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4. Single-Cell RNA Sequencing Shows that Circulating Monocytes Enriched in IFN Signaling Are Associated with Nontuberculous Mycobacteria Pulmonary Disease in Cystic Fibrosis.

Author

Lorè, Nicola I., Gramegna, Andrea, de Pretis, Stefano, Di Marco, Federico, Giannese, Francesca, Saliu, Fabio, Oneto, Caterina, Contarini, Martina, Cariani, Lisa, Blasi, Francesco, and Cirillo, Daniela M.

Subjects
MONONUCLEAR leukocytes, GENE expression, DENSITY gradient centrifugation, KILLER cells, GENE expression profiling, EXOCRINE pancreatic insufficiency
Abstract

This letter discusses a study that used single-cell RNA sequencing to analyze the gene expression profiles of peripheral blood mononuclear cells (PBMCs) in people with cystic fibrosis (pwCFs) who have different stages of Mycobacterium abscessus lung disease. The study identified 10 distinct cell populations within the PBMCs and found that there was no significant cellular variation among pwCFs with different risks of M. abscessus lung disease. However, the CD14+ monocyte cluster in the MABSC-PD group displayed the highest number of upregulated genes compared to other cellular clusters. The study suggests that single-cell transcriptomic profiling of PBMCs could be used to identify diagnostic signatures or therapeutic targets for pwCFs with NTM infection. [Extracted from the article]

Published
2024
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5. New insight into the catalytic -dependent and -independent roles of METTL3 in sustaining aberrant translation in chronic myeloid leukemia

Author

Ianniello, Zaira, Sorci, Melissa, Ceci Ginistrelli, Lavinia, Iaiza, Alessia, Marchioni, Marcella, Tito, Claudia, Capuano, Ernestina, Masciarelli, Silvia, Ottone, Tiziana, Attrotto, Cristina, Rizzo, Manuela, Franceschini, Luca, de Pretis, Stefano, Voso, Maria Teresa, Pelizzola, Mattia, Fazi, Francesco, and Fatica, Alessandro

Published
2021
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11. Single Cells RNA Sequencing Reveals that Circulating Hyperinflammatory Monocytes are Associated with Mycobacterium abscessus Pulmonary Disease

Author

Lore, Nicola Ivan, primary, Gramegna, Andrea, additional, de Pretis, Stefano, additional, Di Marco, Federico, additional, Giannese, Francesca, additional, Saliu, Fabio, additional, Oneto, Caterina, additional, Contarini, Martina, additional, Cariani, Lisa, additional, Blasi, Francesco, additional, and Cirillo, Daniela, additional

Published
2023
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12. Motor neurons use push-pull signals to direct vascular remodeling critical for their connectivity

Author

Martins, Luis F., primary, Brambilla, Ilaria, additional, Motta, Alessia, additional, de Pretis, Stefano, additional, Bhat, Ganesh Parameshwar, additional, Badaloni, Aurora, additional, Malpighi, Chiara, additional, Amin, Neal D., additional, Imai, Fumiyasu, additional, Almeida, Ramiro D., additional, Yoshida, Yutaka, additional, Pfaff, Samuel L., additional, and Bonanomi, Dario, additional

Published
2022
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20. An early Myc-dependent transcriptional program orchestrates cell growth during B-cell activation

Author

Tesi, A, de Pretis, S, Furlan, M, Filipuzzi, M, Morelli, M, Andronache, A, Doni, M, Verrecchia, A, Pelizzola, M, Amati, B, Sabò, A, Tesi, Alessandra, de Pretis, Stefano, Furlan, Mattia, Filipuzzi, Marco, Morelli, Marco J, Andronache, Adrian, Doni, Mirko, Verrecchia, Alessandro, Pelizzola, Mattia, Amati, Bruno, Sabò, Arianna, Tesi, A, de Pretis, S, Furlan, M, Filipuzzi, M, Morelli, M, Andronache, A, Doni, M, Verrecchia, A, Pelizzola, M, Amati, B, Sabò, A, Tesi, Alessandra, de Pretis, Stefano, Furlan, Mattia, Filipuzzi, Marco, Morelli, Marco J, Andronache, Adrian, Doni, Mirko, Verrecchia, Alessandro, Pelizzola, Mattia, Amati, Bruno, and Sabò, Arianna

Abstract

Upon activation, lymphocytes exit quiescence and undergo substantial increases in cell size, accompanied by activation of energy-producing and anabolic pathways, widespread chromatin decompaction, and elevated transcriptional activity. These changes depend upon prior induction of the Myc transcription factor, but how Myc controls them remains unclear. We addressed this issue by profiling the response to LPS stimulation in wild-type and c-myc-deleted primary mouse B-cells. Myc is rapidly induced, becomes detectable on virtually all active promoters and enhancers, but has no direct impact on global transcriptional activity. Instead, Myc contributes to the swift up- and down-regulation of several hundred genes, including many known regulators of the aforementioned cellular processes. Myc-activated promoters are enriched for E-box consensus motifs, bind Myc at the highest levels, and show enhanced RNA Polymerase II recruitment, the opposite being true at down-regulated loci. Remarkably, the Myc-dependent signature identified in activated B-cells is also enriched in Myc-driven B-cell lymphomas: hence, besides modulation of new cancer-specific programs, the oncogenic action of Myc may largely rely on sustained deregulation of its normal physiological targets.

Published
2019

27. Integrated Systems for NGS Data Management and Analysis: Open Issues and Available Solutions

Author

Bianchi, Valerio, primary, Ceol, Arnaud, additional, Ogier, Alessandro G. E., additional, de Pretis, Stefano, additional, Galeota, Eugenia, additional, Kishore, Kamal, additional, Bora, Pranami, additional, Croci, Ottavio, additional, Campaner, Stefano, additional, Amati, Bruno, additional, Morelli, Marco J., additional, and Pelizzola, Mattia, additional

Published
2016
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29. Degradation dynamics of microRNAs revealed by a novel pulse-chase approach

Author

Marzi, Matteo J., primary, Ghini, Francesco, additional, Cerruti, Benedetta, additional, de Pretis, Stefano, additional, Bonetti, Paola, additional, Giacomelli, Chiara, additional, Gorski, Marcin M., additional, Kress, Theresia, additional, Pelizzola, Mattia, additional, Muller, Heiko, additional, Amati, Bruno, additional, and Nicassio, Francesco, additional

Published
2016
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30. Transcription of Mammalian cis-Regulatory Elements Is Restrained by Actively Enforced Early Termination

Author

Austenaa, Liv M I, Barozzi, Iros, Simonatto, Marta, Masella, Silvia, Della Chiara, Giulia, Ghisletti, Serena, Curina, Alessia, de Wit, Elzo, Bouwman, Britta A M, de Pretis, Stefano, Piccolo, Viviana, Termanini, Alberto, Prosperini, Elena, Pelizzola, Mattia, de Laat, Wouter, Natoli, Gioacchino, Austenaa, Liv M I, Barozzi, Iros, Simonatto, Marta, Masella, Silvia, Della Chiara, Giulia, Ghisletti, Serena, Curina, Alessia, de Wit, Elzo, Bouwman, Britta A M, de Pretis, Stefano, Piccolo, Viviana, Termanini, Alberto, Prosperini, Elena, Pelizzola, Mattia, de Laat, Wouter, and Natoli, Gioacchino

Published
2015

31. Transcription of Mammalian cis-Regulatory Elements Is Restrained by Actively Enforced Early Termination

Author

Hubrecht Institute with UMC, Divisie Biomedische Genetica, Cancer, Austenaa, Liv M I, Barozzi, Iros, Simonatto, Marta, Masella, Silvia, Della Chiara, Giulia, Ghisletti, Serena, Curina, Alessia, de Wit, Elzo, Bouwman, Britta A M, de Pretis, Stefano, Piccolo, Viviana, Termanini, Alberto, Prosperini, Elena, Pelizzola, Mattia, de Laat, Wouter, Natoli, Gioacchino, Hubrecht Institute with UMC, Divisie Biomedische Genetica, Cancer, Austenaa, Liv M I, Barozzi, Iros, Simonatto, Marta, Masella, Silvia, Della Chiara, Giulia, Ghisletti, Serena, Curina, Alessia, de Wit, Elzo, Bouwman, Britta A M, de Pretis, Stefano, Piccolo, Viviana, Termanini, Alberto, Prosperini, Elena, Pelizzola, Mattia, de Laat, Wouter, and Natoli, Gioacchino

Published
2015

32. Transcription of Mammalian cis-Regulatory Elements Is Restrained by Actively Enforced Early Termination

Author

Austenaa, Liv M.I., primary, Barozzi, Iros, additional, Simonatto, Marta, additional, Masella, Silvia, additional, Della Chiara, Giulia, additional, Ghisletti, Serena, additional, Curina, Alessia, additional, de Wit, Elzo, additional, Bouwman, Britta A.M., additional, de Pretis, Stefano, additional, Piccolo, Viviana, additional, Termanini, Alberto, additional, Prosperini, Elena, additional, Pelizzola, Mattia, additional, de Laat, Wouter, additional, and Natoli, Gioacchino, additional

Published
2015
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37. Integrative classification of human coding and noncoding genes through RNA metabolism profiles

Author

Mukherjee, Neelanjan, Calviello, Lorenzo, Hirsekorn, Antje, de Pretis, Stefano, Pelizzola, Mattia, and Ohler, Uwe

Abstract

Pervasive transcription of the human genome results in a heterogeneous mix of coding RNAs and long noncoding RNAs (lncRNAs). Only a small fraction of lncRNAs have demonstrated regulatory functions, thus making functional lncRNAs difficult to distinguish from nonfunctional transcriptional byproducts. This difficulty has resulted in numerous competing human lncRNA classifications that are complicated by a steady increase in the number of annotated lncRNAs. To address these challenges, we quantitatively examined transcription, splicing, degradation, localization and translation for coding and noncoding human genes. We observed that annotated lncRNAs had lower synthesis and higher degradation rates than mRNAs and discovered mechanistic differences explaining slower lncRNA splicing. We grouped genes into classes with similar RNA metabolism profiles, containing both mRNAs and lncRNAs to varying extents. These classes exhibited distinct RNA metabolism, different evolutionary patterns and differential sensitivity to cellular RNA-regulatory pathways. Our classification provides an alternative to genomic context-driven annotations of lncRNAs.

Published
2017
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38. Translation is required for miRNA‐dependent decay of endogenous transcripts

Author

Biasini, Adriano, Abdulkarim, Baroj, de Pretis, Stefano, Tan, Jennifer Y., Arora, Rajika, Wischnewski, Harry, Dreos, Rene, Pelizzola, Mattia, Ciaudo, Constance, and Marques, Ana C.

Subjects
RNA metabolic labelling, translation, Dicer knockout mESC, long noncoding RNAs, 3. Good health, miRNA
Abstract

Post-transcriptional repression of gene expression by miRNAs occurs through transcript destabilization or translation inhibition. mRNA decay is known to account for most miRNA-dependent repression. However, because transcript decay occurs co-translationally, whether target translation is a requirement for miRNA-dependent transcript destabilization remains unknown. To decouple these two molecular processes, we used cytosolic long noncoding RNAs (lncRNAs) as models for endogenous transcripts that are not translated. We show that, despite interacting with the miRNA-loaded RNA-induced silencing complex, the steady-state abundance and decay rates of these transcripts are minimally affected by miRNA loss. To further validate the apparent requirement of translation for miRNA-dependent decay, we fused two lncRNA candidates to the 3'-end of a protein-coding gene reporter and found this results in their miRNA-dependent destabilization. Further analysis revealed that the few natural lncRNAs whose levels are regulated by miRNAs in mESCs tend to associate with translating ribosomes, and possibly represent misannotated micropeptides, further substantiating the necessity of target translation for miRNA-dependent transcript decay. In summary, our analyses suggest that translation is required for miRNA-dependent transcript destabilization, and demonstrate that the levels of coding and noncoding transcripts are differently affected by miRNAs., The EMBO Journal, 40 (3), ISSN:0261-4189, ISSN:1460-2075

39. Dynamics of transcriptional and post-transcriptional regulation.

Author

Furlan M, de Pretis S, and Pelizzola M

Subjects
Animals, Humans, Models, Genetic, RNA biosynthesis, RNA genetics, RNA Processing, Post-Transcriptional, Transcription, Genetic
Abstract

Despite gene expression programs being notoriously complex, RNA abundance is usually assumed as a proxy for transcriptional activity. Recently developed approaches, able to disentangle transcriptional and post-transcriptional regulatory processes, have revealed a more complex scenario. It is now possible to work out how synthesis, processing and degradation kinetic rates collectively determine the abundance of each gene's RNA. It has become clear that the same transcriptional output can correspond to different combinations of the kinetic rates. This underscores the fact that markedly different modes of gene expression regulation exist, each with profound effects on a gene's ability to modulate its own expression. This review describes the development of the experimental and computational approaches, including RNA metabolic labeling and mathematical modeling, that have been disclosing the mechanisms underlying complex transcriptional programs. Current limitations and future perspectives in the field are also discussed., (© The Author(s) 2020. Published by Oxford University Press.)

Published
2021
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40. Identification of Genes Post-Transcriptionally Regulated from RNA-seq: The Case Study of Liver Hepatocellular Carcinoma.

Author

de Pretis S, Furlan M, and Pelizzola M

Subjects
Computational Biology methods, Datasets as Topic, Gene Expression Profiling methods, Gene Expression Regulation, Neoplastic, High-Throughput Nucleotide Sequencing methods, Humans, Sequence Analysis, RNA methods, Software, Carcinoma, Hepatocellular genetics, Liver Neoplasms genetics, RNA Processing, Post-Transcriptional genetics, RNA-Seq methods
Abstract

The field of transcriptional regulation generally assumes that changes in transcripts levels reflect changes in transcriptional status of the corresponding gene. While this assumption might hold true for a large population of transcripts, a considerable and still unrecognized fraction of the variation might involve other steps of the RNA lifecycle, that is the processing of the premature RNA, and degradation of the mature RNA. Discrimination between these layers requires complementary experimental techniques, such as RNA metabolic labeling or block of transcription experiments. Nonetheless, the analysis of the premature and mature RNA, derived from intronic and exonic read counts in RNA-seq data, allows distinguishing between transcriptionally and post-transcriptionally regulated genes, although not recognizing the specific step involved in the post-transcriptional response, that is processing, degradation, or a combination of the two. We illustrate how the INSPEcT R/Bioconductor package could be used to infer post-transcriptional regulation in TCGA RNA-seq samples for Hepatocellular Carcinoma.

Published
2021
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