An interactive resource of molecular signalling in the developing human haematopoietic stem cell niche

The emergence of definitive human haematopoietic stem cells (HSCs) from Carnegie Stage (CS) 14 to CS17 in the aorta-gonad-mesonephros (AGM) region is a tightly regulated process. Previously, we conducted spatial transcriptomic analysis of the human AGM region at the end of this period (CS16/CS17) and identified secreted factors involved in HSC development. Here, we extend our analysis to investigate the progression of dorso-ventral polarised signalling around the dorsal aorta over the entire period of HSC emergence. Our results reveal a dramatic increase in ventral signalling complexity from the CS13-CS14 transition, coinciding with the first appearance of definitive HSCs. We further observe stage-specific changes in signalling up to CS17, which may underpin the step-wise maturation of HSCs described in the mouse model. The data-rich resource is also presented in an online interface enabling in silico analysis of molecular interactions between spatially defined domains of the AGM region. This resource will be of particular interest for researchers studying mechanisms underlying human HSC development as well as those developing in vitro methods for the generation of clinically relevant HSCs from pluripotent stem cells.

One pipeline to predict them all? On the prediction of alternative splicing from RNA-Seq data

RNA-Seq has become the standard approach to quantify and compare gene expression and alternative splicing in different conditions. In many cases the limiting factor is not the sequencing itself but the bioinformatic analysis. A variety of software tools exist that predict alternative splicing patterns from RNA-Seq data, but surprisingly, a systematic comparison of the predictions obtained from different pipelines has not been performed. Here we compare results from frequently used bioinformatic tools using a high-quality RNA-Seq dataset. We show that there is little overlap in the splicing changes predicted by different tools and that GO-term analysis of the splicing changes predicted by the individual targets yields very different results. Validation of bioinformatic predictions by RT-PCR suggest a high number of false positives in the splicing changes predicated by each pipeline, which probably dominates GO-term analysis. The validation rate is strongly increased for targets predicted by several tools, offering a strategy to reduce false positives. Based on these results we offer some guidelines that may contribute to make alternative splicing predictions more reliable and may thus increase the impact of conclusions drawn from RNA-Seq studies. Furthermore, we created rmappet, a nextflow pipeline that performs alternative splicing analysis using rMATS and Whippet with subsequent overlapping of the results, enabling robust splicing analysis with only one command (https://github.com/didrikolofsson/rmappet/).

Maternal exposure to perfluorobutane sulfonate (PFBS) during pregnancy: evidence of adverse maternal and fetoplacental effects in New Zealand White (NZW) rabbits

Perfluorobutanesulfonic acid (PFBS) is a replacement for perfluorooctanesulfonic acid (PFOS) that is increasingly detected in drinking water and human serum. Higher PFBS exposure is associated with risk for preeclampsia, the leading cause of maternal and infant morbidity and mortality in the United States. This study investigated relevant maternal and fetal health outcomes after gestational exposure to PFBS in a New Zealand White rabbit model. Nulliparous female rabbits were supplied drinking water containing 0 mg/l (control), 10 mg/l (low), or 100 mg/l (high) PFBS. Maternal blood pressure, body weights, liver and kidney weights histopathology, clinical chemistry panels, and thyroid hormone levels were evaluated. Fetal endpoints evaluated at necropsy included viability, body weights, crown-rump length, and liver and kidney histopathology, whereas placenta endpoints included weight, morphology, histopathology, and full transcriptome RNA sequencing. PFBS-high dose dams exhibited significant changes in blood pressure markers, seen through increased pulse pressure and renal resistive index measures, as well as kidney histopathological changes. Fetuses from these dams showed decreased crown-rump length. Statistical analysis of placental weight via a mixed model statistical approach identified a significant interaction term between PFBS high dose and fetal sex, suggesting a sex-specific effect on placental weight. RNA sequencing identified the dysregulation of angiotensin (AGT) in PFBS high-dose placentas. These results suggest that PFBS exposure during gestation leads to adverse maternal outcomes, such as renal injury and hypertension, and fetal outcomes, including decreased growth parameters and adverse placenta function. These outcomes raise concerns about pregnant women's exposure to PFBS and pregnancy outcomes.

Enzymatically amplified linear dbDNATM as a rapid and scalable solution to industrial lentiviral vector manufacturing

Traditional bacterial fermentation techniques used to manufacture plasmid are time-consuming, expensive, and inherently unstable. The production of sufficient GMP grade material thus imposes a major bottleneck on industrial-scale manufacturing of lentiviral vectors (LVV). Touchlight's linear doggybone DNA (dbDNA^TM) is an enzymatically amplified DNA vector produced with exceptional speed through an in vitro dual enzyme process, enabling industrial-scale manufacturing of GMP material in a fraction of the time required for plasmid. We have previously shown that dbDNA^TM can be used to produce functional LVV; however, obtaining high LVV titres remained a challenge. Here, we aimed to demonstrate that dbDNA^TM could be optimised for the manufacture of high titre LVV. We found that dbDNA^TM displayed a unique transfection and expression profile in the context of LVV production, which necessitated the optimisation of DNA input and construct ratios. Furthermore, we demonstrate that efficient 3' end processing of viral genomic RNA (vgRNA) derived from linear dbDNA^TM transfer vectors required the addition of a strong 3' termination signal and downstream spacer sequence to enable efficient vgRNA packaging. Using these improved vector architectures along with optimised transfection conditions, we were able to produce a CAR19h28z LVV with equivalent infectious titres as achieved using plasmid, demonstrating that dbDNA^TM technology can provide a highly effective solution to the plasmid bottleneck.

Evaluating maternal exposure to an environmental per and polyfluoroalkyl substances (PFAS) mixture during pregnancy: Adverse maternal and fetoplacental effects in a New Zealand White (NZW) rabbit model

Mixtures of per- and polyfluoroalkyl substances (PFAS) are often found in drinking water, and serum PFAS are detected in up to 99% of the population. However, very little is known about how exposure to mixtures of PFAS affects maternal and fetal health. The aim of this study was to investigate maternal, fetal, and placental outcomes after preconceptional and gestational exposure to an environmentally relevant PFAS mixture in a New Zealand White (NZW) rabbit model. Dams were exposed via drinking water to control (no detectable PFAS) or a PFAS mixture for 32 days. This mixture was formulated with PFAS to resemble levels measured in tap water from Pittsboro, NC (10 PFAS compounds; total PFAS load = 758.6 ng/L). Maternal, fetal, and placental outcomes were evaluated at necropsy. Thyroid hormones were measured in maternal serum and kit blood. Placental gene expression was evaluated by RNAseq and qPCR. PFAS exposure resulted in higher body weight (p = 0.01), liver (p = 0.01) and kidney (p = 0.01) weights, blood pressure (p = 0.05), and BUN:CRE ratio (p = 0.04) in dams, along with microscopic changes in renal cortices. Fetal weight, measures, and histopathology were unchanged, but a significant interaction between dose and sex was detected in the fetal: placental weight ratio (p = 0.036). Placental macroscopic changes were present in PFAS-exposed dams. Dam serum showed lower T4 and a higher T3:T4 ratio, although not statistically significant. RNAseq revealed that 11 of the 14 differentially expressed genes (adj. p < 0.1) are involved in placentation or pregnancy complications. In summary, exposure elicited maternal weight gain and signs of hypertension, renal injury, sex-specific changes in placental response, and differential expression of genes involved in placentation and preeclampsia. Importantly, these are the first results to show adverse maternal and placental effects of an environmentally-relevant PFAS mixture in vivo.

Body temperature variation controls pre-mRNA processing and transcription of antiviral genes and SARS-CoV-2 replication

Antiviral innate immunity represents the first defense against invading viruses and is key to control viral infections, including SARS-CoV-2. Body temperature is an omnipresent variable but was neglected when addressing host defense mechanisms and susceptibility to SARS-CoV-2 infection. Here, we show that increasing temperature in a 1.5°C window, between 36.5 and 38°C, strongly increases the expression of genes in two branches of antiviral immunity, nitric oxide production and type I interferon response. We show that alternative splicing coupled to nonsense-mediated decay decreases STAT2 expression in colder conditions and suggest that increased STAT2 expression at elevated temperature induces the expression of diverse antiviral genes and SARS-CoV-2 restriction factors. This cascade is activated in a remarkably narrow temperature range below febrile temperature, which reflects individual, circadian and age-dependent variation. We suggest that decreased body temperature with aging contributes to reduced expression of antiviral genes in older individuals. Using cell culture and in vivo models, we show that higher body temperature correlates with reduced SARS-CoV-2 replication, which may affect the different vulnerability of children versus seniors toward severe SARS-CoV-2 infection. Altogether, our data connect body temperature and pre-mRNA processing to provide new mechanistic insight into the regulation of antiviral innate immunity.

The zinc finger domains in U2AF26 and U2AF35 have diverse functionalities including a role in controlling translation

Recent work has associated point mutations in both zinc fingers (ZnF) of the spliceosome component U2AF35 with malignant transformation. However, surprisingly little is known about the functionality of the U2AF35 ZnF domains in general. Here we have analysed key functionalities of the ZnF domains of mammalian U2AF35 and its paralog U2AF26. Both ZnFs are required for splicing regulation, whereas only ZnF2 controls protein stability and contributes to the interaction with U2AF65. These features are confirmed in a naturally occurring splice variant of U2AF26 lacking ZnF2, that is strongly induced upon activation of primary mouse T cells and localized in the cytoplasm. Using Ribo-Seq in a model T cell line we provide evidence for a role of U2AF26 in activating cytoplasmic steps in gene expression, notably translation. Consistently, an MS2 tethering assay shows that cytoplasmic U2AF26/35 increase translation when localized to the 5'UTR of a model mRNA. This regulation is partially dependent on ZnF1 thus providing a connection between a core splicing factor, the ZnF domains and the regulation of translation. Altogether, our work reveals unexpected functions of U2AF26/35 and their ZnF domains, thereby contributing to a better understanding of their role and regulation in mammalian cells.

Genome-wide identification of alternative splicing events that regulate protein transport across the secretory pathway

Alternative splicing (AS) strongly increases proteome diversity and functionality in eukaryotic cells. Protein secretion is a tightly-controlled process, especially in a tissue-specific and differentiation-dependent manner. While previous work has focussed on transcriptional and post-translational regulatory mechanisms, the impact of AS on the secretory pathway remains largely unexplored. Here we integrate a published screen for modulators of protein transport and RNA-Seq analyses to identify over 200 AS events as secretion regulators. We confirm that splicing events along all stages of the secretory pathway regulate the efficiency of membrane trafficking using Morpholinos and CRISPR/Cas9. We furthermore show that these events are highly tissue-specific and adapt the secretory pathway during T-cell activation and adipocyte differentiation. Our data substantially advance the understanding of AS functionality, add a new regulatory layer to a fundamental cell biological process and provide a resource of alternative isoforms that control the secretory pathway.