Sex and prior exposure jointly shape innate immune responses to a live herpesvirus vaccine

Background

Both sex and prior exposure to pathogens are known to influence responses to immune challenges, but their combined effects are not well established in humans, particularly in early innate responses critical for shaping subsequent outcomes.

Methods

We employed systems immunology approaches to study responses to a replication-defective, herpes simplex virus (HSV) 2 vaccine in men and women either naive or previously exposed to HSV.

Results

Blood transcriptomic and cell population profiling showed substantial changes on day 1 after vaccination, but the responses depended on sex and whether the vaccinee was naive or previously exposed to HSV. The magnitude of early transcriptional responses was greatest in HSV naive women where type I interferon (IFN) signatures were prominent and associated negatively with vaccine-induced neutralizing antibody titers, suggesting that a strong early antiviral response reduced the uptake of this replication-defective virus vaccine. While HSV seronegative vaccine recipients had upregulation of gene sets in type I IFN (IFN-α/β) responses, HSV2 seropositive vaccine recipients tended to have responses focused more on type II IFN (IFN-γ) genes.

Conclusions

These results together show that prior exposure and sex interact to shape early innate responses that then impact subsequent adaptive immune phenotypes.

Funding

Intramural Research Program of the NIH, the National Institute of Allergy and Infectious Diseases, and other institutes supporting the Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation. The vaccine trial was supported through a clinical trial agreement between the National Institute of Allergy and Infectious Diseases and Sanofi Pasteur. Clinical trial number: NCT01915212.

Abstract PR-08: Diabetes affects metabolism, redox signaling, DNA repair capacity and mutational burden in breast cancer

Comorbidities disproportionately affect underserved populations. Diabetes can increase cancer risk and decreases breast cancer survival. Diabetes-associated breast cancer risk impacts African American women more than European Americans. The goal of this study was to understand how diabetes may shape breast tumor biology. We performed an RNA and whole-exome sequencing (WES) analysis, together with global metabolomics, of matched breast tumors from patients with or without diabetes, with the majority being of African American descent. Additionally, as an experimental model, we generated mammary xenografts following orthotopic injection of breast cancer cells (MDA-MB-231, MDA-MB-468, and HS578T) into the mammary fat pad of diabetic mice (NOD.Cg-Rag1 tm1Mom Ins2 Akita Il2rg tm1Wjl/SzJ). After 4-6 weeks we collected the tumors and performed RNAseq and metabolome analysis. Analyzing the metabolome profile of both human breast tumors and xenografts, we observed a distinct metabolite pattern in diabetic breast tumors and diabetic mice. The key observation was the enrichment of food and microbial-derived metabolites under diabetes, indicating that diabetes may promote the accumulation of these metabolites in breast tumors. Next, we analyzed the RNAseq data from the same tumors and xenografts. Here, we applied Gene Set Enrichment Analysis (GSEA) with the transcriptomic data to find specific pathways activated under diabetic conditions. GSEA indicated the enrichment of gene signatures related to mesenchymal and stem cell-like phenotypes both in the patient tumor and xenografts under diabetes. Additionally, we discovered an enrichment of the reactive oxygen species (ROS) pathway in diabetic tumors and xenografts. Consistent with this observation, treating breast cancer cells (MDA-MB-231 and HS578T) with high glucose (25mM) increased superoxide radical production in these cells. Since higher ROS levels could cause DNA damage, we examined DNA damage in breast cancer cells cultured under high glucose. Here we observed an increase in DNA damage under high glucose as indicated by robust nuclear γH2AX and 53BP1 immunostaining. An additional KEGG analysis indicated the inhibition of various DNA repair pathways (e.g. base-excision, nucleotide excision, and mismatch repair) in breast tumors and xenografts. Corroborating this finding with our WES data, we observed a significant enrichment of several mutational signatures (SBS5, SBS15, and SBS30 DNA repair deficiency signatures) in breast tumors of diabetic patients, suggesting that diabetes may interfere with DNA repair pathways in breast tumors. Taken together, this study suggests that diabetes promotes a mesenchymal and stem cell-like phenotype in human breast tumors with higher oxidative stress & DNA damage and a decreased DNA repair capacity. Our data further indicate that breast tumors from diabetic patients may have an increased susceptibility to DNA damage response inhibitors like PARP inhibitors.

Citation Format: Gatikrushna Panigrahi, Tiffany Dorsey, Wei Tang, Julian Candia, Amy Zhang, Stefan Ambs. Diabetes affects metabolism, redox signaling, DNA repair capacity and mutational burden in breast cancer [abstract]. In: Proceedings of the AACR Virtual Conference: 14th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2021 Oct 6-8. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr PR-08.

Abstract PO-234: Relationship between increased concentrations of circulating chemokines and population differences in tumor biology

Genetic ancestry is a significant determinant of multiple aspects of tumor biology, immunity, and inflammatory responses. In lung cancer, in addition to increased incidence in African American (AA) men compared with other racial and ethnic groups in the US, differences in tumor biology between AAs and European Americans (EAs) have been identified. Natural selection is a strong driver of gene selection leading to population differences that can be linked to geographic and genetic ancestry. A classic example involves the Duffy antigen receptor for chemokines, also known as DARC. Individuals with African ancestry are more likely to lack DARC expression on their red blood cells (also known as Duffy null), as this confers resistance to malaria. Loss of erythrocyte expression of DARC is associated with increased circulating chemokine levels in the CXCR and CCR families as DARC serves as a dummy chemokine reservoir. Additionally, Duffy null individuals have lower circulating neutrophils, known as benign ethnic neutropenia. However, loss of DARC expression is exclusive to erythrocytes in Duffy null individuals. As venous endothelial cells and tumor cells also express DARC, we questioned whether the increased circulating bioavailability of DARC ligands in AAs led to increased DARC- dependent signaling in the tumor microenvironment (TME) of AA lung cancer patients. DARC expression on tumor cells is associated with increased aggressiveness and invasion, and endothelial cells have been shown to transcytose DARC ligands into the luminal space. As DARC ligands are associated with angiogenesis and granulocyte recruitment, we hypothesized that tumors of AAs would present with increased blood vessel invasion and granulocyte recruitment to the TME. Using the Somalogic multiplex proteomic assay, we observed significantly elevated levels of the ELR+ CXCR chemokines, with the exception of IL-8 (CXCL8), in serum samples from AA healthy control and stage 1 lung adenocarcinoma patients compared with EAs (samples from the NCI-UMD Case-Control Study), We did not find any evidence of increased angiogenesis as measured by CD31 immunohistochemical staining in AA patients (n= 39) compared with EA patients (n= 107). Immune cell composition did not differ between AAs and EAs as measured by CIBERSORT analysis in both healthy controls and patients between AAs and EAs. Therefore, while AAs have significantly higher levels of circulating DARC ligands compared with EAs, they do not appear to contribute to increased DARC-dependent signaling in normal and tumor lung tissue microenvironment in AAs.

Citation Format: Sheryse Taylor, Julian Candia, Adriana Zingone, John Tsang, Brid Ryan. Relationship between increased concentrations of circulating chemokines and population differences in tumor biology [abstract]. In: Proceedings of the AACR Virtual Conference: Thirteenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2020 Oct 2-4. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(12 Suppl):Abstract nr PO-234.

Abstract PR04: Understanding tumor clonal evolution by single-cell transcriptomic analysis in liver cancer

Tumor evolution is a key feature intrinsic to tumor biology and contributes to intratumor heterogeneity, escape of immune surveillance, treatment failure, and patients’ prognosis. The evolutionary process of tumor is driven by selecting favorable phenotypes in terms of their fitness and survival in a tumor ecosystem. While genomic alterations provide rich materials for tumor evolution, only a few can induce a recognizable phenotypic change with even fewer for a fitness advantage. Thus, transcriptomics, a major molecular feature reflecting functional activities, will be informative in modeling tumor heterogeneity and crucial in understanding tumor evolution. Here, we aim to study tumor clonal evolution by single-cell transcriptomic profiling of hepatocellular carcinoma and intrahepatic cholangiocarcinoma from 37 patients participating the immune checkpoint inhibition trials. By analyzing core biopsies before or after treatment, we determined the single-cell atlas of liver tumors and confidently separated malignant cells and non-malignant cells by inferring chromosomal copy number variations. We developed a consensus clustering model based on machine learning algorithms and statistical methods to identify functional clones from malignant cells within each tumor. We further determined the clonal relationship by constructing the phylogenetic tree of the clones from all tumors. The clonal relationship within each tumor was independently assessed by manifold based single-cell trajectory and RNA-velocity based cell lineage. The analyses revealed a tumor branching evolutionary architecture of the clones. Noticeably, tumor branching evolution was associated with patient outcomes, which was also validated by using bulk transcriptomic data from 765 liver tumors. We found tumors in the poor prognosis branch were enriched in the pathways of hypoxia, epithelial-mesenchymal transition and angiogenesis. Remarkably, the functional role of the clones within a tumor varied, indicating a cooperative tumor cell community. We found a polarization of immune landscape associated with tumor branching evolution driven by tumor cell-specific cytokines. Our results offer insight into the collective behavior of tumor cell communities in liver cancer as well as potential drivers for tumor evolution in response to immunotherapy.

Citation Format: Lichun Ma, Limin Wang, Ching-Wen Chang, Sophia Franck, Dana Dominguez, Marshonna Forgues, Julian Candia, Maria O. Hernandez, Michael Kelly, Yongmei Zhao, Bao Tran, Jonathan M. Hernandez, Jeremy L. Davis, David E. Kleiner, Bradford J. Wood, Tim F. Greten, Xin Wei Wang. Understanding tumor clonal evolution by single-cell transcriptomic analysis in liver cancer [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PR04.

Plasma proteomic signatures predict dementia and cognitive impairment

INTRODUCTION

Biomarker discovery of dementia and cognitive impairment is important to gather insight into mechanisms underlying the pathogenesis of these conditions.

METHODS

In 997 adults from the InCHIANTI study, we assessed the association of 1301 plasma proteins with dementia and cognitive impairment. Validation was conducted in two Alzheimer's disease (AD) case-control studies as well as endophenotypes of AD including cognitive decline, brain amyloid burden, and brain volume.

RESULTS

We identified four risk proteins that were significantly associated with increased odds (peptidase inhibitor 3 (PI3), trefoil factor 3 (TFF3), pregnancy associated plasma protein A (PAPPA), agouti-related peptide (AGRP)) and two protective proteins (myostatin (MSTN), integrin aVb5 (ITGAV/ITGB5)) with decreased odds of baseline cognitive impairment or dementia. Of these, four proteins (MSTN, PI3, TFF3, PAPPA) were associated cognitive decline in subjects that were cognitively normal at baseline. ITGAV/ITGB5 was associated with lower brain amyloid burden, MSTN and ITGAV/ITGB5 were associated with larger brain volume and slower brain atrophy, and PI3, PAPPA, and AGRP were associated with smaller brain volume and/or faster brain atrophy.

DISCUSSION

These proteins may be useful as non-invasive biomarkers of dementia and cognitive impairment.

A Modified Injector and Sample Acquisition Protocol Can Improve Data Quality and Reduce Inter-Instrument Variability of the Helios Mass Cytometer

Mass cytometry is a powerful tool for high-dimensional single cell characterization. Since the introduction of the first commercial CyTOF mass cytometer by DVS Sciences in 2009, mass cytometry technology has matured and become more widely utilized, with sequential platform upgrades designed to address specific limitations and to expand the capabilities of the platform. Fluidigm's third-generation Helios mass cytometer introduced a number of upgrades over the previous CyTOF2. One of these new features is a modified narrow bore sample injector that generates smaller ion clouds, which is expected to improve sensitivity and throughput. However, following rigorous testing, we find that the narrow-bore sample injector may have unintended negative consequences on data quality and result in lower median and higher coefficients of variation in many antibody-associated signal intensities. We describe an alternative Helios acquisition protocol using a wider bore injector, which largely mitigates these data quality issues. We directly compare these two protocols in a multisite study of 10 Helios instruments across 7 institutions and show that the modified protocol improves data quality and reduces interinstrument variability. These findings highlight and address an important source of technical variability in mass cytometry experiments that is of particular relevance in the setting of multicenter studies. © 2019 International Society for Advancement of Cytometry.

The Emergence and Functional Fitness of Memory CD4+ T Cells Require the Transcription Factor Thpok

Memory CD4⁺ T cells mediate long-term immunity, and their generation is a key objective of vaccination strategies. However, the transcriptional circuitry controlling the emergence of memory cells from early CD4⁺ antigen-responders remains poorly understood. Here, using single-cell RNA-seq to study the transcriptome of virus-specific CD4⁺ T cells, we identified a gene signature that distinguishes potential memory precursors from effector cells. We found that both that signature and the emergence of memory CD4⁺ T cells required the transcription factor Thpok. We further demonstrated that Thpok cell-intrinsically protected memory cells from a dysfunctional, effector-like transcriptional program, similar to but distinct from the exhaustion pattern of cells responding to chronic infection. Mechanistically, Thpok- bound genes encoding the transcription factors Blimp1 and Runx3 and acted by antagonizing their expression. Thus, a Thpok-dependent circuitry promotes both memory CD4⁺ T cells' differentiation and functional fitness, two previously unconnected critical attributes of adaptive immunity.

Access to healthcare in Chilean prisons: an inmates' perspective

OBJECTIVES

To analyze the perception of access to Chilean prisons in a representative national sample of persons deprived of liberty as well as to examine the most important covariates of such access.

MATERIALS AND METHODS

This study uses secondary data from the First National Survey on the Quality of Prison Life (2014), which investigated inmates' perceptions regarding access to health services inside the prisons. To do this, it uses descriptive statistics and a logistic regression model.

RESULTS

Descriptive results at the national level show that access to health services in prisons tends to be "difficult" (44.7% of cases in this category). Multivariate logistic regression results indicate that men (OR=0.43) and those who reported better infrastructure (OR=0.70) were less likely to report "difficult access to health services". On the other hand, prison inmates (OR=1.61) and those who had reported higher levels of mistreatment (OR=1.26) were associated with a higher probability of reporting "difficult access to health services".

DISCUSSION

Our study suggests that access to health care is dynamically linked to other aspects of life within prisons such as the composition of the prison population (gender), some of the material aspects of prisons (infrastructure, type of facility), and even some relational aspects (level of mistreatment/abuse). Future studies could further extend the debate on healthcare in prisons, incorporating more complex both variables and analyses.

A multigene array for measurable residual disease detection in AML patients undergoing SCT

AML is a diagnosis encompassing a diverse group of myeloid malignancies. Heterogeneous genetic etiology, together with the potential for oligoclonality within the individual patient, have made the identification of a single high-sensitivity marker of disease burden challenging. We developed a multiple gene measurable residual disease (MG-MRD) RQ-PCR array for the high-sensitivity detection of AML, retrospectively tested on 74 patients who underwent allo-SCT at the NHLBI in the period 1994-2012. MG-MRD testing on peripheral blood samples prior to transplantation demonstrated excellent concordance with traditional BM-based evaluation and improved risk stratification for post-transplant relapse and OS outcomes. Pre-SCT assessment by MG-MRD predicted all clinical relapses occurring in the first 100 days after allo-SCT compared with 57% sensitivity using WT1 RQ-PCR alone. Nine patients who were negative for WT1 prior to transplantation were correctly reclassified into a high-risk MG-MRD-positive group, associated with 100% post-transplant mortality. This study provides proof of principle that a multiple gene approach may be superior to the use of WT1 expression alone for AML residual disease detection.

Comparative study of an Eden model for the irreversible growth of spins and the equilibrium Ising model

The magnetic Eden model (MEM) [N. Vandewalle and M. Ausloos, Phys. Rev. E 50, R635 (1994)] with ferromagnetic interactions between nearest-neighbor spins is studied in (d+1)-dimensional rectangular geometries for d=1,2. In the MEM, magnetic clusters are grown by adding spins at the boundaries of the clusters. The orientation of the added spins depends on both the energetic interaction with already deposited spins and the temperature, through a Boltzmann factor. A numerical Monte Carlo investigation of the MEM has been performed and the results of the simulations have been analyzed using finite-size scaling arguments. As in the case of the Ising model, the MEM in d=1 is noncritical (only exhibits an ordered phase at T=0). In d=2 the MEM exhibits an order-disorder transition of second order at a finite temperature. Such transition has been characterized in detail and the relevant critical exponents have been determined. These exponents are in agreement (within error bars) with those of the Ising model in two dimensions. Further similarities between both models have been found by evaluating the probability distribution of the order parameter, the magnetization, and the susceptibility. Results obtained by means of extensive computer simulations allow us to put forward a conjecture that establishes a nontrivial correspondence between the MEM for the irreversible growth of spins and the equilibrium Ising model. This conjecture is certainly a theoretical challenge and its confirmation will contribute to the development of a framework for the study of irreversible growth processes.

A nasal trumpet orthosis to maintain nares openings and respiratory function for patients with facial burns: a case report

Management of facial burns is a challenge to the burn team because it may lead to functional and cosmetic compromise. Severe scarring of the nares may lead to nasal occlusion. This article introduces a method of maintaining nasal patency that allows respiratory exchange through the use of a custom-fabricated, semirigid tubular orthosis. The technique for fabrication is reviewed, and the use of the device is addressed through a case report. This inexpensive, readily available device is useful in preventing nasal occlusion that results from scar formation.