Functionally active serum and monoclonal antibody responses targeting the pre-erythrocytic stage of Plasmodium falciparum in Tanzanian adults after vaccination with purified, live-attenuated sporozoites

Abstract With 212 million cases worldwide and an estimated 429,000 deaths in 2015, malaria continues to be a serious global health threat. An effective vaccine could significantly decrease malaria-associated morbidity and mortality, especially in children under the age of five years. At present, there is no licensed malaria vaccine available. The most advanced malaria vaccine candidate, the RTS, S/AS01 subunit formulation, showed limited and short-term vaccine efficacy against clinical malaria in phase 3 clinical studies in malaria-endemic populations in sub-Saharan Africa. The only vaccination approach that has ever induced complete sterile protection against controlled human malaria infection (CHMI) in malaria-naïve individuals, is the immunization with live, whole-attenuated sporozoites. The Sanaria® PfSPZ Vaccine (PfSPZ Vaccine) is a pre-erythrocytic vaccine, which is composed of live, radiation-attenuated, aseptic, purified, non-replicating, cryopreserved, whole Plasmodium falciparum (Pf) sporozoites (PfSPZ). In a study at the National Institutes of Health (NIH), the PfSPZ Vaccine was safe and well tolerated and protected 100% (6/6) of malaria-naïve volunteers against homologous CHMI when administered intravenously (IV) at 5 doses of 1.35 x 105 PfSPZ. The overall aims of this thesis included i) the evaluation of the safety, immunogenicity and protective efficacy against homologous CHMI of the PfSPZ Vaccine by direct venous inoculation (DVI) of malaria pre-exposed volunteers from Tanzania and ii) the study of functionally active serum and monoclonal antibody responses against Pf sporozoites induced by malaria pre-exposed Tanzanian volunteers upon immunization with the PfSPZ Vaccine. Building on these objectives, the here presented thesis is structured around three manuscripts: Manuscript 1: Safety, immunogenicity and protective efficacy against controlled human malaria infection of PfSPZ Vaccine in Tanzanian adults This manuscript depicts the first clinical phase I trial on the safety, immunogenicity and protective efficacy against homologous CHMI of PfSPZ Vaccine performed in Africa. The study was conducted in healthy male volunteers aged 20 to 30 years in Bagamoyo, Tanzania. Similar regimen as tested in the NIH study of 5 doses of 1.35 x 105 (low-dose group) or 2.7 x 105 (high-dose group) of PfSPZ Vaccine was administered via DVI to Tanzanian adults. Homologous CHMI was conducted at 3 and 24 weeks after the last vaccination. The PfSPZ Vaccine was safe and well tolerated, but less immunogenic and protective against CHMI as in malaria-naïve US Americans. It is hypothesized that higher individual doses and altering intervals will be required to induce improved protective efficacy and immunogenicity in malaria endemic target populations.   Manuscript 2: Intravenous application of irradiation attenuated Plasmodium falciparum sporozoites elicits long-lived IgG and IgM invasion inhibitory antibodies in malaria pre-exposed volunteers In this study we aimed i) to gain a better understanding of the vaccine-induced humoral immune responses in malaria pre-exposed individuals after immunization with DVI-administered PfSPZ Vaccine and ii) to investigate if sporozoite binding and invasion inhibitory IgM antibodies are induced following PfSPZ vaccination. To address this, we used serum and plasma samples collected from a subset of volunteers who participated in the PfSPZ Vaccine trial described in manuscript 1. Our findings demonstrate that malaria pre-exposed volunteers develop sporozoite invasion inhibitory antibodies and induce anti-CSP IgG and IgM antibodies after repeated PfSPZ vaccination. A subset of these plasma samples was depleted from IgG and IgA antibodies to obtain fractions containing only IgM antibodies. Depleted IgM antibody fractions of 3 volunteers demonstrated sporozoite invasion inhibitory capacity in in vitro inhibition of sporozoite invasion (ISI) assays. These results indicated for the first time that sporozoite-specific IgM antibodies could contribute to protection against malaria infection. Manuscript 3: CSP-specific human monoclonal antibodies inhibiting Plasmodium falciparum liver stage infection target a distinct sequence at the N-terminus To investigate the mechanisms of protection elicited by antibodies following PfSPZ vaccination, we isolated a panel of monoclonal antibodies from the PfSPZ-immunized Tanzanian volunteers who were found protected from homologous CHMI in the study described in manuscript 1. Using an antigen-agnostic approach to identify antibodies that can bind the surface of intact sporozoites, we found that all monoclonal antibodies isolated target the circumsporozoite protein (CSP), confirming its known immunodominance. Functional characterization of these antibodies revealed, that the most effective antibodies reducing Pf liver burden in a humanized mouse model target a distinct epitope located at the junction between the N-terminal end and the NANP repeat, a region which is not included in the RTS, S vaccine. Our results suggest that this identified region could be a component of interest in the future design of effective second generation PfCSP subunit vaccines

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Immunization of malaria pre-exposed volunteers with PfSPZ Vaccine elicits long-lived IgM invasion-inhibitory and complement-fixing antibodies

The assessment of antibody responses after immunization with radiation-attenuated, aseptic, purified, cryopreserved Plasmodium falciparum sporozoites (Sanaria PfSPZ Vaccine) has focused on IgG isotype antibodies. Here, we aimed to investigate if P. falciparum sporozoite binding and invasion-inhibitory IgM antibodies are induced following immunization of malaria-preexposed volunteers with PfSPZ Vaccine.; Using serum from volunteers immunized with PfSPZ, we measured vaccine-induced IgG and IgM antibodies to P. falciparum circumsporozoite protein (PfCSP) via ELISA. Function of this serum as well as IgM antibody fractions was measured via in vitro in an inhibition of sporozoite invasion assay. These IgM antibody fractions were also measured for binding to sporozoites by immunofluorescence assay and complement fixation on whole sporozoites.; We found that in addition to anti-PfCSP IgG, malaria-preexposed volunteers developed anti-PfCSP IgM antibodies after immunization with PfSPZ Vaccine and that these IgM antibodies inhibited P. falciparum sporozoite invasion of hepatocytes in vitro. These IgM plasma fractions also fixed complement to whole P. falciparum sporozoites.; This is the first finding that PfCSP and P. falciparum sporozoite-binding IgM antibodies are induced following immunization of PfSPZ Vaccine in malaria-preexposed individuals and that IgM antibodies can inhibit P. falciparum sporozoite invasion into hepatocytes in vitro and fix complement on sporozoites. These findings indicate that the immunological assessment of PfSPZ Vaccine-induced antibody responses could be more sensitive if they include parasite-specific IgM in addition to IgG antibodies.; NCT02132299

Safety, immunogenicity, and protective efficacy against controlled human malaria infection of Plasmodium falciparum sporozoites vaccine in Tanzanian adults

We are using controlled human malaria infection (CHMI) by direct venous inoculation (DVI) of cryopreserved, infectious; Plasmodium falciparum; (Pf) sporozoites (SPZ) (PfSPZ Challenge) to try to reduce time and costs of developing PfSPZ Vaccine to prevent malaria in Africa. Immunization with five doses at 0, 4, 8, 12, and 20 weeks of 2.7 × 10; 5; PfSPZ of PfSPZ Vaccine gave 65% vaccine efficacy (VE) at 24 weeks against mosquito bite CHMI in U.S. adults and 52% (time to event) or 29% (proportional) VE over 24 weeks against naturally transmitted Pf in Malian adults. We assessed the identical regimen in Tanzanians for VE against PfSPZ Challenge. Twenty- to thirty-year-old men were randomized to receive five doses normal saline or PfSPZ Vaccine in a double-blind trial. Vaccine efficacy was assessed 3 and 24 weeks later. Adverse events were similar in vaccinees and controls. Antibody responses to Pf circumsporozoite protein were significantly lower than in malaria-naïve Americans, but significantly higher than in Malians. All 18 controls developed Pf parasitemia after CHMI. Four of 20 (20%) vaccinees remained uninfected after 3 week CHMI (; P; = 0.015 by time to event,; P; = 0.543 by proportional analysis) and all four (100%) were uninfected after repeat 24 week CHMI (; P; = 0.005 by proportional,; P; = 0.004 by time to event analysis).; Plasmodium falciparum; SPZ Vaccine was safe, well tolerated, and induced durable VE in four subjects. Controlled human malaria infection by DVI of PfSPZ Challenge appeared more stringent over 24 weeks than mosquito bite CHMI in United States or natural exposure in Malian adults, thereby providing a rigorous test of VE in Africa

Public antibodies to malaria antigens generated by two LAIR1 insertion modalities.

In two previously described donors, the extracellular domain of LAIR1, a collagen-binding inhibitory receptor encoded on chromosome 19 (ref. 1), was inserted between the V and DJ segments of an antibody. This insertion generated, through somatic mutations, broadly reactive antibodies against RIFINs, a type of variant antigen expressed on the surface of Plasmodium falciparum-infected erythrocytes. To investigate how frequently such antibodies are produced in response to malaria infection, we screened plasma from two large cohorts of individuals living in malaria-endemic regions. Here we report that 5-10% of malaria-exposed individuals, but none of the European blood donors tested, have high levels of LAIR1-containing antibodies that dominate the response to infected erythrocytes without conferring enhanced protection against febrile malaria. By analysing the antibody-producing B cell clones at the protein, cDNA and gDNA levels, we characterized additional LAIR1 insertions between the V and DJ segments and discovered a second insertion modality whereby the LAIR1 exon encoding the extracellular domain and flanking intronic sequences are inserted into the switch region. By exon shuffling, this mechanism leads to the production of bispecific antibodies in which the LAIR1 domain is precisely positioned at the elbow between the VH and CH1 domains. Additionally, in one donor the genomic DNA encoding the VH and CH1 domains was deleted, leading to the production of a camel-like LAIR1-containing antibody. Sequencing of the switch regions of memory B cells from European blood donors revealed frequent templated inserts originating from transcribed genes that, in rare cases, comprised exons with orientations and frames compatible with expression. These results reveal different modalities of LAIR1 insertion that lead to public and dominant antibodies against infected erythrocytes and suggest that insertion of templated DNA represents an additional mechanism of antibody diversification that can be selected in the immune response against pathogens and exploited for B cell engineering

Sex differences in oncogenic mutational processes

Funder: Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology); doi: https://doi.org/10.13039/501100002790Funder: Genome Canada (Génome Canada); doi: https://doi.org/10.13039/100008762Funder: Canada Foundation for Innovation (Fondation canadienne pour l'innovation); doi: https://doi.org/10.13039/501100000196Funder: Terry Fox Research Institute (Institut de Recherche Terry Fox); doi: https://doi.org/10.13039/501100004376Abstract: Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research

Sex differences in oncogenic mutational processes

Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Peer reviewe

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that -80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAFPeer reviewe