Decreased expression of SCUBE2 is associated with progression and prognosis in colorectal cancer

The biology of SCUBE

The SCUBE [Signal peptide-Complement C1r/C1s, Uegf, Bmp1 (CUB)-Epithelial growth factor domain-containing protein] family consists of three proteins in vertebrates, SCUBE1, 2 and 3, which are highly conserved in zebrafish, mice and humans. Each SCUBE gene encodes a polypeptide of approximately 1000 amino acids that is organized into five modular domains: (1) an N-terminal signal peptide sequence, (2) nine tandem epidermal growth factor (EGF)-like repeats, (3) a large spacer region, (4) three cysteine-rich (CR) motifs, and (5) a CUB domain at the C-terminus. Murine Scube genes are expressed individually or in combination during the development of various tissues, including those in the central nervous system and the axial skeleton. The cDNAs of human SCUBE orthologs were originally cloned from vascular endothelial cells, but SCUBE expression has also been found in platelets, mammary ductal epithelium and osteoblasts. Both soluble and membrane-associated SCUBEs have been shown to play important roles in physiology and pathology. For instance, upregulation of SCUBEs has been reported in acute myeloid leukemia, breast cancer and lung cancer. In addition, soluble SCUBE1 is released from activated platelets and can be used as a clinical biomarker for acute coronary syndrome and ischemic stroke. Soluble SCUBE2 enhances distal signaling by facilitating the secretion of dual-lipidated hedgehog from nearby ligand-producing cells in a paracrine manner. Interestingly, the spacer regions and CR motifs can increase or enable SCUBE binding to cell surfaces via electrostatic or glycan-lectin interactions. As such, membrane-associated SCUBEs can function as coreceptors that enhance the signaling activity of various serine/threonine kinase or tyrosine kinase receptors. For example, membrane-associated SCUBE3 functions as a coreceptor that promotes signaling in bone morphogenesis. In humans, SCUBE3 mutations are linked to abnormalities in growth and differentiation of both bones and teeth. In addition to studies on human SCUBE function, experimental results from genetically modified mouse models have yielded important insights in the field of systems biology. In this review, we highlight novel molecular discoveries and critical directions for future research on SCUBE proteins in the context of cancer, skeletal disease and cardiovascular disease.

The Multifaceted Role of Signal Peptide-CUB-EGF Domain-Containing Protein (SCUBE) in Cancer

Signal peptide, CUB, and EGF-like domain-containing proteins (SCUBE) are secretory cell surface glycoproteins that play key roles in the developmental process. SCUBE proteins participate in the progression of several diseases, including cancer, and are recognized for their oncogenic and tumor suppressor functions depending on the cellular context. SCUBE proteins promote cancer cell proliferation, angiogenesis, invasion, or metastasis, stemness or self-renewal, and drug resistance. The association of SCUBE with other proteins alters the expression of signaling pathways, including Hedgehog, Notch, TGF-β/Smad2/3, and β-catenin. Further, SCUBE proteins function as potential prognostic and diagnostic biomarkers for breast cancer, renal cell carcinoma, endometrial carcinoma, and nasopharyngeal carcinoma. This review presents key features of SCUBE family members, and their structure and functions, and highlights their contribution in the development and progression of cancer. A comprehensive understanding of the role of SCUBE family members offers novel strategies for cancer therapy.

A Combined Feature Screening Approach of Random Forest and Filter-based Methods for Ultra-high Dimensional Data

Background:

Various feature (variable) screening approaches have been proposed in the past decade to mitigate the impact of ultra-high dimensionality in classification and regression problems, including filter based methods such as sure indepen¬dence screening, and wrapper based methods such random forest. However, the former type of methods rely heavily on strong modelling assumptions while the latter ones requires an adequate sample size to make the data speak for themselves. These require¬ments can seldom be met in biochemical studies in cases where we have only access to ultra-high dimensional data with a complex structure and a small number of observations.

Objective:

In this research, we want to investigate the possibility of combing both filter based screening methods and random forest based screening methods in the regression context.

Method:

We have combined four state-of-art filter approaches, namely, sure independence screening (SIS) , robust rank corre¬lation based screening (RRCS), high dimensional ordinary least squares projection (HOLP) and a model free sure independence screening procedure based on the distance correlation (DCSIS) from the statistical community with a random forest based Boruta screening method from the machine learning community for regression problems.

Result:

Among all combined methods, RF-DCSIS performs better than the other methods in terms of screening accuracy and prediction capability on the simulated scenarios and real benchmark datasets.

Conclusion:

By empirical study from both extensive simulation and real data, we have shown that both filter based screening and random forest based screening have their pros and cons while a combination of both may lead to a better feature screening result and prediction capability

Keywords:

feature screening, filter-based method, ultra-high dimensional data, variable selection, random forest,RF-DCSIS

Estrogen receptor-positive breast cancer survival prediction and analysis of resistance-related genes introduction

Background

In recent years, ER+ and HER2- breast cancer of adjuvant therapy has made great progress, including chemotherapy and endocrine therapy. We found that the responsiveness of breast cancer treatment was related to the prognosis of patients. However, reliable prognostic signatures based on ER+ and HER2- breast cancer and drug resistance-related prognostic markers have not been well confirmed, This study in amied to establish a drug resistance-related gene signature for risk stratification in ER+ and HER2- breast cancer.

Methods

We used the data from The Cancer Genoma Atlas (TCGA) breast cancer dataset and gene expression database (Gene Expression Omnibus, GEO), constructed a risk profile based on four drug resistance-related genes, and developed a nomogram to predict the survival of patients with I-III ER+ and HER2- breast cancer. At the same time, we analyzed the relationship between immune infiltration and the expression of these four genes or risk groups.

Results

Four drug resistance genes (AMIGO2, LGALS3BP, SCUBE2 and WLS) were found to be promising tools for ER+ and HER2- breast cancer risk stratification. Then, the nomogram, which combines genetic characteristics with known risk factors, produced better performance and net benefits in calibration and decision curve analysis. Similar results were validated in three separate GEO cohorts. All of these results showed that the model can be used as a prognostic classifier for clinical decision-making, individual prediction and treatment, as well as follow-up.

[The study of mRNA expression profiles of main cell function regulator genes in unchanged colonic mucosa from healthy donors]

A comparative analysis of molecular genetic phenotypes of mucous membrane cells in five anatomical regions of the colon in a group of healthy donors was conducted by comparing mRNA expression profiles of 62 genes involved in the regulation of vital cellular function. We used 181 biopsy samples of morphologically unchanged colonic mucosa, obtained from the colon (ascending, transverse-colon, descending, sigmoid) and rectum sections during prophylactic colonoscopy of 58 donors with no colon pathology. The mRNA levels for 62 genes involved in the regulation of apoptosis, proliferation, transcription, differentiation, cell-cell adhesion, and immune response were assessed by RT-PCR. Statistically significant differences were found for the molecular phenotypes of five sections of the colon. The results of the study can serve as a basis for creating a reference database (values of expression profiles), developing methods of differential diagnostics and screening of various pathologies of the colon.

Circular RNA circ_SETD2 represses breast cancer progression via modulating the miR-155-5p/SCUBE2 axis

Breast cancer (BC) is the leading cause of cancer deaths in women worldwide. Circular RNA circ_SETD2 (circ_SETD2), also termed as hsa_circ_0065173, is reported to be abnormally expressed in BC. Nevertheless, the role and mechanism of circ_SETD2 in BC are unclear. Expression of circ_SETD2, miR-155-5p, and SCUBE2 mRNA was evaluated by quantitative real-time polymerase chain reaction. Cell cycle progression, proliferation, apoptosis, migration, and invasion were determined by flow cytometry, MTT, and transwell assays. The relationship between circ_SETD2 or SCUBE2 and miR-155-5p was verified through a dual-luciferase reporter assay. The role of circ_SETD2 in BC in vivo was confirmed by a xenograft assay. circ_SETD2 and SCUBE2 were downregulated, while miR-155-5p was upregulated in BC tissues and cells. Both circ_SETD2 and SCUBE2 elevation arrested cell cycle progression, inhibited cell proliferation, migration, and invasion, and accelerated cell apoptosis in BC cells. Moreover, circ_SETD2 upregulation repressed BC growth in vivo. Importantly, circ_SETD2 modulated SCUBE2 expression through competitively binding to miR-155-5p in BC cells. Also, the inhibitory impacts of circ_SETD2 enhancement on the malignant behavior of BC cells were restored by miR-155-5p overexpression. Besides, SCUBE2 silencing abolished miR-155-5p downregulation mediated effects on the malignant behavior of BC cells. Therefore, circ_SETD2 curbed BC progression via upregulating SCUBE2 via binding to miR-155-5p.

A 3-gene biomarker signature to predict response to taxane-based neoadjuvant chemotherapy in breast cancer

Breast cancer is the most common cancer in women worldwide, affecting one in eight women in their lifetime. Taxane-based chemotherapy is routinely used in the treatment of breast cancer. The purpose of this study was to develop and validate a predictive biomarker to improve the benefit/risk ratio for that cytotoxic chemotherapy. We explicitly strived for a biomarker that enables secure translation into clinical practice. We used genome-wide gene expression data of the Hatzis et al. discovery cohort of 310 patients for biomarker development and three independent cohorts with a total of 567 breast cancer patients for validation. We were able to develop a biomarker signature that consists of just the three gene products ELF5, SCUBE2 and NFIB, measured on RNA level. Compared to Hatzis et al., we achieved a significant improvement in predicting responders and non-responders in the Hatzis et al. validation cohort with an area under the receiver operating characteristics curve of 0.73 [95% CI, 69%—77%]. Moreover, we could confirm the performance of our biomarker on two further independent validation cohorts. The overall performance on all three validation cohorts expressed as area under the receiver operating characteristics curve was 0.75 [95% CI, 70%—80%]. At the clinically relevant classifier’s operation point to optimize the exclusion of non-responders, the biomarker correctly predicts three out of four patients not responding to neoadjuvant taxane-based chemotherapy, independent of the breast cancer subtype. At the same time, the response rate in the group of predicted responders increased to 42% compared to 23% response rate in all patients of the validation cohorts.

The relationship of serum SCUBE-1, -2 and -3 levels with clinical findings and ultrasonographic skin thickness in systemic sclerosis patients

AIM

This study aimed to investigate the relationship between the level of serum signal peptide-CUB-EGF domain-containing protein (SCUBE)-1, SCUBE-2 and SCUBE-3 and clinical findings and ultrasonographic skin thickness in systemic sclerosis (SSc).

MATERIAL AND METHODS

Thirty patients who met the American College of Rheumatology/European League against Rheumatism 2013 SSc classification criteria and 44 healthy volunteers who were compatible with the patient group in terms of age and gender were included in the study. Serum SCUBE levels were measured by enzyme-linked immunosorbent assay. Ultrasonographic skin thickness measurements were simultaneously performed.

RESULTS

No significant difference was found between the serum SCUBE levels of SSc patients and serum SCUBE levels of the control group. A negative correlation was detected between serum SCUBE-1 level and forced expiratory volume in 1 second (FEV₁ ). While a positive correlation was detected between serum SCUBE-2 level and the Duruöz Hand Index and serum C4 level, a negative correlation was determined with the forced vital capacity (FVC) value. A negative correlation was determined between serum SCUBE-3 level and echocardiographic pulmonary artery pressure (PAP). A correlation could not be determined between serum SCUBE levels and ultrasonographic skin thickness. However, a positive correlation was observed between ultrasonographic skin thickness and the modified Rodnan skin score.

CONCLUSION

In this study, a correlation was observed between serum SCUBE levels and some clinical and laboratory parameters (FEV₁ , FVC, PAP, C4, and Duruöz Hand Index) in SSc patients. New clinical studies are needed to better understand the contribution of these molecules in the progression and pathogenesis of SSc.

Hedgehog Signal and Genetic Disorders

The hedgehog (Hh) family comprises sonic hedgehog (Shh), Indian hedgehog (Ihh), and desert hedgehog (Dhh), which are versatile signaling molecules involved in a wide spectrum of biological events including cell differentiation, proliferation, and survival; establishment of the vertebrate body plan; and aging. These molecules play critical roles from embryogenesis to adult stages; therefore, alterations such as abnormal expression or mutations of the genes involved and their downstream factors cause a variety of genetic disorders at different stages. The Hh family involves many signaling mediators and functions through complex mechanisms, and achieving a comprehensive understanding of the entire signaling system is challenging. This review discusses the signaling mediators of the Hh pathway and their functions at the cellular and organismal levels. We first focus on the roles of Hh signaling mediators in signal transduction at the cellular level and the networks formed by these factors. Then, we analyze the spatiotemporal pattern of expression of Hh pathway molecules in tissues and organs, and describe the phenotypes of mutant mice. Finally, we discuss the genetic disorders caused by malfunction of Hh signaling-related molecules in humans.

Candidate Predisposition Variants in Kaposi Sarcoma as Detected by Whole-Genome Sequencing

Familial clustering of classic Kaposi sarcoma (CKS) is rare with, approximately 100 families reported to date. We studied 2 consanguineous families, 1 Iranian and 1 Israeli, with multiple cases of adult CKS and without overt underlying immunodeficiency. We performed genome-wide linkage analysis and whole-genome sequencing to discover the putative genetic cause for predisposition. A 9-kb homozygous intronic deletion in RP11-259O2.1 in the Iranian family and 2 homozygous variants, 1 in SCUBE2 and the other in CDHR5, in the Israeli family were identified as possible candidates. The presented variants provide a robust starting point for validation in independent samples.

Copy Number Profiling of MammaPrint™ Genes Reveals Association with the Prognosis of Breast Cancer Patients

Purpose

The MammaPrint™ gene signature, currently used in clinical practice, provides prognostic information regarding the recurrence and potential metastasis in breast cancer patients. However, the prognostic information of the 70 genes included can only be estimated at the RNA expression level. In this study, we investigated whether copy number information of MammaPrint™ genes at the DNA level can be used as a prognostic tool for breast cancer, as copy number variations (CNVs) are major contributors to cancer progression.

Methods

We performed CNV profiling of MammaPrint™ genes in 59 breast cancer cell lines and 650 breast cancer patients, using publicly available data in The Cancer Genome Atlas (TCGA) database. Statistical analyses including Fisher exact test, chi-square test, and Kaplan-Meier survival analyses were performed.

Results

All MammaPrint™ genes showed recurrent CNVs, particularly in TCGA cohort. CNVs of 32 and 36 genes showed significant associations with progesterone receptor and estrogen rector, respectively. No genes showed a significant association with human epidermal growth factor receptor 2 status and lymph node status. In addition, only six genes were associated with tumor stages. RFC4, HRASLS, NMU, GPR126, SCUBE2, C20orf46, and EBF4 were associated with reduced survival and RASSF7 and ESM1 were associated with reduced disease-free survival.

Conclusion

Based on these findings, a concordance of CNV-based genomic rearrangement with expression profiling of these genes and their putative roles in disease tumorigenesis was established. The results suggested that the CNV profiles of the MammaPrint™ genes can be used to predict the prognosis of breast cancer patients. In addition, this approach may lead to the development of new cancer biomarkers at the DNA level.

Overexpression of SCUBE2 Inhibits Proliferation, Migration, and Invasion in Glioma Cells

Signal peptide CUB EGF-like domain-containing protein 2 (SCUBE2), a member of the SCUBE family of proteins, was recently found to play an important role in cancer development. However, little is known regarding its biological function in glioma. In the present study, we investigated the effect of SCUBE2 on glioma and explored its relevant mechanisms. The study showed that SCUBE2 had a low expression in glioma tissue and cell lines. SCUBE2 overexpression inhibited glioma cell proliferation in vitro and in vivo as well as suppressed glioma cell migration and invasion in vitro. Furthermore, we found that the Sonic hedgehog (Shh) signaling pathway was involved in the inhibitory effect of SCUBE2 overexpression on glioma cells. In light of the results obtained from our study, SCUBE2 may be regarded as a potential therapeutic target for glioma.