Development of a compact bidirectional promoter-driven dual chimeric antigen receptor (CAR) construct targeting CD19 and CD20 in the Sleeping Beauty (SB) transposon system.

BACKGROUND: A bidirectional promoter-driven chimeric antigen receptor (CAR) cassette provides the simultaneous expression of two CARs, which significantly enhances dual antigen-targeted CAR T-cell therapy. METHODS: We developed a second-generation CAR directing CD19 and CD20 antigens, incorporating them in a head-to-head orientation from a bidirectional promoter using a single Sleeping Beauty transposon system. The efficacy of bidirectional promoter-driven dual CD19 and CD20 CAR T cells was determined in vitro against cell lines expressing either, or both, CD19 and CD20 antigens. In vivo antitumor activity was tested in Raji lymphoma-bearing immunodeficient NOD-scid IL2Rgammanull (NSG) mice. RESULTS: Of all tested promoters, the bidirectional EF-1α promoter optimally expressed transcripts from both sense (CD19-CAR) and antisense (GFP.CD20-CAR) directions. Superior cytotoxicity, cytokine production and antigen-specific activation were observed in vitro in the bidirectional EF-1α promoter-driven CD19/CD20 CAR T cells. In contrast, a unidirectional construct driven by the EF-1α promoter, but using self-cleaving peptide-linked CD19 and CD20 CARs, showed inferior expression and in vitro function. Treatment of mice bearing advanced Raji lymphomas with bidirectional EF-1α promoter-driven CD19/CD20 CAR T cells effectively controlled tumor growth and extended the survival of mice compared with group treated with single antigen targeted CAR T cells. CONCLUSION: The use of bidirectional promoters in a single vector offers advantages of size and robust CAR expression with the potential to expand use in other forms of gene therapies like CAR T cells.

Optimal Annotation of Local Activation Time in Ventricular Tachycardia Substrate Mapping.

BACKGROUND: Accurate annotation of electrogram local activation time (LAT) is critical to the functional assessment of ventricular tachycardia (VT) substrate. Contemporary methods of annotation include: 1) earliest bipolar electrogram (LATearliest); 2) peak bipolar electrogram (LATpeak); 3) latest bipolar electrogram (LATlatest); and 4) steepest unipolar -dV/dt (LAT-dV/dt). However, no direct comparison of these methods has been performed in a large dataset, and it is unclear which provides the optimal functional analysis of the VT substrate. OBJECTIVES: This study sought to investigate the optimal method of LAT annotation during VT substrate mapping. METHODS: Patients with high-density VT substrate maps and a defined critical site for VT re-entry were included. All electrograms were annotated using 5 different methods: LATearliest, LATpeak, LATlatest, LAT-dV/dt, and the novel steepest unipolar -dV/dt using a dynamic window of interest (LATDWOI). Electrograms were also tagged as either late potentials and/or fractionated signals. Maps, utilizing each annotation method, were then compared in their ability to identify critical sites using deceleration zones. RESULTS: Fifty cases were identified with 1,.813 ± 811 points per map. Using LATlatest, a deceleration zone was present at the critical site in 100% of cases. There was no significant difference with LATearliest (100%) or LATpeak (100%). However, this number decreased to 54% using LAT-dV/dt and 76% for LATDWOI. Using LAT-dV/dt, only 33% of late potentials were correctly annotated, with the larger far field signals often annotated preferentially. CONCLUSIONS: Annotation with LAT-dV/dt and LATDWOI are suboptimal in VT substrate mapping. We propose that LATlatest should be the gold standard annotation method, as this allows identification of critical sites and is most suited to automation.

The impact of non-synonymous mutations on miRNA binding sites within the SARS-CoV-2 NSP3 and NSP4 genes.

Non-synonymous mutations in the SARS-CoV-2 spike region affect cell entry, tropism, and immune evasion, while frequent synonymous mutations may modify viral fitness. Host microRNAs, a type of non-coding RNA, play a crucial role in the viral life cycle, influencing viral replication and the host immune response directly or indirectly. Recently, we identified ten miRNAs with a high complementary capacity to target various regions of the SARS-CoV-2 genome. We filtered our candidate miRNAs to those only expressed with documented expression in SARS-CoV-2 target cells, with an additional focus on miRNAs that have been reported in other viral infections. We determined if mutations in the first SARS-CoV-2 variants of concern affected these miRNA binding sites. Out of ten miRNA binding sites, five were negatively impacted by mutations, with three recurrent synonymous mutations present in multiple SARS-CoV-2 lineages with high-frequency NSP3: C3037U and NSP4: G9802U/C9803U. These mutations were predicted to negatively affect the binding ability of miR-197-5p and miR-18b-5p, respectively. In these preliminary findings, using a dual-reporter assay system, we confirmed the ability of these miRNAs in binding to the predicted NSP3 and NSP4 regions and the loss/reduced miRNA bindings due to the recurrent mutations.

Sleeping Beauty kit sets provide rapid and accessible generation of artificial antigen-presenting cells for natural killer cell expansion.

Artificial antigen-presenting cells (aAPCs) offer a cost effective and convenient tool for the expansion of chimeric antigen receptor (CAR)-bearing T cells and NK cells. aAPCs are particularly useful because of their ability to efficiently expand low-frequency antigen-reactive lymphocytes in bulk cultures. Commonly derived from the leukemic cell line K562, these aAPCs lack most major histocompatibility complex expression and are therefore useful for NK cell expansion without triggering allogeneic T-cell proliferation. To combat difficulties in accessing existing aAPC lines, while circumventing the iterative lentiviral gene transfers with antibody-mediated sorting required for the isolation of stable aAPC clones, we developed a single-step technique using Sleeping Beauty (SB)-based vectors with antibiotic selection options. Our SB vectors contain options of two to three genes encoding costimulatory molecules, membrane-bound cytokines as well as the presence of antibiotic-resistance genes that allow for stable transposition-based transfection of feeder cells. Transfection of K562 with SB vectors described in this study allows for the surface expression of CD86, 4-1BBL, membrane-bound (mb) interleukin (IL)-15 and mbIL-21 after simultaneous transposition and antibiotic selection using only two antibiotics. aAPCs successfully expanded NK cells to high purity (80-95%). Expanded NK cells could be further engineered by lentiviral CAR transduction. The multivector kit set is publicly available and will allow convenient and reproducible in-house production of effective aAPCs for the in vitro expansion of primary cells.

COVID-19 monitoring with sparse sampling of sewered and non-sewered wastewater in urban and rural communities.

Equitable SARS-CoV-2 surveillance in low-resource communities lacking centralized sewers is critical as wastewater-based epidemiology (WBE) progresses. However, large-scale studies on SARS-CoV-2 detection in wastewater from low-and middle-income countries is limited because of economic and technical reasons. In this study, wastewater samples were collected twice a month from 186 urban and rural subdistricts in nine provinces of Thailand mostly having decentralized and non-sewered sanitation infrastructure and analyzed for SARS-CoV-2 RNA variants using allele-specific RT-qPCR. Wastewater SARS-CoV-2 RNA concentration was used to estimate the real-time incidence and time-varying effective reproduction number (Re). Results showed an increase in SARS-CoV-2 RNA concentrations in wastewater from urban and rural areas 14-20 days earlier than infected individuals were officially reported. It also showed that community/food markets were "hot spots" for infected people. This approach offers an opportunity for early detection of transmission surges, allowing preparedness and potentially mitigating significant outbreaks at both spatial and temporal scales.

Directed Graph Mapping for Ventricular Tachycardia: A Comparison to Established Mapping Techniques.

BACKGROUND: Understanding underlying mechanism(s) and identifying critical circuit components are fundamental to successful ventricular tachycardia (VT) ablation. Directed graph mapping (DGM) offers a novel technique to identify the mechanism and critical components of a VT circuit. OBJECTIVES: This study sought to evaluate the accuracy of DGM in VT ablation compared with traditional mapping techniques and a commercially available automated conduction velocity mapping (ACVM) tool. METHODS: Patients with structural heart disease who had undergone a VT ablation with entrainment-proven critical isthmus and a high-density electroanatomical activation map were included. Traditional mapping (TM) consisted of a combination of local activation time and entrainment mapping and was considered the gold standard for determining the VT mechanism, circuit, and isthmus location. The same local activation time values were then processed using DGM and a commercially available ACVM (Coherent Mapping, Biosense Webster) tool. The aim of this study was to compare TM vs DGM and ACVM in their ability to identify the VT mechanism, characterize the VT circuit, and locate the critical isthmus. RESULTS: Thirty-five cases were identified. TM classified the VT mechanism as focal in 7 patients and re-entrant in 28 patients. TM classified 11 VTs as single-loop re-entry, 15 as dual-loop re-entry, 1 as complex, and 1 case was indeterminant. The overall agreement between DGM and TM for determining VT mechanism and circuit type was strong (kappa value = 0.79; P < 0.01), as was the agreement between ACVM and TM (kappa value = 0.66; P < 0.01). Both DGM and ACVM identified the putative VT isthmus in 25 (89%) of the re-entrant cases. Focal activation was correctly identified by both techniques in all cases. CONCLUSIONS: DGM is a rapid automated algorithm that has a strong level of agreement with TM for manually re-annotated VT maps.

Retrospective Window of Interest Annotation Provides New Insights Into Functional Channels in Ventricular Tachycardia Substrate.

BACKGROUND: Accurate annotation of local activation time is crucial in the functional assessment of ventricular tachycardia (VT) substrate. A major limitation of modern mapping systems is the standard prospective window of interest (sWOI) is limited to 490 to 500 milliseconds, preventing annotation of very late potentials (LPs). A novel retrospective window of interest (rWOI), which allows annotation of all diastolic potentials, was used to assess the functional VT substrate. OBJECTIVES: This study sought to investigate the utility of a novel rWOI, which allows accurate visualization and annotation of all LPs during VT substrate mapping. METHODS: Patients with high-density VT substrate maps and a defined isthmus were included. All electrograms were manually annotated to latest activation using a novel rWOI. Reannotated substrate maps were correlated to critical sites, with areas of late activation examined. Propagation patterns were examined to assess the functional aspects of the VT substrate. RESULTS: Forty-eight cases were identified with 1,820 ± 826 points per map. Using the novel rWOI, 31 maps (65%) demonstrated LPs beyond the sWOI limit. Two distinct patterns of channel activation were seen during substrate mapping: 1) functional block with unidirectional conduction into the channel (76%); and 2) wave front collision within the channel (24%). In addition, a novel marker termed the zone of early and late crowding was studied in the rWOI substrate maps and found to have a higher positive predictive value (85%) than traditional deceleration zones (69%) for detecting critical sites of re-entry. CONCLUSIONS: The standard WOI of contemporary mapping systems is arbitrarily limited and results in important very late potentials being excluded from annotation. Future versions of electroanatomical mapping systems should provide longer WOIs for accurate local activation time annotation.

Multiple traces of monkeypox detected in non-sewered wastewater with sparse sampling from a densely populated metropolitan area in Asia.

The monkeypox virus is excreted in the feces of infected individuals. Therefore, there is an interest in using viral load detection in wastewater for sentinel early surveillance at a community level and as a complementary approach to syndromic surveillance. We collected wastewater from 63 sewered and non-sewered locations in Bangkok city center between May and August 2022. Monkeypox viral DNA copy numbers were quantified using real-time polymerase chain reaction (PCR) and confirmed positive by Sanger sequencing. Monkeypox viral DNA was first detected in wastewater from the second week of June 2022, with a mean copy number of 16.4 copies/ml (n = 3). From the first week of July, the number of viral DNA copies increased to a mean copy number of 45.92 copies/ml. Positive samples were Sanger sequenced and confirmed the presence of the monkeypox virus. Our study is the first to detect monkeypox viral DNA in wastewater from various locations within Thailand. Results suggest that this could be a complementary source for detecting viral DNA and predicting upcoming outbreaks.

Noise-Reduction and Sensitivity-Enhancement of a Sleeping Beauty-Based Tet-On System.

Tetracycline-inducible systems are widely used control elements for mammalian gene expression. Despite multiple iterations to improve inducibility, their use is still compromised by basal promoter activity in the absence of tetracyclines. In a mammalian system, we previously showed that the introduction of the G72V mutation in the rtTA-M2 tetracycline activator lowers the basal level expression and increases the fold-induction of multiple genetic elements in a long chimeric antigen receptor construct. In this study, we confirmed that the G72V mutation was effective in minimising background expression in the absence of an inducer, resulting in an increase in fold-expression. Loss of responsiveness due to the G72V mutation was compensated through the incorporation of four sensitivity enhancing (SE) mutations, without compromising promoter tightness. However, SE mutations alone (without G72V) led to undesirable leakiness. Although cryptic splice site removal from rtTA did not alter the inducible control of the luciferase reporter gene in this simplified vector system, this is still recommended as a precaution in more complex multi-gene elements that contain rtTA. The optimized expression construct containing G72V and SE mutations currently provides the best improvement of fold-induction mediated by the rtTA-M2 activator in a mammalian system.

Anti-Apoptotic c-FLIP Reduces the Anti-Tumour Activity of Chimeric Antigen Receptor T Cells.

CAR T cell treatment of solid tumours is limited by poor persistence partly due to CD95 ligand (CD95L)-induced apoptosis. Both T cells and cells within the tumour microenvironment (TME) may express CD95L, triggering apoptosis in CD95-receptor-positive CAR T cells. Tonic signalling of CAR T cells may also increase CD95-dependent AICD. Because the intracellular protein c-FLIP protects T cells from AICD, we expressed c-FLIPp43 within a Her-2 targeted CAR cassette and evaluated the potential of c-FLIPp43 through in vitro functional assays and in vivo tumour-bearing xenograft model. cFLIP expression protected against CD95L-induced cell death in the Jurkat T cell lines. However, in primary human CAR T cells containing CAR-CD28 domains, c-FLIPp43 overexpression had minimal additional impact on resistance to CD95L-induded cell death. In vitro cytotoxicity against a breast cancer tumour cell line was not altered by c-FLIPp43 expression, but the expression of c-FLIPp43 in Her2-CAR T cells lowered interferon-γ secretion, without markedly affecting IL-2 levels, and c-FLIPp43-Her2-CAR T cells showed reduced anti-tumour activity in immunodeficient mice with breast cancer. The findings of this study provide a new understanding of the effects of controlling extrinsic apoptosis pathway suppression in CAR T cells, suggesting that c-FLIPp43 expression reduces anti-tumour immunity through the modulation of effector T cell pathways.

MicroRNA-mediated metabolic reprogramming of chimeric antigen receptor T cells.

Advances made in chimeric antigen receptor (CAR) T cell therapy have revolutionized the treatment and management of certain cancers. Currently, B cell malignancies have been among the few cancers to which CAR T cells have shown persistent and resilient anti-tumor responses. A growing body of evidence suggests that the persistence of CAR T cells within patients following infusion is linked to the mitochondrial fitness of the CAR T cell, which could affect clinical outcomes. Analysis of CAR T cells from patients undergoing successful treatment has shown an increase in mitochondrial mass and fusion events, and a reduction in aerobic metabolism, highlighting the importance of mitochondria in CAR T cell function. Consequently, there has been recent interest and investment in approaches that focus on mitochondrial programming. In this regard, miRNAs are promising agents in mitochondrial reprogramming for several reasons: (1) natural and artificial miRNAs are non-immunogenic, (2) one miRNA can simultaneously modulate the expression of multiple genes within a pathway, (3) the small size of a sequence required for producing mature miRNA is ideal for use in viral vectors and (4) different precursor miRNAs (pre-miRNAs) hairpins can be incorporated into a polycistronic miRNA cluster to create a miRNA cocktail. In this perspective, we describe the latest genetic engineering strategies that can be used to achieve the optimal expression of candidate miRNAs alongside a CAR construct. In addition, we include an in silico analysis of rational candidate miRNAs that could promote the mitochondrial fitness of CAR T cells.

Functional Assessment of Ventricular Tachycardia Circuits and Their Underlying Substrate Using Automated Conduction Velocity Mapping.

OBJECTIVES: This study sought to describe the utility of automated conduction velocity mapping (ACVM) in ventricular tachycardia (VT) ablation. BACKGROUND: Identification of areas of slowed conduction velocity (CV) is critical to our understanding of VT circuits and their underlying substrate. Recently, an ACVM called Coherent Mapping (Biosense Webster Inc) has been developed for atrial mapping. However, its utility in VT mapping has not been described. METHODS: Patients with paired high-density VT activation and substrate maps were included. ACVM was applied to paired VT activation and substrate maps to assess regional CV and activation patterns. A combination of ACVM, traditional local activation time maps, electrogram analysis, and off-line calculated CV using triangulation were used to characterize zones of slowed conduction during VT and in substrate mapping. RESULTS: Fifteen patients were included in the study. In all cases, ACVM identified slow CV within the putative VT isthmus, which colocalized to the VT isthmus identified with entrainment. The dimensions of the VT isthmus with local activation time mapping were 37.8 ± 13.7 mm long and 8.7 ± 4.2 mm wide. In comparison, ACVM produced an isthmus that was shorter (length: 25.1 ± 10.6 mm; mean difference: 12.8; 95% CI: 7.5-18.0; P < 0.01) and wider (width: 18.8 ± 8.1 mm; mean difference: 10.1; 95% CI: 6.1-14.2; P < 0.01). In VT, the CV using triangulation at the entrance (8.0 ± 3.6 cm/s) and midisthmus (8.1 ± 4.3 cm/s) was not significantly different (P = 0.92) but was significantly faster at the exit (16.2 ± 9.7 cm/s; P < 0.01). In the paired substrate analysis, traditional local activation time isochronal mapping identified 6.3 ± 2.0 deceleration zones. In contrast, ACVM identified a median of 0 deceleration zones (IQR: 0-1; P < 0.01). CONCLUSIONS: ACVM is a novel complementary tool that can be used to accurately resolve complex VT circuits and identify slow conduction zones in VT but has limited accuracy in identifying slowed conduction during substrate-based mapping.

Controlling Cell Trafficking: Addressing Failures in CAR T and NK Cell Therapy of Solid Tumours.

The precision guiding of endogenous or adoptively transferred lymphocytes to the solid tumour mass is obligatory for optimal anti-tumour effects and will improve patient safety. The recognition and elimination of the tumour is best achieved when anti-tumour lymphocytes are proximal to the malignant cells. For example, the regional secretion of soluble factors, cytotoxic granules, and cell-surface molecule interactions are required for the death of tumour cells and the suppression of neovasculature formation, tumour-associated suppressor, or stromal cells. The resistance of individual tumour cell clones to cellular therapy and the hostile environment of the solid tumours is a major challenge to adoptive cell therapy. We review the strategies that could be useful to overcoming insufficient immune cell migration to the tumour cell mass. We argue that existing 'competitive' approaches should now be revisited as complementary approaches to improve CAR T and NK cell therapy.

Metabolic and Mitochondrial Functioning in Chimeric Antigen Receptor (CAR)-T Cells.

Chimeric antigen receptor (CAR) T-cell therapy has revolutionized adoptive cell therapy with impressive therapeutic outcomes of >80% complete remission (CR) rates in some haematological malignancies. Despite this, CAR T cell therapy for the treatment of solid tumours has invariably been unsuccessful in the clinic. Immunosuppressive factors and metabolic stresses in the tumour microenvironment (TME) result in the dysfunction and exhaustion of CAR T cells. A growing body of evidence demonstrates the importance of the mitochondrial and metabolic state of CAR T cells prior to infusion into patients. The different T cell subtypes utilise distinct metabolic pathways to fulfil their energy demands associated with their function. The reprogramming of CAR T cell metabolism is a viable approach to manufacture CAR T cells with superior antitumour functions and increased longevity, whilst also facilitating their adaptation to the nutrient restricted TME. This review discusses the mitochondrial and metabolic state of T cells, and describes the potential of the latest metabolic interventions to maximise CAR T cell efficacy for solid tumours.

Compact Bidirectional Promoters for Dual-Gene Expression in a Sleeping Beauty Transposon.

Promoter choice is an essential consideration for transgene expression in gene therapy. The expression of multiple genes requires ribosomal entry or skip sites, or the use of multiple promoters. Promoter systems comprised of two separate, divergent promoters may significantly increase the size of genetic cassettes intended for use in gene therapy. However, an alternative approach is to use a single, compact, bidirectional promoter. We identified strong and stable bidirectional activity of the RPBSA synthetic promoter comprised of a fragment of the human Rpl13a promoter, together with additional intron/exon structures. The Rpl13a-based promoter drove long-term bidirectional activity of fluorescent proteins. Similar results were obtained for the EF1-α and LMP2/TAP1 promoters. However, in a lentiviral vector, the divergent bidirectional systems failed to produce sufficient titres to translate into an expression system for dual chimeric antigen receptor (CAR) expression. Although bidirectional promoters show excellent applicability to drive short RNA in Sleeping Beauty transposon systems, their possible use in the lentiviral applications requiring longer and more complex RNA, such as dual-CAR cassettes, is limited.

Optimisation of Tet-On inducible systems for Sleeping Beauty-based chimeric antigen receptor (CAR) applications.

Regulated expression of genetic elements that either encode polypeptides or various types of functional RNA is a fundamental goal for gene therapy. Inducible expression may be preferred over constitutive promoters to allow clinician-based control of gene expression. Existing Tet-On systems represent one of the tightest rheostats for control of gene expression in mammals. However, basal expression in absence of tetracycline compromises the widespread application of Tet-controlled systems in gene therapy. We demonstrate that the order of P2A-linked genes of interest was critical for maximal response and tightness of a chimeric antigen receptor (CAR)-based construct. The introduction of G72V mutation in the activation region of the TetR component of the rtTA further improved the fold response. Although the G72V mutation resulted in a removal of a cryptic splice site within rtTA, additional removal of this splice site led to only a modest improvement in the fold-response. Selective removal of key promoter elements (namely the BRE, TATA box, DPE and the four predicted Inr) confirmed the suitability of the minimal CMV promoter and its downstream sequences for supporting inducible expression. The results demonstrate marked improvement of the rtTA based Tet-On system in Sleeping Beauty for applications such as CAR T cell therapy.

Regulation of human Mcl-1 by a divergently-expressed antisense transcript.

Mcl-1 is a member of the Bcl-2 anti-apoptotic protein family with important roles in the development, lifespan and metabolism of lymphocytes, as well as oncogenesis. Mcl-1 displays the shortest half-life of all Bcl-2 family members, with miRNA interference and proteasomal degradation being major pathways for Mcl-1 downregulation. In this study, we have identified a previously undescribed control mechanism active at the RNA level. A divergently transcribed lncRNA LOC107985203 (named here mcl1-AS1) negatively modulated Mcl-1 expression resulting in downregulation of Mcl-1 at both mRNA and protein level in a time-dependent manner. Using reporter assays, we confirmed that the mcl1-AS1 lncRNA promoter was located within Mcl-1 coding region. We next placed mcl1-AS1 under tetracycline-inducible control and demonstrated decreased viability in HEK293 cells upon doxycycline induction. Inhibition of mcl1-AS1 with shRNA reversed drug sensitivity. Bioinformatics surveys predicted direct mcl1-AS1 lncRNA binding to Mcl-1 transcripts, suggesting its mechanism in Mcl-1 expression is at the transcriptional level, consistent with a common role for anti-sense transcripts. The identification of a bi-directional promoter and lncRNA controlling Mcl-1 expression will have implications for controlling Mcl-1 activity in cancer cells, or for the purpose of enhancing the lifespan and quality of anti-cancer T lymphocytes.

Promoter choice: Who should drive the CAR in T cells?

Chimeric antigen receptor (CAR) T cell therapy is an effective treatment for B cell malignancies, with emerging potential for the treatment of other hematologic cancers and solid tumors. The strength of the promoter within the CAR cassette will alter CAR-polypeptide levels on the cell surface of the T cell-impacting on the kinetics of activation, survival and memory cell formation in T cells. In addition to the CAR, promoters can be used to drive other genes of interest to enhance CAR T cell function. Expressing multiple genes from a single RNA transcript can be effectively achieved by linking the genes via a ribosomal skip site. However, promoters may differ in their ability to transcribe longer RNAs, or could interfere with lentiviral production, or transduction frequencies. In this study we compared the ability of the strong well-characterized promoters CMV, EF-1, hPGK and RPBSA to drive functional expression of a single RNA encoding three products: GFP, CAR, plus an additional cell-survival gene, Mcl-1. Although the four promoters produced similarly high lentiviral titres, EF-1 gave the best transduction efficacy of primary T cells. Major differences were found in the ability of the promoters to drive expression of long RNA encoding GFP, CAR and Mcl-1, highlighting promoter choice as an important consideration for gene therapy applications requiring the expression of long and complex mRNA.

Implications of SARS-CoV-2 Mutations for Genomic RNA Structure and Host microRNA Targeting.

The SARS-CoV-2 virus is a recently-emerged zoonotic pathogen already well adapted to transmission and replication in humans. Although the mutation rate is limited, recently introduced mutations in SARS-CoV-2 have the potential to alter viral fitness. In addition to amino acid changes, mutations could affect RNA secondary structure critical to viral life cycle, or interfere with sequences targeted by host miRNAs. We have analysed subsets of genomes from SARS-CoV-2 isolates from around the globe and show that several mutations introduce changes in Watson-Crick pairing, with resultant changes in predicted secondary structure. Filtering to targets matching miRNAs expressed in SARS-CoV-2-permissive host cells, we identified ten separate target sequences in the SARS-CoV-2 genome; three of these targets have been lost through conserved mutations. A genomic site targeted by the highly abundant miR-197-5p, overexpressed in patients with cardiovascular disease, is lost by a conserved mutation. Our results are compatible with a model that SARS-CoV-2 replication within the human host is constrained by host miRNA defences. The impact of these and further mutations on secondary structures, miRNA targets or potential splice sites offers a new context in which to view future SARS-CoV-2 evolution, and a potential platform for engineering conditional attenuation to vaccine development, as well as providing a better understanding of viral tropism and pathogenesis.

Selecting costimulatory domains for chimeric antigen receptors: functional and clinical considerations.

Costimulatory signals are required to achieve robust chimeric antigen receptor (CAR) T cell expansion, function, persistence and antitumor activity. These can be provided by incorporating intracellular signalling domains from one or more T cell costimulatory molecules, such as CD28 or 4-1BB, into the CAR. The selection and positioning of costimulatory domains within a CAR construct influence CAR T cell function and fate, and clinical experience of autologous anti-CD19 CAR T cell therapies suggests that costimulatory domains have differential impacts on CAR T cell kinetics, cytotoxic function and potentially safety profile. The clinical impacts of combining costimulatory domains and of alternative costimulatory domains are not yet clearly established, and may be construct- and disease-specific. The aim of this review is to summarise the function and effect of established and emerging costimulatory domains and their combinations within CAR T cells.