Copy number analysis from whole-exome sequencing data revealed a novel homozygous deletion in PARK7 leads to severe early-onset Parkinson's disease

Parkinson's disease (PD), a neurodegenerative disease characterized by both motor neuron and non-motor neuron symptoms, is the most frequent neurodegenerative disease after Alzheimer's disease. Both genetic and environmental factors take part in disease etiology. Most cases are considered complex multifactorial diseases. About 15% of PD appear in the familial form, and about 5% of all cases arise from a single gene mutation. Among Mendelian causes of PD, PARK7 is one of the autosomal recessive forms due to loss-of-function mutations in both gene alleles. Both single nucleotide variants (SNVs) and copy number variations (CNVs) are observed in PARK7. This study presents an Iranian family with familial PD where some relatives had psychiatric disorders. A homozygous 1617 bp deletion in a female with early-onset PD was detected through copy-number analysis from whole-exome sequencing (WES) data in this consanguineous family. Further investigation by surveying microhomology revealed that the actual size of the deletion is 3,625 bp. This novel CNV that was in the PARK7gene is supposed to co-relation with early-onset PD and infertility in this family.

Whole-Exome Sequencing Study of Consanguineous Parkinson's Disease Families and Related Phenotypes: Report of Twelve Novel Variants

Parkinson's disease (PD) is a common progressive neurodegenerative disorder with motor and nonmotor symptoms. Recent studies demonstrate various susceptibility loci and candidate genes for familial forms of the disease. However, the genetic basis of the familial form of early-onset PD (EOPD) is not widely studied in the Iranian population. Therefore, the present study aimed to investigate the possible causative genetic variants responsible for developing EOPD among Iranian patients. Iranian patients with a clinical diagnosis of Parkinson's disease were evaluated, and 12 consanguineous families with at least two affected individuals with early-onset PD (EOPD) were chosen to enroll in the present study. An expert neurologist group examined these families. Whole-exome sequencing (WES) was performed on PD patients, and the possible causative genetic variants related to the development of PD were reported. Exome sequencing (WES) was performed on every PD patient and revealed that patients had novel genetic variants in PRKN, PARK7, and PINK1 genes. All the genetic variants were in homozygous status and none of these variants were previously reported in the literature. Moreover, these genetic variants were "pathogenic" based on bioinformatic studies and according to the American College of Medical Genetics (ACMG). The present research revealed some novel variants for EOPD among the Iranian population. Further functional studies are warranted to confirm the pathogenicity of these novel variants and establish their clinical application for the early diagnosis of EOPD.

AOPEP variants as a novel cause of recessive dystonia: Generalized dystonia and dystonia-parkinsonism

INTRODUCTION

The genetic basis of autosomal-recessive dystonia remains poorly understood. Our objective was to report identification of additional individuals with variants in AOPEP, a recently described gene for recessively inherited dystonic disorders (OMIM:619565).

METHODS

Ongoing analysis on a high-throughput genetic platform and international case-recruitment efforts were undertaken.

RESULTS

Novel biallelic, likely pathogenic loss-of-function alleles were identified in two pedigrees of different ethnic background. Two members of a consanguineous Iranian family shared a homozygous c.1917-1G>A essential splice-site variant and featured presentations of adolescence-onset generalized dystonia. An individual of Chinese descent, homozygous for the nonsense variant c.1909G>T (p.Glu637*), displayed childhood-onset generalized dystonia combined with later-manifesting parkinsonism. One additional Iranian patient with adolescence-onset generalized dystonia carried an ultrarare, likely protein-damaging homozygous missense variant (c.1201C>T [p.Arg401Trp]).

CONCLUSIONS

These findings support the implication of AOPEP in recessive forms of generalized dystonia and dystonia-parkinsonism. Biallelic AOPEP variants represent a worldwide cause of dystonic movement-disorder phenotypes and should be considered in dystonia molecular testing approaches.

Exome sequencing identifies RASSF1 and KLK3 germline variants in an Iranian multiple-case breast cancer family

Breast cancer is the most frequent malignancy among women in both developed and developing countries. Although several genes have been identified to harbor germline variants contributing to breast cancer risk, much of the heritability for breast cancer is yet undefined. In the present study, we have performed exome sequencing to detect susceptibility genes in an Iranian family with five first-degree family members affected with breast cancer. We identified novel candidate variants with predicted pathogenicity in RASSF1, KLK3 and FAM81B. The RASSF1 and KLK3 variants, but not the FAM81B variant, partially co-segregated with disease in the investigated pedigree and were not found in additional screenings outside the specific family. RASSF1 p.S135F is a missense substitution abolishing the ATM phosphorylation site, and KLK3 variant p.M1? is a deletion at the initiation codon that is predicted to abolish translation to the functional kallikrein protease, PSA. Our study suggests germline variation in RASSF1 and KLK3 as candidate contributors to familial breast cancer predisposition and illustrates the difficulties to determine the causal genetic risk factor among novel variants restricted to a single family.

Evaluation of COVID-19 trend in Iran; Population response to the recent pandemic overtime

Relative internet search volumes (RSV) is now being consider as a measurement of awareness for most of the trending topics. During the recent coronavirus disease (COVID-19) outbreak, many researchers used the RSVs to interpret the population responses to the pandemic in various ways. By using the RSVs searched by Persian language people, we demonstrated that the Iranian people increased their knowledge and awareness of COVID-19 during the early phases of the disease before the first peak. However, their relative searches about the COVID-19 and its clinical symptoms decreased gradually despite of the gradual rise of the confirmed cases. Their less tendency to seek information about the COVID-19 could be one of the possible explanation for the increasing number of confirmed cases even several days after easing the disease related lockdown.

Cell-based treatment of cerebral palsy: still a long way ahead

BACKGROUND

Cerebral palsy (CP) is a permanent neurodevelopmental disorder with considerable global disability. Various rehabilitation strategies are currently available. However, none represents a convincing curative result. Cellular therapy recently holds much promise as an alternative strategy to repair neurologic defects.

METHOD

In this narrative review, a comprehensive search of the MEDLINE and ClinicalTrials.gov was made, using the terms: "cell therapy" and "cerebral palsy", including published and registered clinical studies, respectively.

RESULTS

The early effects of these studies demonstrated that using cell therapy in CP patients is safe and improves the deficits for a variable duration. Despite such hopeful early bird results, the long-term outcomes are not conclusive.

CONCLUSIONS

Due to the heterogeneous nature of CP, personal factors seem essential to consider. Cell dosage, routes of administration, and repeated dosing are pivotal to establish optimal personalized treatments. Future clinical trials should consider employing other cell types, specific cell modifications before administration, and cell-free platforms.

Developmental regulation and lateralization of N-methyl-d-aspartate (NMDA) receptors in the rat hippocampus

N-methyl-d-aspartate receptors (NMDARs) are expressed abundantly in the brain and play a crucial role in the regulation of central nervous system (CNS) development, learning, and memory. During early neuronal development, NMDARs modulate neurogenesis, neuronal differentiation and migration, and synaptogenesis. The present study aimed to examine the developmental expression of NMDARs subunits, NR1 and NR2B, in the developing hippocampus of neonatal rats during the first two postnatal weeks. Fifty-four male offspring were randomly divided into three age groups, postnatal days (P) 0, 7, and 14. Real-time-PCR, western blotting, and immunohistochemistry (IHC) analyses were employed to examine and compare the hippocampal expression of the NMDA receptor subunits. The highest mRNA expression of NR1 and NR2B subunits was observed at P7, regardless of its laterality. The mRNA expression of both subunits in the right hippocampus was significantly higher than that of the left one at P0 and P7. Similarly, the highest protein level expression of NR1 and NR2B subunits was also observed at P7 in both sides hippocampi. Although the protein expression of NR1 was significantly higher on the right side in all studied days, the NR2B was significantly higher in the right hippocampus only at P7. The analysis of optical density (OD) has shown a marked increase in the distribution pattern of the NR1 and NR2B subunits at P7 in all hippocampal subregions. In conclusion, there is a marked right-left asymmetry in the expression of NR1 and NR2B subunits in the developing rat hippocampus, which might be considered as a probable mechanism for the lateral differences in the structure and function of the hippocampus in rats.

PLA2G6 gene mutation and infantile neuroaxonal degeneration; report of three cases from Iran

OBJECTIVES

Infantile neuroaxonal degeneration (INAD) is a rare subgroup of neurodegeneration with brain iron accumulation (NBIA) disorders. This progressive disorder may develop during the early years of life. Affected individuals mostly manifest developmental delay and/or psychomotor regression as well as other neurological deficits. In the present study, we discussed 3 INAD patients diagnosed before the age of 10 by using Whole-Exome Sequencing (WES).

MATERIALS AND METHODS

We evaluated 3 pediatric patients with clinical phenotypes of INAD who underwent WES. Sanger sequencing was performed for co-segregation analysis of the variants in the families. An in-silico study was conducted for identification of the molecular function of the identified genetic variants in the PLA2G6 gene.

RESULTS

We detected three novel genetic variants in the PLA2G6 gene including a homozygous missense (NM_003560.2; c.1949T>C; p.Phe650Ser), a splicing (NM_001349864; c.1266-1G>A) and a frameshift variant (NM_003560.4; c.1547_1548dupCG; p.Gly517ArgfsTer29). Since the variants were not previously reported in literature or population databases, we performed in-silico studies for these variants and demonstrated their potential pathogenicity.

CONCLUSION

The current study reports novel genetic variants in the PLA2G6 gene in the Iranian population, emphasizing the importance of high-throughput genetic testing in rare diseases.

Scoring Algorithm-Based Genomic Testing in Dystonia: A Prospective Validation Study

BACKGROUND

Despite the established value of genomic testing strategies, practice guidelines for their use do not exist in many indications.

OBJECTIVES

We sought to validate a recently introduced scoring algorithm for dystonia, predicting the diagnostic utility of whole-exome sequencing (WES) based on individual phenotypic aspects (age-at-onset, body distribution, presenting comorbidity).

METHODS

We prospectively enrolled a set of 209 dystonia-affected families and obtained summary scores (0-5 points) according to the algorithm. Singleton (N = 146), duo (N = 11), and trio (N = 52) WES data were generated to identify genetic diagnoses.

RESULTS

Diagnostic yield was highest (51%) among individuals with a summary score of 5, corresponding to a manifestation of early-onset segmental or generalized dystonia with coexisting non-movement disorder-related neurological symptoms. Sensitivity and specificity at the previously suggested threshold for implementation of WES (3 points) was 96% and 52%, with area under the curve of 0.81.

CONCLUSIONS

The algorithm is a useful predictive tool and could be integrated into dystonia routine diagnostic protocols. © 2021 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson Movement Disorder Society.

Telemedicine and Computer-Based Technologies during Coronavirus Disease 2019 Infection; A Chance to Educate and Diagnose

Coronavirus disease 2019 (COVID-19) is now of global concern due to its rapid dissemination across the globe. The rapid spread of this viral infection, along with many of its unknown aspects, has posed new challenges to the health care systems. The main challenging effects of COVID-19 are rapid dissemination through close contact and varying clinical severity among different individuals. Furthermore, the medical staff in endemic areas are becoming exhausted and deal with a considerable level of job burnout, which can negatively affect their medical decision making. Also, due to the variable pulmonary manifestations of COVID-19, some physicians may misdiagnose patients. To overcome these issues, we proposed a web-based software to aid physicians in detecting possible COVID-19 cases through online consultation with different specialists and educate the not-well experienced physicians. Our results demonstrated that this software could improve the diagnostic rate for not-well experienced physicians.

Genetic variants of the phenylalanine hydroxylase gene in patients with phenylketonuria in the northeast of Iran

Background Phenylketonuria (PKU) is a common metabolic disorder with great burden if left untreated or undiagnosed. Genetic variations in the phenylalanine hydroxylase (PAH) gene may be widely varied across different regions of a country. By knowing the most common mutations, diagnostic work-ups will be offered sooner and with lower costs for patients. The present study defines the most common genetic variations in the PAH gene in Khorasan province of Iran. Methods The present cross-sectional study took place in Khorasan province of Iran within a 6-year period starting from 2012 to 2018. Every patient who had been referred as suspicious PKU cases or referred for prenatal diagnosis was included in the present study. Results A total number of 122 individuals with a mean age of 26.22 years were enrolled in the present study. The most frequent genetic variations in the PAH gene were c.1066-11G > A and c.143 T > C. Exon 7 carried the most genetic variations compared to any single exon. Also, three patients had compound heterozygous status for c.727 C > T/c.1066-11 G > A in exon 7 and 11 of the PAH gene. Conclusions Mutations in the PAH gene are widely varied among different populations, and our results confirmed this fact. Determination of the most prevalent mutations and polymorphisms in each region will reduce the time and cost of diagnosing such preventable diseases and will therefore reduce the disease burden.

Circulating and tissue microRNAs as a potential diagnostic biomarker in patients with thrombotic events

Venous and arterial thrombosis are conditions that have a considerable burden if left untreated. The hypoxia-induced by the occluded vessel can disrupt the circulation of any organ, the cornerstone of treating thrombosis is rapid diagnosis and appropriate treatment. Diagnosis of thrombosis may be made by using laboratory tests or imaging techniques in individuals who have clinical manifestations of a thrombotic event. The use of serum micro ribonucleic acids (RNAs) has recently been applied to the diagnosis of thrombosis. These small RNA molecules are emerging as new diagnostic markers but have had very limited applications in vascular disease. Most of the articles provided various microRNAs with different levels of accuracy. However, there remains a lack of an appropriate panel of the most specific microRNA in the literature. The purpose of the present review was to summarize the existing data on the use of microRNAs as a diagnostic biomarker for venous thrombosis.

ADAMTS7 and ZC3HC1 Share Genetic Predisposition to Coronary Artery Disease and Large Artery Ischemic Stroke

Coronary artery disease (CAD) and ischemic stroke (IS) are commonly considered distinct disease phenotypes. However, there is some evidence in favor of a degree of overlap between genetic susceptibility to CAD and genetic risk factors for IS. In the present study, we aimed to examine the role of two single-nucleotide polymorphisms (SNPs), rs3825807 and rs11556924, located in the ADAMTS7 and ZC3HC1 genes, respectively, associated with CAD in published GWASs in European populations and their possible contribution to the development of coronary atherosclerosis and cerebral LA atherosclerosis in a case-control study of an the Iranian population. The sample size was 400, and the methodology for SNP genotyping was ARMS-PCR. Both SNPs showed strong associations with CAD in the analyses comparing significant CAD and myocardial infarction (MI) with controls. None of them, however, were associated with MI in patients with significant CAD. Our findings further support the role of the ADAMTS7 locus in promoting atherosclerosis in LAs of the brain. Regarding ZC3HC1 rs11556924, our study further supports the observed association of rs11556924 with LA IS coming from previous GWASs. In conclusion, the data showed that common variants in ADAMTS7 and ZC3HC1 genes contribute to an increased risk for both CAD and LA (atherosclerotic) IS.

Prevalence of β-Thalassemia Mutations among Northeastern Iranian Population and their Impacts on Hematological Indices and Application of Prenatal Diagnosis, a Seven-Years Study

BACKGROUND AND OBJECTIVE

β-thalassemia results from a diverse range of mutations inside the hemoglobin subunit β (HBB) gene. In a study of β-thalassemia carriers and some of their at-risk fetuses in the Khorasan province of Iran, we aimed to recognize the most common mutations in the region. We also investigated a possible link between these mutations and some of the relevant hematological indices.

METHODS

Amplification-refractory mutation system-PCR (ARMS-PCR) was used to detect the typical HBB mutations among 1593 individuals, suspected of having a mutated HBB allele from March/2011 to January/2018. Sanger sequencing of HBB had been performed, where ARMS-PCR was uninformative. In some cases, reverse dot blot was utilized. Analysis of variance was used to compare parametric variables.

RESULTS

Among 1273 β-thalassemia carriers, the prevalence of the mutations were reported as follows: IVS-I-5 (42.03%), IVS-II-1 (11.23%), codons 8/9 (4.79%), codon 44 (4.56%), codon 15 (3.53%), Los Angeles (2.91%), codon 5 (2.75%), IVS-I-110 (2.51%), -88 (2.20%) and other mutations were less than 2% of all of the reported mutations. 644 conceptions were subjected to prenatal diagnosis, using chorionic villus sampling. 118 cases were reported as normal. 352 cases were detected as carriers. 174 cases were diagnosed as affected. There was a significant difference in mean corpuscular volume and hemoglobin A2 levels between the nine most commonly reported mutation types (p<0.001).

CONCLUSION

This study makes a reliable guide for β-thalassemia diagnosis in the region. The possibility of a correlation between HBB mutations and hematological indices opens a gate of future investigations.

Assessment of an APOBEC3B truncating mutation, c.783delG, in patients with breast cancer

PURPOSE

APOBEC3B belongs to the family of DNA-editing enzymes. A copy number variant targeting the genomic APOBEC3A-APOBEC3B locus has a significant impact on breast cancer risk, but the relative contribution of APOBEC3B is uncertain. In this study, we investigate a loss-of-function mutation that selectively targets APOBEC3B, for its association with breast cancer risk.

METHODS

We performed exome sequencing on genomic DNA samples of 6 Byelorussian patients with familial breast cancer. We then studied through mutation-specific genotyping four hospital-based breast cancer case-control series from Belarus, Russia, Germany, and Iran, respectively, comprising a total of 3070 breast cancer patients and 2878 healthy females. Results were evaluated using fixed-effects meta-analyses.

RESULTS

Exome sequencing uncovered a frameshift mutation, APOBEC3B*c.783delG, that was recurrent in the study populations. Subsequent genotyping identified this mutation in 23 additional breast cancer cases and 9 healthy female controls, with an adjusted Odds Ratio 2.29 (95% CI 1.04; 5.03, P = 0.04) in the combined analysis. There was an enrichment of the c.783delG mutation in patients with breast cancer diagnosed below 50 years of age (OR 3.22, 95% CI 1.37; 7.56, P = 0.007).

CONCLUSIONS

APOBEC3B*c.783delG showed evidence of modest association with breast cancer and seemed to contribute to earlier onset of the disease. These results may need to be reconciled with proposals to consider APOBEC3B as a possible therapeutic target in breast cancer.

Diabetes in Pregnancy Adversely Affects the Expression of Glycogen Synthase Kinase-3β in the Hippocampus of Rat Neonates

Diabetes during pregnancy causes a wide range of neurodevelopmental and neurocognitive abnormalities in offspring. Glycogen synthase kinase-3 (GSK-3) is widely expressed during brain development and regulates multiple cellular processes, and its dysregulation is implicated in the pathogenesis of diverse neurodegenerative and psychological diseases. This study was designed to examine the effects of maternal diabetes on GSK-3β messenger RNA (mRNA) expression and phosphorylation in the developing rat hippocampus. Female rats were maintained diabetic from a week before pregnancy through parturition, and male offspring was killed immediately after birth. We found a significant bilateral upregulation of GSK-3β mRNA expression in the hippocampus of pups born to diabetic mothers at P0, compared to controls. Moreover, at the same time point, there was a marked bilateral increase in the phosphorylation level of GSK-3β in the diabetic group. Unlike phosphorylation levels, there was a significant upregulation in hippocampal GSK-3β mRNA expression in the insulin-treated group, when compared to controls. The present study revealed that diabetes during pregnancy strongly influences the regulation of GSK-3β in the right/left developing hippocampi. These dysregulations may be part of the cascade of events through which diabetes during pregnancy affects the newborn's hippocampal structure and function.

Analysis of novel mutations in BRCA1 in Iranian families with breast cancer

In Iran and the rest of the world, breast cancer (BC) is the most common malignancy in women. Familial history and age are significant risk factors for the development of this disease in Iran. Most hereditary BCs are associated with inherited mutations in the BRCA1 and BRCA2 genes. Some recent studies demonstrated that BRCA1 mutations are seen in high-risk women with family histories of BC. In this report we investigated all BRCA1 exons from 40 female patients with family histories of BC and one BC twin, and report a novel mutation in this gene in one patient. As controls, BRCA1 exons from 100 normal women and the BC-free twin of the BC twin were also examined for this mutation. None of the women in the normal group harbored the mutation. Whether this variation is specific for the Iranian population or for special subgroups remains to be determined.

Chromosome duplication (14q) and the genotype phenotype correlation

The rearrangement of chromosome 14 is a rare cytogenetic finding. Changes in the number or structure of chromosome 14 can have a variety of effects, such as delayed growth and development, and distinctive facial features. The human chromosome 14 plays an important role in imprinting events importunes of a structural rearrangement is specifically when a phenotype is caused by imprinting, whereby the interpretation of genotype-phenotype correlation becomes extremely difficult. In this study, we examined a 3 year-old mentally impaired girl with unusual facial features. G-banding showed terminal duplication of chromosome 14 in the karyotype of the patient. In this particular case, we explained a phenotype genotype correlation in a patient with a dup (14) rearrangement, thus emphasizing the importance of prenatal diagnosis for pregnancies with an abnormal nuchal translucency.

Evaluation of a genetic test for diagnose of primary hypolactasia in northeast of iran (khorasan)

OBJECTIVES

Primary or adult type hypolactasia, the most common enzyme deficiency in the world, is due to reduced lactase activity in the intestinal cell after weaning. Lactase non-persistence is inherited as an autosomal recessive trait. A DNA variant, single nucleotide polymorphism C/T-13910 which is located on 13910 base pairs (bp) upstream of the lactase gene (LCT) at chromosome 2 has been show to associate with the lactase persistence/non-persistence. The prevalence of the C/T-13910 variant is different for hypolactasia in European, Asian, African-American and Northern African populations. In this study, we investigated, for the first time the allele frequent of the single nucleotide polymorphism C/T-13910 in the Iranian population in khorasan province with hypolactasia.

MATERIALS AND METHODS

Peripheral blood was collected from 100 subjecs with primary hypolactasia and 100 healthy individuals as a control group. Genomic DNA was extracted. The genotype was analyzed with the PCR-RFLP method. A statistical analysis was performed by chi-square test using SPSS software. A P-value of <0.05 was considered statistically significant.

RESULTS

In case group allelic frequency for SNP T-13910C (C, T) was respectively 95%, 5% vs. control group 86% and 14%. Genotype frequency (CC, CT, TT) in patient group was 90%, 10%, 0% vs. control group 74%, 24% and 2%. So according to our findings, there were significant differences between allelic frequencies (P=0.03), and in genotype frequency between case and control groups (P=0.006).

CONCLUSION

Based on our results, analysis of C\T-13910 polymorphism can be used as a simple genetic test for diagnosis of primary type hypolactasia in the Iranian population.

Sex differences and left-right asymmetries in expression of insulin and insulin-like growth factor-1 receptors in developing rat hippocampus

Sex differences and laterality of rat hippocampus with respect to insulin-like growth factor-1 receptor (IGF-1R) and insulin receptor (InsR) expression as two important contributors to/regulators of developmental and cognitive functions were examined using real-time PCR and western blot analysis at P0, P7 and P14. Expression of the IGF-1R gene was lowest at P0 in all studied hippocampi. In males, we found the highest expression at P7 in the right hippocampus, and at P14 in the left one. In contrast, the peaked IGF-1R expression occurred at P7 in female hippocampi independent of laterality. Hippocampal InsR expression in males decreased significantly between P0 and P7, followed by a marked upregulation at P14. Conversely, the expression of InsR in females peaked at P7 and then decreased again significantly at P14. We found significant interhemispheric differences in IGF-1R mRNA levels in both male and female hippocampi at different time points. In contrast, we only found significant interhemispheric differences in InsR mRNA expression in P14 male rats, with higher values in the left hippocampus. Interestingly, changes in mRNA expression and in protein levels followed the same developmental pattern, indicating that IGF-1R and InsR transcription is not subject to modulatory effects during the first two weeks of development. These findings indicate that there are prominent interhemispheric and sex differences in IGF-1R and InsR expression in the developing rat hippocampus, suggesting a probable mechanism for the control of gender and laterality differences in development and function of the hippocampus.

Decreased expression of angiogenesis antagonist EFEMP1 in sporadic breast cancer is caused by aberrant promoter methylation and points to an impact of EFEMP1 as molecular biomarker

EGF-containing fibulin-like extracellular matrix protein 1 (EFEMP1) was recently described as an antagonist of angiogenesis. Motivated by a strong dependence of tumor growth and metastasis on angiogenesis, we investigated the role of EFEMP1 in human breast cancer. We applied RNA microarray expression analysis and quantitative real-time PCR (QRT) in a total of 45 sporadic breast cancer tissues and found EFEMP1 down-regulation in 59% and 61% of the analyzed tissues, respectively. This down-regulation was confirmed on protein level. Immunohistochemistry in 211 breast cancer tissues resulted in reduced or even abolished EFEMP1 expression in 57-62.5% of the tumors. Bisulphite genomic sequencing in breast cancer cell lines and primary breast cancer tissues revealed promoter methylation as the major cause of this down-regulation. Furthermore, analysis of 203 clinically well characterized primary breast cancers displayed a significant correlation of reduced EFEMP1 protein expression with poor disease-free (p = 0.037) and overall survival (p = 0.032), particularly in those node-positive patients who received adjuvant anthracycline-based chemotherapy, but not in those treated by either cyclophosphamide-methotrexate-5-fluorouracil (CMF) or Tamoxifen. In summary, the presented data demonstrate for the first time the reduced EFEMP1 expression on RNA and protein level in a substantial number of sporadic breast carcinomas and its correlation with epigenetic alterations. Furthermore, these data point towards a possible predictive impact of EFEMP1 expression in primary breast cancer.

Systematic identification and molecular characterization of genes differentially expressed in breast and ovarian cancer

The identification of novel disease-associated genes in gynaecological tumours has important implications for understanding the process of tumourigenesis and the development of novel treatment regimens. cDNA libraries from disease tissues may represent a valuable source to identify such genes. Recently, a bio-informatic procedure based on an 'electronic Northern' approach was established to screen expressed sequence tag (EST) libraries for genes differentially expressed in tumour and normal tissues, and identified 450 candidate genes differentially expressed in breast and ovarian cancer. In this report, the validation of an initial set of 40 candidate genes, which were selected due to their localization in chromosomal regions frequently altered in gynaecological tumours, is described. Differential expression of 29 of these genes, including three uncharacterized novel genes, was confirmed by applying cancer profiling arrays with 106 matched pairs of tumour/normal cDNAs and quantitative reverse transcription-polymerase chain reaction (RT-PCR) on 60 clinical specimens. The majority of these differentially expressed genes have not been described previously in the context of breast and ovarian cancer, and may constitute novel diagnostic markers for these tumour entities.