Hepatocarcinoma
Conditions
Brief summary
This is a national, observational, retrospective, cross-sectional, non-profit study focused on patients with HCC. The study aims to characterize the expression and function of novel noncoding regulatory transcripts, including those containing TEsin the microenvironment of liver tumors, with emphasis on their role in T cell dysfunction.
Detailed description
We will use TILs, along with other immune, hepatocyte, and stromal cell populations isolated from hepatocellular carcinoma (HCC) tissue, matched adjacent non-tumoral liver, and peripheral blood samples. Single-cell RNA sequencing and spatial transcriptomics will be employed to define the cellular distribution and molecular profiles of TE-containing transcripts, other noncoding RNAs, and associated gene expression programs within the HCC microenvironment. Functional experiments-including CRISPR-Cas13 or ASO-mediated silencing-will be performed to elucidate the role of the novel regulatory transcripts, including TE-transcripts, in modulating cellular identity within the liver TME. In parallel, epigenetic analyses such as ChIPseq, ATAC-seq, DNA methylation profiling, RADICL-seq, and Hi-C will be conducted to map the regulatory networks and chromatin architecture associated with these transcripts
Interventions
GENETICCollection of tumor tissue (Fresh or/and archival FFPE), blood samples
NGS, immunofluorescence analyses, transcriptional and immunophenotypic analyzes, scRNAseq, ChIP-seq/ATAC-seq, DNA methylation, single-cell transcriptomic and TCR sequencing
Sponsors
Niguarda Hospital
San Raffaele University Hospital, Italy
Fondazione Istituto Nazionale Genetica Molecolare - INGM
University of Milan
Study design
Observational model
OTHER
Time perspective
RETROSPECTIVE
Eligibility
Sex/Gender
ALL
Age
18 Years to No maximum
Healthy volunteers
No
Inclusion criteria
1. Histological/radiological (LR-4 o 5)diagnosis of hepatocellular carcinoma (HCC). 2. Solid tumor fresh tissue availability from HCC biospy or surgical resectionas per standard clinical practice, and/orHCC FFPE archival samples availability. 3. Capability of understanding and signing an inform consent form. 4. Known hepatits B and C status, including HBeAg (positive or negative), viral load (HBVDNA e HCV-RNA), HCV genotype, whether sustained virological response (SVR)was obtainedand potential antiviral treatments received (including direct antiretroviral therapy(DAA)and interferon). These parameters will be exploited to stratify patients and analyze the impact of the virological status on microenvironmental immunological features, with particular regards to immunesuppression mechanisms.
Design outcomes
Primary
| Measure | Time frame | Description |
|---|---|---|
| Characterize the molecular mechanisms underlying T cell dysfunction | 5 years | To characterize the molecular mechanisms underlying T cell dysfunction and immune evasion in the tumor microenvironment of hepatocellular carcinoma, through the identification and functional definition of novel non-coding regulatory transcripts - including those containing transposable elements - expressed at single-cell resolution. Identification of TE-containing transcripts expressed in tumor-infiltrating lymphocytes (TILs) and other cellular populations within the HCC tumor microenvironment, using single-cell transcriptomics (scRNA-seq) and spatial transcriptomics technologies. |
Secondary
| Measure | Time frame | Description |
|---|---|---|
| Analyze the epigenetic transcriptional regulatory mechanisms | 5 years | To analyze the epigenetic and transcriptional regulatory mechanisms mediated by the newly identified transcripts from the primary objective, including TEcontaining transcripts, in the cellular components of the HCC tumor microenvironment. Mapping of the genomic occupancy, epigenetic landscape, and three-dimensional chromatin conformation associated with the newly identified regulatory transcripts, including those containing TEs, in TME cells, with particular attention to TILs. |
| Retrospective analysis on FFPE samples | 5 years | Evaluation of the expression dynamics of regulatory transcripts, including those containing TEs, as potential predictive biomarkers of response to immunotherapy, through retrospective analysis on FFPE tissue samples. |
Countries
Italy
Contacts
CONTACTGianluca Mauri, MD
PRINCIPAL_INVESTIGATORGianluca Mauri, MD
ASST Grande Ospedale Metropolitano Niguarda
Outcome results
None listed