Saccharomyces cerevisiae-like 1 (SEC14L1) is a prognostic factor in breast cancer associated with lymphovascular invasion

Copper-mediated SEC14L3 promotes cuproptosis to inhibit hepatocellular carcinoma growth via ERK/YY1/FDX1 axis

Cuproptosis, a copper-triggered cell death pathway, holds therapeutic potential for cancers, but its regulatory mechanisms in hepatocellular carcinoma (HCC) remain undefined. Despite SEC14L3's known roles in cellular signaling, its involvement in HCC progression and cuproptosis regulation is unclear. Here, we reveal that SEC14L3 expression is downregulated in HCC cells and tissues and correlates with advanced stages and poor prognosis. Copper-induced cuproptosis inhibits HCC cell viability, and SEC14L3 positively modulates cuproptosis in HCC cells by promoting DLAT lipoylation and its oligomerization. Mechanistically, SEC14L3-mediated cuproptosis suppressed HCC growth via the ERK/YY1/FDX1 axis both in vitro and in vivo. Additionally, copper enhanced the SEC14L3 expression, which in turn regulated ERK/YY1/FDX1 axis. Our findings show that copper-mediated SEC14L3 promotes cuproptosis via ERK/YY1/FDX1 axis, thereby inhibiting HCC growth. These insights provide a mechanistic foundation for targeting cuproptosis, advancing the development of SEC14L3-driven therapeutic strategies for HCC.

Using parenclitic networks on phaeochromocytoma and paraganglioma tumours provides novel insights on global DNA methylation

Despite the prevalence of sequencing data in biomedical research, the methylome remains underrepresented. Given the importance of DNA methylation in gene regulation and disease, it is crucial to address the need for reliable differential methylation methods. This work presents a novel, transferable approach for extracting information from DNA methylation data. Our agnostic, graph-based pipeline overcomes the limitations of commonly used differential methylation techniques and addresses the "small n, big k" problem. Pheochromocytoma and Paraganglioma (PPGL) tumours with known genetic aetiologies experience extreme hypermethylation genome wide. To highlight the effectiveness of our method in candidate discovery, we present the first phenotypic classifier of PPGLs based on DNA methylation achieving 0.7 ROC-AUC. Each sample is represented by an optimised parenclitic network, a graph representing the deviation of the sample's DNA methylation from the expected non-aggressive patterns. By extracting meaningful topological features, the dimensionality and, hence, the risk of overfitting is reduced, and the samples can be classified effectively. By using an explainable classification method, in this case logistic regression, the key CG loci influencing the decision can be identified. Our work provides insights into the molecular signature of aggressive PPGLs and we propose candidates for further research. Our optimised parenclitic network implementation improves the potential utility of DNA methylation data and offers an effective and complete pipeline for studying such datasets.

Identification of feature genes and molecular mechanisms involved in cell communication in uveal melanoma through analysis of single‑cell sequencing data

Uveal melanoma (UM) is a highly metastatic cancer with resistance to immunotherapy. The present study aimed to identify novel feature genes and molecular mechanisms in UM through analysis of single-cell sequencing data. For this purpose, data were downloaded from The Cancer Genome Atlas and National Center for Biotechnology Information Gene Expression Omnibus public databases. The statistical analysis function of the CellPhoneDB software package was used to analyze the ligand-receptor relationships of the feature genes. The Metascape database was used to perform the functional annotation of notable gene sets. The randomForestSRC package and random survival forest algorithm were applied to screen feature genes. The CIBERSORT algorithm was used to analyze the RNA-sequencing data and infer the relative proportions of the 22 immune-infiltrating cell types. In vitro, small interfering RNAs were used to knockdown the expression of target genes in C918 cells. The migration capability and viability of these cells were then assessed by gap closure and Cell Counting Kit-8 assays. In total, 13 single-cell sample subtypes were clustered by t-distributed Stochastic Neighbor Embedding and annotated by the R package, SingleR, into 7 cell categories: Tissue stem cells, epithelial cells, fibroblasts, macrophages, natural killer cells, neurons and endothelial cells. The interactions in NK cells|Endothelial cells, Neurons|Endothelial cells, CD74_APP, and SPP1_PTGER4 were more significant than those in the other subsets. T-Box transcription factor 2, tropomyosin 4, plexin D1 (PLXND1), G protein subunit α I2 (GNAI2) and SEC14-like lipid binding 1 were identified as the feature genes in UM. These marker genes were found to be significantly enriched in pathways such as vasculature development, focal adhesion and cell adhesion molecule binding. Significant correlations were observed between key genes and immune cells as well as immune factors. Relationships were also observed between the expression levels of the key genes and multiple disease-related genes. Knockdown of PLXND1 and GNAI2 expression led to significantly lower viability and gap closure rates of C918 cells. Therefore, the results of the present study uncovered cell communication between endothelial cells and other cell types, identified innovative key genes and provided potential targets of gene therapy in UM.

Diffuse CNS cortical vein malformations with chromosome 17q microduplication: Possible link to SEC14L1

Partial trisomy of the long arm of chromosome 17 (17q) is a rare but clinically recognized syndrome that involves facial dysmorphisms, skeletal abnormalities, and global developmental delay, as well as various reports of cardiovascular, renal, and central nervous system abnormalities. This report presents a novel neuroradiologic finding of diffuse enlarged, tortuous cortical veins with physiological antegrade flow in a child with a microduplication of the distal end of 17q. To our knowledge, this finding has not been described previously. Although the exact cause for the cortical vascular anomaly is currently unknown, this duplicated region contains genes of interest for future studies that focus on normal and abnormal angiogenesis.

Identification and Expression Analysis of Phosphatidylinositol Transfer Proteins Genes in Rice

The family of phosphatidylinositol transfer proteins (PITPs) is able to bind specific lipids to carry out various biological functions throughout different stages of plant life. But the function of PITPs in rice plant is unclear. In this study, 30 PITPs were identified from rice genome, which showed differences in physicochemical properties, gene structure, conservation domains, and subcellular localization. The promoter region of the OsPITPs genes included at least one type of hormone response element, such as methyl jasmonate (Me JA) and salicylic acid (SA). Furthermore, the expression level of OsML-1, OsSEC14-3, OsSEC14-4, OsSEC14-15, and OsSEC14-19 genes were significantly affected by infection of rice blast fungus Magnaporthe oryzae. Based on these findings, it is possible that OsPITPs may be involved in rice innate immunity in response to M. oryzae infection through the Me JA and SA pathway.

Evaluation of Saccharomyces cerevisiae -like 1 (SEC14L1) in Gynecologic Malignancies Shows Overexpression in Endometrial Serous Carcinoma

Saccharomyces cerevisiae -like 1 ( SEC14L1 ) is a member of the SEC14 family and is involved in liposoluble vitamin transfer, and in a large cohort of breast cancer cases, was one of the genes most significantly associated with lymphovascular invasion (LVI), and had a significant relationship with human epidermal growth factor receptor 2 status, survival, and histologic grade. In this study, 111 separate gynecologic tumors were studied for SEC14L1 protein expression, including: uterine adenosarcoma, ovarian clear cell carcinoma, endometrial stromal sarcoma, endometrioid carcinoma of the uterus, high-grade serous carcinoma, ovarian endometrioid carcinoma, uterine leiomyosarcoma, low-grade serous carcinoma, uterine carcinosarcoma, and uterine serous carcinoma (USC). Overall, LVI was noted in 31/111 (28%) cases, highest in uterine carcinosarcoma (5/11; 45%), high-grade serous carcinoma (9/21; 43%), and ovarian clear cell carcinoma (4/10; 40%). SEC14L1 was positive in 25/111 (23%) cases; the highest percentage and only statistically significant finding by tumor type was USC at 9/12 (75%) cases positive. No relation between LVI or survival and SEC14L1 expression was noted. The relation between USC, a tumor known to show human epidermal growth factor receptor 2 overexpression and SEC14L1 is a novel finding, the significance of which warrants further study.

Commensal microbiota modulates phenotypic characteristics and gene expression in piglet Peyer's patches

The gastrointestinal tract contains a complex microbial community. Peyer's patches (PPs) play an important role in inducing mucosal immune responses in the gastrointestinal tract. However, little is known about the effect of commensal microbiota on the host's PPs. Here, we analyzed the phenotypic-to-transcriptome changes in the intestine PPs of specific pathogen-free (SPF) and germ-free (GF) piglets (fed in an environment with and without commensal microbiota, respectively) to elucidate the role of commensal microbiota in host intestine mucosal immunity. Analyses of anatomical and histological characteristics showed that commensal microbiota deficiency led to PP hypoplasia, especially regarding B and T cells. A total of 12,444 mRNAs were expressed in 12 libraries; 2,156 and 425 differentially expressed (DE) mRNAs were detected in the jejunal PP (JPP) and ileal PP (IPP), respectively (SPF vs. GF). The shared DE mRNAs of the JPP and IPP were mainly involved in basic physiological and metabolic processes, while the specific DE mRNAs were enriched in regulating immune cells in the JPP and microbial responses and cellular immunity in the IPP. Commensal microbiota significantly modulated the expression of genes related to B-cell functions, including activation, proliferation, differentiation, apoptosis, receptor signaling, germinal center formation, and IgA isotype class switching, particularly in the JPP. TLR4 pathway-related genes were induced in response to microbial colonization and in LPS/SCFA-treated B cells. We also detected 69 and 21 DE lncRNAs in the JPP and IPP, respectively, and four one-to-one lncRNA-mRNA pairs were identified. These findings might represent key regulatory axes for host intestine mucosal immunity development during microbial colonization. Overall, the findings of this study revealed that commensal microbiota modulated phenotypic characteristics and gene expression in the piglet intestine PPs and underscored the importance of early microbial colonization for host mucosal immunity development.

Radiomics in Gastric Cancer: First Clinical Investigation to Predict Lymph Vascular Invasion and Survival Outcome Using 18F-FDG PET/CT Images

Background

Lymph vascular invasion (LVI) is an unfavorable prognostic indicator in gastric cancer (GC). However, there are no reliable clinical techniques for preoperative predictions of LVI. The aim of this study was to develop and validate PET/CT-based radiomics signatures for predicting LVI of GC preoperatively. Radiomics nomograms were also established to predict patient survival outcomes.

Methods

This retrospective study registered 148 GC patients with histopathological confirmation for LVI status, who underwent pre-operative PET/CT scans (Discovery VCT 64 PET/CT system) from December 2014 to June 2019. Clinic-pathological factors (age, gender, and tumor grade, etc.) and metabolic PET data (maximum and mean standardized uptake value, total lesion glycolysis and metabolic tumor volume) were analyzed to identify independent LVI predictors. The dataset was randomly assigned to either the training set or test set in a 7:3 ratios. Three-dimensional (3D) radiomics features were extracted from each PET- and CT-volume of interests (VOI) singularly, and then a radiomics signature (RS) associated with LVI status is built by feature selection. Four models with different modalities (PET-RS: only PET radiomics features; CT-RS: only CT radiomics features; PET/CT-RS: both PET and CT radiomics features; PET/CT-RS plus clinical data) were developed to predict LVI. Patients were postoperatively followed up with PET/CT every 6-12 months for the first two years and then annually up to five years after surgery. The PET/CT radiomics score (Rad-scores) was calculated to assess survival outcome, and corresponding nomograms with radiomics (NWR) or without radiomics (NWOR) were established.

Results

Tumor grade and maximum standardized uptake value (SUVmax) were the independent LVI predictor. 1037 CT and PET 3D radiomics features were extracted separately and reduced to 4 and 5 features to build CT-RS and PET-RS, respectively. PET/CT-RS and PET/CT-RS plus clinical data (tumor grade and SUVmax) were also developed. The ROC analysis demonstrated clinical usefulness of PET/CT-RS plus clinical data (AUC values for training and validation, respectively 0.936 and 0.914) and PET/CT-RS (AUC values for training and validation, respectively 0.881 and 0.854), which both are superior to CT-RS (0.838 and 0.824) and PET-RS (0.821 and 0.812). SUVmax and LVI were independent prognostic indicators of both OS and PFS. Decision curve analysis (DCA) demonstrated NWR outperformed NWOR and was established to assess survival outcomes. For estimation of OS and PFS, the C-indexes of the NWR were 0. 88 and 0.88 in the training set, respectively, while the C-indexes of the NWOR were 0. 82 and 0.85 in the training set, respectively.

Conclusions

The PET/CT-based radiomics analysis might serve as a non-invasive approach to predict LVI status in GC patients and provide effective predictors of patient survival outcomes.

A gold revision of the Golgi Dynamics (GOLD) domain structure and associated cell functionalities

The classical secretory pathway is the key membrane-based delivery system in eukaryotic cells. Several families of proteins involved in the secretory pathway, with functionalities going from cargo sorting receptors to the maintenance and dynamics of secretory organelles, share soluble globular domains predicted to mediate protein-protein interactions. One of them is "Golgi Dynamics" (GOLD) domain, named after its strong association with the Golgi apparatus. There are many GOLD-containing protein families, such as the Transmembrane emp24 domain-containing proteins (TMED/p24 family), animal SEC14-like proteins, Human Golgi resident protein ACBD3, a splice variant of TICAM2 called TRAM with GOLD domain and FYCO1. Here, we critically review the state-of-the-art knowledge of the structures and functions of the main representatives of GOLD-containing proteins in vertebrates. We provide the first unified description of the GOLD domain structure across different families since the first high-resolution structure was determined. With a brand-new update on the definition of the GOLD domain, we also discuss how its tertiary structure fits the β-sandwich-like fold map and give exciting new directions for forthcoming studies.

Vitamins D2 and D3 Have Overlapping But Different Effects on the Human Immune System Revealed Through Analysis of the Blood Transcriptome

Vitamin D is best known for its role in maintaining bone health and calcium homeostasis. However, it also exerts a broad range of extra-skeletal effects on cellular physiology and on the immune system. Vitamins D₂ and D₃ share a high degree of structural similarity. Functional equivalence in their vitamin D-dependent effects on human physiology is usually assumed but has in fact not been well defined experimentally. In this study we seek to redress the gap in knowledge by undertaking an in-depth examination of changes in the human blood transcriptome following supplementation with physiological doses of vitamin D₂ and D₃. Our work extends a previously published randomized placebo-controlled trial that recruited healthy white European and South Asian women who were given 15 µg of vitamin D₂ or D₃ daily over 12 weeks in wintertime in the UK (Nov-Mar) by additionally determining changes in the blood transcriptome over the intervention period using microarrays. An integrated comparison of the results defines both the effect of vitamin D₃ or D₂ on gene expression, and any influence of ethnic background. An important aspect of this analysis was the focus on the changes in expression from baseline to the 12-week endpoint of treatment within each individual, harnessing the longitudinal design of the study. Whilst overlap in the repertoire of differentially expressed genes was present in the D₂ or D₃-dependent effects identified, most changes were specific to either one vitamin or the other. The data also pointed to the possibility of ethnic differences in the responses. Notably, following vitamin D₃ supplementation, the majority of changes in gene expression reflected a down-regulation in the activity of genes, many encoding pathways of the innate and adaptive immune systems, potentially shifting the immune system to a more tolerogenic status. Surprisingly, gene expression associated with type I and type II interferon activity, critical to the innate response to bacterial and viral infections, differed following supplementation with either vitamin D₂ or vitamin D₃, with only vitamin D₃ having a stimulatory effect. This study suggests that further investigation of the respective physiological roles of vitamin D₂ and vitamin D₃ is warranted.

Myxovirus resistance 1 (MX1) is an independent predictor of poor outcome in invasive breast cancer

Background

Breast cancer (BC) is a disease with variable morphology, clinical behaviour and response to therapy. Identifying factors associated with the progression of early-stage BC can help understand the risk of metastasis and guide treatment decisions. Myxovirus resistance 1 (MX1), which is involved in the cellular antiviral mechanism, plays a role in some solid tumours; however, its role in invasive BC remains unknown. In this study, we aimed to explore the clinicopathological and prognostic significance of MX1 in BC.

Methods

MX1 was assessed at the protein level using tissue microarrays from a large well-annotated BC cohort (n = 845). The expression of MX1 mRNA was assessed at the transcriptomic level using the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC; n = 1980) and validated using three publicly available cohorts on Breast Cancer Gene-Expression Miner (bc-GenExMiner version 4.4). The associations between MX1 expression and clinicopathological factors, and outcome were evaluated.

Results

High MX1 protein expression was associated with features of aggressiveness, including large tumour size, high tumour grade, high Nottingham prognostic index scores, hormone receptor negativity and high Ki67 expression. High MX1 expression showed an association with poor patient outcome and it was an independent predictor of short BC-specific survival (p = 0.028; HR = 1.5; 95% CI = 1.0–2.2). Consistent with the protein results, high MX1 mRNA levels showed an association with features of aggressive behaviour and with shorter survival.

Conclusion

This study identified MX1 as an independent predictor of poor outcome in patients with BC. Further functional studies are needed to investigate the biological role of MX1 in BC and its potential value as a therapeutic target.

Electronic supplementary material

The online version of this article (10.1007/s10549-020-05646-x) contains supplementary material, which is available to authorized users.

Mitochondrial fission regulator 2 (MTFR2) promotes growth, migration, invasion and tumour progression in breast cancer cells

Introduction: Mitochondrial fission regulator 2 (MTFR2) belongs to the MTFR family, and 2 isoforms of MTFR2 are produced by alternative splicing. The role of MTFR2 in breast cancer (BC) remains unknown.

Results: MTFR2 was upregulated in BC tissues and was strongly associated with tumor characteristics. Moreover, Kaplan-Meier and Cox proportional hazards analyses indicated that high MTFR2 expression was related to poor overall survival. In addition, the capacity for migration and invasion decreased in two BC cell lines after knockdown of MTFR2. The epithelial-mesenchymal transition pathway was inhibited in MTFR2-silenced cells. MTFR2 can switch glucose metabolism from OXPHS to glycolysis in a HIF1α- and HIF2α-dependent manner.

Conclusion: Taken together, our results indicate that increased expression of MTFR2 is associated with tumour progression in breast cancer cells through switching glucose metabolism from OXPHS to glycolysis in a HIF1α- and HIF2α-dependent manner.

Materials and methods: We obtained data from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) to analyse MTFR2 expression in BC. The prognostic value of MTFR2 expression was assessed using the Kaplan-Meier method. The biological influence of MTFR2 on BC cell lines was studied using proliferation, Transwell migration, invasion and mitochondrial function assays.

The prognostic significance of wild-type isocitrate dehydrogenase 2 (IDH2) in breast cancer

BACKGROUND

Lymphovascular invasion (LVI) is a prerequisite step in breast cancer (BC) metastasis. We have previously identified wild-type isocitrate dehydrogenase 2 (IDH2) as a key putative driver of LVI. Thus, we explored the prognostic significance of IDH2 at transcriptome and protein expression levels in pre-invasive and invasive disease.

METHODS

Utlising tissue microarrays from a large well annotated BC cohort including ductal carcinoma in situ and invasive breast cancer (IBC), IDH2 was assessed at the transcriptomic and proteomic level. The associations between clinicopathological factors including LVI status, prognosis and the expression of IDH2 were evaluated.

RESULTS

In pure DCIS and IBC, high IDH2 protein expression was associated with features of aggressiveness including high nuclear grade, larger size, comedo necrosis and hormonal receptor negativity and LVI, higher grade, larger tumour size, high NPI, HER2 positivity, and hormonal receptor negativity, respectively. High expression of IDH2 either in mRNA or in protein levels was associated with poor patient's outcome in both DCIS and IBC. Multivariate analysis revealed that IDH2 protein expression was an independent risk factor for shorter BC specific-survival.

CONCLUSION

Further functional studies to decipher the role of IDH2 and its mechanism of action as a driver of BC progression and LVI are warranted.