Paolo Nanni
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View article: Transcriptomic and proteomic profiling shows dysregulated immune and metabolic pathways in arrhythmogenic cardiomyopathy
Transcriptomic and proteomic profiling shows dysregulated immune and metabolic pathways in arrhythmogenic cardiomyopathy Open
Aims Arrhythmogenic cardiomyopathy (ACM) is a hereditary heart disease characterized by fibrofatty myocardial replacement and a predisposition to malignant ventricular arrhythmias. The underlying pathomechanisms remain incompletely underst…
View article: <i>prolfquapp</i> ─ A User-Friendly Command-Line Tool Simplifying Differential Expression Analysis in Quantitative Proteomics
<i>prolfquapp</i> ─ A User-Friendly Command-Line Tool Simplifying Differential Expression Analysis in Quantitative Proteomics Open
Mass spectrometry is a cornerstone of quantitative proteomics, enabling relative protein quantification and differential expression analysis (DEA) of proteins. As experiments grow in complexity, involving more samples, groups, and identifi…
View article: A Multiyear Longitudinal Harmonization Study of Quality Controls in Mass Spectrometry Proteomics Core Facilities
A Multiyear Longitudinal Harmonization Study of Quality Controls in Mass Spectrometry Proteomics Core Facilities Open
Quality control procedures play a pivotal role in ensuring the reliability and consistency of data generated in mass spectrometry-based proteomics laboratories. However, the lack of standardized quality control practices across laboratorie…
View article: <i>prolfquapp</i>- A User-Friendly Command-Line Tool Simplifying Differential Expression Analysis in Quantitative Proteomics
<i>prolfquapp</i>- A User-Friendly Command-Line Tool Simplifying Differential Expression Analysis in Quantitative Proteomics Open
Mass spectrometry is a cornerstone of quantitative proteomics, enabling relative protein quantification and differential expression analysis ( DEA ) of proteins. As experiments grow in complexity, involving more samples, groups, and identi…
View article: PSXI-16 Using a multi-omics approach to decipher trans-10 shift biomarkers in ruminants
PSXI-16 Using a multi-omics approach to decipher trans-10 shift biomarkers in ruminants Open
The trans-10 shift is a recognized deviation from the normal ruminal biohydrogenation (BH) pathways of the dietary polyunsaturated fatty acids (FA) in the rumen. This phenomenon leads to the formation of the harmful t10-18:1, which is detr…
View article: Protein Network Alterations in G‐CSF Treated Severe Congenital Neutropenia Patients and Beneficial Effects of Oral Health Intervention
Protein Network Alterations in G‐CSF Treated Severe Congenital Neutropenia Patients and Beneficial Effects of Oral Health Intervention Open
Purpose Severe congenital neutropenia (SCN) is a raredisorder characterized by diminished neutrophil levels. Despite granulocytecolony‐stimulating factor (G‐CSF) treatment, SCN patients remain still prone tosevere infections, including per…
View article: A multi-year longitudinal harmonization of quality controls in mass spectrometry proteomics core facilities
A multi-year longitudinal harmonization of quality controls in mass spectrometry proteomics core facilities Open
Quality control procedures play a pivotal role in ensuring the reliability and consistency of data generated in mass spectrometry-based proteomics laboratories. However, the lack of standardized quality control practices across laboratorie…
View article: Probing the salivary proteome for prognostic biomarkers in response to non‐surgical periodontal therapy
Probing the salivary proteome for prognostic biomarkers in response to non‐surgical periodontal therapy Open
Aim This prospective study investigated the salivary proteome before and after periodontal therapy. Materials and Methods Ten systemically healthy, non‐smoking, stage III, grade C periodontitis patients underwent non‐surgical periodontal t…
View article: L’agricoltura e il lavoro agricolo
L’agricoltura e il lavoro agricolo Open
During the Middle Ages agriculture and agricultural labor was involved in a new system of values, due to the expansion of Christianity, and this valorization had a great impact on society and economic development of Western Europe. Agricul…
View article: Multi-omics Characterization of Response to PD-1 Inhibitors in Advanced Melanoma
Multi-omics Characterization of Response to PD-1 Inhibitors in Advanced Melanoma Open
Immunotherapy improves the survival of patients with advanced melanoma, 40% of whom become long-term responders. However, not all patients respond to immunotherapy. Further knowledge of the processes involved in the response and resistance…
View article: Table S5. List of proteins associated with tumor fragmentation. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness
Table S5. List of proteins associated with tumor fragmentation. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness Open
The table shows the list of proteins correlating with TF scores as a continuous response with a FDR<0.05, by Significance Analysis of Microarrays.
View article: Figure S3. Biological processes associated with TF morphotypes from TCGA mRNAseq and WS Mass Spectrometry data. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness
Figure S3. Biological processes associated with TF morphotypes from TCGA mRNAseq and WS Mass Spectrometry data. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness Open
A) gene ontology network visualization of RNAs overexpressed in high (red) and low TF (blue) groups. B) bar plot showing molecular pathways associated with low (blue) and high (red) TF, at the RNA level. C) bar plot showing biological proc…
View article: PRoteomics IDEntifications database from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness
PRoteomics IDEntifications database from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness Open
The PRIDE (PRoteomics IDEntifications database) additional raw and search files of our experiment
View article: Table S3. Association of TF scores with relapse-free survival. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness
Table S3. Association of TF scores with relapse-free survival. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness Open
Survival analysis for human-based TF scores by univariate and multivariate cox regressions. RFS=relapse-free survival; CI=95% confidence interval; Computer: automatic scoring on pan-cytokeratin stained tissue; Human: fragmentation scored b…
View article: Table S1. Complete list of proteins identifications. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness
Table S1. Complete list of proteins identifications. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness Open
The list of proteins identified by mass spectrometry (n=2614) for 48 samples of the WS cohort.
View article: Figure S1. Frequency distributions, intra-tumor heterogeneity and inter-observer variability for TF scores. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness
Figure S1. Frequency distributions, intra-tumor heterogeneity and inter-observer variability for TF scores. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness Open
A) Percentage distribution of computed TF scores for TMA and correlation between matching cores. B) Percentage distribution of computed TF scores for WS and correlation between matching whole sections. C) Percentage distribution of human-b…
View article: Figure S1. Frequency distributions, intra-tumor heterogeneity and inter-observer variability for TF scores. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness
Figure S1. Frequency distributions, intra-tumor heterogeneity and inter-observer variability for TF scores. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness Open
A) Percentage distribution of computed TF scores for TMA and correlation between matching cores. B) Percentage distribution of computed TF scores for WS and correlation between matching whole sections. C) Percentage distribution of human-b…
View article: Table S2. Association of tumor fragmentation with clinico-pathological parameters. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness
Table S2. Association of tumor fragmentation with clinico-pathological parameters. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness Open
The table shows proportions of patients among low and high TF groups (dichotomized at the median TF scores) stratified by clinical parameters. Chi-square tests and Spearman's rank correlations were used for categorical (low/high TF) and co…
View article: Data from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness
Data from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness Open
Accurate stratification of tumors is imperative for adequate cancer management. In addition to staging, morphologic subtyping allows stratification of patients into additional prognostic groups. In this study, we used an image-based comput…
View article: Table S4. Association of human-based TF scores with OS and RFS. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness
Table S4. Association of human-based TF scores with OS and RFS. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness Open
Survival analysis for human-based TF scores on H&E stained sections by univariate and multivariate cox regressions. OS=overall survival; RFS=relapse-free survival; CI=95% confidence interval; TF (low/high): scores dichotomized at the media…
View article: Figure S2. Threshold analysis of tumor fragmentation in correlation with RFS and OS. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness
Figure S2. Threshold analysis of tumor fragmentation in correlation with RFS and OS. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness Open
Series of cox univariate survival analyses are represented for the WS cohort. Data points represent single survival analyses repeated for computed TF scores using different tumor fragments size cut-offs. X-axis indicates the minimal size t…
View article: Table S3. Association of TF scores with relapse-free survival. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness
Table S3. Association of TF scores with relapse-free survival. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness Open
Survival analysis for human-based TF scores by univariate and multivariate cox regressions. RFS=relapse-free survival; CI=95% confidence interval; Computer: automatic scoring on pan-cytokeratin stained tissue; Human: fragmentation scored b…
View article: Data from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness
Data from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness Open
Accurate stratification of tumors is imperative for adequate cancer management. In addition to staging, morphologic subtyping allows stratification of patients into additional prognostic groups. In this study, we used an image-based comput…
View article: PRoteomics IDEntifications database from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness
PRoteomics IDEntifications database from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness Open
The PRIDE (PRoteomics IDEntifications database) additional raw and search files of our experiment
View article: Table S4. Association of human-based TF scores with OS and RFS. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness
Table S4. Association of human-based TF scores with OS and RFS. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness Open
Survival analysis for human-based TF scores on H&E stained sections by univariate and multivariate cox regressions. OS=overall survival; RFS=relapse-free survival; CI=95% confidence interval; TF (low/high): scores dichotomized at the media…
View article: Figure S3. Biological processes associated with TF morphotypes from TCGA mRNAseq and WS Mass Spectrometry data. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness
Figure S3. Biological processes associated with TF morphotypes from TCGA mRNAseq and WS Mass Spectrometry data. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness Open
A) gene ontology network visualization of RNAs overexpressed in high (red) and low TF (blue) groups. B) bar plot showing molecular pathways associated with low (blue) and high (red) TF, at the RNA level. C) bar plot showing biological proc…
View article: Table S1. Complete list of proteins identifications. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness
Table S1. Complete list of proteins identifications. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness Open
The list of proteins identified by mass spectrometry (n=2614) for 48 samples of the WS cohort.
View article: Table S5. List of proteins associated with tumor fragmentation. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness
Table S5. List of proteins associated with tumor fragmentation. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness Open
The table shows the list of proteins correlating with TF scores as a continuous response with a FDR<0.05, by Significance Analysis of Microarrays.