RNA Gene Expression Profiling Research Articles

RNA editing regulates glutamatergic synapses in the frontal cortex of a molecular subtype of Amyotrophic Lateral Sclerosis

BackgroundAmyotrophic Lateral Sclerosis (ALS) is a highly heterogenous neurodegenerative disorder that primarily affects upper and lower motor neurons, affecting additional cell types and brain regions. Underlying molecular mechanisms are still elusive, in part due to disease heterogeneity. Molecular disease subtyping through integrative analyses including RNA editing profiling is a novel approach for identification of molecular networks involved in pathogenesis.MethodsWe aimed to highlight the role of RNA editing in ALS, focusing on the frontal cortex and the prevalent molecular disease subtype (ALS-Ox), previously determined by transcriptomic profile stratification. We established global RNA editing (editome) and gene expression (transcriptome) profiles in control and ALS-Ox cases, utilizing publicly available RNA-seq data (GSE153960) and an in-house analysis pipeline. Functional annotation and pathway analyses identified molecular processes affected by RNA editing alterations. Pearson correlation analyses assessed RNA editing effects on expression. Similar analyses on additional ALS-Ox and control samples (GSE124439) were performed for verification. Targeted re-sequencing and qRT-PCR analysis targeting CACNA1C, were performed using frontal cortex tissue from ALS and control samples (n = 3 samples/group).ResultsWe identified reduced global RNA editing in the frontal cortex of ALS-Ox cases. Differentially edited transcripts are enriched in synapses, particularly in the glutamatergic synapse pathway. Bioinformatic analyses on additional ALS-Ox and control RNA-seq data verified these findings. We identified increased recoding at the Q621R site in the GRIK2 transcript and determined positive correlations between RNA editing and gene expression alterations in ionotropic receptor subunits GRIA2, GRIA3 and the CACNA1C transcript, which encodes the pore forming subunit of a post-synaptic L-type calcium channel. Experimental data verified RNA editing alterations and editing-expression correlation in CACNA1C, highlighting CACNA1C as a target for further study.ConclusionsWe provide evidence on the involvement of RNA editing in the frontal cortex of an ALS molecular subtype, highlighting a modulatory role mediated though recoding and gene expression regulation on glutamatergic synapse related transcripts. We report RNA editing effects in disease-related transcripts and validated editing alterations in CACNA1C. Our study provides targets for further functional studies that could shed light in underlying disease mechanisms enabling novel therapeutic approaches.

Fibroblast-localized lncRNA CFIRL promotes cardiac fibrosis and dysfunction in dilated cardiomyopathy.

CFIRL is a long noncoding RNA (lncRNA), we previously identified as the most significantly upregulated lncRNA in the failing hearts of patients with dilated cardiomyopathy (DCM). In this study, we determined the function of CFIRL and its role in DCM. Real-time polymerase chain reaction and in situ hybridization assays revealed that CFIRL was primarily localized in the nucleus of cardiac fibroblasts and robustly increased in failing hearts. Global knockdown or fibroblast-specific knockout of CFIRL attenuated transverse aortic constriction (TAC)-induced cardiac dysfunction and fibrosis in vivo. Overexpression of CFIRL in vitro promoted fibroblast proliferation and aggravated angiotensin II-induced differentiation to myofibroblasts. CFIRL knockdown attenuated these effects. Mechanistically, RNA pull-down assay and gene expression profiling revealed that CFIRL recruited ENO1, a newly identified noncanonical transcriptional factor, to activate IL-6 transcription. IL-6 exerted a paracrine effect on cardiomyocytes to promote cardiac hypertrophy, which can be prevented by CFIRL knockdown. These findings uncover the critical role of CFIRL, a fibroblast-associated lncRNA, in heart failure by facilitating crosstalk between fibroblasts and cardiomyocytes. CFIRL knockdown might be a potent strategy to prevent cardiac remodeling in heart failure, particularly in DCM.

PRMT5 and CDK4/6 inhibition result in distinctive patterns of alternative splicing in melanoma.

Drugs targeting cyclin-dependent kinases 4 and 6 (CDK4/6) are promising new treatments for melanoma and other solid malignancies. In studies on CDK4/6 inhibitor resistance, protein arginine methyltransferase 5 (PRMT5) regulation of alternative splicing was shown to be an important downstream component of the CDK4/6 pathway. However, the full effects of inhibition of CDK4/6 on splicing events in melanoma and the extent to which they are dependent on PRMT5 has not been established. We performed full-length mRNA sequencing on CHL1 and A375 melanoma cell lines treated with the CDK4/6 inhibitor palbociclib and the PRMT5 inhibitor GSK3326595 and analysed data for differential gene expression and differential pre-mRNA splicing induced by these agents. Changes in gene expression and RNA splicing were more extensive under PRMT5 inhibition than under CDK4/6 inhibition. Although PRMT5 inhibition and CDK4/6 inhibition induced common RNA splicing events and gene expression profiles, the majority of events induced by CDK4/6 inhibition were distinct. Our findings indicate CDK4/6 has the ability to regulate alternative splicing in a manner that is distinct from PRMT5 inhibition, resulting in divergent changes in gene expression under each therapy.

Development of a novel blood-based RNA gene expression platform for early-stage lung cancer diagnosis.

8557 Background: Blood-based methods using circulating tumor DNA (ctDNA) and cell-free DNA (cfDNA) are under development for early and less invasive detection of lung cancer, although detection of the earliest stage cancers (stages 0-II) using these modalities is suboptimal. We hypothesized that a machine learning approach using RNA gene expression may offer important information on the biology of the patient, allowing for gene expression profiles to be used as a surrogate measurement of cancer disease phenotype and as a promising direction for early detection of lung cancer. In a previous study, 23 miRNA biomarkers were successfully discovered and validated for the non-invasive diagnostic classification of lung adenocarcinoma, achieving 97.7% sensitivity, 98.7% specificity in blood obtained from 383 clinical subjects. The aim of this study was to train a machine learning algorithm, from the 23 miRNA features, to test the signature for early lung cancer detection. Methods: A large and diverse clinical cohort was obtained from the NIH Gene Expression Omnibus database, GEO Accession Number GSE137140 ( n=3,744), comprised of miRNA extracted from serum samples consisting of subjects with pre-operative lung cancer ( n=1,566) and non-cancer controls ( n=2,178). Our analytic plan leveraged machine learning methods derived from XGBoost classification, a popular supervised-learning algorithm that uses sequentially built shallow decision trees to provide accurate results and avoidance of overfitting. The algorithm was trained using XGBoost 1.4.1.1 R library programmed with R v3.6.3. Results: The lung cancer cohort was heavily weighted towards early-stage lung cancer (87.7% stage I/II), including representation across prevalent histologic types (adenocarcinoma 77.8%, non-adenocarcinoma 22.2%) and those who self-reported as never smokers (37.9%). The 23-miRNA signature achieved 98% sensitivity, 89% specificity in the held-out test set (Table). When incorporating age and gender, the 23-miRNA signature achieved 95.5% sensitivity, 90.3% specificity. Conclusions: A machine learning approach using RNA gene expression in patient serum achieved high sensitivity and specificity in a large, predominantly early-stage, lung cancer cohort. A multi-analyte, multimodal approach that leverages machine learning algorithms with RNA gene expression profiles and available demographics and clinical risk-factors, represents the possibility to accurately detect lung cancer in the earliest stages. This approach has successfully been translated from microarray to PCR instrumentation, with further validation of this machine learning method and approach currently underway. [Table: see text]

P06.05.A Repeated intracranial administration of ipilimumab and nivolumab in patients with recurrent glioblastoma (rGB): A multi-cohort adaptive phase I clinical trial

Abstract Background Perioperative intracerebral (iCE) administration of ipilimumab (IPI) and nivolumab (NIVO) in combination with IV NIVO was shown to be feasible, safe and associated with an encouraging survival benefit (Duerinck et al. JITC 2021). In subsequent cohorts, combination of iCE administration with biweekly intracavitary (iCA, via an Ommaya reservoir) administration of increasing doses of IPI and NIVO was investigated. Methods Three cohorts were defined according to resectability and postoperative treatment schedule. Patients (pts) in cohort-A and -C underwent a maximal safe resection, pts in cohort-B stereotactic biopsy only. All pts received iCE administration of 10 mg NIVO and 5 mg IPI at the end of the surgical intervention, after which an OR was implanted and an additional 10mg of NIVO and IPI (1, 5 or 10 mg) was administered iCA in cohort-C. All pts received biweekly postoperative NIVO 10 mg IV and iCA administrations of NIVO (3 dose levels were investigated in cohorts-A and -B: 1, 5, or 10 mg) for up to a maximum of 24w postoperatively. In cohort-C, 10 mg of NIVO was complemented with IPI (1, 5, or 10 mg). NGS and RNA gene expression profiling was performed on all tissue samples. Results In total, 44 pts were included (A: n= 16, B: n= 16, C: n= 12 recruitment ongoing). All pts in cohort-A and -B are off study treatment. All pts received the predefined dose of iCE IPI/NIVO and at least one administration of the predefined iCA dose. AE were infrequent and mostly not immune-related. Most common AE were fatigue(n=37), headache(n=25), confusion(n=18) and postoperative fever(n=15). Bacterial colonization of the Ommaya port occurred in 6 pts, subacute neurological deterioration requiring corticosteroids in 8 pts. There were no grade 5 AEs. Median PFS was 13w for cohort-A, 5w in cohort-B and 13w in cohort-C. Median OS is 43weeks in A, 29w in B and is not yet reached in cohort-C after median follow-up of 23w. OS did not differ significantly between study cohorts. OS of pts who underwent surgical resection (cohorts-A and -C) compared favorably to a historical cohort of 469 Belgian patients with rGB (treated in three prospective phase II clinical trials and a large multicenter early acces program for bevacizumab). Conclusions iCE followed by repeated iCA administrations of increasing doses of NIVO with/without IPI in rGB is feasible and safe without dose limiting AEs. A potential survival benefit seems restricted to pts amenable to surgical resection.

Role of Toothbrushes as Gene Expression Profiling Tool for Oral Cancer Screening in Tobacco and Alcohol Users.

Aim: The use of toothbrushes was investigated as a potential RNA source and gene expression profiling tool for oral cancer screening in tobacco and alcohol users. Methodology: A total of 20 subjects were selected on the basis of inclusion and exclusion criteria. They were divided into two groups: group I—healthy controls (n = 6); group II—individuals who consume tobacco and alcohol (n = 14). After the volunteers brushed their teeth using a soft-bristle toothbrush with ~0.5 gm of toothpaste, the toothbrushes were collected, and the gene expression of BAX, BCL2, CDK4, CKDN2A, GNB3, and TCF7L2 was assessed. Results: The gene expression of BAX decreased significantly in alcoholics and smokers (0.13867 ± 0.12014), while the gene expression of BCL2 increased in alcoholics and smokers (1.91001 ± 0.90425) in comparison with healthy controls (p = 0.0054 and p = 0.0055). Although there was increased expression of CDK4, CKDN2A, and TCF7L2 and decreased expression of GNB3 in smokers and alcoholics, the results were not significant. Conclusions: A toothbrush is a good source of RNA, and gene expression analysis can be performed using the genetic material retrieved from toothbrushes, which can aid in the early diagnosis of oral squamous cell carcinoma among tobacco and alcohol users. Further studies with a larger sample size and different durations of toothbrush use should be conducted to explore the role of toothbrushes as a noninvasive tool for disease diagnosis.

Inflammatory molecular endotypes of nasal polyps derived from White and Japanese populations

Emerging evidence suggests that chronic rhinosinusitis with nasal polyps (CRSwNP) is a highly heterogeneous disease with disparate inflammatory characteristics between different racial groups and geographies. Currently, little is known about possible underlying distinguishing factors between these inflammatory differences. Our aim was to interrogate differences in CRSwNP disease between White/non-Asian patients and Japanese patients by using whole transcriptome and single-cell RNA gene expression profiling of nasal polyps (NPs). We performed whole transcriptome RNA sequencing with endotype stratification of NPs from 8 White patients (residing in the United States) and 9 Japanese patients (residing in Japan). Reproducibility was confirmed by quantitative PCR in an independent validation set of 46 White and 31 Japanese patients. Single-cell RNA sequencing (scRNAseq) was used to stratify key cell types for contributory transcriptional signatures. Unsupervised clustering analysis identified 2 major endotypes that were present within both cohorts of patients with NPs and had previously been reported at the cytokine level: (1) type 2 endotype and (2) non-type 2 endotype. Importantly, there was a statistically significant difference in the proportion of these endotypes between these geographically distinct subgroups with NPs (P= .03). Droplet-based single-cell RNA sequencing further identified prominent type 2 inflammatory transcript expression: C-C motif chemokine ligand 13 (CCL13) and CCL18 in M2 macrophages, as well as cystatin SN (CST1) and CCL26 in basal, suprabasal, and secretory epithelial cells. NPs from both racial groups harbor the same 2 major endotypes, which we have determined to be present in differing ratios between each cohort with CRSwNP disease. Distinct inflammatory and epithelial cells contribute to the type 2 inflammatory profiles observed.

CTIM-17. INTRA-CRANIAL ADMINISTRATION OF CTLA-4 AND PD-1 IMMUNE CHECKPOINT-INHIBITING MONOCLONAL ANTIBODIES IN RECURRENT GLIOBLASTOMA PATIENTS: A MULTI-COHORT ADAPTIVE PHASE I CLINICAL TRIAL

Abstract BACKGROUND: Intracerebral (iCE) administration of nivolumab (NIVO) and ipilimumab (IPI) after resection of recurrent glioblastoma (rGB), followed by repeated intravenous(IV) NIVO was recently shown to be feasible, safe and associated with encouraging survival. Subsequent cohorts were defined to investigate the addition of biweekly intracavitary (iCA) or intrathecal (iTH) NIVO +/- IPI administrations. METHODS Four groups were defined according to rGB resectability and postoperative treatment schedule. Group A and D underwent biopsy, B and C maximal safe resection. All patients received iCE injections of 10 mg/1ml NIVO + 5 mg/1ml IPI at the end of surgery, after which an Ommaya catheter was implanted iCA (A, B and C) or iTH (D). Following surgery, all patients received biweekly IV low-dose NIVO(10mg) combined with iCA/iTH 10 mg NIVO (A and B) + 1, 5 or 10 mg IPI (C and D) for up to 24 weeks. NIVO/IPI concentrations were dosed in the cerebrospinal fluid (CSF). Gene sequencing and RNA gene expression profiling were performed on all tissue samples RESULTS 39pts(27 male; 16 in A, 16 in B, 4 in C, 3 in D; recruitment ongoing in C+D) were enrolled. All patients received the predefined dose of iCE IPI/NIVO. Most frequent AEs were fatigue (n=30), headache (n=19), confusion (n=14), dysphasia (n=13), and fever (n=10). Ommaya infection occurred in 5patients, subacute neurological deterioration requiring corticosteroids in 6patients. There were no G5 AEs. irAEs were infrequent and mild. Median PFS and OS were 5w(95% CI 1-8) and 23w(95% CI 0-53) in A and 13w(95% CI 7-19) and 42w(95% CI 30-54) in B, respectively. >90% of CSF samples had elevated protein levels and lymphocytic pleocytosis. There was no evidence for accumulation of NIVO/IPI in the CSF. CONCLUSION Repeated intracavitary or intrathecal administration of NIVO +/- IPI in rGB is feasible and safe. Favourable survival outcome is seen in patients amenable to surgical resection.

Intracerebral administration of CTLA-4 and PD-1 immune checkpoint blocking monoclonal antibodies in patients with recurrent glioblastoma: a phase I clinical trial

BackgroundPatients with recurrent glioblastoma (rGB) have a poor prognosis with a median overall survival (OS) of 30–39 weeks in prospective clinical trials. Intravenous administration of programmed cell death protein 1...

Cardiac Testing in Search for Occult Atrial Fibrillation after Ischemic Stroke

Determining the etiology of ischemic stroke is critical to administering targeted therapy to prevent recurrent stroke and further neurologic deterioration. Ischemic strokes of cardioembolic and cryptogenic etiologies are frequent and are often ultimately attributed to atrial fibrillation (AF). However, the paroxysmal nature of AF presents challenges for accurate and timely detection to prevent a recurrent stroke. The purpose of this review is to evaluate serologic, electrographic, echocardiographic, and radiologic markers of AF after an ischemic stroke. Innovative applications of biotechnologies such as RNA gene expression profiling are being studied to characterize stroke etiology. Extended cardiac rhythm monitoring by implantable and wearable devices allows longer periods to capture paroxysmal AF. Echocardiographic measures including left atrial volume and parameters of left atrial strain increase the probability of detecting AF. Existing radiographic modalities are being investigated in novel ways to assess left atrial abnormalities associated with paroxysmal AF. Emerging technologies and novel applications of existing methods are improving AF diagnostics in cryptogenic stroke patients with a high pre-test probability of this etiology. Future research will continue to optimize AF diagnosis after a cryptogenic ischemic stroke to inform clinical practice and prevent recurrent strokes.

Biomarkers of Immune Checkpoint Blockade Response in Triple-Negative Breast Cancer.

Immune checkpoint blockade (ICB) has revolutionized the treatment landscape across multiple solid tumor types. In triple-negative breast cancer (TNBC), clinical benefit for the addition of ICB to chemotherapy has been shown in both the metastatic and early stage disease settings. A minority of patients with TNBC will truly benefit from ICB, with many tumors unlikely to respond, and ICB can cause additional toxicities for patients to incur. In clinical practice, ICB-based regimens are emerging as standard-of-care treatment options in TNBC subpopulations. Atezolizumab in combination with nab-paclitaxel is recommended as first-line treatment for patients with PD-L1-positive metastatic TNBC. Clinical trials are needed to confirm this benefit and evaluate if additional biomarkers may allow for improved patient selection. Trials investigating ICB in early-stage breast cancer show promise for the benefit of combination ICB with neoadjuvant chemotherapy. However, longer follow-up is required before ICB can be considered as standard-of-care treatment in the early stage setting. In both metastatic and early stage TNBC, novel biomarkers to improve patient selection are now under investigation. These include multiplex IHC to profile immune cell subtypes (such as tumor infiltrating lymphocytes) or RNA gene expression profiling to detect signatures suggestive of a T-cell-inflamed microenvironment. Detecting somatic mutations through tumor next-generation DNA sequencing may predict resistance mechanisms or suggest sensitivity to ICB monotherapy or in combination with other forms of systemic therapy. These biomarker platforms may allow for a more granular analysis of immune activity and should be further investigated in prospective studies with the aim of personalizing ICB-focused therapies in TNBC.

(CDRGI)-Cancer detection through relevant genes identification

Cancer is a genetic disease that is categorized among the most lethal and belligerent diseases. An early staging of the disease can reduce the high mortality rate associated with cancer. The advancement in high throughput sequencing technology and the implementation of several Machine Learning algorithms have led to significant progress in Oncogenomics over the past few decades. Oncogenomics uses RNA sequencing and gene expression profiling for the identification of cancer-related genes. The high dimensionality of RNA sequencing data makes it a complex and large-scale optimization problem. CDRGI presents a Discrete Filtering technique based on a Binary Artificial Bee Colony coupling Support Vector Machine and a two-stage cascading classifier to identify relevant genes and detect cancer using RNA seq data. The proposed approach has been tested for seven different cancers, including Breast Cancer, Stomach Cancer (STAD), Colon Cancer (COAD), Liver Cancer, Lung Cancer (LUSC), Kidney Cancer (KIRC), and Skin Cancer. The results revealed that the CDRGI performs better for feature reduction while achieving better classification accuracy for STAD, COAD, LUSC and KIRC cancer types.

Transcriptome Profiling of Gold Queen Hami Melons under Cold Stress

Hami melon (Cucumis melo L. var. inodorus Jacq) is an important horticultural crop but susceptible to chilling injury during low temperature storage. To characterize the gene expression profiles of Gold Queen Hami melon under the cold stress and discover the key cold stress-induced genes, five cDNA libraries, C0 (control), C12 (control for 12 d), C24 (control for 24 d), L12 (cold treatment at 0.5°C for 12 d) and L24 (cold treatment at 0.5°C for 24 d), were constructed for RNA sequencing (RNA-Seq) and gene expression profiling. A total of 6479 and 7914 differentially expressed genes (DEGs) in L12 and L24 compared with C0 were respectively detected. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses identified the relevant biological functions and metabolic pathways of these differentially expressed genes. In addition, a diverse range of cold response candidate genes were mainly obtained from starch and sucrose metabolism, pentose phosphate pathway and glycolysis/gluconeogenesis, such as genes encoding sucrose-phosphate synthase, α-amylase, β-amylase, sucrose synthase and glucose-6-phosphate dehydrogenase. Various transcription factors with divergent expression patterns were identified. Finally, quantitative real time polymerase chain reaction (qRT-PCR) was conducted to validate the RNA-Seq and gene differentially expression results. This study provides valuable information for further studies on cold response mechanisms and genetic improvement of cold tolerance in Gold Queen Hami melons.

CAMKV Is a Candidate Immunotherapeutic Target in MYCN Amplified Neuroblastoma.

We developed a computational pipeline designed to use RNA sequencing (n = 136) and gene expression profiling (n = 250) data from neuroblastoma tumors to identify cell surface proteins predicted to be highly expressed in MYCN amplified neuroblastomas and with little or no expression in normal human tissues. We then performed ChIP-seq in the MYCN amplified cell lines KELLY, NB-1643, and NGP to identify gene promoters that are occupied by MYCN protein to define the intersection with the differentially-expressed gene list. We initially identified 116 putative immunotherapy targets with predicted transmembrane domains, with the most significant differentially-expressed of these being the calmodulin kinase-like vesicle-associated gene (CAMKV, p = 2 × 10−6). CAMKV encodes a protein that binds calmodulin in the presence of calcium, but lacks the kinase activity of other calmodulin kinase family members. We confirmed that CAMKV is selectively expressed in 7/7 MYCN amplified neuroblastoma cell lines and showed that the transcription of CAMKV is directly controlled by MYCN. From membrane fractionation and immunohistochemistry, we verified that CAMKV is membranous in MYCN amplified neuroblastoma cell lines and patient-derived xenografts. Finally, immunohistochemistry showed that CAMKV is not expressed on normal tissues outside of the central nervous system. Together, these data demonstrate that CAMKV is a differentially-expressed cell surface protein that is transcriptionally regulated by MYCN, making it a candidate for targeting with antibodies or antibody-drug conjugates that do not cross the blood brain barrier.

Integrated bioinformatics analysis to identify 15 hub genes in breast cancer.

The aim of the present study was to identify the hub genes and provide insight into the tumorigenesis and development of breast cancer. To examine the hub genes in breast cancer, integrated bioinformatics analysis was performed. Gene expression profiles were obtained from the Gene Expression Omnibus (GEO) database and the differentially expressed genes (DEGs) were identified using the ‘limma’ package in R. Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis was used to determine the functional annotations and potential pathways of the DEGs. Subsequently, a protein-protein interaction network analysis and weighted correlation network analysis (WGCNA) were conducted to identify hub genes. To confirm the reliability of the identified hub genes, RNA gene expression profiles were obtained from The Cancer Genome Atlas (TCGA)-breast cancer database, and WGCNA was used to screen for genes that were markedly correlated with breast cancer. By combining the results from the GEO and TCGA datasets, 15 hub genes were identified to be associated with breast cancer pathophysiology. Overall survival analysis was performed to examine the association between the expression of hub genes and the overall survival time of patients with breast cancer. Higher expression of all hub genes was associated with significantly shorter overall survival in patients with breast cancer compared with patients with lower levels of expression of the respective gene.

A novel association between GSTM1 null variant and anthracycline-induced cardiac dysfunction (ACD) in childhood cancer survivors (CCS): A COG ALTE03N1 report.

10030 Background: ACD is a leading cause of mortality in CCS. Previous studies have identified genomic variants that moderate the ACD risk. An agnostic evaluation of differential gene expression between those with and without ACD has not been explored, and could provide insights into the mechanism of cardiotoxicity. Methods: Gene expression profiles in leukocyte RNA from anthracycline-exposed non-Hispanic white (NHW) CCS (20 with ACD [cases]; 20 without ACD [controls]) used Illumina HumanHT-12 v4.0 Expression Beadchips. Gene expression profiles in h uman iPSC-derived cardiomyocytes (hiPSC-CMs – Day 30) from 6 childhood cancer patients (3 each with and without CD) treated with 1μM doxorubicin or vehicle for 24 h, used RNA-seq. Genotyping in leukocyte DNA from anthracycline-exposed NHW CCS (65 cases; 76 controls) to determine if the differentially-expressed genes mapped to genetic variants that modified ACD risk, used conditional logistic regression analysis adjusted for sex, age at cancer diagnosis, chest radiation and anthracycline dose. Patient characteristics are in Table. Results: Gene-expression in survivors:Glutathione S transferase mu 1 ( GSTM1) was differentially-expressed; RT q-PCR showed significant downregulation of GSTM1 in cases (0.67±0.57 vs. 1.33±1.33, p=0.049). hiPSC-CMs gene expression: GSTM1 was downregulated in patients with ACD (logFC = -1.4). Genotyping: Using PCR for GSTM1 null, we observed a significant association between CD risk and GSTM1 null genotype (OR=3.0; 95%CI, 1.4-6.2, p=0.003). Conclusions: We report an association between GSTM1 null genotype and ACD, previously unreported likely because GWAS studies did not examined gene deletions. GSTM1 is involved in detoxification of anthracyclines. This finding could facilitate identification of childhood cancer survivors at increased risk of ACD. [Table: see text]

Glucocorticoid‐Driven Transcriptomes in Human Airway Epithelial Cells: Commonalities, Differences and Functional Insight

RATIONALEGlucocorticoids act on the glucocorticoid receptor (GR; NR3C1) to resolve inflammation and, as inhaled corticosteroids (ICS), are the cornerstone of treatment for asthma. However, reduced efficacy in severe disease and during exacerbations indicates a need to improve ICS actions. Since ICS target the epithelium, glucocorticoid‐driven transcriptomes were compared between primary human bronchial epithelial (HBE) cells and common cell lines, pulmonary type II A549 and bronchial epithelial BEAS‐2B cells.METHODSGene expression profiling of RNA extracted from A549, BEAS‐2B and HBE cells following budesonide treatment was performed using Affymetrix PrimeView microarrays. Genes showing significant induction (fold ≥2, P ≤0.05) or repression (fold ≤0.5, P ≤0.05) compared to untreated cells, in any of the cell variants were used for further analyses.RESULTSIn BEAS‐2B cells, budesonide induced or, in a delayed fashion, repressed the expression of 63, 133, 240, and 257 or 15, 56, 236, and 344 mRNAs at 1, 2, 6, and 18 h, respectively. Within the early‐induced mRNAs were multiple transcriptional activators and repressors, thereby providing mechanisms for the subsequent modulation of gene expression. Using the above criteria, 17 (BCL6, BIRC3, CEBPD, ERRFI1, FBXL16, FKBP5, GADD45B, IRS2, KLF9, PDK4, PER1, RGCC, RGS2, SEC14L2, SLC16A12, TFCP2L1, TSC22D3) induced and 8 (ARL4C, FLRT2, IER3, IL11, PLAUR, SEMA3A, SLC4A7, SOX9) repressed mRNAs were common between A549, BEAS‐2B and HBE cells at 6 h. As absolute gene expression change showed greater commonality, lowering the cut‐off (≥1.25 or ≤0.8‐fold) within these groups produced 93 and 82 genes induced or repressed in common. Since large changes in few mRNAs and/or small changes in many mRNAs may drive function, gene ontology (GO)/pathway analyses were performed using both stringency criteria. Budesonide‐induced genes showed GO term enrichment for positive and negative regulation of transcription, signaling, proliferation, apoptosis, and movement, as well as FOXO and PI3K‐Akt signaling pathways. Repressed genes were enriched for inflammatory signaling pathways (TNF, NF‐κB) and GO terms for cytokine activity, chemotaxis and cell signaling. Reduced growth factor expression and effects on proliferation and apoptosis were highlighted.CONCLUSIONSWhile glucocorticoids repress mRNAs associated with inflammation, prior induction of transcriptional activators and repressors may explain longer‐term responses to these agents. Positive and negative effects on signaling, proliferation, migration and apoptosis were revealed. Since many such gene expression changes occurred in human airways post‐ICS inhalation, effects in cell lines and primary HBE cells in vitro may be relevant to ICS in vivo.Support or Funding InformationThis work was supported by: RN grants: Canadian Institutes of Health Research (CIHR), Natural Sciences and Engineering Research Council of Canada (NSERC) discovery grant, and AstraZeneca; MMM studentships: NSERC Postgraduate Scholarship – Doctoral, Queen Elizabeth II Doctoral scholarship, and The Lung Association – Alberta & NWT studentship award.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

The lncRNA TP73-AS1 is linked to aggressiveness in glioblastoma and promotes temozolomide resistance in glioblastoma cancer stem cells

Glioblastoma multiform (GBM) is the most common brain tumor characterized by a dismal prognosis. GBM cancer stem cells (gCSC) or tumor-initiating cells are the cell population within the tumor-driving therapy resistance and recurrence. While temozolomide (TMZ), an alkylating agent, constitutes the first-line chemotherapeutic significantly improving survival in GBM patients, resistance against this compound commonly leads to GBM recurrence and treatment failure. Although the roles of protein-coding transcripts, proteins and microRNA in gCSC, and therapy resistance have been comprehensively investigated, very little is known about the role of long noncoding RNAs (lncRNAs) in this context. Using nonoverlapping, independent RNA sequencing and gene expression profiling datasets, we reveal that TP73-AS1 constitutes a clinically relevant lncRNA in GBM. Specifically, we demonstrate significant overexpression of TP73-AS1 in primary GBM samples, which is particularly increased in the gCSC. More importantly, we demonstrate that TP73-AS1 comprises a prognostic biomarker in glioma and in GBM with high expression identifying patients with particularly poor prognosis. Using CRISPRi to downregulate our candidate lncRNA in gCSC, we demonstrate that TP73-AS1 promotes TMZ resistance in gCSC and is linked to regulation of the expression of metabolism- related genes and ALDH1A1, a protein known to be expressed in cancer stem cell markers and protects gCSC from TMZ treatment. Taken together, our results reveal that high TP73-AS1 predicts poor prognosis in primary GBM cohorts and that this lncRNA promotes tumor aggressiveness and TMZ resistance in gCSC.

Identification of a multidimensional transcriptome signature for survival prediction of postoperative glioblastoma multiforme patients

BackgroundGlioblastoma multiform (GBM) is a devastating brain tumor with maximum surgical resection, radiotherapy plus concomitant and adjuvant temozolomide (TMZ) as the standard treatment. Diverse clinicopathological and molecular features are major obstacles to accurate predict survival and evaluate the efficacy of chemotherapy or radiotherapy. Reliable prognostic biomarkers are urgently needed for postoperative GBM patients.MethodsThe protein coding genes (PCGs) and long non-coding RNA (lncRNA) gene expression profiles of 233 GBM postoperative patients were obtained from The Cancer Genome Atlas (TCGA), TANRIC and Gene Expression Omnibus (GEO) database. We randomly divided the TCGA set into a training (n = 76) and a test set (n = 77) and used GSE7696 (n = 80) as an independent validation set. Survival analysis and the random survival forest algorithm were performed to screen survival associated signature.ResultsSix PCGs (EIF2AK3, EPRS, GALE, GUCY2C, MTHFD2, RNF212) and five lncRNAs (CTD-2140B24.6, LINC02015, AC068888.1, CERNA1, LINC00618) were screened out by a risk score model and formed a PCG-lncRNA signature for its predictive power was strongest (AUC = 0.78 in the training dataset). The PCG-lncRNA signature could divide patients into high- risk or low-risk group with significantly different survival (median 7.47 vs. 18.27 months, log-rank test P < 0.001) in the training dataset. Similar result was observed in the test dataset (median 11.40 vs. 16.80 months, log-rank test P = 0.001) and the independent set (median 8.93 vs. 16.22 months, log-rank test P = 0.007). Multivariable Cox regression analysis verified that it was an independent prognostic factor for the postsurgical patients with GBM. Compared with IDH mutation status, O-(6)-methylguanine DNA methyltransferase promoter methylation status and age, the signature was proved to have a superior predictive power. And stratified analysis found that the signature could further separated postoperative GBM patients who received TMZ-chemoradiation into high- and low-risk groups in TCGA and GEO dataset.ConclusionsThe PCG-lncRNA signature was a novel prognostic marker to predict survival and TMZ-chemoradiation response in GBM patients after surgery.

In the literature: December 2018

The current development of immune checkpoint modulatory treatments has shown durable responses in the treatment of multiple cancer types.1 However, predictive biomarkers beyond PD-1 ligand 1 (PD-L1) expression and high microsatellite instability (MSI-H) to stratify patients and identify those who could benefit of these therapies are needed. In this sense, a recent study published in Science by Cristescu et al 2 describes the potential usefulness of combining the tumour mutational burden (TMB) and the T cell-inflamed gene expression profile (GEP) to jointly predict clinical response to pembrolizumab. Both PD-L1 and the GEP represent a T cell-inflamed tumour microenvironment (TME), whereas TMB and MSI-H are indirect measures of tumour antigenicity generated by somatic tumour mutations. In the mentioned study, TMB was evaluated by whole-exome sequencing (WES) of germline and tumour DNA, and the T cell-inflamed GEP was analysed by targeted gene expression profiling of tumour RNA (with the NanoString platform) from formalin fixed, paraffin-embedded pretreatment samples. To assess the individual and joint clinical utility of TMB and GEP, patients were stratified in four biomarker-defined clinical response groups based on predefined cut-offs for TMB and GEP. Objective response rates were strongest in patients with GEPhi TMBhi (37%–57%), moderate in those with GEPhi TMBlo (12% to 35%) and GEPlo TMBhi (11%–42%) and reduced or absent in those with GEPlo TMBlo (0%–9%). Additionally, longer PFS were seen in patients with higher levels of both TMB and GEP. Findings were comparable when TMB and PD-L1 expression were jointly assessed. Interestingly, more than 300 patient samples with advanced solid tumours and melanoma across 22 tumour types from four KEYNOTE clinical trials were included and analysed. Samples were assessed separately in four cohorts: one discovery, one pan-tumour validation and …