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Forconi CS, Nixon C, Wu HW, Odwar B, Pond-Tor S, Ong'echa JM, Kurtis J, Moormann AM. T follicular helper cell profiles differ by malaria antigen and for children compared to adults. bioRxiv 2024:2024.04.13.589352. [PMID: 38659768 PMCID: PMC11042194 DOI: 10.1101/2024.04.13.589352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Background Circulating T-follicular helper (cT FH ) cells have the potential to provide an additional correlate of protection against Plasmodium falciparum ( Pf) as they are essential to promote B cell production of long-lasting antibodies. Assessing the specificity of cT FH subsets to individual malaria antigens is vital to understanding the variation observed in antibody responses and identifying promising malaria vaccine candidates. Methods Using spectral flow cytometry and unbiased clustering analysis we assessed antigen-specific cT FH cell recall responses in vitro to malaria vaccine candidates Pf SEA-1A and Pf GARP within a cross-section of children and adults living in a malaria holoendemic region of western Kenya. Findings In children, a broad array of cT FH subsets (defined by cytokine and transcription factor expression) were reactive to both malaria antigens, Pf SEA-1A and Pf GARP, while adults had a narrow profile centering on cT FH 17- and cT FH 1/17-like subsets following stimulation with Pf GARP only. Interpretation Because T FH 17 cells are involved in the maintenance of memory antibody responses within the context of parasitic infections, our results suggest that Pf GARP might generate longer lived antibody responses compared to Pf SEA-1A. These findings have intriguing implications for evaluating malaria vaccine candidates as they highlight the importance of including cT FH profiles when assessing interdependent correlates of protective immunity.
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Connelly SV, Brazeau NF, Msellem M, Ngasala BE, Aydemir Ö, Goel V, Niaré K, Giesbrecht DJ, Popkin-Hall ZR, Hennelly CM, Park Z, Moormann AM, Ong'echa JM, Verity R, Mohammed S, Shija SJ, Mhamilawa LE, Morris U, Mårtensson A, Lin JT, Björkman A, Juliano JJ, Bailey JA. Strong isolation by distance and evidence of population microstructure reflect ongoing Plasmodium falciparum transmission in Zanzibar. medRxiv 2024:2023.02.15.23285960. [PMID: 36865135 PMCID: PMC9980253 DOI: 10.1101/2023.02.15.23285960] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The Zanzibar archipelago of Tanzania has become a low-transmission area for Plasmodium falciparum. Despite being considered an area of pre-elimination for years, achieving elimination has been difficult, likely due to a combination of imported infections from mainland Tanzania, and continued local transmission. To shed light on these sources of transmission, we applied highly multiplexed genotyping utilizing molecular inversion probes to characterize the genetic relatedness of 282 P. falciparum isolates collected across Zanzibar and in Bagamoyo District on the coastal mainland from 2016-2018. Overall, parasite populations on the coastal mainland and Zanzibar archipelago remain highly related. However, parasite isolates from Zanzibar exhibit population microstructure due to rapid decay of parasite relatedness over very short distances. This, along with highly related pairs within shehias, suggests ongoing low level local transmission. We also identified highly related parasites across shehias that reflect human mobility on the main island of Unguja and identified a cluster of highly related parasites, suggestive of an outbreak, in the Micheweni district on Pemba island. Parasites in asymptomatic infections demonstrated higher complexity of infection than those in symptomatic infections, but have similar core genomes. Our data support importation as a main source of genetic diversity and contribution to the parasite population on Zanzibar, but they also show local outbreak clusters where targeted interventions are essential to block local transmission. These results highlight the need for preventive measures against imported malaria and enhanced control measures in areas that remain receptive for malaria reemergence due to susceptible hosts and competent vectors.
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Affiliation(s)
- Sean V Connelly
- MD-PhD Program, University of North Carolina, Chapel Hill, NC 27599
| | | | - Mwinyi Msellem
- Research Division, Ministry of Health, Zanzibar, Tanzania
| | - Billy E Ngasala
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Global Health and Migration Unit, Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Özkan Aydemir
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA
| | - Varun Goel
- Carolina Population Center, University of North Carolina, Chapel Hill, NC 27599
| | - Karamoko Niaré
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, 02912 USA
| | - David J Giesbrecht
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, 02912 USA
| | - Zachary R Popkin-Hall
- Institute for Global Health and Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599 USA
| | - Christopher M Hennelly
- Institute for Global Health and Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599 USA
| | - Zackary Park
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599 USA
| | - Ann M Moormann
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA
| | | | - Robert Verity
- MRC Centre for Global Infectious Disease Analysis, Imperial College, London
| | - Safia Mohammed
- Zanzibar Malaria Elimination Program (ZAMEP), Zanzibar, Tanzania
| | - Shija J Shija
- Zanzibar Malaria Elimination Program (ZAMEP), Zanzibar, Tanzania
| | - Lwidiko E Mhamilawa
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Global Health and Migration Unit, Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Ulrika Morris
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Andreas Mårtensson
- Global Health and Migration Unit, Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Jessica T Lin
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599 USA
| | - Anders Björkman
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden
| | - Jonathan J Juliano
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599 USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, 27599 USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599 USA
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, 02912 USA
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Robertson K, Reimold K, Moormann AM, Binder R, Matteson KA, Leftwich HK. Investigating demographic differences in patients' decisions to consent to COVID-19 research. J Matern Fetal Neonatal Med 2023; 36:2148097. [PMID: 36597819 DOI: 10.1080/14767058.2022.2148097] [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: 01/05/2023]
Abstract
OBJECTIVE COVID-19 disease severely impacted pregnant persons, resulting in a significant increase in poor maternal health outcomes, with a disproportionate impact on minority populations and individuals with low socioeconomic status. We sought to determine demographic differences between birthing parents with SARS-CoV-2 infections who consented to research study participation versus those who declined. By analyzing demographic differences, we are able to ensure the generalizability of study outcomes and to aid in future prospective research design, with the ultimate goal of recognizing and ameliorating research disparities. METHODS We conducted a secondary analysis to investigate demographic differences in patients who consented to versus declined study participation, in an effort to confirm the external validity of the study results and ensure minority populations most affected by SARS-CoV-2 infection were accurately represented. An IRB waiver was obtained to conduct retrospective chart review for demographic data collection of all patients approached for the COVID-19 Analysis on Perinatal Specimens Related to ExpoSure (CARES) research study. Pregnant patients with SARS-CoV-2 infection were identified at a single hospital center and approached either in person or via phone, with a translator if primary language listed as non-English. Demographic variables including race, ethnicity, primary language, and insurance type were obtained from the electronic medical record and analyzed via Chi-square to determine significant differences between individuals who consented to participation and those who declined participation. RESULTS One hundred and fifty-eight pregnant patients with SARS-CoV-2 infection were approached for CARES study participation. Eighty-nine patients consented to study participation, while 69 declined study participation. A retrospective chart review was conducted on all 158 patients. Patients who identified as Black race or non-White race were more likely to decline participation (23.2%, p = .031, 68.1%, p = .026), compared to patients who identified as White (31.9%) (Table 1). Patients with public insurance were also more likely to decline study participation (72.5%, p = .049) compared to those with private insurance (27.5%). There was no significant difference between primary language spoken or ethnicity in patients who participated or declined. There was no difference in study participation between patients who identified as Asian race or Other race, compared to patients who identified as White race. CONCLUSIONS We found significant differences in race and insurance type between pregnant patients with SARS-CoV-2 infection who consented versus declined research study participation. Our study showed that patients who identify as Black race or have public insurance are less likely to consent to research study participation. However, when demographics of consented patients are compared to county, state, and national demographics of female patients age 18-49 with confirmed SARS-CoV-2 infection obtained from a dataset collected by the Center for Disease Control and Prevention (CDC), there was no significant difference between race representation of patients who consented to study participation. This suggests that though the external validity of the CARES study is confirmed, more efforts need to be made to address racial and socioeconomic disparities in research participation.
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Affiliation(s)
- Kelly Robertson
- Department of Obstetrics and Gynecology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kimberly Reimold
- Department of Obstetrics and Gynecology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ann M Moormann
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Raquel Binder
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kristen A Matteson
- Department of Obstetrics and Gynecology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Heidi K Leftwich
- Department of Obstetrics and Gynecology, University of Massachusetts Chan Medical School, Worcester, MA, USA
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Willard KA, Barry AP, Oduor CI, Ong'echa JM, Bailey JA, Moormann AM, Luftig MA. Viral and host factors drive a type 1 Epstein-Barr virus spontaneous lytic phenotype. mBio 2023; 14:e0220423. [PMID: 37971257 PMCID: PMC10746244 DOI: 10.1128/mbio.02204-23] [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: 08/22/2023] [Accepted: 09/21/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Epstein-Barr virus (EBV) infects over 95% of adults worldwide. Given its connection to various cancers and autoimmune disorders, it is important to understand the mechanisms by which infection with EBV can lead to these diseases. In this study, we describe an unusual spontaneous lytic phenotype in EBV strains isolated from Kenyan endemic Burkitt lymphoma patients. Because lytic replication of EBV has been linked to the pathogenesis of various diseases, these data could illuminate viral and host factors involved in this process.
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Affiliation(s)
- Katherine A. Willard
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Ashley P. Barry
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Cliff I. Oduor
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | | | - Jeffrey A. Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
| | - Ann M. Moormann
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Micah A. Luftig
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, North Carolina, USA
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5
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Bucci V, Ward DV, Bhattarai S, Rojas-Correa M, Purkayastha A, Holler D, Qu MD, Mitchell WG, Yang J, Fountain S, Zeamer A, Forconi CS, Fujimori G, Odwar B, Cawley C, Moormann AM, Wessolossky M, Maldonado-Contreras A. The intestinal microbiota predicts COVID-19 severity and fatality regardless of hospital feeding method. mSystems 2023; 8:e0031023. [PMID: 37548476 PMCID: PMC10469851 DOI: 10.1128/msystems.00310-23] [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: 03/29/2023] [Accepted: 06/26/2023] [Indexed: 08/08/2023] Open
Abstract
SARS-CoV-2-positive patients exhibit gut and oral microbiome dysbiosis, which is associated with various aspects of COVID-19 disease (1-4). Here, we aim to identify gut and oral microbiome markers that predict COVID-19 severity in hospitalized patients, specifically severely ill patients compared to moderately ill ones. Moreover, we investigate whether hospital feeding (solid versus enteral), an important cofounder, influences the microbial composition of hospitalized COVID-19 patients. We used random forest classification machine learning models with interpretable secondary analyses. The gut, but not the oral microbiota, was a robust predictor of both COVID-19-related fatality and severity of hospitalized patients, with a higher predictive value than most clinical variables. In addition, perturbations of the gut microbiota due to enteral feeding did not associate with species that were predictive of COVID-19 severity. IMPORTANCE SARS-CoV-2 infection leads to wide-ranging, systemic symptoms with sometimes unpredictable morbidity and mortality. It is increasingly clear that the human microbiome plays an important role in how individuals respond to viral infections. Our study adds to important literature about the associations of gut microbiota and severe COVID-19 illness during the early phase of the pandemic before the availability of vaccines. Increased understanding of the interplay between microbiota and SARS-CoV-2 may lead to innovations in diagnostics, therapies, and clinical predictions.
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Affiliation(s)
- Vanni Bucci
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Program of Microbiome Dynamics, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Center for Microbiome Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Doyle V. Ward
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Program of Microbiome Dynamics, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Center for Microbiome Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Shakti Bhattarai
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Program of Microbiome Dynamics, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Center for Microbiome Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Mayra Rojas-Correa
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Program of Microbiome Dynamics, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Center for Microbiome Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Ayan Purkayastha
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Devon Holler
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Program of Microbiome Dynamics, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Center for Microbiome Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Ming Da Qu
- Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - William G. Mitchell
- Department of Internal Medicine/Pediatrics, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Jason Yang
- Department of Medicine - Internal Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Samuel Fountain
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Abigail Zeamer
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Program of Microbiome Dynamics, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Center for Microbiome Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Catherine S. Forconi
- Department of Medicine - Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Gavin Fujimori
- Department of Medicine - Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Boaz Odwar
- Department of Medicine - Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Caitlin Cawley
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Program of Microbiome Dynamics, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Center for Microbiome Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Ann M. Moormann
- Department of Medicine - Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Mireya Wessolossky
- Department of Medicine - Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Ana Maldonado-Contreras
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Program of Microbiome Dynamics, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Center for Microbiome Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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6
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Muriuki BM, Forconi CS, Kirwa EK, Maina TK, Ariera BO, Bailey JA, Ghansah A, Moormann AM, Ong’echa JM. Evaluation of KIR3DL1/KIR3DS1 allelic polymorphisms in Kenyan children with endemic Burkitt lymphoma. PLoS One 2023; 18:e0275046. [PMID: 37647275 PMCID: PMC10468049 DOI: 10.1371/journal.pone.0275046] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 08/15/2023] [Indexed: 09/01/2023] Open
Abstract
Endemic Burkitt lymphoma (eBL) is a fast-growing germinal center B cell lymphoma, affecting 5-10 per 100,000 children annually, in the equatorial belt of Africa. We hypothesize that co-infections with Plasmodium falciparum (Pf) malaria and Epstein-Barr virus (EBV) impair host natural killer (NK) and T cell responses to tumor cells, and thus increase the risk of eBL pathogenesis. NK cell education is partially controlled by killer immunoglobulin-like receptors and variable expression of KIR3DL1 has been associated with other malignancies. Here, we investigated whether KIR3D-mediated mechanisms contribute to eBL, by testing for an association of KIR3DL1/KIR3DS1 genotypes with the disease in 108 eBL patients and 99 healthy Kenyan children. KIR3DL1 allelic typing and EBV loads were assessed by PCR. We inferred previously observed phenotypes from the genotypes. The frequencies of KIR3DL1/KIR3DL1 and KIR3DL1/KIR3DS1 did not differ significantly between cases and controls. Additionally, none of the study participants was homozygous for KIR3DS1 alleles. EBV loads did not differ by the KIR3DL1 genotypes nor were they different between eBL survivors and non-survivors. Our results suggest that eBL pathogenesis may not simply involve variations in KIR3DL1 and KIR3DS1 genotypes. However, considering the complexity of the KIR3DL1 locus, this study could not exclude a role for copy number variation in eBL pathogenesis.
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Affiliation(s)
- Beatrice M. Muriuki
- West African Center for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Catherine S. Forconi
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States of America
| | - Erastus K. Kirwa
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Titus K. Maina
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Bonface O. Ariera
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Jeffrey A. Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, United States of America
| | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Ann M. Moormann
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States of America
| | - John M. Ong’echa
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
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7
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Leftwich HK, Vargas-Robles D, Rojas-Correa M, Yap YR, Bhattarai S, Ward DV, Fujimori G, Forconi CS, Yeboah T, Carter A, Kastrinakis A, Asirwatham AM, Bucci V, Moormann AM, Maldonado-Contreras A. The microbiota of pregnant women with SARS-CoV-2 and their infants. Microbiome 2023; 11:141. [PMID: 37365606 DOI: 10.1186/s40168-023-01577-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 05/16/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND Infants receive their first bacteria from their birthing parent. This newly acquired microbiome plays a pivotal role in developing a robust immune system, the cornerstone of long-term health. RESULTS We demonstrated that the gut, vaginal, and oral microbial diversity of pregnant women with SARS-CoV-2 infection is reduced, and women with early infections exhibit a different vaginal microbiota composition at the time of delivery compared to their healthy control counterparts. Accordingly, a low relative abundance of two Streptococcus sequence variants (SV) was predictive of infants born to pregnant women with SARS-CoV-2 infection. CONCLUSIONS Our data suggest that SARS-CoV-2 infections during pregnancy, particularly early infections, are associated with lasting changes in the microbiome of pregnant women, compromising the initial microbial seed of their infant. Our results highlight the importance of further exploring the impact of SARS-CoV-2 on the infant's microbiome-dependent immune programming. Video Abstract.
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Affiliation(s)
- Heidi K Leftwich
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of Massachusetts Memorial Health, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Daniela Vargas-Robles
- Department of Microbiology and Physiological Systems, Program of Microbiome Dynamics, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Mayra Rojas-Correa
- Department of Microbiology and Physiological Systems, Program of Microbiome Dynamics, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Yan Rou Yap
- Department of Microbiology and Physiological Systems, Program of Microbiome Dynamics, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Shakti Bhattarai
- Department of Microbiology and Physiological Systems, Program of Microbiome Dynamics, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Doyle V Ward
- Department of Microbiology and Physiological Systems, Program of Microbiome Dynamics, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Gavin Fujimori
- Department of Medicine. Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Catherine S Forconi
- Department of Medicine. Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Tracy Yeboah
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of Massachusetts Memorial Health, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Acara Carter
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of Massachusetts Memorial Health, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Alyssa Kastrinakis
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of Massachusetts Memorial Health, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Alison M Asirwatham
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of Massachusetts Memorial Health, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Vanni Bucci
- Department of Microbiology and Physiological Systems, Program of Microbiome Dynamics, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ann M Moormann
- Department of Medicine. Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ana Maldonado-Contreras
- Department of Microbiology and Physiological Systems, Program of Microbiome Dynamics, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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Saikumar Lakshmi P, Oduor CI, Forconi CS, M'Bana V, Bly C, Gerstein RM, Otieno JA, Ong'echa JM, Münz C, Luftig MA, Brehm MA, Bailey JA, Moormann AM. Endemic Burkitt lymphoma avatar mouse models for exploring inter-patient tumor variation and testing targeted therapies. Life Sci Alliance 2023; 6:e202101355. [PMID: 36878637 PMCID: PMC9990458 DOI: 10.26508/lsa.202101355] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 03/08/2023] Open
Abstract
Endemic Burkitt lymphoma (BL) is a childhood cancer in sub-Saharan Africa characterized by Epstein-Barr virus and malaria-associated aberrant B-cell activation and MYC chromosomal translocation. Survival rates hover at 50% after conventional chemotherapies; therefore, clinically relevant models are necessary to test additional therapies. Hence, we established five patient-derived BL tumor cell lines and corresponding NSG-BL avatar mouse models. Transcriptomics confirmed that our BL lines maintained fidelity from patient tumors to NSG-BL tumors. However, we found significant variation in tumor growth and survival among NSG-BL avatars and in Epstein-Barr virus protein expression patterns. We tested rituximab responsiveness and found one NSG-BL model exhibiting direct sensitivity, characterized by apoptotic gene expression counterbalanced by unfolded protein response and mTOR pro-survival pathways. In rituximab-unresponsive tumors, we observed an IFN-α signature confirmed by the expression of IRF7 and ISG15. Our results demonstrate significant inter-patient tumor variation and heterogeneity, and that contemporary patient-derived BL cell lines and NSG-BL avatars are feasible tools to guide new therapeutic strategies and improve outcomes for these children.
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Affiliation(s)
- Priya Saikumar Lakshmi
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Cliff I Oduor
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Catherine S Forconi
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Viriato M'Bana
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Courtney Bly
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Rachel M Gerstein
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Juliana A Otieno
- Jaramogi Oginga Odinga Teaching and Referral Hospital, Ministry of Medical Services, Kisumu, Kenya
| | - John M Ong'echa
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Christian Münz
- Department of Viral Immunobiology, Institute of Experimental Immunology, University of Zürich, Zurich, Switzerland
| | - Micah A Luftig
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Michael A Brehm
- Program in Molecular Medicine and the Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Ann M Moormann
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
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Oluoch PO, Forconi CS, Oduor CI, Ritacco DA, Akala HM, Bailey JA, Juliano JJ, Ong'echa JM, Münz C, Moormann AM. Distinctive Kaposi Sarcoma-Associated Herpesvirus Serological Profile during Acute Plasmodium falciparum Malaria Episodes. Int J Mol Sci 2023; 24:ijms24076711. [PMID: 37047683 PMCID: PMC10095526 DOI: 10.3390/ijms24076711] [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: 02/03/2023] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/14/2023] Open
Abstract
The seroprevalence of Kaposi sarcoma-associated herpesvirus (KSHV) and the incidence of endemic Kaposi sarcoma (KS) overlap with regions of malaria endemicity in sub-Saharan Africa. Multiple studies have shown an increased risk of KSHV seroconversion in children from high malaria compared to low malaria regions; however, the impact of acute episodes of Plasmodium falciparum (P. falciparum) malaria on KSHV's biphasic life cycle and lytic reactivation has not been determined. Here, we examined KSHV serological profiles and viral loads in 134 children with acute malaria and 221 healthy children from high malaria regions in Kisumu, as well as 77 healthy children from low malaria regions in Nandi. We assayed KSHV, Epstein-Barr virus (EBV), and P. falciparum malaria antibody responses in these three by multiplexed Luminex assay. We confirmed that KSHV seroprevalence was significantly associated with malaria endemicity (OR = 1.95, 1.18-3.24 95% CI, p = 0.01) with 71-77% seropositivity in high-malaria (Kisumu) compared to 28% in low-malaria (Nandi) regions. Furthermore, KSHV serological profiles during acute malaria episodes were distinct from age-matched non-malaria-infected children from the same region. Paired IgG levels also varied after malaria treatment, with significantly higher anti-ORF59 at day 0 but elevated ORF38, ORF73, and K8.1 at day 3. Acute malaria episodes is characterized by perturbation of KSHV latency in seropositive children, providing further evidence that malaria endemicity contributes to the observed increase in endemic KS incidence in sub-Saharan Africa.
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Affiliation(s)
- Peter O Oluoch
- Division of Infectious Diseases and Immunology, Department of Medicine, Chan Medical School, University of Massachusetts, Worcester, MA 01605, USA
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu 40100, Kenya
| | - Catherine S Forconi
- Division of Infectious Diseases and Immunology, Department of Medicine, Chan Medical School, University of Massachusetts, Worcester, MA 01605, USA
| | - Cliff I Oduor
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu 40100, Kenya
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02903, USA
| | - Dominic A Ritacco
- Division of Infectious Diseases and Immunology, Department of Medicine, Chan Medical School, University of Massachusetts, Worcester, MA 01605, USA
| | - Hoseah M Akala
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu 40100, Kenya
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02903, USA
| | - Jonathan J Juliano
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - John M Ong'echa
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu 40100, Kenya
| | - Christian Münz
- Viral Immunobiology, Institute of Experimental Immunology, University of Zurich, CH-8057 Zurich, Switzerland
| | - Ann M Moormann
- Division of Infectious Diseases and Immunology, Department of Medicine, Chan Medical School, University of Massachusetts, Worcester, MA 01605, USA
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10
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Vance GH, Lotodo T, Kigen N, Stohler R, Choi H, Njuguna F, Moormann AM, Kirwa E, Langat S, Loehrer P, Vik T. Improvement of diagnosis in children with Burkitt lymphoma in Kenya: feasibility study for the implementation of fluorescence in situ hybridisation testing for MYC and the MYC/IGH translocation. Ecancermedicalscience 2023; 17:1505. [PMID: 37113725 PMCID: PMC10129372 DOI: 10.3332/ecancer.2023.1505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Indexed: 02/11/2023] Open
Abstract
Background Indiana University (IU) initiated fluorescence in situ hybridisation (FISH) methodology for Burkitt Lymphoma (BL) to advance the accuracy and speed of diagnosis in the AMPATH Reference Laboratory at Moi Teaching and Referral Hospital (MTRH) in Eldoret, Kenya. Standard diagnostic testing for BL at MTRH includes morphology of the biopsy specimen or aspirate and limited immunohistochemistry panels. Methods Tumour specimens from 19 children enrolled from 2016 to 2018 in a prospective study to improve the diagnosis and staging of children with suspected BL were evaluated. Touch preps from biopsy specimens or smears from fine needle aspiration were collected, stained with Giemsa and/or H&E and reviewed by pathologists to render a provisional diagnosis. Unstained slides were stored and later processed for FISH. Duplicate slides were split between two laboratories for analysis. Flow cytometry results were available for all specimens. Results from the newly established FISH laboratory in Eldoret, Kenya were cross-validated in Indianapolis, Indiana. Results Concordance studies found 18 of 19 (95%) of specimens studied yielded analysable FISH results for one or both probe sets (MYC and MYC/IGH) in both locations. There was 94% (17/18) concordance of results between the two FISH laboratories. FISH results were 100% concordant for the 16 specimens with a histopathological diagnosis of BL and two of three non-BL cases (one case no result in IU FISH lab). FISH was similarly concordant with flow cytometry for specimens with positive flow results with the exception of a nasopharyngeal tumour with positive flow results for CD10 and CD20 but was negative by FISH. The modal turn-around time for FISH testing on retrospective study specimens performed in Kenya ranged between 24 and 72 hours. Conclusion FISH testing was established, and a pilot study performed, to assess the feasibility of FISH as a diagnostic tool for the determination of BL in a Kenyan paediatric population. This study supports FISH in limited resource settings to improve the accuracy and speed of diagnosis of BL in Africa.
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Affiliation(s)
- Gail H Vance
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Teresa Lotodo
- Department of Pathology, Moi University, Eldoret, Kenya
| | | | - Ryan Stohler
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Haki Choi
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Festus Njuguna
- Department of Child Health and Pediatrics, Moi University, Eldoret, Kenya
| | - Ann M Moormann
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Erastus Kirwa
- Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | | | - Patrick Loehrer
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Terry Vik
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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11
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Agwati EO, Oduor CI, Ayieko C, Ong’echa JM, Moormann AM, Bailey JA. Profiling genome-wide recombination in Epstein Barr virus reveals type-specific patterns and associations with endemic-Burkitt lymphoma. Virol J 2022; 19:208. [PMID: 36482473 PMCID: PMC9733152 DOI: 10.1186/s12985-022-01942-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Endemic Burkitt lymphoma (eBL) is potentiated through the interplay of Epstein Barr virus (EBV) and holoendemic Plasmodium falciparum malaria. To better understand EBV's biology and role in eBL, we characterized genome-wide recombination sites and patterns as a source of genetic diversity in EBV genomes in our well-defined population of eBL cases and controls from Western Kenya. METHODS EBV genomes representing 54 eBL cases and 32 healthy children from the same geographic region in Western Kenya that we previously sequenced were analyzed. Whole-genome multiple sequence alignment, recombination analyses, and phylogenetic inference were made using multiple alignment with fast Fourier transform, recombination detection program 4, and molecular evolutionary genetics analysis. RESULTS We identified 28 different recombination events and 71 (82.6%) of the 86 EBV genomes analyzed contained evidence of one or more recombinant segments. Associated recombination breakpoints were found to occur in a total of 42 different genes, with only 7 (16.67%) being latent genes. Recombination events were major drivers of clustering within genome-wide phylogenetic trees. The occurrence of recombination segments was comparable between genomes from male and female participants and across age groups. More recombinant segments were found in EBV type 1 genomes (p = 6.4e - 06) and the genomes from the eBLs (p = 0.037). Two recombination events were enriched in the eBLs; event 47 (OR = 4.07, p = 0.038) and event 50 (OR = 14.24, p = 0.012). CONCLUSIONS EBV genomes have extensive evidence of recombination likely acquired progressively and cumulatively over time. Recombination patterns display a heterogeneous occurrence rate across the genome with enrichment in lytic genes. Overall, recombination appears to be a major evolutionary force impacting EBV diversity and genome structure with evidence of the association of specific recombinants with eBL.
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Affiliation(s)
- Eddy O. Agwati
- grid.442486.80000 0001 0744 8172Department of Zoology, Maseno University, Maseno, Kenya ,grid.33058.3d0000 0001 0155 5938Center for Global Health Research (CGHR), Kenya Medical Research Institute, Kisumu, Kenya
| | - Cliff I. Oduor
- grid.40263.330000 0004 1936 9094Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02903 USA
| | - Cyrus Ayieko
- grid.442486.80000 0001 0744 8172Department of Zoology, Maseno University, Maseno, Kenya
| | - John Michael Ong’echa
- grid.33058.3d0000 0001 0155 5938Center for Global Health Research (CGHR), Kenya Medical Research Institute, Kisumu, Kenya
| | - Ann M. Moormann
- grid.168645.80000 0001 0742 0364Program in Molecular Medicine and the Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA
| | - Jeffrey A. Bailey
- grid.40263.330000 0004 1936 9094Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02903 USA
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12
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Binder RA, Fujimori GF, Forconi CS, Reed GW, Silva LS, Lakshmi PS, Higgins A, Cincotta L, Dutta P, Salive MC, Mangolds V, Anya O, Calvo Calle JM, Nixon T, Tang Q, Wessolossky M, Wang Y, Ritacco DA, Bly CS, Fischinger S, Atyeo C, Oluoch PO, Odwar B, Bailey JA, Maldonado-Contreras A, Haran JP, Schmidt AG, Cavacini L, Alter G, Moormann AM. SARS-CoV-2 Serosurveys: How Antigen, Isotype and Threshold Choices Affect the Outcome. J Infect Dis 2022; 227:371-380. [PMID: 36314635 PMCID: PMC9891417 DOI: 10.1093/infdis/jiac431] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/21/2022] [Accepted: 10/27/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Evaluating the performance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serological assays and clearly articulating the utility of selected antigens, isotypes, and thresholds is crucial to understanding the prevalence of infection within selected communities. METHODS This cross-sectional study, implemented in 2020, screened PCRconfirmed coronavirus disease 2019 patients (n 86), banked prepandemic and negative samples (n 96), healthcare workers and family members (n 552), and university employees (n 327) for antiSARS-CoV-2 receptor-binding domain, trimeric spike protein, and nucleocapsid protein immunoglobulin (Ig)G and IgA antibodies with a laboratory-developed enzyme-linked immunosorbent assay and tested how antigen, isotype and threshold choices affected the seroprevalence outcomes. The following threshold methods were evaluated: (i) mean 3 standard deviations of the negative controls; (ii) 100 specificity for each antigen-isotype combination; and (iii) the maximal Youden index. RESULTS We found vastly different seroprevalence estimates depending on selected antigens and isotypes and the applied threshold method, ranging from 0.0 to 85.4. Subsequently, we maximized specificity and reported a seroprevalence, based on more than one antigen, ranging from 9.3 to 25.9. CONCLUSIONS This study revealed the importance of evaluating serosurvey tools for antigen-, isotype-, and threshold-specific sensitivity and specificity, to interpret qualitative serosurvey outcomes reliably and consistently across studies.
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Affiliation(s)
- Raquel A Binder
- Correspondence: Raquel A. Binder, University of Massachusetts Chan Medical School, Worcester, MA 01605 ()
| | | | | | - George W Reed
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Leandro S Silva
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Priya Saikumar Lakshmi
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Amanda Higgins
- Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Lindsey Cincotta
- Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Protiva Dutta
- Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Marie-Claire Salive
- Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Virginia Mangolds
- Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Otuwe Anya
- Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - J Mauricio Calvo Calle
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Thomas Nixon
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Qiushi Tang
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Mireya Wessolossky
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Yang Wang
- MassBiologics, University of Massachusetts Medical School, Boston, Massachusetts, USA
| | - Dominic A Ritacco
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Courtney S Bly
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | | | - Caroline Atyeo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Peter O Oluoch
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Boaz Odwar
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, Rhode Island, USA
| | - Ana Maldonado-Contreras
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - John P Haran
- Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA,Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA,Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Lisa Cavacini
- MassBiologics, University of Massachusetts Medical School, Boston, Massachusetts, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
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13
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Becerra-Artiles A, Calvo-Calle JM, Co MD, Nanaware PP, Cruz J, Weaver GC, Lu L, Forconi C, Finberg RW, Moormann AM, Stern LJ. Broadly recognized, cross-reactive SARS-CoV-2 CD4 T cell epitopes are highly conserved across human coronaviruses and presented by common HLA alleles. Cell Rep 2022; 39:110952. [PMID: 35675811 PMCID: PMC9135679 DOI: 10.1016/j.celrep.2022.110952] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 12/18/2021] [Revised: 04/03/2022] [Accepted: 05/23/2022] [Indexed: 11/24/2022] Open
Abstract
Sequence homology between SARS-CoV-2 and common-cold human coronaviruses (HCoVs) raises the possibility that memory responses to prior HCoV infection can affect T cell response in COVID-19. We studied T cell responses to SARS-CoV-2 and HCoVs in convalescent COVID-19 donors and identified a highly conserved SARS-CoV-2 sequence, S811-831, with overlapping epitopes presented by common MHC class II proteins HLA-DQ5 and HLA-DP4. These epitopes are recognized by low-abundance CD4 T cells from convalescent COVID-19 donors, mRNA vaccine recipients, and uninfected donors. TCR sequencing revealed a diverse repertoire with public TCRs. T cell cross-reactivity is driven by the high conservation across human and animal coronaviruses of T cell contact residues in both HLA-DQ5 and HLA-DP4 binding frames, with distinct patterns of HCoV cross-reactivity explained by MHC class II binding preferences and substitutions at secondary TCR contact sites. These data highlight S811-831 as a highly conserved CD4 T cell epitope broadly recognized across human populations.
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Affiliation(s)
| | | | - Mary Dawn Co
- Department of Medicine, UMass Chan Medical School, Worcester, MA 01655, USA
| | - Padma P. Nanaware
- Department of Pathology, UMass Chan Medical School, Worcester, MA 01655, USA
| | - John Cruz
- Department of Pathology, UMass Chan Medical School, Worcester, MA 01655, USA
| | - Grant C. Weaver
- Department of Pathology, UMass Chan Medical School, Worcester, MA 01655, USA
| | - Liying Lu
- Department of Pathology, UMass Chan Medical School, Worcester, MA 01655, USA
| | - Catherine Forconi
- Department of Medicine, UMass Chan Medical School, Worcester, MA 01655, USA
| | - Robert W. Finberg
- Department of Medicine, UMass Chan Medical School, Worcester, MA 01655, USA
| | - Ann M. Moormann
- Department of Medicine, UMass Chan Medical School, Worcester, MA 01655, USA
| | - Lawrence J. Stern
- Department of Pathology, UMass Chan Medical School, Worcester, MA 01655, USA,Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA 01655, USA,Corresponding author
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14
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Topazian HM, Moser KA, Ngasala B, Oluoch PO, Forconi CS, Mhamilawa LE, Aydemir O, Kharabora O, Deutsch-Feldman M, Read AF, Denton M, Lorenzo A, Mideo N, Ogutu B, Moormann AM, Mårtensson A, Odwar B, Bailey JA, Akala H, Ong'echa JM, Juliano JJ. Low Complexity of Infection Is Associated With Molecular Persistence of Plasmodium falciparum in Kenya and Tanzania. Front Epidemiol 2022; 2:852237. [PMID: 38455314 PMCID: PMC10910917 DOI: 10.3389/fepid.2022.852237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/06/2022] [Indexed: 03/09/2024]
Abstract
Background Plasmodium falciparum resistance to artemisinin-based combination therapies (ACTs) is a threat to malaria elimination. ACT-resistance in Asia raises concerns for emergence of resistance in Africa. While most data show high efficacy of ACT regimens in Africa, there have been reports describing declining efficacy, as measured by both clinical failure and prolonged parasite clearance times. Methods Three hundred children aged 2-10 years with uncomplicated P. falciparum infection were enrolled in Kenya and Tanzania after receiving treatment with artemether-lumefantrine. Blood samples were taken at 0, 24, 48, and 72 h, and weekly thereafter until 28 days post-treatment. Parasite and host genetics were assessed, as well as clinical, behavioral, and environmental characteristics, and host anti-malarial serologic response. Results While there was a broad range of clearance rates at both sites, 85% and 96% of Kenyan and Tanzanian samples, respectively, were qPCR-positive but microscopy-negative at 72 h post-treatment. A greater complexity of infection (COI) was negatively associated with qPCR-detectable parasitemia at 72 h (OR: 0.70, 95% CI: 0.53-0.94), and a greater baseline parasitemia was marginally associated with qPCR-detectable parasitemia (1,000 parasites/uL change, OR: 1.02, 95% CI: 1.01-1.03). Demographic, serological, and host genotyping characteristics showed no association with qPCR-detectable parasitemia at 72 h. Parasite haplotype-specific clearance slopes were grouped around the mean with no association detected between specific haplotypes and slower clearance rates. Conclusions Identifying risk factors for slow clearing P. falciparum infections, such as COI, are essential for ongoing surveillance of ACT treatment failure in Kenya, Tanzania, and more broadly in sub-Saharan Africa.
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Affiliation(s)
- Hillary M. Topazian
- Department of Infectious Disease Epidemiology, Imperial College, London, United Kingdom
| | - Kara A. Moser
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
| | - Billy Ngasala
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Peter O. Oluoch
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States
- Center for Global Health Research, Kenyan Medical Research Institute, Kisumu, Kenya
| | - Catherine S. Forconi
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Lwidiko E. Mhamilawa
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Women's and Children's Health, International Maternal and Child Health, Uppsala University, Uppsala, Sweden
| | - Ozkan Aydemir
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, United States
| | - Oksana Kharabora
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
| | - Molly Deutsch-Feldman
- Department of Epidemiology, Gillings School of Global Public Health, Chapel Hill, NC, United States
| | - Andrew F. Read
- Department of Entomology, Penn State University, University Park, PA, United States
| | - Madeline Denton
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
| | - Antonio Lorenzo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Bernhards Ogutu
- Center for Global Health Research, Kenyan Medical Research Institute, Kisumu, Kenya
| | - Ann M. Moormann
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Andreas Mårtensson
- Department of Women's and Children's Health, International Maternal and Child Health, Uppsala University, Uppsala, Sweden
| | - Boaz Odwar
- Center for Global Health Research, Kenyan Medical Research Institute, Kisumu, Kenya
| | - Jeffrey A. Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, United States
| | - Hoseah Akala
- Center for Global Health Research, Kenyan Medical Research Institute, Kisumu, Kenya
| | | | - Jonathan J. Juliano
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
- Department of Epidemiology, Gillings School of Global Public Health, Chapel Hill, NC, United States
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
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15
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Figueiredo JC, Hirsch FR, Kushi LH, Nembhard WN, Crawford JM, Mantis N, Finster L, Merin NM, Merchant A, Reckamp KL, Melmed GY, Braun J, McGovern D, Parekh S, Corley DA, Zohoori N, Amick BC, Du R, Gregersen PK, Diamond B, Taioli E, Sariol C, Espino A, Weiskopf D, Gifoni A, Brien J, Hanege W, Lipsitch M, Zidar DA, McAlearney AS, Wajnberg A, LaBaer J, Lewis EY, Binder RA, Moormann AM, Forconi C, Forrester S, Batista J, Schieffelin J, Kim D, Biancon G, VanOudenhove J, Halene S, Fan R, Barouch DH, Alter G, Pinninti S, Boppana SB, Pati SK, Latting M, Karaba AH, Roback J, Sekaly R, Neish A, Brincks AM, Granger DA, Karger AB, Thyagarajan B, Thomas SN, Klein SL, Cox AL, Lucas T, Furr-Holden D, Key K, Jones N, Wrammerr J, Suthar M, Yu Wong S, Bowman NM, Simon V, Richardson LD, McBride R, Krammer F, Rana M, Kennedy J, Boehme K, Forrest C, Granger SW, Heaney CD, Knight Lapinski M, Wallet S, Baric RS, Schifanella L, Lopez M, Fernández S, Kenah E, Panchal AR, Britt WJ, Sanz I, Dhodapkar M, Ahmed R, Bartelt LA, Markmann AJ, Lin JT, Hagan RS, Wolfgang MC, Skarbinski J. Mission, Organization and Future Direction of the Serological Sciences Network for COVID-19 (SeroNet) Epidemiologic Cohort Studies. Open Forum Infect Dis 2022; 9:ofac171. [PMID: 35765315 PMCID: PMC9129196 DOI: 10.1093/ofid/ofac171] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/22/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Global efforts are needed to elucidate the epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the underlying cause of coronavirus disease 2019 (COVID-19) including seroprevalence, risk factors and long-term sequelae, as well as immune responses following vaccination across populations and the social dimensions of prevention and treatment strategies. In the U.S., the National Cancer Institute in partnership with the National Institute of Allergy and Infectious Diseases, established the SARS-CoV-2 Serological Sciences Network (SeroNet) as the nation’s largest coordinated effort to study COVID-19. The network is comprised of multidisciplinary researchers bridging gaps and fostering collaborations between immunologists, epidemiologists, virologists, clinicians and clinical laboratories, social and behavioral scientists, policy makers, data scientists, and community members. In total, 49 institutions form the SeroNet consortium to study individuals with cancer, autoimmune disease, inflammatory bowel diseases, cardiovascular diseases, HIV, transplant recipients, as well as otherwise healthy pregnant women, children, college students, and high-risk occupational workers (including health care workers and first responders). Several studies focus on underrepresented populations, including ethnic minorities and rural communities. To support integrative data analyses across SeroNet studies, efforts are underway to define common data elements for standardized serology measurements, cellular and molecular assays, self-reported data, treatment, and clinical outcomes. In this paper, we discuss the overarching framework for SeroNet epidemiology studies, critical research questions under investigation, and data accessibility for the worldwide scientific community. Lessons learned will help inform preparedness and responsiveness to future emerging diseases.
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Affiliation(s)
- Jane C Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Fred R Hirsch
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lawrence H Kushi
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Wendy N Nembhard
- Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - James M Crawford
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Nicholas Mantis
- Division of Infectious Diseases Wadsworth Center, New York State Department of Health, New York, NY, USA
| | - Laurel Finster
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Noah M Merin
- Division of Hematology and Cellular Therapy, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Akil Merchant
- Division of Hematology and Cellular Therapy, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Karen L Reckamp
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Gil Y Melmed
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Los Angeles, CA, USA
| | - Jonathan Braun
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Los Angeles, CA, USA
| | - Dermot McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Los Angeles, CA, USA
| | - Samir Parekh
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Douglas A Corley
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Namvar Zohoori
- Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Benjamin C Amick
- Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ruofei Du
- Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Peter K Gregersen
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Betty Diamond
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Emanuela Taioli
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carlos Sariol
- Unit of Comparative Medicine, University of Puerto Rico, Medical Sciences, San Juan, PR
| | - Ana Espino
- Unit of Comparative Medicine, University of Puerto Rico, Medical Sciences, San Juan, PR
| | | | - Alba Gifoni
- La Jolla Institute of Immunology, La Jolla CA, USA
| | - James Brien
- Department of Molecular Microbiology & Immunology, Saint Louis University, St. Louis MI, USA
| | - William Hanege
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Bethesda, MD, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Bethesda, MD, USA
| | - David A Zidar
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Ann Scheck McAlearney
- Department of Family and Community Medicine, Ohio State University College of Medicine, Columbus, OH, USA
| | - Ania Wajnberg
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joshua LaBaer
- Biodesign Virginia G. Piper Center for Personalized Diagnostics, Arizona State University, Tempe AZ, USA
| | - E Yvonne Lewis
- Department of Public Health, Michigan State University, Flint, MI, USA
| | - Raquel A Binder
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ann M Moormann
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Catherine Forconi
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Sarah Forrester
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jennifer Batista
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - John Schieffelin
- Department of Pediatrics, Tulane University School of Medicine, New Orleans, LA, USA
| | - Dongjoo Kim
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Giulia Biancon
- Section of Hematology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Jennifer VanOudenhove
- Section of Hematology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
- Yale Cancer Center, New Haven, CT, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Cancer Center, New Haven, CT, USA
| | - Dan H Barouch
- The Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Galit Alter
- Ragon Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Swetha Pinninti
- Department of Pediatrics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Suresh B Boppana
- Department of Pediatrics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sunil K Pati
- Department of Pediatrics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Misty Latting
- Department of Pediatrics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Andrew H Karaba
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University, Baltimore, MD, USA
| | - John Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Rafick Sekaly
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Andrew Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Ahnalee M Brincks
- Department of Human Development and Family Studies, College of Social Science, Michigan State University, East Lansing, MI, USA
| | - Douglas A Granger
- Institute for Interdisciplinary Salivary Bioscience Research, University of California at Irvine; Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Amy B Karger
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Stefani N Thomas
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Sabra L Klein
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Andrea L Cox
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University, Baltimore, MD, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Todd Lucas
- Division of Public Health, College of Human Medicine, Michigan State University, East Lansing, MI, USA
| | - Debra Furr-Holden
- Division of Public Health, College of Human Medicine, Michigan State University, East Lansing, MI, USA
| | - Kent Key
- Division of Public Health, College of Human Medicine, Michigan State University, East Lansing, MI, USA
| | - Nicole Jones
- Division of Public Health, College of Human Medicine, Michigan State University, East Lansing, MI, USA
| | - Jens Wrammerr
- Department of Pediatrics, Division of Infectious Disease, Emory University, Atlanta, GA, USA
| | - Mehul Suthar
- Department of Pediatrics, Division of Infectious Disease, Emory University, Atlanta, GA, USA
| | - Serre Yu Wong
- The Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Natalie M Bowman
- University of North Carolina School of Medicine, Division of Infectious Diseases, Chapel Hill, NC, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lynne D Richardson
- Institute for Health Equity Research and Department of Emergency Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Russell McBride
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Meenakshi Rana
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joshua Kennedy
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Karl Boehme
- Department of Microbiology and Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Craig Forrest
- Department of Microbiology and Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Christopher D Heaney
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Maria Knight Lapinski
- Department of Communication, Michigan AgBio Research, Michigan State University, East Lansing, MI, USA
| | - Shannon Wallet
- School of Dentistry, Department of Oral and Craniofacial Health Sciences, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Ralph S Baric
- Gillings School of Global Public Health, Department of Epidemiology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Luca Schifanella
- Division of Surgical Outcomes and Precision Medicine Research, Department of Surgery, University of Minnesota, Minneapolis, MN, USA
| | - Marcos Lopez
- Puerto Rico Public Health Trust, Puerto Rico Science, Technology and Research Trust and University of Puerto Rico at Humacao, Medical Sciences, San Juan, PR, USA
| | - Soledad Fernández
- Department of Biomedical Informatics, Center for Biostatistics, Ohio State University College of Medicine, Columbus, OH, USA
| | - Eben Kenah
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, USA
| | - Ashish R Panchal
- Department of Emergency Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - William J Britt
- Department of Immunology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Iñaki Sanz
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Madhav Dhodapkar
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Rafi Ahmed
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Luther A Bartelt
- Department of Medicine, Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Alena J Markmann
- Department of Medicine, Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jessica T Lin
- Department of Medicine, Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Robert S Hagan
- Department of Medicine, Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Matthew C Wolfgang
- Marsico Lung Institute and Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jacek Skarbinski
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
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16
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Mistry A, Odwar B, Olewe F, Kurtis J, Moormann AM, Ong’echa JM. Pediatric Participant Retention Rates in a Longitudinal Malaria Immunology Study. Am J Trop Med Hyg 2022; 106:tpmd211052. [PMID: 35436763 PMCID: PMC9209909 DOI: 10.4269/ajtmh.21-1052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/20/2021] [Indexed: 11/16/2022] Open
Abstract
The resurgence of drug-resistant Plasmodium falciparum parasites continues to motivate the development of a safe and efficacious malaria vaccine. Immuno-epidemiologic studies of naturally acquired immunity (NAI) have been a useful strategy to identify new malaria vaccine targets. However, retention of pediatric participants throughout longitudinal studies is essential for gathering comprehensive exposure and outcome data. Within the context of a 3-year cohort (N = 400) study involving monthly finger prick and bi-annual venous blood sample collections, we conducted qualitative surveys to assess factors impacting participant retention. Phase 1 was conducted 3 months after enrollment in July 2018 and phase 2, 12 months later. In phase 1, 236 parents/guardians participated in focus groups and three withdrawn participants and 10 community health volunteers (CHVs) in key informant interviews. Qualitative analysis indicated overall satisfaction with the study, with 61.8% (136/220 respondents) reporting no concerns. Focus group discussants associated attendance with benefits such as improved access to comprehensive healthcare services. Community health volunteers reported concerns over village rumors of inappropriate use of blood samples and dangers associated with venous blood draws. Phase 2 involved 205 parents/guardians and revealed continued satisfaction, with 46.3% (95/205) identifying no concerns, but expressed increasing worries regarding the amount of venous blood sample. This concern was reflected in an uptick of missed visits when venous blood samples were scheduled. Future studies will address parental concerns to determine whether community engagement and education measures increase study retention until completion.
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Affiliation(s)
- Anushay Mistry
- University of Massachusetts Chan Medical School, Worcester, Massachusetts
| | - Boaz Odwar
- Kenya Medical Research Institute, Kisumu, Kenya
| | | | | | - Ann M. Moormann
- University of Massachusetts Chan Medical School, Worcester, Massachusetts
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17
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Karger AB, Brien JD, Christen JM, Dhakal S, Kemp TJ, Klein SL, Pinto LA, Premkumar L, Roback JD, Binder RA, Boehme KW, Boppana S, Cordon-Cardo C, Crawford JM, Daiss JL, Dupuis AP, Espino AM, Firpo-Betancourt A, Forconi C, Forrest JC, Girardin RC, Granger DA, Granger SW, Haddad NS, Heaney CD, Hunt DT, Kennedy JL, King CL, Krammer F, Kruczynski K, LaBaer J, Lee FEH, Lee WT, Liu SL, Lozanski G, Lucas T, Mendu DR, Moormann AM, Murugan V, Okoye NC, Pantoja P, Payne AF, Park J, Pinninti S, Pinto AK, Pisanic N, Qiu J, Sariol CA, Simon V, Song L, Steffen TL, Stone ET, Styer LM, Suthar MS, Thomas SN, Thyagarajan B, Wajnberg A, Yates JL, Sobhani K. The Serological Sciences Network (SeroNet) for COVID-19: Depth and Breadth of Serology Assays and Plans for Assay Harmonization. medRxiv 2022:2022.02.27.22271399. [PMID: 35262095 PMCID: PMC8902887 DOI: 10.1101/2022.02.27.22271399] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background In October 2020, the National Cancer Institute (NCI) Serological Sciences Network (SeroNet) was established to study the immune response to COVID-19, and "to develop, validate, improve, and implement serological testing and associated technologies." SeroNet is comprised of 25 participating research institutions partnering with the Frederick National Laboratory for Cancer Research (FNLCR) and the SeroNet Coordinating Center. Since its inception, SeroNet has supported collaborative development and sharing of COVID-19 serological assay procedures and has set forth plans for assay harmonization. Methods To facilitate collaboration and procedure sharing, a detailed survey was sent to collate comprehensive assay details and performance metrics on COVID-19 serological assays within SeroNet. In addition, FNLCR established a protocol to calibrate SeroNet serological assays to reference standards, such as the U.S. SARS-CoV-2 serology standard reference material and First WHO International Standard (IS) for anti-SARS-CoV-2 immunoglobulin (20/136), to facilitate harmonization of assay reporting units and cross-comparison of study data. Results SeroNet institutions reported development of a total of 27 ELISA methods, 13 multiplex assays, 9 neutralization assays, and use of 12 different commercial serological methods. FNLCR developed a standardized protocol for SeroNet institutions to calibrate these diverse serological assays to reference standards. Conclusions SeroNet institutions have established a diverse array of COVID-19 serological assays to study the immune response to SARS-CoV-2 virus and vaccines. Calibration of SeroNet serological assays to harmonize results reporting will facilitate future pooled data analyses and study cross-comparisons.
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Affiliation(s)
- Amy B. Karger
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - James D. Brien
- Department of Molecular Microbiology & Immunology, Saint Louis University, Saint Louis, Missouri
| | - Jayne M. Christen
- Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Santosh Dhakal
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Troy J. Kemp
- Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Sabra L. Klein
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Ligia A. Pinto
- Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC
| | - John D. Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Raquel A. Binder
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts
| | - Karl W. Boehme
- Department of Microbiology & Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Suresh Boppana
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Carlos Cordon-Cardo
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - James M. Crawford
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York
| | | | - Alan P. Dupuis
- Wadsworth Center, New York State Department of Health, Albany, New York
| | - Ana M. Espino
- Department of Microbiology and Medical Zoology, University of Puerto Rico-Medical Sciences Campus, San Juan, Puerto Rico
| | | | - Catherine Forconi
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts
| | - J. Craig Forrest
- Department of Microbiology & Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Roxie C. Girardin
- Wadsworth Center, New York State Department of Health, Albany, New York
| | | | | | - Natalie S. Haddad
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, Georgia
| | - Christopher D. Heaney
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Danielle T. Hunt
- Wadsworth Center, New York State Department of Health, Albany, New York
| | - Joshua L. Kennedy
- Departments of Pediatrics and Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
- Arkansas Children’s Research Institute, Little Rock, Arkansas
| | - Christopher L. King
- Department of Pathology, Case Western Reserve School of Medicine, Cleveland, Ohio
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Kate Kruczynski
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Joshua LaBaer
- Virginia G Piper Center for Personalized Diagnostics, Arizona State University Biodesign Institute, Tempe, Arizona
| | - F. Eun-Hyung Lee
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, Georgia
| | - William T. Lee
- Wadsworth Center, New York State Department of Health, Albany, New York
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York
| | - Shan-Lu Liu
- Center for Retrovirus Research, Department of Veterinary Biosciences, Department of Microbial Infection and Immunity, Viruses and Emerging Pathogens Program, Infectious Disease Institute, The Ohio State University, Columbus, Ohio
| | - Gerard Lozanski
- Department of Pathology, The Ohio State University Medical Center, Columbus, Ohio
| | - Todd Lucas
- Division of Public Health and Department of Epidemiology, College of Human Medicine, Michigan State University, East Lansing, Michigan
| | - Damodara Rao Mendu
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ann M. Moormann
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts
| | - Vel Murugan
- Virginia G Piper Center for Personalized Diagnostics, Arizona State University Biodesign Institute, Tempe, Arizona
| | - Nkemakonam C. Okoye
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York
| | - Petraleigh Pantoja
- Unit of Comparative Medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, Puerto Rico
| | - Anne F. Payne
- Wadsworth Center, New York State Department of Health, Albany, New York
| | - Jin Park
- Virginia G Piper Center for Personalized Diagnostics, Arizona State University Biodesign Institute, Tempe, Arizona
| | - Swetha Pinninti
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Amelia K. Pinto
- Department of Molecular Microbiology & Immunology, Saint Louis University, Saint Louis, Missouri
| | - Nora Pisanic
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Ji Qiu
- Virginia G Piper Center for Personalized Diagnostics, Arizona State University Biodesign Institute, Tempe, Arizona
| | - Carlos A. Sariol
- Unit of Comparative Medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, Puerto Rico
- Department of Internal Medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, Puerto Rico
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Lusheng Song
- Virginia G Piper Center for Personalized Diagnostics, Arizona State University Biodesign Institute, Tempe, Arizona
| | - Tara L. Steffen
- Department of Molecular Microbiology & Immunology, Saint Louis University, Saint Louis, Missouri
| | - E. Taylor Stone
- Department of Molecular Microbiology & Immunology, Saint Louis University, Saint Louis, Missouri
| | - Linda M. Styer
- Wadsworth Center, New York State Department of Health, Albany, New York
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York
| | - Mehul S. Suthar
- Center for Childhood Infections and Vaccines of Children’s Healthcare Atlanta, Department of Pediatrics, Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, Georgia
| | - Stefani N. Thomas
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - Ania Wajnberg
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jennifer L. Yates
- Wadsworth Center, New York State Department of Health, Albany, New York
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York
| | - Kimia Sobhani
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
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18
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Forconi CS, Mulama DH, Saikumar Lakshmi P, Foley J, Otieno JA, Kurtis JD, Berg LJ, Ong’echa JM, Münz C, Moormann AM. Interplay between IL-10, IFN-γ, IL-17A and PD-1 Expressing EBNA1-Specific CD4 + and CD8 + T Cell Responses in the Etiologic Pathway to Endemic Burkitt Lymphoma. Cancers (Basel) 2021; 13:cancers13215375. [PMID: 34771539 PMCID: PMC8582526 DOI: 10.3390/cancers13215375] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/18/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Endemic Burkitt lymphoma (eBL) is a common pediatric cancer in sub-Saharan Africa. The incidence of this aggressive B-cell cancer is linked to Plasmodium falciparum (Pf) malaria and Epstein–Barr virus (EBV) co-infections during childhood. Most eBL tumors contain EBV and are characterized by the Epstein–Barr Nuclear Antigen 1 (EBNA1) latency I pattern of viral gene expression. The aim of our study was to compare the phenotypes and functions of CD4+ and CD8+ T cell responses to EBNA1 in children diagnosed with eBL and in healthy EBV-seropositive children to highlight differences that contribute to the balance between anti-viral immunity and eBL pathogenesis. Abstract Children diagnosed with endemic Burkitt lymphoma (eBL) are deficient in interferon-γ (IFN-γ) responses to Epstein–Barr Nuclear Antigen1 (EBNA1), the viral protein that defines the latency I pattern in this B cell tumor. However, the contributions of immune-regulatory cytokines and phenotypes of the EBNA1-specific T cells have not been characterized for eBL. Using a bespoke flow cytometry assay we measured intracellular IFN-γ, IL-10, IL-17A expression and phenotyped CD4+ and CD8+ T cell effector memory subsets specific to EBNA1 for eBL patients compared to two groups of healthy children with divergent malaria exposures. In response to EBNA1 and a malaria antigen (PfSEA-1A), the three study groups exhibited strikingly different cytokine expression and T cell memory profiles. EBNA1-specific IFN-γ-producing CD4+ T cell response rates were lowest in eBL (40%) compared to children with high malaria (84%) and low malaria (66%) exposures (p < 0.0001 and p = 0.0004, respectively). However, eBL patients did not differ in CD8+ T cell response rates or the magnitude of IFN-γ expression. In contrast, eBL children were more likely to have EBNA1-specific CD4+ T cells expressing IL-10, and less likely to have polyfunctional IFN-γ+IL-10+ CD4+ T cells (p = 0.02). They were also more likely to have IFN-γ+IL-17A+, IFN-γ+ and IL-17A+ CD8+ T cell subsets compared to healthy children. Cytokine-producing T cell subsets were predominantly CD45RA+CCR7+ TNAIVE-LIKE cells, yet PD-1, a marker of persistent activation/exhaustion, was more highly expressed by the central memory (TCM) and effector memory (TEM) T cell subsets. In summary, our study suggests that IL-10 mediated immune regulation and depletion of IFN-γ+ EBNA1-specific CD4+ T cells are complementary mechanisms that contribute to impaired T cell cytotoxicity in eBL pathogenesis.
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Affiliation(s)
- Catherine S. Forconi
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (C.S.F.); (P.S.L.); (J.F.)
| | - David H. Mulama
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu 40100, Kenya; (D.H.M.); (J.M.O.)
| | - Priya Saikumar Lakshmi
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (C.S.F.); (P.S.L.); (J.F.)
| | - Joslyn Foley
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (C.S.F.); (P.S.L.); (J.F.)
| | - Juliana A. Otieno
- Jaramogi Oginga Odinga Teaching and Referral Hospital, Ministry of Medical Services, Kisumu 40100, Kenya;
| | - Jonathan D. Kurtis
- Center for International Health Research, Department of Pathology and Laboratory Medicine, Rhode Island Hospital, The Warren Alpert Medical School of Brown University, Providence, RI 02903, USA;
| | - Leslie J. Berg
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA;
| | - John M. Ong’echa
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu 40100, Kenya; (D.H.M.); (J.M.O.)
| | - Christian Münz
- Department of Viral Immunobiology, Institute of Experimental Immunology, University of Zürich, CH-8057 Zurich, Switzerland;
| | - Ann M. Moormann
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (C.S.F.); (P.S.L.); (J.F.)
- Correspondence: ; Tel.: +508-856-8826
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19
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Haran JP, Bradley E, Zeamer AL, Cincotta L, Salive MC, Dutta P, Mutaawe S, Anya O, Meza-Segura M, Moormann AM, Ward DV, McCormick BA, Bucci V. Inflammation-type dysbiosis of the oral microbiome associates with the duration of COVID-19 symptoms and long COVID. JCI Insight 2021; 6:e152346. [PMID: 34403368 PMCID: PMC8564890 DOI: 10.1172/jci.insight.152346] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [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: 06/15/2021] [Accepted: 08/12/2021] [Indexed: 12/19/2022] Open
Abstract
In the COVID-19 pandemic, caused by SARS-CoV-2, many individuals experience prolonged symptoms, termed long-lasting COVID-19 symptoms (long COVID). Long COVID is thought to be linked to immune dysregulation due to harmful inflammation, with the exact causes being unknown. Given the role of the microbiome in mediating inflammation, we aimed to examine the relationship between the oral microbiome and the duration of long COVID symptoms. Tongue swabs were collected from patients presenting with COVID-19 symptoms. Confirmed infections were followed until resolution of all symptoms. Bacterial composition was determined by metagenomic sequencing. We used random forest modeling to identify microbiota and clinical covariates that are associated with long COVID symptoms. Of the patients followed, 63% developed ongoing symptomatic COVID-19 and 37% went on to long COVID. Patients with prolonged symptoms had significantly higher abundances of microbiota that induced inflammation, such as members of the genera Prevotella and Veillonella, which, of note, are species that produce LPS. The oral microbiome of patients with long COVID was similar to that of patients with chronic fatigue syndrome. Altogether, our findings suggest an association with the oral microbiome and long COVID, revealing the possibility that dysfunction of the oral microbiome may have contributed to this draining disease.
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Affiliation(s)
- John P Haran
- Department of Emergency Medicine.,Department of Microbiology and Physiological Systems.,Program in Microbiome Dynamics, and
| | - Evan Bradley
- Department of Emergency Medicine.,Program in Microbiome Dynamics, and
| | - Abigail L Zeamer
- Department of Microbiology and Physiological Systems.,Program in Microbiome Dynamics, and
| | | | | | | | | | | | | | - Ann M Moormann
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Doyle V Ward
- Department of Microbiology and Physiological Systems.,Program in Microbiome Dynamics, and
| | - Beth A McCormick
- Department of Microbiology and Physiological Systems.,Program in Microbiome Dynamics, and
| | - Vanni Bucci
- Department of Microbiology and Physiological Systems.,Program in Microbiome Dynamics, and
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Muriuki BM, Forconi CS, Oluoch PO, Bailey JA, Ghansah A, Moormann AM, Ong’echa JM. Association of killer cell immunoglobulin-like receptors with endemic Burkitt lymphoma in Kenyan children. Sci Rep 2021; 11:11343. [PMID: 34059753 PMCID: PMC8166913 DOI: 10.1038/s41598-021-90596-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 12/22/2020] [Accepted: 04/09/2021] [Indexed: 02/04/2023] Open
Abstract
Endemic Burkitt lymphoma (eBL) is an aggressive pediatric B cell lymphoma, common in Equatorial Africa. Co-infections with Epstein-Barr virus (EBV) and Plasmodium falciparum, coupled with c-myc translocation are involved in eBL etiology. Infection-induced immune evasion mechanisms to avoid T cell cytotoxicity may increase the role of Natural killer (NK) cells in anti-tumor immunosurveillance. Killer immunoglobulin-like receptor (KIR) genes on NK cells exhibit genotypic and allelic variations and are associated with susceptibility to diseases and malignancies. However, their role in eBL pathogenesis remains undefined. This retrospective study genotyped sixteen KIR genes and compared their frequencies in eBL patients (n = 104) and healthy geographically-matched children (n = 104) using sequence-specific primers polymerase chain reaction (SSP-PCR) technique. The relationship between KIR polymorphisms with EBV loads and eBL pathogenesis was investigated. Possession of ≥ 4 activating KIRs predisposed individuals to eBL (OR = 3.340; 95% CI 1.530-7.825; p = 0.004). High EBV levels were observed in Bx haplogroup (p = 0.016) and AB genotypes (p = 0.042) relative to AA haplogroup and AA genotype respectively, in eBL patients but not in healthy controls. Our results suggest that KIR-mediated NK cell stimulation could mute EBV control, contributing to eBL pathogenesis.
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Affiliation(s)
- Beatrice M. Muriuki
- grid.8652.90000 0004 1937 1485West African Center for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana ,grid.33058.3d0000 0001 0155 5938Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Catherine S. Forconi
- grid.168645.80000 0001 0742 0364Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA USA
| | - Peter O. Oluoch
- grid.33058.3d0000 0001 0155 5938Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya ,grid.168645.80000 0001 0742 0364Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA USA
| | - Jeffrey A. Bailey
- grid.40263.330000 0004 1936 9094Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI USA
| | - Anita Ghansah
- grid.8652.90000 0004 1937 1485Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Ann M. Moormann
- grid.168645.80000 0001 0742 0364Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA USA
| | - John M. Ong’echa
- grid.33058.3d0000 0001 0155 5938Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
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21
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Oluoch PO, Oduor CI, Forconi CS, Ong'echa JM, Münz C, Dittmer DP, Bailey JA, Moormann AM. Kaposi Sarcoma-Associated Herpesvirus Infection and Endemic Burkitt Lymphoma. J Infect Dis 2021; 222:111-120. [PMID: 32072172 DOI: 10.1093/infdis/jiaa060] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 11/26/2019] [Accepted: 02/18/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Endemic Burkitt lymphoma (eBL) is associated with Epstein-Barr virus (EBV) and Plasmodium falciparum malaria coinfections. However, the role of Kaposi sarcoma-associated herpesvirus (KSHV), also endemic in Africa, has not been evaluated as a cofactor in eBL pathogenesis. METHODS Multiplexed seroprofiles for EBV, malaria, and KSHV were generated for 266 eBL patients, 78 non-eBL cancers, and 202 healthy children. KSHV and EBV loads were quantified by PCR. RESULTS KSHV seroprevalence did not differ by study group but was associated with age. Seropositivity, defined by K8.1/LANA or in combination with 5 other KSHV antigens (ORF59, ORF65, ORF61, ORF38, and K5) was associated with antimalarial antibody levels to AMA1 (odds ratio [OR], 2.41, P < .001; OR, 2.07, P < .001) and MSP1 (OR, 2.41, P = .0006; OR, 5.78, P < .001), respectively. KSHV loads did not correlate with antibody levels nor differ across groups but were significantly lower in children with detectable EBV viremia (P = .014). CONCLUSIONS Although KSHV-EBV dual infection does not increase eBL risk, EBV appears to suppress reactivation of KSHV while malaria exposure is associated with KSHV infection and/or reactivation. Both EBV and malaria should, therefore, be considered as potential effect modifiers for KSHV-associated cancers in sub-Saharan Africa.
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Affiliation(s)
- Peter O Oluoch
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Kenya Medical Research Institute/Center for Global Health Research, Kisumu, Kenya
| | - Cliff I Oduor
- Kenya Medical Research Institute/Center for Global Health Research, Kisumu, Kenya.,Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, Rhode Island, USA
| | - Catherine S Forconi
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - John M Ong'echa
- Kenya Medical Research Institute/Center for Global Health Research, Kisumu, Kenya
| | - Christian Münz
- Viral Immunobiology, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Dirk P Dittmer
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, Rhode Island, USA
| | - Ann M Moormann
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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22
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Ondigo BN, Moormann AM, John CC. Time to Reflect on Global Health Agenda in Kenya: A Tribute to our Academic and Biomedical Research Mentors. J Health Care Poor Underserved 2021; 32:xvi-xxi. [PMID: 34120957 DOI: 10.1353/hpu.2021.0085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We submit this column to present a brief biography, a tribute to three departed global health mentors who were instrumental in our careers and for the growth of biomedical research in Kenya. We briefly discuss their educational backgrounds and put forth a set of qualities, values, personal supportive experiences, and achievements that nurtured our careers as scientists. The mentors are Prof. Ayub Opiyo Ofulla, Dr. John F. Kennedy Vulule, and Dr. Peter Odada Sumba. We appeal to the community of researchers in biomedical sciences, global health, and epidemiology who study a particular disease or health risk (conducting interventional and observational research) to mentor, teach, and serve as role models for upcoming scholars. There is a need for a positive and supportive attitude to create a universal environment to nurture the next generation of researchers transcending race, color, nationality, ethnicity, culture, faith, gender identities, sexual orientation, age, ability, and background.
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Forconi CS, Oduor C, Ong’echa JM, Bailey J, Moormann AM. Abstract A60: Transcriptional profile of CD56negCD16pos Natural Killer cells within endemic Burkitt lymphoma. Cancer Res 2020. [DOI: 10.1158/1538-7445.pedca19-a60] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Endemic Burkitt lymphoma (eBL), the most common pediatric cancer in equatorial Africa, has long been associated with two etiologic agents: Epstein-Barr virus (EBV) and Plasmodium falciparum malaria. On the other hand, Natural Killer (NK) cells are essential in the clearance of infected cells as well as play a critical role in tumor immunosurveillance. Despite chronic viral infections as HIV, HCV, which have been found to promote the expansion of a CD56 (negative) NK cell subset with impaired effector function, previous cancer studies have been limited to investigations of CD56dimCD16pos NK cells. We previously published that eBL children had significantly more CD56negCD16pos NK cells compared to age-matched healthy children from a low and high malaria transmission area. Here, we characterized this CD56negCD16pos NK subset using histology staining, multicolor flow cytometry, and RNA-sequencing. We found CD56negCD16pos NK cells to be morphologically similar to CD56dimCD16pos NK cells but had higher expression of FCGR3B (CD16b) (p=0.000008) and MPEG1 (Perforin 2) (p=0.0000007), and lower expression of KLRF1 (NKp80), IL18RAP and IL18R1 (IL18 receptor) (p=0.000003, p=0.000003 and p=0.00005, respectively). Phenotypically, CD56negCD16pos NK cells share characteristics of adaptive NK cells; however, they differ from “memory-like” NK cells, with consistent expression of NKG2C/CD57, lower expression of NKp46 and CD160, and higher expression of KIR3DL1 compared to CD56dimCD16pos NK cells. Finally, higher plasma levels of IL-12p70 and IL-2 (known to help NK cell activation and proliferation) and IL-6 and MIP1a were found in healthy compared to eBL children. Together, these findings suggest that the expansion of CD56negCD16pos NK cells could help explain diminished tumor immunosurveillance and might be a mechanism by which EBV-infected cells evades NK-cell mediated immunity.
Citation Format: Catherine S. Forconi, Cliff Oduor, John M. Ong’echa, Jeff Bailey, Ann M. Moormann. Transcriptional profile of CD56negCD16pos Natural Killer cells within endemic Burkitt lymphoma [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr A60.
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Affiliation(s)
| | - Cliff Oduor
- 2Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University Providence, Providence, RI,
| | - John M. Ong’echa
- 3Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Jeff Bailey
- 2Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University Providence, Providence, RI,
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Forconi CS, Oduor CI, Oluoch PO, Ong'echa JM, Münz C, Bailey JA, Moormann AM. A New Hope for CD56 negCD16 pos NK Cells as Unconventional Cytotoxic Mediators: An Adaptation to Chronic Diseases. Front Cell Infect Microbiol 2020; 10:162. [PMID: 32373555 PMCID: PMC7186373 DOI: 10.3389/fcimb.2020.00162] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 12/16/2019] [Accepted: 03/26/2020] [Indexed: 12/17/2022] Open
Abstract
Natural Killer (NK) cells play an essential role in antiviral and anti-tumoral immune responses. In peripheral blood, NK cells are commonly classified into two major subsets: CD56brightCD16neg and CD56dimCD16pos despite the characterization of a CD56negCD16pos subset 25 years ago. Since then, several studies have described the prevalence of an CD56negCD16pos NK cell subset in viral non-controllers as the basis for their NK cell dysfunction. However, the mechanistic basis for their cytotoxic impairment is unclear. Recently, using a strict flow cytometry gating strategy to exclude monocytes, we reported an accumulation of CD56negCD16pos NK cells in Plasmodium falciparum malaria-exposed children and pediatric cancer patients diagnosed with endemic Burkitt lymphoma (eBL). Here, we use live-sorted cells, histological staining, bulk RNA-sequencing and flow cytometry to confirm that this CD56negCD16pos NK cell subset has the same morphological features as the other NK cell subsets and a similar transcriptional profile compared to CD56dimCD16pos NK cells with only 120 genes differentially expressed (fold change of 1.5, p < 0.01 and FDR<0.05) out of 9235 transcripts. CD56negCD16pos NK cells have a distinct profile with significantly higher expression of MPEG1 (perforin 2), FCGR3B (CD16b), FCGR2A, and FCGR2B (CD32A and B) as well as CD6, CD84, HLA-DR, LILRB1/2, and PDCD1 (PD-1), whereas Interleukin 18 (IL18) receptor genes (IL18RAP and IL18R1), cytotoxic genes such as KLRF1 (NKp80) and NCR1 (NKp46), and inhibitory HAVCR2 (TIM-3) are significantly down-regulated compared to CD56dimCD16pos NK cells. Together, these data confirm that CD56negCD16pos cells are legitimate NK cells, yet their transcriptional and protein expression profiles suggest their cytotoxic potential is mediated by pathways reliant on antibodies such as antibody-dependent cell cytotoxicity (ADCC), antibody-dependent respiratory burst (ADRB), and enhanced by complement receptor 3 (CR3) and FAS/FASL interaction. Our findings support the premise that chronic diseases induce NK cell modifications that circumvent proinflammatory mediators involved in direct cytotoxicity. Therefore, individuals with such altered NK cell profiles may respond differently to NK-mediated immunotherapies, infections or vaccines depending on which cytotoxic mechanisms are being engaged.
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Affiliation(s)
- Catherine S Forconi
- Division of Infectious Diseases, Department of Medicine, University of Massachusetts, Worcester, MA, United States
| | - Cliff I Oduor
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, United States.,Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Peter O Oluoch
- Division of Infectious Diseases, Department of Medicine, University of Massachusetts, Worcester, MA, United States.,Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - John M Ong'echa
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Christian Münz
- Laboratory of Viral Immunology, Experimental Immunology Institute, University of Zurich, Zurich, Switzerland
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, United States
| | - Ann M Moormann
- Division of Infectious Diseases, Department of Medicine, University of Massachusetts, Worcester, MA, United States
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25
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Movassagh M, Oduor C, Forconi C, Moormann AM, Bailey JA. Sensitive detection of EBV microRNAs across cancer spectrum reveals association with decreased survival in adult acute myelocytic leukemia. Sci Rep 2019; 9:20321. [PMID: 31889055 PMCID: PMC6937232 DOI: 10.1038/s41598-019-56472-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 12/06/2019] [Indexed: 02/08/2023] Open
Abstract
Epstein Barr virus (EBV) is the etiologic agent involved in numerous human cancers. After infecting the host, EBV establishes a latent infection, with low levels of messenger RNA (mRNA) and protein expression, evolved to evade immune recognition. Conversely, EBV microRNAs (miRNA) are expressed ubiquitously and abundantly within infected cells. Their role in tumor biology and clinical outcomes across the spectrum of cancer is not fully explained. Here, we applied our bioinformatics pipeline for quantitative EBV miRNA detection to examine sequencing data of 8,955 individual tumor samples across 27 tumor types representing the breadth of cancer. We uncover an association of intermediate levels of viral miRNA with decreased survival in adult acute myeloid leukemia (AML) patients (P = 0.00013). Prognostic modeling of this association suggests that increased EBV miRNA levels represent an independent risk factor for poor patient outcomes. Furthermore, we explore differences in expression between elevated and absent viral miRNA loads in adult AML tumors finding that EBV positivity was associated with proinflammatory signals. Together, given no associations were found for pediatric AML, our analyses suggests EBV positivity has the potential for being a prognostic biomarker and might represent a surrogate measure related to immune impairment in adult patients.
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MESH Headings
- Computational Biology/methods
- Epstein-Barr Virus Infections/complications
- Epstein-Barr Virus Infections/virology
- Gene Expression Regulation, Viral
- Herpesvirus 4, Human/genetics
- Humans
- Kaplan-Meier Estimate
- Leukemia, Myeloid, Acute/complications
- Leukemia, Myeloid, Acute/etiology
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/pathology
- MicroRNAs
- Prognosis
- Proportional Hazards Models
- RNA, Viral
- ROC Curve
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Affiliation(s)
- Mercedeh Movassagh
- Department of Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Cliff Oduor
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
- Department of Biomedical Sciences and Technology, Maseno University, Maseno, Kenya
| | - Catherine Forconi
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ann M Moormann
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jeffrey A Bailey
- Department of Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA.
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA.
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26
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Panea RI, Love CL, Shingleton JR, Reddy A, Bailey JA, Moormann AM, Otieno JA, Ong'echa JM, Oduor CI, Schroeder KMS, Masalu N, Chao NJ, Agajanian M, Major MB, Fedoriw Y, Richards KL, Rymkiewicz G, Miles RR, Alobeid B, Bhagat G, Flowers CR, Ondrejka SL, Hsi ED, Choi WWL, Au-Yeung RKH, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig MA, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus BC, Seshadri V, Kim SY, Gascoyne RD, Levy S, Mukhopadyay M, Dunson DB, Dave SS. The whole-genome landscape of Burkitt lymphoma subtypes. Blood 2019; 134:1598-1607. [PMID: 31558468 PMCID: PMC6871305 DOI: 10.1182/blood.2019001880] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [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] [Received: 06/07/2019] [Accepted: 08/28/2019] [Indexed: 01/10/2023] Open
Abstract
Burkitt lymphoma (BL) is an aggressive, MYC-driven lymphoma comprising 3 distinct clinical subtypes: sporadic BLs that occur worldwide, endemic BLs that occur predominantly in sub-Saharan Africa, and immunodeficiency-associated BLs that occur primarily in the setting of HIV. In this study, we comprehensively delineated the genomic basis of BL through whole-genome sequencing (WGS) of 101 tumors representing all 3 subtypes of BL to identify 72 driver genes. These data were additionally informed by CRISPR screens in BL cell lines to functionally annotate the role of oncogenic drivers. Nearly every driver gene was found to have both coding and non-coding mutations, highlighting the importance of WGS for identifying driver events. Our data implicate coding and non-coding mutations in IGLL5, BACH2, SIN3A, and DNMT1. Epstein-Barr virus (EBV) infection was associated with higher mutation load, with type 1 EBV showing a higher mutational burden than type 2 EBV. Although sporadic and immunodeficiency-associated BLs had similar genetic profiles, endemic BLs manifested more frequent mutations in BCL7A and BCL6 and fewer genetic alterations in DNMT1, SNTB2, and CTCF. Silencing mutations in ID3 were a common feature of all 3 subtypes of BL. In vitro, mass spectrometry-based proteomics demonstrated that the ID3 protein binds primarily to TCF3 and TCF4. In vivo knockout of ID3 potentiated the effects of MYC, leading to rapid tumorigenesis and tumor phenotypes consistent with those observed in the human disease.
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Affiliation(s)
- Razvan I Panea
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
| | - Cassandra L Love
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
| | - Jennifer R Shingleton
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
| | - Anupama Reddy
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI
| | - Ann M Moormann
- Department of Medicine, University of Massachusetts, Worcester, MA
| | - Juliana A Otieno
- Jaramogi Oginga Odinga Teaching and Referral Hospital, Ministry of Health, Kisumu, Kenya
| | | | - Cliff I Oduor
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Kristin M S Schroeder
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
- Bugando Medical Center, Mwanza, Tanzania
| | | | - Nelson J Chao
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
| | - Megan Agajanian
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO
| | - Michael B Major
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO
| | | | | | - Grzegorz Rymkiewicz
- Poland Flow Cytometry Laboratory, Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Institute-Oncology Center, Warsaw, Poland
| | - Rodney R Miles
- Department of Pathology, University of Utah, Salt Lake City, UT
| | - Bachir Alobeid
- Department of Pathology and Cell Biology, Columbia University, New York, NY
| | - Govind Bhagat
- Department of Pathology and Cell Biology, Columbia University, New York, NY
| | | | - Sarah L Ondrejka
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH
| | - Eric D Hsi
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH
| | - William W L Choi
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Rex K H Au-Yeung
- The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Wolfgang Hartmann
- Division of Translational Pathology, Gerhard-Domagk-Institute of Pathology, University Hospital Münster, Münster, Germany
| | - Georg Lenz
- Medical Department A, Hematology, Oncology and Pneumology, University of Münster, Münster, Germany
| | - Howard Meyerson
- Department of Pathology, Case Western Reserve University, Cleveland, OH
| | | | | | - Micah A Luftig
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC
| | - Alexander Waldrop
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
| | - Tushar Dave
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
| | - Devang Thakkar
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
| | - Harshit Sahay
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
| | - Guojie Li
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
| | - Brooke C Palus
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
| | - Vidya Seshadri
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC
| | - So Young Kim
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC
| | - Randy D Gascoyne
- Department of Pathology and Experimental Therapeutics, BC Cancer Agency and BC Cancer Research Centre, Vancouver, BC, Canada
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL; and
| | | | - David B Dunson
- Department of Statistical Science, Duke University, Durham, NC
| | - Sandeep S Dave
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC
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27
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Moormann AM, Nixon CE, Forconi CS. Immune effector mechanisms in malaria: An update focusing on human immunity. Parasite Immunol 2019; 41:e12628. [PMID: 30972776 DOI: 10.1111/pim.12628] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 12/22/2018] [Revised: 04/02/2019] [Accepted: 04/08/2019] [Indexed: 12/12/2022]
Abstract
The past decade has witnessed dramatic decreases in malaria-associated mortality and morbidity around the world. This progress has largely been due to intensified malaria control measures, implementation of rapid diagnostics and establishing a network to anticipate and mitigate antimalarial drug resistance. However, the ultimate tool for malaria prevention is the development and implementation of an effective vaccine. To date, malaria vaccine efforts have focused on determining which of the thousands of antigens expressed by Plasmodium falciparum are instrumental targets of protective immunity. The antigenic variation and antigenic polymorphisms arising in parasite genes under immune selection present a daunting challenge for target antigen selection and prioritization, and is a given caveat when interpreting immune recall responses or results from monovalent vaccine trials. Other immune evasion strategies executed by the parasite highlight the myriad of ways in which it can become a recurrent infection. This review provides an update on immune effector mechanisms in malaria and focuses on our improved ability to interrogate the complexity of human immune system, accelerated by recent methodological advances. Appreciating how the human immune landscape influences the effectiveness and longevity of antimalarial immunity will help explain which conditions are necessary for immune effector mechanisms to prevail.
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Affiliation(s)
- Ann M Moormann
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Christina E Nixon
- Department of Pathology and Lab Medicine, Brown University, Providence, Rhode Island
| | - Catherine S Forconi
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
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Kaymaz Y, Oduor CI, Yu H, Otieno JA, Ong'echa JM, Moormann AM, Bailey JA. Comprehensive Transcriptome and Mutational Profiling of Endemic Burkitt Lymphoma Reveals EBV Type-Specific Differences. Mol Cancer Res 2018; 15:563-576. [PMID: 28465297 PMCID: PMC5471630 DOI: 10.1158/1541-7786.mcr-16-0305] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [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] [Received: 09/12/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 12/17/2022]
Abstract
Endemic Burkitt lymphoma (eBL) is the most common pediatric cancer in malaria-endemic equatorial Africa and nearly always contains Epstein-Barr virus (EBV), unlike sporadic Burkitt lymphoma (sBL) that occurs with a lower incidence in developed countries. Given these differences and the variable clinical presentation and outcomes, we sought to further understand pathogenesis by investigating transcriptomes using RNA sequencing (RNAseq) from multiple primary eBL tumors compared with sBL tumors. Within eBL tumors, minimal expression differences were found based on: anatomical presentation site, in-hospital survival rates, and EBV genome type, suggesting that eBL tumors are homogeneous without marked subtypes. The outstanding difference detected using surrogate variable analysis was the significantly decreased expression of key genes in the immunoproteasome complex (PSMB9/β1i, PSMB10/β2i, PSMB8/β5i, and PSME2/PA28β) in eBL tumors carrying type 2 EBV compared with type 1 EBV. Second, in comparison with previously published pediatric sBL specimens, the majority of the expression and pathway differences was related to the PTEN/PI3K/mTOR signaling pathway and was correlated most strongly with EBV status rather than geographic designation. Third, common mutations were observed significantly less frequently in eBL tumors harboring EBV type 1, with mutation frequencies similar between tumors with EBV type 2 and without EBV. In addition to the previously reported genes, a set of new genes mutated in BL, including TFAP4, MSH6, PRRC2C, BCL7A, FOXO1, PLCG2, PRKDC, RAD50, and RPRD2, were identified. Overall, these data establish that EBV, particularly EBV type 1, supports BL oncogenesis, alleviating the need for certain driver mutations in the human genome. IMPLICATIONS Genomic and mutational analyses of Burkitt lymphoma tumors identify key differences based on viral content and clinical outcomes suggesting new avenues for the development of prognostic molecular biomarkers and therapeutic interventions.
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Affiliation(s)
- Yasin Kaymaz
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Cliff I Oduor
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
- Department of Biomedical Sciences and Technology, Maseno University, Maseno, Kenya
| | - Hongbo Yu
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Juliana A Otieno
- Jaramogi Oginga Odinga Teaching and Referral Hospital, Ministry of Health, Kisumu, Kenya
| | | | - Ann M Moormann
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jeffrey A Bailey
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts.
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
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Oduor CI, Kaymaz Y, Chelimo K, Otieno JA, Ong’echa JM, Moormann AM, Bailey JA. Integrative microRNA and mRNA deep-sequencing expression profiling in endemic Burkitt lymphoma. BMC Cancer 2017; 17:761. [PMID: 29132323 PMCID: PMC5683570 DOI: 10.1186/s12885-017-3711-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 10/30/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Burkitt lymphoma (BL) is characterized by overexpression of the c-myc oncogene, which in the vast majority of cases is a consequence of an IGH/MYC translocation. While myc is the seminal event, BL is a complex amalgam of genetic and epigenetic changes causing dysregulation of both coding and non-coding transcripts. Emerging evidence suggest that abnormal modulation of mRNA transcription via miRNAs might be a significant factor in lymphomagenesis. However, the alterations in these miRNAs and their correlations to their putative mRNA targets have not been extensively studied relative to normal germinal center (GC) B cells. METHODS Using more sensitive and specific transcriptome deep sequencing, we compared previously published small miRNA and long mRNA of a set of GC B cells and eBL tumors. MiRWalk2.0 was used to identify the validated target genes for the deregulated miRNAs, which would be important for understanding the regulatory networks associated with eBL development. RESULTS We found 211 differentially expressed (DE) genes (79 upregulated and 132 downregulated) and 49 DE miRNAs (22 up-regulated and 27 down-regulated). Gene Set enrichment analysis identified the enrichment of a set of MYC regulated genes. Network propagation-based method and correlated miRNA-mRNA expression analysis identified dysregulated miRNAs, including miR-17~95 cluster members and their target genes, which have diverse oncogenic properties to be critical to eBL lymphomagenesis. Central to all these findings, we observed the downregulation of ATM and NLK genes, which represent important regulators in response to DNA damage in eBL tumor cells. These tumor suppressors were targeted by multiple upregulated miRNAs (miR-19b-3p, miR-26a-5p, miR-30b-5p, miR-92a-5p and miR-27b-3p) which could account for their aberrant expression in eBL. CONCLUSION Combined loss of p53 induction and function due to miRNA-mediated regulation of ATM and NLK, together with the upregulation of TFAP4, may be a central role for human miRNAs in eBL oncogenesis. This facilitates survival of eBL tumor cells with the IGH/MYC chromosomal translocation and promotes MYC-induced cell cycle progression, initiating eBL lymphomagenesis. This characterization of miRNA-mRNA interactions in eBL relative to GC B cells provides new insights on miRNA-mediated transcript regulation in eBL, which are potentially useful for new improved therapeutic strategies.
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Affiliation(s)
- Cliff I. Oduor
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
- Department of Biomedical Sciences and Technology, Maseno University, Maseno, Kenya
| | - Yasin Kaymaz
- Department of Bioinformatics & Integrative Biology, University of Massachusetts Medical School, Worcester, MA USA
| | - Kiprotich Chelimo
- Department of Biomedical Sciences and Technology, Maseno University, Maseno, Kenya
| | - Juliana A. Otieno
- Jaramogi Oginga Odinga Teaching and Referral Hospital, Ministry of Health, Kisumu, Kenya
| | | | - Ann M. Moormann
- Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA USA
| | - Jeffrey A. Bailey
- Department of Bioinformatics & Integrative Biology, University of Massachusetts Medical School, Worcester, MA USA
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts Medical School, 368 Plantation St. Albert Sherman Building 41077, Worcester, MA 01605 USA
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Falanga YT, Frascoli M, Kaymaz Y, Forconi C, Ong'echa JM, Bailey JA, Berg LJ, Moormann AM. High pathogen burden in childhood promotes the development of unconventional innate-like CD8+ T cells. JCI Insight 2017; 2:93814. [PMID: 28768916 DOI: 10.1172/jci.insight.93814] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [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: 03/06/2017] [Accepted: 06/20/2017] [Indexed: 11/17/2022] Open
Abstract
Cellular and humoral constituents of the immune system differ significantly between children and adults, yet very little is known about the impact of early-life pathogen exposure on this immunologic transition. We examined CD4+ and CD8+ T cell subsets defined by CCR7 and CD45RA expression in two longitudinal pediatric cohorts experiencing divergent levels of pathogen burden. Using multiparameter flow cytometry, along with serological, cytokine, and transcriptomic data, we show that cumulative pathogen burden promotes the development of atypical CD8dim T cells with an innate-like profile (Granzyme Bhi, IFNγlow, TNFαlow, PLFZhi, ID2hi, IKZF2hi) in contrast to age-matched children residing in a low pathogen-exposure area who display a more conventional CD8bright profile (IFNγ+, TNFα+, CCL4+). Furthermore, these unconventional T cells had stunted proliferation, distinct transcriptional programs, and impaired T cell receptor signaling and were enriched in hallmark TNFα, NF-κB, and IL-6 gene signaling pathways, reminiscent of NK cells and type-1 innate lymphoid cells. Our findings suggest that these unconventional CD8dim T cells arise in a very particular immunological context and may provide a deeper understanding of the heterogeneity in human immune responses.
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Affiliation(s)
- Yves T Falanga
- Department of Pathology.,Program in Molecular Medicine, and
| | | | - Yasin Kaymaz
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | | | | | - Jeffrey A Bailey
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Division of Transfusion Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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Kaymaz Y, Oduor CI, Yu H, Otieno JA, Ong'echa JM, Moormann AM, Bailey JA. Comprehensive Transcriptome and Mutational Profiling of Endemic Burkitt Lymphoma Reveals EBV Type-Specific Differences. Mol Cancer Res 2017; 15:563-576. [PMID: 28465297 PMCID: PMC5471630 DOI: 10.1158/1541-7786.mcr-16-0305-t] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 07/23/2023]
Abstract
UNLABELLED Endemic Burkitt lymphoma (eBL) is the most common pediatric cancer in malaria-endemic equatorial Africa and nearly always contains Epstein-Barr virus (EBV), unlike sporadic Burkitt lymphoma (sBL) that occurs with a lower incidence in developed countries. Given these differences and the variable clinical presentation and outcomes, we sought to further understand pathogenesis by investigating transcriptomes using RNA sequencing (RNAseq) from multiple primary eBL tumors compared with sBL tumors. Within eBL tumors, minimal expression differences were found based on: anatomical presentation site, in-hospital survival rates, and EBV genome type, suggesting that eBL tumors are homogeneous without marked subtypes. The outstanding difference detected using surrogate variable analysis was the significantly decreased expression of key genes in the immunoproteasome complex (PSMB9/β1i, PSMB10/β2i, PSMB8/β5i, and PSME2/PA28β) in eBL tumors carrying type 2 EBV compared with type 1 EBV. Second, in comparison with previously published pediatric sBL specimens, the majority of the expression and pathway differences was related to the PTEN/PI3K/mTOR signaling pathway and was correlated most strongly with EBV status rather than geographic designation. Third, common mutations were observed significantly less frequently in eBL tumors harboring EBV type 1, with mutation frequencies similar between tumors with EBV type 2 and without EBV. In addition to the previously reported genes, a set of new genes mutated in BL, including TFAP4, MSH6, PRRC2C, BCL7A, FOXO1, PLCG2, PRKDC, RAD50, and RPRD2, were identified. Overall, these data establish that EBV, particularly EBV type 1, supports BL oncogenesis, alleviating the need for certain driver mutations in the human genome. IMPLICATIONS Genomic and mutational analyses of Burkitt lymphoma tumors identify key differences based on viral content and clinical outcomes suggesting new avenues for the development of prognostic molecular biomarkers and therapeutic interventions.
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Affiliation(s)
- Yasin Kaymaz
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Cliff I Oduor
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
- Department of Biomedical Sciences and Technology, Maseno University, Maseno, Kenya
| | - Hongbo Yu
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Juliana A Otieno
- Jaramogi Oginga Odinga Teaching and Referral Hospital, Ministry of Health, Kisumu, Kenya
| | | | - Ann M Moormann
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jeffrey A Bailey
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts.
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
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Oduor CI, Movassagh M, Kaymaz Y, Chelimo K, Otieno J, Ong'echa JM, Moormann AM, Bailey JA. Human and Epstein-Barr Virus miRNA Profiling as Predictive Biomarkers for Endemic Burkitt Lymphoma. Front Microbiol 2017; 8:501. [PMID: 28400759 PMCID: PMC5368269 DOI: 10.3389/fmicb.2017.00501] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 11/12/2016] [Accepted: 03/10/2017] [Indexed: 11/17/2022] Open
Abstract
Endemic Burkitt lymphoma (eBL) is an aggressive B cell lymphoma and is associated with Epstein-Barr virus (EBV) and Plasmodium falciparum malaria co-infections. Central to BL oncogenesis is the over-expression of the MYC proto-oncogene which is caused by a translocation of an Ig enhancer in approximation to the myc gene. While whole genome/transcriptome sequencing methods have been used to define driver mutations and transcriptional dysregulation, microRNA (miRNA) dysregulation and differential expression has yet to be fully characterized. We hypothesized that both human and EBV miRNAs contribute to eBL clinical presentation, disease progression, and poor outcomes. Using sensitive and precise deep sequencing, we identified miRNAs from 17 Kenyan eBL patient tumor samples and delineated the complement of both host and EBV miRNAs. One human miRNA, hsa-miR-10a-5p was found to be differentially expressed (DE), being down-regulated in jaw tumors relative to abdominal and in non-survivors compared to survivors. We also examined EBV miRNAs, which made up 2.7% of the miRNA composition in the eBL samples. However, we did not find any significant associations regarding initial patient outcome or anatomical presentation. Gene ontology analysis and pathway enrichment of previously validated targets of miR-10a-5p suggest that it can promote tumor cell survival as well as aid in evasion of apoptosis. To examine miR-10a-5p regulatory effect on gene expression in eBL, we performed a pairwise correlation coefficient analysis on the expression levels of all its validated targets. We found a significant enrichment of correlated target genes consistent with miR-10a-5p impacting expression. The functions of genes and their correlation fit with multiple target genes impacting tumor resilience. The observed downregulation of miR-10a and associated genes suggests a role for miRNA in eBL patient outcomes and has potential as a predictive biomarker that warrants further investigation.
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Affiliation(s)
- Cliff I Oduor
- Center for Global Health Research, Kenya Medical Research InstituteKisumu, Kenya; Department of Biomedical Sciences and Technology, Maseno UniversityMaseno, Kenya
| | - Mercedeh Movassagh
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School Worcester, MA, USA
| | - Yasin Kaymaz
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School Worcester, MA, USA
| | - Kiprotich Chelimo
- Department of Biomedical Sciences and Technology, Maseno University Maseno, Kenya
| | - Juliana Otieno
- Jaramogi Oginga Odinga Teaching and Referral Hospital, Ministry of Medical Services Kisumu, Kenya
| | - John M Ong'echa
- Center for Global Health Research, Kenya Medical Research Institute Kisumu, Kenya
| | - Ann M Moormann
- Program in Molecular Medicine, University of Massachusetts Medical School Worcester, MA, USA
| | - Jeffrey A Bailey
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical SchoolWorcester, MA, USA; Division of Transfusion Medicine, Department of Medicine, University of Massachusetts Medical SchoolWorcester, MA, USA
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Moormann AM, Bailey JA. Malaria - how this parasitic infection aids and abets EBV-associated Burkitt lymphomagenesis. Curr Opin Virol 2016; 20:78-84. [PMID: 27689909 DOI: 10.1016/j.coviro.2016.09.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/06/2016] [Accepted: 09/08/2016] [Indexed: 12/27/2022]
Abstract
Burkitt lymphoma (BL) is >90% EBV-associated when this pediatric cancer is diagnosed in regions heavily burden by endemic Plasmodium falciparum malaria and thus has been geographically classified as endemic BL. The incidence of endemic BL is 10-fold higher compared to BL diagnosed in non-malarious regions of the world. The other forms of BL have been classified as sporadic BL which contain EBV in ∼30% of cases and immunodeficiency BL which occurs in HIV-infected adults with ∼40% of tumors containing EBV. Within malaria endemic regions, epidemiologic studies replicating Denis Burkitt's seminal observation continue to show differences in endemic BL incidence linked to intensity of malaria transmission. However, the mechanisms by which malaria contributes to B cell tumorigenesis have not been resolved to the point of designing cancer prevention strategies. The focus of this review is to summarize our current knowledge regarding the influence of prolonged, chronic malaria exposure on defects in immunosurveillance that would otherwise control persistent EBV infections. And thus, set the stage for ensuing mechanisms by which malaria could instigate B cell activation and aberrant activation-induced cytidine deaminase expression initiating somatic hypermutation and thereby increasing the likelihood of an Ig/Myc translocation, the hallmark of all BL tumors. Malaria appears to play multiple, sequential and simultaneous roles in endemic BL etiology; the complexity of these interactions are being revealed by applying computational methods to human immunology. Remaining questions yet to be addressed and prevention strategies will also be discussed.
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Affiliation(s)
- Ann M Moormann
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Jeffrey A Bailey
- Program for Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
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Buckle G, Maranda L, Skiles J, Ong'echa JM, Foley J, Epstein M, Vik TA, Schroeder A, Lemberger J, Rosmarin A, Remick SC, Bailey JA, Vulule J, Otieno JA, Moormann AM. Factors influencing survival among Kenyan children diagnosed with endemic Burkitt lymphoma between 2003 and 2011: A historical cohort study. Int J Cancer 2016; 139:1231-40. [PMID: 27136063 PMCID: PMC5489240 DOI: 10.1002/ijc.30170] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [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: 03/11/2016] [Accepted: 04/19/2016] [Indexed: 12/23/2022]
Abstract
Discovering how to improve survival and establishing clinical reference points for children diagnosed with endemic Burkitt lymphoma (eBL) in resource-constrained settings has recaptured international attention. Using multivariate analyses, we evaluated 428 children with eBL in Kenya for age, gender, tumor stage, nutritional status, hemoglobin, lactate dehydrogenase (LDH), Epstein-Barr virus (EBV) and Plasmodium falciparum prior to induction of chemotherapy (cyclophosphamide, vincristine, methotrexate and doxorubicin) to identify predictive and prognostic biomarkers of survival. During this 10 year prospective study period, 22% died in-hospital and 78% completed six-courses of chemotherapy. Of those, 16% relapsed or died later; 31% achieved event-free-survival; and 31% were lost to follow-up; the overall one-year survival was 45%. After adjusting for covariates, low hemoglobin (<8 g/dL) and high LDH (>400 mU/ml) were associated with increased risk of death (adjusted Hazard Ratio (aHR) = 1.57 [0.97-2.41]) and aHR = 1.84, [0.91-3.69], respectively). Anemic children with malaria were 3.55 times more likely to die [1.10-11.44] compared to patients without anemia or malarial infection. EBV load did not differ by tumor stage nor was it associated with survival. System-level factors can also contribute to poor outcomes. Children were more likely to die when inadvertently overdosed by more than 115% of the correct dose of cyclophosphamide (a HR = 1.43 [0.84-2.43]) or doxorubicin (a HR = 1.25, [0.66-2.35]), compared with those receiving accurate doses of the respective agent in this setting. This study codifies risk factors associated with poor outcomes for eBL patients in Africa and provides a benchmark by which to assess improvements in survival for new chemotherapeutic approaches.
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Affiliation(s)
- Geoffrey Buckle
- Molecular Medicine, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655
| | - Louise Maranda
- Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North, ASC6.1063, Worcester, MA 01655
| | - Jodi Skiles
- Pediatrics, Hemotology/Oncology, Indiana University School of Medicine, Full address: 705 Riley Hospital Drive, RI 2629, Indianapolis, IN 46202
| | - John Michael Ong'echa
- Center for Global, Health Research Kenya Medical Research Institute, P. O. Box 1578-40100, Kisumu, Kenya
| | - Joslyn Foley
- Molecular Medicine, University of Massachusetts Medical School, 373 Plantation St. Biotech 2, Suite 318, Worcester, MA 01605
| | - Mara Epstein
- Quantitative Health Sciences, University of Massachusetts Medical School, 365 Plantation St. Biotech 1, Suite 100, Worcester, MA 01605
| | - Terry A. Vik
- Pediatrics, Hemotology/Oncology, Indiana University School of Medicine, Full address: 705 Riley Hospital Drive, ROC 4340, Indianapolis, IN 46202
| | | | | | - Alan Rosmarin
- Medicine, Hematology/Oncology, University of Massachusetts Medical School, 55 Lake Avenue North, H8-533, Worcester, MA 01655
| | - Scot C. Remick
- Physician Leader, Oncology and Senior Scientist, Maine Medical Center and Maine Medical Center Research Institute, Portland, ME 04074
| | - Jeffrey A. Bailey
- Medicine, Bioinformatics, University of Massachusetts Medical School, 55 Lake Avenue North, ASC4.1077, Worcester, MA 01655
| | - John Vulule
- Center for Global Health Research, Kenya Medical Research Institute, P. O. Box 1578-40100, Kisumu, Kenya
| | - Juliana A. Otieno
- Jaramogi Oginga Odinga Teaching and Referral Hospital, Kenya Ministry of Health, P.O. Box 849-40100, Kisumu, Kenya
| | - Ann M. Moormann
- Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Biotech 2, Suite 318, Worcester MA, 01605 USA
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Reynaldi A, Schlub TE, Piriou E, Ogolla S, Sumba OP, Moormann AM, Rochford R, Davenport MP. Modeling of EBV Infection and Antibody Responses in Kenyan Infants With Different Levels of Malaria Exposure Shows Maternal Antibody Decay is a Major Determinant of Early EBV Infection. J Infect Dis 2016; 214:1390-1398. [PMID: 27571902 DOI: 10.1093/infdis/jiw396] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 08/17/2016] [Indexed: 11/13/2022] Open
Abstract
The combination of Epstein-Barr virus (EBV) infection and high malaria exposure are risk factors for endemic Burkitt lymphoma, and evidence suggests that infants in regions of high malaria exposure have earlier EBV infection and increased EBV reactivation. In this study we analyzed the longitudinal antibody response to EBV in Kenyan infants with different levels of malaria exposure. We found that high malaria exposure was associated with a faster decline of maternally derived immunoglobulin G antibody to both the EBV viral capsid antigen and EBV nuclear antigen, followed by a more rapid rise in antibody response to EBV antigens in children from the high-malaria-transmission region. We also observed the long-term persistence of anti-viral capsid antigen immunoglobulin M responses in children from the high-malaria region. More rapid decay of maternal antibodies was a major predictor of EBV infection outcome, because decay predicted time to EBV DNA detection, independent of high or low malaria exposure.
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Affiliation(s)
- Arnold Reynaldi
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW Australia, Sydney
| | - Timothy E Schlub
- Sydney School of Public Health, Sydney University, New South Wales, Australia
| | - Erwan Piriou
- Médecins Sans Frontières, Amsterdam, The Netherlands
| | - Sidney Ogolla
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu
| | - Odada P Sumba
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu
| | - Ann M Moormann
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester
| | - Rosemary Rochford
- Department of Immunology and Microbiology, University of Colorado Denver, Aurora
| | - Miles P Davenport
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW Australia, Sydney
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Bowman NM, Juliano JJ, Snider CJ, Kharabora O, Meshnick SR, Vulule J, John CC, Moormann AM. Longevity of Genotype-Specific Immune Responses to Plasmodium falciparum Merozoite Surface Protein 1 in Kenyan Children from Regions of Different Malaria Transmission Intensity. Am J Trop Med Hyg 2016; 95:580-7. [PMID: 27481054 DOI: 10.4269/ajtmh.15-0710] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 06/02/2016] [Indexed: 01/06/2023] Open
Abstract
Naturally acquired immunity to Plasmodium falciparum presents a changing landscape as malaria control programs and vaccine initiatives are implemented. Determining which immunologic indicators remain surrogates of past infection, as opposed to mediators of protection, led us to compare stability of immune responses across regions with divergent malaria transmission intensities. A repeat cross-sectional study of Kenyan children from a malaria-holoendemic area and an epidemic-prone area was used to examine longitudinal antibody and interferon-gamma (IFN-γ) responses to the 3D7 and FVO variants of merozoite surface protein 1 (MSP1). Antibodies to MSP1 were common in both study populations and did not significantly wane over a 21-month time period. IFN-γ responses were less frequent and rapidly disappeared in children after a prolonged period of no malaria transmission. Antibody and IFN-γ responses rarely correlated with each other; however, MSP1-specific IFN-γ response correlated with lack of concurrent P. falciparum parasitemia of the same genotype, though only statistically significantly in the malaria-holoendemic region (odds ratio = 0.31, 95% confidence interval = 0.12-0.84). This study affirms that antimalarial antibodies are informative for evaluation of history of malaria exposure within individuals, whereas cell-mediated immunity, though short lived under natural exposure conditions, might provide an assessment of recent infection and protection from parasitemia.
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Affiliation(s)
- Natalie M Bowman
- Division of Infectious Diseases, University of North Carolina, School of Medicine, Chapel Hill, North Carolina
| | - Jonathan J Juliano
- Division of Infectious Diseases, University of North Carolina, School of Medicine, Chapel Hill, North Carolina. Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina. Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina.
| | - Cynthia J Snider
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Oksana Kharabora
- Division of Infectious Diseases, University of North Carolina, School of Medicine, Chapel Hill, North Carolina
| | - Steven R Meshnick
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - John Vulule
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Chandy C John
- Ryan White Center for Pediatric Infectious Disease and Global Health, Indiana University, Indianapolis, Indiana
| | - Ann M Moormann
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
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Reynaldi A, Schlub TE, Chelimo K, Sumba PO, Piriou E, Ogolla S, Moormann AM, Rochford R, Davenport MP. Impact of Plasmodium falciparum Coinfection on Longitudinal Epstein-Barr Virus Kinetics in Kenyan Children. J Infect Dis 2015; 213:985-91. [PMID: 26531246 DOI: 10.1093/infdis/jiv525] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [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: 06/26/2015] [Accepted: 10/28/2015] [Indexed: 11/12/2022] Open
Abstract
Endemic Burkitt lymphoma is associated with Epstein-Barr virus (EBV) and Plasmodium falciparum coinfection, although how P. falciparum exposure affects the dynamics of EBV infection is unclear. We have used a modeling approach to study EBV infection kinetics in a longitudinal cohort of children living in regions of high and low malaria transmission in Kenya. Residence in an area of high malaria transmission was associated with a higher rate of EBV expansion during primary EBV infection in infants and during subsequent episodes of EBV DNA detection, as well as with longer episodes of EBV DNA detection and shorter intervals between subsequent episodes of EBV DNA detection. In addition, we found that concurrent P. falciparum parasitemia also increases the likelihood of the first and subsequent peaks of EBV in peripheral blood. This suggests that P. falciparum infection is associated with increased EBV growth and contributes to endemic Burkitt lymphoma pathogenesis.
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Affiliation(s)
| | | | | | | | - Erwan Piriou
- SUNY Upstate Medical University, Syracuse, New York
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Dent AE, Nakajima R, Liang L, Baum E, Moormann AM, Sumba PO, Vulule J, Babineau D, Randall A, Davies DH, Felgner PL, Kazura JW. Plasmodium falciparum Protein Microarray Antibody Profiles Correlate With Protection From Symptomatic Malaria in Kenya. J Infect Dis 2015; 212:1429-38. [PMID: 25883384 DOI: 10.1093/infdis/jiv224] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [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: 12/22/2014] [Accepted: 03/25/2015] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Immunoglobulin G antibodies (Abs) to Plasmodium falciparum antigens have been associated with naturally acquired immunity to symptomatic malaria. METHODS We probed protein microarrays covering 824 unique P. falciparum protein features with plasma from residents of a community in Kenya monitored for 12 weeks for (re)infection and symptomatic malaria after administration of antimalarial drugs. P. falciparum proteins recognized by Abs from 88 children (aged 1-14 years) and 86 adults (aged ≥ 18 years), measured at the beginning of the observation period, were ranked by Ab signal intensity. RESULTS Abs from immune adults reacted with a total 163 of 824 P. falciparum proteins. Children gradually acquired Abs to the full repertoire of antigens recognized by adults. Abs to some antigens showed high seroconversion rates, reaching maximal levels early in childhood, whereas others did not reach adult levels until adolescence. No correlation between Ab signal intensity and time to (re)infection was observed. In contrast, Ab levels to 106 antigens were significantly higher in children who were protected from symptomatic malaria compared with those who were not. Abs to antigens predictive of protection included P. falciparum erythrocyte membrane protein 1, merozoite surface protein (MSP) 10, MSP2, liver-stage antigen 3, PF70, MSP7, and Plasmodium helical interspersed subtelomeric domain protein. CONCLUSIONS Protein microarrays may be useful in the search for malaria antigens associated with protective immunity.
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Affiliation(s)
- Arlene E Dent
- Center for Global Health and Diseases, Case Western Reserve University Rainbow Babies and Children's Hospital, Cleveland, Ohio
| | | | - Li Liang
- University of California, Irvine
| | | | - Ann M Moormann
- Center for Global Health Research, University of Massachusetts Medical School, Worcester
| | | | | | | | | | | | | | - James W Kazura
- Center for Global Health and Diseases, Case Western Reserve University
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Taylor SM, Parobek CM, DeConti DK, Kayentao K, Coulibaly SO, Greenwood BM, Tagbor H, Williams J, Bojang K, Njie F, Desai M, Kariuki S, Gutman J, Mathanga DP, Mårtensson A, Ngasala B, Conrad MD, Rosenthal PJ, Tshefu AK, Moormann AM, Vulule JM, Doumbo OK, ter Kuile FO, Meshnick SR, Bailey JA, Juliano JJ. Absence of putative artemisinin resistance mutations among Plasmodium falciparum in Sub-Saharan Africa: a molecular epidemiologic study. J Infect Dis 2015; 211:680-8. [PMID: 25180240 PMCID: PMC4402372 DOI: 10.1093/infdis/jiu467] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [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: 05/28/2014] [Accepted: 07/21/2014] [Indexed: 11/12/2022] Open
Abstract
Plasmodium falciparum parasites that are resistant to artemisinins have been detected in Southeast Asia. Resistance is associated with several polymorphisms in the parasite's K13-propeller gene. The molecular epidemiology of these artemisinin resistance genotypes in African parasite populations is unknown. We developed an assay to quantify rare polymorphisms in parasite populations that uses a pooled deep-sequencing approach to score allele frequencies, validated it by evaluating mixtures of laboratory parasite strains, and then used it to screen P. falciparum parasites from >1100 African infections collected since 2002 from 14 sites across sub-Saharan Africa. We found no mutations in African parasite populations that are associated with artemisinin resistance in Southeast Asian parasites. However, we observed 15 coding mutations, including 12 novel mutations, and limited allele sharing between parasite populations, consistent with a large reservoir of naturally occurring K13-propeller variation. Although polymorphisms associated with artemisinin resistance in P. falciparum in Southeast Asia are not prevalent in sub-Saharan Africa, numerous K13-propeller coding polymorphisms circulate in Africa. Although their distributions do not support a widespread selective sweep for an artemisinin-resistant phenotype, the impact of these mutations on artemisinin susceptibility is unknown and will require further characterization. Rapid, scalable molecular surveillance offers a useful adjunct in tracking and containing artemisinin resistance.
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Affiliation(s)
- Steve M. Taylor
- Division of Infectious Diseases, Department of Medicine
- Duke Global Health Institute, Duke University Medical Center, Durham
- Department of Epidemiology, Gillings School of Global Public Health
| | | | | | - Kassoum Kayentao
- Department of Epidemiology of Parasitic Diseases, Malaria Research and Training Center, Faculty of Medicine, Pharmacy, and Odontostomatology, University of Science, Techniques, and Technologies of Bamako, Mali
- Department of Clinical Sciences, Liverpool School of Tropical Medicine
| | | | - Brian M. Greenwood
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Harry Tagbor
- Department of Community Health, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi
| | - John Williams
- Navrongo Health Research Centre, Ghana Health Service, Navrongo
| | - Kalifa Bojang
- Medical Research Council Laboratories, Banjul, Gambia
| | - Fanta Njie
- Medical Research Council Laboratories, Banjul, Gambia
| | - Meghna Desai
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
- CDC–Kenya
| | | | - Julie Gutman
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Don P. Mathanga
- Malaria Alert Center, University of Malawi College of Medicine, Blantyre
- Department of Community Health, College of Medicine, Lilongwe, Malawi
| | - Andreas Mårtensson
- Malaria Research, Department of Medicine Solna
- Global Health, Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Billy Ngasala
- Department of Parasitology, Muhumbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | | | | | - Antoinette K. Tshefu
- Ecole de Sante Publique, Faculte de Medicine, University of Kinshasa, Democratic Republic of the Congo
| | | | | | - Ogobara K. Doumbo
- Department of Epidemiology of Parasitic Diseases, Malaria Research and Training Center, Faculty of Medicine, Pharmacy, and Odontostomatology, University of Science, Techniques, and Technologies of Bamako, Mali
| | - Feiko O. ter Kuile
- Department of Clinical Sciences, Liverpool School of Tropical Medicine
- Center for Global Health Research, KEMRI, Kisumu, Kenya
| | | | - Jeffrey A. Bailey
- Division of Transfusion Medicine
- Program in Bioinformatics and Integrative Biology, University of Massachusetts School of Medicine, Worcester
| | - Jonathan J. Juliano
- Curriculum in Genetics and Molecular Biology
- Divison of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill
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Noland GS, Jansen P, Vulule JM, Park GS, Ondigo BN, Kazura JW, Moormann AM, John CC. Effect of transmission intensity and age on subclass antibody responses to Plasmodium falciparum pre-erythrocytic and blood-stage antigens. Acta Trop 2015; 142:47-56. [PMID: 25446174 DOI: 10.1016/j.actatropica.2014.10.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 08/27/2014] [Accepted: 10/15/2014] [Indexed: 10/24/2022]
Abstract
Cytophilic immunoglobulin (IgG) subclass responses (IgG1 and IgG3) to Plasmodium falciparum antigens have been associated with protection from malaria, yet the relative importance of transmission intensity and age in generation of subclass responses to pre-erythrocytic and blood-stage antigens have not been clearly defined. We analyzed IgG subclass responses to the pre-erythrocytic antigens CSP, LSA-1, and TRAP and the blood-stage antigens AMA-1, EBA-175, and MSP-1 in asymptomatic residents age 2 years or older in stable (n=116) and unstable (n=96) transmission areas in Western Kenya. In the area of stable malaria transmission, a high prevalence of cytophilic (IgG1 and IgG3) antibodies to each antigen was seen in all age groups. Prevalence and levels of cytophilic antibodies to pre-erythrocytic and blood-stage P. falciparum antigens increased with age in the unstable transmission area, yet IgG1 and IgG3 responses to most antigens for all ages in the unstable transmission area were less prevalent and lower in magnitude than even the youngest age group from the stable transmission area. The dominance of cytophilic responses over non-cytophilic (IgG2 and IgG4) was more pronounced in the stable transmission area, and the ratio of IgG3 over IgG1 generally increased with age. In the unstable transmission area, the ratio of cytophilic to non-cytophilic antibodies did not increase with age, and tended to be IgG3-biased for pre-erythrocytic antigens yet IgG1-biased for blood-stage antigens. The differences between areas could not be attributed to active parasitemia status, as there were minimal differences in antibody responses between those positive and negative for Plasmodium infection by microscopy in the stable transmission area. Individuals in areas of unstable transmission have low cytophilic to non-cytophilic IgG subclass ratios and low IgG3:IgG1 ratios to P. falciparum antigens. These imbalances could contribute to the persistent risk of clinical malaria in these areas and serve as population-level, age-specific biomarkers of transmission.
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Pinkevych M, Chelimo K, Vulule J, Kazura JW, Moormann AM, Davenport MP. Time-to-infection by Plasmodium falciparum is largely determined by random factors. BMC Med 2015; 13:19. [PMID: 25633459 PMCID: PMC4311447 DOI: 10.1186/s12916-014-0252-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 12/10/2014] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The identification of protective immune responses to P. falciparum infection is an important goal for the development of a vaccine for malaria. This requires the identification of susceptible and resistant individuals, so that their immune responses may be studied. Time-to-infection studies are one method for identifying putative susceptible individuals (infected early) versus resistant individuals (infected late). However, the timing of infection is dependent on random factors, such as whether the subject was bitten by an infected mosquito, as well as individual factors, such as their level of immunity. It is important to understand how much of the observed variation in infection is simply due to chance. METHODS We analyse previously published data from a treatment-time-to-infection study of 201 individuals aged 0.5 to 78 years living in Western Kenya. We use a mathematical modelling approach to investigate the role of immunity versus random factors in determining time-to-infection in this cohort. We extend this analysis using a modelling approach to understand what factors might increase or decrease the utility of these studies for identifying susceptible and resistant individuals. RESULTS We find that, under most circumstances, the observed distribution of time-to-infection is consistent with this simply being a random process. We find that age, method for detection of infection (PCR versus microscopy), and underlying force of infection are all factors in determining whether time-to-infection is a useful correlate of immunity. CONCLUSIONS Many epidemiological studies of P. falciparum infection assume that the observed variation in infection outcomes, such as time-to-infection or presence or absence of infection, is determined by host resistance or susceptibility. However, under most circumstances, this distribution appears largely due to the random timing of infection, particularly in children. More direct measurements, such as parasite growth rate, may be more useful than time-to-infection in segregating patients based on their level of immunity.
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Affiliation(s)
| | | | | | | | | | - Miles P Davenport
- Centre for Vascular Research, University of New South Wales Australia, Kensington NSW 2052, Sydney, Australia.
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Abstract
Endemic Burkitt's lymphoma (BL) remains the most prevalent pediatric cancer in sub-Saharan Africa even though it was the first human cancer with a viral etiology described over 50 years ago. Epstein-Barr virus (EBV) was discovered in a BL tumor in 1964 and has since been implicated in other malignancies. The etiology of endemic BL has been linked to EBV and Plasmodium falciparum malaria co-infection. While epidemiologic studies have yielded insight into EBV infection and the etiology of endemic BL, the modulation of viral persistence in children by malaria and deficits in EBV immunosurveillance has more recently been reified. Renewed efforts to design prophylactic and therapeutic EBV vaccines provide hope of preventing EBV-associated BL as well as increasing the ability to cure this cancer.
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Affiliation(s)
- Rosemary Rochford
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY, USA.
| | - Ann M Moormann
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA, 01605, USA.
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Abstract
Determining an immunologic correlate of protection against Plasmodium falciparum malaria has been the holy grail of natural infection studies, and sought after as an endpoint for malaria vaccine trials. An in vitro assay that provides an accurate and precise assessment of protective immunity to malaria would make smaller, short-duration studies feasible, rather than the currently powered study designs that use morbidity or mortality as outcomes. Such a biomarker would be especially desirable in situations where malaria control measures that result in decreases in clinical endpoints and putatively waning protective immunity have been implemented. In an article published in BMC Medicine, Osier and colleagues addressed this problem, and demonstrated that antibodies promoting opsonic phagocytosis of merozoites provide a functional link between antigen-specific responses and protection. Understanding the mechanisms conferring protection against malaria not only improves our knowledge of basic human immunology, but promises to help in the design of an effective malaria vaccine.
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Oduor CI, Chelimo K, Ouma C, Mulama DH, Foley J, Vulule J, Bailey JA, Moormann AM. Interleukin-6 and interleukin-10 gene promoter polymorphisms and risk of endemic Burkitt lymphoma. Am J Trop Med Hyg 2014; 91:649-54. [PMID: 25071000 DOI: 10.4269/ajtmh.13-0616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Overexpression of interleukin-6 (IL-6) and IL-10 in endemic Burkitt lymphoma (eBL) may facilitate tumorigenesis by providing a permissive cytokine milieu. Promoter polymorphisms influence interindividual differences in cytokine production. We hypothesized that children genetically predisposed for elevated cytokine levels may be more susceptible to eBL. Using case-control samples from western Kenya consisting of 117 eBL cases and 88 ethnically matched healthy controls, we tested for the association between eBL risk and IL-10 (rs1800896, rs1800871, and rs1800872) and IL-6 (rs1800795) promoter single nucleotide polymorphisms (SNPs) as well as IL-10 promoter haplotypes. In addition, the association between these variants and Epstein Barr Virus (EBV) load was examined. Results showed that selected IL-10 and IL-6 promoter SNPs and IL-10 promoter haplotypes were not associated with risk eBL or EBV levels in EBV-seropositive children. Findings from this study reveal that common variants within the IL-10 and IL-6 promoters do not independently increase eBL risk in this vulnerable population.
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Affiliation(s)
- Cliff I Oduor
- Department of Biomedical Sciences and Technology, Maseno University, Maseno, Kenya; Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya; Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts; Department of Medicine, Division of Transfusion, and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts; Department of Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Kiprotich Chelimo
- Department of Biomedical Sciences and Technology, Maseno University, Maseno, Kenya; Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya; Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts; Department of Medicine, Division of Transfusion, and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts; Department of Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Collins Ouma
- Department of Biomedical Sciences and Technology, Maseno University, Maseno, Kenya; Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya; Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts; Department of Medicine, Division of Transfusion, and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts; Department of Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, Massachusetts
| | - David H Mulama
- Department of Biomedical Sciences and Technology, Maseno University, Maseno, Kenya; Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya; Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts; Department of Medicine, Division of Transfusion, and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts; Department of Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Joslyn Foley
- Department of Biomedical Sciences and Technology, Maseno University, Maseno, Kenya; Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya; Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts; Department of Medicine, Division of Transfusion, and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts; Department of Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, Massachusetts
| | - John Vulule
- Department of Biomedical Sciences and Technology, Maseno University, Maseno, Kenya; Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya; Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts; Department of Medicine, Division of Transfusion, and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts; Department of Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jeffrey A Bailey
- Department of Biomedical Sciences and Technology, Maseno University, Maseno, Kenya; Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya; Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts; Department of Medicine, Division of Transfusion, and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts; Department of Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Ann M Moormann
- Department of Biomedical Sciences and Technology, Maseno University, Maseno, Kenya; Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya; Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts; Department of Medicine, Division of Transfusion, and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts; Department of Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, Massachusetts
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Pinkevych M, Petravic J, Chelimo K, Vulule J, Kazura JW, Moormann AM, Davenport MP. Decreased growth rate of P. falciparum blood stage parasitemia with age in a holoendemic population. J Infect Dis 2013; 209:1136-43. [PMID: 24265441 DOI: 10.1093/infdis/jit613] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [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: 12/19/2022] Open
Abstract
In malaria holoendemic settings, decreased parasitemia and clinical disease is associated with age and cumulative exposure. The relative contribution of acquired immunity against various stages of the parasite life cycle is not well understood. In particular, it is not known whether changes in infection dynamics can be best explained by decreasing rates of infection, or by decreased growth rates of parasites in blood. Here, we analyze the dynamics of Plasmodium falciparum infection after treatment in a cohort of 197 healthy study participants of different ages. We use both polymerase chain reaction (PCR) and microscopy detection of parasitemia in order to understand parasite growth rates and infection rates over time. The more sensitive PCR assay detects parasites earlier than microscopy, and demonstrates a higher overall prevalence of infection than microscopy alone. The delay between PCR and microscopy detection is significantly longer in adults compared with children, consistent with slower parasite growth with age. We estimated the parasite multiplication rate from delay to PCR and microscopy detections of parasitemia. We find that both the delay between PCR and microscopy infection as well as the differing reinfection dynamics in different age groups are best explained by a slowing of parasite growth with age.
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Affiliation(s)
- Mykola Pinkevych
- Centre for Vascular Research, University of New South Wales, Sydney, New South Wales, Australia
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Buckle GC, Collins JP, Sumba PO, Nakalema B, Omenah D, Stiffler K, Casper C, Otieno JA, Orem J, Moormann AM. Factors influencing time to diagnosis and initiation of treatment of endemic Burkitt Lymphoma among children in Uganda and western Kenya: a cross-sectional survey. Infect Agent Cancer 2013; 8:36. [PMID: 24079452 PMCID: PMC3849966 DOI: 10.1186/1750-9378-8-36] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 09/17/2013] [Indexed: 11/28/2022] Open
Abstract
Background Survival rates for children diagnosed with Burkitt lymphoma (BL) in Africa are far below those achieved in developed countries. Late stage of presentation contributes to poor prognosis, therefore this study investigated factors leading to delays in BL diagnosis and treatment of children in Uganda and western Kenya. Methods Guardians of children diagnosed with BL were interviewed at the Jaramogi Oginga Odinga Teaching and Referral Hospital (JTRH) and Uganda Cancer Institute (UCI) from Jan-Dec 2010. Information on sociodemographics, knowledge, attitudes, illness perceptions, health-seeking behaviors and prior health encounters was collected using a standardized, pre-tested questionnaire. Results Eighty-two guardians were interviewed (20 JTRH, 62 UCI). Median "total delay" (1st symptoms to BL diagnosis) was 12.1 weeks [interquartile range (IQR) 4.9-19.9] in Kenya and 12.9 weeks (IQR 4.3-25.7) in Uganda. In Kenya, median "guardian delay" (1st symptoms to 1st health encounter) and "health system delay" (1st health encounter to BL diagnosis) were 9.0 weeks (IQR 3.6-15.7) and 2.0 weeks (IQR 1.6-5.8), respectively. Data on guardian and health system delay in Uganda were only available for those with < 4 prior health encounters (n = 26). Of these, median guardian delay was 4.3 weeks (range 0.7-149.9), health system delay 2.6 weeks (range 0.1-16.0), and total delay 10.7 weeks (range 1.7-154.3). Guardians in Uganda reported more health encounters than those in Kenya (median 5, range 3–16 vs. median 3, range 2–6). Among Kenyan guardians, source of income was the only independent predictor of delay, whereas in Uganda, guardian delay was influenced by guardians’ beliefs on the curability of cancer, health system delay, by guardians’ perceptions of cancer as a contagious disease, and total delay, by the number of children in the household and guardians’ role as caretaker. Qualitative findings suggest financial costs, transportation, and other household responsibilities were major barriers to care. Conclusions Delays from symptom onset to BL treatment were considerable given the rapid growth rate of this cancer, with guardian delay constituting the majority of total delay in both settings. Future interventions should aim to reduce structural barriers to care and increase awareness of BL in particular and cancer in general within the community, as well as among health professionals.
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Affiliation(s)
- Geoffrey C Buckle
- Department of Pediatrics, University of Massachusetts Medical School, 373 Plantation Street, Suite 318, Worcester 01605, MA, USA.
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Wohlford EM, Asito AS, Chelimo K, Sumba PO, Baresel PC, Oot RA, Moormann AM, Rochford R. Identification of a novel variant of LMP-1 of EBV in patients with endemic Burkitt lymphoma in western Kenya. Infect Agent Cancer 2013; 8:34. [PMID: 24016332 PMCID: PMC3847075 DOI: 10.1186/1750-9378-8-34] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 05/09/2013] [Indexed: 12/24/2022] Open
Abstract
Background Epstein Barr virus (EBV) is a gammaherpesvirus that is associated with nasopharyngeal carcinoma (NPC) and endemic Burkitt lymphoma (eBL). EBV carries several latent genes that contribute to oncogenesis including the latent membrane protein 1 (LMP-1), a known oncogene and constitutively active CD40 homolog. Variation in the C terminal region of LMP-1 has been linked to NPC pathogenesis, but little is known regarding LMP-1 variation and eBL. Results In the present study, peripheral blood samples were obtained from 38 eBL patients and 22 healthy controls in western Kenya, where the disease is endemic. The LMP-1 C-terminal region from these samples was sequenced and analyzed. The frequency of a 30 base pair deletion of LMP-1 previously linked to NPC was not associated with eBL compared to healthy controls. However a novel LMP-1 variant was identified, called K for Kenya and for the G318K mutation that characterizes it. The K variant LMP-1 was found in 40.5% of eBL sequences and 25.0% of healthy controls. All K variant sequences contained mutations in both of the previously described minimal T cell epitopes in the C terminal end of LMP-1. These mutations occurred in the anchor residue at the C-terminal binding groove of both epitopes, a pocket necessary for MHC loading. Conclusions Overall, our results suggest that there is a novel K variant of LMP-1 in Kenya that may be associated with eBL. Further studies are necessary to determine the functional implications of the LMP-1 variant on early events in eBL genesis.
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Affiliation(s)
- Eric M Wohlford
- Center for Global Health and Translational Science, SUNY Upstate Medical University, Syracuse, NY 13210, USA.
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48
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Pinkevych M, Petravic J, Chelimo K, Vulule J, Kazura JW, Moormann AM, Davenport MP. Density-dependent blood stage Plasmodium falciparum suppresses malaria super-infection in a malaria holoendemic population. Am J Trop Med Hyg 2013; 89:850-6. [PMID: 24019439 DOI: 10.4269/ajtmh.13-0049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Recent studies of Plasmodium berghei malaria in mice show that high blood-stage parasitemia levels inhibit the development of subsequent liver-stage infections. Whether a similar inhibitory effect on liver-stage Plasmodium falciparum by blood-stage infection occurs in humans is unknown. We have analyzed data from a treatment-time-to-infection cohort of children < 10 years of age residing in a malaria holoendemic area of Kenya where people experience a new blood-stage infection approximately every 2 weeks. We hypothesized that if high parasitemia blocked the liver stage, then high levels of parasitemia should be followed by a "skipped" peak of parasitemia. Statistical analysis of "natural infection" field data and stochastic simulation of infection dynamics show that the data are consistent with high P. falciparum parasitemia inhibiting liver-stage parasite development in humans.
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Affiliation(s)
- Mykola Pinkevych
- Centre for Vascular Research, University of New South Wales, Sydney, NSW, Australia; Kenya Medical Research Institute, Kisumu, Kenya; Case Western Reserve University, Cleveland, Ohio; University of Massachusetts Medical School, Worcester, Massachusetts
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49
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Mulama DH, Bailey JA, Foley J, Chelimo K, Ouma C, Jura WGZO, Otieno J, Vulule J, Moormann AM. Sickle cell trait is not associated with endemic Burkitt lymphoma: an ethnicity and malaria endemicity-matched case-control study suggests factors controlling EBV may serve as a predictive biomarker for this pediatric cancer. Int J Cancer 2013; 134:645-53. [PMID: 23832374 PMCID: PMC3830732 DOI: 10.1002/ijc.28378] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [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] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 06/19/2013] [Accepted: 06/19/2013] [Indexed: 11/13/2022]
Abstract
Endemic Burkitt lymphoma (eBL) is associated with Epstein–Barr virus (EBV) and Plasmodium falciparum coinfections. Malaria appears to dysregulate immunity that would otherwise control EBV, thereby contributing to eBL etiology. Juxtaposed to human genetic variants associated with protection from malaria, it has been hypothesized that such variants could decrease eBL susceptibility, historically referred to as “the protective hypothesis.” Past studies attempting to link sickle cell trait (HbAS), which is known to be protective against malaria, with protection from eBL were contradictory and underpowered. Therefore, using a case–control study design, we examined HbAS frequency in 306 Kenyan children diagnosed with eBL compared to 537 geographically defined and ethnically matched controls. We found 23.8% HbAS for eBL patients, which was not significantly different compared to 27.0% HbAS for controls [odds ratio (OR) = 0.85; 95% confidence interval (CI) 0.61–1.17; p-value = 0.33]. Even though cellular EBV titers, indicative of the number of latently infected B cells, were significantly higher (p-value < 0.0003) in children residing in malaria holoendemic compared to hypoendemic areas, levels were not associated with HbAS genotype. Combined, this suggests that although HbAS protects against severe malaria and hyperparasitemia, it is not associated with viral control or eBL protection. However, based on receiver operating characteristic curves factors that enable the establishment of EBV persistence, in contrast to those involved in EBV lytic reactivation, may have utility as an eBL precursor biomarker. This has implications for future human genetic association studies to consider variants influencing control over EBV in addition to malaria as risk factors for eBL.
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Affiliation(s)
- David H Mulama
- Center for Global Health Research, Kenyan Medical Research InstituteKisumu, Kenya
- Department of Biomedical Sciences and Technology, Maseno UniversityMaseno, Kenya
| | - Jeffrey A Bailey
- Department of Medicine and Program in Bioinformatics & Computational Biology, University of Massachusetts Medical SchoolWorcester, MA
| | - Joslyn Foley
- Department of Pediatrics, University of Massachusetts Medical SchoolWorcester, MA
| | - Kiprotich Chelimo
- Center for Global Health Research, Kenyan Medical Research InstituteKisumu, Kenya
- Department of Biomedical Sciences and Technology, Maseno UniversityMaseno, Kenya
| | - Collins Ouma
- Department of Biomedical Sciences and Technology, Maseno UniversityMaseno, Kenya
| | | | - Juliana Otieno
- Jaramogi Oginga Odinga Teaching and Referral Hospital, Ministry of Medical ServicesKisumu, Kenya
| | - John Vulule
- Center for Global Health Research, Kenyan Medical Research InstituteKisumu, Kenya
| | - Ann M Moormann
- Department of Pediatrics, University of Massachusetts Medical SchoolWorcester, MA
- Department of Quantitative Health Sciences, University of Massachusetts Medical SchoolWorcester, MA
- Correspondence to: Ann M. Moormann, PhD, MPH, University of Massachusetts Medical School, 373 Plantation St., Biotech 2, Suite 318, Worcester, MA 01605, USA, E-mail:
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Moormann AM, Sumba PO, Chelimo K, Fang H, Tisch DJ, Dent AE, John CC, Long CA, Vulule J, Kazura JW. Humoral and cellular immunity to Plasmodium falciparum merozoite surface protein 1 and protection from infection with blood-stage parasites. J Infect Dis 2013; 208:149-58. [PMID: 23539744 DOI: 10.1093/infdis/jit134] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [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: 01/08/2023] Open
Abstract
BACKGROUND Acquired immunity to malaria develops with increasing age and repeated infections. Understanding immune correlates of protection from malaria would facilitate vaccine development and identification of biomarkers that reflect changes in susceptibility resulting from ongoing malaria control efforts. METHODS The relationship between immunoglobulin G (IgG) antibody and both interferon γ (IFN-γ) and interleukin 10 (IL-10) responses to the 42-kD C-terminal fragment of Plasmodium falciparum merozoite surface protein 1 (MSP142) and the risk of (re)infection were examined following drug-mediated clearance of parasitemia in 94 adults and 95 children in an area of holoendemicity of western Kenya. RESULTS Positive IFN-γ enzyme-linked immunosorbent assay (ELISA) and enzyme-linked immunosorbent spot assay (ELISPOT) responses to MSP142 3D7 were associated with delayed time to (re)infection, whereas high-titer IgG antibodies to MSP142 3D7 or FVO alleles were not independently predictive of the risk of (re)infection. When IFN-γ and IL-10 responses were both present, the protective effect of IFN-γ was abrogated. A Cox proportional hazard model including IFN-γ, IL-10, MSP142 3D7 IgG antibody responses, hemoglobin S genotype, age, and infection status at baseline showed that the time to blood-stage infection correlated positively with IFN-γ responses and negatively with IL-10 responses, younger age, and asymptomatic parasitemia. CONCLUSIONS Evaluating combined allele-specific cellular and humoral immunity elicited by malaria provides a more informative measure of protection relative to evaluation of either measure alone.
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Affiliation(s)
- Ann M Moormann
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio, USA.
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