Abstract
Objectives
To evaluate how telomeres length behaves in adamantinomtous craniopharyngioma (aCP) and if it contributes to the pathogenesis of aCPs with and without CTNNB1 mutations. Design: ...Retrospective cross-sectional study enrolling 42 aCPpatients from two tertiary institutions.
Methods
Clinicopathological features were retrieved from patient's charts. Fresh frozen tumors were used for RNA and DNA analyses. Telomere length was evaluated by qPCR (T/S ratio). Somatic mutations in TERT promoter (TERTp) and CTNNB1 were detected by Sanger and/or whole-exome sequencing. We performed RNA-Seq to identify differentially expressed genes in aCPs presenting with shorter or longer telomere lengths.
Results
Mutations in CTNNB1 were detected in 29 (69%) tumors. There was higher frequency of CTNNB1mutations in aCPs from patients diagnosed under the age of 15 years (85% vs 15%; p=0. 04) and a trend to recurrent disease (76% vs 24%; p=0.1). No mutation was detected in the TERTp region. The telomeres were shorter in CTNNB1-mutated aCPs (0.441, IQR: 0.297-0.597 vs 0.607, IQR: 0.445-0.778; p=0. 04) but it was neither associated with clinicopathological features nor with recurrence. RNAseq identified a total of 387 differentially expressed genes, generating two clusters, being one enriched for short telomere and CTNNB1-mutated aCPs.
Conclusions
CTNNB1 mutations are more frequent in children and adolescents and appear to associate with progressive disease. CTNNB1-mutated aCPs have shorter telomeres. This is the first evidence for a relationship between the Wnt/beta-catenin pathway and telomere biology in the pathogenesis of aCPs.
Presentation: No date and time listed
To evaluate how telomeres length behaves in adamantinomtous craniopharyngioma (aCP) and if it contributes to the pathogenesis of aCPs with and without CTNNB1 mutations.
Retrospective cross-sectional ...study enrolling 42 aCP patients from two tertiary institutions.
Clinicopathological features were retrieved from patient's charts. Fresh frozen tumors were used for RNA and DNA analyses. Telomere length was evaluated by qPCR (T/S ratio). Somatic mutations in TERT promoter (TERTp) and CTNNB1 were detected by Sanger and/or whole-exome sequencing. We performed RNA-Seq to identify differentially expressed genes in aCPs presenting with shorter or longer telomere lengths.
Mutations in CTNNB1 were detected in 29 (69%) tumors. There was higher frequency of CTNNB1 mutations in aCPs from patients diagnosed under the age of 15 years (85% vs 15%; p=0.04) and a trend to recurrent disease (76% vs 24%; p=0.1). No mutation was detected in the TERTp region. The telomeres were shorter in CTNNB1-mutated aCPs (0.441, IQR:0.297-0.597 vs 0.607, IQR:0.445-0.778; p=0.04) but it was neither associated with clinicopathological features nor with recurrence. RNAseq identified a total of 387 differentially expressed genes, generating two clusters, being one enriched for short telomere and CTNNB1-mutated aCPs.
CTNNB1 mutations are more frequent in children and adolescents and appear to associate with progressive disease. CTNNB1-mutated aCPs have shorter telomeres, demonstrating a relationship between the Wnt/β-catenin pathway and telomere biology in the pathogenesis of aCPs.
Abstract 4611
The PML-RARα fusion protein plays a pivotal role in acute promyelocytic leukemia (APL) genesis and one of the mechanisms through which this fusion protein exerts its activity is the ...epigenetic suppression of gene transcription. PML-RARα physically interacts with epigenetic-modifying enzymes including DNA methyltransferases leading to hypermethylation and silencing of target genes. Nevertheless, the nature of the genes critical to APL oncogenesis is unclear, particularly in humans. We compared the methylation patterns at diagnosis and at remission in four patients with APL and four healthy controls. In order to isolate myeloid progenitors in the bone marrow (BM) samples from patients at remission and healthy controls, CD117 positive cells were sorted. Genomic DNA was sodium bisulfite converted and methylation analysis was performed using Illumina HumanMethylation27 BeadChip Platform (which analyzes methylation sites, including promoter and methylation hotspots of over 14,000 genes). DNA methylation values from the bead array hybridizations were scored as b-values. The high-variance features (> 0.05) were identified and filtered, and the three groups (APL at diagnosis, at remission and healthy controls) were analyzed in two-way comparisons. The functional categories of differentially methylated genes were determined using the Ingenuity Pathway Analysis (IPA, Ingenuity Systems). After filtering, 2,996 out of 27,578 features from the platform were selected. One hundred and eighteen hypermethylated loci were exclusively found in APL at diagnosis, and 72 were commonly found in healthy subjects and patients in remission, pointing out the similarity between the 2 groups. Clustering based on the filtered set of features showed distinct methylation patterns for three of the four samples at diagnosis, and for two of the samples of APL at remission and three in healthy samples. The genes found hypermethylated at diagnosis were mainly associated with cell death regulation (IPA score=31) and cancer development (IPA score=13). In order to correlate methylation and gene expression profiles, the number of transcripts of 214 genes was analyzed by real time PCR using three platforms of PCR Array (SABioscience-Qiagen). We analyzed the methylation status and gene expression of 20 genes detected hypermethylated in APL at diagnosis, of which nine were downregulated (EGF, ERBB2, FHIT, IL1A, JAK2, MLH1, MMP-7, TERT and WNT2) and two upregulated (RARA and WT1) when compared to samples of healthy controls (Table). The analysis of WT1 expression is of special relevance because it has been used for minimal residual disease detection in APL. Our results suggest that the aberrant expression of WT1 is not dependent on the epigenetic control by PML/RARa. Among the genes founded hypermethylated and downregulated, TERT, that encodes the catalytic subunit of telomerase and which transcription seems to be repressed in differentiating cells, has been demonstrated to be regulated by WT1. This is not the reflection of differentiation, since only CD117+ cells were analyzed. We also analyzed the expression of six genes detected hypermethylated in samples of healthy controls, of interest BRCA2 and HGF genes were hypermethylated but their expression was down and upregulated, respectively. Aberrant expression HGF is frequent in AML and leads to the autocrine activation of its receptor tyrosine kinase, MET, which promotes cell growth and survival of HGF-expressing AML cells. In conclusion, our results provide a first glimpse of the variation in DNA methylation among samples from APL patients at diagnosis and at remission compared to healthy controls, and identified potential target genes capable of conferring survival advantage to the leukemic cell.
TableCorrelation between gene methylation and expression in APL at diagnosis (D), remission (R) and in healthy controls (HC)Gene SymbolMethylated GroupExpression (Fold Change) D × HCp valueBCL2HC/RNSBRCA2HC−3.20.02CD5DNSCDH1DNSCDKN1CDNSCDKN2BDNSEGFD−12.660.04ERBB2D−2.150.001FHITD−6.430.02GREB1HCNSHGFHC21.530.04IL1AD−11.030.04JAK2D−2.550.03LEPDNSMETDNSMLH1D−3.520.001MMP-7D−6.430.01FN1HCNSNF1ADNSRARAD3.720.002SFNDNSTERTD−12.380.03TESCDNSTNFHC/RNSWNT2D−7.320.03WT1D111.520.05HC, Healthy Controls; R, Remission; D, Diagnosis; NS, not significant.
No relevant conflicts of interest to declare.
We present here the clinical and molecular data of two patients with acromegaly treated with octreotide LAR after non-curative surgery, and who presented different responses to therapy. Somatostatin ...receptor type 2 and 5 (SSTR2 and SSTR5), and aryl hydrocarbon receptor-interacting protein (AIP) expression levels were analyzed by qPCR. In both cases, high SSTR2 and low SSTR5 expression levels were detected; however, only one of the patients achieved disease control after octreotide LAR therapy. When we analyzed AIP expression levels of both cases, the patient whose disease was controlled after therapy exhibited AIP expression levels that were two times higher than the patient whose disease was still active. These two cases illustrate that, although the currently available somatostatin analogs bind preferentially to SSTR2, some patients are not responsive to therapy despite high expression of this receptor. This difference could be explained by differences in post-receptor signaling pathways, including the recently described involvement of AIP.
Adrenocortical tumors (ACT) are more frequent during childhood, but they can appear at any age. ACTs can be classified in functioning, nonfunctioning (mainly observed in adults) and mixed. The ...diagnosis is based on clinical, biochemical findings and imaging. In children, in order to classify ACT as benign or malignant, tumor staging classification is recommended. Regarding molecular markers some studies should be taken into account: besides TP53 mutations, previous studies have also provided evidences of IGF2 involvement in 90% of the malignant ACT. Mutations altering exon 3 of CTNNB1 gene have been found in 6% of childhood ACTs. In addition, microRNAs can act as negative regulators of gene expression by targeting mRNA controlling cell growth, differentiation and apoptosis and have been implicated in adrenal tumorigenesis. High-throughput methods to analyze genome-wide expression have been developed over the last decade and identified a subset of tumors with good or poor prognosis. In the future, these studies can provide the basis of specific drug development, which can treat patients according to specific altered signaling pathway.
Environmental temperatures influence ectotherms’ physiology and capacity to perform activities necessary for survival and reproduction. Time available to perform those activities is determined by ...thermal tolerances and environmental temperatures. Estimates of activity time might enhance our ability to predict suitable areas for species’ persistence in face of climate warming, compared to the exclusive use of environmental temperatures, without considering thermal tolerances. We compare the ability of environmental temperatures and estimates of activity time to predict the geographic distribution of a tropical lizard, Tropidurus torquatus. We compared 105 estimates of activity time, resulting from the combination of four methodological decisions: 1) how to estimate daily environmental temperature variation (modeling a sinusoid wave ranging from monthly minimum to maximum temperature, extrapolating from operative temperatures measured in field or using biophysical projections of microclimate)? 2) In which temperature range are animals considered active? 3) Should these ranges be determined from body temperatures obtained in laboratory or in field? And 4) should thermoregulation simulations be included in estimations? We show that models using estimates of activity time made with the sinusoid and biophysical methods had higher predictive accuracy than those using environmental temperatures alone. Estimates made using the central 90% of temperatures measured in a thermal gradient as the temperature range for activity also ranked higher than environmental temperatures. Thermoregulation simulations did not improve model accuracy. Precipitation ranked higher than thermally related predictors. Activity time adds important information to distribution modeling and should be considered as a predictor in studies of the distribution of ectotherms. The distribution of T. torquatus is restricted by precipitation and by the effect of lower temperatures on their time of activity and climate warming could lead to range expansion. We provide an R package ‘Mapinguari’ with tools to generate spatial predictors based on the processes described herein.
Predicting immunotherapy response through genomics Cormedi, Marina Candido Visontai; Van Allen, Eliezer M; Colli, Leandro Machado
Current opinion in genetics & development,
February 2021, 2021-Feb, 2021-02-00, 20210201, Letnik:
66
Journal Article
Recenzirano
•Biomarkers are key to maximize clinical benefit of treatment with anti-CTLA4, anti-PD1 and anti-PDL1 drugs.•Genomic correlates of neoantigen load, such as defective mismatch repair and tumour ...mutation burden, are clinically applicable, but fail to completely explain differences in response patterns to immune checkpoint inhibitors.•HLA genotype, interferon expression and copy number variation are other promising biomarkers related to immune response pathways.•Somatic mutations in genes such as TP53, PTEN, PBRM1 and ARID1A may also help identify responders to immunotherapy.
Immune checkpoint inhibitors (ICI) aim to restore the immune system anti-tumor function by blocking two inhibitory axes: CTLA-4/CD28 and PD1/PDL1. ICI is established as a treatment option for multiple cancers, but their remarkable clinical impact is observed only in a fraction of patients. Together with their adverse effects and high cost, it’s imperative to identify patients who are likely to benefit from this type of treatment. Genomic features represent promising candidates as predictive biomarkers of response to ICI, with agnostic FDA-approvals of an anti-PD1 drug for tumors with microsatellite instability and tumors with a high mutational burden. Other genomic markers are also emerging to help refine patient selection. In this review, we discuss recent progress in genomic biomarkers development and its challenges, with a focus on alterations in the neoantigen burden, immune, and oncogenic pathways.
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