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Our research examined how gut bacteria might influence vaccine effectiveness in different parts of the world. We studied adults from the United States, Rwanda, and Uganda who received an experimental HIV vaccine. We found that participants from East Africa had more diverse gut bacteria than those from the United States, but their immune responses to the vaccine were weaker. This is the first study to directly show this relationship between higher gut bacterial diversity and reduced vaccine effectiveness in the same group of people. We also identified specific types of bacteria that were linked to either stronger or weaker immune responses. These findings are particularly relevant now as we use vaccines globally to fight diseases like COVID-19, as they suggest that regional differences in gut bacteria Bacteroidota and Bacillota might help explain why vaccines work better in some places than others. This could inform how we design and test future vaccines.

HIV type 1 (HIV-1) remains a global health concern, with the greatest burden in sub-Saharan Africa. Despite 40 years of research, no vaccine candidate has shown durable and protective efficacy against HIV-1 acquisition. Although pre-exposure prophylaxis in groups with high vulnerability can be very effective, barriers to its use, such as perceived low acquisition risk, fear of stigma, and concerns about side-effects, remain. Thus, a population-based approach, such as an HIV-1 vaccine, is needed. The current study aimed to evaluate the efficacy and safety of a heterologous HIV-1 vaccine regimen, consisting of a tetravalent mosaic adenovirus 26-based vaccine (Ad26.Mos4.HIV) and aluminium phosphate-adjuvanted clade C glycoprotein (gp) 140, in young women at risk of acquiring HIV-1 in southern Africa. This randomised, double-blind, phase 2b study enrolled sexually active women without HIV-1 or HIV-2 aged 18–35 years at 23 clinical research sites in Malawi, Mozambique, South Africa, Zambia, and Zimbabwe. Participants were centrally randomly assigned (1:1) to receive intramuscular injections of vaccine or saline placebo in stratified permuted blocks via an interactive web response system. Study participants, study site personnel (except those with primary responsibility for study vaccine preparation and dispensing), and investigators were masked to treatment group allocation. The vaccine regimen consisted of Ad26.Mos4.HIV administered at months 0 and 3 followed by Ad26.Mos4.HIV administered concurrently with aluminium phosphate-adjuvanted clade C gp140 at months 6 and 12. The primary efficacy outcome was vaccine efficacy in preventing laboratory-confirmed HIV-1 acquisition diagnosed between visits at month 7 and month 24 after the first vaccination (VE[7–24]) in the per-protocol population, which included participants who had not acquired HIV-1 4 weeks after the third vaccination, received all planned vaccinations at the first three vaccination visits within the protocol-specified windows, and had no major protocol deviations that could affect vaccine efficacy. Primary safety outcomes were assessed in randomly assigned participants who received one study injection or more based on the actual injection received. The primary safety endpoints were the incidences of unsolicited adverse events (AEs), solicited local and systemic AEs, serious AEs, AEs of special interest, and AEs leading to discontinuation of vaccination. This trial is registered with ClinicalTrials.gov, NCT03060629, and is complete. Between Nov 3, 2017, and June 30, 2019, 2654 women were randomly assigned, of whom 2636 women (median age of 23 years [IQR 20–25]) were enrolled and received at least one study injection (1313 assigned vaccine, 1323 placebo; 1317 received vaccine, 1319 placebo). Analysis of the primary efficacy outcome in the per-protocol cohort included 1080 women in the vaccine group and 1108 women in the placebo group; the incidence of HIV-1 acquisition per 100 person-years over months 7–24 after the first vaccination was 3·38 (95% CI 2·54–4·41) in the vaccine group and 3·94 (3·04–5·03) in the placebo group, with an estimated VE(7–24) of 14·10% (95% CI –22·00 to 39·51; p=0·40). There were no serious unsolicited AEs, AEs of special interest, or deaths related to the study vaccine. In the vaccine group, 663 (50·3%) of 1317 participants had grade 1 or 2 solicited local AEs and ten (0·8%) of 1317 participants had grade 3 or 4 solicited local AEs. In the placebo group, 305 (23·1%) of 1319 participants had grade 1 or 2 solicited local AEs and three (0·2%) of 1319 participants had grade 3 or 4 solicited local AEs. 863 (65·5%) of 1317 participants in the vaccine group had grade 1 or 2 solicited systemic AEs and 34 (2·6%) of 1317 participants had grade 3 or 4 solicited systemic AEs. 763 (57·8%) of 1319 participants in the placebo group had grade 1 or 2 solicited systemic AEs and 20 (1·5%) of 1319 participants had grade 3 or 4 solicited systemic AEs. Overall, three (0·2%) of 1317 participants in the vaccine group and three (0·2%) of 1319 participants in the placebo group discontinued vaccination due to an unsolicited AE, and three (0·2%) of 1317 participants in the vaccine group and one (0·1%) of 1319 participants in the placebo group discontinued vaccination due to a solicited AE. The heterologous Ad26.Mos4.HIV and clade C gp140 vaccine regimen was safe and well tolerated but did not show efficacy in preventing HIV-1 acquisition in a population of young women in southern Africa at risk of HIV-1. Division of AIDS at the National Institute of Allergy and Infectious Diseases through the HIV Vaccine Trials Network, Bill & Melinda Gates Foundation, Janssen Vaccines & Prevention, US Army Medical Materiel Development Activity, and Ragon Institute.

Mosaic immunogens are bioinformatically engineered human immunodeficiency virus type 1 (HIV-1) sequences designed to elicit clade-independent coverage against globally circulating HIV-1 strains. This phase 1, double-blinded, randomized, placebo-controlled trial enrolled healthy HIV-uninfected adults who received 2 doses of a modified vaccinia Ankara (MVA)-vectored HIV-1 bivalent mosaic immunogen vaccine or placebo on days 0 and 84. Two groups were enrolled: those who were HIV-1 vaccine naive (n = 15) and those who had received an HIV-1 vaccine (Ad26.ENVA.01) 4-6 years earlier (n = 10). We performed prespecified blinded cellular and humoral immunogenicity analyses at days 0, 14, 28, 84, 98, 112, 168, 270, and 365. All 50 planned vaccinations were administered. Vaccination was safe and generally well tolerated. No vaccine-related serious adverse events occurred. Both cellular and humoral cross-clade immune responses were elicited after 1 or 2 vaccinations in all participants in the HIV-1 vaccine-naive group. Env-specific responses were induced after a single immunization in nearly all subjects who had previously received the prototype Ad26.ENVA.01 vaccine. No safety concerns were identified, and multiclade HIV-1-specific immune responses were elicited. NCT02218125.

Reliable quantitative dopamine transporter imaging is critical for early and accurate diagnosis of Parkinson's disease (PD). Image quantitation is made difficult by the variability introduced by manual interventions during the quantitative processing steps. A fully automated objective striatal analysis (OSA) program was applied to dopamine transporter images acquired from PD subjects with early symptoms of suspected parkinsonism and compared with manual analysis by a trained image-processing technologist. A total of 101 (123)I-beta-CIT SPECT scans were obtained of subjects recruited to participate in the Query-PD Study. Data were reconstructed and then analyzed according to a package of scripts (OSA) that reorients the SPECT brain volume to the standard geometry of an average scan, automatically locates the striata and occipital structures, locates the caudate and putamen, and calculates the background-subtracted striatal uptake ratio (V3''). The striatal uptake ratio calculated by OSA was compared with manual analysis by a trained image-processing technologist. Several parameters were varied in the automated analysis, including the number of summed transverse slices and the size and separation of the regions of interest applied to the caudate and putamen to determine the optimum OSA analysis. The parameters giving V3'' with the closest correlation to the manual analysis were accepted as optimal. The optimal comparison between the V3'' obtained by the human analyst and that obtained by the automated OSA analysis yielded a correlation coefficient of 0.96. Our optimized OSA delivers V3'' evaluations that closely correlate with a similar evaluation manually applied by a highly trained image-processing technologist.

The SHHF/Mcc- fa cp (spontaneous hypertension and heart failure) rat is advanced as a novel and suitable non-primate model of pregnancy-associated hypertension and fetal growth restriction because it simultaneously has spontaneous pregnancy-associated hypertension, small for gestational age (SGA) offsprings, and altered placental gene expression. Pregnancy-associated hypertension is a major contributor to maternal and fetal morbidity and mortality with the potential to result in maternal death and the need for iatrogenic preterm delivery. It has been reported to develop spontaneously in humans, but not in animals; consequently, progress in identifying the cause and pathogenesis of this disorder has been hampered. Spontaneous hypertension and heart failure rats develop hypertension spontaneously as they age, therefore we sought to determine whether these rats developed hypertension and SGA offsprings during pregnancy. Our results show that systolic blood pressure (BP) increased >40 mm Hg by the end of the first trimester and remained at this elevated level for the remainder of pregnancy, but decreased after parturition. Placenta weights of SHHF rats (0.60 ± 0.02 g, n = 36) were significantly higher than Wistar-Kyoto (WKY) rats (0.42 ± 0.01 g, n = 22, P < .05), but pup weights were significantly lower (2.68 ± 0.06 g for SHHF rats compared to 3.24 ± 0.06 g for WKY controls, P < .05). Histologic examination revealed pathologic lesions in neither heart, liver, placenta, nor kidney. l-Arginine administered in drinking water prevented the elevation of BP, particularly during the third trimester. Placentas from SHHF rats displayed altered expression of several genes whose protein products have been implicated in preeclampsia, including serotonin receptor, sodium channel, carbonic anhydrase, estrogen receptor regulator, major histocompatibility complex proteins, superoxide dismutase, and angiotensiogen. In addition, gene expression profiling showed alteration of a number of subcellular putative myristoylproteins not previously associated with preeclampsia, particularly those engaged in post-translational modifications in the placenta. Thus, SHHF rats may be a valuable tool, because it simultaneously has spontaneous pregnancy-associated hypertension, SGA offsprings, and altered placental gene expression.

The STE12 protein of the yeast Saccharomyces cerevisiae binds to the pheromone response element (PRE) present in the upstream region of genes whose transcription is induced by pheromone. Using DNaseI footprinting assays with bacterially made STE12 fragments, I localized the DNA-binding domain to 164 amino acids near the amino terminus, a domain that contains similarities to the homeodomain. A DNaseI footprinting assay showed that the N-terminal 215 amino acids of STE12 has 5-10 fold higher binding affinity to two adjacent sites than to a single site. On a fragment containing multiple PREs, the 215 amino acid STE12 fragment protected both a consensus PRE as well as a degenerate PRE containing an additional residue. Mutation of the degenerate site led to a 5-10 fold decrease in binding; mutation of the consensus site led to a 25 fold decrease in binding. The ability of PREs to function as pheromone-inducible upstream activation sequences in yeast correlated with their ability to bind the STE12 domain in vitro. To investigate the role of STE12 in$\\alpha$ -specific gene activation, I cloned the STE12 functional homolog from the closely related yeast species Kluyveromyces lactis. The K. lactis STE12 (Kl STE12) contains 666 amino acids and is therefore similar in size to the S. cerevisiae STE12 (Sc STE12). The DNA-binding domains of these two STE12 proteins are highly conserved (78% identity) and they bind to the pheromone response element with similar affinity in vitro. However, the remainder of the proteins, required for uninduced transcription and pheromone-induced transcription, is very divergent (10 to 20% identity) with the exception of three short stretches of 9-15 residues. I introduced genes encoding Kl STE12 or both Kl STE12 and the K. lactis MAT $\\alpha$ 1 protein (Kl$\\alpha$ 1) into ste12 $\\Delta$strains of S. cerevisiae and examined their effects on mating. The Kl STE12 gene in low copy number can partially restore mating to S. cerevisiae a ste12 $\\Delta$cells, but little complementation occurs in$\\alpha$ste12$\\Delta$cells. However, the low level of Kl STE12 combined with Kl$\\alpha$ 1 complements the mating defect in$\\alpha$ste12 $\\Delta$cells. This enhancement suggests that STE12 may interact with$\\alpha$ 1 in a complex that is responsible for$\\alpha$ -specific gene activation. In addition, by generating hybrids of the S. cerevisiae and K. lactis STE12 proteins, I determined that the C-terminal activation domain of Kl STE12 is responsible for the inefficient mating observed in$\\alpha$ste12 $\\Delta$cells.

Drought is one of the most important environmental constraints limiting plant growth and agricultural productivity. To understand the underlying mechanism of drought tolerance and to identify genes for improving this important trait, we conducted a gain-of-function genetic screen for improved drought tolerance in Arabidopsis thaliana. One mutant with improved drought tolerance was isolated and designated as enhanced drought tolerance1. The mutant has a more extensive root system than the wild type, with deeper roots and more lateral roots, and shows a reduced leaf stomatal density. The mutant had higher levels of abscisic acid and Pro than the wild type and demonstrated an increased resistance to oxidative stress and high levels of superoxide dismutase. Molecular genetic analysis and recapitulation experiments showed that the enhanced drought tolerance is caused by the activated expression of a T-DNA tagged gene that encodes a putative homeodomain-START transcription factor. Moreover, overexpressing the cDNA of the transcription factor in transgenic tobacco also conferred drought tolerance associated with improved root architecture and reduced leaf stomatal density. Therefore, we have revealed functions of the homeodomain-START factor that were gained upon altering its expression pattern by activation tagging and provide a key regulator that may be used to improve drought tolerance in plants.

BackgroundThere is growing consensus that spatial biology is the key to unlocking the underlying mechanisms of cancer immunotherapy and to predicting patient outcomes. Indeed, a recent example using the Akoya Phenoptics technology revealed a unique phenotypic signature of CD8/Foxp3 positive cells embedded within the tumor microenvironment of patients that responded favorably to PD-1 checkpoint inhibition.1 In this case, the combination of both multiparameter and spatial readouts was required to correlate significantly with outcome. As the number of treatment options expands and knowledge regarding cell types that contribute to treatment mechanisms improves, so too do the number of markers required to analyze responses that enable discovery of new signatures.MethodsHere, we present data from the analysis of human FFPE cancer tissues using an expanded CODEX antibody catalog targeting a variety of immune, immune checkpoint and transcription factors. CODEX enables the highly multiplexed detection of more than 40 targets within the same tissue sample, with single cell resolution and without degradation of the sample.ResultsOur expanded target list enables detection of key macrophage populations, T and B cell subtypes, granulocytes, dendritic cells, natural killer cells, stromal, tumor and epithelial cells. Additionally, the activation state of these immune and tumor cell types can be measured through detection of key immune checkpoints, including PD-1 and PD-L1. Through the addition of these critical markers, both cells known to contribute to treatment outcome and new biomarker signatures can be identified.ConclusionsContinued expansion of spatial biology discovery capabilities will be critical to continuing to improve patient outcomes and to develop new treatment options of solid tumors using cancer immunotherapies.ReferenceBerry S, Taube J, et al. Analysis of multispectral imaging with the AstroPath platform informs efficacy of PD-1 blockade. Science. 2021; 372: 6547.

Large language models (LLMs) are increasingly used to extract clinical data from electronic health records (EHRs), offering significant improvements in scalability and efficiency for real-world data (RWD) curation in oncology. However, the adoption of LLMs introduces new challenges in ensuring the reliability, accuracy, and fairness of extracted data, which are essential for research, regulatory, and clinical applications. Existing quality assurance frameworks for RWD and artificial intelligence do not fully address the unique error modes and complexities associated with LLM-extracted data. In this paper, we propose a comprehensive framework for evaluating the quality of clinical data extracted by LLMs. The framework integrates variable-level performance benchmarking against expert human abstraction, automated verification checks for internal consistency and plausibility, and replication analyses comparing LLM-extracted data to human-abstracted datasets or external standards. This multidimensional approach enables the identification of variables most in need of improvement, systematic detection of latent errors, and confirmation of dataset fitness-for-purpose in real-world research. Additionally, the framework supports bias assessment by stratifying metrics across demographic subgroups. By providing a rigorous and transparent method for assessing LLM-extracted RWD, this framework advances industry standards and supports the trustworthy use of AI-powered evidence generation in oncology research and practice.