NIFK, a Potential Prognostic and Immunological Biomarker in Pan-- Cancer Analysis, Significantly Regulates Proliferation and Metastasis of Colorectal Cancer.

BACKGROUND: As a binding protein of Ki67, NIFK plays an important role in the mitosis of cells and is closely related to the progression of specific types of tumors. However, there is still a lack of systematic analysis of NIFK in pan-cancer and insufficient research to explore its role in human tumors. METHODS: We systematically evaluated the pan-cancer expression and mutation of NIFK in human cancers using data from The Cancer Genome Atlas (TCGA) through large-scale bioinformatics analysis. In addition, we explored the pan-cancer immunological characteristics of NIFK, especially in colorectal adenocarcinoma (COAD). Furthermore, we used single-cell sequencing to analyze the expression of NIFK in different cells of COAD tissues and performed GO, KEGG, and gene set enrichment analysis of NIFK in COAD. Lastly, we evaluated the effects of NIFK knockdown on the colorectal cancer cell lines in in vitro experiment. RESULTS: We found that NIFK was overexpressed in almost all types of tumors and showed significant prognostic efficacy. Additionally, correlations between NIFK and specific immune features, such as immune cell infiltration, immune checkpoint genes, TMB, and MSI, suggest that NIFK may be used to guide immunotherapy. Subsequently, it was found that the expression of NIFK was significantly upregulated in tumor cells through single-cell sequencing analysis, and the NIFK gene was closely associated with tumor progression and immune therapy response. Finally, we further elucidated the role of NIFK in colorectal cancer and found that downregulation of NIFK expression could inhibit the proliferation, migration, and invasion ability of colorectal cancer cells. CONCLUSION: The results of this study demonstrated that NIFK, as a member of the pan-cancer genes, will serve as a biomarker and a potential therapeutic target for a range of cancer types, providing new insight into precision medicine.

Cysteine-Specific Multifaceted Bioconjugation of Peptides and Proteins Using 5-Substituted 1,2,3-Triazines.

Peptide and protein postmodification have gained significant attention due to their extensive impact on biomolecule engineering and drug discovery, of which cysteine-specific modification strategies are prominent due to their inherent nucleophilicity and low abundance. Herein, the study introduces a novel approach utilizing multifunctional 5-substituted 1,2,3-triazine derivatives to achieve multifaceted bioconjugation targeting cysteine-containing peptides and proteins. On the one hand, this represents an inaugural instance of employing 1,2,3-triazine in biomolecular-specific modification within a physiological solution. On the other hand, as a powerful combination of precision modification and biorthogonality, this strategy allows for the one-pot dual-orthogonal functionalization of biomolecules utilizing the aldehyde group generated simultaneously. 1,2,3-Triazine derivatives with diverse functional groups allow conjugation to peptides or proteins, while bi-triazines enable peptide cyclization and dimerization. The examination of the stability of bi-triazines revealed their potential for reversible peptide modification. This work establishes a comprehensive platform for identifying cysteine-selective modifications, providing new avenues for peptide-based drug development, protein bioconjugation, and chemical biology research.

Integrative analysis of cancer-associated fibroblast signature in gastric cancer.

Background: CAFs regulate the signaling of GC cells by promoting their migration, invasion, and proliferation and the function of immune cells as well as their location and migration in the TME by remodeling the extracellular matrix (ECM). This study explored the understanding of the heterogeneity of CAFs in TME and laid the groundwork for GC biomarker and precision treatment development. Methods: The scRNA-seq and bulk RNA-seq datasets were obtained from GEO and TCGA. The prognostic significance of various CAFs subtypes was investigated using ssGSEA combined with Kaplan-Meier analysis. POSTN expression in GC tissues and CAFs was detected using immunohistochemistry, immunofluorescence, and Western blotting. Differential expression analysis identified the differentially expressed genes (DEGs) between normal and tumor samples in TCGA-STAD. Pearson correlation analysis identified DEGs associated with adverse prognosis CAF subtype, and univariate Cox regression analysis determined prognostic genes associated with CAFs. LASSO regression analysis and Multivariate Cox regression were used to build a prognosis model for CAFs. Results: We identified five CAFs subtypes in GC, with the CAF_0 subtype associated with poor prognosis. The abundance of CAF_0 correlated with T stage, clinical stage, histological type, and immune cell infiltration levels. Periostin (POSTN) exhibited increased expression in both GC tissues and CAFs and was linked to poor prognosis in GC patients. Through LASSO and multivariate Cox regression analysis, three genes (CXCR4, MATN3, and KIF24) were selected to create the CAFs-score. We developed a nomogram to facilitate the clinical application of the CAFs-score. Notably, the CAFs signature showed significant correlations with immune cells, stromal components, and immunological scores, suggesting its pivotal role in the tumor microenvironment (TME). Furthermore, CAFs-score demonstrated prognostic value in assessing immunotherapy outcomes, highlighting its potential as a valuable biomarker to guide therapeutic decisions. Conclusion: CAF_0 subtype in TME is the cause of poor prognosis in GC patients. Furthermore, CAFs-score constructed from the CAF_0 subtype can be used to determine the clinical prognosis, immune infiltration, clinicopathological characteristics, and assessment of personalized treatment of GC patients.

Whole exome sequencing of well-differentiated liposarcoma and dedifferentiated liposarcoma in older woman: a case report.

Background: Common kinds of soft tissue sarcomas (STS) include well-differentiated liposarcoma (WDLPS) and dedifferentiated liposarcoma (DDLPS). In this case, we present a comprehensive clinical profile of a patient who underwent multiple recurrences during the progression from WDLPS to DDLPS. Case presentation: A 62-year-old Asian female underwent retroperitoneal resection of a large tumor 11 years ago, the initial pathology revealed a fibrolipoma-like lesion. Over the next six years, the patient underwent three resections for recurrence of abdominal tumors. Postoperative histology shows mature adipose tissue with scattered "adipoblast"-like cells with moderate-to-severe heterogeneous spindle cells, pleomorphic cells, or tumor giant cells. Immunohistochemistry (IHC) demonstrated positive staining for MDM2 and CDK4, confirming that the abdominal tumor was WDLPS and gradually progressing to DDLPS. Post-operative targeted sequencing and IHC confirmed the POC1B::ROS1 fusion gene in DDLPS. Whole-exome sequencing (WES) revealed that WDLPS and DDLPS shared similar somatic mutations and copy number variations (CNVs), whereas DDLPS had more mutated genes and a higher and more concentrated amplification of the chromosome 12q region. Furthermore, somatic mutations in DDLPS were significantly reduced after treatment with CDK4 inhibitors, while CNVs remained elevated. Conclusion: Due to the high likelihood of recurrence of liposarcoma, various effective treatments should be taken into consideration even if surgery is the primary treatment for recurrent liposarcoma. To effectively control the course of the disease following surgery, combination targeted therapy may be a viable alternative to chemotherapy and radiotherapy in the treatment of liposarcoma.

The DNA damage repair-related lncRNAs signature predicts the prognosis and immunotherapy response in gastric cancer.

Background: Gastric cancer (GC) is one of the most prevalent cancers, and it has unsatisfactory overall treatment outcomes. DNA damage repair (DDR) is a complicated process for signal transduction that causes cancer. lncRNAs can influence the formation and incidence of cancers by influencing DDR-related mRNAs/miRNAs. A DDR-related lncRNA prognostic model is urgently needed to improve treatment strategies. Methods: The data of GC samples were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. A total of 588 mRNAs involved in DDR were selected from MSigDB, 62 differentially expressed mRNAs from TCGA-STAD were obtained, and 137 lncRNAs were correlated with these mRNAs. Univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression analyses were used to develop a DDR-related lncRNA prognostic model. Based on the risk model, the differentially expressed gene signature A/B in the low-risk and high-risk groups of TCGA-STAD was identified for further validation. Results: The prognosis model of 5 genes (AC145285.6, MAGI2-AS3, AL590705.3, AC007405.3, and LINC00106) was constructed and classified into two risk groups. We found that GC patients with a low-risk score had a better OS than those with a high-risk score. We found that the high-risk group tended to have higher TME scores. We also found that patients in the high-risk group had a higher proportion of resting CD4 T cells, monocytes, M2 macrophages, resting dendritic cells, and resting mast cells, whereas the low-risk subgroup had a greater abundance of activated CD4 T cells, follicular helper T cells, M0 macrophages, and M1 macrophages. We observed significant differences in the T-cell exclusion score, T-cell dysfunction, MSI, and TMB between the two risk groups. In addition, we found that patients treated with immunotherapy in the low-RS score group had a longer survival and a better prognosis than those in the high-RS score group. Conclusion: The prognostic model has a significant role in the TME, clinicopathological characteristics, prognosis, MSI, and drug sensitivity. We also discovered that patients treated with immunotherapy in the low-RS score group had a better prognosis. This work provides a foundation for improving the prognosis and response to immunotherapy among patients with GC.

Rapid screening and identification of metabolites of murpanicin in rats by UHPLC/Q-TOF-MS/MS combined with diagnostic fragment ions (DFIs) and multiple mass defect filter.

Murpanicin is a main coumarin with obvious anti-inflammatory effect isolated from Murraya species. The primary aim of this research is to identify and characterize the possible metabolites of murpanicin in rats. The metabolites generated in the plasma, urine, bile, and feces of rats were identified and characterized employing ultra-high performance liquid chromatography coupled with quadrupole-time of flight tandem mass spectrometry (UHPLC/Q-TOF-MS/MS) based on diagnostic fragment ions (DFIs) and multiple mass defect filter (MMDF). A total of 67 metabolites were identified, among which 55 are phase I and 12 are phase II reacted products. The plausible structures of the metabolites and the probable metabolic pathways were deduced based on the diagnostic fragment ions, mass ppm error, and mass fragmentation pattern, as well as the MetabolitePilot™ software. The majority of phase I metabolites were generated by demethylation, deethylation, dehydrogenation, hydroxylation, and reduction, while phase II metabolites were mainly generated by glucuronidation and sulfation. Moreover, some rare phase II metabolic pathways, such as N-acetylcysteine conjugation, cysteine conjugation, and S-cysteine conjugation were also observed. In conclusion, our study first expounded the metabolites of murpanicin in rats and provided reference for further clarification of the in vivo therapeutic material basis of murpanicin and other 8-prenylcoumarin derivatives. Moreover, UHPLC/Q-TOF-MS combined with MMDF and DFIs has been proved to be an effective method for rapid identification of the homolog-gathered natural products and their metabolites.

Optimization of 4,6-Disubstituted Pyrido[3,2-d]pyrimidines as Dual MNK/PIM Inhibitors to Inhibit Leukemia Cell Growth.

Mitogen-activated protein kinase-interacting kinases (MNKs) and provirus integration in maloney murine leukemia virus kinases (PIMs) are downstream enzymes of cell proliferation signaling pathways associated with the resistance of tyrosine kinase inhibitors. MNKs and PIMs have complementary effects to regulate cap-dependent translation of oncoproteins. Dual inhibitors of MNKs and PIMs have not been developed. We developed a novel 4,6-disubstituted pyrido[3,2-d]pyrimidine compound 21o with selective inhibition of MNKs and PIMs. The IC50's of 21o to inhibit MNK1 and MNK2 are 1 and 7 nM and those to inhibit PIM1, PIM2, and PIM3 are 43, 232, and 774 nM, respectively. 21o inhibits the growth of myeloid leukemia K562 and MOLM-13 cells with GI50's of 2.1 and 1.2 µM, respectively. 21o decreases the levels of p-eIF4E and p-4EBP1, the downstream products of MNKs and PIMs, as well as cap-dependent proteins c-myc, cyclin D1, and Mcl-1. 21o inhibits the growth of MOLM-13 cell xenografts without causing evident toxicity. 21o represents an innovative dual MNK/PIM inhibitor with a good pharmacokinetic profile.

Carbazole alkaloids with potential cytotoxic activities targeted on PCK2 protein from Murraya microphylla.

From the 95% aqueous ethanol extract of Murraya microphylla, five pairs of new carbazole alkaloid enantiomers, (+/-)-microphylines N-R (1a/1b-5a/5b), were isolated, together with 20 known carbazole alkaloids. The structures of the new compounds were determined by the HRMS and NMR spectroscopic data, along with the calculated electronic circular dichroism (ECD) and Mo2(AcO)4-induced CD data. The known compound (+)-mahanine (21) showed significant cytotoxicities against Du145, HepG2, HeLa, and HCT-116 cell lines, and its possible mechanism was deduced to target on phosphoenolpyruvate carboxykinase 2 (PCK2) protein via surface plasmon resonance (SPR) and molecular docking.

Four circulating exosomal miRNAs as novel potential biomarkers for the early diagnosis of human colorectal cancer.

Colorectal cancer (CRC) is the second leading cause of cancer-related deaths worldwide. Our study aimed to identify novel circulating miRNAs as early diagnostic biomarkers of CRC. The Gene Expression Omnibus (GEO) datasets were analyzed by using the online tool GEO2R. Isolated exosomes were verified by using the transmission electron microscope (TEM), Nanosight, and western blot. qRT-PCR was implemented to examine miRNA expression. The diagnostic value of circulating exosomal miRNAs was identified by using the receiver operating characteristic curve (ROC). In this study, we found that serum exosomal miRNAs are more suitable for diagnosing CRC when compared to serum miRNAs. Furthermore, we identified four exosomal miRNAs (miR-126, miR-1290, miR-23a, and miR-940) in the serum of CRC patients as novel potential biomarkers for the early diagnosis of CRC because they showed high diagnostic values to differentiate CRC patients at TNM stage I from healthy controls (HCs). In addition, our data suggested that CRC cells may secrete miRNAs into the extracellular environment through exosomes regardless of intracellular miRNA expression. In conclusion, we identified serum exosomal miR-126, miR-1290, miR-23a, and miR-940 as novel potential biomarkers for the early diagnosis of CRC.

METTL14 Inhibits Hepatocellular Carcinoma Metastasis Through Regulating EGFR/PI3K/AKT Signaling Pathway in an m6A-Dependent Manner.

PURPOSE: Hepatocellular carcinoma (HCC) ranks as the fourth leading cause of cancer-related deaths worldwide. N6-methyladenosine (m6A) RNA methylation is the most common modification of messenger RNAs (mRNAs). The prognosis of HCC patients with metastasis remains poor. Our study aimed to elucidate the regulatory role of m6A on HCC metastasis. PATIENTS AND METHODS: All HCC patients were enrolled from The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University. The expression levels of gene were tested by quantitative polymerase chain reaction (qPCR), Western blot, or immunohistochemistry (IHC) analysis. Wound healing assay, Transwell invasion assay, and lung metastasis model were implemented to investigate the migration and invasion ability of HCC cells. Candidate targets were selected by a comprehensive analysis of RNA-sequencing and m6A-sequencing of HepG2 cells. RESULTS: In this study, we demonstrated that METTL14 was significantly downregulated in HCC and significantly associated with the prognosis of HCC patients. METTL14 knockdown promoted the migration, invasion, and epithelial-mesenchymal transition (EMT) of HCC cells in vitro and in vivo. In addition, overlapping RNA-sequencing and m6A-sequencing data, we identified EGFR as a direct target of METTL14 in HCC. Mechanistically, METTL14 was found to inhibit HCC cell migration, invasion, and EMT through modulating EGFR/PI3K/AKT signaling pathway in an m6A-dependent manner. CONCLUSION: Targeting METTL14/EGFR/PI3K/AKT signaling pathway may facilitate the development of a new treatment strategy against the metastasis of HCC.

Identification of Tumorigenic and Prognostic Biomarkers in Colorectal Cancer Based on microRNA Expression Profiles.

OBJECTIVE: Although noncoding RNAs, especially the microRNAs, have been found to play key roles in CRC development in intestinal tissue, the specific mechanism of these microRNAs has not been fully understood. METHODS: GEO and TCGA database were used to explore the microRNA expression profiles of normal mucosa, adenoma, and carcinoma. And the differential expression genes were selected. Computationally, we built the SVM model and multivariable Cox regression model to evaluate the performance of tumorigenic microRNAs in discriminating the adenomas from normal tissues and risk prediction. RESULTS: In this study, we identified 20 miRNA biomarkers dysregulated in the colon adenomas. The functional enrichment analysis showed that MAPK activity and MAPK cascade were highly enriched by these tumorigenic microRNAs. We also investigated the target genes of the tumorigenic microRNAs. Eleven genes, including PIGF, TPI1, KLF4, RARS, PCBP2, EIF5A, HK2, RAVER2, HMGN1, MAPK6, and NDUFA2, were identified to be frequently targeted by the tumorigenic microRNAs. The high AUC value and distinct overall survival rates between the two risk groups suggested that these tumorigenic microRNAs had the potential of diagnostic and prognostic value in CRC. CONCLUSIONS: The present study revealed possible mechanisms and pathways that may contribute to tumorigenesis of CRC, which could not only be used as CRC early detection biomarkers, but also be useful for tumorigenesis mechanism studies.

Exosomal miR-1246 in serum as a potential biomarker for early diagnosis of gastric cancer.

BACKGROUND: Gastric cancer (GC) patients are usually diagnosed in advanced stages which results in high mortality. This study aimed to identify novel circulating miRNAs as biomarkers for the early detection of GC. METHODS: Candidate miRNA was identified after integrated analysis of two Gene Expression Omnibus (GEO) datasets and clinical serum samples. Exosomes extracted were verified using transmission electron microscopy (TEM) and western blot. The expressions of miRNAs were tested through qRT-PCR. Receiver operating characteristic curve (ROC) analysis was used to explore the diagnostic utility of miRNAs. RNA pull-down assay was used to find RNA binding proteins (RBPs) which transport candidate miRNA into exosomes. Bioinformatics analysis of candidate miRNA was conducted using DAVID and Cytoscape. RESULTS: After integrated analysis of two GEO datasets, six circulating miRNAs were found to be consistently upregulated in GC patients. Then, qRT-PCR demonstrated that serum miR-1246 was the one with the largest fold change. Studies in vitro revealed that elevated serum miR-1246 was tumor-derived by being packaged into exosomes with the help of ELAVL1. Thereafter, we discovered that exosomal miR-1246 expressions in serum could differentiate GC patients with TNM stage I from healthy controls (HCs) and patients with benign diseases (BDs) with area under the curve (AUC) of 0.843 and 0.811, respectively. Bioinformatics analysis revealed miR-1246, as a tumor suppressor in GC, could regulate several signaling pathways. CONCLUSION: Circulating exosomal miR-1246 was a potential biomarker for the early diagnosis of GC.

Glucoconjugated Monoterpene Indole Alkaloids from Uncaria rhynchophylla.

Twenty-six glucoconjugated monoterpene indole alkaloids, including 12 new compounds, rhynchophyllosides A-L (1-12), and 14 known ones, 13-26, were obtained from the hook-bearing stems of Uncaria rhynchophylla (Miq.) Miq. ex Havil. Their structures were unambiguously elucidated by analyses of UV, MS, NMR, ECD, and single-crystal X-ray diffraction data. The ESI-MSn behavior of the new glucoalkaloids was also elucidated. Although comprising the same glucosyl moiety, the aglycone skeletons and glucosidic numbers and linkage varied greatly, implying the diversity in biosynthetic pathways. This is the first report of such structurally diverse glucoconjugated monoterpene indole alkaloids from U. rhynchophylla. Compound 1 represents a new subtype of oxindole alkaloid with a seven-membered D-ring, 10 is a rare monoterpene indole alkaloid with the glucosyl moiety located at C-9, 4 and 5 are the first two oxindole alkaloid diglycosides, and 11 and 12 represent the first two examples of alkaloids with a quinolone nucleus from the genus Uncaria. Compound 10 exhibited moderate acetylcholinesterase (AChE) inhibitory activity with an IC50 value of 10.5 µM. Molecular docking was performed to explore the binding mode of inhibitor 10 at the active site of AChE.

IL­10 secreted by cancer­associated macrophages regulates proliferation and invasion in gastric cancer cells via c­Met/STAT3 signaling.

Gastric cancer is one of the most common types of human cancer, and it is additionally one of the leading causes of cancer­associated mortality worldwide. Previous studies have suggested that interleukin (IL)­10 may contribute to the pathogenesis of gastric cancer. However, the underlying mechanisms remain unclear. In the present study, it was observed that the expression of IL­10 was significantly upregulated in gastric tumor tissues and serum samples of patients with gastric cancer. Furthermore, IL­10 was increased in the cell culture supernatant of cancer­associated macrophages (CAMs). Treatment with cell culture supernatant from CAMs induced a significant increase in proliferation and migration, while it suppressed apoptosis, in MGC­803 and BGC­823 gastric cancer cells. Notably, application of an inhibitory IL­10 antibody partially blocked the cell culture supernatant of CAM­induced oncogenic effects. RNA­sequencing analysis was then performed to identify the differentially expressed genes in MGC­803 cells treated with IL­10. Based on the sequencing results and in vitro analysis, it was demonstrated that IL­10­induced carcinogenic behaviors in MGC­803 cells were potentially mediated by activation of the c­Met/STAT3 signaling pathway. In conclusion, the present results demonstrated that IL­10 secreted by CAMs may be involved in the pathogenesis of gastric cancer, suggesting that IL­10 may serve as a potential therapeutic target for the treatment of gastric cancer.

Fecal microbiota transplantation treatment for refractory ulcerative colitis with allergy to 5-aminosalicylic acid: A case report.

INTRODUCTION: Fecal microbiota transplantation (FMT) is currently being explored as a potential therapy for ulcerative colitis (UC). Here, we report the first case of a UC patient with allergy to 5-aminosalicylic acid (5-ASA) who underwent FMT and achieved clinical remission. CASE PRESENTATION: This patient had a 9-year history of UC and was allergic to 5-ASA. He suffered from gradually aggravated abdominal pain and frequent bloody diarrhea. There was a continuous distribution of superficial erosion and ulceration by colonoscopy. After steroid therapy failed, he underwent FMT. The donated fecal microbes were purified in laboratory and then transplanted into the terminal ileum and right colon of the patient by colonoscopy. During the 9 months' follow-up, FMT has proved its efficacy in inducing and maintaining clinical and endoscopic remission of the patient. CONCLUSION: The choice of treatment for refractory UC patients who are allergic to 5-ASA is relatively limited. In our case, we highlight the specific role of FMT for refractory UC with absence of 5-ASA through intestinal microbiota reconstruction.

Ubiquilin-mediated Small Molecule Inhibition of Mammalian Target of Rapamycin Complex 1 (mTORC1) Signaling.

Mammalian target of rapamycin complex 1 (mTORC1) is a master regulator of cellular metabolism, growth, and proliferation. mTORC1 has been implicated in many diseases such as cancer, diabetes, and neurodegeneration, and is a target to prolong lifespan. Here we report a small molecule inhibitor (Cbz-B3A) of mTORC1 signaling. Cbz-B3A inhibits the phosphorylation of eIF4E-binding protein 1 (4EBP1) and blocks 68% of translation. In contrast, rapamycin preferentially inhibits the phosphorylation of p70(S6k) and blocks 35% of translation. Cbz-B3A does not appear to bind directly to mTORC1, but instead binds to ubiquilins 1, 2, and 4. Knockdown of ubiquilin 2, but not ubiquilins 1 and 4, decreases the phosphorylation of 4EBP1, suggesting that ubiquilin 2 activates mTORC1. The knockdown of ubiquilins 2 and 4 decreases the effect of Cbz-B3A on 4EBP1 phosphorylation. Cbz-B3A slows cellular growth of some human leukemia cell lines, but is not cytotoxic. Thus Cbz-B3A exemplifies a novel strategy to inhibit mTORC1 signaling that might be exploited for treating many human diseases. We propose that Cbz-B3A reveals a previously unappreciated regulatory pathway coordinating cytosolic protein quality control and mTORC1 signaling.