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Laser Microdissection in Cancer Research and Clinical Oncology

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molecular machines industries -bibliography vol 1 no 1 2008 issue on lasermicrodissection in cancer research and clinical oncology includes the mmi bibliography cancer www.molecular-machines.com mmi-bibliography 1

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»lead the way to scientific results« contents in this issue technology introduction review articles lasermicrodissection and dna analysis lasermicrodissection and rna analysis lasermicrodissection for proteomics new developments references lmd-bibliography online www.molecular-machines.com/news the lmd-bibliograhy is published by molecular machines industries.com issn 1662-8535 editor dr antje plaschke-schluetter e-mail schluetter@molecular-machines.com editorial board andrea curtis norbert brill andre imhof prof stefan seeger concept layout kathrin plaschke ­ grafik design ­ hamburg the mmi caplift technology is a patented trademark of molecular machines industries www.molecular-machines.com mmi-bibliography 2

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»lead the way together with you« editorial the whole area of laser mediated micromanipulation continues to raise interesting scientific developments particularly in the areas outside of traditional research in cancer and personalized medicine these developments will enable us to establish new protocols for cellular and molecular analysis with diagnostic and therapeutic impact in the fight against life-threatening disease we are pleased to introduce to you this very first issue of the mmi-bibliography series with focus on cancer and clinical oncology together with a series of seminars conferences and one-to-one meetings we look forward to strengthen the relationship with our collaborators and our customers we value your opinion and input which will help us to further strengthen our technical developments based on your needs watch out for the seminar announcements on our web-page and the scheduled meetings the whole mmi team hopes that you enjoy this issue and we look forward to »lead the way together with you« dr antje plaschke-schluetter mmi ag zuerich www.molecular-machines.com mmi-bibliography 3

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»lead the way to cutting edge technology« technology the mmi caplift based laser microdissection technology in cancer research and clinical oncology introduction laser microdissection is a technology to isolate specific cell populations from a heterogeneous tissue section under microscopic observation by means of a highly focused laser beam a high number of publications 300 ­ 400 year in the main medical and scientific journals show its increasing importance and usage not only basic scientific questions are addressed by means of laser microdis section but more importantly the main fields of application are within biomedical research for example molecular profiling of specific cell populations is desired in cancer research studies of neurology related diseases parkinson alzheimer immunology caused diseases inflammation rheumatism in dermatology as well as in cardiology the microscopic visualization of the cells permits the specific selection of affected versus non-affected cells of normal premalignant and malignant cells the most common methods employed for molecular profiling of laser microdissected tissue are usually rna and protein based microarray techniques these methods are constantly undergoing optimization towards the use of smaller and smaller amounts of starting material the development of a single cell transcriptom is imminent principle of microdissection fast precise and contamination-free review articles the most current and comprehensive review articles have been written by espina and liotta espina et al 2006 espina et al 2007 they do not only provide innovative and useful hands on tips and tricks but also review on the future impact of laser microdissection in molecular diagnostics patient profiling and biomarker discovery computer-controlled movements uv-cut software-controlled laser focus and energy articles on dna mediated analysis laser microdissected material has been used to successfully analyse genetic aberrations by means of comparative genomic hybridization cgh loss of heterocygocity analysis loh moreno-bueno et al 2002 the detection of point mutations moreno-bueno et al 2002 schipper et al 2003 pugh et al 2007 short tandem repeat analysis wang and zhu 2006 or epigenetic techniques like gene promotor methylation sanchez-aguilera et al 2004 gjerdum and colleagues used laser microdissection for the detection of cytokeratins and epstein-barr virus gene products in head and neck carcinoma gjerdum et al 2005a products in head and neck carcinoma gjerdum et al 2005a for high-speed ultra fine laser cutting the maintenance-free solidstate uva laser is focused through the microscope`s objective onto a microscopic sample to enable a cut width of as small as 0.3 µm with the 100x objective this combined with a very short pico-second pulse duration and a high repetition rate provides an ultra precise and fast target excision articles on rna mediated analysis the strong focus on rna mediated analysis of microdissected tissue and cancer biopsies lead to the elucidation of the molecular changes that occur during cancer progression the development of improved protocols combined with the patentwww.molecular-machines.com mmi-bibliography 4

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»lead the way to a next generation technology« technology ed mmi caplift technology for successful laser microdissection bohm et al 1997 has allowed for the isolation of one of the most delicate molecules in nature rna gjerdrum et al 2001 gjerdrum et al 2004 gjerdrum and hamilton-dutoit 2005a gjerdrum and hamilton-dutoit 2005b kube et al 2007 the first papers were dedicated to the detection of single transcripts and their altered expression in normal versus diseased tissue by means of rt-pcr and northernblotting kumar-sinha et al 2004 kasper et al 2005a kasper et al 2005b scarpino et al 2004a scarpino et al 2004b scarpino et al 2005 scarpino et al 2007a scarpino et al 2007b zhang et al 2003b zhang et al 2003a the combined application of laser microdissection and microarray studies is even more recent and has greatly increased during the last couple of years generating a remarkable body of literature in a combined approach lcm and microarrays have proven to be a very useful tool to study gene expression in many different cancer types such as breast cancer dahl et al 2006 prostate cancer ashida et al 2004 ashida et al 2006 tomlins et al 2006 tomlins et al 2007 tamura et al 2007 liver adenocarcinomas obama et al 2005 esophageal squamous cell carcinomas yamabuki et al 2006 bladder carcinoma takata et al 2005 ovarian carcinomas buckanovich et al 2007 it was used to investigate the mechanisms of tumor vascularization as described by zhang et al and to analyze the homeostasis of intestinal stem cells depending on a change in the wnt/beta catenin signaling fevr et al 2007 all these studies proof the ability to perform microarrays on pure cell populations thereby increasing accuracy and data quality recently lcm has been associated with a combined approach that includes immunohistochemistry immuno-lcm can be used to localize and with high specificity identify the target cell populations of interest from the tumor microenvironment buckanovich et al 2006 sample preparation on frame slide with pet membrane cryo or paraffin-preserved tissue single cells smears or cytospins chromosomes others e.g sperms c elegans for the sample preparation of any source such as frozen or paraffin embedded smears or cytospins and chromosomes spreads the mmi cellcut system uses the mmi membraneslides the different types of samples are prepared on this membrane and are covered with a normal glass slide for protection against contamination articles on proteomics after lmd proteomics based protocols are of increasing interest to many researchers and are based on either gelelectrophoresis or mass spectroscopic analysis cowherd et al 2004 espina et al 2004 hatakeyama et al 2006 kondo et al 2003 kondo and hirohashi 2006 in his current work orimo et al examined the global protein expression profiles of surgically resected tissues including hepatocellular carcinoma hcc nontumor tissue and normal liver tissue this group around prof kondo used proteomic profiling based on 2d gelelectrophoresis to reveal the molecular signature behind the progression of hcc and the prognostic value of adenomatous polyposis coli-end-binding protein 1 eb1 orimo et al 2008 in press new developments new developments in the area of single cell analysis will allow for the isolation of rare cells in suspension from blood and bone marrow on the same lmd instrument platform a new workflow for the isolation of residual tumor cells has been introduced by tveito et al tveito et al 2007 the protocol is based on a two step isolation procedure in a first pre-enrichment step immunomagnetic targeting of cells is performed this is followed by specific collection of individual bead rosetted cells with the newly developed mmi cellector deposition of cells is either onto a grid or into a pcr tube for downstream analysis in molecular patient profiling www.molecular-machines.com mmi-bibliography 5

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»lead the way to an easy operation« references ashida s furihata m katagiri t tamura k anazawa y yoshioka h miki t fujioka t shuin t nakamura y and nakagawa h 2006 ashida s nakagawa h katagiri t furihata m iiizumi m anazawa y tsunoda t takata r kasahara k miki t fujioka t shuin t and nakamura y 2004 bohm m wieland i schutze k and rubben h 1997 buckanovich r j sasaroli d o`brien-jenkins a botbyl j conejo-garcia j r benencia f liotta l a gimotty p a and coukos g 2006 buckanovich r j sasaroli d o`brien-jenkins a botbyl j hammond r katsaros d sandaltzopoulos r liotta l a gimotty p a and coukos g 2007 cowherd s m espina v a petricoin e f iii and liotta l a 2004 dahl e kristiansen g gottlob k klaman i ebner e hinzmann b hermann k pilarsky c durst m klinkhammerschalke m blaszyk h knuechel r hartmann a rosenthal a and wild p.j 2006 espina v dettloff k a cowherd s petricoin e f iii and liotta l a 2004 espina v heiby m pierobon m and liotta l a 2007 espina v wulfkuhle j d calvert v s vanmeter a zhou w coukos g geho d h petricoin e f iii and liotta l a 2006 fevr t robine s louvard d and huelsken j 2007 gjerdrum l m abrahamsen h n villegas b sorensen b s schmidt h and hamilton-dutoit s j 2004 gjerdrum l m and hamilton-dutoit s 2005a gjerdrum l.m and hamilton-dutoit s 2005b gjerdrum l m lielpetere i rasmussen l m bendix k and hamilton-dutoit s 2001 hatakeyama h kondo t fujii k nakanishi y kato h fukuda s and hirohashi s 2006 kasper g vogel a klaman i grone j petersen i weber b castanos-velez e staub e and mennerich d 2005a kasper g weiser a a rump a sparbier k dahl e hartmann a wild p schwidetzky u castanos-velez e and lehmann k 2005b kondo t and hirohashi s 2006 expression of novel molecules mical2-pv mical2 prostate cancer variants increases with high gleason score and prostate cancer progression clin cancer res 12 2767-2773 molecular features of the transition from prostatic intraepithelial neoplasia pin to prostate cancer genome-wide gene-expression profiles of prostate cancers and pins cancer res 64 5963-5972 microbeam moment non-contact laser microdissection of membrane-mounted native tissue am j pathol 151 63-67 use of immuno-lcm to identify the in situ expression profile of cellular constituents of the tumor microenvironment cancer biol ther 5 635-642 tumor vascular proteins as biomarkers in ovarian cancer j clin oncol 25 852-861 proteomic analysis of human breast cancer tissue with laser-capture microdissection and reversephase protein microarrays clin breast cancer 5 385-392 molecular profiling of laser-microdissected matched tumor and normal breast tissue identifies karyopherin alpha2 as a potential novel prognostic marker in breast cancer clin cancer res 12 3950-3960 use of proteomic analysis to monitor responses to biological therapies expert opin biol ther 4 83-93 laser capture microdissection technology laser-capture microdissection expert rev mol diagn 7 647-657 nat protoc 1 586-603 wnt/beta-catenin is essential for intestinal homeostasis and maintenance of intestinal stem cells mol cell biol 27 7551-7559 the influence of immunohistochemistry on mrna recovery from microdissected frozen and formalin-fixed paraffin-embedded sections diagn mol pathol 13 224-233 laser-assisted microdissection of membrane-mounted sections following immunohistochemistry and in situ hybridization methods mol biol 293 139-149 laser-assisted microdissection of membrane-mounted tissue sections methods mol biol 293 127-138 laser-assisted microdissection of membrane-mounted paraffin sections for polymerase chain reaction analysis identification of cell populations using immunohistochemistry and in situ hybridization j mol diagn 3 105-110 protein clusters associated with carcinogenesis histological differentiation and nodal metastasis in esophageal cancer proteomics 6 6300-6316 the human laptm4b transcript is upregulated in various types of solid tumours and seems to play a dual functional role during tumour progression cancer lett 224 93-103 expression levels of the putative zinc transporter liv-1 are associated with a better outcome of breast cancer patients int j cancer 117 961-973 application of highly sensitive fluorescent dyes cydye dige fluor saturation dyes to laser microdissection and two-dimensional difference gel electrophoresis 2d-dige for cancer proteomics nat protoc 1 2940-2956 kondo t seike m mori y fujii k yamada t and hirohashi s 2003 application of sensitive fluorescent dyes in linkage of laser microdissection and two-dimensional gel electrophoresis as a cancer proteomic study tool proteomics 3 1758-1766 optimization of laser capture microdissection and rna amplification for gene expression profiling of prostate cancer bmc mol biol 8 25 elevated alpha-methylacyl-coa racemase enzymatic activity in prostate cancer am j pathol 164 787-793 kube d m savci-heijink c d lamblin a f kosari f vasmatzis g cheville j c connelly d p and klee g g 2007 kumar-sinha c shah r b laxman b tomlins s a harwood j schmitz w conzelmann e sanda m.g wei j t rubin m a and chinnaiyan a m 2004 www.molecular-machines.com mmi-bibliography 6

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»lead the way to microscopic manipulation« references moreno-bueno g hardisson d sanchez c sarrio d cassia r garcia-rostan g prat j guo m herman j g matias-guiu x esteller m and palacios j 2002 obama k ura k li m katagiri t tsunoda t nomura a satoh s nakamura y and furukawa y 2005 orimo t ojima o hiraoka n saito s kosuge t kakisaka t yokoo h nakanshi k karniyama t todo s hirohashi s kondo t 2008 pugh t j bebb g barclay l sutcliffe m fee j salski c o`connor r ho c murray n melosky b english j vielkind j horsman d laskin j j and marra m a 2007 sanchez-aguilera a delgado j camacho f i sanchez-beato m sanchez l montalban c fresno m f martin c piris m a and garcia j f 2004 scarpino s cancellario d f di n a pasquini a marzullo a and ruco l p 2004a scarpino s di n a melotti f talerico c cancrini a and ruco l 2007a scarpino s di n a rapazzotti-onelli m pilozzi e and ruco l 2004b scarpino s di n a stoppacciaro a antonelli m pilozzi e chiarle r palestro g marino m facciolo f rendina e a webster k e kinkel s a scott h s and ruco l 2007b scarpino s di n a taraboletti g cancrini a and ruco l p 2005 schipper h papp t johnen g pemsel h bastrop r muller k m wiethege t jaworska m krismann m schiffmann d and rahman q 2003 takata r katagiri t kanehira m tsunoda t shuin t miki t namiki m kohri k matsushita y fujioka t and nakamura y 2005 tamura k furihata m tsunoda t ashida s takata r obara w yoshioka h daigo y nasu y kumon h konaka h namiki m tozawa k kohri k tanji n yokoyama m shimazui t akaza h mizutani y miki t fujioka t shuin t nakamura y and nakagawa h 2007 tomlins s a mehra r rhodes d r cao x wang l dhanasekaran s m kalyana-sundaram s wei j t rubin m va pienta k j shah r.vb and chinnaiyan a m 2007 tomlins s a mehra r rhodes d r shah r b rubin m a bruening e makarov v and chinnaiyan a m 2006 tveito s maelandsmo g m hoifodt h k rasmussen h and fodstad o 2007 wang l and zhu h 2006 yamabuki t daigo y kato t hayama s tsunoda t miyamoto m ito t fujita m hosokawa m kondo s and nakamura y 2006 zhang l yang n conejo-garcia j r katsaros d mohamed-hadley a fracchioli s schlienger k toll a levine b rubin s c and coukos g 2003a zhang l yang n park j.w katsaros d fracchioli s cao g o`brien-jenkins a randall t c rubin s c and coukos g 2003b abnormalities of the apc/beta-catenin pathway in endometrial cancer oncogene 21 7981-7990 genome-wide analysis of gene expression in human intrahepatic cholangiocarcinoma hepatology 41 1339-1348 proteomic profiling reveals the prognostic value of adenomatous polyposis coli-end-binding protein 1 in hepatocellular carcinoma journal of hepatology in press correlations of egfr mutations and increases in egfr and her2 copy number to gefitinib response in a retrospective analysis of lung cancer patients bmc cancer 7 128 silencing of the p18ink4c gene by promoter hypermethylation in reed-sternberg cells in hodgkin lymphomas blood 103 2351-2357 increased expression of met protein is associated with up-regulation of hypoxia inducible factor-1 j pathol 202 352-358 hif-1 in tumour cells in papillary carcinoma of the thyroid papillary carcinoma of the thyroid low expression of ncam cd56 is associated with downregulation of vegf-d production by tumour cells j pathol 212 411-419 papillary carcinoma of the thyroid methylation is not involved in the regulation of met expression br j cancer 91 703-706 expression of autoimmune regulator gene aire and t regulatory cells in human thymomas clin exp immunol 149 504-512 hepatocyte growth factor hgf downregulates thrombospondin 1 tsp-1 expression in thyroid papillary carcinoma cells j pathol 205 50-56 mutational analysis of the nf2 tumour suppressor gene in three subtypes of primary human malignant mesotheliomas int j oncol 22 1009-1017 predicting response to methotrexate vinblastine doxorubicin and cisplatin neoadjuvant chemotherapy for bladder cancers through genome-wide gene expression profiling clin cancer res 11 2625-2636 molecular features of hormone-refractory prostate cancer cells by genome-wide gene expression profiles cancer res 67 5117-5125 integrative molecular concept modeling of prostate cancer progression nat genet 39 41-51 whole transcriptome amplification for gene expression profiling and development of molecular archives neoplasia 8 153-162 specific isolation of disseminated cancer cells a new method permitting sensitive detection of target molecules of diagnostic and therapeutic value clin exp metastasis 24 317-327 clonal analysis of palmar fibromatosis a study whether palmar fibromatosis is a real tumor j transl med 4 21 genome-wide gene expression profile analysis of esophageal squamous cell carcinomas int j oncol 28 1375-1384 expression of endocrine gland-derived vascular endothelial growth factor in ovarian carcinoma clin cancer res 9 264-272 tumor-derived vascular endothelial growth factor up-regulates angiopoietin-2 in host endothelium and destabilizes host vasculature supporting angiogenesis in ovarian cancer cancer res 63 3403-3412 to be continued www.molecular-machines.com mmi-bibliography 7

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s pecific at ions cellcut with olympus ix2 microscopes item system components samples microscopic systems picosecond uva solid-state laser caplift technology nosepiece uis2 objectives digital camera with ultra high sensitivity uv-cut software basic functions for all application-relevant samples cryo or paraffin-preserved tissues single cells cell compartiments cytospins chromosomes etc olympus ix71 or ix81 computer-controlled wavelength 355 nm pulse duration 500 psec pulse energy/average energy 1 joule/appr 4 mw repetition rate 5 khz sw-controlled covering full slides unique contamination-free sandwich technology 6-position nosepiece na and wd specified to be selected according to application requirements excellent uv/ir transmission digital colour digital monochrome 1,392 x 1,040 pixels compact housing and firewire connection laser energy and focus control full slide and petri dish control inspection mode with positive target identification saving multi user profiles multigroup function across entire sample/slides autodocumentation for sample images and parameters pc and monitor motorised stage motorised nosepiece z-focus for ix81 condenser/contrast methods fluorescence options penscreen system operation cellexplorer image analysis software multicap motorised multislide motorised possible cellcut system upgrade cellmanipulator optical tweezer system new cellector ultra precise contact-free manipulation of microscopic particles with up to 10 independent beams based on a high-quality yag-type infrared laser a fully automated single cell sorting device sensitive 21 pen screen monitor for user-friendly system operationand to allow direct target identification with a special pen identifies and cuts out automatically defined targets based on user settings allows automatic collection of targets in up to 8 different isolationcaps for microdissection of up to 3 slide assemblies 10 nm step size and 1 m reproducibility independent of movement direction fine/coarse movement with 3 mm/sec max speed bf phase and rc contrast and dic application-oriented 6-cube turret dual-level laser coupling specifications will be continuously updated according to market development windows xp 19 lcd monitor computer-controlled for high-precision movement/cutting travelling range 120 x 100 mm step width 0.075 m repositioning accuracy 1 m specification the manufacturer reserves the right to make technical changes without prior notice mmi ag flughofstrasse 37 8152 glattbrugg switzerland phone +41 44 809 10 10 fax +41 44 809 10 11 mail info@molecular-machines.com www.molecular-machines.com mmi gmbh breslauer strasse 2 85386 eching germany phone +49 89 319 048 40 fax +49 89 319 048 59 mail info@molecular-machines.com www.molecular-machines.com mmi inc p.o box 348 haslett mi 48840 usa phone +1 603 629 95 36 fax +1 321 978 0304 october 2008 mail sales_us@molecular-machines.com www.molecular-machines.com

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