In Situ Clonal Heterogeneity in Prostatic Diagnostic Biopsies

Prostate Cancer Clinical Trial

Official title:

In Situ Clonal Heterogeneity in Prostatic Diagnostic Biopsies: Impact on Prostate Cancer Evolution and Clinical Outcome. A Retrospective, Proof of Concept Study

Clinical Trial Details — Status: Terminated

Administrative data

• NCT number: NCT04873427
• Other study ID #: CLM_RAD_001
• Status: Terminated
• Start date: April 15, 2021
• Est. completion date: January 15, 2023

Study information

• Verified date: February 2023
• Source: Clinica Luganese Moncucco
• Contact: n/a
• Is FDA regulated: No
• Study type: Observational

Clinical Trial Summary

This is a retrospective, proof of concept study, which aims at reconstructing the cellular heterogeneity of the tumor in multi-needle diagnostic prostate biopsy as well as any biopsy containing potentially pre-malignant tissue, to study its implications in the clinical history of the disease. For each patient, 2 or more samples will be prepared starting from the FFPE diagnostic material. The biopsy used for assigning the Gleason score will be sequenced, together with two or more of the local peri-proximal biopsies with a higher level of differentiation. Samples will undergo Whole Exome Sequencing with an average coverage of 300x at the Wellcome Sanger Institute (WSI, Hinxton, UK). Sequencing data will be analysed for single nucleotide variants, copy number variants and structural variants by using state-of-the-art data analysis pipeline at WSI. 1. Reconstruction of local PCa heterogeneity in multi-needle diagnostic biopsy with different Gleason scores (6-10) using high-coverage whole exome sequencing (WES) and DP-based clonal analysis; 2. Characterization of the relationships between pathological differentiation (Gleason score) and genomics-measured heterogeneity and malignancy features; 3. Assessment of clinical implications of clonal heterogeneity. The study will include an average of 150 prostatic diagnostic biopsies from a cohort of 20 early metastatic PC patients and 20 non-relapsing/non-metastatic patients with indolent malignant disease.

Description:

Prostate cancer (PCa) is the leading malignancy of the male population. In current clinical practice, diagnostic confirmation of PCa is based on image-guided multi-needle biopsy, in order to capture the intrinsic biological heterogeneity of tumors and to provide a more accurate prediction of clinical outcomes. However, current morphology-based approaches (Gleason score) may not completely describe the complexity of a malignant gland. Not enough is currently known on the impact of genomic heterogeneity in a poorly-differentiated prostate, especially with regards to the development of an indolent versus metastatic prostate malignancy This is a retrospective, proof of concept study, which aims at reconstructing the cellular heterogeneity of the tumor in multi-needle diagnostic prostate biopsy as well as any biopsy containing potentially pre-malignant tissue, to study its implications in the clinical history of the disease. For each patient, 2 or more samples will be prepared starting from the FFPE diagnostic material. The biopsy used for assigning the Gleason score will be sequenced, together with two or more of the local peri-proximal biopsies with a higher level of differentiation. Samples will undergo Whole Exome Sequencing with an average coverage of 300x at the Wellcome Sanger Institute (WSI, Hinxton, UK). Sequencing data will be analysed for single nucleotide variants, copy number variants and structural variants by using state-of-the-art data analysis pipeline at WSI. 1. Reconstruction of local PCa heterogeneity in multi-needle diagnostic biopsy with different Gleason scores (6-10) using high-coverage whole exome sequencing (WES) and DP-based clonal analysis; 2. Characterization of the relationships between pathological differentiation (Gleason score) and genomics-measured heterogeneity and malignancy features; 3. Assessment of clinical implications of clonal heterogeneity. The study will include an average of 150 prostatic diagnostic biopsies from a cohort of 20 early metastatic PC patients and 20 non-relapsing/non-metastatic patients with indolent malignant disease. Descriptive statistics will be carried out and a Mann-Whitney test will be applied on a synthetic parameter for each patient biopsy heterogeneity result, grouped by indolent vs aggressive disease cohort. The null hypotheses (no difference between the two cohort in heterogeneity) will be rejected if p < 0.05. The proposed project will evaluate the impact of diagnostic intra-prostatic cell heterogeneity on the clinical course of PCa. The potential prognostic value of local disease clonality could indeed impact the clinical practice: patient with Gleason <7 and lower level of clonal heterogeneity may be moved from an active disease treatment to an active surveillance (AS) approach, avoiding overtreatment for the subjects. Conversely, patients with a similar Gleason score but a more heterogenous malignant population may be required to undergo more aggressive procedures.

Recruitment information / eligibility

• Status: Terminated
• Enrollment: 40
• Est. completion date: January 15, 2023
• Est. primary completion date: January 15, 2023
• Accepts healthy volunteers: No
• Gender: Male
• Age group: N/A and older

Eligibility

The inclusion criteria for the subjects in the indolent cohort will be:

• a local disease with Gleason = 7 (3+4, i.e. more differentiated tissue is found in diagnostic biopsies, better overall prognosis)
• no metastasis whatsoever during the follow-up;

The inclusion criteria in the early-metastatic aggressive cohort will be:

• an advanced prostatic neoplasia with Gleason score = 7 (4+3, i.e. less differentiated tissue is found in diagnostic biopsies, worse overall prognosis)
• multiple synchronous or metachronous metastasis.

Exclusion Criteria:

• insufficient material on the tissue biopsy to be left in archives for further evaluations/analyses;
• insufficient amount of tumor cells at baseline;

Related Conditions & MeSH terms

• Disease Susceptibility
• Genetic Predisposition
• Genetic Predisposition to Disease
• Prostate Cancer
• Prostatic Neoplasms

Intervention

Genetic:
• clonal heterogeneity evaluation
Reconstruction of local PCa heterogeneity in multi-needle diagnostic biopsy with different Gleason scores (6-10) using high-coverage whole exome sequencing (WES) and DP-based clonal analysis

Locations

Country	Name	City	State
Switzerland	Alessandra Franzetti Pellanda	Lugano	Ticino

Sponsors (1)

Lead Sponsor	Collaborator
Clinica Luganese Moncucco

Country where clinical trial is conducted

Switzerland, 

References & Publications (23)

Altmann A, Weber P, Bader D, Preuss M, Binder EB, Muller-Myhsok B. A beginners guide to SNP calling from high-throughput DNA-sequencing data. Hum Genet. 2012 Oct;131(10):1541-54. doi: 10.1007/s00439-012-1213-z. Epub 2012 Aug 11. — View Citation

Beltran H, Prandi D, Mosquera JM, Benelli M, Puca L, Cyrta J, Marotz C, Giannopoulou E, Chakravarthi BV, Varambally S, Tomlins SA, Nanus DM, Tagawa ST, Van Allen EM, Elemento O, Sboner A, Garraway LA, Rubin MA, Demichelis F. Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer. Nat Med. 2016 Mar;22(3):298-305. doi: 10.1038/nm.4045. Epub 2016 Feb 8. — View Citation

Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014 Aug 1;30(15):2114-20. doi: 10.1093/bioinformatics/btu170. Epub 2014 Apr 1. — View Citation

Bolli N, Avet-Loiseau H, Wedge DC, Van Loo P, Alexandrov LB, Martincorena I, Dawson KJ, Iorio F, Nik-Zainal S, Bignell GR, Hinton JW, Li Y, Tubio JM, McLaren S, O' Meara S, Butler AP, Teague JW, Mudie L, Anderson E, Rashid N, Tai YT, Shammas MA, Sperling AS, Fulciniti M, Richardson PG, Parmigiani G, Magrangeas F, Minvielle S, Moreau P, Attal M, Facon T, Futreal PA, Anderson KC, Campbell PJ, Munshi NC. Heterogeneity of genomic evolution and mutational profiles in multiple myeloma. Nat Commun. 2014;5:2997. doi: 10.1038/ncomms3997. — View Citation

Chen X, Schulz-Trieglaff O, Shaw R, Barnes B, Schlesinger F, Kallberg M, Cox AJ, Kruglyak S, Saunders CT. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics. 2016 Apr 15;32(8):1220-2. doi: 10.1093/bioinformatics/btv710. Epub 2015 Dec 8. — View Citation

Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, Gabriel S, Meyerson M, Lander ES, Getz G. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013 Mar;31(3):213-9. doi: 10.1038/nbt.2514. Epub 2013 Feb 10. — View Citation

Epstein JI, Allsbrook WC Jr, Amin MB, Egevad LL; ISUP Grading Committee. The 2005 International Society of Urological Pathology (ISUP) Consensus Conference on Gleason Grading of Prostatic Carcinoma. Am J Surg Pathol. 2005 Sep;29(9):1228-42. doi: 10.1097/01.pas.0000173646.99337.b1. No abstract available. — View Citation

Epstein JI, Zelefsky MJ, Sjoberg DD, Nelson JB, Egevad L, Magi-Galluzzi C, Vickers AJ, Parwani AV, Reuter VE, Fine SW, Eastham JA, Wiklund P, Han M, Reddy CA, Ciezki JP, Nyberg T, Klein EA. A Contemporary Prostate Cancer Grading System: A Validated Alternative to the Gleason Score. Eur Urol. 2016 Mar;69(3):428-35. doi: 10.1016/j.eururo.2015.06.046. Epub 2015 Jul 10. — View Citation

Ferguson, T. S., 1973. A Bayesian analysis of some nonparametric problems.. Annals of Statistics, Volume 1, pp. 209-230.

Gandellini P, Casiraghi N, Rancati T, Benelli M, Doldi V, Romanel A, Colecchia M, Marenghi C, Valdagni R, Demichelis F, Zaffaroni N. Core Biopsies from Prostate Cancer Patients in Active Surveillance Protocols Harbor PTEN and MYC Alterations. Eur Urol Oncol. 2019 May;2(3):277-285. doi: 10.1016/j.euo.2018.08.010. Epub 2018 Sep 10. Erratum In: Eur Urol Oncol. 2021 Feb;4(1):129. — View Citation

Hamid AA, Gray KP, Shaw G, MacConaill LE, Evan C, Bernard B, Loda M, Corcoran NM, Van Allen EM, Choudhury AD, Sweeney CJ. Compound Genomic Alterations of TP53, PTEN, and RB1 Tumor Suppressors in Localized and Metastatic Prostate Cancer. Eur Urol. 2019 Jul;76(1):89-97. doi: 10.1016/j.eururo.2018.11.045. Epub 2018 Dec 12. — View Citation

Helpap B, Egevad L. Modified Gleason grading. An updated review. Histol Histopathol. 2009 May;24(5):661-6. doi: 10.14670/HH-24.661. — View Citation

Hofman MS, Emmett L. Tumour Heterogeneity and Resistance to Therapy in Prostate Cancer: A Fundamental Limitation of Prostate-specific Membrane Antigen Theranostics or a Key Strength? Eur Urol. 2019 Oct;76(4):479-481. doi: 10.1016/j.eururo.2019.07.030. Epub 2019 Jul 25. No abstract available. — View Citation

Hugosson J, Carlsson S. Overdetection in screening for prostate cancer. Curr Opin Urol. 2014 May;24(3):256-63. doi: 10.1097/MOU.0000000000000054. — View Citation

Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009 Jul 15;25(14):1754-60. doi: 10.1093/bioinformatics/btp324. Epub 2009 May 18. — View Citation

Maura F, Bolli N, Angelopoulos N, Dawson KJ, Leongamornlert D, Martincorena I, Mitchell TJ, Fullam A, Gonzalez S, Szalat R, Abascal F, Rodriguez-Martin B, Samur MK, Glodzik D, Roncador M, Fulciniti M, Tai YT, Minvielle S, Magrangeas F, Moreau P, Corradini P, Anderson KC, Tubio JMC, Wedge DC, Gerstung M, Avet-Loiseau H, Munshi N, Campbell PJ. Genomic landscape and chronological reconstruction of driver events in multiple myeloma. Nat Commun. 2019 Aug 23;10(1):3835. doi: 10.1038/s41467-019-11680-1. — View Citation

Middleton LW, Shen Z, Varma S, Pollack AS, Gong X, Zhu S, Zhu C, Foley JW, Vennam S, Sweeney RT, Tu K, Biscocho J, Eminaga O, Nolley R, Tibshirani R, Brooks JD, West RB, Pollack JR. Genomic analysis of benign prostatic hyperplasia implicates cellular re-landscaping in disease pathogenesis. JCI Insight. 2019 May 16;5(12):e129749. doi: 10.1172/jci.insight.129749. — View Citation

Nik-Zainal S, Alexandrov LB, Wedge DC, Van Loo P, Greenman CD, Raine K, Jones D, Hinton J, Marshall J, Stebbings LA, Menzies A, Martin S, Leung K, Chen L, Leroy C, Ramakrishna M, Rance R, Lau KW, Mudie LJ, Varela I, McBride DJ, Bignell GR, Cooke SL, Shlien A, Gamble J, Whitmore I, Maddison M, Tarpey PS, Davies HR, Papaemmanuil E, Stephens PJ, McLaren S, Butler AP, Teague JW, Jonsson G, Garber JE, Silver D, Miron P, Fatima A, Boyault S, Langerod A, Tutt A, Martens JW, Aparicio SA, Borg A, Salomon AV, Thomas G, Borresen-Dale AL, Richardson AL, Neuberger MS, Futreal PA, Campbell PJ, Stratton MR; Breast Cancer Working Group of the International Cancer Genome Consortium. Mutational processes molding the genomes of 21 breast cancers. Cell. 2012 May 25;149(5):979-93. doi: 10.1016/j.cell.2012.04.024. Epub 2012 May 17. — View Citation

Nik-Zainal S, Van Loo P, Wedge DC, Alexandrov LB, Greenman CD, Lau KW, Raine K, Jones D, Marshall J, Ramakrishna M, Shlien A, Cooke SL, Hinton J, Menzies A, Stebbings LA, Leroy C, Jia M, Rance R, Mudie LJ, Gamble SJ, Stephens PJ, McLaren S, Tarpey PS, Papaemmanuil E, Davies HR, Varela I, McBride DJ, Bignell GR, Leung K, Butler AP, Teague JW, Martin S, Jonsson G, Mariani O, Boyault S, Miron P, Fatima A, Langerod A, Aparicio SA, Tutt A, Sieuwerts AM, Borg A, Thomas G, Salomon AV, Richardson AL, Borresen-Dale AL, Futreal PA, Stratton MR, Campbell PJ; Breast Cancer Working Group of the International Cancer Genome Consortium. The life history of 21 breast cancers. Cell. 2012 May 25;149(5):994-1007. doi: 10.1016/j.cell.2012.04.023. Epub 2012 May 17. Erratum In: Cell. 2015 Aug 13;162(4):924. — View Citation

Pernar CH, Ebot EM, Wilson KM, Mucci LA. The Epidemiology of Prostate Cancer. Cold Spring Harb Perspect Med. 2018 Dec 3;8(12):a030361. doi: 10.1101/cshperspect.a030361. — View Citation

Pietzak EJ, Resnick MJ, Mucksavage P, Van Arsdalen K, Wein AJ, Malkowicz SB, Guzzo TJ. Multiple repeat prostate biopsies and the detection of clinically insignificant cancer in men with large prostates. Urology. 2014 Aug;84(2):380-5. doi: 10.1016/j.urology.2014.04.029. Epub 2014 Jun 12. — View Citation

Shen R, Seshan VE. FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing. Nucleic Acids Res. 2016 Sep 19;44(16):e131. doi: 10.1093/nar/gkw520. Epub 2016 Jun 7. — View Citation

Sved PD, Gomez P, Manoharan M, Kim SS, Soloway MS. Limitations of biopsy Gleason grade: implications for counseling patients with biopsy Gleason score 6 prostate cancer. J Urol. 2004 Jul;172(1):98-102. doi: 10.1097/01.ju.0000132135.18093.d6. — View Citation

* Note: There are 23 references in all — Click here to view all references

Outcome

Type	Measure	Description	Time frame	Safety issue
Primary	reconstruction of local PCa heterogeneity	Primary endpoint is the reconstruction of local PCa heterogeneity in multi-needle diagnostic biopsy with different Gleason scores (6-10) using high-coverage whole exome sequencing (WES) and DP-based clonal analysis	through study completion, an average of 2 years
Secondary	relationships between pathological differentiation (Gleason score) and genomics-measured heterogeneity	Secondary endpoints are characterization of the relationships between pathological differentiation (Gleason score) and genomics-measured heterogeneity and malignancy features; and assessment of clinical implications of clonal heterogeneity.	through study completion, an average of 2 years