PO.BCS01.05 · 生物信息与计算
RNA-seq图谱分析鉴定FOX基因作为潜在的CRC生物标志物
RNA-seq profiling identifies FOX genes as potential CRC biomarkers
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
结直肠癌（CRC）仍是全球（包括波多黎各）癌症相关死亡的主要原因，凸显了对可靠生物标志物的迫切需求，以实现更早、更准确的检测。FOX转录因子家族调控关键细胞过程，包括细胞增殖、凋亡、代谢和免疫调节。然而，其在居住于波多黎各的西班牙裔个体（HPR）中的表达模式和诊断效用尚未得到表征。本研究旨在表征健康个体与CRC个体的FOX基因表达谱，并评估其在HPR中的预后和诊断性能。
使用来自波多黎各家族性结直肠癌登记处（PURIFICAR）队列28名参与者（13例对照——健康正常黏膜、7例早期和8例晚期CRC肿瘤）的组织样本进行RNA提取和bulk RNA测序。差异基因表达分析使用DESeq2进行（|log2倍数变化|>2，校正p<0.05）。使用基因集变异分析（Gene Set Variation Analysis）从显著的非共线性FOX基因（VIF<10）构建了四个FOX特征评分。利用公开可获得的结肠癌数据，对每个差异表达的FOX基因进行Kaplan-Meier生存分析。使用二项广义线性模型（GLM）评估基因与CRC状态的关联，包括未校正模型和校正年龄及BMI的模型。使用敏感性、特异性和AUC-ROC评估诊断性能。显著性水平设为0.05。统计分析使用R version 4.3.3进行。35个FOX基因的表达谱将样本按CRC早期、晚期和对照分为不同的聚类。在12个差异表达基因中，5个基因上调（FOXC1、FOXC2-AS1、FOXH1、FOXN2、FOXQ1），7个基因下调（FOXA1、FOXA3、FOXD2、FOXD3-AS1、FOXE3、FOXF2、FOXO1），相对于对照而言在CRC中如此。Kaplan-Meier分析显示，4个基因（FOXA3、FOXC1、FOXF2、FOXQ1）的较高表达与CRC患者生存概率降低相关，而FOXA1和FOXN2的较高表达与生存改善相关（p<0.05）。在未校正分析中，FOXQ1表达以及包含FOXC1和FOXQ1的6基因FOX特征显著增加CRC风险（p<0.05），而7个基因显著降低CRC风险。在校正年龄和BMI后，FOXE3（OR：0.19）和FOXD2（OR：0.42）呈现保护性关联，而FOXQ1（OR：1.45）和FOXC1（OR：2.83）显示出最大的CRC风险增加。
多个FOX基因在CRC中差异表达，其中FOXC1和FOXQ1与CRC患者生存和疾病风险均显示出显著关联。FOX基因特征进一步提高了诊断性能。这些发现支持FOX转录因子作为HPR中具有临床意义的生物标志物的潜力。
查看英文原文 English abstract
Colorectal cancer (CRC) remains a leading cause of cancer-related deaths worldwide, including Puerto Rico, highlighting the urgent need for reliable biomarkers to enable earlier and more accurate detection. The FOX family of transcription factors regulates key cellular processes, including cell proliferation, apoptosis, metabolism, and immune regulation. However, their expression patterns and diagnostic utility in Hispanics individuals living in Puerto Rico (HPR) have not been characterized. The aim of this study is to characterize FOX gene expression profiles across healthy and CRC individuals and evaluate their prognostic and diagnostic performance in HPR.
Tissue samples from 28 participants in the Puerto Rico Familial Colorectal Cancer Registry (PURIFICAR) cohort (13 controls-healthy normal mucosa, 7 early-stage, and 8 advanced-stage CRC tumors) were used for RNA extraction and bulk RNA sequencing. Differential gene expression was performed using DESeq2 (|log2 fold change|>2, adjusted p<0.05). Four FOX signature scores were constructed from significant non-collinear FOX genes (VIF<10) using Gene Set Variation Analysis. Kaplan Meier survival analysis was performed for each differentially expressed FOX gene using publicly available colon cancer data. Gene associations with CRC status were evaluated using binomial generalized linear models (GLM), unadjusted and adjusted for age and BMI. Diagnostic performance was assessed using sensitivity, specificity, and AUC-ROC. Significance was set at 0.05. Statistical analyses were performed using R, version 4.3.3.Expression profiles of 35 FOX genes separated samples into distinct clusters by early- and advanced-stages of CRC and controls. Of 12 differentially expressed genes, 5 genes were upregulated (FOXC1, FOXC2-AS1, FOXH1, FOXN2, FOXQ1), while 7 were downregulated (FOXA1, FOXA3 FOXD2, FOXD3-AS1, FOXE3, FOXF2, FOXO1) in CRC relative to controls. Kaplan-Meier analysis showed that higher expression of 4 genes (FOXA3, FOXC1, FOXF2, FOXQ1) was associated with reduced survival probabilities in CRC patients, whereas higher expression of FOXA1 and FOXN2 was associated with improved survival (p<0.05). In unadjusted analysis, FOXQ1 expression and a 6-gene FOX signature, including FOXC1 and FOXQ1, significantly increased CRC odds (p<0.05), while 7 genes significantly decreased CRC odds. After adjusting for age and BMI, protective associations were observed for FOXE3 (OR:0.19), and FOXD2 (OR:0.42), while FOXQ1 (OR:1.45) and FOXC1 (OR:2.83) showed the largest increased odds of CRC.
Multiple FOX genes were differentially expressed in CRC, with FOXC1 and FOXQ1 showing significant associations with both survival of CRC patients and disease risk. A FOX gene signature further improved diagnostic performance. These findings support the potential of FOX transcription factors as clinically relevant biomarkers for HPR.
利益披露 Disclosure
Y. N. Ortiz-Maldonado, None..
H. Centeno-Girona, None..
C. Zenon-Melendez, None..
S. N. Lopez-Acevedo, None..
E. V. Caraballo, None.