A note on the early transcriptional response in leaves and root of potato plants to cadmium exposure

Potato plants can accumulate a high amount of cadmium (Cd) in the tuber when grown in soils rich in Cd. The molecular mechanisms governing Cd accumulation in the potato plant are poorly understood. Here we performed an RNA-sequencing experiment to identify genes differentially expressed in the leaf and root of potato during early stages of Cd exposure. Results did not identify any significant transcriptional response in leaves under 1 or 5 mg kg−1 Cd after 72 h. However, in the roots we did identify 2,846 genes that were significantly differentially expressed after 72 h between plants grown in 5 mg kg−1 Cd and controls. These included genes involved in photosynthesis and autophagy being up-regulated, and genes involved in intracellular transport being down-regulated. This study is the first report on the transcriptome-wide response of potato to Cd stress, providing insight into the molecular mechanisms involved in the response.

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Integrated Insight into the Molecular Mechanisms of Spontaneous Abortion during Early Pregnancy in Pigs

International Journal of Molecular Sciences ◽

10.3390/ijms22126644 ◽

2021 ◽

Vol 22 (12) ◽

pp. 6644

Author(s):

Xupeng Zang ◽

Ting Gu ◽

Wenjing Wang ◽

Chen Zhou ◽

Yue Ding ◽

...

Keyword(s):

Immune Response ◽

Spontaneous Abortion ◽

Molecular Mechanisms ◽

Gene Set Enrichment Analysis ◽

Differentially Expressed ◽

Gene Set ◽

Cerna Network ◽

Major Interest ◽

End Stage ◽

Insight Into

Due to the high rate of spontaneous abortion (SAB) in porcine pregnancy, there is a major interest and concern on commercial pig farming worldwide. Whereas the perturbed immune response at the maternal–fetal interface is an important mechanism associated with the spontaneous embryo loss in the early stages of implantation in porcine, data on the specific regulatory mechanism of the SAB at the end stage of the implantation remains scant. Therefore, we used high-throughput sequencing and bioinformatics tools to analyze the healthy and arresting endometrium on day 28 of pregnancy. We identified 639 differentially expressed lncRNAs (DELs) and 2357 differentially expressed genes (DEGs) at the end stage of implantation, and qRT-PCR was used to verify the sequencing data. Gene set variation analysis (GSVA), gene set enrichment analysis (GSEA), and immunohistochemistry analysis demonstrated weaker immune response activities in the arresting endometrium compared to the healthy one. Using the lasso regression analysis, we screened the DELs and constructed an immunological competitive endogenous RNA (ceRNA) network related to SAB, including 4 lncRNAs, 11 miRNAs, and 13 genes. In addition, Blast analysis showed the applicability of the constructed ceRNA network in different species, and subsequently determined HOXA-AS2 in pigs. Our study, for the first time, demonstrated that the SAB events at the end stages of implantation is associated with the regulation of immunobiological processes, and a specific molecular regulatory network was obtained. These novel findings may provide new insight into the possibility of increasing the litter size of sows, making pig breeding better and thus improving the efficiency of animal husbandry production.

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Blunted transcriptional response to skeletal muscle ischemia in rats with chronic kidney disease: potential role for impaired ischemia-induced angiogenesis

Physiological Genomics ◽

10.1152/physiolgenomics.00124.2016 ◽

2017 ◽

Vol 49 (4) ◽

pp. 230-237 ◽

Cited By ~ 1

Author(s):

Rafael U. Heiss ◽

Fabian B. Fahlbusch ◽

Johannes Jacobi ◽

Christoph Daniel ◽

Arif B. Ekici ◽

...

Keyword(s):

Skeletal Muscle ◽

Chronic Kidney Disease ◽

Kidney Disease ◽

Molecular Mechanisms ◽

Transcriptional Response ◽

Differentially Expressed ◽

Early Gene ◽

Male Rats ◽

Pcr Analysis ◽

Cardiovascular Morbidity And Mortality

Chronic kidney disease (CKD) is associated with increased cardiovascular morbidity and mortality. Previous studies indicated an impairment of ischemia-induced angiogenesis in skeletal muscle of rats with CKD. We performed a systematic comparison of early gene expression in response to ischemia in rats with or without CKD to identify potential molecular mechanisms underlying impaired angiogenesis in CKD. CKD was induced in male rats by 5/6 nephrectomy (SNX); control rats were sham operated (sham). Eight weeks later, ischemia of the right limb was induced by ligation and resection of the femoral artery. Rats were killed 24 h after the onset of ischemia, and RNA was extracted from the musculus soleus of the ischemic and the nonischemic hindlimb. To identify differentially expressed transcripts, we analyzed RNA with Affymetrix GeneChip Rat Genome 230 2.0 Arrays. RT-PCR analysis of selected genes was performed to validate observed changes. Hindlimb ischemia upregulated 239 genes in CKD and 299 genes in control rats (66% overlap), whereas only a few genes were downregulated (14 in CKD and 34 in controls) compared with the nonischemic limb of the same animals. Comparison between the ischemic limbs of CKD and controls revealed downregulation of 65 genes in CKD; 37 of these genes were also among the ischemia-induced genes in controls. Analysis of functional groups (other than angiogenesis) pointed to genes involved in leukocyte recruitment and fatty acid metabolism. Transcript expression profiling points to a relatively small number of differentially expressed genes that may underlie the impaired postischemic angiogenesis in CKD.

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Posttranslational processing of a human myeloid lysosomal protein, myeloperoxidase

Blood ◽

10.1182/blood.v70.4.1143.1143 ◽

1987 ◽

Vol 70 (4) ◽

pp. 1143-1150 ◽

Cited By ~ 42

Author(s):

WM Nauseef

Keyword(s):

Lysosomal Enzymes ◽

Intracellular Transport ◽

Molecular Mechanisms ◽

Human Neutrophils ◽

Weak Bases ◽

Glucosidase Inhibitors ◽

Oligosaccharide Processing ◽

Insight Into ◽

Lysosomal Protein

Abstract Myeloperoxidase (MPO) is a lysosomal enzyme present in the azurophilic granules of human neutrophils and monocytes and is important for optimal oxygen-dependent killing of microorganisms. The native molecule is a heterodimer composed of a pair of heavy-light protomers, each containing a 59-kDa and 13.5-kDa subunit. The intracellular processing during biosynthesis of MPO was examined in the human promyelocytic cell line HL-60. Endoglycosidase H and F digestion of immunoprecipitated pro- MPO demonstrated the presence of five N-linked--high-mannose oligosaccharide side chains and no complex mannose units. Incorporation of the threonine analogue beta-hydroxynorvaline produced species approximately 2.5 kDa and approximately 5 kDa smaller than the fully glycosylated pro-MPO, suggesting that two of the glycans were in the asparagine-X-threonine tripeptide sequence. Processing of pro-MPO occurred very rapidly, within approximately five minutes, and was best identified using glucosidase inhibitors. The presence of such inhibitors resulted in synthesis of a 92-kDa glycoprotein rather than the usually identified 89-kDa peptide. Swainsonine, a Golgi mannosidase inhibitor, did not alter the size of the earliest synthesized protein, suggesting that pro-MPO exited the endoplasmic reticulum or cis-Golgi proximal to the site of mannosidases. Intracellular transport and proteolytic maturation of MPO was retarded by weak bases (NH4Cl, chloroquine) or monensin at concentrations shown to raise intralysosomal pH. However, these agents did not qualitatively alter transport nor increase secretion. Thus, although MPO biosynthesis resembled that of other lysosomal enzymes, significant differences exist, including only limited oligosaccharide processing and intracellular transport and proteolytic maturation of pro-MPO that was only retarded by alkalinizing lysosomes without affecting the products or the fraction of pro-MPO secreted. Characterization of the determinants for targeting and of the regulatory factors in processing lysosomal enzymes in myeloid cells will provide insight into the molecular mechanisms underlying common disorders such as myeloperoxidase deficiency.

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Posttranslational processing of a human myeloid lysosomal protein, myeloperoxidase

Blood ◽

10.1182/blood.v70.4.1143.bloodjournal7041143 ◽

1987 ◽

Vol 70 (4) ◽

pp. 1143-1150 ◽

Cited By ~ 1

Author(s):

WM Nauseef

Keyword(s):

Lysosomal Enzymes ◽

Intracellular Transport ◽

Molecular Mechanisms ◽

Human Neutrophils ◽

Weak Bases ◽

Glucosidase Inhibitors ◽

Oligosaccharide Processing ◽

Insight Into ◽

Lysosomal Protein

Myeloperoxidase (MPO) is a lysosomal enzyme present in the azurophilic granules of human neutrophils and monocytes and is important for optimal oxygen-dependent killing of microorganisms. The native molecule is a heterodimer composed of a pair of heavy-light protomers, each containing a 59-kDa and 13.5-kDa subunit. The intracellular processing during biosynthesis of MPO was examined in the human promyelocytic cell line HL-60. Endoglycosidase H and F digestion of immunoprecipitated pro- MPO demonstrated the presence of five N-linked--high-mannose oligosaccharide side chains and no complex mannose units. Incorporation of the threonine analogue beta-hydroxynorvaline produced species approximately 2.5 kDa and approximately 5 kDa smaller than the fully glycosylated pro-MPO, suggesting that two of the glycans were in the asparagine-X-threonine tripeptide sequence. Processing of pro-MPO occurred very rapidly, within approximately five minutes, and was best identified using glucosidase inhibitors. The presence of such inhibitors resulted in synthesis of a 92-kDa glycoprotein rather than the usually identified 89-kDa peptide. Swainsonine, a Golgi mannosidase inhibitor, did not alter the size of the earliest synthesized protein, suggesting that pro-MPO exited the endoplasmic reticulum or cis-Golgi proximal to the site of mannosidases. Intracellular transport and proteolytic maturation of MPO was retarded by weak bases (NH4Cl, chloroquine) or monensin at concentrations shown to raise intralysosomal pH. However, these agents did not qualitatively alter transport nor increase secretion. Thus, although MPO biosynthesis resembled that of other lysosomal enzymes, significant differences exist, including only limited oligosaccharide processing and intracellular transport and proteolytic maturation of pro-MPO that was only retarded by alkalinizing lysosomes without affecting the products or the fraction of pro-MPO secreted. Characterization of the determinants for targeting and of the regulatory factors in processing lysosomal enzymes in myeloid cells will provide insight into the molecular mechanisms underlying common disorders such as myeloperoxidase deficiency.

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The expression of chondrogenesis-related and arthritis-related genes in human ONFH cartilage with different Ficat stages

PeerJ ◽

10.7717/peerj.6306 ◽

2019 ◽

Vol 7 ◽

pp. e6306 ◽

Cited By ~ 2

Author(s):

Gaoyang Chen ◽

Lei Zhong ◽

Qingyu Wang ◽

Zhaoyan Li ◽

Jing Shang ◽

...

Keyword(s):

Articular Cartilage ◽

Antigen Processing ◽

Molecular Mechanisms ◽

Differentially Expressed Gene ◽

Stage Iv ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Control Group ◽

Neck Fracture ◽

Insight Into

Background It has been well known that the degeneration of hip articular cartilage with osteonecrosis of the femoral head (ONFH) increases the instability of hip and accelerates the development process of ONFH. A better understanding of the expression of chondrogenesis-related and arthritis-related genes of cartilage along with the progression of ONFH seems to be essential for further insight into the molecular mechanisms of ONFH pathogenesis. Methods We analyzed the differentially expressed gene profile (GSE74089) of human hip articular cartilage with ONFH. The functions and pathway enrichments of differentially expressed genes (DEGs) were analyzed via GO and KEGG analysis. The expression of six selected critical chondrogenesis-related and four arthritis-related genes in eight human hip articular cartilage with femoral neck fracture (FNF) and 26 human hip articular cartilage with different stages ONFH (6 cases of Ficat stage II, 10 cases of Ficat stage III and 10 cases of Ficat stage IV) were detected. Results A total of 2,174 DEGs, including 1,482 up-regulated and 692 down-regulated ones, were obtained in the ONFH cartilage specimens compared to the control group. The GO and KEGG enrichment analysis indicated that the function of these DEGs mainly enriched in extracellular matrix, angiogenesis, antigen processing and presentation. The results showed a significant stepwise up-expression of chondrogenesis-related genes, including MMP13, ASPN, COL1A1, OGN, COL2A1 and BMP2, along with the progression of ONFH. The arthritis-related genes IL1β, IL6 and TNFα were only found up-expressed in Ficat IV stage which indicated that the arthritis-related molecular changes were not significant in the progression of ONFH before Ficat III stage. However, the arthritis-related gene PTGS2 was significant stepwise up-expression along with the progression of ONFH which makes it to be a sensitive arthritis-related biomarker of ONFH. Conclusion Expression changes of six chondrogenesis-related and four arthritis-related genes were found in hip articular cartilage specimens with different ONFH Ficat stages. These findings are expected to a get a further insight into the molecular mechanisms of ONFH progression.

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Comprehensive microRNA analysis in bleomycin-induced pulmonary fibrosis identifies multiple sites of molecular regulation

Physiological Genomics ◽

10.1152/physiolgenomics.00222.2010 ◽

2011 ◽

Vol 43 (9) ◽

pp. 479-487 ◽

Cited By ~ 73

Author(s):

Ting Xie ◽

Jiurong Liang ◽

Rishu Guo ◽

Ningshan Liu ◽

Paul W. Noble ◽

...

Keyword(s):

Lung Fibrosis ◽

Molecular Mechanisms ◽

Target Genes ◽

Expression Patterns ◽

Differentially Expressed ◽

Toll Like Receptor ◽

Mirna Array ◽

Differentially Expressed Mirnas ◽

Mouse Lungs ◽

Insight Into

The molecular mechanisms of lung injury and fibrosis are incompletely understood. MicroRNAs (miRNAs) are crucial biological regulators that act by suppressing their target genes and are involved in a variety of pathophysiological processes. To gain insight into miRNAs in the regulation of lung fibrosis, total RNA was isolated from mouse lungs harvested at different days after bleomycin treatment, and miRNA array with 1,810 miRNA probes was performed thereafter. MiRNAs expressed in lungs with bleomycin treatment at different time points were compared with miRNAs expressed in lungs without bleomycin treatment, resulting in 161 miRNAs differentially expressed. Furthermore, miRNA expression patterns regulated in initial and late periods after bleomycin were identified. Target genes were predicted in silico for differentially expressed miRNAs, including let-7f, let-7g, miR-196b, miR-16, miR-195, miR-25, miR-144, miR-351, miR-153, miR-468, miR-449b, miR-361, miR-700, miR-704, miR-717, miR-10a, miR-211, miR-34a, miR-367, and miR-21. Target genes were then cross-referenced to the molecular pathways, suggesting that the differentially expressed miRNAs regulate apoptosis, Wnt, Toll-like receptor, and TGF-β signaling. Our study demonstrated a relative abundance of miRNA levels in bleomycin-induced lung fibrosis. The miRNAs and their potential target genes identified may contribute to the understanding of the complex transcriptional program of lung fibrosis.

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Identification of Differentially Expressed Genes Associated with Papillary Thyroid Carcinoma

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207323666200402085832 ◽

2020 ◽

Vol 23 (6) ◽

pp. 546-553

Author(s):

Hongyuan Cui ◽

Mingwei Zhu ◽

Junhua Zhang ◽

Wenqin Li ◽

Lihui Zou ◽

...

Keyword(s):

Papillary Thyroid Carcinoma ◽

Thyroid Carcinoma ◽

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Cellular Proliferation ◽

Mrna Level ◽

Thyroid Tissue ◽

Differentially Expressed ◽

Thyroid Tumors ◽

Papillary Thyroid

Objective: Next-generation sequencing (NGS) was performed to identify genes that were differentially expressed between normal thyroid tissue and papillary thyroid carcinoma (PTC). Materials & Methods: Six candidate genes were selected and further confirmed with quantitative real-time polymerase chain reaction (qRT-PCR), and immunohistochemistry in samples from 24 fresh thyroid tumors and adjacent normal tissues. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was used to investigate signal transduction pathways of the differentially expressed genes. Results: In total, 1690 genes were differentially expressed between samples from patients with PTC and the adjacent normal tissue. Among these, SFRP4, ZNF90, and DCN were the top three upregulated genes, whereas KIRREL3, TRIM36, and GABBR2 were downregulated with the smallest p values. Several pathways were associated with the differentially expressed genes and involved in cellular proliferation, cell migration, and endocrine system tumor progression, which may contribute to the pathogenesis of PTC. Upregulation of SFRP4, ZNF90, and DCN at the mRNA level was further validated with RT-PCR, and DCN expression was further confirmed with immunostaining of PTC samples. Conclusion: These results provide new insights into the molecular mechanisms of PTC. Identification of differentially expressed genes should not only improve the tumor signature for thyroid tumors as a diagnostic biomarker but also reveal potential targets for thyroid tumor treatment.

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Systems Biology Approaches Reveal a Multi-stress Responsive WRKY Transcription Factor and Stress Associated Gene Co-expression Networks in Chickpea

Current Bioinformatics ◽

10.2174/1574893614666190204152500 ◽

2019 ◽

Vol 14 (7) ◽

pp. 591-601 ◽

Cited By ~ 1

Author(s):

Aravind K. Konda ◽

Parasappa R. Sabale ◽

Khela R. Soren ◽

Shanmugavadivel P. Subramaniam ◽

Pallavi Singh ◽

...

Keyword(s):

Expression Pattern ◽

Gene Networks ◽

Molecular Mechanisms ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Wrky Transcription Factor ◽

Functional Enrichment ◽

Differentially Expressed ◽

Callose Deposition ◽

Significant Probability

Background: Chickpea is a nutritional rich premier pulse crop but its production encounters setbacks due to various stresses and understanding of molecular mechanisms can be ascribed foremost importance. Objective: The investigation was carried out to identify the differentially expressed WRKY TFs in chickpea in response to herbicide stress and decipher their interacting partners. Methods: For this purpose, transcriptome wide identification of WRKY TFs in chickpea was done. Behavior of the differentially expressed TFs was compared between other stress conditions. Orthology based cofunctional gene networks were derived from Arabidopsis. Gene ontology and functional enrichment analysis was performed using Blast2GO and STRING software. Gene Coexpression Network (GCN) was constructed in chickpea using publicly available transcriptome data. Expression pattern of the identified gene network was studied in chickpea-Fusarium interactions. Results: A unique WRKY TF (Ca_08086) was found to be significantly (q value = 0.02) upregulated not only under herbicide stress but also in other stresses. Co-functional network of 14 genes, namely Ca_08086, Ca_19657, Ca_01317, Ca_20172, Ca_12226, Ca_15326, Ca_04218, Ca_07256, Ca_14620, Ca_12474, Ca_11595, Ca_15291, Ca_11762 and Ca_03543 were identified. GCN revealed 95 hub genes based on the significant probability scores. Functional annotation indicated role in callose deposition and response to chitin. Interestingly, contrasting expression pattern of the 14 network genes was observed in wilt resistant and susceptible chickpea genotypes, infected with Fusarium. Conclusion: This is the first report of identification of a multi-stress responsive WRKY TF and its associated GCN in chickpea.

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Clinical Candidates Targeting the ATR–CHK1–WEE1 Axis in Cancer

Cancers ◽

10.3390/cancers13040795 ◽

2021 ◽

Vol 13 (4) ◽

pp. 795

Author(s):

Lukas Gorecki ◽

Martin Andrs ◽

Jan Korabecny

Keyword(s):

Cell Cycle ◽

Cancer Cells ◽

Molecular Mechanisms ◽

Patient Survival ◽

Current Status ◽

Future Perspectives ◽

Phase Ii Trials ◽

Anticancer Treatment ◽

Positive Outlook ◽

Insight Into

Selective killing of cancer cells while sparing healthy ones is the principle of the perfect cancer treatment and the primary aim of many oncologists, molecular biologists, and medicinal chemists. To achieve this goal, it is crucial to understand the molecular mechanisms that distinguish cancer cells from healthy ones. Accordingly, several clinical candidates that use particular mutations in cell-cycle progressions have been developed to kill cancer cells. As the majority of cancer cells have defects in G1 control, targeting the subsequent intra‑S or G2/M checkpoints has also been extensively pursued. This review focuses on clinical candidates that target the kinases involved in intra‑S and G2/M checkpoints, namely, ATR, CHK1, and WEE1 inhibitors. It provides insight into their current status and future perspectives for anticancer treatment. Overall, even though CHK1 inhibitors are still far from clinical establishment, promising accomplishments with ATR and WEE1 inhibitors in phase II trials present a positive outlook for patient survival.

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Comparative transcriptomic and metabolomic analyses of carotenoid biosynthesis reveal the basis of white petal color in Brassica napus

Planta ◽

10.1007/s00425-020-03536-6 ◽

2021 ◽

Vol 253 (1) ◽

Author(s):

Ledong Jia ◽

Junsheng Wang ◽

Rui Wang ◽

Mouzheng Duan ◽

Cailin Qiao ◽

...

Keyword(s):

Brassica Napus ◽

Molecular Mechanisms ◽

Flower Color ◽

Carotenoid Biosynthesis ◽

Differentially Expressed ◽

Transcriptome Data ◽

Oilseed Crops ◽

Qrt Pcr ◽

Carotenoid Metabolism ◽

Rapeseed Cultivar

Abstract Main conclusion The molecular mechanism underlying white petal color in Brassica napus was revealed by transcriptomic and metabolomic analyses. Abstract Rapeseed (Brassica napus L.) is one of the most important oilseed crops worldwide, but the mechanisms underlying flower color in this crop are known less. Here, we performed metabolomic and transcriptomic analyses of the yellow-flowered rapeseed cultivar ‘Zhongshuang 11’ (ZS11) and the white-flowered inbred line ‘White Petal’ (WP). The total carotenoid contents were 1.778-fold and 1.969-fold higher in ZS11 vs. WP petals at stages S2 and S4, respectively. Our findings suggest that white petal color in WP flowers is primarily due to decreased lutein and zeaxanthin contents. Transcriptome analysis revealed 10,116 differentially expressed genes with a fourfold or greater change in expression (P-value less than 0.001) in WP vs. ZS11 petals, including 1,209 genes that were differentially expressed at four different stages and 20 genes in the carotenoid metabolism pathway. BnNCED4b, encoding a protein involved in carotenoid degradation, was expressed at abnormally high levels in WP petals, suggesting it might play a key role in white petal formation. The results of qRT-PCR were consistent with the transcriptome data. The results of this study provide important insights into the molecular mechanisms of the carotenoid metabolic pathway in rapeseed petals, and the candidate genes identified in this study provide a resource for the creation of new B. napus germplasms with different petal colors.

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