Collection of Gastrointestinal Malignant and Non-malignant Human Samples
Conditions: Inflammatory Bowel Diseases, Colo-rectal Cancer
Sponsor: University of Texas at Austin

Research Proposal 
 
 
The University of Texas at Austin                                                                                                          Page 1 of 10 
Institutional Review Board- Revised October 2014 
 
 
Study Title: Collection of gastrointestinal malignant and non-malignant human samples 
Document Approval Date: August 15, 2018 
 
 

Research Proposal 
 
 
The University of Texas at Austin                                                                                                          Page 2 of 10 
Institutional Review Board- Revised October 2014 
 
 
 
1. Title 
Collection of gastrointestinal malignant and non-malignant human samples 
 
2. Principal Investigator 
Hyun Jung Kim, hk9746, Biomedical Engineering 
 
3. Purpose 
The purpose of the proposed research is to collect tissue, blood and fecal samples from 
patients undergoing standard of care for their gastrointestinal disease, including Inflammatory 
Bowel Disease (IBD), and Colorectal Cancer (CRC). Tissue and blood samples will be 
obtained during procedures that are part of normal treatment, including blood and fecal 
collection, surgical resection, and biopsy collection. Samples will be obtained from consenting 
patients at Seton Dell Medical Center at the University of Texas (SDMCUT), or other relevant 
facilities (see section 6.i below), and only tissue not required for histopathological analysis will 
be collected. Initially, the focus will be on IBD, and CRC, where there are extensive previous 
studies to draw from.  
 
The collected samples of the proposed study will be used to establish biomimetic human 
organ-on-a-chip platforms by leveraging microfluidic tissue culture technology. Another focus 
of the research will be study the human intestinal microbiome that is highly associated with 
the pathogenesis of human gastrointestinal diseases. We have developed the microchip 
technology to mimic the structure and physiological function of human intestine by integrating 
tools developed in a microfluidic device, tissue engineering, and clinical microbiology, using 
intestinal cell lines. To recreate more reliable intestinal disease models and to further 
investigate the host-gut microbiome interactions in our experimental platforms, we are 
transitioning to use human clinical samples. We will use tissue biopsies to culture human 
intestinal cells including epithelium, endothelium, connective tissues on-chip. We will obtain 
blood samples to isolate peripheral blood mononuclear cells (PBMC) that represent mixed 
population of white blood cells (WBC). Isolated WBCs will be co-cultured with intestinal cells. 
We will also further investigate any potential application of microbiome-related therapies such 
as fecal microbiota transplantation (FMT).  
 
4. Procedures 
Tissue samples will be obtained from consenting patients at (SDMCUT), or other relevant 
facilities (see section 6.i below), in accordance with protocols approved by the University of 
Texas Institutional Review Board (UTIRB). Patients who meet eligibility criteria will have their 
tumors collected at the time of their surgical resection, or 6-10 additional biopsies collected 
during endoscopy (upper gastrointestinal endoscopy or colonoscopy). All samples will be 
obtained during a procedure that is part of normal treatment, with no variation from standard 
of care with respect to the performance of this research.  
During the initial clinic visit with surgeon, patient will be presented with educational 
materials related to this study and a copy of the consent for consideration, as well as contact 
information of research staff available to answer any questions or concerns for the patient. 

Research Proposal 
 
 
The University of Texas at Austin                                                                                                          Page 3 of 10 
Institutional Review Board- Revised October 2014 
 
 
Consenting will occur at subsequent clinic visits if applicable, or may need to occur on the day 
of surgery if no further clinic visits are needed prior to surgery. Every effort will be made to 
ensure the patient has had adequate time to consider consenting to participation, as well as 
any questions or concerns addressed. If consent is to be made on the day of surgery, extra 
precaution will be taken to ensure the patient is clear and comfortable with all aspects 
regarding participation in the study. 
No more than 10 mL of whole blood will be drawn from each patient, kept in a heparin 
treated tube to prevent coagulation, and transported to Kim lab by a member of Dr. Kim’s lab. 
PBMC will be isolated from the whole blood samples and subpopulation of the isolated 
immune cells will be further analyzed using a flow cytometry in the UT Core Facility. Blood 
collection will occur at a pre-op clinic visit or on the day of surgery. 
Tissue will be used to verify disease status by the pathologist. Tissue samples not required 
for histopathological analysis will be used to generate organoid lines as follows. All biopsy 
samples should contain intestinal crypt possessing the intestinal stem cells. In IBD patients 
diagnosed with either ulcerative colitis or Crohn’s disease (CD), biopsy during colonoscopy or 
surgical resection should be done in the fully inflamed region as well as the non-inflamed 
region but adjacent from the inflamed region. Amount of biopsy depends on the surgeon’s 
consideration. The number of additional biopsies required for research are 3-5 each of 
affected region and normal, adjacent region of the intestinal lining, for a total of 6-10 additional 
biopsies. Each additional biopsy is <0.05 g. In CRC patients, we need biopsies obtained from 
CRC region as well as non-CRC but adjacent region. Collected human tissue samples (less 
than 5 g) will be placed in ice-cold phosphate buffered saline (PBS) containing antibiotics (100 
U penicillin and 0.1 mg streptomycin/mL) and transferred on ice in a biosafety carrier to the 
designated location (BME 4.318 at UT Austin) within 30 min by a member of Dr. Kim’s lab.  
To grow intestinal organoids using biopsy samples, we will incubate the biopsies in 8mM 
EDTA for 1 hour with vigorous shaking. After transferring biopsies into 1-2 mL complete 
medium (Advanced DMEM/F12, penicillin/streptomycin, HEPES, glutaMAX, B27 supplement, 
N2 supplement, 50% L-WRN conditioned medium, murine epidermal growth factor (EGF), 
Jagged-1, SB 431542, Y-27632, A-8301), we will vigorously pipette to release intestinal crypts 
and filter the tissues using a cell strainer (cutoff size, 100 μm) at room temperature. We will 
collect crypts by centrifugation at 200×g for 5 min and remove the supernatant. We will 
resuspend the crypts (target crypt density, 200 crypts per 50 μL Matrigel) in the Matrigel 
solution (4 °C), drop 50 μL of crypt/Matrigel suspension into 24 well cell culture plate, solidify 
the crypt suspension to gel at 37 °C for 1 h, then add the pre-warmed complete medium. We 
will keep the well plate in the humidified 37 °C CO2 incubator by changing medium every other 
day, and pass the sufficiently grown organoids (average size 500 μm in diameter) every 7 
days into the new Matrigel.  
Fecal samples will be collected during patient’s visit at clinics, normally prior to surgery, 
because it is required to flash freeze the sample to minimize loss of viable anaerobic bacteria. 
Individual patients will collect fecal sample using the lidded sterile container and a sterile 
plastic stick or cotton swab. Because the samples are required to be proceeded further in an 
anaerobic glove box, we will flash freeze the collected samples and transport to the Kim lab 
(BME 4.318). The aliquot (5 g) of samples will be then diluted in 25 mL of sterile NaCl solution 

Research Proposal 
 
 
The University of Texas at Austin                                                                                                          Page 4 of 10 
Institutional Review Board- Revised October 2014 
 
 
(0.85%, w/v; autoclaved or filter-sterilized by 0.22 µm) inside an anaerobic glove box at room 
temperature, and then filtered sequentially using sieves (cutoff sizes at 100, 70, and 40 μm) 
to remove slurries. The filtered suspension will be centrifuged at 6,000× g for 15 min at room 
temperature. The concentrated fecal bacteria suspension (approximately 1010 cells/mL) will 
be mixed with sterile pharmaceutical grade glycerol (final concentration 10%, v/v in PBS) and 
stored in a deep freezer (-80°C) until use. Any biopsy sample that is not used on the day of 
collection will be discarded following the biosafety protocols (IBC-2016-00002). Fecal matter, 
blood samples and/or cells, and organoids derived from patient tissue samples will be stored 
in a liquid nitrogen for future use in this study, or for use in future studies. 
  
 
5. Location 
Patient consent and specimen collection will occur at (SDMCUT), or other relevant clinic or 
hospital facility (see section 6.i below). 
 
All research related to this study will occur in BME 4.318 at UT Austin 
 
For a multi-site study in which the University is the lead or coordinating institution, provide the 
following:  
 
i. 
Tissue samples will be collected during surgical resection, biopsy collection, blood 
collection, or fecal collection at Dell Seton Medical Center at the University of Texas, 
other facilities in the Seton Healthcare Network, and St. David’s Healthcare 
Partnership.  
 
ii. 
Each participating institution has been confirmed to have an active FWA according to 
the current United States Department of Health and Human Services (USHHS) Office 
for Human Research Protections (OHRP) Database (FWA00004937, FWA00004937, 
FWA00006399, respectively). 
 
iii. 
Dr. Declan Fleming will act as the PI contact at each institution.  
 
iv. 
This study will operate in accordance with approval by the UTIRB, and site approval 
will be obtained from each institution. In addition, Dr. Fleming will communicate with 
the medical director at St. David’s Medical Center as well as Seton Healthcare 
Network. Moreover, once approved by UTIRB, this protocol will be shared with Matt 
Cowperthwaite at St. David’s IRB. 
 
v. 
Dr. Jennifer McKinney will act as the contact and facilitator of communication between 
institutions, and will maintain the responsibility of addressing any unanticipated 
problems involving risks to subjects or others, and other study-related information.  
 
6. Resources 

Research Proposal 
 
 
The University of Texas at Austin                                                                                                          Page 5 of 10 
Institutional Review Board- Revised October 2014 
 
 
Kenneth Rainin Foundation, Innovator Awards 
Texas 4000 
 
7. Study Timeline 
Aug 2017 – Jul 2022  
 
 
8. Measures 
Subjects will be informed and consents will be obtained from the participants prior to the 
surgery according to the IRB protocol. Please see Appendix A for the patient demographic 
information to be gathered at the time the tissue sample is collected. 
We need to verify if the biopsy/surgery tissue samples representatively reflect the disease 
status of patients. For instance, we have to collect biopsies isolated from CRC region & non-
CRC but adjacent region for testing our hypothesized idea. The degree of CRC should be also 
identified to sort out different lines of CRC-derived organoids. For the IBD patients, same 
criterion is applied as described in CRC case. Disease status will be confirmed by the 
pathology staff. 
To determine the gut microbiota from human fecal sample, total DNA from fecal sample 
will be extracted with PureLink Microbiome DNA Purification Kit (Thermo Fisher Scientific). 
The extracted metagenomics DNA will be quantitatively analyzed by 16S rRNA gene 
amplification in V4-V5 region. The raw DNA sequences will be analyzed by CLC genomics 
workbench v9.5.1. which includes the CLC Microbial Genomics Module v1.6.1. (Qiagen). 
Upon the patients’ specimen are grown into the intestinal organoids and cultured inside 
the microfluidic devices, their viability and differentiation-specific markers will be analyzed by 
live/dead assay and immunofluorescence staining using confocal microscopy (BME 4.318). 
Other assays to verify pathological characteristics will be performed following references 
published in scientific journals. Patients will be consented to be allowed to be contacted by 
clinical staff or research coordinator to obtain follow-up information regarding their disease 
status. 
All the research results will be published in the appropriate scientific journals and will be 
presented at the scientific meetings. 
 
9. Participants 
a. Target Population 
No special populations are targeted for accrual to this study. However, racial background 
may play a role in disease etiology, and a variety of races is optimal for this study to 
address that question. Thus, the patient’s race information will be included with the 
sample.  
 
b. Inclusion/Exclusion 
The study will not exclude potential subjects from participation on the basis of ethnic origin 
or gender. Subjects recruited will include men, women, and all ethnic origins, provided 
they meet all eligibility criteria as follows: 

Research Proposal 
 
 
The University of Texas at Austin                                                                                                          Page 6 of 10 
Institutional Review Board- Revised October 2014 
 
 
 
a) Biopsy-proven colorectal cancer scheduled to have surgical resection of primary site, 
at participating and approved facilities. Since it is standard clinical care to resect 
certain suspicious gastrointestinal masses without a pre-existing biopsy, patients who 
are undergoing resections for highly suspicious masses believed to be cancer, may 
be consented. 
b) Diagnosed with IBD or CD, scheduled to have biopsy and/or fecal collection. 
c) Patients undergoing colon resection due to trauma, or non-malignant disease, such 
as diverticulitis. 
d) Age ³18 years old. 
e) Ability to understand and willingness to sign a written informed consent document. 
 
c. Benefits 
There is no known benefit to subjects for their participation in this study. 
 
d. Risks 
Removal of tissue sample during surgery: There is low risk from participation in this study, 
as the subjects will not undergo any additional procedures for this research study. Tissue 
will only be taken when the patient is undergoing a surgical procedure as part of their 
standard care. The tissue samples will be obtained from tissue removal and will only be 
taken from tissue not needed for the patient’s medical care. No additional tissue will be 
taken as part of this procedure, thus no additional risk is added to the patient, and no 
additional time for the patient under anesthesia. 
 
Removal of tissue during endoscopy or colonoscopy: There is negligible increased risk to 
the patient, as the tissue collected will be a very small quantity, measuring approximately 
0.03 g per additional biopsy, and obtained during a procedure that is part of normal 
treatment. Each additional biopsy specimen takes <15 sec to acquire, thus additional time 
for patient under anesthesia is expected to be <3 min. There is a very small additional risk 
of bleeding, infection, or perforation (0.016-0.2%) associated with acquiring the additional 
biopsy samples. 
 
Blood sample: The risks of obtaining a blood sample are minimal, similar to any time blood 
is collected, and include pain, bleeding, bruising, infection, and skin irritation (from 
cleaning agents used to sterilize the skin, or bandages). 
 
e. Recruitment 
Up to 300 patients will be recruited from the various approved facilities. Because there 
exists a treatment relationship with the patient, no recruitment authorization will be 
required to be signed by the patient. There will be no study specific patient advertising or 
supplemental recruitment materials used for this study. 
 
f. Obtaining Informed Consent 

Research Proposal 
 
 
The University of Texas at Austin                                                                                                          Page 7 of 10 
Institutional Review Board- Revised October 2014 
 
 
Patients with IBD or CRC scheduled for surgery or biopsy removal at an approved facility 
will be asked to participate in the study prior to the procedure. Subjects will be consented 
by qualified study personnel, i.e., a research coordinator and/or investigator. These 
personnel will understand the research study and will have completed IRB training as 
directed by institutional requirements. The investigators, clinic nurses or research 
coordinator will provide the subject with information regarding the research study. 
 
During the initial clinic visit with surgeon, patient will be presented with educational 
materials related to this study and a copy of the consent for consideration, as well as 
contact information of research staff available to answer any questions or concerns for the 
patient. Consenting will occur at subsequent clinic visits if applicable, or may need to occur 
on the day of surgery if no further clinic visits are needed prior to surgery. Every effort will 
be made to ensure the patient has had adequate time to consider consenting to 
participation, as well as any questions or concerns addressed. If consent is to be made 
on the day of surgery, extra precaution will be taken to ensure the patient is clear and 
comfortable with all aspects regarding participation in the study. 
 
Consent will be obtained in a quiet setting prior to the initiation of any study procedures 
and the subject will be given ample time to consider the consent form and ask questions. 
Every effort will be made to ensure that the patient has an understanding of the consent 
formed based upon his or her verbal response. 
 
Qualified personnel as listed above, prior to the initiation of study procedures, will obtain 
written consent from the eligible patient. For Spanish speaking subjects, a professionally-
translated version of the consent will be provided. All subjects will receive a signed and 
dated copy of the consent form. 
 
 
10. Privacy and Confidentiality 
This project will require the use of a coded identifier which will have a direct link to 
protected health information (PHI). Identifying PHI, such as name, phone, and address will 
not be provided to research staff. A HIPAA authorization form will be provided to the patient 
at the time of consent. This authorization will designate the specific health information that will 
be required to be released. A signed and dated authorization will be collected by the qualified 
study staff at the time the subject is consented.  
Paper records for this study will be maintained in locked cabinets in Dr. Kim’s research 
laboratory. Electronic records for this study will be maintained on password-protected 
computers on which security is protected by firewalls. At the time of consent, each patient will 
receive a study-generated number that will be used to identify the patient. Each specimen will 
be given a specimen number that is related to the patient identifier. All PHI will be entered by 
the consenting staff into the secure, HIPAA compliant online database, REDCap. Restricted 
access to REDCap will be given to Dr. Kim and his staff (e.g., they will be given access to 
patient data except for name, phone number, and address). Any clinical information regarding 

Research Proposal 
 
 
The University of Texas at Austin                                                                                                          Page 8 of 10 
Institutional Review Board- Revised October 2014 
 
 
study subjects will not be stored within the laboratory. Files containing patient data will be 
stored in a locked office and/or on a password protected computer with access granted only 
to those individuals listed on the HIPAA Authorization form. 
Blood, tissue, and fecal samples obtained for this study will be retained in and used by Dr. 
Kim’s lab for future research purposes, or they may be disposed of, or shared with other 
researchers. Specimens which are shared will be coded and will not have any identifying 
information. Patients will not be charged or receive compensation for use of reposited 
specimens, or from any commercial ventures based on this research or any research in the 
future. Results from future research will not be shared with the patient. Patients may contact 
the clinical or research staff at any time to request that samples be withdrawn from research 
use, and any samples still in possession at that time will be destroyed.  
  
Confidentiality of the Data or Samples 
a. Demographic data will be collected at the time of consent. Blood and tissue samples will 
be collected during procedures that are part of normal care for the patient as described 
above. Fecal samples will be collected during a normal clinic visit if possible (e.g., at the 
time of consent), or just prior to the procedure if applicable. 
b. Samples and data will be securely stored in Kim lab facilities, which have access codes 
for the doors to the labs where the samples will be kept. Samples located in the lab will be 
labeled with the tissue type, specimen number, and coded patient identifier only. 
c. Collected biopsy samples will be kept in the Kim lab no more than 1 day. After biopsies 
are grown into organoids, the organoids will be kept in a liquid nitrogen tank for the 
purpose of storage and furture studies by Dr. Kim, or other researchers. Collected blood 
and fecal bacteria will be stored in the Kim lab at -80°C for the purpose of storage and 
future studies by Dr. Kim, or other researchers. 
d. Data and samples obtained in this study will be stored in Kim lab facilities, and may be 
shared with other researchers for future research use. All data and samples will be 
identified by the coded patient identifier, thus PHI will not be shared with any current or 
furture research staff. The utmost precautions will be taken to ensure that PHI is not 
compromised. 
e. Any biopsy sample that is not used on the day of collection will be discarded following the 
biosafety protocols (IBC-2016-00002). Fecal matter, blood samples and/or cells, and 
organoids derived from patient tissue samples will be stored in a liquid nitrogen for future 
use in this study, or for use in future studies. 
 
11. Compensation 
No compensation will be provided to participants of this study. 
 
 
 
 

Research Proposal 
 
 
The University of Texas at Austin                                                                                                          Page 9 of 10 
Institutional Review Board- Revised October 2014 
 
 
 
 
Appendix A 
 
Patient Demographics 
 
Patient Demographics 
Name 
 
Medical Record Number 
 
LCI Research Number 
 
Date of Birth 
 
Age 
 
Gender 
 
Race/ethnicity 
 
Name of Physician or Surgeon 
 
Type of procedure 
 
Signed Consent 
 
Signed HIPAA 
 
Signed Repository Consent 
 
Specimen(s) given 
 
Tissue from 
 
Blood given 
 
Fecal sample given 
 
Type of Cancer/disease 
 
Diagnosis date 
 
Stage at diagnosis 
 
TMN at diagnosis 
 
Metastatic Disease date 
 
Stage at consent 
 
Previous surgery/procedure 
 
Date  
Comments  
Angio-lymphatic invasion  
Previous radiation 
 
Date  
Comments  
Previous Chemotherapy 
 
Date(s)/# lines  
Comments  
# organs with mets 
 
Current medications 
 
Comments  

Research Proposal 
 
 
The University of Texas at Austin                                                                                                          Page 10 of 10 
Institutional Review Board- Revised October 2014 
 
 
Comorbidities 
 
Smoker 
 
Drinker 
 
Alcoholic intake amount  
Recreational Drug use 
 
Type  
Frequency  
Prior Cancer 
 
Comments  
Family history of cancer 
 
Comments  
Vegetarian diet 
 
Date last contact 
 
Red meat intake 
 
Frequency  
Antibiotics 
 
Type (if known)  
Date last use  
Probiotics 
 
Type (if known)  
Frequency  
Date last use  
Artificial sweetener 
 
Type  
Vitamins and minerals 
 
Type