Human Tissue Repository & Tissue Analysis

The Human Tissue Repository and Tissue Analysis Shared Resource (HTR-TASR) are jointly funded by the Cancer Center and the Department of Pathology. They have been set up to facilitate the translational research of the faculty in the Cancer Center, the Department of Pathology, the School of Medicine and across Institutes. This website describes the services offered and contact details of HTR-TASR staff members who can advise on specimen availability and all aspects of histology and molecular pathology.

Purpose

To facilitate the acquisition, storage, and distribution of high quality human tissue samples to UNM researchers for use in scientific investigations while observing appropriate ethical, scientific, and legislative principles and regulations.

We use the NCI Best Practices for Biospecimen Resources as our guide.

About HTR-Tissue

The HTR-Tissue Shared Resource:

  • Benefits future patients by allowing researchers access to well preserved and maintained tissues that might not otherwise be available
  • Benefits UNM HSC by strengthening mission of providing quality patient care through fostering innovative and clinically valuable research
  • Honest broker function of the HTR in dispensing de-identified specimens devoid of the 18 HIPAA personal identifiers protects researchers from potential HIPAA complications/violations

The TASR provides a variety of histology services, including various types of immunohistochemical and immunofluorescence staining, as well as various molecular pathology techniques such as PCR, Real-Time PCR, DNA and RNA extraction from tissues and fluids and immunofluorescence.

Summary of HTR-TASR Services for Grant Applications

The Human Tissue Repository and Tissue Analysis Shared Resource (HTR-TASR) has the capability to perform a number of techniques and offers a variety of services on a fee for service basis.

The HTR-TASR collects matched normal and tumor tissue primarily from left-over discard surgical specimens, and stores them either frozen or as formalin-fixed paraffin embedded (FFPE) blocks. Investigators can request the tissues, with approvals required from the IRB (Human Research Protections Office) and Tissue Research Oversight Committee (TROC, formerly SRC).

The HTR-TASR can also provide a number of different histology and molecular services, such as sectioning and H&E staining, immunohistochemistry and immunofluorescence using the Ventana Discovery Ultra Platform, creation of custom Tissue Microarrays (TMAs), slide digitizing (brightfield and fluorescent) via the Aperio Versa 200, and image analysis using the HALO™ Platform (from Indica Labs, headquarters in Albuquerque, NM).

Various types of blood processing is available, including performance of cell count and viability via the Nexelom Cellometer 1000.

Some investigators require specially prepared specimens or have specific specimen requirements. For these approved studies, HTR personnel will prospectively collect the specimens and process tailored to the researchers’ needs. In addition, some molecular services are available, such as DNA and RNA extraction, PCR and real-time PCR.  A feasibility meeting should be set up with the Technical Manager and Operations Manager to discuss desired services.

To acknowledge use of this shared resource, please include the following in your publications:

This research was partially supported by UNM Comprehensive Cancer Center Support Grant NCI P30CA118100 and made use of the Human Tissue Repository and Tissue Analysis Shared Resource, which receives additional support from The University of New Mexico School of Medicine Department of Pathology.

Contact HTR-Tissue

Phone: (505) 272-1127
Email: tissuebank@salud.unm.edu
Fitz Hall rooms 306B, and 306C
UNM HSC School of Medicine
Department of Pathology
MSC 08-4640
915 Camino de Salud, NE
Albuquerque, NM 87131

HTR-TA Personnel

Dennis McCance, PhDDennis J McCance PhD

Research Professor, Pathology

Scientific Director

Oversees all aspects of the Resource

Edgar Fischer, MDEdgar Fischer MD

Professor, Pathology

Medical Director

Oversees quality control aspects of the Resource

Cathleen Martinez, PDCathleen Martinez PA

Technical Manager

Oversees the technical aspects of the Resource

Sadie La Bauve, PhDSadie La Bauve PhD

Operational Specialist

Manages day to day responsibilities

Fred Schultz, MAFred Schultz, MA

Informatics Management

Histology and Molecular Pathology Services

Tissue processing and paraffin-embedding or snap freezing of tissue. The tissue can be stained with an H&E stain or remain unstained.

The laboratory can stain tissue sections with standard antibodies using protocols already in place. Alternatively, the laboratory can work up antibodies using the VENTANA DISCOVERY platform that allows for multiple staining combinations to optimize staining results.

HER-2 and ER Image
Dual Staining for HER-2 and ER

Fluorescence-tagged antibodies can also be used to detect your protein of interest.

HTR Tissue Microarrays - e-cadherin

Tissue microarray design and construction: This entails collecting donor paraffin blocks, selecting the areas of interest to core, and placing the cores in a blank recipient paraffin block. The advantages are in speed and cost, as multiple samples may be assessed on one slide. The typical TMA contains approximately 50 to 200 cores of 0.6mm-2.0 mm diameter. Approximately 50 sections may be obtained from one TMA block.

 

(At right: E-cadherin)

The HTR-TASR personnel can retrieve archival tissue blocks from UNM Hospital.

This usually comprises collection of excess or remnant tissues left over at the time of surgical resection after diagnostic samples have been taken for surgical pathologist microscopic review and enough specimen is retained in paraffin for potential future testing for patient care. HTR-TASR personnel will collect the tissues in the Gross Dissection Room of UNM HSC Surgical Pathology. Currently, the HTR does not perform venipunctures but will bank such specimens as requested by researchers.

HTR-TASR project consultants can collect pathology and clinical data that are stripped of HIPAA identifiers while coded to matching samples.

  1. DNA and RNA isolations from multiple types of specimens (e.g., fresh/frozen blood, transformed cells, frozen tissue, paraffin embedded tissue); including quantitation and quality assessment of the RNA.
  2. Polymerase Chain Reaction (PCR) amplification from DNA or RNA targets, including primer design, PCR optimization, set up PCR and RT-PCR, and gel electrophoresis for quality assurance.
  3. Gene expression quantitation (real time PCR): including primer design.

Image Analysis

Images of H&E or immunohistochemically stained tissue sections or immunofluorescence sections are captured on the Leica Versa 200 digital scanner and uploaded to the HALO imaging and annotation software.

The HALO software allows you to annotate the tissue (tumor, stroma, muscle, fat etc.) and then count cells that are positive for protein of choice (Figure, right) within each of these annotated regions. It will also enable you to analyze and quantify nearest neighbor interactions.

The software includes a figure-making tool that can create multi-panel photos of images in publishable formats including reference frames and scale bar

Quantitative Results Image

This figure shows quantification of staining for Ki67 in breast cancer. The top left panel shows the tissue microarray sample, the middle panel shows Ki67 staining (brown) without the HALO markup and the right panel show the same image with the HALO markup.

The markup shows low level staining (yellow), moderate staining (brown) and high levels (red) of Ki67 in the nucleus of tumor cells. Blue staining are cells that are negative for Ki67. The software can independently count Ki67 staining in the stoma of the tumor.

The table shows a read out of the number and percentage of cells in each staining category and the histogram shows the distribution of staining.

How to Apply for Specimens

Contact Cathy Martinez or Sadie LaBauve to schedule.

Open Your Account in iLab:

  1. Navigate to the iLabs login page.
  2. In the upper right-hand corner of the screen, select sign up
  3. Complete the registration form on the sign-up page.
  4. Receive a welcome email from from iLab with login credentials and instructions

Requesting Services in iLab:

  1. Establish a Purchase Requisition (PR) through your department. Email the PR to Sabrina Samudio-Ruiz and Abel Tarango-Prieto requesting it be added under your lab in the iLab system.
  2. Go to the iLabs login page.
  3. In the upper right corner of this page, enter your username and password.
  4. Under the “Request Services” tab, click “Initiate Request” next to the service of interest (Human Tissue Repository vs Molecular Pathology Services).
  5. Complete the form and provide payment information for your request prior to submitting the request to the HTR.
    1. Make sure Project Title and TROC/HRRC/IACUC numbers match those on your approval letters.
    2. Under each category of services, enter the desired number and click on “Add selected services” tab. Services will be added at the bottom of the form.
    3. Use the “Additional Information” box to add any important details, and attach/upload any relevant documents, such as a specimen list or orientation description.
  6. Requests will be pending review by the HTR, which will make any necessary changes and submit back for your approval. You will receive an email from iLab regarding your updated project request.
  1. Submit your proposal to the Tissue Research Oversight Committee (TROC). Contact Karen Capobianco for guidance in this process.
  2. Once the TROC approves your proposal, send the approval letter with your application to the UNM Human Research Review Committee (HRRC) Institutional Review Board (IRB).

To navigate the IRB application process:

  1. On the above link, click the “Click IRB” button to the left
  2. Click the IRB tab at the top of the screen
  3. Click the “Create New Study” button to the left
  4. Fill out the form
  5. At question #7, click the link to go to the library and select the appropriate protocol for your study
    1. If your study requires only de-identified materials select the Exempt Category 4 Protocol (HRP-582). *Note: De-identified discard tissues may not require consent
    2. If your study does not require obtaining any information about living individuals, select Nonhuman Subject Research (HRP-585)
    3. You may submit for an expedited submission if your study involves only specimens that have been collected solely for non-research purposes (such as medical treatment and diagnosis)
  6. Following HRRC approval, submit a tissue request to the HTR through iLab. You will upload your SRC and IRB approval letters, and have an active PR in the system.
  1. Contact the HTR-TASR for a planning/feasibility session.
  2. Submit your proposal to the Tissue Research Oversight Committee (TROC). Contact Karen Capobianco for guidance on this process.
  3. Once the TROC has approved your proposal, send the approval letter with your application to the UNM Human Research Review Committee (HRRC) Institutional Review Board (IRB) (see instructions above).
  4. Contact the HTR-TASR for an additional planning session (usually required to clarify details of the process. This meeting includes obtaining approval from the Division Chief of Surgical Pathology to ensure availability of the specimens while maintaining compliance with national laboratory regulations and best patient care.
  5. If you have tissue remaining after closure of your investigation, you must return it to the HTR
  1. You must obtain approval from the local Human Research Review Committee if any portion of the collected tissue may potentially be used for research.
  2. The Division Chief of Surgical Pathology or their designee must approve the method of sample collection to ensure that sufficient representative tissue is retained for clinical care

Inventory

Site of Tissues Collected

(Includes archival tissue from UNM and prospective collection for investigators for specific studies.)

  • Bladder, Blood, Bone, Bone Marrow, Brain, Breast
  • Chest wall, Colorectal
  • Diaphragm
  • Gallbladder
  • Head and Neck
  • Kidney
  • Liver, Lung, Lymph node
  • Mediastinum
  • Omentum, Ovary
  • Pancreas, Penis, Peritoneum, Prostate
  • Saliva, Salivary Gland, Skin, Small Intestine, Soft Tissue, Spleen, Stomach
  • Testis, Thymus, Thyroid
  • Uterus and Cervix
  • Vagina/Vulva

Expanded Breast Cancer Registry (EBCR)

This is a complicated tissue collection consisting of over 400 consented patients with multiple time points and types of tissue collected. The following were collected on each patient:

  • 5 serum aliquots maximum/participant/collection (like Baseline or FUP time)
  • 10 plasma aliquots maximum/participant/collection
  • 10 DNA aliquots from whole blood/participant/collection
  • 2 DNA aliquots maximum from mouthwash or swab/participant/collection
  • breast tissue (fine needle aspirates, vials and OCT molds) - all cases are different.

Please contact the HTR-TASR for more detailed query of this dataset.