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| Name | Class |
|---|---|
| Università degli Studi di Trento | OTHER |
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The study aims to develop PRIME (PRostate cancer plasma Integrative Multi-modal Evaluation) liquid biopsy test and to implement its use to query prospectively collected samples in advanced prostate cancer (PCa) clinical trials and/or clinical settings. In order to maximise the utility of liquid biopsies for advanced PCa, PRIME is focused on the development of novel computational and sequencing approaches that integrate multiple information from plasma circulating elements: i) cell free DNA (cfDNA) gene mutation data with accurate quantitation of cfDNA structural genomic changes, ii) cfDNA genomic profiling with cfDNA methylation status, and iii) the information provided by extracellular vesicles (EVs) and EV-associated cargo (including DNA, RNA and proteins).
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| Label | Type | Description | Intervention Names |
|---|---|---|---|
| Metastatic Castration Resistant Prostate Cancer (mCRPC) patients | This group includes mCRPC patients treated with serial lines of treatment. For each line of treatment, blood samples are collected:
|
| |
| Metastatic Hormon Sensitive Prostate Cancer (mHSPC) patients | This group includes mHSPC patients treated with hormone therapy. In the hormone sensitive setting, blood samples are collected:
|
|
| Name | Type | Description | Arm Group Labels | Other Names |
|---|---|---|---|---|
| Analysis of cell free DNA, and extracellular vesicles (EVs) and EV-associated molecular components (including RNA, DNA, proteins) | Diagnostic Test | Plasma and buffy coat samples are shipped from the recruiting clinical sites to the lab of Professor Francesca Demichelis at the University of Trento (UniTN). At UniTN, samples are stored in dedicated freezers with restricted access and subsequently used as follows:
Nucleic acids sequencing library preparations and all downstream omics analyses are performed by Prof. Demichelis team. |
| Measure | Description | Time Frame |
|---|---|---|
| Quantification of circulating tumor DNA (ctDNA) in the plasma | Number of circulating tumor DNA (ctDNA) in the plasma | From enrolment across different lines of treatment |
| Quantification of the fraction of cfDNA hypo/hypermethylation | Rate of cfDNA hypo/hypermethylation | From enrolment across different lines of treatment |
| Presence of recurrent somatic aberrations in ctDNA (such as loss of RB1, TP53, BRCA1/2, or AR amplification). | Assessment (yes/no) of recurrent somatic aberrations in ctDNA (such as loss of RB1, TP53, | From enrolment across different lines of treatment |
| Presence of Copy Number Variants (CNVs) in ctDNA | Assessment (yes/no) of Copy Number Variants (CNVs) in ctDNA | From enrolment across different lines of treatment |
| Identification of EV-associated biomarkers | Assessment (yes/no) of EV-associated biomarkers | From enrolment across different lines of treatment |
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Inclusion Criteria:
Exclusion Criteria:
- Histological diagnosis other than prostate cancer
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Patients are selected at oncology care clinics at participating clinical sites.
| Name | Role | Phone | Extension | |
|---|---|---|---|---|
| Orazio Caffo | Contact | +39 0461902121 | orazio.caffo@apss.tn.it |
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| Facility | Status | City | State | ZIP | Country | Contacts |
|---|---|---|---|---|---|---|
| Istituto Romagnolo per lo Studio dei Tumori | Recruiting | Meldola | Forlì-Cesena | 47014 | Italy |
| PubMed Identifier | Type | Citation | Retractions |
|---|---|---|---|
| 38046436 | Background | Mugoni V, Ciani Y, Quaini O, Tomasini S, Notarangelo M, Vannuccini F, Marinelli A, Leonardi E, Pontalti S, Martinelli A, Rossetto D, Pesce I, Mansy SS, Barbareschi M, Ferro A, Caffo O, Attard G, Di Vizio D, D'Agostino VG, Nardella C, Demichelis F. Integrating extracellular vesicle and circulating cell-free DNA analysis using a single plasma aliquot improves the detection of HER2 positivity in breast cancer patients. J Extracell Biol. 2023 Sep;2(9):e108. doi: 10.1002/jex2.108. Epub 2023 Sep 25. | |
| 35664542 |
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| ID | Term |
|---|---|
| D011471 | Prostatic Neoplasms |
| ID | Term |
|---|---|
| D005834 | Genital Neoplasms, Male |
| D014565 | Urogenital Neoplasms |
| D009371 | Neoplasms by Site |
| D009369 | Neoplasms |
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| ID | Term |
|---|---|
| D059371 | DNA, B-Form |
| ID | Term |
|---|---|
| D004247 | DNA |
| D009696 | Nucleic Acids |
| D009706 | Nucleic Acids, Nucleotides, and Nucleosides |
| D009690 | Nucleic Acid Conformation |
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Plasma and buffy coat:
|
| Azienda Ospedaliera San Luigi | Recruiting | Orbassano | Torino | 10043 | Italy |
|
| Istituto Oncologico Veneto | Recruiting | Padova | 35128 | Italy |
|
| Santa Chiara Hospital | Recruiting | Trento | 38122 | Italy |
|
| Background |
| Orlando F, Romanel A, Trujillo B, Sigouros M, Wetterskog D, Quaini O, Leone G, Xiang JZ, Wingate A, Tagawa S, Jayaram A, Linch M; PEACE Consortium; Jamal-Hanjani M, Swanton C, Rubin MA, Wyatt AW, Beltran H, Attard G, Demichelis F. Allele-informed copy number evaluation of plasma DNA samples from metastatic prostate cancer patients: the PCF_SELECT consortium assay. NAR Cancer. 2022 May 27;4(2):zcac016. doi: 10.1093/narcan/zcac016. eCollection 2022 Jun. |
| 34605002 | Background | Conteduca V, Scarpi E, Wetterskog D, Brighi N, Ferroni F, Rossi A, Romanel A, Gurioli G, Bleve S, Gianni C, Schepisi G, Lolli C, Cortesi P, Matteucci F, Barone D, Paganelli G, Demichelis F, Beltran H, Attard G, De Giorgi U. Plasma tumor DNA is associated with increased risk of venous thromboembolism in metastatic castration-resistant cancer patients. Int J Cancer. 2022 Apr 1;150(7):1166-1173. doi: 10.1002/ijc.33834. Epub 2021 Oct 13. |
| 32669676 | Background | Conteduca V, Wetterskog D, Scarpi E, Romanel A, Gurioli G, Jayaram A, Lolli C, Tandefelt DG, Schepisi G, Casadei C, Wingate A, Matteucci F, Paganelli G, Gonzalez-Billalabeitia E, Demichelis F, De Giorgi U, Attard G. Plasma tumour DNA as an early indicator of treatment response in metastatic castration-resistant prostate cancer. Br J Cancer. 2020 Sep;123(6):982-987. doi: 10.1038/s41416-020-0969-5. Epub 2020 Jul 16. |
| 32149736 | Background | Wu A, Cremaschi P, Wetterskog D, Conteduca V, Franceschini GM, Kleftogiannis D, Jayaram A, Sandhu S, Wong SQ, Benelli M, Salvi S, Gurioli G, Feber A, Pereira MB, Wingate AM, Gonzalez-Billalebeitia E, De Giorgi U, Demichelis F, Lise S, Attard G. Genome-wide plasma DNA methylation features of metastatic prostate cancer. J Clin Invest. 2020 Apr 1;130(4):1991-2000. doi: 10.1172/JCI130887. |
| 32091413 | Background | Beltran H, Romanel A, Conteduca V, Casiraghi N, Sigouros M, Franceschini GM, Orlando F, Fedrizzi T, Ku SY, Dann E, Alonso A, Mosquera JM, Sboner A, Xiang J, Elemento O, Nanus DM, Tagawa ST, Benelli M, Demichelis F. Circulating tumor DNA profile recognizes transformation to castration-resistant neuroendocrine prostate cancer. J Clin Invest. 2020 Apr 1;130(4):1653-1668. doi: 10.1172/JCI131041. |
| 31524989 | Background | Prandi D, Demichelis F. Ploidy- and Purity-Adjusted Allele-Specific DNA Analysis Using CLONETv2. Curr Protoc Bioinformatics. 2019 Sep;67(1):e81. doi: 10.1002/cpbi.81. |
| 30108686 | Background | Vagner T, Spinelli C, Minciacchi VR, Balaj L, Zandian M, Conley A, Zijlstra A, Freeman MR, Demichelis F, De S, Posadas EM, Tanaka H, Di Vizio D. Large extracellular vesicles carry most of the tumour DNA circulating in prostate cancer patient plasma. J Extracell Vesicles. 2018 Aug 7;7(1):1505403. doi: 10.1080/20013078.2018.1505403. eCollection 2018. |
| 26537258 | Background | Romanel A, Gasi Tandefelt D, Conteduca V, Jayaram A, Casiraghi N, Wetterskog D, Salvi S, Amadori D, Zafeiriou Z, Rescigno P, Bianchini D, Gurioli G, Casadio V, Carreira S, Goodall J, Wingate A, Ferraldeschi R, Tunariu N, Flohr P, De Giorgi U, de Bono JS, Demichelis F, Attard G. Plasma AR and abiraterone-resistant prostate cancer. Sci Transl Med. 2015 Nov 4;7(312):312re10. doi: 10.1126/scitranslmed.aac9511. |
| 25232177 | Background | Carreira S, Romanel A, Goodall J, Grist E, Ferraldeschi R, Miranda S, Prandi D, Lorente D, Frenel JS, Pezaro C, Omlin A, Rodrigues DN, Flohr P, Tunariu N, S de Bono J, Demichelis F, Attard G. Tumor clone dynamics in lethal prostate cancer. Sci Transl Med. 2014 Sep 17;6(254):254ra125. doi: 10.1126/scitranslmed.3009448. |
| 25160065 | Background | Prandi D, Baca SC, Romanel A, Barbieri CE, Mosquera JM, Fontugne J, Beltran H, Sboner A, Garraway LA, Rubin MA, Demichelis F. Unraveling the clonal hierarchy of somatic genomic aberrations. Genome Biol. 2014 Aug 26;15(8):439. doi: 10.1186/s13059-014-0439-6. |
| 38197680 | Result | Franceschini GM, Quaini O, Mizuno K, Orlando F, Ciani Y, Ku SY, Sigouros M, Rothmann E, Alonso A, Benelli M, Nardella C, Auh J, Freeman D, Hanratty B, Adil M, Elemento O, Tagawa ST, Feng FY, Caffo O, Buttigliero C, Basso U, Nelson PS, Corey E, Haffner MC, Attard G, Aparicio A, Demichelis F, Beltran H. Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation. Cancer Discov. 2024 Mar 1;14(3):424-445. doi: 10.1158/2159-8290.CD-23-0754. |
| D005832 |
| Genital Diseases, Male |
| D000091662 | Genital Diseases |
| D000091642 | Urogenital Diseases |
| D011469 | Prostatic Diseases |
| D052801 | Male Urogenital Diseases |
| D008968 | Molecular Conformation |
| D015394 | Molecular Structure |
| D001669 | Biochemical Phenomena |
| D055598 | Chemical Phenomena |
| D040342 | Genetic Structures |
| D055614 | Genetic Phenomena |