Discrepant mRNA and Protein Expression in Immune Cells

With the development of single-cell mRNA sequencing (scRNA-seq), researchers have attempted to identify new methods for performing in-depth studies of immune cells. However, the discrepancies between the mRNA levels and the levels of surface proteins have confused many researchers. Here, we report a significant and interesting phenomenon in which the mRNA and protein expression levels were mismatched in immune cells. We concluded that scRNA-seq should be combined with other sequencing methods in single-cell studies (e.g., CITE-seq). The simultaneous assessment of both mRNA and protein expression will enhance the precision and credibility of the results.

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Single‐Cell Analysis of Cytokine mRNA and Protein Expression by Flow Cytometry

Current Protocols in Cytometry ◽

10.1002/cpcy.69 ◽

2020 ◽

Vol 92 (1) ◽

Author(s):

Rubina Pal ◽

Jayne Schaubhut ◽

Darcey Clark ◽

Lynette Brown ◽

Jennifer J. Stewart

Keyword(s):

Flow Cytometry ◽

Protein Expression ◽

Single Cell ◽

Single Cell Analysis ◽

Cell Analysis ◽

Cytokine Mrna ◽

Mrna And Protein Expression

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Increased galectin-3 levels are associated with abdominal aortic aneurysm progression and inhibition of galectin-3 decreases elastase-induced AAA development

Clinical Science ◽

10.1042/cs20171142 ◽

2017 ◽

Vol 131 (22) ◽

pp. 2707-2719 ◽

Cited By ~ 13

Author(s):

Carlos-Ernesto Fernandez-García ◽

Carlos Tarin ◽

Raquel Roldan-Montero ◽

Diego Martinez-Lopez ◽

Monica Torres-Fonseca ◽

...

Keyword(s):

Abdominal Aortic Aneurysm ◽

Aortic Aneurysm ◽

Protein Expression ◽

Potential Role ◽

Control Group ◽

Mrna Levels ◽

Abdominal Aortic ◽

Stat3 Phosphorylation ◽

Galectin 3 ◽

Mrna And Protein Expression

Abdominal aortic aneurysm (AAA) evolution is unpredictable and no specific treatment exists for AAA, except surgery to prevent aortic rupture. Galectin-3 has been previously associated with CVD, but its potential role in AAA has not been addressed. Galectin-3 levels were increased in the plasma of AAA patients (n=225) compared with the control group (n=100). In addition, galectin-3 concentrations were associated with the need for surgical repair, independently of potential confounding factors. Galectin-3 mRNA and protein expression were increased in human AAA samples compared with healthy aortas. Experimental AAA in mice was induced via aortic elastase perfusion. Mice were treated intravenously with the galectin-3 inhibitor modified citrus pectin (MCP, 10 mg/kg, every other day) or saline. Similar to humans, galectin-3 serum and aortic mRNA levels were also increased in elastase-induced AAA mice compared with control mice. Mice treated with MCP showed decreased aortic dilation, as well as elastin degradation, vascular smooth muscle cell (VSMC) loss, and macrophage content at day 14 postelastase perfusion compared with control mice. The underlying mechanism(s) of the protective effect of MCP was associated with a decrease in galectin-3 and cytokine (mainly CCL5) mRNA and protein expression. Interestingly, galectin-3 induced CCL5 expression by a mechanism involving STAT3 activation in VSMC. Accordingly, MCP treatment decreased STAT3 phosphorylation in elastase-induced AAA. In conclusion, increased galectin-3 levels are associated with AAA progression, while galectin-3 inhibition decreased experimental AAA development. Our data suggest the potential role of galectin-3 as a therapeutic target in AAA.

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Pseudogene HLA-DRB6 Regulates Immune Microenvironment of Cutaneous Melanoma by miR-338/CXCL10 Axis

10.21203/rs.3.rs-1228103/v1 ◽

2022 ◽

Author(s):

Jianmin Ren ◽

Jinglu Yu ◽

Yang Shi ◽

Inam Ullah Khan ◽

Jiansheng Huang

Keyword(s):

Single Cell ◽

Immune Cells ◽

Cutaneous Melanoma ◽

Target Genes ◽

Mrna Levels ◽

Sequencing Data ◽

Immune Microenvironment ◽

Potential Biomarker ◽

Tumor Immune Microenvironment ◽

The Relationship

Abstract Background: The relationship between the pseudogene and tumor immune microenvironment in cutaneous melanoma is unclear. In this study, we analyzed the role of the pseudogene HLA-DRB6 and its effect on the tumor immune microenvironment in skin cutaneous melanoma (SKCM) using bioinformatics tools. Method: The GEPIA database was used to analyze the expression of HLA-DRB6 and CXCL10 mRNA in tumor tissues. The TIMER database was used to analyze the relationship between mRNA levels and the infiltration of immune cells. The enrichment of HLA-DRB6 and CXCL10 in melanoma tissues was analyzed by single cell portal. The binding sites of HLA-DRB6 with its target genes was predicted via starBase database. The gene expression profiling and clinical data from GEO database (GSE94873) was used to verify the potential of CXCL10 as a biomarker. Result: The expression of HLA-DRB6 in SKCM tumor is higher than in normal tissues, and patients with high HLA-DRB6 expression had a better prognosis (P<0.05). Furthermore, HLA-DRB6 is positively correlated with the infiltration of immune cells such as B cells, CD4+ T, and CD8+ T lymphocytes, and the expression of immune checkpoint molecules such as PD-1, PD-L1, and CTLA-4. Single cell transcriptome sequencing data showed that HLA-DRB6 is mainly enriched in macrophages and had the highest correlation with CXCL10 than other chemokines (cor=0.66, P<0.0001). In addition, we found that CXCL10 can be used as a potential biomarker for predicting responsiveness and survival rate in SKCM patients who treated with Tremelimumab (a human anti-CTLA-4 antibody). Conclusion: In the microenvironment of SKCM, HLA-DRB6 is mainly enriched in macrophages and regulates the expression of CXCL10 through the ceRNA mechanism. Furthermore, the CXCL10 in peripheral blood can be used as a biomarker to predict the responsiveness and the prognosis for patients treated with tremelimumab.

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Yiqi Huoxue Recipe Improves Liver Regeneration in Rats after Partial Hepatectomy via JNK Pathway

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2020/9085801 ◽

2020 ◽

Vol 2020 ◽

pp. 1-9

Author(s):

Wen-cong Li ◽

Su-xian Zhao ◽

Wei-guang Ren ◽

Hui-juan Du ◽

Yu-guo Zhang ◽

...

Keyword(s):

Protein Expression ◽

Liver Regeneration ◽

Partial Hepatectomy ◽

Underlying Mechanism ◽

Mrna Levels ◽

Protective Effects ◽

Jnk Pathway ◽

Expression Levels ◽

Protein Levels ◽

Mrna And Protein Expression

The liver is the only visceral organ that exhibits a remarkable capability of regenerating in response to partial hepatectomy (PH) or chemical injury. Improving liver regeneration (LR) ability is the basis for the favourable treatment outcome of patients after PH, which can serve as a potential indicator for postoperative survival. The present study aimed to investigate the protective effects of Yiqi Huoxue recipe (YQHX) on LR after PH in rats and further elucidate its underlying mechanism. A two-thirds PH rat model was used in this study. Wistar rats were randomly divided into four groups: sham-operated, PH, YQHX + PH, and Fuzheng Huayu decoction (FZHY) + PH groups. All rats were sacrificed under anesthesia at 24 and 72 h after surgery. The rates of LR were calculated, and the expression levels of cyclin D1 and c-jun were determined by immunohistochemical staining. The protein levels of p-JNK1/2, JNK1/2, p-c-jun, c-jun, Bax, and Bcl-2 were detected by Western blotting, while the mRNA levels of JNK1, JNK2, c-jun, Bax, and Bcl-2 were examined by real-time polymerase chain reaction (RT-PCR). At the corresponding time points, YQHX and FZHY administration dramatically induced the protein levels of p-JNK1/2 compared to the PH group p<0.05, while FZHY + PH group showed prominently increase in p-JNK1/2 protein levels compared to the YQHX + PH group p<0.05. A similar trend was observed for the expression levels of p-c-jun. Compared to the PH group, YQHX and FZHY markedly reduced the mRNA and protein expression levels of Bax at 24 h after PH, while those in the FZHY + PH group decreased more obviously p<0.05. Besides, in comparison with the PH group, YQHX and FZHY administration predominantly upregulated the mRNA and protein expression levels of Bcl-2 at 24 and 72 h after PH p<0.05. In conclusion, YQHX improves LR in rats after PH by inhibiting hepatocyte apoptosis via the JNK signaling pathway.

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Hormonal and environmental regulation of epithelial calcium channel in gill of rainbow trout (Oncorhynchus mykiss)

AJP Regulatory Integrative and Comparative Physiology ◽

10.1152/ajpregu.00026.2006 ◽

2006 ◽

Vol 291 (5) ◽

pp. R1490-R1498 ◽

Cited By ~ 21

Author(s):

Arash Shahsavarani ◽

Steve F. Perry

Keyword(s):

Protein Expression ◽

Fold Increase ◽

Mrna Levels ◽

Uptake Capacity ◽

Pavement Cells ◽

Protein Levels ◽

Rainbow Trout Oncorhynchus Mykiss ◽

Uptake Rates ◽

Mrna And Protein Expression ◽

Trout Gill

We indirectly tested the idea that the epithelial Ca2+ channel (ECaC) of the trout gill is regulated in an appropriate manner to adjust rates of Ca2+ uptake. This was accomplished by assessing the levels of gill ECaC mRNA and protein in fish exposed to treatments known to increase or decrease Ca2+ uptake capacity. Exposure of trout to soft water ([Ca2+] = 20–30 nmol/l) for 5 days (a treatment known to increase Ca2+ uptake capacity) caused a significant increase in ECaC mRNA levels and an increase in ECaC protein expression. The inducement of hypercalcemia by infusing fish with CaCl2 (a treatment known to reduce Ca2+ uptake) was associated with a significant decrease in ECaC mRNA levels, yet protein levels were unaltered. ECaC mRNA and protein expression were increased in fish treated with the hypercalcemic hormone cortisol. Finally, exposure of trout to 48 h of hypercapnia (∼7.5 mmHg, a treatment known to increase Ca2+ uptake capacity) elicited an ∼100-fold increase in the levels of ECaC mRNA and a significant increase in protein expression. Immunocytochemical analysis of the gills from hypercapnic fish suggested a marked increase in the apical expression of ECaC on pavement cells and a subpopulation of mitochondria-rich cells. The results of this study provide evidence that Ca2+ uptake rates are, in part, regulated by the numbers of apical membrane Ca2+ channels that, in turn, modulate the inward flux of Ca2+ into gill epithelial cells.

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Age-Related Changes in Sirtuin 7 Expression in Calorie-Restricted and Refed Rats

Gerontology ◽

10.1159/000441603 ◽

2015 ◽

Vol 62 (3) ◽

pp. 304-310 ◽

Cited By ~ 17

Author(s):

Agata Wronska ◽

Aleksandra Lawniczak ◽

Piotr M. Wierzbicki ◽

Zbigniew Kmiec

Keyword(s):

Gene Expression ◽

Protein Expression ◽

Calorie Restriction ◽

Ribosome Biogenesis ◽

Healthy Aging ◽

Mrna Levels ◽

Age Related ◽

Mrna And Protein Expression ◽

Old Rats ◽

Age Related Changes

Background: Sirtuins (SIRT1-7) have been implicated to mediate the beneficial effects of calorie restriction for healthy aging. While the physiological functions of SIRT7 are still poorly understood, SIRT7 has recently been shown to affect ribosome biogenesis, mitochondrial gene expression, and hepatic lipid metabolism. Objective: To analyze the effects of age and short-term calorie restriction (SCR) and subsequent refeeding on SIRT7 expression in key metabolic tissues. Methods: Four- and 24-month-old male Wistar rats were subjected to 40% SCR for 30 days, followed by ad libitum feeding for 2 or 4 days. Liver, white adipose tissue (WAT), heart and skeletal muscle samples were analyzed by real-time PCR and Western blotting for SIRT7 mRNA and protein expression, respectively. Results: Aging had diverse effects on SIRT7 levels in lipogenic tissues: both the mRNA and protein levels increased in the retroperitoneal depot (rWAT), did not change in the epididymal depot (eWAT), and decreased in the subcutaneous depot (sWAT) and the liver of old as compared to young animals. In the heart, extensor digitorum longus muscle (EDL) and soleus muscle (SOL), Sirt7 gene but not protein expression was lower in old than in young control rats. SCR did not affect SIRT7 expression in WAT and the liver in both age groups. In the heart of young animals, SCR did not affect SIRT7 mRNA or protein level. In EDL, SIRT7 protein but not mRNA levels decreased after SCR and remained reduced upon refeeding. In SOL, both SIRT7 mRNA and protein expression were inhibited by refeeding. In old rats, cardiac Sirt7 expression increased after SCR and refeeding. In old rats' EDL and SOL muscles, SIRT7 protein expression was inhibited by refeeding. Conclusion: Age-related changes of SIRT7 gene expression in key organs of energy homeostasis are tissue dependent.

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Regulation of α7-integrin expression in vascular smooth muscle by injury-induced atherosclerosis

AJP Heart and Circulatory Physiology ◽

10.1152/ajpheart.00939.2003 ◽

2004 ◽

Vol 287 (1) ◽

pp. H381-H389 ◽

Cited By ~ 14

Author(s):

Jun-Tzu Chao ◽

Gerald A. Meininger ◽

Jan L. Patterson ◽

Sarah A. L. Jones ◽

Charles R. Partridge ◽

...

Keyword(s):

Smooth Muscle ◽

Vascular Smooth Muscle ◽

Protein Expression ◽

Mrna Expression ◽

Vascular Injury ◽

Pyrrolidine Dithiocarbamate ◽

Integrin Subunit ◽

Integrin Expression ◽

Mrna Levels ◽

Mrna And Protein Expression

Injury of vascular smooth muscle cells (VSMCs) by allylamine (AAM) leads to phenotypic changes associated with atherogenic progression including increased proliferation, migration, and alterations in cell adhesion. In the present study, the relationship between AAM-induced vascular injury and expression of the α7-integrin subunit was investigated. The α7-mRNA and protein expression were examined using real-time RT-PCR, fluorescence-activated cell sorting analysis (FACS), immunohistochemistry, and immunoblotting. In cultured VSMCs from aortas of AAM-treated rats (70 mg/kg for 20 days), α7-mRNA levels were increased more than twofold compared with control cells. No change was seen in β1-integrin expression. FACS analysis revealed increased cell surface expression of α7-protein (25 ± 9%; * P < 0.05). AAM treatment of naive VSMCs enhanced α7-mRNA expression (2.4 ± 0.7-fold, mean ± SE; * P < 0.05). The increased α7-mRNA expression was attenuated by the amine oxidase inhibitor semicarbazide and the antioxidant pyrrolidine dithiocarbamate, which confirms a role for oxidative stress in modulating α7-expression. In vivo α7-mRNA and protein expression were enhanced in the aortas of AAM-treated rats. In addition, increased α7-integrin expression facilitated AAM VSMC adhesion to laminin more efficiently compared with control (51 ± 2%; * P < 0.05). Chemical injury induced by AAM significantly enhances α7-integrin expression in VSMCs. These findings implicate for the first time the expression of α7-integrin during the response of VSMCs to vascular injury.

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Filamin A is reduced and contributes to the CASR sensitivity in human parathyroid tumors

Journal of Molecular Endocrinology ◽

10.1530/jme-16-0184 ◽

2017 ◽

Vol 58 (2) ◽

pp. 91-103 ◽

Cited By ~ 4

Author(s):

Alessandra Mingione ◽

Chiara Verdelli ◽

Stefano Ferrero ◽

Valentina Vaira ◽

Vito Guarnieri ◽

...

Keyword(s):

Protein Expression ◽

Hek293 Cells ◽

Erk Signaling ◽

Mrna Levels ◽

Filamin A ◽

Expression Levels ◽

Parathyroid Tumors ◽

Erk Phosphorylation ◽

Mrna And Protein Expression ◽

Signaling Activation

Parathyroid tumors display reduced sensitivity to extracellular calcium ([Ca2+]o). [Ca2+]o activates calcium-sensing receptor (CASR), which interacts with the scaffold protein filamin A (FLNA). The study aimed to investigate: (1) the FLNA expression in human parathyroid tumors, (2) its effects on the CASR mRNA and protein expression, and (3) on ERK signaling activation, (4) the effect of the carboxy-terminal CASR variants and (5) of the treatment with the CASR agonist R568 on FLNA-mediated ERK phosphorylation in HEK293 cells. Full-length FLNA immunostaining was variably reduced in parathyroid tumors. Immunofluorescence showed that FLNA localized in membrane and cytoplasm and co-localized with CASR in parathyroid adenomas (PAds)-derived cells. Cleaved C-terminus FLNA fragment could also be detected in PAds nuclear protein fractions. In HEK293 cells transfected with 990R-CASR or 990G-CASR variants, silencing of endogenous FLNA reduced CASR mRNA levels and total and membrane-associated CASR proteins. In agreement, FLNA mRNA levels positively correlated with CASR expression in a series of 74 PAds; however, any significant correlation with primary hyperparathyroidism severity could be detected and FLNA transcript levels did not differ between PAds harboring 990R or 990G CASR variants. R568 treatment was efficient in restoring 990R-CASR and 990G-CASR sensitivity to [Ca2+]o in the absence of FLNA. In conclusion, FLNA is downregulated in parathyroid tumors and parallels the CASR expression levels. Loss of FLNA reduces CASR mRNA and protein expression levels and the CASR-induced ERK phosphorylation. FLNA is involved in receptor expression, membrane localization and ERK signaling activation of both 990R and 990G CASR variants.

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Immunohistochemistry as a valuable tool to assess CD30 expression in peripheral T-cell lymphomas: high correlation with mRNA levels

Blood ◽

10.1182/blood-2014-07-584953 ◽

2014 ◽

Vol 124 (19) ◽

pp. 2983-2986 ◽

Cited By ~ 40

Author(s):

Céline Bossard ◽

Maria Pamela Dobay ◽

Marie Parrens ◽

Laurence Lamant ◽

Edoardo Missiaglia ◽

...

Keyword(s):

T Cell ◽

Protein Expression ◽

Mrna Levels ◽

Clinical Tool ◽

T Cell Lymphomas ◽

Key Points ◽

Mrna And Protein Expression ◽

Highly Correlated ◽

Peripheral T Cell Lymphomas

Key Points IHC is a valuable clinical tool for assessing CD30+ PTCL patients who may respond to CD30-targeting treatment. CD30 mRNA and protein expression are highly correlated.

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The Expression and Prognostic Value of SUMO1-Activating Enzyme Subunit 1 and Its Potential Mechanism in Triple-Negative Breast Cancer

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.729211 ◽

2021 ◽

Vol 9 ◽

Author(s):

Qingshui Wang ◽

Wenting Zhong ◽

Lin Deng ◽

Qili Lin ◽

Youyu Lin ◽

...

Keyword(s):

Breast Cancer ◽

Cell Cycle ◽

Protein Expression ◽

Single Cell ◽

Prognostic Model ◽

Triple Negative ◽

Single Cell Analysis ◽

Cell Analysis ◽

Mrna And Protein Expression

Background: Triple-negative breast cancer (TNBC) is the most invasive and metastatic subtype of breast cancer. SUMO1-activating enzyme subunit 1 (SAE1), an E1-activating enzyme, is indispensable for protein SUMOylation. SAE1 has been found to be a relevant biomarker for progression and prognosis in several tumor types. However, the role of SAE1 in TNBC remains to be elucidated.Methods: In the research, the mRNA expression of SAE1 was analyzed via the cancer genome atlas (TCGA) and gene expression omnibus (GEO) database. Cistrome DB Toolkit was used to predict which transcription factors (TFs) are most likely to increase SAE1 expression in TNBC. The correlation between the expression of SAE1 and the methylation of SAE1 or quantity of tumor-infiltrating immune cells was further invested. Single-cell analysis, using CancerSEA, was performed to query which functional states are associated with SAE1 in different cancers in breast cancer at the single-cell level. Next, weighted gene coexpression network (WGCNA) was applied to reveal the highly correlated genes and coexpression networks of SAE1 in TNBC patients, and a prognostic model containing SAE1 and correlated genes was constructed. Finally, we also examined SAE1 protein expression of 207 TNBC tissues using immunohistochemical (IHC) staining.Results: The mRNA and protein expression of SAE1 were increased in TNBC tissues compared with adjacent normal tissues, and the protein expression of SAE1 was significantly associated with overall survival (OS) and disease-free survival (DFS). Correlation analyses revealed that SAE1 expression was positively correlated with forkhead box M1 (FOXM1) TFs and negatively correlated with SAE1 methylation site (cg14042711) level. WGCNA indicated that the genes coexpressed with SAE1 belonged to the green module containing 1,176 genes. Through pathway enrichment analysis of the module, 1,176 genes were found enriched in cell cycle and DNA repair. Single-cell analysis indicated that SAE1 and its coexpression genes were associated with cell cycle, DNA damage, DNA repair, and cell proliferation. Using the LASSO COX regression, a prognostic model including SAE1 and polo-like kinase 1 (PLK1) was built to accurately predict the likelihood of DFS in TNBC patients.Conclusion: In conclusion, we comprehensively analyzed the mRNA and protein expression, prognosis, and interaction genes of SAE1 in TNBC and constructed a prognostic model including SAE1 and PLK1. These results might be important for better understanding of the role of SAE1 in TNBC. In addition, DNA methyltransferase and TFs inhibitor treatments targeting SAE1 might improve the survival of TNBC patients.

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