ABSTRACT We tested the hypothesis that a panel of placental mammal-specific miRNAs and their targets play important to establish receptivity to implantation and their dysregulated expression may be a feature in women with early pregnancy loss. Relative expression levels of miR-340-5p, −542-3p, and −671-5p all increased following treatment of Ishikawa cells with progesterone (10 μg/ml) for 24 hrs (p < 0.05). RNA sequencing of these P4-treated cells identified co-ordinate changes to 6,367 transcripts of which 1713 were predicted targets of miR-340-5p, 670 of miR-542-3p, and 618 of miR-671-5p. Quantitative proteomic analysis of Ishikawa cells transfected with mimic or inhibitor (48 hrs: n=3 biological replicates) for each of the P4-regulated miRNAs was carried out to identify targets of these miRNAs. Excluding off target effects, mir-340-5p mimic altered 1,369 proteins while inhibition changed expression of 376 proteins (p < 0.05) of which, 72 were common to both treatments. A total of 280 proteins were identified between predicted (mirDB) and confirmed ( in vitro ) targets. In total, 171 proteins predicted to be targets by mirDB were altered in vitro by treatment with miR-340-5p mimic or inhibitor and were also altered by treatment of endometrial epithelial cells with P4. In vitro targets of miR-542-3p identified 1,378 proteins altered by mimic while inhibition altered 975 a core of 200 proteins were changed by both. 100 protein targets were predicted and only 46 proteins were P4 regulated. miR-671-mimic altered 1,252 proteins with inhibition changing 492 proteins of which 97 were common to both, 95 were miDB predicted targets and 46 were also P4-regulated. All miRNAs were detected in endometrial biopsies taken from patients during the luteal phase of their cycle, irrespective of prior or future pregnancy outcomes Expression of mir-340-5p showed an overall increase in patients who had previously suffered a miscarriage and had a subsequent miscarriage, as compared to those who had infertility or previous miscarriage and subsequently went on to have a life birth outcome. The regulation of these miRNAs and their protein targets regulate the function of transport and secretion, and adhesion of the endometrial epithelia required for successful implantation in humans. Dysfunction of these miRNAs (and therefore the targets they regulate) may contribute to endometrial-derived recurrent pregnancy loss in women.
The unicellular protozoan parasite Leishmania causes the neglected tropical disease leishmaniasis, affecting 12 million people in 98 countries. In South America, where the Viannia subgenus predominates, so far only L. ( Viannia ) braziliensis and L. ( V. ) panamensis have been sequenced, assembled and annotated as reference genomes. Addressing this deficit in molecular information can inform species typing, epidemiological monitoring and clinical treatment. Here, L. ( V. ) naiffi and L. ( V. ) guyanensis genomic DNA was sequenced to assemble these two genomes as draft references from short sequence reads. The methods used were tested using short sequence reads for L. braziliensis M2904 against its published reference as a comparison. This assembly and annotation pipeline identified 70 additional genes not annotated on the original M2904 reference. Phylogenetic and evolutionary comparisons of L. guyanensis and L. naiffi with 10 other Viannia genomes revealed four traits common to all Viannia : aneuploidy, 22 orthologous groups of genes absent in other Leishmania subgenera, elevated TATE transposon copies and a high NADH-dependent fumarate reductase gene copy number. Within the Viannia , there were limited structural changes in genome architecture specific to individual species: a 45 Kb amplification on chromosome 34 was present in all bar L. lainsoni , L. naiffi had a higher copy number of the virulence factor leishmanolysin, and laboratory isolate L. shawi M8408 had a possible minichromosome derived from the 3’ end of chromosome 34 . This combination of genome assembly, phylogenetics and comparative analysis across an extended panel of diverse Viannia has uncovered new insights into the origin and evolution of this subgenus and can help improve diagnostics for leishmaniasis surveillance.
ABSTRACT Environmental stressors to which a foetus is exposed, affect a range of physiological functions in post-natal offspring. Such stressors include disproportionate steroid hormone concentrations in the uterine environment. We aimed to determine the in-utero effect of steroid hormones on reproductive potential of female offspring using a porcine model. Hypothesising that an in-utero sex bias will influence ovarian reserve and endometrial morphology in the breeding gilt. Reproductive tracts of pigs from female-biased litters (>65% female, n=15), non-biased litters (45-54.9% female, n=15), and male-biased litters (<35% females, n=9) were collected at slaughter (95-115 kg). Ovaries and uterine horns were processed for histological approaches and stained using H&E or IHC techniques. All measurements were conducted in QuPath (Bankhead et al, 2017). Variability of data within groups was analysed with a Levenes test, whilst data was analysed using linear models in R. In the ovarian reserve, there was a significant interaction between the birth weight and the sex ratio of a litter from which a pig originated (p=.015), with low-birth-weight pigs from male-biased litters having a higher number of primordial follicles and the opposite trend seen in pigs from female-biased litters. This was not reflected in recruited, nor atretic follicles. In the uterine horn sex bias held no effect on development as seen in this study. Birth weight held more effects on the gilts. A lower BW decreased the proportion of glands found in the endometrium (p=.045). BW was found to be far more variable in both male-biased and female-biased litters (p=.026). The variability of primordial follicles from male-biased litters was greater than non-and female-biased litters (p=.014). Similarly, endometrial stromal nuclei had a greater range in male- and female-biased litters than non-biased litters (p=.028). There was a greater effect on both ovarian reserve and uterine development of piglet BW than the litter bias. There seems a benefit of being androgenised on ovarian reserve whilst no effects were found for the morphology or endometrial gland proliferation of the uterine horns. However, a crucial finding was in the variability of the data. Both primordial follicles in the male-biased ovary, and stromal nuclei in the male- and female-biased uterine horns had a wider spread in numbers than non-biased litters. This could be inflating the variability of reproductive success seen in animals form male-biased litters by two means. Firstly, by a higher likelihood of insufficient primordial pools. Secondly, through a potential impact on stromal-derived growth factors or insufficient support of the underlying implantation structures, leading to an increased variability in uterine implantation capabilities, and thus survival of the embryo.
Abstract Expanded CAG/CTG repeat disorders affect over 1 in 2500 individuals worldwide. Potential therapeutic avenues include gene silencing and modulation of repeat instability. However, there are major mechanistic gaps in our understanding of these processes, which prevent the rational design of an efficient treatment. To address this, we developed a novel system, ParB/ANCHOR-mediated Inducible Targeting (PInT), in which any protein can be recruited at will to a GFP reporter containing an expanded CAG/CTG repeat. Previous studies have implicated the histone deacetylase HDAC5 and the DNA methyltransferase DNMT1 as modulators of repeat instability via mechanisms that are not fully understood. Using PInT, we found no evidence that HDAC5 or DNMT1 modulate repeat instability upon targeting to the expanded repeat, suggesting that their effect is independent of local chromatin structure. Unexpectedly, we found that expanded CAG/CTG repeats reduce the effectiveness of gene silencing mediated by targeting HDAC5 and DNMT1. The repeat-length effect in gene silencing by HDAC5 was abolished by a small molecule inhibitor of HDAC3. Our results have important implications on the design of epigenome editing approaches for expanded CAG/CTG repeat disorders. PInT is a versatile synthetic system to study the effect of any sequence of interest on epigenome editing.
Targeted DNA sequencing approaches will improve how the size of short tandem repeats is measured for diagnostic tests and preclinical studies. The expansion of these sequences causes dozens of disorders, with longer tracts generally leading to a more severe disease. Interrupted alleles are sometimes present within repeats and can alter disease manifestation. Determining repeat size mosaicism and identifying interruptions in targeted sequencing datasets remains a major challenge. This is in part because standard alignment tools are ill-suited for repetitive and unstable sequences. To address this, we have developed Repeat Detector (RD), a deterministic profile weighting algorithm for counting repeats in targeted sequencing data. We tested RD using blood-derived DNA samples from Huntington's disease and Fuchs endothelial corneal dystrophy patients sequenced using either Illumina MiSeq or Pacific Biosciences single-molecule, real-time sequencing platforms. RD was highly accurate in determining repeat sizes of 609 blood-derived samples from Huntington's disease individuals and did not require prior knowledge of the flanking sequences. Furthermore, RD can be used to identify alleles with interruptions and provide a measure of repeat instability within an individual. RD is therefore highly versatile and may find applications in the diagnosis of expanded repeat disorders and in the development of novel therapies.
Abstract Expanded CAG/CTG repeats cause at least 15 different neurodegenerative and neuromuscular diseases that all remain without an effective disease modifying treatment. Because the size of the repeat tract accounts for the majority of the variation in disease severity, contracting them presents an attractive therapeutic avenue. Here, we show that the CRISPR-Cas9 nickase targeting the CAG/CTG repeat itself leads to efficient contractions in Huntington’s disease patient-derived neurons and astrocytes, as well as in myotonic dystrophy type 1 patient-derived neurons. Using single-cell DNA sequencing, PCR-free whole genome sequencing, and targeted long-read sequencing of the HTT locus, we found no off-target mutations above background in neurons and astrocytes. Furthermore, we delivered the Cas9 nickase and sgRNA stereotactically to a mouse model of Huntington’s disease using adeno-associated viruses, and found contractions accumulating in over half of the infected cells over a period of 5 months. We also found that the Cas9 nickase was prone to silencing, further improving the safety of the approach. Our results provide the proof of concept for using the Cas9 nickase to contract the repeat tract safely in multiple cell types and diseases.
We tested the hypothesis that conserved placental mammal-specific microRNAs and their targets facilitate endometrial receptivity to implantation. Expression of miR-340-5p, -542-3p, and -671-5p was regulated by exposure of endometrial epithelial cells to progesterone (10 μg/ml) for 24 h coordinate with 1,713 of their predicted targets. Proteomic analysis of cells transfected with miRNA mimic/inhibitor (48 h: n = 3) revealed 1,745 proteins altered by miR-340-5p (mimic; 1,369, inhibitor; 376) of which 171 were predicted targets and P4-regulated. MiR-542-3p altered 2,353 (mimic; 1,378, inhibitor; 975) 100 which were mirDB predicted, including 46 P4-regulated. MiR-671-5p altered 1,744 proteins (mimic; 1,252, inhibitor; 492) 95 of which were predicted targets and 46 P4-regulated. All miRNAs were detected in luteal phase endometrial biopsies, irrespective of pregnancy outcomes. miR-340-5p expression increased in biopsies from individuals suffering previous and subsequent miscarriage compared to those with subsequent live birth. Dysfunction of these miRNAs and their targets contribute to endometrial-derived recurrent pregnancy loss.
Expanded CAG/CTG repeats cause at least 15 different diseases, including Huntington's disease. It affects about 1 in 10,000 people world-wide and remains without an effective treatment. Thus, the development of new therapies remains a major unmet medical need. The size of the repeat tract scales with disease severity, therefore, inducing CAG/CTG repeat contractions is an attractive treatment avenue. Our lab has developed the first method capable of achieving this. Here, we show that the CRISPR-Cas9 nickase targeted to the CAG/CTG repeat itself leads to efficient contractions in multiple cellular systems, amongst them, in HD iPSC-derived neurons and astrocytes. Indeed, we found that this approach is specific for the expanded allele and off-targets mutations remained undetected using the whole genome sequencing. This indicates that our approach is a safe for further in vivo work.
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