Evolution and divergence of the genetic lineage Desmodus rotundus/Artibeus lituratus of rabies virus in São Paulo State

The last record of a rabies case caused by the dog-specific rabies virus (RABV) lineage in dogs or cats in São Paulo State was in 1998. From 2002 to 2021, 57 cases of rabies in these animals were reported, and the vast majority (51) were genetically characterized as belonging to the Desmodus rotundus/Artibeus lituratus RABV lineage. However, it is not currently possible to infer which of these bats is the source of infection by genome sequencing of RABV isolates. The aims of this study were (a) to characterize the Desmodus rotundus/Artibeus lituratus lineage to determine the relationships between the RABV lineages and each reservoir, (b) to assess the phylogeny and common ancestors of the RABV lineages found in D. rotundus and A. lituratus, and (c) to further understand the epidemiology and control of rabies. In this study, we genetically analyzed 70 RABV isolates from São Paulo State that were received by the Virology Laboratory of the Pasteur Institute of São Paulo between 2006 and 2015. Of these isolates, 33 were associated with the hematophagous bat D. rotundus and 37 with the fruit bat A. lituratus. A genomic approach using phylogenetic analysis and nucleotide sequence comparisons demonstrated that these isolates belonged to the same genetic lineage of RABV. We also found that, in São Paulo State, the D. rotundus/A. lituratus lineage could be subdivided into at least four phylogenetic sublineages: two associated with D. rotundus and two with A. lituratus. These results are of importance for the epidemiological surveillance of rabies in São Paulo.

Abstract P5-03-19: Frequency of germline TP53 p.R337H variant among women at risk of hereditary breast cancer in a public health system of Central-West of Brazil

Background: Breast Cancer (BC) is one of the most common cancers diagnosed in Li-Fraumeni Syndrome (LFS). Most studies about the frequency of germline pathogenic variant (PV) TP53 p.R337H have been conducted in the South and Southeastern regions of Brazil reaching rates as high as 8% of detection. There is a lack of data on the frequency of this germline PV in other Brazilian regions, especially among patients without access to genetic tests. Objective: This study aims to evaluate the detection rate of TP53 p.R337H in patients (pts) at risk of hereditary breast cancer (HBC) and describe the clinical and demographic profile of the study cohort. Methodology: Hereditary cancer risk assessment based on the National Comprehensive Cancer Network Criteria (NCCN), version 1.2020, was performed in women with BC who were being followed in a public hospital (DF, Brazil) between January 2021 and January 2022. All pts eligible for germline genetic testing according to HBC NCCN criteria were referred for genetic counseling and genetic testing. For those patients who could not afford a comprehensive genetic test, a real time PCR test specifically searching for TP53 p.R337H variant was performed. In case of TP53 p.R337H detection in the proband, genetic counseling and familial variant testing were offered to family members. Results: Among 221 pts eligible for this study, 180 pts performed germline testing, including 100 pts tested only for the TP53 p.R337H variant (real-time PCR) and 80 pts performed out of pocket BC multigene panel testing (including TP53 sequencing). This cohort was mostly represented by pts from Central-West (47%) and Northeast (35%) regions of Brazil. The median age of BC diagnosis was 44 y.o. (18 - 78). Invasive ductal carcinoma represented 92% (n=203) of the tumors, 50% were ER/PR+ HER2-, 25% HER2 +, 25% ER/PR- HER2- (triple negative). Regarding stage at diagnosis, 59% (n=130) were stages IIB-IIIC and 13% IV. The detection rate of TP53 p.R337H was 1.1% (2/180). Among the pts who met the revised Chompret criteria for LFS, this frequency was 5% (2/40). One of them was diagnosed with a stage IIIB IDC ER/PR+HER2- at 28 y.o. and had no relevant family history of cancer. The other pt was diagnosed with a stage IV IDC ER/PR+HER2- at 44 y.o. and the family history revealed four sisters and one niece with BC, and one nephew with brain tumor at 4 y.o. The family members from these two families received genetic counseling and genetic testing. Cascade testing was able to identify 12 additional carriers. All carriers were referred for post-testing follow-up. Conclusion: According to these results, we expect to identify at least one p.R337H carrier in each 90 BC pts treated in the Federal’s District Public Health setting who fulfill HBC NCCN criteria. In a limited resources setting, in Brazil, testing the TP53 p.R337H variant with PCR is a low-cost test that should be considered at least for pts that meet the revised Chompret criteria. The overall detection rate of TP53 p.R337H carriers was lower in comparison to other Brazilian studies from the South/Southeast of the country. Both cases identified in this cohort had advanced local disease or metastatic disease at BC diagnosis, raising the concern about the importance of LFS diagnosis, and high-risk surveillance and risk reduction strategies in this subgroup of pts. Despite the low detection rate of TP53 p.R337H in this cohort, there was a high familial impact through cascade testing.

Citation Format: Tatiana S. Correa, Renata L. Sandoval, Eduarda S. Oliveira, Ana Carolina R. Leite, Luiza Nardin Weis, Maria Isabel Achatz, Claudiner P. Oliveira, Paula Fontes Asprino, Romualdo Barroso-Sousa. Frequency of germline TP53 p.R337H variant among women at risk of hereditary breast cancer in a public health system of Central-West of Brazil [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-03-19.

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.

Disruption of the oral microbiota is associated with a higher risk of relapse after allogeneic hematopoietic stem cell transplantation

Intestinal microbiota (IM) diversity and composition regulates host immunity and affects outcomes after allogeneic stem cell transplantation (allo-HSCT). We evaluated if the oral mucosa microbiota (OM) could impact the outcomes in patients who underwent allo-HSCT. Samples from the oral mucosa of 30 patients were collected at three time points: before the conditioning regimen, at aplasia, and at engraftment. We analyzed the associations of OM diversity and composition with allo-HSCT outcomes. Lower OM diversity at preconditioning was associated with a higher risk of relapse at 3 years (68% versus 33%, respectively; P = 0.04). Dominance (relative abundance ≥ 30%) by a single genus at preconditioning was also associated with a higher risk of relapse (63% versus 36% at 3 years, respectively; P = 0.04), as well as worse progression-free survival (PFS; 19% versus 55%, respectively; P = 0.01), and overall survival (OS) at 3 years (38% versus 81%, respectively; P = 0.02). In our study we observed that OM dysbiosis is associated with a higher risk of relapse and worse survival after allo-HSCT.

Deletion of miRNA-22 Induces Cardiac Hypertrophy in Females but Attenuates Obesogenic Diet-Mediated Metabolic Disorders

BACKGROUND/AIMS

Obesity is a risk factor associated with cardiometabolic complications. Recently, we reported that miRNA-22 deletion attenuated high-fat diet-induced adiposity and prevented dyslipidemia without affecting cardiac hypertrophy in male mice. In this study, we examined the impact of miRNA-22 in obesogenic diet-induced cardiovascular and metabolic disorders in females.

METHODS

Wild type (WT) and miRNA-22 knockout (miRNA-22 KO) females were fed a control or an obesogenic diet. Body weight gain, adiposity, glucose tolerance, insulin tolerance, and plasma levels of total cholesterol and triglycerides were measured. Cardiac and white adipose tissue remodeling was assessed by histological analyses. Echocardiography was used to evaluate cardiac function and morphology. RNA-sequencing analysis was employed to characterize mRNA expression profiles in female hearts.

RESULTS

Loss of miRNA-22 attenuated body weight gain, adiposity, and prevented obesogenic diet-induced insulin resistance and dyslipidemia in females. WT obese females developed cardiac hypertrophy. Interestingly, miRNA-22 KO females displayed cardiac hypertrophy without left ventricular dysfunction and myocardial fibrosis. Both miRNA-22 deletion and obesogenic diet changed mRNA expression profiles in female hearts. Enrichment analysis revealed that genes associated with regulation of the force of heart contraction, protein folding and fatty acid oxidation were enriched in hearts of WT obese females. In addition, genes related to thyroid hormone responses, heart growth and PI3K signaling were enriched in hearts of miRNA-22 KO females. Interestingly, miRNA-22 KO obese females exhibited reduced mRNA levels of Yap1, Egfr and Tgfbr1 compared to their respective controls.

CONCLUSION

This study reveals that miRNA-22 deletion induces cardiac hypertrophy in females without affecting myocardial function. In addition, our findings suggest miRNA-22 as a potential therapeutic target to treat obesity-related metabolic disorders in females.

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.

Revealing the BRD4-NOTCH3 fusion: A novel hill in the cancer landscape

OBJECTIVES

Gene fusions are becoming more evident in cancer scenario for either being the driver alterations, or for the great therapeutic target potential in many cases. Our aim was to characterize the BRD4-NOTCH3 fusion correlating with clinical features, and to determine the frequency of this fusion in the oncological population.

MATERIAL AND METHODS

One patient diagnosed with lung adenocarcinoma at Hospital Sírio-Libanês (Brazil) was included. Foundation Medicine database was searched for all BRD4-NOTCH3 fusions among 233,804 specimens.

RESULTS

A 76-year-old male patient was diagnosed with lung adenocarcinoma. Molecular assessments demonstrated negative ALK and EGFR, with PD-L1 expression positive by 60 %. He was treated with first line chemotherapy and second line immunotherapy. Subsequent treatments resume re-exposures to chemotherapy with poor responses. A next-generation sequencing (NGS) based assay was performed in the tumor biopsy, revealing mainly mutation in STK11, microsatellite stability, TMB-intermediate, MYC amplification and a BRD4-NOTCH3 fusion. The breakpoint analysis of this fusion indicates that BRD4 active domains are preserved, suggesting that it maintained DNA binding activity, as well as its capacity to be halt by BET inhibitors. Foundation Medicine database was searched for all BRD4-NOTCH3 fusions among more than 230-thousand specimens and it was found in 87 new cases in a rate of 0.04 % occurrence in solid tumors, predominately in gynecological cancers. The same rate was found when we analyzed a different dataset.

CONCLUSION

In conclusion, this is the first report of the BRD4-NOTCH3 gene fusion associated with clinical characterization and, although rare, the occurrence of this fusion is constant in different population. Our data suggest that this fusion has great potential to targeted-therapy.

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.

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.

Overexpression of miR-21-5p as a predictive marker for complete tumor regression to neoadjuvant chemoradiotherapy in rectal cancer patients

Background

Neoadjuvant chemoradiotherapy (nCRT) followed by radical surgery is the preferred treatment strategy for locally advanced rectal cancer. However, complete tumor regression is observed in a significant proportion of patients after nCRT, making them ideal candidates for alternative treatment strategies to this considerably morbid procedure. Identification of such patients based on clinical findings (complete clinical response - cCR) is difficult mainly because it relies on subjective clinical and imaging studies. Our goal was to identify biomarkers capable of predicting complete response to nCRT.

Methods

We analyzed miRNA expression profile using deep sequencing in rectal tumor biopsies prior to nCRT. Differential expression was investigated by EdgeR for a training (n = 27) and a validation (n = 16) set of patients to identify miRNAs associated with treatment response (complete vs. incomplete). In vitro experiments with two cancer cell lines were also performed in order to evaluate the possible role of miRNAs on response to nCRT.

Results

We found 4 miRNAs differentially expressed between complete and incomplete responders to nCRT. In addition, validation was performed using an independent group of patients and miR-21-5p was confirmed as being overexpressed in complete responders. Overall sensitivity and specificity of miR-21-5p expression in predicting complete response to nCRT was 78% and 86% respectively. Interestingly, in a subset of patients with cCR followed by early local recurrence, the expression level of miR-21-5p was considerably low, similarly to incomplete responders. We also found SATB1, a miR-21-5p target gene and known multidrug resistance gene, whose expression was inversely correlated with miR-21-5p expression. Finally, we performed functional experiments and showed that miR-21-5p and SATB1 may be directly involved with poor response to nCRT in rectal cancer patients.

Conclusions

This study suggests miR-21-5p as a promising predictive biomarker, which should aid in the selection of patients with cCR to nCRT that potentially could be spared from radical surgery.

Electronic supplementary material

The online version of this article (doi:10.1186/s12920-014-0068-7) contains supplementary material, which is available to authorized users.

Intratumoral heterogeneity of ADAM23 promotes tumor growth and metastasis through LGI4 and nitric oxide signals

Intratumoral heterogeneity (ITH) represents an obstacle for cancer diagnosis and treatment, but little is known about its functional role in cancer progression. The A Desintegrin And Metalloproteinase 23 (ADAM23) gene is epigenetically silenced in different types of tumors, and silencing is often associated with advanced disease and metastasis. Here, we show that invasive breast tumors exhibit significant ADAM23-ITH and that this heterogeneity is critical for tumor growth and metastasis. We demonstrate that while loss of ADAM23 expression enhances invasion, it causes a severe proliferative deficiency and is not itself sufficient to trigger metastasis. Rather, we observed that, in ADAM23-heterotypic environments, ADAM23-negative cells promote tumor growth and metastasis by enhancing the proliferation and invasion of adjacent A23-positive cells through the production of LGI4 (Leucine-rich Glioma Inactivated 4) and nitric oxide (NO). Ablation of LGI4 and NO in A23-negative cells significantly attenuates A23-positive cell proliferation and invasion. Our work denotes a driving role of ADAM23-ITH during disease progression, shifting the malignant phenotype from the cellular to the tissue level. Our findings also provide insights for therapeutic intervention, enforcing the need to ascertain ITH to improve cancer diagnosis and therapy.

Simultaneous detection of the C282Y, H63D and S65C mutations in the hemochromatosis gene using quenched-FRET real-time PCR

Hereditary hemochromatosis (HH) is a common autosomal disorder of iron metabolism mainly affecting Caucasian populations. Three recurrent disease-associated mutations have been detected in the hemochromatosis gene (HFE): C282Y, H63D, and S65C. Although HH phenotype has been associated with all three mutations, C282Y is considered the most relevant mutation responsible for hemochromatosis. Clinical complications of HH include cirrhosis of the liver, congestive cardiac failure and cardiac arrhythmias, endocrine pancreatic disease, which can be prevented by early diagnosis and treatment. Therefore, a reliable genotyping method is required for presymptomatic diagnosis. We describe the simultaneous detection of the C282Y, H63D and S65C mutations in the hemochromatosis gene by real-time PCR followed by melting curve analysis using fluorescence resonance energy transfer (FRET) probes. The acceptor fluorophore may be replaced by a quencher, increasing multiplex possibilities. Real-time PCR results were compared to the results of sequencing and conventional PCR followed by restriction digestion and detection by agarose gel electrophoresis (PCR-RFLP). Genotypes from 80 individuals obtained both by the conventional PCR-RFLP method and quenched-FRET real-time PCR were in full agreement. Sequencing also confirmed the results obtained by the new method, which proved to be an accurate, rapid and cost-effective diagnostic assay. Our findings demonstrate the usefulness of real-time PCR for the simultaneous detection of mutations in the HFE gene, which allows a reduction of a significant amount of time in sample processing compared to the PCR-RFLP method, eliminates the use of toxic reagents, reduces the risk of contamination in the laboratory, and enables full process automation.