Weighted gene co-expression network analysis identifies molecular pathways and hub genes involved in broiler White Striping and Wooden Breast myopathies

Abstract

In recent years, the poultry industry has experienced an increased incidence of myopathies affecting breasts of fast-growing broilers, such as White Striping (WS) and Wooden Breast (WB) defects. To explore the molecular mechanisms and genes involved in WS and WB onset, we decided to perform a Weighted Gene Co-expression Network Analysis (WGCNA) using the gene expression profile and meat quality parameters of Pectoralis major muscles analysed in our previous study. Among the 212 modules identified by WGCNA, the red, darkred, midnightblue and paleturquoise4 modules were chosen for subsequent analysis. Functional analysis evidenced pathways involved in extracellular matrix (ECM) organization, collagen metabolism, cellular signaling and unfolded protein response. The hub gene analysis showed several genes coding for ECM components as the most interconnected nodes in the gene network (e.g. COL4A1, COL4A2, LAMA2, LAMA4, FBLN5 and FBN1). In this regard, this study suggests that alterations in ECM composition could somehow activate the cascade of biological reactions that result in the growth-related myopathies onset, and the involvement of Collagen IV alterations in activating the endoplasmic reticulum (ER) stress response may be hypothesized. Therefore, our findings provide further and innovative knowledge concerning the molecular mechanisms related to the breast abnormalities occurrence in modern broilers.

Insights Into Transcriptome Profiles Associated With Wooden Breast Myopathy in Broilers Slaughtered at the Age of 6 or 7 Weeks

“…In conclusion, our findings were congruent with the proposed model of ECM disorders in the pathogenesis of growth-related myopathies in broilers (Bordini et al, 2021). The present study further provides an observation on the alteration of ECMmediated FA signaling.…”

“…Furthermore, reduced expression of LAMC1 was previously reported in patients with abnormal coronary atherogenesis ( Hebbel et al, 2020 ), suggesting maladaptive activities of the cells when LAMC1 expression was low. The importance of LAMC1 in WB myopathy was recently evidenced in the study of Bordini et al (2021) as it was defined as one of the hub genes interconnecting the DE gene network in WB and WS affected broilers.…”

Differential Expression of Myogenic and Calcium Signaling-Related Genes in Broilers Affected With White Striping

“…White Striping has been one of the main issues in poultry production in the last years. A number of studies have been conducted to understand the onset and development of WS, and other myopathies in chickens and some biological pathways have been associated to the occurrence of these conditions, such as extracellular calcium level, oxidative stress, localized hypoxia, possible fiber-type switching, and cellular repairing ( Mutryn et al, 2015 ; Beauclercq et al, 2017 ; Kuttappan et al, 2017 ; Boerboom et al, 2018 ; Lake et al, 2019 ; Marchesi et al, 2019 ; Abasht et al, 2021 ; Bordini et al, 2021 ). In the present study, 15 functional candidate genes important for tissue development were investigated in normal and WS-affected broilers, and six of them ( CA2 , CSRP3 , PLIN1 , CALM2 , DNASE1L3 , and MYLK2 ) were differentially expressed.…”

Exploring protein-protein interactions at the proteome level

“…Since its introduction in 2005, the weighted gene co-expression network analysis (WGCNA) has become one of the most effective and widely used methods for gene co-expression network analysis (Zhang and Horvath, 2005;Langfelder and Horvath, 2008;Zhao et al, 2010). WGCNA has been successfully used to unravel important functional correlations in cancer research (Giulietti et al, 2017;Li et al, 2019;Liu et al, 2021), proteomics, and transcriptomics (Zheng et al, 2021;Bordini et al, 2021;Liu et al, 2021;He et al, 2021). High-throughput experiments have made it possible to measure the expression profiles of genes on the genome level, which can be easily accessible via open libraries or web servers, but they can also be noisy and populated by false positives.…”