New insights into the genetics of neuroblastoma

The Regulatory Mechanisms and Clinical Significance of Lnc SNHG4 in Cancer

BACKGROUND

LncRNAs have been reported to be involved in a variety of biological functions, including gene expression, cell growth, and differentiation. They may also serve as oncogenes or tumor suppressor genes in diseases. lncRNAs that can encode small nucleolar RNAs (snoRNAs) have been named small nucleolar RNA host genes (SNHGs).

OBJECTIVE

In this review article, we readily review the regulatory mechanisms and clinical significance of Lnc SNHG4 in cancer.

METHODS

We systematically investigated databases, like Scopus, PubMed, Embase, Google Scholar, and Cochrane Library database for all research articles, and have provided an overview regarding the biological functions and mechanisms of lncRNA SNHG4 in tumorigenesis.

RESULTS

Compared to neighboring normal tissues, SNHG4 is significantly dysregulated in various tumor tissues. SNHG4 upregulation is mainly associated with advanced tumor stage, tumor size, TNM stage, and decreased overall survival. In addition, aberrant SNHG4 expression promotes cell proliferation, metastasis, migration, and invasion of cancer cells.

CONCLUSION

SNHG4 may serve as a new therapeutic target and prognostic biomarker in patients with cancer.

Mediastinal neuroblastoma, ganglioneuroblastoma, and ganglioneuroma: Pathology review and diagnostic approach

Neuroblastic tumors are a group of tumors of the sympathetic ganglia and adrenal medulla that derive from primordial neural crest cells. These tumors include neuroblastoma, intermixed ganglioneuroblastoma, nodular ganglioneuroblastoma, and ganglioneuroma. Neuroblastomas are the most common extracranial solid tumor arising in childhood and may occur in different anatomic sites. Neuroblastic tumors are common mesenchymal tumors of the mediastinum. Herein, we describe advances in our understanding of neuroblastic tumor biology. Pathologists should be aware of diagnostic challenges associated with these tumors to ensure correct histologic diagnosis and appropriate clinical management. We describe updated mediastinal neuroblastic tumor pathology, focusing on morphological, immunohistochemical, and molecular features and differential diagnoses.

Emerging Neuroblastoma 3D In Vitro Models for Pre-Clinical Assessments

The potential of tumor three-dimensional (3D) in vitro models for the validation of existing or novel anti-cancer therapies has been largely recognized. During the last decade, diverse in vitro 3D cell systems have been proposed as a bridging link between two-dimensional (2D) cell cultures and in vivo animal models, both considered gold standards in pre-clinical settings. The latest awareness about the power of tailored therapies and cell-based therapies in eradicating tumor cells raises the need for versatile 3D cell culture systems through which we might rapidly understand the specificity of promising anti-cancer approaches. Yet, a faithful reproduction of the complex tumor microenvironment is demanding as it implies a suitable organization of several cell types and extracellular matrix components. The proposed 3D tumor models discussed here are expected to offer the required structural complexity while also assuring cost-effectiveness during pre-selection of the most promising therapies. As neuroblastoma is an extremely heterogenous extracranial solid tumor, translation from 2D cultures into innovative 3D in vitro systems is particularly challenging. In recent years, the number of 3D in vitro models mimicking native neuroblastoma tumors has been rapidly increasing. However, in vitro platforms that efficiently sustain patient-derived tumor cell growth, thus allowing comprehensive drug discovery studies on tailored therapies, are still lacking. In this review, the latest neuroblastoma 3D in vitro models are presented and their applicability for a more accurate prediction of therapy outcomes is discussed.

Dendrimer Nanodevices and Gallic Acid as Novel Strategies to Fight Chemoresistance in Neuroblastoma Cells

Human neuroblastoma (NB), a pediatric tumor inclined to relapse, after an initial response to therapy, usually develops resistance. Since several chemotherapeutics exert anticancer effect by increasing reactive oxygen species (ROS), NB cells overproduce antioxidant compounds becoming drugs-resistant. A strategy to sensitize NB cells to chemotherapy involves reducing their antioxidant defenses and inducing ROS overproduction. Concerning this, although affected by several issues that limit their clinical application, antioxidant/pro-oxidant polyphenols, such as gallic acid (GA), showed pro-oxidant anti-cancer effects and low toxicity for healthy cells, in several kind of tumors, not including NB. Herein, for the first time, free GA, two GA-dendrimers, and the dendrimer adopted as GA reservoir were tested on both sensitive and chemoresistant NB cells. The dendrimer device, administered at the dose previously found active versus sensitive NB cells, induced ROS-mediated death also in chemoresistant cells. Free GA proved a dose-dependent ROS-mediated cytotoxicity on both cell populations. Intriguingly, when administered in dendrimer formulations at a dose not cytotoxic for NB cells, GA nullified any pro-oxidant activity of dendrimer. Unfortunately, due to GA, nanoformulations were inactive on NB cells, but GA resized in nanoparticles showed considerable ability in counteracting, at low dose, ROS production and oxidative stress, herein induced by the dendrimer.

TP53BP2 decreases cell proliferation and induces autophagy in neuroblastoma cell lines

Tumor protein p53-binding protein 2 (TP53BP2), a member of the apoptosis-stimulating protein of p53 (ASPP) family, has previously been reported to be associated with tumor development. However, to the best of our knowledge, the role of TP53BP2 in neuroblastoma has not been elucidated. The aim of the present study was to investigate the function of TP53BP2 in the proliferation and autophagy of neuroblastoma. An expression vector that expresses TP53BP2-specific short hairpin RNA (shTP53BP2) was used for the experimental group and green fluorescent protein short hairpin RNA was used as a control. Cell proliferation was measured using MTT assays, self-renewal was evaluated using soft agar assays, light chain 3 (LC3) II expression level was examined by western blot and immunofluorescence analysis, and the autophagy-related 3 homolog (ATG3), autophagy-related 5 homolog (ATG5) and autophagy-related 9 homolog (ATG7) expression levels were examined using the reverse transcription-quantitative polymerase chain reaction (RT-qPCR). A genomics analysis revealed that TP53BP2 expression was associated with the survival of patients with neuroblastoma. Western blot and RT-qPCR assays indicated that TP53BP2 could be implicated in neuroblastoma, as the proliferative ability of the experimental group decreased compared with that of the control group (P<0.001) and the expression levels of genes associated with autophagy, including LC3 II. ATG3, ATG5 and ATG7, increased in the experimental group. In conclusion, an increased expression of TP53BP2 in patients with neuroblastoma may be associated with poor survival and shTP53BP2 may decrease the proliferative abilities of neuroblastoma cells, including BE(2)C and SK-N-DZ cell lines. In addition, the LC3 II, ATG3, ATG5 and ATG7 expression levels increased and were associated with increased rates of autophagy following upregulation of TP53BP2.

Dissecting Intra-Tumor Heterogeneity by the Analysis of Copy Number Variations in Single Cells: The Neuroblastoma Case Study

Tumors often show intra-tumor heterogeneity because of genotypic differences between all the cells that compose it and that derive from it. Recent studies have shown significant aspects of neuroblastoma heterogeneity that may affect the diagnostic-therapeutic strategy. Therefore, we developed a laboratory protocol, based on the combination of the advanced dielectrophoresis-based array technology and next-generation sequencing to identify and sort single cells individually and carry out their copy number variants analysis. The aim was to evaluate the cellular heterogeneity, avoiding overestimation or underestimation errors, due to a bulk analysis of the sample. We tested the above-mentioned protocol on two neuroblastoma cell lines, SK-N-BE(2)-C and IMR-32. The presence of several gain or loss chromosomal regions, in both cell lines, shows a high heterogeneity of the copy number variants status of the single tumor cells, even if they belong to an immortalized cell line. This finding confirms that each cell can potentially accumulate different alterations that can modulate its behavior. The laboratory protocol proposed herein provides a tool able to identify prevalent behaviors, and at the same time highlights the presence of particular clusters that deviate from them. Finally, it could be applicable to many other types of cancer.

Aberrant MRP14 expression in thyroid follicular cells mediates chemokine secretion through the IL-1β/MAPK pathway in Hashimoto's thyroiditis

Myeloid-related protein 14 (MRP14) is responsible for inflammatory reactions. However, the correlation between MRP14 and Hashimoto's thyroiditis (HT) is still not clear. In this study, we examined the status of MRP14 in thyroid tissues and sera of HT patients and explored the mechanism of IL-1β-mediated regulation of MRP14 expression, as well as the effects of MRP14 on pro-inflammatory chemokine secretion in thyroid follicular cells (TFCs), to elucidate the role of MRP14 in HT development. Our results showed dramatically increased MRP14 expression in thyroid tissues and sera from HT patients. In addition, IL-1β significantly promoted the expression of MRP14 in TFCs, which was mediated by activation of the MAPK/NF-κB signalling pathway. More importantly, IL-1β induced the secretion of the chemokines GRO-2, CXCL9 and CCL22, which was dependent on the regulation of MRP14 in TFCs. Therefore, these findings suggested that under pro-inflammatory conditions, TFCs secreted chemokines with the help of MRP14 regulation, which might suggest a potential pathological mechanism of lymphocyte infiltration into the thyroid gland in HT.

Research progress of neuroblastoma related gene variations

Neuroblastoma, the most common extracranial solid tumor among children, is an embryonal tumor originating from undifferentiated neural crest cell. Neuroblastomas are highly heterogeneous, represented by the wide range of clinical presentations and likelihood of cure, ranging from spontaneous regression to relentless progression despite rigorous multimodal treatments. Approximately, 50% of cases are high-risk with overall survival rates less than 40%. With the efforts to collect large numbers of clinically annotated specimens and the advancements in technologies, researchers have revealed numerous genetic alterations that may drive tumor growth. However, the most lack mutations in genes that are recurrently mutated, which inspires researchers to identify disrupted pathways instead of single mutated genes to unearth biological systems perturbed in neuroblastoma. Stratification of patients and target therapy based on their molecular signatures have been the center of focus. This review provides a comprehensive summary of the recent advances in identification of candidate genes variations, targeted approaches to high-risk neuroblastoma and evaluates the methods utilized for detection, which will provide new avenues to develop therapies and further genetic researches.

HSD17B12 gene rs11037575 C>T polymorphism confers neuroblastoma susceptibility in a Southern Chinese population

A previous genome-wide association study (GWAS) identified four genetic polymorphisms (rs1027702 near DUSP12, rs10055201 in IL31RA, rs2619046 in DDX4, and rs11037575 in HSD17B12 gene) that were associated with neuroblastoma susceptibility, especially for low-risk subjects. The aim of this study was to examine the association between these four polymorphisms and neuroblastoma susceptibility in a Southern Chinese population composed of 256 cases and 531 controls. Overall, among all the polymorphisms, single-locus analysis only revealed significant association between the HSD17B12 rs11037575 C>T polymorphism and neuroblastoma susceptibility (CT vs CC: adjusted odds ratio [OR] =0.71, 95% confidence interval [CI] =0.51-0.97, P=0.030). Moreover, stratified analysis indicated that the rs11037575 T allele was associated with decreased neuroblastoma risk among the children aged 0-18 months (adjusted OR =0.60, 95% CI =0.37-0.97, P=0.036); regarding the tumor site, this polymorphism protected against tumor in the mediastinum (adjusted OR =0.59, 95% CI =0.37-0.94, P=0.025). When risk genotypes were combined, we found that girls with two to four risk genotypes were at a significantly increased risk of neuroblastoma (adjusted OR =1.65, 95% CI =1.03-2.64, P=0.039). In terms of clinical stages, individuals with two to four risk genotypes had a tendency toward the development of stage III/IV diseases (adjusted OR =1.69, 95% CI =1.12-2.54, P=0.012). In conclusion, we verified that the HSD17B12 rs11037575 T allele might negatively associate with neuroblastoma risk. These findings need further validation by prospective studies with larger sample size and different ethnicities.

Primary rare anaplastic large cell lymphoma, ALK positive in small intestine: case report and review of the literature

Background

Primary anaplastic large cell lymphoma, ALK positive in small intestine is clinically rare and the clinical, radiological and pathological information are generally not available. Here, we report a case of 32-year-old male with ALK positive anaplastic large cell lymphoma at the junction of jejunum and ileum, and highlight the clinicopathological features and the differential diagnosis of this type lymphoma.

Case presentation

The patient presented with right middle abdominal mass for 1 month with sporadic pain. Computed tomography (CT) showed a mass measured 8.5 × 7.4 × 4 cm at the junction of jejunum and ileum. The diagnosis was made after pathological examination of the excised tissue by enterectomy. Grossly, the mass was located predominately in intestinal wall with grayish appearance and blurry boundary. Microscopically, almost all layers of the intestinal wall were infiltrated by pleomorphic tumor cells with diffuse and cohesive growth pattern. The neoplastic cells were mainly medium to large size with moderate basophilic cytoplasm. Most of them had hyperchromatic nuclei and prominent nucleoli. “Hallmark” cells were easily detected. Immunohistochemically, tumor cells are characterized by CD30, ALK, CD5, TIA-1, Granzyme B, EMA positive staining, and CD2, CD3, CD7, CD4, CD8, CD20, CD79a negative staining. The Epstein-Barr virus encoded RNAs (EBERs) genome was also negative. A diagnosis as primary small intestinal ALK positive anaplastic large cell lymphoma was finally made. The patient received CHOP chemotherapy and is alive till now without recurrence 5 months after enterectomy.

Conclusions

Primary small intestinal ALK positive anaplastic large cell lymphoma is rare. The accurate diagnosis should be based on combined consideration of clinical characteristics, CT image and pathological features, and should be distinguished from other lymphomas or solid tumors in small intestine.

The Association between GWAS-identified BARD1 Gene SNPs and Neuroblastoma Susceptibility in a Southern Chinese Population

A previous genome-wide association study (GWAS) has found that some common variations in the BARD1 gene were associated with neuroblastoma susceptibility especially for high-risk subjects, and the associations have been validated in Caucasians and African-Americans. However, the associations between BARD1 gene polymorphisms and neuroblastoma susceptibility have not been studied among Asians, not to mention Chinese subjects. In the present study, we investigated the association of three BARD1 polymorphisms (rs7585356 G>A, rs6435862 T>G and rs3768716 A>G) with neuroblastoma susceptibility in 201 neuroblastoma patients and 531 controls using TaqMan methodology. Overall, none of these polymorphisms was significantly associated with neuroblastoma susceptibility. However, stratified analysis showed a more profound association between neuroblastoma risk and rs6435862 TG/GG variant genotypes among older children (adjusted OR=1.55, 95% CI=1.04-2.31), and children with adrenal gland-originated disease (adjusted OR=2.94, 95% CI=1.40-6.18), or with ISSN clinical stages III+IV disease (adjusted OR=1.75, 95% CI=1.09-2.84). Similar results were observed for the variant genotypes of rs3768716 A>G polymorphism among these three subgroups. Our results suggest that the BARD1 rs6435862 T>G and rs3768716 A>G polymorphisms may contribute to increased susceptibility to neuroblastoma, especially for the subjects at age ≥12 months, with adrenal gland-originated or with late clinical stage neuroblastoma. These findings need further validation by prospective studies with larger sample size with subjects enrolled from multicenter, involving different ethnicities.

Genome-wide pathway analysis for diabetic nephropathy in type 1 diabetes

OBJECTIVE

The aim of this study was to identify candidate single-nucleotide polymorphisms (SNPs) that might play a role in susceptibility to diabetic nephropathy (DN) in type 1 diabetes, elucidate their potential mechanisms, and generate SNP-to-gene-to-pathway hypotheses.

METHODS

A genome-wide association study (GWAS) dataset of DN in type 1 diabetes, which included 345,363 SNPs from a total of 1,705 samples (820 DN cases and 885 normoalbuminuric controls) of European ancestry, was used in this study. The Identify Candidate Causal SNPs and Pathways (ICSNPathway) analysis was applied to the GWAS dataset.

RESULTS

ICSNPathway analysis identified 14 candidate SNPs, 10 genes, and 19 pathways, which in turn revealed 10 hypothetical biological mechanisms. The strongest hypothetical biological mechanism was one in which rs4740 altered the role of EBI3 in various pathways and processes, including regulation of the cytokine biosynthetic process, cytokine metabolic process, positive regulation of the cytokine biosynthetic process, regulation of the interferon gamma biosynthetic process, and interferon gamma production (0.008 ≤ p < 0.001; 0.047 ≤ false discovery rate [FDR] ≤ 0.002). This next most strongly supported hypothesis was the modulation of NMUR2 by rs982715, rs4958531, 4958532, rs1895245, and rs4958535 to affect its role in various pathways and processes, including calcium-mediated signaling and peptide receptor activity, and G-protein activity (p < 0.001, 0.002; FDR = 0.005, 0.049, respectively).

CONCLUSIONS

By using the ICSNPathway to analyze the DN GWAS data, we identified 14 candidate SNPs, 10 genes (including EBI3, NMUR2, and EFNA1), and 19 pathways that likely contribute to the susceptibility to DN in type 1 diabetes.

The Cancer Genomics Resource List 2014

CONTEXT

Genomic sequencing for cancer is offered by commercial for-profit laboratories, independent laboratory networks, and laboratories in academic medical centers and integrated health networks. The variability among the tests has created a complex, confusing environment.

OBJECTIVE

To address the complexity, the Personalized Health Care (PHC) Committee of the College of American Pathologists proposed the development of a cancer genomics resource list (CGRL). The goal of this resource was to assist the laboratory pathology and clinical oncology communities.

DESIGN

The PHC Committee established a working group in 2012 to address this goal. The group consisted of site-specific experts in cancer genetic sequencing. The group identified current next-generation sequencing (NGS)-based cancer tests and compiled them into a usable resource. The genes were annotated by the working group. The annotation process drew on published knowledge, including public databases and the medical literature.

RESULTS

The compiled list includes NGS panels offered by 19 laboratories or vendors, accompanied by annotations. The list has 611 different genes for which NGS-based mutation testing is offered. Surprisingly, of these 611 genes, 0 genes were listed in every panel, 43 genes were listed in 4 panels, and 54 genes were listed in 3 panels. In addition, tests for 393 genes were offered by only 1 or 2 institutions. Table 1 provides an example of gene mutations offered for breast cancer genomic testing with the annotation as it appears in the CGRL 2014.

CONCLUSIONS

The final product, referred to as the Cancer Genomics Resource List 2014, is available as supplemental digital content.

Clinical features of ATRX or DAXX mutated neuroblastoma

PURPOSE

Previously, we reported that alternative lengthening of telomere (ALT) may be a biomarker for chemo-sensitivity and late recurrence in neuroblastoma (NBL). In this study, alterations of ATRX or DAXX, which both encode chromatin remodeling proteins in telomeric region, and their relationship to ALT were examined in NBLs.

METHODS

Our previous report on 121 NBLs revealed 11 NBLs with elongated telomeres by ALT. In these NBLs, ATRX or DAXX gene alterations were identified using next-generation sequencing and compared to clinical and other biological factors.

RESULTS

In 11 ALT cases, DAXX mutations were detected in one case, and ATRX alterations were detected in 10 cases. Except for one case, no DAXX or ATRX alterations were detected in 110 tumors with normal or shortened telomeres. MYCN amplification was not detected in ATRX altered tumors. In ALT cases, three infants showed ATRX deletions, and all seven cases detected after 18months of age showed poor prognosis.

CONCLUSIONS

In NBLs, ALT was caused by ATRX or DAXX alterations. ATRX altered cases without MYCN amplification detected at greater than 18months showed poor prognosis, suggesting that ATRX or DAXX alterations are a particular NBL subtype. Since these tumors showed chemo-resistance and late recurrence, complete resection in a surgical approach should be performed to improve patient prognosis.

Inhibition of H3K9 methyltransferase G9a repressed cell proliferation and induced autophagy in neuroblastoma cells

Histone methylation plays an important role in gene transcription and chromatin organization and is linked to the silencing of a number of critical tumor suppressor genes in tumorigenesis. G9a is a histone methyltransferase (HMTase) for histone H3 lysine 9. In this study, we investigated the role of G9a in neuroblastoma tumor growth together with the G9a inhibitor BIX01294. The exposure of neuroblastoma cells to BIX01294 resulted in the inhibition of cell growth and proliferation, and BIX01294 treatment resulted in the inhibition of the tumorigenicity of neuroblastoma cells in NOD/SCID mice. Therefore, G9a may be a potential therapeutic target in neuroblastoma. Moreover, we found several specific characteristics of autophagy after BIX01294 treatment, including the appearance of membranous vacuoles and microtubule-associated protein light chain 3 (LC3B). Similar results were observed in G9a-knockdown cells. In conclusion, our results demonstrated that G9a is a prognostic marker in neuroblastoma, and revealed a potential role of G9a in regulating the autophagy signaling pathway in neuroblastoma.

Downregulation of tumor suppressor menin by miR-421 promotes proliferation and migration of neuroblastoma

Neuroblastoma, featured by a high rate of spontaneous remissions, is the most common extra-cranial solid tumor in infants and children. Numerous reports have demonstrated that MicroRNAs (miRNAs) play essential roles in cancer progression, including cell proliferation, apoptosis, invasion, metastasis and angiogenesis. miR-421 functions as an onco-miR in some malignancies. However, its role in neuroblastoma remains poorly understood. In the present study, we found that miR-421 was increased in neuroblastoma tissues compared with matched adjacent normal tissues. Forced overexpression of miR-421 substantially enhanced cell proliferation, cell-cycle progression, migration, and invasion of neuroblastoma cells. At the molecular level, tumor suppressor menin was found to be a target of miR-421. Furthermore, downregulation of menin by small interfering RNA oligos exhibited similar effects with overexpression of miR-421. On the other hand, overexpression of menin partially reversed the proliferative effects of miR-421 in neuroblastoma cells. Collectively, miR-421 may promote neuroblastoma cell growth and motility partially by targeting menin.

Genome-wide pathway analysis in neuroblastoma

The aim of this study was to identify candidate single-nucleotide polymorphisms (SNPs) that might play a role in susceptibility to neuroblastoma, elucidate their potential mechanisms, and generate SNP-to-gene-to-pathway hypotheses. A genome-wide association study (GWAS) dataset of neuroblastoma that included 442,976 SNPs from 1,627 neuroblastoma patients and 3,254 control subjects of European descent was used in this study. The identify candidate causal SNPs and pathways (ICSNPathway) analysis was applied to the GWAS dataset. ICSNPathway analysis identified 15 candidate SNPs, 10 genes, and 31 pathways, which revealed 10 hypothetical biological mechanisms. The strongest hypothetical biological mechanism was one wherein SNPrs40401 modulates the role of IL3 in several pathways and conditions, including the stem pathway, asthma (hsa05310), the dendritic cell pathway, and development (0.001 < p < 0.004; 0.001 < FDR < 0.033). The second strongest mechanism identified was that in which rs1048108 and rs16852600 alter the function of BARD1, which negatively regulates developmental process and modulates processes including cell development and programmed cell death (0.001 < p < 0.004; 0.001 < FDR < 0.033). The third mechanism identified was one wherein rs1939212 modulated CFL1, resulting in negative regulation of development, cell death, neural crest cell migration, and apoptosis (0.001 < p < 0.004; 0.001 < FDR < 0.033). By using the ICSNPathway to analyze neuroblastoma GWAS data, 15 candidate SNPs, 10 genes including IL3, BARD1, and CFL, and 31 pathways were identified that might contribute to the susceptibility of patients to neuroblastoma.