Genomic Surveillance of SARS-CoV-2 Sequence Variants at Universities in Southwest Idaho.

Although the impact of the SARS-CoV-2 pandemic on major metropolitan areas is broadly reported and readily available, regions with lower populations and more remote areas in the United States are understudied. The objective of this study is to determine the progression of SARS-CoV-2 sequence variants in a frontier and remote intermountain west state among university-associated communities. This study was conducted at two intermountain west universities from 2020 to 2022. Positive SARS-CoV-2 samples were confirmed by quantitative real-time reverse transcription-polymerase chain reaction and variants were identified by the next-generation sequencing of viral genomes. Positive results were obtained for 5355 samples, representing a positivity rate of 3.5% overall. The median age was 22 years. Viral genomic sequence data were analyzed for 1717 samples and phylogeny was presented. Associations between viral variants, age, sex, and reported symptoms among 1522 samples indicated a significant association between age and the Delta variant (B 1.167.2), consistent with the findings for other regions. An outbreak event of AY122 was detected August-October 2021. A 2-month delay was observed with respect to the timing of the first documented viral infection within this region compared to major metropolitan regions of the US.

A new solid target design for the production of 89Zr and radiosynthesis of high molar activity [89Zr]Zr-DBN.

Due to the advent of various biologics like antibodies, proteins, cells, viruses, and extracellular vesicles as biomarkers for disease diagnosis, progression, and as therapeutics, there exists a need to have a simple and ready to use radiolabeling synthon to enable noninvasive imaging trafficking studies. Previously, we reported [89Zr]zirconium-p-isothiocyanatobenzyl-desferrioxamine ([89Zr]Zr-DBN) as a synthon for the radiolabeling of biologics to allow PET imaging of cell trafficking. In this study, we focused on improving the molar activity (Am) of [89Zr]Zr-DBN, by enhancing 89Zr production on a low-energy cyclotron and developing a new reverse phase HPLC method to purify [89Zr]Zr-DBN. To enhance 89Zr production, a new solid target was designed, and production yield was optimized by varying, thickness of yttrium foil, beam current, irradiation duration and proton beam energy. After optimization, 4.78±0.33 GBq (129.3±8.9 mCi) of 89Zr was produced at 40 µA for 180 min (3 h) proton irradiation decay corrected to the end of bombardment with a saturation yield of 4.56±0.31 MBq/µA. Additionally, after reverse phase HPLC purification the molar activity of [89Zr]Zr-DBN was found to be in 165-316 GBq/µmol range. The high molar activity of [89Zr]Zr-DBN also allowed radiolabeling of low concentration of proteins in relatively higher yield. The stability of [89Zr]Zr-DBN was measured over time with and without the presence of ascorbic acid. The newly designed solid target assembly and HPLC method of [89Zr]Zr-DBN purification can be adopted in the routine production of 89Zr and [89Zr]Zr-DBN, respectively.

MicroRNA Regulation of Bone Marrow Mesenchymal Stem Cell Chondrogenesis: Toward Articular Cartilage.

The production of a clinically useful engineered cartilage is an outstanding and unmet clinical need. High-throughput RNA sequencing provides a means of characterizing the molecular phenotype of populations of cells and can be leveraged to better understand differences among source cells, derivative engineered tissues, and target phenotypes. In this study, small RNA sequencing is utilized to comprehensively characterize the microRNA transcriptomes (miRNomes) of native human neonatal articular cartilage and human bone marrow-derived mesenchymal stem cells (hBM-MSCs) differentiating into cartilage organoids, contrasting the microRNA regulation of engineered cartilage with that of a promising target phenotype. Five dominant microRNAs are upregulated during cartilage organoid differentiation and disproportionately regulate transcription factors: miR-148a-3p, miR-140-3p, miR-27b-3p, miR-140-5p, and miR-181a-5p. Two microRNAs that dominate the miRNomes of hBM-MSCs, miR-21-5p and miR-143-3p, persist throughout the differentiation process and may limit the ability of these cells to differentiate into an engineered cartilage resembling target native articular cartilage. By using predictive bioinformatics tools and antagomir inhibition, these persistent microRNAs are shown to destabilize the mRNA of genes with known or potential roles in cartilage biology including FGF18, TGFBR2, TET1, STOX2, ARAP2, N4BP2L1, LHX9, NFIA, and RPS6KA5. These results shed light on the extent to which only a few microRNAs contribute to the complex regulatory environment of hBM-MSCs for engineered tissues. Impact statement MicroRNAs are emerging as important controlling elements in the differentiation of human bone marrow-derived mesenchymal stem cells (hBM-MSCs). By using a robust bioinformatic approach and further validation in vitro, here we provide a comprehensive characterization of the microRNA transcriptomes (miRNomes) of a commonly studied and clinically promising source of multipotent cells (hBM-MSCs), a gold standard model of in vitro chondrogenesis (hBM-MSC-derived cartilage organoids), and an attractive in vivo target phenotype for clinically useful engineered cartilage (neonatal articular cartilage). These analyses highlighted a specific set of microRNAs involved in the chondrogenic program that could be manipulated to acquire a more robust articular cartilage-like phenotype. This characterization provides researchers in the cartilage tissue engineering field a useful atlas with which to contextualize microRNA involvement in complex differentiation pathways.

Transcriptome dynamics of long noncoding RNAs and transcription factors demarcate human neonatal, adult, and human mesenchymal stem cell-derived engineered cartilage.

The engineering of a native-like articular cartilage (AC) is a long-standing objective that could serve the clinical needs of millions of patients suffering from osteoarthritis and cartilage injury. An incomplete understanding of the developmental stages of AC has contributed to limited success in this endeavor. Using next generation RNA sequencing, we have transcriptionally characterized two critical stages of AC development in humans-that is, immature neonatal and mature adult, as well as tissue-engineered cartilage derived from culture expanded human mesenchymal stem cells. We identified key transcription factors (TFs) and long noncoding RNAs (lncRNAs) as candidate drivers of the distinct phenotypes of these tissues. AGTR2, SCGB3A1, TFCP2L1, RORC, and TBX4 stand out as key TFs, whose expression may be capable of reprogramming engineered cartilage into a more expandable and neonatal-like cartilage primed for maturation into biomechanically competent cartilage. We also identified that the transcriptional profiles of many annotated but poorly studied lncRNAs were dramatically different between these cartilages, indicating that lncRNAs may also be playing significant roles in cartilage biology. Key neonatal-specific lncRNAs identified include AC092818.1, AC099560.1, and KC877982. Collectively, our results suggest that tissue-engineered cartilage can be optimized for future clinical applications by the specific expression of TFs and lncRNAs.