Establishing cut-off points with clinical relevance for bcl-2, cyclin D1, p16, p21, p27, p53, Sox11 and WT1 expression in glioblastoma - a short report

OTUD4 promotes the progression of glioblastoma by deubiquitinating CDK1 and activating MAPK signaling pathway

Glioblastoma, IDH-Wild type (GBM, CNS WHO Grade 4) is a highly heterogeneous and aggressive primary malignant brain tumor with high morbidity, high mortality, and poor patient prognosis. The global burden of GBM is increasing notably due to limited treatment options, drug delivery problems, and the lack of characteristic molecular targets. OTU deubiquitinase 4 (OTUD4) is a potential predictive factor for several cancers such as breast cancer, liver cancer, and lung cancer. However, its function in GBM remains unknown. In this study, we found that high expression of OTUD4 is positively associated with poor prognosis in GBM patients. Moreover, we provided in vitro and in vivo evidence that OTUD4 promotes the proliferation and invasion of GBM cells. Mechanism studies showed that, on the one hand, OTUD4 directly interacts with cyclin-dependent kinase 1 (CDK1) and stabilizes CDK1 by removing its K11, K29, and K33-linked polyubiquitination. On the other hand, OTUD4 binds to fibroblast growth factor receptor 1 (FGFR1) and reduces FGFR1's K6 and K27-linked polyubiquitination, thereby indirectly stabilizing CDK1, ultimately influencing the activation of the downstream MAPK signaling pathway. Collectively, our results revealed that OTUD4 promotes GBM progression via OTUD4-CDK1-MAPK axis, and may be a prospective therapeutic target for GBM treatment.

PINK1 Immunoexpression Predicts Survival in Patients Undergoing Hepatic Resection for Colorectal Liver Metastases

PTEN-induced kinase-1 (PINK1) is the initiator of the canonical mitophagy pathway. Our aim was to study the immunoexpression of PINK1 in surgical specimens from ninety patients with metastatic colorectal adenocarcinoma (CRC) to the liver (CRLM). Tissue arrays were produced, and immunohistochemical studies were analyzed by the H-Score method. The mean immunoexpression of PINK1 in normal tissues was between 40 to 100 points. In tumoral tissues, positive PINK1 immunoexpression was observed in all samples, and no differences were noted between CRCs. In CRLMs, a significant under-expression was noted for PINK1 from the rectum (71.3 ± 30.8; p < 0.042) compared to other sites. Altered PINK1 immunoexpression in CRCs, either higher than 100 points or lower than 40 points, was associated with worse overall survival (OS) (p < 0.012) due to a shorter post-metastatic survival (PMS) (p < 0.023), and it was found to be a significant independent predictor of prognosis in a multivariate model for OS and PMS (HR = 1.972, 95% CI 0.971–4.005; p = 0.022. HR = 2.023, 95% CI 1.003–4.091; p = 0.037, respectively). In conclusion, altered PINK1 immunoexpression determined in CRCs with resected CRLM predicts a worse prognosis, possibly due to the abnormal function of mitophagy.

Prognostic value of Ki-67 index in primary intracranial tumors of infants

OBJECTIVE

Primary intracranial tumors are rare tumors in infants. They differ from those found in other pediatric age groups in terms of clinical presentation, histopathological diagnosis, adjuvant therapies, and outcome. Ki-67 index has also shown promising results as a prognostic factor in different types of intracranial tumors in children and adults. However, the importance and the best cutoff point of Ki-67 index in primary intracranial tumors of infants remains unclear. We aimed to analyze prognostic value of Ki-67 index in primary intracranial tumors of infants.

METHODS

This study retrospectively reviewed the records of 28 infants undergoing surgical resection for primary intracranial tumors between April 2016 and March 2021. We analyzed clinical characteristics, tumor location, extent of resection, histopathological diagnosis, Ki-67 index, and overall survival (OS). To define the most relevant cutoff value for Ki-67 index, "Cutoff Finder" was used.

RESULTS

The median age at diagnosis was 188 days for all patients. Fifteen of the patients were boys and 13 were girls. Tumors were located supratentorial in 13 patients and infratentorial in 15 patients. Gross total resection was performed in 7 of 13 supratentorial tumors and 9 of 15 infratentorial tumors. The mean Ki-67 index of the supratentorial tumors was 49.6%, the median was 55%; for infratentorial tumors, the mean was 49.9%, and the median was 70%. Tumor grade (p = 0.019) and Ki-67 index (p = 0.003) were found as significant predictors of OS in log-rank testing for Kaplan-Meier survival analysis. Univariate cox regression analysis identified high Ki-67 index as prognostic factor for worse OS, with hazard ratio of 8.852 (95% CI 1.95-64.80; p = 0.0108). High Ki-67 index was found as independent prognostic factor for worse OS in multivariate cox regression analysis (HR 7.036; 95% CI 1.229-65.82; p = 0.0457).

CONCLUSION

High-grade and high Ki-67 index were associated with worse outcome. Ki-67 index did show a distinct prognostic value for OS within our cohort at a cutoff value of 72.5%.

The Role of Network Science in Glioblastoma

Network science has long been recognized as a well-established discipline across many biological domains. In the particular case of cancer genomics, network discovery is challenged by the multitude of available high-dimensional heterogeneous views of data. Glioblastoma (GBM) is an example of such a complex and heterogeneous disease that can be tackled by network science. Identifying the architecture of molecular GBM networks is essential to understanding the information flow and better informing drug development and pre-clinical studies. Here, we review network-based strategies that have been used in the study of GBM, along with the available software implementations for reproducibility and further testing on newly coming datasets. Promising results have been obtained from both bulk and single-cell GBM data, placing network discovery at the forefront of developing a molecularly-informed-based personalized medicine.

TRIM47 promotes malignant progression of renal cell carcinoma by degrading P53 through ubiquitination

Background

Renal cell carcinoma (RCC) is one of the most common malignant tumors originating from the renal parenchymal urinary epithelial system. Tripartite motif 47 (TRIM47) is a member of the TRIM family proteins, which has E3 ligase activity and has been demonstrated to be involved in the occurrence and prognosis of many tumors. The main purpose of this study is to explore the role and potential mechanism of TRIM47 in promoting malignant biological behavior of RCC.

Materials and methods

TRIM47 mRNA and protein levels in human renal cancer and paired normal adjacent tissues were detected by qRT-PCR and Western blot. The effects of TRIM47 knockdown and overexpression in renal cell carcinoma cells on cell proliferation, invasion and xenograft tumor growth in nude mice were analyzed. The molecular mechanism was explored by mass spectrometric exploration,Western blot and immunoprecipitation assays.

Results

TRIM47 promoted RCC cell proliferation in vitro and in vivo as an oncogene. Mechanistically, TRIM47 exerted an E3 ligase activity by interacting with P53 protein to increase its ubiquitination and degradation, which further promoted the malignant biological behavior of RCC.

Conclusions

Our study demonstrated that the TRIM47-P53 axis played a functional role in RCC progression and suggested a potential therapeutic target for RCC.

WT1 Clone 6F-H2 Cytoplasmic Expression Differentiates Astrocytic Tumors from Astrogliosis and Associates with Tumor Grade, Histopathology, IDH1 Status, Apoptotic and Proliferative Indices: A Tissue Microarray Study

OBJECTIVES

This tissue microarray (TMA) immunohistochemical (IHC) study elucidates the role of Wilms' tumor 1 protein (WT1) in diagnosis and prognostication of astrocytic tumors.

METHODS

IHC was applied to 75 astrocytic lesions (18 astrogliosis and 57 astrocytic tumors) using antibodies directed against WT1 clone 6F-H2, isocitrate dehydrogenase 1(IDH1), Bcl2 and Ki67. WT1 IHC staining was evaluated and scored blindly by 2 pathologists. Bcl2 and Ki67 scores and labelling indices were assessed and IDH1 status determined. Statistical analysis was performed using the appropriate methodology.

RESULTS

WT1 cytoplasmic expression was detected in 89.5% of astrocytic tumors but not in astrogliosis. Positive WT1 differentiated astrocytic tumors (92.6% accuracy) and grade II diffuse astrocytomas (93.5% accuracy) from astrogliosis with high sensitivity, specificity and positive predictive values (p<0.001). Increased WT1 score significantly associated higher Bcl2 and Ki67 labelling indices, increasing WHO tumor grade and tumor's histopathologic type (p<0.05) showing staining pattern variability by tumor entity and cell type. Glioblastomas, gliosarcomas and subependymal giant cell astrocytomas were the most frequently WT1 expressing tumors with frequent +3 WT1 score. About 21.4% of pilocytic astrocytomas had +3WT1 score in association with increased Bcl2 and Ki67 indices. Low WT1 scores in grade II and III diffuse astrocytomas were linked to the high frequency of IDH1 positivity, and were associated with low Bcl2 and Ki67 labelling indices. In glioblastomas, WT1 significantly associated poor prognostic variables: older age, negative-IDH1 status, high Bcl2 and Ki67 labelling indices (p=0.04, <0.001, =0.001 and.

The prognostic and predictive potential of Ki-67 in triple-negative breast cancer

As a cell proliferation biomarker, Ki-67 is principally used in ER+/HER2− breast cancer. However, the importance and the best cutoff point of Ki-67 in triple-negative breast cancer (TNBC) remains unclear and was evaluated in this study.A total of 1800 patients with early invasive TNBC between 2011 and 2016 at Fudan University Shanghai Cancer Center were consecutively recruited for this study. The optimal cutoff for Ki-67 was assessed by Cutoff Finder. Propensity score matching (PSM, ratio = 1:2) was performed to match the Ki-67^low group with the Ki-67^high group. Overall survival (OS) and disease-free survival (DFS) were compared between the two groups using the Kaplan-Meier method and Cox regression model. The most relevant cutoff value for Ki-67 for prognosis was 30% (p = 0.008). At the cutoff point of 30%, worse DFS and OS were observed in the Ki-67^high group. In multivariate analyses, N-stage (p < 0.001), T-stage (p = 0.038), and Ki-67 at the 30% threshold (p = 0.020) were independently linked to OS. In subgroup analysis, Ki-67 cutoff at 30% had prognostic and predictive potential for DFS with either tumor size ≤2 cm (p = 0.008) or lymph node-negative (N−) (p = 0.038) and especially with T₁N₀M₀ (stage I) TNBCs. For 945 N− TNBC patients, adjuvant chemotherapy (CT) was associated with better OS in the Ki-67^high group (p = 0.017) than in the Ki-67^low group (p = 0.875). For stage I/Ki-67^low patients, adjuvant CT did not affect DFS (p = 0.248). Thus, Ki-67 cutoff at 30% had early independent prognostic and predictive potential for OS and DFS in TNBCs, and Ki-67 > 30% was significantly associated with worse prognosis, especially for stage I patients. For stage I/Ki-67^low TNBC patients, the advantage of CT is unclear, providing the basis for future de-escalation therapy.

An Immunohistochemical Study of Cyclin D1 Expression in Astrocytic Tumors and its Correlation with Tumor Grade

Background & Objective:

Glioblastoma-multiforme is the high grade form of astrocytic tumors with a short survival time, which are the most common type of brain tumors. Therefore, finding new therapeutic options is essential. Cyclin D1 is expressed in some human malignancies and can be a potential target for therapeutic intervention. The aim of the present study was to determine this relationship.

Methods:

This is a cross-sectional study conducted in the pathology department of Al-Zahra Hospital in Isfahan, Iran. In this study, 100 samples diagnosed with astrocytic tumors between 2011 and 2015 that met the study’s requirements were studied and immunohistochemical staining for cyclin D1 was performed for each specimen. At the end, the relationship between the expression of cyclin D1 and various variables including tumor grades, tumor subtypes and patient demographic features were examined using appropriate statistical tests.

Results:

Of the 100 samples, cyclin D1 was positive in 60 samples and negative in 40 samples. Moreover, in 26 samples, the amount of the marker was low, while in 34 samples it was high. Following the results of the study, there was a significant difference (P =0.038) in the expression of the cyclin D1 marker among the four different grades of astrocytic tumors.

Conclusion:

The results showed that the expression of cyclin D1 was associated with different tumor grades, especially the high level of expression in grade 4, and the amount of cyclin D1 increased as the level of grade glioma increased.

Evaluate Cutpoints: Adaptable continuous data distribution system for determining survival in Kaplan-Meier estimator

BACKGROUND AND OBJECTIVE

Growing evidence of transcriptional and metabolomic differentiation induced many studies which analyze such differentiation in context of outcome of disease progression, treatment or influence of many different factors affecting cellular and tissue metabolism. Particularly, cancer researchers are looking for new biomarkers that can serve as a diagnostic/prognostic factor and its further corresponding relationship regarding clinical effects. As a result of the increasing interest in use of dichotomization of continuous variables involving clinical or epidemiological data (gene expression, biomarkers, biochemical parameters, etc.) there is a large demand for cutoff point determination tools with simultaneous lack of software offering stratification of patients based on continuous and binary variables. Therefore, we developed "Evaluate Cutpoints" application offering wide set of statistical and graphical methods for cutpoint optimization enabling stratification of population into two or three groups.

METHODS

Application is based on R language including algorithms of packages such as survival, survMisc, OptimalCutpoints, maxstat, Rolr, ggplot2, GGally and plotly offering Kaplan-Meier plots and ROC curves with cutoff point determination.

RESULTS

All capabilities of Evaluate Cutpoints were illustrated with example analysis of estrogen, progesterone and human epidermal growth factor 2 receptors in breast cancer cohort. Through ROC curve the cutoff points were established for expression of ESR1, PGR and ERBB2 in correlation with their immunohistochemical status (cutoff: 1301.253, 243.35, 11,434.438, respectively; sensitivity: 94%, 85%, 64%, respectively; specificity: 93%, 86%, 91%, respectively). Through disease-free survival analysis we divided patients into two and three groups regarding expression of ESR1, PGR and ERBB2. Example algorithm cutp showed that lowered expression of ESR1 and ERBB2 was more favorable (HR = 2.07, p = 0.0412; HR = 2.79, p = 0.0777, respectively), whereas heightened PGR expression was correlated with better prognosis (HR = 0.192, p = 0.0115).

CONCLUSIONS

This work presents application Evaluate Cutpoints that is freely available to download at http://wnbikp.umed.lodz.pl/Evaluate-Cutpoints/. Currently, many softwares are used to split continuous variables such as Cutoff Finder and X-Tile, which offer distinct algorithms. Unlike them, Evaluate Cutpoints allows not only dichotomization of populations into groups according to continuous variables and binary variables, but also stratification into three groups as well as manual selection of cutoff point thus preventing potential loss of information.

Tumor autophagy is associated with survival outcomes in patients with resected non-small cell lung cancer

OBJECTIVES

LC3A protein is associated with autophagosomes, and LC3A immunohistochemistry (IHC) is used for the detection of autophagy activity. The aim of this study was to assess the prognostic value of LC3A expression in patients with resected non-small cell lung cancer (NSCLC).

MATERIALS AND METHODS

We used tissue microarrays (TMAs) constructed from 116 resected stage IB-III NSCLC patients. Standard immunohistochemistry was performed on formalin-fixed paraffin-embedded tissue sections using antibody against LC3A autophagic potein. Stained slides were scanned by Olympus dotSlide Digital Virtual Microscopy System (Japan) and the LC3A staining was evaluated digitally. Groups were compared using the Mann Whitney U test, and correlations were assessed using Spearman's rank test. Survival was calculated using Kaplan-Meier analysis. Primary study endpoint was overall survival (OS), secondardy study endpoint disease-free survival (DFS). Cut-off optimization for LC3A prognostic value was performed using the "cut-off finder' 'software (Charite, Berlin, Germany). In addition, the Kaplan Meier plotter (KmPlot) was used to assess the relationship between LC3A mRNA expression and clinical outcome (OS and DFS) in patients with NSCLC.

RESULTS

From 116 patients, 88 tissue samples were available for final examination. No significant association was found between LC3A staining and other clinicopathological variables, including tumor grade, stage and histological subtype. A higher number of LC3A stone-like structures (SLSs) (>20), was significanly associated with poor OS (HR = 2.27, p = 0.011) and DFS (HR = 2.27, p = 0.003). A significant association between high LC3A mRNA and both a worse OS and worse DFS was found by KMPlot analysis in patients with stage I-III NSCLC.

CONSLUSION

This retrospective study suggests that SLSs as assessed by LC3A IHC as well as LC3A mRNA expression has a clinically relevant negative prognostic value in patients with resected NSCLC, and should be further investigated.