Claudia Cava

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

PhD in Bioinformatics

About

73
Publications
27,171
Reads
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2,922
Citations
Additional affiliations
March 2020 - June 2020
University of Milan
Position
  • Professor
Description
  • https://www.unimi.it/it/corsi/insegnamenti-dei-corsi-di-laurea/2020/biostatistica-e-bioinformatica
March 2018 - July 2018
University of Milan
Position
  • Professor
Description
  • https://www.unimi.it/it/corsi/insegnamenti-dei-corsi-di-laurea/2018/informatica-e-statistica-le-biotecnologie

Publications

Publications (73)
Article
Full-text available
Prostate cancer (PC) is a male common neoplasm and is the second leading cause of cancer death in American men. PC is traditionally diagnosed by the evaluation of prostate secreted antigen (PSA) in the blood. Due to the high levels of false positives, digital rectal examination and transrectal ultrasound guided biopsy are necessary in uncertain cas...
Article
Full-text available
Alzheimer’s disease (AD) is a neurodegenerative disease characterized by rapid brain cell degeneration affecting different areas of the brain. Hippocampus is one of the earliest involved brain regions in the disease. Modern technologies based on high-throughput data have identified transcriptional profiling of several neurological diseases, includi...
Article
Full-text available
Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease characterized by the neurodegeneration of motoneurons. About 10% of ALS is hereditary and involves mutation in 25 different genes, while 90% of the cases are sporadic forms of ALS (sALS). The diagnosis of ALS includes the detection of early symptoms and, as disease progresses,...
Article
Full-text available
Unbalanced diets and altered micronutrient intake are prevalent in the aging adult population. We conducted a systematic review to appraise the evidence regarding the association between single (α-carotene, β-carotene, lutein, lycopene, β-cryptoxanthin) or total carotenoids and frailty syndrome in the adult population. The literature was screened f...
Article
Full-text available
Prostate cancer (PC) is one of the major male cancers. Differential diagnosis of PC is indispensable for the individual therapy, i.e., Gleason score (GS) that describes the grade of cancer can be used to choose the appropriate therapy. However, the current techniques for PC diagnosis and prognosis are not always effective. To identify potential mar...
Article
Full-text available
Breast cancer is a heterogeneous disease classified into four main subtypes with different clinical outcomes, such as patient survival, prognosis, and relapse. Current genetic tests for the differential diagnosis of BC subtypes showed a poor reproducibility. Therefore, an early and correct diagnosis of molecular subtypes is one of the challenges in...
Article
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Background: The coronavirus disease-2019 (COVID-19), caused by a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is now spread worldwide. Therefore, informative and reliable data related to the exact effects of COVID-19 on fertility and pregnancy is still of great interest until the pandemic is declared over. General guidelines regard...
Article
Full-text available
Amyotrophic lateral sclerosis (ALS) is a fatal disease related to upper and lower motor neurons degeneration. Although the environmental and genetic causes of this disease are still unclear, some factors involved in ALS onset such as oxidative stress may be influenced by diet. A higher risk of ALS has been correlated with a high fat and glutamate i...
Article
Full-text available
Amyotrophic lateral sclerosis (ALS) is a complex disease with a late onset and is characterized by the progressive loss of muscular and respiratory functions. Although recent studies have partially elucidated ALS’s mechanisms, many questions remain such as what the most important molecular pathways involved in ALS are and why there is such a large...
Article
Aim: SARS-CoV-2, an emerging betacoronavirus, is the causative agent of COVID-19. Currently, there are few specific and selective antiviral drugs for the treatment and vaccines to prevent contagion. However, their long-term effects can be revealed after several years, and new drugs for COVID-19 should continue to be investigated. Materials & method...
Article
Full-text available
Coronavirus disease 2019 (COVID-19), a global pandemic, is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Angiotensin-converting enzyme 2 (ACE2) is the receptor for SARS-CoV-2 and transmembrane serine protease 2 (TMPRSS2) facilitates ACE2-mediated virus entry. Moreover, the expression of ACE2 in the testes of infertile men...
Article
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Radiomics allows the extraction quantitative features from imaging, as imaging biomarkers of disease. The objective of this exploratory study is to implement a reproducible radiomic-pipeline for the extraction of a magnetic resonance imaging (MRI) signature for prostate cancer (PCa) aggressiveness. One hundred and two consecutive patients performin...
Article
Full-text available
Triple negative breast cancer (TNBC) accounts for about a fifth of all breast cancers and includes a diverse group of cancers. The heterogeneity of TNBC and the lack of target receptors on the cell surface make it difficult to develop specific therapeutic treatments. These aspects cause the high negative prognosis of patients with this type of tumo...
Article
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Background and Objectives: Breast cancer is a heterogeneous disease categorized into four subtypes. Previous studies have shown that copy number alterations of several genes are implicated with the development and progression of many cancers. This study evaluates the effects of DNA copy number alterations on gene expression levels in different brea...
Article
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The development of new computational approaches that are able to design the correct personalized drugs is the crucial therapeutic issue in cancer research. However, tumor heterogeneity is the main obstacle to developing patient-specific single drugs or combinations of drugs that already exist in clinics. In this study, we developed a computational...
Article
Non-obstructive azoospermia (NOA) is the most clinical problem in case of infertility. About 70% of NOA patients are idiopathic with uncharacterized molecular mechanisms. This study aimed to analyze the possible pathogenic miRNA–target gene interaction and lncRNA–miRNA association involved in NOA. In the current study, differentially expressed (DE)...
Article
Full-text available
MicroRNAs (miRNAs) are small noncoding RNAs that have emerged as new potential epigenetic biomarkers. Here, we evaluate the efficacy of six circulating miRNA previously described in the literature as biomarkers for the diagnosis of temporal lobe epilepsy (TLE) and/or as predictive biomarkers to antiepileptic drug response. We measured the differenc...
Preprint
Full-text available
BackgroundSARS-CoV-2 coronavirus, an emerging Betacoronavirus, is the causative agent of the severe acute respiratory distress syndrome outbreak in 2019 (COVID-19). Currently, there are neither specific and selective antiviral drugs for the treatment nor vaccines to prevent contagion. Here we propose a bioinformatic approach in order to test in sil...
Article
Full-text available
Molecular docking in the pharmaceutical industry is a powerful in silico approach for discovering novel therapies for unmet medical needs predicting drug–target interactions. It not only provides binding affinity between drugs and targets at the atomic level, but also elucidates the fundamental pharmacological properties of specific drugs. The purp...
Article
Full-text available
Background: Severe acute respiratory syndrome coronavirus (SARS-CoV-2), an emerging Betacoronavirus, is the causative agent of COVID-19. Angiotensin converting enzyme 2 (ACE2), being the main cell receptor of SARS-CoV-2, plays a role in the entry of the virus into the cell. Currently, there are neither specific antiviral drugs for the treatment or...
Article
Metastases are the main cause of death in advanced breast cancer (BC) patients. Although chemotherapy and hormone therapy are current treatment strategies, drug resistance is frequent and still not completely understood. In this study, a bioinformatics analysis was performed on BC patients to explore the molecular mechanisms associated with BC meta...
Preprint
Full-text available
Background: Severe acute respiratory syndrome coronavirus (SARS-CoV-2), an emerging Betacoronavirus, is the causative agent of COVID-19. Angiotensin converting enzyme 2 (ACE2), being the main cell receptor of SARS-CoV-2, plays a role in the entry of the virus into the cell. Currently, there are no specific antiviral drugs for the treatment and neit...
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
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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
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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
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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
Full-text available
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
Full-text available
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
Full-text available
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...
Preprint
Full-text available
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
Full-text available
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...
Preprint
Full-text available
Cancer is a complex and heterogeneous disease. It is crucial to identify the key driver genes and their role in cancer mechanisms with attention to different cancer stages, types or subtypes. Cancer driver genes are elusive and their discovery is complicated by the fact that the same gene can play a diverse role in different contexts. Key biologica...
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
Full-text available
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
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...
Article
Full-text available
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...
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...