VSTM2A suppresses colorectal cancer and antagonizes Wnt signaling receptor LRP6

Fusobacterium nucleatum modulates the Wnt/β-catenin pathway in colorectal cancer development

The Wnt/β-catenin signalling pathway normally maintains cellular and tissue homeostasis by regulating cellular differentiation and survival in a controlled manner. An aberrantly regulated Wnt/β-catenin signalling pathway can transform into an oncogenic pathway, which is associated with Colorectal cancer (CRC) as well as other cancers. CRC is one of the most frequently occurring gastrointestinal cancers worldwide. In CRC tissues, deregulation of Wnt/β-catenin pathway is observed, which indicates that this oncogenic pathway directly promotes CRC malignancy, cell migration, angiogenesis, chemoresistance, as well as shorter lifespan of a patient. Growing evidence suggests that human commensal microbes have a strong association with carcinogenesis, particularly the prevalence and high enrichment of Fusobacterium nucleatum in CRC progression. The Wnt/β-catenin pathway is one of the targeted pathways by F. nucleatum in CRC, where Fusobacterium adhesin attaches to E-cadherin to initiate infection. Also, Wnt/β-catenin pathway can be a potential target for the treatment of both CRC and F. nucleatum-positive CRC. Here, we discuss the underlying mechanisms of F. nucleatum-positive CRC development through modulation of Wnt/β-catenin signalling and its possibility for the application in targeted therapy of F. nucleatum-positive CRC.

Nanomedicine innovations in colon and rectal cancer: advances in targeted drug and gene delivery systems

Nanotechnology has revolutionized cancer diagnostics and therapy, offering unprecedented possibilities to overcome the constraints of conventional treatments. This study provides a detailed overview of the current progress and difficulties in the creation of nanostructured materials, with a specific emphasis on their use in drug and gene delivery systems. The study examines tactics that attempt to improve the effectiveness and safety of chemotherapeutic drugs such as doxorubicin (Dox) by focusing on the potential of antibody-drug conjugates and functionalized nanoparticles. Moreover, it clarifies the challenges encountered in administering nanoparticles orally for gastrointestinal treatments, emphasizing the crucial physicochemical properties that affect their behavior in the gastrointestinal system. This study highlights the transformational potential of nanostructured materials in precision oncology by examining advanced breakthroughs such cell membrane-camouflaged nanoparticles and inorganic nanoparticles designed for gastrointestinal disorders. The text investigates the processes involved in the absorption of nanoparticles and their destruction in lysosomes, revealing the many methods in which enterocytes take up these particles. This study strongly supports the use of advanced nanoparticle-based methods to reduce the harmful effects on the whole body and improve the effectiveness of therapy, based on a thorough examination of current experiments on animals and humans. The main objective of this paper is to provide a fundamental comprehension that will stimulate more investigation and practical use in the field of cancer nanomedicine, advancing its boundaries.

Loss of VSTM2A promotes adipocyte hypertrophy and disrupts metabolic homeostasis

OBJECTIVE

Adipose tissue expands through hyperplasia and hypertrophy to store excess lipids, a process that is essential for the maintenance of metabolic homeostasis. The mechanisms regulating adipocyte recruitment from progenitors remain unclear. We have previously identified V-set and transmembrane domain-containing protein 2A (VSTM2A) as a factor promoting fat cell development in vitro. Whether VSTM2A impacts adipose tissue and systemic metabolism in vivo is still unknown.

METHODS

We generated VSTM2A knockout mice (Vstm2a-/-) using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) and fed them either a chow or high-fat diet. These mice were evaluated for body weight, adiposity, blood parameters, and glucose homeostasis.

RESULTS

Vstm2a-/- mice were viable and showed no body weight differences. Although adipose mass was similar, Vstm2a-/- mice had larger adipocytes, an effect linked to inflammation, ectopic lipid deposition, and impaired glucose and lipid metabolism. Transcriptomic analysis revealed that VSTM2A loss affects the expression of several genes in adipose tissue, including some related to the lysosome. Interestingly, acute lysosomal inhibition early in life is sufficient to cause adipocyte hypertrophy in adults.

CONCLUSIONS

VSTM2A is dispensable for adipose tissue formation, but its loss causes adipocyte hypertrophy and impairs glucose and lipid homeostasis. Our study also underscores a critical role of the lysosome in initiating adipogenesis.

Exosomal miR-502-5p suppresses the progression of gastric cancer by repressing angiogenesis through the Wnt/β-catenin pathway

BACKGROUND

Gastric cancer (GC) is a significant global health concern, ranking as the fifth most common cancer and the third leading cause of cancer-related deaths. The role of miR-502-5p in various cancers has been studied, but its specific impact on gastric cancer through exosomes is not well understood. This study aimed to investigate the role and mechanism of exosome-derived miR-502-5p in gastric cancer.

METHODS

Differential expression of miR-502-5p in tissues or serum of GC patients was determined using qRT-PCR. The impact of miR-502-5p on cell proliferation, migration, and invasion was assessed through in vitro and in vivo experiments. The potential of exosome-miR-502-5p to inhibit metastatic ability was also explored by using vivo and vitro assay. Furthermore, the underlying mechanism of miR-502-5p in gastric cancer was investigated using western blotting.

RESULTS

It was found that miR-502-5p suppressed the proliferation, migration, and invasion of gastric cancer cells. Exosome-miR-502-5p expression was negatively linked to metastatic ability and demonstrated inhibition of metastasis in vitro and in vivo. Additionally, miR-502-5p appeared to inhibit angiogenesis through the Wnt/β-catenin pathway in gastric cancer.

CONCLUSIONS

Exosomal miR-502-5p acts as a suppressor in the development and progression of gastric cancer, suggesting its potential as a target for anti-cancer therapy or as a diagnostic biomarker.

VSTM2A reverses immunosuppression in colorectal cancer by antagonizing the PD-L1/PD-1 interaction

Immunoglobulin (Ig) VSTM2A (V-set and transmembrane domain containing 2A) is a top-ranked secretory protein frequently silenced during colorectal carcinogenesis; however, its role in immune modulation remains largely unknown. Bioinformatic and immunohistochemistry analysis of human colorectal specimens and Vstm2a+/- knockout mice indicated that VSTM2A positively correlated with CD8a and immune infiltration in both physiological and pathological conditions. We then utilized liquid chromatography-mass spectrometry to pinpoint programmed death ligand 1 (PD-L1) as a membrane receptor of VSTM2A. A series of in vitro biochemistry assays further revealed the binding pattern and kinetics between VSTM2A and PD-L1 proteins through their IgV domains at a dissociation constant of 0.7-2.5 nM. Recombinant VSTM2A protein inhibited the PD-1/PD-L1 interaction and induced NFAT response element (RE) luciferase activity dose dependently. Furthermore, interleukin (IL)-2 production from DO11.10 T cells upon co-culture with mouse non-T splenocytes was upregulated in the presence of VSTM2A conditioned medium. Finally, tumor killing assay and ex vivo data from human peripheral blood mononuclear cells and autologous dendritic cell-T cell co-culture demonstrated that VSTM2A significantly enhanced immune activation via the release of granzyme B and interferon (IFN)-γ cytokines. In conclusion, our study demonstrates the tumor-extrinsic role of VSTM2A in sterically blocking the PD-L1/PD-1 interaction at a picomole to nanomole affinity, which leads to the enhanced anti-tumor effect of cytotoxic T cells.

Targeting LRP6: A new strategy for cancer therapy

Targeting specific molecular drivers of tumor growth is a key approach in cancer therapy. Among these targets, the low-density lipoprotein receptor-related protein 6 (LRP6), a vital component of the Wnt signaling pathway, has emerged as an intriguing candidate. As a cell-surface receptor and vital co-receptor, LRP6 is frequently overexpressed in various cancer types, implicating its pivotal role in driving tumor progression. The pursuit of LRP6 as a target for cancer treatment has gained substantial traction, offering a promising avenue for therapeutic intervention. Here, this comprehensive review explores recent breakthroughs in our understanding of LRP6's functions and underlying molecular mechanisms, providing a profound discussion of its involvement in cancer pathogenesis and drug resistance. Importantly, we go beyond discussing LRP6's role in cancer by discussing diverse potential therapeutic approaches targeting this enigmatic protein. These approaches encompass a wide spectrum, including pharmacological agents, natural compounds, non-coding RNAs, epigenetic factors, proteins, and peptides that modulate LRP6 expression or disrupt its interactions. In addition, also discussed the challenges associated with developing LRP6 inhibitors and their advantages over Wnt inhibitors, as well as the drugs that have entered phase II clinical trials. By shedding light on these innovative strategies, we aim to underscore LRP6's significance as a valuable and multifaceted target for cancer treatment, igniting enthusiasm for further research and facilitating translation into clinical applications.

Gene of the month: VSTM2A

The V-set and transmembrane domain containing 2A (VSTM2A) gene is located on chromosome 7. In the physiological state, VSTM2A regulates preadipocyte cell differentiation. VSTM2A is highly expressed in normal human brain tissue and minimally expressed in other normal tissues. Mucinous tubular and spindle cell carcinoma (MTSCC) of the kidney is a distinct renal tumour subtype with signature chromosomal copy number alterations and an indolent outcome in the majority of cases. VSTM2A overexpression is highly enriched in this renal cancer subtype and has been shown to have potential diagnostic value in distinguishing MTSCC from renal tumours with overlapping histological appearances.

Examining the expression of low-density lipoprotein receptor (LDLR) and low-density lipoprotein receptor-related protein 6 (LRP6) genes in breast cancer cell lines

Cholesterol and the Wnt/β-catenin pathway have an effective role in the proliferation, survival, drug resistance, immune exhaustion, and metastasis of all types of cancer cells. Considering the role of LDLR and LRP6 proteins in cholesterol uptake by cells and activation of Wnt/β-catenin pathway, this study aims to examine the gene expression of LDLR and LRP6 in cell lines of breast cancer. Human breast cancer cell lines MCF7, MD468 and SKBR3 were cultured in suitable conditions and after extracting total RNA from them, real-Time PCR was used to measure the levels of gene expression for LDLR and LRP6. Our results showed that the expression of LDLR and LRP6 genes is significantly increased in MCF7 and MD468 cells compared to SKBR3 cells. These results suggest that LRP6 and LDLR can be considered as a therapeutic target in tumors that have a genetic profile similar to MCF7 and MD468 cells.

Prognostic model development for classification of colorectal adenocarcinoma by using machine learning model based on feature selection technique boruta

Colorectal cancer (CRC) is the third most prevalent cancer type and accounts for nearly one million deaths worldwide. The CRC mRNA gene expression datasets from TCGA and GEO (GSE144259, GSE50760, and GSE87096) were analyzed to find the significant differentially expressed genes (DEGs). These significant genes were further processed for feature selection through boruta and the confirmed features of importance (genes) were subsequently used for ML-based prognostic classification model development. These genes were analyzed for survival and correlation analysis between final genes and infiltrated immunocytes. A total of 770 CRC samples were included having 78 normal and 692 tumor tissue samples. 170 significant DEGs were identified after DESeq2 analysis along with the topconfects R package. The 33 confirmed features of importance-based RF prognostic classification model have given accuracy, precision, recall, and f1-score of 100% with 0% standard deviation. The overall survival analysis had finalized GLP2R and VSTM2A genes that were significantly downregulated in tumor samples and had a strong correlation with immunocyte infiltration. The involvement of these genes in CRC prognosis was further confirmed on the basis of their biological function and literature analysis. The current findings indicate that GLP2R and VSTM2A may play a significant role in CRC progression and immune response suppression.

LSM12 facilitates the progression of colorectal cancer by activating the WNT/CTNNB1 signaling pathway

Aberrant activation of the WNT signaling pathway is a joint event in colorectal cancer (CRC), but the molecular mechanism is still unclear. Recently, RNA-splicing factor LSM12 (like-Sm protein 12) is highly expressed in CRC tissues. This study aimed to verify whether LSM12 is involved in regulating CRC progression via regulating the WNT signaling pathway. Here, we found that LSM12 is highly expressed in CRC patient-derived tissues and cells. LSM12 is involved in the proliferation, invasion, and apoptosis of CRC cells, similar to the function of WNT signaling in CRC. Furthermore, protein interaction simulation and biochemical experiments proved that LSM12 directly binds to CTNNB1 (also known as β-Catenin) and regulates its protein stability to affect the CTTNB1-LEF1-TCF1 transcriptional complex formation and the associated WNT downstream signaling pathway. LSM12 depletion in CRC cells decreased the in vivo tumor growth through repression of cancer cell growth and acceleration of cancer cell apoptosis. Taken together, we suggest that the high expression of LSM12 is a novel factor leading to aberrant WNT signaling activation, and that strategies targeting this molecular mechanism may contribute to developing a new therapeutic method for CRC.

Emerging tools for studying receptor endocytosis and signaling

Ligands, agonists, or antagonists use receptor-mediated endocytosis (RME) to reach their intracellular targets. After the internalization of ligand-receptor complexes, it traffics through different subcellular organelles such as early endosome, recycling endosome, lysosome, etc. Further, after the ligand binding to the receptor, different second messengers are generated, such as cGMP, cAMP, IP₃, etc. Several methods have been used, such as radioligand binding assay, western blotting, co-immunoprecipitation (co-IP), qRT-PCR, immunofluorescence and confocal microscopy, microRNA/siRNA, and bioassays to understand the various events, such as internalization, subcellular trafficking, signaling, metabolic degradation, etc. This chapter briefly discusses the key principles and methods used to study internalization, subcellular trafficking, signaling, and metabolic degradation of numerous receptors.

Wnt signaling in colorectal cancer: pathogenic role and therapeutic target

Background

The Wnt signaling pathway is a complex network of protein interactions that functions most commonly in embryonic development and cancer, but is also involved in normal physiological processes in adults. The canonical Wnt signaling pathway regulates cell pluripotency and determines the differentiation fate of cells during development. The canonical Wnt signaling pathway (also known as the Wnt/β-catenin signaling pathway) is a recognized driver of colon cancer and one of the most representative signaling pathways. As a functional effector molecule of Wnt signaling, the modification and degradation of β-catenin are key events in the Wnt signaling pathway and the development and progression of colon cancer. Therefore, the Wnt signaling pathway plays an important role in the pathogenesis of diseases, especially the pathogenesis of colorectal cancer (CRC).

Objective

Inhibit the Wnt signaling pathway to explore the therapeutic targets of colorectal cancer.

Methods

Based on studying the Wnt pathway, master the biochemical processes related to the Wnt pathway, and analyze the relevant targets when drugs or inhibitors act on the Wnt pathway, to clarify the medication ideas of drugs or inhibitors for the treatment of diseases, especially colorectal cancer.

Results

Wnt signaling pathways include: Wnt/β-catenin or canonical Wnt signaling pathway, planar cell polarity (Wnt-PCP) pathway and Wnt-Ca²⁺ signaling pathway. The Wnt signaling pathway is closely related to cancer cell proliferation, stemness, apoptosis, autophagy, metabolism, inflammation and immunization, microenvironment, resistance, ion channel, heterogeneity, EMT/migration/invasion/metastasis. Drugs/phytochemicals and molecular preparations for the Wnt pathway of CRC treatment have now been developed. Wnt inhibitors are also commonly used clinically for the treatment of CRC.

Conclusion

The development of drugs/phytochemicals and molecular inhibitors targeting the Wnt pathway can effectively treat colorectal cancer clinically.

miR-1269a and miR-1269b: Emerging Carcinogenic Genes of the miR-1269 Family

miRNAs play an important role in the occurrence and development of human cancer. Among them, hsa-mir-1269a and hsa-mir-1269b are located on human chromosomes 4 and 17, respectively, and their mature miRNAs (miR-1269a and miR-1269b) have the same sequence. miR-1269a is overexpressed in 9 cancers. The high expression of miR-1269a not only has diagnostic significance in hepatocellular carcinoma and non-small cell lung cancer but also is related to the poor prognosis of cancer patients such as esophageal cancer, hepatocellular carcinoma, and glioma. miR-1269a can target 8 downstream genes (CXCL9, SOX6, FOXO1, ATRX, RASSF9, SMAD7, HOXD10, and VASH1). The expression of miR-1269a is regulated by three non-coding RNAs (RP11-1094M14.8, LINC00261, and circASS1). miR-1269a participates in the regulation of the TGF-β signaling pathway, PI3K/AKT signaling pathway, p53 signaling pathway, and caspase-9-mediated apoptotic pathway, thereby affecting the occurrence and development of cancer. There are fewer studies on miR-1269b compared to miR-1269a. miR-1269b is highly expressed in hepatocellular carcinoma, non-small cell lung cancer, oral squamous cell carcinoma, and pharyngeal squamous cell carcinoma, but miR-1269b is low expressed in gastric cancer. miR-1269b can target downstream genes (METTL3, CDC40, SVEP1, and PTEN) and regulate the PI3K/AKT signaling pathway. In addition, sequence mutations on miR-1269a and miR-1269b can affect their regulation of cancer. The current studies have shown that miR-1269a and miR-1269b have the potential to be diagnostic and prognostic markers for cancer. Future research on miR-1269a and miR-1269b can focus on elucidating more of their upstream and downstream genes and exploring the clinical application value of miR-1269a and miR-1269b.At present, there is no systematic summary of the research on miR-1269a and miR-1269b. This paper aims to comprehensively analyze the abnormal expression, diagnostic and prognostic value, and molecular regulatory pathways of miR-1269a and miR-1269b in multiple cancers. The overview in our work can provide useful clues and directions for future related research.

Robust Glycogene-Based Prognostic Signature for Proficient Mismatch Repair Colorectal Adenocarcinoma

Background

Proficient mismatch repair (pMMR) colorectal adenocarcinoma (CRAC) metastasizes to a greater extent than MMR-deficient CRAC. Prognostic biomarkers are preferred in clinical practice. However, traditional biomarkers screened directly from sequencing are often not robust and thus cannot be confidently utilized.

Methods

To circumvent the drawbacks of blind screening, we established a new strategy to identify prognostic biomarkers in the conserved and specific oncogenic pathway and its regulatory RNA network. We performed RNA sequencing (RNA-seq) for messenger RNA (mRNA) and noncoding RNA in six pMMR CRAC patients and constructed a glycosylation-related RNA regulatory network. Biomarkers were selected based on the network and their correlation with the clinicopathologic information and were validated in multiple centers (n = 775).

Results

We constructed a competing endogenous RNA (ceRNA) regulatory network using RNA-seq. Genes associated with glycosylation pathways were embedded within this scale-free network. Moreover, we further developed and validated a seven-glycogene prognosis signature, GlycoSig (B3GNT6, GALNT3, GALNT8, ALG8, STT3B, SRD5A3, and ALG6) that prognosticate poor-prognostic subtype for pMMR CRAC patients. This biomarker set was validated in multicenter datasets, demonstrating its robustness and wide applicability. We constructed a simple-to-use nomogram that integrated the risk score of GlycoSig and clinicopathological features of pMMR CRAC patients.

Conclusions

The seven-glycogene signature served as a novel and robust prognostic biomarker set for pMMR CRAC, highlighting the role of a dysregulated glycosylation network in poor prognosis.

RING-finger protein 6 promotes colorectal tumorigenesis by transcriptionally activating SF3B2

RNF6 is a RING finger protein with oncogenic potential. In this study, we established colon-specific RNF6 transgenic (tg) mice, and demonstrated that RNF6 overexpression accelerated colorectal carcinogenesis compared to wild-type littermates in a chemically induced colorectal cancer (CRC) model. To understand whether transcriptional activity of RNF6 underlies its oncogenic effect, we performed integrated chromatin immunoprecipitation (ChIP)-sequencing and RNA-sequencing analysis to identify splicing factor 3b subunit 2 (SF3B2) as a potential downstream target of RNF6. RNF6 binds to the SF3B2 promoter and the overexpression of RNF6 activates SF3B2 expression in CRC cells, primary CRC organoids, and RNF6 tg mice. SF3B2 knockout abrogated the tumor promoting effect of RNF6 overexpression, whereas the reexpression of SF3B2 recused cell growth and migration/invasion in RNF6 knockout cells, indicating that SF3B2 is a functional downstream target of RNF6 in CRC. Targeting of RNF6-SF3B2 axis with SF3B2 inhibitor with pladienolide B suppressed the growth of CRC cells with RNF6 overexpression in vitro and in vivo. Moreover, the combination of 5-fluorouracil (5-FU) plus pladienolide B exerted synergistic effects in CRC with high RNF6 expression, leading to tumor regression in xenograft models. These findings indicate that tumor promoting effect of RNF6 is achieved mainly via transcriptional upregulation of SF3B2, and that RNF6-SF3B2 axis is a promising target for CRC therapy.

Regulation of the Low-Density Lipoprotein Receptor-Related Protein LRP6 and Its Association With Disease: Wnt/β-Catenin Signaling and Beyond

Wnt signaling plays crucial roles in development and tissue homeostasis, and its dysregulation leads to various diseases, notably cancer. Wnt/β-catenin signaling is initiated when the glycoprotein Wnt binds to and forms a ternary complex with the Frizzled and low-density lipoprotein receptor-related protein 5/6 (LRP5/6). Despite being identified as a Wnt co-receptor over 20 years ago, the molecular mechanisms governing how LRP6 senses Wnt and transduces downstream signaling cascades are still being deciphered. Due to its role as one of the main Wnt signaling components, the dysregulation or mutation of LRP6 is implicated in several diseases such as cancer, neurodegeneration, metabolic syndrome and skeletal disease. Herein, we will review how LRP6 is activated by Wnt stimulation and explore the various regulatory mechanisms involved. The participation of LRP6 in other signaling pathways will also be discussed. Finally, the relationship between LRP6 dysregulation and disease will be examined in detail.

lncRNA HIF1A-AS2: A potential oncogene in human cancers (Review)

Long non-coding RNAs (lncRNAs) are transcripts that are >200 nucleotides, but with no open reading frame. An increasing number of lncRNAs have been identified following the development of second-generation sequencing technologies, and they have since become a research hotspot. Functionally, they play a vital role in tumor progression, including in tumor proliferation, migration, invasion, apoptosis and acquisition of drug resistance. They regulate gene expression primarily through interaction with DNA, RNA and proteins at the epigenetic, transcriptional and post-transcriptional levels. Endogenous hypoxia-inducible factor 1α antisense RNA 2 (lncRNA HIF1A-AS2) is aberrantly expressed and involved the development/progression of various types of tumors, such as bladder cancer, glioblastoma, breast cancer and osteosarcoma. It plays a vital role in the proliferation, apoptosis, migration, invasion and epithelial-mesenchymal transformation of various tumor cells. This review summarizes the current body of knowledge on the biological functions and related molecular mechanisms of lncRNA HIF1A-AS2 in the development/progression of human tumors and other diseases.

Regulation of Tumor Necrosis Factor-α by Peptide Lv in Bone Marrow Macrophages and Synovium

Background: Bone marrow-derived monocytes/macrophages are recruited into synovial tissue, where they contribute to synovial inflammation in osteoarthritis through inflammatory cytokine production. Recent studies have suggested that V-Set and transmembrane domain-containing 4 (VSTM4) and its fragment, peptide Lv, exhibit immunosuppressive activity on T cells and vascular endothelial growth factor (VEGF)-like activity, respectively. Given that evidence suggests that VEGF may play a role in macrophage function, we investigated peptide Lv-mediated regulation of inflammatory cytokines in bone marrow macrophages (BMMs) and synovial inflammation. Method: To investigate the effects of peptide Lv, BMMs were stimulated with vehicle, LPS, or LPS + peptide Lv, and Tnfa, Il1b, Il6, and Ifng expression were evaluated using quantitative PCR (qPCR). TNF-α and IFN-γ production was measured using ELISA. To examine the effect of peptide Lv deficiency on macrophages and synovitis, peptide Lv-deficient mice were generated using genome editing. LPS-induced Tnfa and Ifng expression and TNF-α and IFN-γ production were evaluated in BMM isolated from wild-type and peptide Lv-deficient mice. Additionally, Tnfa and Ifng expression levels were compared between wild-type and peptide Lv-deficient mice before and after knee injury. Results: Peptide Lv suppressed the LPS-mediated elevation in TNF-α and IFN-γ. LPS stimulation significantly increased TNF-α and IFN-γ production in BMM derived from peptide Lv-deficient mice compared to wild-type mice. Synovial TNF-α expression in the injured knee was elevated in peptide Lv-deficient compared to wild-type mice. Conclusion: Peptide Lv suppressed TNF-α in macrophages and plays a role in synovial inflammation. Thus, peptide Lv may be a useful therapeutic target for synovitis.

Transcriptome profiling by combined machine learning and statistical R analysis identifies TMEM236 as a potential novel diagnostic biomarker for colorectal cancer

Colorectal cancer (CRC) is a common cause of cancer-related deaths worldwide. The CRC mRNA gene expression dataset containing 644 CRC tumor and 51 normal samples from the cancer genome atlas (TCGA) was pre-processed to identify the significant differentially expressed genes (DEGs). Feature selection techniques Least absolute shrinkage and selection operator (LASSO) and Relief were used along with class balancing for obtaining features (genes) of high importance. The classification of the CRC dataset was done by ML algorithms namely, random forest (RF), K-nearest neighbour (KNN), and artificial neural networks (ANN). The significant DEGs were 2933, having 1832 upregulated and 1101 downregulated genes. The CRC gene expression dataset had 23,186 features. LASSO had performed better than Relief for classifying tumor and normal samples through ML algorithms namely RF, KNN, and ANN with an accuracy of 100%, while Relief had given 79.5%, 85.05%, and 100% respectively. Common features between LASSO and DEGs were 38, from them only 5 common genes namely, VSTM2A, NR5A2, TMEM236, GDLN, and ETFDH had shown statistically significant survival analysis. Functional review and analysis of the selected genes helped in downsizing the 5 genes to 2, which are VSTM2A and TMEM236. Differential expression of TMEM236 was statistically significant and was markedly reduced in the dataset which solicits appreciation for assessment as a novel biomarker for CRC diagnosis.

Network analysis identifies DAPK3 as a potential biomarker for lymphatic invasion and colon adenocarcinoma prognosis

Colon adenocarcinoma is a prevalent malignancy with significant mortality. Hence, the identification of molecular biomarkers with prognostic significance is important for improved treatment and patient outcomes. Clinical traits and RNA-Seq of 551 patient samples in the UCSC Toil Recompute Compendium of The Cancer Genome Atlas TARGET and Genotype Tissue Expression project datasets (primary_site = colon) were used for weighted gene co-expression network analysis to reveal the association between gene networks and cancer cell invasion. One module, containing 151 genes, was significantly correlated with lymphatic invasion, a histopathological feature of higher risk colon cancer. DAPK3 (death-associated protein kinase 3) was identified as the pseudohub of the module. Gene ontology identified gene enrichment related to cytoskeletal organization and apoptotic signaling processes, suggesting modular involvement in tumor cell survival, migration, and epithelial-mesenchymal transformation. Although DAPK3 expression was reduced in patients with colon cancer, high expression of DAPK3 was significantly correlated with greater lymphatic invasion and poor overall survival.

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WCGNA reveals a gene module linked to lymphatic invasion in colon adenocarcinoma

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DAPK3 is a pseudohub gene with differential expression in colon cancer

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Gene ontology identified relationships to cytoskeletal organization and apoptosis

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DAPK3 was correlated with lymphatic invasion and poor overall survival

The Engaged Role of Tumor Microenvironment in Cancer Metabolism: Focusing on Cancer-Associated Fibroblast and Exosome Mediators

Metabolic reprogramming is a significant property of various cancer cells, which most commonly arises from the Tumor Microenvironment (TME). The events of metabolic pathways include the Warburg effect, shifting in Krebs cycle metabolites, and the rate of oxidative phosphorylation, potentially providing energy and structural requirements for the development and invasiveness of cancer cells. TME and tumor metabolism shifting have a close relationship through bidirectional signaling pathways between stromal and tumor cells. Cancer- Associated Fibroblasts (CAFs), as the most dominant cells of TME, play a crucial role in the aberrant metabolism of cancer. Furthermore, the stated relationship can affect survival, progression, and metastasis in cancer development. Recently, exosomes are considered one of the most prominent factors in cellular communications considering effective content and bidirectional mediatory effect between tumor and stromal cells. In this regard, CAF-Derived Exosomes (CDE) exhibit an efficient obligation to induce metabolic reprogramming for promoting growth and metastasis of cancer cells. The understanding of cancer metabolism, including factors related to TME, could lead to the discovery of a potential biomarker for diagnostic and therapeutic approaches in cancer management. This review focuses on the association between metabolic reprogramming and engaged microenvironmental, factors such as CAFs, and the associated derived exosomes.

Control of adipogenic commitment by a STAT3-VSTM2A axis

White adipose tissue (WAT) is a dynamic organ that plays crucial roles in controlling metabolic homeostasis. During development and periods of energy excess, adipose progenitors are recruited and differentiate into adipocytes to promote lipid storage capability. The identity of adipose progenitors and the signals that promote their recruitment are still incompletely characterized. We have recently identified V-set and transmembrane domain-containing protein 2A (VSTM2A) as a novel protein enriched in preadipocytes that amplifies adipogenic commitment. Despite the emerging role of VSTM2A in promoting adipogenesis, the molecular mechanisms regulating Vstm2a expression in preadipocytes are still unknown. To define the molecular mechanisms controlling Vstm2a expression, we have treated preadipocytes with an array of compounds capable of modulating established regulators of adipogenesis. Here, we report that Vstm2a expression is positively regulated by PI3K/mTOR and cAMP-dependent signaling pathways and repressed by the MAPK pathway and the glucocorticoid receptor. By integrating the impact of all the molecules tested, we identified signal transducer and activator of transcription 3 (STAT3) as a novel downstream transcription factor affecting Vstm2a expression. We show that activation of STAT3 increased Vstm2a expression, whereas its inhibition repressed this process. In mice, we found that STAT3 phosphorylation is elevated in the early phases of WAT development, an effect that strongly associates with Vstm2a expression. Our findings identify STAT3 as a key transcription factor regulating Vstm2a expression in preadipocytes.NEW & NOTEWORTHY cAMP-dependent and PI3K-mTOR signaling pathways promote the expression of Vstm2a. STAT3 is a key transcription factor that controls Vstm2a expression in preadipocytes. STAT3 is activated in the early phases of WAT development, an effect that strongly associates with Vstm2a expression.

Identification of a Five-Gene Prognostic Model and Its Potential Drug Repurposing in Colorectal Cancer Based on TCGA, GTEx and GEO Databases

Colorectal cancer (CRC) is a major cause of cancer deaths worldwide. Unfortunately, many CRC patients are still being diagnosed at an advanced stage of the cancer, and the 5-year survival rate is only ~30%. Effective prognostic markers of CRC are therefore urgently needed. To address this issue, we performed a detailed bioinformatics analysis based on the Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and Gene Expression Omnibus (GEO) databases to identify prognostic biomarkers for CRC, which in turn help in exploring potential drug-repurposing. We identified five hub genes (PGM2, PODXL, RHNO1, SCD, and SEPHS1), which had good performance in survival prediction and might be involved in CRC through three key pathways (“Cell cycle,” “Purine metabolism,” and “Spliceosome” KEGG pathways) identified by a KEGG pathway enrichment analysis. What is more, we performed a co-expression analysis between five hub genes and transcription factors to explore the upstream regulatory region. Furthermore, we screened the potential drug-repurposing for the five hub genes in CRC according to the Binding DB and ZINC15 databases. Taking together, we constructed a five-gene signature to predict overall survival of CRC and found the potential drug-repurposing, which may improve the outcome of CRC in the future.

Cytoplasmic SHMT2 drives the progression and metastasis of colorectal cancer by inhibiting β-catenin degradation

Introduction: Serine hydroxymethyltransferase 2 (SHMT2) plays a critical role in serine-glycine metabolism to drive cancer cell proliferation. However, the nonmetabolic function of SHMT2 in tumorigenesis, especially in human colorectal cancer (CRC) progression, remains largely unclear.

Methods: SHMT2 expression in human CRC cells was identified by western blot and immunofluorescence assay. The CRC cell proliferation, migration, and invasion after SHMT2 knockdown or overexpression were explored through in vitro and in vivo assays. Immunofluorescence, mRNA-seq, co-immunoprecipitation, chromatin immunoprecipitation-qPCR and immunohistochemistry assays were used to investigate the underlying mechanisms behind the SHMT2 nonmetabolic function.

Results: We demonstrated that SHMT2 was distributed in the cytoplasm and nucleus of human CRC cells. SHMT2 knockdown resulted in the significant inhibition of CRC cell proliferation, which was not restored by serine, glycine, or formate supplementation. The invasion and migration of CRC cells were suppressed after SHMT2 knockdown. Mechanistically, SHMT2 interacted with β-catenin in the cytoplasm. This interaction inhibited the ubiquitylation-mediated degradation of β-catenin and subsequently modulated the expression of its target genes, leading to the promotion of CRC cell proliferation and metastasis. Notably, the lysine 64 residue on SHMT2 (SHMT2^K64) mediated its interaction with β-catenin. Moreover, transcription factor TCF4 interacted with β-catenin, which in turn increased SHMT2 expression, forming an SHMT2/β-catenin positive feedback loop. In vivo xenograft experiments confirmed that SHMT2 promoted the growth and metastasis of CRC cells. Finally, the level of SHMT2 was found to be significantly increased in human CRC tissues. The SHMT2 level was correlated with an increased level of β-catenin, associated with CRC progression and predicted poor patient survival.

Conclusion: Taken together, our findings reveal a novel nonmetabolic function of SHMT2 in which it stabilizes β-catenin to prevent its ubiquitylation-mediated degradation and provide a potential therapeutic strategy for CRC therapy.

Identification of Dysregulated Genes for Late-Onset Alzheimer's Disease Using Gene Expression Data in Brain

BACKGROUND

Alzheimer's Disease (AD) is a neurodegenerative complex brain disease that represents a public health concern. AD is considered the fifth leading cause of death in Americans who are older than 65 years which prioritizes the importance of understanding the etiology of AD in its early stages before the onset of symptoms. This study attempted to further understand Alzheimer's disease (AD) etiology by investigating the dysregulated genes using gene expression data from multiple brain regions.

METHODS

A linear mixed-effects model for differential gene expression analysis was used in a sample of 15 AD and 30 control subjects, each with data from four different brain regions, in order to deal with the hierarchical multilevel data. Post-hoc Gene Ontology and pathway enrichment analyses provided insights on the biological implications in AD progression. Supervised machine learning algorithms were used to assess the discriminative power of the top 10 candidate genes in distinguishing between the two groups.

RESULTS

Enrichment analyses revealed biological processes and pathways that are related to structural constituents and organization of the axons and synapses. These biological processes and pathways imply dysfunctional axon and synaptic transmission between neuronal cells in AD. Random Forest classification algorithm gave the best accuracy on the test data with F1-score of 0.88.

CONCLUSION

The differentially expressed genes were associated with axon and synaptic transmissions which affect the neuronal connectivity in cognitive systems involved in AD pathophysiology. These genes may open ways to explore new effective treatments and early diagnosis before the onset of clinical symptoms.

HOXA13 promotes colon cancer progression through β-catenin-dependent WNT pathway

Human class I homeobox A13 (HOXA13) was initially identified as a transcription factor and has an important role in embryonic development and malignant transformation. However, the clinical significance and the molecular mechanisms of HOXA13 in colon cancer development and progression are still unknown. In this study, we found that HOXA13 was highly expressed in colon cancer tissues, and its expression was associated with histological grade, T stage, N stage and tumour size. In vitro studies showed that HOXA13 promoted colon cancer cell proliferation, migration and invasion. Bioinformatics analysis revealed that HOXA13 expression was positively correlated with the WNT signalling pathway. In vitro studies showed that HOXA13 promoted the malignant phenotype of colon cancer cells by facilitating the nuclear translocation of β-Catenin. Moreover, XAV939, an inhibitor of β-Catenin, reversed the HOXA13-mediated effects on invasion and proliferation of colon cancer cells. In vivo studies further verified that HOXA13 promoted tumour formation through the Wnt/β-Catenin pathway. Collectively, these results suggest that HOXA13 is a potential oncogene that functions by promoting the nuclear translocation of β-Catenin, thereby maintaining the proliferation and metastasis of colon cancer.

New Advances in Canonical Wnt/β-Catenin Signaling in Cancer

Wnt/β-catenin-mediated signaling is a key pathway regulating tissue growth and development, and tumorigenesis, and has received increasing attention in recent years. In addition to participating in healthy tissue and organ development, ectopic activation of the pathway can cause a variety of tumors and other pathologies. The pathway plays a critical role in many processes such as proliferation, differentiation, apoptosis, migration, invasion, epithelial–mesenchymal transition and cancer cell stemness. The importance of the Wnt signal is self-evident. This review describes the underlying mechanism of Wnt signaling pathway and highlights the latest findings on the relationship between Wnt signaling pathway and tumorigenesis. In addition, the potential relationship between miRNAs and Wnt signaling is presented. Furthermore, we discuss the intrinsic link between Wnt signaling and cancer cell stemness, which shed light on the malignant progression of tumor cells. Finally, cancer treatment strategies based on the canonical Wnt signaling pathway are summarized, hoping to help clinical development.

MicroRNA‑590 inhibits migration, invasion and epithelial‑to‑mesenchymal transition of esophageal squamous cell carcinoma by targeting low‑density lipoprotein receptor‑related protein 6

MicroRNA-590 (miR-590) has been revealed as a tumor suppressor, while low-density lipoprotein receptor-related protein 6 (LRP6) is considered to act as a tumor promoter. However, their roles and underlying molecular regulatory mechanisms in esophageal squamous cell carcinoma (ESCC) have yet to be fully elucidated. Therefore, the present study aimed to investigate these mechanisms. The expression levels of miR-590 and LRP6 in human ESCC samples and cell lines were determined using reverse transcription-quantitative PCR. Bioinformatics analysis was used to predict the relationship between miR-590 and LRP6, and luciferase assay was performed to validate the relationship between these factors. Transwell assays were used to determine cell migration and invasion, while western blotting assays were used to detect the protein expression levels of LRP6, E-cadherin, N-cadherin and Vimentin. The present study demonstrated that miR-590 was downregulated and LRP6 was upregulated in ESCC tissues and cell lines. Furthermore, it was found that miR-590 overexpression and LRP6 knockdown inhibited cell migration, invasion and epithelial-to-mesenchymal transition (EMT) in ESCC cell lines. Additional mechanistic studies identified that LRP6 was a target of, and was inhibited by, miR-590. Collectively, the present findings suggested that miR-590 inhibited the invasion, migration and EMT of ESCC cells by mediating LRP6.

KRAS Mutation-Responsive miR-139-5p inhibits Colorectal Cancer Progression and is repressed by Wnt Signaling

Introduction: Colorectal cancer (CRC) frequently harbors KRAS mutations that result in chemoresistance and metastasis. MicroRNAs (miRNAs) are usually dysregulated and play important regulatory roles in tumor progression. However, the KRAS mutation-responsive miRNA profile in CRC remains uninvestigated. Methods: miR-139-5p was identified and evaluated by small RNA sequencing, qRT-PCR and in situ hybridization. The roles of miR-139-5p in CRC cells with and without KRAS mutation were determined by Cell Counting Kit-8 (CCK-8), colony formation, flow cytometry and transwell assays in vitro and by tumorigenesis and metastasis assays in vivo. Microarrays followed by bioinformatic analyses, luciferase reporter assays and Western blotting were applied for mechanistic studies. Results: miR-139-5p was significantly downregulated in KRAS-mutated CRC cells and tissues compared with their wild-type counterparts. Low miR-139-5p expression was associated with aggressive phenotypes and poor prognosis in CRC patients. miR-139-5p overexpression inhibited CRC cell proliferation, migration and invasion in vitro, sensitized tumors to chemotherapy, and impaired tumor growth and metastasis in vivo. Transcriptomic profiling identified multiple modulators in the Ras (JUN and FOS) and Wnt (CTNNB1 and DVL1) signaling pathways and the epithelial-to-mesenchymal transition (EMT) process (ZEB1) as direct targets of miR-139-5p, and inverse correlations were confirmed in CRC clinical tissues. Aberrantly activated Wnt signaling in KRAS-mutant cells was demonstrated to transcriptionally repress miR-139-5p through TCF4, forming a miR-139-5p/Wnt signaling double-negative feedback loop. Conclusions: We identified miR-139-5p as a KRAS-responsive miRNA and demonstrated its involvement in CRC progression. KRAS mutation disrupted the miR-139-5p/Wnt signaling reciprocal negative feedback mechanism, which might cause miR-139-5p downregulation and derepression of oncogenic signaling pathways and EMT. These results reveal a transcriptional regulatory mode of KRAS-driven malignant transformation and highlight miR-139-5p as a novel regulator of crosstalk between the Ras and Wnt signaling pathways in CRC.

Comparative and selection sweep analysis of CNV was associated to litter size in Dazu black goats

This study aims to identify the relative Copy number variation (CNV) associated with the litter size of Dazu black goats based on the unpublished CNV analytical results of our previously published sequencing data, in which the litter-size groups were classified into extreme low- and high-yield groups. Firstly, to compare the existence of valuable CNV in Dazu black goats with different fertility levels with mixed pools. We obtained 4992 and 4888 CNVs from the HY and LY, which overlapping 1461 genes, and classified on the original CNV type. Three genes [LOC108633278, PPP1R12A, and YIPF4] were observed in the intersection between the HY deletion and the LY duplication groups. Secondly, on individuals level, we identified a novel candidate CNV (Chr1_50215501, F_ST = 0.148, V_ST = 0.347) from 214 autosomal credible CNVs to be significant with litter size in the Dazu black goat, which located in the CBLB gene. This finding indicates the CBLB gene may affect the litter size of the Dazu black goats through structural variations, and Chr1_50215501 can be an effective genetic marker for marker-assisted selection breeding, and this study was also helps understand the molecular mechanism related to the goat litter size.