Risk Stratification with Sarculator and MSKCC in Patients with Primary and Secondary Angiosarcoma

BACKGROUND

Sarculator and Memorial Sloan Kettering Cancer Center (MSKCC) nomograms are freely available risk prediction scores for surgically treated patients with primary sarcomas. Due to the rarity of angiosarcomas, these scores have only been tested on small cohorts of angiosarcoma patients. In neither the original patient cohort upon which the Sarculator is based nor in subsequent studies was a distinction made between primary and secondary angiosarcomas, as the app is intended to be applied to primary sarcomas. Therefore, the objective of our investigation was to assess whether the Sarculator reveals a difference in prognosis and whether such differentiation aligns with actual clinical data.

PATIENTS AND METHODS

Thirty-one patients with primary or secondary soft tissue angiosarcoma, treated at our Sarcoma Center from 2001 to 2023, were included in the study. Actual survival rates were compared with nomogram-derived data for predicted 5-year survival (Sarculator), as well as 4-, 8- and 12-year sarcoma-specific death probabilities (MSKCC). Harrell's c-index was utilized to assess predictive validity.

RESULTS

In total, 31 patients were analyzed. The actual overall 5-year survival was 22.57% with a predicted 5-year survival rate of 25.97%, and the concordance index was 0.726 for the entire cohort. The concordance index results from MSKCC for angiosarcoma patients were below 0.7 indicating limited predictive accuracy in this cohort, particularly when compared to Sarculator.

SUMMARY

Nomogram-based predictive models are valuable tools in clinical practice for rapidly assessing prognosis. They can streamline the decision-making process for adjuvant treatments and improve patient counselling especially in the treatment of rare and complicated tumor entities such as angiosarcomas.

[The neuro-urological expert opinion in statutory accident insurance : Consensual recommendations for diagnostics and for the assessment of reduction of earning capacity]

BACKGROUND

Previous assessment guidelines from standard sources for urologic expert opinions show considerable differences in the recommended percentages for the assessment of reduction of earning capacity (MdE) for accident sequelae in the neuro-urological specialty.

OBJECTIVES

To develop a "revised and standardized version of the MdE assessments of neuro-urological accident sequelae (in tabular form) as a guideline/manual" for expert opinions in the legal area of the German and Austrian Statutory Accident Insurance ( www.dguv.de , www.auva.at ).

MATERIALS AND METHODS

A working group of neuro-urologists from spinal cord injury centers of different BG ("Berufsgenossenschaft") clinics was formed within the working group Neuro-Urology of DMGP (German-speaking Medical Society for Paraplegiology; www.dmgp.de ). Between January 2017 and September 2022, a total of 7 working meetings and 2 video conferences were held. The consensus of the developed documents was reached by formal consensus finding in a nominal group process and in a final consensus conference.

RESULTS

The necessary bases for a targeted, legally sound diagnosis of accident consequences in the neuro-urological field were elaborated and, based on the experience of many years of expert opinion activity, a "matrix" for a uniform, graduated assessment of the level of reduction of earning capacity in the (neuro-)urological field in the case of confirmed neuro-urological accident consequences was created.

CONCLUSION

In the interest of equal treatment of all insured persons, it is of great importance to make a uniform and comprehensible assessment of the amount of the MdE on the basis of "table values" that reflect the available empirical values.

MRNA COVID-19 VACCINE-ASSOCIATED BULLOUS FIXED DRUG ERUPTION

Introduction

Fixed drug eruptions are unique cutaneous drug reactions that recur in the same location upon re-exposure to the offending agent. We report a dilemma of how to proceed with the vaccination after a rare complication of the mRNA covid-19 vaccine.

Case Description

A 47-year-old female referred to us after developing a rash to the mRNA covid-19 vaccine for evaluation of safety and plan on how to proceed with the booster vaccine. After the 1^st dose on her left deltoid, she developed persistent right arm pruritus from mid-forearm to wrist that gradually became well-demarcated and erythematous by day four. Rash improved within seven days of using hydrocortisone but left hyperpigmentation of the skin. Two weeks after receiving her 2^nd dose on her left deltoid, the same location on her right forearm flared up with more pronounced pruritus, erythema and a few bullous lesions. Rash improved after a week of using hydrocortisone leaving behind hyperpigmentation. The patient denied using any prior medications and had no other skin or mucosal involvement. We decided to proceed with another brand of mRNA covid-19 vaccine instead and prophylactically apply clobetasol twice daily to the affected area for 7-days post-vaccine. She tolerated the vaccine without any flare-up of the rash.

Discussion

Fixed drug eruptions more frequently occur with drugs including antimicrobials, NSAIDs, acetaminophen and anti-convulsants. Very rarely has it been reported in association with the administration of the Covid-19 vaccines. This case illustrates a unique predicament after an unusual complication of bullous fixed drug eruption after mRNA covid-19 vaccine administration.

Public Health benefits by implementing digital symptom diaries for COVID patients from Cologne

Background

High rate of people infected with SARS-CoV-2 and their contacts in Cologne, Germany required innovative tools for notification, monitoring and reporting. The digital tool for COVID19 (DiKoMa) provides self-service symptom diaries allowing (a) the stratification for prioritized telephone contact by the health authority and (b) training a machine learning (ML) model that predicts infections with prevailing dominant variant (PDV) from early symptom profiles (SP).

Methods

Pseudononymized SP covering the first week of diary recordings were included for training (16646 index, 11582 contacts). A balanced random forest (BRF) model was trained to differentiate early predictive symptom patterns of different PDV and contact persons. Model evaluation was performed using sex and age stratified cross validation (CV), the model was validated on SP recorded from days 1 and 6.

Results

From 03/20 to 02/22, 90478 indeces and 75444 contact persons reported symptoms and health status, covering 46% and 42% of all reported cases, respectively. Diaries contained between 1-52 entries (566791, median 2). Daily analysis of entries, prioritized according to age, prevalent co-morbidities and detoriation of symptoms allowed risk adjusted follow up even during phases with high case notification rates. The top 5 predictive factors of the BRF were immunization, cough, dysgeusia and dysnosmia, fatigue, and sniffles to differentiate infection between wildtype, three PDV and contact persons (CV AUC 80.6%, Validation AUC 77.1%).

Conclusions

The use of digital symptom diary surveillance helps to provide appropriate medical support for patients on a large scale. Machine learning shows potential for symptom based risk assessment to differentiate PDV for future outbreaks and can thus become a valuable tool alongside specific laboratory diagnostics.

Key messages

• Digital symptom diaries are a powerful and widely accepted tool to attend COVID19 patients in isolation. They allow risk stratification for follow up and are a low-threshold service.

• Machine learning supports index case identification by symptom analysis and can thus become a valuable tool alongside specific laboratory diagnostics.

Stability of Hepatitis E Virus After Drying on Different Surfaces

The hepatitis E virus (HEV) causes acute and chronic hepatitis in humans. The zoonotic HEV genotype 3 is mainly transmitted by consumption of contaminated food produced from infected animals. However, transmission via contaminated surfaces has also to be considered. Here, the genotype 3c strain 47832c was dried on steel, wood, plastics and ceramics, stored at 23 °C or 3 °C for up to 8 weeks and remaining infectivity was titrated on cell culture. During the drying process, only a mean 0.2 log₁₀ decrease of HEV infectivity was observed. At 23 °C, remaining infectious virus was detected until week 4 on most surfaces, but HEV was completely inactivated (> 4 log₁₀ decrease) after 8 weeks. At 3 °C, HEV was detectable up to 8 weeks on most surfaces, with an average 2.3 log₁₀ decrease. HEV showed the highest stability on plastics, which was lower on ceramics and steel, and lowest on wood. The addition of bovine serum albumin mimicking high protein load had only a slight stabilizing effect. In conclusion, HEV shows a high stability against drying and subsequent storage on different surfaces. Strict application of hygienic measures during food production is therefore crucial in order to prevent HEV persistence on surfaces and subsequent cross-contamination.

OUP accepted manuscript

Bloom syndrome (BS) is an autosomal recessive disease clinically characterized by primary microcephaly, growth deficiency, immunodeficiency and predisposition to cancer. It is mainly caused by biallelic loss-of-function mutations in the BLM gene, which encodes the BLM helicase, acting in DNA replication and repair processes. Here, we describe the gene expression profiles of three BS fibroblast cell lines harboring causative, biallelic truncating mutations obtained by single-cell (sc) transcriptome analysis. We compared the scRNA transcription profiles from three BS patient cell lines to two age-matched wild-type controls and observed specific deregulation of gene sets related to the molecular processes characteristically affected in BS, such as mitosis, chromosome segregation, cell cycle regulation and genomic instability. We also found specific upregulation of genes of the Fanconi anemia pathway, in particular FANCM, FANCD2 and FANCI, which encode known interaction partners of BLM. The significant deregulation of genes associated with inherited forms of primary microcephaly observed in our study might explain in part the molecular pathogenesis of microcephaly in BS, one of the main clinical characteristics in patients. Finally, our data provide first evidence of a novel link between BLM dysfunction and transcriptional changes in condensin complex I and II genes. Overall, our study provides novel insights into gene expression profiles in BS on an sc level, linking specific genes and pathways to BLM dysfunction.

Prediction of successful hearing aid treatment in first-time and experienced hearing aid users: Using the International Outcome Inventory for Hearing Aids

OBJECTIVE

Primarily to understand whether clinically relevant factors affect the International Outcome Inventory (IOI-HA) scores and to examine if IOI-HA scores improve when renewing the hearing aids (HA) for experienced users. Secondly, to estimate the overall HA effectiveness using the IOI-HA.

DESIGN

A prospective observational study.

STUDY SAMPLE

In total, 1961 patients with hearing loss were included. All patients underwent a hearing examination, were fitted with HAs, and answered the IOI-HA. Factor analysis of IOI-HA separated the items into a Factor 1 (use of HA, perceived benefits, satisfaction, and quality of life) and Factor 2 (residual activity limitation, residual participation restriction and impact on others) score.

RESULTS

Degree of hearing loss, word recognition score, motivation, HA usage time, tinnitus, asymmetry, and sex were significantly associated with total IOI-HA, Factor 1, or Factor 2 scores. The seven IOI-HA items increased on average by 0.4 (p < 0.001) when renewing HAs. The total median IOI-HA score at follow-up was 29 (7) for experienced (n = 460) and first-time users (n = 1189), respectively.

CONCLUSIONS

Degree of hearing loss, word recognition score, motivation, tinnitus, asymmetry, and sex may be used to identify patients who require special attention to become successful HA users.

Hedgehog signaling in endocrine and folliculo-stellate cells of the adult pituitary

Ubiquitous overactivation of Hedgehog signaling in adult pituitaries results in increased expression of proopiomelanocortin (Pomc), growth hormone (Gh) and prolactin (Prl), elevated adrenocorticotropic hormone (Acth) production and proliferation of Sox2+ cells. Moreover, ACTH, GH and PRL-expressing human pituitary adenomas strongly express the Hedgehog target GLI1. Accordingly, Hedgehog signaling seems to play an important role in pathology and probably also in homeostasis of the adult hypophysis. However, the specific Hedgehog-responsive pituitary cell type has not yet been identified. We here investigated the Hedgehog pathway activation status and the effects of deregulated Hedgehog signaling cell-specifically in endocrine and non-endocrine pituitary cells. We demonstrate that Hedgehog signaling is unimportant for the homeostasis of corticotrophs, whereas it is active in subpopulations of somatotrophs and folliculo-stellate cells in vivo. Reinforcement of Hedgehog signaling activity in folliculo-stellate cells stimulates growth hormone production/release from somatotrophs in a paracrine manner, which most likely is mediated by the neuropeptide vasoactive intestinal peptide. Overall, our data show that Hedgehog signaling affects the homeostasis of pituitary hormone production via folliculo-stellate cell-mediated regulation of growth hormone production/secretion.

Stability of hepatitis E virus at high hydrostatic pressure processing

Hepatitis E virus (HEV) is the causative agent of acute and chronic hepatitis in humans. The zoonotic HEV genotype 3 is the main genotype in Europe. The foodborne transmission via consumption of meat and meat products prepared from infected pigs or wild boars is considered the major transmission route of this genotype. High hydrostatic pressure processing (HPP) is a technique, which can be used for inactivation of pathogens in food. Here, preparations of a cell culture-adapted HEV genotype 3 strain in phosphate-buffered saline (PBS) were subjected to HPP and the remaining infectivity was titrated in cell culture by counting fluorescent foci of replicating virus. A gradual decrease in infectivity was found by application of 100 to 600 MPa for 2 min. At 20 °C, infectivity reduction of 0.5 log₁₀ at 200 MPa and 1 log₁₀ at 400 MPa were observed. Slightly higher infectivity reduction of 1 log₁₀ at 200 MPa and 2 log₁₀ at 400 MPa were found by application of the pressure at 4 °C. At both temperatures, the virus was nearly completely inactivated (>3.5 log₁₀ infectivity decrease) at 600 MPa; however, low amounts of remaining infectious virus were observed in one of three replicates in both cases. Transmission electron microscopy showed disassembled and distorted particles in the preparations treated with 600 MPa. Time-course experiments at 400 MPa showed a continuous decline of infectivity from 30 s to 10 min, leading to a 2 log₁₀ infectivity decrease at 20 °C and to a 2.5 log₁₀ infectivity decrease at 4 °C for a 10 min pressure application each. Predictive models for inactivation of HEV by HPP were generated on the basis of the generated data. The results show that HPP treatment can reduce HEV infectivity, which is mainly dependent on pressure height and duration of the HPP treatment. Compared to other viruses, HEV appears to be relatively stable against HPP and high pressure/long time combinations have to be applied for significant reduction of infectivity.

Effect of Sodium Chloride, Sodium Nitrite and Sodium Nitrate on the Infectivity of Hepatitis E Virus

Hepatitis E virus (HEV) infection can cause acute and chronic hepatitis in humans. The zoonotic HEV genotype 3, which is highly prevalent in Europe, is mainly transmitted by consumption of raw meat and raw meat products produced from infected pigs or wild boars. High salt concentrations represent an important measure to preserve meat products and to inactivate foodborne pathogens. Here, an HEV preparation in phosphate-buffered saline (PBS) was subjected to different salt concentrations and the remaining infectivity was measured in a cell culture assay. Treatments with up to 20% sodium chloride for 24 h at 23 °C, with and without addition of 0.015% sodium nitrite or 0.03% sodium nitrate, did not lead to virus inactivation as compared to PBS only. Conditions usually applied for short-term and long-term fermented raw sausages were simulated by incubation at 22 °C for up to 6 days and at 16 °C for up to 8 weeks, respectively. Only 2% sodium chloride with 0.015% sodium nitrite showed a weak (< 1 log₁₀), but significant, infectivity reduction after 2 and 4 days as compared to PBS only. Addition of 2% sodium chloride and 0.03% sodium nitrate showed a slight, but not significant, decrease in infectivity after 2 and 8 weeks as compared to PBS only. In conclusion, HEV is highly stable at high salt concentrations and at salt conditions usually applied to preserve raw meat products.

Stability of hepatitis E virus at different pH values

Infection with the hepatitis E virus (HEV) can cause acute and chronic hepatitis in humans. The zoonotic HEV genotype 3 is mainly transmitted by consumption of raw and fermented meat products prepared from infected pigs or wild boars. Lowering of pH during fermentation is one of the microbiological hurdles considered to inhibit growth of certain pathogens. However, no data are currently available on pH stability of HEV. As a reliable and reproducible measurement of HEV infectivity in meat products is not established so far, the stability of the cell culture-adapted HEV genotype 3 strain 47832c was analyzed here in phosphate-buffered saline (PBS) at different pH values. Only a minimal decrease of infectivity (up to 0.6 log₁₀ focus forming units) was found after treatment at pH 2 to 9 for 3 h at room temperature. At pH 10, a decrease of about 3 log₁₀ was evident, whereas no remaining virus (>3.5 log₁₀ decrease) was detected at pH 1. The conditions usually achieved during curing of raw sausages were simulated using D/L-lactic acid added to PBS resulting in pH 4.5 to 6.5. After incubation at 4 °C for 7 days at these conditions, no significant differences as compared to a standard PBS solution at pH 7.7 were evident. At room temperature, a 0.8 log₁₀ decrease was found at pH 4.7 after 7 days incubation compared to pH 7.7, but less at the other pH values. In conclusion, only minimal inactivating effects were found at pH conditions commonly occurring during food processing. Therefore, remaining infectious virus might be present in fermented meat products if HEV-contaminated starting material was used. Additional effects of other factors like high salt concentrations and low a_w values should be investigated in future studies.

[Medicaments and oral healthcare. Systematic review of the -literature assessing the effect of drugs on the salivary glands]

Evidence-based reviews of drugs causing medication-induced salivary gland dysfunction, such as xerostomia (sensation of oral dryness) and subjective sialorrhea are lacking. To compile a list of medicaments that influence salivary gland function, electronic databases were searched for relevant articles published up to June 2013. A total of 269 papers out of 3,867 records located satisfied the inclusion criteria (relevance, quality of methodology, strength of evidence). A total of 56 active substances with a higher level of evidence and 50 active substances with a moderate level of evidence of causing salivary gland dysfunction are described in this article. While xerostomia was a commonly reported outcome, the objective effect on salivary secretion was rarely measured. Xerostomia was, moreover, mostly reported as a negative side effect instead of the intended effect of that drug. A comprehensive list of medications having documented effects on salivary gland function or symptoms was compiled, which may assist practitioners in assessing patients who complain of dry mouth while taking medications.

PI3K: A master regulator of brain metastasis-promoting macrophages/microglia

Mutations and activation of the PI3K signaling pathway in breast cancer cells have been linked to brain metastases. However, here we describe that in some breast cancer brain metastases samples the protein expression of PI3K signaling components is restricted to the metastatic microenvironment. In contrast to the therapeutic effects of PI3K inhibition on the breast cancer cells, the reaction of the brain microenvironment is less understood. Therefore we aimed to quantify the PI3K pathway activity in breast cancer brain metastasis and investigate the effects of PI3K inhibition on the central nervous system (CNS) microenvironment. First, to systematically quantify the PI3K pathway activity in breast cancer brain metastases, we performed a prospective biomarker study using a reverse phase protein array (RPPA). The majority, namely 30 out of 48 (62.5%) brain metastatic tissues examined, revealed high PI3K signaling activity that was associated with a median overall survival (OS) of 9.41 months, while that of patients, whose brain metastases showed only moderate or low PI3K activity, amounted to only 1.93 and 6.71 months, respectively. Second, we identified PI3K as a master regulator of metastasis-promoting macrophages/microglia during CNS colonization; and treatment with buparlisib (BKM120), a pan-PI3K Class I inhibitor with a good blood-brain-barrier penetrance, reduced their metastasis-promoting features. In conclusion, PI3K signaling is active in the majority of breast cancer brain metastases. Since PI3K inhibition does not only affect the metastatic cells but also re-educates the metastasis-promoting macrophages/microglia, PI3K inhibition may hold considerable promise in the treatment of brain metastasis and the respective microenvironment.

Improving Health Outcomes for People With Cancer in Rural and Regional Areas by Embedding Evidence-Based Smoking-Cessation Strategies Into Usual Care: A Study Protocol

Background: Smoking following a diagnosis of cancer is a powerful clinical risk indicator, with known poorer health outcomes and associated health care costs. In Australia, smoking rates are higher in rural and regional areas. There are established and effective interventions to promote smoking cessation after a diagnosis of cancer yet these are not in routine practice. Aim: This protocol paper reports on a study that aims to embed evidence-based smoking cessation strategies for people with cancer who are current smokers into routine care, resulting in in system wide improvements, an implemented program and model for further dissemination. Methods: Across three rural/regional sites, and with partners Quit Victoria and Western Alliance, this study employs a variety of methodologies to embed smoking cessation support to improve outcomes for people with cancer who currently smoke. Specifically, the project will embed a system of responsibilities and training in rural and regional health services to routinely engage people with cancer who smoke in support services. The program will: · Promote routine delivery of smoking cessation care by trained oncology staff (oncologists/nurses/ allied health) · Establish referral pathways to Quitline · Correspond with general practitioners, to: i) outline the benefits of quitting in this context, ii) promote access to nicotine replacement therapy and iii) support quitting in the community. · Improve routine recording of smoking status and documentation of provision of brief intervention (personalised advice given, resources provided) and outcomes. Participants: are oncology staff and general practitioners across three health services: Ballarat Health Service, East Grampians Health Service (Ararat), Wimmera Health Care Group (Horsham), all located in Victoria, Australia. Data collection will occur across four sources: 1) Oncology staff: qualitative and quantitative data collection understanding confidence and views on provision on cessation advice; 2) Monitoring Quitline calls, 3) Interview with local general practitioners and 4) Medical record reviews to explore frequency of recording of smoking status. Data will be collected pre/postintervention. Results: The project is underway with the intervention manuals in development. The project is due for completion in 2020. Conclusion: This project takes a health services approach to integration of smoking cessation support in routine care for people with cancer in rural and regional areas. This program of work has capacity to determine best approaches to integrate smoking cessation into routine care, resulting in reduced mortality and morbidity, improved effectiveness of anticancer treatments, and reduced health care costs; by establishing internationally relevant, embedded health care interventions.

Electrostimulation of the lingual nerve by an intraoral device may lead to salivary gland regeneration: A case series study

Background

Salivary gland function is controlled by the salivary reflex, whose efferent arm is composed by the parasympathetic and the sympathetic divisions of the autonomic nervous system. Parenchymal injury is the main salivary gland involvement of Sjögren’s syndrome and head and neck radiotherapy, but neural damage has been reported as well. Recently an intraoral device for electrostimulation of the lingual nerve in vicinity to the lower third molar has been introduced. At this point this nerve carries efferent fibers for the innervation of the submandibular, sublingual and several minor salivary glands and afferent fibers of the salivary reflex. Therefore, excitation of these fibers potentially leads to increased secretion of all salivary glands. Thus, the study objective was to assess whether comprehensive neural activation by electrostimulation of the lingual nerve carries the potential to induce the regeneration of damaged salivary glands.

Material and Methods

The device was tested on three patients with no collectable resting and stimulated secretion of saliva during a double blind, sham controlled period of two months and nine open-label months.

Results

All three subjects developed the capacity to spit saliva, not only in direct response to the electrostimulation but also after free intervals without electrostimulation. In addition, their symptoms of dry mouth severity and frequency improved.

Conclusions

This recovery is probably due to the combined effect of increase in secretory functional gland mass and regain of nervous control of the secretory elements and blood vessels. Both are phenomena that would contribute to gland regeneration.

Key words:Xerostomia, dry mouth, saliva, electrostimulation, regeneration.

Modelling of focused ion beam induced increases in sample temperature: a case study of heat damage in biological samples

Ion beam induced heat damage in soft materials and biological samples is not yet well understood in Focused Ion Beam systems (FIBs). The work presented here discusses the physics behind the ion beam - sample interactions and the effects which lead to increases in sample temperature and potential heat damage. A model by which heat damage can be estimated and which allows parameters to be determined that reduce/prevent heat damage was derived from Fourier's law of heat transfer and compared to finite element simulations, numerical modelling results and experiments. The results suggests that ion beam induced heat damage can be prevented/minimised by reducing the ion beam current (local dose rate), decreasing the beam overlap (reduced local ion dose) and by introducing a blur (increased surface cross-section area, reduced local dose) while sputtering, patterning or imaging soft material and nonresin-embedded biological samples using FIBs.

LAY DESCRIPTION

FIB/SEMs, which combine a scanning electron microscope with a focused ion beam in a single device, have found increasing interest biological research. The device allows to cut samples at precisely selected areas and reveal sub surface information as well as preparing transmission electron microscope samples from bulk materials. Preparing biological samples has proven to be challenging due to the induced heat damage. This work explores the physics behind the sample cutting and proposes a model and a method, based on physical principles which allows the user to estimate the induced heat during the cutting process and to select cutting parameters which avoid heat damage in the sample.

Multi-Valent Group 14 Chalcogenide Architectures from Ionic Liquids: 0D-{[Cs@SnII4 (GeIV4 Se10 )4 ]7- } and 2D-{[SnII (GeIV4 Se10 )]2- }

In order to explore if and how salts comprising polycations and salts comprising polyanions might interact, the [AlBr₄ ]^- salt of the [Pt@Bi₁₀ ]⁴⁺ cluster cation was added to the reaction mixture for the synthesis of the supersphere cluster anion [Ge₂₄ Sn₃₆ Se₁₃₂ ]^24- from Cs₄ [Ge₄ Se₁₀ ]⋅H₂ O and SnCl₄ ⋅5 H₂ O under ionothermal conditions at 120 °C. Indeed, the reaction yields two new compounds, depending on the cation of the used ionic liquid. Apparently, the polycation is not retained under the given conditions, but it acts as a reductant affording Sn^II . In a (C₄ C₁ C₁ im)⁺ -based ionic liquid mixture, a unique supertetrahedral anion is obtained that embeds a Cs⁺ cation, 0D-{[Cs@Sn^II₄ (Ge^IV₄ Se₁₀ )₄ ]^7- }, while (C₄ C₁ im)⁺ cations stabilize an unprecedented ternary layered anion, 2D-{[Sn^II (Ge^IV₄ Se₁₀ )]^2- }. Test reactions with common sources of Sn^II did not afford the new compounds, indicating the necessity of an in situ reduction, for which the polycation seems appropriate.

A comparative study of RNA-Seq and microarray data analysis on the two examples of rectal-cancer patients and Burkitt Lymphoma cells

Background

Pipeline comparisons for gene expression data are highly valuable for applied real data analyses, as they enable the selection of suitable analysis strategies for the dataset at hand. Such pipelines for RNA-Seq data should include mapping of reads, counting and differential gene expression analysis or preprocessing, normalization and differential gene expression in case of microarray analysis, in order to give a global insight into pipeline performances.

Methods

Four commonly used RNA-Seq pipelines (STAR/HTSeq-Count/edgeR, STAR/RSEM/edgeR, Sailfish/edgeR, TopHat2/Cufflinks/CuffDiff)) were investigated on multiple levels (alignment and counting) and cross-compared with the microarray counterpart on the level of gene expression and gene ontology enrichment. For these comparisons we generated two matched microarray and RNA-Seq datasets: Burkitt Lymphoma cell line data and rectal cancer patient data.

Results

The overall mapping rate of STAR was 98.98% for the cell line dataset and 98.49% for the patient dataset. Tophat’s overall mapping rate was 97.02% and 96.73%, respectively, while Sailfish had only an overall mapping rate of 84.81% and 54.44%. The correlation of gene expression in microarray and RNA-Seq data was moderately worse for the patient dataset (ρ = 0.67–0.69) than for the cell line dataset (ρ = 0.87–0.88). An exception were the correlation results of Cufflinks, which were substantially lower (ρ = 0.21–0.29 and 0.34–0.53). For both datasets we identified very low numbers of differentially expressed genes using the microarray platform. For RNA-Seq we checked the agreement of differentially expressed genes identified in the different pipelines and of GO-term enrichment results.

Conclusion

In conclusion the combination of STAR aligner with HTSeq-Count followed by STAR aligner with RSEM and Sailfish generated differentially expressed genes best suited for the dataset at hand and in agreement with most of the other transcriptomics pipelines.

Abstract OT1-02-03: TBCRC 044: A randomized phase II study of pembrolizumab in combination with carboplatin versus carboplatin alone in breast cancer patients with chest wall disease

Background: Patients with breast cancer (BC) and chest wall disease have limited treatment options. We hypothesize that checkpoint inhibition may be an effective treatment approach due to the inflammatory nature of chest wall infiltration, and the association of PD-1 expression with lymphocytic infiltration. Platinum chemotherapy may facilitate anti-tumor immunity in a synergistic manner, and clinical studies of the PD-1 inhibitor pembrolizumab with platinum combinations have been effective in the treatment of advanced lung cancer. In this study, we will evaluate the combination of carboplatin and pembrolizumab in BC patients with chest wall disease.

Methods: This is a randomized phase II multicenter study in the TBCRC including patients with advanced, unresectable BC with hormone resistant or triple negative chest wall disease. Patients may have had prior surgery, prior chest wall radiation is not required, and other sites of distant metastases are allowed. Eighty-four patients at TBCRC sites will be randomized 2:1 to receive pembrolizumab and carboplatin (n=56, Arm A) or carboplatin alone (n=28, Arm B) until disease progression. Patients randomized to Arm B may cross-over following progression to pembrolizumab alone (Arm Bx). Patients in Arm A will be treated with pembrolizumab 200 mg IV and carboplatin AUC 5 IV every 3 weeks for at least 6 cycles followed by maintenance pembrolizumab 200 mg IV every 3 weeks if stable or responding disease. Patients in Arm B will be treated with carboplatin AUC 5 IV every 3 weeks until progression, then may cross-over to pembrolizumab 200 mg IV every 3 weeks alone (Arm Bx). An interim analysis for futility will be performed after 18 patients are enrolled into Arm B to allow early closure of that arm for lack of efficacy. The primary endpoint is disease control rate at 18 weeks of treatment; the study is powered to detect a 20% difference in disease control rates between arms (hazard ratio 0.52, α= 0.10, β= 0.20). Secondary endpoints include progression free survival, toxicity, and response based on PD-L1 expression and irRECIST. Exploratory endpoints include association of response with a number of biomarkers including tumor PD-L1 gene expression, tumor and peripheral blood immune composition and cytokine expression, peripheral T-cell PD-1 expression, circulating tumor DNA, circulating tumor cells, and tumor MYC genomic expression using tumor biopsy and peripheral blood testing before and after treatment. This study should be open to accrual by August of 2017. (NCT03095352)

Citation Format: Vidula N, Goga A, Krummel M, Hwang J, Liu M, Park BH, Nanda R, Pohlmann P, Storniolo AM, Van Poznak C, Brufsky A, Abramson V, Wolff A, Rugo HS. TBCRC 044: A randomized phase II study of pembrolizumab in combination with carboplatin versus carboplatin alone in breast cancer patients with chest wall disease [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr OT1-02-03.

Abstract OT3-05-08: PALLAS: PALbociclib CoLlaborative Adjuvant Study: A randomized phase 3 trial of palbociclib with standard adjuvant endocrine therapy versus standard adjuvant endocrine therapy alone for HR+/HER2- early breast cancer

Background:

Cell cycle inhibition is a proven target for novel cancer therapeutics. Palbociclib (P) is an orally active inhibitor of CDK4/6, and arrests the cell cycle at the G1-S transition. P in combination with endocrine therapy (ET) has demonstrated efficacy in phase II and III randomized trials for patients with newly diagnosed and recurrent hormone receptor positive/HER2 negative (HR+/HER2-) metastatic breast cancer (MBC), and is approved in these settings. Given confirmed benefits of P and ET for MBC, the PALLAS study was designed to determine if the addition of P to adjuvant ET improves outcomes over ET alone in HR+/HER2- early breast cancer.

Trial Design:

PALLAS is an international open-label phase III trial randomizing (1:1) patients (pts) to 2 years of P (125 mg daily, 21 days on 7 days off in a 28-day cycle) combined with at least 5 years of provider choice ET (AI, tamoxifen, +/- LHRH agonist), versus ET alone. The primary objective of the study is to compare invasive disease-free survival (iDFS) for the combination of P and ET, versus ET alone. Secondary objectives include comparison of iDFS excluding cancer of non-breast origin, DRFS, LRRFS, OS, as well as safety. The principal objective of the translational investigations is to determine the predictive or prognostic utility of defined genomic subgroups with respect to iDFS and OS. Additional objectives include evaluation of cfDNA and tissue biomarkers predictive of benefit or resistance, pharmacogenomics, adherence, and patient-reported QOL. Eligible pts are pre- or post-menopausal women or men with stage II-III, HR+/HER2- breast cancer. Patients may have already initiated ET, but must be randomized within 12 months of diagnosis and 6 months of initiation of adjuvant ET. Trial sample size is 4600 pts and stage IIA pts will be capped at a total accrual of 1000 pts. Interim analyses for safety, futility/efficacy and sample size re-estimation are planned. PALLAS opened in 9/2015 and accrual is ongoing. Contact information: emayer@partners.org

Key words: palbociclib, CDK4/6 inhibition, HR+/HER2- early breast cancer, adjuvant endocrine therapy.

Citation Format: Mayer E, DeMichele A, Gnant M, Barry W, Pfeiler G, Metzger O, Burstein H, Miller K, Rastogi P, Loibl S, Goulioti T, Zardavas D, Fesl C, Koehler M, Huang-Bartlett C, Huang X, Piccart M, Winer E, Wolff A. PALLAS: PALbociclib CoLlaborative Adjuvant Study: A randomized phase 3 trial of palbociclib with standard adjuvant endocrine therapy versus standard adjuvant endocrine therapy alone for HR+/HER2- early breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr OT3-05-08.

Abstract P3-04-01: Molecular determinants of post-mastectomy breast cancer recurrence

Introduction

The management of breast cancer (BC) patients who undergo mastectomy in the setting of 1-3 positive lymph nodes has been controversial. This retrospective Translational Breast Cancer Research Consortium study evaluated the molecular aberrations associated with locoregional recurrence (LRR) or distant metastasis (DM) compared to controls in an effort to identify molecular predictors associated with recurrence.

Methods/Materials

We identified 115 HER2 negative, therapy naïve, T 1-3 and N 0-1 BC patients treated with mastectomy and no post mastectomy radiation therapy from 1997 to present with available FFPE tissue blocks. The cohort included 32 patients with LRR, 34 with DM, and 49 controls (without recurrence) who were matched for stage, grade, hormone receptor status, age ≤ or &gt; 50, chemotherapy receipt, and margin status. Matched primary and recurrent LRR samples were available for 3 patients. Hybrid capture next generation sequencing (NGS) of 142 cancer related genes and RNAseq were performed to identify DNA/RNA alterations associated with LRR or DM. The frequency of common alterations on NGS was compared with Fisher's exact test. Expression of each gene from mRNA-Seq was treated as an explanatory variable. Immunohistochemistry (IHC) was performed for PTEN, Ki-67 and cleaved caspase 3 (CC3). PTEN loss and percentage of Ki-67 and CC3 positive cells were compared between groups with Fisher's exact test and nonparametric methods, respectively.

Results

RNAseq was performed on 115 patients; there was no difference in RNA expression levels between the groups. DNA analysis was performed on 57 patients (17 LRR, 15 DM and 25 controls), NF1 mutation rate was significantly elevated in both the LRR (24%) and DM (27%) samples compared to controls 0%; (p=0.0070). The mitogen activated protein kinase (MAPK) pathway was significantly mutated in both LRR (47%) and DM (40%) samples compared to the controls 0%; (p&lt;0.0001). There was no significant difference in the rate of alterations of the PI3K/Akt/mTOR pathway among the three groups. Of three patients with matched primary vs LRR samples, one had concordant mutations. The second patient had additional mutations in the LRR, including gain of a NF1 mutation. The third patient had complete discordance of mutations identified in primary and LRR and had gain of HER2 amplification, suggestive of a new primary. There was no significant association between the groups and the loss of PTEN expression or CC3 expression. There was a significant difference between Ki 67 positive cells in patients with LRR (mean 29%), DM (mean 26%) versus controls (mean 14%, p= 0.0011). HR+ patients were significantly more likely to have a positive PTEN, lower Ki-67 and lower CC3 expression, p=0.0004, p&lt;0.0001, and p&lt;0.0001 respectively.

Conclusions

In this matched cohort analysis, mutations in the MAPK pathway, specifically NF1, were associated with both LRR and DM, suggesting that alterations in this pathway are associated with a more aggressive tumor phenotype. However, there were no molecular features that discriminated between those likely to recur locally alone versus distantly. Further study is needed to validate these findings, and to determine whether targeting alterations in this pathway could decrease the risk of recurrence.

Citation Format: Keene KS, King T, Hwang ES, Peng B, McGuire K, Tapia C, Zhang H, Bae S, Nakhlis F, Klauber-Demore N, Meszoely I, Sabel MS, Willey SC, Eterovic KA, Hudis C, Wolff A, De Los Santos J, Thompson A, Mills GB, Meric-Bernstam F. Molecular determinants of post-mastectomy breast cancer recurrence [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-04-01.

Abstract P5-23-01: Clinical and biological characterization of male breast cancer (BC) EORTC 10085/TBCRC 029/BOOG 2013-02/BIG 2-07: Baseline results from the prospective registry

BACKGROUND: Through the International Male Breast Cancer Program, a prospective registry for male BC was created with the goals of evaluating 1) the clinical and biological features of this disease and 2) assessing feasibility of a prospective therapeutic clinical trial.

METHODS: All men, with any stage histologically proven invasive breast cancer, age 3 18 years, and newly presenting at the participating institutions (within 3 months prior) were eligible. Patients were enrolled for 30 months after activation of the first center, through February 2017. Per the study design, if &lt;100 men enrolled, the study would be considered a failure and therapeutic trials would not be pursued through this network. Epidemiologic data, staging, pathologic features, and BRCA status were collected. Treatment and outcome data collection is ongoing. Optional collection of FFPE tumor samples, blood, and QOL were performed in the US, the Netherlands, and Latin America. Clinical database lock for this report was May 30, 2017. We currently report patient and disease characteristics and will update with patterns of treatment for the presentation. Outcomes and biological samples will be analyzed in the future.

RESULTS: 557 patients were enrolled: 75% in Europe, 20% in United States, 5% in other countries. 6.3% of patients had missing forms. Median age was 67 years (range 26-92). 93% were diagnosed 2010-2017. Among patients with complete data, 79% presented with a breast mass. 88% were M0 and 12% M1. Among M0 patients: 47%, 39%, 2%, and 11% had T1, T2, T3, and T4 disease respectively; 52% were N0. Overall, 98% had ER+ disease and 11% had HER2+ cancer. 14% had grade 1, 56% had grade 2, and 30% had grade 3 tumors. Among 112 men who underwent BRCA1 testing, 1 was positive. Among 118 men who had BRCA2 testing, 18 (15%) were positive. 21% of men had prior or concurrent malignancies, with the following most common sites: prostate, non-melanoma skin, colorectal, and melanoma. The prevalence of previously identified possible risk factors for male breast cancer were: overweight/obesity (72%), former/current smoker (51%), current alcohol 31 drink daily (41%), family history of breast cancer (35%), gynecomastia (16%), history radiation exposure (8%), use of anti-androgens (1%), and use of estrogens (1%).

CONCLUSION: Through an international collaborative effort, we were able to prospectively accrue 557 patients to a male breast cancer registry. These results demonstrate feasibility of pursuing a therapeutic clinical trial in men with breast cancer. In addition, this study shows the relatively low uptake of BRCA testing, high rates of concurrent/prior malignancy, and the rates of potentially modifiable risk factors in this patient population.

Funding from Breast Cancer Research Foundation, Susan G. Komen, Dutch Pink Ribbon Foundation, Swedish Breast Cancer Association (BRO) and EBCC Council.

Citation Format: Giordano SH, Schröder CP, Poncet C, van Leeuwen-Stok E, Linderholm B, Abreu MH, Rubio I, Van Poznak C, Morganstern D, Cameron D, Vleugel MM, Smilde TJ, Bozovic-Spasojevic I, Korde L, Russell NS, den Hoed IDM, Honkoop AH, van der Velden AWG, van 't Riet M, Dijkstra N, Bogler O, Goulioti T, Hilsenbeck S, Ruddy KJ, Wolff A, van Deurzen CHM, Martens J, Bartlett JMS, Aalders K, Tryfonidis K, Cardoso F. Clinical and biological characterization of male breast cancer (BC) EORTC 10085/TBCRC 029/BOOG 2013-02/BIG 2-07: Baseline results from the prospective registry [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P5-23-01.

Presenting XML-based Medical Discharge Letters According to CDA

The HL7 Clinical Document Architecture (CDA) is an important XML-based standard for the representation of clinical documents.

Objectives: The use of Markup Languages could satisfy the demands of involved healthcare staff as well as the needs of patients, to receive an overview of the patient’s treatment during the hospital stay. The standardization efforts of different groups dealing with this problem have demonstrated progress, but have not, as yet, achieved a routinely usable result. In particular, differentiating information according to a hierarchical order has not been published to date.

Methods: A retrospective analysis of 60 discharge letters from a cardiology ward (ward A) as well as 60 discharge letters from a gastroenterology ward (ward B) were extracted from the central hospital information system, by taking every fifth discharge letter issued over a one year period.

Results: An XML-based prototype for medical discharge letters has been put in place representing the required information units and information elements. By means of an XSL-stylesheet, a detailed representation of the conventional discharge letter has been produced that is platform independent and permits the recurrent use of information units.

Conclusions: Through the introduction of definitions like information elements and information units, progress in the development of CDA level two and three might be realized. We present a method by which discharge letters can be used by an Internal Medicine Department. This concept is implemented in a XML-based prototype allowing a special view on XML data to generate this document type.

Using RNA-Seq Data for the Detection of a Panel of Clinically Relevant Mutations

Somatic single nucleotide variants (SNVs) are genomic events with increasing implications in cancer treatment. The clinical standard for SNVs detection is whole genome/exome sequencing (WGS/WES) in matched tumor-normal samples. Yet, this is a very costly approach both economically and biologically and very often only tumor samples are sequenced. On the other hand, RNA sequencing (RNA-Seq) is the most popular technology to study gene expression, and has also the potential for a cost-effective identification of SNVs as an alternative to tumor-only WES. Here we present a method for the identification of SNVs in tumor-only RNA-Seq data putting a special focus on a small panel of clinically relevant SNVs. For evaluation purposeswe analyzed matched tumor-normal WEStumor-only RNA-Seq data from 14 cancer patients. We compared SNVs detected in i) RNA-Seq by our method, ii) WES tumor-only by Mutect2 and iii) WES matched tumor-normal by Mutect2. We did a detailed evaluation for a reduced panel of clinically relevant SNVs and reliably identified in RNA-Seq data a subset of mutations for which we had pathological annotation. Hence, RNA-Seq rises as a cost-effective option to detect in parallel gene expression as well as a small panel of clinically relevant SNVs in research.

Mechanistic exploration of the copper(i) phosphide synthesis in phosphonium-based and phosphorus-free ionic liquids

The mechanism of the synthesis of copper(i) phosphide (Cu_3-xP) in the ionic liquid (IL) trihexyl(tetradecyl)phosphonium chloride ([P₆₆₆₁₄][Cl]) was investigated. The phosphide formation is promoted by a transformation of red phosphorus (P_red) into mobile P₄ molecules and a surface activation of copper caused by the IL including the Brønsted acidic impurity. The surface activation is important to obtain a quantitative product yield. Moreover, we demonstrate that single-phase Cu_3-xP can also be synthesized in the nitrogen-based IL tetrabutylammonium chloride ([N₄₄₄₄][Cl]). Further substitution of the anion of the IL using tetrabutylammonium bromide ([N₄₄₄₄][Br]) or the complete replacement of the IL by a deep eutectic solvent consisting of adipic acid and betaine do not lead to single-phase Cu_3-xP. Therefore, the nature of the anions present in the IL also seems to be relevant for the convenient phosphidization reaction.

Ror2 Signaling and Its Relevance in Breast Cancer Progression

Breast cancer is a heterogeneous disease and has been classified into five molecular subtypes based on gene expression profiles. Signaling processes linked to different breast cancer molecular subtypes and different clinical outcomes are still poorly understood. Aberrant regulation of Wnt signaling has been implicated in breast cancer progression. In particular Ror1/2 receptors and several other members of the non-canonical Wnt signaling pathway were associated with aggressive breast cancer behavior. However, Wnt signals are mediated via multiple complex pathways, and it is clinically important to determine which particular Wnt cascades, including their domains and targets, are deregulated in poor prognosis breast cancer. To investigate activation and outcome of the Ror2-dependent non-canonical Wnt signaling pathway, we overexpressed the Ror2 receptor in MCF-7 and MDA-MB231 breast cancer cells, stimulated the cells with its ligand Wnt5a, and we knocked-down Ror1 in MDA-MB231 cells. We measured the invasive capacity of perturbed cells to assess phenotypic changes, and mRNA was profiled to quantify gene expression changes. Differentially expressed genes were integrated into a literature-based non-canonical Wnt signaling network. The results were further used in the analysis of an independent dataset of breast cancer patients with metastasis-free survival annotation. Overexpression of the Ror2 receptor, stimulation with Wnt5a, as well as the combination of both perturbations enhanced invasiveness of MCF-7 cells. The expression-responsive targets of Ror2 overexpression in MCF-7 induced a Ror2/Wnt module of the non-canonical Wnt signaling pathway. These targets alter regulation of other pathways involved in cell remodeling processing and cell metabolism. Furthermore, the genes of the Ror2/Wnt module were assessed as a gene signature in patient gene expression data and showed an association with clinical outcome. In summary, results of this study indicate a role of a newly defined Ror2/Wnt module in breast cancer progression and present a link between Ror2 expression and increased cell invasiveness.

The adaptation of colorectal cancer cells when forming metastases in the liver: expression of associated genes and pathways in a mouse model

Background

Colorectal cancer (CRC) is the second leading cause of cancer-related death in men and women. Systemic disease with metastatic spread to distant sites such as the liver reduces the survival rate considerably. The aim of this study was to investigate the changes in gene expression that occur on invasion and expansion of CRC cells when forming metastases in the liver.

Methods

The livers of syngeneic C57BL/6NCrl mice were inoculated with 1 million CRC cells (CMT-93) via the portal vein, leading to the stable formation of metastases within 4 weeks. RNA sequencing performed on the Illumina platform was employed to evaluate the expression profiles of more than 14,000 genes, utilizing the RNA of the cell line cells and liver metastases as well as from corresponding tumour-free liver.

Results

A total of 3329 differentially expressed genes (DEGs) were identified when cultured CMT-93 cells propagated as metastases in the liver. Hierarchical clustering on heat maps demonstrated the clear changes in gene expression of CMT-93 cells on propagation in the liver. Gene ontology analysis determined inflammation, angiogenesis, and signal transduction as the top three relevant biological processes involved. Using a selection list, matrix metallopeptidases 2, 7, and 9, wnt inhibitory factor, and chemokine receptor 4 were the top five significantly dysregulated genes.

Conclusion

Bioinformatics assists in elucidating the factors and processes involved in CRC liver metastasis. Our results support the notion of an invasion-metastasis cascade involving CRC cells forming metastases on successful invasion and expansion within the liver. Furthermore, we identified a gene expression signature correlating strongly with invasiveness and migration. Our findings may guide future research on novel therapeutic targets in the treatment of CRC liver metastasis.

Electronic supplementary material

The online version of this article (doi:10.1186/s12885-017-3342-1) contains supplementary material, which is available to authorized users.

Metal-Free CVD Graphene Synthesis on 200 mm Ge/Si(001) Substrates

Good quality, complementary-metal-oxide-semiconductor (CMOS) technology compatible, 200 mm graphene was obtained on Ge(001)/Si(001) wafers in this work. Chemical vapor depositions were carried out at the deposition temperatures of 885 °C using CH₄ as carbon source on epitaxial Ge(100) layers, which were grown on Si(100), prior to the graphene synthesis. Graphene layer with the 2D/G ratio ∼3 and low D mode (i.e., low concentration of defects) was measured over the entire 200 mm wafer by Raman spectroscopy. A typical full-width-at-half-maximum value of 39 cm^-1 was extracted for the 2D mode, further indicating that graphene of good structural quality was produced. The study also revealed that the lack of interfacial oxide correlates with superior properties of graphene. In order to evaluate electrical properties of graphene, its 2 × 2 cm² pieces were transferred onto SiO₂/Si substrates from Ge/Si wafers. The extracted sheet resistance and mobility values of transferred graphene layers were ∼1500 ± 100 Ω/sq and μ ≈ 400 ± 20 cm²/V s, respectively. The transferred graphene was free of metallic contaminations or mechanical damage. On the basis of results of DFT calculations, we attribute the high structural quality of graphene grown by CVD on Ge to hydrogen-induced reduction of nucleation probability, explain the appearance of graphene-induced facets on Ge(001) as a kinetic effect caused by surface step pinning at linear graphene nuclei, and clarify the orientation of graphene domains on Ge(001) as resulting from good lattice matching between Ge(001) and graphene nucleated on such nuclei.

Computational Identification of Key Regulators in Two Different Colorectal Cancer Cell Lines

Transcription factors (TFs) are gene regulatory proteins that are essential for an effective regulation of the transcriptional machinery. Today, it is known that their expression plays an important role in several types of cancer. Computational identification of key players in specific cancer cell lines is still an open challenge in cancer research. In this study, we present a systematic approach which combines colorectal cancer (CRC) cell lines, namely 1638N-T1 and CMT-93, and well-established computational methods in order to compare these cell lines on the level of transcriptional regulation as well as on a pathway level, i.e., the cancer cell-intrinsic pathway repertoire. For this purpose, we firstly applied the Trinity platform to detect signature genes, and then applied analyses of the geneXplain platform to these for detection of upstream transcriptional regulators and their regulatory networks. We created a CRC-specific position weight matrix (PWM) library based on the TRANSFAC database (release 2014.1) to minimize the rate of false predictions in the promoter analyses. Using our proposed workflow, we specifically focused on revealing the similarities and differences in transcriptional regulation between the two CRC cell lines, and report a number of well-known, cancer-associated TFs with significantly enriched binding sites in the promoter regions of the signature genes. We show that, although the signature genes of both cell lines show no overlap, they may still be regulated by common TFs in CRC. Based on our findings, we suggest that canonical Wnt signaling is activated in 1638N-T1, but inhibited in CMT-93 through cross-talks of Wnt signaling with the VDR signaling pathway and/or LXR-related pathways. Furthermore, our findings provide indication of several master regulators being present such as MLK3 and Mapk1 (ERK2) which might be important in cell proliferation, migration, and invasion of 1638N-T1 and CMT-93, respectively. Taken together, we provide new insights into the invasive potential of these cell lines, which can be used for development of effective cancer therapy.

An impedance method for spatial sensing of 3D cell constructs--towards applications in tissue engineering

We present the characterisation and validation of multiplexed 4-terminal (4T) impedance measurements as a method for sensing the spatial location of cell aggregates within large three-dimensional (3D) gelatin scaffolds. The measurements were performed using an array of four rectangular chambers, each having eight platinum needle electrodes for parallel analysis. The electrode positions for current injection and voltage measurements were optimised by means of finite element simulations to maximise the sensitivity field distribution and spatial resolution. Eight different 4T combinations were experimentally tested in terms of the spatial sensitivity. The simulated sensitivity fields were validated using objects (phantoms) with different conductivity and size placed in different positions inside the chamber. This provided the detection limit (volume sensitivity) of 16.5%, i.e. the smallest detectable volume with respect to the size of the measurement chamber. Furthermore, the possibility for quick single frequency analysis was demonstrated by finding a common frequency of 250 kHz for all the presented electrode combinations. As final proof of concept, a high density of human hepatoblastoma (HepG2) cells were encapsulated in gelatin to form artificial 3D cell constructs and detected when placed in different positions inside large gelatin scaffolds. Taken together, these results open new perspectives for impedance-based sensing technologies for non-invasive monitoring in tissue engineering applications providing spatial information of constructs within biologically relevant 3D environments.

World Workshop on Oral Medicine VI: a systematic review of medication-induced salivary gland dysfunction

The aim of this paper was to perform a systematic review of the pathogenesis of medication-induced salivary gland dysfunction (MISGD). Review of the identified papers was based on the standards regarding the methodology for systematic reviews set forth by the World Workshop on Oral Medicine IV and the PRISMA statement. Eligible papers were assessed for both the degree and strength of relevance to the pathogenesis of MISGD as well as on the appropriateness of the study design and sample size. A total of 99 papers were retained for the final analysis. MISGD in human studies was generally reported as xerostomia (the sensation of oral dryness) without measurements of salivary secretion rate. Medications may act on the central nervous system (CNS) and/or at the neuroglandular junction on muscarinic, α-and β-adrenergic receptors and certain peptidergic receptors. The types of medications that were most commonly implicated for inducing salivary gland dysfunction were those acting on the nervous, cardiovascular, genitourinary, musculoskeletal, respiratory, and alimentary systems. Although many medications may affect the salivary flow rate and composition, most of the studies considered only xerostomia. Thus, further human studies are necessary to improve our understanding of the association between MISGD and the underlying pathophysiology.