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CRISPR effector proteins introduce double-stranded breaks into the mammalian genome, facilitating gene editing by non-homologous end-joining or homology-directed repair. Unlike the more commonly studied Cas9, the CRISPR effector protein Cas12a/Cpf1 recognizes a T-rich protospacer adjacent motif (PAM) and can process its own CRISPR RNA (crRNA) array, simplifying the use of multiple guide RNAs. We observed that the Cas12a ortholog of Lachnospiraceae bacterium MA2020 (Lb2Cas12a) edited mammalian genes with efficiencies comparable to those of AsCas12a and LbCas12a. Compared to these well-characterized Cas12a orthologs, Lb2Cas12a is smaller and recognizes a narrow set of PAM TTTV. We introduced two mutations into Lb2Cas12a, Q571K and C1003Y, that increased its cleavage efficiency for a range of target sequences beyond those of the commonly used Cas12a orthologs AsCas12a and LbCas12a. In addition to the canonical TTTV PAM, this variant, Lb2-KY, also efficiently cleaved target regions with CTTN PAMs. Finally, we demonstrated that Lb2-KY ribonucleoprotein (RNP) complexes edited two hemoglobin target regions useful for correcting common forms of sickle-cell anemia more efficiently than commercial AsCas12a RNP complexes. Thus, Lb2-KY has distinctive properties useful for modifying a range of clinically relevant targets in the human genome., Graphical Abstract, CRISPR-Cas12a effector proteins edit mammalian genomes using a T-rich PAM with few off-targets. Tran et al. engineered a Cas12a nuclease from Lachnospiraceae bacterium MA2020. They demonstrated that this variant recognized a broadened PAM and edited mammalian genomes with higher efficiencies than commonly used orthologs, expanding Cas12a utility in genome engineering.

B cells have been engineered ex vivo to express an HIV-1 broadly neutralizing antibody (bNAb). B-cell reprograming may be scientifically and therapeutically useful, but current approaches limit B-cell repertoire diversity and disrupt the organization of the heavy-chain locus. A more diverse and physiologic B-cell repertoire targeting a key HIV-1 epitope could facilitate evaluation of vaccines designed to elicit bNAbs, help identify more potent and bioavailable bNAb variants, or directly enhance viral control in vivo. Here we address the challenges of generating such a repertoire by replacing the heavy-chain CDR3 (HCDR3) regions of primary human B cells. To do so, we identified and utilized an uncharacterized Cas12a ortholog that recognizes PAM motifs present in human JH genes. We also optimized the design of 200 nucleotide homology-directed repair templates (HDRT) by minimizing the required 3’-5’ deletion of the HDRT-complementary strand. Using these techniques, we edited primary human B cells to express a hemagglutinin epitope tag and the HCDR3 regions of the bNAbs PG9 and PG16. Those edited with bNAb HCDR3 efficiently bound trimeric HIV-1 antigens, implying they could affinity mature in vivo in response to the same antigens. This approach generates diverse B-cell repertoires recognizing a key HIV-1 neutralizing epitope.

Widespread use of gene therapy technologies is limited in part by the lack of small genetic switches with wide dynamic ranges that control transgene expression without the requirement of additional protein components1-5. In this study, we engineered a class of type III hammerhead ribozymes to develop RNA switches that are highly efficient at cis-cleaving mammalian mRNAs and showed that they can be tightly regulated by a steric-blocking antisense oligonucleotide. Our variant ribozymes enabled in vivo regulation of adeno-associated virus (AAV)-delivered transgenes, allowing dose-dependent and up to 223-fold regulation of protein expression over at least 43 weeks. To test the potential of these reversible on-switches in gene therapy for anemia of chronic kidney disease6, we demonstrated regulated expression of physiological levels of erythropoietin with a well-tolerated dose of the inducer oligonucleotide. These small, modular and efficient RNA switches may improve the safety and efficacy of gene therapies and broaden their use.

B cells have been engineered ex vivo to express an HIV-1 broadly neutralizing antibody (bNAb). B-cell reprograming may be scientifically and therapeutically useful, but current approaches limit B-cell repertoire diversity and disrupt the organization of the heavy-chain locus. A more diverse and physiologic B-cell repertoire targeting a key HIV-1 epitope could facilitate evaluation of vaccines designed to elicit bNAbs, help identity more potent and bioavailable bNAb variants, or directly enhance viral control in vivo. Here we address the challenges of generating such a repertoire by replacing the heavy-chain CDR3 (HCDR3) regions of primary human B cells. To do so, we identified and utilized an uncharacterized Cas12a ortholog that recognizes PAM motifs present in human JH genes. We also optimized the design of 200 nucleotide homology-directed repair templates (HDRT) by minimizing the required 3’-5’ deletion of the HDRT-complementary strand. Using these techniques, we edited primary human B cells to express a hemagglutinin epitope tag and the HCDR3 regions of the bNAbs PG9 and CH01. Those edited with bNAb HCDR3 efficiently bound trimeric HIV-1 antigens, implying they could affinity mature in vivo in response to the same antigens. This approach generates diverse B-cell repertoires recognizing a key HIV-1 neutralizing epitope.

Background: Given the scale of the ongoing COVID-19 pandemic, the development of vaccines based on different platforms is essential, particularly in light of emerging viral variants, the absence of information on vaccine-induced immune durability, and potential paediatric use. We aimed to assess the safety and immunogenicity of an MF59-adjuvanted subunit vaccine for COVID-19 based on recombinant SARS-CoV-2 spike glycoprotein stabilised in a pre-fusion conformation by a novel molecular clamp (spike glycoprotein-clamp [sclamp]). Methods: We did a phase 1, double-blind, placebo-controlled, block-randomised trial of the sclamp subunit vaccine in a single clinical trial site in Brisbane, QLD, Australia. Healthy adults (aged ≥18 to ≤55 years) who had tested negative for SARS-CoV-2, reported no close contact with anyone with active or previous SARS-CoV-2 infection, and tested negative for pre-existing SARS-CoV-2 immunity were included. Participants were randomly assigned to one of five treatment groups and received two doses via intramuscular injection 28 days apart of either placebo, sclamp vaccine at 5 μg, 15 μg, or 45 μg, or one dose of sclamp vaccine at 45 μg followed by placebo. Participants and study personnel, except the dose administration personnel, were masked to treatment. The primary safety endpoints included solicited local and systemic adverse events in the 7 days after each dose and unsolicited adverse events up to 12 months after dosing. Here, data are reported up until day 57. Primary immunogenicity endpoints were antigen-specific IgG ELISA and SARS-CoV-2 microneutralisation assays assessed at 28 days after each dose. The study is ongoing and registered with ClinicalTrials.gov, NCT04495933. Findings: Between June 23, 2020, and Aug 17, 2020, of 314 healthy volunteers screened, 120 were randomly assigned (n=24 per group), and 114 (95%) completed the study up to day 57 (mean age 32·5 years [SD 10·4], 65 [54%] male, 55 [46%] female). Severe solicited reactions were infrequent and occurred at similar rates in participants receiving placebo (two [8%] of 24) and the SARS-CoV-2 sclamp vaccine at any dose (three [3%] of 96). Both solicited reactions and unsolicited adverse events occurred at a similar frequency in participants receiving placebo and the SARS-CoV-2 sclamp vaccine. Solicited reactions occurred in 19 (79%) of 24 participants receiving placebo and 86 (90%) of 96 receiving the SARS-CoV-2 sclamp vaccine at any dose. Unsolicited adverse events occurred in seven (29%) of 24 participants receiving placebo and 35 (36%) of 96 participants receiving the SARS-CoV-2 sclamp vaccine at any dose. Vaccination with SARS-CoV-2 sclamp elicited a similar antigen-specific response irrespective of dose: 4 weeks after the initial dose (day 29) with 5 μg dose (geometric mean titre [GMT] 6400, 95% CI 3683–11 122), with 15 μg dose (7492, 4959–11 319), and the two 45 μg dose cohorts (8770, 5526–13 920 in the two-dose 45 μg cohort; 8793, 5570–13 881 in the single-dose 45 μg cohort); 4 weeks after the second dose (day 57) with two 5 μg doses (102 400, 64 857–161 676), with two 15 μg doses (74 725, 51 300–108 847), with two 45 μg doses (79 586, 55 430–114 268), only a single 45 μg dose (4795, 2858–8043). At day 57, 67 (99%) of 68 participants who received two doses of sclamp vaccine at any concentration produced a neutralising immune response, compared with six (25%) of 24 who received a single 45 μg dose and none of 22 who received placebo. Participants receiving two doses of sclamp vaccine elicited similar neutralisation titres, irrespective of dose: two 5 μg doses (GMT 228, 95% CI 146–356), two 15 μg doses (230, 170–312), and two 45 μg doses (239, 187–307). Interpretation: This first-in-human trial shows that a subunit vaccine comprising mammalian cell culture-derived, MF59-adjuvanted, molecular clamp-stabilised recombinant spike protein elicits strong immune responses with a promising safety profile. However, the glycoprotein 41 peptide present in the clamp created HIV diagnostic assay interference, a possible barrier to widespread use highlighting the criticality of potential non-spike directed immunogenicity during vaccine development. Studies are ongoing with alternative molecular clamp trimerisation domains to ameliorate this response. Funding: Coalition for Epidemic Preparedness Innovations, National Health and Medical Research Council, Queensland Government, and further philanthropic sources listed in the acknowledgments.

Background: We assessed the safety and immunogenicity of an MF59-adjuvanted subunit vaccine for COVID-19 based on recombinant SARS-CoV-2 spike glycoprotein stabilised in a prefusion conformation by a novel molecular clamp (Sclamp). Methods: Phase 1, double-blind, placebo-controlled trial conducted in Australia (July 2020–ongoing; ClinicalTrials.gov NCT04495933). Healthy adults (18-55 years) received two doses of placebo, 5-μg, 15-μg, or 45-μg SARS-CoV-2 Sclamp, or one 45-μg dose of SARS-CoV-2 Sclamp followed by placebo, 28 days apart (n=120; 24 per group). Safety, humoral immunogenicity (ELISA, microneutralisation, pseudovirus neutralisation), and cellular immunogenicity (antigen-specific CD4+/CD8+ T-cells, antibody-secreting cells) were assessed up to 56 days after the first dose. Findings: The SARS-CoV-2 Sclamp vaccine was very well tolerated with few systemic reactions. All two-dose regimens elicited robust, broadly neutralising humoral responses. Geometric mean titres were higher than in sera from convalescent COVID-19 patients and strongly neutralised spike variants of concern, including N501Y. Moreover, humoral and cellular responses were highly correlated. However, antibodies elicited to a peptide sequence used in the molecular clamp derived from human immunodeficiency virus-1 (HIV-1) gp41 cross-reacted weakly with some HIV diagnostic screening tests. Interpretation: These first-in-human results demonstrate that a subunit vaccine comprising mammalian cell culture-derived, molecular clamp-stabilised recombinant spike protein formulated in a squalene-in-oil adjuvant elicits strong immune responses with an excellent safety profile. However, the gp41 peptide induced diagnostic interference, creates a likely barrier to widespread use and highlights the criticality of potential off-target immunogenicity during vaccine development. Studies are ongoing with alternative molecular clamp trimerisation domains to ameliorate this response. Clinical Trial Registration: ClinicalTrials.gov (NCT04495933). Funding: Coalition for Epidemic Preparedness Innovations; National Health and Medical Research Council, Queensland Government, and philanthropic sources. Declaration of Interests: KJC and DW report grants from the Coalition for Epidemic Preparedness Innovations, the National Health and Medical Research Council of Australia, and the Queensland Government, during the conduct of the study; other from ViceBio Limited, outside the submitted work; and has patents pending (AU 2018241252; BR112019019813.0; CA 3057171; CH 201880022016.9; EP 18775234.0; IN 201917038666; ID P00201909145; IL 269534; JP 2019-553883; MX/a/2019/011599; NZ 757178; KR 0-2019-7031415; SG 11201908280S; US 16/498865). JB reports personal fees from CSL Limited, during the conduct of the study, and other from CSL Limited, outside the submitted work. WZ reports grants from the National Health and Medical Research Council of Australia, the Research Grants Council of the Hong Kong Special Administrative Region, China, and the Jack Ma Foundation, during the conduct of the study. SM-H reports grants from Canarian Foundation Doctor Manuel Morales, during the conduct of the study. KJS reports grants from the the Australian Medical Research Future Fund, during the conduct of the study. AWC reports grants from the Australian Medical Research Future Fund and a National Health and Medical Research Council of Australia Career Development Fellowship, during the conduct of the study. BDW reports grants from the National Health and Medical Research Council of Australia, the Australian Medical Research Future Fund, and the Victorian State Government, during the conduct of the study. PMH reports grants from the Australian Medical Research Future Fund, during the conduct of the study. DP reports grants from the National Health and Medical Research Council of Australia, the A2 Milk Foundation, and the Jack Ma Foundation, during the conduct of the study. CR reports grants from the Coalition for Epidemic Preparedness Innovations, during the conduct of the study. PRY reports grants from the Coalition for Epidemic Preparedness Innovations, the National Health and Medical Research Council of Australia, and the Queensland Government, during the conduct of the study; grants from ViceBio Limited, outside the submitted work; and a patent issued (US 2020/0040042). FLM, Zl, DKW, PE, JAL, STMC, NM, SA, CLH, KH, PG, LH, THON, MHT, PT, JB, PCR, SN, SC, TH, KK, KS, and TPM have nothing to disclose. Ethics Approval Statement: The protocol was approved by the Alfred Health Human Research Ethics Committee (2020001376/334/20).

Senescent endothelial cells (EC) have been identified in cardiovascular disease, in angiogenic tumour associated vessels and in aged individuals. We have previously identified a novel anti-inflammatory senescent phenotype of EC. We show here that caveolae are critical in the induction of this anti-inflammatory senescent state. Senescent EC induced by either the overexpression of ARHGAP18/SENEX or by H₂O₂ showed significantly increased numbers of caveolae and associated proteins Caveolin-1, cavin-1 and cavin-2. Depletion of these proteins by RNA interference decreased senescence induced by ARHGAP18 and by H₂O₂. ARHGAP18 overexpression induced a predominantly anti-inflammatory senescent population and depletion of the caveolae-associated proteins resulted in the preferential reduction in this senescent population as measured by neutrophil adhesion and adhesion protein expression after TNFα treatment. In confirmation, EC isolated from the aortas of CAV-1(-/-) mice failed to induce this anti-inflammatory senescent cell population upon expression of ARHGAP18, whereas EC from wild-type mice showed a significant increase. NF-κB is one of the major transcription factors mediating the induction of E-selectin and VCAM-1 expression, adhesion molecules responsible for leucocyte attachment to EC. TNFα-induced activation of NF-κB was suppressed in ARHGAP18-induced senescent EC, and this inhibition was reversed by Caveolin-1 knock-down. Thus, out results demonstrate that an increase in caveolae and its component proteins in senescent ECs is associated with inhibition of the NF-kB signalling pathway and promotion of the anti-inflammatory senescent pathway.

The aim of this study is to examine the prevalence of smoking during pregnancy by the individual mother's sociodemographic characteristics and ecological factors at the community level (suburbs). This analysis combined 1996 Australia Census and data on 3424 women attending Well-Baby-Clinics (WBC) between January 1996 and February 1998 within a region in South Western Sydney (SWS), Australia. The prevalence of maternal smoking was 31%. Maternal factors such as marital status, country of birth, education, occupation, socioeconomic status (SES), and types of antenatal care (ANC) were independent risk factors for maternal smoking. Small area analysis revealed suburbs within SWS with high rates of maternal smoking (47-57%). Community level characteristics such as low income, low educational level, young mothers, and unemployment can explain 85.7% of the variation in maternal smoking in SWS. Smoking during pregnancy is recognised as a serious risk factor to the unborn child. The present study draws attention to local community level factors, other than individual SES, which may be important when developing strategies for maternal smoking prevention programs.

Schistosomes express a family of integral membrane proteins, called tetraspanins (TSPs), in the outer surface membranes of the tegument. Two of these tetraspanins, Sm-TSP-1 and Sm-TSP-2, confer protection as vaccines in mice, and individuals who are naturally resistant to S. mansoni infection mount a strong IgG response to Sm-TSP-2. To determine their functions in the tegument of S. mansoni we used RNA interference to silence expression of Sm-tsp-1 and Sm-tsp-2 mRNAs. Soaking of parasites in Sm-tsp dsRNAs resulted in 61% (p = 0.009) and 74% (p = 0.009) reductions in Sm-tsp-1 and Sm-tsp-2 transcription levels, respectively, in adult worms, and 67%–75% (p = 0.011) and 69%–89% (p = 0.004) reductions in Sm-tsp-1 and Sm-tsp-2 transcription levels, respectively, in schistosomula compared to worms treated with irrelevant control (luciferase) dsRNA. Ultrastructural morphology of adult worms treated in vitro with Sm-tsp-2 dsRNA displayed a distinctly vacuolated and thinner tegument compared with controls. Schistosomula exposed in vitro to Sm-tsp-2 dsRNA had a significantly thinner and more vacuolated tegument, and morphology consistent with a failure of tegumentary invaginations to close. Injection of mice with schistosomula that had been electroporated with Sm-tsp-1 and Sm-tsp-2 dsRNAs resulted in 61% (p = 0.005) and 83% (p = 0.002) reductions in the numbers of parasites recovered from the mesenteries four weeks later when compared to dsRNA-treated controls. These results imply that tetraspanins play important structural roles impacting tegument development, maturation or stability., Author Summary Schistosomes, or blood flukes, reside in the blood vessels surrounding the liver and bowel of their human hosts. They infect 200 million people and kill many thousands each year in developing countries. The parasites cover themselves in a unique series of cell membranes called the tegument. Molecules in the tegument membranes are a major target for the development of new drugs and vaccines against the parasite. Here we show that at least one member of a family of tegument membrane proteins called tetraspanins, Sm-TSP-2, is integral to the proper formation of the tegument and subsequent survival of the parasite in its human host, providing a potential mechanism by which a vaccine based on Sm-TSP-2 protects immunized hosts.

Background Schistosomes cause more mortality and morbidity than any other human helminth, but control primarily relies on a single drug that kills adult worms. The newly transformed schistosomulum stage is susceptible to the immune response and is a target for vaccine development and rational drug design. Methodology/Principal Findings To identify genes which are up-regulated during the maturation of Schistosoma mansoni schistosomula in vitro, we cultured newly transformed parasites for 3 h or 5 days with and without erythrocytes and compared their transcriptional profiles using cDNA microarrays. The most apparent changes were in the up-regulation of genes between 3 h and 5 day schistosomula involved in blood feeding, tegument and cytoskeletal development, cell adhesion, and stress responses. The most highly up-regulated genes included a tegument tetraspanin Sm-tsp-3 (1,600-fold up-regulation), a protein kinase, a novel serine protease and serine protease inhibitor, and intestinal proteases belonging to distinct mechanistic classes. The inclusion of erythrocytes in the culture medium resulted in a general but less pronounced increase in transcriptional activity, with the highest up-regulation of genes involved in iron metabolism, proteolysis, and transport of fatty acids and sugars. Conclusions We have identified the genes that are up-regulated during the first 5 days of schistosomula development in vitro. Using a combination of gene silencing techniques and murine protection studies, some of these highly up-regulated transcripts can be targeted for future development of new vaccines and drugs., Author Summary Schistosome blood flukes cause more mortality and morbidity than any other human worm infection, but current control methods primarily rely on a single drug. There is a desperate need for new approaches to control this parasite, including vaccines. People become infected when the free-swimming larva, the cercaria, enters through the skin and becomes the schistosomulum. Schistosomula are susceptible to immune responses during their first few days in the host before they become adult parasites. We characterised the genes that these newly transformed parasites switch on when they enter the host to identify molecules that are critical for survival in the human host. Some of these highly up-regulated genes can be targeted for future development of new vaccines and drugs.

The schistosomulum is the main target of vaccine-induced protective immunity; however, most studies have utilized schistosomula produced by mechanical transformation of infective larvae followed by in vitro culture rather than larvae isolated directly from the lungs of infected mammals. Using transmission electron microscopy, we demonstrated that there was little difference in the ultrastructure of Schistosoma japonicum schistosomula obtained by the two methods. However, significant differences in gene expression profiles were apparent when we used an oligonucleotide microarray to compare the gene expression profiles of schistosomula obtained in vivo from lung tissue with those maintained in vitro, and with adult worms of S. japonicum. It is likely that host environmental factors, which cannot be reliably reproduced in vitro, do influence the growth, development and overall biology of schistosomes. Thus caution is urged when using in vitro-cultured schistosomes and mechanically transformed/cultured schistosomula in molecular, biochemical and immunological studies.

Schistosomes are blood-dwelling flukes that infect 200 million people worldwide and are responsible for hundreds of thousands of deaths annually. Using a signal sequence trap, we cloned from Schistosoma mansoni two cDNAs, Sm-tsp-1 and Sm-tsp-2, encoding the tetraspanin (TSP) integral membrane proteins TSP-1 and TSP-2. We raised antibodies to recombinant TSP fusion proteins and showed that both proteins are exposed on the surface of S. mansoni. Recombinant TSP-2, but not TSP-1, is strongly recognized by IgG1 and IgG3 (but not IgE) from naturally resistant individuals but is not recognized by IgG from chronically infected or unexposed individuals. Vaccination of mice with the recombinant proteins followed by challenge infection with S. mansoni resulted in reductions of 57% and 64% (TSP-2) and 34% and 52% (TSP-1) for mean adult worm burdens and liver egg burdens, respectively, over two independent trials. Fecal egg counts were reduced by 65-69% in both test groups. TSP-2 in particular provided protection in excess of the 40% benchmark set by the World Health Organization for progression of schistosome vaccine antigens into clinical trials. When coupled with its selective recognition by naturally resistant people, TSP-2 seems to be an effective vaccine antigen against S. mansoni.

The aim of this study is to examine the prevalence of smoking during pregnancy by the individual mother's sociodemographic characteristics and ecological factors at the community level (suburbs). This analysis combined 1996 Australia Census and data on 3424 women attending Well-Baby-Clinics (WBC) between January 1996 and February 1998 within a region in South Western Sydney (SWS), Australia. The prevalence of maternal smoking was 31%. Maternal factors such as marital status, country of birth, education, occupation, socioeconomic status (SES), and types of antenatal care (ANC) were independent risk factors for maternal smoking. Small area analysis revealed suburbs within SWS with high rates of maternal smoking (47-57%). Community level characteristics such as low income, low educational level, young mothers, and unemployment can explain 85.7% of the variation in maternal smoking in SWS. Smoking during pregnancy is recognised as a serious risk factor to the unborn child. The present study draws attention to local community level factors, other than individual SES, which may be important when developing strategies for maternal smoking prevention programs.

The onset of intracranial metastases is a common development during the course of malignancy. The treatment of these patients represents a significant workload in any radiation oncology department. Much debate has occurred regarding the most appropriate fractionation schedules employed given the perception of limited life expectancy and symptomatic relief following cranial radiation. The aim of this study was to identify the spectrum of primary sites in patients developing intracranial metastases and to assess survival postradiation for the group overall and for selected subgroups. The records of 378 patients undergoing palliative cranial radiation in the years 1993-1998 at Sydney's Mater and Royal North Shore hospitals were analysed retrospectively. Major primary sites were lung (42%), breast (18%), colorectal (9%), melanoma (7%), and unknown primary (7%). Overall median survival post-treatment was 3 months. Lung cancer patients showed a median survival of 6 months, breast 5 months, colorectal 4 months and melanoma 3 months. Long-term survivors were noted with up to 15% of certain groups alive beyond 12 months and 2% alive at 24 months. Multivariate analysis revealed improved survival in patients undergoing resection, and those receiving higher dose radiation justifying a more aggressive approach in selected patients.