Human immune diversity: from evolution to modernity

A quantitative comparison of the deleteriousness of missense and nonsense mutations using the structurally resolved human protein interactome

The complex genotype-to-phenotype relationships in Mendelian diseases can be elucidated by mutation-induced disturbances to the networks of molecular interactions (interactomes) in human cells. Missense and nonsense mutations cause distinct perturbations within the human protein interactome, leading to functional and phenotypic effects with varying degrees of severity. Here, we structurally resolve the human protein interactome at atomic-level resolutions and perform structural and thermodynamic calculations to assess the biophysical implications of these mutations. We focus on a specific type of missense mutation, known as "quasi-null" mutations, which destabilize proteins and cause similar functional consequences (node removal) to nonsense mutations. We propose a "fold difference" quantification of deleteriousness, which measures the ratio between the fractions of node-removal mutations in datasets of Mendelian disease-causing and non-pathogenic mutations. We estimate the fold differences of node-removal mutations to range from 3 (for quasi-null mutations with folding ΔΔG ≥2 kcal/mol) to 20 (for nonsense mutations). We observe a strong positive correlation between biophysical destabilization and phenotypic deleteriousness, demonstrating that the deleteriousness of quasi-null mutations spans a continuous spectrum, with nonsense mutations at the extreme (highly deleterious) end. Our findings substantiate the disparity in phenotypic severity between missense and nonsense mutations and suggest that mutation-induced protein destabilization is indicative of the phenotypic outcomes of missense mutations. Our analyses of node-removal mutations allow for the potential identification of proteins whose removal or destabilization lead to harmful phenotypes, enabling the development of targeted therapeutic approaches, and enhancing comprehension of the intricate mechanisms governing genotype-to-phenotype relationships in clinically relevant diseases.

Inflammatory reactivity is unrelated to childhood adversity or provoked modulation of nociception

ABSTRACT

Adversity in childhood elevates the risk of persistent pain in adulthood. Neuroimmune interactions are a candidate mechanistic link between childhood adversity and persistent pain. We aimed to clarify whether immune reactivity is associated with provoked differences in nociceptive processing in adults with a range of childhood adversity. Pain-free adults (n = 96; 61 female; median [range] age: 23 [18-65] years old) with a history of mild to severe childhood adversity underwent psychophysical assessments before and after in vivo neural provocation (high-frequency electrical stimulation) and, separately, before and after in vivo immune provocation (influenza vaccine administration). Psychophysical assessments included the surface area of secondary hyperalgesia after neural provocation and change in conditioned pain modulation (test stimulus: pressure pain threshold; conditioning stimulus: cold water immersion) after immune provocation. Immune reactivity was operationalised as interleukin-6 and tumour necrosis factor-α expression after in vitro lipopolysaccharide provocation of whole blood. We hypothesised associations between immune reactivity and (1) childhood adversity, (2) induced secondary hyperalgesia, and (3) vaccine-associated change in conditioned pain modulation. We found that provoked expression of proinflammatory cytokines was not statistically associated with childhood adversity, induced secondary hyperalgesia, or vaccine-associated change in conditioned pain modulation. The current findings from a heterogenous sample cast doubt on 2 prominent ideas: that childhood adversity primes the inflammatory system for hyper-responsiveness in adulthood and that nociceptive reactivity is linked to inflammatory reactivity. This calls for the broader inclusion of heterogeneous samples in fundamental research to investigate the psychoneuroimmunological mechanisms underlying vulnerability to persistent pain.

Immunosequencing identifies signatures of T cell responses for early detection of nasopharyngeal carcinoma

To identify nasopharyngeal carcinoma (NPC)-relevant T cell receptors (TCRs), we profile the repertoires of peripheral blood TCRβ chains from 228 NPC patients, 241 at-risk controls positive for serum Epstein-Barr virus (EBV) VCA-IgA antibody, and 251 seronegative controls. We develop a TCR-based signature (T-score) based on 208 NPC-enriched CDR3β sequences, which accurately diagnoses NPC in both the original and independent validation cohorts. Notably, a higher T-score, associated with a shorter time interval to NPC diagnosis, effectively identifies early-stage NPC among EBV-seropositive at-risk individuals prior to clinical diagnosis. These NPC-enriched TCRs react against not only EBV-specific antigens but also non-EBV antigens expressed by NPC cells, indicating a broad range of specificities. Moreover, the abundance of NPC-enriched CD8+ T cells in blood correlates with the infiltration of non-exhausted T cell counterparts in tumors and predicts prolonged survival, suggesting that these NPC-enriched T cells have significant potential for disease monitoring and therapeutic applications.

Chemoradiotherapy efficacy in patients with stage III non-small cell lung cancer (NSCLC): A prognostic clinical and biomarker-based model

BACKGROUND

Chemoradiotherapy (CRT) followed by adjuvant durvalumab is the standard of care for fit patients with unresectable stage III non-small cell lung cancer (NSCLC). However, 20-25 % of the patients do not survive longer than 1 year after treatment initiation, i.e. receive futile treatment. We aimed to develop a prognostic model that can identify patients at high risk of early mortality during and after CRT.

METHODS

Patients with stage III NSCLC treated with CRT were included in the development- (N = 328; MAASTRO Biobank, 2004-2020, NCT01084785) and validation cohorts (N = 39; NCT02921854, NCT04432142). Both clinical parameters (age, sex, body mass index, performance status (PS), tumor stage (UICC 8), and sequence of chemotherapy administration) and peripheral immune-related biomarkers were included in the model development. Futile treatment was defined as death within one year after the first fraction of RT.

RESULTS

In the multivariable logistic regression analysis, PS ≥ 2 (OR = 2.89, 95 % CI 1.25-6.66, p = 0.013), stage IIIC (OR = 3.07, 95 % CI 3.07-6.9, p = 0.007), sequential chemotherapy (OR = 2.07, 95 % CI 1.19-3.62, p = 0.010), IL-6 (OR = 2.17, 95 % CI 1.27-3.70, p = 0.005), IP-10 (OR = 1.58, 95 % CI 0.92-2.73, p = 0.099), and soluble programmed death-ligand 1 (sPD-L1) (OR = 3.24, 95 % CI 1.90-5.54, p < 0.001) were identified as independent risk factors of early mortality. A nomogram was developed to calculate the risk of receiving futile treatment for each patient. The AUC of the development and validation cohort was 0.774 (95 % CI 0.716-0.832) and 0.734 (95 % CI 0.568-0.902), respectively. Patients classified as intermediate or high risk to receive futile treatment presented 23.7 % of the total cohort.

CONCLUSIONS

A prognostic model was developed that can identify patients who are at high risk of early mortality during and after CRT. These patients may be included in clinical trials aiming to improve their outcome.

The Effects of a Mediterranean Diet on Metabolic Hormones and Cytokines in Amyotrophic Lateral Sclerosis Patients: A Prospective Interventional Study

Background: Amyotrophic lateral sclerosis (ALS) is a prevalent neurodegenerative disease but lacks effective treatments. Dietary interventions, notably the Mediterranean diet, promise to modulate disease pathways. This study aimed to investigate the impact of the Mediterranean diet on gut hormones and cytokines in patients with amyotrophic lateral sclerosis (ALS). Methods: We conducted a 12-month, single-center prospective study on a total of 44 ALS patients. After a 6-month observation period, the patients were placed on a dairy-free Mediterranean diet for the next 6 months. We evaluated the patients at baseline (T0), 6 months (T1), and 12 months (T2). We measured the ALS Functional Rating Scale-Revised (ALSFRS-R) scores and a panel of metabolic hormones and cytokines. Results: The ALSFRS-R scores declined over 12 months (37.59 ± 6.32 at T0 vs. 30.23 ± 8.91 at T2, p < 0.001), indicating expected disease progression with no significant difference in the rate of decline before and after the dietary intervention. The leptin levels significantly decreased from T0 to T1 (T0: 4956 ± 3994 pg/mL vs. T1: 3196 ± 2807 pg/mL, p = 0.038). The insulin and GLP-1 levels showed significant drops at T2 (insulin T0: 480 ± 369 vs. T2: 214 ± 213 pmol/L, p < 0.01; GLP-1 T0: 118 ± 76 vs. T2: 60 ± 57 pg/mL, p < 0.01). C-peptide increased at T2 (T0: 3814 ± 1967 vs. T2: 9532 ± 4000 pg/mL, p < 0.001). Among the cytokines, the levels of IL-12P70, IL-13, IL-9, and IL-2 significantly decreased from T0 to T2 (all p < 0.05), while IL-17A and TNFα significantly increased between T1 and T2 (p < 0.01). Conclusions: The Mediterranean diet intervention in ALS patients modulated several metabolic hormones and cytokines but with no evidence of impacting the disease's evolution or of a slowed clinical progression. These findings suggest a potential role for dietary intervention, particularly the Mediterranean diet, in modulating gut hormones and cytokines in ALS patients, but its impact on disease course is unclear. Future randomized studies are needed to confirm these changes and to determine whether dietary intervention can have any benefit in ALS.

From immunobiology to intervention: Pathophysiology of autoimmune encephalitis

Autoimmune encephalitides (AEs) are neurological disorders caused by autoantibodies against neuronal and glial surface proteins. Nearly 20 years after their discovery, AE have evolved from being frequently misdiagnosed and untreated to a growing group of increasingly well-characterized conditions where patients benefit from targeted therapeutic strategies. This narrative review provides an immunological perspective on AE, focusing on NMDAR, CASPR2 and LGI1 encephalitis as the three most common forms of AE associated with anti-neuronal surface autoantibodies. We examine the autoreactive B cell subsets, the tolerance checkpoints that may fail, and the known triggers and predispositions contributing to disease. In addition, we discuss the roles of other immune cells, including T cells and microglia, in the pathogenesis of AE. By analyzing therapeutic strategies and treatment responses we draw insights into AE pathophysiology. Written at a time of transformative therapeutic advancements through cell therapies this work underscores the synergy between detailed immunological research and the development of innovative therapies.

Associations of exposure to acrylamide and glycidamide with psoriasis among adults: Findings from a population-based study

Acrylamide (AA), a hazardous chemical prevalent in the environment and human diet, and its metabolite glycidamide (GA) are suspected contributors to psoriasis. However, the relationship between AA, GA exposure and psoriasis incidence remains unclear. Using data from the National Health and Nutrition Examination Survey (NHANES) cycles 2003-2004, 2005-2006, and 2013-2014, we conducted a cross-sectional study involving 6999 participants. While no overall association was observed between AA-hemoglobin adduct (HbAA), HbGA levels, and psoriasis risk, subgroup analyses revealed positive relationships among individuals aged 20-40 years and those with serum cotinine levels between 0.011 and 10 ng/mL. We also assessed the relationship between HbAA, HbGA exposure and various laboratory biomarkers. HbAA exposure was positively associated with high-density lipoprotein (HDL) and white blood cell counts, but negatively associated with folate. HbGA exposure was negatively associated with HDL and vitamin B12. Interaction analyses indicated that higher levels of serum HDL, folate, vitamin B12, and peripheral white blood cell and monocyte counts attenuated the detrimental effects of HbGA exposure on psoriasis risk. Sensitivity analysis based on dietary AA intake from NHANES 24-hour dietary recall data (2003-2004, 2005-2006 cycles, N = 4932) yielded results consistent with those observed for HbAA and HbGA exposure. These findings suggest that AA and GA exposure may contribute to psoriasis incidence, particularly among younger adults and smokers, and that improving nutritional intake and lifestyle factors could help mitigate this risk. Further research is needed to confirm these associations in diverse populations and elucidate the underlying mechanisms of AA/GA-related psoriasis pathogenesis.

Inflammatory reactivity is unrelated to childhood adversity or provoked modulation of nociception

Adversity in childhood elevates the risk of persistent pain in adulthood. Neuroimmune interactions are a candidate mechanistic link between childhood adversity and persistent pain. We aimed to clarify whether immune reactivity is associated with provoked differences in nociceptive processing in adults with a range of childhood adversity. Pain-free adults (n=96; 61 female; median (range) age: 23 (18-65) years old) with a history of mild to severe childhood adversity underwent psychophysical assessments before and after in vivo neural provocation (high-frequency electrical stimulation) and, separately, before and after in vivo immune provocation (influenza vaccine administration). Psychophysical assessments included the surface area of secondary hyperalgesia after neural provocation and change in conditioned pain modulation (test stimulus: pressure pain threshold; conditioning stimulus: cold water immersion) after immune provocation. Immune reactivity was operationalised as IL-6 and TNF-α expression after in vitro lipopolysaccharide provocation of whole blood. We hypothesised associations between immune reactivity and (1) childhood adversity, (2) induced secondary hyperalgesia, and (3) vaccine-associated change in conditioned pain modulation. We found that provoked expression of pro-inflammatory cytokines was not statistically associated with childhood adversity, induced secondary hyperalgesia, or vaccine-associated change in conditioned pain modulation. The current findings from a heterogenous sample cast doubt on two prominent ideas: that childhood adversity primes the inflammatory system for hyper-responsiveness in adulthood and that nociceptive reactivity is linked to inflammatory reactivity. This calls for the broader inclusion of heterogeneous samples in fundamental research to investigate the psychoneuroimmunological mechanisms underlying vulnerability to persistent pain.

Systems Human Immunology and AI: Immune Setpoint and Immune Health

The immune system, critical for human health and implicated in many diseases, defends against pathogens, monitors physiological stress, and maintains tissue and organismal homeostasis. It exhibits substantial variability both within and across individuals and populations. Recent technological and conceptual progress in systems human immunology has provided predictive insights that link personal immune states to intervention responses and disease susceptibilities. Artificial intelligence (AI), particularly machine learning (ML), has emerged as a powerful tool for analyzing complex immune data sets, revealing hidden patterns across biological scales, and enabling predictive models for individualistic immune responses and potentially personalized interventions. This review highlights recent advances in deciphering human immune variation and predicting outcomes, particularly through the concepts of immune setpoint, immune health, and use of the immune system as a window for measuring health. We also provide a brief history of AI; review ML modeling approaches, including their applications in systems human immunology; and explore the potential of AI to develop predictive models and personal immune state embeddings to detect early signs of disease, forecast responses to interventions, and guide personalized health strategies.

Optimal Annual COVID-19 Vaccine Boosting Dates Following Previous Booster Vaccination or Breakthrough Infection

BACKGROUND

COVID-19 booster vaccinations mitigate transmission and reduce the morbidity and mortality associated with infection. However, the optimal date for booster administration remains uncertain. Geographic variation in infection rates throughout the year makes it challenging to intuit the best yearly booster administration date to effectively prevent infection, and also challenging to provide best guidance on how to alter booster administration in response to a breakthrough infection.

METHODS

We leveraged longitudinal antibody and reinfection probabilities with spatiotemporal projections of COVID-19 incidence to develop a geographically informed approach to optimizing the timing of booster vaccination. We assessed the delay in booster vaccination that is warranted following breakthrough infections whenever they occur during the year, enabling a personalized assessment of optimal timing that acknowledges and respects diversity of COVID-19 immune status, addressing a substantial barrier to uptake.

RESULTS

Yearly booster vaccination on any date is beneficial to prevention of infection. However, each location exhibits as much as a 3-4-fold range in degree of protection by date of uptake. Optimal COVID-19 booster vaccination dates are location-specific, typically in early autumn in the Northern Hemisphere. Infection late in the interval between boosts substantially alters the optimal boosting date.

CONCLUSIONS

Considerable benefit accrues from aptly timing COVID-19 booster vaccination campaigns, which can be tailored to specific locations. Individuals can acquire the greatest benefit from booster vaccination by timing it optimally, including delaying in cases of infection late in the interval between boosts. These results provide location-specific guidance for public health policy, healthcare provider recommendations, and individual decision-making.

Engineering the physical characteristics of biomaterials for innate immune-mediated cancer immunotherapy

It has recently been recognized that the physical characteristics of biomaterials - such as size, structure, shape, charge, mechanical strength, hydrophobicity, and multivalency - regulate immunological functions in innate immune cells. In immuno-oncology applications, biomaterials are engineered with distinct physical properties to achieve desired innate immune responses. In this review, we discuss how physical characteristics influence effector functions and innate immune signaling pathways in distinct innate immune cell subtypes. We highlight how physical properties of biomaterials impact phagocytosis regulation, biodistribution, and innate immune cell targeting. We outline the recent advances in physical engineering of biomaterials that directly or indirectly induce desired innate immune responses for cancer immunotherapy. Lastly, we discuss the challenges in current biomaterial approaches that need to be addressed to improve clinical applicability.

Efficacy and Safety of Nivolumab Plus Ipilimumab for Metastatic Renal Cell Carcinoma in Patients 75 Years and Older: Multicenter Retrospective Study

BACKGROUND/OBJECTIVES

The efficacy and safety of nivolumab plus ipilimumab (NIVO + IPI) for elderly patients with metastatic renal cell carcinoma have not been reported with sufficient evidence. Our study therefore aimed to compare the efficacy and safety of NIVO + IPI between patients ≥75 years and patients <75 years with metastatic renal cell carcinoma.

METHODS

We retrospectively analyzed a multi-center cohort of the 156 patients that received NIVO + IPI treatment at eight institutions. Among them, 33 patients were ≥75 years old, and the remainder were <75 years old.

RESULTS

Patient demographics and tumor characteristics were not significantly different between the two groups except for age. The objective response rate, disease control rate, progression-free survival, or cancer-specific survival were not significantly different between the groups. However, overall survival in the patients ≥75 years was significantly shorter than that in the patients <75 years (median: 18 months vs. 46 months, p = 0.01). In addition, an age ≥75 years was shown in multivariable analysis to be a significant independent predictor of poor overall survival. Toxicity did not show any significant variation between the groups.

CONCLUSIONS

Although the clinical efficacy and safety of NIVO + IPI was demonstrated in patients ≥75 years old, it is suggested that the indication for NIVO + IPI in this age group should be carefully considered, taking into account patients' expected life expectancy.

Human immune system: Exploring diversity across individuals and populations

The immune response is an intricate system that involves the complex connection of cellular and molecular components, each with distinct functional specialisations. It has a distinct capacity to adjust and mould the immune response in accordance with specific stimuli, influenced by both genetic and environmental factors. The presence of genetic diversity, particularly across different ethnic and racial groups, significantly contributes to the impact of incidence of diseases, disease susceptibility, autoimmune disorders, and cancer risks in specific regions and certain populations. Environmental factors, including geography and socioeconomic status, further modulate the variety of the immune system responses. These, in turn, affect the susceptibility to infectious diseases and development of autoimmune disorders. Despite the complexity of the relationship, there remains a gap in understanding the specificity of immune indices across races, immune reference ranges among populations, highlighting the need for deeper understanding of immune diversity for personalized approaches in diagnostics and therapeutics. This review systematically organizes these findings, with the goal of emphasizing the potential of targeted interventions to address health disparities and advance translational research, enabling a more comprehensive strategy. This approach promises significant advancements in identifying specific immunological conditions, focusing on personalized interventions, through both genetic and environmental factors.

Phyto-Fingerprinting of Putranjiva roxburghii Wall. Leaf Extract and its In Vitro Anti-Inflammatory Activity

Putranjiva roxburghii is an important medicinal plant utilized for remedy of female reproductive ailments. Its seed extract is being used as a uterine health booster due to the presence of several pharmaceutically important phytochemicals. However, the presence of phytochemicals in its leaf is still unexplored. The present study was designed to explore phytochemical finger printing and assessment of anti-oxidant and anti-inflammatory activities of hydroalcoholic leaf extract of P. roxburghii (HALEPR). The qualitative, quantitative phytochemical of flavonoid, phenol and HRA-MS analysis of HALEPR carried out along with antioxidant and in vitro membrane stabilization and protein denaturation assay of anti-inflammatory activity were have been analyzed. Results of qualitative phytochemical screening of HALEPR denotes the existence of phenol, flavonoids, alkaloids, coumarins, steroids, saponins, tannins, anthroquinone and carbohydrates. The quantitative phytochemical of flavonoid and phenol was done which revealed the presents of total phenol and flavonoid. High resolution accurate-mass spectrometry (HRA-MS) study was also done for the identification of bioactive compounds from the HALEPR, which showed the presence of various phytochemicals such as luteolin 3'- (3″-acetylglucuronide), luteolin 4'-methyl ether 7-glucoside, quercetin-3β-D-glucoside, 8-hydroxyluteolin 4'-methyl ether 8-glucuronide, quercetin 3-xylosyl- (1- > 2) -rha mnosyl- (1- > 6) -glucoside, quercetin-3β-D-glucoside, myricetin 3- (3-6-diacetylglucosyl) - (1- > 4) - (2″,3″-diacetylrhamnoside), apigetrin, isorhamnetin, catechin 7,3'-Di-O-β-D glucopyranoside, luteolin 7-methylglucuronide, apigenin-8-C-α -l-arabinopyranoside, naringenin 7- O-β-D-glucoside 6″-acetate,ohobanin, shogaol, ginkgetin and amoritin. The HELPER is shown to have the presence of anti-oxidant and anti-inflammatory activities as demonstrated by DPPH (1, 1-diphenyl,2-picrylhydrazyl) and membrane lysis assays. Our findings reveal the presence of phytochemicals in HALEPR that have significant antioxidant and anti-inflammatory activity. The bioactivities were identified using chemical characterization like HRA/MS and biological assessments like anti-inflammatory and antioxidant assays. Future research may focus on isolating specific molecules, conducting in vivo tests, and creating HALEPR-based formulations for clinical application as anti-inflammatory drugs.

The autoimmune disease risk variant NCF1-His90 is associated with a reduced risk of tuberculosis in women

Introduction

The neutrophil cytosolic factor 1 (NCF1) rs201802880 polymorphism is a missense mutation resulting in an amino acid substitution from arginine to histidine at position 90, which impairs the function of NADPH oxidase. This casual variant confers an increased risk for multiple autoimmune disorders, including primary Sjögren's syndrome and systemic lupus erythematosus. Given the high prevalence of this autoimmune disease risk variant in East Asia, we hypothesized that it may confer an evolutionary advantage by providing protection against infectious diseases.

Methods

To test this hypothesis, we investigated whether the NCF1 rs201802880 variant offers a protective effect against tuberculosis (TB), a historically significant and deadly infectious disease. Our study included 490 healthy controls and 492 TB patients who were genotyped for the NCF1 rs201802880 polymorphism.

Results

Our results showed that the NCF1 rs201802880 AA genotype was associated with a reduced risk of TB in women (OR= 0.25, 95% CI: 0.09-0.68, p=0.0023). Additionally, healthy individuals with the NCF1 rs201802880 AA genotype had significantly lower circulating white blood cell (5.56 ± 1.78 vs 6.43 ± 1.59, p=0.003) and neutrophil (3.23 ± 1.20 vs 3.74 ± 1.23, p = 0.02) counts compared to those with the GG or GA genotypes, with this difference being more pronounced in women than in men.

Conclusion

This study demonstrates that the autoimmune disease-causal NCF1 variant is associated with a protective effect against TB infection.

Next generation bioelectronic medicine: making the case for non-invasive closed-loop autonomic neuromodulation

The field of bioelectronic medicine has advanced rapidly from rudimentary electrical therapies to cutting-edge closed-loop systems that integrate real-time physiological monitoring with adaptive neuromodulation. Early innovations, such as cardiac pacemakers and deep brain stimulation, paved the way for these sophisticated technologies. This review traces the historical and technological progression of bioelectronic medicine, culminating in the emerging potential of closed-loop devices for multiple disorders of the brain and body. We emphasize both invasive techniques, such as implantable devices for brain, spinal cord and autonomic regulation, while we introduce new prospects for non-invasive neuromodulation, including focused ultrasound and newly developed autonomic neurography enabling precise detection and titration of inflammatory immune responses. The case for closed-loop non-invasive autonomic neuromodulation (incorporating autonomic neurography and splenic focused ultrasound stimulation) is presented through its applications in conditions such as sepsis and chronic inflammation, illustrating its capacity to revolutionize personalized healthcare. Today, invasive or non-invasive closed-loop systems have yet to be developed that dynamically modulate autonomic nervous system function by responding to real-time physiological and molecular signals; it represents a transformative approach to therapeutic interventions and major opportunity by which the bioelectronic field may advance. Knowledge gaps remain and likely contribute to the lack of available closed loop autonomic neuromodulation systems, namely, (1) significant exogenous and endogenous noise that must be filtered out, (2) potential drift in the signal due to temporal change in disease severity and/or therapy induced neuroplasticity, and (3) confounding effects of exogenous therapies (e.g., concurrent medications that dysregulate autonomic nervous system functions). Leveraging continuous feedback and real-time adjustments may overcome many of these barriers, and these next generation systems have the potential to stand at the forefront of precision medicine, offering new avenues for individualized and adaptive treatment.

Immune dynamics throughout life in relation to sex hormones and perspectives gained from gender-affirming hormone therapy

Biological sex is closely associated with the properties and extent of the immune response, with males and females showing different susceptibilities to diseases and variations in immunity. Androgens, predominantly in males, generally suppress immune responses, while estrogens, more abundant in females, tend to enhance immunity. It is also established that sex hormones at least partially explain sex biases in different diseases, particularly autoimmune diseases in females. These differences are influenced by hormonal, genetic, and environmental factors, and vary throughout life stages. The advent of gender-affirming hormone therapy offers a novel opportunity to study the immunological effects of sex hormones. Despite the limited studies on this topic, available research has revealed that testosterone therapy in transgender men may suppress certain immune functions, such as type I interferon responses, while increasing inflammation markers like TNF-α. Transgender women on estrogen therapy also experience alterations in coagulation-related and inflammatory characteristics. Furthermore, other possible alterations in immune regulation can be inferred from the assessment of inflammatory and autoimmune markers in transgender individuals receiving hormone therapy. Understanding the complex interactions between sex hormones and the immune system, particularly through the unique perspective offered by gender-affirming hormone therapies, may facilitate the development of targeted therapies for infections and autoimmune diseases while also improving healthcare outcomes for transgender individuals. Here we review immune dynamics throughout life in both sexes and provide a summary of novel findings drawn from studies exploring gender-affirming hormone therapy.

Advancing Cancer Drug Delivery with Nanoparticles: Challenges and Prospects in Mathematical Modeling for In Vivo and In Vitro Systems

Mathematical models are crucial for predicting the behavior of drug conjugate nanoparticles and optimizing drug delivery systems in cancer therapy. These models simulate interactions among nanoparticle properties, tumor characteristics, and physiological conditions, including drug resistance and targeting specificity. However, they often rely on assumptions that may not accurately reflect in vivo conditions. In vitro studies, while useful, may not fully capture the complexities of the in vivo environment, leading to an overestimation of nanoparticle-based therapy effectiveness. Advancements in mathematical modeling, supported by preclinical data and artificial intelligence, are vital for refining nanoparticle-based therapies and improving their translation into effective clinical treatments.

Genetic predisposition to high circulating levels of interleukin 6 and risk for Alzheimer's disease. Discovery and replication

IMPORTANCE

Aging is accompanied by immune dysregulation, which has been implicated in Alzheimer's disease (AD) pathogenesis. Individuals who are genetically predisposed to elevated levels of proinflammatory mediators might be at increased risk for AD.

OBJECTIVE

To investigate whether genetic propensity for higher circulating levels of interleukin 6 (IL-6) is associated with AD risk.

DESIGN

We analyzed data from the Hellenic Longitudinal Investigation of Aging and Diet (HELIAD). Mean follow-up was 2.9 (SD, 0.8) years. Baseline assessment was from 11/2009 to 11/2016, and cognitive follow-up from 01/2013 to 07/2019. Associations of interest were also examined in the UK Biobank (UKB) for replication purposes (mean follow-up was 12.9 (SD, 2.4) years; baseline assessment was from 12/2006 to 10/2010).

SETTING

Population-based study.

PARTICIPANTS

The HELIAD sample included 622 participants ≥65 years of age without baseline dementia or amnestic mild cognitive impairment (aMCI-the prodromal stage of AD). The UKB sample included 142,637 participants ≥60 years of age without prevalent dementia.

EXPOSURES

Genetic predisposition to elevated circulating levels of IL-6 was estimated using a polygenic risk score (PRS), calculated based on the summary statistics of a current GWAS meta-analysis.

MAIN OUTCOMES AND MEASURES

AD and MCI diagnoses were based on standard clinical criteria [HELIAD], or hospital records and death registry data [UKB]. Associations with AD or aMCI incidence [HELIAD] and AD incidence [UKB] were examined with Cox regression models.

RESULTS

In HELIAD, mean age was 73.4 (SD, 5.0) years; 363 (58%) women. An increase in IL-6 PRS by 1 standard deviation unit (SDU) was associated with up to a 43% increase in the risk for incident AD/aMCI (HRGWAS significance threshold of 0.01, 1.43 [95%CI, 1.14 - 1.80]). In UKBB, mean age was 64.2 (SD, 2.8) years; 73,707 (52%) women. A 1 SDU increase in IL-6 PRS was associated with up to an 8% increase in the risk for incident AD (HRGWAS significance threshold of 0.2, 1.08 [95%CI, 1.04 - 1.12]).

CONCLUSIONS AND RELEVANCE

Genetic predisposition to higher circulating levels of IL-6 was associated with an increased risk for AD, supporting the role of IL-6-related pathways in AD pathogenesis, and suggesting that genetic predisposition to proinflammatory states might trigger or accelerate AD-related neuropathology.

Genome-wide local ancestry and the functional consequences of admixture in African and European cattle populations

Bos taurus (taurine) and Bos indicus (indicine) cattle diverged at least 150,000 years ago and, since that time, substantial genomic differences have evolved between the two lineages. During the last two millennia, genetic exchange in Africa has resulted in a complex tapestry of taurine-indicine ancestry, with most cattle populations exhibiting varying levels of admixture. Similarly, there are several Southern European cattle populations that also show evidence for historical gene flow from indicine cattle, the highest levels of which are found in the Central Italian White breeds. Here we use two different software tools (MOSAIC and ELAI) for local ancestry inference (LAI) with genome-wide high- and low-density SNP array data sets in hybrid African and residually admixed Southern European cattle populations and obtained broadly similar results despite critical differences in the two LAI methodologies used. Our analyses identified genomic regions with elevated levels of retained or introgressed ancestry from the African taurine, European taurine, and Asian indicine lineages. Functional enrichment of genes underlying these ancestry peaks highlighted biological processes relating to immunobiology and olfaction, some of which may relate to differing susceptibilities to infectious diseases, including bovine tuberculosis, East Coast fever, and tropical theileriosis. Notably, for retained African taurine ancestry in admixed trypanotolerant cattle we observed enrichment of genes associated with haemoglobin and oxygen transport. This may reflect positive selection of genomic variants that enhance control of severe anaemia, a debilitating feature of trypanosomiasis disease, which severely constrains cattle agriculture across much of sub-Saharan Africa.

Inflammaging Markers in the Extremely Cold Climate: A Case Study of Yakutian Population

Yakutia is one of the coldest permanently inhabited regions in the world, characterized by a subarctic climate with average January temperatures near -40 °C and the minimum below -60 °C. Recently, we demonstrated accelerated epigenetic aging of the Yakutian population in comparison to their Central Russian counterparts, residing in a considerably milder climate. In this paper, we analyzed these cohorts from the inflammaging perspective and addressed two hypotheses: a mismatch in the immunological profiles and accelerated inflammatory aging in Yakuts. We found that the levels of 17 cytokines displayed statistically significant differences in the mean values between the groups (with minimal p-value = 2.06 × 10-19), and 6 of them are among 10 SImAge markers. We demonstrated that five out of these six markers (PDGFB, CD40LG, VEGFA, PDGFA, and CXCL10) had higher mean levels in the Yakutian cohort, and therefore, due to their positive chronological age correlation, might indicate a trend toward accelerated inflammatory aging. At the same time, a statistically significant biological age acceleration difference between the two cohorts according to the inflammatory SImAge clock was not detected because they had similar levels of CXCL9, CCL22, and IL6, the top contributing biomarkers to SImAge. We introduced an explainable deep neural network to separate individual inflammatory profiles between the two groups, resulting in over 95% accuracy. The obtained results allow for hypothesizing the specificity of cytokine and chemokine profiles among people living in extremely cold climates, possibly reflecting the effects of long-term human (dis)adaptation to cold conditions related to inflammaging and the risk of developing a number of pathologies.

In utero exposure to per - and polyfluoroalkyl substances (PFAS) associates with altered human infant T helper cell development

Background

Environmental exposures to chemical toxicants during gestation and infancy can dysregulate multiple developmental processes, causing lifelong effects. There is compelling evidence of PFAS-associated immunotoxicity in adults and children. However, the effect of developmental PFAS exposure on infant T-cell immunity is unreported, and, if present, could be implicated in immune-related health outcomes.

Objectives

We seek to model longitudinal changes in CD4+ T-cell subpopulations from birth through 12 months and their association with in-utero PFAS exposure and postnatal CD4+ T-cell frequencies and functions.

Methods

Maternal-infant dyads were recruited as part of the UPSIDE-ECHO cohort during the first trimester between 2015 and 2019 in Rochester, New York; dyads were followed through the infant's first birthday. Maternal PFAS concentrations (PFOS, PFOA, PFNA, and PFHXS) were quantified in serum during the second trimester using high-performance liquid chromatography and tandem mass spectrometry. Infant lymphocyte frequencies were assessed at birth, 6- and 12-months using mass cytometry and high-dimensional clustering methods. Linear mixed-effects models were employed to analyze the relationship between maternal PFAS concentrations and CD4+ T-cell subpopulations (n=200). All models included a PFAS and age interaction and were adjusted for parity, infant sex, and pre-pregnancy body mass index.

Results

In-utero PFAS exposure correlated with multiple CD4+ T-cell subpopulations in infants. The greatest effect sizes were seen in T-follicular helper (Tfh) and T-helper 2 (Th2) cells at 12 months. A log 2 -unit increase in PFOS was associated with lower Tfh [0.17% (95%CI: -0.30, -0.40)] and greater Th2 [0.27% (95%CI: 0.18, 0.35)] cell percentages at 12 months. Similar trends were observed for PFOA, PFNA, and PFHXS.

Discussion

Maternal PFAS exposures correlate with cell-specific changes in the infant T-cell compartment, including key CD4+ T-cell subpopulations that play central roles in coordinating well-regulated, protective immunity. Future studies into the role of PFAS-associated T-cell distribution and risk of adverse immune-related health outcomes in children are warranted.

Big Epidemiology: The Birth, Life, Death, and Resurgence of Diseases on a Global Timescale

Big Epidemiology represents an innovative framework that extends the interdisciplinary approach of Big History to understand disease patterns, causes, and effects across human history on a global scale. This comprehensive methodology integrates epidemiology, genetics, environmental science, sociology, history, and data science to address contemporary and future public health challenges through a broad historical and societal lens. The foundational research agenda involves mapping the historical occurrence of diseases and their impact on societies over time, utilizing archeological findings, biological data, and historical records. By analyzing skeletal remains, ancient DNA, and artifacts, researchers can trace the origins and spread of diseases, such as Yersinia pestis in the Black Death. Historical documents, including chronicles and medical treatises, provide contextual narratives and quantitative data on past disease outbreaks, societal responses, and disruptions. Modern genetic studies reveal the evolution and migration patterns of pathogens and human adaptations to diseases, offering insights into co-evolutionary dynamics. This integrative approach allows for temporal and spatial mapping of disease patterns, linking them to social upheavals, population changes, and economic transformations. Big Epidemiology also examines the roles of environmental changes and socioeconomic factors in disease emergence and re-emergence, incorporating climate science, urban development, and economic history to inform public health strategies. The framework reviews historical and contemporary policy responses to pandemics, aiming to enhance future global health governance. By addressing ethical, legal, and societal implications, Big Epidemiology seeks to ensure responsible and effective epidemiological research and interventions. This approach aims to profoundly impact how we understand, prevent, and respond to diseases, leveraging historical perspectives to enrich modern scientific inquiry and global public health strategies.

Protective and stochastic correlation between infectious diseases and autoimmune disorders

A priori, early exposure to a wide range of bacteria, viruses, and parasites appears to fortify and regulate the immune system, potentially reducing the risk of autoimmune diseases. However, improving hygiene conditions in numerous societies has led to a reduction in these microbial exposures, which, according to certain theories, could contribute to an increase in autoimmune diseases. Indeed, molecular mimicry is a key factor triggering immune system reactions; while it seeks pathogens, it can bind to self-molecules, leading to autoimmune diseases associated with microbial infections. On the other hand, a hygiene-based approach aimed at reducing the load of infectious agents through better personal hygiene can be beneficial for such pathologies. This review sheds light on how the evolution of the innate immune system, following the evolution of molecular patterns associated with microbes, contributes to our protection but may also trigger autoimmune diseases linked to microbes. Furthermore, it addresses how hygiene conditions shield us against autoimmune diseases related to microbes but may lead to autoimmune pathologies not associated with microbes.

Lifestyle score is associated with cellular immune profiles in healthy Tanzanian adults

Immune system and vaccine responses vary across geographical locations worldwide, not only between high and low-middle income countries (LMICs), but also between rural and urban populations within the same country. Lifestyle factors such as housing conditions, exposure to microorganisms and parasites and diet are associated with rural-and urban-living. However, the relationships between these lifestyle factors and immune profiles have not been mapped in detail. Here, we profiled the immune system of 100 healthy Tanzanians living across four rural/urban areas using mass cytometry. We developed a lifestyle score based on an individual's household assets, housing condition and recent dietary history and studied the association with cellular immune profiles. Seventeen out of 80 immune cell clusters were associated with living location or lifestyle score, with eight identifiable only using lifestyle score. Individuals with low lifestyle score, most of whom live in rural settings, showed higher frequencies of NK cells, plasmablasts, atypical memory B cells, T helper 2 cells, regulatory T cells and activated CD4+ T effector memory cells expressing CD38, HLA-DR and CTLA-4. In contrast, those with high lifestyle score, most of whom live in urban areas, showed a less activated state of the immune system illustrated by higher frequencies of naïve CD8+ T cells. Using an elastic net machine learning model, we identified cellular immune signatures most associated with lifestyle score. Assuming a link between these immune profiles and vaccine responses, these signatures may inform us on the cellular mechanisms underlying poor responses to vaccines, but also reduced autoimmunity and allergies in low- and middle-income countries.

The evolution of immune profiling: will there be a role for nanoparticles?

Immune profiling provides insights into the functioning of the immune system, including the distribution, abundance, and activity of immune cells. This understanding is essential for deciphering how the immune system responds to pathogens, vaccines, tumors, and other stimuli. Analyzing diverse immune cell types facilitates the development of personalized medicine approaches by characterizing individual variations in immune responses. With detailed immune profiles, clinicians can tailor treatment strategies to the specific immune status and needs of each patient, maximizing therapeutic efficacy while minimizing adverse effects. In this review, we discuss the evolution of immune profiling, from interrogating bulk cell samples in solution to evaluating the spatially-rich molecular profiles across intact preserved tissue sections. We also review various multiplexed imaging platforms recently developed, based on immunofluorescence and imaging mass spectrometry, and their impact on the field of immune profiling. Identifying and localizing various immune cell types across a patient's sample has already provided important insights into understanding disease progression, the development of novel targeted therapies, and predicting treatment response. We also offer a new perspective by highlighting the unprecedented potential of nanoparticles (NPs) that can open new horizons in immune profiling. NPs are known to provide enhanced detection sensitivity, targeting specificity, biocompatibility, stability, multimodal imaging features, and multiplexing capabilities. Therefore, we summarize the recent developments and advantages of NPs, which can contribute to advancing our understanding of immune function to facilitate precision medicine. Overall, NPs have the potential to offer a versatile and robust approach to profile the immune system with improved efficiency and multiplexed imaging power.

Harnessing Variability Signatures and Biological Noise May Enhance Immunotherapies' Efficacy and Act as Novel Biomarkers for Diagnosing and Monitoring Immune-Associated Disorders

Lack of response to immunotherapies poses a significant challenge in treating immune-mediated disorders and cancers. While the mechanisms associated with poor responsiveness are not well defined and change between and among subjects, the current methods for overcoming the loss of response are insufficient. The Constrained Disorder Principle (CDP) explains biological systems based on their inherent variability, bounded by dynamic boundaries that change in response to internal and external perturbations. Inter and intra-subject variability characterize the immune system, making it difficult to provide a single therapeutic regimen to all patients and even the same patients over time. The dynamicity of the immune variability is also a significant challenge for personalizing immunotherapies. The CDP-based second-generation artificial intelligence system is an outcome-based dynamic platform that incorporates personalized variability signatures into the therapeutic regimen and may provide methods for improving the response and overcoming the loss of response to treatments. The signatures of immune variability may also offer a method for identifying new biomarkers for early diagnosis, monitoring immune-related disorders, and evaluating the response to treatments.

Metabolic reprogramming tips vaccinia virus infection outcomes by stabilizing interferon-γ induced IRF1

Interferon (IFN) induced activities are critical, early determinants of immune responses and infection outcomes. A key facet of IFN responses is the upregulation of hundreds of mRNAs termed interferon-stimulated genes (ISGs) that activate intrinsic and cell-mediated defenses. While primary interferon signaling is well-delineated, other layers of regulation are less explored but implied by aberrant ISG expression signatures in many diseases in the absence of infection. Consistently, our examination of tonic ISG levels across uninfected human tissues and individuals revealed three ISG subclasses. As tissue identity and many comorbidities with increased virus susceptibility are characterized by differences in metabolism, we characterized ISG responses in cells grown in media known to favor either aerobic glycolysis (glucose) or oxidative phosphorylation (galactose supplementation). While these conditions over time had a varying impact on the expression of ISG RNAs, the differences were typically greater between treatments than between glucose/galactose. Interestingly, extended interferon-priming led to divergent expression of two ISG proteins: upregulation of IRF1 in IFN-γ/glucose and increased IFITM3 in galactose by IFN-α and IFN-γ. In agreement with a hardwired response, glucose/galactose regulation of interferon-γ induced IRF1 is conserved in unrelated mouse and cat cell types. In galactose conditions, proteasome inhibition restored interferon-γ induced IRF1 levels to that of glucose/interferon-γ. Glucose/interferon-γ decreased replication of the model poxvirus vaccinia at low MOI and high MOIs. Vaccinia replication was restored by IRF1 KO. In contrast, but consistent with differential regulation of IRF1 protein by glucose/galactose, WT and IRF1 KO cells in galactose media supported similar levels of vaccinia replication regardless of IFN-γ priming. Also associated with glucose/galactose is a seemingly second block at a very late stage in viral replication which results in reductions in herpes- and poxvirus titers but not viral protein expression. Collectively, these data illustrate a novel layer of regulation for the key ISG protein, IRF1, mediated by glucose/galactose and imply unappreciated subprograms embedded in the interferon response. In principle, such cellular circuitry could rapidly adapt immune responses by sensing changing metabolite levels consumed during viral replication and cell proliferation.

Metabolic reprogramming tips vaccinia virus infection outcomes by stabilizing interferon-γ induced IRF1

Interferon (IFN) induced activities are critical, early determinants of immune responses and infection outcomes. A key facet of IFN responses is the upregulation of hundreds of mRNAs termed interferon-stimulated genes (ISGs) that activate intrinsic and cell-mediated defenses. While primary interferon signaling is well-delineated, other layers of regulation are less explored but implied by aberrant ISG expression signatures in many diseases in the absence of infection. Consistently, our examination of tonic ISG levels across uninfected human tissues and individuals revealed three ISG subclasses. As tissue identity and many comorbidities with increased virus susceptibility are characterized by differences in metabolism, we characterized ISG responses in cells grown in media known to favor either aerobic glycolysis (glucose) or oxidative phosphorylation (galactose supplementation). While these conditions over time had a varying impact on the expression of ISG RNAs, the differences were typically greater between treatments than between glucose/galactose. Interestingly, extended interferon-priming led to divergent expression of two ISG proteins: upregulation of IRF1 in IFN-γ/glucose and increased IFITM3 in galactose by IFN-α and IFN-γ. In agreement with a hardwired response, glucose/galactose regulation of interferon-γ induced IRF1 is conserved in unrelated mouse and cat cell types. In galactose conditions, proteasome inhibition restored interferon-γ induced IRF1 levels to that of glucose/interferon-γ. Glucose/interferon-γ decreased replication of the model poxvirus vaccinia at low MOI and high MOIs. Vaccinia replication was restored by IRF1 KO. In contrast, but consistent with differential regulation of IRF1 protein by glucose/galactose, WT and IRF1 KO cells in galactose media supported similar levels of vaccinia replication regardless of IFN-γ priming. Also associated with glucose/galactose is a seemingly second block at a very late stage in viral replication which results in reductions in herpes- and poxvirus titers but not viral protein expression. Collectively, these data illustrate a novel layer of regulation for the key ISG protein, IRF1, mediated by glucose/galactose and imply unappreciated subprograms embedded in the interferon response. In principle, such cellular circuitry could rapidly adapt immune responses by sensing changing metabolite levels consumed during viral replication and cell proliferation.

Intravital Imaging of the Human Cornea Reveals the Differential Effects of Season on Innate and Adaptive Immune Cell Morphodynamics

PURPOSE

Defining how the in vivo immune status of peripheral tissues is shaped by the external environment has remained a technical challenge. We recently developed Functional in vivo confocal microscopy (Fun-IVCM) for dynamic, longitudinal imaging of corneal immune cells in living humans. This study investigated the effect of seasonal-driven environmental factors on the morphodynamic features of human corneal immune cell subsets.

DESIGN

Longitudinal, observational clinical study.

PARTICIPANTS

Sixteen healthy participants (aged 18-40 years) attended 2 visits in distinct seasons in Melbourne, Australia (Visit 1, November-December 2021 [spring-summer]; Visit 2, April-June 2022 [autumn-winter]).

METHODS

Environmental data were collected over each period. Participants underwent ocular surface examinations and corneal Fun-IVCM (Heidelberg Engineering). Corneal scans were acquired at 5.5 ± 1.5-minute intervals for up to 5 time points. Time-lapse Fun-IVCM videos were created to analyze corneal immune cells, comprising epithelial T cells and dendritic cells (DCs), and stromal macrophages. Tear cytokines were analyzed using a multiplex bead-based immunoassay.

MAIN OUTCOME MEASURES

Difference in the density, morphology, and dynamic parameters of corneal immune cell subsets over the study periods.

RESULTS

Visit 1 was characterized by higher temperature, lower humidity, and higher air particulate and pollen levels compared with Visit 2. Clinical ocular surface parameters and the density of immune cell subsets were similar across visits. At Visit 1 , corneal epithelial DCs were larger, with a lower dendrite probing speed (0.38 ± 0.21 vs. 0.68 ± 0.33 μm/min; P < 0.001) relative to Visit 2; stromal macrophages were more circular and had less dynamic activity (Visit 1, 7.2 ± 1.9 vs. Visit 2, 10.3 ± 3.7 dancing index; P < 0.001). Corneal T cell morphodynamics were unchanged across periods. Basal tear levels of interleukin 2 and CXCL10 were relatively lower during spring-summer.

CONCLUSIONS

This study identifies that the in vivo morphodynamics of innate corneal immune cells (DCs, macrophages) are modified by environmental factors, but such effects are not evident for adaptive immune cells (T cells). The cornea is a potential in vivo window to investigate season-dependent environmental influences on the human immune system.

FINANCIAL DISCLOSURE(S)

Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

Into the storm: the imbalance in the yin-yang immune response as the commonality of cytokine storm syndromes

There is a continuous cycle of activation and contraction in the immune response against pathogens and other threats to human health in life. This intrinsic yin-yang of the immune response ensures that inflammatory processes can be appropriately controlled once that threat has been resolved, preventing unnecessary tissue and organ damage. Various factors may contribute to a state of perpetual immune activation, leading to a failure to undergo immune contraction and development of cytokine storm syndromes. A literature review was performed to consider how the trajectory of the immune response in certain individuals leads to cytokine storm, hyperinflammation, and multiorgan damage seen in cytokine storm syndromes. The goal of this review is to evaluate how underlying factors contribute to cytokine storm syndromes, as well as the symptomatology, pathology, and long-term implications of these conditions. Although the recognition of cytokine storm syndromes allows for universal treatment with steroids, this therapy shows limitations for symptom resolution and survival. By identifying cytokine storm syndromes as a continuum of disease, this will allow for a thorough evaluation of disease pathogenesis, consideration of targeted therapies, and eventual restoration of the balance in the yin-yang immune response.

A Bioinformatics Investigation of Hub Genes Involved in Treg Migration and Its Synergistic Effects, Using Immune Checkpoint Inhibitors for Immunotherapies

This study aimed to identify hub genes involved in regulatory T cell (Treg) function and migration, offering insights into potential therapeutic targets for cancer immunotherapy. We performed a comprehensive bioinformatics analysis using three gene expression microarray datasets from the GEO database. Differentially expressed genes (DEGs) were identified to pathway enrichment analysis to explore their functional roles and potential pathways. A protein-protein interaction network was constructed to identify hub genes critical for Treg activity. We further evaluated the co-expression of these hub genes with immune checkpoint proteins (PD-1, PD-L1, CTLA4) and assessed their prognostic significance. Through this comprehensive analysis, we identified CCR8 as a key player in Treg migration and explored its potential synergistic effects with ICIs. Our findings suggest that CCR8-targeted therapies could enhance cancer immunotherapy outcomes, with breast invasive carcinoma (BRCA) emerging as a promising indication for combination therapy. This study highlights the potential of CCR8 as a biomarker and therapeutic target, contributing to the development of targeted cancer treatment strategies.

A mutation in Themis contributes to anaphylaxis severity following oral peanut challenge in CC027 mice

BACKGROUND

The development of peanut allergy is due to a combination of genetic and environmental factors, although specific genes have proven difficult to identify. Previously, we reported that peanut-sensitized Collaborative Cross strain CC027/GeniUnc (CC027) mice develop anaphylaxis upon oral challenge to peanut, in contrast to C3H/HeJ (C3H) mice.

OBJECTIVE

This study aimed to determine the genetic basis of orally induced anaphylaxis to peanut in CC027 mice.

METHODS

A genetic mapping population between CC027 and C3H mice was designed to identify the genetic factors that drive oral anaphylaxis. A total of 356 CC027xC3H backcrossed mice were generated, sensitized to peanut, then challenged to peanut by oral gavage. Anaphylaxis and peanut-specific IgE were quantified for all mice. T-cell phenotyping was conducted on CC027 mice and 5 additional Collaborative Cross strains.

RESULTS

Anaphylaxis to peanut was absent in 77% of backcrossed mice, with 19% showing moderate anaphylaxis and 4% having severe anaphylaxis. There were 8 genetic loci associated with variation in response to peanut challenge-6 associated with anaphylaxis (temperature decrease) and 2 associated with peanut-specific IgE levels. There were 2 major loci that impacted multiple aspects of the severity of acute anaphylaxis, at which the CC027 allele was associated with worse outcome. At one of these loci, CC027 has a private genetic variant in the Themis gene. Consistent with described functions of Themis, we found that CC027 mice have more immature T cells with fewer CD8+, CD4+, and CD4+CD25+CD127- regulatory T cells.

CONCLUSIONS

Our results demonstrate a key role for Themis in the orally reactive CC027 mouse model of peanut allergy.

Interactions between immune cell types facilitate the evolution of immune traits

An essential prerequisite for evolution by natural selection is variation among individuals in traits that affect fitness1. The ability of a system to produce selectable variation, known as evolvability2, thus markedly affects the rate of evolution. Although the immune system is among the fastest-evolving components in mammals3, the sources of variation in immune traits remain largely unknown4,5. Here we show that an important determinant of the immune system's evolvability is its organization into interacting modules represented by different immune cell types. By profiling immune cell variation in bone marrow of 54 genetically diverse mouse strains from the Collaborative Cross6, we found that variation in immune cell frequencies is polygenic and that many associated genes are involved in homeostatic balance through cell-intrinsic functions of proliferation, migration and cell death. However, we also found genes associated with the frequency of a particular cell type that are expressed in a different cell type, exerting their effect in what we term cyto-trans. The vertebrate evolutionary record shows that genes associated in cyto-trans have faced weaker negative selection, thus increasing the robustness and hence evolvability2,7,8 of the immune system. This phenomenon is similarly observable in human blood. Our findings suggest that interactions between different components of the immune system provide a phenotypic space in which mutations can produce variation with little detriment, underscoring the role of modularity in the evolution of complex systems9.

A suite of selective pressures supports the maintenance of alleles of a Drosophila immune peptide

The innate immune system provides hosts with a crucial first line of defense against pathogens. While immune genes are often among the fastest evolving genes in the genome, in Drosophila , antimicrobial peptides (AMPs) are notable exceptions. Instead, AMPs may be under balancing selection, such that over evolutionary timescales multiple alleles are maintained in populations. In this study, we focus on the Drosophila antimicrobial peptide Diptericin A, which has a segregating amino acid polymorphism associated with differential survival after infection with the Gram-negative bacteria Providencia rettgeri . Diptericin A also helps control opportunistic gut infections by common Drosophila gut microbes, especially those of Lactobacillus plantarum . In addition to genotypic effects on gut immunity, we also see strong sex-specific effects that are most prominent in flies without functional diptericin A . To further characterize differences in microbiomes between different diptericin genotypes, we used 16S metagenomics to look at the microbiome composition. We used both lab reared and wild caught flies for our sequencing and looked at overall composition as well as the differential abundance of individual bacterial families. Overall, we find flies that are homozygous for one allele of diptericin A are better equipped to survive a systemic infection from P. rettgeri , but in general have a shorter lifespans after being fed common gut commensals. Our results suggest a possible mechanism for the maintenance of genetic variation of diptericin A through the complex interactions of sex, systemic immunity, and the maintenance of the gut microbiome.

Non-invasive ventral cervical magnetoneurography as a proxy of in vivo lipopolysaccharide-induced inflammation

Maintenance of autonomic homeostasis is continuously calibrated by sensory fibers of the vagus nerve and sympathetic chain that convey compound action potentials (CAPs) to the central nervous system. Lipopolysaccharide (LPS) intravenous challenge reliably elicits a robust inflammatory response that can resemble systemic inflammation and acute endotoxemia. Here, we administered LPS intravenously in nine healthy subjects while recording ventral cervical magnetoneurography (vcMNG)-derived CAPs at the rostral Right Nodose Ganglion (RNG) and the caudal Right Carotid Artery (RCA) with optically pumped magnetometers (OPM). We observed vcMNG RNG and RCA neural firing rates that tracked changes in TNF-α levels in the systemic circulation. Further, endotype subgroups based on high and low IL-6 responders segregate RNG CAP frequency (at 30-120 min) and based on high and low IL-10 response discriminate RCA CAP frequency (at 0-30 min). These vcMNG tools may enhance understanding and management of the neuroimmune axis that can guide personalized treatment based on an individual's distinct endophenotype.

Long-read RNA-seq demarcates cis- and trans-directed alternative RNA splicing

Genetic regulation of alternative splicing constitutes an important link between genetic variation and disease. Nonetheless, RNA splicing is regulated by both cis-acting elements and trans-acting splicing factors. Determining splicing events that are directed primarily by the cis- or trans-acting mechanisms will greatly inform our understanding of the genetic basis of disease. Here, we show that long-read RNA-seq, combined with our new method isoLASER, enables a clear segregation of cis- and trans-directed splicing events for individual samples. The genetic linkage of splicing is largely individual-specific, in stark contrast to the tissue-specific pattern of splicing profiles. Analysis of long-read RNA-seq data from human and mouse revealed thousands of cis-directed splicing events susceptible to genetic regulation. We highlight such events in the HLA genes whose analysis was challenging with short-read data. We also highlight novel cis-directed splicing events in Alzheimer's disease-relevant genes such as MAPT and BIN1. Together, the clear demarcation of cis- and trans-directed splicing paves ways for future studies of the genetic basis of disease.

Integrating population and single-cell variations in vaccine responses identifies a naturally adjuvanted human immune setpoint

Multimodal single-cell profiling methods can capture immune cell variations unfolding over time at the molecular, cellular, and population levels. Transforming these data into biological insights remains challenging. Here, we introduce a framework to integrate variations at the human population and single-cell levels in vaccination responses. Comparing responses following AS03-adjuvanted versus unadjuvanted influenza vaccines with CITE-seq revealed AS03-specific early (day 1) response phenotypes, including a B cell signature of elevated germinal center competition. A correlated network of cell-type-specific transcriptional states defined the baseline immune status associated with high antibody responders to the unadjuvanted vaccine. Certain innate subsets in the network appeared "naturally adjuvanted," with transcriptional states resembling those induced uniquely by AS03-adjuvanted vaccination. Consistently, CD14+ monocytes from high responders at baseline had elevated phospho-signaling responses to lipopolysaccharide stimulation. Our findings link baseline immune setpoints to early vaccine responses, with positive implications for adjuvant development and immune response engineering.

Comprehensive peripheral blood immunoprofiling reveals five immunotypes with immunotherapy response characteristics in patients with cancer

The lack of comprehensive diagnostics and consensus analytical models for evaluating the status of a patient's immune system has hindered a wider adoption of immunoprofiling for treatment monitoring and response prediction in cancer patients. To address this unmet need, we developed an immunoprofiling platform that uses multiparameter flow cytometry to characterize immune cell heterogeneity in the peripheral blood of healthy donors and patients with advanced cancers. Using unsupervised clustering, we identified five immunotypes with unique distributions of different cell types and gene expression profiles. An independent analysis of 17,800 open-source transcriptomes with the same approach corroborated these findings. Continuous immunotype-based signature scores were developed to correlate systemic immunity with patient responses to different cancer treatments, including immunotherapy, prognostically and predictively. Our approach and findings illustrate the potential utility of a simple blood test as a flexible tool for stratifying cancer patients into therapy response groups based on systemic immunoprofiling.

Modeling and predicting individual variation in COVID-19 vaccine-elicited antibody response in the general population

As we learned during the COVID-19 pandemic, vaccines are one of the most important tools in infectious disease control. To date, an unprecedentedly large volume of high-quality data on COVID-19 vaccinations have been accumulated. For preparedness in future pandemics beyond COVID-19, these valuable datasets should be analyzed to best shape an effective vaccination strategy. We are collecting longitudinal data from a community-based cohort in Fukushima, Japan, that consists of 2,407 individuals who underwent serum sampling two or three times after a two-dose vaccination with either BNT162b2 or mRNA-1273. Using the individually reconstructed time courses of the vaccine-elicited antibody response based on mathematical modeling, we first identified basic demographic and health information that contributed to the main features of the antibody dynamics, i.e., the peak, the duration, and the area under the curve. We showed that these three features of antibody dynamics were partially explained by underlying medical conditions, adverse reactions to vaccinations, and medications, consistent with the findings of previous studies. We then applied to these factors a recently proposed computational method to optimally fit an "antibody score", which resulted in an integer-based score that can be used as a basis for identifying individuals with higher or lower antibody titers from basic demographic and health information. The score can be easily calculated by individuals themselves or by medical practitioners. Although the sensitivity of this score is currently not very high, in the future, as more data become available, it has the potential to identify vulnerable populations and encourage them to get booster vaccinations. Our mathematical model can be extended to any kind of vaccination and therefore can form a basis for policy decisions regarding the distribution of booster vaccines to strengthen immunity in future pandemics.

A multi-organ map of the human immune system across age, sex and ethnicity

Understanding tissue biology's heterogeneity is crucial for advancing precision medicine. Despite the centrality of the immune system in tissue homeostasis, a detailed and comprehensive map of immune cell distribution and interactions across human tissues and demographics remains elusive. To fill this gap, we harmonised data from 12,981 single-cell RNA sequencing samples and curated 29 million cells from 45 anatomical sites to create a comprehensive compositional and transcriptional healthy map of the healthy immune system. We used this resource and a novel multilevel modelling approach to track immune ageing and test differences across sex and ethnicity. We uncovered conserved and tissue-specific immune-ageing programs, resolved sex-dependent differential ageing and identified ethnic diversity in clinically critical immune checkpoints. This study provides a quantitative baseline of the immune system, facilitating advances in precision medicine. By sharing our immune map, we hope to catalyse further breakthroughs in cancer, infectious disease, immunology and precision medicine.

Tissue-specific nonheritable influences drive endometrial immune system variation

Although human twin studies have revealed the combined contribution of heritable and environmental factors in shaping immune system variability in blood, the contribution of these factors to immune system variability in tissues remains unexplored. The human uterus undergoes constant regeneration and is exposed to distinct environmental factors. To assess uterine immune system variation, we performed a system-level analysis of endometrial and peripheral blood immune cells in monozygotic twins. Although most immune cell phenotypes in peripheral blood showed high genetic heritability, more variation was found in endometrial immune cells, indicating a stronger influence by environmental factors. Cytomegalovirus infection was identified to influence peripheral blood immune cell variability but had limited effect on endometrial immune cells. Instead, hormonal contraception shaped the local endometrial milieu and immune cell composition with minor influence on the systemic immune system. These results highlight that the magnitude of human immune system variation and factors influencing it can be tissue specific.

Immunological factors linked to geographical variation in vaccine responses

Vaccination is one of medicine's greatest achievements; however, its full potential is hampered by considerable variation in efficacy across populations and geographical regions. For example, attenuated malaria vaccines in high-income countries confer almost 100% protection, whereas in low-income regions these same vaccines achieve only 20-50% protection. This trend is also observed for other vaccines, such as bacillus Calmette-Guérin (BCG), rotavirus and yellow fever vaccines, in terms of either immunogenicity or efficacy. Multiple environmental factors affect vaccine responses, including pathogen exposure, microbiota composition and dietary nutrients. However, there has been variable success with interventions that target these individual factors, highlighting the need for a better understanding of their downstream immunological mechanisms to develop new ways of modulating vaccine responses. Here, we review the immunological factors that underlie geographical variation in vaccine responses. Through the identification of causal pathways that link environmental influences to vaccine responsiveness, it might become possible to devise modulatory compounds that can complement vaccines for better outcomes in regions where they are needed most.

Unique immune profiles in collaborative cross mice linked to survival and viral clearance upon infection

The response to infection is generally heterogeneous and diverse, with some individuals remaining asymptomatic while others present with severe disease or a diverse range of symptoms. Here, we address the role of host genetics on immune phenotypes and clinical outcomes following viral infection by studying genetically diverse mice from the Collaborative Cross (CC), allowing for use of a small animal model with controlled genetic diversity while maintaining genetic replicates. We demonstrate variation by deeply profiling a broad range of innate and adaptive immune cell phenotypes at steady-state in 63 genetically distinct CC mouse strains and link baseline immune signatures with virologic and clinical disease outcomes following infection of mice with herpes simplex virus 2 (HSV-2) or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This work serves as a resource for CC strain selection based on steady-state immune phenotypes or disease presentation upon viral infection, and further, points to possible pre-infection immune correlates of survival and early viral clearance upon infection.

Single-cell analytical technologies: uncovering the mechanisms behind variations in immune responses

The immune landscape varies among individuals. It determines the immune response and results in surprisingly diverse symptoms, even in response to similar external stimuli. However, the detailed mechanisms underlying such diverse immune responses have remained mostly elusive. The utilization of recently developed single-cell multimodal analysis platforms has started to answer this question. Emerging studies have elucidated several molecular networks that may explain diversity with respect to age or other factors. An elaborate interplay between inherent physical conditions and environmental conditions has been demonstrated. Furthermore, the importance of modifications by the epigenome resulting in transcriptome variation among individuals is gradually being revealed. Accordingly, epigenomes and transcriptomes are direct indicators of the medical history and dynamic interactions with environmental factors. Coronavirus disease 2019 (COVID-19) has recently become one of the most remarkable examples of the necessity of in-depth analyses of diverse responses with respect to various factors to improve treatment in severe cases and to prevent viral transmission from asymptomatic carriers. In fact, determining why some patients develop serious symptoms is still a pressing issue. Here, we review the current "state of the art" in single-cell analytical technologies and their broad applications to healthy individuals and representative diseases, including COVID-19.

Pre-vaccination immunotypes reveal weak and robust antibody responders to influenza vaccination

Effective vaccine-induced immune responses are particularly essential in older adults who face an increased risk of immunosenescence. However, the complexity and variability of the human immune system make predicting vaccine responsiveness challenging. To address this knowledge gap, our study aimed to characterize immune profiles that are predictive of vaccine responsiveness using "immunotypes" as an innovative approach. We analyzed an extensive set of innate and adaptive immune cell subsets in the whole blood of 307 individuals (aged 25-92) pre- and post-influenza vaccination which we associated with day 28 hemagglutination inhibition (HI) antibody titers. Building on our previous work that stratified individuals into nine immunotypes based on immune cell subsets, we identified two pre-vaccination immunotypes associated with weak and one showing robust day 28 antibody response. Notably, the weak responders demonstrated HLA-DR+ T-cell signatures, while the robust responders displayed a high naïve-to-memory T-cell ratio and percentage of nonclassical monocytes. These specific signatures deepen our understanding of the relationship between the baseline of the immune system and its functional potential. This approach could enhance our ability to identify individuals at risk of immunosenescence. Our findings highlight the potential of pre-vaccination immunotypes as an innovative tool for informing personalized vaccination strategies and improving health outcomes, particularly for aging populations.

Highly heterogenous humoral immune response in Lyme disease patients revealed by broad machine learning-assisted antibody binding profiling with random peptide arrays

Introduction

Lyme disease (LD), a rapidly growing public health problem in the US, represents a formidable challenge due to the lack of detailed understanding about how the human immune system responds to its pathogen, the Borrelia burgdorferi bacterium. Despite significant advances in gaining deeper insight into mechanisms the pathogen uses to evade immune response, substantial gaps remain. As a result, molecular tools for the disease diagnosis are lacking with the currently available tests showing poor performance. High interpersonal variability in immune response combined with the ability of the pathogen to use a number of immune evasive tactics have been implicated as underlying factors for the limited test performance.

Methods

This study was designed to perform a broad profiling of the entire repertoire of circulating antibodies in human sera at the single-individual level using planar arrays of short linear peptides with random sequences. The peptides sample sparsely, but uniformly the entire combinatorial sequence space of the same length peptides for profiling the humoral immune response to a B.burg. infection and compare them with other diseases with etiology similar to LD and healthy controls.

Results

The study revealed substantial variability in antibody binding profiles between individual LD patients even to the same antigen (VlsE protein) and strong similarity between individuals diagnosed with Lyme disease and healthy controls from the areas endemic to LD suggesting a high prevalence of seropositivity in endemic healthy control.

Discussion

This work demonstrates the utility of the approach as a valuable analytical tool for agnostic profiling of humoral immune response to a pathogen.

Immunosenescence and Cytomegalovirus: Exploring Their Connection in the Context of Aging, Health, and Disease

Aging induces numerous physiological alterations, with immunosenescence emerging as a pivotal factor. This phenomenon has attracted both researchers and clinicians, prompting profound questions about its implications for health and disease. Among the contributing factors, one intriguing actor in this complex interplay is human cytomegalovirus (CMV), a member of the herpesvirus family. Latent CMV infection exerts a profound influence on the aging immune system, potentially contributing to age-related diseases. This review delves into the intricate relationship between immunosenescence and CMV, revealing how chronic viral infection impacts the aging immune landscape. We explore the mechanisms through which CMV can impact both the composition and functionality of immune cell populations and induce shifts in inflammatory profiles with aging. Moreover, we examine the potential role of CMV in pathologies such as cardiovascular diseases, cancer, neurodegenerative disorders, COVID-19, and Long COVID. This review underlines the importance of understanding the complex interplay between immunosenescence and CMV. It offers insights into the pathophysiology of aging and age-associated diseases, as well as COVID-19 outcomes among the elderly. By unraveling the connections between immunosenescence and CMV, we gain a deeper understanding of aging's remarkable journey and the profound role that viral infections play in transforming the human immune system.

Pattern and Prevalence of Intestinal Helminthiasis among Human Immunodeficiency Virus-Infected Children at the University of Nigeria Teaching Hospital, Ituku-Ozalla, Enugu State

BACKGROUND

Children infected with the human immunodeficiency virus (HIV) may be more prone to helminthic infestation because they have depleted immunity, which increases their susceptibility to infection and infestations, even with minimally pathogenic organisms such as helminths.

AIM

The prevalence and pattern of intestinal helminthiasis among children living with HIV attending the University of Nigeria Teaching Hospital (UNTH), Ituku-Ozalla, Enugu.

PATIENTS AND METHODS

A cross-sectional study in which 70 HIV-infected children were consecutively recruited from the Pediatric HIV clinic and matched for age and sex with 70 children recruited from the children outpatient clinic (CHOP) of UNTH Ituku-Ozalla. Stool samples of study participants were collected and analyzed using the Kato-Katz method and subsequently examined under the microscope for helminths' eggs and larvae. The worm intensity was determined using the theoretical analytic sensitivity (TAS) of 24 eggs per gram (EPG) to obtain the number of eggs per gram of feces. The CD4+ count, which describes the severity of immunosuppression in HIV-positive children was determined using the PARTEC Cyflow counter for the CD4+ lymphocyte count, whereas HIV screening was performed using the rapid diagnostic tests for HIV (Determine, Statpack and Unigold). Data were analyzed using IBM SPSS.

RESULTS

The prevalence of intestinal helminthiasis among HIV-infected and non-infected children was 27.1% and 12.9%, respectively (P = 0.038). HIV-positive children were more likely to have intestinal helminthiasis than HIV-negative children (odds ratio [OR] =2.525, 95% confidence interval [CI]: 1.052-6.063). Ascaris lumbricoides was the predominant helminthic species in both HIV-infected and non-infected groups; however, there was no statistical significance between intestinal helminthic species and HIV status (P = 0.655) but the severity of intestinal helminthiasis was significantly associated with decreasing CD4+ count (P = 0.028). The risk factors for intestinal helminthic infestation examined were similar in both HIV-positive and HIV-negative children (P > 0.05).

CONCLUSION

There was a significantly higher prevalence of helminthic infestation among HIV-infected children compared to their HIV-negative counterparts. The severity of intestinal helminthiasis was significantly associated with decreasing CD4+ count.

A molecular signature for IL-10-producing Th1 cells in protozoan parasitic diseases

Control of visceral leishmaniasis (VL) depends on proinflammatory Th1 cells that activate infected tissue macrophages to kill resident intracellular parasites. However, proinflammatory cytokines produced by Th1 cells can damage tissues and require tight regulation. Th1 cell IL-10 production is an important cell-autologous mechanism to prevent such damage. However, IL-10-producing Th1 (type 1 regulatory; Tr1) cells can also delay control of parasites and the generation of immunity following drug treatment or vaccination. To identify molecules to target in order to alter the balance between Th1 and Tr1 cells for improved antiparasitic immunity, we compared the molecular and phenotypic profiles of Th1 and Tr1 cells in experimental VL caused by Leishmania donovani infection of C57BL/6J mice. We also identified a shared Tr1 cell protozoan signature by comparing the transcriptional profiles of Tr1 cells from mice with experimental VL and malaria. We identified LAG3 as an important coinhibitory receptor in patients with VL and experimental VL, and we reveal tissue-specific heterogeneity of coinhibitory receptor expression by Tr1 cells. We also discovered a role for the transcription factor Pbx1 in suppressing CD4+ T cell cytokine production. This work provides insights into the development and function of CD4+ T cells during protozoan parasitic infections and identifies key immunoregulatory molecules.