A Fluorescent Reporter Mouse for In Vivo Assessment of Genome Editing with Diverse Cas Nucleases and Prime Editors

CRISPR-based genome-editing technologies, including nuclease editing, base editing, and prime editing, have recently revolutionized the development of therapeutics targeting disease-causing mutations. To advance the assessment and development of genome editing tools, a robust mouse model is valuable, particularly for evaluating in vivo activity and delivery strategies. In this study, we successfully generated a knock-in mouse line carrying the Traffic Light Reporter design known as TLR-multi-Cas variant 1 (TLR-MCV1). We comprehensively validated the functionality of this mouse model for both in vitro and in vivo nuclease and prime editing. The TLR-MCV1 reporter mouse represents a versatile and powerful tool for expediting the development of editing technologies and their therapeutic applications.

Divalent siRNAs are bioavailable in the lung and efficiently block SARS-CoV-2 infection

The continuous evolution of SARS-CoV-2 variants complicates efforts to combat the ongoing pandemic, underscoring the need for a dynamic platform for the rapid development of pan-viral variant therapeutics. Oligonucleotide therapeutics are enhancing the treatment of numerous diseases with unprecedented potency, duration of effect, and safety. Through the systematic screening of hundreds of oligonucleotide sequences, we identified fully chemically stabilized siRNAs and ASOs that target regions of the SARS-CoV-2 genome conserved in all variants of concern, including delta and omicron. We successively evaluated candidates in cellular reporter assays, followed by viral inhibition in cell culture, with eventual testing of leads for in vivo antiviral activity in the lung. Previous attempts to deliver therapeutic oligonucleotides to the lung have met with only modest success. Here, we report the development of a platform for identifying and generating potent, chemically modified multimeric siRNAs bioavailable in the lung after local intranasal and intratracheal delivery. The optimized divalent siRNAs showed robust antiviral activity in human cells and mouse models of SARS-CoV-2 infection and represent a new paradigm for antiviral therapeutic development for current and future pandemics.

Intratracheally administered LNA gapmer antisense oligonucleotides induce robust gene silencing in mouse lung fibroblasts

The lung is a complex organ with various cell types having distinct roles. Antisense oligonucleotides (ASOs) have been studied in the lung, but it has been challenging to determine their effectiveness in each cell type due to the lack of appropriate analytical methods. We employed three distinct approaches to study silencing efficacy within different cell types. First, we used lineage markers to identify cell types in flow cytometry, and simultaneously measured ASO-induced silencing of cell-surface proteins CD47 or CD98. Second, we applied single-cell RNA sequencing (scRNA-seq) to measure silencing efficacy in distinct cell types; to the best of our knowledge, this is the first time scRNA-seq has been applied to measure the efficacy of oligonucleotide therapeutics. In both approaches, fibroblasts were the most susceptible to locally delivered ASOs, with significant silencing also in endothelial cells. Third, we confirmed that the robust silencing in fibroblasts is broadly applicable by silencing two targets expressed mainly in fibroblasts, Mfap4 and Adam33. Across independent approaches, we demonstrate that intratracheally administered LNA gapmer ASOs robustly induce gene silencing in lung fibroblasts. ASO-induced gene silencing in fibroblasts was durable, lasting 4-8 weeks after a single dose. Thus, lung fibroblasts are well aligned with ASOs as therapeutics.

Abstract 1119: Induced pluripotency in adult keratinocytes through downregulation of ΔNp63 or DGCR8

The roles of microRNAs (miRNAs) and the miRNA processing machinery in the regulation of stem cell biology are not well understood. Here, we show that the p53 family member and p63 isoform, ΔNp63, is a critical transcriptional activator of a co-factor pivotal for miRNA processing, DGCR8. This regulation is important in the terminal differentiation of adult keratinocytes and likely of other cells. Loss of ΔNp63 or DGCR8 induces pluripotency in these cells.

Generation of a conditional ΔNp63 knock-out mouse model with the help of a Cre-LoxP system led to the development of mice with single layered fragile and disorganized epidermis. Analysis of the skin with immunohistochemistry and immmunofluorescence exhibit aberrant expression of differentiation markers like keratin 5,14,10, loricrin and filaggrin, suggesting a defect in terminal differentiation and BrdU incorporation assay suggested hyperproliferation and self-renewal. Further characterization of stem cell marker expression in the epidermal cells from these embryos was found to be high. Chromatin immunoprecipitation assay and luciferase assays demonstrated the transcriptional activation of the DGCR8 promoter by ΔNp63. Overexpression of DGCR8 in the epidermal cells with the help of a lentiviral doxycycline inducible DGCR8 construct forced these cells to undergo differentiation as validated by in vitro differentiation assay and teratoma formation assay. These cells were also capable of generating chimeras when injected into blastocysts. Lentiviral knock-down of ΔNp63 or DGCR8 in normal human epidermal keratinocytes led to the development of induced pluripotent stem cells capable of forming teratomas as analyzed by differentiation markers AFP, MyoD and Nestin for various lineages like endoderm, mesoderm and ectoderm respectively.

Low expression of key miRNAs in ΔNp63 deficient cells results in the failure to repress genes required for stem cell pluripotency, Oct4, Sox2, and Nanog. Strikingly, ΔNp63-/- epidermal cells display profound defects in terminal differentiation and express markers and miRNAs of pluripotency at levels comparable to those in embryonic stem cells. Moreover, these cells can differentiate into multiple cell fates in vitro and in vivo. We found that human primary keratinocytes depleted of ΔNp63 or DGCR8 become pluripotent. For the first time we demonstrate a novel role for ΔNp63 in the transcriptional regulation of DGCR8 to maintain stem cell pluripotency. Importantly, our findings identify a simple method of generating human induced pluripotent stem cells through the knockdown of a single gene.

Citation Format: Deepavali Chakravarti, Xiaohua Su, Minsoon Cho, Young Jin Gi, Ashley Benham, Cristian Coarfa, Avinashnarayan Venkatanarayan, Jennifer Alana, Chad Creighton, weimin Xiao, Marco Leung, Harina Vin, Io Long Chan, Arianexys Aquino, Nicole Müller, Jan Parker-Thornburg, Kenneth Y. Tsai, Preethi H. Gunarante, Elsa R. Flores. Induced pluripotency in adult keratinocytes through downregulation of ΔNp63 or DGCR8. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1119. doi:10.1158/1538-7445.AM2013-1119

TAp63 is a master transcriptional regulator of lipid and glucose metabolism

TAp63 prevents premature aging, suggesting a link to genes that regulate longevity. Further characterization of TAp63-/- mice revealed that these mice develop obesity, insulin resistance, and glucose intolerance similar to those seen in mice lacking two key metabolic regulators, Silent information regulator T1 (Sirt1) and AMPK. While the roles of Sirt1 and AMPK in metabolism have been well studied, their upstream regulators are not well understood. We found that TAp63 is important in regulating energy metabolism by accumulating in response to metabolic stress and transcriptionally activating Sirt1, AMPKα2, and LKB1, resulting in increased fatty acid synthesis and decreased fatty acid oxidation. Moreover, we found that TAp63 lowers blood glucose levels in response to metformin. Restoration of Sirt1, AMPKα2, and LKB1 in TAp63-/- mice rescued some of the metabolic defects of the TAp63-/- mice. Our study defines a role for TAp63 in metabolism and weight control.

ΔNp63 transcriptionally regulates brachyury, a gene with diverse roles in limb development, tumorigenesis and metastasis

The phenotypes of the p63 mutant mice are complex and diverse. The p63-/- mice develop severe defects in morphogenesis of ectodermal appendages, and p63+/- mice are tumor prone. Transcriptional targets of p63 with functions in both of these biological processes likely exist. Here, we identified one such direct transcriptional target of p63, brachyury, a gene with diverse roles in limb development and tumorigenesis. We found that brachyury is not expressed in developing p63-/- mouse embryos, and that in osteosarcomas, ΔNp63 and brachyury are expressed at high levels. Knock down of ΔNp63 in tumor cells resulted in a concomitant diminution of brachyury, cell proliferation, migration and invasion. These data provide evidence that suppression of ΔNp63 in tumors may lead to tumor regression through loss of cell proliferative and metastatic potential.

Use of central venous lines in paediatrics--a local experience

Central venous catheters are widely used in the care of critically ill patients. This paper reviews our experience with central lines in paediatric patients requiring intensive care, between the period August 1994 and August 1995. A total of 57 insertions were performed in 40 patients, all less than 12 years of age. We found that the most common indication for catheter use was nutritional support (40%). The overall complication rate was 58%. Catheter-related infection was the most serious problem, occurring in 32% of all insertions. Coagulase-negative Staphylococcus aureus was the organism most frequently isolated. Maintenance problems affected 17 of our catheters in which 9 were blocked. Both infected and blocked catheters were promptly removed. We had 3 cases of perforation and 2 cases of thrombosis. There were no deaths directly attributed to catheter use. Recommendations made include: 1) staff education and new guidelines for catheter care, 2) use of bacteria filters, 3) careful prospective monitoring of catheter infection rate, 4) heparinisation when infusion rate less than 2 ml/h, 5) eliminate use of stiff polyethylene catheters and 6) routine confirmatory X-ray or waveform monitoring before catheter use, if possible. We concluded that central venous catheterisations greatly facilitated the management of our patients. However, one must bear in mind that the use of such catheters is associated with problems which must be recognised early and promptly treated and, if possible, prevented with safe practice.