Francesca Pia Caruso
A5090470125- Glioma Diagnosis and Treatment
- Epigenetics and DNA Methylation
- Cancer Immunotherapy and Biomarkers
- Histone Deacetylase Inhibitors Research
- Cancer Genomics and Diagnostics
- Single-cell and spatial transcriptomics
- Immunotherapy and Immune Responses
- Ferroptosis and cancer prognosis
- Radiomics and Machine Learning in Medical Imaging
- MicroRNA in disease regulation
- Immune cells in cancer
- Protein Degradation and Inhibitors
- Cancer-related molecular mechanisms research
- Neuroinflammation and Neurodegeneration Mechanisms
- CAR-T cell therapy research
- Extracellular vesicles in disease
- RNA modifications and cancer
- Mitochondrial Function and Pathology
- vaccines and immunoinformatics approaches
- Renal and related cancers
- Occupational and environmental lung diseases
- Ubiquitin and proteasome pathways
- Hepatitis B Virus Studies
- SARS-CoV-2 and COVID-19 Research
- Circular RNAs in diseases
Biogem
2016-2025
Information Technology University
2024
University of Naples Federico II
2020-2024
University of Sannio
2016-2023
University of Siena
2022
National Research Council
2022
Fondazione IRCCS Istituto Nazionale dei Tumori
2022
Fondazione Istituto G. Giglio di Cefalù
2021
Single-cell RNA sequencing is the reference technology to characterize composition of tumor microenvironment and study heterogeneity at high resolution. Here we report Single CEll Variational ANeuploidy analysis (SCEVAN), a fast variational algorithm for deconvolution clonal substructure tumors from single-cell RNA-seq data. It uses multichannel segmentation exploiting assumption that all cells in given copy number clone share same breakpoints. Thus, smoothed expression profile every...
Despite the successes of immunotherapy in cancer treatment over recent decades, less than <10%–20% cases have demonstrated durable responses from immune checkpoint blockade. To enhance efficacy immunotherapies, combination therapies suppressing multiple evasion mechanisms are increasingly contemplated. better understand cell surveillance and diverse tumor tissues, we comprehensively characterized landscape more 1,000 tumors across ten different cancers using CPTAC pan-cancer proteogenomic...
Abstract Background Glioblastoma (GBM) is a complex disease with extensive molecular and transcriptional heterogeneity. GBM can be subcategorized into four distinct subtypes; tumors that shift towards the mesenchymal phenotype upon recurrence are generally associated treatment resistance, unfavorable prognosis, infiltration of pro-tumorigenic macrophages. Results We explore regulatory networks mesenchymal-associated tumor-associated macrophages (MA-TAMs), which drive malignant phenotypic...
Glioblastoma (GBM) is resistant to multimodality therapeutic approaches. A high burden of tumor-specific mutant peptides (neoantigens) correlates with better survival and response immunotherapies in selected solid tumors but how neoantigens impact clinical outcome GBM remains unclear. Here, we exploit the similarity between tumor infectious disease-derived immune epitopes apply a neoantigen fitness model for identifying high-quality human pan-glioma dataset. We find that quality stratifies...
Association with hypomethylating agents is a promising strategy to improve the efficacy of immune checkpoint inhibitors-based therapy. The NIBIT-M4 was phase Ib, dose-escalation trial in patients advanced melanoma agent guadecitabine combined anti-CTLA-4 antibody ipilimumab that followed traditional 3 + design (NCT02608437). Patients received 30, 45 or 60 mg/m2/day subcutaneously on days 1 5 every weeks starting week 0 for total four cycles, and mg/kg intravenously day cycles. Primary...
Sampling restrictions have hindered the comprehensive study of invasive non-enhancing (NE) high-grade glioma (HGG) cell populations driving tumor progression. Here, we present an integrated multi-omic analysis spatially matched molecular and multi-parametric magnetic resonance imaging (MRI) profiling across 313 multi-regional biopsies, including 111 from NE, 68 HGG patients. Whole exome RNA sequencing uncover unique genomic alterations to unresectable NE tumor, subclonal events, which inform...
ABSTRACT Background Single-cell RNA sequencing is the reference technique for characterizing heterogeneity of tumor microenvironment. The composition various cell types making up microenvironment can significantly affect way in which immune system activates cancer rejection mechanisms. Understanding cross-talk signals between cells and fundamental importance identification immuno-oncology therapeutic targets. Results We present a novel method, single-cell Tumor–Host Interaction tool (scTHI),...
Abstract Background Glioblastoma multiforme (GBM) is a highly aggressive primary brain tumor, that refractory to standard treatment and immunotherapy with immune-checkpoint inhibitors (ICI). Noteworthy, melanoma metastases (MM-BM), share the same niche as GBM, frequently respond current ICI therapies. Epigenetic modifications regulate GBM cellular proliferation, invasion, prognosis may negatively cross-talk between malignant cells immune in tumor milieu, likely contributing limit efficacy of...
Abstract We evaluate deconvolution methods, which infer levels of immune infiltration from bulk expression tumor samples, through a community-wide DREAM Challenge. assess six published and 22 community-contributed methods using in vitro silico transcriptional profiles admixed cancer healthy cells. Several predict most cell types well, though they either were not trained to all functional CD8+ T states or do so with low accuracy. address this gap, including deep learning-based approach, whose...
The biological and clinical relevance of the DNA methylation landscape in metastatic melanoma (MM) remains underexplored. In a retrospective cohort 191 MM lesions from 165 AJCC Stage III IV patients (EPICA cohort) we identified four tumor subsets (i.e. DEMethylated, LOW, INTermediate CIMP) with progressively increasing levels methylation. These findings were validated TCGA MM. EPICA, LOW tumors exhibited significantly longer survival lower progression rate to more advanced stages, compared...
Abstract Background Co-targeting of immune checkpoint inhibitors (ICI) CTLA-4 and PD-1 has recently become the new first-line standard care therapy pleural mesothelioma (PM) patients, with a significant improvement overall survival (OS) over conventional chemotherapy. The analysis by tumor histotype demonstrated greater efficacy ICI compared to chemotherapy in non-epithelioid (non-E) vs. epithelioid (E) PM, although some E PM patients also benefit from treatment. This evidence suggests that...
Human microsatellite-stable (MSS) colorectal cancers (CRCs) are immunologically "cold" tumour subtypes characterized by reduced immune cytotoxicity. The molecular linkages between immune-resistance and human MSS CRC is not clear. We used transcriptome profiling, in silico analysis, immunohistochemistry, western blot, RT-qPCR immunofluorescence staining to characterize novel biomarkers. effects of selective antagonists were tested vitro assays long term viability analysis kinase active forms...
Improvement of efficacy immune checkpoint blockade (ICB) remains a major clinical goal. Association ICB with immunomodulatory epigenetic drugs is an option. However, inhibitors show heterogeneous landscape activities. Analysis transcriptional programs induced in neoplastic cells by distinct classes may foster identification the most promising agents. Melanoma cell lines, characterized for mutational and differentiation profile, were treated DNA methyltransferases (guadecitabine), histone...
Melanoma is the deadliest form of skin cancer and metastatic disease associated with a significant survival rate drop. There an urgent need for consistent tumor biomarkers to scale precision medicine reduce mortality. Here, we aimed identify melanoma-specific circulating microRNA signature assess its value as diagnostic tool.The study consisted discovery phase two validation phases. Circulating plasma extracellular vesicles (pEV) profiles were obtained from cohort melanoma patients normal...
Abstract Purpose/methods The determination of tumour biomarkers is paramount to advancing personalized medicine, more so in rare tumours like medullary thyroid carcinoma (MTC), whose diagnosis still challenging. aim this study was identify non-invasive circulating MTC. To achieve goal, paired MTC tissue and plasma extracellular vesicle samples were collected from multiple centres microRNA (miRNA) expression levels evaluated. Results a discovery cohort 23 patients analysed using miRNA arrays....
Abstract A novel two-step bioinformatics strategy was applied for identification of signatures with therapeutic implications in hepatitis-associated HCC. Transcriptional profiles from HBV- and HCV-associated HCC samples were compared non-tumor liver controls. Resulting modulated genes subsequently different tissue samples. Two related identified, namely “HCC-associated” “HCC-specific”. Expression data validated by RNA-Seq analysis carried out on unrelated protein expression confirmed...
Tumor heterogeneity underlies resistance and disease progression in glioblastoma (GBM), tumors most commonly recur adjacent to the surgical resection margins contrast non-enhancing (NE) regions. To date, no targeted therapies have meaningfully altered overall patient survival up-front setting. The aim of this study was characterize intratumoral recurrent GBM using bulk samples from primary taken contrast-enhancing (EN) NE regions.Whole exome RNA sequencing were performed on matched multiple...
(1) Purpose: The methyl donor S-Adenosylmethionine (AdoMet) has been widely explored as a therapeutic compound, and its application-alone or in combination with other molecules-is emerging potential effective strategy for the treatment chemoprevention of tumours. In this study, we investigated antitumor activity AdoMet Laryngeal Squamous Cell Carcinoma (LSCC), exploring underlying mechanisms. (2) Results: We demonstrated that induced ROS generation triggered autophagy consistent increase...
Abstract Radiation therapy is part of the standard care for gliomas and kills a subset tumor cells, while also altering microenvironment. Tumor cells with stem‐like properties preferentially survive radiation give rise to glioma recurrence. Various techniques enriching quantifying have been used, including fluorescence activated cell sorting (FACS)‐based side population (SP) assay, which functional assay that enriches cells. In these analyses, mouse models used understand biology this...
Abstract We evaluate deconvolution methods, which infer levels of immune infiltration from bulk expression tumor samples, through a community-wide DREAM Challenge. assess six published and 22 community-contributed methods using in vitro silico transcriptional profiles admixed cancer healthy cells. Several predict most cell types well, though they either were not trained to all functional CD8+ T states or do so with low accuracy. address this gap, including deep learning-based approach, whose...
Ribonucleoprotein (RNP) condensates are crucial for controlling RNA metabolism and splicing events in animal cells. We used spatial proteomics transcriptomic to elucidate RNP interaction networks at the centrosome, main microtubule-organizing center found a number of cell-type specific centrosome-associated spliceosome interactions localized subcellular structures involved nuclear division ciliogenesis. A component BUD31 was validated as an interactor centriolar satellite protein OFD1....
ABSTRACT Here we report Single CEll Variational ANeuploidy analysis (SCEVAN), a fast variational algorithm for the deconvolution of clonal substructure tumors from single cell data. It uses multichannel segmentation exploiting assumption that all cells in given copy number clone share same breakpoints. Thus, smoothed expression profile every individual constitutes part evidence each subclone. SCEVAN can automatically and accurately discriminate between malignant non-malignant cells,...