RNA-Seq analysis in giant pandas reveals the differential expression of multiple genes involved in cataract formation

Yuyan You,Xin Hu,Wei Wang,Suhui Xu,Tianchun Pu,Yanqiang Yin,Chenglin Zhang,Maohua Xia,Xuefeng Li ,Qing Liu ,Yan Liu,Chao Bai,Yucun Chen,Jun Zhou,Yan Lu,Liqin Wang,Lili Niu,Tao Ma,Yanxia Ni,Ting Jia,Zengshuai Zhang

doi:10.1186/s12863-021-00996-x

Yuyan You, Xin Hu + Show 19 more

Open Access

https://doi.org/10.1186/s12863-021-00996-x

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Abstract

BackgroundThe giant panda (Ailuropoda melanoleuca) is an endangered mammalian species native to China. Fewer than 2500 giant pandas are known to exist, many of which are bred in captivity as a means to preserve and repopulate the species. Like other captive mammals, giant pandas acquire age-related cataracts, reducing their quality of life. Recent comparative genome-wide methylation analysis revealed 110 differentially methylated genes associated with cataract formation including six also associated with the formation of age-related cataracts in humans.ResultsTo investigate the pathological pathway in greater detail, here we used RNA-Seq analysis to investigate the differential expression profiles of genes in three giant pandas with cataracts and three healthy controls. We identified more than 700 differentially expressed genes, 29 of which were selected for further analysis based on their low q-value. We found that many of the genes encoded regulatory and signaling proteins associated with the control of cell growth, migration, differentiation and apoptosis, supporting previous research indicating a key role for apoptosis in cataract formation.ConclusionThe identification of genes involved in the formation of age-related cataracts could facilitate the development of predictive markers, preventative measures and even new therapies to improve the life of captive animals.

Highlights

The giant panda (Ailuropoda melanoleuca) is an endangered mammalian species native to China
Previous studies identified changes in DNA methylation associated with cataract formation in several mammals [14,15,16] and we recently reported that 110 genes with functions relevant to cataract pathogenesis are differentially methylated in giant pandas, including six genes known to be associated with age-related cataracts in humans [17]
Samples Peripheral blood samples were collected from six giant pandas ranging in age from 19 to 37, with three of the females affected by cataracts and the other specimens defined as healthy based on regular physical examinations (Table 1)

Summary

Introduction

The giant panda (Ailuropoda melanoleuca) is an endangered mammalian species native to China. Previous studies identified changes in DNA methylation associated with cataract formation in several mammals [14,15,16] and we recently reported that 110 genes with functions relevant to cataract pathogenesis are differentially methylated in giant pandas, including six genes known to be associated with age-related cataracts in humans [17]. Epigenetic modifications such as DNA methylation affect gene expression and control the availability of the corresponding gene products. The identification of genes that are overexpressed or suppressed during the formation of cataracts could lead to the development of new diagnostics, preventative treatments and therapeutic approaches to improve the quality of life for captive giant pandas and other mammals

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