Targeted regulation of transcription in primary cells using CRISPRa and CRISPRi.

Targeted transcriptional activation or interference can be induced with the CRISPR-Cas9 system (CRISPRa/CRISPRi) using nuclease-deactivated Cas9 fused to transcriptional effector molecules. These technologies have been used in cancer cell lines, particularly for genome-wide functional genetic screens using lentiviral vectors. However, CRISPRa and CRISPRi have not yet been widely applied to ex vivo cultured primary cells with therapeutic relevance owing to a lack of effective and nontoxic delivery modalities. Here we develop CRISPRa and CRISPRi platforms based on RNA or ribonucleoprotein (RNP) delivery by electroporation and show transient, programmable gene regulation in primary cells, including human CD34+ hematopoietic stem and progenitor cells (HSPCs) and human CD3+ T cells. We show multiplex and orthogonal gene modulation using multiple sgRNAs and CRISPR systems from different bacterial species, and we show that CRISPRa can be applied to manipulate differentiation trajectories of HSPCs. These platforms constitute simple and effective means to transiently control transcription and are easily adopted and reprogrammed to new target genes by synthetic sgRNAs. We believe these technologies will find wide use in engineering the transcriptome for studies of stem cell biology and gene function, and we foresee that they will be implemented to develop and enhance cellular therapeutics.

CRISPR-Cas-mediated transcriptional modulation: The therapeutic promises of CRISPRa and CRISPRi.

The CRISPR-Cas system is commonly known for its ability to cleave DNA in a programmable manner, which has democratized gene editing and facilitated recent breakthroughs in gene therapy. However, newer iterations of the technology using nuclease-disabled Cas enzymes have spurred a variety of different types of genetic engineering platforms such as transcriptional modulation using the CRISPR activation (CRISPRa) and CRISPR interference (CRISPRi) systems. This review introduces the creation of these programmable transcriptional modulators, various methods of delivery utilized for these systems, and recent technological developments. CRISPRa and CRISPRi have also been implemented in genetic screens for interrogating gene function and discovering genes involved in various biological pathways. We describe recent compelling examples of how these tools have become powerful means to unravel genetic networks and uncovering important information about devastating diseases. Finally, we provide an overview of preclinical studies in which transcriptional modulation has been used therapeutically, and we discuss potential future directions of these novel modalities.

Amdoparvovirus-associated disease in red pandas (Ailurus fulgens).

The roster of amdoparvoviruses (APVs) in small carnivores is growing rapidly, but in most cases, the consequences of infection are poorly understood. Red panda amdoparvovirus (RPAV) is highly prevalent in zoo-housed red pandas and has been detected in both healthy and sick animals. Clarifying the clinical impact of RPAV in this endangered species is critical, and zoological collections offer a unique opportunity to examine viral disease association in carefully managed populations. We evaluated the potential impact of RPAV in captive red pandas with a combination of prospective and retrospective analyses. First, we collected feces from 2 healthy animals from one collection over a 6-year period and detected virus in 72/75 total samples, suggesting that RPAV can be a long-term subclinical infection. We next investigated the infections using a retrospective study of infection status and tissue distribution in a cohort of necropsied animals. We performed polymerase chain reaction and in situ hybridization on 43 necropsy cases from 4 zoo collections (3 from the United States, 1 from Europe, 1997-2022). RPAV was present in these populations for at least 2 decades before its discovery and is detectable in common and significant lesions of zoo-housed red pandas, including myocarditis (3/3 cases), nephritis (9/10), and interstitial pneumonia (2/4). RPAV is also detectable in sporadic lesions, including multisystemic pyogranulomatous inflammation, oral/pharyngeal mucosal inflammation, and dermatitis. The colocalization of virus with lesions supports a role in causation, suggesting that despite the apparently persistent and subclinical carriage of most infections, RPAV may have a significant impact in zoo collections.

Therapeutic gene editing in haematological disorders with CRISPR/Cas9.

The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas)9 platform offers an efficient way of making precise genetic changes to the human genome. This can be employed for disruption, addition and correction of genes, thereby enabling a new class of genetic therapies that can be applied to haematological disorders. Here we review recent technological advances in the CRISPR/Cas9 methodology and applications in haematology for curing monogenic genetic disorders and for engineering novel chimeric antigen receptor (CAR) T cells to treat haematological malignancies. Furthermore, we discuss current challenges for full clinical implementation of CRISPR/Cas9, and reflect on future trajectories of the technology.

Natural RNA circles function as efficient microRNA sponges.

MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that act by direct base pairing to target sites within untranslated regions of messenger RNAs. Recently, miRNA activity has been shown to be affected by the presence of miRNA sponge transcripts, the so-called competing endogenous RNA in humans and target mimicry in plants. We previously identified a highly expressed circular RNA (circRNA) in human and mouse brain. Here we show that this circRNA acts as a miR-7 sponge; we term this circular transcript ciRS-7 (circular RNA sponge for miR-7). ciRS-7 contains more than 70 selectively conserved miRNA target sites, and it is highly and widely associated with Argonaute (AGO) proteins in a miR-7-dependent manner. Although the circRNA is completely resistant to miRNA-mediated target destabilization, it strongly suppresses miR-7 activity, resulting in increased levels of miR-7 targets. In the mouse brain, we observe overlapping co-expression of ciRS-7 and miR-7, particularly in neocortical and hippocampal neurons, suggesting a high degree of endogenous interaction. We further show that the testis-specific circRNA, sex-determining region Y (Sry), serves as a miR-138 sponge, suggesting that miRNA sponge effects achieved by circRNA formation are a general phenomenon. This study serves as the first, to our knowledge, functional analysis of a naturally expressed circRNA.

Women's experiences of postterm induction of labor: A systematic review of qualitative studies.

BACKGROUND: Over the last decade, induction of labor (IOL) in postterm pregnancies has increased. Studies have shown the medical advantages of postterm IOL, but less is known about the perspectives of the pregnant women. This review aimed to summarize the current qualitative evidence on women's experience of postterm IOL. METHODS: A systematic literature search was performed in three databases. A total of 3193 publications were identified, but only eight studies met the inclusion criteria. Thematic analysis guided the data extraction and synthesis. The Confidence in the Evidence for Reviews of Qualitative research (CERQual) approach was used to assess confidence in the findings. RESULTS: Three major findings were identified. First, for some women, IOL required a shift in expectations because the hope of spontaneous labor had to be given up. Second, the IOL decision was considered a recommendation from health care professionals and was experienced as a nondecision. Finally, the induction process was experienced as a sequential set of steps where the women were expected to fit into the existing hospital organization. The CERQual assessment suggested moderate confidence in all findings. DISCUSSION: The negative experiences identified in this review can be greatly reduced by a communicative and patient-centered approach. To support informed choice and shared decision making, women need high-quality, unbiased information about IOL, alternative options, and potential outcomes, in addition to time for reflection on their personal values and preferences. Women may need a professionally initiated and supported opportunity to re-evaluate their hopes and expectations before IOL.

The association between Bacillus Calmette-Guérin vaccination (1331 SSI) skin reaction and subsequent scar development in infants.

BACKGROUND: The Bacillus Calmette-Guérin vaccine (BCG) against tuberculosis is administered intradermally, and vaccination is often followed by a scar at the injection site. Among BCG-vaccinated individuals, having a scar has been associated with lower mortality. We aimed to examine the impact of vaccination technique for scarring in a high income setting, by assessing the associations between the post injection reaction, the wheal size, and the probability of developing a scar, and scar size. METHODS: This study was nested within a clinical multicenter study randomizing 4262 infants to either BCG vaccination (BCG 1331 SSI) or no intervention. In this substudy, including 492 vaccinated infants, the immediate post BCG vaccination reaction was registered as either wheal (a raised, blanched papule at the injection site), bulge (a palpable element at the injection site), or no reaction. The presence or absence of a BCG scar and the size the scar was measured at 13 months of age. RESULTS: Of 492 infants included, 87% had a wheal after vaccination, 11% had a bulge, and 2% had no reaction. The mean wheal size was 3.8 mm (95% confidence interval 3.7-3.9). Overall, 95% (442/466, 26 lost to follow-up) of BCG-vaccinated infants had a scar at 13 months of age. In infants with a wheal, the probability of developing a scar was 96%, declining to 87% in the case of a bulge, and to 56% in the case of no reaction (p for same probability = 0.03). Wheal size was positively correlated with the probability of getting a scar and scar size. CONCLUSION: Scarring after BCG vaccination has been associated with lower infant mortality. In a high-income setting, we found that correct injection technique is highly important for the development of a BCG scar and that registration of the category of BCG skin reaction (as wheal, bulge, or no reaction) may be used to identify infants at risk of scar failure. Finally, the wheal size was positively associated with both the probability of getting a scar and scar size. TRIAL REGISTRATION: The study was registered at www.ClinicalTrials.gov with trial registration number NCT01694108 .

Effects of Polar Bear and Killer Whale Derived Contaminant Cocktails on Marine Mammal Immunity.

Most controlled toxicity studies use single chemical exposures that do not represent the real world situation of complex mixtures of known and unknown natural and anthropogenic substances. In the present study, complex contaminant cocktails derived from the blubber of polar bears (PB; Ursus maritimus) and killer whales (KW; Orcinus orca) were used for in vitro concentration-response experiments with PB, cetacean and seal spp. immune cells to evaluate the effect of realistic contaminant mixtures on various immune functions. Cytotoxic effects of the PB cocktail occurred at lower concentrations than the KW cocktail (1 vs 16 µg/mL), likely due to differences in contaminant profiles in the mixtures derived from the adipose of each species. Similarly, significant reduction of lymphocyte proliferation occurred at much lower exposures in the PB cocktail (EC50: 0.94 vs 6.06 µg/mL; P < 0.01), whereas the KW cocktail caused a much faster decline in proliferation (slope: 2.9 vs 1.7; P = 0.04). Only the KW cocktail modulated natural killer (NK) cell activity and neutrophil and monocyte phagocytosis in a concentration- and species-dependent manner. No clear sensitivity differences emerged when comparing cetaceans, seals and PB. Our results showing lower effect levels for complex mixtures relative to single compounds suggest that previous risk assessments underestimate the effects of real world contaminant exposure on immunity. Our results using blubber-derived contaminant cocktails add realism to in vitro exposure experiments and confirm the immunotoxic risk marine mammals face from exposure to complex mixtures of environmental contaminants.

Changes in incontinence after hysterectomy.

PURPOSE: Information about the perioperative incontinence following hysterectomy is limited. To advance the postoperative rehabilitation further we need more information about qualitative changes in incontinence, fatigue and physical function of patients undergoing hysterectomy. METHODS: 108 patients undergoing planned hysterectomy were compared pre- and postoperatively. In a sub-study of the prospective follow-up study the changes in incontinence, postoperative fatigue, quality of life, physical function, and body composition were evaluated preoperatively, 13 and 30 days postoperatively. Sample size calculation indicated that 102 women had to be included. The incontinence status was estimated by a Danish version of the ICIG questionnaire; further, visual analogue scale, dynamometer for hand grip, knee extension strength and balance were applied. Work capacity was measured ergometer cycle together with lean body mass by impedance. Quality of life was assessed using the SF-36 questionnaire. Patients were examined preoperatively and twice postoperatively. RESULTS: In total 41 women improved their incontinence after hysterectomy and 10 women reported deterioration. Preoperative stress incontinence correlated with BMI (r = 0.25, p < 0.01) and urge incontinence with age (r = 0.24, p < 0.02). Further, improvement after hysterectomy in stress incontinence was associated with younger age (r = 0.20, p < 0.04). Improvement in urge incontinence was positively associated with BMI (r = 0.22, p = 0.02). A slight but significant loss was seen in lean body mass 13 and 30 days postoperatively. CONCLUSIONS: Hysterectomy was not significantly associated with the risk of incontinence; in particular, when no further vaginal surgery is performed. Hysterectomy may even have a slightly positive effect on incontinence and de-novo cure.

EVALUATION OF A COMMERCIAL COMPETITIVE ENZYME-LINKED IMMUNOSORBENT ASSAY FOR DETECTION OF AVIAN INFLUENZA VIRUS SUBTYPE H5 ANTIBODIES IN ZOO BIRDS.

The hemagglutination inhibition (HI) test is the current gold standard for detecting antibodies to avian influenza virus (AIV). Enzyme-linked immunosorbent assays (ELISAs) have been explored for use in poultry and certain wild bird species because of high efficiency and lower cost. This study compared a commercial ELISA for detection of AIV subtype H5 antibodies with HI test of 572 serum samples from zoo birds. There was no significant difference between the results of the two tests when statistically compared by a McNemar χ2 test (P = 0.86) and assessment of κ (κ = 0.87). With a specificity of 94.2% (95% confidence interval [CI], 0.92-0.97), a sensitivity of 93.9% (95% CI, 0.91-0.97), and an excellent correlation between the two tests, this ELISA can be recommended as an alternative to the HI test for preliminary screening of zoo bird sera for antibodies to AIV subtype H5.

Influenza A(H10N7) virus in dead harbor seals, Denmark.

Since April 2014, an outbreak of influenza in harbor seals has been ongoing in northern Europe. In Denmark during June-August, 152 harbor seals on the island of Anholt were found dead from severe pneumonia. We detected influenza A(H10N7) virus in 2 of 4 seals examined.

Overlap of symptoms of gastroesophageal reflux disease, dyspepsia and irritable bowel syndrome in the general population.

INTRODUCTION: Gastroesophageal reflux disease (GERD), functional dyspepsia (FD) and irritable bowel syndrome (IBS) are common functional gastrointestinal conditions with significant impact on the daily lives of individuals. The objective was to investigate the prevalence and overlap of the three conditions in a Western general population. MATERIAL AND METHODS: A nationwide study of 100,000 individuals 20 years and above, randomly selected in the general population. A web-based questionnaire survey formed the basis of this study. Questions regarding FD and IBS were extracted from the ROME III adult questionnaire. Questions regarding GERD were developed based on the Montreal definition. Prevalence estimates for GERD, FD IBS were calculated in total and for each sex separately and for four age groups. A Venn diagram was constructed, illustrating the overlap between the three conditions. RESULTS: The overall response rate was 52.2%. The prevalence of GERD, FD and IBS was 11.2%, 7.7% and 10.5%, respectively, and overlap between two or three of these conditions was seen among 6.5% of the respondents. Among individuals meeting the criteria of one or more of the conditions GERD, FD and IBS, 30.7% had overlap between two or all three conditions. CONCLUSION: GERD, FD and IBS are common conditions in the general population and the overlap between these conditions is also quite common. When diagnosing patients with GERD, FD and IBS, physicians should keep in mind that these patients could be suffering from more than one of these conditions.

Novel nucleotide-packaging vaccine delivers antigen and poly(I:C) to dendritic cells and generate a potent antibody response in vivo.

An issue with many current vaccines is the dependency on broadly inflammatory adjuvants, such as aluminum hydroxide or aluminum salts that affect many immune- and non-immune cells. These adjuvants are not necessarily activating all antigen-presenting cells (APCs) that take up the antigen and most likely they also activate APCs with no antigen uptake, as well as many non-immune cells. Conjugation of antigen and adjuvant would enable the use of smaller amounts of adjuvant and avoid unnecessary tissue damage and activation of bystander cells. It would ensure that all APCs that take up the antigen would also become activated and avoid that immature and non-activated APCs present the antigen to T cells without a co-stimulatory signal, leading to tolerogenesis. We have developed a novel vaccine that co-deliver antigen and a nucleotide adjuvant to the same APC and lead to a strong activation response in dendritic cells and macrophages. The vaccine is constructed as a fusion-protein with an antigen fused to the DNA/RNA-binding domain from the Hc2 protein from Chlamydia trachomatis. We have found that the fusion protein is able to package polyinosinic:polycytidylic acid (poly(I:C)) or dsDNA into small particles. These particles were taken up by macrophages and dendritic cells and led to strong activation and maturation of these cells. Immunization of mice with the fusion protein packaged poly(I:C) led to a stronger antibody response compared to immunization with a combination of poly(I:C) and antigen without the Hc2 DNA/RNA-binding domain.

Application of Machine Learning for Automating Behavioral Tracking of Captive Bornean Orangutans (Pongo Pygmaeus).

This article applies object detection to CCTV video material to investigate the potential of using machine learning to automate behavior tracking. This study includes video tapings of two captive Bornean orangutans and their behavior. From a 2 min training video containing the selected behaviors, 334 images were extracted and labeled using Rectlabel. The labeled training material was used to construct an object detection model using Create ML. The use of object detection was shown to have potential for automating tracking, especially of locomotion, whilst filtering out false positives. Potential improvements regarding this tool are addressed, and future implementation should take these into consideration. These improvements include using adequately diverse training material and limiting iterations to avoid overfitting the model.

Did algal toxin and Klebsiella infections cause the unexplained 2007 mass mortality event in Danish and Swedish marine mammals?

An unusual mass mortality event (MME) of harbour seals (Phoca vitulina) and harbour porpoises (Phocoena phocoena) occurred in Denmark and Sweden in June 2007. Prior to this incident, the region had experienced two MMEs in harbour seals caused by Phocine Distemper Virus (PDV) in 1988 and 2002. Although epidemiology and symptoms of the 2007 MME resembled PDV, none of the animals examined for PDV tested positive. Thus, it has been speculated that another - yet unknown - pathogen caused the June 2007 MME. To shed new light on the likely cause of death, we combine previously unpublished veterinary examinations of harbour seals with novel analyses of algal toxins and algal monitoring data. All harbour seals subject to pathological examination showed pneumonia, but were negative for PDV, influenza and coronavirus. Histological analyses revealed septicaemia in multiple animals, and six animals tested positive for Klebsiella pneumonia. Furthermore, we detected the algal Dinophysis toxin DTX-1b (1-115 ng g-1) in five seals subject to toxicology, representing the first time DTX-1b has been detected in marine vertebrates. However, no animals tested positive for both Klebsiella and toxins. Thus, while our relatively small sample size prevent firm conclusions on causative agents, we speculate that the unexplained MME may have been caused by a chance incidence of multiple pathogens acting in parallel in June 2007, including Dinophysis toxin and Klebsiella. Our study illustrates the complexity of wildlife MMEs and highlights the need for thorough sampling during and after MMEs, as well as additional research on and monitoring of DTX-1b and other algal toxins in the region.

SAM68 directs STING signaling to apoptosis in macrophages.

DNA is a danger signal sensed by cGAS to engage signaling through STING to activate innate immune functions. The best-studied downstream responses to STING activation include expression of type I interferon and inflammatory genes, but STING also activates other pathways, including apoptosis. Here, we report that STING-dependent induction of apoptosis in macrophages occurs through the intrinsic mitochondrial pathway and is mediated via IRF3 but acts independently of gene transcription. By intersecting four mass spectrometry datasets, we identify SAM68 as crucial for the induction of apoptosis downstream of STING activation. SAM68 is essential for the full activation of apoptosis. Still, it is not required for STING-mediated activation of IFN expression or activation of NF-κB. Mechanistic studies reveal that protein trafficking is required and involves SAM68 recruitment to STING upon activation, with the two proteins associating at the Golgi or a post-Golgi compartment. Collectively, our work identifies SAM68 as a STING-interacting protein enabling induction of apoptosis through this DNA-activated innate immune pathway.

Hepatitis E virus variant in farmed mink, Denmark.

Hepatitis E virus (HEV) is a zoonotic virus for which pigs are the primary animal reservoir. To investigate whether HEV occurs in mink in Denmark, we screened feces and tissues from domestic and wild mink. Our finding of a novel HEV variant supports previous findings of HEV variants in a variety of species.

Proliferation indices of phosphohistone H3 and Ki67: strong prognostic markers in a consecutive cohort with stage I/II melanoma.

Cellular proliferation is correlated with the progression of melanoma. Accordingly, the proliferation index of H&E-stained thin melanomas was recently included in the staging system of the American Joint Committee on Cancer. Yet, the immunohistochemical markers of proliferation phosphohistone H3 and Ki67 may improve such indices. To accurately quantify these markers, they should be combined with a melanocytic marker, for example, MART1 in an immunohistochemical double stain; also enabling automated quantification by image analysis. The aim of the study was to compare the prognostic impact of phosphohistone H3/MART1, Ki67/MART1, and H&E stains in primary cutaneous melanoma, and to determine the difference between indices established in hot spots and the global tumor areas. The study included 153 consecutive stage I/II melanoma-patients. The follow-up time was 8-14 years for event-free melanoma. Recurrent disease occurred in 43 patients; 37 died of melanoma. Both events occurred in only three thin melanomas. Their paraffin-embedded tissue was stained for phosphohistone H3/MART1, Ki67/MART1, and with H&E. And proliferation indices were established in 1-mm(2) hot spots and in the global tumor areas. In multivariate Cox analyses, only hot spot indices of phosphohistone H3/MART1 and Ki67/MART1 were independent prognostic markers. Phosphohistone H3/MART1 tended to be better than Ki67/MART1 with adjusted hazard ratios of 3.66 (95% CI, 1.40-9.55; P=0.008) for progression-free survival and 3.42 (95% CI, 1.29-9.04; P=0.013) for melanoma-specific death. In all stains, prognostic performance was substantially improved by using hot spots instead of the global tumor areas. In conclusion, phosphohistone H3/MART1 and Ki67/MART1 were superior to H&E stains, and hot spots superior to the global tumor areas. Given the potential for automated analysis, these double stains seem to be robust alternatives to conventional mitotic detection by H&E in stage I/II melanomas in general. This was particularly true for thick melanomas whereas no specific analyses for thin melanomas only could be performed.

Enrichment of transgene integrations by transient CRISPR activation of a silent reporter gene.

CRISPR-Cas-mediated site-specific integration of transgenes by homology-directed repair (HDR) is challenging, especially in primary cells, where inferior editing efficiency may impede the development of gene- and cellular therapies. Various strategies for enrichment of cells with transgene integrations have been developed, but most strategies either generate unwanted genomic scars or rely on permanent integration and expression of a reporter gene used for selection. However, stable expression of a reporter gene may perturb cell homeostasis and function. Here we develop a broadly applicable and versatile enrichment strategy by harnessing the capability of CRISPR activation (CRISPRa) to transiently induce expression of a therapeutically relevant reporter gene used for immunomagnetic enrichment. This strategy is readily adaptable to primary human T cells and CD34+ hematopoietic stem and progenitor cells (HSPCs), where enrichment of 1.8- to 3.3-fold and 3.2- to 3.6-fold was achieved, respectively. Furthermore, chimeric antigen receptor (CAR) T cells were enriched 2.5-fold and demonstrated improved cytotoxicity over non-enriched CAR T cells. Analysis of HDR integrations showed a proportion of cells harboring deletions of the transgene cassette arising either from impartial HDR or truncated adeno-associated virus (AAV) vector genomes. Nonetheless, this novel enrichment strategy expands the possibility to enrich for transgene integrations in research settings and in gene and cellular therapies.

Increasing use of computed tomography scans in the North Denmark Region raises patient safety concern.

PURPOSE: Use of computed tomography (CT) scans raises safety concern as lifetime cumulative ionising radiation exposure is associated with risk of developing malignancies. This study aimed to investigate use of abdominal CT scans in the Danish health care sector. METHODS: Data on abdominal CT scans performed annually in the North Denmark Region between 2005 and 2018 were extracted from the regional registry with emphasis on patients with a medical history of a repeated abdominal CT scan within 28 days. An audit of the medical files was subsequently conducted in 100 randomly selected patient cases to evaluate clinical information being provided, in addition to justification for a repeated abdominal CT scan, and finally if other radiology modalities could have been applied. RESULTS: Number of annually performed abdominal CT scans in this demographically stable regional population increased by a factor 4.3 from 15 in 2005 to 65 in 2018 per 1,000 inhabitants. The audit revealed that 31% of the secondabdominal CT scans within a 28 days period were categorized as either doubtful whether justified or not justified. Moreover, 20% of theCT scans were considered replaceable by ultrasonography. CONCLUSIONS: Annual performance of abdominal CT scans increased fourfold during the 14 years period. This tendency is probably attributable to changes in the Danish health care sector by which CT scan examination are used more frequently aiming at more accelerated patient investigation flow in conjunction with shorter length of hospitalization stay. Alertness is strongly warranted towards the associated risk of cancer due to life-time cumulative ionising radiation exposure by this strategy.