Antigen Gene Research Articles

Utilizing Massively Parallel Sequencing (MPS) of Human Leukocyte Antigen (HLA) Gene Polymorphism to Assess Relatedness in Deficiency Parentage Testing.

In the realm of DNA testing with legal implications, the reliability and precision of genetic markers play a pivotal role in confirming or negating paternity claims. This study aimed to assess the potential utility of human leukocyte antigen (HLA) gene polymorphism through massively parallel sequencing (MPS) technology as robust forensic markers for parentage testing involving genetic deficiencies. It sought to redefine the significance of HLA genes in this context. Data on autosomal short tandem repeat (aSTR) mutational events across 18 paternity cases involving 16 commonly employed microsatellite loci were presented. In instances where traditional aSTR analysis failed to establish statistical certainty, kinship determination was pursued via HLA genotyping, encompassing the amplification of 17 linked HLA loci. Within the framework of this investigation, phase-resolved genotypes for HLA genes were meticulously generated, resulting in the definition of 34 inherited HLA haplotypes. An impressive total of 274 unique HLA alleles, which were classified at either the field 3 or 4 level, were identified, including the discovery of four novel HLA alleles. Likelihood ratio (LR) values, which indicated the likelihood of the observed data under a true biological relationship versus no relationship, were subsequently calculated. The analysis of the LR values demonstrated that the HLA genes significantly enhanced kinship determination compared with the aSTR analysis. Combining LR values from aSTR markers and HLA loci yielded conclusive outcomes in duo paternity cases, showcasing the potential of HLA genes and MPS technology for deeper insights and diversity in genetic testing. Comprehensive reference databases and high-resolution HLA typing across diverse populations are essential. Reintegrating HLA alleles into forensic identification complements existing markers, creating a potent method for future forensic analysis.

P1192 Deciphering the colonic immune landscape of UC from cellular senescence by integrated bioinformatics analysis and machine learning

Abstract Background Nowadays, there has been extensive interest in cellular senescence in gastrointestinal diseases. However, the pathological mechanism of cellular senescence in UC and its involvement in colonic immune characteristics remain enigmatic. Therefore, we aimed to investigate the contribution of cellular senescence-related signatures to the colonic immune landscape in UC based on bioinformatics combined machine learning strategy. Methods Three gene sets of UC were selected from the Gene Expression Omnibus database, including two training sets and one testing set. We identified cellular senescence-associated differentially expressed genes (DEGs) in UC and performed functional enrichment analysis. Afterwards, signature genes were determined by machine learning algorithms including least absolute shrinkage and selection operator (LASSO) regression, support vector machine recursive feature elimination (SVM-RFE), and artificial neural network (ANN). Furthermore, distinct immune microenvironment abnormalities in UC were comprehensively explored, and the correlation between the signature genes and the colonic immune landscape of UC was also evaluated. Based on the signature genes, we clustered UC samples into distinct subtypes by consensus clustering analysis. Finally, we performed validation of the signature genes in dextran sulfate sodium salt (DSS)-induced colitis. Results 41 cellular senescence-associated DEGs in UC were identified by intersecting DEGs with the cellular senescence-associated genes from the CellAge database, which were associated with cellular senescence and immune pathways. Following that, seven signature genes were determined by the machine learning method of LASSO regression, SVM-RFE, and ANN, comprising CXCL1, MMP9, CYR61, BAG3, PEX19, RPS6KA6, and ETS2, which were also validated in the testing set. Furthermore, we obtained the most correlated pairs of UC signature genes-immunocytes and found these signature genes were highly corelated with neutrophils and activated CD4+ memory T cells. Additionally, the expression profiling of human leukocyte antigen genes and immune checkpoints were also analyzed. Subsequently, two molecular subtypes related to senescence that exhibit significantly different immune characteristics were identified. Finally, the mRNA levels of the signature genes were confirmed in DSS-induced colitis, which were congruent with results gained from the datasets. Conclusion In summary, the result has emphasized the essential function of cellular senescence-associated genes in controlling the immune microenvironment for UC. The exploration of the etiopathogenesis of UC through cellular senescence is anticipated to lead to novel advancements in disease diagnosis and potential treatments.

A novel avian intestinal epithelial cell line: its characterization and exploration as an in vitro infection culture model for Eimeria species

BackgroundThe gastrointestinal epithelium plays an important role in directing recognition by the immune system, and epithelial cells provide the host's front line of defense against microorganisms. However, it is difficult to cultivate avian intestinal epithelial cells in vitro for lengthy periods, and the lack of available cell lines limits the research on avian intestinal diseases and nutritional regulation. Chicken coccidiosis is a serious intestinal disease that causes significant economic losses in the poultry industry. In vitro, some cell line models are beneficial for the development of Eimeria species; however, only partial reproduction can be achieved. Therefore, we sought to develop a new model with both the natural host and epithelial cell phenotypes.MethodsIn this study, we use the SV40 large T antigen (SV40T) gene to generate an immortalized cell line. Single-cell screening technology was used to sort positive cell clusters with epithelial characteristics for passage. Polymerase chain reaction (PCR) identification, immunofluorescence detection, and bulk RNA sequencing analysis and validation were used to check the expression of epithelial cell markers and characterize the avian intestinal epithelial cell line (AIEC). AIECs were infected with sporozoites, and their ability to support the in vitro endogenous development of Eimeria tenella was assessed.ResultsThis novel AIEC consistently expressed intestinal epithelial markers. Transcriptome assays revealed the upregulation of genes associated with proliferation and downregulation of genes associated with apoptosis. We sought to compare E. tenella infection between an existing fibroblast cell line (DF-1) and several passages of AIEC and found that the invasion efficiency was significantly increased relative to that of chicken fibroblast cell lines.ConclusionsAn AIEC will serve as a better in vitro research model, especially in the study of Eimeria species development and the mechanisms of parasite–host interactions. Using AIEC helps us understand the involvement of intestinal epithelial cells in the digestive tract and the immune defense of the chickens, which will contribute to the epithelial innate defense against microbial infection in the gastrointestinal tract.Graphical

CanVaxKB: a web-based cancer vaccine knowledgebase.

Cancer vaccines have been increasingly studied and developedto prevent or treat various types of cancers. To systematically survey and analyze different reported cancer vaccines, we developed CanVaxKB (https://violinet.org/canvaxkb), the first web-based cancer vaccine knowledgebase that compiles over 670 therapeutic or preventive cancer vaccines that have been experimentally verified to be effective at various stages. Vaccine construction and host response data are also included. These cancer vaccines are developed against various cancer types such as melanoma, hematological cancer, and prostate cancer. CanVaxKB has stored 263 genes or proteins that serve as cancer vaccine antigen genes, which we have collectively termed 'canvaxgens'. Top three mostly used canvaxgens are PMEL, MLANA and CTAG1B, often targeting multiplecancer types. A total of 193 canvaxgens are also reported in cancer-related ONGene, Network of Cancer Genes and/or Sanger Cancer Gene Consensus databases. Enriched functional annotations and clusters of canvaxgens were identified and analyzed. User-friendly web interfaces are searchable for querying and comparing cancer vaccines. CanVaxKB cancer vaccines are also semantically represented bythe community-based Vaccine Ontology to support data exchange. Overall, CanVaxKB is a timely and vital cancer vaccine source that facilitates efficient collection and analysis, further helping researchers and physicians to better understand cancer mechanisms.

Melanoma Antigen Family A (MAGE A) as Promising Biomarkers and Therapeutic Targets in Bladder Cancer.

The Melanoma Antigen Gene (MAGE) is a large family of highly conserved proteins that share a common MAGE homology domain. Interestingly, many MAGE family members exhibit restricted expression in reproductive tissues but are abnormally expressed in various human malignancies, including bladder cancer, which is a common urinary malignancy associated with high morbidity and mortality rates. The recent literature suggests a more prominent role for MAGEA family members in driving bladder tumorigenesis. This review highlights the role of MAGEA proteins, the potential for them to serve as diagnostic or prognostic biomarker(s), and as therapeutic targets for bladder cancer.

Unwrap RAP1's Mystery at Kinetoplastid Telomeres.

Although located at the chromosome end, telomeres are an essential chromosome component that helps maintain genome integrity and chromosome stability from protozoa to mammals. The role of telomere proteins in chromosome end protection is conserved, where they suppress various DNA damage response machineries and block nucleolytic degradation of the natural chromosome ends, although the detailed underlying mechanisms are not identical. In addition, the specialized telomere structure exerts a repressive epigenetic effect on expression of genes located at subtelomeres in a number of eukaryotic organisms. This so-called telomeric silencing also affects virulence of a number of microbial pathogens that undergo antigenic variation/phenotypic switching. Telomere proteins, particularly the RAP1 homologs, have been shown to be a key player for telomeric silencing. RAP1 homologs also suppress the expression of Telomere Repeat-containing RNA (TERRA), which is linked to their roles in telomere stability maintenance. The functions of RAP1s in suppressing telomere recombination are largely conserved from kinetoplastids to mammals. However, the underlying mechanisms of RAP1-mediated telomeric silencing have many species-specific features. In this review, I will focus on Trypanosoma brucei RAP1's functions in suppressing telomeric/subtelomeric DNA recombination and in the regulation of monoallelic expression of subtelomere-located major surface antigen genes. Common and unique mechanisms will be compared among RAP1 homologs, and their implications will be discussed.

Class II HLA-DRB4 is a predictive biomarker for survival following immunotherapy in metastatic non-small cell lung cancer

Immune checkpoint inhibitors (ICI) are important treatment options for metastatic non-small cell lung cancer (mNSCLC). However, not all patients benefit from ICIs and can experience immune-related adverse events (irAEs). Limited understanding exists for germline determinants of ICI efficacy and toxicity, but Human Leukocyte Antigen (HLA) genes have emerged as a potential predictive biomarker. We performed HLA typing on 85 patients with mNSCLC, on ICI therapy and analyzed the impact of HLA Class II genotype on progression free survival (PFS), overall survival (OS), and irAEs. Most patients received pembrolizumab (83.5%). HLA-DRB4 genotype was seen in 34/85 (40%) and its presence correlated with improved OS in both univariate (p = 0.022; 26.3 months vs 10.2 months) and multivariate analysis (p = 0.011, HR 0.49, 95% CI [0.29, 0.85]). PFS did not reach significance (univariate, p = 0.12, 8.2 months vs 5.1 months). Eleven patients developed endocrine irAEs. HLA-DRB4 was the predominant genotype among these patients (9/11, 81.8%). Cumulative incidence of endocrine irAEs was higher in patients with HLA-DRB4 (p = 0.0139). Our study is the first to suggest that patients with metastatic NSCLC patients on ICI therapy with HLA-DRB4 genotype experience improved survival outcomes. Patients with HLA-DRB4 had the longest median OS (26.3 months). Additionally, we found a correlation between HLA-DRB4 and the occurrence of endocrine irAEs.

Association of KIR Genes with Middle East Respiratory Syndrome Coronavirus Infection in South Koreans.

Middle East respiratory syndrome (MERS) is a lower respiratory tract disease caused by a beta coronavirus (CoV) called MERS-CoV, characterized by a high mortality rate. We aimed to evaluate the association between genetic variation in killer cell immunoglobulin-like receptors (KIRs) and the risk of MERS in South Koreans. KIR genes were genotyped by multiplex polymerase chain reaction with sequence-specific primers (PCR-SSP). A case-control study was performed to identify the odds ratios (OR) of KIR genes for MERS and the association of KIR genes and their ligands, human leukocyte antigens (HLA) genes. KIR2DS4D and KIR3DP1F showed higher frequencies in the group of all patients infected with MERS-CoV than in the control group (p = 0.023, OR = 2.4; p = 0.039, OR = 2.7). KIR2DL1, KIR2DP1, and KIR3DP1D were significantly associated with moderate/mild (Mo/Mi) cases. KIR2DL2, KIR2DS1, and KIR3DP1F were affected in severe cases. When we investigated the association between KIR genes and their ligands in MERS patient and control groups, KIR3DL1+/Bw4(80I)+, KIR3DL1+/Bw6+, KIR3DL1+/Bw6-, KIR2DS1+/C2+, and KIR3DS+/Bw4(80I)+ were associated with MERS. KIR3DL1+/Bw6- was found in Mo/Mi cases. KIR2DS1+/C2+ and KIR2DS2+/C1+ were found in severe cases. Further investigations are needed to prove the various immune responses of MERS-CoV-infected cells according to variations in the KIR gene and ligand gene. A treatment strategy based on current research on the KIR gene and MERS-CoV will suggest potential treatment targets.

The inhibition of colon cancer development by black rice bran on BALB/C Mice

<p>Black rice bran (BRB) is well-known for its high antioxidant activity and its pivotal role in preventing colon cancer. The present study aims to investigate the effects of BRB administration on BALB/C mice induced with azoxymethane (AOM) and dextran sodium sulphate (DSS). The 24 mice were divided into three groups: the group induced by colon cancer (C+), the group induced by cancer and given the BRB diet (C+BRB), and the normal group (C−). Both the C− and C+ groups were given a standard AIN-93 M diet containing cellulose fiber. After 16 weeks, the mice were anesthetized, and the colonic tissue was identified for nodule distribution, histopathological observation, and mRNA expression analysis of proliferating cell nuclear antigen (PCNA), caspase-3, and caspase-8 genes using qRT PCR technique. Nodule distribution in the C+BRB group showed a significant decrease compared to the C+ group, with 1.65 ± 0.71 nodule/cm2 vs. 5.73 ± 2.93 nodule/cm<sup>2</sup>. Then, the colon weight was significantly decreased in the C+BRB group, at 0.19 ± 0.04 (g) compared to 0.25 ± 0.03 (g) in the C+ group. Also, the BRB diet in the C+BRB group significantly decreased PCNA mRNA expression compared to the C+ group, with values of 0.58 ± 0.09-fold change vs. 5.22 ± 0.80-fold change. Conversely, increased the mRNA expression of caspase-3 (0.91 ± 0.20-fold change vs. 0.36 ± 0.15-fold change) and caspase-8 (0.51 ± 0.18-fold change vs. 0.13 ± 0.31-fold change). In conclusion, administration of BRB inhibited the rate of cancer development by suppressing cancer cell proliferation and inducing apoptosis.</p>

Human leucocyte antigens and Japanese patients with polymyalgia rheumatica: the protective effect of DRB1*09:01

ObjectiveThe hallmarks of the chronic inflammatory disease polymyalgia rheumatica (PMR) include pain, and morning stiffness in areas of the neck, shoulder and pelvic girdle. The human leucocyte antigen (HLA) gene...

Molecular prevalence, associated risk factors and phylogenetic evaluation of Theileria lestoquardi in the blood samples of small ruminants.

Raising small ruminants is the main source of income for farmers in Pakistan especially in rural areas of Dera Ghazi Khan in Punjab. Despite having large sheep population, the prevalence of intra-erythrocytic protozoa, Theileria (T.) lestoquardi, has never been reported from this area. This study was conducted to fill this knowledge gap and 333 blood samples of apparently healthy small ruminants (168 sheep and 165 goats) along with their epidemiological data were collected from Dera Ghazi Khan district during August till November 2022. The polymerase chain reaction (PCR) analysis amplified a 785 base pair amplicon specific for the Merozoite surface antigen (ms 1-2) gene of T. lestoquardi in 2 out of the 168 (3.3%) sheep blood samples, while no goat blood sample out of 165 was found to be infected with T. lestoquardi. DNA sequencing confirmed the presence of Theileria lestoquardi in both samples and phylogenetic analysis revealed that these amplicon resembled the partial ms 1-2 gene sequences detected in small ruminants from Pakistan, India Iran and Egypt. All the studied epidemiological factors (age, sex, breed, size of herd, dogs with herd, composition of herd, size of herd and Tick burden on sheep) were not found associated with the prevalence of T. lestoquardi. In conclusion, this study reports a low prevalence of T. lestoquardi infection in the Dera Ghazi Khan District of Punjab, Pakistan. The data generated from this work will help pave the way for the prophylactic detection and control of ovine and caprine theileriosis in the region.

Prevalence of Rickettsia spp., Anaplasma spp. and Ehrlichia spp. in Ornithodoros lahorensis from southern Xinjiang, China

Ticks are important vectors for pathogens and transmit a variety of diseases in humans and animals. Numerous studies have reported the presence of Ixodidae ticks and tick-borne pathogens in southern Xinjiang. However, data pertaining to argasid ticks and argasid tick-associated pathogens are sparse. This study collected a total of 407 ticks from southern Xinjiang. The tick species were identified on the basis of their morphological and mitochondrial 16S ribosomal DNA (16S rDNA) characteristics. The citrate synthase gene (gltA), 17-kilodalton antigen gene (17-kDa), and outer membrane protein A and B genes (ompA, ompB) were amplified using four sets of primers. The species of rickettsiae were further identified on the basis of concatenated sequences. To detect Anaplasma and Ehrlichia, nested PCR was used to amplify the Ehrlichia and Anaplasma 16S rRNA genes, respectively. All 407 ticks were Ornithodoros lahorensis. A total of 109 Rickettsia-positive samples and 19 Anaplasma-positive samples were detected in DNA samples from the 407 ticks. R. sibirica, R. massiliae, Candidatus R. barbariae, A. ovis, A. marginale, and A. phagocytophilum were found. All DNA samples from Or. lahorensis were tested for the presence of the Ehrlichia spp. nucleotide, but none of the samples were positive for such pathogens. This is the first time that R. sibirica, R. massiliae, and A. marginale were detected in Or. lahorensis from southern Xinjiang.

Identification and Blood Transfusion of a Rare A1.02/BA.02 Genotype.

The aim was to analyze the serological and molecular genetic characteristics of a rare B(A) subtype pedigree, explore its pathogenesis, and discuss transfusion strategies. ABO blood typing serological tests were conducted on a female subject and her family member using standard serological methods. Sequencing analysis of the ABO gene exons 6 and 7 was performed using PCR technique for the female subject and her family member to examine the blood types of the participants. The serological test results showed a discrepancy between the forward and reverse typings of the female subject. The forward typing was similar to that of AB subtype serological forward typing, while the reverse typing indicated AB blood type. Based on the sequencing results, it is inferred that the female subject and her son have 8 mutations on one BA.02 chain: 297A>G, 526C>G, 657C>T, 700C>G, 703G>A, 796C>A, 803G>C, and 930G>A. Comparing these eight mutation sites with the Blood Group Antigen Gene Mutation Database (BGMUT), it was found that the female subject had a heterozygous mutation at c.700C>G in the 7th exon of the B.01 gene, consistent with the characteristics of the BA.02 allele. The genotype of the female subject was determined as A1.02/ BA.02, while the genotype of her son was determined as O.01.01/BA.02. The serological presentation of the B(A) subtype for the female subject reported in this study was unique. It differed from previously reported cases, indicating that the determination of B(A) subtypes cannot solely rely on serological testing. It requires a comprehensive analysis combining the results of genetic testing and pedigree investigation.

Characterization and molecular identification of the lumpy skin disease virus in cattle in the Mekong Delta of Vietnam.

Lumpy skin disease (LSD) is caused by a virus belonging to the genus Capripoxvirus, exhibiting clinical symptoms ranging from mild signs to the development of nodules. LSD emerged in Asia and Southeast Asia, including Vietnam, in October 2020 and has since spread throughout the region, resulting in productivity and economic losses. This study aimed to investigate the virus-causing papular dermatitis in cattle from the Mekong Delta region of Vietnam by analyzing its GPCR gene and assessing its evolutionary relationship with sequences in the GenBank database. Blood samples (n = 180) were collected from cattle farms in Ben Tre, Tien Giang, and Tra Vinh provinces. PCR targeting the P32 antigen gene was utilized to detect LSDV presence, and GPCR gene amplification was performed to assess genetic variability. LSDV was detected in 8.33% (15/180) of the samples using PCR targeting the P32 antigen gene. Each sample that tested positive for LSDV demonstrated complete amplification of the GPCR gene. Sequence alignments and phylogenetic analyses of the GPCR gene revealed that Mekong Delta LSDV isolates shared genetic similarities and possessed a 12-nucleotide insertion comparable to strains from China in 2019 and Northern Vietnam in 2020. This study provides preliminary insights into the molecular characteristics of LSDV in cattle from the Mekong Delta region of Vietnam. The observed genetic relatedness to other LSDV sequences from Asia and Southeast Asia underscores the importance of regional surveillance and control measures. These findings contribute to the development of effective strategies for LSDV control and prevention.

Detection and quantification of Babesia bovis and Babesia bigemina using different target genes

Molecular assays have been widely used for the detection and quantification of bovine babesiosis due to their high sensitivity and specificity. However, variations in the sensitivity of pathogen detection may occur depending on the selected target gene. Thus, this study aimed to compare the detection sensitivity (DS) of Babesia bovis and B. bigemina infection levels in artificially and naturally infected cattle using quantitative PCR (qPCR) and six target genes. For B. bovis, the merozoite surface antigen genes 2b and 2c (msa-2b and msa-2c), and the mitochondrial cytochrome b gene (cybmt) were used. For B. bigemina, the genes encoding the proteins associated with rhoptry 1c (rap-1c), rap-1a, and cybmt were used. Six bovines, free of babesiosis, were artificially infected with 1 × 10−8 red blood cells infected (iRBC) with B. bovis (n = 3) or 1 × 10−6B. bigemina iRBC (n = 3). The animals were evaluated daily until parasitemia was confirmed (≥ 2.0%). The quantity of iRBC present in each animal was determined by examining blood smears. Blood samples were then subjected to DNA extraction, serial dilution, and qPCR analysis to determine the DS of each target gene. In addition, 30 calves naturally infected by Babesia spp. were also evaluated using the same six target genes. Regarding the artificial infection, B. bovis cybmt showed 25-fold higher sensitivity than the msa-2b and msa-2c genes, while the B. bigemina cybmt exhibited 5-fold and 25-fold higher sensitivity than the rap-1a and rap-1c genes, respectively. The rap-1a gene was found to be 5 times more sensitive than the rap-1c gene, while the B. bovis msa-2b and msa-2c genes exhibited similar DS. The positive frequencies of naturally infected calves for the target cybmt, msa-2b, and msa-2c genes (B. bovis) were: 100%, 33.3% and 50%, while cybmt, rap-1a, and rap-1c genes (B. bigemina) were 90%, 83.3%, and 63.3%, respectively. This study may contribute to the selection of suitable genes for molecular monitoring of bovine babesiosis. Mitochondrial genes could be considered as an alternative to improve the sensitivity of B. bovis and B. bigemina detection using qPCR.

Prognosis and immunotherapy significances of a cancer-associated fibroblasts-related gene signature in lung adenocarcinoma.

Cells associated with cancer (CAFs) contribute significantly to the stroma of a tumor microenvironment (TME), which is related to the occurrence, treatment, and prognosis of lung adenocarcinoma (LUAD). Therefore, this study investigated the function of CAF-associated genes in the microenvironment of LUAD. The Cancer Genome Atlas (TCGA) database was used to download RNA-seq data from the TCGA Lung Adenocarcinoma cohort (TCGA-LUAD). The GSE68465 dataset, as the external validation set, was from the Gene Expression Omnibus (GEO) database. Besides, CAF-associated genes were sourced from the GeneCards and Molecular Signatures Database (MsigDB). For LUAD, differentially expressed CAF-related genes were selected from overlapping CAF and LUAD patient and control samples. Next, LASSO and Univariate Cox analyses were used to construct the risk model. Additionally, an analysis of Cox regression was used to construct a nomogram. Next, the immune infiltration in malignant tumour tissues was compared between high- and low-risk groups using Estimation of STromal and Immune cells in MAlignant Tumours (ESTIMATE) tissues and Cell-type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT). The sensitivity differences of immunotherapy between the two risk groups were estimated by Tumor Immune Dysfunction and Exclusion (TIDE), and compared by rank-sum test. Finally, the model genes were detected by fluorescent real-time quantitative polymerase chain reaction (qRT-PCR). A total of 57 DE-CAFGs were acquired, and 9 of them (SHCBP1, CCNA2, AKAP12, CCNB1, GALNT3, SCGB1A1, CPS1, CDC6, and CXCL13) were selected as prognostic biomarkers. The Cox independent prognosis revealed the RiskScore and Stage were the two LUAD independent prognosis factors Moreover, 11 types of immune cells (memory B cells, resting natural killer cells (NK cells), Eosinophils, Macrophages M0, CD4 memory resting T cells, CD4 memory activated T cells, resting Mast cells, naive B cells, T cells regulatory (Tregs), neutrophils, and plasma cell), and 18 human leukocyte antigen (HLA) genes were different with the two risk groups. Lastly, the TIDE analysis showed differences between the two risk groups for TIDE, T cell dysfunction, and T cell exclusion, PD-L1 treatment scores. Lastly, Both LUAD and normal samples expressed the 9 model genes differently. A CAF-related prognostic model was constructed, which may have potential immunotherapy guiding significance for LUAD patients.

Genomic characterization of Bordetella pertussis in South Africa, 2015-2019.

Pertussis remains a public health concern in South Africa, with an increase in reported cases and outbreaks in recent years. Whole genome sequencing was performed on 32 Bordetella pertussis isolates sourced from three different surveillance programmes in South Africa between 2015 and 2019. Genome sequences were characterized using multilocus sequence typing, vaccine antigen genes (ptxP, ptxA, ptxB, prn and fimH) and overall genome structure. All isolates were sequence type 2 and harboured the pertussis toxin promoter allele ptxP3. The dominant genotype was ptxP3-ptxA1-ptxB2-prn2-fimH2 (31/32, 96.9 %), with no pertactin-deficient or other mutations in vaccine antigen genes identified. Amongst 21 isolates yielding closed genome assemblies, eight distinct genome structures were detected, with 61.9 % (13/21) of the isolates exhibiting three predominant structures. Increases in case numbers are probably not due to evolutionary changes in the genome but possibly due to other factors such as the cyclical nature of B. pertussis disease, waning immunity due to the use of acellular vaccines and/or population immunity gaps.

Multiplex Assays for Analysis of Antibody Responses to South Asian Plasmodium falciparum and Plasmodium vivax Malaria Infections.

Malaria remains a major global health challenge, causing over 0.6 million yearly deaths. To understand naturally acquired immunity in adult human populations in malaria-prevalent regions, improved serological tools are needed, particularly where multiple malaria parasite species co-exist. Slide-based and bead-based multiplex approaches can help characterize antibodies in malaria patients from endemic regions, but these require pure, well-defined antigens. To efficiently bypass purification steps, codon-optimized malaria antigen genes with N-terminal FLAG-tag and C-terminal Ctag sequences were expressed in a wheat germ cell-free system and adsorbed on functionalized BioPlex beads. In a pilot study, 15 P. falciparum antigens, 8 P. vivax antigens, and a negative control (GFP) were adsorbed individually on functionalized bead types through their Ctag. To validate the multiplexing powers of this platform, 10 P. falciparum-infected patient sera from a US NIH MESA-ICEMR study site in Goa, India, were tested against all 23 parasite antigens. Serial dilution of patient sera revealed variations in potency and breadth of antibodies to various parasite antigens. Individual patients revealed informative variations in immunity to P. falciparum versus P. vivax. This multiplex approach to malaria serology captures varying immunity to different human malaria parasite species and different parasite antigens. This approach can be scaled to track the dynamics of antibody production during one or more human malaria infections.

Genetic Susceptibility of HLA Alleles to Non-Steroidal Anti-Inflammatory Drug Hypersensitivity in the Taiwanese Population.

Human leukocyte antigen (HLA) genes are important in many immune processes and contribute to many adverse drug reactions. Whether genetic variations in the HLA region are associated with non-steroid anti-inflammatory drug (NSAID) hypersensitivity remains uncertain. Therefore, the aim of our study was to identify HLA genetic variations in patients with NSAID hypersensitivity in the Taiwanese population. This hospital-based, retrospective case-control study enrolled 37,156 participants with NSAID exposure from the Taiwan Precision Medicine Initiative (TPMI), who were all genotyped and imputed to fine map HLA typing. Our study assigned 1217 cases to the NSAID allergy group and 12,170 controls to a matched group. Logistic regression analyses were utilized to explore associations between HLA alleles and NSAID hypersensitivity. Overall, 13,387 patients were genotyped for eight major HLA alleles. Allele frequencies were different between the two groups. In the NSAID allergy group, the genotype frequencies of HLA-A*02:01, HLA-A*34:01, and HLA-DQA1*06:01 were found to be markedly elevated compared to the control group, a significance that persisted even after applying the Bonferroni correction. Furthermore, the risk of NSAID allergy demonstrated a significant association with HLA-A*02:01 (OR = 1.29, p < 0.001) and HLA-A*34:01 (OR = 9.90, p = 0.001), in comparison to their respective counterparts. Notably, the genotype frequency of HLA-B*46:01 exhibited a significant increase in the severe allergy group when compared with the mild allergy group. We identified HLA genotypes linked to the onset and severity of NSAID hypersensitivity. Our findings establish a basis for precision prescription in future clinical applications.

Expression of Melanoma Antigen Genes A11 and A12 in Non-Small Cell Lung Cancer

Highlights:1. In this study, new primers designed using the semi-nested polymerase chain reaction (PCR) method were utilized to identify MAGE-A11 and MAGE-A12 expressions in specimens collected from core biopsy, forcep biopsy, and bronchoalveolar lavage.2. The histopathological analysis revealed positive expressions of MAGE-A11 and MAGE-A12 in specimens diagnosed with non-small cell lung cancer (NSCLC) as well as in specimens with no malignant cells. AbstractThe melanoma antigen gene (MAGE) belongs to the group of cancer testis antigens that are exclusively expressed in germ cells but may be re-expressed in cancer cells. The highly expressed MAGE-A subfamily in lung cancer may potentially be a diagnostic and prognostic biomarker. This study aimed to identify MAGE-A11 and MAGE-A12 expressions in lung tumors obtained from core biopsy, forceps biopsy, and bronchoalveolar lavage specimens. A cross-sectional observational study was conducted on 90 patients clinically diagnosed with lung tumors. These patients received core biopsy, forceps biopsy, and bronchoalveolar lavage interventions after ethical approval was obtained. The complementary deoxyribonucleic acid (cDNA) quality was assessed by the polymerase chain reaction (PCR) of glyceraldehyde-3-phosphate dehydrogenase (GAPDH). The assessment was performed to ascertain if all specimens exhibited positive PCR amplification of the GAPDH gene. MAGE-A11 and MAGE-A12 were identified through a semi-nested reverse transcription PCR. The positive results were detected by measuring the PCR products, with MAGE-A11 and MAGE-A12 measuring at base pairs (bp) of 858 and 496 in the first and second rounds, respectively. The expressions of MAGE-A11 and MAGE-A12 were observed in 3 (3.33%) and 40 (44.44%) out of 90 specimens, respectively. The prevalence rate of non-small cell lung cancer (NSCLC) was 31.11% (28/90). Among these cases, 3.57% (1/28) showed the expression of MAGE-A11, while 32.14% (9/28) exhibited the expression of MAGE-A12. Sixty-two (68.89%) out of 90 patients were diagnosed with no tumor cell malignancy. Out of 62 cases, 2 (3.23%) exhibited the expression of MAGE-A11, while 31 (50%) demonstrated the expression of MAGE-A12. MAGE-A11 and MAGE-A12 were detected in NSCLC and in certain specimens with a pathological diagnosis that indicated the absence of malignant cells. In conclusion, MAGE A11 and MAGE A12 have potential markers that can improve the pathological diagnosis of lung cancer. Further investigation is necessary to explore the expression of MAGE-A in correlation with lung cancer progression.