Lung UltrasouNd Guided surfactant therapy in preterm infants: an international multicenter randomized control trial (LUNG study)

BACKGROUND

The management of respiratory distress syndrome (RDS) in premature newborns is based on different types of non-invasive respiratory support and on surfactant replacement therapy (SRT) to avoid mechanical ventilation as it may eventually result in lung damage. European guidelines currently recommend SRT only when the fraction of inspired oxygen (FiO2) exceeds 0.30. The literature describes that early SRT decreases the risk of bronchopulmonary dysplasia (BPD) and mortality. Lung ultrasound score (LUS) in preterm infants affected by RDS has proven to be able to predict the need for SRT and different single-center studies have shown that LUS may increase the proportion of infants that received early SRT. Therefore, the aim of this study is to determine if the use of LUS as a decision tool for SRT in preterm infants affected by RDS allows for the reduction of the incidence of BPD or death in the study group.

METHODS/DESIGN

In this study, 668 spontaneously-breathing preterm infants, born at 25+0 to 29+6 weeks' gestation, in nasal continuous positive airway pressure (nCPAP) will be randomized to receive SRT only when the FiO2 cut-off exceeds 0.3 (control group) or if the LUS score is higher than 8 or the FiO2 requirements exceed 0.3 (study group) (334 infants per arm). The primary outcome will be the difference in proportion of infants with BPD or death in the study group managed compared to the control group.

DISCUSSION

Based on previous published studies, it seems that LUS may decrease the time to administer surfactant therapy. It is known that early surfactant administration decreases BPD and mortality. Therefore, there is rationale for hypothesizing a reduction in BPD or death in the group of patients in which the decision to administer exogenous surfactant is based on lung ultrasound scores.

TRIAL REGISTRATION

ClinicalTrials.gov identifier NCT05198375 . Registered on 20 January 2022.

Systems genetics identifies miRNA-mediated regulation of host response in COVID-19

BACKGROUND

Individuals infected with SARS-CoV-2 vary greatly in their disease severity, ranging from asymptomatic infection to severe disease. The regulation of gene expression is an important mechanism in the host immune response and can modulate the outcome of the disease. miRNAs play important roles in post-transcriptional regulation with consequences on downstream molecular and cellular host immune response processes. The nature and magnitude of miRNA perturbations associated with blood phenotypes and intensive care unit (ICU) admission in COVID-19 are poorly understood.

RESULTS

We combined multi-omics profiling-genotyping, miRNA and RNA expression, measured at the time of hospital admission soon after the onset of COVID-19 symptoms-with phenotypes from electronic health records to understand how miRNA expression contributes to variation in disease severity in a diverse cohort of 259 unvaccinated patients in Abu Dhabi, United Arab Emirates. We analyzed 62 clinical variables and expression levels of 632 miRNAs measured at admission and identified 97 miRNAs associated with 8 blood phenotypes significantly associated with later ICU admission. Integrative miRNA-mRNA cross-correlation analysis identified multiple miRNA-mRNA-blood endophenotype associations and revealed the effect of miR-143-3p on neutrophil count mediated by the expression of its target gene BCL2. We report 168 significant cis-miRNA expression quantitative trait loci, 57 of which implicate miRNAs associated with either ICU admission or a blood endophenotype.

CONCLUSIONS

This systems genetics study has given rise to a genomic picture of the architecture of whole blood miRNAs in unvaccinated COVID-19 patients and pinpoints post-transcriptional regulation as a potential mechanism that impacts blood traits underlying COVID-19 severity. The results also highlight the impact of host genetic regulatory control of miRNA expression in early stages of COVID-19 disease.

Selective growth inhibition of cancer cells with doxorubicin-loaded CB[7]-modified iron-oxide nanoparticles

Cucurbit[7]uril-modified iron-oxide nanoparticles (CB[7]NPs) were loaded with doxorubicin hydrochloride (Dox) and tested as a drug delivery system.

Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans

A key challenge of functional genomics today is to generate well-annotated data sets that can be interpreted across different platforms and technologies. Large-scale functional genomics data often fail to connect to standard experimental approaches of gene characterization in individual laboratories. Furthermore, a lack of universal annotation standards for phenotypic data sets makes it difficult to compare different screening approaches. Here we address this problem in a screen designed to identify all genes required for the first two rounds of cell division in the Caenorhabditis elegans embryo. We used RNA-mediated interference to target 98% of all genes predicted in the C. elegans genome in combination with differential interference contrast time-lapse microscopy. Through systematic annotation of the resulting movies, we developed a phenotypic profiling system, which shows high correlation with cellular processes and biochemical pathways, thus enabling us to predict new functions for previously uncharacterized genes.

The ZW10 and Rough Deal checkpoint proteins function together in a large, evolutionarily conserved complex targeted to the kinetochore

The zeste-white 10 (zw10) and rough deal (rod) genes of Drosophila both encode kinetochore components, and mutations in either gene greatly increase the missegregation of sister chromatids during mitosis. Here, we present genetic, cytological and biochemical evidence for a close, evolutionarily conserved relationship between the ROD and ZW10 proteins. We show that the phenotypes caused by disruption of either gene’s function are similar in Drosophila and in C. elegans. No additive effects are observed in zw10; rod double null mutants. In flies, the two proteins always colocalize and, moreover, require each other for their recruitment to the mitotic apparatus. The human ROD and ZW10 homologs also colocalize on HeLa cell kinetochores or kinetochore microtubules throughout most but not all of mitosis. Finally, we show that in both Drosophila and human cells, ROD and ZW10 are in fact physically associated, and in Drosophila these proteins are together constituents of a large (700-900 kDa), soluble macromolecular complex.

RNAi analysis of genes expressed in the ovary of Caenorhabditis elegans

As a step towards comprehensive functional analysis of genomes, systematic gene knockout projects have been initiated in several organisms [1]. In metazoans like C. elegans, however, maternal contribution can mask the effects of gene knockouts on embryogenesis. RNA interference (RNAi) provides an alternative rapid approach to obtain loss-of-function information that can also reveal embryonic roles for the genes targeted [2,3]. We have used RNAi to analyze a random set of ovarian transcripts and have identified 81 genes with essential roles in embryogenesis. Surprisingly, none of them maps on the X chromosome. Of these 81 genes, 68 showed defects before the eight-cell stage and could be grouped into ten phenotypic classes. To archive and distribute these data we have developed a database system directly linked to the C. elegans database (Wormbase). We conclude that screening cDNA libraries by RNAi is an efficient way of obtaining in vivo function for a large group of genes. Furthermore, this approach is directly applicable to other organisms sensitive to RNAi and whose genomes have not yet been sequenced.

Evidence for redundancy but not trans factor-cis element coevolution in the regulation of Drosophila Yp genes

In Drosophila melanogaster and the endemic Hawaiian species D. grimshawi three Yolk protein (Yp) genes are expressed in a similar sex- and tissue-specific pattern. In contrast, DNA sequence comparisons of promoter/enhancer regions show low levels of similarity. We tested the functional significance of these observations by transforming D. melanogaster with the genomic region that includes the divergently transcribed D. grimshawi DgYp1 and DgYp2 genes; we found that the introduced genes were expressed in female fat body and in ovaries but not in males. Moreover, we found D. grimshawi proteins in the hemolymph and accumulating in ovaries. Using reporter constructs we showed that the intergenic region from D. grimshawi was sufficient to drive accurate expression, but some low level of ectopic expression was seen in males. Transforming D. melanogaster with constructs bearing deletions within the D. grimshawi intergenic region revealed only subtle effects in the overall level of expression, suggesting a high level of redundancy. Testing mutants in the sex-specific regulator doublesex revealed that it is capable of repressing the DgYp genes in males. Together, these data show that D. melanogaster trans-acting factors can regulate the in vivo pattern of DgYp expression and support the notion of a redundant and complex system of cis-acting elements.

Atypical protein kinase C cooperates with PAR-3 to establish embryonic polarity in Caenorhabditis elegans

Asymmetric cell divisions, critically important to specify cell types in the development of multicellular organisms, require polarized distribution of cytoplasmic components and the proper alignment of the mitotic apparatus. In Caenorhabditis elegans, the maternally expressed protein, PAR-3, is localized to one pole of asymmetrically dividing blastomeres and is required for these asymmetric divisions. In this paper, we report that an atypical protein kinase C (PKC-3) is essential for proper asymmetric cell divisions and co-localizes with PAR-3. Embryos depleted of PKC-3 by RNA interference die showing Par-like phenotypes including defects in early asymmetric divisions and mislocalized germline-specific granules (P granules). The defective phenotypes of PKC-3-depleted embryos are similar to those exhibited by mutants for par-3 and another par gene, par-6. Direct interaction of PKC-3 with PAR-3 is shown by in vitro binding analysis. This result is reinforced by the observation that PKC-3 and PAR-3 co-localize in vivo. Furthermore, PKC-3 and PAR-3 show mutual dependence on each other and on three of the other par genes for their localization. We conclude that PKC-3 plays an indispensable role in establishing embryonic polarity through interaction with PAR-3.

Phylogeny of the island populations of the Hawaiian Drosophila grimshawi complex: evidence from combined data

The picture-winged species Drosophila grimshawi is unique among Hawaiian Drosophila in its wide geographic range, having populations on several islands of the Hawaiian archipelago. This distribution contrasts with the pattern of single-island endemism observed in most of the picture-winged group; significantly, it does not concur with predictions of the founder theory, where speciation is the typical outcome of founder events involving colonization of a new island. To examine this anomalous situation, we have taken a phylogenetic approach in an attempt to resolve the relationships among taxa and decipher the most probable colonization scenario. We have obtained both morphological and molecular data for all the D. grimshawi populations as well as the closely related species D. pullipes, and two outgroup species, using scanning electron microscopy to score ultrastructural features of the chorion or eggshell, and PCR amplification and nucleotide sequencing to acquire sequence data on Yp1, one of the three Yolk protein genes. In addition, we have used available data on Yolk Protein electrophoretic pattern and jousting, oviposition, and mating behavioral characters. Analyses of these data sets, either individually or in combination, indicate that there are two separate and ecologically distinct clades within this species complex. One clade includes the Kauai and Oahu populations of grimshawi, as well as the closely related species D. pullipes from Hawaii, all of which are classified as ecological specialists with respect to their oviposition and breeding substrate. The other clade includes all the ecologically generalist grimshawi populations of the Maui Nui island complex. The phylogenetic results do not concur with the previously proposed hypothesis that D. pullipes originated from a founder derived from the Maui Nui complex and further suggest that these taxa are in need of taxonomic revision.

Phylogenetic analysis of DNA length mutations in a repetitive region of the Hawaiian Drosophila yolk protein gene Yp2

Nucleotide sequence analysis has demonstrated that interspecific size variation in the YP2 yolk protein among Hawaiian Drosophila is due to in-frame insertions and deletions in two repetitive segments of the coding region of the Yp2 gene. Sequence comparisons of the complex repetitive region close to the 5' end of this gene across 34 endemic Hawaiian taxa revealed five length morphs, spanning a length difference of 21 nucleotides (nt). A phylogenetic character reconstruction of the length mutations on an independently derived molecular phylogeny showed clade-specific length variants arising from six ancient events: two identical insertions of 6 nt, and four deletions, one of 6 nt, one of 12 nt, and two identical but independent deletions of 15 nt. These mutations can be attributed to replication slippage with nontandem trinucleotide repeats playing a major role in the slipped-strand mispairing. Geographic analysis suggests that the 15 nt deletion which distinguishes the planitibia subgroup from the cyrtoloma subgroup occurred on Oahu about 3 million years ago. The homoplasies observed caution against relying too heavily on nucleotide insertions/deletions for phylogenetic inference. In contrast to the extensive repeat polymorphisms within other Drosophila and the human species, the more complex 5' Yp2 repetitive region analyzed here appears to lack polymorphism among Hawaiian Drosophila, perhaps due to founder effects, low population sizes, and hitchhiking effects of selection on the immediately adjacent 5' region.

Pattern of ecological shifts in the diversification of Hawaiian Drosophila inferred from a molecular phylogeny

BACKGROUND

The endemic Hawaiian drosophilids, a unique group that are remarkable for their diversity and rapid proliferation, provide a model for analysis of the process of insular speciation. Founder events and accompanying random drift, together with shifts in sexual selection, appear to explain the dramatic divergence in male morphology and mating behaviour among these flies, but these forces do not account for their spectacular ecological diversification into a wide array of breeding niches. Although recognized as contributing to the success of this group, the precise role of adaptive shifts has not been well defined.

RESULTS

To delineate the pattern of ecological diversification in the evolution of Hawaiian Drosophila, we generated a molecular phylogeny, using nucleotide sequences from the yolk protein gene Yp1, of 42 endemic Hawaiian and 5 continental species. By mapping ecological characters onto this phylogeny, we demonstrate that monophagy is the primitive condition, and that decaying leaves were the initial substrate for oviposition and larval development. Shifts to decaying stems, bark and tree fluxes followed in more derived species. By plotting female reproductive strategies, as reflected in ovarian developmental type, on the molecular tree, we also demonstrate a phylogenetic trend toward increasing fecundity. We find some statistical support for correlations between ecological shifts and shifts in female reproductive strategies.

CONCLUSIONS

Because of the short branches at the base of the phylogram, which lead to ecologically diverse lineages, we conclude that much of the adaptive radiation into alternate breeding substrates occurred rapidly, early in the group's evolution in Hawaii. Furthermore, we conclude that this ecological divergence and the correlated changes in ovarian patterns that adapt species to their ecological habitats were contributing factors in the major phyletic branching within the Hawaiian drosophilid fauna.