Bioinformatics-based analysis of programmed cell death pathway and key prognostic genes in gastric cancer: Implications for the development of therapeutics.

BACKGROUND: Gastric cancer (GC) represents a major global health burden as a result of its high incidence and poor prognosis. The present study examined the role of the programmed cell death (PCD) pathway and identified key genes influencing the prognosis of patients with GC. METHODS: Bioinformatics analysis, machine learning techniques and survival analysis were systematically integrated to identify core prognostic genes from the The Cancer Genome Atlas Stomach Adenocarcinoma (TCGA-STAD) dataset. A prognostic model was then developed to stratify patients into high-risk and low-risk groups, and further validated in the GSE84437 dataset. The model also demonstrated clinical relevance with tumor staging and histopathology. Immune infiltration analysis and the potential benefits of immunotherapy for each risk group were assessed. Finally, subgroup analysis was performed based on the expression of three key prognostic genes. RESULTS: Three core prognostic genes (CAV1, MMP9 and MAGEA3) were identified. The prognostic model could effectively differentiate patients into high-risk and low-risk groups, leading to significantly distinct survival outcomes. Increased immune cell infiltration was observed in the high-risk group, and better potential for immunotherapy outcomes was observed in the low-risk group. Pathways related to cancer progression, such as epithelial-mesenchymal transition and tumor necrosis factor-α signaling via nuclear factor-kappa B, were enriched in the high-risk group. By contrast, the low-risk group showed a number of pathways associated with maintenance of cell functionality and immune responses. The two groups differed in gene mutation patterns and drug sensitivities. Subgroup analysis based on the expression of the three key genes revealed two distinct clusters with distinct survival outcomes, tumor immune microenvironment characteristics and pathway enrichment. CONCLUSIONS: The present study offers novel insights into the significance of PCD pathways and identifies key genes associated with the prognosis of patients with GC. This robust prognostic model, along with the delineation of distinct risk groups and molecular subtypes, provides valuable tools for risk stratification, treatment selection and personalized therapeutic interventions for GC.

Bioinformatics Analysis and Experimental Validation of Differential Genes and Pathways in Bone Nonunions.

Non-union fractures pose a significant clinical challenge, often leading to prolonged pain and disability. Understanding the molecular mechanisms underlying non-union fractures is crucial for developing effective therapeutic interventions. This study integrates bioinformatics analysis and experimental validation to unravel key genes and pathways associated with non-union fractures. We identified differentially expressed genes (DEGs) between non-union and fracture healing tissues using bioinformatics techniques. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were employed to elucidate the biological processes and pathways involved. Common DEGs were identified, and a protein-protein interaction (PPI) network was constructed. Fibronectin-1 (FN1), Thrombospondin-1 (THBS1), and Biglycan (BGN) were pinpointed as critical target genes for non-union fracture treatment. Experimental validation involved alkaline phosphatase (ALP) and Alizarin Red staining to confirm osteogenic differentiation. Our analysis revealed significant alterations in pathways related to cell behavior, tissue regeneration, wound healing, infection, and immune responses in non-union fracture tissues. FN1, THBS1, and BGN were identified as key genes, with their upregulation indicating potential disruptions in the bone remodeling process. Experimental validation confirmed the induction of osteogenic differentiation. The study provides comprehensive insights into the molecular mechanisms of non-union fractures, emphasizing the pivotal roles of FN1, THBS1, and BGN in extracellular matrix dynamics and bone regeneration. The findings highlight potential therapeutic targets and pathways for further investigation. Future research should explore interactions between these genes, validate results using in vivo fracture models, and develop tailored treatment strategies for non-union fractures, promising significant advances in clinical management.

Elucidating the role of T-cell exhaustion-related genes in colorectal cancer: a single-cell bioinformatics perspective.

Colorectal cancer (CRC) remains a significant global health issue. In this study, the role of T-cell exhaustion-related genes (TEXs) in CRC was investigated using single-cell and bulk RNA-seq analysis. This research involved extensive data analysis using multiple databases, including the TCGA-COAD cohort, GSE14333, and GSE39582. Through single-cell analysis, distinct cell populations within CRC samples were identified and classified T-cells into four subgroups: regulatory T-cells (Tregs), conventional CD4+ T-cells (CD4+ T conv), CD8+ T, and CD8+ T exhausted cells. Intercellular communication networks and signaling pathways associated with TEXs using computational tools such as CellChat and PROGENy. Additionally, TEX-related alterations in tumor gene pathways were analyzed through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. Prognostic models were developed, and their correlation with immune infiltration was assessed. The study revealed the presence of distinct cell populations within CRC, with TEXs playing a crucial role in the tumor microenvironment. CD8+ T exhausted cells exhibited expression of specific markers, indicating their involvement in tumor immune evasion. CellChat and PROGENy analyses revealed intricate communication networks and signaling pathways associated with TEXs, including RNA splicing and viral carcinogenesis. Furthermore, the prognostic risk model developed on the basis of TEXs demonstrated its efficacy in stratifying CRC patients. This risk model exhibited strong correlations with immune infiltration by various effector immune cells, highlighting the influence of TEXs on the tumor immune response. The complex interactions and signaling pathways underlying TEX-associated immune dysregulation in CRC were revealed by employing advanced analytical approaches. The development of a prognostic risk model based on TEXs offers a promising tool for prognostic stratification in patients with CRC. Furthermore, the correlations observed between TEXs and immune infiltration provide valuable insights into the potential of TEXs as therapeutic targets and highlight the need for further investigation into TEX-mediated immune evasion mechanisms. This study thus provides valuable insights into the role of TEXs in CRC.

Effects of Heavy Metals on Stomata in Plants: A Review.

Stomata are one of the important structures for plants to alleviate metal stress and improve plant resistance. Therefore, a study on the effects and mechanisms of heavy metal toxicity to stomata is indispensable in clarifying the adaptation mechanism of plants to heavy metals. With the rapid pace of industrialization and urbanization, heavy metal pollution has been an environmental issue of global concern. Stomata, a special physiological structure of plants, play an important role in maintaining plant physiological and ecological functions. Recent studies have shown that heavy metals can affect the structure and function of stomata, leading to changes in plant physiology and ecology. However, although the scientific community has accumulated some data on the effects of heavy metals on plant stomata, the systematic understanding of the effects of heavy metals on plant stomata remains limited. Therefore, in this review, we present the sources and migration pathways of heavy metals in plant stomata, analyze systematically the physiological and ecological responses of stomata on heavy metal exposure, and summarize the current mechanisms of heavy metal toxicity on stomata. Finally, the future research perspectives of the effects of heavy metals on plant stomata are identified. This paper can serve as a reference for the ecological assessment of heavy metals and the protection of plant resources.

Exome sequencing improves genetic diagnosis of fetal increased nuchal translucency.

OBJECTIVE: The aim of this retrospective study is to determine the monogenic syndromes in fetuses with isolated first-trimester increased nuchal translucency (NT) in order to provide more accurate parental counseling. METHODS: Medical trio exome sequencing (ES) was performed on DNA extracted from chorionic villi in 73 fetuses with isolated first-trimester increased NT (≥3.5 mm) and normal chromosomal microarray analysis (CMA). This testing targets coding exons for 4200 clinically relevant disease-causing genes. The interpretation of variants was performed according to the American College of Medical Genetics guidelines. RESULTS: Pathogenic variants were detected in four cases in which phenotypes and genotypes correlate well. Medical trio ES offered a 5.5% (4/73) increase in diagnostic rate over CMA in cases with isolated increased NT. Three of four cases with pathogenic variants developed structural anomalies on ultrasound at mid pregnancy, leading to the pregnancy termination. Only one case with a pathogenic variant demonstrated normal ultrasound throughout pregnancy. CONCLUSION: Our results indicate that after a normal CMA, fetuses with isolated first-trimester increased NT have a 1.4% (1/73) risk of significant childhood genetic syndromes caused by known disease-causing variants, which will not be detectable on prenatal ultrasound. This information may be useful in parental counseling.

A clinical-radiomics nomogram for the preoperative prediction of lung metastasis in colorectal cancer patients with indeterminate pulmonary nodules.

OBJECTIVES: To develop and validate a clinical-radiomics nomogram for preoperative prediction of lung metastasis for colorectal cancer (CRC) patients with indeterminate pulmonary nodules (IPN). METHODS: 194 CRC patients with lung nodules were enrolled in this study (136 in the training cohort and 58 in the validation cohort). To evaluate the probability of lung metastasis, we developed three models, the clinical model with significant clinical risk factors, the radiomics model with radiomics features constructed by the least absolute shrinkage and selection operator algorithm, and the clinical-radiomics model with significant variables selected by the stepwise logistic regression. The Akaike information criterion (AIC) was used to compare the relative strength of different models, and the area under the curve (AUC) was used to quantify the predictive accuracy. The nomogram was developed based on the most appropriate model. Decision-curve analysis was applied to assess the clinical usefulness. RESULTS: The clinical-radiomics model (AIC = 98.893) with the lowest AIC value compared with that of the clinical-only model (AIC = 138.502) or the radiomics-only model (AIC = 116.146) was identified as the best model. The clinical-radiomics nomogram was also successfully developed with favourable discrimination in both training cohort (AUC = 0.929, 95% CI: 0.885-0.974) and validation cohort (AUC = 0.922, 95% CI: 0.857-0.986), and good calibration. Decision-curve analysis confirmed the clinical utility of the clinical-radiomics nomogram. CONCLUSIONS: In CRC patients with IPNs, the clinical-radiomics nomogram created by the radiomics signature and clinical risk factors exhibited favourable discriminatory ability and accuracy for a metastasis prediction. KEY POINTS: • Clinical features can predict lung metastasis of colorectal cancer patients. • Radiomics analysis outperformed clinical features in assessing the risk of pulmonary metastasis. • A clinical-radiomics nomogram can help clinicians predict lung metastasis in colorectal cancer patients.

Prenatal diagnosis of 17q12 deletion syndrome: a retrospective case series.

The 17q12 deletion syndrome is a chromosomal anomaly resulting from the interstitial microdeletion of the long arm of chromosome 17. The aim of this study was to present the experience on prenatal diagnosis of 17q12 deletion to further define the prenatal phenotypes of this syndrome. Eleven pregnancies with foetal 17q12 deletion detected by chromosomal microarray (CMA) were retrospectively included at a single Chinese tertiary medical centre. Clinical data were reviewed for these cases, including the maternal demographics, foetal ultrasound findings, CMA results and pregnancy outcomes. The deletion sizes of 17q12 ranged from 1.42 to 1.94 Mb. The deletion had arisen de novo in 10 cases and inherited from one of the parents in one case. Variable kidney abnormalities were found by ultrasound in all of the cases, with bilateral or unilateral hyperechogenic kidneys being the most common findings. This study indicates that a strikingly high correlation between prenatal hyperechogenic kidneys and 17q12 deletion, and prenatal testing with CMA should be offered to the foetal cases of hyperechogenic kidneys. Impact statement What is already known on this subject? 17q12 deletion syndrome is a cause of renal abnormalities, maturity-onset diabetes of the young and neurodevelopmental disorders. Prenatal diagnosis has been reported in several isolated cases with the use of microarray-based technologic means. What do the results of this study add? The results provide further evidence that a strikingly high correlation between prenatal hyperechogenic kidneys and 17q12 deletion, and genetic testing should be offered to foetal cases with hyperechogenic kidneys. A rare prenatal case of 17q12 deletion with multiple structural malformations and anhydramnios is presented. What are the implications of these findings for clinical practice and/or further research? There should be a high index of suspicion of carriers in parents when 17q12 deletion is confirmed prenatally. An extremely wide phenotype spectrum of this deletion should be emphasised in the prenatal counselling.

Congenital Cystic Diaphragm with Diaphragmatic Eventration in a Fetus: A Case Presentation.

Introduction: Congenital diaphragmatic eventration (CDE) is defined as the abnormal elevation of the diaphragm, due to incomplete muscularization of the diaphragm with a thin membranous sheet replacing normal diaphragmatic muscle. Case report: We report a prenatal case with a diaphragmatic mesothelial cyst combined with CDE. Conclusion: A large cystic mass between the thoracic wall and the liver in early pregnancy is highly suggestive of cystic diaphragm.

Application of noninvasive prenatal testing in pregnancies with fetal double bubble sign: Is it feasible?

OBJECTIVE: To evaluate the application of noninvasive prenatal testing as an alternative to invasive diagnostic testing in pregnancies with the double bubble sign. METHODS: This was a retrospective analysis of 92 pregnancies with fetal double bubble identified by prenatal ultrasound, in which invasive diagnostic testing was performed for genetic investigations using quantitative fluorescence PCR and chromosomal microarray. Noninvasive prenatal testing was assumed to provide to patients for screening for the common aneuploidies. RESULTS: Fetal trisomy 21 was detected in 8 of the 92 patients with prenatal double bubble. No other chromosomal anomalies or microscopic pathogenic copy-number variations (CNV) were found. Noninvasive prenatal testing could theoretically identified the affected pregnancies with trisomy 21 in this group with decreased number of invasive diagnostic testing. CONCLUSIONS: Noninvasive prenatal testing could be recommended for genetic evaluation of the etiology of prenatal double bubble after thorough pretest counseling.

δ-Thalassemia with Complete Absence of Hb A2 in a Chinese Family.

A Chinese family with δ-thalassemia (δ-thal) was found, in which the daughter is homozygous for δ-thal (HBD: c.-127T>C) with complete deficiency of Hb A2 and the mother is a heterozygote with low level of Hb A2. The father, however, is a heterozygote with a normal Hb A2 value due to coinheritance of a ß-thalassemia (ß-thal). Although no abnormal clinical or hematological findings were noted in the individuals with δ-thal, one should keep in mind that ß-thal can be missed during routine preliminary screening when ß-thal and δ-thal coexist in a subject.

What would be missed in the first trimester if nuchal translucency measurement is replaced by cell free DNA foetal aneuploidy screening?

The aim of this study was to evaluate which chromosomal abnormalities in our cohort of foetuses with increased nuchal translucency (NT) in the first trimester of pregnancy could be detected by cell free (cf)DNA screening as well. There were 775 singleton pregnancies referred for cytogenetic testing due to an increased NT (≥3.0 mm). Chromosome aberrations were investigated using karyotyping or chromosomal microarray analysis (CMA). Karyotyping had been chosen for foetal cytogenetic testing by 446 patients, and CMA by 329 patients. Common aneuploidies (trisomies 21, 18, 13 and sex aneuploidies) were detected in 2.2% (99/446) and 1.8% (59/329) cases, respectively. In 329 with CMA testing, clinically significant copy number variations (CNVs) other than common aneuploidies were detected in 2.7% cases; among these, five had a pathogenic microscopic CNV, which could have been detected by karyotyping. There were four cases (1.2%) having a pathogenic submicroscopic CNV, which could have been missed by karyotyping. The total CMA detection rate (23.4%) was not statistically different from that (24.2%) by karyotyping (p > .05). The percentage of chromosomal aberrations, which cfDNA screening would miss in patients with increased NT in the first trimester, might be the same as in those with normal NT. Impact statement What is already known about this topic? First trimester NT is a powerful marker for screening for common aneuploidies. cfDNA screening is more accurate than any standard screening with NT. The need of NT in the era of prenatal screening using cfDNA is debated. What does this study add? An increased NT did not identify any additional aneuploidies that were detected by cfDNA screening. What are the implications of these findings for clinical practice and/or further research? The percentage of chromosomal aberrations which cfDNA screening would miss in patients with increased NT might be the same as in those with normal NT.

Two α1-Globin Gene Point Mutations Causing Severe Hb H Disease.

Hb H disease is generally a moderate form of α-thalassemia (α-thal) that rarely requires regular blood transfusions. In this study, two Chinese families with members carrying transfusion-dependent Hb H disease were investigated for rare mutations on the α-globin genes (HBA1, HBA2). In one family, Hb Zürich-Albisrieden [α59(E8)Gly→Arg; HBA1: c.178G>C] in combination with the Southeast Asian (- -SEA) deletion was the defect responsible for the severe phenotype. In another family, a novel hemoglobin (Hb) variant named Hb Sichuan (HBA1: c.393_394insT), causes α-thal and a severe phenotype when associated with the - -SEA deletion. As these two HBA1 mutations can present as continuous blood transfusion-dependent α-thal, it is important to take this point into account for detecting the carriers, especially in couples in which one partner is already a known α0-thal carrier.

Hb A2-Tianhe (HBD: c.323G>A): First Report in a Chinese Family with Normal Hb A2-ß-Thalassemia Trait.

Coinheritance of δ-globin variants along with ß-globin gene defects can interfere with correct diagnosis of ß-thalassemia (ß-thal) trait. In this report, we present the coinheritance of a δ-globin variant, Hb A2-Tianhe [δ107(G9)Gly→Asp; HBD: c.323G>A] and a heterozygous ß-thal in a Chinese individual with microcytosis, hypochromia and a normal Hb A2 level.

A Novel Frameshift Mutation at Codons 138/139 (HBB: c.417_418insT) on the ß-Globin Gene Leads to ß-Thalassemia.

We describe a new ß-thalassemic mutation in a Chinese subject. This allele develops by insertion of one nucleotide (+T) between codons 138 and 139 in the third exon of the ß-globin gene. The mutation causes a frameshift that leads to a termination codon at codon 139. In the heterozygote, this allele has the phenotype of classical ß-thalassemia (ß-thal) minor.

Hb Hornchurch [ß43(CD2)Glu→Lys; HBB: c.130G>A] Compromises the Molecular Diagnosis of ß-Thalassemia in a Chinese Family.

The combination of ß-thalassemia (ß-thal) and a hemoglobin (Hb) variant is not uncommon in regions with a high prevalence of thalassemia. Although most of the ß-globin chain variants will not aggravate the ß-thal, some can compromise the accurate molecular diagnosis. In this study, we present a rare case of coinheritance of ß-thal and Hb Hornchurch [ß43(CD2)Glu→Lys; HBB: c.130G>A], that compromises the molecular diagnosis of homozygous ß-thal.

Increased first-trimester nuchal translucency associated with a dicentric chromosome and 9q34.3 microdeletion syndrome.

We present prenatal diagnosis and chromosomal microarray analysis (CMA) of 9q34.3 microdeletion in a foetus with an increased nuchal translucency (NT). Conventional G-banding analysis showed a de novo translocation: 45, XX, dic (9;13)(q34;p13). CMA revealed a 3.6 Mb 9q34.3 microdeletion encompassing an OMIM gene of EHMT1 consistent with the diagnosis of Kleefstra syndrome and 9q subtelomeric deletion syndrome. We suggest an application of CMA at prenatal diagnosis in pregnancies with increased NT and an apparent balanced translocation on conventional karyotype.

Small Interfering RNA Targeted to ASPP2 Promotes Progression of Experimental Proliferative Vitreoretinopathy.

Background. Epithelial-mesenchymal transition (EMT) of retinal pigment epithelium (RPE) is vital in proliferative vitreoretinopathy (PVR) development. Apoptosis-stimulating proteins of p53 (ASPP2) have recently been reported to participate in EMT. However, the role of ASPP2 in PVR pathogenesis has not been identified. Methods. Immunohistochemistry was used to investigate the expression of ASPP2 in epiretinal membranes of PVR patients. ARPE-19 cells were transfected with ASPP2-siRNA, followed with measurement of cell cytotoxicity, proliferation, and migration ability. EMT markers and related inflammatory and fibrosis cytokines were measured by western blot or flow cytometry. Additionally, PVR rat models were induced by intravitreal injection of ARPE-19 cells transfected with ASPP2-siRNA and evaluated accordingly. Results. Immunofluorescence analysis revealed less intense expression of ASPP2 in PVR membranes. ASPP2 knockdown facilitated the proliferation and migration of RPE cells and enhanced the expression of mesenchymal markers such as alpha smooth muscle actin, fibronectin, and ZEB1. Meanwhile, ASPP2-siRNA increased EMT-related and inflammatory cytokines, including TGF-ß, CTGF, VEGF, TNF-α, and interleukins. PVR severities were more pronounced in the rat models with ASPP2-siRNA treatment. Conclusions. ASPP2 knockdown promoted EMT of ARPE-19 cells in vitro and exacerbated the progression of experimental PVR in vivo, possibly via inflammatory and fibrosis cytokines.

Identification of proteins that interact with alpha A-crystallin using a human proteome microarray.

PURPOSE: To identify proteins interacting with alpha A-crystallin (CRYAA) and to investigate the potential role that these protein interactions play in the function of CRYAA using a human proteome (HuProt) microarray. METHODS: The active full-length CRYAA protein corresponding to amino acids 1-173 of CRYAA was recombined. A HuProt microarray composed of 17,225 human full-length proteins with N-terminal glutathione S-transferase (GST) tags was used to identify protein-protein interactions. The probes were considered detectable when the signal to noise ratio (SNR) was over 1.2. The identified proteins were subjected to subsequent bioinformatics analysis using the DAVID database. RESULTS: The HuProt microarray results showed that the signals of 343 proteins were higher in the recombinant CRYAA group than in the control group. The SNR of 127 proteins was ≥ 1.2. The SNR of the following eight proteins was > 3.0: hematopoietic cell-specific Lyn substrate 1 (HCLS1), Kelch domain-containing 6 (KLHDC6), sarcoglycan delta (SGCD), KIAA1706 protein (KIAA1706), RNA guanylyltransferase and 5'-phosphatase (RNGTT), chromosome 10 open reading frame 57 (C10orf57), chromosome 9 open reading frame 52 (C9orf52), and plasminogen activator, urokinase receptor (PLAUR). The bioinformatics analysis revealed 127 proteins associated with phosphoproteins, alternative splicing, acetylation, DNA binding, the nuclear lumen, ribonucleotide binding, the cell cycle, WD40 repeats, protein transport, transcription factor activity, GTP binding, and cellular response to stress. Functional annotation clustering showed that they belong to cell cycle, organelle or nuclear lumen, protein transport, and DNA binding and repair clusters. CRYAA interacted with these proteins to maintain their solubility and decrease the accumulation of denatured target proteins. The protein-protein interactions may help CRYAA carry out multifaceted functions. CONCLUSIONS: One-hundred and twenty-seven of 17,225 human full-length proteins were identified that interact with CRYAA. The advent of microarray analysis enables a better understanding of the functions of CRYAA as a molecular chaperone.