Comprehensive proteogenomic characterization of rare kidney tumors

Non-clear cell renal cell carcinomas (non-ccRCCs) encompass diverse malignant and benign tumors. Refinement of differential diagnosis biomarkers, markers for early prognosis of aggressive disease, and therapeutic targets to complement immunotherapy are current clinical needs. Multi-omics analyses of 48 non-ccRCCs compared with 103 ccRCCs reveal proteogenomic, phosphorylation, glycosylation, and metabolic aberrations in RCC subtypes. RCCs with high genome instability display overexpression of IGF2BP3 and PYCR1. Integration of single-cell and bulk transcriptome data predicts diverse cell-of-origin and clarifies RCC subtype-specific proteogenomic signatures. Expression of biomarkers MAPRE3, ADGRF5, and GPNMB differentiates renal oncocytoma from chromophobe RCC, and PIGR and SOSTDC1 distinguish papillary RCC from MTSCC. This study expands our knowledge of proteogenomic signatures, biomarkers, and potential therapeutic targets in non-ccRCC.

Multiple Sessions vs. Single Session Image-Based Intracavitary Brachytherapy for Locally Advanced Cervical Cancer: A Randomized Control Trial

PURPOSE/OBJECTIVE(S)

The objectives of this study are: 1) To compare the acute toxicity caused in the treatment of locally advanced cervical cancer (LACC) treated with weekly multiple applications vs. a single application for image-guided intracavitary High Dose Rate (HDR) brachytherapy (BT) after External Beam Radiation Therapy (EBRT) 2) To compare the loco-regional control of cancer at six months in the two arms MATERIALS/METHODS: In a prospective study, 40 patients with biopsy-proven LACC with FIGO-2018 stage IIB-IIIC1 disease, underwent EBRT to the pelvis at a dose of 50.4 Gy/ 28 fractions over 5.5 weeks with weekly concurrent cisplatin. After completion of EBRT, they were randomized into two arms with 20 patients each. In the Control arm (Arm-A), BT sessions were given with weekly 3 applications whereas, in the experimental arm (Arm-B), all the sessions were given with a single application at 6-12 hours intervals with aim of the high-risk clinical target volume receiving >80 Gy EQD2 and 2 cm3 of the bladder and rectum/sigmoid receiving <85 Gy and <75 Gy, respectively. The OAR contouring was done on CT RESULTS: All 40 patients were treated as per protocol. The mean duration of treatment including EBRT and BT was 73.15 days [95% CI 68.63-77.66] in Arm A and 55.85 days [95% CI 52.11-59.58] in Arm B which was significant. After 6 months, 37 patients came for follow-up, all 19 patients in Arm A had Grade 1 or Grade 2 rectal toxicity. In Arm B as well all 18 patients had Grade 1 or Grade 2 rectal toxicity. Bladder toxicity was Grade 1 or Grade 2 in 18 patients and Grade 3 severity in 1 patient among Arm A. Among 18 patients of Arm B, bladder toxicity of Grade 1 or Grade 2 was seen in 16 patients, and 2 patients had grade 3 toxicity. 2 patients in Arm A and 3 in Arm B complained of Grade 1 urinary incontinence. Moreover, Abdominal pain at 6 months was of Grade 1 in around 6 patients in Arm A but 14 patients had abdominal pain in Arm B which was of Grade 1 in 8, 4 had grade 2 and 2 patients had grade 3 severity abdominal pain. In the monthly analysis of acute toxicity, none of the patients showed Grade 3 or 4 toxicity at the 1st, 2nd, or 3rd month of completion of treatment. When comparing local control in both arms at 6 months, 2 patients had treatment failure in the Experimental Arm compared to only 1 patient in the Control Arm CONCLUSION: Single Application Multiple Fraction Intracavitary Brachytherapy post concurrent CTRT is a safe option for the treatment of locally advanced cervical cancer. When compared to the weekly application arm, single-application ICRT showed a comparable acute toxicity profile and comparable local control rates as well. Some patients in Single Application Arm showed abdominal pain which needs to be investigated with further trials. The overall treatment time in the single application arm is significantly lower than the standard weekly application arm.

Characterization of Intercalated Cell Markers KIT and LINC01187 in Chromophobe Renal Cell Carcinoma and Other Renal Neoplasms

Introduction. Chromophobe renal cell carcinoma (chromophobe RCC) is the third major subcategory of renal tumors after clear cell RCC and papillary RCC, accounting for approximately 5% of all RCC subtypes. Other oncocytic neoplasms seen commonly in surgical pathology practice include the eosinophilic variant of chromophobe RCC, renal oncocytoma, and low-grade oncocytic unclassified RCC. Methods. In our recent next-generation sequencing based study, we nominated a lineage-specific novel biomarker LINC01187 (long intergenic non-protein coding RNA 1187) which was found to be enriched in chromophobe RCC. Like KIT (cluster of differentiation 117; CD117), a clinically utilized chromophobe RCC related biomarker, LINC01187 is expressed in intercalated cells of the nephron. In this follow-up study, we performed KIT immunohistochemistry and LINC01187 RNA in situ hybridization (RNA-ISH) on a cohort of chromophobe RCC and other renal neoplasms, characterized the expression patterns, and quantified the expression signals of the two biomarkers in both primary and metastatic settings. Results. LINC01187, in comparison to KIT, exhibits stronger and more uniform expression within tumors while maintaining temporal and spatial consistency. LINC01187 also is devoid of intra-tumoral heterogeneous expression pattern, a phenomenon commonly noted with KIT. Conclusions. LINC01187 expression can augment the currently utilized KIT assay and help facilitate easy microscopic analyses in routine surgical pathology practice.

Abstract 3127: Comprehensive proteogenomic characterization of rare kidney tumors

Non-clear cell renal cell carcinomas (non-ccRCCs) represent ~15-20% RCCs cases comprising nearly 20 different disease subtypes and a wide spectrum of clinical behavior from benign to highly aggressive course. Clinically, metastatic non-ccRCC patients, regardless of subtypes with distinct genomic aberrations, are all treated with the same standard of care therapies, underscoring the need for precision therapeutic strategies. Diagnostic challenges also exist as benign and malignant entities often display overlapping histomorphologies that current diagnostic cytokeratin markers cannot resolve. Therefore, identification of more reliable diagnostic and prognostic non-ccRCC biomarkers remains an unmet need in this field.

As part of the Clinical Tumor Analysis Consortium (CPTAC), we performed integrative analysis of multi-omics data including genomic next generation sequencing-based whole exome, whole genome, RNAseq, snRNAseq and mass spectrometry-based proteomics, post translational modifications (glycosylation and phosphorylation) and metabolomic profiles generated by CPTAC. The composition of the kidney tumor cohort (n=151) included 103 ccRCC, 15 oncocytomas, 13 papillary RCC (PRCC), 11 other rare tumors and 8 unclassified RCCs. Our multi-omic analysis revealed both unique and shared molecular features of RCC subtypes. We characterized proteogenomic, PTM and glycoproteome impact of genome instability (GI), a feature that is associated with poor prognosis in both ccRCC and non-ccRCC and affects 10-15% of cases. These analyses identified new prognostic signatures, outlier targetable kinase expression patterns, kinase-substrate relationships and differential protein glycosylation events. Glycoproteome analysis also revealed variation in cell-type specific marker expression among RCC subtypes such as FUT8 (core-fucosyltransferase) associated protein glycosylation in PRCC. Integrative analysis of snRNA-seq data predicted diverse tumor cell-of-origin and stratified RCC subtype specific proteogenomic signatures. Differential expression analysis revealed several novel diagnostic makers including MAPRE3, GPNMB, PIGR, SOSTDC1. These biomarkers were validated by IHC and their addition to existing panels results in improved diagnostic specificity. Metabolic characterization revealed RCC subtype-specific differences and increased oncometabolite SAICAR in oncocytomas that may have functional significance. The valuable proteogenomic data resource we generated contains several rare tumor types that are hard to obtain for proteogenomic characterization at the scale described here, and will certainly aid in future pan-RCC studies.

Citation Format: Ginny Xiaohe Li, Yi Hsiao, Lijun Chen, Rahul Mannan, Yuping Zhang, Francesca Petralia, Hanbyul Cho, Noshad Hosseini, Anna Calinawan, Yize Li, Shankara Anand, Aniket Dagar, Yifat Geffen, Felipe V. Leprevost, Anne Le, Sean Ponce, Michael Schnaubelt, Nataly Naser Al Deen, Wagma Caravan, Andrew Houston, Chandan Kumar-Sinha, Xiaoming Wang, Seema Chugh, Gilbert S. Omenn, Daniel W. Chan, Christopher Ricketts, Rohit Mehra, Arul Chinnaiyan, Li Ding, Marcin Cieslik, Hui Zhang, Saravana M. Dhanasekaran, Alexey I. Nesvizhskii. Comprehensive proteogenomic characterization of rare kidney tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3127.

Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness

Clear cell renal cell carcinomas (ccRCCs) represent ∼75% of RCC cases and account for most RCC-associated deaths. Inter- and intratumoral heterogeneity (ITH) results in varying prognosis and treatment outcomes. To obtain the most comprehensive profile of ccRCC, we perform integrative histopathologic, proteogenomic, and metabolomic analyses on 305 ccRCC tumor segments and 166 paired adjacent normal tissues from 213 cases. Combining histologic and molecular profiles reveals ITH in 90% of ccRCCs, with 50% demonstrating immune signature heterogeneity. High tumor grade, along with BAP1 mutation, genome instability, increased hypermethylation, and a specific protein glycosylation signature define a high-risk disease subset, where UCHL1 expression displays prognostic value. Single-nuclei RNA sequencing of the adverse sarcomatoid and rhabdoid phenotypes uncover gene signatures and potential insights into tumor evolution. In vitro cell line studies confirm the potential of inhibiting identified phosphoproteome targets. This study molecularly stratifies aggressive histopathologic subtypes that may inform more effective treatment strategies.