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HOX family genes show specific high expression, validated by RT-qPCR, and network analysis links Hox alterations to proliferation and metabolic remodeling. 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BMC Medical Genomics (2023) 16:153 [https://doi.org/10.1186/s12920-023-01588-7](https://doi.org/10.1186/s12920-023-01588-7)  \nBMC Medical Genomics  \n RESEARCH Open Access  \nGenomic and transcriptional  \ncharacterization of early esophageal squamous cell carcinoma  \nJingjing Zhao1,2†, Xiya Jia2†, Qiaojuan Li2, Hena Zhang2, Jianjun Wang3, Shenglin Huang2, Zhixiang Hu 1,2* and Caiping Li 1*  \nAbstract  \nBackground Esophageal squamous cell carcinoma (ESCC) is a highly heterogeneous cancer that lacks comprehensive understanding and effective treatment. Although multi-omics study has revealed features and underlying drivers of advanced ESCC, research on molecular characteristics of the early stage ESCC is quite limited.  \nMaterials and methods We presented characteristics of genomics and transcriptomics in 10 matched pairs of tumor and normal tissues of early ESCC patients in the China region.  \nResults We identified the specific patterns of cancer gene mutations and copy number variations. We also found a dramatic change in the transcriptome, with more than 4,000 genes upregulated in cancer. Among them, more than one-third of HOX family genes were specifically and highly expressed in early ESCC samples of China and validated by RT-qPCR. Gene regulation network analysis indicated that alteration of Hox family genes promoted the proliferation and metabolism remodeling of early ESCC.  \nConclusions We characterized the genomic and transcriptomic landscape of 10 paired normal adjacent and early ESCC tissues in the China region, and provided a new perspective to understand the development of ESCC and insight into potential prevention and diagnostic targets for the management of early ESCC in China.  \nKeywords Early Esophageal squamous cell carcinoma, Whole-exome sequencing, Genetic variation, HOX family, Tumor immune microenvironment  \n†Jingjing Zhao and Xiya Jia contributed equally to this work.  \n*Correspondence:  \nZhixiang Hu [zhixiang_hu@fudan.edu.cn](zhixiang_hu@fudan.edu.cn)[ ](zhixiang_hu@fudan.edu.cn)Caiping Li [yangrouchuan@189.cn](yangrouchuan@189.cn)  \n1 Department of Gastroenterology, Second Affiliated Hospital of Fujian Medical University, Quanzhou, China  \n2 Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China  \n3 Department of Pediatric Medicine, Gansu Provincial People’s Hospital, Lanzhou City, , Gansu Province, China  \nBackground  \nEsophageal cancer (EC), one of the most lethal cancers, is the seventh common cancer type and the sixth leading cause of cancer-related death in the world [1] . In China, there will be approximately 346,600 people newly diagnosed and 323,600 people dying from EC in 2022 [2] . Esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC) are the two main subtypes of EC, and have almost completely distinct geographic patterns, and primary risk factors. ESCC accounts for the vast majority of EC cases worldwide, especially in Asia [3] . The risk factors of ESCCare complicated in different countries and regions and  \n© The Author(s) 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit","cbCaieO6KscHsqwq","https://ap.wps.com/l/cbCaieO6KscHsqwq","pdf",2154065,12,"English","# Abstract\n## Background\n## Materials and methods\n## Results\n## Conclusions\n# Keywords","[{\"question\":\"What problem does the study address about early ESCC?\",\"answer\":\"Early-stage esophageal squamous cell carcinoma has limited molecular characterization. The study targets genomic and transcriptomic features to improve understanding and identify potential targets.\"},{\"question\":\"How was the dataset structured in this research?\",\"answer\":\"The research analyzed 10 matched pairs of tumor and normal tissues from early ESCC patients in the China region.\"},{\"question\":\"Which gene family showed notable early ESCC expression patterns, and how were they validated?\",\"answer\":\"More than one-third of HOX family genes were specifically and highly expressed in early ESCC samples in China, and the findings were validated by RT-qPCR.\"}]","Genomic and transcriptional characterization of early esophageal squamous cell carcinoma | PDF",1790244692]