Genetic analysis of osteogenesis imperfecta in a large Brazilian cohort

INTRODUCTION

Osteogenesis imperfecta (OI) is a genetically and clinically heterogeneous disorder caused by disruption of type I collagen synthesis. Previous Brazilian molecular OI studies have been restricted to case reports or small cohorts. The Brazilian OI Network (BOIN) is a multicenter study collecting clinical OI treatment data from five reference centers in three regions of Brazil.

OBJECTIVE

To describe the molecular analysis of a large cohort of OI registered at BOIN.

METHODS

Targeted next-generation sequencing (NGS) was performed at a centralized laboratory with the Ion Torrent platform, covering 99.6 % of the coding regions of 18 OI-associated genes. Clinical information was obtained from a clinical database.

RESULTS

We included 156 subjects in the molecular analyses. Variants were detected in 121 subjects: 65 (53.7 %) in COL1A1, 42 (34.7 %) in COL1A2, 2 (1.7 %) in IFITM5, one (0.8 %) in CRTAP, three (2.5 %) in P3H1, two (1.7 %) in PPIB, four (3.3 %) FKBP10, one (0.8 %) in SERPINH1, and one (0.8 %) in TMEM38B. Ninety-one distinct variants were identified, of which 26 were novel. Of the 107 variants identified in COL1A1 and COL1A2, 24.5 % cause mild OI, while the remaining 75.5 % cause moderate, severe, or lethal OI, of which 49.3 % are glycine to serine substitutions. A single variant in FKBP10 (c.179A>C; p.Gln60Pro) was found in three unrelated and non-consanguineous participants living in the same geographic area in Northeast Brazil, suggesting a possible founder effect.

CONCLUSION

Consistent with the literature, 88.4 % of the subjects had a variant in the COL1A1 and COL1A2 genes, with 10 % inherited in an autosomal recessive manner. Notably, one variant in FKBP10 with a potential founder effect requires further investigation. Data from this large cohort improves our understanding of genotype-phenotype correlations for OI in Brazil.

Burden of phenylketonuria in Latin American patients: a systematic review and meta-analysis of observational studies

Background

Phenylketonuria (PKU) is an inborn error of metabolism caused by a deficiency of the enzyme phenylalanine hydroxylase. If untreated, the complications of PKU lead to significant neucognitive and neuropsychiatric impairments, placing a burden on both the individual’s quality of life and on the healthcare system. We conducted a systematic literature review to characterize the impact of PKU on affected individuals and on healthcare resources in Latin American (LATAM) countries.

Methods

Searches of the global medical literature as well as regional and local medical literature up to September 2021. Observational studies on patients with PKU from any LATAM country. Pairs of reviewers independently screened eligible articles, extracted data from included studies, and assessed their risk of bias.

Results

79 unique studies (47 cross-sectional studies, 18 case series, 12 case reports, and two cohort studies) with a total of 4090 patients were eligible. Of these studies, 20 had data available evaluating early-diagnosed PKU patients for meta-analysis of burden outcomes. Intellectual disability in the pooled studies was 18% [95% Confidence Interval (CI) 0.04–0.38; I² = 83.7%, p = 0.0133; two studies; n = 114]. Motor delay was 15% [95% CI 0.04–0.30; I² = 74.5%, p = 0.0083; four studies; n = 132]. Speech deficit was 35% [95% CI 0.08–0.68; I² = 93.9%, p < 0.0001; five studies; n = 162].

Conclusions

There is currently evidence of high clinical burden in PKU patients in LATAM countries. Recognition that there are many unmet neuropsychological needs and socioeconomic challenges faced in the LATAM countries is the first step in planning cost-effective interventions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13023-022-02450-2.

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.

Abstract 5392: Exosomal miRNA expression profiling in triple-negative breast cancer

Exosomes are extracellular vesicles that are present in body fluids and known to play key roles in intercellular signaling communication. Exosomes carry several types of molecules of their tumor of origin, including miRNAs, and therefore present potential as biomarkers for cancer prognosis and treatment. Triple-negative breast cancer (TNBC) is a clinically aggressive subtype of breast cancer, associated with treatment resistance, recurrence and high mortality rates. These tumors are molecularly heterogeneous, which impairs the identification of effective prognostic molecular markers and target therapies. The main objective of this study was to characterize the miRNA expression profile of exosomes derived from TNBC cells in comparison to normal controls and to the luminal A (LA) breast cancer subtype. The exosomal miRNAs were isolated from 19 serum samples of breast cancer patients (10 with the LA and 9 with the TNBC subtype) and 10 serum samples of healthy women (control group) using the exosome precipitation method. Exosome characterization and quantification was assessed by Western blot using the exosomal surface markers, CD6 and CD9, and Nanotracking analysis. The tumor and normal exosomal samples were combined into 6 different pools (of at least 4 samples in each group) and sequenced in the Ion Torrent Proton platform (Applied Biosystems). RNA-seq analysis revealed differentially expressed (DE) levels of exosomal miRNAs, with log2FC ranging from 1.2 to 3.6, among the four groups studied (control, cancer (TNBC+LA), TNBC and LA groups): 22 DE miRNAs were observed in the cancer vs. control, 19 in the LA vs control, 30 in the TNBC vs. control and 7 in the LA vs. TNBC groups. Eleven miRNAs were commonly DE in the cancer, LA and TNBC groups when compared to the control group, which included miRNAs, such as miR-103a-3p, miR-107 and miR-423-5p, involved in the biosynthesis of unsaturated fatty acids and neutrophin signaling pathways. Nine miRNAs were only observed DE in the TNBC group (vs. control), with the majority of them being downregulated. The top 10 significant functional enriched pathways affected by these miRNAs included proteoglycans, pathways in cancer and TGF-beta signaling pathways. Only three miRNAs were observed DE in the TNBC vs. LA groups, all with downregulated expression in the TNBC group. These miRNAs were observed mostly involved in fatty acid biosynthesis, proteoglycans in cancer and TGF-beta signaling pathways. In conclusion, our results indicate that expression alterations of exosomal miRNAs affect critical cancer-associated signaling pathways, suggesting their potential use as noninvasive cancer biomarkers. Additional studies should be performed to determine whether the expression patterns of these exosomal miRNAs reflect the ones observed in the corresponding patients' TNBC tissue.

Funding: CAPES, PPSUS-Fundação Araucária, Brazil.

Citation Format: Patricia M. Ozawa, Débora S. Lemos, Evelyn Vieira, Ingrid L. Souza, Silvio M. Zanata, Vânia C. Pankievicz, Thalita R. Tuleski, Emanuel M. Souza, Rosiane V. Silva, Pryscilla F. Wowk, Rodrigo C. Almeida, Iglenir J. Cavalli, Danielle M. Ferreira, Luciane R. Cavalli, Enilze M. Ribeiro. Exosomal miRNA expression profiling in triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5392.

Differentially expressed miRNAs in triple negative breast cancer between African-American and non-Hispanic white women

Triple Negative Breast Cancer (TNBC), a clinically aggressive subtype of breast cancer, disproportionately affects African American (AA) women when compared to non-Hispanic Whites (NHW). MiRNAs(miRNAs) play a critical role in these tumors, through the regulation of cancer driver genes. In this study, our goal was to characterize and compare the patterns of miRNA expression in TNBC of AA (n = 27) and NHW women (n = 30). A total of 256 miRNAs were differentially expressed between these groups, and distinct from the ones observed in their respective non-TNBC subtypes. Fifty-five of these miRNAs were mapped in cytobands carrying copy number alterations (CNAs); 26 of them presented expression levels concordant with the observed CNAs. Receiving operating characteristic (ROC) analysis showed a good power (AUC ≥ 0.80; 95% CI) for over 65% of the individual miRNAs and a high combined power with superior sensitivity and specificity (AUC = 0.88 (0.78−0.99); 95% CI) of the 26 miRNA panel in discriminating TNBC between these populations. Subsequent miRNA target analysis revealed their involvement in the interconnected PI3K/AKT, MAPK and insulin signaling pathways. Additionally, three miRNAs of this panel were associated with early age at diagnosis. Altogether, these findings indicated that there are different patterns of miRNA expression between TNBC of AA and NHW women and that their mapping in genomic regions with high levels of CNAs is not merely physical, but biologically relevant to the TNBC phenotype. Once validated in distinct cohorts of AA women, this panel can potentially represent their intrinsic TNBC genome signature.

Abstract 3431: The oncogenic role of miR-150-5p in triple-negative breast cancer

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer that confers disease recurrence, treatment resistance and high mortality rates. MicroRNAs are a class of noncoding RNAs, that when dysregulated, impact tumorigenesis through the control of the expression of multiple mRNA targets involved in critical cancer signaling pathways. MiR-150-5p has been shown to control the expression of several driver oncogenes and/or tumor suppressor genes involved in these critical pathways. Its pattern of expression varies according to the cancer type; it has been observed mostly downregulated in hematological diseases and GI cancers, and upregulated in hormonal dependent cancers, such as prostate and breast cancer. The main objective of this study was to assess the patterns of expression of miR-150-5p in TNBC and determine its functional role in affecting the tumor phenotype. Archived paraffin samples of 113 patients with ductal breast carcinoma (56 of the TNBC and 57 of the non-TNBC subtype) and 49 adjacent normal tissue (ANT), obtained from the the pathology tumor bank of Lombardi Comprehensive Cancer Center, Washington DC, were profiled for miRNA using the wide-genome Nanostring platform and a Taqman specific miRNA-150-5p assay. Significant overexpression levels of miRNA-150-5p were observed in the tumor tissues when compared to the ANT and in the TNBC cases when compared to the non-TNBC cases, demonstrating its tumor and TNBC subtype specificity, respectively. Overexpressed levels of miRNA-150-5p were also preferentially observed in the TNBC cases from patients that presented with LN metastasis and breast cancer recurrence, indicating its association with poor prognosis. Interestingly, the TNBC of African-American patients, which is the ethnic group mostly affected by this cancer subtype, presented overexpression levels of this miRNA when compared to the Non-Hispanic White patients. Functional analysis performed in the TNBC cell lines, MDA-MB-231 and HCC1806, showed after transfection with miR-150-5p inhibitor, reduced levels on cell proliferation, clonogenicity, migration, drug resistance and expression of the EMT promoter markers, SLUG and SNAIL. These findings, indicate an oncogenic type of action of miRNA-150-5p in TNBC. In summary, miRNA-150-5p is upregulated in TNBC clinical cases in association with poor prognostic parameters and its functional inhibition, directly confers to the cells a reduction of their tumorigenic phenotype.

Funding: This project was supported by the Georgetown University Center of Excellence in Regulatory Science and Innovation (CERSI U01FD004319), a collaborative effort between the university and the U.S. Food and Drug Administration to promote regulatory science through innovative research and education. This research does not necessarily reflect the views of the FDA. Scholarship to B.S. was provided by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES).

Citation Format: Bruna M. Sugita, Yara Zabala, Aline Fonseca, Rodrigo Almeida, Yuriy Gusev, Simina Boca, Iglenir J. Cavalli, Enilze M. Ribeiro, Luciane R. Cavalli. The oncogenic role of miR-150-5p in triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3431. doi:10.1158/1538-7445.AM2017-3431

Abstract 5100: Genomic profiling of triple negative breast cancer from South of Brazil

Triple negative breast cancer (TNBC) are defined by the lack of expression of ER, PR and HER2 receptors and characterized by an aggressive clinical history and poor outcome. Considering that these tumors do not present a good response to the available adjuvant target therapies (hormonal and HER-2 based therapies), there is a critical need to identify new markers to improve treatment options for these patients. The use of genome-wide methodologies is a progress towards this direction, through the identification of biomarkers that can be translated into novel target-based therapies. We report the genomic profiling performed by array-CGH (Agilent 4x44K) in 33 cases of TNBC obtained from Hospital N.S. das Gracas and Hospital das Clinicas (UFPR), Curitiba, South of Brazil. Copy number alterations in potentially therapeutic target genes for TNBC (involved in the PI3K-AKT pathway) were evaluated by TaqMan copy number assay (Applied Biosystems). The data was correlated with pathological parameters from the patients. Copy number changes were observed by array-CGH in 87% (25/30) of the TNBC cases analyzed, with a median of 9.97+12.37 alterations per case. Based on this value, the samples were divided into two categories (&gt;10 and &lt;10 alterations); no significantly difference was observed between these categories and tumor size (t=1.74;P&gt;0.05) or the presence of lymph node (LN) metastasis (≥2=1.8;P&gt;0.10) and tumor grade (≥2=1.18;P&gt;0.20). Although a high degree of molecular heterogeneity was observed, amplification on 8q was observed in 50% (15/30) of the cases, mostly involving 8q24.3. Tumor size was not significantly different among the cases with or without 8q amplification (t=1,88; P&gt;0.20). These cases were also equally distributed in relation to LN metastasis (≥2=2.67;P&gt;0.10) and tumor grade (≥2=0.5;P&gt;0.50). Finally, alterations in at least one gene involved in the PIK3/AKT pathway were observed in 88% (29/33) of the cases and in more than three genes in 45% (13/29) of the cases. PIK3CA and PTEN were the most frequently altered genes: gained and lost in 42% and 40% of the cases respectively. AKT2, AKT1, and FGFR2 genes were observed gained in 24%, 21% and 21% of the cases respectively. Alterations in those genes were also not significantly correlated with tumor size (t=0.95; P&gt;0.30), LN metastasis (≥2=0.16; P&gt;0.50) and tumor grade (≥2=3.23; P&gt;0.05). Our results indicate a high level of DNA copy number changes in TNBC cases, involving mostly chromosome 8q. Alterations on genes involved in the PIK3/AKT pathway were also common; immunohistochemistry analyses are in progress to evaluate those alterations at the expression level. No significant correlations were observed among the genomic alterations and the pathological parameters from the patients. This lack of correlation can be due to the limited sample size or can indicate that in our set of TNBC cases tumor size, LN metastasis and tumor grade are not associated with an elevated genomic instability.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5100. doi:1538-7445.AM2012-5100

Clonal chromosomal alterations in fibroadenomas of the breast

A cytogenetic study on short-term cell cultures from 10 fibroadenomas of the breast is reported. Clonal chromosomal alterations were observed in all cases analyzed, involving preferentially chromosomes X, 12, 14, 20, and 22. Normal karyotypes were found in 34.9% of the cells. The present findings are discussed together with the reports on fibroadenomas and other benign lesions of the breast described in the literature. Although no specific chromosome abnormality to date can be attributed to a particular type of benign breast pathology, some recurrent alterations are starting to emerge and may characterize these benign breast lesions, differentiating them from their malignant counterparts.

Noval mutation (Y184C) in exon 4 of the beta-sarcoglycan gene identified in a Portuguese patient. Mutations in brief no. 177. Online

We report a novel beta-sarcoglycan gene mutation identified in a 21-year-old Portuguese male with a progressive myopathy of intermediate severity, who had been misdiagnosed as Becker Muscular Dystrophy (BMD) based on clinical observations and muscle immunocytochemical anaylsis with dystrophin antibodies only. Since no detectable deletions or duplications were found in the dystrophin gene, we screened for mutations in the sarcoglycan genes by PCR-SSCP. The patient's sample showed a band of increased mobility in exon 4 of the beta-sarcoglycan gene which, upon sequencing, was found to represent a homozygous A-->G transversion at nucleotide 551, resulting in a tyrosine to cysteine substitution at position 184 (Y184C). Carrier status was ascertained in both parents and a sister. These aberrant conformers were not detected in 85 unrelated control individuals screened by PCR-SSCP analysis. All seven beta-sarcoglycan mutations reported to date are associated with a severe phenotype and occur in exons 3 and 4, which correspond to the immediate extracellular domain of the protein. This region contains five conserved cysteine residues. In our patient, the presence of an extra cysteine residue could interefere with intra- and/or inter-molecular disulphide bond formation. The intermediate phenotype could perhaps result from the assembly of both normal and abnormal complexes, depending on the formation of the disulphide bonds.

Clonal karyotypic abnormalities in gynecomastia

Gynecomastia is a benign condition that frequently occurs in the male breast gland; however, the cytogenetic data on this entity are very limited. To our knowledge, three cases have been reported in the literature, and the only one with an abnormal karyotype had a concomitant breast carcinoma. In this study we report clonal chromosomal alterations in a gynecomastia sample without any signs of adjacent malignant tissue. The nonrandom abnormalities observed were a deletion of 12p, monosomies of chromosomes 9, 17, 19, and 20, and the presence of a marker chromosome. Most of these alterations have been previously described in the literature in other breast lesions, including benign and malignant (male and female) tumors, indicating their recurrence and nonrandomness in abnormal processes of the mammary gland.

Say syndrome: report of a familial case

We describe a new case of Say syndrome. This syndrome is an autosomal dominant condition characterized by cleft palate, short stature of prenatal onset, large protruding ears and microcephaly, delayed bone age, and renal anomalies. The first report was in 1975 by Say et al. in three generations of a family. Three additional reports of isolated cases were published. Our propositus is a 12-month-old boy with the cardinal signs of the syndrome whose mother has only microcephaly. To our knowledge this is the second familial report with evidence of highly variable expressivity. The occurrence of renal anomalies in a son of a normal sister of his mother suggests incomplete penetrance.

Cytogenetic analysis in human bone marrow transplantation

Bone marrow transplantation (BMT) is a therapeutic process used to treat a variety of hematologic diseases. After BMT, the documentation of engrafting with the use of genetic markers is obligatory. C-band polymorphism is an excellent genetic marker because it occurs with high frequency in all populations studied and shows a high stability in vitro and in vivo. We studied a total of 36 patients: 15 with myeloid leukemia and 21 with severe aplastic anemia (SAA), submitted to BMT. The majority of the patients with chronic granulocyte leukemia (CGL; 10/15, 67%) and with SAA (17/21, 81%) showed a frequency of host cells around 15% (CGL) and 8% (SAA) in the first period analyzed (day +30 post-BMT); with a decrease in the others (+90, +180 to CGL and SAA and +365 only to CGL). In our study, the persistence of host cells in these proportions did not imply an unfavorable prognosis. On the contrary, some patients with myeloid leukemia (5/15 33%) and SAA (4/21, 19%) showed high proportions of host cells in one or more periods analyzed. If compared to the first group, these patients had, in general, a poor clinical evolution, with rejections, relapses, and deaths in greater numbers. These results show the important contribution of cytogenetic analysis in the follow-up of patients submitted to BMT.

Trisomy 4 in acute nonlymphocytic leukemia: the first Brazilian case

We report the first South American case of acute nonlymphocytic leukemia, French-American-British (FAB) subtype M1, [1] with trisomy 4 as the sole chromosome abnormality. The patient denied exposure to toxic or carcinogenic substances.

High effectiveness of aerosolized chick embryo fibroblast measles vaccine in seven-month-old and older infants

Neither the presence of hypertonic sugar nor the absence of 1% human albumin in the aerosolized chick embryo fibroblast (CEF) measles vaccine was previously found to be responsible for its inadequacy in infants with titers of maternal plaque-neutralizing (PN) antibody at which human diploid cell measles vaccine was immunogenic. Eight weeks after administration of CEF measles vaccine containing 1% human albumin, antibody had developed in all 10 infants 7-10 months old and all 11 children 12-35 months old but in only 26% of 23 infants 3-5 months old and 67% of 9 infants 6 months of age. Failure of antibody development was associated with prevaccination PN antibody titers of greater than or equal to 1:50 (with one exception at a titer of 1:25). The PN antibody response to CEF vaccine (diluted 1:10, approximately 10(5) pfu/ml) in infants under seven months of age (geometric mean titer [GMT], 1:421) was significantly lower (P less than .005) than in older infants (GMT, 1:1,564). At a 1:1,000 dilution of vaccine, only 50% of 10 infants 13-25 months old, 20% of 15 infants 7-10 months old, and none of 8 infants 6 months old developed antibody.