Lúcio Queiroz

Universidade Federal de Minas Gerais

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Claudio Zanettini

Cornell University

Glória Regina Franco

Universidade Federal de Minas Gerais

Izabela Mamede

Universidade Federal de Minas Gerais

Nayara Evelin de Toledo

Universidade Federal de Minas Gerais

Thomaz Lüscher Dias

Universidade Federal de Minas Gerais

Nádia Skorupa Parachin

Universidade de Brasília

Helder I. Nakaya

Universidade de São Paulo

Gabriel Quintanilha‐Peixoto

Universidade Federal de Minas Gerais

Fenícia Brito Santos

Universidade Federal de Minas Gerais

Ana Paula de Abreu

Universidade Federal de Minas Gerais

Cooperative Institutions

Universidade Federal de Minas Gerais

Cornell University

Weill Cornell Medicine

Presbyterian Hospital

NewYork–Presbyterian Hospital

New York Hospital Queens

Addgene

Universidade de São Paulo

Memorial Sloan Kettering Cancer Center

Harvard University

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Can multifunctional livelihoods including recreational ecosystem services (RES) and non timber forest products (NTFP) maintain biodiverse forests in the Brazilian Amazon?

Ecosystem Services (2018)

Sónia Maria Carvalho Ribeiro Britaldo Soares Filho William Costa Laura Bachi Amanda Ribeiro de Oliveira

Forest product

Brazil nut

10.1016/j.ecoser.2018.03.016

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Citations (37)

SARS-CoV-2 Selectively Induces the Expression of Unproductive Splicing Isoforms of Interferon, Class I MHC, and Splicing Machinery Genes

International Journal of Molecular Sciences (2024)

Thomaz Lüscher Dias Izabela Mamede Nayara Evelin de Toledo Lúcio Queiroz Ícaro Maia Santos de Castro

RNA processing is a highly conserved mechanism that serves as a pivotal regulator of gene expression. Alternative processing generates transcripts that can still be translated but lead to potentially nonfunctional proteins. A plethora of respiratory viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), strategically manipulate the host’s RNA processing machinery to circumvent antiviral responses. We integrated publicly available omics datasets to systematically analyze isoform-level expression and delineate the nascent peptide landscape of SARS-CoV-2-infected human cells. Our findings explore a suggested but uncharacterized mechanism, whereby SARS-CoV-2 infection induces the predominant expression of unproductive splicing isoforms in key IFN signaling, interferon-stimulated (ISGs), class I MHC, and splicing machinery genes, including IRF7, HLA-B, and HNRNPH1. In stark contrast, cytokine and chemokine genes, such as IL6 and TNF, predominantly express productive (protein-coding) splicing isoforms in response to SARS-CoV-2 infection. We postulate that SARS-CoV-2 employs an unreported tactic of exploiting the host splicing machinery to bolster viral replication and subvert the immune response by selectively upregulating unproductive splicing isoforms from antigen presentation and antiviral response genes. Our study sheds new light on the molecular interplay between SARS-CoV-2 and the host immune system, offering a foundation for the development of novel therapeutic strategies to combat COVID-19.

Antigen processing

10.3390/ijms25115671

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Citations (0)

condathis: Run Any CLI Tool on a 'Conda' Environment

Lúcio Queiroz Claudio Zanettini

10.32614/cran.package.condathis

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Citations (0)

Uma estratégia para engajamento de participantes de eventos online

Alfahelix eBooks (2021)

Diego Mariano Wylerson Guimarães Nogueira Wanessa Goes Roselane Gonçalves dos Santos Rodrigo Bentes Kato

removidos).

10.51780/978-6-599-275326-19

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Citations (1)

Optimal fluid volume for detecting malignancy in serous effusions: a single institution experience

Journal of the American Society of Cytopathology (2023)

Shaham Beg Claudio Zanettini Lúcio Queiroz Luigi Marchionni Susan Alperstein

Ascitic fluid

Pericardial fluid

10.1016/j.jasc.2023.06.003

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Citations (5)

Metformin Treatment Modulates Long Non-Coding RNA Isoforms Expression in Human Cells

Non-Coding RNA (2022)

Izabela Mamede Thomaz Lüscher Dias Lúcio Queiroz Ana Gabrielle B. de Melo Carlos Renato Machado

Long noncoding RNAs (lncRNAs) undergo splicing and have multiple transcribed isoforms. Nevertheless, for lncRNAs, as well as for mRNA, measurements of expression are routinely performed only at the gene level. Metformin is the first-line oral therapy for type 2 diabetes mellitus and other metabolic diseases. However, its mechanism of action remains not thoroughly explained. Transcriptomic analyses using metformin in different cell types reveal that only protein-coding genes are considered. We aimed to characterize lncRNA isoforms that were differentially affected by metformin treatment on multiple human cell types (three cancer, two non-cancer) and to provide insights into the lncRNA regulation by this drug. We selected six series to perform a differential expression (DE) isoform analysis. We also inferred the biological roles for lncRNA DE isoforms using in silico tools. We found the same isoform of an lncRNA (AC016831.6-205) highly expressed in all six metformin series, which has a second exon putatively coding for a peptide with relevance to the drug action. Moreover, the other two lncRNA isoforms (ZBED5-AS1-207 and AC125807.2-201) may also behave as cis-regulatory elements to the expression of transcripts in their vicinity. Our results strongly reinforce the importance of considering DE isoforms of lncRNA for understanding metformin mechanisms at the molecular level.

10.3390/ncrna8050068

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Citations (6)

SARS-CoV-2 selectively induces the expression of unproductive splicing isoforms of interferon, class I MHC and splicing machinery genes

bioRxiv (Cold Spring Harbor Laboratory) (2023)

Thomaz Lüscher Dias Izabela Mamede Nayara Evelin de Toledo Lúcio Queiroz Ícaro Maia Santos de Castro

Abstract Splicing is a highly conserved, intricate mechanism intimately linked to transcription elongation, serving as a pivotal regulator of gene expression. Alternative splicing may generate specific transcripts incapable of undergoing translation into proteins, designated as unproductive. A plethora of respiratory viruses, including Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), strategically manipulate the host’s splicing machinery to circumvent antiviral responses. During the infection, SARS-CoV-2 effectively suppresses interferon (IFN) expression, leading to B cell and CD8+ T cell leukopenia, while simultaneously increasing the presence of macrophages and neutrophils in patients with severe COVID-19. In this study, we integrated publicly available omics datasets to systematically analyze transcripts at the isoform level and delineate the nascent-peptide translatome landscapes of SARS-CoV-2-infected human cells. Our findings reveal a hitherto uncharacterized mechanism whereby SARS-CoV-2 infection induces the predominant expression of unproductive splicing isoforms in key IFN signaling genes, interferon-stimulated genes (ISGs), class I MHC genes, and splicing machinery genes, including IRF7, OAS3, HLA-B, and HNRNPH1. In stark contrast, cytokine and chemokine genes, such as IL6, CXCL8, and TNF, predominantly express productive (protein-coding) splicing isoforms in response to SARS-CoV-2 infection. We postulate that SARS-CoV-2 employs a previously unreported tactic of exploiting the host splicing machinery to bolster viral replication and subvert the immune response by selectively upregulating unproductive splicing isoforms from antigen presentation and antiviral response genes. Our study sheds new light on the molecular interplay between SARS-CoV-2 and the host immune system, offering a foundation for the development of novel therapeutic strategies to combat COVID-19.

10.1101/2023.04.12.536671

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Citations (0)

Genetic basis for hyper production of hyaluronic acid in natural and engineered microorganisms

Microbial Cell Factories (2016)

Juliana Davies de Oliveira Lucas Silva Carvalho Antônio Milton Vieira Gomes Lúcio Queiroz Beatriz Simas Magalhães

Hyaluronic acid, or HA, is a rigid and linear biopolymer belonging to the class of the glycosaminoglycans, and composed of repeating units of the monosaccharides glucuronic acid and N-acetylglucosamine. HA has multiple important functions in the human body, due to its properties such as bio-compatibility, lubricity and hydrophilicity, it is widely applied in the biomedical, food, health and cosmetic fields. The growing interest in this molecule has motivated the discovery of new ways of obtaining it. Traditionally, HA has been extracted from rooster comb-like animal tissues. However, due to legislation laws HA is now being produced by bacterial fermentation using Streptococcus zooepidemicus, a natural producer of HA, despite it being a pathogenic microorganism. With the expansion of new genetic engineering technologies, the use of organisms that are non-natural producers of HA has also made it possible to obtain such a polymer. Most of the published reviews have focused on HA formulation and its effects on different body tissues, whereas very few of them describe the microbial basis of HA production. Therefore, for the first time this review has compiled the molecular and genetic bases for natural HA production in microorganisms together with the main strategies employed for heterologous production of HA.

Biopolymer

Industrial microbiology

Rooster

10.1186/s12934-016-0517-4

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Citations (120)

From In-Person to the Online World: Insights Into Organizing Events in Bioinformatics

Frontiers in Bioinformatics (2021)

Alessandra Lima da Silva Ana Paula de Abreu Diego Mariano Felipe Caixeta Fenícia Brito Santos

Bioinformatics is a fast-evolving research field, requiring effective educational initiatives to bring computational knowledge to Life Sciences. Since 2017, an organizing committee composed of graduate students and postdoctoral researchers from the Universidade Federal de Minas Gerais (Brazil) promotes a week-long event named Summer Course in Bioinformatics (CVBioinfo). This event aims to diffuse bioinformatic principles, news, and methods mainly focused on audiences of undergraduate students. Furthermore, as the advent of the COVID-19 global pandemic has precluded in-person events, we offered the event in online mode, using free video transmission platforms. Herein, we present and discuss the insights obtained from promoting the Online Workshop in Bioinformatics (WOB) organized in November 2020, comparing it to our experience in previous in-person editions of the same event.

Pandemic

2019-20 coronavirus outbreak

10.3389/fbinf.2021.711463

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Citations (2)

Abstract 6849: Characterizing a discernible stromal fibroblastic gene signature in the shift from high-grade prostatic intraepithelial neoplasia to aggressive prostate cancer

Cancer Research (2024)

Mohammad K. Alexanderani Lúcio Queiroz Mohamed Omar Claudio Zanettini Hubert Pakula

Abstract Background: High-grade prostatic intraepithelial neoplasia (HGPIN) is a preneoplastic lesion that precedes the development of both indolent and aggressive variants of prostate cancer (PCa). However, the specific stromal molecular mechanisms underlying the progression of HGPIN and their contribution to epithelial cancer cell motility and invasiveness remain poorly understood. This study aims to elucidate the driver genomic alterations involved in shaping the perineoplastic stroma of HGPIN, with the goal of unraveling their role in promoting cancer invasion, and metastasis. Methods: We performed gene expression profiling on laser capture microdissected perineoplastic stroma of HGPIN and PCa in tissue samples from 25 PCa cases, including 12 low-grade (Gleason 6) and 13 high-grade (Gleason >/= 8) cases. We used the standard moderated t-test from the Bioconductor limma package to assess the statistical significance of differential gene expression between perineoplastic stroma high grade PCa and perineoplastic stroma HGPIN, as well as between perineoplastic stroma low grade PCa and HGPIN. The -log10 p-values represents the level of statistical significance for each gene, while the log2 fold change represents the magnitude of gene expression difference between the two comparison groups. Additionally, we computed Gene Set Enrichment Analysis (GSEA) scores using the Bioconductor package and discerned the leading-edge genes among the pathways. This study is supported by the NIH-NCI-T32 program for next-generation pathologists at our institution. Results: In the gene expression analysis comparing High Grade PCa and HGPIN, several genes, including POSTN, BGN, GREM1, C1QA, THBS4, COL1A1, COL1A2, SFRP4, RNU6-847P, FCGR2P, and TOMM22, exhibited the highest level of both biological and statistical significance. GSEA revealed that the multi-invasive pathway had the highest enrichment score (>2). Notably, the top overexpressed genes in this pathway exhibited a fibroblastic signature (in bold), including POSTN, BGN, GREM1, FBN1, COL1A2, COL3A1, COL5A2, ASPN, SPARC, VCAN, COMP, INHBA, THBS2, and SFRP4. The presence of this signature indicates the invasiveness of the disease. Importantly, these genes were not associated with the progression to low grade PCa, indicating their exclusive association with the aggressive variant. Conclusion: To our knowledge, this study is the first to explore the stroma's role in HGPIN-to-aggressive PCa progression. It highlights a key stromal pathway enriched with fibroblastic gene signature. These findings offer potential biomarkers for targeted therapies and improved care through HGPIN patient stratification. Citation Format: Mohammad K. Alexanderani, Lucio Queiroz, Mohamed Omar, Claudio Zanettini, Hubert Pakula, Luigi Marchionni, Massimo Loda. Characterizing a discernible stromal fibroblastic gene signature in the shift from high-grade prostatic intraepithelial neoplasia to aggressive prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6849.

10.1158/1538-7445.am2024-6849

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