Small Indels in the Androgen Receptor Gene: Phenotype Implications and Mechanisms of Mutagenesis

CONTEXT

Despite high abundance of small indels in human genomes, their precise roles and underlying mechanisms of mutagenesis in Mendelian disorders require further investigation.

OBJECTIVE

To profile the distribution, functional implications, and mechanisms of small indels in the androgen receptor (AR) gene in individuals with androgen insensitivity syndrome (AIS).

METHODS

We conducted a systematic review of previously reported indels within the coding region of the AR gene, including 3 novel indels. Distribution throughout the AR coding region was examined and compared with genomic population data. Additionally, we assessed their impact on the AIS phenotype and investigated potential mechanisms driving their occurrence.

RESULTS

A total of 82 indels in AIS were included. Notably, all frameshift indels exhibited complete AIS. The distribution of indels across the AR gene showed a predominance in the N-terminal domain, most leading to frameshift mutations. Small deletions accounted for 59.7%. Most indels occurred in nonrepetitive sequences, with 15.8% situated within triplet regions. Gene burden analysis demonstrated significant enrichment of frameshift indels in AIS compared with controls (P < .00001), and deletions were overrepresented in AIS (P < .00001).

CONCLUSION

Our findings underscore a robust genotype-phenotype relationship regarding small indels in the AR gene in AIS, with a vast majority presenting complete AIS. Triplet regions and homopolymeric runs emerged as prone loci for small indels within the AR. Most were frameshift indels, with polymerase slippage potentially explaining half of AR indel occurrences. Complex frameshift indels exhibited association with palindromic runs. These discoveries advance understanding of the genetic basis of AIS and shed light on potential mechanisms underlying pathogenic small indel events.

A novel program of infiltrative control in astrocytomas: ADAM23 depletion promotes cell invasion by activating -secretase complex

Background

Infiltration is a life-threatening growth pattern in malignant astrocytomas and a significant cause of therapy resistance. It results in the tumor cell spreading deeply into the surrounding brain tissue, fostering tumor recurrence and making complete surgical resection impossible. We need to thoroughly understand the mechanisms underlying diffuse infiltration to develop effective therapies.

Methods

We integrated in vitro and in vivo functional assays, RNA sequencing, clinical, and expression information from public data sets to investigate the role of ADAM23 expression coupling astrocytoma's growth and motility.

Results

ADAM23 downregulation resulted in increased infiltration, reduced tumor growth, and improved overall survival in astrocytomas. Additionally, we show that ADAM23 deficiency induces γ-secretase (GS) complex activity, contributing to the production and deposition of the Amyloid-β and release of NICD. Finally, GS ablation in ADAM23-low astrocytomas induced a significant inhibitory effect on the invasive programs.

Conclusions

Our findings reveal a role for ADAM23 in regulating the balance between cell proliferation and invasiveness in astrocytoma cells, proposing GS inhibition as a therapeutic option in ADAM23 low-expressing astrocytomas.

Association between tumor mutational burden (TMB) and mutational profile and its effect on overall survival: A post hoc analysis of patients with TMB-high and TMB-low metastatic cancer treated with immune checkpoint inhibitors (ICI)

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Background: High-TMB was recently approved as an agnostic biomarker for pembrolizumab in advanced cancers. Still, several patients with high-TMB do not respond to ICI, while some patients with low-TMB benefit from immunotherapy. Methods: We collected genomic (MSK-IMPACTassay) and survival data from 1,661 patients and assessed OS (Kaplan-Meier method) according to the mutational status. To better qualify patients with TMB ≥ 10 mut/Mb (TMB-H) (N = 488, 29%) and TMB < 10 mut/Mb (TMB-L) (N = 1,173, 71%) for ICI treatment, we analyzed single gene alterations impacting OS (P < 0.05). For all genes exhibiting a correlation with OS, we conducted a Cox multivariate analysis stratified by median TMB, sex, median age, microsatellite instability (MSI) status, and histology. Results: Survival to ICI increased with higher TMB. Median OS was 42 and 15 months for TMB-H and TMB-L (P < 0.05), respectively. For TMB-H tumors, 5 genes ( STK11, KEAP1, CIC, E2F3, TP53) exhibited reduced OS on ICI, and 22 genes ( NTRK3, TERT, NOTCH3, RNF43, TET1, PTPRD, NCOA3, TENT5C, ZFHX3, RIT1, CCNE1, PPM1D, GATA2, ALK, DNMT1, PTPRT, MET, EPHA7, BCL6, SMO, CDK6, MED12) were associated with better OS, P < 0.05. Cox multivariate analysis confirmed a correlation between mutations in STK11 and E2F3 with worse OS, while mutations in NTRK, PTPRD, RNF43, TENT5C, TET1, and ZFHX3 were associated with better OS (P < 0.05). Histology did not play a relevant role in ICI response except for melanoma (better OS; P < 0.05). MSI status did not significantly affect OS. For TMB-L tumors, 20 genes were related with reduced OS ( TP53, H3C2, DAXX, SMARC4, STK11, SOX17, RB1, PIK3CA, CTNNB1, KMT2D, HLA-A, FBXW7, CDH1, RBM10, KEAP1, IGF1R, H3C11, EGFR, RUNX1, B2M), while 8 genes were associated with better OS ( VHL, SETD2, PBRM1, BRAF, KDM5C, MAP2K1, CSF1R, RET), P < 0.05. Cox multivariate analysis confirmed 15 genes associated with superior ( KDM5C, PBRM1, and VHL) and inferior ( CTNNB1, DAXX, FBXW7, H3C2, H3C1, IGF1R, KMT2D, PIK3CA , RB1, SMARC4, SOX17, TP53) OS (P < 0.05). In the TMB-L context, melanoma histology and MSI status (except among VHL-mutated tumors) were independently associated with better OS. Conclusions: This pan-cancer analysis demonstrates that genomic alterations in single cancer genes can help define outcomes of TMB-H and TMB-L patients treated with ICI. [Table: see text]

Identification of NID1 as a novel candidate susceptibility gene for familial non-medullary thyroid carcinoma using whole-exome sequencing

The genetics underlying non-syndromic familial non-medullary thyroid carcinoma (FNMTC) is still poorly understood. To identify susceptibility genes for FNMTC, we performed whole-exome sequencing (WES) in a Brazilian family affected by papillary thyroid carcinoma (PTC) in three consecutive generations. WES was performed in four affected and two unaffected family members. Manual inspection in over 100 previously reported susceptibility genes for FNMTC showed that no variants in known genes co-segregated with disease phenotype in this family. Novel candidate genes were investigated using PhenoDB and filtered using Genome Aggregation (gnomAD) and Online Archive of Brazilian Mutations (ABraOM) population databases. The missense variant p.Ile657Met in the NID1 gene was the only variant that co-segregated with the disease, while absent in unaffected family members and controls. The allele frequency for this variant was <0.0001 in the gnomAD and ABbraOM databases. In silico analysis predicted the variant to be deleterious or likely damaging to the protein function. Somatic mutations in NID1 gene were found in nearly 500 cases of different cancer subtypes in the intOGen platform. Immunohistochemistry analysis showed NID1 expression in PTC cells, while it was absent in normal thyroid tissue. Our findings were corroborated using data from the TCGA cohort. Moreover, higher expression of NID1 was associated with higher likelihood of relapse after treatment and N1b disease in PTCs from the TCGA cohort. Although replication studies are needed to better understand the role of this variant in the FNMTC susceptibility, the NID1 variant (c.1971T>G) identified in this study fulfills several criteria that suggest it as a new FNMTC predisposing gene.

Molecular Signature Expands the Landscape of Driver Negative Thyroid Cancers

Thyroid cancer is the most common endocrine malignancy. However, the cytological diagnosis of follicular thyroid carcinoma (FTC), Hürthle cell carcinoma (HCC), and follicular variant of papillary thyroid carcinoma (FVPTC) and their benign counterparts is a challenge for preoperative diagnosis. Nearly 20-30% of biopsied thyroid nodules are classified as having indeterminate risk of malignancy and incur costs to the health care system. Based on that, 120 patients were screened for the main driver mutations previously described in thyroid cancer. Subsequently, 14 mutation-negative cases that are the main source of diagnostic errors (FTC, HCC, or FVPTC) underwent RNA-Sequencing analysis. Somatic variants in candidate driver genes (ECD, NUP98,LRP1B, NCOR1, ATM, SOS1, and SPOP) and fusions were described. NCOR1 and SPOP variants underwent validation. Moreover, expression profiling of driver-negative samples was compared to 16 BRAF V600E, RAS, or PAX8-PPARg positive samples. Negative samples were separated in two clusters, following the expression pattern of the RAS/PAX8-PPARg or BRAF V600E positive samples. Both negative groups showed distinct BRS, ERK, and TDS scores, tumor mutation burden, signaling pathways and immune cell profile. Altogether, here we report novel gene variants and describe cancer-related pathways that might impact preoperative diagnosis and provide insights into thyroid tumor biology.

Evidence of Cooperation between Hippo Pathway and RAS Mutation in Thyroid Carcinomas

Thyroid cancer incidences have been steadily increasing worldwide and are projected to become the fourth leading cancer diagnosis by 2030. Improved diagnosis and prognosis predictions for this type of cancer depend on understanding its genetic bases and disease biology. RAS mutations have been found in a wide range of thyroid tumors, from benign to aggressive thyroid carcinomas. Based on that and in vivo studies, it has been suggested that RAS cooperates with other driver mutations to induce tumorigenesis. This study aims to identify genetic alterations or pathways that cooperate with the RAS mutation in the pathogenesis of thyroid cancer. From a cohort of 120 thyroid carcinomas, 11 RAS-mutated samples were identified. The samples were subjected to RNA-Sequencing analyses. The mutation analysis in our eleven RAS-positive cases uncovered that four genes that belong to the Hippo pathway were mutated. The gene expression analysis revealed that this pathway was dysregulated in the RAS-positive samples. We additionally explored the mutational status and expression profiling of 60 RAS-positive papillary thyroid carcinomas (PTC) from The Cancer Genome Atlas (TCGA) cohort. Altogether, the mutational landscape and pathway enrichment analysis (gene set enrichment analysis (GSEA) and Kyoto Encyclopedia of Genes and Genome (KEGG)) detected the Hippo pathway as dysregulated in RAS-positive thyroid carcinomas. Finally, we suggest a crosstalk between the Hippo and other signaling pathways, such as Wnt and BMP.

Global changes in nitration levels and DNA binding profile of Trypanosoma cruzi histones induced by incubation with host extracellular matrix

Adhesion of T. cruzi trypomastigotes to components of the extracellular matrix (ECM) is an important step in mammalian host cell invasion. We have recently described a significant increase in the tyrosine nitration levels of histones H2A and H4 when trypomastigotes are incubated with components of the ECM. In this work, we used chromatin immunoprecipitation (ChIP) with an anti-nitrotyrosine antibody followed by mass spectrometry to identify nitrated DNA binding proteins in T. cruzi and to detect alterations in nitration levels induced upon parasite incubation with the ECM. Histone H1, H2B, H2A and H3 were detected among the 9 most abundant nitrated DNA binding proteins using this proteomic approach. One nitrated tyrosine residue (Y29) was identified in Histone H2B in the MS/MS spectrum. In addition, we observed a significant increase in the nitration levels of histones H1, H2B, H2A and H4 upon parasite incubation with ECM. Finally, we used ChIP-Seq to map global changes in the DNA binding profile of nitrated proteins. We observed a significant change in the binding pattern of nitrated proteins to DNA after parasite incubation with ECM. This work provides the first global profile of nitrated DNA binding proteins in T. cruzi and additional evidence for modification in the nitration profile of histones upon parasite incubation with ECM. Our data also indicate that the parasite interaction with the ECM induces alterations in chromatin structure, possibly affecting nuclear functions.

Comprehensive germline mutation analysis and clinical profile in a large cohort of Brazilian xeroderma pigmentosum patients

BACKGROUND

Xeroderma pigmentosum (XP) patients present a high risk of developing skin cancer and other complications at an early age. This disease is characterized by mutations in the genes related to the DNA repair system.

OBJECTIVES

To describe the clinical and molecular findings in a cohort of 32 Brazilian individuals who received a clinical diagnosis of XP.

METHODS

Twenty-seven families were screened for germline variants in eight XP-related genes.

RESULTS

All patients (N = 32) were diagnosed with bi-allelic germline pathogenic or potentially pathogenic variants, including nine variants previously undescribed. The c.2251-1G>C XPC pathogenic variant, reported as the founder mutation in Comorian and Pakistani patients, was observed in 15 cases in homozygous or compound heterozygous. Seven homozygous patients for POLH/XPV variants developed their symptoms by an average age of 7.7 years. ERCC2/XPD, DDB2/XPE and ERCC5/XPG variants were found in a few patients. Aside from melanoma and non-melanoma skin tumours, a set of patients developed skin sebaceous carcinoma, leiomyosarcoma, angiosarcoma, mucoepidermoid carcinoma, gastric adenocarcinoma and serous ovarian carcinoma.

CONCLUSIONS

We reported a high frequency of XPC variants in 32 XP Brazilian patients. Nine new variants in XP-related genes, unexpected non-skin cancer lesions and an anticipation of the clinical manifestation in POLH/XPV cases were also described.

Tumor mutational burden (TMB) and BCG responsiveness in high-risk non-muscle invasive bladder cancer (NMIBC)

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Background: Despite optimal management of NMIBC with transurethral resection of bladder tumor (TURBT) and intravesical BCG therapy, a significant proportion of patients (pts) will eventually present with disease recurrence or progression. To date, there is no validated predictive biomarker to guide patient selection for the most appropriate therapy in this setting. Methods: We retrospectively identified pts with high-risk NMIBC treated with TURBT, repeat TUR and intravesical BCG (≥ 6 instillations) from 2009 to 2016. Patients were classified as BCG-responsive (BCG-R) and BCG-unresponsive (BCG-UR) based on the International Bladder Cancer Group criteria. Whole exome sequencing was performed using archival FFPE tumor tissue from pre-BCG TURBT samples. Association of genomic variables and outcomes was evaluated by Cox proportional hazards survival analysis and likelihood ratio tests. Results: Thirty-five patients were included (BCG-R = 17, BCG-UR = 18). Median follow-up was 46 months for BCG-R and 52 months for BCG-UR pts. The majority of pts was male (91.4%), former smoker (60%), and presented with high-grade urothelial carcinoma (85.7%) and/or T1 staging (71.4%). Median time for relapse and progression was 10.5 and 19 months, respectively, in the BCG-UR group. In this cohort, TMB was significantly different in BCG-R and BCG-UR groups, with a median TMB of 5.53 +- 4.60 and 3.17 +- 1.82 mutations/Mb, respectively ( P= 0.045). TMB was also associated with relapse-free survival (RFS), with a median RFS of 38 and 15 months in high versus low TMB groups, respectively ( P= 0.0092). Intratumoral genetic heterogeneity assessed by mutant-allele tumor heterogeneity (MATH) was not statistically different between the groups, with a median MATH score of 31.8 and 21.9 for BCG-R and BCG-UR ( P= 0.14), respectively. On multivariate analysis, age and TMB were independently associated with RFS. Conclusions: In this exploratory biomarker study, high TMB was associated with benefit from immunotherapy with BCG for NMIBC. The identification of predictive biomarkers in this setting is an important unmet need and integrative analysis of TMB with other potential predictive biomarkers should be assessed in larger datasets.

Histopathological Characterization and Whole Exome Sequencing of Ectopic Thyroid: Fetal Architecture in a Functional Ectopic Gland from Adult Patient

Ectopic thyroid results from a migration defect of the developing gland during embryogenesis causing congenital hypothyroidism. But it has also been detected in asymptomatic individuals. This study aimed to investigate the histopathological, functional, and genetic features of human ectopic thyroids. Six samples were histologically examined, and the expression of the specific thyroid proteins was assessed by immunohistochemistry. Two samples were submitted to whole exome sequencing. An oropharynx sample showed immature fetal architecture tissue with clusters or cords of oval thyrocytes and small follicles; one sample exhibited a normal thyroid pattern while four showed colloid goiter. All ectopic thyroids expressed the specific thyroid genes and T4 at similar locations to those observed in normal thyroid. No somatic mutations associated with ectopic thyroid were found. This is the first immature thyroid fetal tissue observed in an ectopic thyroid due to the arrest of structural differentiation early in the colloid stage of development that proved able to synthesize thyroid hormone but not to respond to TSH. Despite the ability of all ectopic thyroids to synthetize specific thyroid proteins and T4, at some point in life, it may be insufficient to support body growth leading to hypothyroidism, as observed in some of the patients.

Abstract A26: Analysis of alternative splicing events in high- and low-grade bladder tumors

Functioning primarily in the rearrangement of identical pre-mRNA into different molecules, the alternative splicing (AS) contributes to the organism proteomic diversity. There are still unknown AS events, especially the aberrant splicing events that are associated to nonfunctional final products or tumorigenesis. For instance, hallmarks, such as apoptosis, metastasis, and angiogenesis, of certain types of cancer are known to be affected by some kind of aberrant splicing event. As examples, for BCLX gene, antiapoptotic and proapoptotic isoforms have been discovered, and, for the VEGFA gene, changes between proangiogenic and antiangiogenic isoforms expression have been detected in tumors and normal-matched samples, as well as among several distinct tissues. We hypothesize that AS events can also be associated and contribute to the origin and maintenance of specific tumor types and sub-types. We characterized the AS events in 35 samples of primary bladder tumors, classified as 20 high-grade (cells poorly differentiated, invasive and metastatic tumor), 11 low-grade (cell differentiated, noninvasive tumor), and 5 normal tissues. To access the AS events, we generated in total 2.5 billion of reads using RNAseq. The next step was mapping these reads against the human reference genome, using a set of in-house and publicly available pipelines to detect AS events in high-/low-grade bladder samples and normal tissues. As result, we observed 992 significant splicing events on high-grade tumors as compared to normal samples, 796 significant events on low-grade versus normal samples, and 871 significant events on low-grade versus high-grade tumors. After looking for some of these events in combinations of tumor grades and control, we found a tumor-specific isoform for RPS24 gene and five splicing events of genes RPL13A, RPL3, RPL37A, RPS27A, and RPL34 that are unique to high-grade tumors. We believe that these low-/high-grade AS specific events should be further studied in order to contribute to the understanding and to the development of new drugs for bladder tumors presenting low- or high-grade.

Citation Format: André Luiz Ventura Sávio, Ricardo Piuco, Katia Ramos Moreira Leite, Daisy Maria Favero Salvadori, Pedro Alexandre Favoretto Galante, Luiz Otavio Ferraz Penalva. Analysis of alternative splicing events in high- and low-grade bladder tumors [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr A26.

Abstract A54: Circulating miR-15a, miR-101, and miR-144 to distinguish between benign and malignant breast lesions in women with BI-RADS 4 mammography

BI-RADS 4 category reports suspicious breast lesions in mammograms, which have 23-34% chance of malignancy and require core biopsies for diagnosis confirmation. New biomarkers are needed and have been sought to improve diagnose in those patients. Once the human plasma contains a large number of circulating microRNAs (miRNAs), variations in their circulating levels have been associated with pathologic conditions, including cancer. We hypothesized that miRNA circulating level can be used to separate malignant from benign breast lesions in BI-RADS 4 patients. In this context, here we compared the circulating levels of 1,805 miRNAs in cancer patients (BI-RADS 5 or 6 mammography) and controls (BI-RADS 1 or 2 mammography) using miRNome PCR array to identify cancer-associated alterations in circulating miRNA levels. miRNAs with altered circulating levels in cancer patients were validated by qRT-PCR in an independent cohort and then investigated as biomarkers to distinguish between benign and malignant breast lesions in women with BI-RADS 4 mammography. We identified 12 miRNAs with different circulating levels (&gt;1.5x and a p-value &lt; 0.05) between controls and cancer patients. Altered circulating levels for 3 of these miRNAs (miR-15a, miR-101, and miR-144) were validated in an independent cohort of cancer patients. Next, we investigated the level of those three miRNAs in BI-RADS 4 patients and constructed an artificial neural network to test the capacity of this miRNA circulating profile to detect malignant breast lesions in women with BI-RADS 4 mammography. We found that the circulating levels of miR-15a, miR-101, and miR-144 were efficient to distinguish benign from malignant breast lesion with 92% of accuracy. In this work, we demonstrated how miRNAs circulating levels can be used as biomarkers to distinguish between benign and malignant breast lesions in women with BI-RADS 4 mammography and concluded that circulating miRNAs can be useful to improve breast cancer diagnosis.

Citation Format: Julia Alejandra Pezuk, Thiago Luiz Araujo Miller, José Luiz Barbosa Bevilacqua, Alfredo Carlos Simões Barros, Felipe Eduardo Martins de Andrade, Luiza Freire de Andrade e Macedo, Amanda Natasha Menardo Claro, Anamaria Aranha Camargo, Pedro Alexandre Favoretto Galante, Luiz Fernando Lima Reis. Circulating miR-15a, miR-101, and miR-144 to distinguish between benign and malignant breast lesions in women with BI-RADS 4 mammography [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr A54.

Abstract B22: High prevalence of TSC2 germline missense mutations in nontuberous sclerosis patients with gastroenteropancreatic neuroendocrine neoplasia

Background: Neuroendocrine neoplasias (NENs) are sporadic diseases, with only a few cases occurring in patients with predisposing syndromes, such as multiple endocrine neoplasia type 1 and type 2, von Hippel-Lindau disease, neurofibromatosis, and tuberous sclerosis. Nevertheless, epidemiologic researches have demonstrated that, even for previously healthy people, there is a higher risk for developing gastroenteropancreatic (GEP) NENs when a relative is affected by these neoplasms. The molecular basis to explain this familial pattern is, however, still unrecognized. We examined germline genes of GEP NEN nonsyndromic patients and looked for mutations that could justify this genetic susceptibility.

Methods: Patients with GEP NEN who were in medical care between March to November 2015 at Hospital Sírio-Libanês or Instituto do Câncer do Estado de São Paulo (both in São Paulo, Brazil) were invited to participate of the study. We excluded patients with previously known mutation in any gene surveyed in this study (MEN1, RET, VHL, NF1, TSC1, and TSC2). All participating patients signed the written informed consent form. Targeted next-generation sequencing of the coding region of the 6 genes which are associated with NEN physiopathology was performed in germline DNA. Only mutations with damaging impact by SIFT or PolyPhen2 functional predictors; with minor allele frequency (MAF) lower than 0.1% and with confirmed analysis by Sanger sequencing, were considered for the results. Enrichment of mutations in the evaluated genes in GEP NEN patients was verified by Fisher's exact test, contrasting the results of the GEP NEN group with the ExAC populational database.

Results: Ninety-three patients were included in the study (54.8% males) with the median age at diagnosis of 52 years. No patients had clinical phenotype of any syndromes related to NENs predisposition. The majority of patients had neoplasia grades 1 and 2 (38.7% and 41.9%), with primary site in pancreas (44.1%) or small bowel (35.5%) and were not associated with functional syndrome (74.2%). Eight patients (8.6%) have germline missense mutations in the TSC2 gene, and 1 patient (1.1%) in RET. There were no clear differences on age at diagnosis, neoplasia differentiation, site of the primary tumor, or diagnosis of functional syndrome when comparing patients with or without mutations. Populational analysis have shown an odds ratio of 3.8 (IC95% 1.42-7.42; p-value=0.004) for detecting TSC2 mutation in GEP NEN patients comparing with ExAC database. All mutations detected in the TSC2 are not diagnostic for tuberous sclerosis by consensus criteria. No association was seen in RET mutation (OR=1.00).

Conclusion: GEP NEN patients without clinical phenotype of any syndrome related to NENs susceptibility are significantly enriched for germline damaging missense mutation in the TSC2 gene. There is no enrichment of mutations in other evaluated genes. Taking into account the increasingly consistent evidence about hereditary predisposition in GEP NEN, as well as the already established relationship of truncated tuberin protein with predisposition of NENs, these findings strongly suggest that TSC2 damaging missense mutation is implicated in the genesis of GEP NEN in some nonsyndromic patients. Although these mutations are not associated with classical phenotype of tuberous sclerosis, this condition could be considered a new feature of a mild tuberous sclerosis.

Funding: This research was supported by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) and by Ludwig Institute for Cancer Research São Paulo.

Citation Format: Rudinei Diogo Marques Linck, Paula Fontes Asprino, Jônatas Eduardo da Silva Cesar, Florêncio Porto Freitas, Fernanda Christtanini Koyama, Rachel Simões Pimenta Riechelmann, Pedro Alexandre Favoretto Galante, Frederico Perego Costa, Paulo Marcelo Gehm Hoff, Diogo Meyer, Anamaria Aranha Camargo, Jorge Sabbaga. High prevalence of TSC2 germline missense mutations in nontuberous sclerosis patients with gastroenteropancreatic neuroendocrine neoplasia [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr B22.

Abstract A24: Contribution of aberrant splicing mechanisms in glioblastoma development

According to the World Health Organization, glioblastoma multiforme (GBM) represents 15-20% of all primary intracranial tumors and it is one of the most worrisome types of tumor, due to its high aggressiveness with low response to treatments. Currently, most patients diagnosed with GBM survive less than 15 months after diagnosis. Thus, there is a growing interest in the study of molecular signatures that contribute to a more effective therapy. Given the high prevalence of defects in splicing mechanisms found in cancer, small modulating splicing molecules have been presented as novel therapeutic strategies for the treatment of this malignant disease. In addition, alternative splicing appears to be more active in the nervous system compared to that detected in other tissues. In the last decade, some studies have reinforced the hypothesis that aberrant alternative splicing of RNA contributes to tumorigenesis, especially in GBM, and that changes in splicing mechanism of some genes could redirect this process. RNA binding proteins (RBPs) are the main regulators of alternative splicing mechanisms and thus could contribute to the acquisition of the malignant phenotype. A recent study from our group, focused exclusively in GBM, has shown several RBPs with deregulated expression on GBM compared to normal tissue (Correa et al., 2016). Among them, the MAGOH, an EJC complex component that plays a key role in mRNA metabolism, seems to participate on splicing regulation and has been implicated as possible oncogenic factor. Furthermore, the previous study from our group has also showed that MAGOH significantly increased the survival and proliferation of glioblastoma cell lines. Knowing that splicing machinery is a tangible target, we believe it is a possible new therapeutic route for GBM treatment. Thus, due to MAGOH participation in splicing regulation and on acquisition of GBM malignant phenotype, we have proposed to characterize, for the first time, new regulatory routes of gliomagenesis by a global analysis of MAGOH effects on alternative splicing pathways in GBM. By global analysis of public data, we identified aberrantly expressed genes on GBM compared to normal brain tissue. In addition, after MAGOH knockdown, we have identified some aberrantly expressed genes and also altered splicing events in glioblastoma cells compared to wild type. Together, the results corroborate our hypothesis that MAGOH contributes to glioma cells' malignant transformation with controlling splicing mechanism and interfering on gene expression.

Citation Format: Fabiana Marcelino Meliso, Luis Penalva, Pedro Alexandre Favoretto Galante. Contribution of aberrant splicing mechanisms in glioblastoma development [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr A24.

A straightforward assay to evaluate DNA integrity and optimize next-generation sequencing for clinical diagnosis in oncology

Next generation sequencing (NGS) has become an informative tool to guide cancer treatment and conduce a personalized approach in oncology. The biopsy collected for pathologic analysis is usually stored as formalin-fixed paraffin-embedded (FFPE) blocks and then availed for molecular diagnostic, resulting in DNA molecules that are invariably fragmented and chemically modified. In an attempt to improve NGS based diagnostics in oncology we developed a straightforward DNA integrity assessment assay based on qPCR, defining clear parameters to whether NGS sequencing results is accurate or when it should be analyzed with caution. We performed DNA extraction from 12 tumor samples from diverse tissues and accessed DNA integrity by straightforward qPCR assays. In order to perform a cancer panel NGS sequencing, DNA library preparation was performed using RNA capture baits. Reads were aligned to the reference human genome and mutation calls were further validated by Sanger sequencing. Results obtained by the DNA integrity assays correlated to the efficiency of the pre-capture library preparation in up to 0.94 (Pearson's test). Moreover, sequencing results showed that poor integrity DNA leads to high rates of false positive mutation calls, specially C:G>T:A and C:G>A:T. Poor quality FFPE DNA samples are prone to generating false positive mutation calls. These are especially perilous in cases in which subclonal populations are expected, such as in advance disease, since it could lead clinicians to erroneous conclusions and equivocated conduct.

Measuring plasma levels of three microRNAs can improve the accuracy for identification of malignant breast lesions in women with BI-RADS 4 mammography

A BI-RADS category of 4 from a mammogram indicates suspicious breast lesions, which require core biopsies for diagnosis and have an approximately one third chance of being malignant. Human plasma contains many circulating microRNAs, and variations in their circulating levels have been associated with pathologies, including cancer. Here, we present a novel methodology to identify malignant breast lesions in women with BI-RADS 4 mammography. First, we used the miRNome array and qRT-PCR to define circulating microRNAs that were differentially represented in blood samples from women with breast tumor (BI-RADS 5 or 6) in comparison to controls (BI-RADS 1 or 2). Next, we used qRT-PCR to quantify the level of this circulating microRNAs in patients with mammograms presenting with BI-RADS category 4. Finally, we developed a machine learning method (Artificial Neural Network - ANN) that receives circulating microRNA levels and automatically classifies BI-RADS 4 breast lesions as malignant or benign. We identified a minimum set of three circulating miRNAs (miR-15a, miR-101 and miR-144) with altered levels in patients with breast cancer. These three miRNAs were quantified in plasma from 60 patients presenting biopsy-proven BI-RADS 4 lesions. Finally, we constructed a very efficient ANN that could correctly classify BI-RADS 4 lesions as malignant or benign with approximately 92.5% accuracy, 95% specificity and 88% sensibility. We believe that our strategy of using circulating microRNA and a machine learning method to classify BI-RADS 4 breast lesions is a non-invasive, non-stressful and valuable complementary approach to core biopsy in women with BI-RADS 4 lesions.

A genetic cluster of patients with variant xeroderma pigmentosum with two different founder mutations

BACKGROUND

Xeroderma pigmentosum (XP) is a rare human syndrome associated with hypersensitivity to sunlight and a high frequency of skin tumours at an early age. We identified a community in the state of Goias (central Brazil), a sunny and tropical region, with a high incidence of XP (17 patients among approximately 1000 inhabitants).

OBJECTIVES

To identify gene mutations in the affected community and map the distribution of the affected alleles, correlating the mutations with clinical phenotypes.

METHODS

Functional analyses of DNA repair capacity and cell-cycle responses after ultraviolet exposure were investigated in cells from local patients with XP, allowing the identification of the mutated gene, which was then sequenced to locate the mutations. A specific assay was designed for mapping the distribution of these mutations in the community.

RESULTS

Skin primary fibroblasts showed normal DNA damage removal but abnormal DNA synthesis after ultraviolet irradiation and deficient expression of the Polη protein, which is encoded by POLH. We detected two different POLH mutations: one at the splice donor site of intron 6 (c.764 +1 G>A), and the other in exon 8 (c.907 C>T, p.Arg303X). The mutation at intron 6 is novel, whereas the mutation at exon 8 has been previously described in Europe. Thus, these mutations were likely brought to the community long ago, suggesting two founder effects for this rare disease.

CONCLUSIONS

This work describes a genetic cluster involving POLH, and, particularly unexpected, with two independent founder mutations, including one that likely originated in Europe.

MicroRNA Expression Signature Is Altered in the Cardiac Remodeling Induced by High Fat Diets

Recent studies have revealed the involvement of microRNAs (miRNAs) in the control of cardiac hypertrophy and myocardial function. In addition, several reports have demonstrated that high fat (HF) diet induces cardiac hypertrophy and remodeling. In the current study, we investigated the effect of diets containing different percentages of fat on the cardiac miRNA expression signature. To address this question, male C57Bl/6 mice were fed with a low fat (LF) diet or two HF diets, containing 45 kcal% fat (HF45%) and 60 kcal% fat (HF60%) for 10 and 20 weeks. HF60% diet promoted an increase on body weight, fasting glycemia, insulin, leptin, total cholesterol, triglycerides, and induced glucose intolerance. HF feeding promoted cardiac remodeling, as evidenced by increased cardiomyocyte transverse diameter and interstitial fibrosis. RNA sequencing analysis demonstrated that HF feeding induced distinct miRNA expression patterns in the heart. HF45% diet for 10 and 20 weeks changed the abundance of 64 and 26 miRNAs in the heart, respectively. On the other hand, HF60% diet for 10 and 20 weeks altered the abundance of 27 and 88 miRNAs in the heart, respectively. Bioinformatics analysis indicated that insulin signaling pathway was overrepresented in response to HF diet. An inverse correlation was observed between cardiac levels of GLUT4 and miRNA-29c. Similarly, we found an inverse correlation between expression of GSK3β and the expression of miRNA-21a-3p, miRNA-29c-3p, miRNA-144-3p, and miRNA-195a-3p. In addition, miRNA-1 overexpression prevented cardiomyocyte hypertrophy. Taken together, our results revealed differentially expressed miRNA signatures in the heart in response to different HF diets. J. Cell. Physiol. 231: 1771-1783, 2016. © 2015 Wiley Periodicals, Inc.

A Mouse Model of Targeted Musashi1 Expression in Whole Intestinal Epithelium Suggests Regulatory Roles in Cell Cycle and Stemness

The intestinal epithelium is very peculiar for its continuous cell renewal, fuelled by multipotent stem cells localized within the crypts of Lieberkühn. Several lines of evidence have established the evolutionary conserved RNA-binding protein Musashi1 as a marker of adult stem cells, including those of the intestinal epithelium, and revealed its roles in stem cell self-renewal and cell fate determination. Previous studies from our laboratories have shown that Musashi1 controls stem cell-like features in medulloblastoma, glioblastoma, and breast cancer cells, and has pro-proliferative and pro-tumorigenic properties in intestinal epithelial progenitor cells in vitro. To undertake a detailed study of Musashi1's function in the intestinal epithelium in vivo, we have generated a mouse model, referred to as v-Msi, overexpressing Musashi1 specifically in the entire intestinal epithelium. Compared with wild type litters, v-Msi1 mice exhibited increased intestinal crypt size accompanied by enhanced proliferation. Comparative transcriptomics by RNA-seq revealed Musashi1's association with gut stem cell signature, cell cycle, DNA replication, and drug metabolism. Finally, we identified and validated three novel mRNA targets that are stabilized by Musashi1, Ccnd1 (Cyclin D1), Cdk6, and Sox4. In conclusion, the targeted expression of Musashi1 in the intestinal epithelium in vivo increases the cell proliferation rate and strongly suggests its action on stem cells activity. This is due to the modulation of a complex network of gene functions and pathways including drug metabolism, cell cycle, and DNA synthesis and repair.

SurfaceomeDB: a cancer-orientated database for genes encoding cell surface proteins

Cell surface proteins (CSPs) are excellent targets for the development of diagnostic and therapeutic reagents, and it is estimated that 10-20% of all genes in the human genome encode CSPs. In an effort to integrate all data publicly available for genes encoding cell surface proteins, a database (SurfaceomeDB) was developed. SurfaceomeDB is a gene-centered portal containing different types of information, including annotation for gene expression, protein domains, somatic mutations in cancer, and protein-protein interactions for all human genes encoding CSPs. SurfaceomeDB was implemented as an integrative and relational database in a user-friendly web interface, where users can search for gene name, gene annotation, or keywords. There is also a streamlined graphical representation of all data provided and links to the most important data repositories and databases, such as NCBI, UCSC Genome Browser, and EBI.

Analysis of allelic differential expression in the human genome using allele-specific serial analysis of gene expression tags

Recent reports have demonstrated that a significant proportion of human genes display allelic differential expression (ADE). ADE is associated with phenotypic variability and may contribute to complex genetic diseases. Here, we present a computational analysis of ADE using allele-specific serial analysis of gene expression (SAGE) tags representing 1295 human genes. We identified 472 genes for which unequal representation (>3-fold) of allele-specific SAGE tags was observed in at least one SAGE library, suggesting the occurrence of ADE. For 235 out of these 472 genes, the difference in the expression level between both allele-specific SAGE tags was statistically significant (p < 0.05). Eleven candidate genes were then subjected to experimental validation and ADE was confirmed for 8 out of these 11 genes. Our results suggest that at least 25% of the human genes display ADE and that allele-specific SAGE tags can be efficiently used for the identification of such genes.

Detection and evaluation of intron retention events in the human transcriptome

Alternative splicing is a very frequent phenomenon in the human transcriptome. There are four major types of alternative splicing: exon skipping, alternative 3' splice site, alternative 5' splice site, and intron retention. Here we present a large-scale analysis of intron retention in a set of 21,106 known human genes. We observed that 14.8% of these genes showed evidence of at least one intron retention event. Most of the events are located within the untranslated regions (UTRs) of human transcripts. For those retained introns interrupting the coding region, the GC content, codon usage, and the frequency of stop codons suggest that these sequences are under selection for coding potential. Furthermore, 26% of the introns within the coding region participate in the coding of a protein domain. A comparison with mouse shows that at least 22% of all informative examples of retained introns in human are also present in the mouse transcriptome. We discuss that the data we present suggest that a significant fraction of the observed events is not spurious and might reflect biological significance. The analyses also allowed us to generate a reliable set of intron retention events that can be used for the identification of splicing regulatory elements.