Identification of Genomic Regions Influencing N-Metabolism and N-Excretion in Lactating Holstein- Friesians

Honerlagen, Hanne; Reyer, Henry; Oster, Michael; Ponsuksili, Siriluck; Trakooljul, Nares; Kuhla, Björn; Reinsch, Norbert; Wimmers, Klaus

doi:10.3389/fgene.2021.699550

Cited by 8 publications

(3 citation statements)

References 60 publications

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“…It has been reported that DKK1 functioned as a prognostic or diagnostic marker for OS assessment, and DKK1 immunodepletion may also be used as an additional treatment for OS ( 48 ). TMCC2 acts as a member of transmembrane and coiled-coil domain family, and its-encoding proteins might locate in endoplasmic reticulum and invovled in amyloid precursor protein metabolic process and bone marrow hematopoiesis ( 49 , 50 ). In addition, TMCC2 is identified as a potential biomarker of steroid-induced osteonecrosis of the femoral head ( 51 ).…”

Section: Discussionmentioning

confidence: 99%

Integration of single-cell RNA sequencing and bulk RNA sequencing to reveal an immunogenic cell death-related 5-gene panel as a prognostic model for osteosarcoma

et al. 2022

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BackgroundDespite the comparatively low prevalence of osteosarcoma (OS) compared to other cancer types, metastatic OS has a poor overall survival rate of fewer than 30%. Accumulating data has shown the crucial functions of immunogenic cell death (ICD) in various cancers; nevertheless, the relationship between ICD and OS was not previously well understood. This research aims to determine the function of ICD in OS and construct an ICD-based prognostic panel.MethodsSingle cell RNA sequencing data from GSE162454 dataset distinguished malignant cells from normal cells in OS. The discrepancy in ICD scores and corresponding gene expression was intensively explored between malignant cells and normal cells. Using the RNA sequencing data of the TARGET-OS, GSE16091, GSE21257, and GSE39058 datasets, the molecular subtype of OS was determined by clustering seventeen ICD-related genes obtained from the literature. Differentially expressed genes (DEGs) between different molecular subtypes were identified to develop a novel ICD-associated prognostic panel.ResultsThe malignant cells had a remarkable decrease in the ICD scores and corresponding gene expression compared with normal cells. A total of 212 OS patients were successfully stratified into two subtypes: C1 and C2. C1-like OS patients were characterized by better prognostic outcomes, overexpression of ICD genes, activation of the ICD pathway, high inflitration abundance of immunocytes, and low expression levels of immune checkpoint genes (ICGs); however, the reverse is true in C2-like OS patients. Utilizing the limma programme in R, the DEGs between two subtypes were determined, and a 5-gene risk panel consisting of BAMBI, TMCC2, NOX4, DKK1, and CBS was developed through LASSO-Cox regression analysis. The internal- and external-verification cohorts were employed to verify the efficacy and precision of the risk panel. The AUC values of ROC curves indicated excellent prognostic prediction values of our risk panel.ConclusionsOverall, ICD represented a protective factor against OS, and our 5-gene risk panel serving as a biomarker could effectively evaluate the prognostic risk in patients with OS.

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Section: Discussionmentioning

confidence: 99%

Integration of single-cell RNA sequencing and bulk RNA sequencing to reveal an immunogenic cell death-related 5-gene panel as a prognostic model for osteosarcoma

et al. 2022

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“…The SFI1 gene, or centrin-binding protein also on OAR17, has been associated with reproductive traits [ 96 ], metabolic digestion [ 97 ], and interestingly, cold adaptation, as it affects basal metabolic rate [ 98 ]. In addition, in humans, this gene was proved to be associated with glycosylated haemoglobin [ 99 ], a marker of average blood glucose levels.…”

Section: Discussionmentioning

confidence: 99%

Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds

Lukic,

Curik,

Drzaic

et al. 2023

J Animal Sci Biotechnol

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Background The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations. Sheep production system is extensive and generally carried out in traditional systems without intensive systematic breeding programmes for high uniform trait production (carcass, wool and milk yield). Therefore, eight indigenous Croatian sheep breeds from eastern Adriatic treated here as metapopulation (EAS), are generally considered as multipurpose breeds (milk, meat and wool), not specialised for a particular type of production, but known for their robustness and resistance to certain environmental conditions. Our objective was to identify genomic regions and genes that exhibit patterns of positive selection signatures, decipher their biological and productive functionality, and provide a "genomic" characterization of EAS adaptation and determine its production type. Results We identified positive selection signatures in EAS using several methods based on reduced local variation, linkage disequilibrium and site frequency spectrum (eROHi, iHS, nSL and CLR). Our analyses identified numerous genomic regions and genes (e.g., desmosomal cadherin and desmoglein gene families) associated with environmental adaptation and economically important traits. Most candidate genes were related to meat/production and health/immune response traits, while some of the candidate genes discovered were important for domestication and evolutionary processes (e.g., HOXa gene family and FSIP2). These results were also confirmed by GO and QTL enrichment analysis. Conclusions Our results contribute to a better understanding of the unique adaptive genetic architecture of EAS and define its productive type, ultimately providing a new opportunity for future breeding programmes. At the same time, the numerous genes identified will improve our understanding of ruminant (sheep) robustness and resistance in the harsh and specific Mediterranean environment.

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“…Generally, neither the cow individual N-uptake nor the content of N in urine and feces is measurable in practice operating dairy farms. Thus, in the last years the cow-specific MU concentration has been considered as a substitute trait (Burgos et al, 2007 , 2010 ; König et al, 2008 ; Honerlagen et al, 2021 ; Jahnel et al, 2021 ). MU values are available to breeding companies at a large scale due to the results of monthly milk records.…”

Section: Introductionmentioning

confidence: 99%

Ruminal background of predisposed milk urea (MU) concentration in Holsteins

Honerlagen

Reyer

Segelke³

et al. 2022

Front. Microbiol.

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Efforts to reduce nitrogen (N) emissions are currently based on the optimization of dietary- N supply at average herd N requirements. The implementation of the considerable individual differences and predispositions in N- use efficiency and N- excretion in breeding programs is hampered by the difficulty of data collection. Cow individual milk urea (MU) concentration has been proposed as an easy-to-measure surrogate trait, but recent studies questioned its predictive power. Therefore, a deeper understanding of the biological mechanisms underlying predisposed higher (HMUg) or lower (LMUg) MU concentration in dairy cows is needed. Considering the complex N- metabolism in ruminants, the distinction between HMUg and LMUg could be based on differences in (i) the rumen microbial community, (ii) the host-specific transcription processes in the rumen villi, and (iii) the host–microbe interaction in the rumen. Therefore, rumen fluid and rumen epithelial samples from 10 HMUg and 10 LMUg cows were analyzed by 16S sequencing and HiSeq sequencing. In addition, the effect of dietary-N reduction on ruminal shifts was investigated in a second step. In total, 10 differentially abundant genera (DAG) were identified between HMUg and LMUg cows, elucidating greater abundances of ureolytic Succinivibrionaceae_UCG-002 and Ruminococcaceae_unclassified in LMUg animals and enhanced occurrences of Butyvibrio in HMUg cows. Differential expression analysis revealed genes of the bovine Major Histocompatibility Complex (BOLA genes) as well as MX1, ISG15, and PRSS2 displaying candidates of MU predisposition that further attributed to enhanced immune system activities in LMUg cows. A number of significant correlations between microbial genera and host transcript abundances were uncovered, including strikingly positive correlations of BOLA-DRA transcripts with Roseburia and Lachnospiraceae family abundances that might constitute particularly prominent microbial–host interplays of MU predisposition. The reduction of feed-N was followed by 18 DAG in HMUg and 19 DAG in LMUg, depicting pronounced interest on Shuttleworthia, which displayed controversial adaption in HMUg and LMUg cows. Lowering feed-N further elicited massive downregulation of immune response and energy metabolism pathways in LMUg. Considering breeding selection strategies, this study attributed information content to MU about predisposed ruminal N-utilization in Holstein–Friesians.

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Identification of Genomic Regions Influencing N-Metabolism and N-Excretion in Lactating Holstein- Friesians

Cited by 8 publications

References 60 publications

Integration of single-cell RNA sequencing and bulk RNA sequencing to reveal an immunogenic cell death-related 5-gene panel as a prognostic model for osteosarcoma

Integration of single-cell RNA sequencing and bulk RNA sequencing to reveal an immunogenic cell death-related 5-gene panel as a prognostic model for osteosarcoma

Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds

Ruminal background of predisposed milk urea (MU) concentration in Holsteins

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