Integrative Analysis Reveals a Molecular Stratification of Systemic Autoimmune Diseases

OBJECTIVE

Clinical heterogeneity, a hallmark of systemic autoimmune diseases, impedes early diagnosis and effective treatment, issues that may be addressed if patients could be classified into groups defined by molecular pattern. This study was undertaken to identify molecular clusters for reclassifying systemic autoimmune diseases independently of clinical diagnosis.

METHODS

Unsupervised clustering of integrated whole blood transcriptome and methylome cross-sectional data on 955 patients with 7 systemic autoimmune diseases and 267 healthy controls was undertaken. In addition, an inception cohort was prospectively followed up for 6 or 14 months to validate the results and analyze whether or not cluster assignment changed over time.

RESULTS

Four clusters were identified and validated. Three were pathologic, representing "inflammatory," "lymphoid," and "interferon" patterns. Each included all diagnoses and was defined by genetic, clinical, serologic, and cellular features. A fourth cluster with no specific molecular pattern was associated with low disease activity and included healthy controls. A longitudinal and independent inception cohort showed a relapse-remission pattern, where patients remained in their pathologic cluster, moving only to the healthy one, thus showing that the molecular clusters remained stable over time and that single pathogenic molecular signatures characterized each individual patient.

CONCLUSION

Patients with systemic autoimmune diseases can be jointly stratified into 3 stable disease clusters with specific molecular patterns differentiating different molecular disease mechanisms. These results have important implications for future clinical trials and the study of nonresponse to therapy, marking a paradigm shift in our view of systemic autoimmune diseases.

Lysyl oxidase-like 3 is required for melanoma cell survival by maintaining genomic stability

Lysyl oxidase-like 3 (LOXL3) is a member of the lysyl oxidase family comprising multifunctional enzymes with depicted roles in extracellular matrix maturation, tumorigenesis, and metastasis. In silico expression analyses followed by experimental validation in a comprehensive cohort of human cell lines revealed a significant upregulation of LOXL3 in human melanoma. We show that LOXL3 silencing impairs cell proliferation and triggers apoptosis in various melanoma cell lines. Further supporting a pro-oncogenic role in melanoma, LOXL3 favors tumor growth in vivo and cooperates with oncogenic BRAF in melanocyte transformation. Upon LOXL3 depletion, melanoma cells display a faulty DNA damage response (DDR), characterized by ATM checkpoint activation and inefficient ATR activation leading to the accumulation of double-strand breaks (DSBs) and aberrant mitosis. Consistent with these findings, LOXL3 binds to proteins involved in the maintenance of genome integrity, in particular BRCA2 and MSH2, whose levels dramatically decrease upon LOXL3 depletion. Moreover, LOXL3 is required for efficient DSB repair in melanoma cells. Our results reveal an unexpected role for LOXL3 in the control of genome stability and melanoma progression, exposing its potential as a novel therapeutic target in malignant melanoma, a very aggressive condition yet in need for more effective treatment options.

NF-κB-direct activation of microRNAs with repressive effects on monocyte-specific genes is critical for osteoclast differentiation

Background

Monocyte-to-osteoclast conversion is a unique terminal differentiation process that is exacerbated in rheumatoid arthritis and bone metastasis. The mechanisms implicated in upregulating osteoclast-specific genes involve transcription factors, epigenetic regulators and microRNAs (miRNAs). It is less well known how downregulation of osteoclast-inappropriate genes is achieved.

Results

In this study, analysis of miRNA expression changes in osteoclast differentiation from human primary monocytes revealed the rapid upregulation of two miRNA clusters, miR-212/132 and miR-99b/let-7e/125a. We demonstrate that they negatively target monocyte-specific and immunomodulatory genes like TNFAIP3, IGF1R and IL15. Depletion of these miRNAs inhibits osteoclast differentiation and upregulates their targets. These miRNAs are also upregulated in other inflammatory monocytic differentiation processes. Most importantly, we demonstrate for the first time the direct involvement of Nuclear Factor kappa B (NF-κB) in the regulation of these miRNAs, as well as with their targets, whereby NF-κB p65 binds the promoters of these two miRNA clusters and NF-κB inhibition or depletion results in impaired upregulation of their expression.

Conclusions

Our results reveal the direct involvement of NF-κB in shutting down certain monocyte-specific genes, including some anti-inflammatory activities, through a miRNA-dependent mechanism for proper osteoclast differentiation.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0561-5) contains supplementary material, which is available to authorized users.

Regulating girlhood: Evaluative language, discourses of gender socialization and relational aggression

Placing the discursive psychological analysis of sexuality at its centre, this article considers a number of overlapping fields of linguistics: women’s language, construction of gender identities and language and sexuality. By encompassing these fields, in spite of potential differences in terms of theoretical stance and foci of analysis, the present study suggests a wider stance in the analysis of language, gender and sexuality. The study considers two important post-structuralist concepts: performativity and heteronormativity. More precisely, the analysis shows how the sexual identities of British heterosexual female teenagers are discursively constructed and regulated via language use when aggressively relating to other girls in Facebook. The analysis is based on the assumption that sexuality is but one aspect of identity. Although on the surface these British teenagers’ constructions present masculine ‘negative’ mean girls, a closer analysis reveals that more subversive and challenging interpretations can be applied.

Carbon mineralisation and plant growth in soil amended with compost samples at different degrees of maturity

The carbon and nitrogen mineralisation of a composting mixture of brewing yeast and lemon tree prunings was studied, at different degrees of stabilisation of this matrix, within an incubation experiment in soil. Meanwhile, a growth test in pots with ryegrass (Lolium perenne L.) was carried out using the selected soil and equal amounts of the composting mixture taken at different maturation steps, in order to evaluate the additions of these organic amendments in terms of fertilising value. Samples of the composting mixture, when poorly transformed through the biostabilisation process, showed high CO2-C releases in the soil, due to the microbial attack on easily degradable organic fractions still present in the mixture, with 24.7% mineralisation of the initial total organic carbon (TOC) after a 70 day incubation. On the other hand, mature compost was the most stable matrix, with only 5.4% of TOC mineralised after 70 days. Furthermore, amendments with the initial composting mixture led to negative net N-mineralisation during 56 days of incubation with soil. Only slight negative values of the net N-mineralisation were detected with fully stabilised compost. Nevertheless, pot experiments with ryegrass revealed that mature compost may promote N mineralisation to certain extents. Moreover, mature compost did not produce any phytotoxic effect, behaving as a slow-action organic fertiliser with N made available through a progressive mineralisation. Thus, the results gained through this study are a confirmation that the fertilising quality of a compost destined for agricultural uses is heavily affected by the complete exhaustion of the maturation reactions.

Composting of the solid fraction of olive mill wastewater with olive leaves: organic matter degradation and biological activity

The flocculated solid fraction of olive mill wastewaters, obtained from two different olive oil extraction systems (FOMW1 and FOMW2) was composted, with olive leaves (OL) as bulking agent, by the static pile system (Rutgers). The dynamic of organic matter (OM) degradation during composting and its relationship with the basal respiration and fluorescein diacetate (FDA) hydrolytic activity, as indicators of biological activity, were studied. Two mixtures were prepared: C1, from 65% FOMW1 plus 35% OL; and C2, from 74% FOMW2 plus 25% OL and 1% urea. The biooxidative phase of composting in C1, which had a high initial C/N ratio, was long, leading to a high OM degradation, mainly of the lignocellulosic compounds. The water-soluble organic carbon content, C/N ratio and the urea supplied as a N source for the C2 compost make this mixture more adequate for composting, as it had a shorter composting time than C1, and developed a microbial population with a high metabolic activity. The results for basal respiration in C1 and C2 were correlated at a high probability level with those of FDA hydrolysis, and both parameters can be used for establishing the degree of biological stability of the composting material.

HLA genes in Arabic-speaking Moroccans: close relatedness to Berbers and Iberians

The gene profile of Arabic-speaking Moroccans has been compared with those of other Mediterranean populations in order to provide additional information about the history of their origins. Our HLA data suggest that most Moroccans are of a Berber (Imazighen) origin and that Arabs who invaded North Africa and Spain in the 7th century A.D. did not substantially contributed to the gene pool; however, they imposed their advanced culture and their religion. Present-day Egyptians are also related to Moroccan Berbers and this supports an ancient Saharan origin for part of the present-day Mediterraneans, particularly for the Arabic-speaking ones (also Algerians) and also for the older substratum of Mediterranean people.