Table Info

Table 1.

Clinical, genomic characteristics, and Decipher^® results

Case characteristics	Case 1	Case 2	Case 3	Case 4
Age/Sex	72/Male	57/Male	80/Female	64/Male
Upper tract location	Renal pelvis and ureter	Renal pelvis and ureter	Renal pelvis	Renal pelvis
Initial stage	III	IV	III	IV
Metastatic (Y/N); sites	N; N/A	Y; lung, bronchus	Y; RP nodes, liver	Y; spine osseous
Neoadjuvant chemo (Y/N); cycles	Y; 3	N; N/A	N; N/A	N; N/A
Treatment response	Residual ypT3 after NAC but without metastatic disease	Progressive disease	Progressive disease	Initial stable disease then progressive disease
Final clinical stage	Stage III	Stage IV	Stage IV	Stage IV
Final pT stage	ypT3	pT3cN1cM1	pT3cN2Mx	pT3aNxM1
Variant histology	HG UTUC with glandular and focal squamous differentiation	HG UTUC with squamous differentiation of 40%	Pure HG UTUC	HG UTUC with 30% sarcomatoid features and 20% necrosis
Decipher^® subtype probability	Basal probability 53.4%/Basal Claudin-low 43%	Basal probability 80.4%	Basal probability 82.4%	Basal probability 39.4%/Basal Claudin-low probability 43.5%
Decipher subtype	Basal/Basal Claudin-low	Basal	Basal	Basal/Basal Claudin-low
Consensus subtype	Stroma-rich	Basal/Squamous	Basal/Squamous	Stroma-rich
UNC subtype	Basal	Basal	Basal	Basal
FGFR3 activity class	inactive	inactive	inactive	inactive
Immune190 score	0.70	0.27	0.68	0.48
ESTIMATE stromal score	3,675	–875	1,889	2,245
Foundation medicine (NGS results)	N/A	PD-L1 TPS 1%; MS-Stable; TMB—6 Muts/Mb; CASP8 loss exons 3-7; CDKN2A loss; CDKN2B loss; HRAS G12S; MTAP loss; TERT promoter -124C>T; VUS: BTK Y418H; CDH1 V794I; CSF1R V48M; HRAS L163fs*52; MITF E207G; NOTCH3 S872F; RBM10 G280V; RPTOR D821N; SNCAIP R269Q; TSC2 R1268H	MS-Stable; TMB—11 Muts/Mb; AKT2 amplification; CDKN2A loss; CDKN2B loss; ERBB3 E332K; KDM6A Q670*; MTAP loss; RAF1 amplification; TERT promoter -124C>T; TP53 loss	N/A
Overall survival	36.6 mos	8.7 mos	10.8 mos	14.2 mos
Progression free survival	N/A	6 mos	0.7 mos	2.5 mos
Decipher gene outlier category	Immune activation/angiogenesis	FGF/ADC	Immune activation/angiogenesis	Immune activation

HG UTUC: high-grade upper tract urothelial carcinoma; mos: months; N/A: not applicable; NAC: neoadjuvant chemotherapy; RP: retroperitoneal; TPS: tumor proportion score; VUS: variants of unknown significance; UNC: University of North Carolina; NGS: next generation sequencing; PD-L1: programmed death ligand 1; TMB: tumor mutational burden; FGFR: fibroblast growth factor receptor

Declarations

Acknowledgments

Special thanks to Inova Schar Cancer Institute Clinical trials research office under Stephanie Van Bebber. Acknowledgement to Ewan Gibb, PhD, former Vericyte Scientist for the conduct of this study. This study was in part included as presented Belay et al., Journal of Clinical Oncology; 41 (16) suppl e16578 at the American Society Clinical Oncology (ASCO) Annual Meeting 2023 (cited Reference # 12).

Author contributions

JBAC: Conceptualization, Investigation, Writing—original draft, Writing—review & editing, Validation, Supervision. JJdJ and ED: Conceptualization, Investigation, Writing—original draft, Writing—review & editing, Validation. WL: Writing—original draft, Writing—review & editing, Visualization, Investigation. MWH, SB, and JK: Writing—original draft, Writing—review & editing, Investigation. All authors read and approved the submitted version.

Conflicts of interest

JBAC received Speakers’ Bureau and Advisory board fees from BMS, Astellas/Seagen Pfizer, EMD Serono, Merck KGaA; and also received advisory board fees from Pfizer, EMD Serono, Merck, AVEO, Immunomedics, Astellas/Seagen, Jannsen, Bayer, Novartis. JJdJ reports being a consultant for Veracyte. ED reports employee of Veracyte. All other authors declare that they have no conflicts of interest.

Ethical approval

This study was approved by the Inova IRB (Inova IRB # 16-2259).

Consent to participate

Consent to participate was waived and exempt according to the section 46.116 (d) conditions of the IRB approval and review expedited.

Consent to publication

Consent to publication was waived and exempt according to the section 46.116 (d) conditions of the IRB approval and review expedited.

Availability of data and materials

The raw data supporting the conclusions of this manuscript will be made available by the authors, without undue reservation, to any qualified researcher.

Funding

This project was funded by the Inova Institutional Research Seed Grant. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Copyright

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