Surveying the landscape of RNA isoform diversity and expression across 9 GTEx tissues using long-read sequencing data

Even though alternative RNA splicing was discovered in 1977 (nearly 50 years ago), we still understand very little about most isoforms arising from a single gene, including in which tissues they are expressed and if their functions differ. Human gene annotations suggest remarkable transcriptional complexity, with approximately 252,798 distinct RNA isoform annotations from 62,710 gene bodies (Ensembl v109; 2023), emphasizing the need to understand their biological effects. For example, 256 gene bodies have ≥50 annotated isoforms and 30 have ≥100, where one protein-coding gene (MAPK10) even has 192 distinct RNA isoform annotations. Whether such isoform diversity results from biological noise (i.e., spurious alternative splicing) or whether it represents biological intent and specialized functions (even if subtle) remains a mystery. Recent studies by Aguzzoli-Heberle et al., Leung et al., and Glinos et al. demonstrate long-read RNAseq enables improved RNA isoform quantification for essentially any tissue, cell type, or biological condition (e.g., disease, development, aging, etc.) making it possible to better assess individual isoform expression and function. While each study provided important discoveries related to RNA isoform diversity, deeper exploration is needed. We sought, in part, to quantify real isoform usage across tissues (compared to annotations) and explore whether observed diversity is biological noise or intent. We used long-read RNAseq data from 58 GTEx samples across nine tissues (three brain, two heart, muscle, lung, liver, and cultured fibroblasts) generated by Glinos et al. and found considerable isoform diversity within and across tissues. Cerebellar hemisphere was the most transcriptionally complex tissue (22,522 distinct isoforms; 3,726 unique); liver was least diverse (12,435 isoforms; 1,039 unique). We highlight gene clusters exhibiting high tissue-specific isoform diversity per tissue (e.g., TPM1 expresses 19 in heart's atrial appendage), and specific genes (PAX6 and TPM1) that counterintuitively exhibit evidence that their expressed isoform diversity results from both biological noise and intent. We also validated 447 of the 700 new isoforms discovered by Aguzzoli-Heberle et al. and found that 88 were expressed in all nine tissues, while 58 were specific to a single tissue. This study represents a broad survey of the RNA isoform landscape, demonstrating isoform diversity across nine tissues and emphasizes the need to better understand how individual isoforms from a single gene body contribute to human health and disease.

Using deep long-read RNAseq in Alzheimer's disease brain to assess medical relevance of RNA isoform diversity

Due to alternative splicing, human protein-coding genes average over eight RNA isoforms, resulting in nearly four distinct protein coding sequences per gene. Long-read RNAseq (IsoSeq) enables more accurate quantification of isoforms, shedding light on their specific roles. To assess the medical relevance of measuring RNA isoform expression, we sequenced 12 aged human frontal cortices (6 Alzheimer's disease cases and 6 controls; 50% female) using one Oxford Nanopore PromethION flow cell per sample. Our study uncovered 53 new high-confidence RNA isoforms in medically relevant genes, including several where the new isoform was one of the most highly expressed for that gene. Specific examples include WDR4 (61%; microcephaly), MYL3 (44%; hypertrophic cardiomyopathy), and MTHFS (25%; major depression, schizophrenia, bipolar disorder). Other notable genes with new high-confidence isoforms include CPLX2 (10%; schizophrenia, epilepsy) and MAOB (9%; targeted for Parkinson's disease treatment). We identified 1,917 medically relevant genes expressing multiple isoforms in human frontal cortex, where 1,018 had multiple isoforms with different protein coding sequences, demonstrating the need to better understand how individual isoforms from a single gene body are involved in human health and disease, if at all. Exactly 98 of the 1,917 genes are implicated in brain-related diseases, including Alzheimer's disease genes such as APP (Aβ precursor protein; five), MAPT (tau protein; four), and BIN1 (eight). As proof of concept, we also found 99 differentially expressed RNA isoforms between Alzheimer's cases and controls, despite the genes themselves not exhibiting differential expression. Our findings highlight the significant knowledge gaps in RNA isoform diversity and their medical relevance. Deep long-read RNA sequencing will be necessary going forward to fully comprehend the medical relevance of individual isoforms for a "single" gene.

The Polygenic Risk Score Knowledge Base offers a centralized online repository for calculating and contextualizing polygenic risk scores

The process of identifying suitable genome-wide association (GWA) studies and formatting the data to calculate multiple polygenic risk scores on a single genome can be laborious. Here, we present a centralized polygenic risk score calculator currently containing over 250,000 genetic variant associations from the NHGRI-EBI GWAS Catalog for users to easily calculate sample-specific polygenic risk scores with comparable results to other available tools. Polygenic risk scores are calculated either online through the Polygenic Risk Score Knowledge Base (PRSKB; https://prs.byu.edu ) or via a command-line interface. We report study-specific polygenic risk scores across the UK Biobank, 1000 Genomes, and the Alzheimer's Disease Neuroimaging Initiative (ADNI), contextualize computed scores, and identify potentially confounding genetic risk factors in ADNI. We introduce a streamlined analysis tool and web interface to calculate and contextualize polygenic risk scores across various studies, which we anticipate will facilitate a wider adaptation of polygenic risk scores in future disease research.

Analysis of high-risk pedigrees identifies 11 candidate variants for Alzheimer's disease

Introduction

Analysis of sequence data in high‐risk pedigrees is a powerful approach to detect rare predisposition variants.

Methods

Rare, shared candidate predisposition variants were identified from exome sequencing 19 Alzheimer's disease (AD)‐affected cousin pairs selected from high‐risk pedigrees. Variants were further prioritized by risk association in various external datasets. Candidate variants emerging from these analyses were tested for co‐segregation to additional affected relatives of the original sequenced pedigree members.

Results

AD‐affected high‐risk cousin pairs contained 564 shared rare variants. Eleven variants spanning 10 genes were prioritized in external datasets: rs201665195 (ABCA7), and rs28933981 (TTR) were previously implicated in AD pathology; rs141402160 (NOTCH3) and rs140914494 (NOTCH3) were previously reported; rs200290640 (PIDD1) and rs199752248 (PIDD1) were present in more than one cousin pair; rs61729902 (SNAP91), rs140129800 (COX6A2, AC026471), and rs191804178 (MUC16) were not present in a longevity cohort; and rs148294193 (PELI3) and rs147599881 (FCHO1) approached significance from analysis of AD‐related phenotypes. Three variants were validated via evidence of co‐segregation to additional relatives (PELI3, ABCA7, and SNAP91).

Discussion

These analyses support ABCA7 and TTR as AD risk genes, expand on previously reported NOTCH3 variant identification, and prioritize seven additional candidate variants.

A lever action hypothesis for pendulous hummingbird flowers: experimental evidence from a columbine

BACKGROUND AND AIMS

Pendulous flowers (due to a flexible pedicel) are a common, convergent trait of hummingbird-pollinated flowers. However, the role of flexible pedicels remains uncertain despite several functional hypotheses. Here we present and test the 'lever action hypothesis': flexible pedicels allow pendulous flowers to move upwards from all sides, pushing the stigma and anthers against the underside of the feeding hummingbird regardless of which nectary is being visited.

METHODS

To test whether this lever action increased pollination success, we wired emasculated flowers of serpentine columbine, Aquilegia eximia, to prevent levering and compared pollination success of immobilized flowers with emasculated unwired and wire controls.

KEY RESULTS

Seed set was significantly lower in wire-immobilized flowers than unwired control and wire control flowers. Video analysis of visits to wire-immobilized and unwired flowers demonstrated that birds contacted the stigmas and anthers of immobilized flowers less often than those of flowers with flexible pedicels.

CONCLUSIONS

We conclude that flexible pedicels permit the levering of reproductive structures onto a hovering bird. Hummingbirds, as uniquely large, hovering pollinators, differ from flies or bees which are too small to cause levering of flowers while hovering. Thus, flexible pedicels may be an adaptation to hummingbird pollination, in particular due to hummingbird size. We further speculate that this mechanism is effective only in radially symmetric flowers; in contrast, zygomorphic hummingbird-pollinated flowers are usually more or less horizontally oriented rather than having pendulous flowers and flexible pedicels.

Comparison of concentric condensation technique with laterally condensed gutta-percha

Sixty mandibular premolars with large, straight canals and 60 nonjoining narrow, curved canals from mesial mandibular molar roots were obturated with gutta-percha via 1 of 3 methods: lateral condensation with sealer, or concentric condensation without sealer. The sealer used was a zinc oxide-eugenol without radiopacifiers. The premolar teeth were radiographed next to a step wedge, both before and after obturation. All teeth were exposed to India ink as a test for linear dye leakage, then cleared, and the leakage recorded. The pre- and postobturation radiographs were scanned at 2 and 6 mm from the apex using a Joyce-Loebel microdensitometer to establish the radiographic density of the obturation material, and a density ratio for the obturation was calculated using the cross-sectional diameter of the obturating material. The incidence of gutta-percha extrusion and Micro-Flow Compactor breakage was recorded. Two-way analysis of variance for linear dye leakage revealed no significant differences between the lateral and concentric condensation groups when sealer was used (p > 0.05). The concentric condensation without sealer groups exhibited significantly greater leakage (p < 0.00001) than the other groups, showing the importance of using sealers. One-way analysis of variance found no significant differences in radiographic density ratios between groups at 2 mm (p > 0.05) or 6 mm from the apex (p > 0.05). The incidence of extrusion was not significant, but a high rate of #30 condensor breakage was found.

Childhood bereavement after the death of a sibling

The article describes a study designed to explore the processes of sibling bereavement and to compare children's impressions with those of their parents. The Institute of Medicine model was used as a sensitizing framework for the study. Constant comparative technique was used to analyze data from a pilot study of 18 bereaved siblings aged 4 to 23 years. Sadness was the most common reaction after sibling death. Mothers were most often cited as being helpful; friends and fathers were also helpful. People who were not actively supportive were not helpful. Many children described feeling protective of their parents, and several children described personal growth.

Are serological tests of value in diagnosing and monitoring response to treatment of syphilis in patients infected with human immunodeficiency virus?

To assess the value of serological tests in diagnosing and monitoring the response to treatment of syphilis in patients infected with the human immunodeficiency virus (HIV), case notes of eight homosexual men with a history of treated syphilis, positive reactions to serological tests for syphilis, and documented subsequent conversion to HIV seropositivity were studied. No change was noted in serological markers of syphilis after HIV infection. The case notes of one man with primary syphilis, four men with secondary syphilis, and three men with latent syphilis, of whom all were HIV seropositive, were also studied. In seven of these patients the serological responses to infection and after treatment were consistent with the experience of syphilis in HIV seronegative patients. In one man treated for secondary syphilis, and confirmed as HIV seropositive eight months after treatment, the rapid plasma reagin (RPR) test result continued to be positive at a high titre for up to 20 months after treatment.

Human trypanosomiasis in Southern Africa

Five cases of human trypanosomiasis are presented. The clinical picture and course of the disease, and the results of haematological, immunological and other special examinations, are presented. The persistence of decreased total haemolytic complement, increased serum igM levels, decreased plasma fibrinogen levels, raised plasma and urinary fibrinogen split products, cryofibrinogenaemia and significant proteinuria in the presence of apparent clinical cure, tends to indicate the continuation of an immune complex process in spite of eradication of the parasite.