H&E image analysis pipeline for quantifying morphological features.

Detecting cell types from histopathological images is essential for various digital pathology applications. However, large number of cells in whole-slide images (WSIs) necessitates automated analysis pipelines for efficient cell type detection. Herein, we present hematoxylin and eosin (H&E) Image Processing pipeline (HEIP) for automatied analysis of scanned H&E-stained slides. HEIP is a flexible and modular open-source software that performs preprocessing, instance segmentation, and nuclei feature extraction. To evaluate the performance of HEIP, we applied it to extract cell types from ovarian high-grade serous carcinoma (HGSC) patient WSIs. HEIP showed high precision in instance segmentation, particularly for neoplastic and epithelial cells. We also show that there is a significant correlation between genomic ploidy values and morphological features, such as major axis of the nucleus.

Electrically Induced Blink for the Prevention of Ocular Symptoms and Blurred Vision in Patients With Acute Facial Nerve Palsy.

Objectives: Facial nerve palsy causes blurred vision and ocular discomfort due to deficits in blinking and eye closure. The objective of this study was to determine whether eye-blinks could be elicited by electrical stimulation and whether electrically induced blink would have an effect on the visual acuity and ocular symptoms in patients with acute facial nerve palsy. Methods: The zygomatic branch of the facial nerve of fifteen participants with acute facial nerve palsy was electrically stimulated in order to elicit a blink. In successful cases, the participant proceeded with a two-hour TV watching session in which an electrically induced blink was delivered every 5 seconds. The control condition consisted of an otherwise similar TV watching session without electrically induced blinking. Subjective ocular symptoms were evaluated with a Dry Eye Questionnaire and visual acuity was assessed with a Logarithm of the Minimum Angle of Resolution (LogMAR) chart before and after both sessions. Results: The stimulation produced a blink in 8 participants (53%). The visual acuity in the affected eye decreased during the control session, whereas no significant change occurred during the stimulation session. The ocular symptoms were significantly reduced during the stimulation session. Conclusions: Electrically elicited blink is a promising method for reducing the eye symptoms in individuals with acute facial nerve palsy.

FUNGI: FUsioN Gene Integration toolset.

MOTIVATION: Fusion genes are both useful cancer biomarkers and important drug targets. Finding relevant fusion genes is challenging due to genomic instability resulting in a high number of passenger events. To reveal and prioritize relevant gene fusion events we have developed FUsionN Gene Identification toolset (FUNGI) that uses an ensemble of fusion detection algorithms with prioritization and visualization modules. RESULTS: We applied FUNGI to an ovarian cancer dataset of 107 tumor samples from 36 patients. Ten out of 11 detected and prioritized fusion genes were validated. Many of detected fusion genes affect the PI3K-AKT pathway with potential role in treatment resistance. AVAILABILITYAND IMPLEMENTATION: FUNGI and its documentation are available at https://bitbucket.org/alejandra_cervera/fungi as standalone or from Anduril at https://www.anduril.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Agile workflow for interactive analysis of mass cytometry data.

MOTIVATION: Single-cell proteomics technologies, such as mass cytometry, have enabled characterization of cell-to-cell variation and cell populations at a single-cell resolution. These large amounts of data, require dedicated, interactive tools for translating the data into knowledge. RESULTS: We present a comprehensive, interactive method called Cyto to streamline analysis of large-scale cytometry data. Cyto is a workflow-based open-source solution that automates the use of state-of-the-art single-cell analysis methods with interactive visualization. We show the utility of Cyto by applying it to mass cytometry data from peripheral blood and high-grade serous ovarian cancer (HGSOC) samples. Our results show that Cyto is able to reliably capture the immune cell sub-populations from peripheral blood and cellular compositions of unique immune- and cancer cell subpopulations in HGSOC tumor and ascites samples. AVAILABILITYAND IMPLEMENTATION: The method is available as a Docker container at https://hub.docker.com/r/anduril/cyto and the user guide and source code are available at https://bitbucket.org/anduril-dev/cyto. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Three-Dimensional Printing of the Nasal Cavities for Clinical Experiments.

3D printing has produced many beneficial applications for surgery. The technique´s applicability in replicating nasal cavity anatomy for clinical use has not been studied. Our aim was to determine whether 3D printing could realistically replicate the nasal cavities and the airflow passing through them from a clinical point of view. We included Cone Beam Computed Tomography (CBCT) scans of five patients with symptoms of chronic nasal congestion. These CBCT scans were used to print plastic 3D prints of the nasal cavities, which were also CBCT scanned and the measurements were compared. The results in vivo were higher than the results in vitro in maxillary sinus volumes with a ratio of 1.05 ± 0.01 (mean ± SD) and in the nasal cavities with a ratio of 1.20 ± 0.1 (mean ± SD). Linear measurements in vitro were very close to those in vivo. Rhinomanometric results showed some differences, but rhinomanometric graphs in vitro were close to the graphs in vivo. 3D printing proved to be a suitable and fast method for replicating nasal cavity structures and for the experimental testing of nasal function. It can be used as a complementary examination tool for rhinomanometry.

Effect of pulse waveforms on movement amplitudes and perceived discomfort in electric muscle stimulation in unresolved facial nerve palsy.

Studies on the effects of the pulse waveform used in electrical muscle stimulation on the activations and perceived discomfort of the waveform have been mainly executed on limb muscles with variable results, however, knowledge of these effects on facial muscles is currently lacking. We studied two waveforms, square wave and sinusoidal wavelet, for the activation of the frontalis muscle in 9 individuals with unresolved facial nerve palsy. Both waveforms produced a movement that was greater in amplitude compared with the maximal voluntary movement of the affected side in 8 participants and at least as great as the healthy side's maximal voluntary movement in 4 participants. Both waveforms were equally successful in producing movements, and there was no significant difference in perceived discomfort ratings between the two waveforms. These findings will be useful for the future development of neuroprosthetic applications for reanimating facial muscles using electrical stimulation. Trial registration: ClinicalTrials.gov NCT03496025, registration date March 19, 2018.

Drug screening approach combines epigenetic sensitization with immunochemotherapy in cancer.

BACKGROUND: The epigenome plays a key role in cancer heterogeneity and drug resistance. Hence, a number of epigenetic inhibitors have been developed and tested in cancers. The major focus of most studies so far has been on the cytotoxic effect of these compounds, and only few have investigated the ability to revert the resistant phenotype in cancer cells. Hence, there is a need for a systematic methodology to unravel the mechanisms behind epigenetic sensitization. RESULTS: We have developed a high-throughput protocol to screen non-simultaneous drug combinations, and used it to investigate the reprogramming potential of epigenetic inhibitors. We demonstrated the effectiveness of our protocol by screening 60 epigenetic compounds on diffuse large B-cell lymphoma (DLBCL) cells. We identified several histone deacetylase (HDAC) and histone methyltransferase (HMT) inhibitors that acted synergistically with doxorubicin and rituximab. These two classes of epigenetic inhibitors achieved sensitization by disrupting DNA repair, cell cycle, and apoptotic signaling. The data used to perform these analyses are easily browsable through our Results Explorer. Additionally, we showed that these inhibitors achieve sensitization at lower doses than those required to induce cytotoxicity. CONCLUSIONS: Our drug screening approach provides a systematic framework to test non-simultaneous drug combinations. This methodology identified HDAC and HMT inhibitors as successful sensitizing compounds in treatment-resistant DLBCL. Further investigation into the mechanisms behind successful epigenetic sensitization highlighted DNA repair, cell cycle, and apoptosis as the most dysregulated pathways. Altogether, our method adds supporting evidence in the use of epigenetic inhibitors as sensitizing agents in clinical settings.

Simple 3D culture of dissociated kidney mesenchyme mimics nephron progenitor niche and facilitates nephrogenesis Wnt-independently.

Kidney mesenchyme (KM) and nephron progenitors (NPs) depend on WNT activity, and their culture in vitro requires extensive repertoire of recombinant proteins and chemicals. Here we established a robust, simple culture of mouse KM using a combination of 3D Matrigel and growth media supplemented with Fibroblast Growth Factor 2 (FGF2) and Src inhibitor PP2. This allows dissociated KM to spontaneously self-organize into spheres. To reassess the requirement of WNT activity in KM self-organization and NPs maintenance, cells were cultured with short pulse of high-dose GSK3ß inhibitor BIO, on a constant low-dose or without BIO. Robust proliferation at 48 hours and differentiation at 1 week were observed in cultures with high BIO pulse. Importantly, dissociated KM cultured without BIO, similarly to that exposed to constant low dose of BIO, maintained NPs up to one week and spontaneously differentiated into nephron tubules at 3 weeks of culture. Our results show that KM is maintained and induced to differentiate in a simple culture system. They also imply that GSK3ß/WNT-independent pathways contribute to the maintenance and induction of mouse KM. The robust and easy 3D culture enables further characterization of NPs, and may facilitate disease modeling when applied to human cells.

Facial muscle reanimation by transcutaneous electrical stimulation for peripheral facial nerve palsy.

Reanimation of paralysed facial muscles by electrical stimulation has been studied extensively in animal models, but human studies in this field are largely lacking. Twenty-four subjects with a peripheral facial nerve palsy with a median duration of three years were enrolled. We studied activations of four facial muscles with electrical stimulation using surface electrodes. In subjects whose voluntary movement was severely impaired or completely absent, the electrical stimulation produced a movement that was greater in amplitude compared with the voluntary effort in 10 out of 18 subjects in the frontalis muscle, in 5 out of 14 subjects in the zygomaticus major muscle, and in 3 out of 8 subjects in the orbicularis oris muscle. The electrical stimulation produced a stronger blink in 8 subjects out of 22 compared with their spontaneous blinks. The stimulation could produce a better movement even in cases where the muscles were clinically completely paretic, sometimes also in palsies that were several years old, provided that the muscle was not totally denervated. Restoring the function of paralysed facial muscles by electrical stimulation has potential as a therapeutic option in cases where the muscle is clinically paretic but has reinnervation.

FGFR4 phosphorylates MST1 to confer breast cancer cells resistance to MST1/2-dependent apoptosis.

Cancer cells balance with the equilibrium of cell death and growth to expand and metastasize. The activity of mammalian sterile20-like kinases (MST1/2) has been linked to apoptosis and tumor suppression via YAP/Hippo pathway-independent and -dependent mechanisms. Using a kinase substrate screen, we identified here MST1 and MST2 among the top substrates for fibroblast growth factor receptor 4 (FGFR4). In COS-1 cells, MST1 was phosphorylated at Y433 residue in an FGFR4 kinase activity-dependent manner, as assessed by mass spectrometry. Blockade of this phosphorylation by Y433F mutation induced MST1 activation, as indicated by increased threonine phosphorylation of MST1/2, and the downstream substrate MOB1, in FGFR4-overexpressing T47D and MDA-MB-231 breast cancer cells. Importantly, the specific knockdown or short-term inhibition of FGFR4 in endogenous models of human HER2+ breast cancer cells likewise led to increased MST1/2 activation, in conjunction with enhanced MST1 nuclear localization and generation of N-terminal cleaved and autophosphorylated MST1. Unexpectedly, MST2 was also essential for this MST1/N activation and coincident apoptosis induction, although these two kinases, as well as YAP, were differentially regulated in the breast cancer models analyzed. Moreover, pharmacological FGFR4 inhibition specifically sensitized the HER2+ MDA-MB-453 breast cancer cells, not only to HER2/EGFR and AKT/mTOR inhibitors, but also to clinically relevant apoptosis modulators. In TCGA cohort, FGFR4 overexpression correlated with abysmal HER2+ breast carcinoma patient outcome. Therefore, our results uncover a clinically relevant, targetable mechanism of FGFR4 oncogenic activity via suppression of the stress-associated MST1/2-induced apoptosis machinery in tumor cells with prominent HER/ERBB and FGFR4 signaling-driven proliferation.

Anduril 2: upgraded large-scale data integration framework.

SUMMARY: Anduril is an analysis and integration framework that facilitates the design, use, parallelization and reproducibility of bioinformatics workflows. Anduril has been upgraded to use Scala for pipeline construction, which simplifies software maintenance, and facilitates design of complex pipelines. Additionally, Anduril's bioinformatics repository has been expanded with multiple components, and tutorial pipelines, for next-generation sequencing data analysis. AVAILABILITYAND IMPLEMENTATION: Freely available at http://anduril.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PROX1 is a transcriptional regulator of MMP14.

The transcription factor PROX1 is essential for development and cell fate specification. Its function in cancer is context-dependent since PROX1 has been shown to play both oncogenic and tumour suppressive roles. Here, we show that PROX1 suppresses the transcription of MMP14, a metalloprotease involved in angiogenesis and cancer invasion, by binding and suppressing the activity of MMP14 promoter. Prox1 deletion in murine dermal lymphatic vessels in vivo and in human LECs increased MMP14 expression. In a hepatocellular carcinoma cell line expressing high endogenous levels of PROX1, its silencing increased both MMP14 expression and MMP14-dependent invasion in 3D. Moreover, PROX1 ectopic expression reduced the MMP14-dependent 3D invasiveness of breast cancer cells and angiogenic sprouting of blood endothelial cells in conjunction with MMP14 suppression. Our study uncovers a new transcriptional regulatory mechanism of cancer cell invasion and endothelial cell specification.

Hyper-phosphorylation of Sequestosome-1 Distinguishes Resistance to Cisplatin in Patient Derived High Grade Serous Ovarian Cancer Cells.

Platinum-resistance is a major limitation to effective chemotherapy regimens in high-grade serous ovarian cancer (HGSOC). To better understand the mechanisms involved we characterized the proteome and phosphoproteome in cisplatin sensitive and resistant HGSOC primary cells using a mass spectrometry-based proteomic strategy. PCA analysis identified a distinctive phosphoproteomic signature between cisplatin sensitive and resistant cell lines. The most phosphorylated protein in cisplatin resistant cells was sequestosome-1 (p62/SQSTM1). Changes in expression of apoptosis and autophagy related proteins Caspase-3 and SQSTM1, respectively, were validated by Western blot analysis. A significant increase in apoptosis in the presence of cisplatin was observed in only the sensitive cell line while SQSTM1 revealed increased expression in the resistant cell line relative to sensitive cell line. Furthermore, site-specific phosphorylation on 20 amino acid residues of SQSTM1 was detected indicating a hyper-phosphorylation phenotype. This elevated hyper-phosphorylation of SQSTM1 in resistant HGSOC cell lines was validated with Western blot analysis. Immunofluoresence staining of s28-pSQSTM1 showed inducible localization to autophagosomes upon cisplatin treatment in the sensitive cell line while being constitutively expressed to autophagosomes in the resistant cell. Furthermore, SQSTM1 expression was localized in cancer cells of clinical high-grade serous tumors. Here, we propose hyper-phosphorylation of SQSTM1 as a marker and a key proteomic change in cisplatin resistance development in ovarian cancers by activating the autophagy pathway and influencing down-regulation of apoptosis.

Somatic MED12 Nonsense Mutation Escapes mRNA Decay and Reveals a Motif Required for Nuclear Entry.

MED12 is a key component of the transcription-regulating Mediator complex. Specific missense and in-frame insertion/deletion mutations in exons 1 and 2 have been identified in uterine leiomyomas, breast tumors, and chronic lymphocytic leukemia. Here, we characterize the first MED12 5' end nonsense mutation (c.97G>T, p.E33X) identified in acute lymphoblastic leukemia and show that it escapes nonsense-mediated mRNA decay (NMD) by using an alternative translation initiation site. The resulting N-terminally truncated protein is unable to enter the nucleus due to the lack of identified nuclear localization signal (NLS). The absence of NLS prevents the mutant MED12 protein to be recognized by importin-α and subsequent loading into the nuclear pore complex. Due to this mislocalization, all interactions between the MED12 mutant and other Mediator components are lost. Our findings provide new mechanistic insights into the MED12 functions and indicate that somatic nonsense mutations in early exons may avoid NMD.

SePIA: RNA and small RNA sequence processing, integration, and analysis.

BACKGROUND: Large-scale sequencing experiments are complex and require a wide spectrum of computational tools to extract and interpret relevant biological information. This is especially true in projects where individual processing and integrated analysis of both small RNA and complementary RNA data is needed. Such studies would benefit from a computational workflow that is easy to implement and standardizes the processing and analysis of both sequenced data types. RESULTS: We developed SePIA (Sequence Processing, Integration, and Analysis), a comprehensive small RNA and RNA workflow. It provides ready execution for over 20 commonly known RNA-seq tools on top of an established workflow engine and provides dynamic pipeline architecture to manage, individually analyze, and integrate both small RNA and RNA data. Implementation with Docker makes SePIA portable and easy to run. We demonstrate the workflow's extensive utility with two case studies involving three breast cancer datasets. SePIA is straightforward to configure and organizes results into a perusable HTML report. Furthermore, the underlying pipeline engine supports computational resource management for optimal performance. CONCLUSION: SePIA is an open-source workflow introducing standardized processing and analysis of RNA and small RNA data. SePIA's modular design enables robust customization to a given experiment while maintaining overall workflow structure. It is available at http://anduril.org/sepia.

A survey on the feasibility of surface EMG in facial pacing.

A survey on the feasibility of surface electromyography (EMG) measurements in facial pacing is presented. Pacing for unilateral facial paralysis consists of the measurement of activity from the healthy side of the face and functional electrical stimulation to reanimate the paralyzed one. The goal of this study is to evaluate the feasibility of surface EMG as a measurement method to detect muscle activations and to determine their intensities. Prior work is discussed, and results from experiments where 12 participants carried out a set of facial movements are presented. EMG was registered from zygomaticus major (smile), orbicularis oris (lip pucker), orbicularis oculi (eye blink), corrugator supercilii (frown), and masseter (chew). Most important facial functions that are limited due to the paralysis are blinking, smiling, and puckering. With majority of the participants, crosstalk between the measured EMG channels was found to be acceptably small to be able to pace smiling and puckering based on detecting their contraction intensities from the healthy side. However, pacing blinking based on orbicularis oculi EMG measurement does not seem possible due to crosstalk from other muscles, but the electro-oculographic (EOG) signals that couple to the same measurement channel could help to detect eye blinks and trigger stimuli. Futhermore, masseter greatly disturbs EMG measurement of most facial muscles, which needs to be addressed in the pacing system to avoid falsely interpreting its activity as the activity of another muscle.

MMP16 Mediates a Proteolytic Switch to Promote Cell-Cell Adhesion, Collagen Alignment, and Lymphatic Invasion in Melanoma.

Lymphatic invasion and accumulation of continuous collagen bundles around tumor cells are associated with poor melanoma prognosis, but the underlying mechanisms and molecular determinants have remained unclear. We show here that a copy-number gain or overexpression of the membrane-type matrix metalloproteinase MMP16 (MT3-MMP) is associated with poor clinical outcome, collagen bundle assembly around tumor cell nests, and lymphatic invasion. In cultured WM852 melanoma cells derived from human melanoma metastasis, silencing of MMP16 resulted in cell-surface accumulation of the MMP16 substrate MMP14 (MT1-MMP) as well as L1CAM cell adhesion molecule, identified here as a novel MMP16 substrate. When limiting the activities of these trans-membrane protein substrates toward pericellular collagen degradation, cell junction disassembly, and blood endothelial transmigration, MMP16 supported nodular-type growth of adhesive collagen-surrounded melanoma cell nests, coincidentally steering cell collectives into lymphatic vessels. These results uncover a novel mechanism in melanoma pathogenesis, whereby restricted collagen infiltration and limited mesenchymal invasion are unexpectedly associated with the properties of the most aggressive tumors, revealing MMP16 as a putative indicator of adverse melanoma prognosis.

Workflow for automated quantification of cerebromicrovascular gelatinase activity.

The gelatinase enzymes, matrix metalloproteinases -2 and -9, are central mediators of blood-brain barrier disruption, actively studied in experimental models of neurological disease. Staining with in situ zymography (ISZ) allows visualization of gelatinase activity directly in brain tissue sections. However, quantifying microvascular gelatinase activity from ISZ-images is challenging and time consuming, as surrounding cell types often show significant confounding activity. We describe validation and performance of a workflow for automated image analysis of cerebromicrovascular gelatinase activity, now released for open-access use. In comparison to manual analysis, the automated workflow showed superior accuracy, was faster to execute and allows for more detailed analysis of heterogeneity in the microvasculature. We further suggest recommendations for quantifying and reporting this type of activity in experimental studies, focusing on ischemic stroke.

mTORC1 controls PNS myelination along the mTORC1-RXRγ-SREBP-lipid biosynthesis axis in Schwann cells.

Myelin formation during peripheral nervous system (PNS) development, and reformation after injury and in disease, requires multiple intrinsic and extrinsic signals. Akt/mTOR signaling has emerged as a major player involved, but the molecular mechanisms and downstream effectors are virtually unknown. Here, we have used Schwann-cell-specific conditional gene ablation of raptor and rictor, which encode essential components of the mTOR complexes 1 (mTORC1) and 2 (mTORC2), respectively, to demonstrate that mTORC1 controls PNS myelination during development. In this process, mTORC1 regulates lipid biosynthesis via sterol regulatory element-binding proteins (SREBPs). This course of action is mediated by the nuclear receptor RXRγ, which transcriptionally regulates SREBP1c downstream of mTORC1. Absence of mTORC1 causes delayed myelination initiation as well as hypomyelination, together with abnormal lipid composition and decreased nerve conduction velocity. Thus, we have identified the mTORC1-RXRγ-SREBP axis controlling lipid biosynthesis as a major contributor to proper peripheral nerve function.