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Clinical Nutrition (Edinburgh, Scotland) Dec 2023Maternal diet influences the milk composition, yet little information is available on the impact of maternal diet on milk miRNAs expression. Further, the association of... (Clinical Trial)
Clinical Trial
BACKGROUND
Maternal diet influences the milk composition, yet little information is available on the impact of maternal diet on milk miRNAs expression. Further, the association of human milk miRNAs to maternal diet and milk microbiota is not explored. In addition, the role of milk miRNAs on the infant gut microbiota, infant growth and development has not been investigated.
METHODS
Milk samples were collected from 60 healthy lactating women at ≤15d post-partum, HTG transcriptome assay was performed to examine milk miRNA profile. Maternal clinical and dietary clusters information were available and infant anthropometric measures were followed up to one year of age. Milk and infant microbiota were analyzed by 16S rRNA gene sequencing and integrative multi-omics data analysis was performed to identify potential association between microRNA, maternal dietary nutrients and microbiota.
RESULTS
Discriminant analysis revealed that the milk miRNAs were clustered into groups according to the maternal protein source. Interestingly, 31 miRNAs were differentially expressed (P adj < 0.05) between maternal dietary clusters (Cluster 1: enriched in plant protein and fibers and Cluster 2: enriched in animal protein), with 30 miRNAs downregulated in the plant protein group relative to animal protein group. Pathway analysis revealed that the top enriched pathways (P adj < 0.01) were involved in cell growth and proliferation processes. Furthermore, significant features contributing to the clustering were associated with maternal dietary nutrients and milk microbiota (r > 0.70). Further, miR-378 and 320 family miRNAs involved in adipogenesis were positively correlated to the infant BMI-z-scores, weight, and weight for length-z-scores at 6 months of age.
CONCLUSIONS
Maternal dietary source impacts the milk miRNA expression profile. Further, miRNAs were associated with maternal dietary nutrients, milk microbiota and to the infant gut microbiota and infant growth and development.
CLINICAL TRIAL
The study is registered in ClinicalTrials.gov. The identification number is NCT03552939.
Topics: Female; Humans; Infant; Diet; Gastrointestinal Microbiome; Lactation; MicroRNAs; Milk, Human; Nutrients; Plant Proteins; RNA, Ribosomal, 16S
PubMed: 37931372
DOI: 10.1016/j.clnu.2023.10.011 -
Antibiotics (Basel, Switzerland) Aug 2023Microcin C7 (McC) as a viable form of antimicrobial has gained substantial attention due to its distinctive antimicrobial activity, by targeting aspartyl tRNA...
Microcin C7 (McC) as a viable form of antimicrobial has gained substantial attention due to its distinctive antimicrobial activity, by targeting aspartyl tRNA synthetase. McC can be a potential solution against pathogenic microbial infections in the postantibiotic era. However, considering that degradation by digestive enzymes can disrupt the function of this peptide in the gastrointestinal tract, in this study, we attempt to design McC variants to overcome several barriers that may affect its stability and biological activity. The gene encoding the McC peptide precursor was mutated and 12 new McC variants with trypsin resistance were found. The YejrimL strain was used as an indicator to determine the minimum inhibitory concentrations (MICs). The results showed that three variants, including R2A, R2T and R2Q, among 12 variants formed by the replacement of the second arginine of the McC peptide with different amino acids, were resistant to trypsin and had an outstanding antimicrobial ability, with MIC values of 12.5, 25, and 25 μg/mL, respectively. Taken together, our findings show that the engineering of the site-directed mutagenesis of McC significantly enhances McC trypsin resistance and maintains a great antimicrobial activity.
PubMed: 37760643
DOI: 10.3390/antibiotics12091346 -
Heliyon Jan 2024Diabetic nephropathy (DN) is one of the most common microvascular complications of diabetes mellitus. Periodontitis (PD) is a microbially-induced chronic inflammatory...
Diabetic nephropathy (DN) is one of the most common microvascular complications of diabetes mellitus. Periodontitis (PD) is a microbially-induced chronic inflammatory disease that is thought to have a bidirectional relationship with diabetes mellitus. DN and PD are recognized as models associated with accelerated aging. This study is divided into two parts, the first of which explores the bidirectional causal relationship through Mendelian randomization (MR). The second part aims to investigate the relationship between PD and DN in terms of potential crosstalk genes, aging-related genes, biological pathways, and processes using bioinformatic methods. MR analysis showed no evidence to support a causal relationship between DN and PD ( = 0.34) or PD and DN ( = 0.77). Using the GEO database, we screened 83 crosstalk genes overlapping in two diseases. Twelve paired genes identified by Pearson correlation and the four hub genes in the key cluster were jointly evaluated as key crosstalk-aging genes. Using support vector machine recursive feature elimination (SVM-RFE) and maximal clique centrality (MCC) algorithms, feature selection established five genes as the key crosstalk-aging genes. Based on five key genes, an ANN diagnostic model with reliable diagnosis of two diseases was developed. Gene enrichment analysis indicates that AGE-RAGE pathway signaling, the complement system, and multiple immune inflammatory pathways may be involved in common features of both diseases. Immune infiltration analysis reveals that most immune cells are differentially expressed in PD and DN, with dendritic cells and T cells assuming vital roles in both diseases. Overall, although there is no causal link, CSF1R, CXCL6, VCAM1, JUN and IL1B may be potential crosstalk-aging genes linking PD and DN. The common pathways and markers explored in this study could contribute to a deeper understanding of the common pathogenesis of both diseases in the context of aging and provide a theoretical basis for future research.
PubMed: 38304805
DOI: 10.1016/j.heliyon.2024.e24872 -
Journal of Cancer Research and Clinical... Aug 2023Lung cancer is the most common form of cancer and the leading cause of cancer death. For familial lung cancer, identification of causing genetic factors is essential for...
OBJECTIVES
Lung cancer is the most common form of cancer and the leading cause of cancer death. For familial lung cancer, identification of causing genetic factors is essential for prevention and control of non-lung cancer in carriers.
MATERIALS AND METHODS
We studied two generations of a family with suspected inherited lung cancer susceptibility. Four individuals in this family had lung adenocarcinoma. To identify the gene(s) that cause the lung cancer in this pedigree, we extracted DNA from the peripheral blood of four cancer individuals and blood from three cancer-free family members as the control and performed whole-genome sequencing. Our filtering strategy includes, assessment of allele frequency, functional affection on amino acids, mutation accumulation, phased blocks and evolution analysis towards the alterations.
RESULTS
We identified two possible mutations, including PLEKHM2 (D134N) and MCC (R448Q) in all affected family members but did not found in the control group. Then, we performed a genetic susceptibility screening for 10 non-lung cancer relatives and found two individuals with PLEKHM2 (D134N) mutation, two with MCC (R448Q) mutation and one carrying both mutations. 3 carriers performed LDCT scan and 2 of them carried MCC (R448Q) also had ground-glass opacity (GGO) lesion in their lung.
CONCLUSION
Our data suggested that WGS together with our filtering strategy was successful in identifying PLEKHM2 (D134N) and MCC (R448Q) as the possible driver mutations in this family. Genetic susceptibility screening of non-lung cancer carriers will be a useful approach to prevent and control lung cancer in families with high-risk for the disease.
Topics: Aged; Aged, 80 and over; Female; Humans; Male; Middle Aged; Adenocarcinoma of Lung; Gene Frequency; Genetic Predisposition to Disease; Germ-Line Mutation; Lung Neoplasms; Pedigree; Tumor Suppressor Proteins; Tomography, X-Ray Computed; Lung
PubMed: 36781503
DOI: 10.1007/s00432-023-04616-2 -
Clinical Genetics Jun 2024Multiple congenital contractures (MCC) due to fetal akinesia manifest across a broad spectrum of diseases, ranging from mild distal arthrogryposis to lethal fetal...
Multiple congenital contractures (MCC) due to fetal akinesia manifest across a broad spectrum of diseases, ranging from mild distal arthrogryposis to lethal fetal akinesia deformation sequence. We hereby present a series of 26 fetuses displaying severe MCC phenotypes from 18 families and describe detailed prenatal ultrasound findings, postmortem clinical evaluations, and genetic investigations. Most common prenatal findings were abnormal facial profile (65%), central nervous system abnormalities (62%), polyhydramnios (50%), increased nuchal translucency (50%), and fetal hydrops (35%). Postmortem examinations unveiled additional anomalies including facial dysmorphisms, dysplastic skeletal changes, ichthyosis, multiple pterygia, and myopathy, allowing preliminary diagnosis of particular Mendelian disorders in multiple patients. Evaluation of the parents revealed maternal grip myotonia in one family. By exome sequencing and targeted testing, we identified causative variants in ACTC1, CHST14, COG6, DMPK, DOK7, HSPG2, KLHL7, KLHL40, KIAA1109, NEB, PSAT1, RAPSN, USP14, and WASHC5 in 15 families, and one patient with a plausible diagnosis associated with biallelic NEB variants. Three patients received a dual diagnosis. Pathogenic alterations in newly discovered genes or in previously known genes recently linked to new MCC phenotypes were observed in 44% of the cohort. Our results provide new insights into the clinical and molecular landscape of lethal MCC phenotypes.
Topics: Humans; Female; Male; Arthrogryposis; Phenotype; Fetus; Exome Sequencing; Contracture; Pregnancy; Ultrasonography, Prenatal; Mutation; Abnormalities, Multiple
PubMed: 38278647
DOI: 10.1111/cge.14490 -
BioRxiv : the Preprint Server For... Nov 2023Merkel Cell Carcinoma (MCC) is a highly aggressive neuroendocrine cutaneous malignancy arising from either ultraviolet-induced mutagenesis or Merkel cell polyomavirus...
Merkel Cell Carcinoma (MCC) is a highly aggressive neuroendocrine cutaneous malignancy arising from either ultraviolet-induced mutagenesis or Merkel cell polyomavirus (MCPyV) integration. It is the only known neuroendocrine tumor (NET) with a virus etiology. Despite extensive research, our understanding of the molecular mechanisms driving the transition from normal cells to MCC remains limited. To address this knowledge gap, we assessed the impact of inducible MCPyV T antigens into normal human fibroblasts by performing RNA sequencing. Our findings suggested that the WNT signaling pathway plays a critical role in the development of MCC. To test this model, we bioinformatically evaluated various perturbagens for their ability to reverse the MCC gene expression signature and identified pyrvinium pamoate, an FDA-approved anthelminthic drug known for its anti-tumor potential in multiple cancers. Leveraging transcriptomic, network, and molecular analyses, we found that pyrvinium effectively targets multiple MCC vulnerabilities. Specifically, pyrvinium not only reverses the neuroendocrine features of MCC by modulating canonical and non-canonical WNT signaling pathways but also inhibits cancer cell growth by activating the p53-mediated apoptosis pathway, disrupting mitochondrial function, and inducing endoplasmic reticulum (ER) stress. Pyrvinium also effectively inhibits tumor growth in an MCC mouse xenograft model. These findings offer new avenues for the development of therapeutic strategies for neuroendocrine cancer and highlight the utility of pyrvinium as a potential treatment for MCC.
PubMed: 37961132
DOI: 10.1101/2023.11.01.565218 -
Journal of the Neurological Sciences Aug 2023Cylindrical spirals (CSs) are ultrastructurally distinct, intracytoplasmic inclusions characterized by concentrically wrapped lamellae, which are rarely found in...
Cylindrical spirals (CSs) are ultrastructurally distinct, intracytoplasmic inclusions characterized by concentrically wrapped lamellae, which are rarely found in skeletal muscle biopsies on electron microscopy (EM). CSs are often confused with other EM concentric structures including concentric laminated bodies and mitochondrial concentric cristae (MCC), due to similarities in these ultrastructures. In this study, we found CSs in 9 muscle biopsies from 9 patients, accounting for 0.5% of the biopsies examined routinely by EM. The frequency of CSs in these muscles varied from sparse and segregated to focally frequent and aggregated. CS-associated features included muscle fiber denervation atrophy in all 9 cases, fiber type grouping in 7/8 cases, tubular aggregates in 3/9 cases, and MCC in 2/9 cases. We also compared the concentric structures and highlighted their differences to distinguish CSs from other similar structures. Clinically, 8 out of 9 patients were adults aged 41-74 years and only one patient was 17 month-old. CSs were associated with several neurological diseases including Huntington's disease, amyotrophic lateral sclerosis, Mitochondrial Encephalopathy, Lactic Acidosis, and Stroke-like episodes, and other complex neurological disorders with neuropathy/encephalopathy, as well as anti-MDA5+ dermatomyositis. Eight of nine patients had genetic findings such as trinucleotide repeat expansion of huntingtin gene, ALS2 variant, MT-TL1 m.3243A > G mutation, and PMP 22 gene deletion. These results suggest that CSs may be highly variable in frequency and likely are under-reported/under-detected; they may be associated with neurogenic myopathy or central/peripheral nervous system disorders including some genetic neurological/neuromuscular diseases. Our findings of more CS-associated neurological diseases and an association of CSs with muscle neurogenic features may contribute to a better understanding of the clinico-pathological significance of CSs.
Topics: Adult; Humans; Infant; Muscle, Skeletal; Muscular Diseases; Neuromuscular Diseases; Huntington Disease; Muscular Atrophy
PubMed: 37478793
DOI: 10.1016/j.jns.2023.120734 -
Frontiers in Immunology 2024Over the past decades, immune dysregulation has been consistently demonstrated being common charactoristics of endometriosis (EM) and Inflammatory Bowel Disease (IBD) in...
INTRODUCTION
Over the past decades, immune dysregulation has been consistently demonstrated being common charactoristics of endometriosis (EM) and Inflammatory Bowel Disease (IBD) in numerous studies. However, the underlying pathological mechanisms remain unknown. In this study, bioinformatics techniques were used to screen large-scale gene expression data for plausible correlations at the molecular level in order to identify common pathogenic pathways between EM and IBD.
METHODS
Based on the EM transcriptomic datasets GSE7305 and GSE23339, as well as the IBD transcriptomic datasets GSE87466 and GSE126124, differential gene analysis was performed using the limma package in the R environment. Co-expressed differentially expressed genes were identified, and a protein-protein interaction (PPI) network for the differentially expressed genes was constructed using the 11.5 version of the STRING database. The MCODE tool in Cytoscape facilitated filtering out protein interaction subnetworks. Key genes in the PPI network were identified through two topological analysis algorithms (MCC and Degree) from the CytoHubba plugin. Upset was used for visualization of these key genes. The diagnostic value of gene expression levels for these key genes was assessed using the Receiver Operating Characteristic (ROC) curve and Area Under the Curve (AUC) The CIBERSORT algorithm determined the infiltration status of 22 immune cell subtypes, exploring differences between EM and IBD patients in both control and disease groups. Finally, different gene expression trends shared by EM and IBD were input into CMap to identify small molecule compounds with potential therapeutic effects.
RESULTS
113 differentially expressed genes (DEGs) that were co-expressed in EM and IBD have been identified, comprising 28 down-regulated genes and 86 up-regulated genes. The co-expression differential gene of EM and IBD in the functional enrichment analyses focused on immune response activation, circulating immunoglobulin-mediated humoral immune response and humoral immune response. Five hub genes (SERPING1、VCAM1、CLU、C3、CD55) were identified through the Protein-protein Interaction network and MCODE.High Area Under the Curve (AUC) values of Receiver Operating Characteristic (ROC) curves for 5hub genes indicate the predictive ability for disease occurrence.These hub genes could be used as potential biomarkers for the development of EM and IBD. Furthermore, the CMap database identified a total of 9 small molecule compounds (TTNPB、CAY-10577、PD-0325901 etc.) targeting therapeutic genes for EM and IBD.
DISCUSSION
Our research revealed common pathogenic mechanisms between EM and IBD, particularly emphasizing immune regulation and cell signalling, indicating the significance of immune factors in the occurence and progression of both diseases. By elucidating shared mechanisms, our study provides novel avenues for the prevention and treatment of EM and IBD.
Topics: Humans; Endometriosis; Female; Inflammatory Bowel Diseases; Protein Interaction Maps; Transcriptome; Computational Biology; Gene Expression Profiling; Databases, Genetic; Gene Regulatory Networks; Biomarkers; Gene Expression Regulation
PubMed: 38660311
DOI: 10.3389/fimmu.2024.1339647 -
Journal of Cancer Research and Clinical... Sep 2023Class I selective histone deacetylase inhibitors (HDACi) have been previously demonstrated to not only increase major histocompatibility complex class I surface...
BACKGROUND
Class I selective histone deacetylase inhibitors (HDACi) have been previously demonstrated to not only increase major histocompatibility complex class I surface expression in Merkel cell carcinoma (MCC) cells by restoring the antigen processing and presentation machinery, but also exert anti-tumoral effect by inducing apoptosis. Both phenomena could be due to induction of type I interferons (IFN), as has been described for HDACi. However, the mechanism of IFN induction under HDACi is not fully understood because the expression of IFNs is regulated by both activating and inhibitory signaling pathways. Our own preliminary observations suggest that this may be caused by suppression of HES1.
METHODS
The effect of the class I selective HDACi domatinostat and IFNα on cell viability and the apoptosis of MCPyV-positive (WaGa, MKL-1) and -negative (UM-MCC 34) MCC cell lines, as well as, primary fibroblasts were assessed by colorimetric methods or measuring mitochondrial membrane potential and intracellular caspase-3/7, respectively. Next, the impact of domatinostat on IFNA and HES1 mRNA expression was measured by RT-qPCR; intracellular IFNα production was detected by flow cytometry. To confirm that the expression of IFNα induced by HDACi was due to the suppression of HES1, it was silenced by RNA interference and then mRNA expression of IFNA and IFN-stimulated genes was assessed.
RESULTS
Our studies show that the previously reported reduction in viability of MCC cell lines after inhibition of HDAC by domatinostat is accompanied by an increase in IFNα expression, both of mRNA and at the protein level. We confirmed that treatment of MCC cells with external IFNα inhibited their proliferation and induced apoptosis. Re-analysis of existing single-cell RNA sequencing data indicated that induction of IFNα by domatinostat occurs through repression of HES1, a transcriptional inhibitor of IFNA; this was confirmed by RT-qPCR. Finally, siRNA-mediated silencing of HES1 in the MCC cell line WaGa not only increased mRNA expression of IFNA and IFN-stimulated genes but also decreased cell viability.
CONCLUSION
Our results demonstrate that the direct anti-tumor effect of HDACi domatinostat on MCC cells is at least in part mediated via decreased HES1 expression allowing the induction of IFNα, which in turn causes apoptosis.
Topics: Humans; Carcinoma, Merkel Cell; Histone Deacetylase Inhibitors; Interferon Type I; Skin Neoplasms; RNA, Messenger; Cell Line, Tumor; Transcription Factor HES-1
PubMed: 37071208
DOI: 10.1007/s00432-023-04733-y -
Cancer Letters Mar 2024The highly heterogenous nature of colorectal cancer can significantly hinder its early and accurate diagnosis, eventually contributing to high mortality rates. The... (Review)
Review
The highly heterogenous nature of colorectal cancer can significantly hinder its early and accurate diagnosis, eventually contributing to high mortality rates. The adenoma-carcinoma sequence and serrated polyp-carcinoma sequence are the two most common sequences in sporadic colorectal cancer. Genetic alterations in adenomatous polyposis coli (APC), v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) and tumour protein 53 (TP53) genes are critical in adenoma-carcinoma sequence, whereas v-Raf murine sarcoma viral oncogene homolog B (BRAF) and MutL Homolog1 (MLH1) are driving oncogenes in the serrated polyp-carcinoma sequence. Sporadic mutations in these genes contribute differently to colorectal cancer pathogenesis by introducing distinct alterations in several signalling pathways that rely on the endosome-lysosome system. Unsurprisingly, the endosome-lysosome system plays a pivotal role in the hallmarks of cancer and contributes to specialised colon function. Thus, the endosome-lysosome system might be distinctively influenced by different mutations and these alterations may contribute to the heterogenous nature of sporadic colorectal cancer. This review highlights potential connections between major sporadic colorectal cancer mutations and the diverse pathogenic mechanisms driven by the endosome-lysosome system in colorectal carcinogenesis.
Topics: Animals; Mice; Humans; Proto-Oncogene Proteins B-raf; Proto-Oncogene Proteins p21(ras); Colorectal Neoplasms; Mutation; Adenoma; Carcinoma
PubMed: 38290660
DOI: 10.1016/j.canlet.2024.216639