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Article ; Online: A new absolute quantitative method for peptide and metabolite detection.

Brogna, Carlo / Cristoni, Simone

2023 Volume 59, Issue 1, Page(s) e4991

Abstract: Mass spectrometry is widely employed in various analytical fields for both compound identification and quantification. While in the case of compound identification, the high-resolution instrument has increased selectivity and characterization efficiency; ...

Abstract	Mass spectrometry is widely employed in various analytical fields for both compound identification and quantification. While in the case of compound identification, the high-resolution instrument has increased selectivity and characterization efficiency; in the case of quantitative analysis, some critical tasks actually remain. In particular, different compounds exhibit different ionization efficiency, and this introduces the need to have a calibration standard for each analyte. In this paper, we present a new elaborative data technology, which makes it possible to standardize calibration between different instruments and molecules, making it absolute. The method was applied to data acquired by means of liquid chromatography mass spectrometry by means of an ion trap analyzer. The approach is based on the correlation of the ion trap space charge effect and the analyte concentration. The method was validated in the analysis of compounds having different polarity: hydrossitirosol, arginine, thyodiglicolic acid, and a peptide mixture of bacteria cultures derived the human gut microbiome where was found poliovirus. Moreover, it was used to obtain the absolute quantitation of peptides originating from the tryptic digestion of bacterial proteins in the fecal samples. It was therefore possible to identify and quantify different derived bacterial proteins of the poliomyelitis virus coded in bacteria derived from the gastrointestinal tract.
MeSH term(s)	Humans ; Research Design ; Arginine ; Bacterial Proteins ; Calibration ; Peptides
Chemical Substances	Arginine (94ZLA3W45F) ; Bacterial Proteins ; Peptides
Language	English
Publishing date	2023-12-18
Publishing country	England
Document type	Journal Article
ZDB-ID	1221763-3
ISSN	1096-9888 ; 1076-5174
ISSN (online)	1096-9888
ISSN	1076-5174
DOI	10.1002/jms.4991
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Article ; Online: Enhanced molecular release from elderly bone samples using collagenase I: insights into fatty acid metabolism alterations.

Malvandi, Amir Mohammad / Halilaj, Esra / Faraldi, Martina / Mangiavini, Laura / Cristoni, Simone / Leoni, Valerio / Lombardi, Giovanni

Journal of translational medicine

2024 Volume 22, Issue 1, Page(s) 143

Abstract: Background: Bone is a metabolically active tissue containing different cell types acting as endocrine targets and effectors. Further, bone is a dynamic depot for calcium, phosphorous and other essential minerals. The tissue matrix is subjected to a ... ...

Abstract	Background: Bone is a metabolically active tissue containing different cell types acting as endocrine targets and effectors. Further, bone is a dynamic depot for calcium, phosphorous and other essential minerals. The tissue matrix is subjected to a constant turnover in response to mechanical/endocrine stimuli. Bone turnover demands high energy levels, making fatty acids a crucial source for the bone cells. However, the current understanding of bone cell metabolism is poor. This is partly due to bone matrix complexity and difficulty in small molecules extraction from bone samples. This study aimed to evaluate the effect of metabolite sequestering from a protein-dominated matrix to increase the quality and amount of metabolomics data in discovering small molecule patterns in pathological conditions. Methods: Human bone samples were collected from 65 to 85 years old (the elderly age span) patients who underwent hip replacement surgery. Separated cortical and trabecular bone powders were treated with decalcifying, enzymatic (collagenase I and proteinase K) and solvent-based metabolite extraction protocols. The extracted mixtures were analyzed with the high-resolution mass spectrometry (HRMS). Data analysis was performed with XCMS and MetaboAnalystR packages. Results: Fast enzymatic treatment of bone samples before solvent addition led to a significantly higher yield of metabolite extraction. Collagenase I and proteinase K rapid digestion showed more effectiveness in cortical and trabecular bone samples, with a significantly higher rate (2.2 folds) for collagenase I. Further analysis showed significant enrichment in pathways like de novo fatty acid biosynthesis, glycosphingolipid metabolism and fatty acid oxidation-peroxisome. Conclusion: This work presents a novel approach for bone sample preparation for HRMS metabolomics. The disruption of bone matrix conformation at the molecular level helps the molecular release into the extracting solvent and, therefore, can lead to higher quality results and trustable biomarker discovery. Our results showed β-oxidation alteration in the aged bone sample. Future work covering more patients is worthy to identify the effective therapeutics to achieve healthy aging.
MeSH term(s)	Humans ; Aged ; Aged, 80 and over ; Endopeptidase K ; Metabolomics/methods ; Collagenases ; Solvents ; Fatty Acids
Chemical Substances	Endopeptidase K (EC 3.4.21.64) ; Collagenases (EC 3.4.24.-) ; Solvents ; Fatty Acids
Language	English
Publishing date	2024-02-09
Publishing country	England
Document type	Journal Article
ZDB-ID	2118570-0
ISSN	1479-5876 ; 1479-5876
ISSN (online)	1479-5876
ISSN	1479-5876
DOI	10.1186/s12967-024-04948-8
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Article ; Online: Correction: Enhanced molecular release from elderly bone samples using collagenase I: insights into fatty acid metabolism alterations.

Malvandi, Amir Mohammad / Halilaj, Esra / Faraldi, Martina / Mangiavini, Laura / Cristoni, Simone / Leoni, Valerio / Lombardi, Giovanni

Journal of translational medicine

2024 Volume 22, Issue 1, Page(s) 303

Language	English
Publishing date	2024-03-24
Publishing country	England
Document type	Published Erratum
ZDB-ID	2118570-0
ISSN	1479-5876 ; 1479-5876
ISSN (online)	1479-5876
ISSN	1479-5876
DOI	10.1186/s12967-024-05074-1
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Article ; Online: The importance of the gut microbiome in the pathogenesis and transmission of SARS-CoV-2.

Brogna, Carlo / Viduto, Valentina / Fabrowski, Mark / Cristoni, Simone / Marino, Giuliano / Montano, Luigi / Piscopo, Marina

Gut microbes

2023 Volume 15, Issue 1, Page(s) 2244718

Abstract: Zhou et al. study nicely traces a significant topic in COVID-19 infection: the persistence of the virus within the intestinal tract. Many pathological mechanisms have been noted in the current literature about the mode of infection and propagation of ... ...

Abstract	Zhou et al. study nicely traces a significant topic in COVID-19 infection: the persistence of the virus within the intestinal tract. Many pathological mechanisms have been noted in the current literature about the mode of infection and propagation of SARS-CoV-2 in the human body. Nevertheless, there are still many concerns about this: only some things seem well understood. We present a different point of view by illustrating the importance of the gut microbiome in the pathogenesis of COVID-19 disorders.
MeSH term(s)	Humans ; SARS-CoV-2 ; Gastrointestinal Microbiome ; COVID-19
Language	English
Publishing date	2023-08-10
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	2575755-6
ISSN	1949-0984 ; 1949-0984
ISSN (online)	1949-0984
ISSN	1949-0984
DOI	10.1080/19490976.2023.2244718
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Article ; Online: Ion mobility mass spectrometry with surface activated chemical ionisation as a method for studying the domain of water clusters.

Cristoni, Simone / Larini, Martina / Madama, Simone / Zorloni, Ilaria / Donato, Kevin / Paolacci, Stefano / Bertelli, Matteo

Journal of preventive medicine and hygiene

2022 Volume 63, Issue 2 Suppl 3, Page(s) E289–E296

Abstract: Water holds great relevance in various biological and biochemical systems. Water behaves as an excellent solvent, a reactant, a product and a catalyst of the reaction. The organisation of the water molecules, synergised by hydrogen bonds, builds up the ... ...

Abstract	Water holds great relevance in various biological and biochemical systems. Water behaves as an excellent solvent, a reactant, a product and a catalyst of the reaction. The organisation of the water molecules, synergised by hydrogen bonds, builds up the structure of the water clusters. These water clusters significantly influence biological functions. To study the domain of water clusters using Ion mobility mass spectrometry with surface activated chemical ionisation. The experimental analysis was aimed to determine the water behaviour in terms of cluster formation before and after the application of a physical effect, namely low-frequency irradiation. A sanist platform-based spectrometer, manufactured by ISB srl with SACI version for protein analysis, was used as the equipment. Furthermore, for samples, we used pure de-ionised water, a part of which was used virgin, and another part was irradiated. Ion-mobility mass spectrometry (IM-MS) procedure was adopted as the experimental method. An electromagnetic frequency fields generator was used to subject the test samples to electromagnetic radiations between 7 Hz to 80 Hz. The presence of neutral water species was confirmed in the water samples. For the same m/z, water ion clusters in the untreated water were found to have a much higher intensity than the electromagnetically treated water. The presence of a water cluster near the (M+H)
MeSH term(s)	Humans ; Water ; Research Design ; Mass Spectrometry
Chemical Substances	Water (059QF0KO0R)
Language	English
Publishing date	2022-10-17
Publishing country	Italy
Document type	Journal Article
ZDB-ID	1102926-2
ISSN	2421-4248 ; 1121-2233
ISSN (online)	2421-4248
ISSN	1121-2233
DOI	10.15167/2421-4248/jpmh2022.63.2S3.2771
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Zs.B 990: Show issues

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Article ; Online: Detection of recombinant Spike protein in the blood of individuals vaccinated against SARS-CoV-2: Possible molecular mechanisms.

Brogna, Carlo / Cristoni, Simone / Marino, Giuliano / Montano, Luigi / Viduto, Valentina / Fabrowski, Mark / Lettieri, Gennaro / Piscopo, Marina

Proteomics. Clinical applications

2023 Volume 17, Issue 6, Page(s) e2300048

Abstract: Purpose: The SARS-CoV-2 pandemic prompted the development and use of next-generation vaccines. Among these, mRNA-based vaccines consist of injectable solutions of mRNA encoding for a recombinant Spike, which is distinguishable from the wild-type protein ...

Abstract	Purpose: The SARS-CoV-2 pandemic prompted the development and use of next-generation vaccines. Among these, mRNA-based vaccines consist of injectable solutions of mRNA encoding for a recombinant Spike, which is distinguishable from the wild-type protein due to specific amino acid variations introduced to maintain the protein in a prefused state. This work presents a proteomic approach to reveal the presence of recombinant Spike protein in vaccinated subjects regardless of antibody titer. Experimental design: Mass spectrometry examination of biological samples was used to detect the presence of specific fragments of recombinant Spike protein in subjects who received mRNA-based vaccines. Results: The specific PP-Spike fragment was found in 50% of the biological samples analyzed, and its presence was independent of the SARS-CoV-2 IgG antibody titer. The minimum and maximum time at which PP-Spike was detected after vaccination was 69 and 187 days, respectively. Conclusions and clinical relevance: The presented method allows to evaluate the half-life of the Spike protein molecule "PP" and to consider the risks or benefits in continuing to administer additional booster doses of the SARS-CoV-2 mRNA vaccine. This approach is of valuable support to complement antibody level monitoring and represents the first proteomic detection of recombinant Spike in vaccinated subjects.
MeSH term(s)	Humans ; COVID-19 Vaccines ; SARS-CoV-2/genetics ; Proteomics ; Spike Glycoprotein, Coronavirus/genetics ; COVID-19/prevention & control ; RNA, Messenger/genetics ; Vaccination
Chemical Substances	COVID-19 Vaccines ; spike protein, SARS-CoV-2 ; Spike Glycoprotein, Coronavirus ; RNA, Messenger
Language	English
Publishing date	2023-08-31
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2261788-7
ISSN	1862-8354 ; 1862-8346
ISSN (online)	1862-8354
ISSN	1862-8346
DOI	10.1002/prca.202300048
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Zs.A 6575: Show issues

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Article ; Online: A retrospective cohort study on early antibiotic use in vaccinated and unvaccinated COVID-19 patients.

Brogna, Carlo / Montano, Luigi / Zanolin, Maria Elisabetta / Bisaccia, Domenico Rocco / Ciammetti, Gianluca / Viduto, Valentina / Fabrowski, Mark / Baig, Abdul M / Gerlach, Joachim / Gennaro, Iapicca / Bignardi, Elio / Brogna, Barbara / Frongillo, Aquilino / Cristoni, Simone / Piscopo, Marina

Journal of medical virology

2024 Volume 96, Issue 3, Page(s) e29507

Abstract: The bacteriophage behavior of SARS-CoV-2 during the acute and post-COVID-19 phases appears to be an important factor in the development of the disease. The early use of antibiotics seems to be crucial to inhibit disease progression-to prevent viral ... ...

Abstract	The bacteriophage behavior of SARS-CoV-2 during the acute and post-COVID-19 phases appears to be an important factor in the development of the disease. The early use of antibiotics seems to be crucial to inhibit disease progression-to prevent viral replication in the gut microbiome, and control toxicological production from the human microbiome. To study the impact of specific antibiotics on recovery from COVID-19 and long COVID (LC) taking into account: vaccination status, comorbidities, SARS-CoV-2 wave, time of initiation of antibiotic therapy and concomitant use of corticosteroids and nonsteroidal anti-inflammatory drugs (NSAIDs). A total of 211 COVID-19 patients were included in the study: of which 59 were vaccinated with mRNA vaccines against SARS-CoV-2 while 152 were unvaccinated. Patients were enrolled in three waves: from September 2020 to October 2022, corresponding to the emergence of the pre-Delta, Delta, and Omicron variants of the SARS-CoV-2 virus. The three criteria for enrolling patients were: oropharyngeal swab positivity or fecal findings; moderate symptoms with antibiotic intake; and measurement of blood oxygen saturation during the period of illness. The use of antibiotic combinations, such as amoxicillin with clavulanic acid (875 + 125 mg tablets, every 12 h) plus rifaximin (400 mg tablets every 12 h), as first choice, as suggested from the previous data, or azithromycin (500 mg tablets every 24 h), plus rifaximin as above, allows healthcare professionals to focus on the gut microbiome and its implications in COVID-19 disease during patient care. The primary outcome measured in this study was the estimated average treatment effect, which quantified the difference in mean recovery between patients receiving antibiotics and those not receiving antibiotics at 3 and 9 days after the start of treatment. In the analysis, both vaccinated and unvaccinated groups had a median illness duration of 7 days (interquartile range [IQR] 6-9 days for each; recovery crude hazard ratio [HR] = 0.94, p = 0.700). The median illness duration for the pre-Delta and Delta waves was 8 days (IQR 7-10 days), while it was shorter, 6.5 days, for Omicron (IQR 6-8 days; recovery crude HR = 1.71, p < 0.001). These results were confirmed by multivariate analysis. Patients with comorbidities had a significantly longer disease duration: median 8 days (IQR 7-10 days) compared to 7 days (IQR 6-8 days) for those without comorbidities (crude HR = 0.75, p = 0.038), but this result was not confirmed in multivariate analysis as statistical significance was lost. Early initiation of antibiotic therapy resulted in a significantly shorter recovery time (crude HR = 4.74, p < 0.001). Concomitant use of NSAIDs did not reduce disease duration and in multivariate analysis prolonged the disease (p = 0.041). A subgroup of 42 patients receiving corticosteroids for a median of 3 days (IQR 3-6 days) had a longer recovery time (median 9 days, IQR 8-10 days) compared to others (median 7 days, IQR 6-8 days; crude HR = 0.542, p < 0.001), as confirmed also by the adjusted HR. In this study, a statistically significant reduction in recovery time was observed among patients who received early antibiotic treatment. Early initiation of antibiotics played a crucial role in maintaining higher levels of blood oxygen saturation. In addition, it is worth noting that a significant number of patients who received antibiotics in the first 3 days and for a duration of 7 days, during the acute phase did not develop LC.
MeSH term(s)	Humans ; Anti-Bacterial Agents/therapeutic use ; COVID-19/prevention & control ; Rifaximin ; SARS-CoV-2 ; Post-Acute COVID-19 Syndrome ; COVID-19 Vaccines ; Retrospective Studies ; Anti-Inflammatory Agents, Non-Steroidal ; Adrenal Cortex Hormones
Chemical Substances	Anti-Bacterial Agents ; Rifaximin (L36O5T016N) ; COVID-19 Vaccines ; Anti-Inflammatory Agents, Non-Steroidal ; Adrenal Cortex Hormones
Language	English
Publishing date	2024-03-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.29507
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Article: Who Is the Intermediate Host of RNA Viruses? A Study Focusing on SARS-CoV-2 and Poliovirus.

Brogna, Carlo / Bisaccia, Domenico Rocco / Costanzo, Vincenzo / Lettieri, Gennaro / Montano, Luigi / Viduto, Valentina / Fabrowski, Mark / Cristoni, Simone / Prisco, Marina / Piscopo, Marina

Microorganisms

2024 Volume 12, Issue 4

Abstract: The COVID-19 pandemic has sparked a surge in research on microbiology and virology, shedding light on overlooked aspects such as the infection of bacteria by RNA virions in the animal microbiome. Studies reveal a decrease in beneficial gut bacteria ... ...

Abstract	The COVID-19 pandemic has sparked a surge in research on microbiology and virology, shedding light on overlooked aspects such as the infection of bacteria by RNA virions in the animal microbiome. Studies reveal a decrease in beneficial gut bacteria during COVID-19, indicating a significant interaction between SARS-CoV-2 and the human microbiome. However, determining the origins of the virus remains complex, with observed phenomena such as species jumps adding layers to the narrative. Prokaryotic cells play a crucial role in the disease's pathogenesis and transmission. Analyzing previous studies highlights intricate interactions from clinical manifestations to the use of the nitrogen isotope test. Drawing parallels with the history of the Poliovirus underscores the need to prioritize investigations into prokaryotic cells hosting RNA viruses.
Language	English
Publishing date	2024-03-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms12040643
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Article ; Online: Toxin-like peptides in plasma, urine and faecal samples from COVID-19 patients.

Brogna, Carlo / Cristoni, Simone / Petrillo, Mauro / Querci, Maddalena / Piazza, Ornella / Van den Eede, Guy

F1000Research

2021 Volume 10, Page(s) 550

Abstract: Background: ...

Abstract	Background:
MeSH term(s)	COVID-19 ; Feces ; Humans ; Pandemics ; Peptides ; SARS-CoV-2
Chemical Substances	Peptides
Language	English
Publishing date	2021-07-08
Publishing country	England
Document type	Journal Article
ZDB-ID	2699932-8
ISSN	2046-1402 ; 2046-1402
ISSN (online)	2046-1402
ISSN	2046-1402
DOI	10.12688/f1000research.54306.2
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Article ; Online: Increase of SARS-CoV-2 RNA load in faecal samples prompts for rethinking of SARS-CoV-2 biology and COVID-19 epidemiology.

Petrillo, Mauro / Brogna, Carlo / Cristoni, Simone / Querci, Maddalena / Piazza, Ornella / Van den Eede, Guy

F1000Research

2021 Volume 10, Page(s) 370

Abstract: Background Scientific evidence for the involvement of human microbiota in the development of COVID-19 disease has been reported recently. SARS-CoV-2 RNA presence in human faecal samples and SARS-CoV-2 activity in faeces from COVID-19 patients have been ... ...

Abstract	Background Scientific evidence for the involvement of human microbiota in the development of COVID-19 disease has been reported recently. SARS-CoV-2 RNA presence in human faecal samples and SARS-CoV-2 activity in faeces from COVID-19 patients have been observed. Methods Starting from these observations, an experimental design was developed to cultivate
MeSH term(s)	Biology ; COVID-19 ; Feces ; Humans ; RNA, Viral ; SARS-CoV-2
Chemical Substances	RNA, Viral
Language	English
Publishing date	2021-05-11
Publishing country	England
Document type	Journal Article
ZDB-ID	2699932-8
ISSN	2046-1402 ; 2046-1402
ISSN (online)	2046-1402
ISSN	2046-1402
DOI	10.12688/f1000research.52540.2
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