Comprehensive genomic profiling by liquid biopsy captures tumor heterogeneity and identifies cancer vulnerabilities in patients with RAS/BRAFV600E wild type metastatic colorectal cancer in the CAPRI 2-GOIM trial.

BACKGROUND: Emerging evidence supports tumor tissue-based comprehensive genomic profiling (CGP) in metastatic colorectal cancer (mCRC). Data on liquid biopsy-based circulating tumor DNA (ctDNA) CGP are scarce and mainly retrospective. Prospective comparison between the two tests is not currently available. METHODS: The CAPRI 2-GOIM trial investigates efficacy and safety of ctDNA-driven, cetuximab-based, sequence of three treatment lines in patients with RAS/BRAFV600E wild type (WT) mCRC, as determined by local laboratory. Before first-line therapy, CGP is performed with FoundationOne (F1) CDx and F1 Liquid (F1L) CDx (324 genes) on tumor tissue DNA and plasma ctDNA, respectively. RESULTS: For 2/207 (0.96%) patients, no ctDNA was detected by F1L CDx. No patient displayed tumor fraction (TF) below 1%, whereas elevated ctDNA (TF≥10%) was detected among 140/205 (68.3%) patients. 1013 genomic variants were identified. F1L CDx found KRAS, NRAS or BRAFV600E alterations in 19 patients, whose tumors were classified as RAS/BRAFV600E WT by local laboratory. Both F1 CDx and F1L CDx were available for 164/205 (80%) patients. Concordance of 61.4% between the two tests was observed. Concordance increased to 72.7% for F1L CDx with TF ≥10%. Concordance for genes potentially involved in anti-epidermal growth factor receptor (EGFR) resistance was found in 137/164 (83%) patients, increasing to 91.5% for F1L CDx with TF ≥10%. A higher number of genomic alterations was detected by F1L CDx compared with F1 CDx, including 6 cases with KRAS and NRAS alterations. Overall, 109/205 (53.2%) patients displayed at least one actionable genomic alteration (I to IIIB), according to the ESMO Scale for Clinical Actionability of Molecular Targets (ESCAT). CONCLUSION: Baseline liquid biopsy-based CGP is feasible, it has high concordance with tumor tissue-based CGP, it could better recapitulate tumor heterogeneity, and it is clinically informative by identifying additional actionable genomic alterations in approximately half of RAS/BRAFV600E WT mCRC patients.

Where Environment Meets Cognition: A Focus on Two Developmental Intellectual Disability Disorders.

One of the most challenging questions in neuroscience is to dissect how learning and memory, the foundational pillars of cognition, are grounded in stable, yet plastic, gene expression states. All known epigenetic mechanisms such as DNA methylation and hydroxymethylation, histone modifications, chromatin remodelling, and noncoding RNAs regulate brain gene expression, both during neurodevelopment and in the adult brain in processes related to cognition. On the other hand, alterations in the various components of the epigenetic machinery have been linked to well-known causes of intellectual disability disorders (IDDs). Two examples are Down Syndrome (DS) and Fragile X Syndrome (FXS), where global and local epigenetic alterations lead to impairments in synaptic plasticity, memory, and learning. Since epigenetic modifications are reversible, it is theoretically possible to use epigenetic drugs as cognitive enhancers for the treatment of IDDs. Epigenetic treatments act in a context specific manner, targeting different regions based on cell and state specific chromatin accessibility, facilitating the establishment of the lost balance. Here, we discuss epigenetic studies of IDDs, focusing on DS and FXS, and the use of epidrugs in combinatorial therapies for IDDs.

Nucleosome loss facilitates the chemotactic response of macrophages.

BACKGROUND: High mobility group box 1 (HMGB1) is a small nuclear protein with two functions. In the nucleus, it helps to wrap DNA around nucleosomes. When secreted, it recruits inflammatory cells and induces cytokine production. Before HMGB1 is secreted from inflammatory cells, it relocates to the cytoplasm, which partially or totally depletes cell nuclei of HMGB1. We previously showed that cells lacking HMGB1 contain 20% fewer nucleosomes and 30% more RNA transcripts levels genome-wide. OBJECTIVE: We hypothesized that the depletion of nuclear HMGB1 plays a role in inflammation that can enhance or complement the role of extracellular HMGB1. METHODS: We analysed the transcriptional profile of wild-type and Hmgb1-/- mouse embryonic fibroblasts (MEFs) as a proxy for cells that have lost HMGB1 from their nuclei. We explored the transcriptome of wild-type and Hmgb1-/- macrophages differentiated in the presence of granulocyte-macrophage colony-stimulating factor, before and after exposure to LPS/IFN-γ. In the same cells, histones and nuclear HMGB1 were quantified. RESULTS: We found that Hmgb1-/- MEFs show a transcriptional profile associated with stress and inflammation responses. Moreover, wild-type macrophages that have secreted HMGB1 because of LPS/IFN-γ exposure rapidly reduce their histone content as much as cells that genetically lack HMGB1. Importantly, unstimulated Hmgb1-/- macrophages activate transcriptional pathways associated with cell migration and chemotaxis. CONCLUSIONS: We suggest that nucleosome loss is an early event that facilitates transcriptional responses of macrophages to inflammation, particularly chemotaxis. HMGB1's dual roles in the nucleus and in the extracellular space appear to be complementary.

Immunomodulatory effects of BCG in patients with recurrent respiratory papillomatosis.

BACKGROUND: Recurrent respiratory papillomatosis (RRP) is a rare manifestation of human papilloma virus (HPV) infection with extremely high relapse frequency, poorly understood immunopathogenesis, and lack of efficient treatment. Immunotherapy with Calgevax (BCG) in combination with CO2 surgery significantly improves the outcome of RRP. The present study investigates cellular immunity parameters in RRP patients, and the effects of 20-month Calgevax immunomodulation. MATERIALS AND METHODS: RRP patients (n = 15) subjected to combined therapy were tested before, 6, 12 and 20 months after the start of immunomodulation. Absolute counts and percentage of T, B and NK cells, effector T1 (CD8 + IFNgamma+); Th1 (CD4+IFNgamma+), Th17 (CD4+IL-17+) and regulatory (CD4+FoxP3+) T lymphocytes, as well as the in vitro stimulated secretion of IL-2, IL-4, IL-5, IL-10, IFNgamma and TNFalpha were determined by flow cytometry (FACSCanto II, BD). RESULTS: While no significant changes were detected in the circulating T, B and NK subsets, RRP patients presented increased proportions of Tc1, Th1 and Th17 cells, and significantly reduced IFNgamma/IL-4 and IFNgamma/IL-10 ratios as compared to healthy controls (15% vs. 8%), (58 vs. 139 and 15 vs. 26, respectively), p < 0.05 for all comparisons. Increased Treg (9% vs. 4%), and decreased Th17 effectors share (0.7% vs. 0.4%) were observed at 12 months, while IFNgamma/IL-4 and IFNgamma/IL-10 ratios were restored after 20 months of Calgevax application. CONCLUSIONS: Antiviral response closely depends on cytokine background. Calgevax potentiates Treg differentiation at the expense of proinflammatory Th17, limits hyperactivation and virus-specific T cell clones depletion, and restores a Th1 cytokine background.

Effects of perfusion and cyclic compression on in vitro tissue engineered meniscus implants.

PURPOSE: The purpose of this study was to investigate the influence of continuous perfusion and mechanical stimulation on bone marrow stromal cells seeded on a collagen meniscus implant. METHODS: Bone marrow aspirates from 6 donors were amplified in vitro. 10(6) human BMSC were distributed on a collagen meniscus implant. Scaffolds were cultured under static conditions (control) or placed into a bioreactor system where continuous perfusion (10 ml/min) or perfusion and mechanical stimulation (8 h of 10% cyclic compression at 0.5 Hz) were administered daily. After 24 h, 7 and 14 days, cell proliferation, synthesis of procollagen I and III peptide (PIP, PIIIP), histology, and the equilibrium modulus of the constructs were analyzed. RESULTS: Proliferation demonstrated a significant increase over time in all groups (p < 0.001). PIP synthesis was found to increase from 0.1 ± 0.0 U/ml/g protein after 24 h to 2.0 ± 0.5 (perfusion), 3.8 ± 0.3 (mechanical stimulation), and 1.8 ± 0.2 U/ml/g protein (static control, lower than perfusion and mechanical stimulation, p < 0.05). These differences were also evident after 2 weeks (2.7 ± 0.3, 4.0 ± 0.6, and 1.8 ± 0.2 U/ml/g protein, p < 0.01); PIIIP synthesis was found to increase from 0.1 ± 0.0 U/ml/g protein after 24 h to 2.9 ± 0.7 (perfusion), 3.1 ± 0.9 (mechanical stimulation), and 1.6 ± 0.3 U/ml/g protein (controls) after 1 week and remained significantly elevated under the influence of perfusion and mechanical stimulation (p < 0.01) after 2 weeks. Mechanical stimulation increased the equilibrium modulus more than static culture and perfusion after 2 weeks (24.7 ± 7.6; 12.3 ± 3.7; 15.4 ± 2.6 kPa; p < 0.02). CONCLUSION: Biomechanical stimulation and perfusion have impact on collagen scaffolds seeded with BMSCs. Cell proliferation can be enhanced using continuous perfusion and differentiation is fostered by mechanical stimulation.

[Biological monitoring and exposure to silica: application of new dose and effect biomarkers]. / Monitoraggio biologico ed esposizione a silice: applicazione di nuovi indicatori di dose e di effetto.

Si-CAE was measured in 16 composite marble industry workers furthermore, a spirometry was performed and 8oxoGua, 8oxoGuo 8oxodGuo, SP-A, SP-D, CC16 and HO-1 were dosed. A lower spirometric values (FEV1 and FVC) were observed among workers compared with controls and the following markers were increased: Si-CAE, 8oxoGuo and HO-1 expression. This study shows that exposure to silica can increase the levels of Si-CAE, which can be used to estimate the dose to the target. Finally, nonspecific spirometric abnormalities and an increase in biomarkers of effect were observed.

Re-establishment of the epigenetic state and rescue of kinome deregulation in Ts65Dn mice upon treatment with green tea extract and environmental enrichment.

Down syndrome (DS) is the main genetic cause of intellectual disability due to triplication of human chromosome 21 (HSA21). Although there is no treatment for intellectual disability, environmental enrichment (EE) and the administration of green tea extracts containing epigallocatechin-3-gallate (EGCG) improve cognition in mouse models and individuals with DS. Using proteome, and phosphoproteome analysis in the hippocampi of a DS mouse model (Ts65Dn), we investigated the possible mechanisms underlying the effects of green tea extracts, EE and their combination. Our results revealed disturbances in cognitive-related (synaptic proteins, neuronal projection, neuron development, microtubule), GTPase/kinase activity and chromatin proteins. Green tea extracts, EE, and their combination restored more than 70% of the phosphoprotein deregulation in Ts65Dn, and induced possible compensatory effects. Our downstream analyses indicate that re-establishment of a proper epigenetic state and rescue of the kinome deregulation may contribute to the cognitive rescue induced by green tea extracts.

Dependence of maternal serum [AFP]/[hCG] median ratios on age of gestation: comparison of trisomy 21 to euploid pregnancies.

BACKGROUND: Current risk calculations for trisomy 21, which are based on multiples of median (MoM), do not take into account possible differences between euploid and trisomy 21 pregnancies that may develop with gestational age. In order to optimize the predictive value of screening tests, we calculated the ratio between maternal serum concentration of alpha-fetoprotein (AFP) and that of human chorionic gonadotropin (hCG) in euploid and in trisomy 21 pregnancies. METHODS: The medians of the concentration ratios, [AFP]/[hCG] at 16-21 weeks of gestation, were plotted as a function of gestational age for 307 cases of trisomy 21 and were compared with the medians of 30 549 normal karyotype cases. RESULTS: [AFP]/[hCG] ratio medians were independent of body weight and maternal age. There was a significant difference in the [AFP]/[hCG] ratio when comparing trisomy 21 and euploid pregnancies at each week. This difference became greater with advancing gestational age (P < 0.01). CONCLUSION: There is a significant difference in ratios of [AFP]/[hCG] between euploid and trisomy 21 pregnancies, which may be used to improve detection rates of Down syndrome screening.

Overweight Mice Show Coordinated Homeostatic and Hedonic Transcriptional Response across Brain.

Obesogenic diets lead to overeating and obesity by inducing the expression of genes involved in hedonic and homeostatic responses in specific brain regions. However, how the effects on gene expression are coordinated in the brain so far remains largely unknown. In our study, we provided mice with access to energy-dense diet, which induced overeating and overweight, and we explored the transcriptome changes across the main regions involved in feeding and energy balance: hypothalamus, frontal cortex, and striatum. Interestingly, we detected two regulatory processes: a switch-like regulation with differentially expressed (DE) genes changing over 1.5-fold and "fine-tuned" subtler changes of genes whose levels correlated with body weight and behavioral changes. We found that genes in both categories were positioned within specific topologically associated domains (TADs), which were often differently regulated across different brain regions. These TADs were enriched in genes relevant for the physiological and behavioral observed changes. Our results suggest that chromatin structure coordinates diet-dependent transcriptional regulation.

Implication of Long noncoding RNAs in the endothelial cell response to hypoxia revealed by RNA-sequencing.

Long noncoding RNAs (lncRNAs) are non-protein coding RNAs regulating gene expression. Although for some lncRNAs a relevant role in hypoxic endothelium has been shown, the regulation and function of lncRNAs is still largely unknown in the vascular physio-pathology. Taking advantage of next-generation sequencing techniques, transcriptomic changes induced by endothelial cell exposure to hypoxia were investigated. Paired-end sequencing of polyadenylated RNA derived from human umbilical vein endothelial cells (HUVECs) exposed to 1% O2 or normoxia was performed. Bioinformatics analysis identified ≈2000 differentially expressed genes, including 122 lncRNAs. Extensive validation was performed by both microarray and qPCR. Among the validated lncRNAs, H19, MIR210HG, MEG9, MALAT1 and MIR22HG were also induced in a mouse model of hindlimb ischemia. To test the functional relevance of lncRNAs in endothelial cells, knockdown of H19 expression was performed. H19 inhibition decreased HUVEC growth, inducing their accumulation in G1 phase of the cell cycle; accordingly, p21 (CDKN1A) expression was increased. Additionally, H19 knockdown also diminished HUVEC ability to form capillary like structures when plated on matrigel. In conclusion, a high-confidence signature of lncRNAs modulated by hypoxia in HUVEC was identified and a significant impact of H19 lncRNA was shown.

Structure and function of fibroblast growth factor.

We describe some structural requirements of the fibroblast growth factor (FGF) signaling system for the stimulation of the mitogenic response in terms of the design, synthesis and mitogenic activity of linear peptides related to the human FGF-1 sequence and the structural requirements of heparin for the potentiation of the mitogenic activity of FGF-1. The best mitogenic peptide we have synthesized so far is Ac-WFVGLKKNGSSKRGPRT-NH2, that has been shown: 1) to bind to heparin-Sepharose columns with moderate affinity, requiring about 0.5 M NaCl to be eluted from the resin; 2) to be mitogenic upon BALB/c 3T3 fibroblasts in culture (ED50 = 10-20 microM) and 3) to compete with human FGF-1 for cellular binding (ID50 = 30-50 microM). The potentiating activity of heparin upon FGF-1 has shown to be dependent on the oligosaccharide size, degree of sulfation and carboxylation. Apparently, these same requirements hold for the heparan sulfate molecules. Based on the reported studies, we propose some important requirements of an oligosaccharide to potentiate FGF-1 mitogenic activity: 1) to have a minimum of twelve units, organized as disaccharides where one of the units is a uronic acid and the second is glycosamine; 2) to have at least one iduronic acid sulfated at position 2 and 3) to have N-sulfated glycosamines, preferentially 6-O-sulfated. To have groups of negative charges is not enough: they need to be localized in a correct conformation.

Structuring clinical workflows for diabetes care: an overview of the OntoHealth approach.

BACKGROUND: Electronic health records (EHRs) play an important role in the treatment of chronic diseases such as diabetes mellitus. Although the interoperability and selected functionality of EHRs are already addressed by a number of standards and best practices, such as IHE or HL7, the majority of these systems are still monolithic from a user-functionality perspective. The purpose of the OntoHealth project is to foster a functionally flexible, standards-based use of EHRs to support clinical routine task execution by means of workflow patterns and to shift the present EHR usage to a more comprehensive integration concerning complete clinical workflows. OBJECTIVES: The goal of this paper is, first, to introduce the basic architecture of the proposed OntoHealth project and, second, to present selected functional needs and a functional categorization regarding workflow-based interactions with EHRs in the domain of diabetes. METHODS: A systematic literature review regarding attributes of workflows in the domain of diabetes was conducted. Eligible references were gathered and analyzed using a qualitative content analysis. Subsequently, a functional workflow categorization was derived from diabetes-specific raw data together with existing general workflow patterns. RESULTS: This paper presents the design of the architecture as well as a categorization model which makes it possible to describe the components or building blocks within clinical workflows. The results of our study lead us to identify basic building blocks, named as actions, decisions, and data elements, which allow the composition of clinical workflows within five identified contexts. CONCLUSIONS: The categorization model allows for a description of the components or building blocks of clinical workflows from a functional view.

Epidural analgesia in labor for a woman with an intrathecal baclofen pump.

A 28-year-old woman in active labor at 38 weeks of gestation requested epidural analgesia. She had previously received an intrathecal baclofen infusion pump to relieve the spasticity of cerebral palsy. She had right hemiparesis and cerebral palsy but was otherwise healthy. The patient had been seen one month before her expected delivery date by a staff anesthesiologist. A lumbar X-ray demonstrated the intrathecal catheter entering the L3-4 interspace and extending to the mid-thoracic region. For labor analgesia the epidural space was identified at L4-5 with the patient sitting, using a standard 17-gauge Tuohy needle. An epidural catheter was threaded to 5 cm and provided effective analgesia until delivery four hours later. There were no postnatal complications.

Advances in renal (patho)physiology using multiphoton microscopy.

Multiphoton excitation fluorescence microscopy is a state-of-the-art confocal imaging technique ideal for deep optical sectioning of living tissues. It is capable of performing ultrasensitive, quantitative imaging of organ functions in health and disease with high spatial and temporal resolution which other imaging modalities cannot achieve. For more than a decade, multiphoton microscopy has been successfully used with various in vitro and in vivo experimental approaches to study many functions of different organs, including the kidney. This study focuses on recent advances in our knowledge of renal (patho)physiological processes made possible by the use of this imaging technology. Visualization of cellular variables like cytosolic calcium, pH, cell-to-cell communication and signal propagation, interstitial fluid flow in the juxtaglomerular apparatus (JGA), real-time imaging of tubuloglomerular feedback (TGF), and renin release mechanisms are reviewed. A brief summary is provided of kidney functions that can be measured by in vivo quantitative multiphoton imaging including glomerular filtration and permeability, concentration, dilution, and activity of the intrarenal renin-angiotensin system using this minimally invasive approach. New visual data challenge a number of existing paradigms in renal (patho)physiology. Also, quantitative imaging of kidney function with multiphoton microscopy has tremendous potential to eventually provide novel non-invasive diagnostic and therapeutic tools for future applications in clinical nephrology.

In vivo skin relief measurement using a new optical profilometer.

BACKGROUND/AIMS: Usually, skin topography is quantified by means of 2D profilometry using negative- or positive-replicas. To allow a direct in vivo measurement, a new profilometer is built, based on an optical triangulation principle. CONCLUSION: High speed of measurement can be reached using a non contact profilometer. The ability of a position sensing detector to read the center of gravity of the spot reflected by the skin surface, allows one to reduce the effects of the enlargement due to the skin absorption of the laser beam.

Mitogenic activity of peptides related to the sequence of human fibroblast growth factor-1.

Linear synthetic peptides related to the human Fibroblast Growth Factor-1 (hFGF-1) segment [112-147] were tested for their capacity of mimicking FGF mitogenic activity, binding to heparin-Sepharose columns, stimulating DNA synthesis and competing with hFGF-1 for the cellular receptors. The results obtained indicated that the activity of these compounds is dependent on the presence of the sequence WFVGLK in their structures. The affinity for the cellular receptors increased when this sequence was elongated in order to incorporate amino acid residues that are important for FGF-heparin binding.

Structure and function of fibroblast growth factor

We describe some structural requirements od the fibroblast growth factor (FGF) signaling system for the stimulation of the mitogenic response in terms of the design, synthesis and mitogenic activity of linear peptides related to the human FGF-1 sequence and the structural requirements of heparin for the potentiation of the mitogenic activity of FGF-1. The best mitogenic peptide we have synthesized so far is Ac-WFVGLKKNGSSKRGPRT-NH2, that has been shown: 1)to bind to heparin-Sepharose columns with moderate affinity, requiring about 0.5 M NaCl to be eluted from the resin; 2) to be mitogenic upon BALB/c 3T3 fibroblasts in culture (ED50=10-20 muM) and 3)to compete with human FGF-1 for cellular binding (ID50=30-50 muM). The potentiating activity of heparin upon FGF-1 has shown to be dependent on the oligosaccharide size, degree of sulfation and carboxylation. Apparently, these same requirements hold for the heparan sulfate molecules. Based on the reported studies, ee propose some important requirements of an oligosaccharide to potentiate FGF-1 mitogenic activity: 1) to have a minimum of twelve units, organized as disaccharides where one of the units is a uronic acid and the second is glycosamine; 2) to have at least one iduronic acid sulfated at position 2 and 3) to have N-sulfated glycosamines, preferentially 6-O-sulfated. To have groups of negative charges is not enough: they need to be localized in a correct conformation.