An integrated analysis of cancer genes in thyroid cancer

FHOD3 shows clinical significance in progression of ovarian cancer through regulation of caspase-3 signaling pathway

Ovarian cancer is a malignant disease threatening women's life. Traditional therapies bring little benefits for the patients with distant metastasis or recurrence. FHOD3 gene was reported to promote progression in cancer. However, the role of FHOD3 in ovarian cancer is not known yet. To investigate the role of FHOD3 gene in the progression of ovarian cancer and its molecular mechanism, FHOD3 gene was successfully knocked down in ovarian cancer cell lines. Then cell behaviors includes proliferation, migration, invasion, and apoptosis were detected. The data demonstrated that cell proliferation, migration, and invasion ability were suppressed after FHOD3 knockdown. Cell apoptosis was induced reversely. Moreover, caspase-3-mediated signaling pathway was activated after FHOD3 knockdown, and activity of caspase-3 further supported this finding. In addition, PARP inhibitor, Olaparib showed much more potent inhibition in ovarian cancer cells with FHOD3 knockdown. In clinical ovarian cancer tissues, FHOD3 gene showed increased expression compared to adjacent normal tissues. And FHOD3 gene expression level was negatively correlated to the patients' survival. Overall, these findings shed light on the significance of FHOD3 gene in progression of ovarian cancer. This study showed that FHOD3 gene might be exploited as a new target to improve the clinical outcome of ovarian cancer.

DrGA: cancer driver gene analysis in a simpler manner

Background

To date, cancer still is one of the leading causes of death worldwide, in which the cumulative of genes carrying mutations was said to be held accountable for the establishment and development of this disease mainly. From that, identification and analysis of driver genes were vital. Our previous study indicated disagreement on a unifying pipeline for these tasks and then introduced a complete one. However, this pipeline gradually manifested its weaknesses as being unfamiliar to non-technical users, time-consuming, and inconvenient.

Results

This study presented an R package named DrGA, developed based on our previous pipeline, to tackle the mentioned problems above. It wholly automated four widely used downstream analyses for predicted driver genes and offered additional improvements. We described the usage of the DrGA on driver genes of human breast cancer. Besides, we also gave the users another potential application of DrGA in analyzing genomic biomarkers of a complex disease in another organism.

Conclusions

DrGA facilitated the users with limited IT backgrounds and rapidly created consistent and reproducible results. DrGA and its applications, along with example data, were freely provided at https://github.com/huynguyen250896/DrGA.

Formins in Human Disease

Almost 25 years have passed since a mutation of a formin gene, DIAPH1, was identified as being responsible for a human inherited disorder: a form of sensorineural hearing loss. Since then, our knowledge of the links between formins and disease has deepened considerably. Mutations of DIAPH1 and six other formin genes (DAAM2, DIAPH2, DIAPH3, FMN2, INF2 and FHOD3) have been identified as the genetic cause of a variety of inherited human disorders, including intellectual disability, renal disease, peripheral neuropathy, thrombocytopenia, primary ovarian insufficiency, hearing loss and cardiomyopathy. In addition, alterations in formin genes have been associated with a variety of pathological conditions, including developmental defects affecting the heart, nervous system and kidney, aging-related diseases, and cancer. This review summarizes the most recent discoveries about the involvement of formin alterations in monogenic disorders and other human pathological conditions, especially cancer, with which they have been associated. In vitro results and experiments in modified animal models are discussed. Finally, we outline the directions for future research in this field.

Large contribution of copy number alterations in early stage of Papillary Thyroid Carcinoma

Papillary Thyroid Carcinoma (PTC) accounts for approximately 85% of patients with thyroid cancer. Despite its indolent nature, progression to higher stages is expected in a subgroup of patients. Hence, genomic characterization of the early stages of PTC may help to identify this subgroup, leading to better clinical management. Here, we conducted a comprehensive mutational and somatic copy number alteration (SCNA) investigation on 277 stage one PTC from TCGA. SCNA analysis revealed amplification and deletion of several cancer related genes. We found amplification of 60 oncogenes (Oncs), from which 15 were recurrently observed. Deletion of 58 tumor suppressors (TSs) was also detected. MAPK, PI3K-Akt, Rap1 and Ras were the signaling pathways with large numbers of amplified Oncs. On the other hand, deleted TSs belonged mostly to cell cycle, PI3K-Akt, mTOR and cellular senescence pathways. This suggests that despite heterogeneity in SCNA events, the final results would be the activation/deactivation of a few cancer signaling pathways. Of note, despite large amounts of heterogeneity in stage one PTC, recurrent broad deletion on Chr22 was detected in 21 individuals, leading to deletion of several tumor suppressors. In parallel, the oncogenic/pathogenic mutations in the RTK-RAS and PI3k-Akt pathways were detected. However, no pathogenic mutation was identified in known tumor suppressor genes. In order to identify a potential subgroup of BRAF (V600E) positive patients, who might progress to higher stages, low frequency mutations accompanying BRAF (V600E) were also identified. In conclusion, our findings imply that SCNA have a substantial contribution to early stages of PTC. Experimental validation of the observed genomic alterations could help to stratify patients at the time of diagnosis, and to move toward precision medicine in PTC.

Noncanonical Functions and Cellular Dynamics of the Mammalian Signal Recognition Particle Components

The signal recognition particle (SRP) is a ribonucleoprotein complex fundamental for co-translational delivery of proteins to their proper membrane localization and secretory pathways. Literature of the past two decades has suggested new roles for individual SRP components, 7SL RNA and proteins SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72, outside the SRP cycle. These noncanonical functions interconnect SRP with a multitude of cellular and molecular pathways, including virus-host interactions, stress response, transcriptional regulation and modulation of apoptosis in autoimmune diseases. Uncovered novel properties of the SRP components present a new perspective for the mammalian SRP as a biological modulator of multiple cellular processes. As a consequence of these findings, SRP components have been correlated with a growing list of diseases, such as cancer progression, myopathies and bone marrow genetic diseases, suggesting a potential for development of SRP-target therapies of each individual component. For the first time, here we present the current knowledge on the SRP noncanonical functions and raise the need of a deeper understanding of the molecular interactions between SRP and accessory cellular components. We examine diseases associated with SRP components and discuss the development and feasibility of therapeutics targeting individual SRP noncanonical functions.

Generation and Differentiation of Adult Tissue-Derived Human Thyroid Organoids

Total thyroidectomy as part of thyroid cancer treatment results in hypothyroidism requiring lifelong daily thyroid hormone replacement. Unbalanced hormone levels result in persistent complaints such as fatigue, constipation, and weight increase. Therefore, we aimed to investigate a patient-derived thyroid organoid model with the potential to regenerate the thyroid gland. Murine and human thyroid-derived cells were cultured as organoids capable of self-renewal and which expressed proliferation and putative stem cell and thyroid characteristics, without a change in the expression of thyroid tumor-related genes. These organoids formed thyroid-tissue-resembling structures in culture. (Xeno-)transplantation of 600,000 dispersed organoid cells underneath the kidney capsule of a hypothyroid mouse model resulted in the generation of hormone-producing thyroid-resembling follicles. This study provides evidence that thyroid-lineage-specific cells can form organoids that are able to self-renew and differentiate into functional thyroid tissue. Subsequent (xeno-)transplantation of these thyroid organoids demonstrates a proof of principle for functional miniature gland formation.

FHOD3 promotes carcinogenesis by regulating RhoA/ROCK1/LIMK1 signaling pathway in medulloblastoma

PURPOSE

Medulloblastoma (MB) is a malignant brain disease in young children. The overall survival of MB patients is disappointing due to absence of effective therapeutics and this could be attributed to the lack of molecular mechanism underlying MB. FHOD3 was an important gene during cardio-genesis and was reported to promote cell migration in cancer. However, its role in MB is not clear to date.

METHODS

RT-qPCR and IHC analysis were used to determine expression of FHOD3. Survival curve was drawn by K-M analysis. FHOD3 was knocked down by RNAi technology. The effects of FHOD3 on medulloblastoma cells were determined by CCK-8 assay, colony formation assay, transwell assay and FACs analysis.

RESULTS

FHOD3 expression increased by 1.5 fold in tumor tissues compared to the control and IHC analysis further confirmed strong expression of FHOD3 in medulloblastoma tissues. Then higher FHOD3 expression was associated with shorter survival time in MB patients (13.0 months versus 43.8 months). In medulloblastoma cells such as Daoy and D283med, FHOD3 also displayed abundant expression. When FHOD3 was knocked down, the ability of cell proliferation and colony formation was reduced over greatly. The capability of cell migration and invasion was also inhibited significantly. However, cell apoptotic rate increased significantly reversely. Mechanistically, the phosphorylation level of RhoA, ROCK1, and LIMK1 was decreased when FHOD3 was knocked down but increased reversely when FHOD3 was over-expressed in Daoy cells.

CONCLUSIONS

FHOD3 was associated with overall survival time in medulloblastoma patients and was essential to cell proliferation, growth and survival in medulloblastoma and might regulates activation of RhoA/ROCK1/LIMK1 signaling pathway.

Improving existing analysis pipeline to identify and analyze cancer driver genes using multi-omics data

The cumulative of genes carrying mutations is vital for the establishment and development of cancer. However, this driver gene exploring research line has selected and used types of tools and models of analysis unsystematically and discretely. Also, the previous studies may have neglected low-frequency drivers and seldom predicted subgroup specificities of identified driver genes. In this study, we presented an improved driver gene identification and analysis pipeline that comprises the four most widely focused analyses for driver genes: enrichment analysis, clinical feature association with expression profiles of identified driver genes as well as with their functional modules, and patient stratification by existing advanced computational tools integrating multi-omics data. The improved pipeline's general usability was demonstrated straightforwardly for breast cancer, validated by some independent databases. Accordingly, 31 validated driver genes, including four novel ones, were discovered. Subsequently, we detected cancer-related significantly enriched gene ontology terms and pathways, probable drug targets, two co-expressed modules associated significantly with several clinical features, such as number of positive lymph nodes, Nottingham prognostic index, and tumor stage, and two biologically distinct groups of BRCA patients. Data and source code of the case study can be downloaded at https://github.com/hauldhut/drivergene.

The Integrated Analyses of Driver Genes Identify Key Biomarkers in Thyroid Cancer

AIM

Thyroid cancer is the most common endocrine cancer, the incidence rate has continuously increased worldwide. However, there are still lack of effective molecular biomarkers for the diagnosis and treatment of the disease. The study was conducted to identify driver genes that may serve as potential biomarkers for the disease.

METHODS

The computational tools oncodriveCLUST, oncodriveFM, icages and drgap were used to detect driver genes in thyroid cancer using somatic mutations from The Cancer Genome Atlas database. Integrated analyses were performed on the driver genes using multiomics data from the TCGA database.

RESULTS

A set of 291 driver genes were identified in thyroid cancer. BRAF, NRAS, HRAS, OTUD4, EIF1AX were the top 5 frequently mutated genes in thyroid cancer. The weighted gene co-expression network analysis identified 4 coexpression modules. The modules 1-3 were significantly associated with patients' tumor size, residual tumor, cancer stage, distant metastasis and multifocality. SEC24B, MET and ITGAL were the hub genes in the modules 1-3 respectively. Hierarchical clustering analysis of the 20 driver genes with the most frequent copy number changes revealed 3 clusters of PRAD patients. Cluster 1 tumors exhibited significantly older age, tumor size, cancer stages, and poorer prognosis than cluster 2 and 3 tumors. 16 genes were significantly associated with number of lymph nodes, tumor size and pathologic stage, such as IL7 R, IRS1, PTK2B, MAP3K3 and FGFR2.

CONCLUSIONS

The set of cancer genes and subgroups of patients shed insight on the tumorigenesis of thyroid cancer and open up avenues for developing prognostic biomarkers and driver gene-targeted therapies in thyroid cancer.

Heterozygous loss of Srp72 in mice is not associated with major hematological phenotypes

OBJECTIVES

Familial cases of hematological malignancies are associated with germline mutations. In particular, heterozygous mutations of SRP72 correlate with the development of myelodysplasia and bone marrow aplasia in two families. The signal recognition particle 72 kDa protein (SRP72) is part of the SRP complex, responsible for targeting of proteins to the endoplasmic reticulum. The main objective of this study is to investigate the role of SRP72 in the hematopoietic system, thus explaining why a reduced dose could increase susceptibility to hematological malignancies.

METHODS

We developed an Srp72 null mouse model and characterized its hematopoietic system using flow cytometry, bone marrow transplantations, and gene expression analysis.

RESULTS

Heterozygous loss of Srp72 in mice is not associated with major changes in hematopoiesis, although causes mild reductions in blood and BM cellularity and minor changes within the stem/progenitor compartment. We did not observe any hematological disorder. Interestingly, gene expression analysis demonstrated that genes encoding secreted factors, including cytokines and receptors, were transcriptionally down-regulated in Srp72^+/- animals.

CONCLUSIONS

The Srp72^+/- mouse model only partially recapitulates the phenotype observed in families with inherited SRP72 lesions. Nonetheless, these results can provide mechanistic insights into why SRP72 mutations are associated with aplasia and myelodysplasia in humans.

Detection of genetic alterations in gastric cancer patients from Saudi Arabia using comparative genomic hybridization (CGH)

Background

The present study was conducted to discover genetic imbalances such as DNA copy number variations (CNVs) associated with gastric cancer (GC) and to examine their association with different genes involved in the process of gastric carcinogenesis in Saudi population.

Methods

Formalin-fixed paraffin-embedded (FFPE) tissues samples from 33 gastric cancer patients and 15 normal gastric samples were collected. Early and late stages GC samples were genotyped and CNVs were assessed by using Illumina HumanOmni1-Quad v.1.0 BeadChip.

Results

Copy number gains were more frequent than losses throughout all GC samples compared to normal tissue samples. The mean number of the altered chromosome per case was 64 for gains and 40 for losses, and the median aberration length was 679115bp for gains and 375889bp for losses. We identified 7 high copy gain, 52 gains, 14 losses, 32 homozygous losses, and 10 copy neutral LOHs (loss of heterozygosities). Copy number gains were frequently detected at 1p36.32, 1q12, 1q22, 2p11.1, 4q23-q25, 5p12-p11, 6p21.33, 9q12-q21.11, 12q11-q12, 14q32.33, 16p13.3, 17p13.1, 17q25.3, 19q13.32, and losses at 1p36.23, 1p36.32, 1p32.1, 1q44, 3q25.2, 6p22.1, 6p21.33, 8p11.22, 10q22.1, 12p11.22, 14q32.12 and 16q24.2. We also identified 2 monosomy at chromosome 14 and 22, 52 partially trisomy and 22 whole chromosome 4 neutral loss of heterozygosities at 13q14.2-q21.33, 5p15.2-p15.1, 5q11.2-q13.2, 5q33.1-q34 and 3p14.2-q13.12. Furthermore, 11 gains and 2 losses at 1p36.32 were detected for 11 different GC samples and this region has not been reported before in other populations. Statistical analysis confirms significant association of H. pylori infection with T4 stage of GC as compare to control and other stages.

Conclusions

We found that high frequency of copy number gains and losses at 1p36.23, 1p32.1, 1p36.32, 3q25.2, 6p21.33 and 16q24.2 may be common events in gastric cancer. While novel CNVs at 1p36.32 harbouring PRDM16, TP73 and TP73-AS1 genes showed 11 gains and 2 losses for 11 different GC cases and this region is not reported yet in Database of Genomic Variants may be specific to Saudi population.

Inhibition of the AKT/mTOR Pathway Augments the Anticancer Effects of Sorafenib in Thyroid Cancer

BACKGROUND

Sorafenib is a multikinase inhibitor that has been approved for the treatment of patients with advanced ¹³¹iodine (¹³¹I) refractory differentiated thyroid cancer (DTC). However, the progression-free survival of patients with advanced ¹³¹I refractory DTC is short, and most DTC patients eventually acquire resistance to sorafenib. Therefore, new therapeutic strategies need to be developed.

MATERIALS AND METHODS

The thyroid cancer cell lines 8505C and FTC133 were treated with sorafenib in the presence or absence of BEZ235 or small interfering RNA (siRNA) directed against AKT. A CCK8 kit was used to evaluate cell viability. Protein expression levels of relevant genes were determined by Western blotting analysis, whereas messenger RNA expression levels were determined by real-time PCR analysis. Flow cytometry was performed to assess the number of apoptotic cells.

RESULTS

The results indicate that sorafenib simultaneously inhibited the activities of the MAPK and PI3K/AKT/mTOR pathways in thyroid cancer cells. Treatment of 8505C and FTC133 cells with NVP-BEZ235, siRNA against AKT, or sorafenib induced tumor cell apoptosis and led to reduced tumor cell proliferation. Sorafenib in combination with PI3K/AKT/mTOR inhibition by NVP-BEZ235 or AKT siRNA enhanced apoptosis and proliferation suppression.

CONCLUSIONS

The evidence of this study suggests that a combinatorial approach that inhibits both the MAPK and PI3K/AKT/mTOR pathways exerts a greater antitumor effect than sorafenib alone in thyroid cancer cell lines.

Predictive and Prognostic Implications of Mutation Profiling and Microsatellite Instability Status in Patients with Metastatic Colorectal Carcinoma

To investigate whether mutation profiling and microsatellite instability (MSI) status were associated with clinicopathological features and the prognosis in metastatic colorectal cancer (mCRC), mutations in RAS (including KRAS, NRAS, and HRAS) and BRAF were determined by Sanger sequencing. Tumor mismatch repair proteins and MSI status were examined using immunohistochemistry and polymerase chain reaction, respectively. The clinical value of these abnormalities was statistically analyzed, and prognostic value of different treatment regimens was also evaluated. Among 461 mCRC patients, mutations in RAS, BRAF, and MSI-high (MSI-H) status were observed in 45.3% (209/461), 5.6% (26/461), and 6.5% (30/461) of cases, respectively. Brain metastasis and high carcinoembryonic antigen level were highly correlated with KRAS mutation (P = 0.011 and P < 0.001), and tumors from females or located in the right colon tended to harbor BRAF mutation (P = 0.039 and P = 0.001). RAS/BRAF mutations may predict brain and/or lung metastases. Although neither clinical nor prognostic importance of MSI status was identified in our study, KRAS and BRAF mutations were demonstrated to be independent prognostic factors for overall survival and progression-free survival. Besides, in wild-type group, patients treated with chemotherapy plus targeted therapy exhibited the most favorable prognosis. Therefore, RAS/BRAF mutations may serve as indicators for prognosis and treatment options in mCRC.

Comprehensive characterization of differentially expressed genes in thyroid cancer

AIM

To explore the patterns of gene expression and functionally characterize the differentially expressed genes (DEGs) in thyroid cancer.

METHODS

DEGs were determined between 57 paired thyroid cancer and noncancerous tissues using DESeq2. Subsequently, the main functions of the DEGs were studied by a variety of analyses.

RESULTS

We identified a cohort of 752 upregulated and 309 downregulated DEGs in thyroid cancer. Several hub DEGs were found in the protein-protein interaction networks. We also revealed a set of DEGs that were dysmethylated, involved in copy number variations and associated with clinical features in thyroid cancer.

CONCLUSION

These results provide some novel findings on DEGs in thyroid cancer, which will be useful to guide further investigation and target therapy for this disease. [Formula: see text].

Prevalence and phenotypic correlations of EIF1AX mutations in thyroid nodules

The EIF1AX gene mutations have been recently found in papillary thyroid carcinoma (PTC) and anaplastic thyroid carcinoma (ATC). The prevalence of these mutations in other types of thyroid cancers and benign nodules is unknown. In this study, we analyzed the occurrence of EIF1AX mutations in exons 2, 5, and 6 of the gene in a series of 266 thyroid tumors and hyperplastic nodules by either Sanger or next-generation sequencing (ThyroSeq v.2). In addition, 647 thyroid fine-needle aspiration (FNA) samples with indeterminate cytology were analyzed. Using surgically removed samples, EIF1AX mutations were detected in 3/86 (2.3%) PTC, 1/4 (25%) ATC, 0/53 follicular carcinomas, 0/12 medullary carcinomas, 2/27 (7.4%) follicular adenomas, and 1/80 (1.3%) hyperplastic nodules. Among five mutation-positive FNA samples with surgical follow-up, one nodule was PTC and others were benign follicular adenomas or hyperplastic nodules. Overall, among 33 mutations identified, A113_splice mutation at the intron 5/exon 6 splice site of EIF1AX was the most common. All four carcinomas harbored A113_splice mutation and three of them had one or more coexisting mutations, typically RAS All PTC carrying EIF1AX mutations were encapsulated follicular variants. In summary, this study shows that EIF1AX mutations occur not only in thyroid carcinomas, but also in benign nodules. The most common mutation hotspot is the A113_splice, followed by a cluster of mutations in exon 2. When found in thyroid FNA samples, EIF1AX mutations confer ~20% risk of cancer; the risk is likely to be higher in nodules carrying a A113_splice mutation and when EIF1AX coexists with RAS mutations.