Molecular Pathology Shared Resource (HICCC)

The Molecular Pathology Shared Resource (MPSR), managed by the Herbert Irving Comprehensive Cancer Center, provides members with a diverse set of services, including tumor banking, histology and immunohistochemistry, full pathological evaluation of human material and mouse models, traditional and “next generation” (nucleic acids-based) tumor banking, as well as start-to-finish tissue-based research project management. The core is directed by Hanina Hibshoosh, MD. MPSR is located in the Lasker Biomedical Research Building, and the histology and tumor banking services are located in room 455 in the Black Building. More information on each service is below

Histology Service: The histology service offers routine and specialized histology services including grossing, embedding, tissue processing, sectioning and staining. It operates on frozen and FFPE tissue. On average, it has processed more than 13,000 blocks and an excess of 161,000 sections were generated.

Tumor bank: The tumor bank procures, bar codes, stores, annotates, processes, and distributes to investigators tumor and normal frozen tissue for research purposes. The bank operates under IRB approval, is HIPAA compliant, is licensed by the New York State Department of Health, follows NCI best practices for biospecimen resources, and is governed by a tissue utilization committee. The bank contains more than 19,000 tumor cases, collects approximately 1,800 cases per year, and distributes over 1,000 cases to investigators per year. It has a database (Freezerworks 3.1.08.1 multi-user version) that utilizes caBIG compliant terminology.

Macromolecule Platform (next-generation banking): The macromolecule platform is a research platform designed to facilitate, Columbia University wide and beyond, cancer research and foster collaboration by evaluating systematically the procured frozen tumors in our tumor bank. The platform provides thoroughly characterized frozen tumors and normal tissue, corresponding DNA/RNA, corresponding tissue, microarrays, whole section banks of formalin fixed slides corresponding to cases, frozen tissue for Western Blots/IHC, database linking clinical/pathological and basic science characteristics, professional services, and expertise in tissue based analysis (extraction, storage, expression, and immune and molecular genetic characterization). The platform works closely with the histology service and tumor bank to maximize value. The platform currently focuses on systematic evaluation of all tumors in the bank corresponding to breast, prostate, bladder, and pancreas. The platform contains hundreds of tumors in each organ ready for biomarker analysis and correlation providing an “off the shelf”, highly characterized and robust resource.

Molecular Biology Service: The molecular biology service helps investigators operating on fresh/frozen or FFPE tissues or analytes prepared by the next-generation biobanking service. The service provides professional, efficient, and cost-effective services: high throughput RNA/DNA extraction service; Affymetrix/Agilent microarray labeling; quantitation of macromolecules; and Realtime PCR and RT-PCR.

Equipment

  • Primera Cassettes Labeler
  • Sakura Tissue-Tek VIP 5 Tissue Processor
  • Sakura Tissue-Tek TEC 5 Embedding Station
  • Leica Microtome (3)
  • Leica IP S Automated Slides Labeler
  • Tissue Tek S76411 Automated H&E Stainer
  • Leica CV5030 Automated Coverslipper
  • Leica CM3050 S Cryostat
  • Thermo Scientific Cryotome FSE Cryostat
  • Leica VT1000 S Vibratome
  • Beecher Tissue Arrayer
  • Leica SCN400 Sl801 Whole Slide Scanner with Autoloader
  • Revco -80°C Freezers  (12)
  • Dako Autostainer
  • Nikon Eclipse 50i Binocular Microscope (2)
  • Qiagen QIAsymphony SP Automated Extractor
  • Thermo Scientific NanoDrop 8000 Spectrophotometer 
  • Agilent 2100 G2939A Bioanalyzer 
  • Invitrogen Qubit 4 Fluorometer
  • ThermoFisher QuantStudio 3 Real-Time PCR System
  • Qiagen TissueLyser II  
     

The Molecular Pathology Shared Resource (MPSR)has a diverse set of equipment to support its varied activities. The histology services of the MPSR utilize multiple automated platforms achieving high throughput with high quality, consistency and low cost. The Primera Signature cassette printer is directly linked with users’ requisition forms in the iLab Core Facility management System using an in-house developed program. This printer significantly increases the efficiency of the lab and reduces the risk of mislabeling of specimens, and can print text, graphics and barcodes directly onto face of the cassettes.The Sakura Tissue-Tek tissue processor stationprocesses fixed tissues before embedding. It features an automated reagent transfer, continuous mixing, and bottle connection check that ensures smooth performance and efficient processing.The Sakura Tissue-Tek embedding station includes two-component system with an embedding and cryo module. The Leica microtomes are fully automated high-performance microtomes capable of cutting paraffin sections in a thickness range from 0.5µm to 100µm.The Leica slide labeler is directly linked with users’ requisition forms in iLab, using an in-house developed program. This printer can print text, graphics and barcodes directly onto face of the slides, significantly increases efficiency, and reduces the risk of mislabeling of slides. The Sakura Tissue-Tek H&E Slide AutoStainer is an automated, fully programmable H&E stainer that can stain both frozen and paraffin H&E with up to 180 slides per hour. The Leica CV5030 cover slipper is a fully automated slide cover slipper which can cover slides at a rate of up to 400 slides per hour. 

We have two cryostats (Leica and Thermo Electron Cryotome) that are fully automated for cutting frozen sections at a thickness range of 0.5µm-300µm, and can operate at temperature range of 0°C to -40°C.The Leica Vibratome is a fully automated tissue vibrating blade microtome that can cut tissue at thickness range from 1m-999m. The Beecher Tissue Arrayer, used for tissue microarray (TMA) construction, can operate at 4 different needle sizes (0.6mm, 1mm,1.5mm and 2mm) and constructs up to 162 cores (0.6mm size) per TMA block.

The DAKO Auto-Stainer, used for automated IHC, processes slides for the staining of paraffin-embedded and frozen tissue sections, cytospins, cell smears and fine needle aspirates. This system is designed to automate manual regular staining methods and can process up to 48 slides with 1-48 antibodies per run. The Leica SCN400is used for image digitalization and whole slide scanning with a 384 slide auto loader. This whole slide scanner can scan entire slides, including slides labels for up to 40x with options of 40x, 20x or 10x. The DIH (digital image hub) software incorporated with the slide scanner allows researchers to analyze with fully customized algorithms, annotate, convert and share the images.  For slide review and image capture, we have Nikon florescent and bright field microscopes (Eclipse 90i and 50i).   

Tissue banking services are supported by our 12°C, -80°C,  and -20°C freezers. Freezerworks, a customizable client/server software, is used to manage our database of frozen specimens. Currently, our tissue bank -80°C freezers contain more than 36,000 cases of frozen specimens collected since 1992.

Next Generation Banking Equipment:   We have several -80°C Thermo Revco freezers to stores frozen tissue blocks, sections, lysates and RNA samples.The Qiagen QIAsymphony SP is an automated, magnetic bead-based nucleic acid extraction system used to extract DNA or RNA from frozen or FFPE samples in under 3 hours. The Thermo ScientificSpectrophotometer NanoDrop 8000is a micro-volume UV-Vis spectrophotometer for DNA, RNA and protein quantification. The instrument can measure up to 8 samples simultaneously using only 1-2µl of sample with 8-channel pipette. 

The Agilent Bioanalyzer 2100 is a high-resolution microfluidic chip based, automated electrophoresis system for DNA or RNA quality control. The Invitrogen Qubit 4 Fluorometer accurately measures DNA, RNA, and protein quantity, and RNA integrity and quality using the highly sensitive Qubit assays. The ABI QuantStudio real-time PCR system has software for simple one plate setup and analysis, and cross-plate data analysis. The Qiagen TissueLyser II homogenizer disrupts multiple biological samples through high-speed shaking in plastic tubes with stainless steel beads for RNA extraction from frozen or fresh tissue/cells. 

Standards, Rigor, and Reproducibility

Quality control procedures recommended by the instrument manufacturer are in place to ensure proper instrument operation. To abide rigor and reproducibility, all analytical services include standard operating protocols and are routinely validated using technical replicas.