is reduced by a factor of 10 compared with a pyrimidine-rich DNA of identical length. These results provide insight into the mechanism of RPA-DNA binding and are consistent with RPA recognition of DNA-damage playing a critical role in NER.
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Affiliation(s)
- S M Patrick
- Department of Biochemistry and Molecular Biology, Wright State University School of Medicine, Dayton, Ohio 45435, USA
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13
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Kim S, Patrick SM, Braunstein NS, Thomas JL, Leonard EF. Modeling of early events in T cell signal transduction after controlled T cell activation by peptide major histocompatibility complex. Ann Biomed Eng 2001; 29:373-83. [PMID: 11400719 DOI: 10.1114/1.1366671] [Citation(s) in RCA: 4] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Calcium signaling was observed in murine T cells over time, starting at a precise moment of contact with a layer of fibroblasts expressing a stimulatory major histocompatibility class II-peptide complex. The contact was controlled by a film-thinning apparatus. Intracellular calcium levels were followed with the ratiometric dye, Fura-2. The calcium response was highly synchronized and well fitted by a mathematical model. The model includes three components: a sequence of reactions occurring after T cell receptor (TCR) triggering; InsP3-mediated calcium release from intracellular stores (Meyer and Stryer, Proc. Natl. Acad. Sci. USA 85: 5051-5055, 1988); and slow changes in levels phospholipase C-gammal (PLCgammal) reflecting a decrease in receptor triggering rate. Each component in the model controls a different part of the response-the initial delay, the sharp rise, and the slow decay, respectively. Kinetic parameters determined from curve fitting were the initial delay in calcium signaling defined as the time when [PLCgammal] reached its half of its maximum (76 s), the coefficient characterizing calcium efflux from endoplasmic reticulum (ER) (2.86 microM s(-1), expressed per liter of cell volume), and a rate constant characterizing the diminishing yield of production of PLCgammal (0.00046 s(-1)) by active TCR. Only the parameter representing PLCgammal production varied much from cell to cell.
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Affiliation(s)
- S Kim
- Department of Chemical Engineering and Applied Chemistry, Columbia University, New York, NY 10027, USA
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14
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Patrick SM, Kim S, Braunstein NS, Maldarelli CM, Thomas JL, Leonard EF. Controlled cell deformation produces defined areas of contact between cells and ligand-coated surfaces. Ann Biomed Eng 2001; 29:1-8. [PMID: 11219503 DOI: 10.1114/1.1332081] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A method which allows precise control of the time of initiation and the area of contact of T cells with immobilized ligands has been developed. Cells are trapped in an asymmetric film that can be quantitatively thinned by reducing the film's capillary pressure. Ligands adsorbed to the base of the apparatus are forced into close contact with the cells as the air-liquid interface is drawn down. Using interference microscopy and microbeads to indicate the film height, the amount of thinning can be controlled to within 1 microm. In this study, this system was used to produce contact areas of 182 and 356 microm2 between T cells and anti-CD3 coated surfaces. These contact areas were measured using fluorescent dye exclusion microscopy. This apparatus can be used for quantitative studies of T cell activation, as is reported in Patrick et al., J. Immunol. Method. 24:97-108, 2000.
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Affiliation(s)
- S M Patrick
- Department of Chemical Engineering, Columbia University, New York, New York 10027, USA
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15
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Patrick SM, Kim S, Braunstein NS, Thomas JL, Leonard EF. Dependence of T cell activation on area of contact and density of a ligand-coated surface. J Immunol Methods 2000; 241:97-108. [PMID: 10915852 DOI: 10.1016/s0022-1759(00)00216-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
An apparatus which allows precise control of the time of initiation and the area of contact of cells with immobilized ligands has been developed. Cells are trapped in an asymmetric film that can be quantitatively thinned, forcing the cells into close contact with ligands adsorbed on the base of the apparatus. Using microbeads to indicate the film height, the amount of thinning can be controlled to within 1 microm, producing known contact areas between cells and the ligand-coated surface. This system was used with anti-CD3-coated surfaces of different densities to examine the effect of ligand density on T cell activation, while keeping the number of ligands presented to the cells constant. T cell activation was observed individually in each cell as intracellular calcium mobilization. In these experiments both the percent of T cell activation and the rate of calcium rise were found to depend only on the number of anti-CD3 molecules presented and not on their density. This implies that the spacing between molecules is not important in the range studied, and suggests that receptor clustering to levels higher than dimers may not be necessary for induction of calcium mobilization by anti-CD3.
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Affiliation(s)
- S M Patrick
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
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16
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Abstract
We have undertaken the systematic isolation and characterization of mammalian proteins which display an affinity for cisplatin-damaged DNA. Fractionation of human cell extracts has led to the identification of two classes of proteins. The first includes proteins that bind duplex DNA in the absence of cisplatin damage and retain their affinity for DNA in the presence of cisplatin-DNA adducts. The DNA-dependent protein kinase (DNA-PK) falls into this class. The inhibition of DNA-PK phosphorylation activity by cisplatin-damaged DNA has led to the hypothesis that cisplatin sensitization of mammalian cells to ionizing radiation may be mediated by DNA-PK. The second class of proteins identified are those which display a high relative affinity for cisplatin-damaged DNA and a low affinity for undamaged duplex DNA. Proteins that fall into this class include high mobility group 1 protein (HMG-1), replication protein A (RPA) and xeroderma pigmentosum group A protein (XPA). Each protein has been isolated and purified in the lab. The interaction of each protein with cisplatin-damaged DNA has been assessed in electrophoretic mobility shift assays. A series of DNA binding experiments suggests that RPA binds duplex DNA via denaturation and subsequent preferential binding to the undamaged DNA strand of the partial duplex. DNA substrates prepared with photo-reactive base analogs on either the damaged or undamaged DNA strand have also been employed to investigate the mechanism and specific protein-DNA interactions that occur as each protein binds to cisplatin-damaged DNA. Results suggest both damage and strand specificity for RPA and XPA binding cisplatin-damaged DNA.
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Affiliation(s)
- J J Turchi
- Department of Biochemistry and Molecular Biology, Wright State University School of Medicine, Dayton, OH 45435, USA.
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Vaisman A, Lim SE, Patrick SM, Copeland WC, Hinkle DC, Turchi JJ, Chaney SG. Effect of DNA polymerases and high mobility group protein 1 on the carrier ligand specificity for translesion synthesis past platinum-DNA adducts. Biochemistry 1999; 38:11026-39. [PMID: 10460158 DOI: 10.1021/bi9909187] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Translesion synthesis past Pt-DNA adducts can affect both the cytotoxicity and mutagenicity of the platinum adducts. We have shown previously that the extent of replicative bypass in vivo is influenced by the carrier ligand of platinum adducts. The specificity of replicative bypass may be determined by the DNA polymerase complexes that catalyze translesion synthesis past Pt-DNA adducts and/or by DNA damage-recognition proteins that bind to the Pt-DNA adducts and block translesion replication. In the present study, primer extension on DNA templates containing site-specifically placed cisplatin, oxaliplatin, JM216, or chlorodiethylenetriamine-Pt adducts revealed that the eukaryotic DNA polymerases beta, zeta, gamma, and human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) had a similar specificity for translesion synthesis past Pt-DNA adducts (dien >> oxaliplatin >/= cisplatin > JM216). Primer extension assays performed in the presence of high mobility group protein 1 (HMG1), which is known to recognize cisplatin-damaged DNA, revealed that inhibition of translesion synthesis by HMG1 also depended on the carrier ligand of the Pt-DNA adduct (cisplatin > oxaliplatin = JM216 >> dien). These data were consistent with the results of gel-shift experiments showing similar differences in the affinity of HMG1 for DNA modified with the different platinum adducts. Our studies show that both DNA polymerases and damage-recognition proteins can impart specificity to replicative bypass of Pt-DNA adducts. This information may serve as a model for further studies of translesion synthesis.
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Affiliation(s)
- A Vaisman
- Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina, Chapel Hill 27599-7260, USA
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18
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Patrick SM, Turchi JJ. Replication protein A (RPA) binding to duplex cisplatin-damaged DNA is mediated through the generation of single-stranded DNA. J Biol Chem 1999; 274:14972-8. [PMID: 10329699 DOI: 10.1074/jbc.274.21.14972] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Replication protein A (RPA) is a heterotrimeric protein composed of 70-, 34-, and 14-kDa subunits that has been shown to be required for DNA replication, repair, and homologous recombination. We have previously shown preferential binding of recombinant human RPA (rhRPA) to duplex cisplatin-damaged DNA compared with the control undamaged DNA (Patrick, S. M., and Turchi, J. J. (1998) Biochemistry 37, 8808-8815). Here we assess the binding of rhRPA to DNA containing site-specific cisplatin-DNA adducts. rhRPA is shown to bind 1.5-2-fold better to a duplex 30-base pair substrate containing a single 1,3d(GpXpG) compared with a 1,2d(GpG) cisplatin-DNA intrastrand adduct, consistent with the difference in thermal stability of DNA containing each adduct. Consistent with these data, a 21-base pair DNA substrate containing a centrally located single interstrand cisplatin cross-link resulted in less binding than to the undamaged control DNA. A series of experiments measuring rhRPA binding and concurrent DNA denaturation revealed that rhRPA binds duplex cisplatin-damaged DNA via the generation of single-stranded DNA. Single-strand DNA binding experiments show that rhRPA binds 3-4-fold better to an undamaged 24-base DNA compared with the same substrate containing a single 1,2d(GpG) cisplatin-DNA adduct. These data are consistent with a low affinity interaction of rhRPA with duplex-damaged DNA followed by the generation of single-stranded DNA and then high affinity binding to the undamaged DNA strand.
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Affiliation(s)
- S M Patrick
- Department of Biochemistry and Molecular Biology, Wright State University School of Medicine, Dayton, Ohio 45435, USA
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Abstract
Fractionation of human cell extracts by cisplatin-DNA affinity chromatography was employed to identify proteins capable of binding cisplatin-damaged DNA. A specific protein-DNA complex, termed DRP-3, was identified in an electrophoretic mobility shift assay (EMSA) using a cisplatin-damaged DNA probe. Using this assay we purified DRP-3 and the final fraction contained proteins of 70, 53, 46, 32, and 14 kDa. On the basis of subunit molecular weights, antibody reactivity, and DNA binding activities, DRP-3 was identified as human replication protein A (hRPA). Therefore, we assessed the binding of recombinant human RPA (rhRPA) to duplex cisplatin-damaged DNA in vitro. Global treatment of a highly purified completely duplex 44-bp DNA with cisplatin resulted in a 10-20-fold increase in rhRPA binding compared to the undamaged control. The stability of the RPA-DNA complexes was assessed, and NaCl and MgCl2 concentrations that completely inhibited rhRPA binding to undamaged DNA had only a minimal effect on binding to duplex platinated DNA. We assessed rhRPA binding to a duplex DNA containing a single site-specific 1,2-d(GpG) cisplatin adduct, and the results revealed a 4-6-fold increase in binding to this DNA substrate compared to an undamaged control DNA of identical sequence. These results are consistent with RPA being involved in the initial recognition of cisplatin-damaged DNA, possibly mediating DNA repair events. Therefore, we assessed how another cisplatin DNA binding protein, HMG-1, affected the ability of rhRPA to bind damaged DNA. Competition binding assays show minimal dissociation of either protein from cisplatin-damaged DNA during the course of the reaction. Simultaneous addition experiments revealed that HMG-1 binding to cisplatin-damaged DNA was minimally affected by rhRPA, while HMG-1 inhibited the damaged-DNA binding activity of rhRPA. These data are consistent with HMG-1 blocking DNA repair and possibly having the capability to enhance the cytotoxic efficacy of the drug cisplatin.
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Affiliation(s)
- S M Patrick
- Department of Biochemistry and Molecular Biology, Wright State University School of Medicine, Dayton, Ohio 45435, USA
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Patrick SM, Henkels KM, Turchi JJ. High-mobility group 1 protein inhibits helicase catalyzed displacement of cisplatin-damaged DNA. Biochim Biophys Acta 1997; 1354:279-90. [PMID: 9427537 DOI: 10.1016/s0167-4781(97)00136-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We have determined the effect of HMG-1 bound to cisplatin-damaged DNA on the activities of calf helicase E. DNase I protection analysis demonstrated HMG-1 bound a cisplatin-damaged 24 base oligonucleotide annealed to M13mp18. Exonuclease digestion experiments revealed that greater than 90% of the DNA substrates contained a single site specific cisplatin adduct and, maximally, 65% of the substrates were bound by HMG-1. Helicase E catalyzed displacement of the cisplatin-damaged DNA oligonucleotide was inhibited by HMG-1 in a concentration-dependent manner. Time course experiments revealed a decreased rate of displacement in reactions containing HMG-1. The maximum inhibition observed was 55% and taking into account that only 65% of the substrates had HMG-1 bound, approximately 85% inhibition was observed on platinated DNA substrates containing HMG-1. Inhibition of helicase activity was proportional to the amount of substrate bound by HMG-1 based on the displacement and exonuclease assays at varying HMG-1 concentrations. The ability of helicase E to displace an undamaged DNA oligonucleotide from a cisplatin-damaged DNA template was also inhibited by HMG-1. Interestingly, HMG-1 had no effect on the rate of DNA-dependent ATP hydrolysis catalyzed by helicase E on the same DNA substrate. The inhibition of helicase activity by HMG-1 binding cisplatin-damaged DNA further supports a role for HMG-1 inhibiting DNA repair which may contribute to cellular sensitivity to cisplatin.
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Affiliation(s)
- S M Patrick
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH 45435, USA
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Patrick SM, An H, Harris MB, Ivanov IB, Braunstein NS, Leonard EF. Controlling receptor-ligand contact to examine kinetics of T cell activation. Ann Biomed Eng 1997; 25:1072-80. [PMID: 9395052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A method for controlling the contact of cell-surface receptors with immobilized ligands has been developed. Cells are trapped in an asymmetric liquid film that can be quantitatively thinned by reducing the film's capillary pressure. Ligands adsorbed to the liquid-solid interface are forced into increasingly tighter contact with the cells as the air-liquid interface is drawn down. Controlling the degree of thinning allows study of repulsive forces, and controlling its time course produces a definite time 0 for analyzing signal transduction. This system was tested by examining the time course of calcium mobilization in T cells upon activation with anti-CD3 antibody at different dilutions and ionic strengths. The averaged calcium transient of the responding cells was essentially the same for each condition. However, the fraction of responding cells decreased with anti-CD3 dilution, and indicated that the critical ligand density for T cell activation lies between approximately 35 and 70 molecules of anti-CD3 per microm2. Decreasing the medium's ionic strength from the normal value of 157 mM to 57 mM did not affect either the average calcium response profile or the fraction of responding cells, but strongly affected receptor-ligand contact, decreasing the percent of spontaneous activation from 38% to 5%. Such an imposed decrease sets the stage for film thinning to impose much greater control of receptor-ligand contact.
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Affiliation(s)
- S M Patrick
- Department of Chemical Engineering, Columbia University, NY, NY 10027, USA
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Abstract
We have determined the mechanism of DNA-dependent protein kinase (DNA-PK) inhibition by cis-diamminedichloroplatinum(II)-(cisplatin-) damaged DNA. We previously have demonstrated that Ku, the DNA binding subunit of DNA-PK, is capable of binding to DNA duplexes globally damaged with cisplatin but was unable to stimulate DNA-PKcs, the catalytic subunit [Turchi & Henkels (1996) J. Biol. Chem. 271, 2992-3000]. In this report we have assessed Ku binding and DNA-PK stimulation using a series of DNA substrates containing single, site-specific d(GpG), d(ApG), and d(GpXpG) intrastrand cisplatin adducts and a substrate with a single interstrand cisplatin adduct. Results demonstrate that Ku binding is marginally decreased by the presence of cisplatin adducts on each substrate. When assayed for the ability to stimulate DNA-PK, each cisplatin-damaged substrate resulted in significantly decreased activity compared to undamaged DNA controls. The degree of inhibition of both Ku binding and kinase activity varied depending on the specific adduct employed. The inhibition of DNA-PK activity by cisplatin-damaged DNA was observed using either a synthetic peptide or human replication protein A as a substrate. Autophosphorylation of the DNA-PKcs and Ku subunits was also inhibited in reactions performed with cisplatin-damaged DNA, demonstrating that increased autophosphorylation of DNA-PKcs does not account for the decreased kinase activity observed with cisplatin-damaged DNA. Equilibrium binding and initial velocity experiments revealed a less than 2-fold increase in the Kd of Ku and the Km of DNA-PK for DNA containing a single 1,2-d(GpG) cisplatin adduct. The mechanism of DNA-PK inhibition by cisplatin-damaged DNA can be attributed to a large decrease in the Vmax and small increase in Km.
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Affiliation(s)
- J J Turchi
- Department of Biochemistry and Molecular Biology, Wright State University School of Medicine, Dayton, Ohio 45435, USA.
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