Biochemical Genetics最新文献

Esophageal cancer is a deadly tumor with a high mortality rate and unsatisfactory treatment effect. Circular RNAs (circRNAs), as a new kind of noncoding RNA molecules, were found to play a key role in variety of tumors. This study aimed to explore the participation of hsa_circ_0062558 (circMMP11) in the recurrence of ESCC and its role in ESCC progression. The expression of circMMP11 in tissue specimens and cells was measured using the RT-qPCR method. RNase R treatment assay and Actinomycin D treatment assay verified the stability of circMMP11. Receiver Operating Characteristic (ROC) curve was conducted to evaluate the clinical significance of circMMP11 in predicting postoperative recurrence. The capacities of circMMP11 on cellular behaviors were measured using cell counting kit (CCK-8) and Transwell assays. The circMMP11 expression was raised in ESCC tissues. The circMMP11 in tumor tissues of the recurrence/metastasis group was higher than that in the non-recurrence/metastasis group. ROC curve showed that circMMP11 in tumor tissues could detect the postoperative recurrence/metastasis of the patients with an area under the ROC curve (AUC) of 0.838. Silencing circMMP11 led to a reduction in the proliferative, migratory, and invasive capacities of ESCC cells, and miR-671-5p inhibitor partially diminished the inhibitory effects of si-circMMP11. The high circMMP11 expression in postoperative tissues of patients with ESCC is correlated with recurrence and metastasis, and it has potential predictive value for postoperative recurrence and metastasis of patients. Inhibition of circMMP11 repressed ESCC cell behaviors by regulating miR-671-5p, which may be a potential target for early diagnosis of recurrence and treatment of ESCC.

Arisaema takesimense (Araceae) is a unique species found exclusively in Ulleung Island of Korea. This study presents the complete chloroplast (cp.) genome of A. takesimense, which comprises 174, 361 base pairs and exhibits a typical tetrad structure. The genome encodes 112 unique genes, including 78 protein-coding genes (CDS), 30 tRNA genes, and 4 rRNA genes. In this study, a total of 49 long repeats and 139 simple sequence repeats (SSRs) were identified, predominantly located in intergenic spacer regions (IGS). Additionally, several hotspot regions, including trnS-G, accD-psaI, ndhF and rps15-ycf1, were identified, which are commonly shared among Araceae species. The analysis of these repeats revealed species-specific SSR types and hotspot regions that can be utilized for population genetic studies and species identification. A comparative genomic analysis of eleven Arisaema taxa revealed that the large single copy region (LSC) exhibits the most variability, with non-coding genes displaying more variation than coding genes. The borders between the LSC-IR-SSC regions in Arisaema taxa were generally well-preserved, and there were notable exceptions in the positions of LSC/IRa, LSC/IRb and SSC/IRb junctions for A. takesimense, A. ringens, and A. nepenthoides. A phylogenetic analysis based on the cp. genome revealed a close relationship between A. takesimense and A. bockii. The outcomes of this study substantially increase the genomic resources available for Araceae, serving as a valuable resource for species identification and evaluating intraspecific diversity within the Arisaema genus.

This study aimed to explore the mechanisms through which microRNAs (miRNAs) regulate 5-fluorouracil (5-FU) sensitivity in colorectal cancer (CRC) using organoid models. Fresh tissue samples from CRC tumors were collected, and CRC organoids were isolated and cultured. The consistency between CRC organoids and their derived tissues was validated. CRC organoids were treated with 5-FU, and ATP activity was measured. High-throughput sequencing of CRC organoids, combined with Gene Expression Omnibus (GEO) data analysis, was performed to examine miRNA expression following 5-FU treatment. Next, we investigated the cellular function of miR-526b-5p in CRC organoids and cells. Dual-luciferase reporter assays validated the binding of miR-526b-5p to the 3' UTR of TP53 mRNA. We successfully established CRC organoids that exhibited characteristics consistent with their source tissues. 5-FU treatment suppressed the proliferation and ATP activity of CRC organoids. High-throughput sequencing of CRC organoids, combined with GEO data analysis and quantitative reverse transcription polymerase chain reaction (qRT-PCR) validation, revealed that hsa-miR-526b-5p levels were elevated following 5-FU treatment in CRC organoids and cells. Furthermore, hsa-miR-526b-5p was upregulated in CRC tissues compared to adjacent normal tissues, correlating with poor survival in CRC patients. Overexpression of hsa-miR-526b-5p mitigated the inhibitory effects of 5-FU on CRC organoid proliferation, migration, invasion, and ferroptosis. In contrast, silencing of hsa-miR-526b-5p impaired cell function and ferroptosis. Additionally, overexpression of hsa-miR-526b-5p decreased TP53 mRNA and protein levels while increasing the expression of SLC7A11 mRNA and protein. Silencing of hsa-miR-526b-5p resulted in the opposite effect. hsa-miR-526b-5p directly targeted and inhibited TP53 expression. Overexpression of TP53 diminished the promotive effect of hsa-miR-526b-5p on ferroptosis-related proteins GPX4 and SLC7A11, whereas inhibition of TP53 reversed the impact of hsa-miR-526b-5p silencing. Our study demonstrates that hsa-miR-526b-5p targets TP53 to regulate 5-FU sensitivity in CRC through the ferroptosis pathway based on CRC organoid models.

Intramuscular fat, which is closely related to the traits of tenderness, juiciness, and flavor of pork, is regulated by numerous molecular regulatory mechanisms that have been regarded as an important agricultural research area. Long noncoding RNAs (lncRNAs) are emerging regulators involved in adipogenesis due to their functional diversity. In this study, we identified a novel lncRNA related to porcine adipogenesis, named lncIMF1, based on previous RNA sequencing results. Our results suggested that lncIMF1 was most abundantly expressed in adipose tissue and located in both the cytoplasm and nucleus. Besides, lncIMF1 promoted the proliferation and differentiation, while inhibited apoptosis of intramuscular preadipocytes. Moreover, lncIMF1 could act as a molecular sponge for miR-187, inhibiting the binding of miR-187 and SMAD1, thereby promoting the expression of SMAD1 and enhancing the adipogenic differentiation of intramuscular preadipocytes. Additionally, we found that lncIMF1-miR187-SMAD1 axis could activate the p38-mitogen-activated protein kinase (MAPK) pathway. Taken together, our study provided new insights into the role of lncRNAs in the regulation of pork quality.

Porcine reproductive and respiratory syndrome (PRRS) is one of the most economically devastating diseases affecting the global pig industry. Host microRNAs directly target viral gene regions to exert their disease-fighting effects. PRRS virus (PRRSV) infection upregulates miR-361-3p expression; however, it is unclear whether it can exert inhibitory effects by directly targeting viral genes. Bioinformatic and experimental findings revealed that miR-361-3p inhibited PRRSV replication by directly targeting the PRRSV ORF1b and ORF1a loci. Intramuscular injection of pcDNA3.1-pri-miR-361 verified the expression of miR-361-3p in mammals. In summary, miR-361-3p plays an important role in infection and may be a promising therapeutic target for PRRS, providing insights into possible drug therapies.

Non-syndromic hearing loss (NSHL) is a genetically heterogeneous disorder accounting for almost 70% of the total congenital hearing loss. The implementation of rapid advanced sequencing methods has significantly contributed to the correct molecular diagnosis for several rare genetic disorders, including NHSL. Features of two probands with NHSL were clinically and genetically evaluated. One of the affected individuals was subjected to exome sequencing (ES) using standard methods. 3D protein modeling was performed to check the effect of mutation on the protein structure. ES data analysis revealed a homozygous nonsense variant [c.1144A > T; p.Lys382*] within the GPR156 gene (NM_153002.3) associated with rare NSHL. Sanger sequencing supported its recessive segregation within the family. The in silico predictions and 3D protein modeling further affirmed its disease-causing nature. The present study reported a nonsense variant in the GPR156 and its association with NSHL susceptibility, which requires further studies to unveil its key role and disease-related pathophysiology.

IKZF1 deletions (ΔIKZF1) are common in precursor B-cell acute lymphoblastic leukemia (B-ALL) and are assumed to have a prognostic impact. We aimed to determine the prognostic implications of ΔIKZF1 and CRLF2 overexpression in pediatric B-ALL. Furthermore, we sought to compare the multiplex polymerase chain reaction (PCR) assay with standard multiplex ligand-dependent probe amplification (MLPA) methods to ascertain IKZF1 status in a clinical context. Seventy-nine diagnoses and 43 relapse B-ALL samples were evaluated for deletions of IKZF1 Δ2-7, Δ4-7, and Δ4-8 by conventional PCR and then sequenced by targeted sequencing. Subsequently, MLPA analysis was performed for ΔIKZF1 detection, and CRLF2 expression was evaluated in 42 diagnose time B-ALL patients by QRT-PCR. ΔIKZF1 was detected in 10 out of 79 diagnose samples (12.66%) and eight of the 43 first relapsed materials (18.60%). Our results revealed no association between survival outcomes with ΔIKZF1 or CRLF2 overexpression status in pediatric B-ALL patients. However, we found ΔIKZF1 was more frequent among relapsed samples, and the deletions showed consistency between diagnose-first/second relapse pairs of samples. These results suggest that ΔIKZF1 may contribute to the development of treatment failure in B-ALL. Furthermore, we demonstrated methodological adjustments in conventional PCR and MLPA for selected alterations in ΔIKZF1.

To analyze whether the single-nucleotide polymorphisms (SNPs) in Matrix metalloproteinases 2, 3, and 9 (MMP2, MMP3, and MMP9), Tissue Inhibitor of Metalloproteinases 1 and 2 (TIMP1 and TIMP2), methionine synthase (MTR) and methionine synthase reductase (MTRR) influence delayed deciduous tooth eruption (DDTE). This cross-sectional study included 1060 biologic unrelated children (aged between 6 and 36 months) of both sexes, selected from 25 public schools in Nova Friburgo, Rio de Janeiro, Brazil. Oral examination was conducted and DDTE was defined by the absence of gingival eruption according to a chronology based on the Brazilian population. Genotyping of selected SNPs (rs243847, rs52261, rs17576, rs4898, rs7501477, rs1805087, and rs1801394) was performed using TaqMan real-time PCR with genomic DNA extracted from buccal cells. The association between genotypes and DDTE was evaluated using univariate and multivariate analyses (p < 0.05). A total of 224 children and caregivers were included after the eligibility criteria. The heterozygous genotype for the SNPs MTR (rs11805087) was associated with DDTE in both the univariate (p = 0.004) and multivariate (p < 0.001) codominant models, as well as in the univariate (p = 0.010) and multivariate (p = 0.001) recessive models. TIMP1 (rs4898) and MMP3 (rs522616) were associated with DDTE only in the univariate model (p < 0.05). The SNPs in MTR (rs11805087), MMP3 (rs522616) and TIMP (rs4898) genes are associated with DDTE. The factors affecting the chronology of deciduous tooth eruption has been insufficiently studied. This article brings novel knowledge regarding the role of genetics polymorphisms on timing variation of deciduous tooth eruption. Understanding the factors that impact tooth eruption is crucial for the fields of pediatric dentistry and orthodontics.

Indian Himalayan Region (IHR) supports a plethora of biodiversity with a unique assemblage of many charismatic and endemic species. We assessed the genetic diversity, demographic history, and habitat suitability of blue sheep (Pseudois nayaur) in the IHR through the analysis of the mitochondrial DNA (mtDNA) control region (CR) and Cytochrome b gene, and 14 ecological predictor variables. We observed high genetic divergence and designated them into two genetic lineage groups, i.e., the Himalayan blue sheep (P. n. nayaur) in the western part, and the Chinese blue sheep (P. n. szechuanensis) in the eastern part. They exhibited poor connectivity due to landscape resistance. The genetic distance value suggested substantial genetic differentiation between them. The habitat selection by blue sheep indicated the disparity between the residence preferences in the western and eastern Himalayas. In both the regions, the habitat suitability was mostly influenced by the minimum temperature of the coldest month. However, in the eastern Himalayas, precipitation seasonality emerged as a significant variable influencing habitat suitability. These findings provided strong support for the presumption that the habitats preferred by blue sheep in the western Himalayas are dryer, compared with the preferred habitats in the eastern region, which were moister. The identification of two separate lineages of P. nayaur in the IHR has significant conservation implications as it underlines the necessity for a unique management approach for each lineage. In order to preserve genetic integrity, conservation efforts must make sure that each population is maintained and monitored separately, as genetic divergence across the lineages that might indicate reproductive isolation. This study has potential conservation implications as it provides insights on the crucial ecological information of a relatively lesser-known ungulates species of Himalaya essential for effective conservation planning.

Idiopathic pulmonary fibrosis (IPF) is a rapidly progressive interstitial lung disease of unknown pathogenesis with no effective treatment currently available. Given the regulatory roles of lncRNAs (TP53TG1, LINC00342, H19, MALAT1, DNM3OS, MEG3), miRNAs (miR-218-5p, miR-126-3p, miR-200a-3p, miR-18a-5p, miR-29a-3p), and their target protein-coding genes (PTEN, TGFB2, FOXO3, KEAP1) in the TGF-β/SMAD3, Wnt/β-catenin, focal adhesion, and PI3K/AKT signaling pathways, we investigated the expression levels of selected genes in peripheral blood mononuclear cells (PBMCs) and lung tissue from patients with IPF. Lung tissue and blood samples were collected from 33 newly diagnosed, treatment-naive patients and 70 healthy controls. Gene expression levels were analyzed by RT-qPCR. TaqMan assays and TaqMan MicroRNA assay were employed to quantify the expression of target lncRNAs, mRNAs, and miRNAs. Our study identified significant differential expression in PBMCs from IPF patients compared to healthy controls, including lncRNAs MALAT1 (Fold Change = 3.809, P = 0.0001), TP53TG1 (Fold Change = 0.4261, P = 0.0021), and LINC00342 (Fold Change = 1.837, P = 0.0448); miRNAs miR-126-3p (Fold Change = 0.102, P = 0.0028), miR-200a-3p (Fold Change = 0.442, P = 0.0055), and miR-18a-5p (Fold Change = 0.154, P = 0.0034); and mRNAs FOXO3 (Fold Change = 4.604, P = 0.0032) and PTEN (Fold Change = 2.22, P = 0.0011). In lung tissue from IPF patients, significant expression changes were observed in TP53TG1 (Fold Change = 0.2091, P = 0.0305) and DNM3OS (Fold Change = 4.759, P = 0.05). Combined analysis of PBMCs expression levels for TP53TG1, MALAT1, miRNA miR-126-3p, and PTEN distinguished IPF patients from healthy controls with an AUC = 0.971, sensitivity = 0.80, and specificity = 0.955 (P = 6 × 10^-8). These findings suggest a potential involvement of the identified ncRNAs and mRNAs in IPF pathogenesis. However, additional functional validation studies are needed to elucidate the precise molecular mechanisms by which these lncRNAs, miRNAs, and their targets contribute to PF.