PeerJ最新文献

{"title":"Common laboratory results-based artificial intelligence analysis achieves accurate classification of plasma cell dyscrasias.","authors":"Bihua Yao, Yicheng Liu, Yuwei Wu, Siyu Mao, Hangbiao Zhang, Lei Jiang, Cheng Fei, Shuang Wang, Jijun Tong, Jianguo Wu","doi":"10.7717/peerj.18391","DOIUrl":"https://doi.org/10.7717/peerj.18391","url":null,"abstract":"<p><strong>Background: </strong>Plasma cell dyscrasias encompass a diverse set of disorders, where early and precise diagnosis is essential for optimizing patient outcomes. Despite advancements, current diagnostic methodologies remain underutilized in applying artificial intelligence (AI) to routine laboratory data. This study seeks to construct an AI-driven model leveraging standard laboratory parameters to enhance diagnostic accuracy and classification efficiency in plasma cell dyscrasias.</p><p><strong>Methods: </strong>Data from 1,188 participants (609 with plasma cell dyscrasias and 579 controls) collected between 2018 and 2023 were analyzed. Initial variable selection employed Kruskal-Wallis and Wilcoxon tests, followed by dimensionality reduction and variable prioritization using the Shapley Additive Explanations (SHAP) approach. Nine pivotal variables were identified, including hemoglobin (HGB), serum creatinine, and β₂-microglobulin. Utilizing these, four machine learning models (gradient boosting decision tree (GBDT), support vector machine (SVM), deep neural network (DNN), and decision tree (DT) were developed and evaluated, with performance metrics such as accuracy, recall, and area under the curve (AUC) assessed through 5-fold cross-validation. A subtype classification model was also developed, analyzing data from 380 cases to classify disorders such as multiple myeloma (MM) and monoclonal gammopathy of undetermined significance (MGUS).</p><p><strong>Results: </strong>1. Variable selection: The SHAP method pinpointed nine critical variables, including hemoglobin (HGB), serum creatinine, erythrocyte sedimentation rate (ESR), and β₂-microglobulin. 2. Diagnostic model performance: The GBDT model exhibited superior diagnostic performance for plasma cell dyscrasias, achieving 93.5% accuracy, 98.1% recall, and an AUC of 0.987. External validation reinforced its robustness, with 100% accuracy and an F1 score of 98.5%. 3. Subtype Classification: The DNN model excelled in classifying multiple myeloma, MGUS, and light-chain myeloma, demonstrating sensitivity and specificity above 90% across all subtypes.</p><p><strong>Conclusions: </strong>AI models based on routine laboratory results significantly enhance the precision of diagnosing and classifying plasma cell dyscrasias, presenting a promising avenue for early detection and individualized treatment strategies.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11542560/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142605995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of habitual physical activity on motor performance and prefrontal cortex activity during implicit motor learning.","authors":"Fu-Miao Tan, Wei-Peng Teo, Jessie Siew-Pin Leuk, Alicia M Goodwill","doi":"10.7717/peerj.18217","DOIUrl":"https://doi.org/10.7717/peerj.18217","url":null,"abstract":"<p><strong>Background: </strong>Acute bouts of exercise have been shown to improve motor learning. However, whether these benefits can be observed from habitual physical activity (PA) levels remains unclear and has important implications around PA guidelines to promote motor learning across the lifespan. This study investigated the effect of habitual PA levels on brain activity within the dorsolateral prefrontal cortex (DLPFC) during procedural motor skill acquisition.</p><p><strong>Methods: </strong>Twenty-six right-handed healthy young adults had physical activity levels quantified by calculating the metabolic equivalent of task (METs) in minutes per week, derived from the International Physical Activity Questionnaire (IPAQ). Functional near-infrared spectroscopy (fNIRS) over the DLPFC was recorded to measure neural activation during a serial reaction time task (SRTT). Behavioural indicators of procedural motor skill acquisition were quantified as reaction time and accuracy of correct trials during the SRTT. DLPFC activation was characterised as task-related changes in oxyhaemoglobin (∆[HbO₂]).</p><p><strong>Results: </strong>Findings showed that higher PA levels were associated with improvements in reaction time during procedural motor skill acquisition (<i>p</i> = 0.03). However, no significant effects of PA levels on accuracy or ∆[HbO₂] during procedural motor skill acquisition were observed. These findings show that while habitual PA may promote motor performance in young adults, this is not reflected by changes in the DLPFC area of the brain.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11542559/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142606013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Citizen science enhances understanding of sea turtle distribution in the Gulf of California.","authors":"Stephanie J Rousso, María Dinorah Herrero Perezrul, Agnese Mancini, Alan A Zavala-Norzagaray, Jesse F Senko","doi":"10.7717/peerj.18203","DOIUrl":"https://doi.org/10.7717/peerj.18203","url":null,"abstract":"<p><p>Citizen science is a valuable tool for addressing spatial distribution gaps in endangered species, especially in data-limited regions. Given the logistical and financial challenges of studying migratory species, this cost-effective approach contributes to strategic conservation planning. The Bay of La Paz, located in Baja California Sur, México, is considered an ecologically important region within the larger Gulf of California. Due to its rich biodiversity and abundant natural resources, the region serves as a hub for ecotourism and fishing, affording diverse opportunities for community-based scientific initiatives. This paper examines the value of citizen science contributions from three diverse community groups (<i>i.e.</i>, coastal residents, SCUBA divers, and artisanal fishers) to help scientists obtain information on sea turtle distribution in the Bay of La Paz. Our findings represent the first records of loggerhead turtles (Caretta caretta) in the bay based on ten citizen science reports that include live and dead turtles (either observed swimming, as bycatch, or stranded), providing new information on an endangered pelagic species identified in a coastal bay. Although the sample size is small, our diversity of sources and sighting types highlight the value of collaborative citizen science initiatives in complementing traditional research methods.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11542562/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142605992","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic complexity and clinical significance of the RCCX locus.","authors":"Vladimir V Shiryagin, Andrey A Devyatkin, Oleg D Fateev, Ekaterina S Petriaikina, Viktor P Bogdanov, Zoia G Antysheva, Pavel Yu Volchkov, Sergey M Yudin, Mary Woroncow, Veronika I Skvortsova","doi":"10.7717/peerj.18243","DOIUrl":"https://doi.org/10.7717/peerj.18243","url":null,"abstract":"<p><p>Nearly identical, repetitive elements in the genome contribute to the variability in genetic inheritance patterns, particularly in regions like the RCCX locus, where such repeats can lead to structural variations. In addition, during the formation of gametes as a result of meiosis, variants of loci with repetitive elements that do not code for the required proteins may occur. As a result, an individual with certain genetic rearrangements in this region may have an increased risk of developing a congenital disorder, particularly in cases where the non-functional allele is inherited dominantly. At the same time, there is still no routine or generally recognized diagnostic method to determine the sequence of the repetitive fragments. The functionally important RCCX locus consists of such repetitive fragments. The available knowledge about the genomic variants of the RCCX locus is fragmented, as there is no standardized method to determine its structure. It should be noted that in some structural variants of the RCCX locus, the sequence of protein-coding genes is disrupted, leading to the development of diseases such as congenital adrenal hyperplasia (CAH). Although genetic testing is generally accepted as a gold standard for CAH diagnosis, there are a myriad of strategies on which exact methods to use and in which order. The reason for this inconsistency lies in the complexity of the RCCX locus and the fact that each patient or carrier may have a highly individualized mutation or combination thereof. In this review, we have discussed all known methods that can be used to study the structure of the RCCX locus. As a result, optimal approaches are proposed for the diagnosis of the most common disease caused by lesions in the RCCX-CAH due to <i>CYP21A2</i> deficiency.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11542561/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142606014","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dietary reference intake for military operations: a scoping review.","authors":"Ryoko Mizushima, Motohiko Miyachi, Eiichi Yoshimura, Yoichi Hatamoto, Mai Matsumoto, Yuka Hamada, Mana Hatanaka, Aya Maeno, Chifumi Shimomura, Hidemi Takimoto","doi":"10.7717/peerj.18353","DOIUrl":"https://doi.org/10.7717/peerj.18353","url":null,"abstract":"<p><strong>Background: </strong>Reports that collect and organize dietary reference intake (DRI) data for military operations in different countries and regions worldwide are limited.This scoping review aimed to collect and organize information on the status of formulating a DRI for military operations in each country.</p><p><strong>Methodology: </strong>For the information search, we queried PubMed and Google for literature and reports on the DRI for military operations and summarized the content of the adopted literature and reports.</p><p><strong>Results: </strong>The content and rationale for DRI for military operations in Australia, the United Kingdom (UK), the United States of America (USA), and the North Atlantic Treaty Organization (NATO) can be summarized as follows: (1) Energy requirements: Four reports formulated physical activity levels (PALs) and corresponding energy requirements that differed from those for the civilian public. The PAL range for the military was set as high as 1.50-3.20, as opposed to the standard civilian upper PAL set at 1.20-2.20. (2) Protein: Three military reports outside of the UK had different standards than those for the civilian public with an increased intake in accordance with the high PAL while simultaneously preventing excessive intake.In the military, values were formulated 1.2-4.8 times higher than the standards for civilians (45-65 g/day to 55-307 g/day). (3) Macronutrient energy distribution: Four military reports established macronutrient energy distributions that differed from those for the civilian public. The DRI for the Australian and UK militaries was formulated such that as PAL increased, protein decreased, fat decreased or remained unchanged, and carbohydrate increased. (4) Sodium: Considering that military personnel sweat more due to high physical activity and their environment, two Australian and NATO reports were established with sodium levels that were twice as high as that of the civilian public (460-2,300 mg/day to 920-3,200 mg/day). Increasing sodium intake to <4,800 mg/day is recommended for individuals who sweat a lot or are not accustomed to hot environments.</p><p><strong>Conclusions: </strong>The DRI in Australia, the UK, USA, and NATO consider the physical activity and operating environment of military personnel, differing from those of the civilian population in terms of (1) energy requirements, (2) protein, (3) macronutrient energy distribution, and (4) sodium.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11542563/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142606011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel nomogram to predict the risk of requiring mechanical ventilation in patients with sepsis within 48 hours of admission: a retrospective analysis.","authors":"Bin Wang, Jian Ouyang, Rui Xing, Jiyuan Jiang, Manzhen Ying","doi":"10.7717/peerj.18500","DOIUrl":"10.7717/peerj.18500","url":null,"abstract":"<p><strong>Objective: </strong>To establish a model that can predict the risk of requiring mechanical ventilation within 48 h after admission in patients with sepsis.</p><p><strong>Methods: </strong>Data for patients with sepsis admitted to Dongyang People's Hospital from October 2011 to October 2023 were collected and divided into a modeling group and a validation group. Independent risk factors in the modeling group were analyzed, and a corresponding predictive nomogram was established. The model was evaluated for discriminative power (the area under the curve of the receiver operating characteristic curve, AUC), calibration degree (Hosmer-Lemeshow test), and clinical benefit (decision curve analysis, DCA). Models based on the Sequential Organ Failure Assessment (SOFA) scores, the National Early Warning Score (NEWS) scores and multiple machine learning methods were also established.</p><p><strong>Results: </strong>The independent factors related to the risk of requiring mechanical ventilation in patients with sepsis within 48 h included lactic acid, pro-brain natriuretic peptide (PRO-BNP), and albumin levels, as well as prothrombin time, the presence of lung infection, and D-dimer levels. The AUC values of nomogram model in the modeling group and validation group were 0.820 and 0.837, respectively. The nomogram model had a good fit and clinical value. The AUC values of the models constructed using SOFA scores and NEWSs were significantly lower than those of the nomogram (<i>P</i> < 0.01). The AUC value of the integrated machine-learning model for the validation group was 0.849, comparable to that of the nomogram model (<i>P</i> = 0.791).</p><p><strong>Conclusion: </strong>The established nomogram could effectively predict the risk of requiring mechanical ventilation within 48 h of admission by patients with sepsis. Thus, the model can be used for the treatment and management of sepsis.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533908/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142574860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Application of composite reference intervals in the diagnosis of subclinical hypothyroidism in the elderly: a retrospective study.","authors":"Peijuan Li, Wenming Yang, Guohua Tang, Zhipeng Li","doi":"10.7717/peerj.18417","DOIUrl":"10.7717/peerj.18417","url":null,"abstract":"<p><strong>Background: </strong>Thyroid stimulating hormone releasing hormone (TSH) is a key indicator for diagnosing subclinical hypothyroidism (SCH). We evaluated factors affecting TSH levels in elderly SCH, establishing a composite reference interval, and comparing it with traditional one in diagnosis.</p><p><strong>Methods: </strong>We collected data on patients aged ≥60 undergoing physical examinations in Chengdu, screening the influencing factors associated with TSH. Then, a two-dimensional composite reference interval was established for TSH and FT4, and the differences between the new and traditional diagnosing methods were compared.</p><p><strong>Results: </strong>The incidence of subclinical thyroid dysfunction was about 14%, with SCH accounting for 97%. Regression analysis found that TSH levels increase as FT4 and uric acid levels decrease. Compared with the two-dimensional composite reference interval, the traditional one has a higher incidence rate of SCH.</p><p><strong>Conclusion: </strong>Compared with the two-dimensional composite reference interval, the traditional one is more likely to overestimate the incidence rate of SCH, leading to excessive diagnosis and treatment.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533903/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142574861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prognosis of hepatitis B virus reactivation in newly diagnosed multiple myeloma in modern era therapy: a retrospective study.","authors":"Weiran Lv, Xiaojin Li, Jingbo Xu, Yun Wang, Hanying Huang, Fang Hu, Yingying Cui, Yuanbin Song, Lezong Chen, Bingyi Wu, Yang Liang","doi":"10.7717/peerj.18475","DOIUrl":"10.7717/peerj.18475","url":null,"abstract":"<p><p>Studies on the prognosis of hepatitis B virus (HBV) reactivation following modern therapies for newly diagnosed MM (NDMM) are lacking. In this retrospective study, we aimed to assess the incidence, risk factors and prognosis of HBV reactivation in NDMM. A total of 33 of 355 patients with NDMM and HBV reactivation were included in this study. Multivariable analysis showed that hepatitis B surface antigen-positivity, hepatitis B core antibody-positivity, bortezomib-containing regimens, autologous stem cell transplantation, and gain of 1q21 were identified as independent risk factors of HBV reactivation in NDMM patients. The NDMM patients with HBV reactivation had poorer 3-year overall survival (OS) and progression-free survival (PFS) than did those without HBV reactivation, as confirmed by multivariate analysis. In conclusion, HBV reactivation in patients with NDMM constitutes a significant complication, correlating with reduced OS and PFS, and emerges as a potential adverse prognostic factor in the contemporary era of treatment.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533906/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142575306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Applying stacking ensemble method to predict chronic kidney disease progression in Chinese population based on laboratory information system: a retrospective study.","authors":"Jialin Du, Jie Gao, Jie Guan, Bo Jin, Nan Duan, Lu Pang, Haiming Huang, Qian Ma, Chenwei Huang, Haixia Li","doi":"10.7717/peerj.18436","DOIUrl":"10.7717/peerj.18436","url":null,"abstract":"<p><strong>Background and objective: </strong>Chronic kidney disease (CKD) is a major public health issue, and accurate prediction of the progression of kidney failure is critical for clinical decision-making and helps improve patient outcomes. As such, we aimed to develop and externally validate a machine-learned model to predict the progression of CKD using common laboratory variables, demographic characteristics, and an electronic health records database.</p><p><strong>Methods: </strong>We developed a predictive model using longitudinal clinical data from a single center for Chinese CKD patients. The cohort included 987 patients who were followed up for more than 24 months. Fifty-three laboratory features were considered for inclusion in the model. The primary outcome in our study was an estimated glomerular filtration rate ≤15 mL/min/1.73 m² or kidney failure. Machine learning algorithms were applied to the modeling dataset (<i>n</i> = 296), and an external dataset (<i>n</i> = 71) was used for model validation. We assessed model discrimination <i>via</i> area under the curve (AUC) values, accuracy, sensitivity, specificity, positive predictive value, negative predictive value, and F1 score.</p><p><strong>Results: </strong>Over a median follow-up period of 3.75 years, 148 patients experienced kidney failure. The optimal model was based on stacking different classifier algorithms with six laboratory features, including 24-h urine protein, potassium, glucose, urea, prealbumin and total protein. The model had considerable predictive power, with AUC values of 0.896 and 0.771 in the validation and external datasets, respectively. This model also accurately predicted the progression of renal function in patients over different follow-up periods after their initial assessment.</p><p><strong>Conclusions: </strong>A prediction model that leverages routinely collected laboratory features in the Chinese population can accurately identify patients with CKD at high risk of progressing to kidney failure. An online version of the model can be easily and quickly applied in clinical management and treatment.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533905/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142575020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Potential molecular mechanisms of ETV6-RUNX1-positive B progenitor cell cluster in acute lymphoblastic leukemia revealed by single-cell RNA sequencing.","authors":"Ning Qu, Yue Wan, Xin Sui, Tianyi Sui, Yang Yang","doi":"10.7717/peerj.18445","DOIUrl":"10.7717/peerj.18445","url":null,"abstract":"<p><strong>Aim: </strong>This study was to explore role of immune landscape and the immune cells in acute lymphoblastic leukemia (ALL) progression.</p><p><strong>Background: </strong>The most prevalent genetic alteration in childhood ALL is the ETV6-RUNX1 fusion. The increased proliferation of B progenitor cells could expedite the disease's progression due to irregularities in the cell cycle. Nevertheless, the mechanisms by which particular cell clusters influence the cell cycle and promote the advancement of ALL are still not well understood.</p><p><strong>Objective: </strong>This study was to explore role of immune landscape and the immune cells in ALL progression.</p><p><strong>Methods: </strong>Single-cell RNA sequencing (scRNA-seq) data of ETV6-RUNX1 and healthy pediatric samples obtained from GSE132509 were clustered and annotated using the Seurat package, and differentially highly expressed genes identified in each cluster were analyzed using DAVID for pathway annotation. Chromosome amplification and deletion were analyzed using the inferCNV package. SCENIC evaluated the regulation of transcription factors and target gene formation in cells. cellphoneDB and CellChat were served to infer ligand-receptor pairs that mediate interactions between subpopulations. The role of the target gene in regulating ALL progression was assessed using RT-qPCR, Transwell and scratch healing assays.</p><p><strong>Results: </strong>The bone marrow mononuclear cells (BMMCs) from ETV6-RUNX1 and healthy pediatric samples in GSE132509 were divided into 11 clusters, and B cell cluster 1 was identified as B progenitor cell, which was amplified on chromosome 6p. B progenitor cells were divided into seven clusters. Expression levels of amplified genes in chromosome 6p of B progenitor cell cluster 5 were the highest, and its specific highly expressed genes were annotated to pathways promoting cell cycle progression. Regulons formed in B progenitor cell cluster 5 were all involved in promoting cell cycle progression, so it was regarded as the B progenitor cell cluster that drives cell cycle progression. The key regulator of the B progenitor cell is E2F1, which promotes the migration and invasion ability of the cell line HAP1. The major ligand-receptor pairs that mediate the communication of B progenitor cell cluster 5 with cytotoxic NK/T cells or naive T cells included FAM3C-CLEC2D, CD47-SIRPG, HLAE-KLRC2, and CD47-KLRC2. HLAE-KLRC1 and TGFB1-(TGFBR1+TGFBR2).</p><p><strong>Conclusion: </strong>This study outlined the immune cell landscape of ETV6-RUNX1 ALL and identified chromosome 6p amplification in B progenitor cells, described the major B progenitor cell cluster driving cell cycle progression and its potential regulatory mechanisms on NK cells and T cells, providing cellular and molecular insights into ETV6-RUNX1 ALL.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533907/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142575147","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}