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Uemura T, Kawashima A, Jingushi K, Motooka D, Saito T, Nesrine S, Oka T, Okuda Y, Yamamoto A, Yamamichi G, Tomiyama E, Ishizuya Y, Yamamoto Y, Kato T, Hatano K, Tsujikawa K, Wada H, Nonomura N. Bacteria-derived DNA in serum extracellular vesicles are biomarkers for renal cell carcinoma. Heliyon 2023; 9:e19800. [PMID: 37810127 PMCID: PMC10559165 DOI: 10.1016/j.heliyon.2023.e19800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 08/25/2023] [Accepted: 09/01/2023] [Indexed: 10/10/2023] Open
Abstract
This is the first study to determine the clinical importance of circulating bacterial DNA in patients with renal cell carcinoma (RCC). We performed 16S rRNA metagenomic analysis of serum extracellular vesicles (EVs) from 88 patients with RCC and 10 healthy donors and identified three abundant bacterial DNA: Bacteroidia, TM7-1, and Sphingomonadales. Combining characteristic bacterial DNA information (three bacteria-derived DNA), a BTS index was created to diagnose patients with RCC. The BTS index showed high sensitivity not only in the discovery cohort, but also in the validation cohort, suggesting that it was useful as a screening test. Furthermore, in nivolumab treatment of RCC, patients with higher levels of Bacteroidia DNA in serum EVs had significantly poorer progression-free and overall survival than did those with lower levels. This study showed that circulating Bacteria-derived DNA could be used as a biomarker for RCC.
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Affiliation(s)
- Toshihiro Uemura
- Department of Urology, Osaka University, Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Atsunari Kawashima
- Department of Urology, Osaka University, Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kentaro Jingushi
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Genome Information Research Center, Osaka University Research Institute for Microbial Diseases, Suita, Osaka, 565-0871, Japan
| | - Takuro Saito
- Department of Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
- Department of Clinical Research in Tumor Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Sassi Nesrine
- Department of Urology, Osaka University, Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Toshiki Oka
- Department of Urology, Osaka University, Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yohei Okuda
- Department of Urology, Osaka University, Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Akinaru Yamamoto
- Department of Urology, Osaka University, Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Gaku Yamamichi
- Department of Urology, Osaka University, Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Eisuke Tomiyama
- Department of Urology, Osaka University, Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yu Ishizuya
- Department of Urology, Osaka University, Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yoshiyuki Yamamoto
- Department of Urology, Osaka University, Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Taigo Kato
- Department of Urology, Osaka University, Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Koji Hatano
- Department of Urology, Osaka University, Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kazutake Tsujikawa
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hisashi Wada
- Department of Clinical Research in Tumor Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Norio Nonomura
- Department of Urology, Osaka University, Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
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Addo SO, Bentil RE, Yartey KN, Ansah-Owusu J, Behene E, Opoku-Agyeman P, Bruku S, Asoala V, Mate S, Larbi JA, Baidoo PK, Wilson MD, Diclaro JW, Dadzie SK. First molecular identification of multiple tick-borne pathogens in livestock within Kassena-Nankana, Ghana. ANIMAL DISEASES 2023. [DOI: 10.1186/s44149-022-00064-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
AbstractThe risk of pathogen transmission continues to increase significantly in the presence of tick vectors due to the trade of livestock across countries. In Ghana, there is a lack of data on the incidence of tick-borne pathogens that are of zoonotic and veterinary importance. This study, therefore, aimed to determine the prevalence of such pathogens in livestock using molecular approaches. A total of 276 dry blood spots were collected from cattle (100), sheep (95) and goats (81) in the Kassena-Nankana Districts. The samples were analyzed using Polymerase Chain Reaction (qPCR) and conventional assays and Sanger sequencing that targeted pathogens including Rickettsia, Coxiella, Babesia, Theileria, Ehrlichia and Anaplasma. An overall prevalence of 36.96% was recorded from the livestock DBS, with mixed infections seen in 7.97% samples. Furthermore, the prevalence of infections in livestock was recorded to be 19.21% in sheep, 14.13% in cattle, and 3.62% in goats. The pathogens identified were Rickettsia spp. (3.26%), Babesia sp. Lintan (8.70%), Theileria orientalis (2.17%), Theileria parva (0.36%), Anaplasma capra (18.48%), Anaplasma phagocytophilum (1.81%), Anaplasma marginale (3.26%) and Anaplasma ovis (7.25%). This study reports the first molecular identification of the above-mentioned pathogens in livestock in Ghana and highlights the use of dry blood spots in resource-limited settings. In addition, this research provides an update on tick-borne pathogens in Ghana, suggesting risks to livestock production and human health. Further studies will be essential to establish the distribution and epidemiology of these pathogens in Ghana.
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Mosaic Evolution of Beta-Barrel-Porin-Encoding Genes in Escherichia coli. Appl Environ Microbiol 2022; 88:e0006022. [PMID: 35285711 DOI: 10.1128/aem.00060-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial porin-encoding genes are often found under positive selection. Local recombination has also been identified in a few of them to facilitate bacterial rapid adaptation, although it remains unknown whether it is a common evolutionary mechanism for the porins or outer membrane proteins in Gram-negative bacteria. In this study, we investigated the beta-barrel (β-barrel) porin-encoding genes in Escherichia coli that were reported under positive Darwinian selection. Besides fhuA that was found with ingenic local recombination previously, we identified four other genes, i.e., lamB, ompA, ompC, and ompF, all showing the similar mosaic evolution patterns. Comparative analysis of the protein sequences disclosed a list of highly variable regions in each family, which are mostly located in the convex of extracellular loops and coinciding with the binding sites of bacteriophages. For each of the porin families, mosaic recombination leads to unique combinations of the variable regions with different sequence patterns, generating diverse protein groups. Structural modeling indicated a conserved global topology among the different porins, with the extracellular surface varying a lot due to individual or combinatorial variable regions. The conservation of global tertiary structure would ensure the channel activity, while the wide diversity of variable regions may represent selection to avoid the invasion of phages, antibiotics or immune surveillance factors. Our study identified multiple bacterial porin genes with mosaic evolution. We hypothesize that this could be generalized strategy for outer membrane proteins to both maintain normal life processes and evade the attack of unfavored factors rapidly. IMPORTANCE Microevolution studies can disclose more elaborate evolutionary mechanisms of genes, appearing especially important for genes with multifaceted function such as those encoding outer membrane proteins. However, in most cases, the gene is considered as a whole unit, and the evolutionary patterns are disclosed. Here, we report that multiple bacterial porin proteins follow mosaic evolution, with local ingenic recombination combined with spontaneous mutations based on positive Darwinian selection, and conservation for most structural regions. This could represent a common mechanism for bacterial outer membrane proteins. The variable regions within each porin family showed large coincidence with the binding sites of bacteriophages, antibiotics, and immune factors and therefore would represent effective targets for the development of new antibacterial agents or vaccines.
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Belkahia H, Ben Abdallah M, Andolsi R, Selmi R, Zamiti S, Kratou M, Mhadhbi M, Darghouth MA, Messadi L, Ben Said M. Screening and Analysis of Anaplasma marginale Tunisian Isolates Reveal the Diversity of lipA Phylogeographic Marker and the Conservation of OmpA Protein Vaccine Candidate. Front Vet Sci 2021; 8:731200. [PMID: 34746278 PMCID: PMC8566978 DOI: 10.3389/fvets.2021.731200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 09/16/2021] [Indexed: 01/18/2023] Open
Abstract
Bovine anaplasmosis caused by Anaplasma marginale is a disease responsible for serious animal health problems and great economic losses all over the world. Thereby, the identification of A. marginale isolates from various bioclimatic areas in each country, the phylogeographic analysis of these isolates based on the most informative markers, and the evaluation of the most promising candidate antigens are crucial steps in developing effective vaccines against a wide range of A. marginale strains. In order to contribute to this challenge, a total of 791 bovine samples from various bioclimatic areas of Tunisia were tested for the occurrence of A. marginale DNA through msp4 gene fragment amplification. Phylogeographic analysis was performed by using lipA and sucB gene analyses, and the genetic relationship with previously characterized A. marginale isolates and strains was analyzed by applying similarity comparison and phylogenetic analysis. To evaluate the conservation of OmpA protein vaccine candidate, almost complete ompA nucleotide sequences were also obtained from Tunisian isolates, and various bioinformatics software were used in order to analyze the physicochemical properties and the secondary and tertiary structures of their deduced proteins and to predict their immunodominant epitopes of B and T cells. A. marginale DNA was detected in 19 bovine samples (2.4%). Risk factor analysis shows that cattle derived from subhumid bioclimatic area were more infected than those that originated from other areas. The analysis of lipA phylogeographic marker indicated a higher diversity of Tunisian A. marginale isolates compared with other available worldwide isolates and strains. Molecular, phylogenetic, and immuno-informatics analyses of the vaccine candidate OmpA protein demonstrated that this antigen and its predicted immunodominant epitopes of B and T cells appear to be highly conserved between Tunisian isolates and compared with isolates from other countries, suggesting that the minimal intraspecific modifications will not affect the potential cross-protective capacity of humoral and cell-mediated immune responses against multiple A. marginale worldwide strains.
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Affiliation(s)
- Hanène Belkahia
- Service de Microbiologie et Immunologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisia
| | - Meriem Ben Abdallah
- Service de Microbiologie et Immunologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisia
| | - Rihab Andolsi
- Service de Microbiologie et Immunologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisia
| | - Rachid Selmi
- Service de Microbiologie et Immunologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisia.,Ministère de la Défense Nationale, Direction Générale de la Santé Militaire, Service Vétérinaire, Tunis, Tunisia
| | - Sayed Zamiti
- Service de Parasitologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisia
| | - Myriam Kratou
- Service de Microbiologie et Immunologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisia
| | - Moez Mhadhbi
- Service de Parasitologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisia
| | - Mohamed Aziz Darghouth
- Service de Parasitologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisia
| | - Lilia Messadi
- Service de Microbiologie et Immunologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisia
| | - Mourad Ben Said
- Service de Microbiologie et Immunologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisia.,Département des Sciences Fondamentales, Institut Supérieur de Biotechnologie de Sidi Thabet, University of Manouba, Sidi Thabet, Tunisia
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