bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of long-term climate trends on the methane and CO2 exchange processes of Toolik Lake, Alaska
Authors: Eugster Werner , DelSontro Tonya , Laundre James A. , Dobkowski Jason , Shaver Gaius R. , Kling George W.
Published: September 2022

Methane and carbon dioxide effluxes from aquatic systems in the Arctic will affect and likely amplify global change. As permafrost thaws in a warming world, more dissolved organic carbon (DOC) and greenhouse gases are produced and move from soils to surface waters where the DOC can be oxidized to CO2 and also released to the atmosphere. Our main study objective is to measure the release of carbon to the atmosphere via effluxes of methane (CH4) and carbon dioxide (CO2) from Toolik Lake, a deep, dimictic, low-arctic lake in northern Alaska. By combining direct eddy covariance flux measurements with continuous gas pressure measurements in the lake surface waters, we quantified the k600 piston velocity that controls gas flux across the air–water interface. Our measured k values for CH4 and CO2 were substantially above predictions from several models at low to moderate wind speeds, and only converged on model predictions at the highest wind speeds. We attribute this higher flux at low wind speeds to effects on water-side turbulence resulting from how the surrounding tundra vegetation and topography increase atmospheric turbulence considerably in this lake, above the level observed over large ocean surfaces. We combine this process-level understanding of gas exchange with the trends of a climate-relevant long-term (30 + years) meteorological data set at Toolik Lake to examine short-term variations (2015 ice-free season) and interannual variability (2010–2015 ice-free seasons) of CH4 and CO2 fluxes. We argue that the biological processing of DOC substrate that becomes available for decomposition as the tundra soil warms is important for understanding future trends in aquatic gas fluxes, whereas the variability and long-term trends of the physical and meteorological variables primarily affect the timing of when higher or lower than average fluxes are observed. We see no evidence suggesting that a tipping point will be reached soon to change the status of the aquatic system from gas source to sink. We estimate that changes in CH4 and CO2 fluxes will be constrained with a range of +30% and −10% of their current values over the next 30 years.
qPCRtools: An R package for qPCR data processing and visualization
Authors: Li Xiang , Wang Yingmin , Li Jingyu , Mei Xinyue , Liu Yixiang , Huang Huichuan
Published: September 2022

In biological research, qPCR is a technique that is frequently used to measure gene expression levels. The calculation of gene amplification efficiency is a critical step in the processing of qPCR data since it helps to decide which method to employ to compute gene expression levels. Here, we introduce the R package qPCRtools, which enables users to analyze the efficiency of gene amplification. Additionally, this software can determine gene expression levels using one of three approaches: the conventional curve-based method, the 2−ΔΔCt method, and the SATQPCR method. The qPCRtools package produces a table with the statistical data of each method as well as a figure with a box or bar plot illustrating the results. The R package qPCRtools is freely available at CRAN (https://CRAN.R-project.org/package=qPCRtools) or GitHub (https://github.com/lixiang117423/qPCRtools/tree/main/CRAN/qPCRtools).
Microtubule modification defects underlie cilium degeneration in cell models of retinitis pigmentosa associated with pre-mRNA splicing factor mutations
Authors: Nazlamova Liliya , Villa Vasquez Suly Saray , Lord Jenny , Karthik Varshini , Cheung Man-Kim , Lakowski Jörn , Wheway Gabrielle
Published: September 2022

Retinitis pigmentosa (RP) is the most common cause of hereditary blindness, and may occur in isolation as a non-syndromic condition or alongside other features in a syndromic presentation. Biallelic or monoallelic mutations in one of eight genes encoding pre-mRNA splicing factors are associated with non-syndromic RP. The molecular mechanism of disease remains incompletely understood, limiting opportunities for targeted treatment. Here we use CRISPR and base edited PRPF6 and PRPF31 mutant cell lines, and publicly-available data from human PRPF31+/− patient derived retinal organoids and PRPF31 siRNA-treated organotypic retinal cultures to confirm an enrichment of differential splicing of microtubule, centrosomal, cilium and DNA damage response pathway genes in these cells. We show that genes with microtubule/centrosome/centriole/cilium gene ontology terms are enriched for weak 3′ and 5′ splice sites, and that subtle defects in spliceosome activity predominantly affect efficiency of splicing of these exons. We suggest that the primary defect in PRPF6 or PRPF31 mutant cells is microtubule and centrosomal defects, leading to defects in cilium and mitotic spindle stability, with the latter leading to DNA damage, triggering differential splicing of DNA damage response genes to activate this pathway. Finally, we expand understanding of “splicing factor RP” by investigating the function of TTLL3, one of the most statistically differentially expressed genes in PRPF6 and PRPF31 mutant cells. We identify that TTLL3 is the only tubulin glycylase expressed in the human retina, essential for monoglycylation of microtubules of the cilium, including the retinal photoreceptor cilium, to prevent cilium degeneration and retinal degeneration. Our preliminary data suggest that rescue of tubulin glycylation through overexpression of TTLL3 is sufficient to rescue cilium number in PRPF6 and PRPF31 mutant cells, suggesting that this defect underlies the cellular defect and may represent a potential target for therapeutic intervention in this group of disorders.
Investigation of chicken housekeeping genes using next-generation sequencing data
Authors: Hasanpur Karim , Hosseinzadeh Sevda , Mirzaaghayi Atiye , Alijani Sadegh
Published: September 2022

Accurate normalization of the gene expression assays, using housekeeping genes (HKGs), is critically necessary. To do so, selection of a proper set of HKGs for a specific experiment is of great importance. Despite many studies, there is no consensus about the suitable set of HKGs for implementing in the quantitative real-time PCR analyses of chicken tissues. A limited number of HKGs have been widely used. However, wide utilization of a little number of HKGs for all tissues is challenging. The emergence of high-throughput gene expression RNA-seq data has enabled the simultaneous comparison of the stability of multiple HKGs. Therefore, employing the average coefficient of variations of at least three datasets per tissue, we sorted all reliably expressed genes (REGs; with FPKM ≥ 1 in at least one sample) and introduced the top 10 most suitable and stable reference genes for each of the 16 chicken tissues. We evaluated the consistency of the results of five tissues using the same methodology on other datasets. Furthermore, we assessed 96 previously widely used HKGs (WU-HKGs) in order to challenge the accuracy of the previous studies. The New Tuxedo software suite was used for the main analyses. The results revealed novel, different sets of reference genes for each of the tissues with 17 common genes among the top 10 genes lists of 16 tissues. The results did disprove the suitability of WU-HKGs such as Actb, Ldha, Scd, B2m, and Hprt1 for any of the tissues examined. On the contrary, a total of 6, 13, 14, 23, and 32 validated housekeeping genes (V-HKGs) were discovered as the most stable and suitable reference genes for muscle, spleen, liver, heart, and kidney tissues, respectively. Although we identified a few new HKGs usable for multiple tissues, the selection of suitable HKGs is required to be tissue specific. The newly introduced reference genes from the present study, despite lacking experimental validation, will be able to contribute to the more accurate normalization for future expression analysis of chicken genes.
Synergistic effects of rare variants of ARHGAP31 and FBLN1 in vitro in terminal transverse limb defects
Authors: Tian Hong , Chu Fan , Li Yingjie , Xu Mengmeng , Li Wenjiao , Li Chuanzhou
Published: September 2022

Background: Aplasia cutis congenita (ACC) and terminal transverse limb defects (TTLDs) are the most common features of Adams-Oliver syndrome (AOS). ARHGAP31 is one of the causative genes for autosomal dominant forms of AOS, meanwhile its variants may only cause isolated TTLD. Here, we report a proband presented with apparent TTLD but not ACC.

Methods: Whole exome sequencing (WES) and Sanger sequencing were applied to identify causative genes. Expression vectors were constructed for transfections in mammalian cell cultures followed by biochemical and functional analysis including immunoblotting, immunofluorescence staining, and cell counting kit-8 assay.

Results: WES and Sanger sequencing suggested that the proband inherited rare ARHGAP31 variant [c.2623G > A (p.Glu875Lys)] and a rare FBLN1 variant [c.1649G > A (p.Arg550His)] from one of her asymptomatic parents, respectively. Given FBLN1 variation has also been linked to syndactyly, we suspected that the two genes together contributed to the TTLD phenotype and explored their possible roles in vitro. Mutant FBLN1 showed reduced expression resulted from impaired protein stability, whereas ARHGAP31 protein expression was unaltered by mutation. Functional assays showed that only in the co-transfected group of two mutants cell viability was decreased, cell proliferation was impaired, and apoptosis was activated. Cdc42 activity was declined by both ARHGAP31 mutation and FBLN1 mutation alone, and the two together. Furthermore, the MAPK/ERK pathway was only activated by two mutants co-transfected group compared with two wild-type transfections.

Conclusion: We report a case carrying two rare variants of limb defects associated genes, ARHGAP31 and FBLN1, and provide in vitro evidence that synergistic disruption of cellular functions attributed by the two mutants may potentiate the penetrance of clinical manifestations, expanding our knowledge of clinical complexity of causal gene interactions in TTLD and other genetic disorders.
miR-21-5p/PRKCE axis implicated in immune infiltration and poor prognosis of kidney renal clear cell carcinoma
Authors: Wang Jinxiang , Jin Jie , Liang Yanling , Zhang Yihe , Wu Nisha , Fan Mingming , Zeng Fangyin , Deng Fan
Published: September 2022

Kidney renal clear cell carcinoma (KIRC or ccRCC) is the most notorious subtype of renal cell carcinoma for its poor prognosis. Mounting evidence has highlighted the key role of PRKCE in the initiation and development of several types of human cancer, including kidney renal clear cell carcinoma (KIRC). However, the mechanism of PRKCE aberrant expression and the specific clinical correlation of PRKCE expression with immune cell infiltration in KIRC remains elusive. Therefore, we analyzed the relationship between PRKCE and KIRC using many databases, including Oncomine, TCGA, GTEx, TIMER, and GEO. We found that PRKCE decreased in KIRC tumor tissue compared to normal tissue. The Kaplan-Meier Plotter analysis and Univariate and Multivariate Cox analyses were used to evaluate the association between PRKCE and clinicopathological variables and prognosis. Low PRKCE expression was associated with poor survival and histologic grade, T stage, pathologic stage, and M stage. Besides, the C-indexes and calibration plots of the nomogram based on multivariate analysis showed an effective predictive performance for KIRC patients. In addition, PRKCE may be positively correlated with inflammation and negatively correlated with proliferation, metastasis, and invasion as identified by CancerSEA. Moreover, overexpression of PRKCE suppressed ACHN and Caki-1 cell proliferation, migration, and invasion in vitro. Additionally, methylation level data acquired from UALCAN, DiseaseMeth, CCLE, LinkedOmics, and MEXPRESS was used to investigate the relationship between PRKCE expression and PRKCE methylation level. Furthermore, upstream potential miRNA predictions were further performed to explore the mechanism of PRKCE decreased expression in KIRC using multiple online databases available on publicly assessable bioinformatics platforms. High PRKCE methylation levels and hsa-miR-21-5p may contribute to PRKCE low expression in KIRC. Finally, an analysis of immune infiltration indicated that PRKCE was associated with immune cell infiltration. Importantly, PRKCE may affect prognosis partially by regulating immune infiltration in KIRC. In summary, PRKCE may serve as a novel prognostic biomarker reflecting immune infiltration level and a novel therapeutic target in KIRC.
Methylmercury-induced DNA methylation—From epidemiological observations to experimental evidence
Authors: Cediel-Ulloa Andrea , Yu Ximiao , Hinojosa Maria , Johansson Ylva , Forsby Anna , Broberg Karin , Rüegg Joëlle
Published: September 2022

Methylmercury (MeHg) is a developmental neurotoxicant, and one potential mechanism of MeHg toxicity is epigenetic dysregulation. In a recent meta-analysis of epigenome-wide association studies (EWAS), associations between prenatal MeHg exposure and DNA methylation at several genomic sites were identified in blood from newborns and children. While EWASs reveal human-relevant associations, experimental studies are required to validate the relationship between exposure and DNA methylation changes, and to assess if such changes have implications for gene expression. Herein, we studied DNA methylation and gene expression of five of the top genes identified in the EWAS meta-analysis, MED31, MRPL19, GGH, GRK1, and LYSMD3, upon MeHg exposure in human SH-SY5Y cells exposed to 8 or 40 nM of MeHg during differentiation, using bisulfite-pyrosequencing and qPCR, respectively. The concentrations were selected to cover the range of MeHg concentrations in cord blood (2–8.5 μg/L) observed in the cohorts included in the EWAS. Exposure to MeHg increased DNA methylation at MED31, a transcriptional regulator essential for fetal development. The results were in concordance with the epidemiological findings where more MED31 methylation was associated with higher concentrations of MeHg. Additionally, we found a non-significant decrease in DNA methylation at GGH, which corresponds to the direction of change observed in the EWAS, and a significant correlation of GGH methylation with its expression. In conclusion, this study corroborates some of the EWAS findings and puts forward candidate genes involved in MeHg’s effects on the developing brain, thus highlighting the value of experimental validation of epidemiological association studies.
Discovery of the first PD-1 ligand encoded by a pathogen
Authors: Martínez-Vicente Pablo , Poblador Francesc , Leitner Judith , Farré Domènec , Steinberger Peter , Engel Pablo , Angulo Ana
Published: September 2022

Large double-stranded DNA viruses deploy multiple strategies to subvert host immune defenses. Some of these tactics are mediated by viral gene products acquired by horizontal gene transfer from the corresponding hosts and shaped throughout evolution. The programmed death-1 (PD-1) receptor and its ligands, PD-L1 and PD-L2, play a pivotal role attenuating T-cell responses and regulating immune tolerance. In this study, we report the first functional PD-L1 homolog gene (De2) found in a pathogen. De2, captured by a γ-herpesvirus from its host during co-evolution around 50 million years ago, encodes a cell-surface glycoprotein that interacts with high affinity and stability with host PD-1. We also find that mutations evolved by the viral protein result in a significant loss of its ability to interact in cis with CD80, an interaction that for PD-L1:CD80 has been reported to block PD-1 inhibitory pathways. Furthermore, we demonstrate that the viral protein strongly inhibits T-cell signaling. Our observations suggest that PD-L1 homologs may enable viruses to evade T cell responses, favor their replication, and prevent excessive tissue damage. Altogether, our findings reveal a novel viral immunosuppressive strategy and highlight the importance of the modulation of the PD-1/PD-L1 axis during viral infections.
Dietary mannan oligosaccharides strengthens intestinal immune barrier function via multipath cooperation during Aeromonas Hydrophila infection in grass carp (Ctenopharyngodon Idella)
Authors: Lu Zhi-Yuan , Feng Lin , Jiang Wei-Dan , Wu Pei , Liu Yang , Jiang Jun , Kuang Sheng-Yao , Tang Ling , Li Shu-Wei , Zhong Cheng-Bo , Zhou Xiao-Qiu
Published: September 2022

In recent years, mannose oligosaccharide (MOS) as a functional additive is widely used in aquaculture, to enhance fish immunity. An evaluation of the effect of dietary MOS supplementation on the immune barrier function and related signaling molecules mechanism of grass carp (Ctenopharyngodon idella) was undertaken in the present study. Six diets with graded amounts of MOS supplementation (0, 200, 400, 600, 800, and 1000 mg/kg) were fed to 540 grass carp over 60 days. To examine the immune response and potential mechanisms of MOS supplementation on the intestine, a challenge test was conducted using injections ofAeromonas hydrophilafor 14 days. Results of the study on the optimal supplementation with MOS were found as follows (1) MOS enhances immunity partly related to increasing antibacterial substances content and antimicrobial peptides expression; (2) MOS attenuates inflammatory response partly related to regulating the dynamic balance of intestinal inflammatory cytokines; (3) MOS regulates immune barrier function may partly be related to modulating TLRs/MyD88/NFκB and TOR/S6K1/4EBP signalling pathways. Finally, the current study concluded that MOS supplementation could improve fish intestinal immune barrier function underAeromonas hydrophilainfected conditions.
Comparison between HIV self-testing and facility-based HIV testing approach on HIV early detection among men who have sex with men: A cross-sectional study
Authors: Zhou Yi , Huang Shaoli , Cui Mingting , Guo Zhihui , Tang Haotong , Lyu Hang , Ni Yuxin , Lu Ying , Feng Yunlong , Wang Yuyu , Jing Fengshi , Huang Shanzi , Li Jiarun , Xu Yao , Mei Wenhua
Published: September 2022

Background

To assess whether HIV self-testing (HIVST) has a better performance in identifying HIV-infected cases than the facility-based HIV testing (HIVFBT) approach.

Methods

A cross-sectional study was conducted among men who have sex with men (MSM) by using an online questionnaire (including information on sociodemographic, sexual biography, and HIV testing history) and blood samples (for limiting antigen avidity enzyme immunoassay, gene subtype testing, and taking confirmed HIV test). MSM who were firstly identified as HIV positive through HIVST and HIVFBT were compared. Chi-square or Fisher’s exact test was used to explore any association between both groups and their subgroups.

Results

In total, 124 MSM HIV cases were identified from 2017 to 2021 in Zhuhai, China, including 60 identified through HIVST and 64 through HIVFBT. Participants in the HIVST group were younger (≤30 years, 76.7% vs. 46.9%), were better educated (>high school, 61.7% vs. 39.1%), and had higher viral load (≥1,000 copies/ml, 71.7% vs. 50.0%) than MSM cases identified through HIVFBT. The proportion of early HIV infection in the HIVST group was higher than in the HIVFBT group, identified using four recent infection testing algorithms (RITAs) (RITA 1, 46.7% vs. 25.0%; RITA 2, 43.3% vs. 20.3%; RITA 3, 30.0% vs. 14.1%; RITA 4, 26.7% vs. 10.9%; all p < 0.05).

Conclusions

The study showed that HIVST has better HIV early detection among MSM and that recent HIV infection cases mainly occur in younger and better-educated MSM. Compared with HIVFBT, HIVST is more accessible to the most at-risk population on time and tends to identify the case early. Further implementation studies are needed to fill the knowledge gap on this medical service model among MSM and other target populations.
The diagnosis of immune-related pancreatitis disguised as multifocal lesions on MRI by endoscopic ultrasound-guided fine-needle biopsy: A case report
Authors: Shi Wen , Tan Bei , Li Yuan , Zhu Liang , Feng Yunlu , Jiang Qingwei , Qian Jiaming
Published: September 2022

Immune checkpoint inhibitor (ICI)–related acute pancreatitis (irAP) is a rare, potentially life-threatening immune-related adverse event. Whereas CT and MRI remain first-line diagnostic imaging modalities, more patients are presenting with atypical irAP as ICI use increases. To appropriately manage these events, it is important to catalog these presentations and provide comprehensive clinical, radiological, and pathological descriptions to guide evidence-based practice. Here, we present the case of a 66-year-old man with advanced lung adenocarcinoma who, after the fifth course of toripalimab, developed epigastric discomfort and elevated serum amylase and lipase. irAP was suspected, but MRI revealed atypical, multifocal pancreatic lesions. To exclude metastases, an endoscopic ultrasound-guided fine-needle biopsy (EUS-FNB) was performed. EUS revealed a slightly swollen pancreas with heterogeneous echoic signals and scattered hyperechoic areas in the parenchyma without an obvious mass. Histopathological examination of the FNB revealed retention of the normal lobular pancreatic architecture with focal acinar atrophy associated with a CD8+ T lymphocyte-predominant infiltrate, further confirming the diagnosis of irAP. After starting glucocorticoids, his symptoms resolved, serum amylase and lipase rapidly decreased to normal, and the abnormal MRI features diminished. irAP can, therefore, present as multifocal lesions on MRI, and, when metastatic disease requires exclusion, EUS-FNB is an effective way to establish a definitive diagnosis. Refining the histopathological and immunopathological criteria for the diagnosis of irAP is now warranted.
The Euroflow PID Orientation Tube in the diagnostic workup of primary immunodeficiency: Daily practice performance in a tertiary university hospital
Authors: Neirinck Jana , Emmaneel Annelies , Buysse Malicorne , Philippé Jan , Van Gassen Sofie , Saeys Yvan , Bossuyt Xavier , De Buyser Stefanie , Burg Mirjam van der , Pérez-Andrés Martín , Orfao Alberto , van Dongen Jacques J. M. , Lambrecht Bart N. , Kerre Tessa , Hofmans Mattias , Haerynck Filomeen , Bonroy Carolien
Published: September 2022

Introduction

Multiparameter flow cytometry (FCM) immunophenotyping is an important tool in the diagnostic screening and classification of primary immunodeficiencies (PIDs). The EuroFlow Consortium recently developed the PID Orientation Tube (PIDOT) as a universal screening tool to identify lymphoid-PID in suspicious patients. Although PIDOT can identify different lymphoid-PIDs with high sensitivity, clinical validation in a broad spectrum of patients with suspicion of PID is missing. In this study, we investigated the diagnostic performance of PIDOT, as part of the EuroFlow diagnostic screening algorithm for lymphoid-PID, in a daily practice at a tertiary reference center for PID.

Methods

PIDOT was tested in 887 consecutive patients suspicious of PID at the Ghent University Hospital, Belgium. Patients were classified into distinct subgroups of lymphoid-PID vs. non-PID disease controls (non-PID DCs), according to the IUIS and ESID criteria. For the clinical validation of PIDOT, comprehensive characterization of the lymphoid defects was performed, together with the identification of the most discriminative cell subsets to distinguish lymphoid-PID from non-PID DCs. Next, a decision-tree algorithm was designed to guide subsequent FCM analyses.

Results

The mean number of lymphoid defects detected by PIDOT in blood was 2.87 times higher in lymphoid-PID patients vs. non-PID DCs (p < 0.001), resulting in an overall sensitivity and specificity of 87% and 62% to detect severe combined immunodeficiency (SCID), combined immunodeficiency with associated or syndromic features (CID), immune dysregulation disorder (ID), and common variable immunodeficiency (CVID). The most discriminative populations were total memory and switched memory B cells, total T cells, TCD4+cells, and naive TCD4+cells, together with serum immunoglobulin levels. Based on these findings, a decision-tree algorithm was designed to guide further FCM analyses, which resulted in an overall sensitivity and specificity for all lymphoid-PIDs of 86% and 82%, respectively.

Conclusion

Altogether, our findings confirm that PIDOT is a powerful tool for the diagnostic screening of lymphoid-PID, particularly to discriminate (S)CID, ID, and CVID patients from other patients suspicious of PID. The combination of PIDOT and serum immunoglobulin levels provides an efficient guide for further immunophenotypic FCM analyses, complementary to functional and genetic assays, for accurate PID diagnostics.
CD1d-independent NK1.1+ Treg cells are IL2-inducible Foxp3+ T cells co-expressing immunosuppressive and cytotoxic molecules
Authors: Park Hyun Jung , Lee Sung Won , Park Yun Hoo , Kim Tae-Cheol , Van Kaer Luc , Hong Seokmann
Published: September 2022

Regulatory T cells (Treg) play pivotal roles in maintaining self-tolerance and preventing immunological diseases such as allergy and autoimmunity through their immunosuppressive properties. Although Treg cells are heterogeneous populations with distinct suppressive functions, expression of natural killer (NK) cell receptors (NKR) by these cells remains incompletely explored. Here we identified that a small population of Foxp3+CD4+ Treg cells in mice expresses the NK1.1 NKR. Furthermore, we found that rare NK1.1+ subpopulations among CD4+ Treg cells develop normally in the spleen but not the thymus through CD1d-independent pathways. Compared with NK1.1- conventional Treg cells, these NK1.1+ Treg cells express elevated Treg cell phenotypic hallmarks, pro-inflammatory cytokines, and NK cell-related cytolytic mediators. Our results suggest that NK1.1+ Treg cells are phenotypically hybrid cells sharing functional properties of both NK and Treg cells. Interestingly, NK1.1+ Treg cells preferentially expanded in response to recombinant IL2 stimulation in vitro, consistent with their increased IL2Rαβ expression. Moreover, DO11.10 T cell receptor transgenic NK1.1+ Treg cells were expanded in an ovalbumin antigen-specific manner. In the context of lipopolysaccharide-induced systemic inflammation, NK1.1+ Treg cells downregulated immunosuppressive molecules but upregulated TNFα production, indicating their plastic adaptation towards a more pro-inflammatory rather than regulatory phenotype. Collectively, we propose that NK1.1+ Treg cells might play a unique role in controlling inflammatory immune responses such as infection and autoimmunity.
Association between germ-line HLA and immune-related adverse events
Authors: Jiang Ning , Yu Yue , Zhang Min , Tang Yu , Wu Dawei , Wang Shuhang , Fang Yuan , Zhang Yu , Meng Lin , Li Yingying , Miao Huilei , Ma Peiwen , Huang Huiyao , Li Ning
Published: September 2022

Background

In recent years, significant progress has been made in immune checkpoint inhibitors (ICIs). However, accompanied by remarkable efficacy, a growing number of immune-related adverse events (irAEs) also arose. The mechanism of irAEs remains unclear. Previous studies indicated a positive association between specific human leukocyte antigen (HLA) variants and irAEs. Therefore, we planned and initiated a large cohort study aiming to uncover the relationship between irAEs and divergent HLA types.

Methods

We screened all patients who have been treated in the clinical research ward, Cancer Hospital of the Chinese Academy of Medical Sciences. All participants were diagnosed with malignant tumors with complete AE follow-up data in the original electronic medical records. Sequencing libraries were generated using a customized panel, and four-digit formatted HLA alleles were extracted for further analysis. Association analysis was performed between HLA variants and different irAEs. We introduced two external reference groups and a non-irAE control group within the study cohort to control the type I error. We also explored the relationship between the zygosity of HLA genes, the evolutionary divergence of HLA class I genotype (HED), and irAEs.

Results

530 participants received at least two doses of ICIs. The median follow-up time was 10.3 months. 97% of patients received anti-PD-1/PD-L1 treatment. The occurrence of overall irAEs showed no significant difference between the HLA homozygous group and the HLA heterozygous group. We did not find any significant association between irAEs and HED. We found that some HLA types are associated with irAEs of different organs and detected a significant association between HLA-DRB3*01:01 and thrombocytopenia (OR 3.48 (1.19,9.42), p = 0.011), HLA-DPB1*04:02 and hypokalemia/hyponatremia (OR 3.44 (1.24,9.1), p = 0.009), leukopenia (OR 2.1 (0.92,4.8), p = 0.037), anemia (OR 2.33 (1.0,5.41), p = 0.026), HLA-A*26:01 and bilirubin elevation (OR 2.67 (0.92,8.31), p = 0.037).

Conclusions

IrAEs in specific organs and tissues may be associated with certain HLA types, while HLA heterogeneity has no significant influence on the happening of irAEs. More research is needed to explore the role of germline genetic changes in the risk assessment of irAEs.
An integrated bioinformatic investigation of mitochondrial energy metabolism genes in colon adenocarcinoma followed by preliminary validation of CPT2 in tumor immune infiltration
Authors: Cao Zichao , Lin Jianwei , Fu Gang , Niu Lingshan , Yang Zheyu , Cai Wei
Published: September 2022

Background

The prognosis for colon adenocarcinoma (COAD) today remains poor. Changes in mitochondria-related genes and metabolic reprogramming are related to tumor growth, metastasis, and immune evasion and are key factors in tumor genesis and development.

Methods

TCGA database was used to analyze the differentially expressed mitochondrial energy metabolism pathway-related genes (MMRGs) in COAD patients, and the mutation of MMRG in tumor cells, the biological processes involved, and the correlation with tumor immunity were also analyzed. Then, MMRG and MMRG-related genes were used to divide COAD patients into different subtypes, and immunocorrelation analysis and survival analysis were performed. Finally, univariate regression analysis and LASSO regression analysis were used to construct a prognostic risk model for COAD patients, which was verified by the GEO database and evaluated by Kaplan–Meier (K-M) and receiver operating characteristic (ROC) curves, and the correlation between the risk model and immunity and clinical subtypes based on MMRG was analyzed.

Results

In this study, the MMRG patterns and tumor immune microenvironment characteristics in COAD patients were systematically evaluated by clustering the expression of 188 MMRGs. We identified two subtypes of COAD with different clinical and immunological characteristics. Eight of the 28 differentially expressed MMRG genes were used to construct risk scores. ROC and K-M curves suggested that the risk model could well predict the prognosis of COAD patients, and the risk model was related to immune cell infiltration and immune function.

Conclusions

The two COAD subtypes identified by MMRG are helpful for the clinical differentiation of patients with different prognoses and tumor progressions, and the risk score can assist the clinical evaluation of patient prognosis. Our results suggest that CPT2 contributes to the recruitment and regulation of neutrophils in COAD. CPT2 may act as a valuable biomarker for COAD immunotherapy.
Rumen and fecal microbiota profiles associated with immunity of young and adult goats
Authors: Luo Tao , Li Yongtao , Zhang Wenying , Liu Jianxin , Shi Hengbo
Published: September 2022

Low immunity at birth increases risk of disease of young livestock, such as goat kids. Microbiomes change as animals mature, and a healthy microbiome is related to decreased risk of disease. The relationship between microbiota profiles and immunity at different developmental stages remains unclear. Young (female, n = 12, 30 d) and adult (female, n = 12, 2 yrs. old) Saanen dairy goats were used to investigate changes in rumen microbiomes, fecal microbiomes, and their correlations to circulating immune factors. Serum IgG (P = 0.02) and IgM (P < 0.01) were higher at 2 years than 30 d of age, but there were no differences in IgA (P = 0.34), IL-2 (P = 0.05), IL-4 (P = 0.37) and IL-6 (P = 0.73) between ages. Amplicon sequencing analysis revealed young goats had a higher diversity of bacterial communities in rumen and lower diversity in feces compared with adult goats. Ten genera in rumen and 14 genera in feces were positively correlated with serum IgM concentration across both ages. Olsenella, Methanosphaera, Quinella, Candidatus_Saccharimonas, and Methanobrevibacter in rumen and Ruminobacter, Treponema, Rikenelaceae_ RC9_ gut_ Group in feces were positively correlated with the concentration of IgG. The correlation analysis using weighted gene co-expression network analysis showed the MEblue module was positively associated with the IgG and IgM. These data provide novel insight into the association between rumen-feces microbiota and immune response. Further experiments are needed to investigate whether inoculating young livestock with immune-related bacteria identified can improve the immune status. Our data suggest a possible strategy to improve the immunity of the kids by alterative microbiota profiles.
Bibliometric analysis of global research trends on pyroptosis in lung disease
Authors: Mo Wei , Li Quanfu , Zhou Huanping , Shi Xuan , Yang Hao , Xiao Zhuoran , Wei Juan , Lv Xin
Published: September 2022

Background

Pyroptosis is a lytic pro-inflammatory programmed cell death mode that depends on caspase, inflammasome, and Gasdermin D (GSDMD). A growing number of studies have shown that pyroptosis is closely related to the pathophysiological mechanism of lung. The purpose of this study is to analyze the literature from Science Citation Index Expanded (SCI-expanded) of Web of Science Core Collection (WoSCC) and visualize the current trends and hotspots in the research of pyroptosis in lung disease.

Methods

On February 20, 2022, we retrieved all articles on pyroptosis in lung disease from SCI-expanded of WoSCC. Original articles and reviews published in English from 2007 to 2021 were included in the analysis. VOSviewer 1.6.17 and CiteSpace 5.8.R2 were used to analyze the retrieved data and visualize the results.

Result

1798 qualified original articles and reviews on pyroptosis in lung disease were included in the bibliometric analysis. So far, the research in this field is still in a period of growth, and the number of global publications has increased yearly. Among the 66 countries that have published relevant articles, China ranked first in the number of publications, and the USA ranked first in the number of cited articles. Holian,A. was the author with the largest number of articles, including 21 published. The University of California System in the USA was the organization with the largest number of articles, totaling 55. Frontiers in Immunology was the journal with the most publications in pyroptosis. After bibliometric analysis, the frequently used keywords are: “NOD-like receptor3 (NLRP3) inflammasome”, “inflammation”, “oxidative stress”, and “acute lung injury (ALI)”.

Conclusion

The research on pyroptosis in lung disease is in its growth stage. The information released in this article may help researchers better understand the hotspots and developmental trends in this field, the cooperation network information of authors, countries, and institutions, and the citation correlation between articles. With the in-depth study of the mechanism of pyroptosis, the focus has shifted to increasing research on the connections and influences of different diseases. So far, increasing attention has been paid to the research field of the relationship between ALI and pyroptosis related to COVID-19.
Single-cell RNA-seq uncovered hemocyte functional subtypes and their differentiational characteristics and connectivity with morphological subpopulations in Litopenaeus vannamei
Authors: Cui Chuang , Tang Xiaoqian , Xing Jing , Sheng Xiuzhen , Chi Heng , Zhan Wenbin
Published: September 2022

Hemocytes play central roles in shrimp immune system, whereas whose subclasses have not yet been completely defined. At present, the morphological classification of hemocytes is inadequate to classify the complete hemocyte repertoire and elucidate the functions and differentiation and maturation processes. Based on single-cell RNA sequencing (scRNA-seq) of hemocytes in healthy Litopenaeus vannamei, combined with RNA-FISH and flow cytometric sorting, we identified three hemocyte clusters including TGase+ cells, CTL+ cells and Crustin+ cells, and further determined their functional properties, potential differentiation trajectory and correspondence with morphological subpopulations. The TGase+ cells were mainly responsible for the coagulation, exhibiting distinguishable characteristics of hyalinocyte, and appeared to be developmentally arrested at an early stage of hemocyte differentiation. The CTL+ cells and Crustin+ cells arrested at terminal stages of differentiation mainly participated in recognizing foreign pathogens and initiating immune defense responses, owning distinctive features of granule-containing hemocytes. Furthermore, we have revealed the functional sub-clusters of three hemocyte clusters and their potential differentiation pathways according to the expression of genes involved in cell cycle, cell differentiation and immune response, and the successive differentiation and maturation of hyalinocytes to granule-containing hemocytes have also mapped. The results revealed the diversity of shrimp hemocytes and provide new theoretical rationale for hemocyte classification, which also facilitate systematic research on crustacean immunity.
Modulating cholesterol-rich lipid rafts to disrupt influenza A virus infection
Authors: Li Yu-Jyun , Chen Chi-Yuan , Yang Jeng-How , Chiu Ya-Fang
Published: September 2022

Influenza A virus (IAV) is widely disseminated across different species and can cause recurrent epidemics and severe pandemics in humans. During infection, IAV attaches to receptors that are predominantly located in cell membrane regions known as lipid rafts, which are highly enriched in cholesterol and sphingolipids. Following IAV entry into the host cell, uncoating, transcription, and replication of the viral genome occur, after which newly synthesized viral proteins and genomes are delivered to lipid rafts for assembly prior to viral budding from the cell. Moreover, during budding, IAV acquires an envelope with embedded cholesterol from the host cell membrane, and it is known that decreased cholesterol levels on IAV virions reduce infectivity. Statins are commonly used to inhibit cholesterol synthesis for preventing cardiovascular diseases, and several studies have investigated whether such inhibition can block IAV infection and propagation, as well as modulate the host immune response to IAV. Taken together, current research suggests that there may be a role for statins in countering IAV infections and modulating the host immune response to prevent or mitigate cytokine storms, and further investigation into this is warranted.
Changes in macrophage-like cells characterized by en face optical coherence tomography after retinal stroke
Authors: Zeng Yunkao , Wen Feng , Mi Lan , Ji Yuying , Zhang Xiongze
Published: September 2022

Purpose

The retina could serve as a window of neuroinflammation, but the in vivo changes in macrophage-like cell (MLC), such as microglia, in acute ischemic retinal stroke remain unclear. Thus, the current study aimed to investigate the in vivo changes in MLC characterized by en face optical coherence tomography (OCT) after acute ischemic retinal stroke.

Methods

Twenty patients with unilateral acute nonarteritic reperfused central retinal artery occlusion (CRAO) were participated in this study, and their contralateral eyes served as control group. A 3 μm en face OCT slab on the inner limiting membrane of the optic nerve head (ONH) region or macular region was used to visualize and binarize the MLCs. The MLCs were binarized and quantified using a semiautomated method. OCT angiography was used to evaluate the reperfusion status and obtain the structural data of the inner retina in the ONH and macula. The thickness of the ganglion cell complex in the macular region was measured. The optical intensity and optical intensity ratio of the inner retina were calculated to evaluate the ischemia severity.

Results

In the ONH region, decreased vessel densities of radial peripapillary capillaries accompanied by increased thickness of the retinal nerve fiber layer were found in the CRAO eyes in comparison to the unaffected eyes (p=0.001, p=0.009, respectively). In the macular region, significantly lower vessel densities in both the superficial and deep capillary plexus and increased thickness of the ganglion cell complex were also found in the CRAO eyes (all p ≤ 0.001). The ONH and macular MLC quantities and densities in CRAO eyes were significantly higher than those in the unaffected eyes (both p<0.001). Larger and plumper MLCs were observed in the CRAO eyes compared with their unaffected eyes. ONH and macular MLC densities were positively associated with the disease duration in the acute phase and the optical intensity ratio of inner retina.

Conclusions

The increased density and morphological changes of MLCs may indicate the aggregation and activation of MLCs following acute reperfused CRAO. The aggregation of MLCs may be more pronounced in CRAO eyes with longer disease duration and more severe ischemia. MLCs characterized by en face OCT may serve as an in vivo visual tool to investigate neuroinflammation in the ischemic-reperfusion process of stroke.
Global alteration of colonic microRNAome landscape associated with inflammatory bowel disease
Authors: Boros Éva , Hegedűs Zoltán , Kellermayer Zoltán , Balogh Péter , Nagy István
Published: September 2022

Inflammatory Bowel Disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract that associates with, among others, increased risk of colorectal cancer. There is a growing evidence that miRNAs have important roles in pathological processes, such as inflammation or carcinogenesis. Understanding the molecular mechanisms such as alterations in microRNAome upon chronic intestinal inflammation is critical for understanding the exact pathomechanism of IBD. Hence, we conducted a genome wide microRNAome analysis by applying miRNA-Seq in a rat model of experimental colitis, validated the data by QPCR, examined the expression of a selection of precursor and mature miRNAs, performed in depth biological interpretation using Ingenuity Pathway Analysis and tested the obtained results on samples derived from human patients. We identified specific, interdependent expression pattern of activator/repressor transcription factors, miRNAs and their direct targets in the inflamed colon samples. Particularly, decreased expression of the miR-200 family members (miR-200a/b/c,-141, and -429) and miR-27b correlates with the reduced level of their enhancers (HNF1B, E2F1), elevated expression of their repressors (ZEB2, NFKB1) and increased expression of their target genes (ZEB2, RUNX1). Moreover, the marked upregulation of six miR-27b target genes (IFI16, GCA, CYP1B1, RUNX1, MEF2C and MMP13) in the inflamed colon tissues is a possible direct consequence of the lack of repression due to the downregulated miRNA-27b expression. Our data indicate that changes in microRNAome are associated with the pathophysiology of IBD, consequently, microRNAs offer potential targets for the diagnosis, prognosis and treatment of IBD.
Artificial intelligence approach for recommendation of pupil dilation test using medical interview and basic ophthalmologic examinations
Authors: Ahn Hyunmin , Jun Ikhyun , Seo Kyoung Yul , Kim Eung Kweon , Kim Tae-im
Published: September 2022

Purpose

To evaluate the value of artificial intelligence (AI) for recommendation of pupil dilation test using medical interview and basic ophthalmologic examinations.

Design

Retrospective, cross-sectional study.

Subjects

Medical records of 56,811 patients who visited our outpatient clinic for the first time between 2017 and 2020 were included in the training dataset. Patients who visited the clinic in 2021 were included in the test dataset. Among these, 3,885 asymptomatic patients, including eye check-up patients, were initially included in test dataset I. Subsequently, 14,199 symptomatic patients who visited the clinic in 2021 were included in test dataset II.

Methods

All patients underwent a medical interview and basic ophthalmologic examinations such as uncorrected distance visual acuity, corrected distance visual acuity, non-contact tonometry, auto-keratometry, slit-lamp examination, dilated pupil test, and fundus examination. A clinically significant lesion in the lens, vitreous, and fundus was defined by subspecialists, and the need for a pupil dilation test was determined when the participants had one or more clinically significant lesions in any eye. Input variables of AI consisted of a medical interview and basic ophthalmologic examinations, and the AI was evaluated with predictive performance for the need of a pupil dilation test.

Main outcome measures

Accuracy, sensitivity, specificity, and positive predictive value.

Results

Clinically significant lesions were present in 26.5 and 59.1% of patients in test datasets I and II, respectively. In test dataset I, the model performances were as follows: accuracy, 0.908 (95% confidence interval (CI): 0.880–0.936); sensitivity, 0.757 (95% CI: 0.713–0.801); specificity, 0.962 (95% CI: 0.947–0.977); positive predictive value, 0.878 (95% CI: 0.834–0.922); and F1 score, 0.813. In test dataset II, the model had an accuracy of 0.949 (95% CI: 0.934–0.964), a sensitivity of 0.942 (95% CI: 0.928–956), a specificity of 0.960 (95% CI: 0.927–0.993), a positive predictive value of 0.971 (95% CI: 0.957–0.985), and a F1 score of 0.956.

Conclusion

The AI model performing a medical interview and basic ophthalmologic examinations to determine the need for a pupil dilation test had good sensitivity and specificity for symptomatic patients, although there was a limitation in identifying asymptomatic patients.