Human inversions and their functional consequences

Polymorphic inversions are a type of structural variants that are difficult to analyze owing to their balanced nature and the location of breakpoints within complex repeated regions. So far, only a handful of inversions have been studied in detail in humans and current knowledge about their possible functional effects is still limited. However, inversions have been related to phenotypic changes and adaptation in multiple species. In this review, we summarize the evidences of the functional impact of inversions in the human genome. First, given that inversions have been shown to inhibit recombination in heterokaryotes, chromosomes displaying different orientation are expected to evolve independently and this may lead to distinct gene-expression patterns. Second, inversions have a role as disease-causing mutations both by directly affecting gene structure or regulation in different ways, and by predisposing to other secondary arrangements in the offspring of inversion carriers. Finally, several inversions show signals of being selected during human evolution. These findings illustrate the potential of inversions to have phenotypic consequences also in humans and emphasize the importance of their inclusion in genome-wide association studie

Exceptional human longevity is associated with a specific plasma phenotype of ether lipids

A lipid profile resistant to oxidative damage is an inherent trait associated with animal lifespan. However, there is a lack of lipidomic studies on human longevity. Here we use mass spectrometry based technologies to detect and quantify 137 ether lipids to define a phenotype of healthy humans with exceptional lifespan. Ether lipids were chosen because of their antioxidant properties and ability to modulate oxidative stress. Our results demonstrate that a specific ether lipid signature can be obtained to define the centenarian state. This profile comprises higher level of alkyl forms derived from phosphatidylcholine with shorter number of carbon atoms and double bonds; and decreased content in alkenyl forms from phosphatidylethanolamine with longer chain length and higher double bonds. This compositional pattern suggests that ether lipids from centenarians are more resistant to lipid peroxidation, and that ether lipid signature expresses an optimized feature associated with exceptional human longevity. These results are in keeping with the free radical theory of aging.We acknowledge funding from the Spanish Ministry of Education and Science (ref. SAF2013–44663-R), and from the ‘Red Tematica de Investigación Cooperativa en Envejecimiento y Fragilidad’ (RETICEF) (ref. ISCIII2012-RED-43-029) to J.V.; and from the Spanish Ministry of Economy and Competitiveness/Institute of Health Carlos III (ref. PI14/00328), and the Autonomous Government of Catalonia, Department of Health (ref. SLT002/16/00250) and Department of Business and Knowledge (ref. 2017SGR696) to R.P. This study has been co-financed by FEDER funds from the European Union (“Una manera de hacer Europa”). I.P. was supported by a University of Lleida Predoctoral Fellowship. K.H. was supported by a Dementia Australia Research Foundation Scholarship

Determining the impact of uncharacterized inversions in the human genome by droplet digital PCR

Despite the interest in characterizing genomic variation, the presence of large repeats at the breakpoints hinders the analysis of many structural variants. This is especially problematic for inversions, since there is typically no gain or loss of DNA. Here, we tested novel linkage-based droplet digital PCR (ddPCR) assays to study 20 inversions ranging from 3.1 to 742 kb flanked by inverted repeats (IRs) up to 134 kb long. Of those, we validated 13 inversions predicted by different genome-wide techniques. In addition, we obtained new experimental human population information across 95 African, European, and East Asian individuals for 16 inversions, including four already validated variants without high-throughput genotyping methods. Through comparison with previous data, independent replicates and both inversion breakpoints, we demonstrate that the technique is highly accurate and reproducible. Most studied inversions are widespread across continents, and their frequency is negatively correlated with genetic length. Moreover, all except two show clear signs of being recurrent, and we could better define the factors affecting recurrence levels and estimate the inversion rate across the genome. Finally, the generated genotypes have allowed us to check inversion functional effects, validating gene expression differences reported before for two inversions and finding new candidate associations. Therefore, the developed methodology makes it possible to screen these and other complex genomic variants quickly in a large number of samples for the first time, highlighting the importance of direct genotyping to assess their potential consequences and clinical implications

Reduced humoral response 3 months following BNT162b2 vaccination in SARS-CoV-2 uninfected residents of long-term care facilities

SARS-CoV-2 vaccination is the most effective strategy to protect older residents of long-term care facilities (LTCF) against severe COVID-19, but primary vaccine responses are less effective in older adults. Here, we characterised the humoral responses of institutionalised seniors 3 months after they had received the mRNA/BNT162b2 vaccine. plasma levels of SARS-CoV-2-specific total IgG, IgM and IgA antibodies were measured before and 3 months after vaccination in older residents of LTCF. Neutralisation capacity was assessed in a pseudovirus neutralisation assay against the original WH1 and later B.1.617.2/Delta variants. A group of younger adults was used as a reference group. three months after vaccination, uninfected older adults presented reduced SARS-CoV-2-specific IgG levels and a significantly lower neutralisation capacity against the WH1 and Delta variants compared with vaccinated uninfected younger individuals. In contrast, COVID-19-recovered older adults showed significantly higher SARS-CoV-2-specific IgG levels after vaccination than their younger counterparts, whereas showing similar neutralisation activity against the WH1 virus and an increased neutralisation capacity against the Delta variant. Although, similarly to younger individuals, previously infected older adults elicit potent cross-reactive immune responses, higher quantities of SARS-CoV-2-specific IgG antibodies are required to reach the same neutralisation levels. although hybrid immunity seems to be active in previously infected older adults 3 months after mRNA/BNT162b2 vaccination, humoral immune responses are diminished in COVID-19 uninfected but vaccinated older residents of LTCF. These results suggest that a vaccine booster dose should be prioritised for this particularly vulnerable population

Study protocol for the evaluation of the health effects of superblocks in barcelona : The "salut als carrers" (health in the streets) project

Superblocks are currently being introduced in Barcelona to respond to the city's scarcity of green spaces and high levels of air pollution, traffic injuries, and sedentariness. The aim is to calm the streets by reducing the number of square meters dedicated to private vehicles and to reclaim part of this public space for people. Salut als Carrers (Health in the Streets) is a project to evaluate the potential environmental and health effects of the superblock model with an equity perspective in Barcelona. This study aims to explain the various interventions implemented in different neighborhoods in Barcelona and the methods that will be used to evaluate them in a quasi-experimental and health impact assessment (HIA) approaches. Given the complexity of the intervention evaluated, the project employs mixed methodologies. Quantitative methods include: (a) a pre-post health survey of 1200 people randomly selected from the municipal register asked about self-perceived health and quality of life, social support, mental health, mobility, physical activity, neighborhood characteristics, and housing; (b) pre-post environmental measurements, mainly of nitrogen dioxide (NO), particulate matter of less than 10 µm (PM), and particulate matter of less than 2.5 µm (PM) and black carbon; (c) pre-post environmental walkability measures using the Microscale Audit of Pedestrian Streetscapes (MAPS) tool; (d) use of public space and physical activity levels using the System for Observing Play and Recreation in Communities (SOPARC), a validated observation tool; (e) pre-post traffic injury measures with a comparison group; and (f) the comparison and integration of pre-post assessment with previous HIAs and the improvement of future HIAs. Qualitative studies will be performed to analyze residents' perception of these effects by using: (a) various focus groups according to different participant characteristics who are more or less likely to use the superblocks; and (b) a guerrilla ethnography, which is a method that combines ethnographic observation and semi-structured interviews. This study, which evaluates the impact of an ambitious urban-renewal program on health, will help to assess the effectiveness of public policy in terms of health and health inequalities

GCAT|Panel, a comprehensive structural variant haplotype map of the Iberian population from high-coverage whole-genome sequencing

The combined analysis of haplotype panels with phenotype clinical cohorts is a common approach to explore the genetic architecture of human diseases. However, genetic studies are mainly based on single nucleotide variants (SNVs) and small insertions and deletions (indels). Here, we contribute to fill this gap by generating a dense haplotype map focused on the identification, characterization, and phasing of structural variants (SVs). By integrating multiple variant identification methods and Logistic Regression Models (LRMs), we present a catalogue of 35 431 441 variants, including 89 178 SVs (≥50 bp), 30 325 064 SNVs and 5 017 199 indels, across 785 Illumina high coverage (30x) whole-genomes from the Iberian GCAT Cohort, containing a median of 3.52M SNVs, 606 336 indels and 6393 SVs per individual. The haplotype panel is able to impute up to 14 360 728 SNVs/indels and 23 179 SVs, showing a 2.7-fold increase for SVs compared with available genetic variation panels. The value of this panel for SVs analysis is shown through an imputed rare Alu element located in a new locus associated with Mononeuritis of lower limb, a rare neuromuscular disease. This study represents the first deep characterization of genetic variation within the Iberian population and the first operational haplotype panel to systematically include the SVs into genome-wide genetic studies

DPP9 as a Potential Novel Mediator in Gastrointestinal Virus Infection

Dipeptidyl peptidase 9 (DPP9) is a member of the dipeptidyl peptidase IV family. Inhibition of DPP9 has recently been shown to activate the nucleotide-binding domain leucine-rich repeat 1 (NLRP1) inflammasome. NLRP1 is known to bind nucleic acids with high affinity and directly interact with double stranded RNA, which plays a key role in viral replication. DPP9 has also recently emerged as a key gene related to lung-inflammation in critical SARS-CoV-2 infection. Importantly, DPP9 activity is strongly dependent on the oxidative status. Here, we explored the potential role of DPP9 in the gastrointestinal tract. We performed transcriptomics analyses of colon (microarray, n = 37) and jejunal (RNA sequencing, n = 31) biopsies from two independent cohorts as well as plasma metabolomics analyses in two independent cohorts (n = 37 and n = 795). The expression of DPP9 in the jejunum, colon, and blood was significantly associated with circulating biomarkers of oxidative stress (uric acid, bilirubin). It was also associated positively with the expression of transcription factors (NRF-2) and genes (SOD, CAT, GPX) encoding for antioxidant enzymes, but negatively with that of genes (XDH, NOX) and transcription factors (NF-KB) involved in ROS-generating enzymes. Gene co-expression patterns associated with DPP9 identified several genes participating in antiviral pathways in both tissues. Notably, DPP9 expression in the colon and plasma was strongly positively associated with several circulating nucleotide catabolites (hypoxanthine, uric acid, 3-ureidopropionic acid) with important roles in the generation of ROS and viral infection, as well as other metabolites related to oxidative stress (Resolvin D1, glutamate-containing dipeptides). Gene-drug enrichment analyses identified artenimol, puromycin, anisomycin, 3-phenyllactic acid, and linezolid as the most promising drugs targeting these DPP9-associated genes. We have identified a novel potential pathogenic mechanism of viral infection in the digestive tract and promising existing drugs that can be repositioned against viral infection.This work was partially supported by Fundació Marató de TV3 research grant number 201612-31 and by Instituto de Salud Carlos III (ISCIII, Madrid, Spain) through the project PI20/01090 (co-funded by the European Union under the European Regional Development Fund (FEDER). “A way to make Europe”) to J.M.-P. Á.d.C.-I. is funded by Girona Biomedical Research Institute (Girona, Spain) through the Horizon 2020 Framework Programme of the European Union under the Marie Skłodowska-Curie Innovative Training Network grant agreement No 859890. M.A.-R. is funded by Instituto de Salud Carlos III (Madrid, Spain) through a predoctoral Río Hortega contract CM19/00190 (co-funded by European Regional Development Fund “Investing in your future”). J.M.-P. is funded by Instituto de Salud Carlos III (Madrid, Spain) through the Miguel Servet Program CP18/00009 (co-funded by European Regional Development Fund “Investing in your future”)

All-cause mortality in the cohorts of the Spanish AIDS Research Network (RIS) compared with the general population: 1997Ł2010

Abstract Background: Combination antiretroviral therapy (cART) has produced significant changes in mortality of HIVinfected persons. Our objective was to estimate mortality rates, standardized mortality ratios and excess mortality rates of cohorts of the AIDS Research Network (RIS) (CoRIS-MD and CoRIS) compared to the general population. Methods: We analysed data of CoRIS-MD and CoRIS cohorts from 1997 to 2010. We calculated: (i) all-cause mortality rates, (ii) standardized mortality ratio (SMR) and (iii) excess mortality rates for both cohort for 100 personyears (py) of follow-up, comparing all-cause mortality with that of the general population of similar age and gender. Results: Between 1997 and 2010, 8,214 HIV positive subjects were included, 2,453 (29.9%) in CoRIS-MD and 5,761 (70.1%) in CoRIS and 294 deaths were registered. All-cause mortality rate was 1.02 (95% CI 0.91-1.15) per 100 py, SMR was 6.8 (95% CI 5.9-7.9) and excess mortality rate was 0.8 (95% CI 0.7-0.9) per 100 py. Mortality was higher in patients with AIDS, hepatitis C virus (HCV) co-infection, and those from CoRIS-MD cohort (1997. Conclusion: Mortality among HIV-positive persons remains higher than that of the general population of similar age and sex, with significant differences depending on the history of AIDS or HCV coinfection

Functional analysis of position effects of inversion 2j in Drosophila buzzatii: gene CG13617 silencing and its adpative significance

És sabut de fa molt temps que les inversions cromosòmiques son mantenides per selecció natural a les poblacions de Drosophila. No obstant, els mecanismes moleculars que generen aquest valor adaptatiu encara no es coneixen. A les poblacions naturals de D. buzzatii, la inversió 2j forma un polimorfisme equilibrat amb l’ordenació 2st, en què els individus 2j tenen una mida més gran y un temps de desenvolupament més llarg en comparació amb els 2st. En aquest treball hem posat a provat la hipòtesi de que un efecte de posició d’un dels punts de trencament podria ser la causa d’aquests canvis fenotípics. Per a fer-ho hem analitzat l’expressió d’un gen adjacent al punt de trencament proximal, CG13617, en línies de D. buzzatii amb i sense la inversió 2j. Hem trobat que els embrions 2j presenten un nivell d’expressió de CG13617 cinc vegades menor causat per un RNA antisense originat en una còpia d’un transposó de la família Galileo inserit al punt de trencament. Les conseqüències funcionals de la reducció de l’expressió de CG13617 s’han investigat utilitzant la tècnica de RNA interferència per reproduir aquest silenciament a D. melanogaster. Els experiments de microarrays i RT-PCR en temps real comparant larves de primer estadi amb i sense expressió de CG13617 han revelat que 41 gens mostren nivells d’expressió reduïts quan CG13617 és silenciat, mentre que cap gen presenta un increment. A més, hi ha un excés significatiu de gens implicats en la replicació del DNA i el cicle celular entre els afectats pel silenciament de CG13617. Nou de deu d’aquests gens van ser analitzats a D. buzzatii i també tenen un nivell d’expressió reduït en embrions 2j, però no en larves de primer estadi, una fase en què la diferència d’expressió de CG13617 entre ordenacions cromosòmiques és menor i el RNA antisense ja no es transcriu. Per a esbrinar la possible funció d’aquest gen hem dut a terme un exhaustiu anàlisi de seqüències nucleotídiques i proteiques en els 12 genomes de Drosophila disponibles i també en altres organismes. La proteïna CG13617 conté un dit de zinc tipus C2H2 molt conservat, tres regions que poden formar coiled coils, dues seqüències PEST i senyals de localització i exportació nuclear. També presenta similitud amb la proteïna humana DZIP1 i amb Iguana, un component de la via de senyalització Hedgehog al peix zebra, fet que indica que el seu paper dins la cèl·lula podria estar relacionat amb el transport de factors de transcripció cap a dins i cap a fora del nucli. Aquests resultats suggereixen que el gen CG13617 podria estar implicat en la regulació de la replicació del DNA i que l’efecte de posició en els portadors de la inversió 2j podria contribuir a explicar les diferències fenotípiques observades entre els individus 2st i 2j, així com el valor adaptatiu d’aquesta inversió.Chromosomal inversions have been known for a long time to be maintained by natural selection in Drosophila populations. However, the molecular mechanisms underlying their adaptive value remain uncertain. In D. buzzatii natural populations, inversion 2j forms a balanced polymorphism with the 2st arrangement, in which 2j individuals have a larger size and a longer developmental time compared to 2st carriers. In this work we tested the hypothesis that a position effect of one of the inversion breakpoints could be the cause of these phenotypic changes by analyzing the expression of a gene adjacent to the proximal breakpoint, CG13617, in D. buzzatii lines with and without inversion 2j. We have found that in 2j embryos an antisense RNA originated in a copy of a Galileo family transposon inserted at the breakpoint causes a 5-fold decrease of the expression level of CG13617. In order to investigate the functional consequences of the reduction in CG13617 expression, we have used RNA interference to reproduce this silencing in D. melanogaster. Microarray and real-time RT-PCR experiments comparing first instar larvae with and without CG13617 expression revealed that 41 genes show reduced expression levels when CG13617 is silenced, while none is up-regulated. Interestingly, genes involved in DNA replication and cell cycle are significantly enriched among those affected by CG13617 silencing. Nine out of ten of these genes analyzed in D. buzzatii also show a reduced expression level in 2j embryos, but not in first instar larvae, a stage where the CG13617 expression difference between chromosomal arrangements is lower and the antisense RNA is no longer transcribed. To gain insight into the potential function of this gene we have carried out a comprehensive nucleotide and protein sequence analysis in the 12 available Drosophila genomes and also in other organisms. CG13617 protein contains a conserved C2H2 zinc finger, three coiled coil regions, two PEST sequences, and putative nuclear localization and export signals, and shows similarity to human DZIP1 and zebrafish Iguana (a component of the Hedgehog signaling pathway) proteins, which indicates that its cellular role could be related to the transport of transcription factors in and out of the nucleus. These results suggest that gene CG13617 could be involved in the regulation of DNA replication and that the position effect in 2j carriers might contribute to explain the phenotypic differences observed between 2st and 2j individuals as well as the adaptive value of the inversion