Publications by authors named "Elisa Cattaneo"

23 Publications

  • Page 1 of 1

Expanding the Molecular Spectrum of Gene Defects in 33 Patients with a Clinical Presentation of KBG Syndrome.

Int J Mol Sci 2022 May 25;23(11). Epub 2022 May 25.

Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, 20142 Milan, Italy.

KBG syndrome (KBGS) is a neurodevelopmental disorder caused by the Ankyrin Repeat Domain 11 () haploinsufficiency. Here, we report the molecular investigations performed on a cohort of 33 individuals with KBGS clinical suspicion. By using a multi-testing genomic approach, including gene sequencing, Chromosome Microarray Analysis (CMA), and RT-qPCR gene expression assay, we searched for pathogenic alterations in . A molecular diagnosis was obtained in 22 out of 33 patients (67%). sequencing disclosed pathogenic or likely pathogenic variants in 18 out of 33 patients. CMA identified one full and one terminal pathogenic deletions, and one partial duplication and one intronic microdeletion, with both possibly being pathogenic. The pathogenic effect was established by RT-qPCR, which confirmed haploinsufficiency only for the three deletions. Moreover, RT-qPCR applied to six molecularly unsolved KBGS patients identified gene downregulation in a clinically typical patient with previous negative tests, and further molecular investigations revealed a cryptic deletion involving the gene promoter. In conclusion, pathogenic variants could also involve the regulatory regions of the gene. Moreover, the application of a multi-test approach along with the innovative use of RT-qPCR improved the diagnostic yield in KBGS suspected patients.
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http://dx.doi.org/10.3390/ijms23115912DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9180463PMC
May 2022

Progressive Clinical and Neuroradiological Findings in a Child with BCL11B Missense Mutation: Expanding the Phenotypic Spectrum of Related Disorder.

Neuropediatrics 2021 Nov 29. Epub 2021 Nov 29.

Department of Pediatric Radiology and Neuroradiology, "Vittore Buzzi" Children's Hospital - ASST Fatebenefratelli-Sacco, Milan, Italy.

We report a patient affected by -related disorder, providing the first extensive demonstration of clinical and neuroradiological progressive course of the disease, with possible implications on the way it is studied and followed-up. Never described clinical aspects such as toes abnormalities and hypospadias widen the range of dysmorphisms associated with this condition. Our data suggest that mutations may be implicated not only in impaired morphogenesis and hematopoiesis but also in progressive central nervous system damage, which remains to be further investigated and clarified.
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http://dx.doi.org/10.1055/s-0041-1736193DOI Listing
November 2021

Autosomal Dominant Hypophosphatemic Rickets: A Case Report and Review of the Literature.

Int J Environ Res Public Health 2021 08 19;18(16). Epub 2021 Aug 19.

Department of Pediatrics, V. Buzzi Children's Hospital, Università di Milano, Via Lodovico Castelvetro, 32, 20154 Milan, Italy.

Autosomal dominant hypophosphatemic rickets (ADHR) is an extremely rare form of genetic rickets caused by mutations in the fibroblast growth factor 23 gene. ADHR is characterized by hypophosphatemia secondary to isolated renal phosphate wasting. Only a few cases of ADHR have been reported in the literature to date. We describe the case of a 17-month-old girl who presented with severe failure to thrive (length: -4.08 standard deviation (SD), weight: -2.2 SD) and hypotonia. Hypophosphatemia, decreased tubular phosphate reabsorption (69%), and rachitic lesions were found. Genetic analysis showed the heterozygous variant c.536G>A (NM_020638.3:c.536G>A) in exon 3 of the FGF23 gene, leading to the diagnosis of ADHR. She was treated with phosphate salts and oral alfacalcidol. After 4 years of treatment, at 5 years of age, the patient's ADHR resolved spontaneously. Considering the lack of knowledge regarding ADHR, we reviewed the literature to describe the features of this rare and poorly understood disease. Eleven ADHR pediatric cases have been described thus far, with cases tending to be more common in females than males. Similar to the general population, two groups of patients with ADHR can be described depending on the mutations present: patients with an R179 and R176 mutation have early-onset of disease and higher frequency of rickets, and a milder and late-onset of disease, respectively. Symptoms and disease severity may fluctuate. Spontaneous remission may occur during the pediatric age.
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http://dx.doi.org/10.3390/ijerph18168771DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8392413PMC
August 2021

Electroclinical features of MEF2C haploinsufficiency-related epilepsy: A multicenter European study.

Seizure 2021 May 30;88:60-72. Epub 2021 Mar 30.

Maternal and Pediatric Department, Fondazione IRCCS Casa Sollievo della Sofferenza, Poliambulatorio "Giovanni Paolo II", Viale Padre Pio, snc, San Giovanni Rotondo (FG) 71013, Italy.

Purpose: Epilepsy is a main manifestation in the autosomal dominant mental retardation syndrome caused by heterozygous variants in MEF2C. We aimed to delineate the electro-clinical features and refine the genotype-phenotype correlations in patients with MEF2C haploinsufficiency.

Methods: We thoroughly investigated 25 patients with genetically confirmed MEF2C-syndrome across 12 different European Genetics and Epilepsy Centers, focusing on the epileptic phenotype. Clinical features (seizure types, onset, evolution, and response to therapy), EEG recordings during waking/sleep, and neuroimaging findings were analyzed. We also performed a detailed literature review using the terms "MEF2C", "seizures", and "epilepsy".

Results: Epilepsy was diagnosed in 19 out of 25 (~80%) subjects, with age at onset <30 months. Ten individuals (40%) presented with febrile seizures and myoclonic seizures occurred in ~50% of patients. Epileptiform abnormalities were observed in 20/25 patients (80%) and hypoplasia/partial agenesis of the corpus callosum was detected in 12/25 patients (~50%). Nine patients harbored a 5q14.3 deletion encompassing MEF2C and at least one other gene. In 7 out of 10 patients with myoclonic seizures, MIR9-2 and LINC00461 were also deleted, whereas ADGRV1 was involved in 3/4 patients with spasms.

Conclusion: The epileptic phenotype of MEF2C-syndrome is variable. Febrile and myoclonic seizures are the most frequent, usually associated with a slowing of the background activity and irregular diffuse discharges of frontally dominant, symmetric or asymmetric, slow theta waves with interposed spike-and-waves complexes. The haploinsufficiency of ADGRV1, MIR9-2, and LINC00461 likely contributes to myoclonic seizures and spasms in patients with MEF2C syndrome.
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http://dx.doi.org/10.1016/j.seizure.2021.03.025DOI Listing
May 2021

Cerebellar dysplasia related to PIK3CA mutation: a three-case series.

Neurogenetics 2021 03 8;22(1):27-32. Epub 2020 Sep 8.

Department of Pediatric Radiology and Neuroradiology, ASST FBF SACCO - V. Buzzi Children's Hospital, Milan, Italy.

The term PROS (PIK3CA-Related Overgrowth Spectrum) indicates a wide spectrum of overgrowth disorders related to somatic mutations in PIK3CA (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) pathway. We present three cases with PIK3CA mutation and clinical characteristics encompassing MCAP (megalencephaly-capillary malformation) condition but lacking all criteria to a certain diagnosis, most of all showing prevalent and peculiar involvement of cerebellar structures at MRI (magnetic resonance imaging) mainly consisting in cortical rim thickening and abnormal orientation of folia axis. These cases expand the spectrum of intracranial MRI features in PIK3CA disorders.
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http://dx.doi.org/10.1007/s10048-020-00628-zDOI Listing
March 2021

Natural history of non-lethal Raine syndrome during childhood.

Orphanet J Rare Dis 2020 04 16;15(1):93. Epub 2020 Apr 16.

Department of Pediatrics, Vittore Buzzi Children's Hospital, Department of Biomedical and Clinical Science L. Sacco, Università degli Studi di Milano, Milan, Italy.

Background: Raine syndrome (RS) is a rare autosomal recessive disorder caused by biallelic loss-of-function mutations of FAM20C. The most common clinical features are microcephaly, exophthalmos, hypoplastic nose and severe midface hypoplasia, leading to choanal atresia. The radiological findings include generalized osteosclerosis and brain calcifications. RS is usually lethal during the neonatal period due to severe respiratory distress. However, there exists a non-lethal RS form, the phenotype of which is extremely heterogeneous. There is paucity of data about clinical course and life expectancy of these patients.

Results: This is the first description of follow-up features of non-lethal RS patients. Moreover, we present three unpublished cases. There are five Asian and two Arab patients. All were born to consanguineous parents. The most common neonatal comorbidity was respiratory distress secondary to choanal atresia. A variable degree of neurodevelopmental delay was seen in the majority of our cases and seizures and hearing or vision involvement were also frequent. Neurological and orthopedic issues were the most frequent complications seen at follow-up in our group. Persistent hypophosphatemic rickets was the most striking endocrinological manifestation, which was scarcely responsive to therapy with phosphate salts and alfacalcidol. Life expectancy of our patients goes beyond childhood, with the oldest of those described being 18 years old at present.

Conclusions: Manifestations of RS in those surviving the neonatal period are being increasingly recognized. Our study supports previous findings and provides clinical and biochemical observations and data from longer follow up. Finally, we propose multidisciplinary follow up for patients with non-lethal RS.
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http://dx.doi.org/10.1186/s13023-020-01373-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7164176PMC
April 2020

CD10 and CD34 as markers in vascular malformations with PIK3CA and TEK mutations.

Hum Pathol 2020 05 6;99:98-106. Epub 2020 Apr 6.

Unit of Human Pathology, Department of Health Sciences, Santi Paolo e Carlo Hospital Medical School, University of Milan, Milan, 20142, Italy.

Aims: Vascular malformations (vMs) encompass a wide range of diseases often associated with somatic or, more rarely, germinal genetic mutations. A mutation in the PIK3Ca/mTOR pathway is more often involved in various vMs. CD10 and CD34 are cellular markers that may play a role in mesenchymal differentiation and proliferation. The aim of our study was to find a possible link between the immunohistochemical expression of CD10 and CD34 in vMs and their relationship with mutations in the PIK3CA/mTOR signaling pathway.

Methods And Results: Our study on 58 samples of vMs showed that in endothelial cells, CD10 was significantly expressed in PIK3CA-mutated samples compared with samples without any mutation (p < 0.05), especially and even more consistently when compared with samples with mutation in other pathways (p < 0.0001). Conversely, in the same PIK3CA-mutated samples, CD34 expression in endothelial cells was significantly reduced compared with samples either without any mutation or mutations in other pathways (p < 0.05 and p < 0.0005). Compared with samples with mutations in other pathways, a significant overexpression of endothelial CD10 was also found in samples with TEK/TIE2 mutation, a gene linked to the PIK3CA/mTOR pathway (p < 0.01). However, CD34 expression was not altered. In samples with PIK3CA mutation, the CD10 expression was significantly increased in the stroma compared with samples with TEK/TIE2 gene or other gene mutations (p < 0.05).

Conclusion: Therefore, the CD10 and CD34 immunohistochemical profile could suggest/support the presence of mutations in the PIK3CA/mTOR pathway in samples of vMs.
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http://dx.doi.org/10.1016/j.humpath.2020.04.001DOI Listing
May 2020

Currarino syndrome and microcephaly due to a rare 7q36.2 microdeletion: a case report.

Ital J Pediatr 2018 May 25;44(1):59. Epub 2018 May 25.

Pediatric Department, "V. Buzzi" Children's Hospital, University of Milan, Via Castelvetro 32, 20154, Milan, Italy.

Background: Currarino syndrome is a rare condition characterized by presacral mass, anorectal malformation and sacral dysgenesis.

Case Presentation: We report the case of a child that presented chronic constipation, encopresis and mycrocephaly. The characteristics were initially compatible with a case of functional constipation and a therapy with polyethylene glycol was prescribed. After a year, because of poor response, a plain abdominal X-ray was performed, detecting sacrum abnormalities. Finally, a CGH-array analysis was performed and a form of Currarino Syndrome caused by a rare 7q36 microdeletion, was diagnosed.

Conclusion: Occult spinal dysraphism should be suspected in case of poor polyethylene glycol responder constipation, even when evident sacral abnormalities on the physical examination are not detected.
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http://dx.doi.org/10.1186/s13052-018-0500-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5970537PMC
May 2018

Moebius syndrome: clinical features, diagnosis, management and early intervention.

Ital J Pediatr 2016 Jun 3;42(1):56. Epub 2016 Jun 3.

Medical Genetic Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.

Background: Moebius syndrome (MBS) is rare disease characterized by nonprogressive congenital uni- or bi-lateral facial (i. e. VII cranial nerve) and abducens (i. e. VI cranial nerve) palsy. Although the neurological and ophthalmological findings are quite well-known, data concerning the attendant functional difficulties and their changes over time are seldom addressed. In this study we attempt to estimate the prevalence of clinical and functional data in an Italian cohort affected by MBS.

Methods: The study included 50 children, 21 males and 29 females, aged 1 month to 14 years. The patients entered into a multidisciplinary diagnostic and follow-up protocol that had the specific purpose of detecting clinical and developmental deficits related to MBS.

Results: Involvement of the VII cranial nerve (total/partial, bilateral or unilateral) was present in 96 % of patients, and of the VI nerve in 85 %. Two patients were without impairment of the VII nerve and seven patients had no involvement of the VI nerve and were thus classified as Moebius-like because of the involvement of other CNs. Additional affected CNs were numbers III-IV in 16 %, V in 11 %, VIII and X each in 8 %, the XI in 6 %, the IX, most often partially, in 22 %, and the XII in 48 % of cases. Their development was characterized by global delay at one year of age, motor, emotional and speech difficulties at two years of age, a trend toward normalization at three years of age but with weakness in hand-eye coordination, and achieving average results at five years of age. Overall 90 % of children had a normal developmental quotient whereas only 10 % manifested cognitive deficits.

Conclusion: Early rehabilitation may enhance the recovery of normal function, particularly in vulnerable areas of development. It is possible that early intervention that integrates sensory and visual information with emotional difficulties can improve the prognosis of the child with MBS.
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http://dx.doi.org/10.1186/s13052-016-0256-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4893276PMC
June 2016

Rare interstitial deletion of chromosome 2p11.2p12. Report of a new patient with developmental delay and unusual clinical features.

Eur J Med Genet 2016 Jan 15;59(1):39-42. Epub 2015 Dec 15.

Medical Genetics Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.

De novo interstitial deletions of the short arm of chromosome 2 are rare chromosomal abnormalities. Patients showing these kind of microdeletions have developmental delay/intellectual disability, minor facial anomalies including high forehead, frontal bossing, broad nasal bridge, abnormal ears and congenital defects such as skeletal and genital malformations. We describe the second child of a healthy and non consanguineous couple presenting at birth multiple malformations and minor facial anomalies. Because of the clinical findings, an array CGH analysis was performed using Agilent 60K microarray oligonucleotide. The analysis detected a 9.3 Mb deletion on the short arm of chromosome 2 at band p11.2p12 spanning the bases 77,946,599-87,277,610. The five patients previously described display a minimal common deleted region which explains the clinical features shared by all of them, while their individual characteristics might be explained by the different sizes of the deletion. The common deleted region involves several genes (CTNNA2, LRRTM1, REEP1), highly expressed in the nervous system. The deletion found in this case overlaps with most of those reported in literature but our patient displays extra clinical signs such as bilateral choanal atresia and atrial septal defect. It was impossible to find any direct correlation between the genes involved in the deletion and the choanal atresia and the heart defect. The question remains open as to whether these clinical features are a consequence of the deletion or are due to a second pathogenic event. Our case emphasizes the difficulties to find a close correlation between a large deletion and a well defined clinical picture. As only five patients with 2p11.2p12 deletions, reported in the literature are characterized by array CGH, further reports will be necessary to well define a clinical phenotype related to the 2p11.2p12 microdeletion.
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http://dx.doi.org/10.1016/j.ejmg.2015.12.005DOI Listing
January 2016

A comprehensive look at transcription factor gene expression changes in colorectal adenomas.

BMC Cancer 2014 Jan 29;14:46. Epub 2014 Jan 29.

Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, Zurich 8051, Switzerland.

Background: Biological processes are controlled by transcription networks. Expression changes of transcription factor (TF) genes in precancerous lesions are therefore crucial events in tumorigenesis. Our aim was to obtain a comprehensive picture of these changes in colorectal adenomas.

Methods: Using a 3-pronged selection procedure, we analyzed transcriptomic data on 34 human tissue samples (17 adenomas and paired samples of normal mucosa, all collected with ethics committee approval and written, informed patient consent) to identify TFs with highly significant tumor-associated gene expression changes whose potential roles in colorectal tumorigenesis have been under-researched. Microarray data were subjected to stringent statistical analysis of TF expression in tumor vs. normal tissues, MetaCore-mediated identification of TF networks displaying enrichment for genes that were differentially expressed in tumors, and a novel quantitative analysis of the publications examining the TF genes' roles in colorectal tumorigenesis.

Results: The 261 TF genes identified with this procedure included DACH1, which plays essential roles in the proper proliferation and differentiation of retinal and leg precursor cell populations in Drosophila melanogaster. Its possible roles in colorectal tumorigenesis are completely unknown, but it was found to be markedly overexpressed (mRNA and protein) in all colorectal adenomas and in most colorectal carcinomas. However, DACH1 expression was absent in some carcinomas, most of which were DNA mismatch-repair deficient. When networks were built using the set of TF genes identified by all three selection procedures, as well as the entire set of transcriptomic changes in adenomas, five hub genes (TGFB1, BIRC5, MYB, NR3C1, and TERT) where identified as putatively crucial components of the adenomatous transformation process.

Conclusion: The transcription-regulating network of colorectal adenomas (compared with that of normal colorectal mucosa) is characterized by significantly altered expression of over 250 TF genes, many of which have never been investigated in relation to colorectal tumorigenesis.
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http://dx.doi.org/10.1186/1471-2407-14-46DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4078005PMC
January 2014

First evidence of vertical paternal transmission of osteopatia striata with cranial sclerosis.

Am J Med Genet A 2013 May 13;161A(5):1173-6. Epub 2013 Mar 13.

Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy.

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http://dx.doi.org/10.1002/ajmg.a.35813DOI Listing
May 2013

Molecular pathways undergoing dramatic transcriptomic changes during tumor development in the human colon.

BMC Cancer 2012 Dec 19;12:608. Epub 2012 Dec 19.

Istituto di Studi sui Sistemi Intelligenti per l'Automazione - CNR, Via Amendola 122/D-I, 70126 Bari, Italy.

Background: The malignant transformation of precancerous colorectal lesions involves progressive alterations at both the molecular and morphologic levels, the latter consisting of increases in size and in the degree of cellular atypia. Analyzing preinvasive tumors of different sizes can therefore shed light on the sequence of these alterations.

Methods: We used a molecular pathway-based approach to analyze transcriptomic profiles of 59 colorectal tumors representing early and late preinvasive stages and the invasive stage of tumorigenesis. Random set analysis was used to identify biological pathways enriched for genes differentially regulated in tumors (compared with 59 samples of normal mucosa).

Results: Of the 880 canonical pathways we investigated, 112 displayed significant tumor-related upregulation or downregulation at one or more stages of tumorigenesis. This allowed us to distinguish between pathways whose dysregulation is probably necessary throughout tumorigenesis and those whose involvement specifically drives progression from one stage to the next. We were also able to pinpoint specific changes within each gene set that seem to play key roles at each transition. The early preinvasive stage was characterized by cell-cycle checkpoint activation triggered by DNA replication stress and dramatic downregulation of basic transmembrane signaling processes that maintain epithelial/stromal homeostasis in the normal mucosa. In late preinvasive lesions, there was also downregulation of signal transduction pathways (e.g., those mediated by G proteins and nuclear hormone receptors) involved in cell differentiation and upregulation of pathways governing nuclear envelope dynamics and the G2>M transition in the cell cycle. The main features of the invasive stage were activation of the G1>S transition in the cell cycle, upregulated expression of tumor-promoting microenvironmental factors, and profound dysregulation of metabolic pathways (e.g., increased aerobic glycolysis, downregulation of pathways that metabolize drugs and xenobiotics).

Conclusions: Our analysis revealed specific pathways whose dysregulation might play a role in each transition of the transformation process. This is the first study in which such an approach has been used to gain further insights into colorectal tumorigenesis. Therefore, these data provide a launchpad for further exploration of the molecular characterization of colorectal tumorigenesis using systems biology approaches.
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http://dx.doi.org/10.1186/1471-2407-12-608DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3541196PMC
December 2012

The expression of leucine-rich repeat gene family members in colorectal cancer.

Exp Biol Med (Maywood) 2012 Oct 8;237(10):1123-8. Epub 2012 Oct 8.

Laboratory and Division of Gastroenterology, IRCCS Casa Sollievo della Sofferenza Hospital, Viale Cappuccini n.1, San Giovanni Rotondo (FG), Italy.

This study was conducted to evaluate the association of the leucine-rich repeat (LRR) gene family with colorectal cancer (CRC). The expression of members of the LRR gene family were analyzed in 17 CRC specimens and in 59 healthy colorectal tissues by using Human Exon1.0ST microarray, and in 25 CRC specimens and 32 healthy colorectal tissues by U133Plus2.0 microarray. An association was found for 25 genes belonging to the plant-specific (PS) class of LRR genes (P = 0.05 for Exon1.0 ST and P = 0.04 for U133Plus2.0). In both data-sets, in CRC, we found down-regulation of SHOC2 (P < 0.00003) and LRRC28 (P < 0.01) and up-regulation of LRSAM1 (P < 0.000001), while up-regulation of MFHAS1 (P = 0.0005) and down-regulation of WDFY3 (P = 0.026) were found only in the Exon1.0 ST data-set. The PS LLR gene class encodes proteins that activate immune cells and might play a key role in programmed cell death and autophagy. SHOC2 and LRRC28 genes involved in RAS-mediated signaling, which hinders nutrient deprivation-induced autophagy, might be a possible link between the negative control of autophagy and tumorigenesis.
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http://dx.doi.org/10.1258/ebm.2012.012042DOI Listing
October 2012

Sequencing analysis of SLX4/FANCP gene in Italian familial breast cancer cases.

PLoS One 2012 23;7(2):e31038. Epub 2012 Feb 23.

IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy.

Breast cancer can be caused by germline mutations in several genes that are responsible for different hereditary cancer syndromes. Some of the genes causing the Fanconi anemia (FA) syndrome, such as BRCA2, BRIP1, PALB2, and RAD51C, are associated with high or moderate risk of developing breast cancer. Very recently, SLX4 has been established as a new FA gene raising the question of its implication in breast cancer risk. This study aimed at answering this question sequencing the entire coding region of SLX4 in 526 familial breast cancer cases from Italy. We found 81 different germline variants and none of these were clearly pathogenic. The statistical power of our sample size allows concluding that in Italy the frequency of carriers of truncating mutations of SLX4 may not exceed 0.6%. Our results indicate that testing for SLX4 germline mutations is unlikely to be relevant for the identification of individuals at risk of breast cancer, at least in the Italian population.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0031038PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3285620PMC
August 2012

Common breast cancer susceptibility alleles are associated with tumour subtypes in BRCA1 and BRCA2 mutation carriers: results from the Consortium of Investigators of Modifiers of BRCA1/2.

Breast Cancer Res 2011 2;13(6):R110. Epub 2011 Nov 2.

Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, 2 Worts Causeway, Cambridge, CB1 8RN, UK.

Introduction: Previous studies have demonstrated that common breast cancer susceptibility alleles are differentially associated with breast cancer risk for BRCA1 and/or BRCA2 mutation carriers. It is currently unknown how these alleles are associated with different breast cancer subtypes in BRCA1 and BRCA2 mutation carriers defined by estrogen (ER) or progesterone receptor (PR) status of the tumour.

Methods: We used genotype data on up to 11,421 BRCA1 and 7,080 BRCA2 carriers, of whom 4,310 had been affected with breast cancer and had information on either ER or PR status of the tumour, to assess the associations of 12 loci with breast cancer tumour characteristics. Associations were evaluated using a retrospective cohort approach.

Results: The results suggested stronger associations with ER-positive breast cancer than ER-negative for 11 loci in both BRCA1 and BRCA2 carriers. Among BRCA1 carriers, single nucleotide polymorphism (SNP) rs2981582 (FGFR2) exhibited the biggest difference based on ER status (per-allele hazard ratio (HR) for ER-positive = 1.35, 95% CI: 1.17 to 1.56 vs HR = 0.91, 95% CI: 0.85 to 0.98 for ER-negative, P-heterogeneity = 6.5 × 10-6). In contrast, SNP rs2046210 at 6q25.1 near ESR1 was primarily associated with ER-negative breast cancer risk for both BRCA1 and BRCA2 carriers. In BRCA2 carriers, SNPs in FGFR2, TOX3, LSP1, SLC4A7/NEK10, 5p12, 2q35, and 1p11.2 were significantly associated with ER-positive but not ER-negative disease. Similar results were observed when differentiating breast cancer cases by PR status.

Conclusions: The associations of the 12 SNPs with risk for BRCA1 and BRCA2 carriers differ by ER-positive or ER-negative breast cancer status. The apparent differences in SNP associations between BRCA1 and BRCA2 carriers, and non-carriers, may be explicable by differences in the prevalence of tumour subtypes. As more risk modifying variants are identified, incorporating these associations into breast cancer subtype-specific risk models may improve clinical management for mutation carriers.
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http://dx.doi.org/10.1186/bcr3052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3326552PMC
June 2012

Common alleles at 6q25.1 and 1p11.2 are associated with breast cancer risk for BRCA1 and BRCA2 mutation carriers.

Hum Mol Genet 2011 Aug 18;20(16):3304-21. Epub 2011 May 18.

Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK.

Two single nucleotide polymorphisms (SNPs) at 6q25.1, near the ESR1 gene, have been implicated in the susceptibility to breast cancer for Asian (rs2046210) and European women (rs9397435). A genome-wide association study in Europeans identified two further breast cancer susceptibility variants: rs11249433 at 1p11.2 and rs999737 in RAD51L1 at 14q24.1. Although previously identified breast cancer susceptibility variants have been shown to be associated with breast cancer risk for BRCA1 and BRCA2 mutation carriers, the involvement of these SNPs to breast cancer susceptibility in mutation carriers is currently unknown. To address this, we genotyped these SNPs in BRCA1 and BRCA2 mutation carriers from 42 studies from the Consortium of Investigators of Modifiers of BRCA1/2. In the analysis of 14 123 BRCA1 and 8053 BRCA2 mutation carriers of European ancestry, the 6q25.1 SNPs (r(2) = 0.14) were independently associated with the risk of breast cancer for BRCA1 mutation carriers [hazard ratio (HR) = 1.17, 95% confidence interval (CI): 1.11-1.23, P-trend = 4.5 × 10(-9) for rs2046210; HR = 1.28, 95% CI: 1.18-1.40, P-trend = 1.3 × 10(-8) for rs9397435], but only rs9397435 was associated with the risk for BRCA2 carriers (HR = 1.14, 95% CI: 1.01-1.28, P-trend = 0.031). SNP rs11249433 (1p11.2) was associated with the risk of breast cancer for BRCA2 mutation carriers (HR = 1.09, 95% CI: 1.02-1.17, P-trend = 0.015), but was not associated with breast cancer risk for BRCA1 mutation carriers (HR = 0.97, 95% CI: 0.92-1.02, P-trend = 0.20). SNP rs999737 (RAD51L1) was not associated with breast cancer risk for either BRCA1 or BRCA2 mutation carriers (P-trend = 0.27 and 0.30, respectively). The identification of SNPs at 6q25.1 associated with breast cancer risk for BRCA1 mutation carriers will lead to a better understanding of the biology of tumour development in these women.
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http://dx.doi.org/10.1093/hmg/ddr226DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3652640PMC
August 2011

Preinvasive colorectal lesion transcriptomes correlate with endoscopic morphology (polypoid vs. nonpolypoid).

EMBO Mol Med 2011 Jun 3;3(6):334-47. Epub 2011 May 3.

Institute of Molecular Cancer Research, University of Zurich, Switzerland.

Improved colonoscopy is revealing precancerous lesions that were frequently missed in the past, and ∼30% of those detected today have nonpolypoid morphologies ranging from slightly raised to depressed. To characterize these lesions molecularly, we assessed transcription of 23,768 genes in 42 precancerous lesions (25 slightly elevated nonpolypoid and 17 pedunculated polypoid), each with corresponding samples of normal mucosa. Nonpolypoid versus polypoid morphology explained most gene expression variance among samples; histology, size, and degree of dysplasia were also linked to specific patterns. Expression changes in polypoid lesions frequently affected cell-cycling pathways, whereas cell-survival dysregulation predominated in nonpolypoid lesions. The latter also displayed fewer and less dramatic expression changes than polypoid lesions. Paradigmatic of this trend was progressive loss through the normal > nonpolypoid > polypoid > cancer sequence of TMIGD1 mRNA and protein. This finding, along with TMIGD1 protein expression patterns in tissues and cell lines, suggests that TMIGD1 might be associated with intestinal-cell differentiation. We conclude that molecular dysregulation in slightly elevated, nonpolypoid, precancerous colorectal lesions may be somewhat less severe than that observed in classic adenomatous polyps.
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http://dx.doi.org/10.1002/emmm.201100141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3377079PMC
June 2011

Laser-capture microdissection impairs activity-based protein profiles for serine hydrolase in human lung adenocarcinoma.

J Biomol Tech 2010 Apr;21(1):25-8

Department of Thoracic Surgery, University Hospital Zurich, Switzerland.

Laser-capture microdissection (LCM) enables the selection of a specific and pure cell population from a heterogenous tissue such as tumors. Activity-based protein profiling/profile (ABPP) is a chemical technology using enzyme-specific active site-directed probes to read out the functional state of many enzymes directly in any proteome. The aim of this work was to assess the compatibility of LCM with downstream ABPP for serine hydrolase (SH) in human lung adenocarcinoma. Fresh frozen lung adenocarcinoma tissue was stained with hematoxylin, toluidine blue, or methyl green (MG). Proteome from stained tissue was labeled further with SH-directed probes, and ABPPs were determined on a one-dimensional gel-based approach. This allowed us to assess the impact of staining procedures on their ABPPs. The effect of the LCM process on ABPPs was assessed furthermore using MG-stained lung adenocarcinoma tissue. The staining procedures led to strong changes in ABPPs. However, MG staining seemed the most compatible with downstream ABPP. MG-stained, laser-captured, microdissected tissue showed additional change in profiles as a result of the denaturing property of extraction buffer but not to the microdissection process itself. LCM staining procedures but not microdissection per se interfered with downstream ABPP and led to a strong change in ABPPs of SHs in human lung adenocarcinoma.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2841994PMC
April 2010

The protein tyrosine phosphatase receptor type R gene is an early and frequent target of silencing in human colorectal tumorigenesis.

Mol Cancer 2009 Dec 16;8:124. Epub 2009 Dec 16.

Institute of Molecular Cancer Research, University of Zurich, Switzerland.

Background: Tumor development in the human colon is commonly accompanied by epigenetic changes, such as DNA methylation and chromatin modifications. These alterations result in significant, inheritable changes in gene expression that contribute to the selection of tumor cells with enhanced survival potential.

Results: A recent high-throughput gene expression analysis conducted by our group identified numerous genes whose transcription was markedly diminished in colorectal tumors. One of these, the protein-tyrosine phosphatase receptor type R (PTPRR) gene, was dramatically downregulated from the earliest stages of cellular transformation. Here, we show that levels of both major PTPRR transcript variants are markedly decreased (compared with normal mucosal levels) in precancerous and cancerous colorectal tumors, as well in colorectal cancer cell lines. The expression of the PTPRR-1 isoform was inactivated in colorectal cancer cells as a result of de novo CpG island methylation and enrichment of transcription-repressive histone-tail marks, mainly H3K27me3. De novo methylation of the PTPRR-1 transcription start site was demonstrated in 29/36 (80%) colorectal adenomas, 42/44 (95%) colorectal adenocarcinomas, and 8/8 (100%) liver metastases associated with the latter tumors.

Conclusions: Epigenetic downregulation of PTPRR seems to be an early alteration in colorectal cell transformation, which is maintained during the clonal selection associated with tumor progression. It may represent a preliminary step in the constitutive activation of the RAS/RAF/MAPK/ERK signalling, an effect that will later be consolidated by mutations in genes encoding key components of this pathway.
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http://dx.doi.org/10.1186/1476-4598-8-124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2801661PMC
December 2009

Transcriptome profile of human colorectal adenomas.

Mol Cancer Res 2007 Dec;5(12):1263-75

Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.

Colorectal cancers are believed to arise predominantly from adenomas. Although these precancerous lesions have been subjected to extensive clinical, pathologic, and molecular analyses, little is currently known about the global gene expression changes accompanying their formation. To characterize the molecular processes underlying the transformation of normal colonic epithelium, we compared the transcriptomes of 32 prospectively collected adenomas with those of normal mucosa from the same individuals. Important differences emerged not only between the expression profiles of normal and adenomatous tissues but also between those of small and large adenomas. A key feature of the transformation process was the remodeling of the Wnt pathway reflected in patent overexpression and underexpression of 78 known components of this signaling cascade. The expression of 19 Wnt targets was closely correlated with clear up-regulation of KIAA1199, whose function is currently unknown. In normal mucosa, KIAA1199 expression was confined to cells in the lower portion of intestinal crypts, where Wnt signaling is physiologically active, but it was markedly increased in all adenomas, where it was expressed in most of the epithelial cells, and in colon cancer cell lines, it was markedly reduced by inactivation of the beta-catenin/T-cell factor(s) transcription complex, the pivotal mediator of Wnt signaling. Our transcriptomic profiles of normal colonic mucosa and colorectal adenomas shed new light on the early stages of colorectal tumorigenesis and identified KIAA1199 as a novel target of the Wnt signaling pathway and a putative marker of colorectal adenomatous transformation.
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http://dx.doi.org/10.1158/1541-7786.MCR-07-0267DOI Listing
December 2007
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