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Article ; Online: A Meta-Analysis Approach to Gene Regulatory Network Inference Identifies Key Regulators of Cardiovascular Diseases.

Pepe, Gerardo / Appierdo, Romina / Ausiello, Gabriele / Helmer-Citterich, Manuela / Gherardini, Pier Federico

International journal of molecular sciences

2024 Volume 25, Issue 8

Abstract: Cardiovascular diseases (CVDs) represent a major concern for global health, whose mechanistic understanding is complicated by a complex interplay between genetic predisposition and environmental factors. Specifically, heart failure (HF), encompassing ... ...

Abstract	Cardiovascular diseases (CVDs) represent a major concern for global health, whose mechanistic understanding is complicated by a complex interplay between genetic predisposition and environmental factors. Specifically, heart failure (HF), encompassing dilated cardiomyopathy (DC), ischemic cardiomyopathy (ICM), and hypertrophic cardiomyopathy (HCM), is a topic of substantial interest in basic and clinical research. Here, we used a Partial Correlation Coefficient-based algorithm (PCC) within the context of a meta-analysis framework to construct a Gene Regulatory Network (GRN) that identifies key regulators whose activity is perturbed in Heart Failure. By integrating data from multiple independent studies, our approach unveiled crucial regulatory associations between transcription factors (TFs) and structural genes, emphasizing their pivotal roles in regulating metabolic pathways, such as fatty acid metabolism, oxidative stress response, epithelial-to-mesenchymal transition, and coagulation. In addition to known associations, our analysis also identified novel regulators, including the identification of TFs FPM315 and OVOL2, which are implicated in dilated cardiomyopathies, and TEAD1 and TEAD2 in both dilated and ischemic cardiomyopathies. Moreover, we uncovered alterations in adipogenesis and oxidative phosphorylation pathways in hypertrophic cardiomyopathy and discovered a role for IL2 STAT5 signaling in heart failure. Our findings underscore the importance of TF activity in the initiation and progression of cardiac disease, highlighting their potential as pharmacological targets.
MeSH term(s)	Humans ; Gene Regulatory Networks ; Cardiovascular Diseases/genetics ; Cardiovascular Diseases/metabolism ; Transcription Factors/metabolism ; Transcription Factors/genetics ; Gene Expression Regulation ; Algorithms ; Heart Failure/genetics ; Heart Failure/metabolism
Chemical Substances	Transcription Factors
Language	English
Publishing date	2024-04-11
Publishing country	Switzerland
Document type	Journal Article ; Meta-Analysis
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms25084224
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A "data sharing trust" model for rapid, collaborative science.

Chan, Vincent / Gherardini, Pier Federico / Krummel, Matthew F / Fragiadakis, Gabriela K

Cell

2021 Volume 184, Issue 3, Page(s) 566–570

Abstract: Complex datasets provide opportunities for discoveries beyond their initial scope. Effective and rapid data sharing and management practices are crucial to realize this potential; however, they are harder to implement than post-publication access. Here, ... ...

Abstract	Complex datasets provide opportunities for discoveries beyond their initial scope. Effective and rapid data sharing and management practices are crucial to realize this potential; however, they are harder to implement than post-publication access. Here, we introduce the concept of a "data sharing trust" to maximize the value of large datasets.
MeSH term(s)	Authorship ; Cooperative Behavior ; Humans ; Information Dissemination ; Models, Theoretical ; Research Personnel ; Trust
Language	English
Publishing date	2021-03-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2021.01.006
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Article ; Online: Multiplexed profiling of RNA and protein expression signatures in individual cells using flow or mass cytometry.

Duckworth, Andrew D / Gherardini, Pier Federico / Sykorova, Martina / Yasin, Faten / Nolan, Garry P / Slupsky, Joseph R / Kalakonda, Nagesh

Nature protocols

2019 Volume 14, Issue 3, Page(s) 901–920

Abstract: Advances in single-cell analysis technologies are providing novel insights into phenotypic and functional heterogeneity within seemingly identical cell populations. RNA within single cells can be analyzed using unbiased sequencing protocols or through ... ...

Abstract	Advances in single-cell analysis technologies are providing novel insights into phenotypic and functional heterogeneity within seemingly identical cell populations. RNA within single cells can be analyzed using unbiased sequencing protocols or through more targeted approaches using in situ hybridization (ISH). The proximity ligation assay for RNA (PLAYR) approach is a sensitive and high-throughput technique that relies on in situ and proximal ligation to measure at least 27 specific RNAs by flow or mass cytometry. We provide detailed instructions for combining this technique with antibody-based detection of surface/internal protein, allowing simultaneous highly multiplexed profiling of RNA and protein expression at single-cell resolution. PLAYR overcomes limitations on multiplexing seen in previous branching DNA-based RNA detection techniques by integration of a transcript-specific oligonucleotide sequence within a rolling-circle amplification (RCA). This unique transcript-associated sequence can then be detected by heavy metal (for mass cytometry)- or fluorophore (for flow cytometry)-conjugated complementary detection oligonucleotides. Included in this protocol is methodology to label oligonucleotides with lanthanide metals for use in mass cytometry. When analyzed by mass cytometry, up to 40 variables (with scope for future expansion) can be measured simultaneously. We used the described protocol to demonstrate intraclonal heterogeneity within primary cells from chronic lymphocytic leukemia patients, but it can be adapted to other primary cells or cell lines in suspension. This robust, reliable and reproducible protocol can be completed in 2-3 d and can be paused at several stages for convenience.
MeSH term(s)	Animals ; Antibodies/metabolism ; Antigens/metabolism ; B-Lymphocytes/metabolism ; Computer Simulation ; Flow Cytometry/methods ; Gene Expression Profiling/methods ; Humans ; Ionomycin/pharmacology ; Proteins/genetics ; Proteins/metabolism ; RNA/genetics ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Tetradecanoylphorbol Acetate/pharmacology
Chemical Substances	Antibodies ; Antigens ; Proteins ; RNA, Messenger ; Ionomycin (56092-81-0) ; RNA (63231-63-0) ; Tetradecanoylphorbol Acetate (NI40JAQ945)
Language	English
Publishing date	2019-02-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2244966-8
ISSN	1750-2799 ; 1754-2189
ISSN (online)	1750-2799
ISSN	1754-2189
DOI	10.1038/s41596-018-0120-8
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Article ; Online: Experimental and computational methods for the analysis and modeling of signaling networks.

Gherardini, Pier Federico / Helmer-Citterich, Manuela

New biotechnology

2013 Volume 30, Issue 3, Page(s) 327–332

Abstract: External cues are processed and integrated by signal transduction networks that drive appropriate cellular responses. Characterizing these programs, as well as how their deregulation leads to disease, is crucial for our understanding of cell biology. The ...

Abstract	External cues are processed and integrated by signal transduction networks that drive appropriate cellular responses. Characterizing these programs, as well as how their deregulation leads to disease, is crucial for our understanding of cell biology. The past ten years have witnessed a gradual increase in the number of molecular parameters that can be simultaneously measured in a sample. Moreover our capacity to handle multiple samples in parallel has expanded, thus allowing a deeper profiling of cellular states under diverse experimental conditions. These technological advances have been complemented by the development of computational methods aimed at mining, analyzing and modeling these data. In this review we give a general overview of the most important experimental and computational techniques used in the field and describe several interesting application of these methodologies. We conclude by highlighting the issues that we think will keep researchers in the field busy in the next few years.
MeSH term(s)	Computational Biology ; Humans ; Neoplasms/drug therapy ; Neoplasms/metabolism ; Neoplasms/pathology ; Signal Transduction
Language	English
Publishing date	2013-03-25
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2400836-9
ISSN	1876-4347 ; 1871-6784
ISSN (online)	1876-4347
ISSN	1871-6784
DOI	10.1016/j.nbt.2012.11.007
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Article ; Online: What has proteomics taught us about Leishmania development?

Tsigankov, Polina / Gherardini, Pier Federico / Helmer-Citterich, Manuela / Zilberstein, Dan

Parasitology

2012 Volume 139, Issue 9, Page(s) 1146–1157

Abstract: Leishmania are obligatory intracellular parasitic protozoa that cycle between sand fly mid-gut and phagolysosomes of mammalian macrophages. They have developed genetically programmed changes in gene and protein expression that enable rapid optimization ... ...

Abstract	Leishmania are obligatory intracellular parasitic protozoa that cycle between sand fly mid-gut and phagolysosomes of mammalian macrophages. They have developed genetically programmed changes in gene and protein expression that enable rapid optimization of cell function according to vector and host environments. During the last two decades, host-free systems that mimic intra-lysosomal environments have been devised in which promastigotes differentiate into amastigotes axenically. These cultures have facilitated detailed investigation of the molecular mechanisms underlying Leishmania development inside its host. Axenic promastigotes and amastigotes have been subjected to transcriptome and proteomic analyses. Development had appeared somewhat variable but was revealed by proteomics to be strictly coordinated and regulated. Here we summarize the current understanding of Leishmania promastigote to amastigote differentiation, highlighting the data generated by proteomics.
MeSH term(s)	Adaptation, Physiological ; Animals ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Humans ; Insect Vectors/parasitology ; Leishmania/genetics ; Leishmania/growth & development ; Leishmania/metabolism ; Leishmaniasis/parasitology ; Life Cycle Stages ; Macrophages/parasitology ; Phagosomes/parasitology ; Proteomics/methods ; Protozoan Proteins/genetics ; Protozoan Proteins/metabolism ; Psychodidae/parasitology ; Signal Transduction
Chemical Substances	Protozoan Proteins
Language	English
Publishing date	2012-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	207627-5
ISSN	1469-8161 ; 0031-1820
ISSN (online)	1469-8161
ISSN	0031-1820
DOI	10.1017/S0031182012000157
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Article ; Online: Superpose3D: a local structural comparison program that allows for user-defined structure representations.

Gherardini, Pier Federico / Ausiello, Gabriele / Helmer-Citterich, Manuela

PloS one

2010 Volume 5, Issue 8, Page(s) e11988

Abstract: Local structural comparison methods can be used to find structural similarities involving functional protein patches such as enzyme active sites and ligand binding sites. The outcome of such analyses is critically dependent on the representation used to ... ...

Abstract	Local structural comparison methods can be used to find structural similarities involving functional protein patches such as enzyme active sites and ligand binding sites. The outcome of such analyses is critically dependent on the representation used to describe the structure. Indeed different categories of functional sites may require the comparison program to focus on different characteristics of the protein residues. We have therefore developed superpose3D, a novel structural comparison software that lets users specify, with a powerful and flexible syntax, the structure description most suited to the requirements of their analysis. Input proteins are processed according to the user's directives and the program identifies sets of residues (or groups of atoms) that have a similar 3D position in the two structures. The advantages of using such a general purpose program are demonstrated with several examples. These test cases show that no single representation is appropriate for every analysis, hence the usefulness of having a flexible program that can be tailored to different needs. Moreover we also discuss how to interpret the results of a database screening where a known structural motif is searched against a large ensemble of structures. The software is written in C++ and is released under the open source GPL license. Superpose3D does not require any external library, runs on Linux, Mac OSX, Windows and is available at http://cbm.bio.uniroma2.it/superpose3D.
MeSH term(s)	Binding Sites ; Flavin-Adenine Dinucleotide/metabolism ; Humans ; Models, Molecular ; Molecular Conformation ; Protein Conformation ; Proteins/chemistry ; Proteins/metabolism ; Software ; User-Computer Interface
Chemical Substances	Proteins ; Flavin-Adenine Dinucleotide (146-14-5)
Language	English
Publishing date	2010-08-05
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0011988
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Article ; Online: A Proteome-wide Domain-centric Perspective on Protein Phosphorylation.

Palmeri, Antonio / Ausiello, Gabriele / Ferrè, Fabrizio / Helmer-Citterich, Manuela / Gherardini, Pier Federico

Molecular & cellular proteomics : MCP

2014 Volume 13, Issue 9, Page(s) 2198–2212

Abstract: Phosphorylation is a widespread post-translational modification that modulates the function of a large number of proteins. Here we show that a significant proportion of all the domains in the human proteome is significantly enriched or depleted in ... ...

Abstract	Phosphorylation is a widespread post-translational modification that modulates the function of a large number of proteins. Here we show that a significant proportion of all the domains in the human proteome is significantly enriched or depleted in phosphorylation events. A substantial improvement in phosphosites prediction is achieved by leveraging this observation, which has not been tapped by existing methods. Phosphorylation sites are often not shared between multiple occurrences of the same domain in the proteome, even when the phosphoacceptor residue is conserved. This is partly because of different functional constraints acting on the same domain in different protein contexts. Moreover, by augmenting domain alignments with structural information, we were able to provide direct evidence that phosphosites in protein-protein interfaces need not be positionally conserved, likely because they can modulate interactions simply by sitting in the same general surface area.
MeSH term(s)	Computational Biology/methods ; Humans ; Phosphoproteins/metabolism ; Phosphorylation ; Protein Domains ; Proteome/chemistry ; Proteome/metabolism
Chemical Substances	Phosphoproteins ; Proteome
Language	English
Publishing date	2014-05-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	2075924-1
ISSN	1535-9484 ; 1535-9476
ISSN (online)	1535-9484
ISSN	1535-9476
DOI	10.1074/mcp.M114.039990
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Article ; Online: Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities.

Bianchi, Valerio / Gherardini, Pier Federico / Helmer-Citterich, Manuela / Ausiello, Gabriele

BMC bioinformatics

2012 Volume 13 Suppl 4, Page(s) S17

Abstract: Background: The identification of ligand binding sites is a key task in the annotation of proteins with known structure but uncharacterized function. Here we describe a knowledge-based method exploiting the observation that unrelated binding sites share ...

Abstract	Background: The identification of ligand binding sites is a key task in the annotation of proteins with known structure but uncharacterized function. Here we describe a knowledge-based method exploiting the observation that unrelated binding sites share small structural motifs that bind the same chemical fragments irrespective of the nature of the ligand as a whole. Results: PDBinder compares a query protein against a library of binding and non-binding protein surface regions derived from the PDB. The results of the comparison are used to derive a propensity value for each residue which is correlated with the likelihood that the residue is part of a ligand binding site. The method was applied to two different problems: i) the prediction of ligand binding residues and ii) the identification of which surface cleft harbours the binding site. In both cases PDBinder performed consistently better than existing methods. PDBinder has been trained on a non-redundant set of 1356 high-quality protein-ligand complexes and tested on a set of 239 holo and apo complex pairs. We obtained an MCC of 0.313 on the holo set with a PPV of 0.413 while on the apo set we achieved an MCC of 0.271 and a PPV of 0.372. Conclusions: We show that PDBinder performs better than existing methods. The good performance on the unbound proteins is extremely important for real-world applications where the location of the binding site is unknown. Moreover, since our approach is orthogonal to those used in other programs, the PDBinder propensity value can be integrated in other algorithms further increasing the final performance.
MeSH term(s)	Algorithms ; Animals ; Binding Sites ; Databases, Protein ; Knowledge Bases ; Ligands ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Proteins/chemistry ; Proteins/metabolism
Chemical Substances	Ligands ; Proteins
Language	English
Publishing date	2012-03-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/1471-2105-13-S4-S17
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Article ; Online: Highly multiplexed simultaneous detection of RNAs and proteins in single cells.

Frei, Andreas P / Bava, Felice-Alessio / Zunder, Eli R / Hsieh, Elena W Y / Chen, Shih-Yu / Nolan, Garry P / Gherardini, Pier Federico

Nature methods

2016 Volume 13, Issue 3, Page(s) 269–275

Abstract: To enable the detection of expression signatures specific to individual cells, we developed PLAYR (proximity ligation assay for RNA), a method for highly multiplexed transcript quantification by flow and mass cytometry that is compatible with standard ... ...

Abstract	To enable the detection of expression signatures specific to individual cells, we developed PLAYR (proximity ligation assay for RNA), a method for highly multiplexed transcript quantification by flow and mass cytometry that is compatible with standard antibody staining. When used with mass cytometry, PLAYR allowed for the simultaneous quantification of more than 40 different mRNAs and proteins. In primary cells, we quantified multiple transcripts, with the identity and functional state of each analyzed cell defined on the basis of the expression of a separate set of transcripts or proteins. By expanding high-throughput deep phenotyping of cells beyond protein epitopes to include RNA expression, PLAYR opens a new avenue for the characterization of cellular metabolism.
MeSH term(s)	Flow Cytometry/methods ; High-Throughput Nucleotide Sequencing/methods ; High-Throughput Screening Assays/methods ; Humans ; Jurkat Cells ; Protein Array Analysis/methods ; Proteins/analysis ; Proteins/metabolism ; RNA/analysis ; RNA/metabolism
Chemical Substances	Proteins ; RNA (63231-63-0)
Language	English
Publishing date	2016-01-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2169522-2
ISSN	1548-7105 ; 1548-7091
ISSN (online)	1548-7105
ISSN	1548-7091
DOI	10.1038/nmeth.3742
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Article ; Online: Superpose3D

Pier Federico Gherardini / Gabriele Ausiello / Manuela Helmer-Citterich

PLoS ONE, Vol 5, Iss 8, p e

a local structural comparison program that allows for user-defined structure representations.

2010 Volume 11988

Abstract	Local structural comparison methods can be used to find structural similarities involving functional protein patches such as enzyme active sites and ligand binding sites. The outcome of such analyses is critically dependent on the representation used to describe the structure. Indeed different categories of functional sites may require the comparison program to focus on different characteristics of the protein residues. We have therefore developed superpose3D, a novel structural comparison software that lets users specify, with a powerful and flexible syntax, the structure description most suited to the requirements of their analysis. Input proteins are processed according to the user's directives and the program identifies sets of residues (or groups of atoms) that have a similar 3D position in the two structures. The advantages of using such a general purpose program are demonstrated with several examples. These test cases show that no single representation is appropriate for every analysis, hence the usefulness of having a flexible program that can be tailored to different needs. Moreover we also discuss how to interpret the results of a database screening where a known structural motif is searched against a large ensemble of structures. The software is written in C++ and is released under the open source GPL license. Superpose3D does not require any external library, runs on Linux, Mac OSX, Windows and is available at http://cbm.bio.uniroma2.it/superpose3D.
Keywords	Medicine ; R ; Science ; Q
Subject code	004
Language	English
Publishing date	2010-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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