Intratumoral heterogeneity of DNA content in renal cell carcinoma and its prognostic significance

A non-diploid DNA status is linked to poor prognosis in renal cell cancer

Purpose

DNA ploidy measurement has earlier been suggested as a potentially powerful prognostic tool in many cancer types, but the role in renal tumors is still unclear.

Methods

To clarify its prognostic impact, we analyzed the DNA content of 1320 kidney tumors, including clear cell, papillary and chromophobe renal cell carcinoma (RCC) as well as renal oncocytoma and compared these data with clinico-pathological parameters and patient prognosis.

Results

A non-diploid DNA content was seen in 37% of 1276 analyzable renal tumors with a striking predominance in chromophobe carcinoma (74.3% of 70 cases). In clear cell carcinoma, a non-diploid DNA content was significantly linked to high-grade (ISUP, Fuhrman, Thoenes; p < 0.0001 each), advanced tumor stage (p = 0.0011), distant metastasis (p < 0.0001), shortened overall survival (p = 0.0010), and earlier recurrence (p < 0.0001). In papillary carcinoma, an aberrant DNA content was significantly linked to high Fuhrman grade (p = 0.0063), distant metastasis (p = 0.0138), shortened overall survival (p = 0.0010), and earlier recurrence (p = 0.0003).

Conclusion

In summary, the results of our study identify a non-diploid DNA content as a predictor of an unfavorable prognosis in clear cell and papillary carcinoma.

Electronic supplementary material

The online version of this article (10.1007/s00345-020-03226-8) contains supplementary material, which is available to authorized users.

Intratumoral Genomic Heterogeneity May Hinder Precision Medicine Strategies in Patients with Serous Ovarian Carcinoma

Precision medicine, which includes comprehensive genome sequencing, is a potential therapeutic option for treating high-grade serous carcinoma (HGSC). However, HGSC is a heterogeneous tumor at the architectural, cellular, and molecular levels. Intratumoral molecular heterogeneity currently limits the precision of medical strategies based on the gene mutation status. This study was carried out to analyze the presence of 160 cancer-related genetic alterations in three tissue regions with different pathological features in a patient with HGSC. The patient exhibited histological heterogeneous features with different degrees of large atypical cells and desmoplastic reactions. TP53 mutation, ERBB2 and KRAS amplification, and WT1, CDH1, and KDM6A loss were detected as actionable gene alterations. Interestingly, the ERBB2 and KRAS amplification status gradually changed according to the region examined. The difference was consistent with the differences in pathological features. Our results demonstrate the need for sampling of the appropriate tissue region showing progression of pathological features for molecular analysis to solve issues related to tumor heterogeneity prior to developing precision oncology strategies.

LPAR1 regulates the development of intratumoral heterogeneity in ovarian serous cystadenocarcinoma by activating the PI3K/AKT signaling pathway

Background

To explore the role of lysophosphatidic acid receptor 1 (LPAR1) and its correlation with the PI3K/AKT pathway in the development of intratumoral heterogeneity (ITH) in human ovarian serous cystadenocarcinoma (OSC).

Methods

Immunohistochemical staining was performed to detect LPAR1 expression in matched primary and recurrent lesions from the same patients. Cell models of ITH were established using the limiting dilution methodology and Transwell invasion/migration assays. LPAR1 expression in the ITH cell models was silenced or upregulated with lentiviral particles, and the biological characteristics were evaluated using various in vitro and in vivo assessments of cell function. The levels of phosphorylated PI3K/AKT (p-PI3K/p-AKT) in LPAR1 knockdown and LPAR1-overexpressing cells were detected.

Results

The H-scores for LPAR1 staining in the lymphatic metastatic and recurrent lesions were noticeably higher than in the primary tumor lesions from the same patients (P = 0.024/0.031). High LPAR1 expression was associated with worse progression-free survival and overall survival (P = 0.017/0.039). Biological functions in vitro, including invasion, migration, and proliferation, and tumor formation in vivo were decreased in the LPAR1-silenced cells (all P < 0.05). These cellular functions were significantly increased in the LPAR1-overexpressing cells in vitro and in vivo (all P < 0.05). The levels of p-PI3K and p-AKT were significantly decreased in the LPAR1 knockdown cells and significantly increased in the LPAR1-overexpressing cells (all P < 0.05).

Conclusions

Higher levels of the LPAR1 protein were associated with a poor prognosis. LPAR1 plays essential roles in the invasion, migration, and proliferation of heterogeneous subsets of OSC cell lines and the development of ITH of OSC, possibly by modulating the activity of the PI3K/AKT signaling pathway.

Prognostic Biomarkers in Renal Cell Carcinoma: Relevance of DNA Ploidy in Predicting Disease-Related Survival

Objective

To investigate the prognostic value of DNA ploidy, Ki-67 index and p53 expression in relation to disease-related survival in a consecutive series of patients with renal cell carcinoma (RCC).

Material and methods

The study group consisted of 64 RCC patients treated by radical nephrectomy. Histological type, pathological staging and nuclear anaplasia were assessed according to the WHO classification, TNM system and Fuhrman grading criteria, respectively. Ploidy was determined by DNA flow cytometry using two sampling methods (frozen vs paraffin-embedded tissue). Ki-67 and p53 were evaluated by immunohistochemistry techniques using two cutoff points (10% vs mean value) for staining interpretation. Kaplan-Meier and Cox regression analyses were used for prognostic evaluation.

Results

Thirty-one tumors (48.4%) showed DNA diploidy and 33 (51.6%) were DNA aneuploid. Concordance between both ploidy measurement methods was found in 85.5% of cases (p=0.0455). The mean values for Ki-67 and p53 immunostaining were 3.65% (0–23.5%) and 5.90% (0–55.9%), respectively. DNA ploidy significantly correlated with staging, tumor size (pT), nuclear grading, and Ki-67 (mean value cutoff). Ki-67 (10% cutoff) correlated with staging and pT, while p53 (mean value cutoff) was associated with Ki-67 (mean value cutoff). There were significant differences between survival curves for pathological stage, pT, nuclear grade, ploidy, Ki-67 (both cutoffs), and p53 (10% cutoff). By univariate regression analysis, stage III and stage IV, pT3, aneuploidy, high Ki-67 (both cutoffs), and p53 overexpression (10% cutoff) showed significant correlations with worse disease-related survival. In addition, DNA aneuploidy significantly correlated with poor prognosis within stages I/II (p=0.0355) and stages III/IV (p=0.0138) of the disease.

Conclusion

The results indicate that DNA ploidy has relevant prognostic value in RCC, adding useful information to the classic histopathological indicators of clinical outcome.

Intratumoural heterogeneity may hinder precision medicine strategies in patients with clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is an heterogeneous tumour at architectural, cellular and molecular level, a reason why the 2014 International Society of Urological Pathology consensus recommended wide sampling of RCC masses to include at least 1 block/cm of tumour together with perpendicular sections of the tumour/perinephric fat interface and the tumour/renal sinus interface. Intratumoural molecular heterogeneity may be a limitation at the moment of defining precision medicine strategies based on gene mutation status. This study analyses the presence of any mutation of KRAS, NRAS, BRAF, PIK3CA, ALK, ERBB2, DDR2, MAP2K1, RET and EGFR genes in 20 tissue blocks from a case of ccRCC and its metastasis. We observed the presence of the mutation at pH1047R of PIK3CA gene in five samples of the tumour, while the remaining 15 samples did not show any mutation at PIK3CA or any other investigated gene. There is a great need to develop novel RCC sampling strategies to overcome tumour heterogeneity prior to define precision oncology strategies.

Sunitinib rechallenge in metastatic renal cell carcinoma patients

BACKGROUND

Sunitinib was a standard initial therapy in metastatic renal cell carcinoma (mRCC). Given the fact that many patients progressed through many available therapies and antitumor activity had been demonstrated with sequential vascular endothelial growth factor-targeting approaches, a retrospective review was performed of the experience of rechallenge with sunitinib in sunitinib-refractory mRCC.

METHODS

mRCC patients who received sunitinib therapy after disease progression on prior sunitinib and other therapy were retrospectively identified. Patient characteristics, toxicity, clinical outcome, Response Evaluation Criteria in Solid Tumors (RECIST) objective response rate, and progression-free survival (PFS) were recorded.

RESULTS

Twenty-three mRCC patients who were rechallenged with sunitinib were identified. Upon rechallenge, 5 patients (22%) achieved an objective partial response. The median PFS with initial treatment was 13.7 months and 7.2 months with rechallenge. Patients with >6-month interval between sunitinib treatments had a longer PFS with rechallenge than patients who started the rechallenge within 6 months (median PFS, 16.5 vs 6.0 months; P=.03). There was no significant difference in outcome to sunitinib rechallenge based on number or mechanism of intervening treatments. Substantial new toxicity or significantly increased severity of prior toxicity was not seen during rechallenge in this cohort.

CONCLUSIONS

Sunitinib rechallenge had potential benefits and was tolerated in select metastatic RCC patients. Additional prospective investigation was warranted.

DNA methylation of polycomb group target genes in cores taken from breast cancer centre and periphery

We previously demonstrated that methylation of neugogenic differentiation 1 (NEUROD1) gene, a polycomb group target (PCGT) gene is a predictor of response to neoadjuvant chemotherapy in breast cancer. Here, we address the question whether NEUROD1 methylation provides clinical information independent from its expression level, and whether PCGT methylation is homogeneous in breast cancer. We examined: (1) NEUROD1 methylation and mRNA expression in 9 breast cancer cell lines and 63 tumour specimens, (2) DNA methylation in a training set of 55 PCGT genes taken from the centre (TUC) and periphery (TUP) of 15 breast cancer specimens, and compared this with 22 non neoplastic controls, and finally, (3) validated statistically significant genes in an independent set of 20 cases versus 18 controls. 8/9 cell lines demonstrated NEUROD1 methylation, whereas, there was only one cell-line that showed NEUROD1 expression. There was no association between methylation and expression in breast tumour specimens, with only 14% exhibiting NEUROD1 expression. Of the 55 PCGT genes analysed, 24% (13/55) were shown to be cancer specific (p < 0.05) with a receiver-operating-characteristic (ROC) area-under-the-curve (AUC) of >0.7 (range 0.71-0.95). DNA methylation accurately predicted the presence of cancer in both TUC and TUP. DNA methylation of PCGT genes predicts the presence of breast cancer and is not subject to tumour heterogeneity. Further work will reveal if methylation of PCGT genes will serve as a robust means for the clinical detection and assessment of breast cancer.

Will knowledge of human genome variation result in changing cancer paradigms?

Our incomplete understanding of carcinogenesis may be a significant reason why some cancer mortality rates are still increasing. This lack of understanding is likely due to a research approach that relies heavily on genetic comparison between cancerous and non-cancerous tissues and cells, which has led to the identification of genes of cancer proliferation rather than differentiation. Recent observations showing that a tremendous degree of natural human genetic variation occurs are likely to lead to a shift in the basic paradigms of cancer genetics, in that there is a need to consider both the nature of the genes involved, and the idea that not every genetic variation identified in these genes may be associated with carcinogenesis. Based on studies using LCM and micro-genetic analyses, we propose that significant cancer initiating events may take place during the very early stages of development of cancer-susceptible tissues and that using such techniques might greatly help us in our understanding of carcinogenesis.

Genetic intra-tumour heterogeneity in epithelial ovarian cancer and its implications for molecular diagnosis of tumours

Genetic analysis of solid tumours using DNA or cDNA expression microarrays may enable individualized treatment based on the profiles of genetic changes that are identified from each patient. This could result in better response to adjuvant chemotherapy and, consequently, improved clinical outcome. So far, most research studies that have tested the efficacy of such an approach have sampled only single areas of neoplastic tissue from tumours; this assumes that the genetic profile within solid tumours is homogeneous throughout. The aim of this study was to evaluate the extent of genetic intra-tumour heterogeneity (ITH) within a series of epithelial ovarian cancers. Several different regions (five to eight regions) of tumour tissue from 16 grade 3, serous epithelial ovarian cancers were analysed for genetic alterations using a combination of microsatellite analysis and single nucleotide polymorphism (SNP) analysis, in order to establish the extent of ITH. Maximum parsimony tree analysis was applied to the genetic data from each tumour to evaluate the clonal relationship between different regions within tumours. Extensive ITH was identified within all ovarian cancers using both microsatellite and SNP analysis. Evolutionary analysis of microsatellite data suggested that the origin of all tumours was monoclonal, but that subsequent clonal divergence created mixed populations of genetically distinct cells within the tumour. SNP analysis suggested that ITH was not restricted to random genetic changes, but affected genes that have an important functional role in ovarian cancer development. The frequent occurrence of ITH within epithelial ovarian cancers may have implications for the interpretation of genetic data generated from emerging technologies such as DNA and mRNA expression microarrays, and their use in the clinical management of patients with ovarian cancer. The basis of genetic ITH and the possible implications for molecular approaches to clinical diagnosis of ovarian cancers may apply to other tumour types.

Bcl-2 protein and DNA ploidy in renal cell carcinoma: do they affect patient prognosis?

AIM

The aim of the present study was to correlate bcl-2 protein expression and DNA-ploidy status with established prognostic parameters in renal cell carcinoma (RCC) and to examine their impact on disease progression and patient survival.

METHODS

Both parameters were prospectively measured in 50 consecutive radical nephrectomy specimens using flow cytometry. They were correlated with the tumor grade, stage and histological type. Kaplan-Meier survival analysis for all parameters was performed.

RESULTS

Bcl-2 protein expression was higher in RCC compared to normal renal tissue (P < 0.0001). Aneuploid tumors had higher bcl-2 expression compared to diploid tumors (P = 0.015). Bcl-2 expression and DNA content were not correlated with tumor histological types (P = 0.277/P = 0.419), grades (P = 0.690/P = 0.449), T categories (P = 0.637/P = 0.585) or stages (P = 0.726/P = 0.800). Median follow-up time was 46 months (range, 5-84) with a mean overall survival of 61.8 months (95% confidence interval, 53.7-69.9). Tumor stage was the only statistically important prognostic factor (P = 0.0045).

CONCLUSION

Although Bcl-2 expression was correlated with tumor DNA content, the prognostic value of these two parameters following radical nephrectomy was not established.

Prognostic significance of clinicopathologic and deoxyribonucleic acid flow cytometric variables in non-metastatic renal cell carcinoma in the modern era

OBJECTIVE

The prognostic value of deoxyribonucleic acid (DNA) ploidy in renal cell carcinoma (RCC) is not well-defined among modern surgical nephrectomy series. We sought to determine which variables correlated with overall survival and recurrence-free survival in the modern era.

METHODS

We reviewed all patients from 1992 to 2000, who prospectively had DNA ploidy analysis of their primary tumor determined at the time of nephrectomy for nonmetastatic RCC. Variables examined included age, gender, ethnicity, presentation (incidental vs. symptomatic), preoperative laboratory studies, American Society for Anesthesiology class, tumor size, tumor-nodes-metastasis stage, histology, Fuhrman grade, and diploid versus nondiploid tumor. Statistical analyses of overall survival and recurrence-free survival were performed using the Kaplan-Meier method, log-rank test, and Cox regression model using commercially available software.

RESULTS

Sixty men and 41 women, median age 61 years (range, 23-85), were included. Pathologic stage included T1 (54 patients), T2 (14), and T3 (33). Eighty-four patients had conventional RCC. A total of 58 patients had well-differentiated (Fuhrman Grade 1 [12] or Grade 2 [46]), 28 had moderately differentiated (Grade 3), 12 had poorly differentiated tumors (Grade 4), and 3 were not specified. There were 52 patients who had diploid tumors, and 49 had aneuploid tumors. Median follow-up was 39 months (range, 0-109). Actuarial 5-year overall survival was 70%, and 5-year recurrence-free survival was 76%. Diploid tumors were significantly associated with better recurrence-free survival (P = 0.02) but not overall survival (P = 0.17). On multivariate analysis, the American Society for Anesthesiology class (P = 0.01), abnormal preoperative platelet count (P = 0.03), and tumor differentiation (P = 0.01) were independent predictors of overall survival, whereas only tumor differentiation (P = 0.05) was an independent predictor of recurrence-free survival.

CONCLUSIONS

In the modern era, DNA ploidy is not an independent predictor of either overall survival or recurrence-free survival in patients with nonmetastatic RCC. The most important predictor of recurrence-free survival is tumor differentiation.

Prognostic value of uPA, PAI-1, and DNA content in adult renal cell carcinoma

OBJECTIVES

To examine whether urokinase-type plasminogen activator (uPA) and type 1 plasminogen inhibitor (PAI-1), DNA ploidy, and S-phase fraction (SPF) add supplementary prognostic information relative to stage and Fuhrman's grade in renal cell carcinoma.

METHODS

A total of 100 patients with primary renal adenocarcinoma treated by nephrectomy were followed up for a median of 42 months. Of the 100 patients, 78 with Stage M0N0-Nx tumors were studied by multivariate analysis. The study population was dichotomized on the basis of the median cytosolic uPA and PAI-1 concentrations (30 pg/mg protein and 12.7 ng/mg protein, respectively). DNA content was measured by flow cytometry (FCM) on multiple tumor samples from each patient. DNA aneuploidy was observed in 67% of cases. The SPF was calculated for aneuploid samples.

RESULTS

An FCM classification based on a combination of DNA content and SPF was obtained. High-risk patients were those with aneuploid tumors and high SPF values (greater than 1.7%) and included 23% of patients with M0N0-Nx tumors. Cytosolic uPA and PAI-1 levels were not predictive of metastasis. The stage, grade, SPF, and FCM classification were statistically significant prognostic factors in the univariate analysis, in both the overall population and the M0N0-Nx subgroup. In multivariate analysis, tumor grade and the FCM classification were the only independent predictors of disease-free survival (P = 0.018 and P = 0.046, respectively).

CONCLUSIONS

We defined a group of M0N0-Nx patients with aneuploid tumors and high SPF values who are at a high risk of metastasis and who may benefit from closer long-term follow-up.

[Prognosis factors in pT3 renal carcinoma]

OBJECTIVES

To identify independent predictors of progression and global survival in patients affected by pT3 renal cell carcinoma. To make risk groups by risk factors.

MATERIAL AND METHODS

We evaluated 117 patients with pT3 renal cell carcinoma. 88 was M0 and 29 M1. Most frequent clinical feature: asintomatic patients. 80 males (69%) and 37 females (31%). Mean age 59 (24-82). Median follow up 34 months (mean 44 +/- 39 months).

RESULTS

Pathological stage (TNM 1997) was pT3a in 52 patients (43.6%), pT3b 63 patients (53.6%) and pT3c 2 patients.

HISTOLOGY

clear cell carcinoma 106 patients (90.6%), papillary 5 patients (4.3%) an dchromophobe 4 patients (3.4%). Nuclear grading according Fuhrman's classification: G1 13 patients, G2 45 patients, G3 32 and G4 12 patients. Size > 4 cm (p = 0.005/p = 0.0019), grade 3-4 (p = 0.006/p = 0.0007), N+ (p = 0.034/p = 0.009) and M+ (p = 0.035/p = 0.042) were independent prognosis factors for progression and global survival of the pT3 renal cell carcinoma. Patients M0 with 0 or 1 risk factor have better global survival tanh patients M0 with 3 or 4 risk factors and patients M1.

CONCLUSIONS

Size, grade, N+ and M+ were independent prognosis factors for progression and global survival of the pT3 renal cell carcinoma. Tera are no differencies in global survival between patients M0 with 2 or 3 risk factors and patients M1.

[Clinical features, diagnosis, and prognosis of renal carcinoma]

Significant conceptual changes have taken place in renal tumoral diseases over the last few years. As a result of the authors' broad institutional experience, this overall revision describes the most up-to-date clinical and diagnostic aspects of this condition. Emphasis is made on molecular staging and two variables that guide the prognosis of the disease, a decisive feature to establish treatment and to contribute to change current survival rates.

Proliferative activity of renal cell carcinoma associated with acquired cystic disease of the kidney: comparison with typical renal cell carcinoma

To assess the proliferative activity of renal cell carcinoma (RCC-A) in patients with acquired cystic disease of the kidney (ACDK) after long-term hemodialysis, we analyzed cell cycle, DNA ploidy, and S-phase fraction by flow cytometry (FCM) and proliferating cell nuclear antigen (PCNA) labeling index by immunohistochemistry. The data were compared with those of typical RCC (tRCC). Sixteen (88.9%) of 18 RCC-As showed a diploid pattern. The values of cells at each phase in the cell cycle in RCC-A group (S, 4.36% + 2.16%; G2M, 5.06% + 1.90%; S+G2M, 9.41% + 2.81%; P <.05) were significantly different from those of tRCCs (S, 8.91% + 6.58%; G2M, 8.77% + 5.73%; S+G2M; 17.67% + 7.61%). The PCNA labeling index was statistically significantly lower in the RCC-As (24.01% +/- 13.4%; P <.05) than in tRCCs (42.27% +/- 26.1%). These results indicate that the RCC-As are less proliferative than tRCC and are consistent with the observation that RCC-As are less aggressive neoplasms.