Integrating GWAS with bulk and single-cell RNA-sequencing reveals a role for LY86 in the anti-Candida host response

Contains fulltext : 220669.pdf (publisher's version ) (Open Access)Candida bloodstream infection, i.e. candidemia, is the most frequently encountered life-threatening fungal infection worldwide, with mortality rates up to almost 50%. In the majority of candidemia cases, Candida albicans is responsible. Worryingly, a global increase in the number of patients who are susceptible to infection (e.g. immunocompromised patients), has led to a rise in the incidence of candidemia in the last few decades. Therefore, a better understanding of the anti-Candida host response is essential to overcome this poor prognosis and to lower disease incidence. Here, we integrated genome-wide association studies with bulk and single-cell transcriptomic analyses of immune cells stimulated with Candida albicans to further our understanding of the anti-Candida host response. We show that differential expression analysis upon Candida stimulation in single-cell expression data can reveal the important cell types involved in the host response against Candida. This confirmed the known major role of monocytes, but more interestingly, also uncovered an important role for NK cells. Moreover, combining the power of bulk RNA-seq with the high resolution of single-cell RNA-seq data led to the identification of 27 Candida-response QTLs and revealed the cell types potentially involved herein. Integration of these response QTLs with a GWAS on candidemia susceptibility uncovered a potential new role for LY86 in candidemia susceptibility. Finally, experimental follow-up confirmed that LY86 knockdown results in reduced monocyte migration towards the chemokine MCP-1, thereby implying that this reduced migration may underlie the increased susceptibility to candidemia. Altogether, our integrative systems genetics approach identifies previously unknown mechanisms underlying the immune response to Candida infection

Serous cystic neoplasm of the pancreas: A multinational study of 2622 patients under the auspices of the International Association of Pancreatology and European Pancreatic Club (European Study Group on Cystic Tumors of the Pancreas)

OBJECTIVES: Serous cystic neoplasm (SCN) is a cystic neoplasm of the pancreas whose natural history is poorly known. The purpose of the study was to attempt to describe the natural history of SCN, including the specific mortality. DESIGN: Retrospective multinational study including SCN diagnosed between 1990 and 2014. RESULTS: 2622 patients were included. Seventy-four per cent were women, and median age at diagnosis was 58\u2005years (16-99). Patients presented with non-specific abdominal pain (27%), pancreaticobiliary symptoms (9%), diabetes mellitus (5%), other symptoms (4%) and/or were asymptomatic (61%). Fifty-two per cent of patients were operated on during the first year after diagnosis (median size: 40\u2005mm (2-200)), 9% had resection beyond 1\u2005year of follow-up (3\u2005years (1-20), size at diagnosis: 25\u2005mm (4-140)) and 39% had no surgery (3.6\u2005years (1-23), 25.5\u2005mm (1-200)). Surgical indications were (not exclusive) uncertain diagnosis (60%), symptoms (23%), size increase (12%), large size (6%) and adjacent organ compression (5%). In patients followed beyond 1\u2005year (n=1271), size increased in 37% (growth rate: 4\u2005mm/year), was stable in 57% and decreased in 6%. Three serous cystadenocarcinomas were recorded. Postoperative mortality was 0.6% (n=10), and SCN's related mortality was 0.1% (n=1). CONCLUSIONS: After a 3-year follow-up, clinical relevant symptoms occurred in a very small proportion of patients and size slowly increased in less than half. Surgical treatment should be proposed only for diagnosis remaining uncertain after complete workup, significant and related symptoms or exceptionally when exists concern with malignancy. This study supports an initial conservative management in the majority of patients with SCN

The behavior of osteoblast-like cells on various substrates with functional blocking of integrin-β1 and integrin-β3

This study was designed to examine the influence of integrin subunit-β1 and subunit-β3 on the behavior of primary osteoblast-like cells, cultured on calcium phosphate (CaP)-coated and non coated titanium (Ti). Osteoblast-like cells were incubated with specific monoclonal antibodies against integrin-β1 and integrin-β3 to block the integrin function. Subsequently, cells were seeded on Ti discs, either non coated or provided with a 2 μm carbonated hydroxyapatite coating using Electrostatic Spray Deposition. Results showed that on CaP coatings, cellular attachment was decreased after a pre-treatment with either anti-integrin-β1 or anti-integrin-β3 antibodies. On Ti, cell adhesion was only slightly affected after a pre-treatment with anti-integrin-β3 antibodies. Scanning electron microscopy showed that on both types of substrate, cellular morphology was not changed after a pre-treatment with either antibody. With quantitative PCR, it was shown for both substrates that mRNA expression of integrin-β1 was increased after a pre-treatment with either anti-integrin-β1 or anti-integrin-β3 antibodies. Furthermore, after a pre-treatment with either antibody, mRNA expression of integrin-β3 and ALP was decreased, on both types of substrate. In conclusion, osteoblast-like cells have the ability to compensate to great extent for the blocking strategy as applied here. Still, integrin-β1 and β3 seem to play different roles in attachment, proliferation, and differentiation of osteoblast-like cells, and responses on CaP-coated substrates differ to non coated Ti. Furthermore, the influence on ALP expression suggests involvement of both integrin subunits in signal transduction for cellular differentiation

An amphitropic cAMP-binding protein in yeast mitochondria

ABSTRACT: We describe the first example of a mitochondrial protein with a covalently attached phos-phatidylinositol moiety acting as a membrane anchor. The protein can be metabolically labeled with both stearic acid and inositol. The stearic acid label is removed by phospholipase D whereupon the protein with the retained inositol label is released from the membrane. This protein is a cAMP receptor of the yeast Saccharomyces cereuisiae and tightly associated with the inner mitochondrial membrane. However, it is converted into a soluble form during incubation of isolated mitochondria with Ca2+ and phospholipid (or lipid derivatives). This transition requires the action of a proteinaceous, N-ethylmaleimide-sensitive component of the intermembrane space and is accompanied by a decrease in the lipophilicity of the cAMP receptor. We propose that the component of the intermembrane space triggers the amphitropic behavior of the mitochondrial lipid-modified CAMP-binding protein through a phospholipase activity. Only in recent years specific fatty acids have been recog-nized to play important roles in the association of proteins with membranes. Both noncovalent and covalent interactions be-tween fatty acids and proteins have been reported. Among the latter are GTP-binding proteins (Molenaar et al., 1988)

The Temporal Winner-Take-All Readout

How can the central nervous system make accurate decisions about external stimuli at short times on the basis of the noisy responses of nerve cell populations? It has been suggested that spike time latency is the source of fast decisions. Here, we propose a simple and fast readout mechanism, the temporal Winner-Take-All (tWTA), and undertake a study of its accuracy. The tWTA is studied in the framework of a statistical model for the dynamic response of a nerve cell population to an external stimulus. Each cell is characterized by a preferred stimulus, a unique value of the external stimulus for which it responds fastest. The tWTA estimate for the stimulus is the preferred stimulus of the cell that fired the first spike in the entire population. We then pose the questions: How accurate is the tWTA readout? What are the parameters that govern this accuracy? What are the effects of noise correlations and baseline firing? We find that tWTA sensitivity to the stimulus grows algebraically fast with the number of cells in the population, N, in contrast to the logarithmic slow scaling of the conventional rate-WTA sensitivity with N. Noise correlations in first-spike times of different cells can limit the accuracy of the tWTA readout, even in the limit of large N, similar to the effect that has been observed in population coding theory. We show that baseline firing also has a detrimental effect on tWTA accuracy. We suggest a generalization of the tWTA, the n-tWTA, which estimates the stimulus by the identity of the group of cells firing the first n spikes and show how this simple generalization can overcome the detrimental effect of baseline firing. Thus, the tWTA can provide fast and accurate responses discriminating between a small number of alternatives. High accuracy in estimation of a continuous stimulus can be obtained using the n-tWTA

Satisfaction with care as a quality-of-life predictor for stroke patients and their caregivers

Purpose: We sought to identify indicators associated with the quality of life (QoL) of stroke patients and caregivers. Methods: The cross-sectional study was conducted at nine Dutch stroke service facilities involving 251 stroke patients and their caregivers. We used the EuroQol (EQ-5D) and Satisfaction with Stroke Care questionnaires, and included the variables (1) disability at hospital admission, (2) length of hospital stay, (3) demographic data, and (4) caregivers' relationship with stroke patients. The Actor-Partner (patient-caregiver) Interdependence Model (APIM) was used to examine dependence between patients' and caregivers' QoL scores through dyad membership. Results: Patients' age was significantly related to their QoL, and caregivers' age and educational level were significantly related to their QoL. Patients' disability on hospital admission and length of stay were associated with patients' QoL, and their disability on admission was related to caregivers' QoL. No relationship was found between length of stay and caregivers' QoL. Satisfaction with care was associated with both patients' and caregivers' QoL. Conclusions: The APIM distinguished the different roles of patients and caregivers while acknowledging the interdependence of their QoL scores. Satisfaction with care was identified as important indicator of stroke patients' and caregivers' QoL

Intraductal papillary mucinous neoplasm of the pancreas (IPMN): clinico-pathological correlations and surgical indications

<p>Abstract</p> <p>Background</p> <p>Intraductal papillary mucinous neoplasms (IPMNs) are increasingly recognized entities, whose management remains sometimes controversial, due to the high rate of benign lesions and on the other side to the good survival after resection of malignant ones.</p> <p>Methods</p> <p>Retrospective analysis of a prospectively collected Western series of IPMN.</p> <p>Results</p> <p>Forty cases of IPMN were analysed (1992-2007). Most patients were symptomatic (72.5%); cholangio-MRI had the best diagnostic accuracy both for the tumour nature (83.3%) and for the presence of malignancy (57.1%). ERCP was done in 8 cases (20%), and the results were poor. Thirteen patients were treated by pancreatic resection and 27 were maintained in follow-up. Total pancreatectomy was performed in 46% of the cases; in situ and invasive carcinoma were recognized in 15.4% and 38.4% of the cases, respectively. The mean follow-up was 42 months (range 12-72). One only patients with nodal metastases died 16 months after the operation for disease progression, while 91.6% of the operated patients are disease free. Out of the 27 not resected patients, 2 out of 4 presenting a lesion at high risk for malignancy died, while the remaining are in good conditions and disease free, with a mean follow-up of 31 months.</p> <p>Conclusion</p> <p>Therapeutic indication for IPMNs is mainly based upon radiological evaluation of the risk of malignancy. While the main duct tumours should be resected, preserving whenever possible a portion of the gland, the secondary ducts tumours may be maintained under observation, in absence of radiological elements of suspicion such as size larger than 3 cm, or a wall greater than 3 mm or nodules or papillae in the context of the cyst.</p

Efficiency of stress-adaptive traits chlorophyll fluorescence and membrane thermo- stability in wheat under high temperature

Despite developments in targeted gene sequencing and whole-genome analysis techniques, the robust detection of all genetic variation, including structural variants, in and around genes of interest and in an allele-specific manner remains a challenge. Here we present targeted locus amplification (TLA), a strategy to selectively amplify and sequence entire genes on the basis of the crosslinking of physically proximal sequences. We show that, unlike other targeted re-sequencing methods, TLA works without detailed prior locus information, as one or a few primer pairs are sufficient for sequencing tens to hundreds of kilobases of surrounding DNA. This enables robust detection of single nucleotide variants, structural variants and gene fusions in clinically relevant genes, including BRCA1 and BRCA2, and enables haplotyping. We show that TLA can also be used to uncover insertion sites and sequences of integrated transgenes and viruses. TLA therefore promises to be a useful method in genetic research and diagnostics when comprehensive or allele-specific genetic information is needed

The social and scientific values that shape national climate scenarios: a comparison of the Netherlands, Switzerland and the UK

This paper seeks to understand why climate information is produced differently from country to country. To do this, we critically examined and compared the social and scientific values that shaped the production of three national climate scenarios in the Netherlands, Switzerland and the UK. A comparative analysis of documentary materials and expert interviews linked to the climate scenarios was performed. Our findings reveal a new typology of use-inspired research in climate science for decision-making: (i) innovators, where the advancement of science is the main objective; (ii) consolidators, where knowledge exchanges and networks are prioritised; and (iii) collaborators, where the needs of users are put first and foremost. These different values over what constitutes ‘good’ science for decision-making are mirrored in the way users were involved in the production process: (i) elicitation, where scientists have privileged decision-making power; (ii) representation, where multiple organisations mediate on behalf of individual users; and (iii) participation, where a multitude of users interact with scientists in an equal partnership. These differences help explain why climate knowledge gains its credibility and legitimacy differently even when the information itself might not be judged as salient and usable. If the push to deliberately co-produce climate knowledge is not sensitive to the national civic epistemology at play in each country, scientist–user interactions may fail to deliver more ‘usable’ climate information