Patterns of TPD52 Overexpression in Multiple Human Solid Tumor Types Analyzed by Quantitative PCR

Total Page:16

File Type:pdf, Size:1020Kb

Patterns of TPD52 Overexpression in Multiple Human Solid Tumor Types Analyzed by Quantitative PCR INTERNATIONAL JOURNAL OF ONCOLOGY 44: 609-615, 2014 Patterns of TPD52 overexpression in multiple human solid tumor types analyzed by quantitative PCR �IERRE TENNSTE�T1*, CHARLOTTE BÖLCH2*, GUN�ULA STROBEL2, SARAH MINNER2, LIA BURKHAR�T2, TOBIAS GROB2, SAWINEE MASSER2, GUI�O SAUTER2, THORSTEN SCHLOMM1,3 ��� RONAL� SIMON2 1M������-C�����, 2I�������� �f �������gy, 3���������� �f U����gy, S������ f�� T������������ �������� C����� R�������, U��v�����y M������ C����� H��b��g-E�������f, H��b��g, G�����y Received Septemb�� 24, 2013; Accepted Octob�� 29, 2013 �OI: 10.3892/�j�.2013.2200 Abstract. Tumor���� protein������� �52��� �TPD��52��� is�� located������� at�� chromo������- for �xample tumors �f the breast, �vary, endometrium, lung, some 8q21, a region that is frequently gained or amplified colon, head and neck, urinary bladder, kidney and prostate in multiple human cancer �ypes. TPD52 has been suggested �1,2�. Whereas gains �ften �ffect larg� portions �f 8q or as � potential target for new anticancer therapies. I� order even the entire q-arm, high-level amplifications are typically to analyz� TPD52 �xpression in the most prevalent human focused on the chromosomal bands 8q21 �3-5� and 8q24 �6,7�, cancer �ypes, w� employed quantitativ� �CR to measure thus highlighting the loci �f putativ� oncogenes, including TPD52 mRNA levels in formalin-fixed tissue samples from MYC at 8q24. S�veral candidate oncogenes hav� been more than 900 cancer tissues �btained from 29 different suggested to reside inside the 8q21 region, including tumor human cancer �ypes. TPD52 was �xpressed at varying levels protein �52 �TPD52� �3,8-13�. TPD52 has been suggested to in all tested normal tissues, including �kin, �ymph node, lung, play a role for vesicle trafficking and Ca2+ dependent �xocy- oral mucosa, breast, endometrium, �vary, vulv�, �yometrium, totic secretion, and has been show� to facilitate �ytokinesis in liver, pancreas, stomach, kidney, prostate, testis, urinary rapidly proliferating cells �14,15�. bladder, thyroid gland, brain, muscle and fat tissue. TPD52 I� line with an oncogenic role, TPD52 �verexpression has was upregulated in 18/29 �62%� tested cancer �ypes. Strongest been described from � multitude �f cancer �ypes, including �xpression was found in non-seminoma �56-fold �verexpres- breast �9�, lung prostate �2�, �varian �8�, pancreatic cancer �16�, sion compared to corresponding normal tissue), seminoma multiple �yeloma �17,18�, Burkitt'� �ymphoma �19�, melanoma �42-fold), ductal �28-fold) and lobular breast cancer �14-fold). �20� and testicular germ cell tumors �21�, and has been linked I� these tumor �ypes, TPD52 upregulation was found in the to poor prognosis in breast, medulloblastoma, lung and prostate vast majority �>80%� �f tested samples. Downregulation was cancer patients �22�. Moreov��, cell line �xperiments and in vivo found in 11 �38%� tumor �ypes, most strong�y in papillary analysis in mice support the implication �f TPD52 in tumori- renal cell cancer �-8-fold), leiomyosarcoma �-6-fold), clear genesis and progression to metastasis �23,24�. According�y, cell renal cell cancer �-5-fold), liposarcoma �-5-fold) and lung TPD52 has been suggested as � promising target for antitumor cancer �-4-fold). These results demonstrate that TPD52 is therapies in breast �25� and prostate cancer �24�, and it seems frequently and strong�y upregulated in many human cancer likely that also other tumor �ypes showing TPD52 �verexpres- �ypes, which may represent candidate tumor �ypes for poten- sion could profit from a TPD52 specific therapy. tial anti-TPD52 therapies. A �ystematic analysis �f TPD52 �xpression in human cancers in order to identify tumor types that might benefit Introduction from potential anti-TPD52 therapies is lacking. I� this study, w� hav� employed quantitativ� real-time �CR in more than Copy numb�� increase involving chromosome 8q belong to the 900 tumor samples to compare the prevalence and �xpression most frequent �berrations in human solid cancers, including levels �f TPD52 across 29 important human cancer �ypes and corresponding normal tissues. Materials and methods Correspondence to: Dr Ronald Simon, Institute �f Pathology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Tissue specimens. Formalin-fixed, paraffin embedded tissues �-20246 Hamburg, Germany were selected from the archiv� �f the Institute �f Pathology, E-mail: �.simon@�k�.uni-hamburg.de University Medical Center Hamburg-Eppendorf �Hamburg, * Germany�. A total �f 999 cancer samples and 40 normal Contributed �qually tissue samples were included into the study. A detailed list �f all samples is g�ven in T�ble I. One pathologist reviewed Key words: TPD52, cancer, real-time �CR, �RNA analysis, normal tissue all hematoxylin and eosin stained sections �f all tissues and selected one block per tumor for RNA isolation. For tumor 610 TENNSTE�T et al: TPD52 U�REGULATION IN �IFFERENT TUMOR TY�ES T�b�� I. T����� ������� f�� TPD52 �x�������� ����y���. T����� �y�� O�g�� � O�g�� � N����� Sk�� 2 Pancreas 1 Ly��� ���� 2 S������ 2 L��g 2 K����y 2 O��� ��v���y 2 Prostate 2 B����� 1 T����� 3 E���������� 2 B������ 2 Ov�� 2 T�y���� g���� 2 V��v� 2 B���� 2 My�������� 2 Sk������ ������ 2 L�v�� 3 A������ ������ 2 C����� M���g���� �������� 11 L�v�� ������ 50 L��y�x ��������� 39 Pancreatic ������ 38 L��g ������, ���g� ���� �24�, ����� �68�, ����� ���� �17� ��� �q������ ���� �25� 134 S������ ������ 50 O��� ��v��y ������ 56 R���� ���� ������ 59 B����� ������, ������ �26� ��� ��b���� �27� 53 Prostate ������ 48 E���������� ��������� 31 T����� ������, �������� �30� ��� ���-�������� �29� 59 Ov����� ������ 33 U�����y b������ ������, ���-��v���v� ��T� 27� and invasive (≥pT2 28) 55 U����� ���v�x ��������� 28 T�y���� g���� ������ 40 V��v� ������ 39 L����y�������� 42 C���� ������ 50 L���������� 36 E�����g��� ������, �q������ ���� �23� ��� �������������� �25� 48 samples areas with high tumor cell content (≥60% tumor amplification of TPD52 and the housekeeping gene TB� the cells) were marked on the slide. A hollow needle was used QuantiTect Primer Assay �Qiagen) was used. The following to tak� �w� tissue �ylinders (diameter from 0.5 mm) from conditions were used for �CR: i) initial denaturation step at each tissue block for nucleic acid isolation. The local ethics 95˚C for 10 min; and ii) 40 cycles at 95˚C for 20 sec and committee approved usag� �f the human tissue samples for 55˚C for 40 sec. Relative quantity of TPD52 �xpression in research purposes. tumor samples was calculated by the 2-∆∆C� method standard- �zed to TPD52 �xpression in corresponding normal tissue. RNA extraction and cDNA synthesis. Punched tissue mate- A fold chang� �f 2 was used to determine the frequency �f rial was deparaffinized with xylene and 80% ethanol. After significant TPD52 regulated cancers. digestion with proteinases K at 56˚C overnight, total RNA was isolated using the RNeasy FF�E kit �Qiagen) in � full- Results automated nucleic acid isolation device �QIAcub�, Qiagen). cDNA was �ynthesized in � 96-well plate format using the Technical issue. A total �f 894 cancer samples from 29 different high‑capacity cDNA reverse transcription kit �Applied tumor �ypes and 40 normal tissue samples from 20 different Biosystems) following the manufacturer'� instructions. Total normal tissue �ypes were included in the analysis �T�ble I�. A RNA �1 µg� was used for reverse transcription �f all samples. total �f 105 �10.5%� tumor samples and 3 �7.5%� normal tissue samples were �xcluded from analysis because either the ref��- Quantitative PCR analysis. Real-time �CR was performed ence gene TBP or the target gene TPD52 showed � C� value using the L�ghtCycler LC480 �Roche) detection �ystem, and �xceeding 35, indicating that too little cDNA was generated the QuantiTect SYBR-Green PCR Kit (Qiagen). For specific for reliable TPD52 �xpression analysis. INTERNATIONAL JOURNAL OF ONCOLOGY 44: 609-615, 2014 611 F�gure 1. TPD52 �xpression ��vels in different normal tissue. Relativ� TPD52 �xpression ��vel (log2� was standardized to TPD52 �xpression in testis. TPD52 expression in normal tissues. TPD52 transcript was Prevalence of TPD52 expression in cancer. I� order to estimate found in all analyzed normal tissues. Averag� ∆C� was 2.4±0.4. the variability �f TPD52 �xpression in the analyzed tumor �ypes, For � direct comparison �f the TPD52 �xpression levels �f the w� determined the fraction �f samples showing at least 2-fold different normal tissues, the �xpression levels were normalized up- or downregulation. This analysis revealed that TPD52 �ver- to the TPD52 �xpression level in testis, which had the lowest �xpression was particular frequent �80% �f samples showing �xpression level �f all analyzed normal tissues. According�y, ≥2-fold overexpression) in germ cell tumors (non-seminoma highest TPD52 expression levels [≥32 (25� -fold �verexpression and seminoma), bladder cancer, esophageal carcinoma and as compared to normal testis] were found in normal oral cavity mamma carcinoma, whereas cancer �ypes �ypically showing mucosa �104-fold �verexpression), pancreas �91-fold), thyroid TPD52 downregulation included renal cell carcinoma �90% gland �79-fold), kidney �76-fold), prostate �69-fold), stomach papillary and 68% clear cell), leiomyosarcoma (69%� and lipo- �56-fold), vulv� �45-fold), liv�� �39-fold), �ymph node �38-fold), sarcoma �52%�. All data are show� in F�g. 3. and breast �32-fold). All data are summarized in F�g. 1. Discussion TPD52 expression in cancer. T� compare TPD52 �xpression across the different tumor �ypes, �verag�
Recommended publications
  • Amplification of 8Q21 in Breast Cancer Is Independent of MYC and Associated with Poor Patient Outcome
    Modern Pathology (2010) 23, 603–610 & 2010 USCAP, Inc. All rights reserved 0893-3952/10 $32.00 603 Amplification of 8q21 in breast cancer is independent of MYC and associated with poor patient outcome Matthias Choschzick1, Paula Lassen1, Annette Lebeau1, Andreas Holger Marx1, Luigi Terracciano2, Uwe Heilenko¨tter3, Fritz Jaenicke4, Carsten Bokemeyer5, Jakob Izbicki6, Guido Sauter1 and Ronald Simon1 1Institute of Pathology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany; 2Institute of Pathology, University Hospital Basel, Basel, Switzerland; 3Department of Gynaecology, Hospital Itzehoe, Itzehoe, Germany; 4Department of Gynaecology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany; 5Department of Oncology, Hematology, Bone Marrow Transplantation with Section Pneumology, University Hospital Hamburg-Eppendorf, Hamburg, Germany and 6Department of Surgery, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany Copy number gains involving the long arm of chromosome 8, including high-level amplifications at 8q21 and 8q24, have been frequently reported in breast cancer. Although the role of the MYC gene as the driver of the 8q24 amplicon is well established, the significance of the 8q21 amplicon is less clear. The breast cancer cell line SK-BR-3 contains three separate 8q21 amplicons, the distal two of which correspond to putative target genes TPD52 and WWP1. To understand the effect of proximal 8q21 amplification on breast cancer phenotype and patient prognosis, we analyzed 8q21 copy number changes using fluorescence in situ hybridization (FISH) in a tissue microarray containing more than 2000 breast cancers. Amplification at 8q21 was found in 3% of tumors, and was associated with medullary type (Po0.03), high tumor grade (Po0.0001), high Ki67 labeling index (Po0.05), amplification of MYC (Po0.0001), HER2, MDM2, and CCND1 (Po0.05 each), as well as the total number of gene amplifications (Po0.0001).
    [Show full text]
  • Identification of TPD52 and DNAJB1 As Two Novel Bile Biomarkers for Cholangiocarcinoma by Itraq‑Based Quantitative Proteomics Analysis
    2622 ONCOLOGY REPORTS 42: 2622-2634, 2019 Identification of TPD52 and DNAJB1 as two novel bile biomarkers for cholangiocarcinoma by iTRAQ‑based quantitative proteomics analysis HONGYUE REN1*, MINGXU LUO2,3*, JINZHONG CHEN4, YANMING ZHOU5, XIUMEI LI4, YANYAN ZHAN6, DONGYAN SHEN7 and BO CHEN3 1Department of Pathology, The Affiliated Southeast Hospital of Xiamen University, Zhangzhou, Fujian 363000; 2Department of Gastrointestinal Surgery, Xiamen Humanity Hospital; Departments of 3Gastrointestinal Surgery, 4Endoscopy Center and 5Hepatopancreatobiliary Surgery, Xiamen Cancer Hospital, The First Affiliated Hospital of Xiamen University, Xiamen Fujian 361003; 6Cancer Research Center, Xiamen University Medical College, Xiamen, Fujian 361002; 7Biobank, Xiamen Cancer Hospital, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian 361003, P.R. China Received December 17, 2018; Accepted September 26, 2019 DOI: 10.3892/or.2019.7387 Abstract. Cholangiocarcinoma (CCA) represents a type of proteins may contribute to tumor pathogenesis. In addition, the epithelial cancer with a late diagnosis and poor outcome. expression levels of TPD52 and DNAJB1 were found to be However, the molecular mechanisms responsible for the devel- closely associated with the clinical parameters and prognosis opment of CCA have not yet been fully identified. Thus, in this of patients with CCA. On the whole, the findings of this study study, we aimed to elucidate some of these mechanisms. For indicate that TPD52 and DNAJB1 may serve as novel bile this purpose, isobaric tags for relative and absolute quantifica- biomarkers for CCA. tion (iTRAQ) was performed to analyze the secretory proteins from the 2 CCA cell lines, TFK1 and HuCCT1, as well as from Introduction a normal biliary epithelial cell line, human intrahepatic biliary epithelial cells (HiBECs).
    [Show full text]
  • Chromosomal Aberrations in Head and Neck Squamous Cell Carcinomas in Norwegian and Sudanese Populations by Array Comparative Genomic Hybridization
    825-843 12/9/08 15:31 Page 825 ONCOLOGY REPORTS 20: 825-843, 2008 825 Chromosomal aberrations in head and neck squamous cell carcinomas in Norwegian and Sudanese populations by array comparative genomic hybridization ERIC ROMAN1,2, LEONARDO A. MEZA-ZEPEDA3, STINE H. KRESSE3, OLA MYKLEBOST3,4, ENDRE N. VASSTRAND2 and SALAH O. IBRAHIM1,2 1Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91; 2Department of Oral Sciences - Periodontology, Faculty of Medicine and Dentistry, University of Bergen, Årstadveien 17, 5009 Bergen; 3Department of Tumor Biology, Institute for Cancer Research, Rikshospitalet-Radiumhospitalet Medical Center, Montebello, 0310 Oslo; 4Department of Molecular Biosciences, University of Oslo, Blindernveien 31, 0371 Oslo, Norway Received January 30, 2008; Accepted April 29, 2008 DOI: 10.3892/or_00000080 Abstract. We used microarray-based comparative genomic logical parameters showed little correlation, suggesting an hybridization to explore genome-wide profiles of chromosomal occurrence of gains/losses regardless of ethnic differences and aberrations in 26 samples of head and neck cancers compared clinicopathological status between the patients from the two to their pair-wise normal controls. The samples were obtained countries. Our findings indicate the existence of common from Sudanese (n=11) and Norwegian (n=15) patients. The gene-specific amplifications/deletions in these tumors, findings were correlated with clinicopathological variables. regardless of the source of the samples or attributed We identified the amplification of 41 common chromosomal carcinogenic risk factors. regions (harboring 149 candidate genes) and the deletion of 22 (28 candidate genes). Predominant chromosomal alterations Introduction that were observed included high-level amplification at 1q21 (harboring the S100A gene family) and 11q22 (including Head and neck squamous cell carcinoma (HNSCC), including several MMP family members).
    [Show full text]
  • Epigenome-Wide Exploratory Study of Monozygotic Twins Suggests Differentially Methylated Regions to Associate with Hand Grip Strength
    Biogerontology (2019) 20:627–647 https://doi.org/10.1007/s10522-019-09818-1 (0123456789().,-volV)( 0123456789().,-volV) RESEARCH ARTICLE Epigenome-wide exploratory study of monozygotic twins suggests differentially methylated regions to associate with hand grip strength Mette Soerensen . Weilong Li . Birgit Debrabant . Marianne Nygaard . Jonas Mengel-From . Morten Frost . Kaare Christensen . Lene Christiansen . Qihua Tan Received: 15 April 2019 / Accepted: 24 June 2019 / Published online: 28 June 2019 Ó The Author(s) 2019 Abstract Hand grip strength is a measure of mus- significant CpG sites or pathways were found, how- cular strength and is used to study age-related loss of ever two of the suggestive top CpG sites were mapped physical capacity. In order to explore the biological to the COL6A1 and CACNA1B genes, known to be mechanisms that influence hand grip strength varia- related to muscular dysfunction. By investigating tion, an epigenome-wide association study (EWAS) of genomic regions using the comb-p algorithm, several hand grip strength in 672 middle-aged and elderly differentially methylated regions in regulatory monozygotic twins (age 55–90 years) was performed, domains were identified as significantly associated to using both individual and twin pair level analyses, the hand grip strength, and pathway analyses of these latter controlling the influence of genetic variation. regions revealed significant pathways related to the Moreover, as measurements of hand grip strength immune system, autoimmune disorders, including performed over 8 years were available in the elderly diabetes type 1 and viral myocarditis, as well as twins (age 73–90 at intake), a longitudinal EWAS was negative regulation of cell differentiation.
    [Show full text]
  • Identification of the Downregulation of TPD52-Like3 Gene and NKX2-1 Gene in Type 2 Diabetes Mellitus Via RNA Sequencing
    Archives of Diabetes & Obesity DOI: 10.32474/ADO.2020.03.000156 ISSN: 2638-5910 Opinion Identification of The Downregulation of TPD52-Like3 Gene and NKX2-1 Gene in Type 2 Diabetes Mellitus Via RNA Sequencing Rob N M Weijers* Teaching Hospital , Onze Lieve Vrouwe Gasthuis, Amsterdam, The Netherlands *Corresponding author: Rob NM Weijers, Teacher, Teaching Hospital, Onze Lieve Vrouwe Gasthuis, Oosterparkstraat 9, PO Box 95500, Amsterdam 1090, Netherlands Received: November 02, 2020 Published: November 12, 2020 Abstract between patients with type 2 diabetes mellitus, compared to non-diabetic patients. Ex-post review, based in part on both the A recent study using next-generation RNA sequencing was reported on genome-wide changes in gene expressing in the skin most downregulated gene TPD52L3, and in the gene regulation category the most downregulated gene NKX2-1. There is strong existence of lipid droplets, peridroplet mitochondria and cytoplasmic mitochondria, selected in the gene metabolism category the evidenceKeywords: that these two genes are involved in the disease process of type 2 diabetes mellitus. Gene Expression; Lipid Droplets; Mitochondria; RNA Sequencing; Type 2 Diabetes Mellitus Opinion Although both the peridroplet mitochondria and cytoplasmic mitochondria are similar in their cell membrane composition they In an earlier study, it was proposed that the final consequence of which already emerges in the prediabetic phase. It was thought to hereditary anomaly results in the development of type 2 diabetes, differ in other fundamental respects [3,4]. A comparison of the suggests that peridroplet mitochondria are more elongated, where protons (H+ purified peridroplet mitochondria to cytoplasmic mitochondria occur due to an increased flux, as compared to the healthy controls whereas cytoplasmic mitochondria tend to be smaller.
    [Show full text]
  • Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights Into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle
    animals Article Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle Masoumeh Naserkheil 1 , Abolfazl Bahrami 1 , Deukhwan Lee 2,* and Hossein Mehrban 3 1 Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran; [email protected] (M.N.); [email protected] (A.B.) 2 Department of Animal Life and Environment Sciences, Hankyong National University, Jungang-ro 327, Anseong-si, Gyeonggi-do 17579, Korea 3 Department of Animal Science, Shahrekord University, Shahrekord 88186-34141, Iran; [email protected] * Correspondence: [email protected]; Tel.: +82-31-670-5091 Received: 25 August 2020; Accepted: 6 October 2020; Published: 9 October 2020 Simple Summary: Hanwoo is an indigenous cattle breed in Korea and popular for meat production owing to its rapid growth and high-quality meat. Its yearling weight and carcass traits (backfat thickness, carcass weight, eye muscle area, and marbling score) are economically important for the selection of young and proven bulls. In recent decades, the advent of high throughput genotyping technologies has made it possible to perform genome-wide association studies (GWAS) for the detection of genomic regions associated with traits of economic interest in different species. In this study, we conducted a weighted single-step genome-wide association study which combines all genotypes, phenotypes and pedigree data in one step (ssGBLUP). It allows for the use of all SNPs simultaneously along with all phenotypes from genotyped and ungenotyped animals. Our results revealed 33 relevant genomic regions related to the traits of interest.
    [Show full text]
  • TPD52L2 Polyclonal Antibody Catalog Number:11795-1-AP Featured Product 4 Publications
    For Research Use Only TPD52L2 Polyclonal antibody Catalog Number:11795-1-AP Featured Product 4 Publications www.ptglab.com Catalog Number: GenBank Accession Number: Purification Method: Basic Information 11795-1-AP BC006804 Antigen affinity purification Size: GeneID (NCBI): Recommended Dilutions: 150ul , Concentration: 900 μg/ml by 7165 WB 1:500-1:1000 Nanodrop and 447 μg/ml by Bradford Full Name: IP 0.5-4.0 ug for IP and 1:500-1:1000 method using BSA as the standard; tumor protein D52-like 2 for WB Source: IHC 1:20-1:200 Calculated MW: IF 1:50-1:500 Rabbit 206 aa, 22 kDa Isotype: Observed MW: IgG 25-30 kDa Immunogen Catalog Number: AG2364 Applications Tested Applications: Positive Controls: IF, IHC, IP, WB,ELISA WB : HEK-293 cells, HeLa cells, human brain tissue, Cited Applications: human kidney tissue, Jurkat cells, K-562 cells, MCF-7 IHC, WB cells, mouse brain tissue, rat brain tissue Species Specificity: IP : HEK-293 cells, human, mouse, rat IHC : human breast cancer tissue, human testis tissue Cited Species: human, mouse IF : HepG2 cells, Note-IHC: suggested antigen retrieval with TE buffer pH 9.0; (*) Alternatively, antigen retrieval may be performed with citrate buffer pH 6.0 Tumor protein D52-like proteins (TPD52) are small coiled-coil motif bearing proteins that were first identified in Background Information breast carcinoma. Three human TPD52 members had been identified, named hD52 (TPD52), hD53 (TPD52L1), and hD54 (TPD52L2). The most important characteristic of the protein family is a highly conserved coiled-coil motif that is required for homo- and heteromeric interaction with other TPD52-like proteins.
    [Show full text]
  • MYC-Containing Amplicons in Acute Myeloid Leukemia: Genomic Structures, Evolution, and Transcriptional Consequences
    Leukemia (2018) 32:2152–2166 https://doi.org/10.1038/s41375-018-0033-0 ARTICLE Acute myeloid leukemia Corrected: Correction MYC-containing amplicons in acute myeloid leukemia: genomic structures, evolution, and transcriptional consequences 1 1 2 2 1 Alberto L’Abbate ● Doron Tolomeo ● Ingrid Cifola ● Marco Severgnini ● Antonella Turchiano ● 3 3 1 1 1 Bartolomeo Augello ● Gabriella Squeo ● Pietro D’Addabbo ● Debora Traversa ● Giulia Daniele ● 1 1 3 3 4 Angelo Lonoce ● Mariella Pafundi ● Massimo Carella ● Orazio Palumbo ● Anna Dolnik ● 5 5 6 2 7 Dominique Muehlematter ● Jacqueline Schoumans ● Nadine Van Roy ● Gianluca De Bellis ● Giovanni Martinelli ● 3 4 8 1 Giuseppe Merla ● Lars Bullinger ● Claudia Haferlach ● Clelia Tiziana Storlazzi Received: 4 August 2017 / Revised: 27 October 2017 / Accepted: 13 November 2017 / Published online: 22 February 2018 © The Author(s) 2018. This article is published with open access Abstract Double minutes (dmin), homogeneously staining regions, and ring chromosomes are vehicles of gene amplification in cancer. The underlying mechanism leading to their formation as well as their structure and function in acute myeloid leukemia (AML) remain mysterious. We combined a range of high-resolution genomic methods to investigate the architecture and expression pattern of amplicons involving chromosome band 8q24 in 23 cases of AML (AML-amp). This 1234567890();,: revealed that different MYC-dmin architectures can coexist within the same leukemic cell population, indicating a step-wise evolution rather than a single event origin, such as through chromothripsis. This was supported also by the analysis of the chromothripsis criteria, that poorly matched the model in our samples. Furthermore, we found that dmin could evolve toward ring chromosomes stabilized by neocentromeres.
    [Show full text]
  • Role and Regulation of the P53-Homolog P73 in the Transformation of Normal Human Fibroblasts
    Role and regulation of the p53-homolog p73 in the transformation of normal human fibroblasts Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Bayerischen Julius-Maximilians-Universität Würzburg vorgelegt von Lars Hofmann aus Aschaffenburg Würzburg 2007 Eingereicht am Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Dr. Martin J. Müller Gutachter: Prof. Dr. Michael P. Schön Gutachter : Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am Erklärung Hiermit erkläre ich, dass ich die vorliegende Arbeit selbständig angefertigt und keine anderen als die angegebenen Hilfsmittel und Quellen verwendet habe. Diese Arbeit wurde weder in gleicher noch in ähnlicher Form in einem anderen Prüfungsverfahren vorgelegt. Ich habe früher, außer den mit dem Zulassungsgesuch urkundlichen Graden, keine weiteren akademischen Grade erworben und zu erwerben gesucht. Würzburg, Lars Hofmann Content SUMMARY ................................................................................................................ IV ZUSAMMENFASSUNG ............................................................................................. V 1. INTRODUCTION ................................................................................................. 1 1.1. Molecular basics of cancer .......................................................................................... 1 1.2. Early research on tumorigenesis ................................................................................. 3 1.3. Developing
    [Show full text]
  • Omics Knowledgebase for Mammalian Cellular Signaling Pathways Scott A
    www.nature.com/scientificdata OPEN The Signaling Pathways Project, an ARTICLE integrated ‘omics knowledgebase for mammalian cellular signaling pathways Scott A. Ochsner1, David Abraham1,8, Kirt Martin1,8, Wei Ding2, Apollo McOwiti2, Wasula Kankanamge2, Zichen Wang 3, Kaitlyn Andreano4, Ross A. Hamilton1, Yue Chen1, Angelica Hamilton5, Marin L. Gantner6, Michael Dehart2, Shijing Qu2, Susan G. Hilsenbeck2, Lauren B. Becnel2, Dave Bridges7, Avi Ma’ayan 3, Janice M. Huss5, Fabio Stossi1, Charles E. Foulds1, Anastasia Kralli6, Donald P. McDonnell4 & Neil J. McKenna 1* Mining of integrated public transcriptomic and ChIP-Seq (cistromic) datasets can illuminate functions of mammalian cellular signaling pathways not yet explored in the research literature. Here, we designed a web knowledgebase, the Signaling Pathways Project (SPP), which incorporates community classifcations of signaling pathway nodes (receptors, enzymes, transcription factors and co-nodes) and their cognate bioactive small molecules. We then mapped over 10,000 public transcriptomic or cistromic experiments to their pathway node or biosample of study. To enable prediction of pathway node-gene target transcriptional regulatory relationships through SPP, we generated consensus ‘omics signatures, or consensomes, which ranked genes based on measures of their signifcant diferential expression or promoter occupancy across transcriptomic or cistromic experiments mapped to a specifc node family. Consensomes were validated using alignment with canonical literature knowledge, gene target-level integration of transcriptomic and cistromic data points, and in bench experiments confrming previously uncharacterized node-gene target regulatory relationships. To expose the SPP knowledgebase to researchers, a web browser interface was designed that accommodates numerous routine data mining strategies. SPP is freely accessible at https://www.signalingpathways.org.
    [Show full text]
  • (TPD52) Are Highly Expressed in Colorectal Cancer and Correlated with Poor Prognosis
    RESEARCH ARTICLE The four-transmembrane protein MAL2 and tumor protein D52 (TPD52) are highly expressed in colorectal cancer and correlated with poor prognosis Jingwen Li☯, Yongmin Li☯, He Liu, Yanlong Liu*, Binbin Cui* Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China a1111111111 ☯ These authors contributed equally to this work. a1111111111 * [email protected] (YLL); [email protected] (BBC) a1111111111 a1111111111 a1111111111 Abstract The four-transmembrane protein MAL2 and tumor protein D52 (TPD52) have been shown to be involved in tumorigenesis of various cancers. However, their roles in colorectal cancer OPEN ACCESS (CRC) remain unclear. In this study, we explored the expressions of MAL2 and TPD52 in Citation: Li J, Li Y, Liu H, Liu Y, Cui B (2017) The tumor specimens resected from 123 CRC patients and the prognostic values of the two pro- four-transmembrane protein MAL2 and tumor teins in CRC. Immunohistochemical analyses showed that MAL2 (P<0.001) and TPD52 protein D52 (TPD52) are highly expressed in (P<0.001) were significantly highly expressed in primary carcinoma tissues compared with colorectal cancer and correlated with poor prognosis. PLoS ONE 12(5): e0178515. https://doi. adjacent non-cancerous mucosa tissues. And TPD52 exhibited frequent overexpression in org/10.1371/journal.pone.0178515 liver metastasis tissues relative to primary carcinoma tissues (P = 0.042), while MAL2 in Editor: Aamir Ahmad, University of South Alabama lymphnode and liver metastasis tissues showed no significant elevation. Real-time quantita- Mitchell Cancer Institute, UNITED STATES tive PCR (RT-qPCR) showed the identical results. Correlation analyses by Pearson's chi- Received: April 1, 2017 square test demonstrated that MAL2 in tumors was positively correlated with tumor status (pathological assessment of regional lymph nodes (pN, P = 0.024)), and clinic stage (P = Accepted: May 15, 2017 0.017).
    [Show full text]
  • Mutations Suggests Both Loss-Of-Function and Gain-Of-Function Effects Morag A
    © 2021. Published by The Company of Biologists Ltd | Disease Models & Mechanisms (2021) 14, dmm047225. doi:10.1242/dmm.047225 RESEARCH ARTICLE Hearing impairment due to Mir183/96/182 mutations suggests both loss-of-function and gain-of-function effects Morag A. Lewis1,2,*, Francesca Di Domenico1, Neil J. Ingham1,2, Haydn M. Prosser2 and Karen P. Steel1,2 ABSTRACT birth. However, this is not the cause of the hearing loss; even before The microRNA miR-96 is important for hearing, as point mutations in the onset of normal hearing, homozygote hair cells fail to mature humans and mice result in dominant progressive hearing loss. Mir96 both morphologically and physiologically, remaining in their is expressed in sensory cells along with Mir182 and Mir183, but the immature state, and heterozygote hair cells show a developmental roles of these closely-linked microRNAs are as yet unknown. Here, delay. miR-96 is thus thought to be responsible for coordinating we analyse mice carrying null alleles of Mir182, and of Mir183 and hair cell maturation (Chen et al., 2014; Kuhn et al., 2011). Mir96 together to investigate their roles in hearing. We found that Overexpression of the three miRNAs also results in cochlear defects Mir183/96 heterozygous mice had normal hearing and homozygotes and hearing loss (Weston et al., 2018). The complete loss of all were completely deaf with abnormal hair cell stereocilia bundles and mature miRNAs from the inner ear results in early developmental reduced numbers of inner hair cell synapses at 4 weeks of age. defects including a severely truncated cochlear duct (Friedman Mir182 knockout mice developed normal hearing then exhibited et al., 2009; Soukup et al., 2009).
    [Show full text]