A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans.

As part of the Human Functional Genomics Project, which aims to understand the factors that determine the variability of immune responses, we investigated genetic variants affecting cytokine production in response to ex vivo stimulation in two independent cohorts of 500 and 200 healthy individuals. We demonstrate a strong impact of genetic heritability on cytokine production capacity after challenge with bacterial, fungal, viral, and non-microbial stimuli. In addition to 17 novel genome-wide significant cytokine QTLs (cQTLs), our study provides a comprehensive picture of the genetic variants that influence six different cytokines in whole blood, blood mononuclear cells, and macrophages. Important biological pathways that contain cytokine QTLs map to pattern recognition receptors (TLR1-6-10 cluster), cytokine and complement inhibitors, and the kallikrein system. The cytokine QTLs show enrichment for monocyte-specific enhancers, are more often located in regions under positive selection, and are significantly enriched among SNPs associated with infections and immune-mediated diseases. PAPERCLIP.

iPSC-derived organ-on-a-chip models for personalized human genetics and pharmacogenomics studies.

Genome-wide association studies (GWAS) have now correlated hundreds of genetic variants with complex genetic diseases and drug efficacy. Functional characterization of these factors remains challenging, particularly because of the lack of human model systems. Molecular and nanotechnological advances, in particular the ability to generate patient-specific PSC lines, differentiate them into diverse cell types, and seed and combine them on microfluidic chips, have led to the establishment of organ-on-a-chip (OoC) platforms that recapitulate organ biology. OoC technology thus provides unique personalized platforms for studying the effects of host genetics and environmental factors on organ physiology. In this review we describe the technology and provide examples of how OoCs may be used for disease modeling and pharmacogenetic research.

Cycloartane-type triterpenoids from the whole plants of Macrosolen bidoupensis.

One new cycloartane-type triterpenoid, named macrobidoupoic acid A (as an C-24 epimeric mixture, 4a, 4 b), together with three known ones (1-3), were clarified by different chromatography from the M. bidoupensis whole plants. Triterpenoids (1, 3 & 4) were detected for the first time from the Macrosolen genus. Chemical structures of them were illuminated using HR-ESI-MS, and NMR (1 D & 2 D) assessments. The cytotoxic properties of triterpenoids (3 & 4) were examined against two human cancer cell lines (A549, and RD) by MTT assay. As results shown, triterpenoids (3 & 4) possessed moderate cytotoxic activity against A549 and RD cancer cells (IC50 ranged from 5.44 to 39.52 µM).

Implications of climate change and drought on water requirements in a semi-mountainous region of the Vietnamese Mekong Delta.

As the backbone of Vietnam's economy, the country has recently established a number of policies for promoting and investing in smart agriculture in the Mekong Delta, the country's largest agricultural hub, to foster overall socio-economic development. However, water remains a critical constraint for crop production, with progress being hindered by water scarcity and quality issues, and compounded by socio-economic transformation and climate change. Considering these challenges, this study used the CROPWAT model and a wide spectrum of climate change scenarios to investigate future total water demands in the 2030s and 2050s as well as drought levels in two underdeveloped semi-mountainous reservoir catchments, i.e., O Ta Soc and O Tuk Sa in An Giang province. The results suggest that the usable storage capacity of the O Ta Soc reservoir will increase to 650,000 m3 to meet water supply demands under all climate change scenarios and the medium-term, moderate drought conditions. The useable storage capacity of the O Tuk Sa reservoir will also be increased to 880,000 m3 and the irrigation area would see a marked 70% reduction compared to its design irrigation. Under these circumstances, the O Tuk Sa reservoir will continue to supply water under all climate change scenarios and medium-term droughts. As a core element for strategic planning and to ensure efficient management of water resources, the results highlight the importance of estimating potential runoff and rainfall in semi-mountainous reservoir catchments under various drought conditions in order to propose the suitable expansion of the useable water storage capacities.

May Measurement Month 2019: an analysis of blood pressure screening results from the United Kingdom and Republic of Ireland.

In the UK, heart and circulatory diseases account for 29% of all deaths (14% through coronary heart disease and 8% through stroke). In 2015, the prevalence of hypertension was 20% in the UK and 23% in the Republic of Ireland. In 2019, 14% of people registered with a UK general practice had hypertension and yet it was the attributable risk factor for around half of all deaths from coronary heart disease or stroke. We participated in May Measurement Month 2019 to increase awareness of blood pressure (BP) measurement, and to identify the proportion of undiagnosed hypertension and degree of uncontrolled hypertension in the community. The 2019 campaign set up screening sites within the community at places of worship, supermarkets, GP surgeries, workplaces, charity events, community pharmacies, gyms, and various other public places. We screened 10194 participants (mean age 51 ± 18 years, 60% women) and found that 1013 (9.9%) were on antihypertensive treatment, while 3408 (33.4%) had hypertension. Of the 3408 participants with hypertension, only 33.5% were aware of their condition despite 98.8% having previous BP measurements. In those on antihypertensive medication, only 38.2% had controlled BP (<140 and <90 mmHg). Our UK and Republic of Ireland data demonstrate concerning levels of undiagnosed hypertension and sub-optimal BP control in many individuals with a diagnosis. This evidence supports a critical need for better systematic community and primary care screening initiatives.

Frequent use of colistin-based drug treatment to eliminate extended-spectrum beta-lactamase-producing Escherichia coli in backyard chicken farms in Thai Binh Province, Vietnam.

Reports of livestock infections with extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E) are increasing. Based on interviews conducted over a 6-month period, we found that veterinarians in the Vietnamese province of Thai Binh prefer to prescribe colistin-based drugs (CBD) in chicken farms. We aimed to clarify whether CBD use selects for strains of colistin-resistant ESBL-E. With the cooperation of seven local households, we detected ESBL-E in chickens' feces after treating chickens with CBD. Phylogenetic groupings and the presence of CTX-M/AmpC genes were determined, and the multi-antibiotic susceptibility of isolates was analyzed. Our results showed that ESBL-E presented in seven chickens' feces from two households. Seventy-two percent of ESBL-E isolates harbored CTX-M9 and the phylogenetic group A; the colistin minimum inhibitory concentration (MIC) of all isolated ESBL-E ranged from 0.064 to 1 µg mL-1. Moreover, ESBL-E isolates were used to experimentally select for colistin resistance, and the effect of commercial CBD on ESBL-E was investigated. The results showed that an ESBL-E strain with a colistin MIC of 4 µg mL-1 was able to grow in media with CBD. Although CBD treatment was effective, in vitro experiments demonstrated that ESBL-E can easily acquire colistin resistance. Therefore, restrictions on colistin use are necessary to prevent the emergence of colistin-resistant bacteria.

When intervention becomes imperative: a case report of spontaneous vulvar edema during pregnancy.

Spontaneous idiopathic vulvar edema during the second trimester is a rare condition. The approach to managing this condition involves relieving symptoms, identifying underlying causes, and implementing appropriate treatment. Managing such cases during pregnancy is challenging because of concerns for potential adverse fetal outcomes. Conservative management expects the condition to be relieved spontaneously postpartum, whereas invasive treatment offers a more rapid resolution. Treatment choices are controversial because each method has its pros and cons and influences the delivery process to a certain extent. Surgical drainage becomes a viable option when patients are not responsive to medications. We report a case of spontaneous massive vulvar edema in a 22-year-old primigravida in her 23rd week of pregnancy. After ruling out other notable causes of vulvar edema, we decided to intervene using an invasive procedure because she complained of progressive symptoms and discomfort. Subsequently, the edema subsided postprocedure, and the patient experienced successful labor with no complications. This report aims to alert clinicians that drainage attempts should be considered in pregnant patients with worsening symptoms.

Integration of Candida albicans-induced single-cell gene expression data and secretory protein concentrations reveal genetic regulators of inflammation.

Both gene expression and protein concentrations are regulated by genetic variants. Exploring the regulation of both eQTLs and pQTLs simultaneously in a context- and cell-type dependent manner may help to unravel mechanistic basis for genetic regulation of pQTLs. Here, we performed meta-analysis of Candida albicans-induced pQTLs from two population-based cohorts and intersected the results with Candida-induced cell-type specific expression association data (eQTL). This revealed systematic differences between the pQTLs and eQTL, where only 35% of the pQTLs significantly correlated with mRNA expressions at single cell level, indicating the limitation of eQTLs use as a proxy for pQTLs. By taking advantage of the tightly co-regulated pattern of the proteins, we also identified SNPs affecting protein network upon Candida stimulations. Colocalization of pQTLs and eQTLs signals implicated several genomic loci including MMP-1 and AMZ1. Analysis of Candida-induced single cell gene expression data implicated specific cell types that exhibit significant expression QTLs upon stimulation. By highlighting the role of trans-regulatory networks in determining the abundance of secretory proteins, our study serve as a framework to gain insights into the mechanisms of genetic regulation of protein levels in a context-dependent manner.

Environmental allergen reduction in asthma management: an overview.

Asthma is a prevalent non-communicable disease that affects both children and adults. Many patients with severe, uncontrolled asthma could not achieve total control despite using anti-asthmatic drugs. There is increasing evidence that allergy to environmental allergens, including both indoor and outdoor allergens, is associated with asthma symptoms and severe asthma. Frequently reported sensitized allergens were dust mites, cockroaches, grass pollens, molds, pets, and rodents in allergic asthma patients, although the patterns of widespread allergens differed from each country. Allergen avoidance is the cornerstone of asthma management, especially in sensitized subjects. This review summarizes environmental allergen avoidance and clarifies their effects on asthma control. Despite contrasting results about the impact of allergen exposure reduction on asthma control, several studies supported the beneficial effects of reducing asthma-related symptoms or risk of exacerbations as a nondrug therapy. Identifying environmental allergens is helpful for asthma patients, and further studies on clinically effective avoidance methods are required.

Alterations of lipid-related genes during anti-tuberculosis treatment: insights into host immune responses and potential transcriptional biomarkers.

Background: The optimal diagnosis and treatment of tuberculosis (TB) are challenging due to underdiagnosis and inadequate treatment monitoring. Lipid-related genes are crucial components of the host immune response in TB. However, their dynamic expression and potential usefulness for monitoring response to anti-TB treatment are unclear. Methodology: In the present study, we used a targeted, knowledge-based approach to investigate the expression of lipid-related genes during anti-TB treatment and their potential use as biomarkers of treatment response. Results and discussion: The expression levels of 10 genes (ARPC5, ACSL4, PLD4, LIPA, CHMP2B, RAB5A, GABARAPL2, PLA2G4A, MBOAT2, and MBOAT1) were significantly altered during standard anti-TB treatment. We evaluated the potential usefulness of this 10-lipid-gene signature for TB diagnosis and treatment monitoring in various clinical scenarios across multiple populations. We also compared this signature with other transcriptomic signatures. The 10-lipid-gene signature could distinguish patients with TB from those with latent tuberculosis infection and non-TB controls (area under the receiver operating characteristic curve > 0.7 for most cases); it could also be useful for monitoring response to anti-TB treatment. Although the performance of the new signature was not better than that of previous signatures (i.e., RISK6, Sambarey10, Long10), our results suggest the usefulness of metabolism-centric biomarkers. Conclusions: Lipid-related genes play significant roles in TB pathophysiology and host immune responses. Furthermore, transcriptomic signatures related to the immune response and lipid-related gene may be useful for TB diagnosis and treatment monitoring.

Characteristics of allergen profile, sensitization patterns and Allergic Rhinitis in SouthEast Asia.

PURPOSE OF REVIEW: To highlight the characteristics of allergic rhinitis, local allergic rhinitis (LAR), and importance of allergens in Southeast Asian countries. RECENT FINDINGS: The Asia-Pacific region is very diverse with disparities in the epidemiological data between countries as well as in the unmet needs. The prevalence of allergic rhinitis has markedly increased in the past decades, with a high variation between countries, ranging from 4.5--80.3%. In terms of LAR, the reported prevalence in Southeast Asia is similar to that of other Asian countries (3.7-24.9%) but lower than that in western countries. House dust mites, cockroach, pollens, and molds are major allergens that are known triggers for of allergic rhinitis in this region, whereas the association with helminth infection requires further investigation. SUMMARY: There are gaps and high variation between countries in Southeast Asia regarding the prevalence of allergic rhinitis and LAR. Further studies are needed to fully elucidate the association between allergens and allergic rhinitis in Southeast Asia.

Macrotricolorin A, a new diarylpropanoid from the Vietnamese plant Macrosolen tricolor (Lecomte) Danser.

From the Vietnamese plant Macrosolen tricolor (Lecomte) Danser, one new diarylpropanoid, named macrotricolorin A (1) together with three diarylheptanoids including bisdemethoxycurcumin (2), demethoxycurcumin (3) and curcumin (4), were isolated. Their structures were elucidated by intensive analyses of their IR, UV, HR-ESI-MS and NMR (1 D & 2 D) spectra. It is the first time that diarylalkanoids have been reported from the genus Macrosolen. Compound 1 exhibited anti-inflammatory activity against the nitric oxide (NO) production in lipopolysaccharide (LPS)-induced RAW264.7 with an IC50 value of 27.54 ± 1.75 µM.

Pharmacogenomics of Hypersensitivity to Non-steroidal Anti-inflammatory Drugs.

Non-steroidal anti-inflammatory drugs (NSAIDs) are extensively prescribed in daily clinical practice. NSAIDs are the main cause of drug hypersensitivity reactions all over the world. The inhibition of cyclooxygenase enzymes by NSAIDs can perpetuate arachidonic acid metabolism, shunting to the 5-lipoxygenase pathway and its downstream inflammatory process. Clinical phenotypes of NSAID hypersensitivity are diverse and can be classified into cross-reactive or selective responses. Efforts have been made to understand pathogenic mechanisms, in which, genetic and epigenetic backgrounds are implicated in various processes of NSAID-induced hypersensitivity reactions. Although there were some similarities among patients, several genetic polymorphisms are distinct in those exhibiting respiratory or cutaneous symptoms. Moreover, the expression levels, as well as the methylation status of genes related to immune responses were demonstrated to be involved in NSAID-induced hypersensitivity reactions. There is still a lack of data on delayed type reactions. Further studies with a larger sample size, which integrate different genetic pathways, can help overcome current limitations of gen etic/epigenetic studies, and provide valuable information on NSAID hypersensitivity reactions.

Functional characterization of PD1+TIM3+ tumor-infiltrating T cells in DLBCL and effects of PD1 or TIM3 blockade.

In diffuse large B-cell lymphoma (DLBCL), tumor-infiltrating T lymphocytes (TILs) are involved in therapeutic responses. However, tumor-specific TILs can be dysfunctional, with impaired effector functions. Various mechanisms are involved in this exhaustion, and the increased expression of programmed cell death receptor 1 (PD1) and TIM3 on dysfunctional cells suggests their involvement. However, conflicting data have been published regarding their expression or coexpression in DLBCL. We evaluated the presence and phenotype of CD4+ and CD8+ TILs in freshly collected tumor tissues in DLBCL and compared the results with those in follicular lymphoma, classical Hodgkin lymphoma, and nonmalignant reactive lymphadenopathy. We found that TILs expressing both PD1 and TIM3 were expanded in DLBCL, particularly in the activated B cell-like subgroup. Isolated PD1+TIM3+ TILs exhibited a transcriptomic signature related to T-cell exhaustion associated with a reduction in cytokine production, both compromising the antitumor immune response. However, these cells expressed high levels of cytotoxic molecules. In line with this, stimulated PD1+TIM3+ TILs from DLBCL patients exhibited reduced proliferation and impaired secretion of interferon-γ, but these functions were restored by the blockade of PD1 or TIM3. In summary, the PD1+TIM3+ TIL population is expanded and exhausted in DLBCL but can be reinvigorated with appropriate therapies.

Uncoupling of IL-6 signaling and LC3-associated phagocytosis drives immunoparalysis during sepsis.

Immune deactivation of phagocytes is a central event in the pathogenesis of sepsis. Herein, we identify a master regulatory role of IL-6 signaling on LC3-associated phagocytosis (LAP) and reveal that uncoupling of these two processes during sepsis induces immunoparalysis in monocytes/macrophages. In particular, we demonstrate that activation of LAP by the human fungal pathogen Aspergillus fumigatus depends on ERK1/2-mediated phosphorylation of p47phox subunit of NADPH oxidase. Physiologically, autocrine IL-6/JAK2/Ninein axis orchestrates microtubule organization and dynamics regulating ERK recruitment to the phagosome and LC3+ phagosome (LAPosome) formation. In sepsis, loss of IL-6 signaling specifically abrogates microtubule-mediated trafficking of ERK, leading to defective activation of LAP and impaired killing of bacterial and fungal pathogens by monocytes/macrophages, which can be selectively restored by IL-6 supplementation. Our work uncovers a molecular pathway linking IL-6 signaling with LAP and provides insight into the mechanisms underlying immunoparalysis in sepsis.

Inflammatory Protein Profiles in Plasma of Candidaemia Patients and the Contribution of Host Genetics to Their Variability.

Circulatory inflammatory proteins play a significant role in anti-Candida host immune defence. However, little is known about the genetic variation that contributes to the variability of inflammatory responses in response to C. albicans. To systematically characterize inflammatory responses in Candida infection, we profiled 91 circulatory inflammatory proteins in peripheral blood mononuclear cells (PBMCs) stimulated with C. albicans yeast isolated from 378 individuals of European origin from the 500 Functional Genomics (500FG) cohort of the Human Functional Genomics Project (HFGP) and Lifelines Deep cohort. To identify the genetic factors that determine variation in inflammatory protein responses, we correlated genome-wide single nucleotide polymorphism (SNP) genotypes with protein abundance (protein quantitative trait loci, pQTLs) produced by the Candida-stimulated PBMCs. Furthermore, we investigated whether differences in survival of candidaemia patients can be explained by modulating levels of inflammatory proteins. We identified five genome-wide significant pQTLs that modulate IL-8, MCP-2, MMP-1, and CCL3 in response to C. albicans. In addition, our genetic analysis suggested that GADD45G from rs10114707 locus that reached genome-wide significance could be a potential core gene that regulates a cytokine network upon Candida infection. Last but not least, we observed that a trans-pQTL marked from SNP rs7651677 at chromosome 3 that influences urokinase plasminogen activator (uPA) is strongly associated with patient survival (Psurvival = 3.52 x 10-5, OR 3). Overall, our genetic analysis showed that genetic variation determines the abundance of circulatory proteins in response to Candida infection.

Development of ICT01, a first-in-class, anti-BTN3A antibody for activating Vγ9Vδ2 T cell-mediated antitumor immune response.

Gamma delta T (γδ T) cells are among the most potent cytotoxic lymphocytes. Activating anti­butyrophilin 3A (BTN3A) antibodies prime diverse tumor cell types to be killed by Vγ9Vδ2 T cells, the predominant γδ T cell subset in peripheral circulation, by mechanisms independent of tumor antigen­major histocompatibility complex (MHC) complexes. In this report, we describe the development of a humanized monoclonal antibody, ICT01, with subnanomolar affinity for the three isoforms of BTN3A. We demonstrate that ICT01-activated Vγ9Vδ2 T cells kill multiple tumor cell lines and primary tumor cells, but not normal healthy cells, in an efficient process requiring approximately 20% target occupancy. We show that ICT01 activity is dependent on BTN3A and BTN2A but independent of the phosphoantigen (pAg)­binding B30.2 domain. ICT01 delays the growth of hematologic and solid tumor xenografts and prolongs survival of NOD/SCID/IL2rγnull (NSG) mice adoptively transferred with human Vγ9Vδ2 T cells. In single- and multiple-dose safety studies in cynomolgus macaques that received up to 100 mg/kg once weekly, ICT01 was well tolerated. With respect to pharmacodynamic endpoints, ICT01 selectively activated Vγ9Vδ2 T cells without affecting other BTN3A-expressing lymphocytes such as αß T or B cells. A first-in-human, phase 1/2a, open-label, clinical study of ICT01 was thus initiated in patients with advanced-stage solid tumors (EVICTION: NCT04243499; EudraCT: 2019-003847-31). Preliminary results show that ICT01 was well tolerated and pharmacodynamically active in the first patients. Digital pathology analysis of tumor biopsies of a patient with melanoma suggests that ICT01 may promote immune cell infiltration within the tumor microenvironment.

Functional Annotation of Genetic Loci Associated With Sepsis Prioritizes Immune and Endothelial Cell Pathways.

Due to limited sepsis patient cohort size and extreme heterogeneity, only one significant locus and suggestive associations at several independent loci were implicated by three genome-wide association studies. However, genes from such suggestive loci may also provide crucial information to unravel genetic mechanisms that determine sepsis heterogeneity. Therefore, in this study, we made use of integrative approaches to prioritize genes and pathways affected by sepsis associated genetic variants. By integrating expression quantitative trait loci (eQTL) results from the largest whole-blood eQTL database, cytokine QTLs from pathogen-stimulated peripheral blood mononuclear cells (PBMCs), publicly available blood transcriptome data from pneumoniae-derived sepsis patients, and transcriptome data from pathogen-stimulated PBMCs, we identified 55 potential genes affected by 39 independent loci. By performing pathway enrichment analysis at these loci we found enrichment of genes for adherences-junction pathway. Finally, we investigated the functional role of the only one GWAS significant SNP rs4957796 on sepsis survival in altering transcription factor binding affinity in monocytes and endothelial cells. We also found that transient deficiency of FER and MAN2A1 affect endothelial response to stimulation, indicating that both FER and MAN2A1 could be the causal genes at this locus. Taken together, our study suggests that in addition to immune pathways, genetic variants may also affect non-immune related pathways.

Leukocyte-Released Mediators in Response to Both Bacterial and Fungal Infections Trigger IFN Pathways, Independent of IL-1 and TNF-α, in Endothelial Cells.

In sepsis, dysregulated immune responses to infections cause damage to the host. Previous studies have attempted to capture pathogen-induced leukocyte responses. However, the impact of mediators released after pathogen-leukocyte interaction on endothelial cells, and how endothelial cell responses vary depending on the pathogen-type is lacking. Here, we comprehensively characterized the transcriptomic responses of human leukocytes and endothelial cells to Gram negative-bacteria, Gram positive-bacteria, and fungi. We showed that whole pathogen lysates induced strong activation of leukocytes but not endothelial cells. Interestingly, the common response of leukocytes to various pathogens converges on endothelial activation. By exposing endothelial cells to leukocyte-released mediators, we observed a strong activation of endothelial cells at both transcription and protein levels. By adding IL-1RA and TNF-α antibody in leukocyte-released mediators before exposing to endothelial cells, we identified specific roles for IL-1 and TNF-α in driving the most, but not all, endothelial activation. We also showed for the first time, activation of interferon response by endothelial cells in response to leukocyte-released mediators, independently from IL-1 and TNF-α pathways. Our study therefore, not only provides pathogen-dependent transcriptional changes in leukocytes and endothelial cells during infections, but also reveals a role for IFN, together with IL1 and TNFα signaling, in mediating leukocyte-endothelial interaction in infections.

Isobaric tags for relative and absolute quantitation-based proteome analysis of Vietnamese colorectal carcinoma tissues.

CONTEXT: Colorectal cancer (CRC) is one of the most common malignancies and one of the leading causes of cancer death worldwide. Establishing early detection methods or markers of CRC is central to improve the survival rate of CRC patients. Nowadays, new molecular tools have been developed to acquire further knowledge on tumor progression. AIMS: Comparative proteomics analysis of Vietnamese colorectal carcinoma in different stages was performed to gain an insight into the molecular events taking place in CRC and metastasis. SUBJECTS AND METHODS: In this study, the comparative protein expression analysis of ten paired CRC and its corresponding noncancerous tissue samples was performed using the combination of isobaric tags for relative and absolute quantitation labeling and mass spectrometry (MS). The data obtained were further analyzed with Ingenuity Pathways Analysis (IPA) system. RESULTS: Based on the MS/MS spectra analyzed by ProteinPilot software, 684 proteins were identified, out of which 215 were observed to be differentially expressed in at least 1 sample pair. Individual protein expression and variation have been identified for each patient. IPA system demonstrated cytoskeletal signaling as the top-ranked functional pathway network associated with the oncogenic function. CONCLUSIONS: Our study supplemented the understanding about proteome of Vietnamese CRC patients and identified statistically protein expression differences among samples assisting in finding effective biomarkers for CRC diagnostics.