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| Name | Class |
|---|---|
| San Raffaele University Hospital, Italy | OTHER |
| Fondazione Istituto Nazionale Genetica Molecolare - INGM | UNKNOWN |
| University of Milan | OTHER |
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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.
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
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| Label | Type | Description | Intervention Names |
|---|---|---|---|
| HCC patients | 120 patients will be prospectively recruitedand from whom fresh tumor samples and blood samples will be collected. 150 HCC patients treated by surgery FFPE samples will be retrospectively collected |
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| Name | Type | Description | Arm Group Labels | Other Names |
|---|---|---|---|---|
| Collection of tumor tissue (Fresh or/and archival FFPE), blood samples | Genetic | NGS, immunofluorescence analyses, transcriptional and immunophenotypic analyzes, scRNAseq, ChIP-seq/ATAC-seq, DNA methylation, single-cell transcriptomic and TCR sequencing |
| Measure | Description | Time Frame |
|---|---|---|
| Characterize the molecular mechanisms underlying T cell dysfunction | 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. | 5 years |
| Measure | Description | Time Frame |
|---|---|---|
| Analyze the epigenetic transcriptional regulatory mechanisms | 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. |
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Patients with HCC and eligible for biopsy or surgical resection
| Name | Role | Phone | Extension | |
|---|---|---|---|---|
| Gianluca Mauri, MD | Contact | +39026444 | 3695 | gianluca.mauri@ospedaleniguarda.it |
| Name | Affiliation | Role |
|---|---|---|
| Gianluca Mauri, MD | ASST Grande Ospedale Metropolitano Niguarda | Principal Investigator |
| Facility | Status | City | State | ZIP | Country | Contacts |
|---|---|---|---|---|---|---|
| ASST GOM Niguarda | Recruiting | Milan | Lombardy | 20162 | Italy |
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| ID | Term |
|---|---|
| D006528 | Carcinoma, Hepatocellular |
| ID | Term |
|---|---|
| D000230 | Adenocarcinoma |
| D002277 | Carcinoma |
| D009375 | Neoplasms, Glandular and Epithelial |
| D009370 | Neoplasms by Histologic Type |
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| ID | Term |
|---|---|
| D001800 | Blood Specimen Collection |
| ID | Term |
|---|---|
| D013048 | Specimen Handling |
| D019411 | Clinical Laboratory Techniques |
| D019937 | Diagnostic Techniques and Procedures |
| D003933 | Diagnosis |
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Tumor tissue (fresh and archival FFPE)
| 5 years |
| Retrospective analysis on FFPE samples | 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. | 5 years |
| D009369 | Neoplasms |
| D008113 | Liver Neoplasms |
| D004067 | Digestive System Neoplasms |
| D009371 | Neoplasms by Site |
| D004066 | Digestive System Diseases |
| D008107 | Liver Diseases |
| D011677 | Punctures |
| D013514 | Surgical Procedures, Operative |
| D008919 | Investigative Techniques |