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.

Functional Short-Term Outcomes and Mortality in Children with Severe Traumatic Brain Injury: Comparing Decompressive Craniectomy and Medical Management.

The effect of decompressive craniectomy (DC) on functional outcomes and mortality in children after severe head trauma is strongly debated. The lack of high-quality evidence poses a serious challenge to neurosurgeons' and pediatric intensive care physicians' decision making in critically ill children after head trauma. This study was conducted to compare DC and medical management in severely head-injured children with respect to short-term outcomes and mortality. Data on patients <18 years of age treated in Germany, Austria, and Switzerland during a 10-year period were extracted from TraumaRegister DGU®, forming a retrospective multi-center cohort study. Descriptive and multi-variable analyses were performed to compare outcomes and mortality after DC and medical management. Of 2507 patients, 402 (16.0%) received DC. Mortality was 20.6% after DC and 13.7% after medical management. Poor outcome (death or vegetative state) occurred in 27.6% after DC and in 16.1% after medical management. After risk adjustment by logistic regression modeling, the odds ratio was 1.56 (95% confidence interval 1.01-2.40) for poor outcome at intensive care unit discharge and 1.20 (0.74-1.95) for mortality after DC. In summary, DC was associated with increased odds for poor short-term outcomes in children with severe head trauma. This finding should temper enthusiasm for DC in children until a large randomized controlled trial has answered more precisely if DC in children is beneficial or increases rates of vegetative state.

Targeted RNA-Sequencing Enables Detection of Relevant Translocations and Single Nucleotide Variants and Provides a Method for Classification of Hematological Malignancies-RANKING.

BACKGROUND: Patients with hematological malignancies (HMs) carry a wide range of chromosomal and molecular abnormalities that impact their prognosis and treatment. Since no current technique can detect all relevant abnormalities, technique(s) are chosen depending on the reason for referral, and abnormalities can be missed. We tested targeted transcriptome sequencing as a single platform to detect all relevant abnormalities and compared it to current techniques. MATERIAL AND METHODS: We performed RNA-sequencing of 1385 genes (TruSight RNA Pan-Cancer, Illumina) in bone marrow from 136 patients with a primary diagnosis of HM. We then applied machine learning to expression profile data to perform leukemia classification, a method we named RANKING. Gene fusions for all the genes in the panel were detected, and overexpression of the genes EVI1, CCND1, and BCL2 was quantified. Single nucleotide variants/indels were analyzed in acute myeloid leukemia (AML), myelodysplastic syndrome and patients with acute lymphoblastic leukemia (ALL) using a virtual myeloid (54 genes) or lymphoid panel (72 genes). RESULTS: RANKING correctly predicted the leukemia classification of all AML and ALL samples and improved classification in 3 patients. Compared to current methods, only one variant was missed, c.2447A>T in KIT (RT-PCR at 10-4), and BCL2 overexpression was not seen due to a t(14; 18)(q32; q21) in 2% of the cells. Our RNA-sequencing method also identified 6 additional fusion genes and overexpression of CCND1 due to a t(11; 14)(q13; q32) in 2 samples. CONCLUSIONS: Our combination of targeted RNA-sequencing and data analysis workflow can improve the detection of relevant variants, and expression patterns can assist in establishing HM classification.

Detection of Fusion Genes to Determine Minimal Residual Disease in Leukemia Using Next-Generation Sequencing.

BACKGROUND: Measuring minimal residual disease (MRD), the persistence of leukemic cells after treatment, is important for monitoring leukemia recurrence. The current methods for monitoring MRD are flow cytometry, to assess aberrant immune phenotypes, and digital droplet PCR (ddPCR), to target genetic aberrations such as single-nucleotide variants and gene fusions. We present the performance of an RNA-based next-generation sequencing (NGS) method for MRD gene fusion detection compared with ddPCR. This method may have advantages, including the capacity to analyze different genetic aberrations and patients in 1 experiment. In particular, detection at the RNA level may be highly sensitive if the genetic aberration is highly expressed. METHODS: We designed a probe-based NGS panel targeting the breakpoints of 11 fusion genes previously identified in clinical patients and 2 fusion genes present in cell lines. Blocking probes were added to prevent nonspecific enrichment. Each patient RNA sample was diluted in background RNA, depleted for rRNA and globin mRNA, converted to cDNA, and prepared for sequencing. Unique sequence reads, identified by unique molecular identifiers, were aligned directly to reference transcripts. The same patient and cell-line samples were also analyzed with ddPCR for direct comparison. RESULTS: Our NGS method reached a maximum sensitivity of 1 aberrant cell in 10 000 cells and was mostly within a factor of 10 compared with ddPCR. CONCLUSIONS: Our detection limit was below the threshold of 1:1000 recommended by European Leukemia Net. Further optimizations are easy to implement and are expected to boost the sensitivity of our method to diagnostically obtained ddPCR thresholds.

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.

Gene expression profiling of epithelium-associated FcRL4+ B cells in primary Sjögren's syndrome reveals a pathogenic signature.

In primary Sjögren's syndrome (pSS), FcRL4+ B cells are present in inflamed salivary gland tissue, within or in close proximity to ductal epithelium. FcRL4 is also expressed by nearly all pSS-related mucosa-associated lymphoid tissue (MALT) B cell lymphomas, linking FcRL4 expression to lymphomagenesis. Whether glandular FcRL4+ B cells are pathogenic, how these cells originate, and how they functionally differ from FcRL4- B cells in pSS is unclear. This study aimed to investigate the phenotype and function of FcRL4+ B cells in the periphery and parotid gland tissue of patients with pSS. First, circulating FcRL4+ B cells from 44 pSS and 54 non-SS-sicca patients were analyzed by flow cytometry. Additionally, RNA sequencing of FcRL4+ B cells sorted from parotid gland cell suspensions of 6 pSS patients was performed. B cells were sorted from cell suspensions as mini bulk (5 cells/well) based on the following definitions: CD19+CD27-FcRL4- ('naive'), CD19+CD27+FcRL4- ('memory'), and CD19+FcRL4+ B cells. We found that, although FcRL4+ B cells were not enriched in blood in pSS compared with non-SS sicca patients, these cells generally exhibited a pro-inflammatory phenotype. Genes coding for CD11c (ITGAX), T-bet (TBX21), TACI (TNFRSF13B), Src tyrosine kinases and NF-κB pathway-related genes were, among others, significantly upregulated in glandular FcRL4+ B cells versus FcRL4- B cells. Pathway analysis showed upregulation of B cell activation, cell cycle and metabolic pathways. Thus, FcRL4+ B cells in pSS exhibit many characteristics of chronically activated, pro-inflammatory B cells and their gene expression profile suggests increased risk of lymphomagenesis. We postulate that these cells contribute significantly to the epithelial damage seen in the glandular tissue and that FcRL4+ B cells are an important treatment target in pSS.

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.

A Transcriptionally Distinct CXCL13+CD103+CD8+ T-cell Population Is Associated with B-cell Recruitment and Neoantigen Load in Human Cancer.

The chemokine CXCL13 mediates recruitment of B cells to tumors and is essential for the formation of tertiary lymphoid structures (TLSs). TLSs are thought to support antitumor immunity and are associated with improved prognosis. However, it remains unknown whether TLSs are formed in response to the general inflammatory character of the tumor microenvironment, or rather, are induced by (neo)antigen-specific adaptive immunity. We here report on the finding that the TGFß-dependent CD103+CD8+ tumor-infiltrating T-cell (TIL) subpopulation expressed and produced CXCL13. Accordingly, CD8+ T cells from peripheral blood activated in the presence of TGFß upregulated CD103 and secreted CXCL13. Conversely, inhibition of TGFß receptor signaling abrogated CXCL13 production. CXCL13+CD103+CD8+ TILs correlated with B-cell recruitment, TLSs, and neoantigen burden in six cohorts of human tumors. Altogether, our findings indicated that TGFß plays a noncanonical role in coordinating immune responses against human tumors and suggest a potential role for CXCL13+CD103+CD8+ TILs in mediating B-cell recruitment and TLS formation in human tumors.

Running-wheel activity delays mitochondrial respiratory flux decline in aging mouse muscle via a post-transcriptional mechanism.

Loss of mitochondrial respiratory flux is a hallmark of skeletal muscle aging, contributing to a progressive decline of muscle strength. Endurance exercise alleviates the decrease in respiratory flux, both in humans and in rodents. Here, we dissect the underlying mechanism of mitochondrial flux decline by integrated analysis of the molecular network. Mice were given a lifelong ad libitum low-fat or high-fat sucrose diet and were further divided into sedentary and running-wheel groups. At 6, 12, 18 and 24 months, muscle weight, triglyceride content and mitochondrial respiratory flux were analysed. Subsequently, transcriptome was measured by RNA-Seq and proteome by targeted LC-MS/MS analysis with 13 C-labelled standards. In the sedentary groups, mitochondrial respiratory flux declined with age. Voluntary running protected the mitochondrial respiratory flux until 18 months of age. Beyond this time point, all groups converged. Regulation Analysis of flux, proteome and transcriptome showed that the decline of flux was equally regulated at the proteomic and at the metabolic level, while regulation at the transcriptional level was marginal. Proteomic regulation was most prominent at the beginning and at the end of the pathway, namely at the pyruvate dehydrogenase complex and at the synthesis and transport of ATP. Further proteomic regulation was scattered across the entire pathway, revealing an effective multisite regulation. Finally, reactions regulated at the protein level were highly overlapping between the four experimental groups, suggesting a common, post-transcriptional mechanism of muscle aging.

Somatic Leiomyosarcoma of the Soft Tissues: A Single-Institutional Analysis of Factors Predictive of Survival in 164 Patients.

BACKGROUND: Somatic leiomyosarcoma (LMS) is an aggressive soft tissue sarcoma entity with a high metastatic potential. The purpose of this study was to identify prognostic indicators of survival in patients with somatic LMS of the soft tissues. METHODS: We retrospectively assessed the relationship between local recurrence-free survival (LRFS), disease-specific survival (DSS), overall survival (OS) and potential prognostic factors in 164 patients who were suitable for surgical treatment in curative intent. Patients with soft tissue LMS of the extremities, the truncal wall and the head and neck area were included. The median follow-up time was 4.9 years. RESULTS: In the entire cohort, the 5-year estimate of the DSS, OS and LRFS rate were 74.5% (95% confidence interval [CI] 65.0-81.8), 70.6% (95% CI: 60.9-78.3) and 63.4% (95% CI 53.4-71.9), respectively. Thirty-eight patients (23.2%) developed distant metastases with a median survival time of 1.5 years after diagnosis of metastasis. Surgical margins attained at the initial oncologic resection and eventual re-excisions did not influence DSS, OS and LRFS significantly. Within the R0 subgroup, close and wide negative margins led to similar outcomes. High histologic grade (P < 0.001), size >5 cm (P = 0.002) and subfascial localisation (P = 0.002) were associated with significantly diminished DSS in univariate analysis. In multivariate analysis, only histologic grade was found to be an independent prognostic factor of DSS. CONCLUSIONS: The data from this study could not determine a prognostic significance of surgical margins suggesting that tumour characteristics other than margin status are important. Tumour biology reflected by the histologic grade dictates the final outcome.

A single-institutional review of 68 patients with dermatofibrosarcoma protuberans: wide re-excision after inadequate previous surgery results in a high rate of local control.

BACKGROUND: Dermatofibrosarcoma protuberans (DFSP) is a cutaneous soft tissue sarcoma characterized by an indolent but aggressive local growth. Unplanned excisions with positive margins are common, and the prognostic impact of radical re-excisions is still unclear. The aim of the present study was to identify prognostic indicators of recurrence-free survival (RFS) in patients with DFSP through a long-term follow-up. We tried particularly to determine the prognostic impact of surgical margins and re-excisions in patients after earlier inadequate surgery. METHODS: Seventy-five patients with DFSP were treated surgically at our institution between 1999 and 2015. Analyses were restricted to 68 participants with available information on surgical margins. The median follow-up was 5.4 years. RESULTS: Fifty-four patients (79.4%) had low-grade DFSP and 14 patients (20.6%) intermediate-grade FS-DFSP. The 5-year RFS rates were estimated to be 93.5% (95% CI 81.2-97.9) for low-grade DFSP and 39.7% (95% CI 13.0-65.8) for FS-DFSP (P < 0.0001). Re-excisions were performed in 55 patients (80.9%) following R1 or marginal R0 resections. Negative margins could be attained in a total of 65 patients (95.6%). Negative margin widths >1 cm led to the best local outcome within the R0 subgroup. Significant adverse prognostic features in the multivariate analysis included histologic grade and close margins. CONCLUSIONS: The data from this study underscore the long-term benefit of negative margins. In our analysis, re-excisions were an effective method to achieve a high rate of local control in patients who presented after R1 or marginal R0 resection. To ensure the best outcome, re-excisions should aim at negative margin widths of more than 1 cm in the histologic specimen.

Mutation patterns in small cell and non-small cell lung cancer patients suggest a different level of heterogeneity between primary and metastatic tumors.

Several studies have shown heterogeneity in lung cancer, with parallel existence of multiple subclones characterized by their own specific mutational landscape. The extent to which minor clones become dominant in distinct metastasis is not clear. The aim of our study was to gain insight in the evolution pattern of lung cancer by investigating genomic heterogeneity between primary tumor and its distant metastases. Whole exome sequencing (WES) was performed on 24 tumor and five normal samples of two small cell lung carcinoma (SCLC) and three non-SCLC (NSCLC) patients. Validation of somatic variants in these 24 and screening of 33 additional samples was done by single primer enrichment technology. For each of the three NSCLC patients, about half of the mutations were shared between all tumor samples, whereas for SCLC patients, this percentage was around 95. Independent validation of the non-ubiquitous mutations confirmed the WES data for the vast majority of the variants. Phylogenetic trees indicated more distance between the tumor samples of the NSCLC patients as compared to the SCLC patients. Analysis of 30 independent DNA samples of 16 biopsies used for WES revealed a low degree of intra-tumor heterogeneity of the selected sets of mutations. In the primary tumors of all five patients, variable percentages (19-67%) of the seemingly metastases-specific mutations were present albeit at low read frequencies. Patients with advanced NSCLC have a high percentage of non-ubiquitous mutations indicative of branched evolution. In contrast, the low degree of heterogeneity in SCLC suggests a parallel and linear model of evolution.

Primary and Secondary Soft Tissue Angiosarcomas: Prognostic Significance of Surgical Margins in 43 Patients.

BACKGROUND: Angiosarcomas are aggressive soft tissue sarcomas. Due to their rarity there is a paucity of data regarding the clinical outcome of patients with non-visceral angiosarcomas of the soft tissues. In particular, the prognostic significance of surgical margins remains controversial. PATIENTS AND METHODS: We retrospectively assessed the outcome of 43 patients with localised disease suitable for surgical treatment with curative intent. The median follow-up was 7.5 years. RESULTS: The 5-year overall survival (OS) rate was 46.2%. Sixteen patients (37.2%) were diagnosed with secondary, radiation-induced angiosarcomas. Twenty-four patients (55.8%) developed local recurrences and 15 patients (34.9%) distant metastases. Negative surgical margin emerged as the only statistically significant prognostic factor (5-year OS: R0 51.8% vs. R1/R2 17.1%, p=0.036). As indicated in the regression analysis, close and wide negative margins within the R0 subgroup led to similar outcomes. CONCLUSION: Angiosarcomas have a high risk of local recurrence and metastasis. Surgical resection with negative margins improves the outcome.