1
|
Bordini J, Lenzi C, Frenquelli M, Morabito A, Pseftogas A, Belloni D, Mansouri L, Tsiolas G, Perotta E, Ranghetti P, Gandini F, Genova F, Hägerstrand D, Gavriilidis G, Keisaris S, Pechlivanis N, Davi F, Kay NE, Langerak AW, Pospisilova S, Scarfò L, Makris A, Psomopoulos FE, Stamatopoulos K, Rosenquist R, Campanella A, Ghia P. IκBε deficiency accelerates disease development in chronic lymphocytic leukemia. Leukemia 2024:10.1038/s41375-024-02236-4. [PMID: 38575671 DOI: 10.1038/s41375-024-02236-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 03/11/2024] [Accepted: 03/20/2024] [Indexed: 04/06/2024]
Abstract
The NFKBIE gene, which encodes the NF-κB inhibitor IκBε, is mutated in 3-7% of patients with chronic lymphocytic leukemia (CLL). The most recurrent alteration is a 4-bp frameshift deletion associated with NF-κB activation in leukemic B cells and poor clinical outcome. To study the functional consequences of NFKBIE gene inactivation, both in vitro and in vivo, we engineered CLL B cells and CLL-prone mice to stably down-regulate NFKBIE expression and investigated its role in controlling NF-κB activity and disease expansion. We found that IκBε loss leads to NF-κB pathway activation and promotes both migration and proliferation of CLL cells in a dose-dependent manner. Importantly, NFKBIE inactivation was sufficient to induce a more rapid expansion of the CLL clone in lymphoid organs and contributed to the development of an aggressive disease with a shortened survival in both xenografts and genetically modified mice. IκBε deficiency was associated with an alteration of the MAPK pathway, also confirmed by RNA-sequencing in NFKBIE-mutated patient samples, and resistance to the BTK inhibitor ibrutinib. In summary, our work underscores the multimodal relevance of the NF-κB pathway in CLL and paves the way to translate these findings into novel therapeutic options.
Collapse
Affiliation(s)
| | - Chiara Lenzi
- IRCSS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | | | - Alessia Morabito
- IRCSS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Athanasios Pseftogas
- IRCSS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Daniela Belloni
- IRCSS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Larry Mansouri
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - George Tsiolas
- Centre for Research & Technology, Hellas (CERTH), Thessaloniki, Greece
| | | | | | - Francesca Gandini
- IRCSS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | | | - Daniel Hägerstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | | | - Sofoklis Keisaris
- Centre for Research & Technology, Hellas (CERTH), Thessaloniki, Greece
| | | | - Frederic Davi
- Institution Université Pierre et Marie Curie & Hôpital Pitié-Salpêtrière, Paris, France
| | | | | | - Sarka Pospisilova
- University Hospital Brno, Brno, Czech Republic
- Masaryk University, Brno, Czech Republic
| | - Lydia Scarfò
- IRCSS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Antonios Makris
- Centre for Research & Technology, Hellas (CERTH), Thessaloniki, Greece
| | | | | | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Alessandro Campanella
- IRCSS Ospedale San Raffaele, Milan, Italy.
- Vita-Salute San Raffaele University, Milan, Italy.
| | - Paolo Ghia
- IRCSS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| |
Collapse
|
2
|
Kyritsi M, Tsiolas G, Michailidou S, Koukaras K, Argiriou A. Genomic and 16S metabarcoding data of Holothuria tubulosa Gmelin, 1791. Data Brief 2023; 48:109171. [PMID: 37206897 PMCID: PMC10189087 DOI: 10.1016/j.dib.2023.109171] [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: 12/31/2022] [Revised: 03/29/2023] [Accepted: 04/17/2023] [Indexed: 05/21/2023] Open
Abstract
Holothuria tubulosa Gmelin, 1791 is an edible sea cucumber species widespread in the Mediterranean Sea with ecological and increasing economic importance. Genome data of holothurian species is limited and the availability of genomic data resources is crucial in understanding their biology and adaptability mechanisms. This dataset presents the raw genome sequence data of H. tubulosa sequenced on an Illumina NextSeq 2000 platform. Genome size estimation was performed based on k-mer frequency approach. Additionally, the bacterial microbiome in the stomach and intestine of H. tubulosa collected from the Strymonian Gulf (North Aegean Sea, Greece) through 16S rRNA amplicon metabarcoding sequencing is reported. Sequencing was performed on an Illumina MiSeq platform. Analysis was conducted using the QIIME2 software package, the DADA2 algorithm and a trained classifier for taxonomy assignment. The datasets presented in this work serve as valuable resources for a comprehensive investigation of H. tubulosa at the genome level and for comparative genomics and echinoderms gut microbial studies.
Collapse
Affiliation(s)
- Maria Kyritsi
- Institute of Applied Biosciences / CERTH, P.O. Box 60361, Thermi, Thessaloniki 57001, Greece
| | - George Tsiolas
- Institute of Applied Biosciences / CERTH, P.O. Box 60361, Thermi, Thessaloniki 57001, Greece
| | - Sofia Michailidou
- Institute of Applied Biosciences / CERTH, P.O. Box 60361, Thermi, Thessaloniki 57001, Greece
| | - Konstantinos Koukaras
- Institute of Applied Biosciences / CERTH, P.O. Box 60361, Thermi, Thessaloniki 57001, Greece
| | - Anagnostis Argiriou
- Institute of Applied Biosciences / CERTH, P.O. Box 60361, Thermi, Thessaloniki 57001, Greece
- Department of Food Science and Nutrition, University of the Aegean, Lemnos 81400, Greece
- Corresponding author.
| |
Collapse
|
3
|
Tsiolas G, Michailidou S, Tsoureki A, Argiriou A. Genomic data of two Greek Vitis varieties. Data Brief 2022; 42:108216. [PMID: 35572792 PMCID: PMC9092844 DOI: 10.1016/j.dib.2022.108216] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/15/2022] [Accepted: 04/22/2022] [Indexed: 11/30/2022] Open
Abstract
The genetic material of Vitis varieties is crucial for the wine sector. In addition, genomic technologies applied in vitis germplasm characterization are important for the conservation of indigenous genetic reservoirs. Until recently the most common method to genetically identify vitis varieties was the use of Simple Sequence Repeats (SSR) along with SNP chips. Yet, with the progress in Next Generation Sequencing (NGS) technologies and the reduced sequencing cost per base, a twist in plant species genetic identification methods has occurred. Among them, the low coverage Whole-Genome Sequencing (lcWGS) method with downstream bioinformatic analysis for variant discovery and phylogenetic characterization is gaining scientific attention. In this dataset, shotgun sequencing data of two different Greek Vitis varieties, ‘Razaki’ and ‘Vlachiko’ are presented. Vitis cultivars were collected from the Aristotle University of Thessaloniki's (AUTH) ampelographic collection and have been previously phenotypically and genetically characterized. WGS libraries were sequenced on an IlluminaⓇ NovaSeq 6000 platform with the IlluminaⓇ NovaSeq 6000 S2 Reagent Kit (300 cycles). Raw sequence data used for analysis are available in NCBI under the Sequence Read Archive (SRA), with BioProject ID PRJNA805368. Reads were aligned to the reference genome of Vitis vinifera available from the EnsemblPlants database and formal analysis was conducted with the Genome Analysis Toolkit 4 (GATK4) pipeline. Data can be used to enrich our knowledge related to the genetic background of vitis cultivars and can also serve as a threshold in the scientific community towards the construction of a genomic database of vitis cultivars.
Collapse
Affiliation(s)
- George Tsiolas
- Institute of Applied Biosciences / CERTH, P.O. Box 60361, Thermi 57001, Thessaloniki, Greece
- Corresponding author.
| | - Sofia Michailidou
- Institute of Applied Biosciences / CERTH, P.O. Box 60361, Thermi 57001, Thessaloniki, Greece
| | - Antiopi Tsoureki
- Institute of Applied Biosciences / CERTH, P.O. Box 60361, Thermi 57001, Thessaloniki, Greece
| | - Anagnostis Argiriou
- Institute of Applied Biosciences / CERTH, P.O. Box 60361, Thermi 57001, Thessaloniki, Greece
- Department of Food Science and Nutrition / University of the Aegean, Lemnos 81400, Greece
| |
Collapse
|
4
|
Bantis F, Tsiolas G, Mouchtaropoulou E, Tsompanoglou I, Polidoros AN, Argiriou A, Koukounaras A. Comparative Transcriptome Analysis in Homo- and Hetero-Grafted Cucurbit Seedlings. Front Plant Sci 2021; 12:691069. [PMID: 34777405 PMCID: PMC8582762 DOI: 10.3389/fpls.2021.691069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
Watermelon (Citrullus lanatus) is a valuable horticultural crop with nutritional benefits grown worldwide. It is almost exclusively cultivated as grafted scions onto interspecific squash rootstock (Cucurbita maxima × Cucurbita moschata) to improve the growth and yield and to address the problems of soilborne diseases and abiotic stress factors. This study aimed to examine the effect of grafting (homo- and hetero-grafting) on the transcriptome level of the seedlings. Therefore, we compared homo-grafted watermelon (WW) with non-grafted watermelon control (W), homo-grafted squash (SS) with non-grafted squash control (S), hetero-grafted watermelon onto squash (WS) with SS, and WS with WW. Different numbers of differentially expressed genes (DEGs) were identified in each comparison. In total, 318 significant DEGs were detected between the transcriptomes of hetero-grafts and homo-grafts at 16 h after grafting. Overall, a significantly higher number of downregulated transcripts was detected among the DEGs. Only one gene showing increased expression related to the cytokinin synthesis was common in three out of four comparisons involving WS, SS, and S. The highest number of differentially expressed (DE) transcripts (433) was detected in the comparison between SS and S, followed by the 127 transcripts between WW and W. The study provides a description of the transcriptomic nature of homo- and hetero-grafted early responses, while the results provide a start point for the elucidation of the molecular mechanisms and candidate genes for the functional analyses of hetero-graft and homo-graft systems in Cucurbitaceae and generally in the plants.
Collapse
Affiliation(s)
- Filippos Bantis
- School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - George Tsiolas
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece
| | | | - Ioanna Tsompanoglou
- School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Alexios N. Polidoros
- School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anagnostis Argiriou
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece
- Department of Food Science and Nutrition, University of the Aegean, Myrina, Greece
| | | |
Collapse
|
5
|
Chaintoutis SC, Chassalevris T, Balaska S, Mouchtaropoulou E, Tsiolas G, Vlatakis I, Tychala A, Koutsioulis D, Argiriou A, Skoura L, Dovas CI. A Novel Real-Time RT-PCR-Based Methodology for the Preliminary Typing of SARS-CoV-2 Variants, Employing Non-Extendable LNA Oligonucleotides and Three Signature Mutations at the Spike Protein Receptor-Binding Domain. Life (Basel) 2021; 11:life11101015. [PMID: 34685386 PMCID: PMC8540511 DOI: 10.3390/life11101015] [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: 08/18/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 12/31/2022] Open
Abstract
Mutations resulting in amino-acid substitutions of the SARS-CoV-2 spike protein receptor-binding domain (RBD) have been associated with enhanced transmissibility and immune escape of the respective variants, namely Alpha, Beta, Gamma or Delta. Rapid identification of the aforementioned variants of concern and their discrimination of other variants is thus of importance for public health interventions. For this reason, a one-step real-time RT-PCR assay employing four locked nucleic acid (LNA) modified TaqMan probes was developed, to target signature mutations associated with amino-acid substitutions at positions 478, 484 and 501 present in the receptor-binding motif (RBM) of the spike protein RBD. This region contains most contacting residues of SARS-CoV-2 that bind to ACE2. A novel strategy employing the use of non-extendable LNA oligonucleotide blockers that can reduce non-specific hybridization of probes increased the number of different mutated sites examined in a multiplex PCR. The combinatory analysis of the different fluorescence signals obtained enabled the preliminary differentiation of SARS-CoV-2 variants of concern. The assay is sensitive with a LOD of 263 copies/reaction for the Delta variant, 170 copies/reaction for the Beta variant, amplification efficiencies > 91% and a linear range of >5 log10 copies/reaction against all targets. Validation of the assay using known SARS-CoV-2-positive and negative samples from humans and animals revealed its ability to correctly identify the targeted mutations and preliminary characterize the SARS-CoV-2 variants. The novel approach for mutation typing using LNA oligonucleotide blockers can be modified to target signature mutations at four different sites in the RBM and further expand the range of variants detected.
Collapse
Affiliation(s)
- Serafeim C. Chaintoutis
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 S. Voutyra Str., 54627 Thessaloniki, Greece; (S.C.C.); (T.C.)
| | - Taxiarchis Chassalevris
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 S. Voutyra Str., 54627 Thessaloniki, Greece; (S.C.C.); (T.C.)
| | - Sofia Balaska
- Department of Microbiology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, S. Kyriakidi Str., 54636 Thessaloniki, Greece; (S.B.); (A.T.); (L.S.)
| | - Evangelia Mouchtaropoulou
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001 Thessaloniki, Greece; (E.M.); (G.T.); (A.A.)
| | - George Tsiolas
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001 Thessaloniki, Greece; (E.M.); (G.T.); (A.A.)
| | - Ioannis Vlatakis
- EnzyQuest PC, Science and Technology Park of Crete, 100 N. Plastira Str., Vassilika Vouton, 70013 Heraklion, Greece; (I.V.); (D.K.)
| | - Areti Tychala
- Department of Microbiology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, S. Kyriakidi Str., 54636 Thessaloniki, Greece; (S.B.); (A.T.); (L.S.)
| | - Dimitris Koutsioulis
- EnzyQuest PC, Science and Technology Park of Crete, 100 N. Plastira Str., Vassilika Vouton, 70013 Heraklion, Greece; (I.V.); (D.K.)
| | - Anagnostis Argiriou
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001 Thessaloniki, Greece; (E.M.); (G.T.); (A.A.)
- Department of Food Science and Nutrition, University of the Aegean, 81400 Myrina, Greece
| | - Lemonia Skoura
- Department of Microbiology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, S. Kyriakidi Str., 54636 Thessaloniki, Greece; (S.B.); (A.T.); (L.S.)
| | - Chrysostomos I. Dovas
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 S. Voutyra Str., 54627 Thessaloniki, Greece; (S.C.C.); (T.C.)
- Correspondence: ; Tel.: +30-23-1099-9870
| |
Collapse
|
6
|
Chaintoutis SC, Thomou Z, Mouchtaropoulou E, Tsiolas G, Chassalevris T, Stylianaki I, Lagou M, Michailidou S, Moutou E, Koenen JJH, Dijkshoorn JW, Paraskevis D, Poutahidis T, Siarkou VI, Sypsa V, Argiriou A, Fortomaris P, Dovas CI. Outbreaks of SARS-CoV-2 in naturally infected mink farms: Impact, transmission dynamics, genetic patterns, and environmental contamination. PLoS Pathog 2021; 17:e1009883. [PMID: 34492088 PMCID: PMC8448373 DOI: 10.1371/journal.ppat.1009883] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 09/17/2021] [Accepted: 08/10/2021] [Indexed: 12/14/2022] Open
Abstract
SARS-CoV-2 infection outbreaks in minks have serious implications associated with animal health and welfare, and public health. In two naturally infected mink farms (A and B) located in Greece, we investigated the outbreaks and assessed parameters associated with virus transmission, immunity, pathology, and environmental contamination. Symptoms ranged from anorexia and mild depression to respiratory signs of varying intensity. Although the farms were at different breeding stages, mortality was similarly high (8.4% and 10.0%). The viral strains belonged to lineages B.1.1.218 and B.1.1.305, possessing the mink-specific S-Y453F substitution. Lung histopathology identified necrosis of smooth muscle and connective tissue elements of vascular walls, and vasculitis as the main early key events of the acute SARS-CoV-2-induced broncho-interstitial pneumonia. Molecular investigation in two dead minks indicated a consistently higher (0.3-1.3 log10 RNA copies/g) viral load in organs of the male mink compared to the female. In farm A, the infected farmers were responsible for the significant initial infection of 229 out of 1,000 handled minks, suggesting a very efficient human-to-mink transmission. Subsequent infections across the sheds wherein animals were being housed occurred due to airborne transmission. Based on a R0 of 2.90 and a growth rate equal to 0.293, the generation time was estimated to be 3.6 days, indicative of the massive SARS-CoV-2 dispersal among minks. After the end of the outbreaks, a similar percentage of animals were immune in the two farms (93.0% and 93.3%), preventing further virus transmission whereas, viral RNA was detected in samples collected from shed surfaces and air. Consequently, strict biosecurity is imperative during the occurrence of clinical signs. Environmental viral load monitoring, in conjunction with NGS should be adopted in mink farm surveillance. The minimum proportion of minks that need to be immunized to avoid outbreaks in farms was calculated at 65.5%, which is important for future vaccination campaigns.
Collapse
Affiliation(s)
- Serafeim C. Chaintoutis
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Zoi Thomou
- Pecon Hellas PC, Dispilio, Kastoria, Greece
| | | | - George Tsiolas
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, Greece
| | - Taxiarchis Chassalevris
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ioanna Stylianaki
- Laboratory of Pathology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Maria Lagou
- Laboratory of Pathology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sofia Michailidou
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, Greece
| | - Evangelia Moutou
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | | | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Theofilos Poutahidis
- Laboratory of Pathology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Victoria I. Siarkou
- Laboratory of Microbiology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Vana Sypsa
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Anagnostis Argiriou
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, Greece
- Department of Food Science and Nutrition, University of the Aegean, Myrina, Greece
| | - Paschalis Fortomaris
- Laboratory of Animal Husbandry, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Chrysostomos I. Dovas
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| |
Collapse
|
7
|
Chaintoutis SC, Chassalevris T, Tsiolas G, Balaska S, Vlatakis I, Mouchtaropoulou E, Siarkou VI, Tychala A, Koutsioulis D, Skoura L, Argiriou A, Dovas CI. A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions. J Virol Methods 2021; 296:114242. [PMID: 34274369 PMCID: PMC8282437 DOI: 10.1016/j.jviromet.2021.114242] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/14/2021] [Accepted: 07/14/2021] [Indexed: 11/18/2022]
Abstract
The emergence of SARS-CoV-2 mutations resulting in the S protein amino-acid substitutions N501Y and E484K, which have been associated with enhanced transmissibility and immune escape, respectively, necessitates immediate actions, for which their rapid identification is crucial. For the simultaneous typing of both of these mutations of concern (MOCs), a one-step real-time RT-PCR assay employing four locked nucleic acid (LNA) modified TaqMan probes was developed. The assay is highly sensitive with a LOD of 117 copies/reaction, amplification efficiencies >94 % and a linear range of over 5 log10 copies/reaction. Validation of the assay using known SARS-CoV-2-positive and negative samples from human and animals revealed its ability to correctly identify wild type strains, and strains possessing either one or both targeted amino-acid substitutions, thus comprising a useful pre-screening tool for rapid MOC identification. The basic principles of the methodology for the development of the assay are explained in order to facilitate the rapid design of similar assays able to detect emerging MOCs.
Collapse
Affiliation(s)
- Serafeim C Chaintoutis
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Taxiarchis Chassalevris
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - George Tsiolas
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloniki, Greece
| | - Sofia Balaska
- Department of Microbiology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, 1 Stilponos Kyriakidi str., 54636, Thessaloniki, Greece
| | - Ioannis Vlatakis
- EnzyQuest PC, Science and Technology Park of Crete, 100 Nikolaou Plastira str., Vassilika Vouton, 70013, Heraklion, Greece
| | - Evangelia Mouchtaropoulou
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloniki, Greece
| | - Victoria I Siarkou
- Laboratory of Microbiology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, University Campus, 54134, Thessaloniki, Greece
| | - Areti Tychala
- Department of Microbiology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, 1 Stilponos Kyriakidi str., 54636, Thessaloniki, Greece
| | - Dimitris Koutsioulis
- EnzyQuest PC, Science and Technology Park of Crete, 100 Nikolaou Plastira str., Vassilika Vouton, 70013, Heraklion, Greece
| | - Lemonia Skoura
- Department of Microbiology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, 1 Stilponos Kyriakidi str., 54636, Thessaloniki, Greece
| | - Anagnostis Argiriou
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloniki, Greece; Department of Food Science and Nutrition, University of the Aegean, 81400, Myrina, Lemnos, Greece
| | - Chrysostomos I Dovas
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece.
| |
Collapse
|
8
|
Andreadelli A, Petrakis S, Tsoureki A, Tsiolas G, Michailidou S, Baltzopoulou P, van Merkestein R, Hodgson P, Sceats M, Karagiannakis G, Makris AM. Effects of Magnesium Oxide and Magnesium Hydroxide Microparticle Foliar Treatment on Tomato PR Gene Expression and Leaf Microbiome. Microorganisms 2021; 9:microorganisms9061217. [PMID: 34199815 PMCID: PMC8228823 DOI: 10.3390/microorganisms9061217] [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: 04/19/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 11/20/2022] Open
Abstract
Recently, metal oxides and magnesium hydroxide nanoparticles (NPs) with high surface-to-volume ratios were shown to possess antibacterial properties with applications in biomedicine and agriculture. To assess recent observations from field trials on tomatoes showing resistance to pathogen attacks, porous micron-scale particles composed of nano-grains of MgO were hydrated and sprayed on the leaves of healthy tomato (Solanum lycopersicum) plants in a 20-day program. The results showed that the spray induced (a) a modest and selective stress gene response that was consistent with the absence of phytotoxicity and the production of salicylic acid as a signalling response to pathogens; (b) a shift of the phylloplane microbiota from near 100% dominance by Gram (−) bacteria, leaving extremophiles and cyanobacteria to cover the void; and (c) a response of the fungal leaf phylloplane that showed that the leaf epiphytome was unchanged but the fungal load was reduced by about 70%. The direct microbiome changes together with the low level priming of the plant’s immune system may explain the previously observed resistance to pathogen assaults in field tomato plants sprayed with the same hydrated porous micron-scale particles.
Collapse
Affiliation(s)
- Aggeliki Andreadelli
- Institute of Applied Biosciences, Centre for Research & Technology, Hellas (CERTH), 570 01 Thessaloniki, Greece; (A.A.); (S.P.); (A.T.); (G.T.); (S.M.)
| | - Spyros Petrakis
- Institute of Applied Biosciences, Centre for Research & Technology, Hellas (CERTH), 570 01 Thessaloniki, Greece; (A.A.); (S.P.); (A.T.); (G.T.); (S.M.)
| | - Antiopi Tsoureki
- Institute of Applied Biosciences, Centre for Research & Technology, Hellas (CERTH), 570 01 Thessaloniki, Greece; (A.A.); (S.P.); (A.T.); (G.T.); (S.M.)
| | - George Tsiolas
- Institute of Applied Biosciences, Centre for Research & Technology, Hellas (CERTH), 570 01 Thessaloniki, Greece; (A.A.); (S.P.); (A.T.); (G.T.); (S.M.)
| | - Sofia Michailidou
- Institute of Applied Biosciences, Centre for Research & Technology, Hellas (CERTH), 570 01 Thessaloniki, Greece; (A.A.); (S.P.); (A.T.); (G.T.); (S.M.)
| | - Penelope Baltzopoulou
- Chemical Process & Energy Resources Institute, Centre for Research & Technology, Hellas (CERTH), 570 01 Thessaloniki, Greece; (P.B.); (G.K.)
| | | | - Philip Hodgson
- Calix Limited, Pymble, NSW 2073, Australia; (R.v.M.); (P.H.); (M.S.)
| | - Mark Sceats
- Calix Limited, Pymble, NSW 2073, Australia; (R.v.M.); (P.H.); (M.S.)
| | - George Karagiannakis
- Chemical Process & Energy Resources Institute, Centre for Research & Technology, Hellas (CERTH), 570 01 Thessaloniki, Greece; (P.B.); (G.K.)
| | - Antonios M. Makris
- Institute of Applied Biosciences, Centre for Research & Technology, Hellas (CERTH), 570 01 Thessaloniki, Greece; (A.A.); (S.P.); (A.T.); (G.T.); (S.M.)
- Correspondence: ; Tel.: +30-2311-257-541
| |
Collapse
|
9
|
Michailidis M, Karagiannis E, Tanou G, Samiotaki M, Tsiolas G, Sarrou E, Stamatakis G, Ganopoulos I, Martens S, Argiriou A, Molassiotis A. Novel insights into the calcium action in cherry fruit development revealed by high-throughput mapping. Plant Mol Biol 2020; 104:597-614. [PMID: 32909183 DOI: 10.1007/s11103-020-01063-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/27/2020] [Indexed: 05/26/2023]
Abstract
This work provides the first system-wide datasets concerning metabolic changes in calcium-treated fruits, which reveal that exogenously applied calcium may specifically reprogram sweet cherry development and ripening physiognomy. Calcium modulates a wide range of plant developmental processes; however, the regulation of fruit ripening by calcium remains largely uncharacterized. In this study, transcriptome, proteome and metabolome profiling was used to document the responses of sweet cherry fruit to external calcium application (0.5% CaCl2) at 15, 27 and 37 days after full blossom. Endogenous calcium loading in fruit across development following external calcium feeding was accompanied by a reduction in respiration rate. Calcium treatment strongly impaired water-induced fruit cracking tested by two different assays, and this effect depended on the fruit size, water temperature and light/dark conditions. Substantial changes in the levels of numerous polar/non-polar primary and secondary metabolites, including malic acid, glucose, cysteine, epicatechin and neochlorogenic acid were noticed in fruits exposed to calcium. At the onset of ripening, we identified various calcium-affected genes, including those involved in ubiquitin and cysteine signaling, that had not been associated previously with calcium function in fruit biology. Calcium specifically increased the abundance of a significant number of proteins that classified as oxidoreductases, transferases, hydrolases, lyases, and ligases. The overview of temporal changes in gene expression and corresponding protein abundance provided by interlinked analysis revealed that oxidative phosphorylation, hypersensitive response, DNA repair, stomata closure, biosynthesis of secondary metabolites, and proton-pump activity were mainly affected by calcium. This report provides the fullest characterization of expression patterns in calcium-responsive genes, proteins and metabolites currently available in fruit ripening and will serve as a blueprint for future biological endeavors.
Collapse
Affiliation(s)
- Michail Michailidis
- Laboratory of Pomology, School of Agriculture, Aristotle University of Thessaloniki, 57001, Thermi, Greece
| | - Evangelos Karagiannis
- Laboratory of Pomology, School of Agriculture, Aristotle University of Thessaloniki, 57001, Thermi, Greece
| | - Georgia Tanou
- Institute of Soil and Water Resources, ELGO-DEMETER, 57001, Thessaloniki, Greece
| | - Martina Samiotaki
- Institute of Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", 16672, Vari, Greece
| | - George Tsiolas
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thermi, 570 01, Thessaloniki, Greece
| | - Eirini Sarrou
- Institute of Plant Breeding and Genetic Resources, ELGO-DEMETER, 57001, Thessaloniki, Greece
| | - George Stamatakis
- Institute of Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", 16672, Vari, Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, ELGO-DEMETER, 57001, Thessaloniki, Greece
| | - Stefans Martens
- Department of Food Quality and Nutrition, Centro Ricerca e Innovazione, Fondazione Edmund Mach, 38010 San Michele all'Adige, Trento, Italy
| | - Anagnostis Argiriou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thermi, 570 01, Thessaloniki, Greece
| | - Athanassios Molassiotis
- Laboratory of Pomology, School of Agriculture, Aristotle University of Thessaloniki, 57001, Thermi, Greece.
| |
Collapse
|