Little is known about human crypt stem cells. Although strategies which create and follow visible crypt markers are impractical for humans, it may be possible to analyze endogenous sequences which inherently record crypt histories. To better distinguish between otherwise identical crypts without experimental intervention, epigenetic patterns were used as cell fate markers. Methylation exhibits somatic inheritance and random site independent changes which potentially create binary information strings or tags in adjacent CpG sites that drift with time. Instead of visual examinations, methylation tag contents of individual crypts are sampled and read with bisulfite sequencing. Tags at three presumably neutral loci were different between crypts and between cells within crypts. Methylation increased with aging but was mosaic between crypts, and between alleles and loci within single crypts. Some crypts were quasi‑clonal because they contained more unique tags than expected from a single stem cell. The complex epigenetic patterns analyzed with coalescence theory were more consistent with crypt niches in which multiple stem cells are replaced through periodic symmetric divisions. Methylation tags suggest normal human crypts are long lived, contain multiple stem cells, undergo continuous purification, and accumulate random methylation errors at some loci. Proposed studies will further verify methylation tags as cell fate markers and better characterize stem cell dynamics in normal human colon.

Agency
National Institute of Health (NIH)
Institute
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Type
Exploratory/Developmental Grants (R21)
Project #
5R21DK061140-02
Application #
6524807
Study Section
Special Emphasis Panel (ZDK1-GRB-4 (O1))
Program Officer
May, Michael K
Project Start
2001-09-30
Project End
2005-08-31
Budget Start
2002-09-01
Budget End
2005-08-31
Support Year
2
Fiscal Year
2002
Total Cost
$162,500
Indirect Cost
Name
University of Southern California
Department
Pathology
Type
Schools of Medicine
DUNS #
041544081
City
Los Angeles
State
CA
Country
United States
Zip Code
90089
Kim, Jung Yeon; Tavare, Simon; Shibata, Darryl (2006) Human hair genealogies and stem cell latency. BMC Biol 4:2
Kim, Jung Yeon; Beart, Robert W; Shibata, Darryl (2005) Stability of colon stem cell methylation after neo-adjuvant therapy in a patient with attenuated familial adenomatous polyposis. BMC Gastroenterol 5:19
Kim, Jung Yeon; Siegmund, Kimberly D; Tavare, Simon et al. (2005) Age-related human small intestine methylation: evidence for stem cell niches. BMC Med 3:10
Kim, Jung Yeon; Tavare, Simon; Shibata, Darryl (2005) Counting human somatic cell replications: methylation mirrors endometrial stem cell divisions. Proc Natl Acad Sci U S A 102:17739-44
Calabrese, Peter; Tavare, Simon; Shibata, Darryl (2004) Pretumor progression: clonal evolution of human stem cell populations. Am J Pathol 164:1337-46
Kim, Kyoung-Mee; Shibata, Darryl (2004) Tracing ancestry with methylation patterns: most crypts appear distantly related in normal adult human colon. BMC Gastroenterol 4:8
Kim, Kyoung-Mee; Calabrese, Peter; Tavare, Simon et al. (2004) Enhanced stem cell survival in familial adenomatous polyposis. Am J Pathol 164:1369-77
Calabrese, Peter; Tsao, Jen-Lan; Yatabe, Yasushi et al. (2004) Colorectal pretumor progression before and after loss of DNA mismatch repair. Am J Pathol 164:1447-53
Kim, Kyoung-Mee; Shibata, Darryl (2002) Methylation reveals a niche: stem cell succession in human colon crypts. Oncogene 21:5441-9