Insight into the potential candidate genes and signaling pathways involved in lymphoma disease in dogs using a comprehensive whole blood transcriptome analysis

Sheet, Sunirmal; Oh, Ye In; Arora, D. K.; Choi, Bong-Hwan; Ko, Minjeong; Nam, Yelin; Lim, Youngjo; Lim, Jeong-Hoon; Park, Mirim; Park, Woncheoul; Seo, Kyoung Won; Lee, Kyung-Tai

doi:10.1016/j.gene.2022.146735

Cited by 4 publications

(5 citation statements)

References 80 publications

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“…GO and KEGG pathway enrichment analysis of the DEGs linked to ADG deviation was performed using the DAVID web tool 59 , 60 . The KEGG graphs were obtained from www.kegg.jp/kegg/kegg1.html 61 .…”

Section: Methodsmentioning

confidence: 99%

A transcriptomic analysis of skeletal muscle tissues reveals promising candidate genes and pathways accountable for different daily weight gain in Hanwoo cattle

Sheet,

Jang,

Kim

et al. 2024

Sci Rep

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Cattle traits like average daily weight gain (ADG) greatly impact profitability. Selecting based on ADG considering genetic variability can lead to economic and genetic advancements in cattle breeding. This study aimed to unravel genetic influences on ADG variation in Hanwoo cattle at the skeletal muscle transcriptomic level. RNA sequencing was conducted on longissimus dorsi (LD), semimembranosus (SB), and psoas major (PM) muscles of 14 steers assigned to same feed, grouped by low (≤ 0.71 kg) and high (≥ 0.77 kg) ADG. At P ≤ 0.05 and log2fold > 1.5, the distinct pattern of gene expression was identified with 184, 172, and 210 differentially expressed genes in LD, SB, and PM muscles, respectively. Tissue-specific responses to ADG variation were evident, with myogenesis and differentiation associated JAK-STAT signaling pathway and prolactin signaling pathways enriched in LD and SB muscles, while adipogenesis-related PPAR signaling pathways were enriched in PM muscle. Key hub genes (AXIN2, CDKN1A, MYC, PTGS2, FZD5, SPP1) were upregulated and functionally significant in muscle growth and differentiation. Notably, DPP6, CDKN1A, and FZD5 emerged as possible candidate genes linked to ADG variation. These findings enhance our understanding of genetic factors behind ADG variation in Hanwoo cattle, illuminating skeletal muscle mechanisms influencing ADG.

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Section: Methodsmentioning

confidence: 99%

A transcriptomic analysis of skeletal muscle tissues reveals promising candidate genes and pathways accountable for different daily weight gain in Hanwoo cattle

Sheet,

Jang,

Kim

et al. 2024

Sci Rep

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“…Total RNA was extracted from each homogenized tissue sample obtained from selected necropsied pigs using the Qiagen RNeasy Kit (Qiagen), according to the manufacturer’s instructions. RNA extraction and sequencing data processing, quality analysis, mapping of reads, and DEG analysis were performed as described previously [ 19 ].…”

Section: Methodsmentioning

confidence: 99%

“…To determine the biological significance and significant pathways associated with ASFV infection, DEGs, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed according to our previous study [ 19 ]. The genome of the pig ( Sus scrofa ) was chosen as the background parameter, and a threshold of p < 0.05 was chosen to denote a statistically significant difference.…”

Section: Methodsmentioning

confidence: 99%

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Transcriptome profiles of organ tissues from pigs experimentally infected with African swine fever virus in early phase of infection

Oh,

Sheet,

Bui

et al. 2024

Emerging Microbes & Infections

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African swine fever, caused by African swine fever virus (ASFV), is a highly contagious and fatal disease that poses a significant threat to the global pig industry. The limited information on ASFV pathogenesis and ASFV–host interactions has recently prompted numerous transcriptomic studies. However, most of these studies have focused on elucidating the transcriptome profiles of ASFV-infected porcine alveolar macrophages in vitro . Here, we analyzed dynamic transcriptional patterns in vivo in nine organ tissues (spleen, submandibular lymph node, mesenteric lymph node, inguinal lymph node, tonsils, lungs, liver, kidneys, and heart) obtained from pigs in the early stages of ASFV infection (1 and 3 d after viremia). We observed rapid spread of ASFV to the spleen after viremia, followed by broad transmission to the liver and lungs and subsequently, the submandibular and inguinal lymph nodes. Profound variations in gene expression patterns were observed across all organs and at all time-points, providing an understanding of the distinct defence strategies employed by each organ against ASFV infection. All ASFV-infected organs exhibited a collaborative response, activating immune-associated genes such as S100A8 , thereby triggering a pro-inflammatory cytokine storm and interferon activation. Functional analysis suggested that ASFV exploits the PI3K-Akt signalling pathway to evade the host immune system. Overall, our findings provide leads into the mechanisms underlying pathogenesis and host immune responses in different organs during the early stages of infection, which can guide further explorations, aid the development of efficacious antiviral strategies against ASFV, and identify valuable candidate gene targets for vaccine development.

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“…GO and KEGG pathway enrichment analysis of the DEGs linked to ADG deviation was performed using the DAVID web tool 59,60 . The KEGG graphs were obtained from www.…”

Section: Functional and Pathway Enrichment Analysis Of Degsmentioning

confidence: 99%

A transcriptomic analysis of skeletal muscle tissues reveals promising candidate genes and pathways accountable for different daily weight gain in Hanwoo Cattle

Sheet,

Jang,

Kim

et al. 2023

Preprint

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Cattle traits like average daily weight gain (ADG) greatly impact profitability. Selecting based on ADG considering genetic variability can lead to economic and genetic advancements in cattle breeding. This study aimed to unravel genetic influences on ADG variation in Hanwoo cattle at the skeletal muscle transcriptomic level. RNA sequencing was conducted on longissimus dorsi (LD), semimembranosus (SB), and psoas major (PM) muscles of 14 steers assigned to same feed, grouped by low (≤ 0.78 kg) and high (≥ 0.88 kg) ADG. At P ≤ 0.05 and log2fold > 1.5, distinct gene expression patterns were identified with 200, 172, and 210 differentially expressed genes in LD, SB, and PM muscles, respectively. Tissue-specific responses to ADG variation were evident, with myogenesis and differentiation associated JAK-STAT signaling pathway and prolactin signaling pathways enriched in LD and SB muscles, while adipogenesis-related PPAR signaling pathways were enriched in PM muscle. Key hub genes (AXIN2, CDKN1A, MYC, PTGS2, FZD5, SPP1) were upregulated and functionally significant in muscle growth and differentiation. Notably, DPP6, CDKN1A, and FZD5 emerged as potential candidate genes linked to ADG variation. These findings enhance our understanding of genetic factors behind ADG variation in Hanwoo cattle, illuminating skeletal muscle mechanisms influencing ADG.

show abstract

Insight into the potential candidate genes and signaling pathways involved in lymphoma disease in dogs using a comprehensive whole blood transcriptome analysis

Cited by 4 publications

References 80 publications

A transcriptomic analysis of skeletal muscle tissues reveals promising candidate genes and pathways accountable for different daily weight gain in Hanwoo cattle

A transcriptomic analysis of skeletal muscle tissues reveals promising candidate genes and pathways accountable for different daily weight gain in Hanwoo cattle

Transcriptome profiles of organ tissues from pigs experimentally infected with African swine fever virus in early phase of infection

A transcriptomic analysis of skeletal muscle tissues reveals promising candidate genes and pathways accountable for different daily weight gain in Hanwoo Cattle

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