PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Serum cystatin-C and all-cause mortality in patients with hypertrophic cardiomyopathy: a retrospective cohort study
items: Prognostic implications of microRNA-107 in esophageal cancer: a retrospective cohort study
items: Effect of short-term exposure to air pollution on ischemic stroke incidence and mortality: a five-year time-series study in Jining, China
items: Are caves enough to represent karst groundwater biodiversity? Insights from geospatial analyses applied to European obligate groundwater-dwelling copepods
items: Breaking epigenetic shackles: targeting ARID1A methylation and the PI3K/AKT/mTOR-PD-L1 axis to overcome immune escape in gastric cancer
items: Retrospective study on the association between paternal occupational exposure to agrochemicals and childhood leukemia in Michoacán de Ocampo, México
items: Auditory processing ability in Thai native speakers with the Gaps-In-Noise (GIN) test
items: Analysis of the chitin synthase gene family in Ganoderma lucidum: its structure, phylogeny, and expression patterns
items: CD81 inhibits the proliferation of acute megakaryoblastic leukemia cells
items: Biocontrol-relevant diversity of wheat-associated Pseudomonas: prevalence of P. sivasensis and identification of the novel species P. arvensis sp. nov.

Serum cystatin-C and all-cause mortality in patients with hypertrophic cardiomyopathy: a retrospective cohort study
type: item
type: AcademicArticle
description: Background Numerous studies across various populations have revealed that elevated cystatin-C levels are associated with an excessive risk of mortality. However, the prognostic value of cystatin-C remains unidentified in hypertrophic cardiomyopathy (HCM) patients. The objective of this study was to investigate whether serum cystatin-C could predict all-cause mortality independently in HCM patients. Methods Data from 456 HCM patients treated at West China Hospital were collected and stratified into two groups based on the median baseline serum cystatin-C level. All-cause mortality was the primary outcome. Cox regression models were used to analyze the association between cystatin-C levels and mortality risk. Results A total of 90 deaths were recorded over a median follow-up period of 4.67 years. Patients with higher cystatin-C levels had an increased risk of all-cause mortality (adjusted hazard ratio (HR): 2.11, 95% CI [1.30–3.42], p = 0.003) compared to those with lower levels. Time-dependent area under the curves (AUC) of cystatin-C in different time points, ranging from initial measurement to follow-up, showed a relatively stable fluctuation between 0.70 and 0.80. In comparison, the commonly used renal function markers, estimated glomerular filtration rate (eGFR) and serum creatinine, yielded lower AUC values. Restricted cubic spline curves showed that with median value of cystatin-C (1.01 mg/L) as reference, there was a gradual rise in risk of all-cause mortality with cystatin-C increasing. Subgroup analyses in female, in the patients ≥ 58 years old, and in the patients with eGFR ≥ 60 mL/min/1.73 m2 consistently confirmed robustness of the main findings. Conclusion Elevated serum cystatin-C levels are associated with a higher risk of all-cause mortality in HCM patients, providing valuable prognostic information beyond traditional renal function markers such as eGFR and serum creatinine.
format: application/pdf
format: text/html
creator: Lu Liu
creator: Yi Zheng
creator: Haiyan Ruan
creator: Ziqiong Wang
creator: Xiaoping Chen
creator: Sen He
subject: Cardiology
subject: Epidemiology
subject: Internal Medicine
description: doi:10.7717/peerj.19631
publisher: PeerJ Inc.
rights: © 2025 Liu et al.
abstract: Background Numerous studies across various populations have revealed that elevated cystatin-C levels are associated with an excessive risk of mortality. However, the prognostic value of cystatin-C remains unidentified in hypertrophic cardiomyopathy (HCM) patients. The objective of this study was to investigate whether serum cystatin-C could predict all-cause mortality independently in HCM patients. Methods Data from 456 HCM patients treated at West China Hospital were collected and stratified into two groups based on the median baseline serum cystatin-C level. All-cause mortality was the primary outcome. Cox regression models were used to analyze the association between cystatin-C levels and mortality risk. Results A total of 90 deaths were recorded over a median follow-up period of 4.67 years. Patients with higher cystatin-C levels had an increased risk of all-cause mortality (adjusted hazard ratio (HR): 2.11, 95% CI [1.30–3.42], p = 0.003) compared to those with lower levels. Time-dependent area under the curves (AUC) of cystatin-C in different time points, ranging from initial measurement to follow-up, showed a relatively stable fluctuation between 0.70 and 0.80. In comparison, the commonly used renal function markers, estimated glomerular filtration rate (eGFR) and serum creatinine, yielded lower AUC values. Restricted cubic spline curves showed that with median value of cystatin-C (1.01 mg/L) as reference, there was a gradual rise in risk of all-cause mortality with cystatin-C increasing. Subgroup analyses in female, in the patients ≥ 58 years old, and in the patients with eGFR ≥ 60 mL/min/1.73 m2 consistently confirmed robustness of the main findings. Conclusion Elevated serum cystatin-C levels are associated with a higher risk of all-cause mortality in HCM patients, providing valuable prognostic information beyond traditional renal function markers such as eGFR and serum creatinine.
bibliographic citation: Liu et al. (2025) Serum cystatin-C and all-cause mortality in patients with hypertrophic cardiomyopathy: a retrospective cohort study. PeerJ 13:e19631 https://doi.org/10.7717/peerj.19631
date submitted: 2023-11-07
date accepted: 2025-05-30
issued: 2025-11-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Lu
author list: Agent
  family name: Zheng
  given name: Yi
author list: Agent
  family name: Ruan
  given name: Haiyan
author list: Agent
  family name: Wang
  given name: Ziqiong
author list: Agent
  family name: Chen
  given name: Xiaoping
author list: Agent
  family name: He
  given name: Sen
doi: 10.7717/peerj.19631
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-07
copyright: ©2025 Liu et al.
attribution name: Liu et al.

Prognostic implications of microRNA-107 in esophageal cancer: a retrospective cohort study
type: item
type: AcademicArticle
description: Background Esophageal squamous cell carcinoma (ESCC) imposes a heavy disease burden in China, accounting for over 50% of global cases and approximately 301,000 annual deaths. Current prognostic markers inadequately predict recurrence in early-stage patients. This study investigates microRNA-107 (miR-107) as a novel prognostic biomarker for ESCC. Methods Tumor tissues (n = 66) and adjacent normal tissues (n = 28) were collected from ESCC patients undergoing radical surgery (2010–2012). miR-107 expression was quantified via reverse transcription quantitative polymerase chain reaction (RT-qPCR) (normalized to U6 snRNA). Clinicopathological correlations and survival outcomes were analyzed using χ2 tests, Kaplan–Meier/log-rank tests, and Cox regression. Comparative analysis of miR-107 levels was performed in human esophageal squamous cell carcinoma line 109 (EC109) cancer cells versus human esophageal epithelial cell (HEEC) normal epithelial cells. Results miR-107 expression was significantly lower in esophageal cancer tissues (0.801 ± 0.737) compared to adjacent non-cancerous tissues (1.390 ± 1.346), p = 0.006. Low miR-107 expression (cutoff = median) correlated with advanced tumor, node, metastasis stage (TNM stage) (I vs. V: 100% vs. 21.4%, P < 0.001), lymph node metastasis (73.1% vs. 35%, P < 0.001), and larger tumor size (70% vs. 33.3%, P < 0.001). Patients with low miR-107 had shorter median overall survival (10 vs. 59 months; Hazard Ratio (HR) = 0.475, 95% Confidence Interval (CI) [0.247–0.915]; P < 0.001). Multivariate Cox analysis confirmed miR-107 as an independent prognostic factor alongside TNM stage (HR = 3.586, 95% CI [2.253–5.708]; P < 0.001). Consistently, EC109 cells exhibited 59% lower miR-107 levels than HEEC (P = 0.029). Conclusions miR-107 downregulation is a robust predictor of aggressive ESCC phenotypes and poor survival. It holds promise as a clinical biomarker for risk stratification and personalized therapy. Future studies should validate these …
format: application/pdf
format: text/html
creator: Jie Sun
creator: Jin Zhang
creator: Jingwen Ye
creator: Yuqi Chen
creator: Caifeng Jiang
subject: Clinical Trials
subject: Gastroenterology and Hepatology
subject: Internal Medicine
subject: Oncology
description: doi:10.7717/peerj.20327
publisher: PeerJ Inc.
rights: © 2025 Sun et al.
abstract: Background Esophageal squamous cell carcinoma (ESCC) imposes a heavy disease burden in China, accounting for over 50% of global cases and approximately 301,000 annual deaths. Current prognostic markers inadequately predict recurrence in early-stage patients. This study investigates microRNA-107 (miR-107) as a novel prognostic biomarker for ESCC. Methods Tumor tissues (n = 66) and adjacent normal tissues (n = 28) were collected from ESCC patients undergoing radical surgery (2010–2012). miR-107 expression was quantified via reverse transcription quantitative polymerase chain reaction (RT-qPCR) (normalized to U6 snRNA). Clinicopathological correlations and survival outcomes were analyzed using χ2 tests, Kaplan–Meier/log-rank tests, and Cox regression. Comparative analysis of miR-107 levels was performed in human esophageal squamous cell carcinoma line 109 (EC109) cancer cells versus human esophageal epithelial cell (HEEC) normal epithelial cells. Results miR-107 expression was significantly lower in esophageal cancer tissues (0.801 ± 0.737) compared to adjacent non-cancerous tissues (1.390 ± 1.346), p = 0.006. Low miR-107 expression (cutoff = median) correlated with advanced tumor, node, metastasis stage (TNM stage) (I vs. V: 100% vs. 21.4%, P < 0.001), lymph node metastasis (73.1% vs. 35%, P < 0.001), and larger tumor size (70% vs. 33.3%, P < 0.001). Patients with low miR-107 had shorter median overall survival (10 vs. 59 months; Hazard Ratio (HR) = 0.475, 95% Confidence Interval (CI) [0.247–0.915]; P < 0.001). Multivariate Cox analysis confirmed miR-107 as an independent prognostic factor alongside TNM stage (HR = 3.586, 95% CI [2.253–5.708]; P < 0.001). Consistently, EC109 cells exhibited 59% lower miR-107 levels than HEEC (P = 0.029). Conclusions miR-107 downregulation is a robust predictor of aggressive ESCC phenotypes and poor survival. It holds promise as a clinical biomarker for risk stratification and personalized therapy. Future studies should validate these …
bibliographic citation: Sun et al. (2025) Prognostic implications of microRNA-107 in esophageal cancer: a retrospective cohort study. PeerJ 13:e20327 https://doi.org/10.7717/peerj.20327
date submitted: 2025-04-21
date accepted: 2025-10-13
issued: 2025-11-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Jie
author list: Agent
  family name: Zhang
  given name: Jin
author list: Agent
  family name: Ye
  given name: Jingwen
author list: Agent
  family name: Chen
  given name: Yuqi
author list: Agent
  family name: Jiang
  given name: Caifeng
doi: 10.7717/peerj.20327
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-06
copyright: ©2025 Sun et al.
attribution name: Sun et al.

Effect of short-term exposure to air pollution on ischemic stroke incidence and mortality: a five-year time-series study in Jining, China
type: item
type: AcademicArticle
description: Background Short-term exposure to air pollutants is associated with an increased risk of ischemic stroke incidence and mortality. However, there is a lack of research based on data from disease surveillance systems. This study used disease surveillance system data to quantitatively analyze the association between air pollution and ischemic stroke incidence and mortality in Jining, China. Methods The stroke registration system of the Jining City Center for Disease Control and Prevention (CDC) includes information on confirmed stroke cases reported by all medical institutions in the jurisdiction, covering a population of 8.9 million. Generalized linear regression models combined with distributed lag nonlinear models (DLNM) were used to determine the association between air pollutants and ischemic stroke incidence and mortality. Stratified analyses by sex, age, and season were also conducted. Results During the study period (January 1, 2018, to December 31, 2022), there were 209,949 ischemic stroke incidence cases and 23,565 ischemic stroke-related deaths. There were more ischemic stroke incidence and death cases in males compared to females. The number of incidence cases was higher in the warm season (52.6%) than in the cold season (47.4%), while this pattern was reversed for the number of deaths, with a higher number of deaths in the cold season (55.9%) than in the warm season (44.1%). This study showed that exposure to particulate matter (PM2.5 and PM10), nitrogen dioxide (NO2), and carbon monoxide (CO) was associated with ischemic stroke incidence, and exposure to PM2.5, PM10, sulfur dioxide (SO2), and CO was associated with ischemic stroke mortality. The relative risks (RRs, with 95% CIs) for ischemic stroke incidence at the maximum single-lag effect day for each interquartile range (IQR) increment for PM2.5, PM10, NO2, and CO were 1.007 (1.001–1.014), 1.004 (1.000–1.008); 1.031 (1.011–1.051), and 1.008 (1.001–1.015), respectively. The RRs (with 95% CIs) for morta…
format: application/pdf
format: text/html
creator: Yaohui Kong
creator: Wenhua Duan
creator: Zi Zhang
creator: Peizhen Zhou
creator: Mei Wang
creator: Jing Zhang
creator: Wenjun Wang
subject: Neurology
subject: Public Health
subject: Environmental Health
description: doi:10.7717/peerj.20298
publisher: PeerJ Inc.
rights: © 2025 Kong et al.
abstract: Background Short-term exposure to air pollutants is associated with an increased risk of ischemic stroke incidence and mortality. However, there is a lack of research based on data from disease surveillance systems. This study used disease surveillance system data to quantitatively analyze the association between air pollution and ischemic stroke incidence and mortality in Jining, China. Methods The stroke registration system of the Jining City Center for Disease Control and Prevention (CDC) includes information on confirmed stroke cases reported by all medical institutions in the jurisdiction, covering a population of 8.9 million. Generalized linear regression models combined with distributed lag nonlinear models (DLNM) were used to determine the association between air pollutants and ischemic stroke incidence and mortality. Stratified analyses by sex, age, and season were also conducted. Results During the study period (January 1, 2018, to December 31, 2022), there were 209,949 ischemic stroke incidence cases and 23,565 ischemic stroke-related deaths. There were more ischemic stroke incidence and death cases in males compared to females. The number of incidence cases was higher in the warm season (52.6%) than in the cold season (47.4%), while this pattern was reversed for the number of deaths, with a higher number of deaths in the cold season (55.9%) than in the warm season (44.1%). This study showed that exposure to particulate matter (PM2.5 and PM10), nitrogen dioxide (NO2), and carbon monoxide (CO) was associated with ischemic stroke incidence, and exposure to PM2.5, PM10, sulfur dioxide (SO2), and CO was associated with ischemic stroke mortality. The relative risks (RRs, with 95% CIs) for ischemic stroke incidence at the maximum single-lag effect day for each interquartile range (IQR) increment for PM2.5, PM10, NO2, and CO were 1.007 (1.001–1.014), 1.004 (1.000–1.008); 1.031 (1.011–1.051), and 1.008 (1.001–1.015), respectively. The RRs (with 95% CIs) for morta…
bibliographic citation: Kong et al. (2025) Effect of short-term exposure to air pollution on ischemic stroke incidence and mortality: a five-year time-series study in Jining, China. PeerJ 13:e20298 https://doi.org/10.7717/peerj.20298
date submitted: 2025-02-05
date accepted: 2025-10-06
issued: 2025-11-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Kong
  given name: Yaohui
author list: Agent
  family name: Duan
  given name: Wenhua
author list: Agent
  family name: Zhang
  given name: Zi
author list: Agent
  family name: Zhou
  given name: Peizhen
author list: Agent
  family name: Wang
  given name: Mei
author list: Agent
  family name: Zhang
  given name: Jing
author list: Agent
  family name: Wang
  given name: Wenjun
doi: 10.7717/peerj.20298
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-06
copyright: ©2025 Kong et al.
attribution name: Kong et al.

Are caves enough to represent karst groundwater biodiversity? Insights from geospatial analyses applied to European obligate groundwater-dwelling copepods
type: item
type: AcademicArticle
description: Caves are recognized as biodiversity hotspots for groundwater fauna, including obligate groundwater-dwelling copepods (Crustacea: Copepoda), exhibiting high species richness, endemism, and phylogenetic rarity. However, the extent to which caves alone provide a representative estimate of copepod species richness in karst areas remains uncertain. Taking advantage of the recently published EGCop dataset, the first expert-validated, Europe-wide occurrence dataset for obligate groundwater-dwelling copepods (hereinafter, GW copepods), this study investigates the distribution of GW copepods into karst areas, comparing species richness in caves versus other karst groundwater habitats (e.g., springs, karst streams, artificial wells), within and among the European karst units. The main aims are: (i) identifying karst areas which represent hotpots of GW copepod species richness; (ii) assessing to which extent caves, as open windows to the subterranean environments, contribute to define hotspots of GW copepods’ species richness into karst areas across Europe. EGCop comprises 6,986 records from 588 copepod species/subspecies distributed among four orders: Cyclopoida (3,664 records, 184 species), Harpacticoida (3,288 records, 395 species), Calanoida (32 records, seven species), and Gelyelloida (two records, two species). To perform geospatial analyses, we filtered the dataset by: (i) selecting only the records with spatial uncertainty in the associated coordinates lower than 10 km; (ii) searching for those records falling within, or very close to, the polygons representing European karst areas. Species richness hotspots were then estimated through geospatial analyses in geographic information system (GIS) environment. Within the selected records, those specifically referring to karst habitats (2,526 records, 369 species) are primarily represented by Harpacticoida (1,199 records, 228 species) and Cyclopoida (1,293 records, 132 species). Among species collected from karst habitats,…
format: application/pdf
format: text/html
creator: Emma Galmarini
creator: Mattia Di Cicco
creator: Barbara Fiasca
creator: Nataša Mori
creator: Mattia Iannella
creator: Tiziana Di Lorenzo
creator: Francesco Cerasoli
creator: Diana Maria Paola Galassi
subject: Biodiversity
subject: Conservation Biology
subject: Zoology
subject: Freshwater Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.20285
publisher: PeerJ Inc.
rights: © 2025 Galmarini et al.
abstract: Caves are recognized as biodiversity hotspots for groundwater fauna, including obligate groundwater-dwelling copepods (Crustacea: Copepoda), exhibiting high species richness, endemism, and phylogenetic rarity. However, the extent to which caves alone provide a representative estimate of copepod species richness in karst areas remains uncertain. Taking advantage of the recently published EGCop dataset, the first expert-validated, Europe-wide occurrence dataset for obligate groundwater-dwelling copepods (hereinafter, GW copepods), this study investigates the distribution of GW copepods into karst areas, comparing species richness in caves versus other karst groundwater habitats (e.g., springs, karst streams, artificial wells), within and among the European karst units. The main aims are: (i) identifying karst areas which represent hotpots of GW copepod species richness; (ii) assessing to which extent caves, as open windows to the subterranean environments, contribute to define hotspots of GW copepods’ species richness into karst areas across Europe. EGCop comprises 6,986 records from 588 copepod species/subspecies distributed among four orders: Cyclopoida (3,664 records, 184 species), Harpacticoida (3,288 records, 395 species), Calanoida (32 records, seven species), and Gelyelloida (two records, two species). To perform geospatial analyses, we filtered the dataset by: (i) selecting only the records with spatial uncertainty in the associated coordinates lower than 10 km; (ii) searching for those records falling within, or very close to, the polygons representing European karst areas. Species richness hotspots were then estimated through geospatial analyses in geographic information system (GIS) environment. Within the selected records, those specifically referring to karst habitats (2,526 records, 369 species) are primarily represented by Harpacticoida (1,199 records, 228 species) and Cyclopoida (1,293 records, 132 species). Among species collected from karst habitats,…
bibliographic citation: Galmarini et al. (2025) Are caves enough to represent karst groundwater biodiversity? Insights from geospatial analyses applied to European obligate groundwater-dwelling copepods. PeerJ 13:e20285 https://doi.org/10.7717/peerj.20285
date submitted: 2025-07-24
date accepted: 2025-10-02
issued: 2025-11-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Galmarini
  given name: Emma
author list: Agent
  family name: Di Cicco
  given name: Mattia
author list: Agent
  family name: Fiasca
  given name: Barbara
author list: Agent
  family name: Mori
  given name: Nataša
author list: Agent
  family name: Iannella
  given name: Mattia
author list: Agent
  family name: Di Lorenzo
  given name: Tiziana
author list: Agent
  family name: Cerasoli
  given name: Francesco
author list: Agent
  family name: Galassi
  given name: Diana Maria Paola
doi: 10.7717/peerj.20285
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-06
copyright: ©2025 Galmarini et al.
attribution name: Galmarini et al.

Breaking epigenetic shackles: targeting ARID1A methylation and the PI3K/AKT/mTOR-PD-L1 axis to overcome immune escape in gastric cancer
type: item
type: AcademicArticle
description: Objective AT-rich interaction domain 1A (ARID1A), is frequently mutated in cancer, leading to loss-of-function and posing challenges to therapeutic targeting. This study aimed to systematically explore epigenetic regulation of ARID1A, specifically promoter hypermethylation, in gastric cancer (GC) and its functional/immunological consequences. Methods We employed multi-omics bioinformatics analyses (UALCAN, cBioPortal, MEXPRESS and UCSC Xena) combined with in vitro functional validation in GC cell lines, including pharmacological demethylation using 5-Aza-2’-deoxycytidine (5-aza-CdR) and mechanistic interrogation via AKT agonism (SC79). Results Promoter hypermethylation was identified as a key mechanism silencing ARID1A transcriptional, showing a significant negative correlation between methylation β-values and mRNA expression (Spearman’s ρ = − 0.29, p = 2.06 × 10−8). 5-aza-CdR treatment restored ARID1A expression (p < 0.001), suppressed malignant phenotypes (proliferation, invasion, and apoptosis resistance), and revealed that ARID1A lose activates the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) pathway (elevated p-AKT, p-mTOR) and upregulates PD-L1. Rescue experiments with SC79 reversed 5-aza-CdR’s effects, confirming the ARID1A-PI3K/AKT/mTOR-PD-L1 axis. Integrative analysis linked ARID1A hypermethylation to elevated immune/ESTIMATE scores (p < 0.05). Conclusion ARID1A promoter hypermethylation drives an epigenetic-immune checkpoint cascade in GC. Combined with its association with immune signatures and PD-L1 upregulation, ARID1A hypermethylation emerges as a candidate biomarker for predicting immune checkpoint blockade (ICB) responsiveness and patient stratification in GC. Future studies should evaluate 5-aza-CdR-ICB-AKT inhibitor regimens in advanced models to guide clinical translation.
format: application/pdf
format: text/html
creator: Xueqin Duan
creator: Xingfa Huo
creator: Yuming Zhang
creator: Hongwei Lan
creator: Fangfang Yang
creator: Xiaochun Zhang
creator: Na Zhou
subject: Cell Biology
subject: Molecular Biology
subject: Immunology
subject: Oncology
description: doi:10.7717/peerj.20251
publisher: PeerJ Inc.
rights: © 2025 Duan et al.
abstract: Objective AT-rich interaction domain 1A (ARID1A), is frequently mutated in cancer, leading to loss-of-function and posing challenges to therapeutic targeting. This study aimed to systematically explore epigenetic regulation of ARID1A, specifically promoter hypermethylation, in gastric cancer (GC) and its functional/immunological consequences. Methods We employed multi-omics bioinformatics analyses (UALCAN, cBioPortal, MEXPRESS and UCSC Xena) combined with in vitro functional validation in GC cell lines, including pharmacological demethylation using 5-Aza-2’-deoxycytidine (5-aza-CdR) and mechanistic interrogation via AKT agonism (SC79). Results Promoter hypermethylation was identified as a key mechanism silencing ARID1A transcriptional, showing a significant negative correlation between methylation β-values and mRNA expression (Spearman’s ρ = − 0.29, p = 2.06 × 10−8). 5-aza-CdR treatment restored ARID1A expression (p < 0.001), suppressed malignant phenotypes (proliferation, invasion, and apoptosis resistance), and revealed that ARID1A lose activates the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) pathway (elevated p-AKT, p-mTOR) and upregulates PD-L1. Rescue experiments with SC79 reversed 5-aza-CdR’s effects, confirming the ARID1A-PI3K/AKT/mTOR-PD-L1 axis. Integrative analysis linked ARID1A hypermethylation to elevated immune/ESTIMATE scores (p < 0.05). Conclusion ARID1A promoter hypermethylation drives an epigenetic-immune checkpoint cascade in GC. Combined with its association with immune signatures and PD-L1 upregulation, ARID1A hypermethylation emerges as a candidate biomarker for predicting immune checkpoint blockade (ICB) responsiveness and patient stratification in GC. Future studies should evaluate 5-aza-CdR-ICB-AKT inhibitor regimens in advanced models to guide clinical translation.
bibliographic citation: Duan et al. (2025) Breaking epigenetic shackles: targeting ARID1A methylation and the PI3K/AKT/mTOR-PD-L1 axis to overcome immune escape in gastric cancer. PeerJ 13:e20251 https://doi.org/10.7717/peerj.20251
date submitted: 2025-05-28
date accepted: 2025-09-25
issued: 2025-11-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Duan
  given name: Xueqin
author list: Agent
  family name: Huo
  given name: Xingfa
author list: Agent
  family name: Zhang
  given name: Yuming
author list: Agent
  family name: Lan
  given name: Hongwei
author list: Agent
  family name: Yang
  given name: Fangfang
author list: Agent
  family name: Zhang
  given name: Xiaochun
author list: Agent
  family name: Zhou
  given name: Na
doi: 10.7717/peerj.20251
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-06
copyright: ©2025 Duan et al.
attribution name: Duan et al.

Retrospective study on the association between paternal occupational exposure to agrochemicals and childhood leukemia in Michoacán de Ocampo, México
type: item
type: AcademicArticle
description: Objectives The constant use of agrochemicals in avocado plantations, because of their susceptibility to pests and diseases, continuously exposes those who work or reside near these orchards to health risks. The purpose of this study was to investigate the association between childhood leukemia cases in Michoacán, paternal occupational exposure to agrochemicals, and environmental exposure due to residential proximity. Methods A retrospective observational cohort study was performed. We analyzed 430 cases of leukemia in children under 18 years of age diagnosed between 2010-2023. Logistic regression models were used to estimate odds ratios and 95% confidence intervals, adjusted for sociodemographic factors. Survival was analyzed using Kaplan-Meier curves. Results A total of 46.6% of the parents of children with leukemia in this study had jobs related to the use of agrochemicals (e.g., day laborers, peasants, farmers). Additionally, 65.4% of the leukemia cases occurred in municipalities producing avocado, the most important perennial crop in the state. Regarding the residential area analysis (mapping), many cases were found in contiguous zip codes and in areas densely occupied by avocado orchards. In addition, paternal occupations related to agrochemical use were associated with the avocado-growing zone, with an OR = 1.764 (95% CI [1.034–3.009], p = 0.0379). Interestingly, survival associated with agrochemical-related occupations has a higher mean survival (139.3 months) than all other parental occupations (p = 0.0148). Conclusions The epidemiologic evidence found in this study supports the association between paternal occupational exposure to agrochemicals and childhood leukemia. Furthermore, children with leukemia who live in avocado-growing regions have a higher survival rate.
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creator: Paola Jiménez-Alcántar
creator: Anel Gómez-García
creator: Joel E. López-Meza
creator: Alejandra Ochoa-Zarzosa
creator: Luis Andrés Espino-Barajas
creator: Luis Miguel Morales-Manilla
creator: Eloy Pérez-Rivera
creator: Luz Yadira Zúñiga-Quijano
creator: Sergio Gutiérrez-Castellanos
subject: Epidemiology
subject: Hematology
subject: Oncology
subject: Pediatrics
subject: Environmental Health
description: doi:10.7717/peerj.20219
publisher: PeerJ Inc.
rights: © 2025 Jiménez-Alcántar et al.
abstract: Objectives The constant use of agrochemicals in avocado plantations, because of their susceptibility to pests and diseases, continuously exposes those who work or reside near these orchards to health risks. The purpose of this study was to investigate the association between childhood leukemia cases in Michoacán, paternal occupational exposure to agrochemicals, and environmental exposure due to residential proximity. Methods A retrospective observational cohort study was performed. We analyzed 430 cases of leukemia in children under 18 years of age diagnosed between 2010-2023. Logistic regression models were used to estimate odds ratios and 95% confidence intervals, adjusted for sociodemographic factors. Survival was analyzed using Kaplan-Meier curves. Results A total of 46.6% of the parents of children with leukemia in this study had jobs related to the use of agrochemicals (e.g., day laborers, peasants, farmers). Additionally, 65.4% of the leukemia cases occurred in municipalities producing avocado, the most important perennial crop in the state. Regarding the residential area analysis (mapping), many cases were found in contiguous zip codes and in areas densely occupied by avocado orchards. In addition, paternal occupations related to agrochemical use were associated with the avocado-growing zone, with an OR = 1.764 (95% CI [1.034–3.009], p = 0.0379). Interestingly, survival associated with agrochemical-related occupations has a higher mean survival (139.3 months) than all other parental occupations (p = 0.0148). Conclusions The epidemiologic evidence found in this study supports the association between paternal occupational exposure to agrochemicals and childhood leukemia. Furthermore, children with leukemia who live in avocado-growing regions have a higher survival rate.
bibliographic citation: Jiménez-Alcántar et al. (2025) Retrospective study on the association between paternal occupational exposure to agrochemicals and childhood leukemia in Michoacán de Ocampo, México. PeerJ 13:e20219 https://doi.org/10.7717/peerj.20219
date submitted: 2025-03-20
date accepted: 2025-09-20
issued: 2025-11-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Jiménez-Alcántar
  given name: Paola
author list: Agent
  family name: Gómez-García
  given name: Anel
author list: Agent
  family name: López-Meza
  given name: Joel E.
author list: Agent
  family name: Ochoa-Zarzosa
  given name: Alejandra
author list: Agent
  family name: Espino-Barajas
  given name: Luis Andrés
author list: Agent
  family name: Morales-Manilla
  given name: Luis Miguel
author list: Agent
  family name: Pérez-Rivera
  given name: Eloy
author list: Agent
  family name: Zúñiga-Quijano
  given name: Luz Yadira
author list: Agent
  family name: Gutiérrez-Castellanos
  given name: Sergio
doi: 10.7717/peerj.20219
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-06
copyright: ©2025 Jiménez-Alcántar et al.
attribution name: Jiménez-Alcántar et al.

Auditory processing ability in Thai native speakers with the Gaps-In-Noise (GIN) test
type: item
type: AcademicArticle
description: Introduction Auditory processing disorder (APD) arises from dysfunctions within the central auditory nervous system (CANS). One key tool for assessing temporal auditory processing capabilities is the Gaps-In-Noise (GIN) test. While the GIN test serves as a critical tool, its accuracy may be influenced by linguistic factors. This research aims to establish preliminary normative data for the GIN test among young adult native Thai speakers and to compare potential performance differences across ears and various linguistic backgrounds. Methods This study included 52 native Thai speakers aged 18 to 25, all of whom had normal hearing confirmed through pure-tone audiometry, to examine auditory processing using the GIN test. The testing was conducted in an anechoic chamber to ensure standardized conditions. The results were analyzed based on the approximate gap-detection threshold (A.th.) value and the overall percent correct (OPC) value metrics. Results The study revealed that, among young adult native Thai speakers, the A.th. values were 5.12–0.81 milliseconds (ms.) in the right ear, 5.08–0.81 ms. in the left ear, and 5.04–0.68 ms. for both ears. The corresponding averages of OPC values were 69.94–7.66% for the right ear, 71.37–7.21% for the left ear, and 71.35–6.72% for both ears, respectively. While no significant differences were observed in the threshold between ears, a notable discrepancy in response accuracy was noted, with the right ear showing lower accuracy than the left ear. Significant differences were also found when compared to English, Korean, and Portuguese language users, but not when compared to Polish language users. Conclusion The study revealed comparable temporal processing abilities among young adult native Thai speakers, as indicated by similar A.th. values across both ears. However, differences in the OPC value responses suggest potential asymmetries in auditory processing mechanisms. Additionally, linguistic factors appeared to influence the outco…
format: application/pdf
format: text/html
creator: Supakarn Jeanbunjongkij
creator: Pawichaya Suphinnapong
creator: Patcharaorn Limkitisupasin
creator: Yuttana Roongthumskul
creator: Nattawan Utoomprurkporn
subject: Neuroscience
subject: Neurology
subject: Otorhinolaryngology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.20207
publisher: PeerJ Inc.
rights: © 2025 Jeanbunjongkij et al.
abstract: Introduction Auditory processing disorder (APD) arises from dysfunctions within the central auditory nervous system (CANS). One key tool for assessing temporal auditory processing capabilities is the Gaps-In-Noise (GIN) test. While the GIN test serves as a critical tool, its accuracy may be influenced by linguistic factors. This research aims to establish preliminary normative data for the GIN test among young adult native Thai speakers and to compare potential performance differences across ears and various linguistic backgrounds. Methods This study included 52 native Thai speakers aged 18 to 25, all of whom had normal hearing confirmed through pure-tone audiometry, to examine auditory processing using the GIN test. The testing was conducted in an anechoic chamber to ensure standardized conditions. The results were analyzed based on the approximate gap-detection threshold (A.th.) value and the overall percent correct (OPC) value metrics. Results The study revealed that, among young adult native Thai speakers, the A.th. values were 5.12–0.81 milliseconds (ms.) in the right ear, 5.08–0.81 ms. in the left ear, and 5.04–0.68 ms. for both ears. The corresponding averages of OPC values were 69.94–7.66% for the right ear, 71.37–7.21% for the left ear, and 71.35–6.72% for both ears, respectively. While no significant differences were observed in the threshold between ears, a notable discrepancy in response accuracy was noted, with the right ear showing lower accuracy than the left ear. Significant differences were also found when compared to English, Korean, and Portuguese language users, but not when compared to Polish language users. Conclusion The study revealed comparable temporal processing abilities among young adult native Thai speakers, as indicated by similar A.th. values across both ears. However, differences in the OPC value responses suggest potential asymmetries in auditory processing mechanisms. Additionally, linguistic factors appeared to influence the outco…
bibliographic citation: Jeanbunjongkij et al. (2025) Auditory processing ability in Thai native speakers with the Gaps-In-Noise (GIN) test. PeerJ 13:e20207 https://doi.org/10.7717/peerj.20207
date submitted: 2025-03-05
date accepted: 2025-09-18
issued: 2025-11-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jeanbunjongkij
  given name: Supakarn
author list: Agent
  family name: Suphinnapong
  given name: Pawichaya
author list: Agent
  family name: Limkitisupasin
  given name: Patcharaorn
author list: Agent
  family name: Roongthumskul
  given name: Yuttana
author list: Agent
  family name: Utoomprurkporn
  given name: Nattawan
doi: 10.7717/peerj.20207
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-06
copyright: ©2025 Jeanbunjongkij et al.
attribution name: Jeanbunjongkij et al.

Analysis of the chitin synthase gene family in Ganoderma lucidum: its structure, phylogeny, and expression patterns
type: item
type: AcademicArticle
description: Background Chitin synthases are essential enzymes in fungi, contributing to various biological processes such as hyphal growth, sporulation, and cell wall stability. Despite their well-documented functions in other fungal species, the specific roles of chitin synthases in Ganoderma lucidum remain unexplored. This investigation systematically characterized the complete chitin synthase gene family in Ganoderma lucidum. Methods A comprehensive analysis was conducted using bioinformatics tools to examine genomic localization, gene structure, conserved domains, and phylogenetic evolution. By employing bioinformatic approaches, the study investigated promoter cis-elements and expression patterns to elucidate the regulatory mechanisms of these genes in G. lucidum. Results In G. lucidum, eight chitin synthase (GlCS) family members were identified and phylogenetically classified into five distinct classes. Our investigation revealed stage-specific expression patterns of GlCS genes throughout the fungal development process. GlCS1, GlCS2, GlCS5, GlCS6, and GlCS8 exhibited significantly greater expression levels in the early fruiting body (EA) stage than in the other developmental phases. In the mature fruiting body (MA) stage, GlCS3 was predominantly expressed. In the primordium formation (PR) stage, GlCS7 exhibited peak expression levels. Six genes (GlCS1, GlCS3, GlCS4, GlCS6, GlCS7, and GlCS8) were markedly upregulated under 40 °C thermal stress, suggesting their potential roles in thermotolerance mechanisms. These findings demonstrate functional diversification among GlCS family members across different developmental stages and stress conditions.
format: application/pdf
format: text/html
creator: Linling Liu
creator: Yiming Yang
creator: Jintao Li
creator: Yanliang Gao
creator: Meixia Yan
subject: Agricultural Science
subject: Bioinformatics
subject: Mycology
description: doi:10.7717/peerj.20302
publisher: PeerJ Inc.
rights: © 2025 Liu et al.
abstract: Background Chitin synthases are essential enzymes in fungi, contributing to various biological processes such as hyphal growth, sporulation, and cell wall stability. Despite their well-documented functions in other fungal species, the specific roles of chitin synthases in Ganoderma lucidum remain unexplored. This investigation systematically characterized the complete chitin synthase gene family in Ganoderma lucidum. Methods A comprehensive analysis was conducted using bioinformatics tools to examine genomic localization, gene structure, conserved domains, and phylogenetic evolution. By employing bioinformatic approaches, the study investigated promoter cis-elements and expression patterns to elucidate the regulatory mechanisms of these genes in G. lucidum. Results In G. lucidum, eight chitin synthase (GlCS) family members were identified and phylogenetically classified into five distinct classes. Our investigation revealed stage-specific expression patterns of GlCS genes throughout the fungal development process. GlCS1, GlCS2, GlCS5, GlCS6, and GlCS8 exhibited significantly greater expression levels in the early fruiting body (EA) stage than in the other developmental phases. In the mature fruiting body (MA) stage, GlCS3 was predominantly expressed. In the primordium formation (PR) stage, GlCS7 exhibited peak expression levels. Six genes (GlCS1, GlCS3, GlCS4, GlCS6, GlCS7, and GlCS8) were markedly upregulated under 40 °C thermal stress, suggesting their potential roles in thermotolerance mechanisms. These findings demonstrate functional diversification among GlCS family members across different developmental stages and stress conditions.
bibliographic citation: Liu et al. (2025) Analysis of the chitin synthase gene family in Ganoderma lucidum: its structure, phylogeny, and expression patterns. PeerJ 13:e20302 https://doi.org/10.7717/peerj.20302
date submitted: 2025-07-09
date accepted: 2025-10-07
issued: 2025-11-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Linling
author list: Agent
  family name: Yang
  given name: Yiming
author list: Agent
  family name: Li
  given name: Jintao
author list: Agent
  family name: Gao
  given name: Yanliang
author list: Agent
  family name: Yan
  given name: Meixia
doi: 10.7717/peerj.20302
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-05
copyright: ©2025 Liu et al.
attribution name: Liu et al.

CD81 inhibits the proliferation of acute megakaryoblastic leukemia cells
type: item
type: AcademicArticle
description: CD81 is a cell surface protein that plays an important part in tumor development. Several studies have shown that CD81 plays a role in cancer cell proliferation, invasion, and metastasis, particularly in leukemia. It has been reported that CD81 is overexpressed in non-Down syndrome acute megakaryoblastic leukemia (non-DS AMKL). In this article, we hypothesize that CD81 may play a vital role in acute megakaryoblastic leukemia (AMKL). We constructed the CD81 knockdown cell line using shRNA and found that CD81 knockout can inhibit the proliferation of AMKL and increase the apoptosis of AMKL in vitro. Therefore, CD81 may be a target of AMKL.
format: application/pdf
format: text/html
creator: Narun Su
creator: Xiaohao Hu
subject: Cell Biology
subject: Molecular Biology
subject: Hematology
subject: Pediatrics
description: doi:10.7717/peerj.20286
publisher: PeerJ Inc.
rights: © 2025 Su and Hu
abstract: CD81 is a cell surface protein that plays an important part in tumor development. Several studies have shown that CD81 plays a role in cancer cell proliferation, invasion, and metastasis, particularly in leukemia. It has been reported that CD81 is overexpressed in non-Down syndrome acute megakaryoblastic leukemia (non-DS AMKL). In this article, we hypothesize that CD81 may play a vital role in acute megakaryoblastic leukemia (AMKL). We constructed the CD81 knockdown cell line using shRNA and found that CD81 knockout can inhibit the proliferation of AMKL and increase the apoptosis of AMKL in vitro. Therefore, CD81 may be a target of AMKL.
bibliographic citation: Su et al. (2025) CD81 inhibits the proliferation of acute megakaryoblastic leukemia cells. PeerJ 13:e20286 https://doi.org/10.7717/peerj.20286
date submitted: 2025-03-10
date accepted: 2025-10-02
issued: 2025-11-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Su
  given name: Narun
author list: Agent
  family name: Hu
  given name: Xiaohao
doi: 10.7717/peerj.20286
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-05
copyright: ©2025 Su and Hu
attribution name: Su and Hu

Biocontrol-relevant diversity of wheat-associated Pseudomonas: prevalence of P. sivasensis and identification of the novel species P. arvensis sp. nov.
type: item
type: AcademicArticle
description: The role of microbial communities in plant health and productivity has become increasingly evident. In this study, we investigated the diversity and functional potential of Pseudomonas spp. associated with Belgian cereal crops, focusing on wheat and spelt. From 444 Pseudomonas isolates, we identified 11 species, with several strains exhibiting strong antagonistic activity against major wheat pathogens. Notably, we report the high prevalence and efficient colonization abilities of Pseudomonas sivasensis, including its capacity to translocate from seed to leaf and suppress Zymoseptoria tritici infection in planta. Furthermore, we describe Pseudomonas arvensis sp. nov., a newly characterized species within the wheat microbiome, with DR1PS3 designated as the type strain. Our results advance the understanding of beneficial plant-microbe interactions in cereals and highlight the promise of native Pseudomonas species as biocontrol agents for sustainable disease management.
format: application/pdf
format: text/html
creator: Mathieu Delitte
creator: Benjamin Dubois
creator: Louis Morandini
creator: Alain Bultreys
creator: Jacques Mahillon
creator: Frederic Debode
creator: Claude Bragard
subject: Agricultural Science
subject: Biodiversity
subject: Microbiology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.20177
publisher: PeerJ Inc.
rights: © 2025 Delitte et al.
abstract: The role of microbial communities in plant health and productivity has become increasingly evident. In this study, we investigated the diversity and functional potential of Pseudomonas spp. associated with Belgian cereal crops, focusing on wheat and spelt. From 444 Pseudomonas isolates, we identified 11 species, with several strains exhibiting strong antagonistic activity against major wheat pathogens. Notably, we report the high prevalence and efficient colonization abilities of Pseudomonas sivasensis, including its capacity to translocate from seed to leaf and suppress Zymoseptoria tritici infection in planta. Furthermore, we describe Pseudomonas arvensis sp. nov., a newly characterized species within the wheat microbiome, with DR1PS3 designated as the type strain. Our results advance the understanding of beneficial plant-microbe interactions in cereals and highlight the promise of native Pseudomonas species as biocontrol agents for sustainable disease management.
bibliographic citation: Delitte et al. (2025) Biocontrol-relevant diversity of wheat-associated Pseudomonas: prevalence of P. sivasensis and identification of the novel species P. arvensis sp. nov.. PeerJ 13:e20177 https://doi.org/10.7717/peerj.20177
date submitted: 2024-08-28
date accepted: 2025-09-12
issued: 2025-11-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Delitte
  given name: Mathieu
author list: Agent
  family name: Dubois
  given name: Benjamin
author list: Agent
  family name: Morandini
  given name: Louis
author list: Agent
  family name: Bultreys
  given name: Alain
author list: Agent
  family name: Mahillon
  given name: Jacques
author list: Agent
  family name: Debode
  given name: Frederic
author list: Agent
  family name: Bragard
  given name: Claude
doi: 10.7717/peerj.20177
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-05
copyright: ©2025 Delitte et al.
attribution name: Delitte et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359