# Silencing lncRNA 93358 Inhibits the Apoptosis of Myocardial Cells in Myocardial Infarction Rats by Inducing the Expression of SLC8A1

Authors: Jiumei Cai; Xiaoping Wang; Wei Liao; Yiming Zhong; Lingling Chen; Zhiwei Zhang
Journal: BioMed Research International
 (2022)

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## Abstract

Objective. To explore the inhibitor effects and mechanism of lncRNA 93358 against the apoptosis of myocardial cells in rats with myocardial infarction. Methods. The myocardial infarction model was established in rats, which were identified by cardiac ultrasound. TTC staining was used to evaluate the degree of heart infarction, and HE staining was utilized to determine the pathological state in myocardial tissues. The apoptotic state in myocardial tissues was confirmed by TUNEL assay. lncRNA 93358 was screened out using a high-throughput sequencing which was confirmed by RT-qPCR. The interaction between miR-466c-3p and SLC8A1 was identified using the dual-luciferase reporter assay. The expression level of Bax, Bcl-2, and SLC8A1 was determined in lncRNA 93358 knockdown cells using RT-qPCR and Western blotting Results. Massive myocardial necrosis was observed in model rats according to the results of TTC staining, HE staining, and TUNEL assay. lncRNA 93358 and Bax were found significantly upregulated, and Bcl-2 and SLC8A1 were greatly downregulated in model rats, which were dramatically reversed by the knockdown of lncRNA 93358, accompanied by the decline area of myocardial necrosis and decreased apoptotic myocardial cells. Conclusion. Silencing lncRNA 93358 inhibits the apoptosis of myocardial cells in rats with myocardial infarction by inducing the expression of SLC8A1.


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## Body

## 1. Introduction

Myocardial infarction (MI) is a fatal cardiovascular disease with millions of deaths annually all over the world, the morbidity and mortality of which remains high in recent years [1, 2]. It is reported that physiological and pathological processes, such as inflammatory reactions, cell apoptosis, and fibrosis, play important roles in impacting the prognosis and survival rate of MI patients [3, 4]. Long noncoding RNAs (lncRNAs) are a group of functional molecules at a greater length than 200 nt and play a critical role in multiple cellular progressions, such as proliferation, apoptosis, and differentiation. lncRNA is reported to be involved in the processes of development, differentiation, myocardial hypertrophy, heart failure, and MI by regulating transcription, posttranscriptional gene regulation, competitive endogenous RNA, and protein translation [5, 6]. In addition, lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is regarded as a key gene involved in the development of cardiovascular diseases such as MI [7]. The progression of MI is reported to be abnormally aggravated by lncRNA taurine upregulated gene 1 (TUG1) [8]. lncRNA cardiac conduction regulatory RNA (CCRR) shows significant impacts on cardiac conduction. However, not sufficient importance has been attached to the function of lncRNA in the regulation of myocardial apoptosis post MI. The present study will investigate the differentially expressed lncRNAs in MI through the high-throughput sequencing assay and explore the potential genes related to the function of differentially expressed lncRNAs utilizing the methods of bioinformatics, coexpression network analysis, and fluorescence quantitative PCR.


## 2. Materials and Methods

### 2.1. Animals and MI Modeling

25 SD rats weighing from 220 g to 250 g were raised at the condition of 18°C-26°C temperature and 40%-70% humidity. After being anesthetized by intraperitoneally injected with 2% pentobarbital sodium, the skin on the back of rats was cut off and the trachea was separated out, followed by making a small hole in the trachea with a needle to insert an endotracheal tube. The tidal volume was modulated to 10, and the electrocardiograph was connected, followed by opening the chest to expose the heart. Ligation was performed with a 6-0 circular wire through the upper 1/3 of the left coronary artery until the myocardial tissues turned pale. The successful establishment of the MI model was confirmed by the electrocardiogram. In the sham group, the ligation was absolved. The animal experiments described in this study were authorized by the Committee of the First Affiliated Hospital of Gannan Medical University (No. LLSC-20201022011).


### 2.2. lncRNA High-Throughput Sequencing and Expression Profiling

The samples were myocardial tissue of MI rats and control groups. The TRIzol reagent (Invitrogen, USA) was used to extract RNA and reverse transcription to synthesize cDNA. High-throughput sequencing was performed by Shanghai Jingneng Biotechnology Co., Ltd. Qualified double-stranded cDNA samples were interrupted by the Covaris ultrasonic system and subjected to end repair. A tail and sequencing adapter addition and the sequence of about 200 bp were recovered and enriched by PCR, and then, a cDNA library was established, and the quality of the library was evaluated. After statistics, samples with a mapping ratio lower than 50% were excluded. The DESeq2 software was used to screen the differentially expressed (DE) lncRNAs between the two groups [9]. Differences in gene expression with log2FC≥1 and P value < 0.05 were considered to be significantly differentially expressed.For functional analyses, Gene Ontology (GO,http://geneontology.org/) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG, https://www.kegg.jp/) were used for the functional annotation and classification of pathway according to the DAVID database (https://david.ncifcrf.gov/) [10]. Significantly enriched GO and significant pathways were screened according to P<0.05.


### 2.3. Silencing of lncRNA 93358 in MI Rats

SiRNA (GenScript, Nanjing, China) was designed according to the sequence of lncRNA 93358. MI rats were divided into three groups: model group (injected with the same amount of normal saline), NC group (injected with 100 nM siRNA NC), and shRNA group (injected with 100 nM siRNA lncRNA 93358). Each group received continuous intervention for 5 days.


### 2.4. Primary Cardiomyocyte Culture

Take the rat’s heart and cut the heart into about 1 mm3 tissue pieces. After adding a mixture of digestive enzymes, digest with slow shaking in a 37°C water bath. The single cell suspension was transferred to DMEM complete medium containing 15% fetal bovine serum (FBS) to end the digestion. The above process was repeated until the digestion of the tissue block was complete. All digested cells were collected, filtered through a 200-mesh cell screen, and centrifuged at 1000 rpm/min for 10 min, the supernatant was discarded, the pellet was resuspended in DMEM complete medium with 15% FBS, and the pellet was repeatedly pipetted gently to form a single cell suspension. The cell suspension was transferred to a Petri dish, and the myocardial cells in the supernatant were collected by differentially adhering to the wall for 60 min. The cells were seeded in a sterile 6-well plate precoated with laminin at 5×104 cells per well. After 24 hours of culture, the medium changed. After 48 hours, the myocardial cells were flattened into a monolayer, which could be used for subsequent experiments.


### 2.5. The Establishment of lncRNA 93358 Knockdown Myocardial Cells

ShRNA was designed and analyzed by GenScript (Nanjing, China), which was used to transfect myocardial cells to establish the lncRNA 93358 knockdown myocardial cells. The transfection reagent was Lipofectamine 3000 (Invitrogen, California, USA), and the duration of the transfection was 48 hours. The control group was myocardial cells from sham-operated rats, the model group was untreated MI rat myocardial cells, the NC group was myocardial cells from MI rat transfected with shRNA NC, and the shRNA group was myocardial cells from MI rat transfected with shRNA-lncRNA 93358. The efficacy of transfection was confirmed using the RT-qPCR assay.


### 2.6. Dual-Luciferase Reporter Assay

The synthesized SLC8A1 3′-UTR sequence (RiboBio, Guangzhou, China) or a mutant sequence was cloned into pmirGlo vectors (GenePharm) to construct the luciferase reporters SLC8A1-WT and SLC8A1-MUT. 293 T cells were cotransfected with SLC8A1-WT (or SLC8A1-MUT) and miR-466c-3p mimics (or mimics NC) at 70–80% confluency. The luciferase activities were assessed 48 h posttransfection using a Dual-Luciferase Reporter Assay System (Promega Biotech Co., Madison, USA).


### 2.7. Western Blot

The lysis buffer was utilized to isolate total proteins from rat myocardial tissue, and the isolated proteins were quantified with the BCA kit (Takara, Tokyo, Japan), followed by loading 30μg proteins for each sample onto the 12% SDS-PAGE. After being separated for 1 hour, proteins in the gel were further transferred onto the PVDF membrane (Takara, Tokyo, Japan), followed by incubation with 5% skim milk. Then, the membrane was incubated with the primary antibody against SLC8A1 (1 : 1000, 55075-1-AP, Proteintech, Chicago, USA), Bcl-2 (1 : 1000, bs-34012R, Bioss, Beijing, China), Bax (1 : 1000, 50599-2-lg, Proteintech, Chicago, USA), and Tubulin (1 : 1000, 10094-1-AP, Proteintech, Chicago, USA). Then, the secondary antibody (1 : 2000, ZB-2301, SolelyBio, Shanghai, China) was utilized to incubate with the membrane for 1.5 h at room temperature. Finally, the bands were incubated with the ECL solution, followed by quantification using the ImageJ software.


### 2.8. Quantitative Real-Time PCR (RT-qPCR)

The TRIzol© reagent (Leagene, Beijing, China) was applied for the extraction of total RNAs from myocardial tissues in each group, which were further reverse-transcribed to cDNA using the TaqMan miRNA reverse transcription kit (Invitrogen, California, USA). The RT-PCR was performed with HiScript II Q RT SuperMix (R223-01, Vazyme, Jiangsu, China) using SYBR® Green Real-time PCR Master Mix (Lifeint, Fujian, China). GAPDH was utilized for normalizing gene expression, which was determined using the 2−ΔΔCt method.


### 2.9. Hematoxylin and Eosin (H&E) Staining

After collecting the myocardial tissues from each rat and washing, the tissues were successively dehydrated with a 70%, 80%, and 90% ethanol solution, followed by incubation with equal quality of ethanol and xylene for 15 min. Subsequently, the samples were incubated with equal quality of xylene for another 15 min, followed by repeated incubation until the tissues appeared transparent. Then, the tissues were embedded in paraffin, sectioned, and stained with H&E staining, followed by randomly selecting the images from 5 fields at 100× magnification that were captured, and all phases of follicles and corpora lutea were counted by using an inverted microscope (Olympus, Tokyo, Japan).


### 2.10. TUNEL Assay

The tissue slides were baked in the oven at 65°C for 2 hours, followed by dehydrating with xylene, 100% ethyl alcohol, 95% ethyl alcohol, 80% ethyl alcohol solution, and pure water, successively. The slides were then added to a 50μg/mL proteinase K working solution to incubate at 37°C for 30 min. After 3 washes using PBS buffer, the slides were added with the TUNEL detection buffer to be incubated at 45°C for 2 hours. Lastly, the images were taken under an inverted microscope (Olympus, Tokyo, Japan).


### 2.11. Statistical Analysis

Data achieved was presented asmean±standard deviation (SD) and analyzed using the GraphPad software (Harvey Motulsky). The Student’s t-test was applied to check the difference between the two groups, and the one-way ANOVA method followed by the Tukey post hoc test was applied to check the differences among groups. P<0.05 was regarded as a significant difference.


## 2.1. Animals and MI Modeling

25 SD rats weighing from 220 g to 250 g were raised at the condition of 18°C-26°C temperature and 40%-70% humidity. After being anesthetized by intraperitoneally injected with 2% pentobarbital sodium, the skin on the back of rats was cut off and the trachea was separated out, followed by making a small hole in the trachea with a needle to insert an endotracheal tube. The tidal volume was modulated to 10, and the electrocardiograph was connected, followed by opening the chest to expose the heart. Ligation was performed with a 6-0 circular wire through the upper 1/3 of the left coronary artery until the myocardial tissues turned pale. The successful establishment of the MI model was confirmed by the electrocardiogram. In the sham group, the ligation was absolved. The animal experiments described in this study were authorized by the Committee of the First Affiliated Hospital of Gannan Medical University (No. LLSC-20201022011).


## 2.2. lncRNA High-Throughput Sequencing and Expression Profiling

The samples were myocardial tissue of MI rats and control groups. The TRIzol reagent (Invitrogen, USA) was used to extract RNA and reverse transcription to synthesize cDNA. High-throughput sequencing was performed by Shanghai Jingneng Biotechnology Co., Ltd. Qualified double-stranded cDNA samples were interrupted by the Covaris ultrasonic system and subjected to end repair. A tail and sequencing adapter addition and the sequence of about 200 bp were recovered and enriched by PCR, and then, a cDNA library was established, and the quality of the library was evaluated. After statistics, samples with a mapping ratio lower than 50% were excluded. The DESeq2 software was used to screen the differentially expressed (DE) lncRNAs between the two groups [9]. Differences in gene expression with log2FC≥1 and P value < 0.05 were considered to be significantly differentially expressed.For functional analyses, Gene Ontology (GO,http://geneontology.org/) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG, https://www.kegg.jp/) were used for the functional annotation and classification of pathway according to the DAVID database (https://david.ncifcrf.gov/) [10]. Significantly enriched GO and significant pathways were screened according to P<0.05.


## 2.3. Silencing of lncRNA 93358 in MI Rats

SiRNA (GenScript, Nanjing, China) was designed according to the sequence of lncRNA 93358. MI rats were divided into three groups: model group (injected with the same amount of normal saline), NC group (injected with 100 nM siRNA NC), and shRNA group (injected with 100 nM siRNA lncRNA 93358). Each group received continuous intervention for 5 days.


## 2.4. Primary Cardiomyocyte Culture

Take the rat’s heart and cut the heart into about 1 mm3 tissue pieces. After adding a mixture of digestive enzymes, digest with slow shaking in a 37°C water bath. The single cell suspension was transferred to DMEM complete medium containing 15% fetal bovine serum (FBS) to end the digestion. The above process was repeated until the digestion of the tissue block was complete. All digested cells were collected, filtered through a 200-mesh cell screen, and centrifuged at 1000 rpm/min for 10 min, the supernatant was discarded, the pellet was resuspended in DMEM complete medium with 15% FBS, and the pellet was repeatedly pipetted gently to form a single cell suspension. The cell suspension was transferred to a Petri dish, and the myocardial cells in the supernatant were collected by differentially adhering to the wall for 60 min. The cells were seeded in a sterile 6-well plate precoated with laminin at 5×104 cells per well. After 24 hours of culture, the medium changed. After 48 hours, the myocardial cells were flattened into a monolayer, which could be used for subsequent experiments.


## 2.5. The Establishment of lncRNA 93358 Knockdown Myocardial Cells

ShRNA was designed and analyzed by GenScript (Nanjing, China), which was used to transfect myocardial cells to establish the lncRNA 93358 knockdown myocardial cells. The transfection reagent was Lipofectamine 3000 (Invitrogen, California, USA), and the duration of the transfection was 48 hours. The control group was myocardial cells from sham-operated rats, the model group was untreated MI rat myocardial cells, the NC group was myocardial cells from MI rat transfected with shRNA NC, and the shRNA group was myocardial cells from MI rat transfected with shRNA-lncRNA 93358. The efficacy of transfection was confirmed using the RT-qPCR assay.


## 2.6. Dual-Luciferase Reporter Assay

The synthesized SLC8A1 3′-UTR sequence (RiboBio, Guangzhou, China) or a mutant sequence was cloned into pmirGlo vectors (GenePharm) to construct the luciferase reporters SLC8A1-WT and SLC8A1-MUT. 293 T cells were cotransfected with SLC8A1-WT (or SLC8A1-MUT) and miR-466c-3p mimics (or mimics NC) at 70–80% confluency. The luciferase activities were assessed 48 h posttransfection using a Dual-Luciferase Reporter Assay System (Promega Biotech Co., Madison, USA).


## 2.7. Western Blot

The lysis buffer was utilized to isolate total proteins from rat myocardial tissue, and the isolated proteins were quantified with the BCA kit (Takara, Tokyo, Japan), followed by loading 30μg proteins for each sample onto the 12% SDS-PAGE. After being separated for 1 hour, proteins in the gel were further transferred onto the PVDF membrane (Takara, Tokyo, Japan), followed by incubation with 5% skim milk. Then, the membrane was incubated with the primary antibody against SLC8A1 (1 : 1000, 55075-1-AP, Proteintech, Chicago, USA), Bcl-2 (1 : 1000, bs-34012R, Bioss, Beijing, China), Bax (1 : 1000, 50599-2-lg, Proteintech, Chicago, USA), and Tubulin (1 : 1000, 10094-1-AP, Proteintech, Chicago, USA). Then, the secondary antibody (1 : 2000, ZB-2301, SolelyBio, Shanghai, China) was utilized to incubate with the membrane for 1.5 h at room temperature. Finally, the bands were incubated with the ECL solution, followed by quantification using the ImageJ software.


## 2.8. Quantitative Real-Time PCR (RT-qPCR)

The TRIzol© reagent (Leagene, Beijing, China) was applied for the extraction of total RNAs from myocardial tissues in each group, which were further reverse-transcribed to cDNA using the TaqMan miRNA reverse transcription kit (Invitrogen, California, USA). The RT-PCR was performed with HiScript II Q RT SuperMix (R223-01, Vazyme, Jiangsu, China) using SYBR® Green Real-time PCR Master Mix (Lifeint, Fujian, China). GAPDH was utilized for normalizing gene expression, which was determined using the 2−ΔΔCt method.


## 2.9. Hematoxylin and Eosin (H&E) Staining

After collecting the myocardial tissues from each rat and washing, the tissues were successively dehydrated with a 70%, 80%, and 90% ethanol solution, followed by incubation with equal quality of ethanol and xylene for 15 min. Subsequently, the samples were incubated with equal quality of xylene for another 15 min, followed by repeated incubation until the tissues appeared transparent. Then, the tissues were embedded in paraffin, sectioned, and stained with H&E staining, followed by randomly selecting the images from 5 fields at 100× magnification that were captured, and all phases of follicles and corpora lutea were counted by using an inverted microscope (Olympus, Tokyo, Japan).


## 2.10. TUNEL Assay

The tissue slides were baked in the oven at 65°C for 2 hours, followed by dehydrating with xylene, 100% ethyl alcohol, 95% ethyl alcohol, 80% ethyl alcohol solution, and pure water, successively. The slides were then added to a 50μg/mL proteinase K working solution to incubate at 37°C for 30 min. After 3 washes using PBS buffer, the slides were added with the TUNEL detection buffer to be incubated at 45°C for 2 hours. Lastly, the images were taken under an inverted microscope (Olympus, Tokyo, Japan).


## 2.11. Statistical Analysis

Data achieved was presented asmean±standard deviation (SD) and analyzed using the GraphPad software (Harvey Motulsky). The Student’s t-test was applied to check the difference between the two groups, and the one-way ANOVA method followed by the Tukey post hoc test was applied to check the differences among groups. P<0.05 was regarded as a significant difference.


## 3. Results

### 3.1. lncRNA Screening

According to the comparison of reads, the proportion of each gene occupied in total reads was shown in Figure1, including exons, introns, and intergenic.Figure 1
The pie chart of gene structure distribution. Percent of reads mapped to genome regions. M1-M3: model group; C1-C3: control group. Blue represents exons, orange represents introns, and green represents intergenic.The conditions for screening were shown as follows: (1) transcripts with more than 2 exons were selected; (2) transcripts with a length longer than 200 bp were selected; (3) transcripts with known annotation were selected; and (4) transcripts without coding potential in the intersection of such software as CPC2, CNCI, Pfam, and PLEK were selected. Based on these conditions, the predicted lncRNAs were shown in Table1 and Figures 2(a) and 2(b).Table 1
The number and percentage of lncRNAs achieved by 4 different methods of prediction.
MethodNumber of transcriptsPercentage (%)Assessment noncoding in Pfam700252.45Assessment noncoding in CPC2468035.05Assessment noncoding in PLEK473435.46Assessment noncoding in CNCI447733.53Assessment noncoding in at least one method816961.19Assessment noncoding in all methods299722.45Total transcripts13351100Figure 2
The line chart (a) and Venn diagram (b) of lncRNA concentrations.
(a)(b)


### 3.2. Differentially Expressed lncRNA Identification

As shown in Figure3(a), the data from the control group flocked together, and the difference within the group was small. The distance within the model group was relatively significant, indicating that there was a significant difference among individuals in the model group.Figure 3
Identification of differentially expressed lncRNA. (a) The PCA diagram. (b) Volcano map of differential expression analysis. The horizontal axis represented the expression multiple of the transcript between different groups of samples and the vertical axis represented the statistical significance of changes in transcript expression levels (q value). Red dots represented an upregulated transcript, green dots represented a downregulated transcript, and black represented a nondifferential transcript.
(a)(b)A total of 241 DE lncRNAs were then identified, of which 111 were upregulated and 130 were downregulated. Volcano plots were used to assess the DE lncRNAs between the control and model groups (Figure3(b)).


### 3.3. Functional Enrichment of Differentially Expressed lncRNAs

To further investigate the biological functions of DE lncRNAs, we performed functional enrichment analysis for the DE mRNA regulated by lncRNAs. The GO terms of biological processes, cellular components, and molecular functions were illustrated in Figure4(a). The results showed that DE mRNAs were enriched in cellular process, protein-containing complex, and binding. Moreover, the KEGG analysis showed that the DE mRNAs significantly enriched in cell growth and death, signal transduction, translation, and energy metabolism (Figure 4(b)).Figure 4
Functional enrichment of differentially expressed lncRNAs. (a) GO analysis on the differentially expressed lncRNAs. The horizontal axis represented a functional classification, and the vertical axis represented the number of genes in the classification (right) and their percentage in the total number of genes annotated (left). (b) KEGG analysis on the differentially expressed lncRNAs. The vertical axis represents the pathway category, and the vertical axis represents the number of genes in the classification (right) and its percentage in the total number of annotated genes (left). Different colors represent different categories.
(a)(b)


### 3.4. Validation of Sequencing Data

lncRNA 93358 was proved to be differentially expressed in myocardial tissues in MI rats and by prediction using miRDB (http://mirdb.org/index.html); it was predicted that miR-34a-3p, miR-125b-2-3p, and miR-466c-3p interact with lncRNA 93358. Furthermore, we predicted the potential myocardial diseases that interact with these three miRNAs, which were SLC8A1 and TRPS1. Subsequently, the expression level of lncRNA 93358, miR-34a-3p, miR-125b-2-3p, miR-466c-3p, SLC8A1, and TRPS1 was determined by RT-qPCR. We found that lncRNA 93358 and TRPS1 were significantly upregulated in the model group, while the expression of SLC8A1, miR-34a-3p, miR-125b-2-3p, and miR-466c-3p was downregulated (Figures 5(a) and 5(b)).Figure 5
Validation of sequencing data. (a and b) The expression levels of lncRNA 93358, SLC8A1, and TRPS1 (a) and miR-34a-3p, miR-125b-2-3p, and miR-466c-3p (b) in the rat myocardial tissues were detected by RT-qPCR.∗∗P<0.01.
(a)(b)


### 3.5. SLC8A1 Was a Target of miR-466c-3p

To confirm the regulation among lncRNA 93358, miRNAs, and SLC8A1, we collected heart tissues from each group of rats. RT-qPCR results showed that lncRNA 93358 was highly expressed in the model group, which was significantly downregulated by the knockdown of lncRNA 93358. And the expression levels of miR-466c-3p in the model group and NC group were significantly downregulated, which were greatly reversed after the knockdown of lncRNA 93358 (P<0.05, Figures 6(a) and 6(b)).Figure 6
The regulation axis of lncRNA 93358/miRNA/SLC8A1. (a and b) The expression of lncRNA 93358 and miR-466c-3p in the four rat myocardial tissues was measured by RT-qPCR.∗P<0.05 vs. control, #P<0.05 vs. model, and ^P<0.05 vs. NC group. (c) The binding between SLC8A1 and miR-466c-3p was measured by dual-luciferase reporter. ∗P<0.05.
(a)(b)(c)Compared to the WT-SLC8A1 and WT-SLC8A1+mimic NC groups, the fluorescence value in the WT-SLC8A1+miR-466c group declined significantly (P<0.05). After mutation was induced on the binding site, there was no significant difference in the fluorescence value between the mut-SLC8A1+mimic NC and mut-SLC8A1+miR-466c group. This data indicated that miR-466c interacted with SLC8A1 (Figure 6(c)).


### 3.6. lncRNA 93358 Knockdown Improves Cardiac Function in MI Rats

Further, we investigated the effect of lncRNA 93358 expression on cardiac function in MI rats. Echocardiographic results (Figure7) showed that IVSd, LVIDd, and LVIDs were significantly increased, while LVFE, LVFS, HR, and CO were significantly decreased in the model rats compared with the control group (P<0.05). Interference with lncRNA 93358 expression significantly reduced IVSd, LVIDd, and LVIDs and increased LVFE and LVFS in MI rats. There was no significant difference in LVPWd and LVPWs between the groups (P>0.05).Figure 7
The results of cardiac ultrasound in rats.∗P<0.05 vs. control, #P<0.05 vs. model, and ^P<0.05 vs. NC group. IVSd: interventricular septum size (diastole); IVSs: interventricular septum size (systole); LVIDd: left ventricular internal size (diastolic); LVIDs: internal size of left ventricle (systole); LVPWd: left ventricular posterior wall size (diastolic); LVPWs: posterior wall size of left ventricle (systole); EF: left ventricular ejection fraction (LVEF); FS: percentage of left ventricular fraction shortening; HR: heart rate; CO: cardiac output.The infarcted myocardium appeared white after TTC staining, and the percentage of infarct area in each group was calculated. As shown in Figure8(a), compared to the model and NC groups, the infarct area in the lncRNA 93358-shRNA group declined significantly, indicating that the infarction could be ameliorated by the knockdown of lncRNA 93358.Figure 8
Pathological changes in the heart of rats in each group. (a) TTC staining of rat heart. (b) The images of HE staining.
(a)(b)In the control group, myocardial cells were neatly arranged, clearly defined, and evenly stained, indicating that the myocardial cells were in good condition. Myocardial cells in the model group and NC group were widely dissociated, necrotic and, severely damaged, and the cells showed incomplete contour. In the shRNA group, myocardial cells underwent necrosis, which was less than that in the model group and NC group. Although myocardial cells were damaged, there were still large areas of live myocardial cells (Figure8(b)).


### 3.7. lncRNA 93358 Knockdown Inhibits Apoptosis in MI Rat Cardiomyocytes

As shown in Figure9(a), compared with the control group, a large number of apoptosis cells was observed in the model group and NC group with green fluorescence. However, the green fluorescence was significantly reduced in the shRNA group, indicating that apoptotic cells were significantly reduced after the knockdown of lncRNA 93358.Figure 9
Effect of lncRNA 93358 on apoptosis in myocardial infarction rat cardiomyocytes. (a) The apoptosis of myocardial tissues was determined by TUNEL assay. (b and c) The expression level of Bax, Bcl-2, and SLC8A1 in the myocardial cells was determined by RT-qPCR (b) and Western blotting (c).∗P<0.05 vs. control, #P<0.05 vs. model, and ^P<0.05 vs. NC group.
(a)(b)(c)In addition, the apoptosis-related protein Bax in myocardial cells in the model group and NC group was significantly increased compared with the control group, while the expression of Bcl2 and SLC8A1 was significantly decreased. However, the expression levels of Bax, Bcl2, and SLC8A1 were significantly reversed by the knockdown of lncRNA 93358 (Figures9(b) and 9(c)).


## 3.1. lncRNA Screening

According to the comparison of reads, the proportion of each gene occupied in total reads was shown in Figure1, including exons, introns, and intergenic.Figure 1
The pie chart of gene structure distribution. Percent of reads mapped to genome regions. M1-M3: model group; C1-C3: control group. Blue represents exons, orange represents introns, and green represents intergenic.The conditions for screening were shown as follows: (1) transcripts with more than 2 exons were selected; (2) transcripts with a length longer than 200 bp were selected; (3) transcripts with known annotation were selected; and (4) transcripts without coding potential in the intersection of such software as CPC2, CNCI, Pfam, and PLEK were selected. Based on these conditions, the predicted lncRNAs were shown in Table1 and Figures 2(a) and 2(b).Table 1
The number and percentage of lncRNAs achieved by 4 different methods of prediction.
MethodNumber of transcriptsPercentage (%)Assessment noncoding in Pfam700252.45Assessment noncoding in CPC2468035.05Assessment noncoding in PLEK473435.46Assessment noncoding in CNCI447733.53Assessment noncoding in at least one method816961.19Assessment noncoding in all methods299722.45Total transcripts13351100Figure 2
The line chart (a) and Venn diagram (b) of lncRNA concentrations.
(a)(b)


## 3.2. Differentially Expressed lncRNA Identification

As shown in Figure3(a), the data from the control group flocked together, and the difference within the group was small. The distance within the model group was relatively significant, indicating that there was a significant difference among individuals in the model group.Figure 3
Identification of differentially expressed lncRNA. (a) The PCA diagram. (b) Volcano map of differential expression analysis. The horizontal axis represented the expression multiple of the transcript between different groups of samples and the vertical axis represented the statistical significance of changes in transcript expression levels (q value). Red dots represented an upregulated transcript, green dots represented a downregulated transcript, and black represented a nondifferential transcript.
(a)(b)A total of 241 DE lncRNAs were then identified, of which 111 were upregulated and 130 were downregulated. Volcano plots were used to assess the DE lncRNAs between the control and model groups (Figure3(b)).


## 3.3. Functional Enrichment of Differentially Expressed lncRNAs

To further investigate the biological functions of DE lncRNAs, we performed functional enrichment analysis for the DE mRNA regulated by lncRNAs. The GO terms of biological processes, cellular components, and molecular functions were illustrated in Figure4(a). The results showed that DE mRNAs were enriched in cellular process, protein-containing complex, and binding. Moreover, the KEGG analysis showed that the DE mRNAs significantly enriched in cell growth and death, signal transduction, translation, and energy metabolism (Figure 4(b)).Figure 4
Functional enrichment of differentially expressed lncRNAs. (a) GO analysis on the differentially expressed lncRNAs. The horizontal axis represented a functional classification, and the vertical axis represented the number of genes in the classification (right) and their percentage in the total number of genes annotated (left). (b) KEGG analysis on the differentially expressed lncRNAs. The vertical axis represents the pathway category, and the vertical axis represents the number of genes in the classification (right) and its percentage in the total number of annotated genes (left). Different colors represent different categories.
(a)(b)


## 3.4. Validation of Sequencing Data

lncRNA 93358 was proved to be differentially expressed in myocardial tissues in MI rats and by prediction using miRDB (http://mirdb.org/index.html); it was predicted that miR-34a-3p, miR-125b-2-3p, and miR-466c-3p interact with lncRNA 93358. Furthermore, we predicted the potential myocardial diseases that interact with these three miRNAs, which were SLC8A1 and TRPS1. Subsequently, the expression level of lncRNA 93358, miR-34a-3p, miR-125b-2-3p, miR-466c-3p, SLC8A1, and TRPS1 was determined by RT-qPCR. We found that lncRNA 93358 and TRPS1 were significantly upregulated in the model group, while the expression of SLC8A1, miR-34a-3p, miR-125b-2-3p, and miR-466c-3p was downregulated (Figures 5(a) and 5(b)).Figure 5
Validation of sequencing data. (a and b) The expression levels of lncRNA 93358, SLC8A1, and TRPS1 (a) and miR-34a-3p, miR-125b-2-3p, and miR-466c-3p (b) in the rat myocardial tissues were detected by RT-qPCR.∗∗P<0.01.
(a)(b)


## 3.5. SLC8A1 Was a Target of miR-466c-3p

To confirm the regulation among lncRNA 93358, miRNAs, and SLC8A1, we collected heart tissues from each group of rats. RT-qPCR results showed that lncRNA 93358 was highly expressed in the model group, which was significantly downregulated by the knockdown of lncRNA 93358. And the expression levels of miR-466c-3p in the model group and NC group were significantly downregulated, which were greatly reversed after the knockdown of lncRNA 93358 (P<0.05, Figures 6(a) and 6(b)).Figure 6
The regulation axis of lncRNA 93358/miRNA/SLC8A1. (a and b) The expression of lncRNA 93358 and miR-466c-3p in the four rat myocardial tissues was measured by RT-qPCR.∗P<0.05 vs. control, #P<0.05 vs. model, and ^P<0.05 vs. NC group. (c) The binding between SLC8A1 and miR-466c-3p was measured by dual-luciferase reporter. ∗P<0.05.
(a)(b)(c)Compared to the WT-SLC8A1 and WT-SLC8A1+mimic NC groups, the fluorescence value in the WT-SLC8A1+miR-466c group declined significantly (P<0.05). After mutation was induced on the binding site, there was no significant difference in the fluorescence value between the mut-SLC8A1+mimic NC and mut-SLC8A1+miR-466c group. This data indicated that miR-466c interacted with SLC8A1 (Figure 6(c)).


## 3.6. lncRNA 93358 Knockdown Improves Cardiac Function in MI Rats

Further, we investigated the effect of lncRNA 93358 expression on cardiac function in MI rats. Echocardiographic results (Figure7) showed that IVSd, LVIDd, and LVIDs were significantly increased, while LVFE, LVFS, HR, and CO were significantly decreased in the model rats compared with the control group (P<0.05). Interference with lncRNA 93358 expression significantly reduced IVSd, LVIDd, and LVIDs and increased LVFE and LVFS in MI rats. There was no significant difference in LVPWd and LVPWs between the groups (P>0.05).Figure 7
The results of cardiac ultrasound in rats.∗P<0.05 vs. control, #P<0.05 vs. model, and ^P<0.05 vs. NC group. IVSd: interventricular septum size (diastole); IVSs: interventricular septum size (systole); LVIDd: left ventricular internal size (diastolic); LVIDs: internal size of left ventricle (systole); LVPWd: left ventricular posterior wall size (diastolic); LVPWs: posterior wall size of left ventricle (systole); EF: left ventricular ejection fraction (LVEF); FS: percentage of left ventricular fraction shortening; HR: heart rate; CO: cardiac output.The infarcted myocardium appeared white after TTC staining, and the percentage of infarct area in each group was calculated. As shown in Figure8(a), compared to the model and NC groups, the infarct area in the lncRNA 93358-shRNA group declined significantly, indicating that the infarction could be ameliorated by the knockdown of lncRNA 93358.Figure 8
Pathological changes in the heart of rats in each group. (a) TTC staining of rat heart. (b) The images of HE staining.
(a)(b)In the control group, myocardial cells were neatly arranged, clearly defined, and evenly stained, indicating that the myocardial cells were in good condition. Myocardial cells in the model group and NC group were widely dissociated, necrotic and, severely damaged, and the cells showed incomplete contour. In the shRNA group, myocardial cells underwent necrosis, which was less than that in the model group and NC group. Although myocardial cells were damaged, there were still large areas of live myocardial cells (Figure8(b)).


## 3.7. lncRNA 93358 Knockdown Inhibits Apoptosis in MI Rat Cardiomyocytes

As shown in Figure9(a), compared with the control group, a large number of apoptosis cells was observed in the model group and NC group with green fluorescence. However, the green fluorescence was significantly reduced in the shRNA group, indicating that apoptotic cells were significantly reduced after the knockdown of lncRNA 93358.Figure 9
Effect of lncRNA 93358 on apoptosis in myocardial infarction rat cardiomyocytes. (a) The apoptosis of myocardial tissues was determined by TUNEL assay. (b and c) The expression level of Bax, Bcl-2, and SLC8A1 in the myocardial cells was determined by RT-qPCR (b) and Western blotting (c).∗P<0.05 vs. control, #P<0.05 vs. model, and ^P<0.05 vs. NC group.
(a)(b)(c)In addition, the apoptosis-related protein Bax in myocardial cells in the model group and NC group was significantly increased compared with the control group, while the expression of Bcl2 and SLC8A1 was significantly decreased. However, the expression levels of Bax, Bcl2, and SLC8A1 were significantly reversed by the knockdown of lncRNA 93358 (Figures9(b) and 9(c)).


## 4. Discussion

In the present study, DE lncRNA in MI rats was screened by high-throughput sequencing, namely, lncRNA 93358. It was predicted that lncRNA 93358 might interact with miR-34a-3p, miR-125b-2-3p, and miR-466c-3p by the miRDB method. SLC8A1 and TRPS1 were predicted as a target of these miRNAs. lncRNA 93358 regulated the expression of SLC8A1 and participated in the MI process by acting as a competitive endogenous RNA (ceRNA) through absorbing and inhibiting miRNA function.As further research develops, lncRNAs have proven to play an important role in the occurrence and development of tumors and cardiovascular diseases [11, 12]. lncRNA aggregates in specific regions near transcription sites and forms lncRNA-protein complexes to organize nuclear structure, modify chromatin state, participate in gene expression regulation, and stabilize subcellular structure and protein complexes [13, 14]. Current sequencing results indicate that a variety of lncRNAs play a critical role in the development of heart diseases. For example, the expression level of lncRNA MIAT is increased and maintains a high level after myocardial death [15]. lncRNA CCRR improves cardiac conduction and inhibits arrhythmias by upregulating Cx43 in the myocardial gap [16]. Downregulating lncRNA MEG3 and lncRNA H19 significantly reduces the size of MI and myocardial cell apoptosis [17, 18]. In the present study, lncRNA93358 was screened out by high-throughput sequencing, which was highly expressed in MI rats. In addition, current studies indicate that myocardial cell apoptosis plays an important role in ventricular remodeling and heart failure caused by MI in the early stage of MI. Blocking MI is of great significance for inhibiting myocardial injury [19–21]. Therefore, the present study continued to explore the effects of lncRNA93358 on myocardial apoptosis in MI rats, and cardiac ultrasound results showed that downregulation of lncRNA93358 improved cardiac function in MI rats. The results of HE staining, TTC staining, and TUNEL assay showed that downregulation of lncRNA93358 expression significantly improved the myocardial pathological morphology of MI rats, reduced the myocardial infarction area and myocardial cell apoptosis rate, downregulated Bax, and upregulated Bcl-2. These results suggested that the knockdown of lncRNA93358 significantly ameliorated MI in rats.The solute carrier (SLC) superfamily is a family of membrane proteins capable of transporting solutes. More than 400 members of the SLC family have been identified, encoding passive transporter, ion complex transporter, and exchanger genes, respectively. The sequence identity of SLC superfamily members is about 20%, with diverse functions. For example, SLC6A3, an amine transporter, plays an important role in signal transmission in the nervous system and provides targets for the design of a variety of drugs [22]. SLC22A20, an organic anion transporter, mainly mediates the transmembrane input and output of organic anions [23]. SLC8A1 is a calcium ion exchanger that is expressed in high abundance in cardiomyocytes. SLC8A1 mainly mediates the exchange between Ca2+ and Na+, and its memory loss or mutation may lead to arrhythmia and abnormal cardiac contraction, which further induces cardiac diseases such as heart failure and ischemic injury [24, 25]. Studies on SLC8A1 are mainly focused on diseases such as arrhythmia, diabetes, and cancer, which are mainly mediated by the working mode of Ca2+ entry and Na+ excretion [26]. lncRNA-SLC8A1-AS1 alleviates myocardial injury, inhibits the release of pro-inflammatory factors, and reduces infarct size by regulating SLC8A1 and activating the CGMP-PKG signaling pathway, which finally protects the myocardium from injury [27]. In the present study, the expression of SLC8A1 was significantly decreased in MI rats, which was greatly reversed by the knockdown of lncRNA 93358, accompanied by the ameliorated MI in rats. In addition, the dual-luciferase reporter assay results showed that SLC8A1 interacted with miR-466c, indicating that lncRNA93358 was involved in the MI process by inhibiting the function of miR-466c and regulating the expression of SLC8A1.The injury of cardiomyocytes after MI is an important part of mitochondrial apoptosis. As the antiapoptotic molecule Bcl-2 continues to decrease, the proapoptotic molecule Bax gradually increases, resulting in a large amount of cytochrome C in the mitochondria entering the cytoplasm. The reaction causes procaspase-3 to be cleaved into cleaved-caspase-3 to induce apoptosis. We found that silencing lncRNA 93358 in MI rats can inhibit rat cardiomyocyte apoptosis, which may be a potential target for the treatment of myocardial injury, but more experiments are needed to prove it.In conclusion, lncRNA 93358 in MI rats was obtained by high-throughput sequencing in this study. Downregulation of lncRNA93358 suppressed the apoptosis of myocardial cells in MI rats, which was achieved by inhibiting the function of miR-466c and regulating the expression of SLC8A1. However, the feedback regulation of miR-466c and SLC8A1 needs to be further studied for our future work.



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*Source: 1138709-2022-07-07.xml*