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Murgiano L, Waluk D, Towers R, Wiedemar N, Dietrich J, Jagannathan V, Drögemüller M, Druet T, Galichet A, Penedo MC, Müller E, Roosje P, Welle M, Leeb T. P6015 An intronic MBTPS2 variant results in a splicing defect in horses with brindle coat texture. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement4155a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Reis-Filho JS, Schizas M, Piscuoglio S, Sakr RA, Ng CKY, Lim RS, Carniello JVS, Towers R, Martelotto L, Giri DD, de Andrade VP, Viale A, Solit DB, Weigelt B, King TA. Abstract S4-04: Lobular carcinoma in situ displays intra-lesion genetic heterogeneity and its progression to invasive disease involves clonal selection and variations in mutational processes. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-s4-04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Lobular carcinoma in situ (LCIS) is considered both a risk factor and non-obligate precursor of invasive breast cancer. We sought to determine the genomic landscape of LCIS and the mutational processes involved in the clonal evolution and progression from LCIS to ductal carcinoma in situ (DCIS) and invasive lobular carcinoma (ILC).
Methods: Patients with a history of LCIS undergoing therapeutic or prophylactic mastectomy were prospectively enrolled in an IRB approved protocol. Frozen tissue blocks were collected, screened for lesions of interest (LCIS, DCIS, ILC, invasive ductal carcinomas (IDC)) and subjected to microdissection and DNA/RNA extraction. Matched germline DNA was available for all cases. Whole exome sequencing was performed on a HiSeq2000 and data were aligned to the reference human genome and processed using GATK. Single nucleotide variants (SNVs) and small insertions/deletions were identified using MuTect and Varscan, respectively. Purity and ploidy estimates were calculated using ABSOLUTE. Clonal frequencies were estimated using Pyclone and the clonal structure of each sample was reconstructed using SubcloneSeeker. Shannon index and Simpson index metrics were used to calculate heterogeneity levels. Mutational signatures were defined according to their mutational trinucleotide context, and the expression levels of APOBEC gene family members were assessed by quantitative reverse transcription (qRT)-PCR.
Results: 30 LCIS, 10 ILCs, 7 DCIS and 5 IDCs from 15 patients qualified for data analysis. CDH1 was the most frequently mutated gene and found to be targeted by mutations in 26 LCIS samples (23 somatic, 3 germline). The repertoire of somatic mutations in LCIS was similar to that of luminal A breast cancers, with the exception of the significantly higher frequency of CDH1 mutations and the lower prevalence of TP53 mutations. ILCs were clonally related to at least one LCIS in 10 patients, and in 3/7 patients, DCIS was clonally related to at least one LCIS. Clonal composition analysis revealed that the presence of a minor clone(s) in LCIS, and the levels of intra-tumor genetic heterogeneity were significantly higher in LCIS clonally related with DCIS/ILC than in LCIS unrelated to DCIS/ILC. In two cases, a minor LCIS subclone constituted the major clone in the associated DCIS/ILC. A comparative analysis of the mutational signatures in the truncal and branch mutations of these cases revealed that whilst the truncal mutations displayed an aging signature, branch mutations were enriched for the APOBEC signature. qRT-PCR analysis demonstrated that cases displaying the APOBEC signature also harbored significantly higher levels of APOBEC3B expression than samples with the aging signature.
Conclusions: LCIS displays intra-lesion genetic heterogeneity, and the progression from LCIS to DCIS or ILC may involve the selection of clones resulting from distinct mutational processes during clonal evolution. Our findings also suggest that cytodine deamination driven by the overexpression of APOBEC3B may drive the progression of LCIS to DCIS/ILC in a subset of cases.
Citation Format: Reis-Filho JS, Schizas M, Piscuoglio S, Sakr RA, Ng CKY, Lim RS, Carniello JVS, Towers R, Martelotto L, Giri DD, de Andrade VP, Viale A, Solit DB, Weigelt B, King TA. Lobular carcinoma in situ displays intra-lesion genetic heterogeneity and its progression to invasive disease involves clonal selection and variations in mutational processes. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr S4-04.
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Affiliation(s)
- JS Reis-Filho
- Memorial Sloan Kettering Cancer Center, NY, NY; Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, NY
| | - M Schizas
- Memorial Sloan Kettering Cancer Center, NY, NY; Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, NY
| | - S Piscuoglio
- Memorial Sloan Kettering Cancer Center, NY, NY; Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, NY
| | - RA Sakr
- Memorial Sloan Kettering Cancer Center, NY, NY; Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, NY
| | - CKY Ng
- Memorial Sloan Kettering Cancer Center, NY, NY; Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, NY
| | - RS Lim
- Memorial Sloan Kettering Cancer Center, NY, NY; Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, NY
| | - JVS Carniello
- Memorial Sloan Kettering Cancer Center, NY, NY; Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, NY
| | - R Towers
- Memorial Sloan Kettering Cancer Center, NY, NY; Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, NY
| | - L Martelotto
- Memorial Sloan Kettering Cancer Center, NY, NY; Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, NY
| | - DD Giri
- Memorial Sloan Kettering Cancer Center, NY, NY; Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, NY
| | - VP de Andrade
- Memorial Sloan Kettering Cancer Center, NY, NY; Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, NY
| | - A Viale
- Memorial Sloan Kettering Cancer Center, NY, NY; Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, NY
| | - DB Solit
- Memorial Sloan Kettering Cancer Center, NY, NY; Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, NY
| | - B Weigelt
- Memorial Sloan Kettering Cancer Center, NY, NY; Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, NY
| | - TA King
- Memorial Sloan Kettering Cancer Center, NY, NY; Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, NY
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Reyes SA, Sakr RA, Schizas M, Towers R, Park AY, Ng CKY, Weigelt B, Reis-Filho JS, King TA. Abstract P6-06-02: Germline CDH1 mutations in lobular carcinoma in situ. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-p6-06-02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
BACKGROUND: Germline CDH1 mutations are responsible for the increased risk of both gastric cancer and invasive lobular breast cancer (ILC) in families with hereditary diffuse gastric cancer syndrome; yet germline CDH1 mutations in women with ILC without a family history (FH) of gastric cancer are rare. Lobular carcinoma in situ (LCIS) is both a risk factor and non-obligate precursor of ILC and recent data suggest that germline CDH1 mutations may be present in up to 8% of patients with bilateral LCIS +/- ILC; raising questions about the role of genetic testing in this context. The purpose of this study was to determine the frequency of germline CDH1 mutations in a large prospectively followed cohort of patients with pathologically confirmed bilateral LCIS.
METHODS: Patients with a biopsy proven history of LCIS, entering surveillance or presenting for surgery (prophylactic or therapeutic mastectomy), between 2005 and 2013 were prospectively identified and enrolled in IRB approved protocols at Memorial Sloan-Kettering Cancer Center for the collection of tissue and/or germline DNA (IRB 01-135, 99-030). All biopsies were reviewed to confirm LCIS and mastectomy specimens were subject to extensive sampling of all quadrants. Cases with confirmed bilateral LCIS were chosen for the primary analysis. Cases where bilateral mastectomy tissue sampling confirmed only unilateral LCIS were included for comparison. Germline DNA was anonymized and analyzed for CDH1 mutations using targeted capture sequencing with baits for all exons of CDH1 on HiSeq2000. Germline single nucleotide variants were called using GATK HaplotypeCaller and insertions/deletions by Varscan and Scalpel. Mutations were manually inspected using the Integrative Genomics Viewer (IGV). Clinical data were abstracted prior to anonymization.
RESULTS: Germline DNA was available for 114 patients; 78 underwent bilateral mastectomy for breast cancer (BC), 8 chose prophylactic mastectomy and 28 patients with biopsy proven bilateral LCIS were identified in surveillance. Following mastectomy, tissue sampling confirmed bilateral LCIS in 67/86 (78%) patients, and ruled out bilateral LCIS in 19 patients; yielding 95 patients with bilateral LCIS for the primary analysis. Median age at LCIS diagnosis for bilateral and unilateral cases respectively was 48yrs (range 36-70) and 44 yrs (range 38-63). One patient with bilateral LCIS also reported a FH of gastric cancer. Pathogenic germline CDH1 mutations (D72N (missense) and E35* (nonsense)) were identified in 2/95 (2%) patients with bilateral LCIS, one of whom also had invasive breast cancer (ILC). A germline CDH1 mutation was not identified in the patient with bilateral LCIS and a FH of gastric cancer, nor were CDH1 mutations identified among the 19 patients with unilateral LCIS.
CONCLUSIONS: In this cohort of 95 patients with pathologically documented bilateral LCIS +/- BC, the overall frequency of CDH1 germline mutations was 2%; considerably lower than previously reported. To our knowledge this is the largest series to address this question and these findings do not support germline testing for CDH1 mutations in women with bilateral LCIS.
Citation Format: Reyes SA, Sakr RA, Schizas M, Towers R, Park AY, Ng CKY, Weigelt B, Reis-Filho JS, King TA. Germline CDH1 mutations in lobular carcinoma in situ. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-06-02.
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Affiliation(s)
- SA Reyes
- Memorial Sloan-Kettering Cancer Center, NY, NY
| | - RA Sakr
- Memorial Sloan-Kettering Cancer Center, NY, NY
| | - M Schizas
- Memorial Sloan-Kettering Cancer Center, NY, NY
| | - R Towers
- Memorial Sloan-Kettering Cancer Center, NY, NY
| | - AY Park
- Memorial Sloan-Kettering Cancer Center, NY, NY
| | - CKY Ng
- Memorial Sloan-Kettering Cancer Center, NY, NY
| | - B Weigelt
- Memorial Sloan-Kettering Cancer Center, NY, NY
| | | | - TA King
- Memorial Sloan-Kettering Cancer Center, NY, NY
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Kalkoff M, Chan-Dominy A, Sleigh JW, Jogia PM, Cursons RT, Towers R, La Pine M. Alpha1-adrenergic receptor mRNA and inflammatory mediator expression in circulating leucocytes after cardiac surgery. Anaesth Intensive Care 2008; 36:535-43. [PMID: 18714622 DOI: 10.1177/0310057x0803600406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Vasodilation after coronary artery bypass surgery is a common complication. Inflammatory mediators influence the expression of alpha1-adrenergic receptors. Do patients requiring high doses of postoperative inotropic support have down-regulated alpha-adrenergic receptors? Is there a characteristic pattern of preoperative inflammatory mediator expression that could predict a complicated course after the operation? Forty-four patients undergoing cardiac bypass surgery with extracorporeal circulation were prospectively investigated. Five perioperative blood samples were taken (preoperative, two hours, 12 hours, 36 hours and 72 hours postoperative). The leucocyte mRNA-expression of the three alpha1-adrenergic receptor subtypes (A, B and D) and 11 different pro-inflammatory mediators were investigated with the real-time reverse transcriptase polymerase chain reaction. The patients were divided into three groups (No-noradrenaline [No-NA]= 0 microg/min, Low-noradrenaline [Low-NA]=0.1-7 microg/min, High-noradrenaline [High-NA] >7 microg/min), according to their postoperative noradrenaline requirements. Preoperatively, alpha1(A)-receptor expression was 4.9-fold (High-NA) and 18.7-fold (Low-NA) higher than the No-NA group (P=0.005) and plasma noradrenaline levels were higher in the High-NA group (P=0.005). Across all groups at 12 hours after the operation, alpha1(A) -receptor expression decreased to approximately one-fifth of preoperative levels (P=0.01); but with greater duration and magnitude of relative decrease in the High-NA group. Patients in the No-NA group had significant postoperative increases in leucocyte inflammatory mediator expression for IL-1beta, TLR4, TREM, MPO, MMP9 and TNF genes, whereas the changes in the Low-NA and High-NA groups were not significant. Low preoperative levels of noradrenaline and low expression of alpha1(A)-adrenoreceptors in leucocytes was associated with less probability of requiring noradrenaline support after cardiac surgery.
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Affiliation(s)
- M Kalkoff
- Department of Intensive Care, Waikato Hospital, Hamilton, New Zealand
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Towers R, Naftali T, Gabay G, Carlebach M, Klein A, Novis B. High levels of glucocorticoid receptors in patients with active Crohn's disease may predict steroid resistance. Clin Exp Immunol 2005; 141:357-62. [PMID: 15996200 PMCID: PMC1809436 DOI: 10.1111/j.1365-2249.2005.02846.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Up to 20% of Crohn's disease (CD) patients respond poorly to glucocorticoids (GC). A product of an alternative splicing of the glucocorticoid receptor (GR) premRNA, GRbeta, may play a role as a dominant inhibitor of the glucocorticoid response. Increasing evidence suggests that inflammatory cytokines such as interleukin (IL)-18 alternate the splicing of the primary transcript between the two isoforms GRbeta and GRalpha in hGR gene of CD patients. The aim of this study is to assess the expression of GRalpha and GRbeta in patients with CD and to look for a possible correlation between these receptors and the response to glucocorticoid treatment. Forty-two CD patients and 17 healthy volunteers were studied. Quantitative reverse transcription-polymerase chain reaction (RT-PCR) was performed using real-time PCR techniques. Serum IL-18 protein levels were measured by enzyme-linked immunosorbent assay (ELISA). The amount of hGRalpha-mRNA in patients in remission was significantly lower than in controls (P < 0.05). The amount of hGRbeta-mRNA was significantly higher in GC-resistant patients in the active stage of disease compared with all other groups (P < 0.05). Patients in the active stage of the disease had higher levels of IL-18 than patients in remission and both had higher levels than controls (P < 0.05). The amounts of IL-18 were directly correlated with the amount of hGRbeta mRNA in GC-resistant patients with an active disease. High levels of hGRbeta might be connected to GC resistance. IL-18 might participate in the alternative splicing of the hGR preliminary mRNA of CD patients. The results support the theory that augmented hGRbeta mRNA expression level in PBMC is connected with GC-resistance of CD patients.
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Affiliation(s)
- R Towers
- Institute of Gastroenterology and Liver Diseases, Meir Hospital, Kfar Saba 4428, Israel
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Ramachandran V, McArthur JD, Behm CE, Gutzeit C, Dowton M, Fagan PK, Towers R, Currie B, Sriprakash KS, Walker MJ. Two distinct genotypes of prtF2, encoding a fibronectin binding protein, and evolution of the gene family in Streptococcus pyogenes. J Bacteriol 2004; 186:7601-9. [PMID: 15516573 PMCID: PMC524900 DOI: 10.1128/jb.186.22.7601-7609.2004] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2004] [Accepted: 08/11/2004] [Indexed: 11/20/2022] Open
Abstract
The group A Streptococcus (GAS) is an important pathogen that is responsible for a wide range of human diseases. Fibronectin binding proteins (FBPs) play an important role in promoting GAS adherence and invasion of host cells. The prtF2 gene encodes an FBP and is present in approximately 60% of GAS strains. In the present study we examined 51 prtF2-positive GAS strains isolated from the Northern Territory of Australia, and here we describe two genotypes of prtF2 which are mutually exclusive. The two genotypes have been identified previously as pfbp and fbaB. We show that these genotypes map to the same chromosomal location within the highly recombinatorial fibronectin-collagen-T antigen (FCT) locus, indicating that they arose from a common ancestor, and in this study these genotypes were designated the pfbp type and the fbaB type. Phylogenetic analysis of seven pfbp types, 14 fbaB types, and 11 prtF2-negative GAS strains by pulsed-field gel electrophoresis (PFGE) produced 32 distinct PFGE patterns. Interpretation of evolution based on the PFGE dendrogram by parsimony suggested that the pfbp type had a recent origin compared to the fbaB type. A comparison of multiple DNA sequences of the pfbp and fbaB types revealed a mosaic pattern for the amino-terminal region of the pfbp types. The fbaB type is generally conserved at the amino terminus but varies in the number of fibronectin binding repeats in the carboxy terminus. Our data also suggest that there is a possible association of the pfbp genotype with sof (84.2%), while the fbaB genotype was found in a majority of the GAS strains negative for sof (90.6%), indicating that these two prtF2 subtypes may be under different selective pressures.
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Affiliation(s)
- V Ramachandran
- School of Biological Sciences, University of Wollongong, Darwin, Australia
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McKenna TJ, Loughlin T, Ohman M, Schneider A, Towers R. Mild familial goitrous hypothyroidism associated with prolonged 131-iodine retention: possible defect in thyroglobulin synthesis. J Endocrinol Invest 1989; 12:229-34. [PMID: 2745934 DOI: 10.1007/bf03349971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Four male siblings presented with goitrous hypothyroidism which had been present from the first few years of life. Serum total thyroxine (T4), free T4 index and free T4 levels were low or in the low-normal range while TSH levels were elevated; triiodothyronine (T3) levels were normal. The 131-I-uptake was elevated at 4 and 24 h, 76-93% and 69-82% respectively (normal less than 50%), and remained elevated 96 h after the administration of radioiodine. Administration of potassium perchlorate did not cause a reduction in thyroidal radioiodine. These findings, therefore, were not consistent with defects affecting iodine trapping, iodine organification or iodotyrosine deiodinase. If a coupling defect was the cause of the disorder, iodotyrosines would have to cycle between the thyroid cell and thyroglobulin in the follicular lumen undergoing deiodination, and reorganification continually. To examine this possibility carbimazole, which inhibits organification of iodine was taken orally following administration of 131-I; potassium perchlorate was given to discharge any accumulating nonorganified radioiodine. 131-I uptake changed only from 50 to 48% and from 68 to 71% in the 2 subjects studied. These findings do not support a coupling defect. The possibility of abnormal thyroglobulin synthesis was supported by the finding of inappropriately low serum thyroglobulin levels. A specimen of thyroid tissue demonstrated a 40-fold reduction in normal thyroglobulin content. These findings suggest that our sibship have a rare partial defect in thyroglobulin synthesis and that iodine is incorporated into an alternative complex which is resistant to mobilization.
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Affiliation(s)
- T J McKenna
- Department of Endocrinology, St. Vincent's Hospital, Dublin, Ireland
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