Personalized High-Resolution Genetic Diagnostics of Prostate Adenocarcinoma Guided by Multiparametric Magnetic Resonance Imaging: Results of a Pilot Study
Abstract
1. Introduction
2. Results
2.1. DNA Quality and Quantitative Metrics
2.2. Patient Clinical Characteristics
2.2.1. Patient 1
2.2.2. Patient 2
2.2.3. Patient 3
2.2.4. Patient 4
2.3. TMPRSS2/ERG Fusion Evaluation
2.4. NGS Results
2.5. Clinical Follow-Up
3. Discussion
4. Materials and Methods
4.1. Material Acquisition
4.2. Fluorescence In Situ Hybridization
4.3. DNA Isolation
4.4. Next-Generation Sequencing
4.5. Sanger Sequencing
4.6. Statistical Analysis
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
List of Abbreviations
CGP | Comprehensive Genomic Profiling |
CNV | Copy Number Variation |
FISH | Fluorescence In Situ Hybridization |
FFPE | Formalin-Fixed Paraffin-Embedded |
HP | Histopathology |
HRD | Homologous Recombination Deficiency |
ICD-O | International Classification of Diseases for Oncology |
IHC | Immunohistochemistry |
LUTS | Lower Urinary Tract Symptoms |
MRI | Magnetic Resonance Imaging |
mCRPC | Metastatic Castration-Resistant Prostate Cancer |
NGS | Next-Generation Sequencing |
PARP | Poly(ADP-ribose) Polymerase |
PC | Prostate Cancer |
PI-RADS | Prostate Imaging Reporting and Data System |
PSA | Prostate-Specific Antigen |
PSAD | Prostate-Specific Antigen Density |
SNV | Single Nucleotide Variant |
SV | Structural Variant |
TMB | Tumor Mutational Burden |
TRUS | Transrectal Ultrasound |
US | Ultrasound |
VAF | Variant Allele Frequency |
References
- Didkowska, J.; Barańska, K.; Miklewska, M.J.; Wojciechowska, U. Cancer Incidence and Mortality in Poland in 2023. Nowotw. J. Oncol. 2024, 74, 75–93. [Google Scholar] [CrossRef]
- Owczarek, A.J. Drzewa klasyfikacyjne w medycynie. Ann. Acad. Med. Siles. 2019, 68, 449–456. [Google Scholar]
- Garzotto, M.; Beer, T.M.; Hudson, R.G.; Peters, L.; Hsieh, Y.-C.; Barrera, E.; Klein, T.; Mori, M. Improved Detection of Prostate Cancer Using Classification and Regression Tree Analysis. J. Clin. Oncol. 2005, 23, 4322–4329. [Google Scholar] [CrossRef] [PubMed]
- Cornud, F.; Brolis, L.; Delongchamps, N.B.; Portalez, D.; Malavaud, B.; Renard-Penna, R.; Mozer, P. TRUS-MRI Image Registration: A Paradigm Shift in the Diagnosis of Significant Prostate Cancer. Abdom. Imaging 2013, 38, 1447–1463. [Google Scholar] [CrossRef]
- Logan, J.K.; Rais-Bahrami, S.; Turkbey, B.; Gomella, A.; Amalou, H.; Choyke, P.L.; Wood, B.J.; Pinto, P.A. Current Status of Magnetic Resonance Imaging (MRI) and Ultrasonography Fusion Software Platforms for Guidance of Prostate Biopsies. BJU Int. 2014, 114, 641–652. [Google Scholar] [CrossRef]
- Avolio, P.P.; Lughezzani, G.; Anidjar, M.; Hassan, T.; Rompré-Brodeur, A.; Buffi, N.M.; Lazzeri, M.; Sanchez-Salas, R. The Diagnostic Accuracy of Micro-Ultrasound for Prostate Cancer Diagnosis: A Review. World J. Urol. 2023, 41, 3267–3276. [Google Scholar] [CrossRef]
- Masarwa, I.; Bahouth, Z.; Shefler, A.; Bejar, J.; Shprits, S.; Avitan, O.; Halachmi, S.; Nativ, O. The Value of the SmartBxTM System in Improving the Detection of Prostate Cancer in Patients Undergoing Transrectal Ultrasound-Guided Biopsy. JMCM 2020, 3, 33–36. [Google Scholar] [CrossRef]
- Mandel, P.; Wenzel, M.; Hoeh, B.; Welte, M.N.; Preisser, F.; Inam, T.; Wittler, C.; Humke, C.; Köllermann, J.; Wild, P.; et al. Immunohistochemistry for Prostate Biopsy—Impact on Histological Prostate Cancer Diagnoses and Clinical Decision Making. Curr. Oncol. 2021, 28, 2123–2133. [Google Scholar] [CrossRef]
- Murciano-Goroff, Y.R.; Drilon, A.; Stadler, Z.K. The NCI-MATCH: A National, Collaborative Precision Oncology Trial for Diverse Tumor Histologies. Cancer Cell 2021, 39, 22–24. [Google Scholar] [CrossRef]
- Meric-Bernstam, F.; Ford, J.M.; O’Dwyer, P.J.; Shapiro, G.I.; McShane, L.M.; Freidlin, B.; O’Cearbhaill, R.E.; George, S.; Glade-Bender, J.; Lyman, G.H.; et al. National Cancer Institute Combination Therapy Platform Trial with Molecular Analysis for Therapy Choice (ComboMATCH). Clin. Cancer Res. 2023, 29, 1412–1422. [Google Scholar] [CrossRef]
- Coombs, N.J.; Gough, A.C.; Primrose, J.N. Optimisation of DNA and RNA Extraction from Archival Formalin-Fixed Tissue. Nucleic Acids Res. 1999, 27, e12. [Google Scholar] [CrossRef]
- Schäfer, S.C.; Pfnür, M.; Yerly, S.; Fandel, T.M.; Jichlinski, P.; Lehr, H.-A. Cryopreservation of Prostate Cancer Tissue during Routine Processing of Fresh Unfixed Prostatectomy Specimen: Demonstration and Validation of a New Technique. Prostate 2009, 69, 191–197. [Google Scholar] [CrossRef] [PubMed]
- Hedegaard, J.; Thorsen, K.; Lund, M.K.; Hein, A.-M.K.; Hamilton-Dutoit, S.J.; Vang, S.; Nordentoft, I.; Birkenkamp-Demtröder, K.; Kruhøffer, M.; Hager, H.; et al. Next-Generation Sequencing of RNA and DNA Isolated from Paired Fresh-Frozen and Formalin-Fixed Paraffin-Embedded Samples of Human Cancer and Normal Tissue. PLoS ONE 2014, 9, e98187. [Google Scholar] [CrossRef]
- Schweiger, M.R.; Kerick, M.; Timmermann, B.; Albrecht, M.W.; Borodina, T.; Parkhomchuk, D.; Zatloukal, K.; Lehrach, H. Genome-Wide Massively Parallel Sequencing of Formaldehyde Fixed-Paraffin Embedded (FFPE) Tumor Tissues for Copy-Number- and Mutation-Analysis. PLoS ONE 2009, 4, e5548. [Google Scholar] [CrossRef]
- Spencer, D.H.; Sehn, J.K.; Abel, H.J.; Watson, M.A.; Pfeifer, J.D.; Duncavage, E.J. Comparison of Clinical Targeted Next-Generation Sequence Data from Formalin-Fixed and Fresh-Frozen Tissue Specimens. J. Mol. Diagn. 2013, 15, 623–633. [Google Scholar] [CrossRef]
- Adiconis, X.; Borges-Rivera, D.; Satija, R.; DeLuca, D.S.; Busby, M.A.; Berlin, A.M.; Sivachenko, A.; Thompson, D.A.; Wysoker, A.; Fennell, T.; et al. Comparative Analysis of RNA Sequencing Methods for Degraded or Low-Input Samples. Nat. Methods 2013, 10, 623–629. [Google Scholar] [CrossRef]
- Morlan, J.D.; Qu, K.; Sinicropi, D.V. Selective Depletion of rRNA Enables Whole Transcriptome Profiling of Archival Fixed Tissue. PLoS ONE 2012, 7, e42882. [Google Scholar] [CrossRef]
- Norton, N.; Sun, Z.; Asmann, Y.W.; Serie, D.J.; Necela, B.M.; Bhagwate, A.; Jen, J.; Eckloff, B.W.; Kalari, K.R.; Thompson, K.J.; et al. Gene Expression, Single Nucleotide Variant and Fusion Transcript Discovery in Archival Material from Breast Tumors. PLoS ONE 2013, 8, e81925. [Google Scholar] [CrossRef]
- Högnäs, G.; Kivinummi, K.; Kallio, H.M.L.; Hieta, R.; Ruusuvuori, P.; Koskenalho, A.; Kesseli, J.; Tammela, T.L.J.; Riikonen, J.; Ilvesaro, J.; et al. Feasibility of Prostate PAXgene Fixation for Molecular Research and Diagnostic Surgical Pathology: Comparison of Matched Fresh Frozen, FFPE, and PFPE Tissues. Am. J. Surg. Pathol. 2018, 42, 103–115. [Google Scholar] [CrossRef]
- Menon, R.; Deng, M.; Boehm, D.; Braun, M.; Fend, F.; Boehm, D.; Biskup, S.; Perner, S. Exome Enrichment and SOLiD Sequencing of Formalin Fixed Paraffin Embedded (FFPE) Prostate Cancer Tissue. Int. J. Mol. Sci. 2012, 13, 8933–8942. [Google Scholar] [CrossRef]
- de Schaetzen van Brienen, L.; Larmuseau, M.; Van der Eecken, K.; De Ryck, F.; Robbe, P.; Schuh, A.; Fostier, J.; Ost, P.; Marchal, K. Comparative Analysis of Somatic Variant Calling on Matched FF and FFPE WGS Samples. BMC Med. Genom. 2020, 13, 94. [Google Scholar] [CrossRef] [PubMed]
- Jennings, L.J.; Arcila, M.E.; Corless, C.; Kamel-Reid, S.; Lubin, I.M.; Pfeifer, J.; Temple-Smolkin, R.L.; Voelkerding, K.V.; Nikiforova, M.N. Guidelines for Validation of Next-Generation Sequencing-Based Oncology Panels: A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists. J. Mol. Diagn. 2017, 19, 341–365. [Google Scholar] [CrossRef]
- Yao, Y.; Wang, H.; Li, B.; Tang, Y. Evaluation of the TMPRSS2:ERG Fusion for the Detection of Prostate Cancer: A Systematic Review and Meta-Analysis. Tumour Biol. 2014, 35, 2157–2166. [Google Scholar] [CrossRef] [PubMed]
- Sanguedolce, F.; Cormio, A.; Brunelli, M.; D’Amuri, A.; Carrieri, G.; Bufo, P.; Cormio, L. Urine TMPRSS2: ERG Fusion Transcript as a Biomarker for Prostate Cancer: Literature Review. Clin. Genitourin. Cancer 2016, 14, 117–121. [Google Scholar] [CrossRef] [PubMed]
- Delongchamps, N.B.; Peltier, A.; Potiron, E.; Bladou, F.; Anract, J.; Diamand, R.; Robert, G.; Messas, A.; Van Velthoven, R. Targeted Microwave Ablation of Localised Prostate Cancer: Initial Results of VIOLETTE Trial. BJUI Compass 2024, 5, 1307–1313. [Google Scholar] [CrossRef]
- Sondka, Z.; Bamford, S.; Cole, C.G.; Ward, S.A.; Dunham, I.; Forbes, S.A. The COSMIC Cancer Gene Census: Describing Genetic Dysfunction across All Human Cancers. Nat. Rev. Cancer 2018, 18, 696–705. [Google Scholar] [CrossRef]
- Jiang, H.; Lei, R.; Ding, S.-W.; Zhu, S. Skewer: A Fast and Accurate Adapter Trimmer for next-Generation Sequencing Paired-End Reads. BMC Bioinform. 2014, 15, 182. [Google Scholar] [CrossRef]
- Krzywinski, M.; Schein, J.; Birol, I.; Connors, J.; Gascoyne, R.; Horsman, D.; Jones, S.J.; Marra, M.A. Circos: An Information Aesthetic for Comparative Genomics. Genome Res. 2009, 19, 1639–1645. [Google Scholar] [CrossRef]
n | Sample | Site | Concentration (ng/μL) | Absorbance Ratio (A260/A280) |
---|---|---|---|---|
1 | 20563 | MRI-guided target | 25.9 | 1.92 |
2 | 20564 | MRI-guided target | 25.4 | 1.89 |
3 | 20565 | systematic | 12.9 | 2.18 |
4 | 21116 | MRI-guided target | 33.3 | 1.79 |
5 | 21118 | systematic | 49.6 | 1.9 |
6 | 21119 | MRI-guided target | 46.1 | 1.92 |
7 | 21120 | MRI-guided target | 31.2 | 1.71 |
8 | 21121 | MRI-guided target | 28.5 | 1.67 |
9 | 21122 | MRI-guided target | 43.8 | 1.77 |
10 | 21123 | MRI-guided target | 26.1 | 1.78 |
11 | 21923 | MRI-guided target | 10.5 | 1.81 |
12 | 21924 | MRI-guided target | 8.1 | 1.67 |
13 | 22605 | MRI-guided target | 26.4 | 2.02 |
14 | 22606 | systematic | 18.5 | 2.09 |
15 | 22607 | MRI-guided target | 26.4 | 2 |
16 | 22608 | systematic | 44.5 | 1.9 |
17 | 23212 | MRI-guided target | 22.5 | 1.79 |
18 | 22882 | MRI-guided target | 6.2 | 1.78 |
19 | 22883 | MRI-guided target | 25.4 | 2.11 |
20 | 23213 | systematic | 10.4 | 1.92 |
21 | 22884 | systematic | 10.4 | 1.93 |
22 | 23214 | MRI-guided target | 16.1 | 1.69 |
23 | 22890 | MRI-guided target | 29.1 | 1.88 |
24 | 22891 | MRI-guided target | 34.1 | 1.84 |
25 | 22892 | MRI-guided target | 44.2 | 1.83 |
26 | 22893 | systematic | 57.2 | 1.85 |
27 | 23215 | MRI-guided target | 19.2 | 2.1 |
28 | 23216 | MRI-guided target | 12.3 | 1.83 |
29 | 23217 | MRI-guided target | 5.8 | 1.59 |
30 | 24097 | MRI-guided target | 18.19 | 1.91 |
31 | 24098 | MRI-guided target | 25.24 | 1.84 |
32 | 23972 | systematic | 16.76 | 2.08 |
33 | 24099 | MRI-guided target | 14.93 | 1.97 |
34 | 24100 | MRI-guided target | 21.24 | 1.89 |
35 | 23974 | systematic | 46.88 | 1.95 |
n | Sample | PI-RADS v2 | Concentration (ng/μL) | Absorbance Ratio (A260/A280) |
---|---|---|---|---|
1 | 25484 | 4 | 12.8 | 1.55 |
2 | 25485 | 4 | 21.7 | 1.65 |
3 | 25486 | 3 | 17.2 | 1.67 |
4 | 25487 | 4 | 35.7 | 1.67 |
Case | PI-RADS v2 | FISH Result | % of Cells with Fusion | HP |
---|---|---|---|---|
1 | 4 | nuc ish (TMPRSS2,TMPRSS2,ERG)x2[50] | - | benign prostatic hyperplasia, focal glandular atrophy, and chronic inflammation |
2 | 4 | nuc ish (TMPRSS2,TMPRSS2,ERG)x2[50] | - | mild glandular atrophy, focal chronic inflammatory infiltration, and hyperplastic changes |
3 | 3 | nuc ish (TMPRSS2,ERG)x2(TMPRSS2/TMPRSS2 sep ERG)x1[32/50] | 64% | prostatic acinar adenocarcinoma |
4 | 4 | nuc ish (TMPRSS2,ERG)x2(TMPRSS2/TMPRSS2 sep ERG)x1[42/50] | 84% | prostatic acinar adenocarcinoma |
n | Sample | Aligned Reads (on Target) | Proportion of Aligned Reads (in %) | Duplicate Rate (in %) | Average Coverage | Number of Small Variants |
---|---|---|---|---|---|---|
1 | 22890 | 34.245 | 36.12 | 16.81 | 845.58 | 2636 |
2 | 23215 | 36.773 | 38.62 | 16.8 | 909.18 | 2609 |
3 | 24097 | 33.628 | 34.77 | 15.24 | 832.98 | 2577 |
4 | 24098 | 34.148 | 35.33 | 15.18 | 846.9 | 2585 |
5 | 24099 | 32.563 | 33.81 | 15.58 | 806.42 | 2546 |
6 | 24100 | 32.599 | 34.84 | 17.78 | 810.53 | 2535 |
n | Sample | Aligned Reads (on Target) | Proportion of Aligned Reads (in %) | Duplicate Rate (in %) | Average Coverage | Number of Small Variants |
---|---|---|---|---|---|---|
1 | 25486 | 2.723 | 6.08 | 49.63 | 60.68 | 2939 |
2 | 25487 | 3.175 | 5.88 | 49.11 | 72.6 | 2933 |
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2025 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Wilkosz, J.; Sobieraj, D.W.; Kałużewski, T.; Kaczmarek, J.; Szwalski, J.; Bednarek, M.; Morel, A.; Kasprzyk, Ż.; Kępczyński, Ł.; Sałamunia, J.; et al. Personalized High-Resolution Genetic Diagnostics of Prostate Adenocarcinoma Guided by Multiparametric Magnetic Resonance Imaging: Results of a Pilot Study. Int. J. Mol. Sci. 2025, 26, 5648. https://doi.org/10.3390/ijms26125648
Wilkosz J, Sobieraj DW, Kałużewski T, Kaczmarek J, Szwalski J, Bednarek M, Morel A, Kasprzyk Ż, Kępczyński Ł, Sałamunia J, et al. Personalized High-Resolution Genetic Diagnostics of Prostate Adenocarcinoma Guided by Multiparametric Magnetic Resonance Imaging: Results of a Pilot Study. International Journal of Molecular Sciences. 2025; 26(12):5648. https://doi.org/10.3390/ijms26125648
Chicago/Turabian StyleWilkosz, Jacek, Dariusz Wojciech Sobieraj, Tadeusz Kałużewski, Jakub Kaczmarek, Jarosław Szwalski, Michał Bednarek, Agnieszka Morel, Żaneta Kasprzyk, Łukasz Kępczyński, Jordan Sałamunia, and et al. 2025. "Personalized High-Resolution Genetic Diagnostics of Prostate Adenocarcinoma Guided by Multiparametric Magnetic Resonance Imaging: Results of a Pilot Study" International Journal of Molecular Sciences 26, no. 12: 5648. https://doi.org/10.3390/ijms26125648
APA StyleWilkosz, J., Sobieraj, D. W., Kałużewski, T., Kaczmarek, J., Szwalski, J., Bednarek, M., Morel, A., Kasprzyk, Ż., Kępczyński, Ł., Sałamunia, J., Gach, A., & Kałużewski, B. (2025). Personalized High-Resolution Genetic Diagnostics of Prostate Adenocarcinoma Guided by Multiparametric Magnetic Resonance Imaging: Results of a Pilot Study. International Journal of Molecular Sciences, 26(12), 5648. https://doi.org/10.3390/ijms26125648