Identification of mutant genes with high-frequency, high-risk, and high-expression in lung adenocarcinoma

Control of TGFβ signalling by ubiquitination independent function of E3 ubiquitin ligase TRIP12

Transforming growth factor β (TGFβ) pathway is a master regulator of cell proliferation, differentiation, and death. Deregulation of TGFβ signalling is well established in several human diseases including autoimmune disorders and cancer. Thus, understanding molecular pathways governing TGFβ signalling may help better understand the underlying causes of some of those conditions. Here, we show that a HECT domain E3 ubiquitin ligase TRIP12 controls TGFβ signalling in multiple models. Interestingly, TRIP12 control of TGFβ signalling is completely independent of its E3 ubiquitin ligase activity. Instead, TRIP12 recruits SMURF2 to SMAD4, which is most likely responsible for inhibitory monoubiquitination of SMAD4, since SMAD4 monoubiquitination and its interaction with SMURF2 were dramatically downregulated in TRIP12-/- cells. Additionally, genetic inhibition of TRIP12 in human and murine cells leads to robust activation of TGFβ signalling which was rescued by re-introducing wildtype TRIP12 or a catalytically inactive C1959A mutant. Importantly, TRIP12 control of TGFβ signalling is evolutionary conserved. Indeed, genetic inhibition of Drosophila TRIP12 orthologue, ctrip, in gut leads to a reduced number of intestinal stem cells which was compensated by the increase in differentiated enteroendocrine cells. These effects were completely normalised in Drosophila strain where ctrip was co-inhibited together with Drosophila SMAD4 orthologue, Medea. Similarly, in murine 3D intestinal organoids, CRISPR/Cas9 mediated genetic targeting of Trip12 enhances TGFβ mediated proliferation arrest and cell death. Finally, CRISPR/Cas9 mediated genetic targeting of TRIP12 in MDA-MB-231 breast cancer cells enhances the TGFβ induced migratory capacity of these cells which was rescued to the wildtype level by re-introducing wildtype TRIP12. Our work establishes TRIP12 as an evolutionary conserved modulator of TGFβ signalling in health and disease.

Lung Cancer Subtype Diagnosis by Fusing Image-Genomics Data and Hybrid Deep Networks

Accurate diagnosis of cancer subtypes is crucial for precise treatment, because different cancer subtypes are involved with different pathology and require different therapies. Although deep learning techniques have made great success in computer vision and other fields, they do not work well on Lung cancer subtype diagnosis, due to the distinction of slide images between different cancer subtypes is ambiguous. Furthermore, they often over-fit to high-dimensional genomics data with limited samples, and do not fuse the image and genomics data in a sensible way. In this paper, we propose a hybrid deep network based approach LungDIG for Lung cancer subtype Diagnosis by fusing Image-Genomics data. LungDIG first tiles the tissue slide image into small patches and extracts the patch-level features by fine-tuning an Inception-V3 model. Since the patches may contain some false positives in non-diagnostic regions, it further designs a patch-level feature combination strategy to integrate the extracted patch features and maintain the diversity between different cancer subtypes. At the same time, it extracts the genomics features from Copy Number Variation data by an attention based nonlinear extractor. Next, it fuses the image and genomics features by an attention based multilayer perceptron (MLP) to diagnose cancer subtype. Experiments on TCGA lung cancer data show that LungDIG can not only achieve higher accuracy for cancer subtype diagnosis than state-of-the-art methods, but also have a high authenticity and good interpretability.

The oncogenic E3 ligase TRIP12 suppresses epithelial-mesenchymal transition (EMT) and mesenchymal traits through ZEB1/2

Thyroid hormone receptor interactor 12 (TRIP12) is an E3 ligase most notably involved in the proteolytic degradation of the tumor suppressor p14ARF. Through this process, it is proposed that TRIP12 plays an oncogenic role in tumor initiation and growth. However, its role in other cancer processes is unknown. In this study, using publicly available cancer patient datasets, we found TRIP12 to be associated with distant metastasis-free survival in breast cancer, suggesting an inhibitory role in metastasis. Following TRIP12 depletion, an epithelial-mesenchymal transition (EMT) shift occurred with concomitant changes in EMT cell adhesion markers identified through RNA-seq. In line with EMT changes, TRIP12-depleted cells gained mesenchymal traits such as loss of cell polarity, dislodgement from bulk cells at a higher frequency, and increased cellular motility. Furthermore, ectopic TRIP12 expression sensitized cells to anoikis. Mechanistically, TRIP12 suppresses EMT through inhibiting ZEB1/2 gene expression, and ZEB1/2 depletion rescues EMT markers and mesenchymal behavior. Overall, our study delineates TRIP12's role in inhibition of EMT and implies a potential suppressive role in breast cancer metastasis.

Extracellular Matrix Proteins and Transcription of Matrix-Associated Genes in Mesenchymal Stromal Cells during Modeling of the Effects of Microgravity

We studied the effects of simulated microgravity (10 days) on the production of extracellular matrix proteins and expression of extracellular matrix-associated genes in human mesenchymal stem cells. A decrease in collagen production, reduced expression of TIMP-1, TIMP-3, and MMP-11 genes, and enhanced expression of tenascin and laminin subunit were revealed. The results attest to activation of proteolytic processes in the matrix of mesenchymal stromal cells and weakening of cell adhesion to extracellular matrix under conditions of simulated microgravity.

E3 Ubiquitin Ligase TRIP12: Regulation, Structure, and Physiopathological Functions

The Thyroid hormone Receptor Interacting Protein 12 (TRIP12) protein belongs to the 28-member Homologous to the E6-AP C-Terminus (HECT) E3 ubiquitin ligase family. First described as an interactor of the thyroid hormone receptor, TRIP12’s biological importance was revealed by the embryonic lethality of a murine model bearing an inactivating mutation in the TRIP12 gene. Further studies showed the participation of TRIP12 in the regulation of major biological processes such as cell cycle progression, DNA damage repair, chromatin remodeling, and cell differentiation by an ubiquitination-mediated degradation of key protein substrates. Moreover, alterations of TRIP12 expression have been reported in cancers that can serve as predictive markers of therapeutic response. The TRIP12 gene is also referenced as a causative gene associated to intellectual disorders such as Clark–Baraitser syndrome and is clearly implicated in Autism Spectrum Disorder. The aim of the review is to provide an exhaustive and integrated overview of the different aspects of TRIP12 ranging from its regulation, molecular functions and physio-pathological implications.

Mechanism of autophagy regulating chemoresistance in esophageal cancer cells

The current study aimed to explore the mechanism of autophagy-regulating chemoresistance in esophageal cancer (EC) cells. Methods: 45 cases of esophageal cancer cell tissue and 25 cases of adjacent normal tissue excised in the surgical resection were collected from the tumor pathology department of our hospital from March to November 2017. The above cancer cells and paracancerous cells were cultured according to the cell culture procedures. The autophagy was induced by cisplatin in human esophageal cancer EC9706 cells line. The effect of autophagy on the survival of EC9706 cells was observed by autophagy inhibitor 3-MA. Cell viability was also measured by cell counting kit-8 (CCK-8). Apoptosis and cell cycle were detected by flow cytometry. Furthermore, monodansylcadaverine (MDC) was used to detect autophagy. Western blot was applied to determine the molecular changes during treatment. Diketopyrrolopyrrole (DPP) is able to inhibit cell proliferation, induce cell death and cell cycle arrest in the S phase. In addition, autophagy was activated through PI3K-III pathway. Results: 3-MA inhibitor plus 10% fetal bovine serum were added for culture, and the cell culture temperature and humidity were the best conditions. There were few autophagic vesicles in the stationary cells, where their brightness was weakened. There were more and brighter green fluorescent particles in the DPP group without a 3-MA inhibitor, indicating that autophagic parameters actually exist in this process. The apoptosis rate of DDP-induced cell death was not found to be the best, but was higher than that of the control group (P<0.05). The combination of DDP and 3-MA had a more obvious catalytic effect on apoptosis, and the apoptosis rate was much higher than that of single DDP (P<0.05), indicating that DDP was capable of inducing significant apoptosis after inhibiting autophagy. The combination of DDP and 3-MA had an obvious catalytic effect on apoptosis, and the apoptosis rate was higher than that of DDP alone (P < 0.05), suggesting that DDP could significantly improve the ability to induce apoptosis after inhibiting autophagy. The expression level of autophagy-related proteins was also detected by Western blotting. Our findings indicated that autophagy may be a self-protective mechanism of esophageal cancer cells induced by DDP, and its inhibition may be a new strategy for adjuvant chemotherapy in esophageal cancer.

Expression profile and prognostic values of STAT family members in non-small cell lung cancer

Non-small cell lung cancer (NSCLC) is a highly malignant type of cancer with a poor 5-year survival rate. The development of prognostic biomarkers and novel drug targets are required in order to improve the survival for NSCLC patients. Signal transducer and activator of transcription (STAT) proteins are cytoplasmic transcription factors known to play key roles in many cellular biological processes. However, the roles of STAT family members in the development and progression of NSCLC have not yet been apparently determined. Our study investigated the roles of STATs in the prognosis of NSCLC using cBioPortal, Human Protein Atlas, ONCOMINE, and Kaplan-Meier Plotter databases. High mutation rate of STATs existed in both lung adenocarcinoma (ADE) patients and squamous cell carcinoma (SCC) patients. High mRNA expression of STAT2 was significantly associated with shorter overall survival (OS) in NSCLC patients, while increased STAT5 and STAT6 were associated with better OS in NSCLC patients. We further found that increased mRNA expressions of STAT2 and STAT3 predicted unfavorable overall survival (OS) while high mRNA expression of STAT5B and STAT6 related to favorable OS for lung ADE patients. However, no significant correlation was identified for lung SCC patients. In stratified survival analysis, high expression of STAT2 predicted poor prognosis in stage II NSLCC patients, surgical margins negative patients and female patients. Taken together, our results illustrated that STAT5B and STAT6 could be effective prognostic biomarkers for survivals of NSCLC patients. And STAT2 might be a promising therapeutic target for the treatment of NSCLC as well as ADE.

Cancer gene mutations in congenital pulmonary airway malformation patients

Background

Newborns affected with congenital pulmonary airway malformations (CPAMs) may present with severe respiratory distress or remain asymptomatic. While surgical resection is the definitive treatment for symptomatic CPAMs, prophylactic elective surgery may be recommended for asymptomatic CPAMs owing to the risk of tumour development. However, the implementation of prophylactic surgery is quite controversial on the grounds that more evidence linking CPAMs and cancer is needed. The large gap in knowledge of CPAM pathogenesis results in uncertainties and controversies in disease management. As developmental genes control postnatal cell growth and contribute to cancer development, we hypothesised that CPAMs may be underlain by germline mutations in genes governing airways development.

Methods

Sequencing of the exome of 19 patients and their unaffected parents.

Results

A more than expected number of mutations in cancer genes (false discovery rate q-value <5.01×10⁻⁵) was observed. The co-occurrence, in the same patient, of damaging variants in genes encoding interacting proteins is intriguing, the most striking being thyroglobulin (TG) and its receptor, megalin (LRP2). Both genes are highly relevant in lung development and cancer.

Conclusions

The overall excess of mutations in cancer genes may account for the reported association of CPAMs with carcinomas and provide some evidence to argue for prophylactic surgery by some surgeons.

Congenital pulmonary airway malformation (CPAM) patients have more than expected numbers of damaging variants in genes involved in lung carcinoma; this may provide evidence for clinicians choosing to adopt prophylactic excision in CPAMhttp://ow.ly/h1AE30n4DIe

Express: A database of transcriptome profiles encompassing known and novel transcripts across multiple development stages in eye tissues

Advances in sequencing have facilitated nucleotide-resolution genome-wide transcriptomic profiles across multiple mouse eye tissues. However, these RNA sequencing (RNA-seq) based eye developmental transcriptomes are not organized for easy public access, making any further analysis challenging. Here, we present a new database "Express" (http://www.iupui.edu/∼sysbio/express/) that unifies various mouse lens and retina RNA-seq data and provides user-friendly visualization of the transcriptome to facilitate gene discovery in the eye. We obtained RNA-seq data encompassing 7 developmental stages of lens in addition to that on isolated lens epithelial and fibers, as well as on 11 developmental stages of retina/isolated retinal rod photoreceptor cells from publicly available wild-type mouse datasets. These datasets were pre-processed, aligned, quantified and normalized for expression levels of known and novel transcripts using a unified expression quantification framework. Express provides heatmap and browser view allowing easy navigation of the genomic organization of transcripts or gene loci. Further, it allows users to search candidate genes and export both the visualizations and the embedded data to facilitate downstream analysis. We identified total of >81,000 transcripts in the lens and >178,000 transcripts in the retina across all the included developmental stages. This analysis revealed that a significant number of the retina-expressed transcripts are novel. Expression of several transcripts in the lens and retina across multiple developmental stages was independently validated by RT-qPCR for established genes such as Pax6 and Lhx2 as well as for new candidates such as Elavl4, Rbm5, Pabpc1, Tia1 and Tubb2b. Thus, Express serves as an effective portal for analyzing pruned RNA-seq expression datasets presently collected for the lens and retina. It will allow a wild-type context for the detailed analysis of targeted gene-knockout mouse ocular defect models and facilitate the prioritization of candidate genes from Exome-seq data of eye disease patients.

Dysregulation of miR-605-5p/STAT2 axis predicts an unfavorable survival in patients with gastric cancer

Our present study aimed to reveal the clinical significance of miR-605-5p/STAT2 axis in patients with gastric cancer (GC). The association of STAT2 or miR-605-5p expression with the clinicopathological characteristics and prognosis in patients with GC was analyzed using the tissue microarray and TCGA RNA-seq data. Pearson correlation analysis was used to evaluate the correlation of STAT2 with miRNAs expression in GC tissues. Cox proportional hazard regression model was conducted to assess whether STAT2 or miR-605-5p expressions was an independent prognostic factor in patients with GC. Consequently, we found that STAT2 expression levels were dramatically elevated in GC tissues and acted as an independent prognostic factor of poor survival in patients with GC. The upregulation of STAT2 was attributable to the dysregulation of miR-605-5p rather than its genetic and epigenetic modulation. MiR-605-5p indicated a negative correlation with STAT2 expression and was an independent prognostic factor of poor survival in patients with GC. In conclusion, dysregulation of miR-605-5p/STAT2 axis predicted a poor survival in patients with GC.

[Omics technologies in diagnostics of lung adenocarcinoma]

To date lung adenocarcinoma (LAC) is the most common type of lung cancer. Numerous studies on LAC biology resulted in identification of crucial mutations in protooncogenes and activating neoplastic transformation pathways. Therapeutic approaches that significantly increase the survival rate of patients with LAC of different etiology have been developed and introduced into clinical practice. However, the main problem in the treatment of LAC is early diagnosis, taking into account both factors and mechanisms responsible in tumor initiation and progression. Identification of a wide biomarker repertoire with high specificity and reliability of detection appears to be a solution to this problem. In this context, proteins with differential expression in normal and pathological condition, suitable for detection in biological fluids are the most promising biomarkers. In this review we have analyzed literature data on studies aimed at search of LAC biomarkers. The major attention has been paid to protein biomarkers as the most promising and convenient subject of clinical diagnosis. The review also summarizes existing knowledge on posttranslational modifications, splice variants, isoforms, as well as model systems and transcriptome changes in LAC.

Characterization of the Role of the Malate Dehydrogenases to Lung Tumor Cell Survival

Cellular compartmentalization of biochemical processes in eukaryotic cells is critical for many functions including shuttling of reducing equivalents across membranes. Although coordination of metabolic flux between different organelles is vital for cell physiology, its impact on tumor cell survival is not well understood. By using an integrative approach, we have dissected the role of the key metabolic enzymes Malate dehydrogenases (MDH1 and MDH2) to the survival of Non-small Cell Lung Carcinomas. Here, we report that while both the MDH1 (cytosolic) and the MDH2 (mitochondrial) enzymes display elevated levels in patients compared to normal counterparts, only high expression of MDH1 is associated with poor prognosis. We further show that the MDH1 enzymatic activity is significantly higher in NSCLC cells than that of MDH2. Accordingly, genetic depletion of MDH1 leads to significantly higher toxicity than depletion of MDH2. These findings provide molecular insights into the metabolic characteristics of the malate isoenzymes and mark MDH1 as a potential therapeutic target in these tumors.