Network-Based Analysis to Identify Hub Genes Involved in Spatial Root Response to Mechanical Constrains

Dimitrova, Anastazija; Sferra, Gabriella; Scippa, Gabriella Stefania; Trupiano, Dalila

doi:10.3390/cells11193121

Cited by 3 publications

(1 citation statement)

References 83 publications

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“…During the past decades, hundreds of hyperaccumulator plants have been identified and a wide variety of in-wet experiments have been attempted to achieve a careful description of the biology underlying this trait [45,46]. Despite this, the hyperaccumulation trait still needs to be dissected and, in this sense, bioinformatics may provide tools for the comprehensive analysis and modeling of the related processes, as already applied for various purposes in plant biology studies [4,[47][48][49][50].…”

Section: Discussionmentioning

confidence: 99%

Key Pathways and Genes of Arabidopsis thaliana and Arabidopsis halleri Roots under Cadmium Stress Responses: Differences and Similarities

Sferra

Fantozzi

Scippa

et al. 2023

Plants

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Cadmium (Cd) is among the world’s major health concerns, as it renders soils unsuitable and unsafe for food and feed production. Phytoremediation has the potential to remediate Cd-polluted soils, but efforts are still needed to develop a deep understanding of the processes underlying it. In this study, we performed a comprehensive analysis of the root response to Cd stress in A. thaliana, which can phytostabilize Cd, and in A. halleri, which is a Cd hyperaccumulator. Suitable RNA-seq data were analyzed by WGCNA to identify modules of co-expressed genes specifically associated with Cd presence. The results evidenced that the genes of the hyperaccumulator A. halleri mostly associated with the Cd presence are finely regulated (up- and downregulated) and related to a general response to chemical and other stimuli. Additionally, in the case of A. thaliana, which can phytostabilize metals, the genes upregulated during Cd stress are related to a general response to chemical and other stimuli, while downregulated genes are associated with functions which, affecting root growth and development, determine a deep modification of the organ both at the cellular and physiological levels. Furthermore, key genes of the Cd-associated modules were identified and confirmed by differentially expressed gene (DEG) detection and external knowledge. Together, key functions and genes shed light on differences and similarities among the strategies that the plants use to cope with Cd and may be considered as possible targets for future research.

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Section: Discussionmentioning

confidence: 99%

Key Pathways and Genes of Arabidopsis thaliana and Arabidopsis halleri Roots under Cadmium Stress Responses: Differences and Similarities

Sferra

Fantozzi

Scippa

et al. 2023

Plants

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Network biology and bioinformatics-based framework to identify the impacts of SARS-CoV-2 infections on lung cancer and tuberculosis

Waaje,

Sarkar,

Islam

2024

Preprint

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The severe acute respiratory syndrome coronavirus 2 (SARSCoV 2) is a coronavirus variation responsible for COVID19, the respiratory disease that triggered the COVID19 pandemic. The primary aim of our study is to elucidate the complex network of interactions between SARS CoV 2, tuberculosis, and lung cancer employing a bioinformatics and network biology approach. Lung cancer is the leading cause of significant illness and death connected to cancer worldwide. Tuberculosis (TB) is a prevalent medical condition induced by the Mycobacterium bacteria. It mostly affects the lungs but may also have an influence on other areas of the body. Coronavirus disease (COVID19) causes a risk of respiratory complications between lung cancer and tuberculosis. SARSCoV 2 impacts the lower respiratory system and causes severe pneumonia, which can significantly increase the mortality risk in individuals with lung cancer. We conducted transcriptome analysis to determine molecular biomarkers and common pathways in lung cancer, TB, and COVID19, which provide understanding into the association of SARSCoV 2 to lung cancer and tuberculosis. Based on the compatible RNA-seq data, our research employed GREIN and NCBI's Gene Expression Omnibus (GEO) to perform differential gene expression analysis. Our study exploited three RNAseq datasets from the Gene Expression Omnibus (GEO) GSE171110, GSE89403, and GSE81089 to identify distinct relationships between differentially expressed genes (DEGs) in SARSCoV 2, tuberculosis, and lung cancer. We identified 30 common genes among SARSCoV 2, tuberculosis, and lung cancer (25 upregulated genes and 5 downregulated genes). We analyzed the following five databases: WikiPathway, KEGG, Bio Carta, Elsevier Pathway and Reactome. Using Cytohubba's MCC and Degree methods, We determined the top 15 hub genes resulting from the PPI interaction. These hub genes can serve as potential biomarkers, leading to novel treatment strategies for disorders under investigation. Transcription factors (TFs) and microRNAs (miRNAs) were identified as the molecules that control the differentially expressed genes (DEGs) of interest, either during transcription or after transcription. We identified 35 prospective therapeutic compounds that form significant differentially expressed genes (DEGs) in SARSCoV 2, lung cancer, and tuberculosis, which could potentially serve as medications. We hypothesized that the potential medications that emerged from this investigation may have therapeutic benefits.

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The Course of Mechanical Stress: Types, Perception, and Plant Response

Kouhen

Dimitrova

Scippa

et al. 2023

Biology

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Mechanical stimuli, together with the corresponding plant perception mechanisms and the finely tuned thigmomorphogenetic response, has been of scientific and practical interest since the mid-17th century. As an emerging field, there are many challenges in the research of mechanical stress. Indeed, studies on different plant species (annual/perennial) and plant organs (stem/root) using different approaches (field, wet lab, and in silico/computational) have delivered insufficient findings that frequently impede the practical application of the acquired knowledge. Accordingly, the current work distils existing mechanical stress knowledge by bringing in side-by-side the research conducted on both stem and roots. First, the various types of mechanical stress encountered by plants are defined. Second, plant perception mechanisms are outlined. Finally, the different strategies employed by the plant stem and roots to counteract the perceived mechanical stresses are summarized, depicting the corresponding morphological, phytohormonal, and molecular characteristics. The comprehensive literature on both perennial (woody) and annual plants was reviewed, considering the potential benefits and drawbacks of the two plant types, which allowed us to highlight current gaps in knowledge as areas of interest for future research.

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Network-Based Analysis to Identify Hub Genes Involved in Spatial Root Response to Mechanical Constrains

Cited by 3 publications

References 83 publications

Key Pathways and Genes of Arabidopsis thaliana and Arabidopsis halleri Roots under Cadmium Stress Responses: Differences and Similarities

Key Pathways and Genes of Arabidopsis thaliana and Arabidopsis halleri Roots under Cadmium Stress Responses: Differences and Similarities

Network biology and bioinformatics-based framework to identify the impacts of SARS-CoV-2 infections on lung cancer and tuberculosis

The Course of Mechanical Stress: Types, Perception, and Plant Response

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