In Silico Analysis of HSP70 Gene Family in Bovine Genome

Tripathy, Kabita; Sodhi, Monika; Kataria, R. S.; Chopra, Meenu; Mukesh, Manishi

doi:10.1007/s10528-020-09994-7

Cited by 11 publications

(11 citation statements)

References 35 publications

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“…This finding was consistent with many previous ones (Gade et al, 2010; Nikbin et al, 2014). Thus, it is a highly conserved gene (Tripathy et al, 2021), explaining its rapid expression and production during stress (Silver & Noble, 2012). Several studies have reported that polymorphisms may exist in the HSP70 gene (Abhijith et al, 2021;Mohalik et al, 2021;Raza et al, 2021).…”

Section: Discussionsupporting

confidence: 92%

Genetic profiling of HSP70 gene in local Iraqi goats

2022

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Animals display numerous physiological and behavioral responses that reduce the effects of heat stress. Moreover, genetic variance is strongly associated with responses to heat stress, including variants of heat shock proteins (HSPs) that are necessary for thermoregulation and stress resistance. Herein, we performed the molecular profiling of the HSP70 gene, and its polymorphism was demonstrated as a possible factor in the stress tolerance of local Iraqi goats. A number of different mutations were found owing to seven main polymorphisms. Results indicated the occurrence of silent and missense mutations in sequences obtained for Iraqi local goats. Genetic diversity was observed in the HSP70 gene of Iraqi local goats on the basis of phylogenetic-tree analysis as some mutations occurred once whereas others occurred multiple times. The polymorphisms LC616787, LC616788, and LC616791 were combined with the reference gene in the same branch, whereas polymorphisms (LC616785 and LC616786) and (LC616789 and LC616790) met in different branches, respectively. Moreover, all studied proteins had mismatches in their threedimensional structures. Therefore, the presence of specific genetic differences within the HSP70 gene in Iraqi goats can increase the possibility of selecting animals more suitable to various levels of stress.

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Section: Discussionsupporting

confidence: 92%

Genetic profiling of HSP70 gene in local Iraqi goats

2022

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“…Notably, we identified the HSPa17 gene in the M. mercenaria and C. sinensis genomes, which was not reported in the oyster (Zhang et al, 2012) and scallop genomes (Cheng et al, 2016;Hu et al, 2019). The HSPa17 gene was also identified in the human (Brocchieri et al, 2008), bovine (Tripathy et al, 2021), channel catfish (Song et al, 2016), large yellow croaker (Xu et al, 2018), rainbow trout (Ma and Luo, 2020), and ascidian (Fujikawa et al, 2010) genomes. However, we did not identify HSPa13 in the M. mercenaria genome.…”

Section: Discussionmentioning

confidence: 59%

“…The HSP70 gene family has been studied in humans (Brocchieri et al, 2008), bovines (Tripathy et al, 2021), fish (Song et al, 2016;Xu et al, 2018), the fruit fly Drosophila melanogaster (Gong and Golic, 2004), and nematodes (Heschl and Baillie, 1990;Nikolaidis and Nei, 2004;Guerin et al, 2019). Mollusca is the second largest phylum in Animalia, and as the largest group of species in the Lophotrochozoa, it is central to our understanding of the biology and evolution of this superphylum of protostomes (Zhang et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Massive Heat Shock Protein 70 Genes Expansion and Transcriptional Signatures Uncover Hard Clam Adaptations to Heat and Hypoxia

Song

Feng

et al. 2022

Front. Mar. Sci.

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Heat shock protein 70 (HSP70) members participate in a wide range of housekeeping and stress-related activities in eukaryotic cells. In marine ecosystems, bivalves encounter abiotic stresses, including high temperatures and low dissolved oxygen. Here, 133 MmHSP70 genes were identified through combined methods including Blastp, HMM and manual filtration, based on the whole Mercenaria mercenaria genome. The MmHSP70 genes were unevenly distributed, and 41 genes (33.08%) were located on Chr 7. Phylogenetic analyses indicated that the MmHSP70 gene family mainly consisted of two clusters and the Hspa12 subfamily underwent lineage-specific expansion. A high-density collinear gene block was observed between M. mercenaria Chr 7 and Cyclina sinensis Chr 14. Tandem duplication MmHSP70 gene pairs experienced different levels of purifying selection, which could be an important source of sequence and functional constraints. MmHSP70 genes showed tissue-specific and stress-specific expression. Most tandem duplication HSP70 gene pairs had high expression under hypoxia stress. HSP70 B2 tandem duplication gene pairs showed significantly increased expression under heat plus severe hypoxia stress. This study provided a comprehensive understanding of the MmHSP70 gene family in the M. mercenaria and laid a significant foundation for further studies on the functional characteristics of MmHSP70 genes during exposure to heat and hypoxia stress.

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“…Thus, we explored the correlation of the IRPRS with these biomarkers. The genes included in the HSP70 family were obtained from a previous study [ 23 ]. The mean expression level of these HSP70 genes was used for correlation analysis.…”

Section: Methodsmentioning

confidence: 99%

Identification and Validation of an Inflammatory Response-Related Polygenic Risk Score as a Prognostic Marker in Hepatocellular Carcinoma

Huang

Feixiong

et al. 2022

Disease Markers

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Aims. We hypothesized that the expression patterns of inflammatory response-related genes may be a potential tool for hepatocellular carcinoma (HCC) risk scoring. Background. Inflammatory response plays a pivotal role in the pathogenesis of HCC. Objective. To establish and validate a hallmark inflammatory response gene-based polygenic risk score as a prognostic tool in HCC. Methods. We screened differentially expressed inflammatory response genes and established an inflammatory response-related polygenic risk score (IRPRS) in an HCC-related dataset. Patients with HCC were categorized into high- and low-risk groups according to the median IRPRS, and the overall survival between the two groups was compared. The IRPRS was validated in an independent external dataset. Tumor-infiltrating lymphocytes (TILs) in high- and low-risk groups were compared, and gene set enrichment analysis was performed to characterize high-risk HCC identified using this IRPRS. Results. Four differentially expressed hallmark inflammatory response genes (CD14, AQP9, SERPINE1, and ITGA5) were identified to construct the IRPRS. Patients in the high-risk group had significantly shorter overall survival than those in the low-risk group in both the training set and the test set. Furthermore, the IRPRS remained an independent prognostic factor compared to the routine clinicopathological characteristics. Many cancer-related hallmark gene sets and TILs were significantly enriched in the high-risk group. Conclusions. We established and validated a four-hallmark inflammatory response gene-based polygenic risk score, which could successfully divide patients with HCC into high-risk and low-risk groups. These two risk groups of HCC possess significantly distinct prognostic and biological characteristics.

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In Silico Analysis of HSP70 Gene Family in Bovine Genome

Cited by 11 publications

References 35 publications

Genetic profiling of HSP70 gene in local Iraqi goats

Genetic profiling of HSP70 gene in local Iraqi goats

Massive Heat Shock Protein 70 Genes Expansion and Transcriptional Signatures Uncover Hard Clam Adaptations to Heat and Hypoxia

Identification and Validation of an Inflammatory Response-Related Polygenic Risk Score as a Prognostic Marker in Hepatocellular Carcinoma

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