Claudia Cava

Claudia Cava
Institute of Molecular Bioimaging and Physiology · National Research Council

30.33
 · 
PhD in Bioinformatics

About

49
Publications
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1,160
Citations

Publications

Publications (49)
Article
Full-text available
Cancer driver gene alterations influence cancer development, occurring in oncogenes, tumor suppressors, and dual role genes. Discovering dual role cancer genes is difficult because of their elusive context-dependent behavior. We define oncogenic mediators as genes controlling biological processes. With them, we classify cancer driver genes, unveili...
Article
Full-text available
Previous studies reported that Angiotensin converting enzyme 2 (ACE2) is the main cell receptor of SARS-CoV and SARS-CoV-2. It plays a key role in the access of the virus into the cell to produce the final infection. In the present study we investigated in silico the basic mechanism of ACE2 in the lung and provided evidences for new potentially eff...
Article
Full-text available
Personalized medicine relies on the integration and consideration of specific characteristics of the patient, such as tumor phenotypic and genotypic profiling. Background: Radiogenomics aim to integrate phenotypes from tumor imaging data with genomic data to discover genetic mechanisms underlying tumor development and phenotype. Methods: We des...
Article
Full-text available
Human epidermal growth factor receptor 2 (HER2) is overexpressed/amplified in one third of breast cancers (BCs), and is associated with the poorer prognosis and the higher metastatic potential in BC. Emerging evidences highlight the role of microRNAs (miRNAs) in the regulation of several cellular processes, including BC. Methods: Here we identifi...
Article
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Genes that encode proteins playing a role in more than one biological process are frequently dependent on their tissue context, and human diseases result from the altered interplay of tissue- and cell-specific processes. In this work, we performed a computational approach that identifies tissue-specific co-expression networks by integrating miRNAs,...
Article
The knowledge of cancer cell response to conventional therapies is crucial in order to choose the correct therapy of patients affected by cancer. The major problem is generally attributed to the lack of specific biological processes able to predict the therapy efficacy. Here, we optimized a computational method for the analysis of gene networks abl...
Article
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Epilepsy includes a group of disorders of the brain characterized by an enduring predisposition to generate epileptic seizures. Although familial epilepsy has a genetic component and heritability, the etiology of the majority of non-familial epilepsies has no known associated genetic mutations. In epilepsy, recent epigenetic profiles have highlight...
Article
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Background: Despite great development in genome and proteome high-throughput methods, treatment failure is a critical point in the management of most solid cancers, including breast cancer (BC). Multiple alternative mechanisms upon drug treatment are involved to offset therapeutic effects, eventually causing drug resistance or treatment failure. M...
Article
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MicroRNAs play important roles in many biological processes. Their aberrant expression can have oncogenic or tumor suppressor function directly participating to carcinogenesis, malignant transformation, invasiveness and metastasis. Indeed, miRNA profiles can distinguish not only between normal and cancerous tissue but they can also successfully cla...
Article
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Background: There is extensive scientific evidence that radiation therapy (RT) is a crucial treatment, either alone or in combination with other treatment modalities, for many types of cancer, including breast cancer (BC). BC is a heterogeneous disease at both clinical and molecular levels, presenting distinct subtypes linked to the hormone recept...
Article
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Like other cancer diseases, prostate cancer (PC) is caused by the accumulation of genetic alterations in the cells that drives malignant growth. These alterations are revealed by gene profiling and copy number alteration (CNA) analysis. Moreover, recent evidence suggests that also microRNAs have an important role in PC development. Despite efforts...
Article
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Background: Modern high-throughput genomic technologies represent a comprehensive hallmark of molecular changes in pan-cancer studies. Although different cancer gene signatures have been revealed, the mechanism of tumourigenesis has yet to be completely understood. Pathways and networks are important tools to explain the role of genes in functiona...
Article
Cancer heterogeneity represents a major hurdle in the development of effective theranostic strategies, as it prevents to devise unique and maximally efficient diagnostic, prognostic and therapeutic procedures even for patients affected by the same tumor type. Computational techniques can nowadays leverage the huge and ever increasing amount of (epi...
Article
Full-text available
Gene Regulatory Networks (GRNs) control many biological systems, but how such network coordination is shaped is still unknown. GRNs can be subdivided into basic connections that describe how the network members interact e.g., co-expression, physical interaction, co-localization, genetic influence, pathways, and shared protein domains. The important...
Article
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Purpose: We demonstrated that Hsa-miR-567 expression is significantly downregulated in poor prognosis breast cancer, compared to better prognosis breast cancer, having a role in the control of cell proliferation and migration by regulating KPNA4 gene. Methods and results: In this study, based on our previously published in silico results, we pro...
Article
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Background An important challenge in cancer biology is to understand the complex aspects of the disease. It is increasingly evident that genes are not isolated from each other and the comprehension of how different genes are related to each other could explain biological mechanisms causing diseases. Biological pathways are important tools to reveal...
Article
Dysregulation of microRNAs (miRNAs) has a fundamental role in the initiation, development and progression of several human cancers, including breast cancer (BC), since strong evidence has shown that miRNAs can regulate the expression of oncogenes or tumor suppressor genes. A possible role of miRNAs in the diagnosis in BC has been demonstrated. As m...
Article
Understanding the dynamical evolution of cancer, with the final goal of developing effective techniques for diagnosis, prediction and treatment is one of the main challenges of modern biosciences. In this paper we approach the temporal ordering reconstruction problem, which refers to the temporal sorting of a collection of static biological data. T...
Code
Full-text available
SpidermiR: An R/Bioconductor package for integrative network analysis with miRNA data
Article
Full-text available
Prostate cancer (PC) includes several phenotypes, from indolent to highly aggressive cancer. Actual diagnostic and prognostic tools have several limitations, and there is a need for new biomarkers to stratify patients and assign them optimal therapies by taking into account potential genetic and epigenetic differences. MicroRNAs (miRNAs) are small...
Article
Full-text available
The Cancer Genome Atlas (TCGA) research network has made public a large collection of clinical and molecular phenotypes of more than 10 000 tumor patients across 33 different tumor types. Using this cohort, TCGA has published over 20 marker papers detailing the genomic and epigenomic alterations associated with these tumor types. Although many impo...
Article
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Background: Development of human cancer can proceed through the accumulation of different genetic changes affecting the structure and function of the genome. Combined analyses of molecular data at multiple levels, such as DNA copy-number alteration, mRNA and miRNA expression, can clarify biological functions and pathways deregulated in cancer. The...
Article
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In this work an integrated approach was used to identify functional miRNAs regulating gene pathway cross-talk in breast cancer (BC). We first integrated gene expression profiles and biological pathway information to explore the underlying associations between genes differently expressed among normal and BC samples and pathways enriched from these g...
Article
Full-text available
Dysregulation of microRNAs (miRNAs) is involved in the initiation and progression of several human cancers, including breast cancer (BC), as strong evidence has been found that miRNAs can act as oncogenes or tumor suppressor genes. This review presents the state of the art on the role of miRNAs in the diagnosis, prognosis, and therapy of BC. Based...
Conference Paper
Full-text available
Microarray experiments have made possible to identify breast cancer marker gene signatures. However, gene expression-based signatures present limitations because they do not consider metabolic role of the genes and are affected by genetic heterogeneity across patient cohorts. Considering the activity of entire pathways rather than the expression le...
Article
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Defining the aggressiveness and growth rate of a malignant cell population is a key step in the clinical approach to treating tumor disease. The correct grading of breast cancer (BC) is a fundamental part in determining the appropriate treatment. Biological variables can make it difficult to elucidate the mechanisms underlying BC development. To id...
Article
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Copy number alterations (CNAs) represent an important component ofgenetic variations. Such alterations are related with certain type ofcancer including those of the pancreas, colon, and breast, amongothers. CNAs have been used as biomarkers for cancer prognosis inmultiple studies, but few works report on the relation of CNAs withthe disease progres...
Chapter
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Bioinformatics traditionally deals with computational approaches to the analysis of big data from high-throughput technologies as genomics, proteomics, and sequencing. Bioinformatics analysis allows extraction of new information from big data that might help to better assess the biological details at a molecular and cellular level. The wide-scale a...
Conference Paper
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Tamoxifen is currently used for the treatment of breast cancer. Response to tamoxifen in metastatic conditions is a primary issue in cancer development. We used a cohort of breast cancer patients, treated or not with tamoxifen, and combined these data with the gene signature of metastatic samples in order to investigate the genetic mechanism of met...
Conference Paper
Full-text available
Specific genome copy number alterations, such as deletions and amplifications are an important factor in tumor development and progression, and are also associated with changes in gene expression. By combining analyses of gene expression and genome copy number we identified genes as candidate biomarkers of BC which were validated as prognostic fact...
Conference Paper
Full-text available
Copy–number alterations (CNAs) represent an important component of genetic variations and play a significant role in many human diseases. Such alterations are related to certain types of cancers, including those of the pancreas, colon, and breast, among others. CNAs have been used as biomarkers for cancer prognosis in multiple studies, but few work...
Conference Paper
Full-text available
Background / Purpose: We are approaching the temporal ordering reconstruction problem, namely the sorting of a collection of multi-dimensional biological data to reflect an accurate temporal progression of colorectal cancer. Our work is more focused on a specific approach to the temporal problem, previously proposed by Gupta and Bar-Joseph (1), w...
Conference Paper
Full-text available
Background / Purpose: We focus on the role of copy number alteration (CNA) in assessing prognosis of patients with colorectal cancer (CRC) when a particular relational representation of patients is given. Main conclusion: We showed that even a prediction analysis, concerning the progression of CRC, as characterized by the given staging classif...
Article
Full-text available
DNA microarray data are used to identify genes which could be considered prognostic markers. However, due to the limited sample size of each study, the signatures are unstable in terms of the composing genes and may be limited in terms of performances. It is therefore of great interest to integrate different studies, thus increasing sample size. In...

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Projects (4)
Project
Network-based in silico to quantify the therapeutic effect of drugs.
Project
MicroRNAs (miRNAs) are small sequences of non-coding RNA regulating specific genes involved in the onset and development of tumors. Dysregulation of miRNAs has a fundamental role in the initiation, development and progression of several human cancers, including breast cancer (BC), since strong evidence has shown that miRNAs can regulate the expression of oncogenes or tumor suppressor genes. Some miRNAs are emerging as biomarkers of BC for diagnosis , prognosis, and prediction of therapeutic outcomes, and have important roles in the control of BC hallmark functions such as invasion, metastasis, proliferation, resting death, apoptosis, and genomic instability. Other miRNAs are of interest as new, easily accessible, affordable, non-invasive tools for the personalized management of patients with BC because they are circulating in body fluids.