Molecular Cytology. Anna M Bofin. Associate Professor of Pathology Department of Laboratory Medicine, Children s and Women s Health

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1 1 Molecular Cytology Anna M Bofin Associate Professor of Pathology Department of Laboratory Medicine, Children s and Women s Health

2 2 «Fine needle aspiration is a mechanicophysical tumour cell enrichment procedure» Professsor Bjørn Hagmar

3 3 What is molecular cytology? The in situ localization of selected molecules Utilization of advanced technologies that allow for the detection, analysis and quantification of molecules in their natural environment, such as cells, tissues, organs, embryos and tumors. in diagnostics and research. AMB May 2012

4 4 Why molecular cytology? Primary diagnostics Prognostic information Predictive information Determine treatment strategies Monitoring disease Diagnose recurrence Research AMB May 2012

5 5 Cytology Whole interphase cells A complete cell membrane A full set of chromosomes All the cytoplasm Air-dried Cell suspension Snap-frozen Fixed Henrietta Lacks Immortal Cells The Smithsonian Magazine 2010 AMB May 2012

6 6 Whole cells Exfoliated cells Urine, serous fluids, expectorat, vaginal cytology Brushed, scraped or washed from a surface Bronchial cytology, cervical cytology, skin scrape cytology, urinary bladder Fine needle cytology Fine needle aspiration (FNA), fine needle sampling (FNS)

7 7 Techniques In Situ Hybridization Immunocytochemistry PCR / RT-PCR Flow cytometry cdna microarray

8 8 The molecular biological pathway FISH/CISH/PCR PCR ICC/IHC

9 9 any cell with a nucleus can be examined using (F)ISH techniques JK Blancato, BR Haddad Medical Cytogenetics (Ed HFL Mark) 2000 pp 147

10 10 Fluorescence in situ hybridisation

11 11 Applications Aneuploidy Gene copy number Structural breakpoint analysis Translocation Microdeletion Gene mapping

12 12 ISH probes Metaphase Whole chromosome probes Alpha satellite/centromere probes Unique sequence probes Lodish et al Molecular Cell Biology 2005 Interphase

13 13 Alpha satellite/centromere probe Repetitive sequences Near chromosome centromeres Chromosome specific Detect aneuploidy

14 14 Unique sequence probes (locus specific probes) Target regions NOT repeated in the genome Chromosome deletions Oncogenes c-myc; HER2; EGFR Telomeric and subtelomeric probes

15 15

16 16 Amplification patterns Double minutes = extrachromosomal amplification MYCN FISH in neuroblastoma Interphase Metaphase

17 17 Amplification patterns Homogeneous staining regions = intrachromosomal amplification HER2 FISH in breast cancer Interphase

18 18 HER2/chromosome 17 FISH Looking for gene amplification - breast cancer FNA cytology Ratio 2:2 = 1.0 No gene amplification

19 19 HER2/chromosome 17 FISH Looking for gene amplification - breast cancer FNA cytology Ratio 2:>15=7.5 High grade gene amplification

20 20 Morphology in the fluorescence microscope

21 21 Morphology in the fluorescence microscope

22 22 Morphology in the fluorescence microscope

23 23 Morphology in the fluorescence microscope

24 24 HER2 TOP2A Chromosome17 Brystkreft BRCA1 HER2 TOP2A TP53 Bofin, et al Cytopathology 2003;14: Ingen HER2/TOP2A genamp amp HER2 amp/top2a nonamp

25 25 Translocations Locus specific probes Diagnostics Prognostication Follow-up Leukemia CML brc/abl translokasjon Lymphoma Mantle cell lymphoma t(11;14)(q13;q32) Sarcoma synovial sarcoma - t(x;18)

26 26 Fusion and split translocations Red and green co-localise to detect a known translocation Red and green separate to detect a break without the need to know the translocation partner

27 27 Translocations - fusions

28 28 Translocations - Splits Bishop R Bioscience Horizons 2010;3:85-95

29 29 Screening for disease or relapse Multicolour FISH Cancer of the urinary bladder urine cytology Copy number changes in ch. 3, 7, or 17 in at least 4 cells OR Loss of 9p21 in at least 12 cells Ferras S et al Cancer Cytopathol 2009 Feb 25;117(1):7-14.

30 30 Chromosome copy number Urinary cytology FISH Chromosomes 3,7,17 Locus 9p21 E Berggren/A Bofin

31 31 Pap Urothelial carcinoma WHO grade 2-3 FISH Pap Urothelial carcinoma, WHO grade 3 FISH E Berggren/A Bofin

32 32 Pap Urothelial carcinoma, WHO grade 3 (FISH) Pap Cis,/Urothelial carcinoma, WHO grade 2 FISH E Berggren/A Bofin

33 33 Cytogenetic analyses Karyotyping FISH Lipoma Synovial sarcoma t(x;18) (SYT;SSX) Rhabdomyosarcoma Cohen IJ et al Synovial sarcoma of bone delineated by spectral karyotyping.lancet ;350(9092): Croes R et al Adult sclerosing rhabdomyosarcoma: cytogenetic link with embryonal rhabdomyosarcomavirchows Arch Jan;446(1):64-7 Sandberg AA Updates on the cytogenetics and molecular genetics of bone and soft tissue tumors: lipoma. Cancer Genet Cytogenet Apr 15;150(2):93-115

34 34 FISH in the path lab Contributes to diagnosis Surveillance in patient follow-up Prognostic and predictive information Determining treatment strategies

35 35 FISH - pros and cons Simpler protocol minimal pretreatment No formalin-fixation artefacts Whole nuclei - no truncation artefacts Little background fluorescence Recognisable morphology compared to routine stained smears Cytology not always available

36 36 Artefacts/Problems Smearing artefacts Non-specific background fluorescence Low stringency washing Cross-hybridisation Poorly prepared probe Probe too small Amplification techniques (TSA)

37 37 Immunocytochemistry Cell smears Fine needle aspirates Liquid-based cytology Smears Cell suspension Snap frozen Cell blocks «pseudohistology»

38 38 Immunocytochemistry Cervix Liquid-based cytology HSIL MIB1 p16 INK4a Sahebali et al Immunocytochemistry in liquid based cervical cytology: Analysis of clinical use following a cross sectional study International Journal of Cancer 2005;118:

39 39 Immunocytochemistry Breast carcinoma Diff Quick atypical ductal cells Oestrogen receptor

40 40 Immunocytochemistry Breast carcinoma Reliability of a negative result Snap freezing Fixative/air-drying The epitope may become slightly deformed resultiong in a false neg. Result Cuthbert et al Cytopathology 1990;1: Sauer T, Beraki E, Jebsen P. Anal Quant Cytol Histol 1998;20:122-6 A negative ER on FNA should prompt ER on tissue biopsy Lea D, Bofin A. Er hormonundersøkelse av cytologisk materiale i brystkreftsvulster til å stole på? Bioingeniøren 2011:3;6-12

41 41 Immunocytochemistry Malignant melanoma Atypical melanocytes Immunocytochemistry:HMB45

42 42 Painful subcutaneous tumour S100 protein

43 43 Painful subcutaneous tumour Neurofibroma

44 44 Large tumour in the shoulder FNA smear LCA B-cell lymphoma CD20 CD99

45 45 Soft tissue tumour in a child FNA smear MGG Desmin Alveolar rhabdomyosarcoma Lisa Walaas, Rikshospitalet, Oslo

46 46 ICC - pros and cons Simple procedure air-dried smears LBC Cell blocks Provides additional information in inoperable patients Enables pre-operative chemotherapy Not always enough material for multiple ICC s

47 47 Polymerase Chain Reaction(PCR) Finding small sequences of DNA and making them visible DNA mrna converted to cdna by means of reverse transcriptase DNA is amplified: 5 3 DNA DNA

48 48 RT-PCR (reverse transcriptase) Fluorochrome Probe Quencher DNA DNA

49 49 Real time RT-PCR Relative quantification

50 50 B-RAF mutation in thyroid FNA Diagnostics Determining treatment strategy B-REF mutation detection in papillary carcinoma (45 %) BRAF-mutation in a follicular-like neoplasm indicates a follicular variant of a papillary carcinoma AND total thyroidectomy rather than a diagnostic hemithyroidectomy Canadas-Garre et al Ann Surg 2012 May;255(5):986-92

51 51 PCR- pros and cons Costly, perhaps complicated procedure Requires a reasonable amount of material Quantitation or relative quantitation of small amounts of RNA/DNA

52 52 Flow cytometry Flow cytometry is a method allowing the analysis of of cells or particles suspended and separated in a fluid. The fluid flows past a focused laser beam. The cells are usually labelled using fluorescent probes which bind to specific cell associated molecules Phenotypic, biochemical and molecular characteristics of the individual cells Visualised as a scatter chart or graph

53 53 Flow cytometry Rudbeck laboratory, University of Uppsala

54 54 Flow cytometry FNS/FNA from lymph nodes/lymphoid tissue Particularly in non-hodgkins lymphoma Requires a certain number of cells No morphology keep some material back for microscopy Zeppa et al Cytopathology 2010;21:

55 55 Quality assurance/control Follow procedure particularly posthybridisation washes Qualified readers National and international QA programmes

56 56 Take home message Think special tests - Always