Identification and analysis of key genes related to efferocytosis in colorectal cancer.

The impact of efferocytosis-related genes (ERGs) on the diagnosis of colorectal cancer (CRC) remains unclear. In this study, efferocytosis-associated biomarkers for the diagnosis of CRC were identified by integrating data from transcriptome sequencing and public databases. Finally, the expression of biomarkers was validated by real-time quantitative polymerase chain reaction (RT-qPCR). Our study may provide a reference for CRC diagnosis. BACKGROUND: It has been shown that some efferocytosis related genes (ERGs) are associated with the development of cancer. However, it is still uncertain how ERGs may influence the diagnosis of colorectal cancer (CRC). METHODS: In our study, the CRC cohorts were gained from transcriptome sequencing and the gene expression omnibus (GEO) database (GSE71187). Efferocytosis related biomarkers with diagnostic utility for CRC were identified through combining differentially expressed analysis, machine learning algorithms, and receiver operating characteristic (ROC) analysis. Then, infiltration abundance of immune cells between CRC and control was evaluated. The regulatory networks (including mRNA-miRNA-lncRNA and miRNA/transcription factors (TF)-mRNA networks) were created. Finally, the expression of biomarkers was validated via real-time quantitative polymerase chain reaction (RT-qPCR). RESULTS: There were 3 biomarkers (ELMO3, P2RY12, and PDK4) related diagnosis for CRC patients gained. ELMO3 was highly expressed in CRC group, while P2RY12 and PDK4 was lowly expressed. Besides, the infiltrating abundance of 3 immune cells between CRC and control groups was significantly differential, namely activated CD4 memory T cells, macrophages M0, and resting mast cells. We then constructed a mRNA-miRNA-lncRNA network containing 3 mRNAs, 33 miRNAs, and 22 lncRNAs, and a miRNA/TF-mRNA network including 3 mRNAs, 33 miRNAs, and 7 TFs. Additionally, RT-qPCR results revealed that the expression trends of all biomarkers were consistent with the transcriptome sequencing data and GSE71187. CONCLUSION: Taken together, this study provides three efferocytosis related biomarkers (ELMO3, P2RY12, and PDK4) for diagnosis of CRC, providing a scientific reference for further studies of CRC.

Clinical features and GCDH gene variants in three Chinese families with glutaric aciduria type 1: A case series and literature review.

Aim: To analyze the clinical phenotype and genetic etiology of three cases of glutaric aciduria type 1 (GA1) in Chinese children. Methods: We performed genetic and metabolic testing using tandem mass spectrometry (MS/MS) and gas chromatography-mass spectrometry (GC/MS), followed by trio whole-exome sequencing (trio-WES) and Sanger sequencing. A literature review on glutaric aciduria type 1 (GA1) in Chinese patients was also conducted. Results: Sequencing results showed each case had compound heterozygous variants in GCDH(NM_000159.4): c.214C > G (p.Arg72Gly) and c.411C > G (p.Tyr137Term) (Case 1), c.214C > G (p.Arg72Gly) and c.1204C > T (p.Arg402Trp) (Case 2), and c.1228G > T (p.Val410Leu) and c.395G > A (p.Arg132Gln) (Case 3). These variants were inherited from their respective parents. Notably, the c.214C > G variant found in two children was a novel variant not previously reported. A review of the literature revealed that, clinically, the majority of patients experienced onset in infancy and early childhood (82%). Additionally, 38.36% were diagnosed through newborn screening, with the primary reasons for the initial visit being delayed development (32.43%) and infections (21.61%). The most common clinical manifestations included increased head circumference (77.19%) and motor developmental delay (65.15%). Biochemically, patients exhibited significant elevations in C5DC (98.51%) and C5DC/C8 (94.87%) in blood, as well as GA (94.37%) and 3OHGA (69.39%) in urine. Radiographically, patients showed a high prevalence of abnormalities in cranial MRI (86.15%) and EEG (73.33%). Genetically, 67 distinct GCDH gene variants were identified among 73 patients, with missense variants being the most prevalent type (73.97%). The most frequent variant was c.1244-2 A > C, observed in 17.12% of cases. Additionally, the majority of variant sites were located in exons 11 (25.37%) and 6 (22.39%). Conclusion: GCDH variants were identified as the causative factors in the three children. The discovery of the novel variant (c.214C > G) expands the spectrum of pathogenic GCDH variants. These findings facilitate the diagnosis and treatment of affected children and provide a basis for genetic counseling and prenatal diagnosis for their families.

Coenzyme Q10-loaded microcapsules stabilized by glyceryl monostearate and soy protein isolates-flaxseed gum: Characterization, in vitro release and digestive behavior.

This study aimed to stabilize microcapsules with core materials of glyceryl monostearate (GMS) and octyl and decyl glycerate, and wall materials of soy protein isolates (SPI) and flaxseed gum (FG) by complex coacervation method to overcome the drawbacks of coenzyme Q10 (CoQ10). It was demonstrated by the study that the obtained microcapsules were irregular aggregates. Differential scanning calorimetry and x-ray diffraction patterns indicated that CoQ10 was entrapped inside the disordered semisolid cores of microcapsules. The CoQ10 loading and encapsulation efficiency analysis revealed that GMS and FG helped CoQ10 better encapsulated inside the microcapsules. The in vitro release curve showed a "burst" release of CoQ10 absorbed on the surface of microcapsules for the first 180 min, followed by a sustained release of the encapsulated CoQ10. GMS and FG contributed to the sustained release and the release mechanism of the microcapsules was Fickian diffusion. The in vitro simulated digestion demonstrated that the constructed microcapsules improved the bio-accessibility of CoQ10. Finally, due to the protection of GMS and FG, microcapsules had good storage stability. In conclusion, this study emphasized the potential of using new microcapsules to deliver and protect lipophilic ingredients, providing valuable information for developing functional foods with higher bioavailability.

Preparation and characterization of astaxanthin-loaded microcapsules stabilized by lecithin-chitosan-alginate interfaces with layer-by-layer assembly method.

Astaxanthin is a kind of keto-carotenes with various health benefits. However, its solubility and chemical stability are poor, which leads to low bio-availability. Microcapsules have been reported to improve the solubility, chemical stability, and bio-availability of lipophilic bioactives. Freeze-dried astaxanthin-loaded microcapsules were prepared by layer-by-layer assembly of tertiary emulsions with maltodextrin as the filling matrix. Tertiary emulsions were fabricated by performing chitosan and sodium alginate electrostatic deposition onto soybean lecithin stabilized emulsions. 0.9 wt% of chitosan solution, 0.3 wt% of sodium alginate solution and 20 wt% of maltodextrin were optimized as the suitable concentrations. The prepared microcapsules were powders with irregular blocky structures. The astaxanthin loading was 0.56 ± 0.05 % and the encapsulation efficiency was >90 %. A slow release of astaxanthin could be observed in microcapsules promoted by the modulating of chitosan, alginate and maltodextrin. In vitro simulated digestion displayed that the microcapsules increased the bio-accessibility of astaxanthin to 69 ± 1 %. Chitosan, alginate and maltodextrin can control the digestion of microcapsules. The coating of chitosan and sodium alginate, and the filling of maltodextrin in microcapsules improved the chemical stability of astaxanthin. The constructed microcapsules were valuable to enrich scientific knowledge about improving the application of functional ingredients.

[Clinical and molecular genetic analysis of a child with comorbid 16p11.2 microdeletion syndrome and Rett syndrome].

OBJECTIVE: To explore the genetic characteristics of a child with comorbid 16p11.2 microdeletion syndrome and Rett syndrome (RTT). METHODS: A male infant who was admitted to Gansu Provincial Maternity and Child Health Care Hospital in May 2020 was selected as the study subject. Clinical data of the infant was collected. Genomic DNA was extracted from peripheral blood samples from the infant and his parents, and subjected to whole exome sequencing (WES). Candidate variant was verified by Sanger sequencing. RESULTS: The patient, a 4-day-old male infant, had presented with poor response, poor intake, feeding difficulties, and deceased at 8 months after birth. WES revealed that he has harbored a 0.643 Mb deletion in the 16p11.2 region, which encompassed key genes of the 16p11.2 microdeletion syndrome such as ALDOA, CORO1A, KIFF22, PRRT2 and TBX6. His father has carried the same deletion, but was phenotypically normal. The deletion was predicted to be pathogenic. The child was also found to harbor a maternally derived c.763C>T (p.R255X) hemizygous variant of the MECP2 gene, which was also predicted to be pathogenic (PVS1+PS4+PM2_Supporting). CONCLUSION: The 16p11.2 deletion and the MECP2: c.763C>T (p.R255X) variant probably underlay the pathogenesis in this infant.

A muti-modal feature fusion method based on deep learning for predicting immunotherapy response.

Immune checkpoint therapy (ICT) has greatly improved the survival of cancer patients in the past few years, but only a small number of patients respond to ICT. To predict ICT response, we developed a multi-modal feature fusion model based on deep learning (MFMDL). This model utilizes graph neural networks to map gene-gene relationships in gene networks to low dimensional vector spaces, and then fuses biological pathway features and immune cell infiltration features to make robust predictions of ICT. We used five datasets to validate the predictive performance of the MFMDL. These five datasets span multiple types of cancer, including melanoma, lung cancer, and gastric cancer. We found that the prediction performance of multi-modal feature fusion model based on deep learning is superior to other traditional ICT biomarkers, such as ICT targets or tumor microenvironment-associated markers. In addition, we also conducted ablation experiments to demonstrate the necessity of fusing different modal features, which can improve the prediction accuracy of the model.

[Clinical and genetic analysis of two pedigrees affected with Carnitine-acylcarnitine translocase deficiency due to variant of SLC25A20 gene].

OBJECTIVE: To analyze the clinical phenotype and genotypes of two children with Carnitine-acylcarnitine translocase deficiency (CACTD). METHODS: Two children diagnosed with CACTD at the Gansu Provincial Maternal and Child Health Care Hospital respectively on January 3 and November 19, 2018 were selected as the study subjects. Trio-whole exome sequencing (trio-WES) was carried out, and candidate variants were validated through Sanger sequencing and pathogenicity analysis. RESULTS: Both children were males and had manifested mainly with hypoglycemia. Trio-WES and Sanger sequencing showed that child 1 had harbored compound heterozygous variants of the SLC25A20 gene, namely c.49G>C (p.Gly17Arg) and c.106-2A>G, which were inherited from his father and mother, respectively. Child 2 had harbored homozygous c.199-10T>G variants of the SLC25A20 gene, which were inherited from both of his parents. Among these, the c.106-2A>G and c.49G>C variants were unreported previously. Based on the guidelines from the American College of Medical Genetics and Genomics (ACMG), the c.49G>C (p.Gly17Arg), c.106-2A>G, and c.199-10T>G variants were classified as likely pathogenic (PM2_supporting+PP3+PM3_strong+PP4), pathogenic (PVS1+PM2_supporting+PM5+PP3), and pathogenic (PVS1+PM2_supporting+PP3+PP5), respectively. CONCLUSION: Combined with their clinical phenotype and genetic analysis, both children were diagnosed with CACTD. Above finding has provided a basis for their treatment as well as genetic counseling and prenatal diagnosis for their families.

[Genetic analysis and prenatal diagnosis for a Chinese pedigree affected with co-morbid Ornithine carbamoyl transferase deficiency and MECP2 duplication syndrome].

OBJECTIVE: To explore the genetic basis for a Chinese pedigree affected with co-morbid Ornithine carbamoyl transferase deficiency (OTCD) and MECP2 duplication syndrome. METHODS: A proband who was admitted to the Neonatal Intensive Care Unit of Gansu Provincial Maternal and Child Health Care Hospital on December 19, 2017 was selected as the study subject. High-throughput sequencing and multiplex ligation-dependent probe amplification (MLPA) were carried out for her pedigree, and short tandem repeat-based linkage analysis and chromosome copy number variation sequencing (CNV-seq) were used for the prenatal diagnosis. RESULTS: The proband, a 3-day-old female, was found to harbor heterozygous deletion of exons 7-9 of the OTC gene. Based on the guidelines from the American College of Medical Genetics and Genomics (ACMG), the variant was classified as likely pathogenic (PVS1+PM2_Supporting+PP4). The proband was diagnosed with OTCD , which was in keeping with her acute encephalopathy and metabolic abnormalities (manifesting as hyperammonemia, decreased blood citrulline, and increased urine orotic acid). Prenatal diagnosis was carried out for the subsequent pregnancy. The fetus did not harbor the exons 7-9 deletion of the OTC gene, but was found to carry a duplication in Xq28 region (which encompassed the whole region of MECP2 duplication syndrome) and was positive for the SRY sequence. The same duplication was also found in the proband and her mother. Considering the possible existence of X-chromosome inactivation, the proband was diagnosed with two X-linked recessive disorders including OTCD and MECP2 duplication syndrome, and the fetus was determined as a male affected with the MECP2 duplication syndrome. CONCLUSION: Discoveries of the pathogenic variants underlying the OTCD and MECP2 duplication syndrome have enabled clinical intervention, treatment, genetic counseling and prenatal diagnosis for this pedigree.

Novel biomarkers and interferon signature in secondary progressive multiple sclerosis.

Multiple sclerosis (MS) exhibits poor immune regulation and subnormal interferon (IFN-ß) signaling. Secondary Progressive MS displays waning exacerbations, relentless neurodegeneration, and diminished benefit of therapy. We find dysregulated serum protein balance (Th1/Th2) and excessive gene expression in Relapsing-Remitting MS vs. healthy controls (8700 differentially-expressed genes, DEG) and intermediate levels in SPMS (3900 DEG). Olfactory receptor genes (chemosensing), and WNT/ß-catenin (anti-inflammatory, repair) and metallothionein (anti-oxidant) gene pathways, have less expression in SPMS than RRMS. IFN-ß treatment decreased pro-inflammatory and increased metallothionein gene expression in SPMS. These gene expression biomarkers suggest new targets for immune regulation and brain repair in this neurodegenerative disease.

Sacrificial-Hydroxamate-Enabled Sizable Crystallization of Scandium Carboxylate Metal-Organic Frameworks.

Starting from labile hydroxamic acid ligands that are strong chelators, here, we implemented a sacrificial modulating strategy to prepare a series of scandium carboxylate metal-organic frameworks. Overcoming conventional syntheses that use excessive carboxylate modulators, the present strategy greatly reduces the organics required and produces large single crystals of several Sc-MOFs for X-ray crystallography.

Fabrication and characterization of dihydromyricetin-loaded microcapsules stabilized by glyceryl monostearate and whey protein-xanthan gum.

Dihydromyricetin (DMY) is a lipophilic nutrient with various potential health benefits; however, its poor storage stability and low solubility and bioavailability limit its applications. This study aims to encapsulate DMY in microcapsules by membrane emulsification and freeze-drying methods to overcome these issues. Glyceryl monostearate (GMS, solid lipid) and octyl and decyl glycerate (ODO, liquid lipid) were applied as the inner cores. Whey protein and xanthan gum (XG) were used as wall materials. The prepared microcapsules had an irregular blocky aggregated structure with rough surfaces. All the microcapsules had a DMY loading of 0.85 %-1.1 % and encapsulation efficiency (EE) >85 %. GMS and XG increased the DMY loading and EE. The addition of GMS and an increased XG concentration led to a decrease in the rehydration rate. The in vitro release and digestion studies revealed that GMS and XG controlled the release and digestion of DMY. The chemical stability results indicated that GMS and XG protected DMY against oxidation. An antioxidant capacity study showed that GMS and XG helped DMY in the microcapsules exert antioxidant effects. This research study provides a platform for designing microcapsules with good stability and high bioavailability to deliver lipophilic bioactive compounds.

Defective Nb2 C MXene Cocatalyst on TiO2 Microsphere for Enhanced Photocatalytic CO2 Conversion to Methane.

Sustainable and scalable solar-energy-driven CO2 conversion into fuels requires earth-abundant and stable photocatalysts. In this work, a defective Nb2 C MXene as a cocatalyst and TiO2 microspheres as photo-absorbers, constructed via a coulombic force-driven self-assembly, is synthesized. Such photocatalyst, at an optimized loading of defective Nb2 C MXene (5% def-Nb2 C/TiO2 ), exhibits a CH4 production rate of 7.23 µmol g-1  h-1 , which is 3.8 times higher than that of TiO2 . The Schottky junction at the interface improves charge transfer from TiO2 to defective Nb2 C MXene and the electron-rich feature (nearly free electron states) enables multielectron reaction of CO2 , which apparently leads to high activity and selectivity to CH4 (sel. 99.5%) production. Moreover, DFT calculation demonstrates that the Fermi level (EF ) of defective Nb2 C MXene (-0.3 V vs NHE) is more positive than that of Nb2 C MXene (-1.0 V vs NHE), implying a strong capacity to accept photogenerated electrons and enhance carrier lifetime. This work gives a direction to modify the earth-abundant MXene family as cocatalysts to build high-performance photocatalysts for energy production.

Janus particles with tunable patch symmetry and their assembly into chiral colloidal clusters.

Janus particles, which have an attractive patch on the otherwise repulsive surface, have been commonly employed for anisotropic colloidal assembly. While current methods of particle synthesis allow for control over the patch size, they are generally limited to producing dome-shaped patches with a high symmetry (C∞). Here, we report on the synthesis of Janus particles with patches of various tunable shapes, having reduced symmetries ranging from C2v to C3v and C4v. The Janus particles are synthesized by partial encapsulation of an octahedral metal-organic framework particle (UiO-66) in a polymer matrix. The extent of encapsulation is precisely regulated by a stepwise, asymmetric dewetting process that exposes selected facets of the UiO-66 particle. With depletion interaction, the Janus particles spontaneously assemble into colloidal clusters reflecting the particles' shapes and patch symmetries. We observe the formation of chiral structures, whereby chirality emerges from achiral building blocks. With the ability to encode symmetry and directional bonding information, our strategy could give access to more complex colloidal superstructures through assembly.

FoxO1 knockdown inhibits RANKL-induced osteoclastogenesis by blocking NLRP3 inflammasome activation.

OBJECTIVES: This study aimed to elucidate the connection between osteoclastic forkhead transcription factor O1 (FoxO1) and periodontitis and explore the underlying mechanism by which FoxO1 knockdown regulates osteoclast formation. MATERIALS AND METHODS: A conventional ligature-induced periodontitis model was constructed to reveal the alterations in the proportion of osteoclastic FoxO1 in periodontitis via immunofluorescence staining. Additionally, RNA sequencing (RNA-seq) was performed to explore the underlying mechanisms of FoxO1 knockdown-mediated osteoclastogenesis, followed by western blotting, quantitative polymerase chain reaction, and enzyme-linked immunosorbent assay. RESULTS: FoxO1+ osteoclasts were enriched in the alveolar bone in experimental periodontitis. Moreover, FoxO1 knockdown led to impaired osteoclastogenesis with low expression of osteoclast differentiation-related genes, accompanied by an insufficient osteoclast maturation phenotype. Mechanistically, RNA-seq revealed that the nuclear factor kappa B (NF-κB) and nucleotide-binding oligomerization domain-like receptor family pyrin domain containing 3 (NLRP3) inflammasome signaling pathways were inhibited in FoxO1-knockdown osteoclasts. Consistent with this, MCC950, an effective inhibitor of the NLRP3 inflammasome, substantially attenuated osteoclast formation. CONCLUSIONS: FoxO1 knockdown contributed to the inhibition of osteoclastogenesis by effectively suppressing NF-κB signaling and NLRP3 inflammasome activation. This prospective study reveals the role of FoxO1 in mediating osteoclastogenesis and provides a viable therapeutic target for periodontitis treatment.

[Clinical features and genetic analysis of a child with 3-methylglutenedioic aciduria type VII due to novel variants of CLPB gene].

OBJECTIVE: To explore the clinical features and genetic basis for a child with 3-methylglutaconic aciduria type VII. METHODS: A child who was diagnosed at the Gansu Provincial Maternity and Child Health Care Hospital on August 9, 2019 was selected as the study subject. Clinical data of the child, including urine gas chromatography and mass spectrometry, were collected. The child and her parents were subjected to whole exome sequencing. RESULTS: The child, a female neonate, had presented mainly with intermittent skin cyanosis, convulsions, hypomagnesemia, apnea, neutropenia after birth. Her urine 3-methylpentenedioic acid has increased to 17.53 µmol/L. DNA sequencing revealed that she has harbored compound heterozygous variants of the CLPB gene, namely c.1016delT (p.L339Rfs*5) and c.1087A>G (p.R363G), which were respectively inherited from her mother and father. Both variants were unreported previously. Based on the standards from the American College of Medical Genetics and Genomics (ACMG), the variants were respectively predicted to be pathogenic and likely pathogenic. CONCLUSION: The child was diagnosed with 3-methylglutenedioic aciduria type VII. Discovery of the c.1016delT and c.1087A>G variants has enriched the mutational spectrum of the CLPB gene.

Cell nucleus elastography with the adjoint-based inverse solver.

BACKGROUND AND OBJECTIVES: The mechanics of the nucleus depends on cellular structures and architecture, and impact a number of diseases. Nuclear mechanics is yet rather complex due to heterogeneous distribution of dense heterochromatin and loose euchromatin domains, giving rise to spatially variable stiffness properties. METHODS: In this study, we propose to use the adjoint-based inverse solver to identify for the first time the nonhomogeneous elastic property distribution of the nucleus. Inputs of the inverse solver are deformation fields measured with microscopic imaging in contracting cardiomyocytes. RESULTS: The feasibility of the proposed method is first demonstrated using simulated data. Results indicate accurate identification of the assumed heterochromatin region, with a maximum relative error of less than 5%. We also investigate the influence of unknown Poisson's ratio on the reconstruction and find that variations of the Poisson's ratio in the range [0.3-0.5] result in uncertainties of less than 15% in the identified stiffness. Finally, we apply the inverse solver on actual deformation fields acquired within the nuclei of two cardiomyocytes. The obtained results are in good agreement with the density maps obtained from microscopy images. CONCLUSIONS: Overall, the proposed approach shows great potential for nuclear elastography, with promising value for emerging fields of mechanobiology and mechanogenetics.

3'-O-ß-Glucosyl-4',5'-didehydro-5'-deoxyadenosine Is a Natural Product of the Nucleocidin Producers Streptomyces virens and Streptomyces calvus.

3'-O-ß-Glucosyl-4',5'-didehydro-5'-deoxyadenosine 13 is identified as a natural product of Streptomyces calvus and Streptomyces virens. It is also generated in vitro by direct ß-glucosylation of 4',5'-didehydro-5'-deoxyadenosine 12 with the enzyme NucGT. The intact incorporation of oxygen-18 and deuterium isotopes from (±)[1-18O,1-2H2]-glycerol 14 into C-5' of nucleocidin 1 and its related metabolites precludes 3'-O-ß-glucosyl-4',5'-didehydro-5'-deoxyadenosine 13 as a biosynthetic precursor to nucleocidin 1.

Corrigendum: Adaptive and innate immune responses in multiple sclerosis with anti-CD20 therapy: gene expression and protein profiles.

[This corrects the article DOI: 10.3389/fneur.2023.1158487.].