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Johnson KE, Hernandez-Alvarado N, Blackstad M, Heisel T, Allert M, Fields DA, Isganaitis E, Jacobs KM, Knights D, Lock EF, Rudolph MC, Gale CA, Schleiss MR, Albert FW, Demerath EW, Blekhman R. Human cytomegalovirus in breast milk is associated with milk composition and the infant gut microbiome and growth. Nat Commun 2024; 15:6216. [PMID: 39043677 PMCID: PMC11266569 DOI: 10.1038/s41467-024-50282-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 07/03/2024] [Indexed: 07/25/2024] Open
Abstract
Human cytomegalovirus (CMV) is a highly prevalent herpesvirus that is often transmitted to the neonate via breast milk. Postnatal CMV transmission can have negative health consequences for preterm and immunocompromised infants, but any effects on healthy term infants are thought to be benign. Furthermore, the impact of CMV on the composition of the hundreds of bioactive factors in human milk has not been tested. Here, we utilize a cohort of exclusively breastfeeding full-term mother-infant pairs to test for differences in the milk transcriptome and metabolome associated with CMV, and the impact of CMV in breast milk on the infant gut microbiome and infant growth. We find upregulation of the indoleamine 2,3-dioxygenase (IDO) tryptophan-to-kynurenine metabolic pathway in CMV+ milk samples, and that CMV+ milk is associated with decreased Bifidobacterium in the infant gut. Our data indicate two opposing CMV-associated effects on infant growth; with kynurenine positively correlated, and CMV viral load negatively correlated, with infant weight-for-length at 1 month of age. These results suggest CMV transmission, CMV-related changes in milk composition, or both may be modulators of full-term infant development.
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Affiliation(s)
- Kelsey E Johnson
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA.
| | | | - Mark Blackstad
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Timothy Heisel
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Mattea Allert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - David A Fields
- Department of Pediatrics, Section of Diabetes and Endocrinology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | | | - Katherine M Jacobs
- Department of Obstetrics, Gynecology and Women's Health, Division of Maternal-Fetal Medicine, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Eric F Lock
- Division of Biostatistics and Health Data Science, University of Minnesota School of Public Health, Minneapolis, MN, USA
| | - Michael C Rudolph
- Harold Hamm Diabetes Center, Department of Biochemistry and Physiology, Oklahoma University Health Sciences Center, Oklahoma City, OK, USA
| | - Cheryl A Gale
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Mark R Schleiss
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Frank W Albert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Ellen W Demerath
- Division of Epidemiology and Community Health, University of Minnesota School of Public Health, Minneapolis, MN, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Division of Biological Sciences, University of Chicago, Chicago, IL, USA
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Johnson KE, Heisel T, Fields DA, Isganaitis E, Jacobs KM, Knights D, Lock EF, Rudolph MC, Gale CA, Schleiss MR, Albert FW, Demerath EW, Blekhman R. Human Cytomegalovirus in breast milk is associated with milk composition, the infant gut microbiome, and infant growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.19.549370. [PMID: 37503212 PMCID: PMC10370112 DOI: 10.1101/2023.07.19.549370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Human cytomegalovirus (CMV) is a highly prevalent herpesvirus that is often transmitted to the neonate via breast milk. Postnatal CMV transmission can have negative health consequences for preterm and immunocompromised infants, but any effects on healthy term infants are thought to be benign. Furthermore, the impact of CMV on the composition of the hundreds of bioactive factors in human milk has not been tested. Here, we utilize a cohort of exclusively breastfeeding full term mother-infant pairs to test for differences in the milk transcriptome and metabolome associated with CMV, and the impact of CMV in breast milk on the infant gut microbiome and infant growth. We find upregulation of the indoleamine 2,3- dioxygenase (IDO) tryptophan-to-kynurenine metabolic pathway in CMV+ milk samples, and that CMV+ milk is associated with decreased Bifidobacterium in the infant gut. Our data indicate a complex relationship between milk CMV, milk kynurenine, and infant growth; with kynurenine positively correlated, and CMV viral load negatively correlated, with infant weight-for-length at 1 month of age. These results suggest CMV transmission, CMV-related changes in milk composition, or both may be modulators of full term infant development.
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Affiliation(s)
- Kelsey E Johnson
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, USA
| | - Timothy Heisel
- Division of Neonatology, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - David A Fields
- Department of Pediatrics, Diabetes-Endocrinology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Elvira Isganaitis
- Pediatric, Adolescent and Young Adult Unit, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Katherine M Jacobs
- Department of Obstetrics, Gynecology and Women's Health, Division of Maternal-Fetal Medicine, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Eric F Lock
- Division of Biostatistics, University of Minnesota School of Public Health, Minneapolis, MN, USA
| | - Michael C Rudolph
- Harold Hamm Diabetes Center, Department of Physiology, Oklahoma University Health Sciences Center, Oklahoma City, OK, USA
| | - Cheryl A Gale
- Division of Neonatology, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Mark R Schleiss
- Division of Pediatric Infectious Diseases and Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Frank W Albert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, USA
| | - Ellen W Demerath
- Division of Epidemiology and Community Health, University of Minnesota School of Public Health, Minneapolis, MN, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Division of Biological Sciences, University of Chicago, Chicago, IL, USA
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Ishikawa S, Tasaki M, Saito K, Nakagawa Y, Ikeda M, Takahashi K, Tomita Y. Long-term CMV monitoring and chronic rejection in renal transplant recipients. Front Cell Infect Microbiol 2023; 13:1190794. [PMID: 37384223 PMCID: PMC10294236 DOI: 10.3389/fcimb.2023.1190794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/24/2023] [Indexed: 06/30/2023] Open
Abstract
Introduction Cytomegalovirus (CMV) is well established to be an independent risk factor for graft loss after kidney transplantation (KTx). Monitoring for CMV in the chronic phase is not defined in the current guideline. The effects of CMV infection, including asymptomatic CMV viremia, in the chronic phase are unclear. Methods We performed a single-center retrospective study to investigate incidence of CMV infection in the chronic phase, defined as more than 1 year after KTx. We included 205 patients who received KTx between April 2004 and December 2017. The CMV pp65 antigenemia assays to detect CMV viremia were continuously performed every 1-3 months. Results The median duration of the follow-up was 80.6 (13.1-172.1) months. Asymptomatic CMV infection and CMV disease were observed in 30.7% and 2.9% in the chronic phase, respectively. We found that 10-20% of patients had CMV infections in each year after KTx which did not change over 10 years. The history of CMV infection in the early phase (within 1 year after KTx) and chronic rejection were significantly associated with CMV viremia in the chronic phase. CMV viremia in the chronic phase was significantly associated with graft loss. Discussion This is the first study to examine the incidence of CMV viremia for 10 years post KTx. Preventing latent CMV infection may decrease chronic rejection and graft loss after KTx.
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Affiliation(s)
- Shoko Ishikawa
- Division of Urology, Department of Regenerative & Transplant Medicine, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Masayuki Tasaki
- Division of Urology, Department of Regenerative & Transplant Medicine, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Kazuhide Saito
- Division of Urology, Department of Regenerative & Transplant Medicine, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Yuki Nakagawa
- Division of Urology, Department of Regenerative & Transplant Medicine, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
- Department of Urology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Masahiro Ikeda
- Division of Urology, Department of Regenerative & Transplant Medicine, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | | | - Yoshihiko Tomita
- Division of Urology, Department of Regenerative & Transplant Medicine, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
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Parhizgari N, Zarei Ghobadi M, Rezaei F, Maraashi SM, Khatami MR, Mokhtari-Azad T. Transcriptomic analysis of human cytomegalovirus to survey the indirect effects on renal transplant recipients. Transpl Immunol 2023; 78:101746. [PMID: 36796459 DOI: 10.1016/j.trim.2022.101746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/02/2022] [Accepted: 11/13/2022] [Indexed: 02/17/2023]
Abstract
Post-transplant human cytomegalovirus (HCMV) viremia has been linked to adverse "indirect effects" among transplant patients. HCMV-created immunomodulatory mechanisms could be associated with the indirect effects. OBJECTIVE In the present study, the RNA-Seq whole transcriptome of renal transplant (RT) patients was analyzed to seek the underlying pathobiologic pathways associated with the long-term indirect effects of HCMV. METHODS To investigate the activated biological pathways in HCMV infection, total RNA was extracted from PBMCs of 2 RT patients with active HCMV and 2 RT patients without infection and then were sequenced using RNA-Seq. The resulted raw data were analyzed by conventional RNA-Seq software to determine the Differentially Expressed Genes (DEGs). Afterward, Gene Ontology (GO) and pathway enrichment analyses were conducted to determine the enriched pathways and biological processes by DEGs. Eventually, the relative expressions of some significant genes were validated in the twenty external RT patients. RESULT The analysis of RNA-Seq data related to RT patients with HCMV active viremia led to the identification of 140 up-regulated and 100 down-regulated DEGs. KEGG pathway analysis revealed the enrichment of DEGs in IL18 signaling, AGE-RAGE signaling pathway in diabetic complications, signaling by GPCR, Platelet activation, signaling and aggregation, Estrogen signaling pathway and signaling by Wnt due to HCMV infection. The expression levels of six genes involved in enriched pathways including F3, PTX3, ADRA2B, GNG11, GP9, HBEGF were then verified using RT-qPCR. The results were in consistent with RNA-Seq resultsoutcomes. CONCLUSION This study specifies some pathobiological pathways which are activated in HCMV active infection and could be linked to the adverse indirect effects caused by HCMV infection in transplant patients.
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Affiliation(s)
- Najmeh Parhizgari
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohadeseh Zarei Ghobadi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran; Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Farhad Rezaei
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| | - Seyed Mahdi Maraashi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Talat Mokhtari-Azad
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
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Sigdel TK, Boada P, Kerwin M, Rashmi P, Gjertson D, Rossetti M, Sur S, Munar D, Cimino J, Ahn R, Pickering H, Sen S, Parmar R, Fatou B, Steen H, Schaenman J, Bunnapradist S, Reed EF, Sarwal MM. Plasma proteome perturbation for CMV DNAemia in kidney transplantation. PLoS One 2023; 18:e0285870. [PMID: 37205661 DOI: 10.1371/journal.pone.0285870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 05/03/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Cytomegalovirus (CMV) infection, either de novo or as reactivation after allotransplantation and chronic immunosuppression, is recognized to cause detrimental alloimmune effects, inclusive of higher susceptibility to graft rejection and substantive impact on chronic graft injury and reduced transplant survival. To obtain further insights into the evolution and pathogenesis of CMV infection in an immunocompromised host we evaluated changes in the circulating host proteome serially, before and after transplantation, and during and after CMV DNA replication (DNAemia), as measured by quantitative polymerase chain reaction (QPCR). METHODS LC-MS-based proteomics was conducted on 168 serially banked plasma samples, from 62 propensity score-matched kidney transplant recipients. Patients were stratified by CMV replication status into 31 with CMV DNAemia and 31 without CMV DNAemia. Patients had blood samples drawn at protocol times of 3- and 12-months post-transplant. Additionally, blood samples were also drawn before and 1 week and 1 month after detection of CMV DNAemia. Plasma proteins were analyzed using an LCMS 8060 triple quadrupole mass spectrometer. Further, public transcriptomic data on time matched PBMCs samples from the same patients was utilized to evaluate integrative pathways. Data analysis was conducted using R and Limma. RESULTS Samples were segregated based on their proteomic profiles with respect to their CMV Dnaemia status. A subset of 17 plasma proteins was observed to predict the onset of CMV at 3 months post-transplant enriching platelet degranulation (FDR, 4.83E-06), acute inflammatory response (FDR, 0.0018), blood coagulation (FDR, 0.0018) pathways. An increase in many immune complex proteins were observed at CMV infection. Prior to DNAemia the plasma proteome showed changes in the anti-inflammatory adipokine vaspin (SERPINA12), copper binding protein ceruloplasmin (CP), complement activation (FDR = 0.03), and proteins enriched in the humoral (FDR = 0.01) and innate immune responses (FDR = 0.01). CONCLUSION Plasma proteomic and transcriptional perturbations impacting humoral and innate immune pathways are observed during CMV infection and provide biomarkers for CMV disease prediction and resolution. Further studies to understand the clinical impact of these pathways can help in the formulation of different types and duration of anti-viral therapies for the management of CMV infection in the immunocompromised host.
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Affiliation(s)
- Tara K Sigdel
- Department of Surgery, University of California San Francisco, San Francisco, CA, United States of America
| | - Patrick Boada
- Department of Surgery, University of California San Francisco, San Francisco, CA, United States of America
| | - Maggie Kerwin
- Department of Surgery, University of California San Francisco, San Francisco, CA, United States of America
| | - Priyanka Rashmi
- Department of Surgery, University of California San Francisco, San Francisco, CA, United States of America
| | - David Gjertson
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Maura Rossetti
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Swastika Sur
- Department of Surgery, University of California San Francisco, San Francisco, CA, United States of America
| | - Dane Munar
- Department of Surgery, University of California San Francisco, San Francisco, CA, United States of America
| | - James Cimino
- Department of Surgery, University of California San Francisco, San Francisco, CA, United States of America
| | - Richard Ahn
- Department of Microbiology and Immunology, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Harry Pickering
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Subha Sen
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Rajesh Parmar
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Benoit Fatou
- Department of Pathology, Harvard Medical School, Boston, MA, United States of America
| | - Hanno Steen
- Department of Pathology, Harvard Medical School, Boston, MA, United States of America
| | - Joanna Schaenman
- Department of Medicine, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Suphamai Bunnapradist
- Department of Medicine, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Elaine F Reed
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Minnie M Sarwal
- Department of Surgery, University of California San Francisco, San Francisco, CA, United States of America
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Steinbrink JM, Miller C, Myers RA, Sanoff S, Mazur A, Burke TW, Byrns J, Jackson AM, Luo X, McClain MT. Transcriptional responses define dysregulated immune activation in Hepatitis C (HCV)-naïve recipients of HCV-infected donor kidneys. PLoS One 2023; 18:e0280602. [PMID: 36701416 PMCID: PMC9879532 DOI: 10.1371/journal.pone.0280602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 01/03/2023] [Indexed: 01/27/2023] Open
Abstract
Renal transplantation from hepatitis C (HCV) nucleic acid amplification test-positive (NAAT-positive) donors to uninfected recipients has greatly increased the organ donation pool. However, there is concern for adverse outcomes in these recipients due to dysregulated immunologic activation secondary to active inflammation from acute viremia at the time of transplantation. This includes increased rates of cytomegalovirus (CMV) DNAemia and allograft rejection. In this study, we evaluate transcriptional responses in circulating leukocytes to define the character, timing, and resolution of this immune dysregulation and assess for biomarkers of adverse outcomes in transplant patients. We enrolled 67 renal transplant recipients (30 controls, 37 HCV recipients) and performed RNA sequencing on serial samples from one, 3-, and 6-months post-transplant. CMV DNAemia and allograft rejection outcomes were measured. Least absolute shrinkage and selection operator was utilized to develop gene expression classifiers predictive of clinical outcomes. Acute HCV incited a marked transcriptomic response in circulating leukocytes of renal transplant recipients in the acute post-transplant setting, despite the presence of immunosuppression, with 109 genes significantly differentially expressed compared to controls. These HCV infection-associated genes were reflective of antiviral immune pathways and generally resolved by the 3-month timepoint after sustained viral response (SVR) for HCV. Differential gene expression was also noted from patients who developed CMV DNAemia or allograft rejection compared to those who did not, although transcriptomic classifiers could not accurately predict these outcomes, likely due to sample size and variable time-to-event. Acute HCV infection incites evidence of immune activation and canonical antiviral responses in the human host even in the presence of systemic immunosuppression. After treatment of HCV with antiviral therapy and subsequent aviremia, this immune activation resolves. Changes in gene expression patterns in circulating leukocytes are associated with some clinical outcomes, although larger studies are needed to develop accurate predictive classifiers of these events.
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Affiliation(s)
- Julie M. Steinbrink
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, NC, United States of America
- Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University, Durham, NC, United States of America
- * E-mail:
| | - Cameron Miller
- Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University, Durham, NC, United States of America
| | - Rachel A. Myers
- Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University, Durham, NC, United States of America
| | - Scott Sanoff
- Division of Nephrology, Department of Medicine, Duke University Medical Center, Durham, NC, United States of America
| | - Anna Mazur
- Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University, Durham, NC, United States of America
| | - Thomas W. Burke
- Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University, Durham, NC, United States of America
| | - Jennifer Byrns
- Department of Pharmacy, Duke University Medical Center, Durham, NC, United States of America
| | - Annette M. Jackson
- Departments of Surgery and Immunology, Duke University, Durham, NC, United States of America
| | - Xunrong Luo
- Division of Nephrology, Department of Medicine, Duke University Medical Center, Durham, NC, United States of America
| | - Micah T. McClain
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, NC, United States of America
- Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University, Durham, NC, United States of America
- Division of Infectious Diseases, Durham Veterans Affairs Health Care System, Durham, NC, United States of America
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