Genomic heterogeneity of clear cell renal cell carcinoma

Defects in DNA are an important driver of the behaviour of cancer. One of the challenges in understanding and treating cancer is that tumours of a certain type can differ between each other but also not all cancer cells within a single tumour are identical. Some cells within a tumour can for example be more resistant to chemotherapy than others or be more inclined to metastasize. Pathologist Paranita Ferronika (Department of Genetics, UMCG) studied these differences in the clear cell type of kidney cancer, which is the most common and usually lethal type. She identified many genetic differences between and within these tumours, and also between the tumours and their metastases. She was able to reconstruct the genetic steps in the evolution of metastases from particular regions within the kidney cancer. She also found that patients with defects in a particular combination of genes (PBRM1 and VHL) have a better cancer related survival than patients with tumours lacking that combination. Gaining more insight into the genetic differences between and within this kidney tumours and their metastases can help improving cancer diagnostics and treatment in the future

Mutational heterogeneity between different regional tumour grades of clear cell renal cell carcinoma

Only a limited number of studies have explored the possible associations between tumour grade and mutated genes in clear cell renal cell carcinoma (ccRCC), and we set out to investigate this further using a multiple sampling and next generation sequencing (NGS) approach in a series of ccRCCs. Multiple regions were sampled from formalin-fixated paraffin-embedded ccRCC tumour blocks from seven patients. In 27 samples from six patients, we performed targeted NGS using a custom 42-gene panel based on the most frequently mutated genes in ccRCC reported in public databases. In four samples from the seventh patient, we performed whole exome sequencing (WES) and array comparative genomic hybridisation for detection of copy number variants (CNVs). Mutated genes and the tumour grades of the samples in which they had been identified were compared both within and between all individual tumours. CNVs were compared across all samples from patient 7. We identified clear genetic heterogeneity within and across tumours, but VHL mutations were seen in all patients. Looking across all samples, we identified eleven genes that were only mutated in samples with one particular tumour grade. However, these genes were never mutated in all samples with that tumour grade. Increasing chromosomal instability corresponded with increasing tumour grade, but we observed minimal association between tumour grade and total mutational load in the WES data. Our study confirms the genetic heterogeneity and tumour grade heterogeneity of ccRCC. Although a relatively small number of samples was analysed, genes were identified that could potentially be specific, though insensitive, markers of higher ccRCC tumour grades

Evaluation of a seven gene mutational profile as a prognostic factor in a population-based study of clear cell renal cell carcinoma

In this study, we investigate the influence of the seven genes (VHL, PBRM1, SETD2, BAP1, KDM5C, MTOR and TP53) most frequently mutated in clear cell renal cell cancer (ccRCC) on cancer-specific survival (CSS) in the prospective Netherlands Cohort Study on diet and cancer. DNA isolated from routinely archived formalin-fixed paraffin-embedded tumour blocks from 252 incident ccRCC cases was available for targeted next generation sequencing. Based on the sequencing quality and the completeness of information on clinical characteristics and follow-up, we could use 110 cases for survival analysis. The association with CSS for each mutated gene in these cases was tested using multivariable Cox proportional hazards models to estimate hazards ratios (HR) and confidence intervals (CIs), and we observed mutations in one or more of the seven genes in 64 out of 110 cases (58%). In the multivariable-adjusted analyses, mutations in VHL and PBRM1 were associated with better CSS (HRs (95% CI) 0.34 (0.13‒0.89) and 0.17 (0.04–0.66), respectively), although these results were not statistically significant after multiple testing correction. No association was observed for the other five genes, which may be attributable to limited power

Expression of p63 Cytoplasmic Aberrance, Notch1, and ALDH1A1 in Prostate Lesions

Background: Prostate cancer in Indonesia is the third rank cancer among male and the fifth rank cancer mortality among male. Prognostic markers that can identify aggressive prostate cancer in early lesion which can help select appropriate therapy to finally reduce the mortality are therefore urgently needed. It has been proven that stem cell in prostate gland have a role in initiation, progression, and metastasis of cancer cells, although still in controversy. Maintenance of normal stem cell or reserve cell populations in several epithelia including prostate gland were shown to be regulated by p63 and Notch1. The alteration of p63 expression is considered to have an oncogenic role in prostate cancer. This oncogenic role was also proposed associated with Notch1 expression. Objective: To investigate the role of cancer stem cell and its regulation in initiation and progression of prostate cancer by investigating its association with pathological diagnosis including Gleason score, cell proliferation, and apoptosis. Methods: Cross-sectional study in period of 2009-2010 was performed, in which totally 79 paraffin embedded tissues consisting of Benign Prostatic Hyperplasia, High Grade Prostatic Intraepithelial Neoplasia, and prostate cancer were investigated using IHC staining. The expressions of ALDH1A1, cytoplasmic p63, and Notch1 in different group of prostate lesion were investigated. The association among those three markers was analyzed by Chi-square test. The association of those markers with pathological diagnosis was analyzed by Chisquare test. The association of ALDH1A1 and Notch1 expression with cell proliferation rate (Ki-67) and apoptotic marker (cleaved caspase 3) was analyzed by Mann-Whitney test. Meanwhile, the association of cytoplasmic p63 with Ki67 and cleaved caspase 3 was analyzed by Kruskal-Wallis test. A p-value of <0.05 was considered statistically significant. Results: Patients had mean age at the diagnosis of 69.89 years. Association were found between cytoplasmic p63, Notch1 and ALDH1A1 expression (Chi-square, both p<0.001). ALDH1A1, ectopic cytoplasmic p63, and Notch1 were found to be significantly associated with pathological diagnosis, including Gleason score (Chi-square, p<0.001, p=0.006, and p<0.001 respectively). Moreover, it is also found in this study that cytoplasmic p63 and Notch1 were significantly associated with frequency of proliferating cells in prostate cancers (Kruskall-Wallis, p=0.001 and Mann-Whitney, p=0.009 respectively). Only cytoplasmic p63 that was significantly associated with apoptotic rate (Kruskall-Wallis, p=0.015). Conclusion: The expression of ALDH1A1, p63 cytoplasmic aberrance, and Notch1 is suggested to be important in prostate cancer progression and may be used as molecular markers. The interaction among those components, although still clouded by controversy, needed to be outlined and further investigated

Pattern of skin diseases prompting biopsy before and during the COVID-19 pandemic in Yogyakarta, Indonesia

Introduction: Less biopsies were expected when large scale social restrictions were enforced during COVID-19 pandemic. Aim: To compare the skin diseases prompting biopsy before and during the COVID-19 pandemic. Materials and Methods: A retrospective study of skin diseases was performed; the skin problems were then grouped into major histopathological reactions. Results: A total of 229 biopsies were performed before the COVID-19 outbreak, whereas only 160 biopsies were done during the pandemic. Before versus during the outbreak, the proportion of major reactions were granulomatous 20.52 vs 21.88, neoplasms 17.47 vs 20, psoriasiform 14.85 vs 10, vesiculobullous 9.61 vs 8.75, others 10.92 vs 7.50, interface dermatitis 6.99 vs 10, vasculopathy 6.99 vs 5.63, spongiotic 6.55 vs 8.13, panniculitis 3.49 vs 3.75, and superficial and deep dermal infiltrate 2.62 vs 4.38. Conclusion: A decreased total number of patients prompting less biopsies were reported during the COVID-19 outbreak. However, the three largest percentages of major histopathological reactions were still similar, namely granulomatous, neoplasms, and psoriasiform. © 2022, Malaysian Society of Pathologists. All rights reserved

Pattern of skin diseases prompting biopsy before and during the COVID-19 pandemic in Yogyakarta, Indonesia

ntroduction: Less biopsies were expected when large scale social restrictions were enforced during COVID-19 pandemic. Aim: To compare the skin diseases prompting biopsy before and during the COVID-19 pandemic. Materials and methods: A retrospective study of skin diseases was performed; the skin problems were then grouped into major histopathological reactions. Results: A total of 229 biopsies were performed before the COVID-19 outbreak, whereas only 160 biopsies were done during the pandemic. Before versus during the outbreak, the proportion of major reactions were granulomatous 20.52% vs 21.88%, neoplasms 17.47% vs 20%, psoriasiform 14.85% vs 10%, vesiculobullous 9.61% vs 8.75%, others 10.92% vs 7.50%, interface dermatitis 6.99% vs 10%, vasculopathy 6.99% vs 5.63%, spongiotic 6.55% vs 8.13%, panniculitis 3.49% vs 3.75%, and superficial and deep dermal infiltrate 2.62% vs 4.38%. Conclusion: A decreased total number of patients prompting less biopsies were reported during the COVID-19 outbreak. However, the three largest percentages of major histopathological reactions were still similar, namely granulomatous, neoplasms, and psoriasiform

Stromal Tumor Infiltrating Lymphocytes (sTILs) Were Associated with a Higher Grade and a Lower Stage of Indonesian Triple Negative Breast Cancers

Objective: This study aimed to investigate the association of sTILs with clinicopathological parameters and overall survival (OS) in patients with triple negative breast cancer (TNBC). Methods: One hundred and twenty-five paraffin embedded tissue of patients with TNBC, collected from Dr. Sardjito General Hospital Yogyakarta, Indonesia, between 2008-2017, were used in this study. Stromal TILs were examined from hematoxylin and eosin (H&E)-stained samples, and classified as either low or high score using 20 cut-off. Analysis of the association of sTILs with clinicopathological parameters, relative risk (RR) and OS used 95 confidence interval (CI) with significance set as pIIIa (56), alive (50.4), and with low sTILs (54.4). The results showed significant association between sTILs and a higher grade or a lower stage of tumor (B = 0.259, 95CI = 0.090-0.468, p = 0.004 and B = -0.255, 95CI = -0.433 - -0.080, p = 0.005, respectively ). Meanwhile sTILs were not associated with age at diagnosis (B = 0.027, 95CI = -0.193 – 0.264 p = 0.758 nor 3-year OS of patients (HR = 0.342, 95CI = 0.41 - 1.43 p = 0.402). Conclusion: The results indicate that sTILs may serve as an additional pathological parameter for TNBC. © This work is licensed under a Creative Commons Attribution-Non Commercial 4.0 International Licens

Regulatory T Cells but Not Tumour-Infiltrating Lymphocytes Correlate with Tumour Invasion Depth in Basal Cell Carcinoma

Basal cell carcinoma (BCC) is the most common skin malignancy worldwide. Current evidence suggests tumour-infiltrating lymphocytes (TILs) may influence the clinical outcomes of patients with BCC. The present study aimed to profile the infiltrative characteristics of stromal TILs and regulatory T cells (Treg cells) in the tumour centre (TC), tumour periphery (TP), and normal adjacent tissue (NAT) of BCC. A total of 111 samples from 43 cutaneous BCC cases were examined for TIL (CD3+) and Treg cell (FOXP3+/CD3+) expression using immunohistochemical techniques. The correlations of Treg cells with TILs, invasion depth, and tumour morphological risk were analysed. We identified a high mean proportion of Treg cells within the tumour (TC = 46.9%, TP = 56.1%, NAT = 51.8%) despite a relatively low median of TILs (TC = 12.7%, TP = 10.3%, NAT = 3.6%), supporting the classification of BCC as a cold tumour. A significant positive correlation was observed between the proportion of Treg cells and sTILs (&rho; = 0.325, p &lt; 0.001), suggesting a predominant role of TILs in the infiltration of Treg cells. An inverse correlation discovered between Treg cells and tumour invasion depth (r = &minus;0.36, p = 0.017) might indicate Treg cells&rsquo; anti-tumour capacity in BCC

Comprehensive Profiling of Primary and Metastatic ccRCC Reveals a High Homology of the Metastases to a Subregion of the Primary Tumour

While intratumour genetic heterogeneity of primary clear cell renal cell carcinoma (ccRCC) is well characterized, the genomic profiles of metastatic ccRCCs are seldom studied. We profiled the genomes and transcriptomes of a primary tumour and matched metastases to better understand the evolutionary processes that lead to metastasis. In one ccRCC patient, four regions of the primary tumour, one region of the thrombus in the inferior vena cava, and four lung metastases (including one taken after pegylated (PEG)-interferon therapy) were analysed separately. Each sample was analysed for copy number alterations and somatic mutations by whole exome sequencing. We also evaluated gene expression profiles for this patient and 15 primary tumour and 15 metastasis samples from four additional patients. Copy number profiles of the index patient showed two distinct subgroups: one consisted of three primary tumours with relatively minor copy number changes, the other of a primary tumour, the thrombus, and the lung metastases, all with a similar copy number pattern and tetraploid-like characteristics. Somatic mutation profiles indicated parallel clonal evolution with similar numbers of private mutations in each primary tumour and metastatic sample. Expression profiling of the five patients revealed significantly changed expression levels of 57 genes between primary tumours and metastases, with enrichment in the extracellular matrix cluster. The copy number profiles suggest a punctuated evolution from a subregion of the primary tumour. This process, which differentiated the metastases from the primary tumours, most likely occurred rapidly, possibly even before metastasis formation. The evolutionary patterns we deduced from the genomic alterations were also reflected in the gene expression profiles

Evaluation of a seven gene mutational profile as a prognostic factor in a population-based study of clear cell renal cell carcinoma

In this study, we investigate the influence of the seven genes (VHL, PBRM1, SETD2, BAP1, KDM5C, MTOR and TP53) most frequently mutated in clear cell renal cell cancer (ccRCC) on cancer-specific survival (CSS) in the prospective Netherlands Cohort Study on diet and cancer. DNA isolated from routinely archived formalin-fixed paraffin-embedded tumour blocks from 252 incident ccRCC cases was available for targeted next generation sequencing. Based on the sequencing quality and the completeness of information on clinical characteristics and follow-up, we could use 110 cases for survival analysis. The association with CSS for each mutated gene in these cases was tested using multivariable Cox proportional hazards models to estimate hazards ratios (HR) and confidence intervals (CIs), and we observed mutations in one or more of the seven genes in 64 out of 110 cases (58%). In the multivariable-adjusted analyses, mutations in VHL and PBRM1 were associated with better CSS (HRs (95% CI) 0.34 (0.13‒0.89) and 0.17 (0.04-0.66), respectively), although these results were not statistically significant after multiple testing correction. No association was observed for the other five genes, which may be attributable to limited power