A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci.

Genome-wide association studies (GWAS) have been highly informative in discovering disease-associated loci but are not designed to capture all structural variations in the human genome. Using long-read sequencing data, we discovered widespread structural variation within SINE-VNTR-Alu (SVA) elements, a class of great ape-specific transposable elements with gene-regulatory roles, which represents a major source of structural variability in the human population. We highlight the presence of structurally variable SVAs (SV-SVAs) in neurological disease-associated loci, and we further associate SV-SVAs to disease-associated SNPs and differential gene expression using luciferase assays and expression quantitative trait loci data. Finally, we genetically deleted SV-SVAs in the BIN1 and CD2AP Alzheimer's disease-associated risk loci and in the BCKDK Parkinson's disease-associated risk locus and assessed multiple aspects of their gene-regulatory influence in a human neuronal context. Together, this study reveals a novel layer of genetic variation in transposable elements that may contribute to identification of the structural variants that are the actual drivers of disease associations of GWAS loci.

Transcriptome analysis of the phosphate starvation response sheds light on strigolactone biosynthesis in rice.

Phosphorus (P) is a major element required for plant growth and development. To cope with P shortage, plants activate local and long-distance signaling pathways, such as an increase in the production and exudation of strigolactones (SLs). The role of the latter in mitigating P deficiency is, however, still largely unknown. To shed light on this, we studied the transcriptional response to P starvation and replenishment in wild-type rice and a SL mutant, dwarf10 (d10), and upon exogenous application of the synthetic SL GR24. P starvation resulted in major transcriptional alterations, such as the upregulation of P TRANSPORTER, SYG1/PHO81/XPR1 (SPX) and VACUOLAR PHOSPHATE EFFLUX TRANSPORTER. Gene Ontology (GO) analysis of the genes induced by P starvation showed enrichment in phospholipid catabolic process and phosphatase activity. In d10, P deficiency induced upregulation of genes enriched for sesquiterpenoid production, secondary shoot formation and metabolic processes, including lactone biosynthesis. Furthermore, several genes induced by GR24 treatment shared the same GO terms with P starvation-induced genes, such as oxidation reduction, heme binding and oxidoreductase activity, hinting at the role that SLs play in the transcriptional reprogramming upon P starvation. Gene co-expression network analysis uncovered a METHYL TRANSFERASE that displayed co-regulation with known rice SL biosynthetic genes. Functional characterization showed that this gene encodes an enzyme catalyzing the conversion of carlactonoic acid to methyl carlactonoate. Our work provides a valuable resource to further studies on the response of crops to P deficiency and reveals a tool for the discovery of SL biosynthetic genes.

ZNF91 deletion in human embryonic stem cells leads to ectopic activation of SVA retrotransposons and up-regulation of KRAB zinc finger gene clusters.

Transposable element (TE) invasions have shaped vertebrate genomes over the course of evolution. They have contributed an extra layer of species-specific gene regulation by providing novel transcription factor binding sites. In humans, SINE-VNTR-Alu (SVA) elements are one of three still active TE families; approximately 2800 SVA insertions exist in the human genome, half of which are human-specific. TEs are often silenced by KRAB zinc finger (KZNF) proteins recruiting corepressor proteins that establish a repressive chromatin state. A number of KZNFs have been reported to bind SVAs, but their individual contribution to repressing SVAs and their roles in suppressing SVA-mediated gene-regulatory effects remains elusive. We analyzed the genome-wide binding profile for ZNF91 in human cells and found that ZNF91 interacts with the VNTR region of SVAs. Through CRISPR-Cas9-mediated deletion of ZNF91 in human embryonic stem cells, we established that loss of ZNF91 results in increased transcriptional activity of SVAs. In contrast, SVA activation was not observed upon genetic deletion of the ZNF611 gene encoding another strong SVA interactor. Epigenetic profiling confirmed the loss of SVA repression in the absence of ZNF91 and revealed that mainly evolutionary young SVAs gain gene activation-associated epigenetic modifications. Genes close to activated SVAs showed a mild up-regulation, indicating SVAs adopt properties of cis-regulatory elements in the absence of repression. Notably, genome-wide derepression of SVAs elicited the communal up-regulation of KZNFs that reside in KZNF clusters. This phenomenon may provide new insights into the potential mechanisms used by the host genome to sense and counteract TE invasions.

A strategy for differential abundance analysis of sparse microbiome data with group-wise structured zeros.

Comparing the abundance of microbial communities between different groups or obtained under different experimental conditions using count sequence data is a challenging task due to various issues such as inflated zero counts, overdispersion, and non-normality. Several methods and procedures based on counts, their transformation and compositionality have been proposed in the literature to detect differentially abundant species in datasets containing hundreds to thousands of microbial species. Despite efforts to address the large numbers of zeros present in microbiome datasets, even after careful data preprocessing, the performance of existing methods is impaired by the presence of inflated zero counts and group-wise structured zeros (i.e. all zero counts in a group). We propose and validate using extensive simulations an approach combining two differential abundance testing methods, namely DESeq2-ZINBWaVE and DESeq2, to address the issues of zero-inflation and group-wise structured zeros, respectively. This combined approach was subsequently successfully applied to two plant microbiome datasets that revealed a number of taxa as interesting candidates for further experimental validation.

Multicenter real-world experience with epinephrine 0.5 mg dosing for anaphylaxis with allergen immunotherapy.

Aim: To determine the safety and efficacy of 0.5 mg intramuscular (IM) epinephrine for the treatment of subcutaneous allergen immunotherapy induced anaphylaxis. Patients & methods: Retrospective chart review of patients who received 0.5 mg of IM epinephrine for treatment of anaphylaxis from subcutaneous allergen immunotherapy at two outpatient allergy and immunology practices. Results: Thirty-eight patients received 0.5 mg IM epinephrine. Eleven patients (29%) required a second dose, and two patients (5%) required a third dose of IM epinephrine. Sixteen patients (42%) were transferred to the emergency department with ongoing symptoms. All had eventual resolution of anaphylaxis. There were no adverse reactions or fatalities. Conclusion: IM epinephrine at a dose of 0.5 mg is safe and effective for treatment of anaphylaxis from subcutaneous allergen immunotherapy.

Lay abstract The aim of this study to understand whether a 0.5 mg dose of epinephrine injected into the muscle is safe and effective in treating anaphylaxis (a life-threatening allergic reaction) caused by subcutaneous allergen immunotherapy (allergy shots). We reviewed the charts of all patients who received 0.5 mg of epinephrine at two allergy clinics. Thirty-eight patients received 0.5 mg of epinephrine. Twenty-nine percent of patients required a second dose of epinephrine and 5% required a third dose. Forty-two percent of patients were sent to the emergency department due to ongoing symptoms. Anaphylaxis was successfully treated in all patients. There were no side effects or deaths. Epinephrine at 0.5 mg is safe and effective in treating anaphylaxis from subcutaneous allergen immunotherapy.

Reliability, validity, and sensitivity to change of the lower extremity functional scale in individuals affected by stroke.

OBJECTIVE: To investigate reliability, validity, and sensitivity to change of the Lower Extremity Functional Scale (LEFS) in individuals affected by stroke. The secondary objective was to test the validity and sensitivity of a single-item linear analog scale (LAS) of function. DESIGN: Prospective cohort reliability and validation study. SETTING: A single rehabilitation department in an academic medical center. PATIENTS: Forty-three individuals receiving neurorehabilitation for lower extremity dysfunction after stroke were studied. Their ages ranged from 32 to 95 years, with a mean of 70 years; 77% were men. METHODS: Test-retest reliability was assessed by calculating the classical intraclass correlation coefficient, and the Bland-Altman limits of agreement. Validity was assessed by calculating the Pearson correlation coefficient between the instruments. Sensitivity to change was assessed by comparing baseline scores with end of treatment scores. Measurements were taken at baseline, after 1-3 days, and at 4 and 8 weeks. MAIN OUTCOME MEASUREMENTS: The LEFS, Short-Form-36 Physical Function Scale, Berg Balance Scale, Six-Minute Walk Test, Five-Meter Walk Test, Timed Up-and-Go test, and the LAS of function were used. RESULTS: The test-retest reliability of the LEFS was found to be excellent (ICC = 0.96). Correlated with the 6 other measures of function studied, the validity of the LEFS was found to be moderate to high (r = 0.40-0.71). Regarding the sensitivity to change, the mean LEFS scores from baseline to study end increased 1.2 SD and for LAS 1.1 SD. CONCLUSION: LEFS exhibits good reliability, validity, and sensitivity to change in patients with lower extremity impairments secondary to stroke. Therefore, the LEFS can be a clinically efficient outcome measure in the rehabilitation of patients with subacute stroke. The LAS is shown to be a time-saving and reasonable option to track changes in a patient's functional status.