TCOF1 upregulation in triple-negative breast cancer promotes stemness and tumour growth and correlates with poor prognosis.

BACKGROUND: Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with poor prognosis. By performing multiomic profiling, we recently uncovered super-enhancer heterogeneity between breast cancer subtypes. Our data also revealed TCOF1 as a putative TNBC-specific super-enhancer-regulated gene. TCOF1 plays a critical role in craniofacial development but its function in cancer remains unclear. METHODS: Overall survival and multivariant Cox regression analyses were conducted using the METABRIC data set. The effect of TCOF1 knockout on TNBC growth and stemness was evaluated by in vitro and in vivo assays. RNA-seq and rescue experiments were performed to explore the underlying mechanisms. RESULTS: TCOF1 is frequently upregulated in TNBC and its elevated expression correlates with shorter overall survival. TCOF1 depletion significantly inhibits the growth and stemness of basal-like TNBC, but not of mesenchymal-like cells, highlighting the distinct molecular dependency in different TNBC subgroups. RNA-seq uncovers several stem cell molecules regulated by TCOF1. We further demonstrate that KIT is a downstream effector of TCOF1 in mediating TNBC stemness. TCOF1 expression in TNBC is regulated by the predicted super-enhancer. CONCLUSIONS: TCOF1 depletion potently attenuates the growth and stemness of basal-like TNBC. Expression of TCOF1 may serve as a TNBC prognostic marker and a therapeutic target.

From Bi-Level to One-Level: A Framework for Structural Attacks to Graph Anomaly Detection.

The success of graph neural networks stimulates the prosperity of graph mining and the corresponding downstream tasks including graph anomaly detection (GAD). However, it has been explored that those graph mining methods are vulnerable to structural manipulations on relational data. That is, the attacker can maliciously perturb the graph structures to assist the target nodes in evading anomaly detection. In this article, we explore the structural vulnerability of two typical GAD systems: unsupervised FeXtra-based GAD and supervised graph convolutional network (GCN)-based GAD. Specifically, structural poisoning attacks against GAD are formulated as complex bi-level optimization problems. Our first major contribution is then to transform the bi-level problem into one-level leveraging different regression methods. Furthermore, we propose a new way of utilizing gradient information to optimize the one-level optimization problem in the discrete domain. Comprehensive experiments demonstrate the effectiveness of our proposed attack algorithm BinarizedAttack .

Deep learning-derived spatial organization features on histology images predicts prognosis in colorectal liver metastasis patients after hepatectomy.

Histopathological images of colorectal liver metastases (CRLM) contain rich morphometric information that may predict patients' outcomes. However, to our knowledge, no study has reported any practical deep learning framework based on the histology images of CRLM, and their direct association with prognosis remains largely unknown. In this study, we developed a deep learning-based framework for fully automated tissue classification and quantification of clinically relevant spatial organization features (SOFs) in H&E-stained images of CRLM. The SOFs based risk-scoring system demonstrated a strong and robust prognostic value that is independent of the current clinical risk score (CRS) system in independent clinical cohorts. Our framework enables fully automated tissue classification of H&E images of CRLM, which could significantly reduce assessment subjectivity and the workload of pathologists. The risk-scoring system provides a time- and cost-efficient tool to assist clinical decision-making for patients with CRLM, which could potentially be implemented in clinical practice.

Parenteral N-3 fatty acids modulate inflammatory and immune response in rats undergoing total gastrectomy.

This study investigated the effect of n-3 fatty acid (FA)-containing parenteral nutrition on the circulatory lymphocyte subpopulation, intracellular cytokine and leukocyte adhesion molecule expression, and phagocytic activity in rats undergoing total gastrectomy. Normal rats with internal jugular catheters were assigned to normal control (NC) and two experimental groups and received total parenteral nutrition (TPN). At the same time, a total gastrectomy was performed in the experimental groups, whereas the NC group underwent a sham operation. The TPN solutions were isonitrogenous and identical in nutrient compositions except for differences in fat emulsion contents. The NC and one of the experimental groups received a soybean oil emulsion (SO), and the other experimental group received 50% soybean oil and 50% fish oil emulsion (FO). Half of the rats in each respective group were sacrificed 1 or 3 days after surgery or the sham operation to examine their immune response. The results showed that the FO group had a higher CD4 proportion and CD4/CD8 ratio than those of the SO and NC groups postoperatively. The phagocytic activity of peritoneal macrophages was higher in the FO group than in the NC group, but no difference was found between the SO and NC groups 3 days after surgery. The intracellular interferon (IFN)-gamma distribution in the FO group was higher than that of the SO group on postoperative days. Leukocyte adhesion molecule expressions and peritoneal monocyte chemotactic protein-1 levels were lower in the FO group than in the SO group on postoperative day 3. These results suggest that parenterally infused FO did not result in immunosuppression. In addition, FO administration promotes lymphocyte Th1 cytokine production, enhances peritoneal macrophage phagocytic activity, and reduces leukocyte adhesion molecule expression in rats with total gastrectomy.

Effects of glutamine supplementation on splenocyte cytokine mRNA expression in rats with septic peritonitis.

AIM: To investigate the effects of glutamine (GLN)-enriched diets before and GLN-containing total parenteral nutrition (TPN) after sepsis or both on the secretion of cytokines and their mRNA expression levels in splenocytes of rats with septic peritonitis. METHODS: Rats were assigned to a control group and 4 experimental groups. The control group and experimental groups 1 and 2 were fed a semipurified diet, while experimental groups 3 and 4 had part of the casein replaced by GLN which provided 25% of the total nitrogen. After rats were fed with these diets for 10 d, sepsis was induced by cecal ligation and puncture (CLP), whereas the control group underwent a sham operation, at the same time, an internal jugular vein was cannulated. All rats were maintained on TPN for 3 d. The control group and experimental groups 1 and 3 were infused with conventional TPN, while the TPN in experimental groups 2 and 4 was supplemented with GLN, providing 25% of the total nitrogen in the TPN solution. All rats were kiued 3 d after sham operation or CLP to examine their splenocyte subpopulation distribution and cytokine expression levels. RESULTS: Most cytokines could not be detected in plasma except for IL-10. No difference in plasma IL-10 was observed among the 5 groups. The IL-2, IL-4, IL-10, and TNF-alpha mRNA expression levels in splenocytes were significantly higher in experimental groups 2 and 4 than in the control group and group 1. The mRNA expression of IFN-gamma was significantly higher in the GLN-supplemented groups than in the control group and experimental group 1. The proportion of CD45Ra+ was increased, while those of CD3+ and CD4+ were decreased in experimental group 1 after CLP was performed. There were no differences in spleen CD3+ lymphocyte distributions between the control and GLN-supplemented groups. CONCLUSION: GLN supplementation can maintain T-lymphocyte populations in the spleen and significantly enhance the mRNA expression levels of Th1 and Th2 cytokines and TNF-alpha in the spleen of rats with septic peritonitis.

Effects of arginine supplementation on mucosal immunity in rats with septic peritonitis.

BACKGROUND: Supplemental Arginine (Arg) has been demonstrated to improve the immunologic response and reduce mortality in rodents with sepsis. However, the effects of Arg on gut-associated lymphoid tissue function after infection and sepsis are not clear. The aim of this study was to study the effect of Arg-supplemented diets before and Arg-enriched total parenteral nutrition (TPN) after sepsis or both on the intestinal immunity of rats with septic peritonitis. METHODS: Rats were assigned to four groups. Groups 1 and 2 were fed a semipurified diet, while in the diets of groups 3 and 4, part of the casein was replaced with Arg. After feeding the experimental diets for 10 days, sepsis was induced by cecal ligation and puncture (CLP); at the same time, the internal jugular vein was cannulated. All rats were maintained on TPN for 3 days. Groups 1 and 3 were infused with conventional TPN, while groups 2 and 4 were given a TPN solution supplemented with Arg, which replaced 10% of the total amino acids. All rats were sacrificed 3 days after CLP. Intestinal immunoglobin (Ig) A levels, total lymphocyte yields, and lymphocyte subpopulations in Peyer's patches were analyzed. In vitro cytokine secretion by splenocytes and Peyer's patch lymphocytes were also measured. RESULTS: Total lymphocyte yields in Peyer's patches, and small intestinal immunoglobulin A (IgA) secretion in group 4 were significantly higher than the groups 1 and 2. No differences were observed between groups 3 and 4. There were no differences in the interleukin (IL)-2 and interferon- gamma levels among all groups when splenocytes were stimulated with mitogen. However, in vitro splenocyte IL-10 production in group 4 was significantly higher than those of groups 1 and 2, and had no difference from group 3. There were no differences in the ratios of B and T lymphocyte subpopulations in Peyer's patches among all groups. CONCLUSIONS: Enteral Arg supplementation before sepsis tended to enhance total lymphocyte yields in Peyer's patches and intestinal IgA secretion. Arg administered both before and after CLP had a synergistic effect on improving intestinal immunity, possibly by enhancing systemic IL-10 secretion. However, intravenous Arg administration after CLP had no favorable effects on mucosal immunity in rats with septic peritonitis.

Glutamine supplementation enhances mucosal immunity in rats with Gut-Derived sepsis.

OBJECTIVE: Supplemental glutamine (Gln) has been demonstrated to improve the immunologic response and reduce mortality in rodents with sepsis. However, the effects of Gln on gut-associated lymphoid tissue function after infection and sepsis are not clear. We investigated the effects of Gln-supplemented diets before sepsis, Gln-enriched total parenteral nutrition (TPN) after sepsis, or both on the intestinal immunity in rats with gut-derived sepsis. METHODS: Male Wistar rats were assigned to control and four experimental groups. The control and experimental groups 1 and 2 were fed a semi-purified diet; in experimental groups 3 and 4, part of the casein in the diets was replaced with Gln. After feeding rats the respective diets for 10 d, sepsis was induced by cecal ligation and puncture (CLP) in the experimental groups, whereas the control group underwent a sham operation; at the same time, the internal jugular vein of all rats was cannulated. All rats were maintained on TPN for 3 d. The control group and groups 1 and 3 were infused with conventional TPN, and groups 2 and 4 were given a TPN solution supplemented with Gln, which provided 25% of total amino acid nitrogen. All rats were killed 3 d after the sham operation or CLP. Intestinal immunoglobin A levels, total lymphocyte yields, and lymphocyte subpopulations in Peyer's patches were analyzed. RESULTS: Total Peyer's patch lymphocyte numbers were significantly higher in the Gln-supplemented groups than in the control group. Distributions of CD3+ and CD4+ in group 1 were significantly lower than those in the control group, whereas no differences were observed among the control and Gln-supplemented groups. Plasma immunoglobulin A levels were higher in the Gln-supplemented groups than the control group and group 1. Intestinal immunoglobulin A levels were significantly higher in groups 2 and 4 than in the control group and group 1. CONCLUSIONS: Preventive use of a Gln-supplemented enteral diet before CLP or intravenous Gln supplementation after CLP have similar effects in promoting proliferation of total lymphocyte in gut-associated lymphoid tissue, enhancing IgA secretion, and maintaining T-lymphocyte populations in Peyer's patches. Gln administered before and after CLP did not seem to have a synergistic effect on enhancing mucosal immunity in rats with gut-derived sepsis.

Arginine supplementation enhances peritoneal macrophage phagocytic activity in rats with gut-derived sepsis.

BACKGROUND: Previous reports have shown that arginine (Arg) enhances phagocytic activity of macrophages and is required for macrophage-mediated toxicity toward tumor cells. Few studies have addressed the importance of Arg supplementation on macrophage and neutrophil function after infection and sepsis. This study examined the effect of Arg-supplemented diets before and Arg-enriched total parenteral nutrition (TPN) after sepsis or both on the phagocytic activity of peritoneal macrophages and blood polymorphonuclear cells in rats with gut-derived sepsis. METHODS: Male Wistar rats were assigned to 4 groups. Groups 1 and 2 were fed a semipurified diet, while groups 3 and 4 had part of the casein replaced with 2% of total calories as Arg. After the experimental diets were administered for 10 days, sepsis was induced by cecal ligation and puncture (CLP); at the same time, an internal jugular vein was cannulated. All rats were maintained on TPN for 3 days. Groups 1 and 3 were infused with conventional TPN, while groups 2 and 4 were supplemented with Arg, replacing 10% of total amino acids in the TPN solution. Survival rates were recorded for 3 days after CLP, and all surviving rats were killed 3 days after CLP to examine their immune responses. RESULTS: Aerobic and anaerobic bacteria colony counts in peritoneal lavage fluid were significantly reduced, and the phagocytic activity of peritoneal macrophages was enhanced in groups 3 and 4 but not in the other 2 groups. There were no significant differences in the phagocytic activities of blood polymorphonuclear cells and survival rates among the 4 groups. CONCLUSIONS: Enteral Arg supplementation before sepsis significantly enhanced peritoneal macrophage phagocytic activity and reduced total bacterial counts in peritoneal lavage fluid. Arg administered before and after CLP seemed to have a synergistic effect on enhancing phagocytic activity and on bacterial clearance. However, IV Arg administration after CLP had no favorable effects on phagocytic activity or survival rates in rats with gut-derived sepsis.

Effects of glutamine supplementation on innate immune response in rats with gut-derived sepsis.

The present study examined the effect of glutamine (Gln)-enriched diets before sepsis or Gln-containing total parenteral nutrition (TPN) after sepsis, or both, on the phagocytic activity and blood lymphocyte subpopulation in rats with gut-derived sepsis. Rats were assigned to a control group or one of four experimental groups. The control group and groups 1 and 2 were fed a semipurified diet; groups 3 and 4 had part of casein replaced by Gln. After feeding the diets for 10 d, sepsis was induced by caecal ligation and puncture (CLP); TPN was maintained for 3 d after CLP. The control group and groups 1 and 3 were infused with conventional TPN and groups 2 and 4 were supplemented with Gln in the TPN solution. All rats were killed 3 d after CLP or sham operation to examine their immune responses. The results showed that compared with the control group, the phagocytic activities of peritoneal macrophages were enhanced in groups 3 and 4, but not in groups 1 and 2. The proportion of CD3+ cells in group 1 was significantly lower (P<0.05) than that of the control group, whereas no differences were observed among the control and Gln-supplemented groups. The CD4+ cell proportion was significantly lower (P<0.05) in group 1 compared with the control group and groups 3 and 4. These findings suggest that Gln-enriched diets before CLP significantly enhanced peritoneal macrophage phagocytic activity, preserved CD4+ cells and maintained blood total T lymphocytes in gut-derived sepsis. However, parenteral Gln administration after caecal ligation and puncture had no favourable effects on modulating immune response in septic rats.