一种用于筛选浆细胞相关特征基因以评估骨质疏松症风险和治疗易感性的机器学习框架。
A Machine Learning Framework for Screening Plasma Cell-Associated Feature Genes to Estimate Osteoporosis Risk and Treatment Vulnerability.
作者信息
Wang Shoubao, Zhu Jiafu, Liu Weinan, Liu Aihua
机构信息
Department of Orthopedics, Huai'an Hospital Affiliated to Yangzhou University (The Fifth People's Hospital of Huai'an), Huai'an, 223300, China.
Department of Orthopaedics, Tongde Hospital of Zhejiang Province, Hangzhou, 310012, China.
出版信息
Biochem Genet. 2024 Jun 19. doi: 10.1007/s10528-024-10861-y.
Osteoporosis, in which bones become fragile owing to low bone density and impaired bone mass, is a global public health concern. Bone mineral density (BMD) has been extensively evaluated for the diagnosis of low bone mass and osteoporosis. Circulating monocytes play an indispensable role in bone destruction and remodeling. This work proposed a machine learning-based framework to investigate the impact of circulating monocyte-associated genes on bone loss in osteoporosis patients. Females with discordant BMD levels were included in the GSE56815, GSE7158, GSE7429, and GSE62402 datasets. Circulating monocyte types were quantified via CIBERSORT, with subsequent selection of plasma cell-associated DEGs. Generalized linear models, random forests, extreme gradient boosting (XGB), and support vector machines were adopted for feature selection. Artificial neural networks and nomograms were subsequently constructed for osteoporosis diagnosis, and the molecular machinery underlying the identified genes was explored. SVM outperformed the other tuned models; thus, the expression of several genes (DEFA4, HLA-DPB1, LCN2, HP, and GAS7) associated with osteoporosis were determined. ANNs and nomograms were proposed to robustly distinguish low and high BMDs and estimate the risk of osteoporosis. Clozapine, aspirin, pyridoxine, etc. were identified as possible treatment agents. The expression of these genes is extensively posttranscriptionally regulated by miRNAs and mA modifications. Additionally, they participate in modulating key signaling pathways, e.g., autophagy. The machine learning framework based on plasma cell-associated feature genes has the potential for estimating personalized risk stratification and treatment vulnerability in osteoporosis patients.
骨质疏松症是一个全球公共卫生问题,其特征是由于骨密度低和骨量受损导致骨骼变得脆弱。骨矿物质密度(BMD)已被广泛用于诊断低骨量和骨质疏松症。循环单核细胞在骨破坏和重塑中起着不可或缺的作用。这项研究提出了一个基于机器学习的框架,以研究循环单核细胞相关基因对骨质疏松症患者骨质流失的影响。BMD水平不一致的女性被纳入GSE56815、GSE7158、GSE7429和GSE62402数据集。通过CIBERSORT对循环单核细胞类型进行量化,随后选择与浆细胞相关的差异表达基因(DEG)。采用广义线性模型、随机森林、极端梯度提升(XGB)和支持向量机进行特征选择。随后构建人工神经网络和列线图用于骨质疏松症诊断,并探索已鉴定基因的分子机制。支持向量机的表现优于其他调优模型;因此,确定了几个与骨质疏松症相关的基因(DEFA4、HLA-DPB1、LCN2、HP和GAS7)的表达。提出了人工神经网络和列线图以可靠地区分低BMD和高BMD,并估计骨质疏松症的风险。氯氮平、阿司匹林、吡哆醇等被确定为可能的治疗药物。这些基因的表达在转录后受到微小RNA(miRNA)和N6-甲基腺苷(m6A)修饰的广泛调控。此外,它们参与调节关键信号通路,如自噬。基于浆细胞相关特征基因的机器学习框架具有估计骨质疏松症患者个性化风险分层和治疗易感性的潜力。