Combined analysis of the effects of hypoxia and oxidative stress on DNA methylation and the transcriptome in HTR-8/SVneo trophoblast cells.

The alterations in DNA methylation and transcriptome in trophoblast cells under conditions of low oxygen and oxidative stress have major implications for pregnancy-related disorders. However, the exact mechanism is still not fully understood. In this study, we established models of hypoxia (H group) and oxidative stress (HR group) using HTR-8/SVneo trophoblast cells and performed combined analysis of genome-wide DNA methylation changes using reduced representation bisulphite sequencing and transcriptome expression changes using RNA sequencing. Our findings revealed that the H group exhibited a higher number of differentially methylated genes and differentially expressed genes than the HR group. In the H group, only 0.90% of all differentially expressed genes displayed simultaneous changes in DNA methylation and transcriptome expression. After the threshold was expanded, this number increased to 6.29% in the HR group. Notably, both the H group and HR group exhibited concurrent alterations in DNA methylation and transcriptome expression within Axon guidance and MAPK signalling pathway. Among the top 25 differentially methylated KEGG pathways in the promoter region, 11 pathways were commonly enriched in H group and HR group, accounting for 44.00%. Among the top 25 KEGG pathways in transcriptome with significant differences between the H group and HR group, 10 pathways were consistent, accounting for 40.00%. By integrating our previous data on DNA methylation from preeclamptic placental tissues, we identified that the ANKRD37 and PFKFB3 genes may contribute to the pathogenesis of preeclampsia through DNA methylation-mediated transcriptome expression under hypoxic conditions.

Allelic phenotype prediction of phenylketonuria based on the machine learning method.

BACKGROUND: Phenylketonuria (PKU) is caused by mutations in the phenylalanine hydroxylase (PAH) gene. Our study aimed to predict the phenotype using the allelic genotype. METHODS: A total of 1291 PKU patients with 623 various variants were used as the training dataset for predicting allelic phenotypes. We designed a common machine learning framework to predict allelic genotypes associated with the phenotype. RESULTS: We identified 235 different mutations and 623 various allelic genotypes. The features extracted from the structure of mutations and graph properties of the PKU network to predict the phenotype of PKU were named PPML (PKU phenotype predicted by machine learning). The phenotype of PKU was classified into three different categories: classical PKU (cPKU), mild PKU (mPKU) and mild hyperphenylalaninemia (MHP). Three hub nodes (c.728G>A for cPKU, c.721 for mPKU and c.158G>A for HPA) were used as each classification center, and 5 node attributes were extracted from the network graph for machine learning training features. The area under the ROC curve was AUC = 0.832 for cPKU, AUC = 0.678 for mPKU and AUC = 0.874 for MHP. This suggests that PPML is a powerful method to predict allelic phenotypes in PKU and can be used for genetic counseling of PKU families. CONCLUSIONS: The web version of PPML predicts PKU allele classification supported by applicable real cases and prediction results. It is an online database that can be used for PKU phenotype prediction http://www.bioinfogenetics.info/PPML/ .

Serum IL-24 combined with CA125 as screening and prognostic biomarkers for NSCLC.

Noninvasive and effective methods for early screening of non-small cell lung cancer (NSCLC) still need to be developed. At present, a reasonable conclusion is that a combination of tumor markers is a superior predictor of screening. Cytokines, as important regulators of cancer development, have great potential for the screening and prognosis of NSCLC. This study screened novel biomarkers related to the early screening and prognosis of NSCLC. In the present study, the biological significance and immunoregulation of interleukin-24 (IL-24) were analyzed based on The Cancer Genome Atlas data. Next, 150 serum samples from initially treated patients with NSCLC and 70 controls were collected, and we obtained pathological sections from 60 patients with NSCLC. The ELISA and immunohistochemistry results showed the differential expression of IL-24 and carbohydrate antigen 125 (CA125). The results show that IL-24 is an important tumor suppressor in NSCLC that helps to improve the poor prognosis of these patients. A significantly negative correlation between IL-24 and CA125 levels was also found. Notably, serum IL-24 levels were significantly negatively correlated with the TNM stage of patients with NSCLC, consistent with an important role for tumor suppressors in NSCLC. The receiver operating characteristic curve analysis showed that a combination of IL-24 and CA125 was an effective panel for discriminating patients with NSCLC from HD, and individuals with other lung diseases. Serum IL-24 and CA125 levels were identified as independent prognostic markers for NSCLC. The IL-24 and CA125 panel exhibited good performance in the screening of NSCLC.

A necroptosis-related gene signature to predict prognosis and immune features in hepatocellular carcinoma.

BACKGROUND AND AIM: Necroptosis plays an important role in hepatocellular carcinoma (HCC) development, recurrence, and immunotherapy tolerance. We aimed to build a new prognostic necroptosis-related gene signature that could be used for survival and immunotherapy prediction in HCC patients. METHODS: We found that necroptosis was associated with HCC progression and survival outcomes and was involved in the immune infiltration of HCC. Multiple bioinformatics methods including WGCNA, LASSO-Cox regression, stepwise Cox regression, and Random Forest and Boruta model analysis, were used to establish a prognostic profile related to necroptosis. The necroptosis-related gene signature was validated in ICGC and GSE14520 datasets. RESULTS: This five-gene signature showed excellent predictive performance and was an independent risk factor for patients' overall survival outcome in the three cohorts. Moreover, this signature was an exact predictor using fewer genes than previous gene signatures. Finally, qRT-PCR and immunohistochemical staining investigations were performed in previously collected fresh frozen tumor tissues from HCC patients and their paracancerous normal tissues, and the results were consistent with the bioinformatics results. We found that LGALS3 not only affected the proliferation and migration ability of HepG2 cells but also affected necroptosis and the expression of inflammatory cytokines. CONCLUSION: In summary, we established and validated an individualized prognostic profile related to necroptosis to forecast the therapeutic response to immune therapy, which might offer a potential non-apoptotic therapeutic target for HCC patients.

Identification of phenylketonuria patient genotypes using single-gene full-length sequencing.

BACKGROUND: Phenylketonuria (PKU) is a common, autosomal recessive inborn error of metabolism caused by PAH gene variants. After routine genetic analysis methods were applied, approximately 5% of PKU patients were still not diagnosed with a definite genotype. METHODS: In this study, for the first time, we identified PKU patients with unknown genotypes via single-gene full-length sequencing. RESULTS: The detection rate of PKU genotype increased from 94.6 to 99.4%, an increase of approximately 5%. The variants c.1199 + 502A > T and 1065 + 241C > A were found at a high frequency in Chinese PKU patients. CONCLUSION: Our study suggest that single-gene full-length sequencing is a rapid, efficient and cost-effective tool to improve the genotype detection rate of PKU patients. Moreover, we provides additional case data to support pathogenicity of deep intronic variants in PAH.

Association between HIF-1α, BNIP3, and autophagy in the chorionic villi of missed abortion.

AIM: To investigate the expression of autophagy mediated by the hypoxia-inducible factor 1α (HIF-1α)/BNIP3 signaling pathway in villus tissues of missed abortion and HTR-8/SVneo cells and to elucidate the association of HIF-1α and BNIP3 in autophagy of missed abortion. METHODS: Villus tissues from 30 healthy women with induced abortion and 35 patients with missed abortion were collected, and HTR-8/SVneo cells were cultured under hypoxia and transfected with HIF-1α-siRNA. Real-time polymerase chain reaction was utilized to measure the mRNA levels of HIF-1α and BNIP3; Western blotting was performed to determine the protein levels of HIF-1α, BNIP3, LC3 II/I, and Beclin 1 in villus tissues and HTR-8/SVneo cells. Cellular invasion activity was detected by transwell matrigel assay. The level of autophagy was confirmed by transmission electron microscopy of autophagosome formation. RESULTS: The mRNA levels of HIF-1α and BNIP3 were significantly lower in the missed abortion villi than in the induced abortion samples. The protein levels of HIF-1α, BNIP3, Beclin 1, and LC3II/I were significantly decreased in villus tissues from missed abortion, and autophagosomes were significantly decreased in villus tissues from missed abortion. Under hypoxia, the mRNA expression of HIF-1α and BNIP3 was inhibited after silencing HIF-1α by RNAi, while the protein expression of HIF-1α, BNIP3, Beclin1, and LC3II/I was significantly downregulated. The number of invading cells was significantly decreased, and autophagosomes were significantly decreased after silencing HIF-1α by RNAi in HTR-8/SVneo cells. CONCLUSIONS: Autophagy mediated by the HIF-1α/BNIP3 signaling pathway in villous trophoblast cells may be associated with the progression and development of missed abortion.

WNT3 hypomethylation counteracts low activity of the Wnt signaling pathway in the placenta of preeclampsia.

Preeclampsia is a hypertensive disorder of pregnancy. Many studies have shown that epigenetic mechanisms may play a role in preeclampsia. Moreover, our previous study indicated that the differentially methylated genes in preeclampsia were enriched in the Wnt/ß-catenin signaling pathway. This study aimed to identify differentially methylated Wnt/ß-catenin signaling pathway genes in the preeclamptic placenta and to study the roles of these genes in trophoblast cells in vitro. Using an Illumina Infinium HumanMethylation 850 K BeadChip, we found that the Wnt signaling pathway was globally hypermethylated in the preeclamptic group compared with the term birth group, but hypomethylated in the preeclamptic group compared with the preterm birth group. Among all Wnt/ß-catenin signaling pathway factors, WNT3 was the most significantly differentially expressed gene and was hypomethylated in the preeclamptic group compared to the nonhypertensive groups, namely, the preterm birth group and term birth group. This result was confirmed by pyrosequencing. Through quantitative real-time PCR and western blot analysis, the WNT3 gene was found to be highly expressed in preeclamptic placental tissues, in contrast to other WNT factors, which were previously reported to be expressed at low levels in placental tissues. Additionally, in the HTR8/SVneo cell line, knockdown of WNT3 suppressed the Wnt/ß-catenin signaling pathway, consistent with the findings for other WNT factors. These results prompted us to speculate that the WNT3 gene counteracts the low activation state of the Wnt signaling pathway in the preeclamptic placenta through methylation modification.

Red blood cell distribution width at admission predicts outcome in critically ill patients with kidney failure: a retrospective cohort study based on the MIMIC-IV database.

PURPOSE: We aimed to explore whether red blood cell distribution width (RDW) could serve as a biomarker to predict outcomes in critically ill patients with kidney failure in this study. MATERIALS AND METHODS: This retrospective study was conducted with the Medical Information Mart for Intensive Care IV (MIMIC-IV).A total of 674 patients were divided into three groups based on tertiles of RDW. We used the generalized additive model, Kaplan-Meier curve, and Cox proportional hazards models to evaluate the association between RDW and clinical outcomes. We then performed subgroup analyses to investigate the stability of the associations between RDW and all-cause mortality. RESULTS: Nonlinear and J-shaped curves were observed in the generalized additive model. Kaplan-Meier analysis showed that patients with elevated RDW had a lower survival rate. The Cox regression model indicated that high levels of RDW were most closely associated with ICU mortality and 30-day mortality (HR = 4.71, 95% CI: 1.69-11.64 and HR = 6.62, 95% CI: 2.84-15.41). Subgroup analyses indicated that the associations between RDW and all-cause mortality were stable. CONCLUSIONS: Elevated levels of RDW were associated with an increased risk of all-cause mortality, and RDW could be an independent prognostic factor for kidney failure.

Analysis of the screening results of 24040 potential sperm donors in a human sperm bank in Henan Province, China: a 14-year retrospective cohort study.

STUDY QUESTION: Is there a relation between the characteristics of potential sperm donors and the acceptance rate of these potential donors? SUMMARY ANSWER: A relatively higher acceptance rate was observed for potential sperm donors who were aged ≤ 35 years, were married, had children, and who had received higher education, and acceptance rates were also higher during spring and winter than summer and autumn. WHAT IS KNOWN ALREADY: Recruiting donors to a sperm bank program is difficult and slow owing to the high rates of rejection and dropout. STUDY DESIGN, SIZE, DURATION: A total of 24040 potential sperm donors were screened by the Henan Human Sperm Bank from 2006 to 2019. PARTICIPANTS/MATERIALS, SETTING, METHODS: Potential sperm donors were recruited using the following baseline requirement: height of 168 cm or taller; age 22-45 years; currently attending or had graduated from high school or above. Men who met the criteria for age, height, and education level were invited for semen quality screening. The acceptable criteria for semen samples included liquefaction time < 60min, volume ≥ 2mL, sperm concentration ≥ 60 × 106/mL, progressive motility ≥ 60%, post-thaw motility ≥ 40%, pre-freezing total motile sperm per vial > 30 × 106/mL, post-thaw total motile sperm per vial > 12 × 106/mL, and freeze-thaw survival rate ≥ 60%. Any potential sperm donors meeting the minimum criteria for acceptable semen quality on two consecutive semen samples were scheduled for clinical assessment, physical examination, and laboratory tests. The reasons for sperm donor rejection were analyzed. The characteristics of accepted and rejected donors were compared using the chi-square test, and multivariate logistic regression analyses were conducted to identify factors associated with the acceptance rate of potential sperm donors and the positive rate of sexually transmitted diseases (STDs). MAIN RESULTS AND THE ROLE OF CHANCE: Only 23.38% (5620/24040) of potential sperm donors were accepted. The top four reasons for rejection were suboptimal semen quality (90.27%), STDs (6.26%), dropped out (2.65%), and chromosomal abnormalities (0.35%). The most common reason for the rejection of donors with an STD was a positive test for mycoplasmas (49.05%), followed by hepatitis B virus (27.56%), Chlamydia trachomatis (4.68%), and Escherichia coli (3.03%). n this study, the acceptance rate for men aged ≤ 35 years was significantly higher than that for men aged >35 years (P < 0.05). The acceptance rates were also significantly higher for men with a higher education than for men with lower education, married men than unmarried men, and men with children than men without children (P < 0.05). Moreover, acceptance rates were significantly higher during spring and winter than during summer (P <0.05) but were not significantly higher during autumn than during summer (P >0.05). LIMITATIONS, REASONS FOR CAUTION: This study was not performed to analyze the effect of lifestyle habits, such as alcohol consumption and cigarette smoking, on the acceptance rate of potential sperm donors. WIDER IMPLICATIONS OF THE FINDINGS: Only a small proportion of potential sperm donors were accepted in this anonymous sperm donor program. New strategies for sperm donor recruitment may be required to improve the acceptance rate. In the future, we may have to target potential sperm donors who are aged ≤ 35 years and who received higher education in order to improve the acceptance rate. STUDY FUNDING/COMPETING INTEREST(S): This work was supported by the Joint Construction Project of Henan Medical Science and Technology Research Plan under grant number LHGJ20190389. The authors report no conflict of interest. TRIAL REGISTRATION NUMBER: N/A.

Serum anion gap at admission predicts all-cause mortality in critically ill patients with cerebral infarction: evidence from the MIMIC-III database.

BACKGROUND: Recent studies reported that serum anion gap could be regarded as a prognostic biomarker for patients admitted to intensive care units. However, the association between AG and mortality in cerebral infarction patients remained largely unknown. METHODS: Relevant clinical data were collected from Medical Information Mart for Intensive Care III. Patients were divided into three groups according to tertiles of AG. Kaplan-Meier curve and Cox proportional hazards models were used to evaluate the association between AG levels and all-cause mortality. Subgroup analyses were performed to verify the predictive role of AG on mortality. RESULTS: Kaplan-Meier analysis showed that patients with higher AG had shorter survival time. Cox regression model indicated high AG as an independent risk factor of 30-day, 60-day and 180-day all-cause mortality (30-day: HR = 2.45, 95% CI = 1.21-4.97, 60-day: HR = 2.04, 95% CI = 1.07-3.89, and 180-day: HR = 1.85, 95% CI = 1.02-3.36). However, no significance was observed between AG and 365-day all-cause mortality (HR = 1.56, 95% CI = 0.87-2.78). CONCLUSIONS: High AG was associated with increased risk of all-cause mortality, and AG could be an independent short-term prognostic factor for cerebral infarction.

Age- and sex-related reference intervals of lymphocyte subsets in healthy ethnic Han Chinese children.

Immunophenotyping of blood lymphocytes has become an important tool in the diagnosis of immunologic and hematologic disorders such as immunodeficiencies, lymphoproliferative and autoimmune diseases. Lymphocyte subsets include total T-cells (CD3(+)), TH (T helper, CD3(+) CD4(+)), TC (cytotoxic T cells, CD3(+) CD8(+)), B-cells (CD3(-) CD19(+)), and NK-cells (CD3(-) CD16(+) CD56(+)). Specific lymphocyte subset reference intervals should be locally established for meaningful comparison and to obtain an accurate interpretation of the results. Reference intervals of lymphocyte subsets for Chinese children are scarce. We performed dual-platform flow cytometry to determine the reference intervals of the percentages and absolute counts of lymphocyte subsets, including total T-cells, TH cells, TC cells, B-cells, and NK-cells in 1,027 ethnic Han children aged 4 months to 7 years in Henan, China. The children were divided into seven age groups. The percentages and absolute counts differed significantly with age, with the percentages of TH cells and B cells and the CD4/CD8 ratio peaking during the first year, while the percentages of total T cells, TC cells, and NK cells were obviously increased with age; girls showed a trend toward having a higher percentage of TH cells and a higher CD4/CD8 ratio than boys. The absolute counts of lymphocyte subsets peaked during first year and then decreased steadily with age. The reference intervals of lymphocyte subsets among children from China differed from the reported values in Hong Kong, the United States, Cameroon, and Italy. The differences observed could be due to genetic and environmental factors, coupled with the methodology used. The reference intervals of lymphocyte subsets could be used as initial national reference ranges in guidelines for children aged 4 months to 7 years.

Regulatory effect of N6-methyladenosine on tumor angiogenesis.

Previous studies have demonstrated that genetic alterations governing epigenetic processes frequently drive tumor development and that modifications in RNA may contribute to these alterations. In the 1970s, researchers discovered that N6-methyladenosine (m6A) is the most prevalent form of RNA modification in advanced eukaryotic messenger RNA (mRNA) and noncoding RNA (ncRNA). This modification is involved in nearly all stages of the RNA life cycle. M6A modification is regulated by enzymes known as m6A methyltransferases (writers) and demethylases (erasers). Numerous studies have indicated that m6A modification can impact cancer progression by regulating cancer-related biological functions. Tumor angiogenesis, an important and unregulated process, plays a pivotal role in tumor initiation, growth, and metastasis. The interaction between m6A and ncRNAs is widely recognized as a significant factor in proliferation and angiogenesis. Therefore, this article provides a comprehensive review of the regulatory mechanisms underlying m6A RNA modifications and ncRNAs in tumor angiogenesis, as well as the latest advancements in molecular targeted therapy. The aim of this study is to offer novel insights for clinical tumor therapy.

Immunogenic cell death (ICD) genes predict immunotherapy response and therapeutic targets in acute myeloid leukemia (AML).

Introduction: Numerous studies have demonstrated acute myeloid leukemia (AML) is one of the malignancies with high mortality worldwide. Immunogenic cell death (ICD) is a form of cell death that is specialised in that it triggers the body's immune response, particularly the adaptive immune response. Recent evidence has confirmed that pseudogenes are implicated in multiple human tumorigenesis and progression although lacking the function of coding protein. However, the roles of ICD-associated genes in AML remain largely unascertained. Methods: TCGA-AML and GSE71014 cohorts were picked out and we combined them into a merged dataset by removing the batch effect using the sva package in the R project. A consensus clustering analysis of the ICD genes in AML was performed to define subgroups. Based on the expression of 15 prognostic-related pseudogenes, we developed a prognostic model and categorized AML samples into low and high-risk groups. Results: AML was differentiated into two subgroups (C1 and C2 clusters). Most ICD-related genes were significantly up-regulated in the C2 cluster. The single sample gene set enrichment analysis (ssGSEA) revealed that the immune cell infiltration and immune checkpoint gene expression of the C2 cluster was strongly high, suggesting that the C2 population responded well to immune checkpoint blockade (ICB) therapy and had better survival. The C1 group was sensitive to chemotherapy, including Cytarabine, Midostaurin, and Doxorubicin. On the other hand, 15 ICD-related pseudogenes were identified to be associated with AML prognosis. The receiver operator curve (ROC) analysis and nomogram manifested that our prognostic model had high accuracy in predicting survival. However, the high-risk group was sensitive to ICB therapy and chemotherapy such as Methotrexate, Cytarabine, and Axitinib while the low-risk group benefited from 5-Fluorouracil, Talazoparib, and Navitoclax therapy. Discussion: In summary, we defined two subgroups relying on 33 ICD-related genes and this classification exerted a decisive role in assessing immunotherapy and chemotherapy benefit. Significantly, a prognostic signature identified by critical ICD-related pseudogene was created. The pseudogene prognostic signature had a powerful performance in predicting prognosis and therapeutic efficacy, including immunotherapy and chemotherapy to AML. Our research points out novel implications of ICD in cancer prognosis and treatment approach choice.

Mendelian randomization reveals association of gut microbiota with Henoch-Schönlein purpura and immune thrombocytopenia.

Gut microbiota have been linked to immune thrombocytopenia (ITP) and Henoch-Schönlein purpura (HSP) in recent studies, but a cause-and-effect relationship is unclear. We used Mendelian randomization (MR) to assess causal relationships between gut microbiota and HSP/ITP using summary statistics from the GWAS dataset of the international MiBioGen and FinnGen consortium. The IVW method was used as the main evaluation indicator. MR analysis of 196 intestinal flora and HSP/ITP/sTP phenotypes showed that 12 flora were potentially causally associated with ITP, 6 with HSP, and 9 with sTP. The genes predicted that genus Coprococcus3 (p = 0.0264, OR = 2.05, 95% CI 1.09-3.88)and genus Gordonibacter (p = 0.0073, OR = 1.38; 95% CI 1.09-1.75) were linked to a higher likelihood of developing ITP. Additionally, family Actinomycetaceae (p = 0.02, OR = 0.51, 95% CI 0.28-0.90) and order Actinomycetales (p = 0.0199, OR = 0.50, 95% CI 0.28-0.90) linked to reduced HSP risk. Genus Ruminococcaceae UCG013 (p = 0.0426, OR = 0.44, 95% CI 0.20-0.97) negatively correlated with sTP risk. Our MR analyses offer evidence of a possible cause-and-effect connection between certain gut microbiota species and the likelihood of HSP/ITP.

Dissemination of bla NDM-5 Driven by Horizontal Transfer of IncFIA Plasmid Between Escherichia coli and Klebsiella pneumoniae Co-Isolated from a Patient's Ascitic Fluid.

Purpose: Understanding the horizontal transfer of resistance genes, such as bla NDM-5, is pivotal in developing strategies to control the spread of resistance. In this study, we isolated two bacterial strains, Escherichia coli (designated GYB01) and Klebsiella pneumoniae (designated GYB02), from a single patient. The aim of our research is to explore the biological characteristics of these strains and to investigate the interspecies horizontal transfer of bla NDM-5. Materials and Methods: Strain identification and antimicrobial susceptibility testing were conducted using the Vitek 2 system. Both GYB01 and GYB02 were sequenced with the Illumina HiSeq platform. Bioinformatics analysis tools, including multilocus sequence typing, PlasmidFinder, ResFinder, and others, were utilized to analyze the strains. Additionally, conjugation assays and Galleria mellonella infection assays were employed to assess the strains. Results: The isolates exhibited similar antimicrobial resistance profiles and both harbored the bla NDM-5 gene within the IncFIA plasmids (pGYB01-2, 165.8 kb and pGYB02-2, 211.6 kb, respectively). These plasmids (pGYB01-2 and pGYB02-2) shared over 99% homology, suggesting a common ancestral origin. Conjugation experiments confirmed the transferability of the bla NDM-5 carrying IncFIA plasmids among Enterobacteriaceae. GYB02 possessed an iucACD-iutA gene cluster, exhibited high virulence, and tested positive in the string test. Conclusion: Our findings provide direct evidence of potential in vivo interspecies transfer of a multidrug-resistant plasmid, thus enriching our understanding of the mechanisms driving multidrug resistance (MDR) and aiding in the formulation of containment and treatment strategies.

Unravelling the function of prdm16 in human tumours: A comparative analysis of haematologic and solid tumours.

Extensive research has shown that PR domain 16 (PRDM16) plays a critical role in adipose tissue metabolism, including processes such as browning and thermogenesis of adipocytes, beigeing of adipocytes, and adipogenic differentiation of myoblasts. These functions have been associated with diseases such as obesity and diabetes. Additionally, PRDM16 has been correlated with various other conditions, including migraines, heterochromatin abnormalities, metabolic syndrome, cardiomyopathy, sarcopenia, nonsyndromic cleft lip, and essential hypertension, among others. However, there is currently no systematic or comprehensive conclusion regarding the mechanism of PRDM16 in human tumours, including haematologic and solid tumours. The aim of this review is to provide an overview of the research progress on PRDM16 in haematologic and solid tumours by incorporating recent literature findings. Furthermore, we explore the prospects of PRDM16 in the precise diagnosis and treatment of human haematologic and solid tumours.

Combined analysis of bulk and single-cell RNA sequencing reveals novel natural killer cell-related prognostic biomarkers for predicting immunotherapeutic response in hepatocellular carcinoma.

Introduction: Natural killer (NK) cells play an irreplaceable and important role as a subtype of innate immune cells in the contemporary setting of antitumor immunity. Methods: We chose a total of 1,196 samples for this analysis from the public dataset's six separate cohorts. To identify 42 NK cell marker genes, we first carried out a thorough study of single-cell RNA sequencing data from the GSE149614 cohort of hepatocellular carcinoma (HCC). Results: Using the NK cell marker genes in the TCGA cohort, we next created a seven-gene prognostic signature, separating the patients into two categories with distinct survival patterns. This signature's prognostic prediction ability was well verified across several validation cohorts. Patients with high scores had higher TIDE scores but lower immune cell infiltration percentages. Importantly, low-scoring patients had superior immunotherapy response and prognosis than high-scoring patients in an independent immunotherapy cohort (IMvigor210). Finally, we used CD56 and TUBA1B antibodies for immunohistochemical labeling of HCC tissue sections, and we discovered a lower number of CD56+ cells in the HCC tissue sections with high TUBA1B expression. Discussion: In summary, our research created a unique prognostic profile based on NK cell marker genes that may accurately predict how well immunotherapy would work for HCC patients.

Exploring the relationship between IGHMBP2 gene mutations and spinal muscular atrophy with respiratory distress type 1 and Charcot-Marie-Tooth disease type 2S: a systematic review.

Background: IGHMBP2 is a crucial gene for the development and maintenance of the nervous system, especially in the survival of motor neurons. Mutations in this gene have been associated with spinal muscular atrophy with respiratory distress type 1 (SMARD1) and Charcot-Marie-Tooth disease type 2S (CMT2S). Methods: We conducted a systematic literature search using the PubMed database to identify studies published up to April 1st, 2023, that investigated the association between IGHMBP2 mutations and SMARD1 or CMT2S. We compared the non-truncating mutations and truncating mutations of the IGHMBP2 gene and selected high-frequency mutations of the IGHMBP2 gene. Results: We identified 52 articles that investigated the association between IGHMBP2 mutations and SMARD1/CMT2S. We found 6 hotspot mutations of the IGHMBP2 gene. The truncating mutations in trans were all associated with SMARD1. Conclusion: This study provides evidence that the complete LOF mechanism of the IGHMBP2 gene defect may be an important cause of SMARD1.

The construction of a prognostic model of cervical cancer based on four immune-related LncRNAs and an exploration of the correlations between the model and oxidative stress.

Introduction: The immune-related lncRNAs (IRLs) are critical for the development of cervical cancer (CC), but it is still unclear how exactly ILRs contribute to CC. In this study, we aimed to examine the relationship between IRL and CC in detail. Methods: First, the RNAseq data and clinical data of CC patients were collected from The Cancer Genome Atlas (TCGA) database, along with the immune genes from the Import database. We used univariate cox and least absolute shrinkage and selection operator (lasso) to obtain IRLs for prediction after screening the variables. According to the expression levels and risk coefficients of IRLs, the riskscore were calculated. We analyzed the relationship between the model and oxidative stress. We stratified the risk model into two as the high and low-risk groups. We also evaluated the survival differences, immune cell differences, immunotherapeutic response differences, and drug sensitivity differences between the risk groups. Finally, the genes in the model were experimentally validated. Results: Based on the above analyses, we further selected four IRLs (TFAP2A.AS1, AP000911.1, AL133215.2, and LINC02078) to construct the risk model. The model was associated with oxidative-stress-related genes, especially SOD2 and OGG1. Patients in the high-risk group had a lower overall survival than those in the low-risk group. Riskscore was positively correlated with resting mast cells, neutrophils, and CD8+ T-cells. Patients in the low-risk group showed a greater sensitivity to immunosuppression therapy. In addition, we found that patients with the PIK3CA mutation were more sensitive to chemotherapeutic agents such as dasatinib, afatinib, dinaciclib and pelitinib. The function of AL133215.2 was verified, which was consistent with previous findings, and AL133215.2 exerted a pro-tumorigenic effect. We also found that AL133215.2 was closely associated with oxidative-stress-related pathways. Discussion: The results suggested that risk modeling might be useful for prognosticating patients with CC and opening up new routes for immunotherapy.