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Protein Localization, Identification and Folding Core

In Vivo Animal and Human Studies Core
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Molecular Biology Core

Microbiome and Metabolomics Core

In Vivo Animal and Human Studies Core


Chung Owyang, M.D.

Peter Higgins, M.D., Ph.D.
Associate Core Director and Director of the Clinical Design and Statistics Program

John Kao, M.D.
Associate Core Director and Director of the Biobank Program

Jason Spence, Ph.D.
Associate Core Director and Director of the Organoid/Enteroid Program


The In Vivo Animal and Human Studies Core consists of the following 4 distinct programs.

  1. In Vivo Small Animal Studies Program (Service Request Form)
  2. Organoid/Enteroid Modeling Program (Service Request Form)
  3. Biospecimens Banking Service (Service Request Form)
  4. Clinical Design and Statistics (Service Request Form)

1.  In Vivo Small Animal Studies Program

Animal studies programs are frequently used by Center investigators including: 1) In vivo cellular and molecular imaging for small animals; 2) Small animal endoscopy; 3) Fluorescent-activated cell sorting (FACS) analysis; 4) Electroporation for Direct Transfer of siRNA into targeted neural tissues or GI Organs; and 5) Animal Model development and function studies. The services provided include:

a. Consultation - Program Director Dr. Owyang and other lab personnel (Dr. Xiao-Yin Wu) will consult with members on research projects and how they make use of the Small Animal Studies Program, including the choice of animal models or application of behavior methods to assess physiological questions related to transgenic animal models. This is pertinent to the study of neuropeptides in mediating visceral pain and satiety. Appropriate animal behavior paradigms provide critical validated tools for translational research, allowing investigators to evaluate roles of specific molecules at the whole animal level and are essential for behavioral phenotyping of new transgenic and knockout mice. Other services provided by the Small Animal Studies Program include consultation for, and measurement of, gastric and pancreatic secretion and GI motility and metabolic studies, which are valuable to basic scientists interested in testing functions of specific genes and proteins in whole animal models.

b. Training and Education – The Small Animal Studies Program will offer training in mouse endoscopy, FACS analysis, and pain and feeding behavior studies and will also perform limited studies for pilot data. These services will be provided by Dr. Wu, a senior lab associate who has worked with Dr. Owyang for 10 years. She will instruct Center members on measuring gastric and pancreatic secretion and recording GI motility. Through the NIH-funded In Vivo Cellular and Molecular Imaging Center, the In Vivo Studies Core offers many imaging modalities including fMRI, bioluminescence imaging, microcomputed tomography, and microPET for small animal studies–important tools to study tumor biology, stem cell research, and organogenesis. Members can receive instruction from trained Imaging Center staff on using these imaging modalities in their research. For sophisticated techniques such as in vivo electrophysiological recording of brain stem nuclei or electroporation for direct transfer of siRNA into targeted neural tissue or GI organs, the Small Animal Studies Program can provide technical support and perform limited studies for pilot data.

c. Protocols – The program will provide detailed protocols for the techniques covered by this service.  When new technologies come on-line we will conduct training workshops for potential users. (Service Request Form)

2. Organoid/Enteroid Modeling Program

The goal of the Organoid/Enteroid Modeling Program is to offer expertise, intellectual, and material support to Center members to implement and use these new 3D human model systems. Services provided include:

a. Training – A primary goal of the Organoid/Enteroid Program will be training members to implement organoid and/or enteroid technology.  For iPSC-derived organoids, this will include instruction on directed differentiation to generate 3D structures, followed by teaching in 3D culture techniques (embedding, organoid passaging, microinjection methods).  If investigators need training in iPSC generation, culture or manipulation, they will be referred to the Pluripotent Stem Cell Core (  Enteroids are derived from primary human tissues like biopsy samples and training will be provided in isolating, growing and passaging these cultures.

b. Protocols – Protocols for organoids and enteroids have been developed by Dr. Spence and others and have been tested, modified, and implemented in the Spence lab, enabling the growth of enteroid and organoid tissues. All protocols and media formulations will be available to all Center members.

c. Reagents – A common theme for growing organoids/enteroids is use of robust media with high growth factor signaling activity. Initial publications described using commercially available growth factors, which have exorbitant prices. To offset high prices associated with poor quality commercially available proteins, many labs have turned to using media conditioned by growth factor producing cell lines which elicit more robust activation of cell signaling than their commercial counterparts (data not shown). The UMCGR will generate quality-controlled media (CM)(WNT3A, RSPO2) following optimized protocols.  WNT3A-CM and RSPO@-CM will be tested for activity using TOPflash reporter assays, and will be validated on mouse enteroids. Conditioned media will be distributed to Center members as requested.

d. Consultation – The Program Director, Dr. Spence, and Co-Director, Dr. Linda Samuelson, have experience using 3D model systems. Investigators will be provided with free consultation before embarking on implementing 3D GI systems.  Given that each system has advantages and disadvantages, it will be important to determine the optimal system that can be best leveraged for the experimental question. (Service Request Form)

3.  Biospecimens Banking Service

The goal of the UMCGR Biorespository Core is to offer UMCGR and UM investigators expert consultative service to gain access to clinical specimens and to provide high-quality annotated biosamples along with the associated clinical information to ensure a high rate of success in achieving their scientific objectives.

The Biorespository Core will collect tissues related to 4 categories of GI and liver disease: 1) tissue inflammation and cytokines, 2) cell transformation & neoplasms, 3) enteric neurosciences, and 4) liver pathobiology. Investigators using these services will have access to sophisticated tissue technologies throughout the Medical School and Life Sciences Institutes, helping to achieve the mission of advancing translational medicine. Services provided include:  

a. Training: A primary goal of the Biorepository core is to training UMCGR investigators to access clinical samples to conduct clinically relevant research raising the significance and impact of their research. New investigators or those new to working with human samples, will be referred to our Clinical Studies Design and Statistic Program for instructions on how to write an IRB (see Below) . Additional support services will include collecting biospecimens from endoscopy suites or surgical pathology, special sample collection (e.g. feces for human microbiome research), fresh tissue processing, long-term sample storage, inventory management, and assist in biobank development.
b. Protocols: Standard protocols for cryopreservation of biopsy/surgical tissues, serum, and tissue primary cells will be established according to published biobanking protocols.16-17 The standard protocol for tissue and serum cryopreservation is snap freezing within 20 min before storage at -80°C in 0.5/1.5/2.0 ml screw cap tubes. Protocols to isolate primary immune cells from tissue samples or blood have been established in the lab of Dr. John Kao and others and have been tested, modified, and implemented in the Kao lab, providing the ability to perform ex vivo stimulation to measure antigen-specific immune responses.18-20 
c. Reagents: Commercial grade reagents to process tissue and serum (liquid N2, RNAlater®, Ficoll, Recovery™ Cell Culture Freezing Medium) are available at the Biorepository Core. Special reagents to setup primary tissue cells for ex vivo stimulation (EDTA, collagenase/Liberase, DNAase) are available from the Kao lab on request.
d. Consultation: The Core Director, Dr. John Kao, has worked with primary cell cultures and tissue processing/storage for >12 years. Investigators will receive free consultation before using clinical samples. (Service Request Form)

4.  Clinical Design and Statistics

Carefully planned and analyzed clinical studies are fundamental to the translation of scientific discovery to human biology and the advancement of clinical care in GI.  The ultimate goal of the CSDS is to accelerate the advancement of laboratory-based discoveries to applications, diagnosis, prognosis and therapy in digestive diseases.  One essential final step in this translation process is the ability to demonstrate that these findings change outcomes in patients. The CSDS facilitates the transformation of digestive disease research findings into clinically relevant, testable research, and, ultimately, clinical applications to patient care.  Since our last renewal, the GI Division and the Department of Internal Medicine have provided $200,000 in seed money to enhance the infrastructure for this service, which has been fully operational for the last 2 years. The Services provide include:

a. Consultation – The program will provide consultation services in two areas – Clinical Studies Design and Statistical Analysis.  Consultation will be provided by Program Director Dr. Peter Higgins with the assistance of a Master’s-level statistician (supported by the GI Division) on a variety of topics including:

  • Available and appropriate databases for scientific questions
  • Epidemiologic Study and Design Analysis
  • Clinical Study Design and Analysis
  • Prospective Clinical Trial Design and Analysis

Consultation on the execution of clinical studies will be provided by a dedicated study coordinator on topics including:

  • Study Protocol Development
  • IRB Application and Consent forms
  • Subject Recruitments and Retention
  • Best practices and quality control for biosamples

b. Education and Training – The study coordinator, Elaine Brady, provides training and education to assist Center members getting started in translational and clinical research.  Guidance will be provided to ensure that IRB, HIPAA, and federal standards for clinical research are maintained by Center members who are conducting clinical studies.

Clinical Studies training includes:

  • PEERRS (Program for Education and Evaluation in Responsible Research) training
  • REDCap secure HIPAA- compliant Database Training
  • Best Practices for keeping PHI secure and study HIPAA-compliant
  • Good Clinical Practice (GCP) for Clinical Research
  • Use of 12b2 and EMERSE for subject identification and date extraction
  • Additional study-specific training can be provided as needed

c. Protocols – Standard Operating Procedures (SOPs) for clinical research, covering topics including informed consent, protocol design, telephone contact scripts and standard sampling protocols will be provided and maintained on the In Vivo Studies Core website.  Additional study-specific clinical SOPs will be added as needed for specific projects. (Service Request Form)



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