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Article ; Online: Genomic and transcriptomic analysis of the recent Mpox outbreak.

Giorgi, Federico M / Pozzobon, Daniele / Di Meglio, Antonio / Mercatelli, Daniele

2024 Volume 42, Issue 7, Page(s) 1841–1849

Abstract: The Mpox (formerly named Monkeypox) virus is the etiological cause of a recent multi-country outbreak, with thousands of distinct cases detected outside the endemic areas of Africa as of December 2023. In this article, we analyze the sequences of full ... ...

Abstract	The Mpox (formerly named Monkeypox) virus is the etiological cause of a recent multi-country outbreak, with thousands of distinct cases detected outside the endemic areas of Africa as of December 2023. In this article, we analyze the sequences of full genomes of Mpox virus from Europe and compare them with all available Mpox sequences of historical relevance, annotated by year and geographic origin, as well as related Cowpox and Variola (smallpox) virus sequences. Our results show that the recent outbreak is most likely originating from the West African clade of Mpox, with >99 % sequence identity with sequences derived from historical and recent cases, dating from 1971 to 2017. We analyze specific mutations occurring in viral proteins between the current outbreak, previous Mpox and Cowpox sequences, and the historical Variola virus. Genome-wide sequence analysis of the recent outbreak and other Mpox/Cowpox/Variola viruses shows a very high conservation, with 97.9 % (protein-based) and 97.8 % (nucleotide-based) sequence identity. We identified significant correlation in human transcriptional responses as well, with a conserved immune pathway response induced in human cell cultures by the three families of Pox virus. The similarities identified between the major strains of Pox viruses, as well as within the Mpox clades, both at the genomic and transcriptomic levels, provide a molecular basis for the observed efficacy of Variola vaccines in other Poxviruses.
MeSH term(s)	Animals ; Humans ; Smallpox ; Cowpox ; Mpox (monkeypox)/epidemiology ; DNA, Viral/genetics ; Variola virus ; Poxviridae ; Monkeypox virus/genetics ; Genomics ; Disease Outbreaks ; Gene Expression Profiling
Chemical Substances	DNA, Viral
Language	English
Publishing date	2024-02-03
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	605674-x
ISSN	1873-2518 ; 0264-410X
ISSN (online)	1873-2518
ISSN	0264-410X
DOI	10.1016/j.vaccine.2023.12.086
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Article ; Online: Quantitative and qualitative detection of tRNAs, tRNA halves and tRFs in human cancer samples: Molecular grounds for biomarker development and clinical perspectives.

Cabrelle, Chiara / Giorgi, Federico Manuel / Mercatelli, Daniele

Gene

2023 Volume 898, Page(s) 148097

Abstract: Transfer RNAs (tRNAs) are small non-coding RNAs playing a central role during protein synthesis. Besides translation, growing evidence suggests that in many contexts, precursor or mature tRNAs can also be processed into smaller fragments playing many non- ...

Abstract	Transfer RNAs (tRNAs) are small non-coding RNAs playing a central role during protein synthesis. Besides translation, growing evidence suggests that in many contexts, precursor or mature tRNAs can also be processed into smaller fragments playing many non-canonical regulatory roles in different biological pathways with oncogenic relevance. Depending on the source, these molecules can be classified as tRNA halves (also known as tiRNAs) or tRNA-derived fragments (tRFs), and furtherly divided into 5'-tRNA and 3'-tRNA halves, or tRF-1, tRF-2, tRF-3, tRF-5, and i-tRF, respectively. Unlike DNA and mRNA, high-throughput sequencing of tRNAs is challenging, because of technical limitations of currently developed sequencing methods. In recent years, different sequencing approaches have been proposed allowing the quantification and identification of an increasing number of tRNA fragments with critical functions in distinct physiological and pathophysiological processes. In the present review, we discussed pros and cons of recent advances in different sequencing methods, also introducing the expanding repertoire of bioinformatics tool and resources specifically focused on tRNA research and discussing current issues in the study of these small RNA molecules. Furthermore, we discussed the potential value of tRNA fragments as diagnostic and prognostic biomarkers for different types of cancers.
MeSH term(s)	Humans ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Neoplasms/diagnosis ; Neoplasms/genetics ; Neoplasms/metabolism ; High-Throughput Nucleotide Sequencing
Chemical Substances	RNA, Transfer (9014-25-9)
Language	English
Publishing date	2023-12-19
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	391792-7
ISSN	1879-0038 ; 0378-1119
ISSN (online)	1879-0038
ISSN	0378-1119
DOI	10.1016/j.gene.2023.148097
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Article: The R Language: An Engine for Bioinformatics and Data Science.

Giorgi, Federico M / Ceraolo, Carmine / Mercatelli, Daniele

Life (Basel, Switzerland)

2022 Volume 12, Issue 5

Abstract: The R programming language is approaching its 30th birthday, and in the last three decades it has achieved a prominent role in statistics, bioinformatics, and data science in general. It currently ranks among the top 10 most popular languages worldwide, ... ...

Abstract	The R programming language is approaching its 30th birthday, and in the last three decades it has achieved a prominent role in statistics, bioinformatics, and data science in general. It currently ranks among the top 10 most popular languages worldwide, and its community has produced tens of thousands of extensions and packages, with scopes ranging from machine learning to transcriptome data analysis. In this review, we provide an historical chronicle of how R became what it is today, describing all its current features and capabilities. We also illustrate the major tools of R, such as the current R editors and integrated development environments (IDEs), the R Shiny web server, the R methods for machine learning, and its relationship with other programming languages. We also discuss the role of R in science in general as a driver for reproducibility. Overall, we hope to provide both a complete snapshot of R today and a practical compendium of the major features and applications of this programming language.
Language	English
Publishing date	2022-04-27
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2662250-6
ISSN	2075-1729
ISSN	2075-1729
DOI	10.3390/life12050648
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Article: Geographic and Genomic Distribution of SARS-CoV-2 Mutations.

Mercatelli, Daniele / Giorgi, Federico M

Frontiers in microbiology

2020 Volume 11, Page(s) 1800

Abstract: The novel respiratory disease COVID-19 has reached the status of worldwide pandemic and large efforts are currently being undertaken in molecularly characterizing the virus causing it, SARS-CoV-2. The genomic variability of SARS-CoV-2 specimens scattered ...

Abstract	The novel respiratory disease COVID-19 has reached the status of worldwide pandemic and large efforts are currently being undertaken in molecularly characterizing the virus causing it, SARS-CoV-2. The genomic variability of SARS-CoV-2 specimens scattered across the globe can underly geographically specific etiological effects. In the present study, we gather the 48,635 SARS-CoV-2 complete genomes currently available thanks to the collection endeavor of the GISAID consortium and thousands of contributing laboratories. We analyzed and annotated all SARS-CoV-2 mutations compared with the reference Wuhan genome NC_045512.2, observing an average of 7.23 mutations per sample. Our analysis shows the prevalence of single nucleotide transitions as the major mutational type across the world. There exist at least three clades characterized by geographic and genomic specificity. In particular, clade G, prevalent in Europe, carries a D614G mutation in the Spike protein, which is responsible for the initial interaction of the virus with the host human cell. Our analysis may facilitate custom-designed antiviral strategies based on the molecular specificities of SARS-CoV-2 in different patients and geographical locations.
Keywords	covid19
Language	English
Publishing date	2020-07-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2020.01800
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Article ; Online: Transcriptional network inference and master regulator analysis of the response to ribosome-inactivating proteins in leukemia cells.

Mercatelli, Daniele / Bortolotti, Massimo / Giorgi, Federico M

Toxicology

2020 Volume 441, Page(s) 152531

Abstract: Gene-regulatory networks reconstruction has become a very popular approach in applied biology to infer and dissect functional interactions of Transcription Factors (TFs) driving a defined phenotypic state, termed as Master Regulators (MRs). In the ... ...

Abstract	Gene-regulatory networks reconstruction has become a very popular approach in applied biology to infer and dissect functional interactions of Transcription Factors (TFs) driving a defined phenotypic state, termed as Master Regulators (MRs). In the present work, cutting-edge bioinformatic methods were applied to re-analyze experimental data on leukemia cells (human myelogenous leukemia cell line THP-1 and acute myeloid leukemia MOLM-13 cells) treated for 6 h with two different Ribosome-Inactivating Proteins (RIPs), namely Shiga toxin type 1 (400 ng/mL) produced by Escherichia coli strains and the plant toxin stenodactylin (60 ng/mL), purified from the caudex of Adenia stenodactyla Harms. This analysis allowed us to identify the common early transcriptional response to 28S rRNA damage based on gene-regulatory network inference and Master Regulator Analysis (MRA). Both toxins induce a common response at 6 h which involves inflammatory mediators triggered by AP-1 family transcriptional factors and ATF3 in leukemia cells. We describe for the first time the involvement of MAFF, KLF2 and KLF6 in regulating RIP-induced apoptotic cell death, while receptor-mediated downstream signaling through ANXA1 and TLR4 is suggested for both toxins.
MeSH term(s)	Cell Line, Tumor ; Gene Expression Regulation, Leukemic/drug effects ; Gene Regulatory Networks/drug effects ; Humans ; Lectins/pharmacology ; Leukemia/metabolism ; Membrane Proteins/drug effects ; Membrane Proteins/metabolism ; N-Glycosyl Hydrolases/pharmacology ; Ribosome Inactivating Proteins/pharmacology ; Shiga Toxin 1/pharmacology ; Transcription Factors/metabolism
Chemical Substances	Lectins ; Membrane Proteins ; Shiga Toxin 1 ; Transcription Factors ; N-Glycosyl Hydrolases (EC 3.2.2.-) ; stenodactylin protein, Adenia stenodactyla (EC 3.2.2.-) ; Ribosome Inactivating Proteins (EC 3.2.2.22)
Language	English
Publishing date	2020-06-25
Publishing country	Ireland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	184557-3
ISSN	1879-3185 ; 0300-483X
ISSN (online)	1879-3185
ISSN	0300-483X
DOI	10.1016/j.tox.2020.152531
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Article ; Online: Web tools to fight pandemics: the COVID-19 experience.

Mercatelli, Daniele / Holding, Andrew N / Giorgi, Federico M

Briefings in bioinformatics

2020 Volume 22, Issue 2, Page(s) 690–700

Abstract: The current outbreak of COVID-19 has generated an unprecedented scientific response worldwide, with the generation of vast amounts of publicly available epidemiological, biological and clinical data. Bioinformatics scientists have quickly produced online ...

Abstract	The current outbreak of COVID-19 has generated an unprecedented scientific response worldwide, with the generation of vast amounts of publicly available epidemiological, biological and clinical data. Bioinformatics scientists have quickly produced online methods to provide non-computational users with the opportunity of analyzing such data. In this review, we report the results of this effort, by cataloguing the currently most popular web tools for COVID-19 research and analysis. Our focus was driven on tools drawing data from the fields of epidemiology, genomics, interactomics and pharmacology, in order to provide a meaningful depiction of the current state of the art of COVID-19 online resources.
MeSH term(s)	COVID-19/prevention & control ; COVID-19/virology ; Computational Biology ; Humans ; Internet ; Pandemics ; SARS-CoV-2/isolation & purification
Keywords	covid19
Language	English
Publishing date	2020-10-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbaa261
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Article ; Online: Structural genetics of circulating variants affecting the SARS-CoV-2 spike/human ACE2 complex.

Ortuso, Francesco / Mercatelli, Daniele / Guzzi, Pietro Hiram / Giorgi, Federico Manuel

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 14, Page(s) 6545–6555

Abstract: SARS-CoV-2 entry in human cells is mediated by the interaction between the viral Spike protein and the human ACE2 receptor. This mechanism evolved from the ancestor bat coronavirus and is currently one of the main targets for antiviral strategies. ... ...

Abstract	SARS-CoV-2 entry in human cells is mediated by the interaction between the viral Spike protein and the human ACE2 receptor. This mechanism evolved from the ancestor bat coronavirus and is currently one of the main targets for antiviral strategies. However, there currently exist several Spike protein variants in the SARS-CoV-2 population as the result of mutations, and it is unclear if these variants may exert a specific effect on the affinity with ACE2 which, in turn, is also characterized by multiple alleles in the human population. In the current study, the GBPM analysis, originally developed for highlighting host-guest interaction features, has been applied to define the key amino acids responsible for the Spike/ACE2 molecular recognition, using four different crystallographic structures. Then, we intersected these structural results with the current mutational status, based on more than 295,000 sequenced cases, in the SARS-CoV-2 population. We identified several Spike mutations interacting with ACE2 and mutated in at least 20 distinct patients: S477N, N439K, N501Y, Y453F, E484K, K417N, S477I and G476S. Among these, mutation N501Y in particular is one of the events characterizing SARS-CoV-2 lineage B.1.1.7, which has recently risen in frequency in Europe. We also identified five ACE2 rare variants that may affect interaction with Spike and susceptibility to infection: S19P, E37K, M82I, E329G and G352V.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Angiotensin-Converting Enzyme 2/chemistry ; Angiotensin-Converting Enzyme 2/genetics ; Angiotensin-Converting Enzyme 2/metabolism ; COVID-19/genetics ; COVID-19/virology ; Humans ; Mutation ; Peptidyl-Dipeptidase A/chemistry ; Protein Binding ; SARS-CoV-2/chemistry ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Peptidyl-Dipeptidase A (EC 3.4.15.1) ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2021-02-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2021.1886175
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Article ; Online: Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K.

Di Giacomo, Simone / Mercatelli, Daniele / Rakhimov, Amir / Giorgi, Federico M

Journal of medical virology

2021 Volume 93, Issue 9, Page(s) 5638–5643

Abstract: Several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have emerged, posing a renewed threat to coronavirus disease 2019 containment and to vaccine and drug efficacy. In this study, we analyzed more than 1,000,000 SARS-CoV-2 ... ...

Abstract	Several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have emerged, posing a renewed threat to coronavirus disease 2019 containment and to vaccine and drug efficacy. In this study, we analyzed more than 1,000,000 SARS-CoV-2 genomic sequences deposited up to April 27, 2021, on the GISAID public repository, and identified a novel T478K mutation located on the SARS-CoV-2 Spike protein. The mutation is structurally located in the region of interaction with human receptor ACE2 and was detected in 11,435 distinct cases. We show that T478K has appeared and risen in frequency since January 2021, predominantly in Mexico and the United States, but we could also detect it in several European countries.
MeSH term(s)	COVID-19/virology ; Europe ; Genome, Viral ; Humans ; Mexico ; Mutation ; Phylogeny ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/physiology ; United States
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2021-05-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.27062
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Article ; Online: Geographic and Genomic Distribution of SARS-CoV-2 Mutations

Mercatelli, Daniele / Giorgi, Federico M.

Frontiers in Microbiology

2020 Volume 11

Keywords	Microbiology (medical) ; Microbiology ; covid19
Publisher	Frontiers Media SA
Publishing country	ch
Document type	Article ; Online
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2020.01800
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Article: Geographic and Genomic Distribution of SARS-CoV-2 Mutations

Mercatelli, Daniele / Giorgi, Federico M.

Front. Microbiol.

Abstract	The novel respiratory disease COVID-19 has reached the status of worldwide pandemic and large efforts are currently being undertaken in molecularly characterizing the virus causing it, SARS-CoV-2. The genomic variability of SARS-CoV-2 specimens scattered across the globe can underly geographically specific etiological effects. In the present study, we gather the 48,635 SARS-CoV-2 complete genomes currently available thanks to the collection endeavor of the GISAID consortium and thousands of contributing laboratories. We analyzed and annotated all SARS-CoV-2 mutations compared with the reference Wuhan genome NC_045512.2, observing an average of 7.23 mutations per sample. Our analysis shows the prevalence of single nucleotide transitions as the major mutational type across the world. There exist at least three clades characterized by geographic and genomic specificity. In particular, clade G, prevalent in Europe, carries a D614G mutation in the Spike protein, which is responsible for the initial interaction of the virus with the host human cell. Our analysis may facilitate custom-designed antiviral strategies based on the molecular specificities of SARS-CoV-2 in different patients and geographical locations.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #706306
Database	COVID19

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