AutoCore: A network-based definition of the core module of human autoimmunity and autoinflammation

Although research on rare autoimmune and autoinflammatory diseases has enabled definition of nonredundant regulators of homeostasis in human immunity, because of the single gene-single disease nature of many of these diseases, contributing factors were mostly unveiled in sequential and noncoordinated individual studies. We used a network-based approach for integrating a set of 186 inborn errors of immunity with predominant autoimmunity/autoinflammation into a comprehensive map of human immune dysregulation, which we termed "AutoCore." The AutoCore is located centrally within the interactome of all protein-protein interactions, connecting and pinpointing multidisease markers for a range of common, polygenic autoimmune/autoinflammatory diseases. The AutoCore can be subdivided into 19 endotypes that correspond to molecularly and phenotypically cohesive disease subgroups, providing a molecular mechanism-based disease classification and rationale toward systematic targeting for therapeutic purposes. Our study provides a proof of concept for using network-based methods to systematically investigate the molecular relationships between individual rare diseases and address a range of conceptual, diagnostic, and therapeutic challenges.

Network cartographs for interpretable visualizations

Networks offer an intuitive visual representation of complex systems. Important network characteristics can often be recognized by eye and, in turn, patterns that stand out visually often have a meaningful interpretation. In conventional network layout algorithms, however, the precise determinants of a node's position within a layout are difficult to decipher and to control. Here we propose an approach for directly encoding arbitrary structural or functional network characteristics into node positions. We introduce a series of two- and three-dimensional layouts, benchmark their efficiency for model networks, and demonstrate their power for elucidating structure-to-function relationships in large-scale biological networks.

The VRNetzer platform enables interactive network analysis in Virtual Reality

Networks provide a powerful representation of interacting components within complex systems, making them ideal for visually and analytically exploring big data. However, the size and complexity of many networks render static visualizations on typically-sized paper or screens impractical, resulting in proverbial ‘hairballs’. Here, we introduce a Virtual Reality (VR) platform that overcomes these limitations by facilitating the thorough visual, and interactive, exploration of large networks. Our platform allows maximal customization and extendibility, through the import of custom code for data analysis, integration of external databases, and design of arbitrary user interface elements, among other features. As a proof of concept, we show how our platform can be used to interactively explore genome-scale molecular networks to identify genes associated with rare diseases and understand how they might contribute to disease development. Our platform represents a general purpose, VR-based data exploration platform for large and diverse data types by providing an interface that facilitates the interaction between human intuition and state-of-the-art analysis methods.

Data-rich networks can be difficult to interpret beyond a certain size. Here, the authors introduce a platform that uses virtual reality to allow the visual exploration of large networks, while interfacing with data repositories and other analytical methods to improve the interpretation of big data.

The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity

The WAVE regulatory complex (WRC) is crucial for assembly of the peripheral branched actin network constituting one of the main drivers of eukaryotic cell migration. Here, we uncover an essential role of the hematopoietic-specific WRC component HEM1 for immune cell development. Germline-encoded HEM1 deficiency underlies an inborn error of immunity with systemic autoimmunity, at cellular level marked by WRC destabilization, reduced filamentous actin, and failure to assemble lamellipodia. Hem1^-/- mice display systemic autoimmunity, phenocopying the human disease. In the absence of Hem1, B cells become deprived of extracellular stimuli necessary to maintain the strength of B cell receptor signaling at a level permissive for survival of non-autoreactive B cells. This shifts the balance of B cell fate choices toward autoreactive B cells and thus autoimmunity.

[Melanoma within tattoos: Two cases and a systematic literature review]

BACKGROUND

There have been reports of malignant melanoma arising within tattoos. However, there is no clear relationship between tattoos and the development of cutaneous malignancies. We report two new cases of melanoma and provide a review of cases of melanoma reported in the medical literature.

PATIENTS AND METHODS

Case No. 1: a 61-year-old patient consulted following the appearance one year ago of a nodular lesion measuring 4.5×3cm on a blue and red tattoo on his back. Complete excision of the lesion with histological analysis revealed an ulcerated nodular melanoma with a Breslow depth of 7mm. No secondary sites were found. Case No. 2: a 39-year-old patient with a blue tattoo on his left arm consulted following the appearance of a pigmented lesion a few months earlier. Surgical excision was immediately performed, confirming the diagnosis of SSM, with a Breslow depth of 0.9mm. There was no sign of relapse 9 years later.

DISCUSSION

In our systematic review we noted 34 cases of melanoma occurring in tattoos. There was a high male prevalence (90.3%) and a relatively young mean age (45.9 years). Most tattoos were monochrome (71.0%). The average time between tattooing and onset of melanoma was 13.2 years. The most common sites of melanoma were the upper limbs (53.1%) and trunk (34.4%). Mean tumor size was 11.6mm. Histologic examination revealed 2 cases of melanoma in situ, and in 13 cases, the Breslow depth was 1mm or less. In 5 cases, macroscopic or microscopic lymph node metastasis (sentinel lymph node) was found at diagnosis, and in one case, in transit skin metastases were also observed at the time of diagnosis. We discuss the hypothetical pathogenic role of tattoos in melanoma.

Plasticity of the Cullin-RING Ligase Repertoire Shapes Sensitivity to Ligand-Induced Protein Degradation

Inducing protein degradation via small molecules is a transformative therapeutic paradigm. Although structural requirements of target degradation are emerging, mechanisms determining the cellular response to small-molecule degraders remain poorly understood. To systematically delineate effectors required for targeted protein degradation, we applied genome-scale CRISPR/Cas9 screens for five drugs that hijack different substrate receptors (SRs) of cullin RING ligases (CRLs) to induce target proteolysis. We found that sensitivity to small-molecule degraders is dictated by shared and drug-specific modulator networks, including the COP9 signalosome and the SR exchange factor CAND1. Genetic or pharmacologic perturbation of these effectors impairs CRL plasticity and arrests a wide array of ligases in a constitutively active state. Resulting defects in CRL decommissioning prompt widespread CRL auto-degradation that confers resistance to multiple degraders. Collectively, our study informs on regulation and architecture of CRLs amenable for targeted protein degradation and outlines biomarkers and putative resistance mechanisms for upcoming clinical investigation.

[Teledermatology between two French hospitals: Two years of experience]

BACKGROUND

Teledermatology is currently booming. Due to the shortage of dermatologists in hospitals access to dermatological consultations is very limited in some hospitals. We present our experience of collaboration between an expert center, the dermatology department of the Victor-Dupouy Hospital Centre in Argenteuil, and all medical structures under the André-Mignot Hospital in Versailles (CHV), including 2 prison medical centers (UCSA), traditional departments and emergency department.

PATIENTS AND METHODS

Teledermatology, developed in the form of tele-expertise, began at the UCSA in November 2013. This expertise was then extended in June 2014 to the Internal Medicine department of CHV, and in December 2014 to all departments, including the emergency department. The rules and ethics of teledermatology were strictly adhered to. While UCSA could file all expertise dossiers, only urgent or difficult cases could be filed by other CHV departments.

RESULTS

In 26 months, 347 expertise requests were filed: 231 by prisons and 116 by the other departments of the CHV. No patients refused teledermatology. The quality of information and photographs was considered good or excellent in over 95% of cases. A response was given within 3hours in more than 50% of cases and in all cases within 24hours (on working days). Analysis of diseases diagnosed illustrates the wide variety of conditions encountered in dermatology, with different structures having their own specific features.

CONCLUSION

Our example illustrates the possibility of developing such an inter-hospital platform. However, it does not yet cater for requests made by patients to dermatologists, by dermatologists to dermatologists, or by dermatologists to the hospital teledermatology department. Acceptability was considered excellent by patients (with no refusals), physicians at the CHV, and the expert center.

[Leg ulcers occurring under tyrosine kinase inhibitor therapy (sunitinib, nilotinib)]

BACKGROUND

Certain anticancer drugs are known to induce leg ulcers, mainly chemotherapy agents such as hydroxyurea. We report 2 cases of leg ulcers in cancer patients treated with the tyrosine kinase inhibitors, sunitinib and nilotinib, and we discuss the role of these treatments in the pathogenesis of leg ulcers.

PATIENTS AND METHODS

Case 1. A 62-year-old patient on sunitinib for intrahepatic cholangiocarcinoma developed a lesion on her right foot. The vascular evaluation was negative. After progressive worsening, sunitinib was stopped and healing was observed within a few months. Case 2. A 83-year-old patient had been treated for chronic myeloid leukemia since 2005. Nilotinib was introduced in 2009. Peripheral arterial revascularization was required in May 2013. A few months later, worsening was noted with the onset of ulceration and necrosis of the third toe. Further revascularisation surgery was performed, and nilotinib was suspended and antiplatelets introduced. Healing occurred a few months later.

DISCUSSION

Many skin reactions have been described in patients on nilotinib and sunitinib, but few publications report the development of de novo ulcers in patients without risk factors. The pathophysiology of the development of ulcers in patients receiving tyrosine kinase inhibitors is not clear, and probably involves several mechanisms of action. The increasing use of this type of treatment could lead to an upsurge in the incidence of vascular complications.

CONCLUSION

We report two cases of leg ulcers developing in patients on tyrosine kinase inhibitors and raise the question of causal implication of these treatments in the pathogenesis of ulcers.

Degradation Parameters from Pulse-Chase Experiments

Pulse-chase experiments are often used to study the degradation of macromolecules such as proteins or mRNA. Considerations for the choice of pulse length include the toxicity of the pulse to the cell and maximization of labeling. In the general case of non-exponential decay, varying the length of the pulse results in decay patterns that look different. Analysis of these patterns without consideration to pulse length would yield incorrect degradation parameters. Here we propose a method that constructively includes pulse length in the analysis of decay patterns and extracts the parameters of the underlying degradation process. We also show how to extract decay parameters reliably from measurements taken during the pulse phase.

Bacteria differently regulate mRNA abundance to specifically respond to various stresses

Environmental stress is detrimental to cell viability and requires an adequate reprogramming of cellular activities to maximize cell survival. We present a global analysis of the response of Escherichia coli to acute heat and osmotic stress. We combine deep sequencing of total mRNA and ribosome-protected fragments to provide a genome-wide map of the stress response at transcriptional and translational levels. For each type of stress, we observe a unique subset of genes that shape the stress-specific response. Upon temperature upshift, mRNAs with reduced folding stability up- and downstream of the start codon, and thus with more accessible initiation regions, are translationally favoured. Conversely, osmotic upshift causes a global reduction of highly translated transcripts with high copy numbers, allowing reallocation of translation resources to not degraded and newly synthesized mRNAs.

Quantitative assessment of ribosome drop-off in E. coli

Premature ribosome drop-off is one of the major errors in translation of mRNA by ribosomes. However, repeated analyses of Ribo-seq data failed to quantify its strength inE. coli Relying on a novel highly sensitive data analysis method we show that a significant rate of ribosome drop-off is measurable and can be quantified also when cells are cultured under non-stressing conditions. Moreover, we find that the drop-off rate is highly variable, depending on multiple factors. In particular, under environmental stress such as amino acid starvation or ethanol intoxication, the drop-off rate markedly increases.

[Subcutaneous calcinosis, a late and severe complication of radiotherapy: Three cases]

BACKGROUND

Radiation-induced subcutaneous calcinosis is a rare and special form of potentially severe subcutaneous calcinosis of late onset. Herein, we report three cases of this disease, occurring in each instance more than 10 years after use of radiotherapy as an adjuvant treatment in breast cancer.

PATIENTS AND METHODS

Our report concerns 3 women aged 69-88 years consulting for pre-sternal ulcers (n=2) and/or subcutaneous nodules (n=2). These lesions developed on areas irradiated between 10 and 38 years earlier for breast cancer. In all three cases, radiological explorations showed extensive subcutaneous calcification. In one case, calcification extended into the mediastinum. In each patient, a diagnosis of radiation-induced subcutaneous calcinosis was made and symptomatic treatment was given.

DISCUSSION

Radiation-induced subcutaneous calcinosis is an irreversible and rare complication of high-dose radiation that usually occurs several years after radiotherapy. Its severity is related to potential ulcerations, pain and a risk for in-depth extension up to the mediastina. This complication remains unclear and treatment has not been codified. The only option seems to be "heavy" plastic surgery.

Single-molecule modeling of mRNA degradation by miRNA: Lessons from data

Recent experimental results on the effect of miRNA on the decay of its target mRNA have been analyzed against a previously hypothesized single molecule degradation pathway. According to that hypothesis, the silencing complex (miRISC) first interacts with its target mRNA and then recruits the protein complexes associated with NOT1 and PAN3 to trigger deadenylation (and subsequent degradation) of the target mRNA. Our analysis of the experimental decay patterns allowed us to refine the structure of the degradation pathways at the single molecule level. Surprisingly, we found that if the previously hypothesized network was correct, only about 7% of the target mRNA would be regulated by the miRNA mechanism, which is inconsistent with the available knowledge. Based on systematic data analysis, we propose the alternative hypothesis that NOT1 interacts with miRISC before binding to the target mRNA. Moreover, we show that when miRISC binds alone to the target mRNA, the mRNA is degraded more slowly, probably through a deadenylation-independent pathway. The new biochemical pathway proposed here both fits the data and paves the way for new experimental work to identify new interactions.

[Compression care for venous leg ulcers: Assessment of medical practices in 100 patients]

INTRODUCTION

The etiologic treatment of venous ulcers is based on compression therapy in compliance with the new guidelines promulgated by the French National Authority for Health (HAS) in 2010. Prescriptions often originate from a request by the nurse delivering care in the patient's home. A recent French study demonstrated the positive impact of compression therapy on venous ulcer healing. The objective of this study was to evaluate medical practices in order to target corrective actions.

MATERIALS AND METHODS

We conducted a single-center prospective observational study, using a standardized questionnaire from January to May 2014. Patients with venous ulcers who had an indication for compression therapy were included consecutively. The questionnaire collected demographic and clinical data and also recorded the results of complementary tests and the characteristics of the compression therapy.

RESULTS

One hundred patients were included (61 women and 39 men). The average age was 76 years. Patients were recruited during consultations (n = 69), with a majority of patients living at home (n = 80) and receiving home care delivered by a nurse (n = 81). Thirteen patients were seen for the first time and 87 patients were receiving long-term care. The ulcers evolved for 5.7 years on average. Patients presented peri-lesional edema (n = 58), ankle ankylosis (n = 49), autonomous mobilization (n = 40) and walking problems (n = 60). Physical therapy was prescribed for 39 patients and was effectively carried out for 24. The two main causes were venous varices (n = 66) and post-phlebitis disease (n = 18). Compression therapy was prescribed for 97 patients and the products delivered by the pharmacy were consistent with the prescription for 74 patients. Compliance with compression therapy was faulty for 28 patients because of poor tolerance, misunderstanding, manipulation problems, or inappropriate footwear. At assessment, 66 patients were wearing the bands, but not always correctly (starting at the base of the toes [n = 61], heel included [n = 43], proper stretching [n = 43] up to below the knee [n = 57]). Proper footwear was noted in 70 patients.

CONCLUSION

Data are scarce on compliance with compression banding. This study shows that further efforts are needed to ensure proper patient education and professional training for physicians and allied profession concerning the installation of compression therapy. Total compliance was observed in only 35% of patients. In addition, the products delivered by the pharmacy were not consistent with the prescription in 26% of cases. Many discrepancies were observed between what was prescribed and what the patients achieved. Patient adherence is a crucial issue for compression therapy.

[Phlegmasia cerulea dolens]

BACKGROUND

Herein we report a case of phlegmasia cerulea dolens, a form of venous thrombosis complicated by arterial ischaemia.

PATIENTS AND METHODS

A 69-year-old man presented a bilateral trophic condition of the lower limbs that had appeared 3 weeks earlier. The patient had a history of metastatic urothelial bladder carcinoma and arteritis. Clinical examination revealed right leg ulcers with massive bilateral oedema of the lower limbs, cyanosis and local ischaemia. Doppler ultrasound revealed bilateral and proximal deep vein thrombosis (sural and superficial femoral veins of the right leg; sural and iliac veins of the left leg) without any distal arterial flow. We concluded on a diagnosis of bilateral phlegmasia cerulea dolens.

DISCUSSION

Phlegmasia cerulea dolens is a particular type of deep venous thrombosis in which a proximal venous thrombus is combined with arterial ischaemic signs due to brutal and massive oedema and slowing down of arterial flow. In most cases, the lower limbs are involved, with malignancy being the most common cause. It should be suspected in the presence of the classical triad of "pain, oedema and cyanosis", with confirmation by Doppler ultrasound. There is no general consensus regarding standard management. Traditionally, systemic anticoagulation has been the mainstay of treatment for this condition. Endovascular surgery may be a possibility in some cases. Prompt diagnosis and rapid treatment initiation are paramount in order to improve the prognosis of this severe condition with ominous prospects.

Increased prevalence of psoriasis in patients with coronary artery disease: results from a case-control study

BACKGROUND

The incidence of myocardial events has been reported to be increased in patients with psoriasis.

OBJECTIVES

To investigate whether psoriasis is an independent risk factor for coronary artery disease (CAD).

METHODS

We compared the prevalence of psoriasis between case patients with a diagnosis of CAD based on coronary angiography findings and control patients with no CAD referred to the emergency surgery department for an acute noncardiovascular condition. Case and control patients were examined for the presence of psoriasis by two dermatologists. The prevalence of psoriasis was compared among patients with CAD according to CAD severity. Five-hundred cases and 500 age- and sex-matched controls were included.

RESULTS

Using matched univariate analysis, the prevalence of psoriasis was about twofold higher in CAD case patients than in control patients [8·0% vs. 3·4%, odds ratio (OR) 2·64; 95% confidence interval (CI) 1·42-4·88]. Using unconditional multivariate analysis, the association of psoriasis with CAD appeared to be borderline significant (OR 1·84; 95% CI 0·99-3·40). Psoriasis in patients with CAD was significantly associated with three-vessel involvement relative to one-or two-vessel involvement (13·1% vs. 6·1%; OR 3·07; 95% CI 1·50-6·25).

CONCLUSIONS

The prevalence of psoriasis is twofold higher in patients with CAD than in control patients without CAD. It is associated with a more severe coronary artery involvement.

[Erythrokeratodermia variabilis]

BACKGROUND

Erythrokeratodermia variabilis (EKV) is a rare genodermatosis associated with keratinisation disorders. Mutations are found in genes encoding connexin 31 and 30.3 mapped to chromosome 1 p34-35. We report two cases of EKV, one of which presented dramatic improvement with oral retinoids.

PATIENTS AND METHODS

A 15-month-old boy was referred to us with reddish-brown hyperkeratotic and well-demarcated plaques on the extremities, axillary space and face. The lesions started when he was 6months of age. Cutaneous histopathology showed acanthosis and papillomatosis associated with orthokeratotic hyperkeratosis. Anatomoclinical comparison confirmed the diagnosis of EKV. A second child aged 10years was referred to us with fixed, well-demarcated hyperkeratotic plaques associated with transient red patches. The lesions began when she was 1month old. Anatomoclinical comparison confirmed the diagnosis of EKV and the patient showed dramatic improvement after 2weeks on acitretin.

DISCUSSION

EKV is characterized by the association of fixed well-demarcated plaques and transient erythematous patches. Although cutaneous histopathology is not specific, a typical physical examination and a compatible cutaneous histopathology can aid the diagnosis. Oral retinoids are often very rapidly effective.

[Wound dressing. Nursing knowledge and practice]

BACKGROUND

Wound management constitutes an important public health issue. Health authorities have published numerous recommendations on wound cleansing and dressing. The French law currently authorizes nurses to prescribe wound care with a doctor's agreement. Further, they have an essential role in wound management. In this study, we evaluate nurses' behavior in wound cleansing in outpatients and in hospital settings.

PATIENTS AND METHODS

The survey was conducted from 4/1/11 to 5/6/11 in 111 nurses working at Argenteuil Hospital and in 299 nurses with outpatient activity within two administrative departments (Hauts-de-Seines and Val-d'Oise) in the suburbs of Paris, France. The questionnaire included items relating to the use of antiseptics during cleansing of various types of wounds, with or without signs of super-infection, and with or without medical prescription. The results were compared with French references.

RESULTS

One hundred and ninety-one answers were obtained: 111 (100%) from the hospital and 80 (27%) from nurses with outpatient activity (women: 88%, mean age=36 years). The mean number of wounds seen per week was 18 (0-135). In the absence of a prescription, antiseptics were used by less than 35% of the nurses for chronic wounds and burns but by more than 50% for operative and traumatic wounds. When water or physiological serum was prescribed for wound cleansing, these figures were slightly lower. Conversely, if an antiseptic was prescribed, more than 50% of the nurses used antiseptics. Where nurses disagreed with the medical prescription, more than 60% of the hospital nurses discussed this with the doctor, compared to less than 40% of private nurses. In the event of signs of super-infection, more than 85% of the nurses used antiseptics, with or without medical prescription, and in the case of disagreement, more than 90% called the doctor, whether working in a hospital setting or among outpatients. The alternative to an antiseptic was physiological saline for 60 to 80% of the nurses, with sterile water or tap water being used by less than 45%.

DISCUSSION

Antiseptics continue to be used in situations in which they are no longer recommended (e.g. chronic wounds, operative wounds, super-infected wounds) whereas they are used very little for burns, where they are in fact recommended during the acute phase. This is true both with and without medical prescription. Prescriptions are not always followed in practice and prescriptions of antiseptics are more often respected than prescriptions of water or physiological saline solution. Discussion with the prescribing doctor is more frequent among hospital nurses than among private nurses.

NRAMP1 genetic polymorphisms as a risk factor of tuberculous pleurisy

SETTING

Nrampl encoded by the NRAMP1 gene influences the phagolysosomal function of alveolar macrophage against Mycobacterium tuberculosis. Genetic polymorphisms of NRAMP1 affect innate host resistance through the defective production and function of Nrampl.

OBJECTIVE

To investigate this relationship, the NRAMP1 polymorphisms in patients with tuberculous pleurisy were determined.

DESIGN

Pleural biopsy proven 56 patients were designated to the pleurisy group and 45 healthy adults were designated to the healthy control group. Three NRAMP1 polymorphisms such as single nucleotide change in intron 4(469 + 14G/C, INT4), a non-conservative single-base substitution at codon 543(D543N) and TGTG deletion in the 3' untranslated region (1729 + 55del4, 3'UTR) were determined.

RESULTS

The frequencies of mutant genotypes of INT4 and 3'UTR were significantly high in the pleurisy group (P = 0.01, P = 0.02), but the frequencies of D543N were not significantly different between the two groups. Odds ratios (OR), which are a comparison of the wild with the mutant genotype, were 8.02 (95%CI 2.42 approximately 26.57) for INT4 and 5.73 (95%CI 1.14 approximately 28.92) for 3'UTR which were statistically significant. In the combined analysis of the INT4 and 3'UTR, the ORs were 6.00 (95%CI 1.46 approximately 24.64) for GC/++ genotype and 14.00 (95%CI 1.61 approximately 121.75) for GC/+del when compared with GG/++; these differences were statistically significant.

CONCLUSION

The NRAMP1 genetic polymorphisms, especially INT4 and 3'UTR, were closely related to tuberculous pleurisy.