Heterogeneous Human Population Research Articles

Migration speed of captured breast cancer subpopulations correlates with metastatic fitness.

The genetic alterations contributing to migration proficiency, a phenotypic hallmark of metastatic cells required for colonizing distant organs, remain poorly defined. Here, we used single-cell magneto-optical capture (scMOCa) to isolate fast cells from heterogeneous human breast cancer cell populations, based on their migratory ability alone. We show that captured fast cell subpopulations retain higher migration speed and focal adhesion dynamics over many generations as a result of a motility-related transcriptomic profile. Upregulated genes in isolated fast cells encoded integrin subunits, proto-cadherins and numerous other genes associated with cell migration. Dysregulation of several of these genes correlates with poor survival outcomes in people with breast cancer, and primary tumors established from fast cells generated a higher number of circulating tumor cells and soft tissue metastases in pre-clinical mouse models. Subpopulations of cells selected for a highly migratory phenotype demonstrated an increased fitness for metastasis.

Five commercially-available antibodies react differentially with allelic forms of human HLA-DR beta chain

Allelic variants of HLA-DRB1 have been associated with a variety of autoimmune and infectious diseases. Although the precise molecular mechanisms by which HLA-DRB1 alleles predispose to a particular disease are currently unclear, it has been shown that mRNA expression levels of HLA-DRB1 are dependent on the different alleles. We aimed to measure HLA-DR beta chain levels in peripheral blood mononuclear cells of individuals carrying HLA-DRB1*03:01/*04:01 and HLA-DRB1*03:01/*15:01 alleles by western blotting, using five commercially-available HLA-DRB antibodies. We observed highly heterogeneous binding of the tested antibodies to the different allelic forms of the HLA-DR beta chain. Overall, we show that current immunological research that employs available antibodies to detect HLA-DR beta chains is biased towards detection of specific variants of the protein; this may cause significant discrepancy in quantification of protein expression in a heterogeneous human population.

Mouse Organ-Specific Proteins and Functions

Organ-specific proteins (OSPs) possess great medical potential both in clinics and in biomedical research. Applications of them—such as alanine transaminase, aspartate transaminase, and troponins—in clinics have raised certain concerns of their organ specificity. The dynamics and diversity of protein expression in heterogeneous human populations are well known, yet their effects on OSPs are less addressed. Here, we used mice as a model and implemented a breadth study to examine the panorgan proteome for potential variations in organ specificity in different genetic backgrounds. Using reasonable resources, we generated panorgan proteomes of four in-bred mouse strains. The results revealed a large diversity that was more profound among OSPs than among proteomes overall. We defined a robustness score to quantify such variation and derived three sets of OSPs with different stringencies. In the meantime, we found that the enriched biological functions of OSPs are also organ-specific and are sensitive and useful to assess the quality of OSPs. We hope our breadth study can open doors to explore the molecular diversity and dynamics of organ specificity at the protein level.

Single-cell analysis of human skin identifies CD14+ type 3 dendritic cells co-producing IL1B and IL23A in psoriasis.

Inflammatory skin diseases including atopic dermatitis (AD) and psoriasis (PSO) are underpinned by dendritic cell (DC)-mediated T cell responses. Currently, the heterogeneous human cutaneous DC population is incompletely characterized, and its contribution to these diseases remains unclear. Here, we performed index-sorted single-cell flow cytometry and RNA sequencing of lesional and nonlesional AD and PSO skin to identify macrophages and all DC subsets, including the newly described mature LAMP3+BIRC3+ DCs enriched in immunoregulatory molecules (mregDC) and CD14+ DC3. By integrating our indexed data with published skin datasets, we generated a myeloid cell universe of DC and macrophage subsets in healthy and diseased skin. Importantly, we found that CD14+ DC3s increased in PSO lesional skin and co-produced IL1B and IL23A, which are pathological in PSO. Our study comprehensively describes the molecular characteristics of macrophages and DC subsets in AD and PSO at single-cell resolution, and identifies CD14+ DC3s as potential promoters of inflammation in PSO.

Immunogenicity and antigenicity based T-cell and B-cell epitopes identification from conserved regions of 10664 SARS-CoV-2 genomes.

The surge of SARS-CoV-2 has created a wave of pandemic around the globe due to its high transmission rate. To contain this virus, researchers are working around the clock for a solution in the form of vaccine. Due to the impact of this pandemic, the economy and healthcare have immensely suffered around the globe. Thus, an efficient vaccine design is the need of the hour. Moreover, to have a generalised vaccine for heterogeneous human population, the virus genomes from different countries should be considered. Thus, in this work, we have performed genome-wide analysis of 10,664 SARS-CoV-2 genomes of 73 countries around the globe in order to identify the potential conserved regions for the development of peptide based synthetic vaccine viz. epitopes with high immunogenic and antigenic scores. In this regard, multiple sequence alignment technique viz. Clustal Omega is used to align the 10,664 SARS-CoV-2 virus genomes. Thereafter, entropy is computed for each genomic coordinate of the aligned genomes. The entropy values are then used to find the conserved regions. These conserved regions are refined based on the criteria that their lengths should be greater than or equal to 60 nt and their corresponding protein sequences are without any stop codons. Furthermore, Nucleotide BLAST is used to verify the specificity of the conserved regions. As a result, we have obtained 17 conserved regions that belong to NSP3, NSP4, NSP6, NSP8, RdRp, Helicase, endoRNAse, 2’-O-RMT, Spike glycoprotein, ORF3a protein, Membrane glycoprotein and Nucleocapsid protein. Finally, these conserved regions are used to identify the T-cell and B-cell epitopes with their corresponding immunogenic and antigenic scores. Based on these scores, the most immunogenic and antigenic epitopes are then selected for each of these 17 conserved regions. Hence, we have obtained 30 MHC-I and 24 MHC-II restricted T-cell epitopes with 14 and 13 unique HLA alleles and 21 B-cell epitopes for the 17 conserved regions. Moreover, for validating the relevance of these epitopes, the binding conformation of the MHC-I and MHC-II restricted T-cell epitopes are shown with respect to HLA alleles. Also, the physico-chemical properties of the epitopes are reported along with Ramchandran plots and Z-Scores and the population coverage is shown as well. Overall, the analysis shows that the identified epitopes can be considered as potential candidates for vaccine design.

Multitype branching and graph product theory of infectious disease outbreaks.

The heterogeneity of human populations is a challenge to mathematical descriptions of epidemic outbreaks. Numerical simulations are deployed to account for the many factors influencing the spreading dynamics. Yet, the results from numerical simulations are often as complicated as the reality, leaving us with a sense of confusion about how the different factors account for the simulation results. Here, using a multitype branching together with a graph tensor product approach, I derive a single equation for the effective reproductive number of an infectious disease outbreak. Using this equation I deconvolute the impact of crowd management, targeted testing, contact heterogeneity, stratified vaccination, mask use, and smartphone tracing app use. This equation can be used to gain a basic understanding of infectious disease outbreaks and their simulations.

Topological Analysis for Sequence Variability: Case Study on more than 2K SARS-CoV-2 sequences of COVID-19 infected 54 countries in comparison with SARS-CoV-1 and MERS-CoV.

The pandemic due to novel coronavirus, SARS-CoV-2 is a serious global concern now. More than thousand new COVID-19 infections are getting reported daily for this virus across the globe. Thus, the medical research communities are trying to find the remedy to restrict the spreading of this virus, while the vaccine development work is still under research in parallel. In such critical situation, not only the medical research community, but also the scientists in different fields like microbiology, pharmacy, bioinformatics and data science are also sharing effort to accelerate the process of vaccine development, virus prediction, forecasting the transmissible probability and reproduction cases of virus for social awareness. With the similar context, in this article, we have studied sequence variability of the virus primarily focusing on three aspects: (a) sequence variability among SARS-CoV-1, MERS-CoV and SARS-CoV-2 in human host, which are in the same coronavirus family, (b) sequence variability of SARS-CoV-2 in human host for 54 different countries and (c) sequence variability between coronavirus family and country specific SARS-CoV-2 sequences in human host. For this purpose, as a case study, we have performed topological analysis of 2391 global genomic sequences of SARS-CoV-2 in association with SARS-CoV-1 and MERS-CoV using an integrated semi-alignment based computational technique. The results of the semi-alignment based technique are experimentally and statistically found similar to alignment based technique and computationally faster. Moreover, the outcome of this analysis can help to identify the nations with homogeneous SARS-CoV-2 sequences, so that same vaccine can be applied to their heterogeneous human population.

Human Heterogeneity and Survival of the Species: How Did It Arise and Being Sustained?—The Conundrum Facing Researchers

Current humans, Homo sapiens, are genetically and epigenetically very heterogeneous, and subsequently also biologically and physiologically heterogeneous. Much of this heterogeneity likely arose during evolutionary processes, via various iterations of humanoid lineages, and interbreeding. While advantageous from a species perspective, the heterogeneity of humans poses serious challenges to researchers attempting to understand complex disease processes. While the use of inbred preclinical models makes the research effort more effective at some levels, the findings are often not translatable to the more heterogeneous human populations. This conundrum leads to considerable research activity with inbred preclinical models, but modest progress in understanding many complex human conditions and diseases. This article discusses several of the issues around human heterogeneity and the need to change some directions in preclinical model research. Using newer Artificial Intelligence and Machine Learning approaches can begin to deduce important elements from the complexity of human heterogeneity.

Complexity and critical thresholds in the dynamics of visceral leishmaniasis.

We study a general multi-host model of visceral leishmaniasis including both humans and animals, and where host and vector characteristics are captured via host competence along with vector biting preference. Additionally, the model accounts for spatial heterogeneity in human population and heterogeneity in biting behaviour of sandflies. We then use parameters for visceral leishmaniasis in the Indian subcontinent as an example and demonstrate that the model exhibits backward bifurcation, i.e. it has a human infection and a sandfly population threshold, characterized by a bi-stable region. These thresholds shift as a function of host competence, host population size, vector feeding preference, spatial heterogeneity, biting heterogeneity and control efforts. In particular, if control is applied through human treatment a new and lower human infection threshold is created, making elimination difficult to achieve, before eventually the human infection threshold no longer exists, making it impossible to control the disease by only reducing the infection levels below a certain threshold. A better strategy would be to reduce the human infection below a certain threshold potentially by early diagnosis, control animal population levels and keep the vector population under check. Spatial heterogeneity in human populations lowers the overall thresholds as a result of weak migration between patches.

Characterization of heterogeneous primary human cartilage-derived cell population using non-invasive live-cell phase-contrast time-lapse imaging

Reliable and reproducible cell therapy strategies to treat osteoarthritis demand an improved characterization of the cell and heterogeneous cell population resident in native cartilage tissue. Using live-cell phase-contrast time-lapse imaging (PC-TLI), this study investigates the morphological attributes and biological performance of the three primary biological objects enzymatically isolated from primary human cartilage: connective tissue progenitors (CTPs), non-progenitors (NPs) and multi-cellular structures (MCSs). The authors’ results demonstrated that CTPs were smaller in size in comparison to NPs (P < 0.001). NPs remained part of the adhered cell population throughout the cell culture period. Both NPs and CTP progeny on day 8 increased in size and decreased in circularity in comparison to their counterparts on day 1, although the percent change was considerably less in CTP progeny (P < 0.001). PC-TLI analyses indicated three colony types: single-CTP-derived (29%), multiple-CTP-derived (26%) and MCS-derived (45%), with large heterogeneity with respect to cell morphology, proliferation rate and cell density. On average, clonal (CL) (P = 0.009) and MCS (P = 0.001) colonies exhibited higher cell density (cells per colony area) than multi-clonal (MC) colonies; however, it is interesting to note that the behavior of CL (less cells per colony and less colony area) and MCS (high cells per colony and high colony area) colonies was quite different. Overall effective proliferation rate (EPR) of the CTPs that formed CL colonies was higher than the EPR of CTPs that formed MC colonies (P = 0.02), most likely due to CTPs with varying EPR that formed the MC colonies. Finally, the authors demonstrated that lag time before first cell division of a CTP (early attribute) could potentially help predict its proliferation rate long-term. Quantitative morphological characterization using non-invasive PC-TLI serves as a reliable and reproducible technique to understand cell heterogeneity. Size and circularity parameters can be used to distinguish CTP from NP populations. Morphological cell and colony features can also be used to reliably and reproducibly identify CTP subpopulations with preferred proliferation and differentiation potentials in an effort to improve cell manufacturing and therapeutic outcomes.

Dietary fatty acid intake and gut microbiota determine circulating endocannabinoidome signaling beyond the effect of body fat

The endocannabinoidome encompasses several fatty acid (FA)-derived mediators, including the endocannabinoid anandamide (AEA) and 2-arachidonoyl-glycerol (2-AG), which served as targets for anti-obesity drug development, and their congener N-acyl-ethanolamines (NAEs) and 2-monoacyl-glycerols (2‑MAGs), which are involved in food intake and energy metabolism. Body weight and fat distribution have been suggested as determinants of peripheral endocannabinoid levels. We aimed at investigating factors, beyond body fat composition, that are associated with circulating NAE and 2-MAG levels in a heterogeneous human population. Plasma NAEs and 2-MAGs were measured using LC–MS/MS in a cross-sectional sample of healthy men and women (n = 195) covering a wide range of BMI and individuals before and after a 2-day Mediterranean diet (n = 21). Circulating levels of all 2-MAGs and NAEs, other than N-oleoyl-ethanolamine (OEA), correlated with body fat mass and visceral adipose tissue (0.26 < r < 0.54). NAE levels were elevated in individuals with elevated fat mass, while 2-MAGs were increased in individuals with predominantly visceral body fat distribution. Dietary intakes of specific FAs were associated with 2-AG and omega-3-FA-derived NAEs or 2-MAGs, irrespective of the body fat distribution. Some gut bacterial families (e.g. Veillonellaceae, Peptostreptococcaceae and Akkermansiaceae) were associated with variations in most NAEs or omega-3-FA-derived 2‑MAGs, independently of fat mass and dietary FA intake. Finally, a 2-day Mediterranean diet intervention increased circulating levels of NAEs and 2-MAGs in agreement with changes in FA intake (p < 0.01). Self-reported intake and short-term dietary intervention increased in oleic acid and EPA and DHA intake as well as certain gut microbiota taxa are associated to circulating NAEs and 2‑MAGs independently of adiposity measures, thus highlighting the potential importance of these variables in determining endocannabinoidome signaling in humans.

Intuitive eating is associated with elevated levels of circulating omega-3-polyunsaturated fatty acid-derived endocannabinoidome mediators

The regulation of food intake and eating behaviours involves interactions between different systems. The endocannabinoidome, comprising several fatty acid-derived mediators, plays a central role in the regulation of food intake. Alterations of this system have been suggested to intervene in the aetiology of eating disorders. This study aimed to examine the associations between non-pathological eating behaviours and circulating endocannabinoidome mediators in a heterogeneous human population. Plasma 2-monoacyl-glycerol and N-acyl-ethanolamine congeners were measured by LC-MS/MS in a sample of 190 men and women. Eating behaviours were assessed using the Three-Factor Eating Questionnaire (TFEQ) and the Intuitive Eating Scale-2 (IES-2). Following adjustment for body mass index and age, plasma levels of omega-3 polyunsaturated fatty acid-derived 2-monoacyl-glycerols, 2-eicosapentaenoyl-glycerol (2-EPG) and 2-docosapentaenoyl-glycerol (2-DPG), were associated with higher intuitive eating scores (0.15 ≤ rho ≤ 0.20; p < 0.05). These associations were independent of the dietary intake of the fatty acid precursors of these 2-monoacyl-glycerols. However, almost no association was found between plasma levels of N-acyl-ethanolamine congeners and the TFEQ or the IES-2 scores. The results of the present study suggest the association of 2-monoacyl-glycerols, especially 2-EPG and 2-DPG, in the regulation of intuitive eating and the potential implication therein of bioactive lipids.

The Exposome in Toxicologic Pathology.

The "exposome" is an individual's lifetime spectrum of chemical exposures beginning at conception. An exposome includes general external influences such as pollution and weather; external individual-specific factors (diet, infections, self-selected chemical intake); and internal individual-specific constituents (metabolic byproducts, microbiome derivatives, inflammatory mediators, stress hormones, etc). The exposome paradigm is inherent in animal toxicity testing because laboratory studies are designed so that subjects share a common exposure history encompassing not only exposure(s)/treatment(s) but also other chemical sources (eg, air, bedding, food, water). Toxicologic pathologists should remember that some differences in responsiveness to a test article may reflect subtle differences in individual exposomes of seemingly equivalent test animals. Translation of toxicity data obtained in tests of genetically inbred animals maintained under controlled environmental conditions to produce quasi-identical exposomes at best offers only approximate guidance regarding potential responses in genetically heterogeneous human populations who live in many environmental settings and thus have divergent, complex exposomes.

Monitoring from Battlefield to Bedside: Serum Repositories Help Identify Biomarkers, Perspectives on Mild Traumatic Brain Injury.

Serum repositories are foundations for seroepidemiological data, revealing targeted information about morbidities and existing heterogeneity in human populations. With the recent technological advances, we can perform high-throughput screening at an affordable cost using minimal plasma. Monitoring brain health after an injury is critical since mild Traumatic Brain Injury (mTBI) and other neurological symptoms are under-diagnosed. Our objective in this study is to present our preliminary serological data from one of our ongoing studies on mTBI. In this retrospective study, we used stored plasma samples to understand biomarkers of mTBI. We compared plasma samples from five patients with mTBI following their first concussive episode to five gender and age-matched healthy controls. We assessed multiple biomarkers to show the importance of biorepositories. Most of the estimated plasma factors in mTBI subjects at baseline were comparable to normal healthy individuals except for the astroglial markers S100B and glial fibrillary acidic protein. Fluctuations of these biomarkers can affect the homeostasis of brain parenchyma by altering the neural network signaling, which in turn may result in intermittent behavioral symptoms. Biorepositories are powerful resources for understanding the spectrum of morbidity. Biomarkers serve as a valuable diagnostic and therapeutic tool.

Developement of health risk rating scale for indoor airborne fungal exposure

This paper aims to quantify airborne fungal load in air-conditioned rooms and develop a health risk rating scale for different indoor environments. Five sampling locations in Kolkata frequented by a heterogeneous human population, containing various types of fungal growth-promoting substances (FGPS) like old documents, food items, waste hair, etc. were chosen as sampling locations where an Andersen Two-Stage Cascade Impactor was ran using Rose Bengal agar and Potato Dextrose agar media plates. Total spore load (CFU/m3), species diversity, species dominance, human exposure time, susceptible age and FGPS were considered the risk factors for this study. A risk rating scale was developed after evaluating the relative importance of these different factors in relation to human health. The most dominant genera were Aspergillus, followed by Penicillium. Maximum CFU was observed at library, followed by computer room.

Abstract 4351: Single-cell RNA sequencing reveals transcriptomic heterogeneity in response to epigenetic inhibitors

Abstract Histone modification is a fundamental regulatory mechanism of gene transcription and is associated with multiple diseases including cancer and inflammatory diseases. The factors that place and read these modifications can be co-opted in pathological conditions to give rise to disease-promoting transcriptional states, and thus represent promising targets for therapeutic small molecule inhibition. A central challenge in the development of epigenetic cancer therapy is the identification of transcriptionally sensitive cells within a heterogeneous population as a way to maximize therapeutic efficacy. To explore this challenge, we used single cell RNA-sequencing to characterize the transcriptional response of intrinsically heterogeneous human cancer and primary cell populations to small molecule inhibitors of epigenetic factors including the BET bromodomains, EZH2 methyltransferase, and CBP/EP300 acetyltransferase. Through clustering and differential expression analysis, we show that bulk transcriptional response in a mixed population of primary or tumor cells can be driven by a profound response in a hypersensitive subpopulation. Further, through the use of trajectory analysis, we show that epigenetic inhibitors can skew cell fate or differentiation status depending on the heterogeneity of the starting population. Overall, our results demonstrate the value of single cell transcriptomics for understanding the response of cell populations to epigenetic small molecule inhibitors and for enhancing the therapeutic potential of targeting pathogenic transcriptional programs. Citation Format: Andrew R. Conery, Sungmi Park, Michael J. Steinbaugh, Barbara M. Bryant, Shruti Apte, Patricia J. Keller, C. C. Yuan, Bill Bradley, Archana Bommi-Reddy, Robert J. Sims. Single-cell RNA sequencing reveals transcriptomic heterogeneity in response to epigenetic inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4351.

Physiological Perspective on Therapies of Lymphatic Vessels.

Significance: Growth of distinctive blood vessels of granulation tissue is a central step in the post-developmental tissue remodeling. Even though lymphangiogenesis is a part of the regeneration process, the significance of the controlled restoration of lymphatic vessels has only recently been recognized.Recent Advances: Identification of lymphatic markers and growth factors paved the way for the exploration of the roles of lymphatic vessels in health and disease. Emerging pro-lymphangiogenic therapies use vascular endothelial growth factor (VEGF)-C to combat fluid retention disorders such as lymphedema and to enhance the local healing process.Critical Issues: The relevance of recently identified lymphatic functions awaits verification by their association with pathologic conditions. Further, despite a century of research, the complete etiology of secondary lymphedema, a fluid retention disorder directly linked to the lymphatic function, is not understood. Finally, the specificity of pro-lymphangiogenic therapy depends on VEGF-C transfection efficiency, dose exposure, and the age of the subject, factors that are difficult to standardize in a heterogeneous human population.Future Directions: Further research should reveal the role of lymphatic circulation in internal organs and connect its impairment with human diseases. Pro-lymphangiogenic therapies that aim at the acceleration of tissue healing should focus on the controlled administration of VEGF-C to increase their capillary specificity, whereas regeneration of collecting vessels might benefit from balanced maturation and differentiation of pre-existing lymphatics. Unique features of pre-nodal lymphatics, fault tolerance and functional hyperplasia of capillaries, may find applications outreaching traditional pro-lymphangiogenic therapies, such as immunomodulation or enhancement of subcutaneous grafting.

Nonlinear relationship between biodiversity and human population density: evidence from Southeast Asia

The geographical distribution of terrestrial vertebrate biodiversity was assessed in Southeast Asia, an area characterized by highly heterogeneous human population densities (HPDs). We tested the hypothesis that recent (between 1990 and 2000) population increases may result in increased threats to biodiversity. GIS data were compiled from the International Union for the Conservation of Nature, BirdLife, and the Socioeconomic Data and Applications Center. Polygon data sets were transformed into rasters with different resolutions from 2.5 $$'$$ to 1 $$^{\circ }.$$ Relationships between species diversity were assessed globally and separately for terrestrial vertebrates (mammals, birds, reptiles, and amphibians) and for five countries (Cambodia, Laos, Myanmar, Thailand, and Vietnam). The number of species within a 20 km $$^{2}$$ -cell varied greatly and reached a maximum of 801. The species-rich cells ( $$>700$$ species) were located in a single, almost continuous area across Myanmar, Thailand, Vietnam, and South China. The relationship between vertebrate biodiversity and population density showed that biodiversity increased with HPD until around 10 persons km $$^{-2},$$ then decreased until around 200 persons km $$^{-2}$$ where it stabilized. This relationship was mediated by land cover and protection status with significant interactions between these variables and with population density. The areas with moderately increasing populations between 1990 and 2000 were those with the highest overall diversity (median 607) whereas those with decreasing populations were those with the lowest diversity (median 479). Our results suggest that population pressure on biodiversity has increased between 1990 and 2000 and this is a relatively widespread phenomenon. The presence of a continuous area of high vertebrate biodiversity calls for international action at a regional scale involving China, Laos, Myanmar, Thailand, and Vietnam.

Mouse population-based evaluation of urinary protein and miRNA biomarker performance associated with cisplatin renal injury.

Discovery and qualification of novel biomarkers with improved specificity and sensitivity for detection of xenobiotic-induced injuries is an area of active research across multiple sectors. However, the majority of efforts in this arena have used genetically limited rodent stocks that lack variability in xenobiotic responses inherent to genetically heterogeneous human populations. In this study, genetically diverse Diversity Outbred (DO) mice were used as a surrogate for human clinical populations to investigate performance of urinary kidney biomarkers against classical preclinical kidney injury biomarkers (blood urea nitrogen [BUN] and serum creatinine). In this study, cisplatin was used as a paradigm kidney toxicant, with female adult DO mice exposed to a single injection (5 mg/kg) of cisplatin or vehicle and necropsied 72 h post-exposure and 18 h following overnight urine collection. Interindividual variability in kidney toxicity was observed, with DO mice experiencing either no tubule cell necrosis or minimal-mild necrosis. A panel of urinary protein biomarkers and profiled miRNAs were assessed by receiver-operating characteristic curves as to their ability to distinguish non-responder versus responder animals, as defined by histopathological evidence of renal tubule cell necrosis. A surprising outcome of these studies was that BUN was elevated alongside of urinary miRNA and protein biomarkers in animals with grade 2 proximal tubular cell necrosis; but not elevated with grade 1 necrosis. These studies demonstrate a novel approach for using a rodent population to better assess sensitivity of candidate biomarkers, especially for proposed clinical applications. Impact statement Recent studies have indicated that several urinary proteins and miRNA species may be suitable as biomarkers for acute kidney injury. A major focus on biomarker qualification is demonstrating improved specificity and sensitivity over gold standard tests. In this study, a mouse population model, Diversity Outbred mice, was used to demonstrate that neither the urinary protein markers nor the miRNA species assayed in urine could reliably detect low severity kidney injury better than blood urea nitrogen. This study has implications for use of these biomarkers in the clinic, where interindividual heterogeneity is present within patient populations and for which the underlying tissue pathology may not be known.

Genetic background impacts vaccine-induced reduction of pneumococcal colonization.

Vaccination has been one of the most successful strategies to reduce morbidity and mortality caused by respiratory infections. Recent evidence suggests that differences in the host genetic background and environmental factors may contribute to heterogeneity in the immune response to vaccination. During pre-clinical testing, vaccines are often evaluated in a single mouse inbred strain, which may not translate well to the heterogeneous human population. Here, we examined the influence of host genetic background on vaccine-induced protection against pneumococcal colonization in two commonly used inbred mouse strains, i.e. C57BL/6 and BALB/cas well as the F1 cross of these two strains. Groups of mice were vaccinated intranasally with a vaccine formulation containing a model pneumococcal antigen, i.e. pneumococcal surface protein A (PspA), adjuvanted with cholera toxin subunit B (CTB). Even in the absence of vaccination, differences in colonization density were observed between mouse strains. Although vaccination significantly reduced pneumococcal density in all mouse strains, differences were observed in the magnitude of protection. We therefore examined immunological parameters known to be involved in vaccine-induced mucosal clearance of S. pneumoniae. We found that PspA-specific IgG levels in nasal tissue differed between mouse strains, but in all cases it correlated significantly with a reduction in colonization. Furthermore, increased mucosal IL17A, but not IFNγ, IL10, or IL4, was found to be mouse strain specific. This suggests that the reduction of bacterial load may be accompanied by a Th17 response in all genetic backgrounds, although the cytokine dynamics may differ. Increased insight into the different immune mechanisms that affect pneumococcal carriage will contribute to development of future vaccines against S. pneumoniae.