Tag Archives: Germline

First-in-human nanoparticle HIV vaccine induces broad and publicly targeted helper T cell responses

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Researchers from Fred Hutchinson Cancer Center in Seattle, Scripps Research in La Jolla, California, IAVI and other collaborating institutions have characterized robust T-cell responses in volunteers participating in the IAVI G001 Phase 1 clinical trial to test the safety and immune response of a self-assembling nanoparticle HIV vaccine.

Their work, published in Science Translational Medicine, signals a major step toward development of a vaccine approach to end the HIV/AIDS epidemic worldwide. The antigen used in this study was jointly developed by IAVI and Scripps Research and has been shown in previous analyses to stimulate VRC01-class B cells, an immune response considered promising enough for boosting in further studies.

We were quite impressed that this vaccine candidate produced such a vigorous T-cell response in almost all trial participants who received the vaccine. These results highlight the potential of this HIV-1 nanoparticle vaccine approach to induce the critical T-cell help needed for maturing antibodies toward the pathway of broadly neutralizing against HIV.”

Julie McElrath, MD, PhD, senior vice president and director of Fred Hutch’s Vaccine and Infectious Disease Division and co-senior author of the study

However, she added, this is the first step, and heterologous booster vaccines will still be needed to eventually produce VRC01-class broadly neutralizing antibodies, which in previous studies have demonstrated the ability to neutralize approximately 90% of HIV strains.

“We showed previously that this vaccine induced the desired B-cell responses from HIV broadly neutralizing antibody precursors. Here we demonstrated strong CD4 T-cell responses, and we went beyond what is normally done by drilling down to identify the T cell epitopes and found several broadly immunogenic epitopes that might be useful for developing boosters and for other vaccines,” William Schief, PhD, executive director of vaccine design for IAVI’s Neutralizing Antibody Center at Scripps Research and professor, Department of Immunology and Microbiology, at Scripps Research, who is co-senior author of the study.

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The trial is a phase 1, randomized, double-blind and placebo-controlled study to evaluate the safety and effectiveness of a nanoparticle HIV vaccine in healthy adult volunteers without HIV. It was comprised of two groups with 18 vaccine and six placebo recipients per group, with 48 total enrollees. Participants were given two doses of the vaccine or placebo eight weeks apart.

McElrath acknowledged the groundbreaking work of her lab team, the biostatistical team and Fred Hutch’s Vaccine Trials Unit for their invaluable contributions to the study. The Vaccine Trials Unit conducts multiple vaccine trials and was one of only two sites for this study.

Findings from the study include:

  • Vaccine-specific CD4 T cells were induced in almost all vaccine recipients.
  • Lymph node GC T follicular helper cells increased after vaccination compared to placebo.
  • Lumazine synthase protein, needed for self-assembly of the particle, also induced T-cell responses that can provide additional help to ultimately enhance efficacy in a sequential vaccine strategy.
  • Vaccine-specific CD4 T cells were polyfunctional and had diverse phenotypes.
  • LumSyn-specific CD8 T cells were highly polyfunctional and had a predominantly effector memory phenotype.
  • CD4 T-cell responses were driven by immunodominant epitopes with diverse and promiscuous HLA restriction.
  • CD8 T-cell responses to LumSyn were driven by HLA-A*02-restricted immunodominant epitopes B- and T-cell responses correlated within but not between LN and peripheral blood compartments.

This study was funded by the Bill & Melinda Gates Foundation Collaboration for AIDS Vaccine Discovery; IAVI Neutralizing Antibody Center; National Institute of Allergy and Infectious Diseases; and Ragon Institute of MGH, MIT and Harvard.

Study authors WRS and SM are inventors on a patent filed by Scripps and IAVI on the eOD-GT8 monomer and 60-mer immunogens (patent number 11248027, “Engineered outer domain (eOD) of HIV gp 120 and mutants thereof”). WRS, KWC and MJM are inventors on patents filed by Scripps, IAVI and Fred Hutch on immunodominant peptides from LumSyn (Title: Immunogenic compositions; filing no. 63127975).

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Source:
Journal reference:

Cohen, K. W., et al. (2023) A first-in-human germline-targeting HIV nanoparticle vaccine induced broad and publicly targeted helper T cell responses. Science Translational Medicine. doi.org/10.1126/scitranslmed.adf3309.

A novel approach to quantify personal information contained within gut metagenome data

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In a recent study published in Nature Microbiology, researchers used shotgun sequencing to extract human reads from deoxyribonucleic acid (DNA) in fecal samples of 343 Japanese individuals comprising the main dataset of this study.

They used this gut metagenome data to reconstruct personal information. Some study participants also provided whole genome sequencing (WGS) data for ultra-deep metagenome shotgun sequencing analysis.

Study: Reconstruction of the personal information from human genome reads in gut metagenome sequencing data. Image Credit: KaterynaKon/Shutterstock.comStudy: Reconstruction of the personal information from human genome reads in gut metagenome sequencing data. Image Credit: KaterynaKon/Shutterstock.com

Background

The knowledge regarding the human microbiome, microorganisms inhabiting the human body, has expanded considerably in the last ten years, thanks to rapid advancements in technologies like metagenome shotgun sequencing.

This technology allows the sequencing of the non-bacterial component of the microbiome samples, including host DNA. For instance, in fecal samples, the amount of host DNA is less than 10% but is removed to protect the privacy of donors.

Human germline genotype in metagenome data is substantial to enable the re-identification of individuals. However, researchers and donors should recognize that it is highly confidential, so sharing it with the community requires careful consideration.

Apart from ethical concerns related to sharing this data, it is necessary to understand that if human reads in metagenome data are not removed before deposition, what kind of personal information (e.g., sex and ancestry) could this data help recover?

In addition, human reads in gut metagenome data could be a good resource for stool-based forensics, robust variant calling, and polygenic risk scores based estimates of disease risks (e.g., type 2 diabetes).

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Since this data could help quantitatively and precisely reconstruct genotype information, it could complement human WGS data.

About the study

In the present study, researchers applied a few humans reads in the gut metagenome data of the main study dataset to reconstruct personal information, including genetic sex and ancestry. For predicting genetic sex and the ancestries of these 343 individuals, they used sequencing depth of the sex chromosomes and modified likelihood score-based method, respectively.

In addition, the researchers developed methods to re-identify a person from a genotype dataset. Furthermore, they combined two harmonized genotype-calling approaches, the direct calling of rare variants and the two-step imputation of common variants, to reconstruct genotypes.

The main dataset of the study included 343 Japanese participants, whereas the validation dataset for the genetic sex prediction analysis comprised 113 Japanese individuals.

The multi-ancestry dataset, which helped the researchers validate ancestry prediction analysis, comprised 73 individuals of various nationalities, including samples from individuals in New Delhi, India.

The female and male participants in each dataset were 196 & 147, 65 & 48, and 25 & 48, respectively. Likewise, the age range for these three datasets was 20 to 88, 20 to 81, and 20 to 61 years, respectively.

Results and conclusion

Given that human reads in the gut metagenome data were derived consistently from all chromosomes, the read depth of the X chromosome was nearly double in females and that of the Y chromosome in males.

So, in a logistic regression analysis, when the researchers applied a 0.43 Y:X chromosome read-depth ratio to the validation dataset, which correctly predicted the genetic sex of 97.3% of the study samples.

In human microbiome and genetic research, the feasibility of sex prediction using human gut metagenome data could help remove mislabelled samples.

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The study analysis also helped researchers remarkably predict ancestry in 98.3% of individuals using 1,000 Genomes Project (1KG) data as a reference.

However, the likelihood score-based method often misclassified South Asian (SAS) samples as American (AMR) and European (EUR), especially when the number of human reads was small. It is understandable because the genetic diversity of the SAS population is complex.

The likelihood score-based method also efficiently utilized the data from genomic areas with low coverage demonstrating the quantitative power of gut metagenome data to re-identify individuals and successfully re-identified 93.3% of individuals.

Despite ethical concerns, the re-identification method used in this study could help in the quality control of multi-omics datasets comprising gut metagenome and human germline genotype data.

In addition, the authors successfully reconstructed genome-wide common variants using genomic approaches. Historically researchers used stool samples as a source of germline genomes for wild and domestic animals but not humans.

Thus, further development of suitable methodologies could help efficiently utilize the human genome in gut metagenome data and benefit animal research.

Nonetheless, the study remarkably demonstrated that optimized methods could help reconstruct personal information from the human reads in gut metagenome data.

Moreover, the findings of this study could serve as a guiding resource to devise best practices for using the already accumulated gut metagenome data of humans.

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Journal reference:

Multi-stage HIV vaccine regimen shows promising results in Phase 1 clinical trial

The George Washington University Vaccine Research Unit in partnership with Scripps Research, IAVI, Fred Hutchinson Cancer Center (FHCC) and the National Institutes of Health, National Institute of Allergy and Infectious Diseases Vaccine Research Center published the results of their Phase 1 Clinical Trial in Science. The results show critical new insights into their novel vaccine strategy, which involves a stepwise approach to producing antibodies capable of targeting a wide range of HIV variants.

The trial, known as IAVI G001, tested the first stage in a multi-stage HIV vaccine regimen the researchers are developing. The trial results show that the vaccine had a favorable safety profile and induced the targeted response in 97% of people who were vaccinated. Importantly, the study also provides a detailed immunological analysis of the vaccine responses.

HIV has continued to be a difficult virus to create a vaccine for given its ability to mutate and quickly evade the immune system. The findings from this trial bring new hope to stopping HIV and may help find vaccines for other difficult infectious diseases as well.”

David Diemert, Professor of Medicine, GWU School of Medicine and Health Sciences

The novel vaccine strategy that was tested in this trial is focused on producing broadly neutralizing antibodies (“bnAbs”), which are a rare type of antibody that can fight and protect against many different variants of a virus, including HIV.

The researchers in the study are using a procedure known as ‘germline targeting’ to eventually produce bnAbs that can protect against HIV. The first step of germline targeting involves stimulating the rare immune cells-;known as bnAb-precursor B cells-;that can evolve into the cells that produce the bnAbs needed to block the virus. To accomplish this, the researchers designed a customized molecule-;known as an immunogen-;that would “prime” the immune system and elicit responses from these rare bnAb-precursor cells.

For this clinical trial, a novel method of sampling lymph nodes was developed by the clinical and biorepository teams at GW, FHCC and IAVI, which included ultrasound-guided fine needle aspiration of lymph nodes near the injection site. “This is the first time such a technique has been used routinely in a vaccine clinical trial,” Jeffrey Bethony, professor of microbiology, immunology and tropical medicine at GW SMHS said. “It enabled us to acquire a cell population critical to germline stimulation that do not circulate but remains sequestered in lymph node tissue.”

The GW VRU has partnered with IAVI on two other HIV vaccine-related Phase I clinical trials over the past five years, serving as a lead site, central biorepository and support unit. In addition, the unit has conducted a number of other clinical vaccine trials to date, including a Phase III trial to test the now FDA-authorized COVID-19 vaccine from biotechnology company Moderna; a Phase II clinical trial for a COVID-19 vaccine booster from the biopharmaceutical company Sanofi; and a Phase I trial of a vaccine to prevent Lassa fever, an acute, animal-borne viral disease endemic to parts of West Africa.