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Colon cancer is a heterogeneous tumor driven by a subpopulation of cancer stem cells (CSCs). To study CSCs in colon cancer, we used limiting dilution spheroid and serial xenotransplantation assays to functionally define the frequency of CSCs in a panel of patient-derived cancer organoids. These studies demonstrated cancer organoids to be enriched for CSCs, which varied in frequency between tumors. Whole-transcriptome analysis identified WNT and Hedgehog signaling components to be enhanced in CSC-enriched tumors and in aldehyde dehydrogenase (ALDH)-positive CSCs. Canonical GLI-dependent Hedgehog signaling is a negative regulator of WNT signaling in normal intestine and intestinal tumors. Here, we show that Hedgehog signaling in colon CSCs is autocrine SHH-dependent, noncanonical PTCH1 dependent, and GLI independent. In addition, using small-molecule inhibitors and RNAi against SHH-palmitoylating Hedgehog acyltransferase (HHAT),we demonstrate that non-canonical Hedgehog signaling is a positive regulator of WNT signaling and required for colon CSC survival. [ABSTRACT FROM AUTHOR]

Mutated genes of the RAS family encoding small GTP-binding proteins drive numerous cancers, including pancreatic, colon and lung tumors. Besides the numerous effects of mutant RAS gene expression on aberrant proliferation, transformed phenotypes, metabolism, and therapy resistance, the most striking consequences of chronic RAS activation are changes of the genetic program. By performing systematic gene expression studies in cellular models that allow comparisons of pre-neoplastic with RAS-transformed cells, we and others have estimated that 7 percent or more of all transcripts are altered in conjunction with the expression of the oncogene. In this context, the number of up-regulated transcripts approximates that of down-regulated transcripts. While up-regulated transcription factors such as MYC, FOSL1, and HMGA2 have been identified and characterized as RAS-responsive drivers of the altered transcriptome, the suppressed factors have been less well studied as potential regulators of the genetic program and transformed phenotype in the breadth of their occurrence. We therefore have collected information on downregulated RAS-responsive factors and discuss their potential role as tumor suppressors that are likely to antagonize active cancer drivers. To better understand the active mechanisms that entail anti-RAS function and those that lead to loss of tumor suppressor activity, we focus on the tumor suppressor HREV107 (alias PLAAT3 [Phospholipase A and acyltransferase 3], PLA2G16 [Phospholipase A2, group XVI] and HRASLS3 [HRAS-like suppressor 3]). Inactivating HREV107 mutations in tumors are extremely rare, hence epigenetic causes modulated by the RAS pathway are likely to lead to down-regulation and loss of function. [ABSTRACT FROM AUTHOR]

Summary: Gene expression profiling studies and conventional approaches for the identification of genes involved in the initiation and progression of ovarian cancer have identified a plethora of potential therapeutic targets. This review summarizes the targets that show promise for specific interference in cancer cells, groups them according to their subcellular localization and involved biological processes and discusses their impact on experimental, pre-clinical and clinical therapy. [Copyright &y& Elsevier]

The scope of this project covers the storing of result data produced by generic laboratory devices during processing of analytical experiments, the data describing the examination methods, and the audit trail using the Analytical Information Markup Language (AnIML) standard. This project also considers the integration of generic devices in automated laboratory environments. AnIML is an upcoming ASTM standard format for recording analytical data and workflows with accompanying experimental metadata. Adapting this standard to existing instruments currently requires manual intervention. The goal of this project is to automate as many steps as possible in generating an AnIML document with all its essential information supplied directly by the analytical instrument. Software with such functionality could be integrated into analytical instruments or reside in firmware boxes hooked to the instruments. This would allow a smooth transition to the new standard even in complex existing environments. A set of prerequisites have to be fulfilled before the feasibility of this approach can be shown. The prototype application we describe here integrates the generic description of an instrument using the Laboratory Equipment Control Interface Specification, Object Management Group (LECIS OMG) Device Capability Dataset. Information about the device''s commands and the device''s data stream with its semantics can be found there. The experiment''s metadata are provided by the test order. In both cases, XML schemas contain the information syntax. Using this information, we developed a generic interface that maps the result stream semantically and then transforms it into an AnIML document without manual intervention. At this time, we have completed and tested a prototype implementation and are working to support the full functionality of both the LECIS OMG and the ASTM AnIML standards. [Copyright &y& Elsevier]

Laboratory environments are controlled more and more by automated systems. Written procedures and lab journals are replaced by workflow description languages and electronic notebooks, which not only describe the processes but are used also for the control of the entire workbench, data acquisition, and documentation. Dynamic scheduling is needed in such an environment. Multiple samples with different procedures are processed in parallel, competing for the instruments. The whole environment may be also underlaid by optimization strategies like throughput or minimum sample processing time. The modeling of all components interacting on the workbench—samples, devices, sensors, results, database systems, and so on—needs to rely on concepts building a consistent framework. This article gives a set of terms and definitions used in a dynamic scheduling environment. It describes most of these entities in detail, including their functionality and attributes as well as their logical and physical interactions. It also describes concepts such as workflows with activities and constraints, functional libraries, hidden transport, and dynamic execution. Maintenance, calibration, and error management also are included. Finally, it discusses how the entities interact with the different components in the scheduling system. [Copyright &y& Elsevier]

SpectroML, a markup language for ultraviolet-visible spectroscopy data, has been developed as a “Web-aware” mechanism for instrument-to-instrument, instrument-to-application, and application-to-application data interchange and archiving. This article documents the application of SpectroML to the interchange and archiving of measurement data from three spectrophotometers that are used in the NIST optical filter standards program. It describes how result data from the NIST national reference spectrophotometer and two commercial spectrophotometers are converted into SpectroML format and how SpectroML-formatted data and metadata are imported into the optical filter standards database. [Copyright &y& Elsevier]

Ovarian cancer remains the most lethal gynecologic cancer in women. Despite achievements in surgical and systemic therapy, most patients develop platinum resistance. Thus, new strategies to increase or reverse the platinum sensitivity in ovarian cancer patients are urgently needed. In this study, we aimed to investigate the anti-cancer effect of the leaves of Pistacia lentiscus L medicinal plants used in Algerian traditional medicine on ovarian cancer cells in vitro. Four newly established primary cell lines derived from ascites of patients with high-grade serous and clear cell ovarian cancer were used to test the anti-cancer effect of the leaves of Pistacia lentiscus L. A n experimental study was performed to study the therapeutic effects of the plant leaves substances in patient derived models. The anti- proliferative activity of ethanolic, acetonic and methanolic plant leaves extracts was measured by cell viability assays, and the apoptotic effect assessed using flow cytometry analysis. The impact on constitutive active oncogenic pathways and cytokine release in cell culture supernatant were monitored by Western blotting and ELISA, respectively. Sequencing analysis confirmed the presence of mutations in several genes, such as TP53, RB1, PIK3C , which are commonly mutated in high-grade serous ovarian cancer. Obtained results indicated a cytotoxic effect of the methanolic extract of P. lentiscus L (MEPL) on primary cell line cultures, inhibiting PI3K/AKT and MAPK/ERK signaling pathways, and decreasing the release of IL6 and VEGF by the malignant cells. Moreover, treatment with MEPL enhanced the sensitivity to platinum-based chemotherapy in our primary cell lines of patients. Methanolic extract of P. lentiscus L might be a promising candidate for novel therapeutic approaches in combination with classic chemotherapy for patients with high-grade serous ovarian cancer. [ABSTRACT FROM AUTHOR]

An abstract of the article "Effects of Ras Signaling on Gene Expression Analyzed by Customized Microarray," by Oleg I. Tchernitsa and colleagues is presented.

Targeted therapies for metastatic uveal melanoma have shown limited benefit in biomarker-unselected populations. The Treat20 Plus study prospectively evaluated the feasibility of a precision oncology strategy in routine clinical practice. Fresh biopsies were analyzed by high-throughput genomics (whole-genome, whole-exome, and RNA sequencing). A multidisciplinary molecular and immunologic tumor board (MiTB) made individualized treatment recommendations based on identified molecular aberrations, patient situation, drug, and clinical trial availability. Therapy selection was at the discretion of the treating physician. The primary endpoint was the feasibility of the precision oncology clinical program. Molecular analyses were available for 39/45 patients (87%). The MiTB provided treatment recommendations for 40/45 patients (89%), of whom 27/45 (60%) received ≥1 matched therapy. First-line matched therapies included MEK inhibitors (n = 15), MET inhibitors (n = 10), sorafenib (n = 1), and nivolumab (n = 1). The best response to first-line matched therapy was partial response in one patient (nivolumab based on tumor mutational burden), mixed response in two patients, and stable disease in 12 patients for a clinical benefit of 56%. The matched therapy population had a median progression-free survival and overall survival of 3.3 and 13.9 months, respectively. The growth modulation index with matched therapy was >1.33 in 6/17 patients (35%) with prior systemic therapy, suggesting clinical benefit. A precision oncology approach was feasible for patients with metastatic uveal melanoma, with 60% receiving a therapy matched to identify molecular aberrations. The clinical benefit after checkpoint inhibitors highlights the value of tumor mutational burden testing. • Demonstration of the feasibility of precision oncology for advanced uveal melanoma. • Complete whole-genome and RNA sequencing data were generated for 87% of patients. • Following treatment recommendations, 60% of patients received ≥1 matched therapy. • First-line therapies included inhibitors of MEK, MET, sorafenib, and nivolumab. • Clinical benefit rate in 56% of patients with one partial response under nivolumab. [ABSTRACT FROM AUTHOR]

Reliable and reproducible interpretation of molecular aberrations constitutes a bottleneck of precision medicine. Evidence-based decision management systems may improve rational therapy recommendations. To cope with an increasing amount of complex molecular data in the clinical care of patients with cancer, we established a workflow for the interpretation of molecular analyses. A specialized physician screened results from molecular analyses for potential biomarkers, irrespective of the diagnostic modality. Best available evidence was retrieved and categorized through establishment of an in-house database and interrogation of publicly available databases. Annotated biomarkers were ranked using predefined evidence levels and subsequently discussed at a molecular tumour board (MTB), which generated treatment recommendations. Subsequent translation into patient treatment and clinical outcomes were followed up. One hundred patients were discussed in the MTB between January 2016 and May 2017. Molecular data were obtained for 70 of 100 patients (50 whole exome/RNA sequencing, 18 panel sequencing, 2 immunohistochemistry (IHC)/microsatellite instability analysis). The MTB generated a median of two treatment recommendations each for 63 patients. Thirty-nine patients were treated: 6 partial responses and 12 stable diseases were achieved as best responses. Genetic counselling for germline events was recommended for seven patients. The development of an evidence-based workflow allowed for the clinical interpretation of complex molecular data and facilitated the translation of personalized treatment strategies into routine clinical care. The high number of treatment recommendations in patients with comprehensive genomic data and promising responses in patients treated with combination therapy warrant larger clinical studies. • Evidence-based, flexible workflow for the clinical interpretation of molecular data. • Application to complex data including whole-exome sequencing and RNA-Sequencing in clinical routine. • Initiation of targeted treatment in 39% of patients. • Promising responses in a subset of patients. • Standardisation of precision oncology workflows could help improve prospective trials. [ABSTRACT FROM AUTHOR]

The impact of tumour mutational burden (TMB) on outcome with molecularly matched therapy is unknown. Higher TMB could predict resistance to molecularly matched therapy through co-occurring driver mutations. One hundred and four patients with advanced cancers underwent molecular profiling in the DKTK-MASTER program. Fifty-five patients received systemic therapy excluding immunotherapy. Patients with molecularly matched (n = 35) or non-molecularly informed therapy (n = 20) were analysed for TMB and survival. Results were validated in an independent cohort of patients receiving molecularly matched (n = 68) or non-molecularly informed therapy (n = 40). Co-occurring driver mutations and TMB were analysed in the exploratory cohort and The Cancer Genome Atlas (TCGA) datasets. Patients were stratified by the median TMB of 1.67 mutations per Megabase (mut/Mb) of 35 patients receiving molecularly matched therapy into TMB-high or TMB-low groups. Median overall survival (4 months [95% CI, 3.3–7.6] versus 12.8 months [95% CI, 10-not reached], p < 0.001) and progression-free survival (1.8 months [95% CI, 1.1–3.7] versus 7.9 months [95% CI, 2.8–17.0], p = 0.003) were significantly shorter in the TMB-high group compared to the TMB-low group. In the validation cohort, shorter OS and PFS were identified in the TMB-high group (TMB cut-off of 4 mut/Mb) treated with molecularly matched therapy. No differences were observed in patients receiving non-molecularly informed systemic therapy. A significant correlation between co-occurring driver mutations and TMB (n = 104, r = 0.78 [95% CI, 0.68–0.85], p < 0.001) was found in the exploratory cohort as well as the majority (24/33) of TCGA studies. A high TMB was associated with unfavourable outcome in patients receiving molecularly matched therapy, indicating untargeted resistance pathways. Therefore, TMB should be further investigated as a predictive biomarker in precision oncology programs. • Personalised cancer therapy lacks efficacy for a majority of patients. • Predictive biomarkers for the use of molecularly matched therapy warranted. • Role of tumour mutational burden for molecularly matched therapy unknown. • Analysis of TMB and molecularly matched therapy in two pan-cancer cohorts. • TMB associated with improved outcome with matched but not unmatched therapy. [ABSTRACT FROM AUTHOR]

The COSMIC database (version 94) lists 576 genes in the Cancer Gene Census which have a defined function as drivers of malignancy (oncogenes) or as tumour suppressors (Tier 1). In addition, there are 147 genes with similar functions, but which are less well characterised (Tier 2). Furthermore, next-generation sequencing projects in the context of precision oncology activities are constantly discovering new ones. Since cancer genes differ from their wild-type precursors in numerous molecular and biochemical properties and exert significant differential effects on downstream processes, simple assays that can uncover oncogenic or anti-oncogenic functionality are desirable and may precede more sophisticated analyses. We describe simple functional assays for PTPN11 (protein-tyrosine phosphatase, non-receptor-type 11)/SHP2 mutants, which are typically found in RASopathies and exhibit potential oncogenic activity. We have also designed a functional test for lysyl oxidase (LOX), a prototypical class II tumour suppressor gene whose loss of function may contribute to neoplastic transformation by RAS oncogenes. Moreover, we applied this test to analyse three co-regulated, RAS-responsive genes for transformation-suppressive activity. The integration of these tests into systems biology studies will contribute to a better understanding of cellular networks in cancer. [ABSTRACT FROM AUTHOR]

In colorectal cancer (CRC), the prevalence of NRAS mutations (5–9%) is inferior to that of KRAS mutations (40–50%). NRAS mutations feature lately during tumour progression and drive resistance to anti-EGFR therapy in KRAS wild-type tumours. To elucidate specific functions of NRAS mutations in CRC, we expressed doxycycline-inducible G12D and Q61K mutations in the CRC cell line Caco-2. A focused phospho-proteome analysis based on the Bio-Plex platform, which interrogated the activity of MAPK, PI3K, mTOR, STAT, p38, JNK and ATF2, did not reveal significant differences between Caco-2 cells expressing NRASG12D, NRASQ61K and KRASG12V. However, phenotypic read-outs were different. The NRAS Q61K mutation promoted anchorage-independent proliferation and tumorigenicity, similar to features driven by canonical KRAS mutations. In contrast, expression of NRASG12D resulted in reduced proliferation and apoptosis. At the transcriptome level, we saw upregulation of cytokines and chemokines. IL1A, IL11, CXCL8 (IL-8) and CCL20 exhibited enhanced secretion into the culture medium. In addition, RNA sequencing results indicated activation of the IL1-, JAK/STAT-, NFκB- and TNFα signalling pathways. These results form the basis for an NRASG12D-driven inflammatory phenotype in CRC. [ABSTRACT FROM AUTHOR]