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Axelsson TA, Sydén F, Eisfeldt J, Eriksson Y, Lundberg GG, Jaremko G, Gyllensten OC, Tham E, Brehmer M. Diagnostic and prognostic genomic aberrations in upper tract urothelial carcinoma can be identified in focal barbotage samples. BJU Int 2025; 135:792-801. [PMID: 39654327 PMCID: PMC11975159 DOI: 10.1111/bju.16620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2025]
Abstract
OBJECTIVES To investigate whether genetic analysis of focal barbotage samples obtained at ureterorenoscopy (URS) is possible, and to identify genetic aberrations that might add prognostic information. METHODS This prospective study included barbotage samples from 42 patients with upper urinary tract urothelial carcinoma (UTUC) confirmed at URS. At URS, focal barbotage specimens were collected for cytology and for gene sequencing. Tumour grades were determined from cytology and/or biopsy, or from radical nephroureterectomy samples. Next-generation sequencing using a 385-gene panel was performed and single nucleotide variants (SNVs), deletions/insertions (indels) and copy number aberrations (CNAs) were identified. Manual filtering of the SNVs/indels was performed to identify possible pathogenic mutations. RESULTS Of the 42 samples, two failed quality control, therefore, 40 focal barbotage samples were sequenced. We identified known and suspected pathogenic mutations and other genomic aberrations in 36 samples. The most common variants were in TERT (78%), FGFR3 (50%), KMT2D (42%), KDM6A (42%), ARID1A (39%), TP53 (19%) and deletion of 9q (50%). Known pathogenic mutations in FGFR3 were common in grade 1 and 2 tumours, but not present in any grade 3 tumour. No patients with an FGFR3 mutation died during follow-up. TP53 variants or deletions, as well as amplifications of MDM2, were only present in high-grade (HG) tumours or low-grade (LG) tumours in patients who had metastasis/died from urinary tract carcinoma. CNAs were detected in 36/40 barbotage samples, 91% of the HG samples and 69% of the LG samples, including those from all five patients with LG tumours with metastasis or who died from urinary tract cancer. CONCLUSION Focal barbotage samples enable identification of gene mutations and other genetic aberrations that may add important prognostic information to histopathology and cytology. Refined prognostication of UTUC patients already at diagnosis can guide treatment decisions and follow-up programmes.
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Affiliation(s)
| | - Filip Sydén
- Department of UrologyStockholm South General HospitalStockholmSweden
| | - Jesper Eisfeldt
- Department of Clinical Genetics and GenomicsKarolinska University HospitalStockholmSweden
- Department of Molecular Medicine and SurgeryKarolinska InstitutetStockholmSweden
| | | | | | - Georg Jaremko
- Department of Pathology and Cancer DiagnosticsKarolinska University HospitalStockholmSweden
| | | | - Emma Tham
- Department of Clinical Genetics and GenomicsKarolinska University HospitalStockholmSweden
- Department of Molecular Medicine and SurgeryKarolinska InstitutetStockholmSweden
| | - Marianne Brehmer
- Department of UrologyStockholm South General HospitalStockholmSweden
- Department of Clinical Science and EducationKarolinska InstitutetStockholmSweden
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Jaime-Casas S, Tripathi A, Pal SK, Yip W. Clinical Implications of the Molecular and Genomic Landscape of Upper Tract Urothelial Carcinoma. Curr Urol Rep 2024; 26:11. [PMID: 39379745 PMCID: PMC11461588 DOI: 10.1007/s11934-024-01245-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2024] [Indexed: 10/10/2024]
Abstract
PURPOSE OF REVIEW Upper tract urothelial carcinoma (UTUC) is an aggressive entity with treatment strategies mirroring bladder cancer. Genomic and molecular profiling allows for a better characterization of this disease and allows for patient-tailored approaches. We aim to describe the genomic and molecular implications of this disease. RECENT FINDINGS Technological advances have the potential for early diagnosis and precise molecular analysis in patients with UTUC. Genomic profile clustering, specific mRNA signatures, and pathway-specific protein abundance tools have oncologic and clinical implications. We describe their utility in the context of this disease. In the era of precision medicine, designing clinical trials that explore the diagnostic and prognostic implications of biomolecular signatures in the context of UTUC is of utmost importance. Promising advances in this arena provide tools for physicians to avoid overtreatment in this patient population.
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Affiliation(s)
- Salvador Jaime-Casas
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Abhishek Tripathi
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Sumanta K Pal
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Wesley Yip
- Division of Urology and Urologic Oncology, City of Hope Comprehensive Cancer Center, 1500 East Duarte Road, Duarte, CA, 91010, USA.
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Fukumoto K, Kanatani S, Jaremko G, West Z, Li Y, Takamatsu K, Al Rayyes I, Mikami S, Niwa N, Axelsson TA, Tanaka N, Oya M, Miyakawa A, Brehmer M, Uhlén P. Three-dimensional imaging of upper tract urothelial carcinoma improves diagnostic yield and accuracy. JCI Insight 2024; 9:e175751. [PMID: 39133649 PMCID: PMC11383588 DOI: 10.1172/jci.insight.175751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024] Open
Abstract
Upper tract urothelial carcinoma (UTUC) is a rare form of urothelial cancer with a high incidence of recurrence and a low survival rate. Almost two-thirds of UTUCs are invasive at the time of diagnosis; therefore, improving diagnostic methods is key to increasing survival rates. Histopathological analysis of UTUC is essential for diagnosis and typically requires endoscopy biopsy, tissue sectioning, and labeling. However, endoscopy biopsies are minute, and it is challenging to cut into thin sections for conventional histopathology; this complicates diagnosis. Here, we used volumetric 3-dimensional (3D) imaging to explore the inner landscape of clinical UTUC biopsies, without sectioning, revealing that 3D analysis of phosphorylated ribosomal protein S6 (pS6) could predict tumor grade and prognosis with improved accuracy. By visualizing the tumor vasculature, we discovered that pS6+ cells were localized near blood vessels at significantly higher levels in high-grade tumors than in low-grade tumors. Furthermore, the clustering of pS6+ cells was associated with shorter relapse-free survival. Our results demonstrate that 3D volume imaging of the structural niches of pS6 cells deep inside the UTUC samples improved diagnostic yield, grading, and prognosis prediction.
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Affiliation(s)
- Keishiro Fukumoto
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Department of Urology, Keio University School of Medicine, Tokyo, Japan
| | - Shigeaki Kanatani
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Georg Jaremko
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Zoe West
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Yue Li
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Kimiharu Takamatsu
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ibrahim Al Rayyes
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Shuji Mikami
- Department of Diagnostic Pathology, National Hospital Organization Saitama Hospital, Saitama, Japan
| | - Naoya Niwa
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Nobuyuki Tanaka
- Department of Urology, Keio University School of Medicine, Tokyo, Japan
| | - Mototsugu Oya
- Department of Urology, Keio University School of Medicine, Tokyo, Japan
| | - Ayako Miyakawa
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Division of Urology, Department of Molecular Medicine and Surgery, Karolinska University Hospital, Stockholm, Sweden
| | - Marianne Brehmer
- Department of Urology and Department of Clinical Science and Education, Stockholm South General Hospital, Sweden
| | - Per Uhlén
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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Brehmer M, Osther P. Consultation on UTUC Stockholm 2022. World J Urol 2023; 41:3393-3394. [PMID: 37989789 DOI: 10.1007/s00345-023-04693-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Affiliation(s)
- Marianne Brehmer
- Department of Urology, South General Hospital, Department of Clinical Science and Education, Södersjukhuset, Department of Cinical Sciences, Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden.
| | - Palle Osther
- Department of Urology, Urological Research Center, Lillebælt Hospital, University Hospital of Southern Denmark, Vejle, Denmark
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Mu N, Jylhä C, Axelsson T, Sydén F, Brehmer M, Tham E. Patient-specific targeted analysis of circulating tumour DNA in plasma is feasible and may be a potential biomarker in UTUC. World J Urol 2023; 41:3421-3427. [PMID: 37721600 PMCID: PMC10693512 DOI: 10.1007/s00345-023-04583-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 08/15/2023] [Indexed: 09/19/2023] Open
Abstract
PURPOSE The prognosis of upper urinary tract urothelial carcinoma (UTUC) is associated with tumour grade (G) and stage. Despite preoperative risk stratification and radical treatment, recurrence and progression are common. Thus, prognostic and monitoring biomarkers are needed. This feasibility study aimed to investigate if targeted analyses on circulating tumour DNA (ctDNA) in plasma could identify tumour-specific gene variants, and thus have potential for further evaluation as a biomarker in UTUC. METHODS Nine UTUC patients with genetically characterised tumours were included in this prospective pilot study. Two tumour-specific variants were chosen for targeted analyses with multiplex droplet digital PCR on cell-free DNA (cfDNA) from plasma at diagnosis or from recurrence. RESULTS Of six patients with diagnostic plasma samples, ctDNA was detected in four with G2 or G3 tumours and tumours > 300m2 in size. Three of these patients progressed in their disease and the fourth had the largest G3 tumour at sampling. In contrast, the two patients with undetectable ctDNA in diagnostic plasma had a G1 tumour and G3 carcinoma in situ (CIS), respectively. The patient with G3 CIS had detectable ctDNA later during follow-up and progressed thereafter with aggressive intravesical recurrence and CT-scan-verified CIS progression in the upper urinary tract. In three patients with small recurrent G1 or G2 tumours, none had detectable ctDNA in plasma and all were progression free. CONCLUSION Our early findings demonstrate that ctDNA in plasma can be detected by targeted analysis in patients with UTUC. However, further studies are needed to determine its role as a potential biomarker.
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Affiliation(s)
- Ninni Mu
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Cecilia Jylhä
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Tomas Axelsson
- Division of Urology, Danderyd Hospital, Stockholm, Sweden
| | - Filip Sydén
- Department of Urology, Stockholm South General Hospital, Stockholm, Sweden
| | - Marianne Brehmer
- Department of Urology, Stockholm South General Hospital, Stockholm, Sweden
- Department of Clinical Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
- Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.
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Powles T, Young A, Nimeiri H, Madison RW, Fine A, Zollinger DR, Huang Y, Xu C, Gjoerup OV, Aushev VN, Wu HT, Aleshin A, Carter C, Davarpanah N, Degaonkar V, Gupta P, Mariathasan S, Schleifman E, Assaf ZJ, Oxnard G, Hegde PS. Molecular residual disease detection in resected, muscle-invasive urothelial cancer with a tissue-based comprehensive genomic profiling-informed personalized monitoring assay. Front Oncol 2023; 13:1221718. [PMID: 37601688 PMCID: PMC10433150 DOI: 10.3389/fonc.2023.1221718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/11/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Circulating tumor DNA (ctDNA) detection postoperatively may identify patients with urothelial cancer at a high risk of relapse. Pragmatic tools building off clinical tumor next-generation sequencing (NGS) platforms could have the potential to increase assay accessibility. Methods We evaluated the widely available Foundation Medicine comprehensive genomic profiling (CGP) platform as a source of variants for tracking of ctDNA when analyzing residual samples from IMvigor010 (ClinicalTrials.gov identifier NCT02450331), a randomized adjuvant study comparing atezolizumab with observation after bladder cancer surgery. Current methods often involve germline sampling, which is not always feasible or practical. Rather than performing white blood cell sequencing to filter germline and clonal hematopoiesis (CH) variants, we applied a bioinformatic approach to select tumor (non-germline/CH) variants for molecular residual disease detection. Tissue-informed personalized multiplex polymerase chain reaction-NGS assay was used to detect ctDNA postsurgically (Natera). Results Across 396 analyzed patients, prevalence of potentially actionable alterations was comparable with the expected prevalence in advanced disease (13% FGFR2/3, 20% PIK3CA, 13% ERBB2, and 37% with elevated tumor mutational burden ≥10 mutations/megabase). In the observation arm, 66 of the 184 (36%) ctDNA-positive patients had shorter disease-free survival [DFS; hazard ratio (HR) = 5.77; 95% confidence interval (CI), 3.84-8.67; P < 0.0001] and overall survival (OS; HR = 5.81; 95% CI, 3.41-9.91; P < 0.0001) compared with ctDNA-negative patients. ctDNA-positive patients had improved DFS and OS with atezolizumab compared with those in observation (DFS HR = 0.56; 95% CI, 0.38-0.83; P = 0.003; OS HR = 0.66; 95% CI, 0.42-1.05). Clinical sensitivity and specificity for detection of postsurgical recurrence were 58% (60/103) and 93% (75/81), respectively. Conclusion We present a personalized ctDNA monitoring assay utilizing tissue-based FoundationOne® CDx CGP, which is a pragmatic and potentially clinically scalable method that can detect low levels of residual ctDNA in patients with resected, muscle-invasive bladder cancer without germline sampling.
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Affiliation(s)
- Thomas Powles
- Barts Experimental Cancer Medicine Centre, Barts Cancer Institute, Queen Mary University of London ECMC, Barts Health, London, United Kingdom
| | - Amanda Young
- Foundation Medicine, Cambridge, MA, United States
| | | | | | | | | | - Yanmei Huang
- Foundation Medicine, Cambridge, MA, United States
| | - Chang Xu
- Foundation Medicine, Cambridge, MA, United States
| | | | | | | | | | - Corey Carter
- Roche/Genentech, South San Francisco, CA, United States
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Malm C, Jaremko G, Brehmer M. S-phase - an independent prognostic marker in upper tract urothelial carcinoma. Scand J Urol 2022; 56:397-403. [PMID: 35971571 DOI: 10.1080/21681805.2022.2107065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
OBJECTIVES To evaluate S-phase fraction as a predictor of invasiveness and cancer-specific survival in upper tract urothelial carcinoma (UTUC). PATIENTS AND METHODS One hundred and fifteen patients having undergone radical nephroureterectomy were analysed with histology in radical nephroureterectomy specimens as reference test and S-phase fraction as index test. Ploidy and S-phase were determined using flow cytometry. Differences in S-phase fraction were calculated between stages, grades (WHO 1999 and 2004 classifications), ploidy and patients that died of UTUC and those who did not. Five- and 10-year-cancer-specific survivals were calculated. Areas under the ROC curve (AUCs) of S-phase fraction in relation to tumour stage and to death from UTUC were measured. Multiple Cox regression was performed. RESULTS Independent prognostic markers of death from UTUC were S-phase fraction and stage. Correlation between S-phase fraction and risk of dying from UTUC was strong, with a 17% greater risk of death from UTUC with every 1% increase in S-phase fraction, hazard ratio = 1.17, 95% CI = 1.10-1.25, p < 0.001, Spearman's rho ρ = 0.65. AUCs for S-phase fraction as predictors of stage and death from UTUC were 0.8 (95% CI = 0.705-0.894) and 0.77 (95% CI = 0.67-0.87), respectively. Cancer-specific survival was statistically significantly different between stages, ploidy and WHO 1999 grades, but not between WHO 2004 grades. This was also reflected in S-phase fraction, which differed in LG-G1 compared with LG-G2 and in HG-G2 compared with HG-G3. CONCLUSION S-phase fraction was a good test for predicting both invasiveness and cancer-specific survival. Using both WHO 1999 and 2004 classifications, rather than one system alone, had a higher predictive value of cancer-specific survival.
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Affiliation(s)
- Camilla Malm
- Department of Oncology/Pathology, Karolinska Institute, Stockholm, Sweden.,Stockholm South General Hospital, Stockholm, Sweden
| | - Georg Jaremko
- Department of Oncology/Pathology, Karolinska Institute, Stockholm, Sweden
| | - Marianne Brehmer
- Department of Clinical Sciences, Danderyd Hospital-Karolinska Institute, Stockholm, Sweden
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