Wnk kinases are positive regulators of canonical Wnt/ß-catenin signalling.

Wnt/ß-catenin signalling is central to development and its regulation is essential in preventing cancer. Using phosphorylation of Dishevelled as readout of pathway activation, we identified Drosophila Wnk kinase as a new regulator of canonical Wnt/ß-catenin signalling. WNK kinases are known for regulating ion co-transporters associated with hypertension disorders. We demonstrate that wnk loss-of-function phenotypes resemble canonical Wnt pathway mutants, while Wnk overexpression causes gain-of-function canonical Wnt-signalling phenotypes. Importantly, knockdown of human WNK1 and WNK2 also results in decreased Wnt signalling in mammalian cell culture, suggesting that Wnk kinases have a conserved function in ensuring peak levels of canonical Wnt signalling.

Deep Learning in Surgical Workflow Analysis: A Review of Phase and Step Recognition.

OBJECTIVE: In the last two decades, there has been a growing interest in exploring surgical procedures with statistical models to analyze operations at different semantic levels. This information is necessary for developing context-aware intelligent systems, which can assist the physicians during operations, evaluate procedures afterward or help the management team to effectively utilize the operating room. The objective is to extract reliable patterns from surgical data for the robust estimation of surgical activities performed during operations. The purpose of this article is to review the state-of-the-art deep learning methods that have been published after 2018 for analyzing surgical workflows, with a focus on phase and step recognition. METHODS: Three databases, IEEE Xplore, Scopus, and PubMed were searched, and additional studies are added through a manual search. After the database search, 343 studies were screened and a total of 44 studies are selected for this review. CONCLUSION: The use of temporal information is essential for identifying the next surgical action. Contemporary methods used mainly RNNs, hierarchical CNNs, and Transformers to preserve long-distance temporal relations. The lack of large publicly available datasets for various procedures is a great challenge for the development of new and robust models. As supervised learning strategies are used to show proof-of-concept, self-supervised, semi-supervised, or active learning methods are used to mitigate dependency on annotated data. SIGNIFICANCE: The present study provides a comprehensive review of recent methods in surgical workflow analysis, summarizes commonly used architectures, datasets, and discusses challenges.

Comparison of the toxicological potential of two JUUL ENDS products to reference cigarette 3R4F and filtered air in a 90-day nose-only inhalation toxicity study.

Electronic nicotine delivery systems (ENDS) are generally recognized as less harmful alternatives for those who would otherwise continue to smoke cigarettes. The potential toxicity of aerosols generated from JUUL Device and Virginia Tobacco (VT3) or Menthol (ME3) JUULpods at 3.0% nicotine concentration was assessed in rats exposed at target aerosol concentrations of 1400 µg/L for up to 6 h/day on a 5 day/week basis for at least 90 days (general accordance with OECD 413). 3R4F reference cigarette smoke (250 µg/L) and Filtered Air were used as comparators. JUUL ENDS product aerosol exposures at >5x the 3R4F cigarette smoke level resulted in greater plasma nicotine and cotinine levels (up to 2x). Notable cigarette smoke related effects included pronounced body weight reductions in male rats, pulmonary inflammation evidenced by elevated lactate dehydrogenase, pro-inflammatory cytokines and neutrophils in bronchoalveolar lavage fluid, increased heart and lung weights, and minimal to marked respiratory tract histopathology. In contrast, ENDS aerosol exposed animals had minimal body weight changes, no measurable inflammatory changes and minimal to mild laryngeal squamous metaplasia. Despite the higher exposure levels, VT3 and ME3 did not result in significant toxicity or appreciable respiratory histopathology relative to 3R4F cigarette smoke following 90 days administration.

Key challenges for in vitro testing of tobacco products for regulatory applications: Recommendations for dosimetry.

The Institute for In Vitro Sciences (IIVS) is sponsoring a series of workshops to develop recommendations for optimal scientific and technical approaches for conducting in vitro assays to assess potential toxicity within and across tobacco and various next-generation products (NGPs) including heated tobacco products (HTPs) and electronic nicotine delivery systems (ENDSs). This publication was developed by a working group of the workshop members in conjunction with the sixth workshop in that series entitled "Dosimetry for conducting in vitro evaluations" and focuses on aerosol dosimetry for aerosol exposure to combustible cigarettes, HTP, and ENDS aerosolized tobacco products and summarizes the key challenges as well as documenting areas for future research.

Characterization of a rapid condensate collection apparatus for in vitro assays of electronic nicotine delivery systems.

In vitro testing of Electronic Nicotine Delivery System (ENDS) aerosol condensates is important in evaluating their potential toxicity. Collecting sufficient condensate for these tests is a time consuming and costly procedure. The "triple puff (TP)" is a novel system which collects the aerosol from three ENDS devices sequentially into a single filter pad and impinger. The TP substantially reduces condensate collection time relative to the conventional single ENDS, single puff (SP), device system. Both the TP and SP (using two puffing profiles) were used to generate condensates from JUUL ENDS e-liquid Mint 5.0% (nicotine by weight). Aerosols were collected using the filter pad and ethanol-containing impinger method. Condensates produced with the SP and TP were compared for concentrations of primary constituents and carbonyl compounds as well as for their cytotoxicity (OECD 129), mutagenicity (OECD 471) and genotoxicity (OECD 487). Condensates generated with the SP and TP, regardless of puffing regimen, were very similar chemically and equivalent in the biological assays tested (not cytotoxic, mutagenic, or genotoxic). The TP device significantly reduces production time of ENDS condensates relative to the standard SP method and thus may facilitate further research by reducing the time and effort required to collect ENDS condensates.

Inference of the Selective Auditory Attention Using Sequential LMMSE Estimation.

Attentive listening in a multispeaker environment such as a cocktail party requires suppression of the interfering speakers and the noise around. People with normal hearing perform remarkably well in such situations. Analysis of the cortical signals using electroencephalography (EEG) has revealed that the EEG signals track the envelope of the attended speech stronger than that of the interfering speech. This has enabled the development of algorithms that can decode the selective attention of a listener in controlled experimental settings. However, often these algorithms require longer trial duration and computationally expensive calibration to obtain a reliable inference of attention. In this paper, we present a novel framework to decode the attention of a listener within trial durations of the order of two seconds. It comprises of three modules: 1) Dynamic estimation of the temporal response functions (TRF) in every trial using a sequential linear minimum mean squared error (LMMSE) estimator, 2) Extract the N1 -P2 peak of the estimated TRF that serves as a marker related to the attentional state, and 3) Obtain a probabilistic measure of the attentional state using a support vector machine followed by a logistic regression. The efficacy of the proposed decoding framework was evaluated using EEG data collected from 27 subjects. The total number of electrodes required to infer the attention was four: One for the signal estimation, one for the noise estimation and the other two being the reference and the ground electrodes. Our results make further progress towards the realization of neuro-steered hearing aids.

PTPRD is homozygously deleted and epigenetically downregulated in human hepatocellular carcinomas.

PTPRD (protein tyrosine phosphatase, receptor type, D) is a tumor suppressor gene, frequently inactivated through deletions or epigenetic mechanisms in several cancers with importance for global health. In this study, we provide new and functionally integrated evidence on genetic and epigenetic alterations of PTPRD gene in hepatocellular carcinomas (HCCs). Importantly, HCC is the sixth most common malignancy and the third most common cause of cancer-related mortality worldwide. We used a high throughput single nucleotide polymorphism (SNP) microarray assay (Affymetrix, 10K2.0 Assay) covering the whole genome to screen an extensive panel of HCC cell lines (N=14 in total) to detect DNA copy number changes. PTPRD expression was determined in human HCCs by Q-RT-PCR and immunohistochemistry. Promoter hypermethylation was assessed by combined bisulfite restriction analysis (COBRA). DNA methyl transferase inhibitor 5-azacytidine (5-AzaC) and/or histone deacetylase inhibitor Trichostain A (TSA) were used to restore the expression. We identified homozygous deletions in Mahlavu and SNU475 cells, in the 5'UTR and coding regions, respectively. PTPRD mRNA expression was downregulated in 78.5% of cell lines and 82.6% of primary HCCs. PTPRD protein expression was also found to be lost or reduced in HCC tumor tissues. We found promoter hypermethylation in 22.2% of the paired HCC samples and restored PTPRD expression by 5-AzaC and/or TSA treatments. In conclusion, PTPRD is homozygously deleted and epigenetically downregulated in HCCs. We hypothesize PTPRD as a tumor suppressor candidate and potential cancer biomarker in human HCCs. This hypothesis is consistent with compelling evidences in other organ systems, as discussed in this article. Further functional assays in larger samples may ascertain the contribution of PTPRD to hepatocarcinogenesis in greater detail, not to forget its broader importance for diagnostic medicine and the emerging field of personalized medicine in oncology.

RAB8B is required for activity and caveolar endocytosis of LRP6.

Wnt/ß-catenin signaling plays an important role in embryonic development and adult tissue homeostasis. When Wnt ligands bind to the receptor complex, LRP5/6 coreceptors are activated by phosphorylation and concomitantly endocytosed. In vertebrates, Wnt ligands induce caveolin-dependent endocytosis of LRP6 to relay signal downstream, whereas antagonists such as Dickkopf promote clathrin-dependent endocytosis, leading to inhibition. However, little is known about how LRP6 is directed to different internalization mechanisms, and how caveolin-dependent endocytosis is mediated. In an RNAi screen, we identified the Rab GTPase RAB8B as being required for Wnt/ß-catenin signaling. RAB8B depletion reduces LRP6 activity, ß-catenin accumulation, and induction of Wnt target genes, whereas RAB8B overexpression promotes LRP6 activity and internalization and rescues inhibition of caveolar endocytosis. In Xenopus laevis and Danio rerio, RAB8B morphants show lower Wnt activity during embryonic development. Our results implicate RAB8B as an essential evolutionary conserved component of Wnt/ß-catenin signaling through regulation of LRP6 activity and endocytosis.

Wnt secretion is required to maintain high levels of Wnt activity in colon cancer cells.

Aberrant regulation of the Wnt/ß-catenin pathway has an important role during the onset and progression of colorectal cancer, with over 90% of cases of sporadic colon cancer featuring mutations in APC or ß-catenin. However, it has remained a point of controversy whether these mutations are sufficient to activate the pathway or require additional upstream signals. Here we show that colorectal tumours express elevated levels of Wnt3 and Evi/Wls/GPR177. We found that in colon cancer cells, even in the presence of mutations in APC or ß-catenin, downstream signalling remains responsive to Wnt ligands and receptor proximal signalling. Furthermore, we demonstrate that truncated APC proteins bind ß-catenin and key components of the destruction complex. These results indicate that cells with mutations in APC or ß-catenin depend on Wnt ligands and their secretion for a sufficient level of ß-catenin signalling, which potentially opens new avenues for therapeutic interventions by targeting Wnt secretion via Evi/Wls.

Cell perturbation screens for target identification by RNAi.

Over the last decade, cell-based screening has become a powerful method in target identification and plays an important role both in basic research and drug discovery. The availability of whole genome sequences and improvements in cell-based screening techniques opened new avenues for high-throughput experiments. Large libraries of RNA interference reagents available for many organisms allow the dissection of broad spectrum of cellular processes. Here, we describe the current state of the large-scale phenotype screening with a focus on cell-based screens. We underline the importance and provide details of screen design, scalability, performance, data analysis, and hit prioritization. Similar to classical high-throughput in vitro screens with defined-target approaches in the past, cell-based screens depend on a successful establishment of robust phenotypic assays, the ability to quantitatively measure phenotypic changes and bioinformatics methods for data analysis, integration, and interpretation.

A novel multiplex cell viability assay for high-throughput RNAi screening.

Cell-based high-throughput RNAi screening has become a powerful research tool in addressing a variety of biological questions. In RNAi screening, one of the most commonly applied assay system is measuring the fitness of cells that is usually quantified using fluorescence, luminescence and absorption-based readouts. These methods, typically implemented and scaled to large-scale screening format, however often only yield limited information on the cell fitness phenotype due to evaluation of a single and indirect physiological indicator. To address this problem, we have established a cell fitness multiplexing assay which combines a biochemical approach and two fluorescence-based assaying methods. We applied this assay in a large-scale RNAi screening experiment with siRNA pools targeting the human kinome in different modified HEK293 cell lines. Subsequent analysis of ranked fitness phenotypes assessed by the different assaying methods revealed average phenotype intersections of 50.7±2.3%-58.7±14.4% when two indicators were combined and 40-48% when a third indicator was taken into account. From these observations we conclude that combination of multiple fitness measures may decrease false-positive rates and increases confidence for hit selection. Our robust experimental and analytical method improves the classical approach in terms of time, data comprehensiveness and cost.

Polymorphisms in CTNNBL1 in relation to colorectal cancer with evolutionary implications.

Colorectal cancer (CRC) is a complex disease related to environmental and genetic risk factors. Several studies have shown that susceptibility to complex diseases can be mediated by ancestral alleles. Using RNAi screening, CTNNBL1 was identified as a putative regulator of the Wnt signaling pathway, which plays a key role in colorectal carcinogenesis. Recently, single nucleotide polymorphisms (SNPs) in CTNNBL1 have been associated with obesity, a known risk factor for CRC. We investigated whether genetic variation in CTNNBL1 affects susceptibility to CRC and tested for signals of recent selection. We applied a tagging SNP approach that cover all known common variation in CTNNBL1 (allele frequency >5%; r(2)>0.8). A case-control study was carried out using two well-characterized study populations: a hospital-based Czech population composed of 751 sporadic cases and 755 controls and a family/early onset-based German population (697 cases and 644 controls). Genotyping was performed using allele specific PCR based TaqMan® assays (Applied Biosystems, Weiterstadt, Germany). In the Czech cohort, containing sporadic cases, the ancestral alleles of three SNPs showed evidence of association with CRC: rs2344481 (OR 1.44, 95%CI 1.06-1.95, dominant model), rs2281148 (OR 0.59, 95%CI 0.36-0.96, dominant model) and rs2235460 (OR 1.38, 95%CI 1.01-1.89, AA vs. GG). The associations were less prominent in the family/early onset-based German cohort. Data derived from several databases and statistical tests consistently pointed to a likely shaping of CTNNBL1 by positive selection. Further studies are needed to identify the actual function of CTNNBL1 and to validate the association results in other populations.

Mapping segmental and sequence variations among laboratory mice using BAC array CGH.

We used arrays of 2069 BACs (1303 nonredundant autosomal clones) to map sequence variation among Mus spretus (SPRET/Ei and SPRET/Glasgow) and Mus musculus (C3H/HeJ, BALB/cJ, 129/J, DBA/2J, NIH, FVB/N, and C57BL/6) strains. We identified 80 clones representing 74 autosomal loci of copy number variation (|log(2)ratio| >/= 0.4). These variant loci distinguish laboratory strains. By FISH mapping, we determined that 63 BACs mapped to a single site on C57BL/6J chromosomes, while 17 clones mapped to multiple chromosomes (n = 16) or multiple sites on one chromosome (n = 1). We also show that small ratio changes (Delta log(2)ratio approximately 0.1) distinguish homozygous and heterozygous regions of the genome in interspecific backcross mice, providing an efficient method for genotyping progeny of backcrosses.