Complexity of the genomic landscape of renal cell carcinoma: Implications for targeted therapy and precision immuno-oncology

CASP5 associated with PANoptosis promotes tumorigenesis and progression of clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is a globally severe cancer with an unfavorable prognosis. PANoptosis, a form of cell death regulated by PANoptosomes, plays a role in numerous cancer types. However, the specific roles of genes associated with PANoptosis in the development and advancement of ccRCC remain unclear. Our study developed a risk model utilizing three PANoptosis-associated genes (Caspase 4 (CASP4), TLR3, and CASP5). This model demonstrated a high degree of precision in predicting the prognosis for patients with ccRCC. ccRCC patients in the high-risk group had the strongest immune cell activity, experiencing immune evasion, and might potentially derive advantages from treatment involving combined immune checkpoint inhibitors. CASP5 was highly expressed in ccRCC tissues by RT-qPCR, western blotting, and immunofluorescence. Stable CASP5 knockdown cell lines were constructed by lentivirus in vitro transfection technique. Reducing CASP5 level suppressed the growth, migration, and invasion of ccRCC cells, while encouraging cell apoptosis. In addition, the results of in vivo tumorigenesis experiments showed that down-regulating CASP5 expression inhibited the tumorigenic ability of 786-O cells. Together, the innovative risk model using PANoptosis-associated genes effectively forecasts the tumor microenvironment and survival rates for ccRCC, offering a novel approach to the early, precise diagnosis of ccRCC and the advancement of personalized treatment strategies.

Construction and validation of a ferroptosis-related long noncoding RNA signature in clear cell renal cell carcinoma

Background

Clear cell renal cell carcinoma (ccRCC) is characterized by the accumulation of lipid-reactive oxygen species. Ferroptosis, due to the lipid peroxidation, has been reported to be strongly correlated with tumorigenesis and progression. However, the functions of the ferroptosis process in ccRCC remain unclear.

Methods

After sample cleaning, data integration, and batch effect removal, we used the Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases to screen out the expression and prognostic value of ferroptosis-related lncRNAs and then performed the molecular subtyping using the K-means method. Then, the functional pathway enrichment and immune microenvironment infiltration between the different clusters were carried out. The results showed a significant difference in immune cell infiltration between the two clusters and the associated marker responded to individualized differences in treatment. Then, least absolute shrinkage and selection operator (LASSO) Cox regression was used to establish a prognostic signature based on 5 lncRNAs. This signature could accurately predicted patient prognosis and served as an independent clinical risk factor. We then combined significant clinical parameters in multivariate Cox regression and the prognostic signature to construct a clinical predictive nomogram, which provides appropriate guidance for predicting the overall survival of ccRCC patients.

Results

The prognostic differentially expressed ferroptosis-related LncRNAs (DEFRlncRNAs) were found, and 5 lncRNAs were finally used to establish the prognostic signature in the TCGA cohort, with subsequently validation in the internal and external cohorts. Moreover, we conducted the molecular subtyping and divided the patients in the TCGA cohort into two clusters showing differences in Hallmark pathways, immune infiltration, immune target expression, and drug therapies. Differences between clusters contributed to individualizing treatment. Furthermore, a nomogram was established to better predict the clinical outcomes of the ccRCC patients.

Conclusions

Our study conducted molecular subtyping and established a novel predictive signature based on the ferroptosis-related lncRNAs, which contributed to the prognostic prediction and individualizing treatment of ccRCC patients.

The 2022 revision of World Health Organization classification of tumors of the urinary system and male genital organs: advances and challenges

The fifth edition of the World Health Organization (WHO) classification of urinary and male genital organ tumors has been recently published in 2022. The application of molecular profiling has made a substantial impact on classification of urologic tumors. The new WHO classification introduces a group of molecularly well-defined renal tumor subtypes. The significant changes include addition of a category of "other oncocytic tumors" with oncocytoma/chromophobe renal cell carcinoma (chRCC)-like features, elimination of the subcategorization of type1/2 papillary RCC and inclusion of eosinophilic solid and cystic RCC as an independent tumor entity. The WHO/ISUP grading now has been recommended for all RCCs. Major nomenclature changes include replacement of histologic 'variants' by 'subtypes', 'clear cell papillary renal cell carcinoma' to 'clear cell renal cell tumor','TCEB1-mutated RCC' to 'ELOC-mutated RCC', 'hereditary leiomyomatosis and renal cell carcinoma' to 'fumarate hydratase-deficient RCC', 'RCC-Unclassified' to 'RCC-NOS', 'primitive neuroectodermal tumor' to 'embryonic neuroectodermal tumor', 'testicular carcinoid' to 'testicular neuroendocrine tumor', and 'basal cell carcinoma of the prostate' to 'adenoid-cystic (basal-cell) carcinoma of the prostate'. Metastatic, hematolymphoid, mesenchymal, melanocytic, soft tissue and neuroendocrine tumors are collectively discussed in separate chapters. It has been suggested that the morphological classification of urothelial cancer be replaced with a new molecular taxonomic classification system.

Clinicopathologic and Immunohistochemical Characterization of Sarcomatoid Chromophobe Renal Cell Carcinoma: An Analysis of 22 Cases

Sarcomatoid differentiation in chromophobe renal cell carcinoma (ChRCC) is a rare finding and a significant predictor of worse outcomes. When the sarcomatoid component overgrows the conventional component or is the only component on a biopsy, the differential diagnoses encompass a variety of entities. Therefore, we reviewed 22 sarcomatoid ChRCCs and characterized the immunophenotype. Given that renal carcinomas with sarcomatoid features may benefit from immune checkpoint inhibitor-based therapy we also assessed the programmed death-ligand 1 (PD-L1) (28-8) expression. DOG1, CD117, cytokeratin 7, and PAX8 were negative in 100%, 88%, 63%, and 44% of the sarcomatoid components, respectively. GATA3 was expressed in 31% of the conventional components and in 50% of the sarcomatoid components. One conventional and 3 sarcomatoid components expressed PD-L1. Sarcomatoid ChRCCs have a high propensity for metastases and cancer progression. Distant metastatic disease was seen in 73% of the cases and median survival in this cohort was <1 year. The sarcomatoid portion had increased expression of PD-L1 and frequent loss of expression of multiple immunohistochemical markers associated with ChRCC. Half of the sarcomatoid ChRCC exhibited GATA3 expression, 3 of which did not express PAX8.

Effects of LncRNA HCP5/miR-214-3p/MAPK1 Molecular Network on Renal Cell Carcinoma Cells

Background

Recent researches have shown that long non-coding RNA (LncRNA) is often disordered and acts in many carcinomas. Clear cell renal cell carcinoma (ccRCC) is the main reason for carcinoma-related deaths, which are mainly caused by the metastasis. HCP5 is a newly discovered LcnRNA. Early studies have found that HCP5 acts in neoplasm metastasis, but the mechanism of HCP5 in ccRCC is still unclear.

Methods

The expression of HCP5 in human renal cell carcinoma (RCC) was detected by real-time quantitative PCR. The biological effect of LncRNAs in proliferation, migration, invasion and metastasis of RCC cells was explored by gain-of-function and loss-of-function tests. The molecular mechanism of LncRNAs was explored by RNA immunoprecipitation and Western blot.

Results

qRT-PCR revealed that HCP5 was enhanced in neoplasm tissues of ccRCC patients and correlated with the metastatic characteristics of RCC. Over-expression of HCP5 promoted the proliferation, migration and invasion of renal carcinoma cells. The deletion of HCP5 inhibited the proliferation, migration and invasion of RCC in vitro and the metastasis of RCC in vivo. Mechanically, HCP5 inhibited the growth and metastasis of ccRCC cells by regulating miR-214-3p/MAPK1 axis.

Conclusion

HCP5, as a key LncRNA, can promote ccRCC metastasis by regulating miR-214-3p/MAPK1 axis and may be a biomarker and be helpful for judging the prognosis of ccRCC.

Analysis of the concordance of 20 immunohistochemical tissue markers in metastasectomy lesions in patients with metastatic renal cell carcinoma: A retrospective study using tissue microarray

Purpose

This study aimed to characterize the different expressions of 20 tissue markers in multiple metastatic lesions and organs in patients with metastatic renal cell carcinoma (mRCC).

Materials and Methods

Sixty-six patients with mRCC, harboring 162 metastasectomy tissue lesions (MTLs), were enrolled. Immunohistochemical analysis for the following tissue markers was performed: BAP1; CD31; CD 34; HIF1α and 2α; Ki67; pS6; PBRM1; PDGFRα and β; PDL1; PSMA; PTEN; α-SMA; TGase2; VEGFR1, 2, and 3; VHL loss; and CA9. Cases were identified pathologically using the semi-quantitative H-score (0–300), including the intensity score (0, 1, 2, 3). The concordance rate was calculated as the number of patients with concordant binary score out of the total number of patients in that comparison.

Results

The specimens from 66 patients were divided into those from the same organs and those from different organs. Forty-two patients (44 cases) with 96 MTLs and 39 with 83 MTLs were examined. Among the 20 tissue markers, only BAP1, PSMA, VEGFR3, PDGFRα, and pS6 tissue showed high concordance ratio (>0.7) regardless of different metastatic tissues and different metastatic lesions within the tumor.

Conclusions

The study demonstrated the intratumoral heterogeneity of mRCC with a low-concordance index of most tissue markers. However, some had high concordance with a similar expression regardless of the metastatic organs, metastatic sites, or presence of recurrence.

Knockdown of ALPK2 blocks development and progression of renal cell carcinoma

Renal cell carcinoma (RCC) is one of the most common malignant tumors in the urinary system, whose molecular mechanism is still not clear. ALPK2 is a member of alpha protein kinase family, and its relationship with RCC is never reported. In this study, expression of ALPK2 in tumor tissues or cells of RCC was detected by qPCR, western blotting and immunohistochemical analysis. The effects of ALPK2 knockdown on cell proliferation, colony formation, cell migration and apoptosis were assessed by MTT, colony formation assay, wound-healing assay, Transwell assay and flow cytometry, respectively. The influence of ALPK2 knockdown on tumor growth in vivo was evaluated by mice xenograft models. The results demonstrated that ALPK2 was upregulated in tumor tissues of RCC and its high expression was significantly associated with advanced stage and poor prognosis. Knockdown of ALPK2 could inhibited cell proliferation, colony formation and cell migration of RCC cells, while promoting cell apoptosis. The suppression of tumor growth in vivo by ALPK2 knockdown was also showed by using mice xenograft models. Moreover, the regulation of RCC by ALPK2 may involve Akt, CDK6, Cyclin D1 and PIK3CA signaling. Therefore, our studies suggested that ALPK2 may act as a tumor promotor in the development and progression of RCC, and could be considered as a novel therapeutic target for RCC treatment.

Computational analysis of pathological images enables a better diagnosis of TFE3 Xp11.2 translocation renal cell carcinoma

TFE3 Xp11.2 translocation renal cell carcinoma (TFE3-RCC) generally progresses more aggressively compared with other RCC subtypes, but it is challenging to diagnose TFE3-RCC by traditional visual inspection of pathological images. In this study, we collect hematoxylin and eosin- stained histopathology whole-slide images of 74 TFE3-RCC cases (the largest cohort to date) and 74 clear cell RCC cases (ccRCC, the most common RCC subtype) with matched gender and tumor grade. An automatic computational pipeline is implemented to extract image features. Comparative study identifies 52 image features with significant differences between TFE3-RCC and ccRCC. Machine learning models are built to distinguish TFE3-RCC from ccRCC. Tests of the classification models on an external validation set reveal high accuracy with areas under ROC curve ranging from 0.842 to 0.894. Our results suggest that automatically derived image features can capture subtle morphological differences between TFE3-RCC and ccRCC and contribute to a potential guideline for TFE3-RCC diagnosis.

Translocation renal cell carcinoma is an aggressive form of renal cancer that is often misdiagnosed to other subtypes. Here the authors demonstrated that by using machine learning and H&E stained whole-slide images, an accurate diagnose of this particular type of renal cancer can be achieved.

Immunotherapy in renal cell carcinoma from poverty to the spoiled of choice

Management of metastatic renal cell carcinoma has been enriched by the advent of new therapeutic compounds. The approval of new combination strategies between targeted agents and immune-checkpoint inhibitors as well as the administration of combinations between immune-checkpoint inhibitors has clearly demonstrated significant improvement toward patients' prognosis and other clinical outcomes. Due to the availability of different treatments, the choice between them may be a difficult issue in our clinical practice. We have summarized current knowledge about available treatments focusing on criteria, which may help clinicians to make decisions.

Toward a genome-based treatment landscape for renal cell carcinoma

Knowledge about molecular mechanisms driving development and progression of renal cell carcinoma has been elucidated by different studies. In few years we discovered a large difference between genomic landscapes of clear cell and non-clear cell carcinoma. Moreover, tumor heterogeneity and different acquisition of gene mutations during tumor progression are issues of particular interest. In this review we focalized our attention on principal genomic alterations identified among RCC subtypes. Acquired gene mutations may be an adaptive response to several external pressure including metabolic, treatment, genomic and immune-related external pressure. Thus we correlated and discussed principal genomic alterations adopted by tumor to escape from each external pressures. The aim of the present work is to summarize current knowledge about genomic alterations in RCC with special interest of treatment strategies tailored on the basis of disease mutations assessment.

Best treatment options for advanced renal cell carcinoma (RCC) patients: a Delphi consensus study

The introduction of targeted therapy for the treatment of advanced renal cell carcinoma (RCC) has improved the outcome of these patients in the last decade. However, many patients still relapse. The aim of this consensus study was to establish common recommendations about the best treatment options in patients with RCC. A two-round Delphi methodology was used. A total of 25 statements were submitted to a panel of 30 specialists. If consensus was not obtained in the first round a second and last round was performed. Agreement was achieved for 19 of the proposed 25 statements (76%). When making a decision about the treatment option, considering the efficiency and response rate to previous treatment, drug's toxicity and the patients' clinical features are very relevant.

Novel therapeutic roles of MC-4 in combination with everolimus against advanced renal cell carcinoma by dual targeting of Akt/pyruvate kinase muscle isozyme M2 and mechanistic target of rapamycin complex 1 pathways

Current clinical trials of new anticancer therapies against metastatic renal cell carcinoma (RCC), including molecular-targeted therapies, have not shown promise. The purpose of this study was to preclinically assess the antitumor effects of MC-4, a partially purified material of Artemisia annua L., as a monotherapy or in combination with the known mechanistic target of rapamycin complex 1 (mTORC1) inhibitor, everolimus, against Caki-1 (Von Hippel-Lindau (VHL)+/+) and 786-O (VHL-/-) human RCC cells. MC-4 monotherapy significantly increased tumor growth inhibition and autophagic cell death in RCC cells in vitro and in vivo. Everolimus led to compensatory Akt activation by inhibiting only mTORC1 signaling pathway. In contrast to everolimus, MC-4 enhanced phosphatase and tensin homolog expression and reduced its downstream effector, Akt/pyruvate kinase muscle isozyme M2 (PKM2), leading to decreased expression of glucose transporter 1, which is associated with cancer cell metabolism. The synergistic antitumor and anti-metastatic effects induced by co-administration of MC-4 and everolimus involve cell growth inhibition and autophagic cell death via dual targeting of phosphatidylinositol 3-kinase (PI3K)/Akt/PKM2 and mTORC1. These findings suggest that MC-4 is a novel Akt/PKM2 inhibitor that can overcome the limitation of existing mTOR inhibitors and can be considered a novel strategy to treat patients with rapidly progressing advanced RCC.

Genomic classifications of renal cell carcinoma: a critical step towards the future application of personalized kidney cancer care with pan-omics precision

Over the past 20 years, classifications of kidney cancer have undergone major revisions based on morphological refinements and molecular characterizations. The 2016 WHO classification of renal tumors recognizes more than ten different renal cell carcinoma (RCC) subtypes. Furthermore, the marked inter- and intra-tumor heterogeneity of RCC is now well appreciated. Nevertheless, contemporary multi-omics studies of RCC, encompassing genomics, transcriptomics, proteomics, and metabolomics, not only highlight apparent diversity but also showcase and underline commonality. Here, we wish to provide an integrated perspective concerning the future 'functional' classification of renal cancer by bridging gaps among morphology, biology, multi-omics, and therapeutics. This review focuses on recent progress and elaborates the potential value of contemporary pan-omics approaches with a special emphasis on cancer genomics unveiled through next-generation sequencing technology, and how an integrated multi-omics approach might impact precision-based personalized kidney cancer care in the near future. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Morphological spectrum of renal cell carcinoma, unclassified: an analysis of 136 cases

AIMS

Renal cell carcinoma, unclassified (RCCU) is a category that includes a morphologically and biologically heterogeneous group of tumours that are unable to be diagnosed as other well-defined entities. We aim to describe the morphological findings of tumours within this category and to determine the most frequent morphological features leading to classification difficulty.

METHODS AND RESULTS

One hundred and thirty-six cases of RCCU were examined. Patients ranged in age from 23 to 87 years. Seventy-seven patients were men and 59 were women. International Society of Urological Pathology (ISUP) grade was most commonly 3 (n = 66), followed by 2 (n = 42) and 4 (n = 28). Tumour size ranged from 0.6 to 24.9 cm. The American Joint Committee on Cancer (AJCC) pathological T categories included pT1a (n = 50), pT1b (n = 14), pT2a (n = 7), pT2b (n = 4), pT3a (n = 50) and pT4 (n = 9). Forty-four cases included lymph node(s), 41% of which (n = 18) had metastases. Tumours were assessed for a variety of histological features and assigned to the following morphological groups: predominantly oncocytoma/chromophobe RCC-like; clear cell RCC-like; papillary RCC-like; collecting duct-like; and pure sarcomatoid differentiation. The majority of the oncocytoma/chromophobe and clear cell RCC-like phenotypes were low stage (pT1 or pT2). The papillary RCC-like, collecting duct-like and pure sarcomatoid phenotypes were mainly high stage (pT3 or pT4).

CONCLUSIONS

Renal cell carcinoma, unclassified is a term that encompasses tumours with a variety of morphological features and a wide biological spectrum. The most common source of diagnostic difficulty was tumours composed of predominantly eosinophilic cells.