The FUT2 Variant c.461G>A (p.Trp154*) Is Associated With Differentially Expressed Genes and Nasopharyngeal Microbiota Shifts in Patients With Otitis Media

Otitis media (OM) is a leading cause of childhood hearing loss. Variants in FUT2, which encodes alpha-(1,2)-fucosyltransferase, were identified to increase susceptibility to OM, potentially through shifts in the middle ear (ME) or nasopharyngeal (NP) microbiotas as mediated by transcriptional changes. Greater knowledge of differences in relative abundance of otopathogens in carriers of pathogenic variants can help determine risk for OM in patients. In order to determine the downstream effects of FUT2 variation, we examined gene expression in relation to carriage of a common pathogenic FUT2 c.461G>A (p.Trp154*) variant using RNA-sequence data from saliva samples from 28 patients with OM. Differential gene expression was also examined in bulk mRNA and single-cell RNA-sequence data from wildtype mouse ME mucosa after inoculation with non-typeable Haemophilus influenzae (NTHi). In addition, microbiotas were profiled from ME and NP samples of 65 OM patients using 16S rRNA gene sequencing. In human carriers of the FUT2 variant, FN1, KMT2D, MUC16 and NBPF20 were downregulated while MTAP was upregulated. Post-infectious expression in the mouse ME recapitulated these transcriptional differences, with the exception of Fn1 upregulation after NTHi-inoculation. In the NP, Candidate Division TM7 was associated with wildtype genotype (FDR-adj-p=0.009). Overall, the FUT2 c.461G>A variant was associated with transcriptional changes in processes related to response to infection and with increased load of potential otopathogens in the ME and decreased commensals in the NP. These findings provide increased understanding of how FUT2 variants influence gene transcription and the mucosal microbiota, and thus contribute to the pathology of OM.

Nm-Nano: Predicting 2′-O-methylation (Nm) Sites in Nanopore RNA Sequencing Data

Nm (2′-O-methylation) is one of the most abundant modifications of mRNAs and non-coding RNAs occurring when a methyl group (–CH3) is added to the 2′ hydroxyl (–OH) of the ribose moiety. This modification can appear on any nucleotide (base) regardless of the type of nitrogenous base, because each ribose sugar has a hydroxyl group and so 2′-O-methyl ribose can occur on any base. Nm modification has a great contribution in many biological processes such as the normal functioning of tRNA, the protection of mRNA against degradation by DXO, and the biogenesis and specificity of rRNA. Recently, the single-molecule sequencing techniques for long reads of RNA sequences data offered by Oxford Nanopore technologies have enabled the direct detection of RNA modifications on the molecule that is being sequenced, but to our knowledge there was only one research attempt that applied this technology to predict the stoichiometry of Nm-modified sites in RNA sequence of yeast cells. To this end, in this paper, we extend this research direction by proposing a bio-computational framework, Nm-Nano for predicting Nm sites in Nanopore direct RNA sequencing reads of human cell lines. Nm-Nano framework integrates two supervised machine learning models for predicting Nm sites in Nanopore sequencing data, namely Xgboost and Random Forest (RF). Each model is trained with set of features that are extracted from the raw signal generated by the Oxford Nanopore MinION device, as well as the corresponding basecalled k-mer resulting from inferring the RNA sequence reads from the generated Nanopore signals. The results on two benchmark data sets generated from RNA Nanopore sequencing data of Hela and Hek293 cell lines show a great performance of Nm-Nano. In independent validation testing, Nm-Nano has been able to identify Nm sites with a high accuracy of 93% and 88% using Xgboost and RF models respectively by training each model with Hela benchmark dataset and testing it for identifying Nm sites on Hek293 benchmark dataset. Thus, Nm-Nano outperforms the Nm sites predictors existing in the literature (not relying on Nanopore technology) that were only limited to predict Nm sites on short reads of RNA sequences and unable to predict Nm sites on long RNA sequence reads. By deploying Nm-Nano to predict Nm sites in Hela cell line, it was revealed that a total of 196 genes was identified to have the most abundance of Nm modification among all other genes that have been modified by Nm in this cell line. Similarly, deploying Nm-Nano to predict Nm sites in Hek393 cell line revealed that a total of 196 genes line was identified to have the most abundance of Nm modification among all other genes that have been modified by Nm in this cell line. According to this, a significant enrichment of a wide range of functional processes like high confidences (adjusted p-val < 0.05) enriched ontologies that were more representative of Nm modification role in immune response and cellular homeostasis were revealed in Hela cell line, and "MHC class 1 protein complex", "mitotic spindle assembly", "response to glucocorticoid", and "nucleocytoplasmic transport" were revealed in Hek293 cell line. The source code of Nm-Nano can be freely accessed https://github.com/Janga-Lab/Nm-Nano.

Engineering Protein Activity into Off-the-Shelf DNA Devices

DNA-based devices are relatively straightforward to design by virtue of their predictable folding, but they lack biological activity. Conversely, protein-based devices offer a myriad of biological functions but are much more difficult to design due to their complex folding. This study bridges the fields of DNA engineering and protein engineering to generate a protein switch that is activated by a specific DNA sequence. A single protein switch, engineered from nanoluciferase using the alternate frame folding mechanism and herein called nLuc-AFF, is paired with different DNA technologies to create a biosensor for a DNA or RNA sequence of choice, sensors for serotonin and ATP, and a computational device that processes two DNA inputs. nLuc-AFF is a genetically-encoded, ratiometric, blue/green-luminescent biosensor whose output can be quantified by cell phone camera. nLuc-AFF is not falsely activated by decoy DNA and it retains full ratiometric readout in 100 % serum. The design approach can be applied to other proteins and enzymes to convert them into DNA-activated switches.

Unraveling Heterogeneity of Aged Hematopoietic Stem Cells By Single-Cell RNA Sequence Analysis

During aging, hematopoietic stem cells (HSCs) alter quantitatively as well as qualitatively due to accumulating damages induced by intrinsic and extrinsic stresses. Functional decline of HSCs causes deregulated hematopoiesis resulting in anemia, immune dysfunction, and increased risk of hematologic malignancies. The absolute number of HSCs in aged mice evidently increases compared to young mice. In addition, aged HSCs show abnormal hematopoiesis such as myeloid-biased differentiation accompanied by low production of lymphocytes. However, the molecular mechanisms underlying age-associated changes in hematopoiesis remain largely unknown. In this study, we performed single-cell RNA sequence analysis (scRNA-seq) of HSCs from young (10-week-old), middle-aged (12-month-old) and aged (20-month-old) mice to gain insight into the dynamics of HSC aging. scRNA-seq analysis revealed three major clusters (A, B, C) and three minor clusters (D, E, F) in young HSCs. Of interest, aged HSCs also showed similar cluster formation. One of the minor clusters was characterized by gene signature associated with inflammatory response and significantly increased with age, while the remaining two minor clusters, which showed cell cycle gene signature, did not change in proportion. One of the major clusters, Cluster C, which showed the strongest expression of HSC-specific gene sets compared with other clusters, moderately increased with age. Our scRNA-seq analysis confirmed upregulation of age-related genes previously reported, such as Selp, Mt1, and Vwf, in a considerable portion of aged HSCs. von Willebrand factor (Vwf) encodes a blood glycoprotein produced by megakaryocytes and endothelial cells. Several groups have reported that Vwf-expressing HSCs show myeloid/platelet-biased differentiation (Joana C et al., Nature 2013; Sandra P et al., Developmental Cell 2018). Importantly, our scRNA-seq data identified that Clusterin (Clu) is rarely expressed in young HSCs and is dramatically upregulated in aged HSCs. Clu expression was predominantly increased in one of the major clusters, Cluster C. Clusterin encodes a secreted chaperone involved in clearance of cellular debris and regulation of apoptosis. We hypothesized that Clu would be useful as a marker of a unique subpopulation of aged HSCs, and thus conducted further analysis by using Clu reporter mice with Clu BAC clone, in which an EGFP reporter gene was inserted at the initiating ATG codon of the Clu gene so that EGFP expression is driven by the regulatory sequences of the BAC gene. Clu/GFP was preferentially expressed in HSCs and at lower frequencies in MPP1 than HSCs in Lineage -Sca-1 +c-Kit + (LSK) cell fraction. Clu-positive HSCs expressed high levels of CD150 and were detected in 10% and 60% of HSCs in 10-week-old young mice and 8-month-old middle-aged mice, respectively, indicating that Clu-positive HSCs increase with aging. We next assessed the function of Clu-positive HSCs in young mice. Clu-positive young HSCs established significantly lower chimerism than Clu-negative young HSCs and preferentially differentiated into myeloid cells in competitive transplantation assays. RNA-seq analysis of Clu-positive and Clu-negative HSCs from young mice confirmed that Clu-positive HSCs show the gene signature of myeloid-biased HSCs. Characterization of Clu-positive and negative subpopulations in aged HSCs is currently underway. These results suggest that Clu-positive HSCs represent myeloid-biased HSCs which expand with aging, thus Clu expression serves as a novel marker to monitor the alterations in HSC heterogeneity with aging. Disclosures Iwama: Nissan Chemical Corporation: Research Funding.

Development of a Bicistronic Anti-CD19/CD20 CAR Construct Including Optimization to Abrogate Retroviral Recombination Events

Anti-CD19 chimeric antigen receptor (CAR) T cells can eliminate lymphoma, but CD19 loss from lymphoma can cause anti-CD19 CAR T-cell treatment failure. To address CD19 loss, we designed a bicistronic construct encoding 2 CARs. The first CAR in the bicistronic construct was the anti-CD19 CAR Hu19-CD828Z, which incorporated a human anti-CD19 single-chain variable fragment (scFv) along with CD28 and CD3ζ domains (Brudno et al. Nature Medicine 2020). The 2nd CAR in the construct was a novel anti-CD20 CAR incorporating a human anti-CD20 scFv, plus 4-1BB and CD3ζ domains. This bicistronic CAR construct, designated Hu1928-Hu20BB-original, was encoded by the mouse stem cell virus-based splice-gag (MSGV1) gamma-retroviral vector. Repeated segments of identical DNA sequence can lead to recombination events when retroviral vectors are utilized. Recombination events driven by repeated identical nucleotide segments can occur during retroviral vector production in packaging cells. Recombination events can also occur in transduced T cells during reverse transcription when repeated segments of identical nucleotides on the same nucleotide strand anneal, which leads to strand switching by the reverse transcriptase enzyme and deletion of part of the sequence. We assessed T cells transduced with Hu1928-Hu20BB-original for evidence of recombination. Southern blots of DNA from T cells transduced with Hu1928-Hu20BB-original showed a dominant band of the expected CAR transgene length and no aberrant bands after 21 hours of exposure; however, with extended exposure of 8 days, an unexpected band indicating shorter transgene length became visible. This aberrant band was consistent with deletion of part of the transgene sequence due to recombination. To investigate possible recombination by a more sensitive method, we assessed RNA from transduced T cells by single-molecule real-time RNA sequencing (SMRT-RNAseq, PacBio). Deletions of Hu1928-Hu20BB-original RNA sequence between segments of identical sequence were detected by SMRT-RNAseq. These findings were consistent with recombination. The most common recombination events were between the CD8α hinge and transmembrane (HT) domains of the 2 CARs of Hu1928-Hu20BB-original. These HT domains shared regions of identical nucleic acid sequence. Less commonly, recombination events occurred between segments of identical sequence shared by the heavy-chain domains and the light-chain domains of the two CARs in the construct. The attached table summarizes deletions consistent with recombination in Hu1928-Hu20BB-original RNA from transduced T cells of one patient. Similar results were obtained in T cells of 3 other patients. We confirmed deletions consistent with recombination in CAR RNA transcripts by short-read RNA sequencing (Illumina). Digital droplet PCR analysis of DNA from transduced T cells showed that recombination events between the HT domains of Hu1928-Hu20BB-original were present in DNA of transduced T cells. We modified the DNA sequence of Hu1928-Hu20BB-original to reduce repeated segments of identical DNA sequence to form a new CAR designated Hu1928-Hu20BB-standard. When T cells transduced with Hu1928-Hu20BB-standard were studied by SMRT RNAseq, deletions of RNA sequence consistent with recombination were substantially reduced (Table). We modified Hu1928-Hu20BB-standard by lengthening the linker in the anti-CD20 scFv to form a construct designated Hu1928-Hu20BB-long. We compared Hu1928-Hu20BB-standard to Hu1928-Hu20BB-long in vitro, and both specifically recognized CD19 and CD20 in assays of degranulation, cytokine release, and proliferation. In vitro assays showed higher interleukin-2 release by T cells transduced with Hu1928-Hu20BB-long versus Hu1928-Hu20BB-standard in response to 3 different CD20+ target cells (P value range 0.001 to 0.036). We tested Hu1928-Hu20BB-long against tumors established in nod-scid common gamma-chain knockout (NSG) mice. Human T cells expressing Hu1928-Hu20BB-long eliminated tumors of the following tumor cell lines: st486 (CD19+, CD20+), st486-CD19-negative (CD20+, CD19 low to negative expression), and NALM6 (CD19+, CD20 low expression). One million Hu1928-Hu20BB-long T cells per mouse eradicated st486 tumors. These optimized anti-CD19/CD20 bicistronic CAR constructs are promising for clinical treatment of B-cell malignancies. Figure 1 Figure 1. Disclosures Lam: Kite, a Gilead Company: Patents & Royalties. Kochenderfer: Bristol Myers Squibb: Research Funding; Kite, a Gilead Company: Patents & Royalties: on anti-CD19 CARs, Research Funding.

Myositis caused by Trachipleistophora hominis in a person with HIV: the first case in Thailand

Background To date, the cases of extraintestinal microsporidiosis have been increasingly reported in both otherwise healthy and immunocompromised individuals. Among them, microsporidial myositis is very rare (2,3). To the best of our knowledge, this is the first report of microsporidial myositis caused by Trachipleistophora hominis in a patient with HIV in Thailand. Case presentation A Thai male with HIV presented with fever and muscle pain at both anterior thighs and left arm for 3 months. Muscle biopsy was performed, and pathology exhibited neutrophils infiltrates and focal aggregations of microsporidial spores. The 18S ribosomal RNA sequence revealed the species of this microsporidium as Trachipleistophora hominis (T. hominis), and albendazole of 800 mg/day was initiated. He gradually improved, and was discharged home 6 weeks after hospitalization. Conclusion to the best of our knowledge, this is the first report of microsporidial myositis caused by Trachipleistophora hominis in a person with HIV in Thailand.